title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2019-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The extent to which cancer patients trust in cancer-related online information: a systematic review link: https://peerj.com/articles/7634 last-modified: 2019-09-30 description: BackgroundThe use of the internet to satisfy information needs is widespread among cancer patients. Patients’ decisions regarding whether to act upon the information they find strongly depend on the trustworthiness of the information and the medium. Patients who are younger, more highly educated and female are more likely to trust online information. The objectives of this systematic review were to examine the extent to which cancer patients trust in cancer-related online information, internet websites as a source of cancer-related information or the internet as a medium of cancer information.MethodsA systematic review was conducted using five databases (PROSPERO registration number: CRD42017070190). Studies of any kind were included if they measured cancer patients’ trust in online health information. Study quality was assessed using the Research Triangle Institute (RTI) item bank. A narrative synthesis was undertaken to examine the included studies.ResultsOf the 7,314 citations obtained by the search, seven cross-sectional studies were included in the synthesis. A total of 1,054 patients reported having some or a great deal of trust in online cancer information; 154 patients reported moderately trusting such information; and 833 patients reported having no or little trust in online cancer information, internet websites as a source of cancer-related information or the internet as a medium of cancer-related information. Two of the seven studies reported between group comparisons for the above-stated patient characteristics. The methodological quality of the included studies was diverse.ConclusionThe results of the included studies indicates that approximately half of cancer patients appear to trust cancer-specific online information, internet websites as a source of cancer-related information or the internet as an information medium. However, the small number of included studies, high heterogeneity of participants, methods and outcomes calls for further systematic research. It is important to understand that cancer patients do and will increasingly use trusted cancer information websites to search for information concerning their disease. Therefore, physicians and other health care providers should provide more support and advice to these patients. creator: Lukas Lange creator: Mona Leandra Peikert creator: Christiane Bleich creator: Holger Schulz uri: https://doi.org/10.7717/peerj.7634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lange et al. title: Computational analysis of functional SNPs in Alzheimer’s disease-associated endocytosis genes link: https://peerj.com/articles/7667 last-modified: 2019-09-30 description: BackgroundFrom genome wide association studies on Alzheimer’s disease (AD), it has been shown that many single nucleotide polymorphisms (SNPs) of genes of different pathways affect the disease risk. One of the pathways is endocytosis, and variants in these genes may affect their functions in amyloid precursor protein (APP) trafficking, amyloid-beta (Aβ) production as well as its clearance in the brain. This study uses computational methods to predict the effect of novel SNPs, including untranslated region (UTR) variants, splice site variants, synonymous SNPs (sSNPs) and non-synonymous SNPs (nsSNPs) in three endocytosis genes associated with AD, namely PICALM, SYNJ1 and SH3KBP1.Materials and MethodsAll the variants’ information was retrieved from the Ensembl genome database, and then different variation prediction analyses were performed. UTRScan was used to predict UTR variants while MaxEntScan was used to predict splice site variants. Meta-analysis by PredictSNP2 was used to predict sSNPs. Parallel prediction analyses by five different software packages including SIFT, PolyPhen-2, Mutation Assessor, I-Mutant2.0 and SNPs&GO were used to predict the effects of nsSNPs. The level of evolutionary conservation of deleterious nsSNPs was further analyzed using ConSurf server. Mutant protein structures of deleterious nsSNPs were modelled and refined using SPARKS-X and ModRefiner for structural comparison.ResultsA total of 56 deleterious variants were identified in this study, including 12 UTR variants, 18 splice site variants, eight sSNPs and 18 nsSNPs. Among these 56 deleterious variants, seven variants were also identified in the Alzheimer’s Disease Sequencing Project (ADSP), Alzheimer’s Disease Neuroimaging Initiative (ADNI) and Mount Sinai Brain Bank (MSBB) studies.DiscussionThe 56 deleterious variants were predicted to affect the regulation of gene expression, or have functional impacts on these three endocytosis genes and their gene products. The deleterious variants in these genes are expected to affect their cellular function in endocytosis and may be implicated in the pathogenesis of AD as well. The biological consequences of these deleterious variants and their potential impacts on the disease risks could be further validated experimentally and may be useful for gene-disease association study. creator: Han Jieh Tey creator: Chong Han Ng uri: https://doi.org/10.7717/peerj.7667 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tey and Ng title: Identification and characterization of hirudin-HN, a new thrombin inhibitor, from the salivary glands of Hirudo nipponia link: https://peerj.com/articles/7716 last-modified: 2019-09-30 description: Transcriptome sequencing data (6.5 Gb) of the salivary glands of the haematophagous leech Hirudo nipponia was obtained by using the BGIseq-500 platform. After identification and analysis, one transcript (Unigene5370) was annotated to hirudin HV3 from Hirudo medicinalis with an e-value of 1e-29 and was named hirudin-HN. This transcript was a new thrombin inhibitor gene belonging to the proteinase inhibitor I14 (hirudin) family. Hirudin-HN, with a 270-bp cDNA, encodes an 89-aa protein containing a 20-aa signal peptide. The mature hirudin-HN protein contains the typical structural characteristics of hirudin, e.g., three conserved disulfide bonds and the PKP and DFxxIP motifs. Proteins (Hir and M-Hir) were obtained via prokaryotic expression, and the mature hirudin-HN protein was shown to have anticoagulant activity and thrombin affinity by using the chromogenic substrate S2238 and surface plasmon resonance (SPR) interaction analysis, respectively. The N-terminal structure of the mature hirudin-HN protein was shown to be important for anticoagulant activity by comparing the activity and thrombin affinity of Hir and M-Hir. The abundances of Hirudin-HN mRNA and protein were higher in the salivary glands of starving animals than in those of feeding or fed leeches. These results provided a foundation for further study on the structure-function relationship of hirudin-HN with thrombin. creator: Boxing Cheng creator: Fei Liu creator: Qiaosheng Guo creator: Yuxi Lu creator: Hongzhuan Shi creator: Andong Ding creator: Chengfeng Xu uri: https://doi.org/10.7717/peerj.7716 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cheng et al. title: Vegetation change in response to climate factors and human activities on the Mongolian Plateau link: https://peerj.com/articles/7735 last-modified: 2019-09-30 description: BackgroundVegetation in the Mongolian Plateau is very sensitive to climate change, which has a significant impact on the regulation of terrestrial carbon cycle.MethodsWe analyzed spatio-temporal changes of both growing season and the seasonal Normalized Difference Vegetation Index (NDVI) using simple linear trend analysis. Besides, correlation analysis was applied to explore the climate factors’ effects on vegetation growth at temporal and spatial scale. Potential effects of human factors on vegetation growth were also explored by residual trend analysis.ResultsThe results indicated that vegetation growth showed a greening trend in the Mongolian Plateau over the past 30 years. At the temporal scale, the growing season NDVI showed an insignificant increasing trend (at a rate of 0.0003 yr−1). At the spatial scale, a large region (53.8% of the whole Mongolian Plateau) with an increasing growing season NDVI, was primarily located in the southern and northern parts of the plateau. The correlation analysis suggested that temperature and precipitation were the main limiting factors that affected vegetation growth in spring and the growing season, respectively. The residual trend analysis showed that human activities primarily stimulated the growth of grasslands and shrublands, while croplands displayed a decreasing trend due to human disturbances, implying that anthropogenic factors may lead to croplands abandonment in favor of grasslands restoration. Our results provided detailed spatial and temporal changes of vegetation growth, and explored how climate and human factors affected vegetation growth, which may offer baseline data and scientific suggestions for local land and resources management, and facilitate the sustainable development of the terrestrial ecosystems. creator: Meng Meng creator: Ni Huang creator: Mingquan Wu creator: Jie Pei creator: Jian Wang creator: Zheng Niu uri: https://doi.org/10.7717/peerj.7735 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Meng et al. title: Incidence and risk of dialysis therapy within 30 days after contrast enhanced computed tomography in patients coded with chronic kidney disease: a nation-wide, population-based study link: https://peerj.com/articles/7757 last-modified: 2019-09-30 description: BackgroundPatients with chronic kidney disease (CKD) are considered at risk of contrast-induced acute kidney injury and possible subsequent need for dialysis therapy. Computed tomography (CT) is the most commonly performed examination requiring intravenous iodinated contrast media (ICM) injection. The actual risk of dialysis in CKD patients undergoing CT with ICM remains controversial. Furthermore, it is also uncertain whether these at-risk patients can be identified by means of administrative data. Our study is conducted in order to determine the incidence and risk of dialysis within 30 days after undergoing contrast enhanced CT in CKD coded patients.MethodsThis longitudinal, nation-wide, populated-based study is carried out by analyzing the Taiwan National Health Insurance Research Database retrospectively. Patients coded under the diagnosis of CKD who underwent CT are identified within randomly selected one million subjects of the database. From January 2012 to December 2013, 487 patients had undergone CT with ICM. A total of 924 patients who underwent CT without ICM are selected as the control group. Patients with advanced CKD or intensive care unit (ICU) admissions are assigned to the subgroups for analysis. The primary outcome is measured by dialysis events within 30 days after undergoing CT scans. The cumulative incidence is assessed by the Kaplan–Meier method and log-rank test. The risk of 30-day dialysis relative to the control group is analyzed by the Cox proportional hazards model after adjusting for age, sex, and baseline comorbidities.ResultsThe numbers and percentages of dialysis events within 30 days after undergoing CT scans are 20 (4.1%) in the CT with ICM group and 66 (7.1%) in the CT without ICM group (p = 0.03). However, the adjusted hazard ratio (aHR) for 30-day dialysis was 0.84 (95% CI [0.46–1.54], p = 0.57), which is statistically non-significant. In both advanced CKD and ICU admission subgroups, there are also no significant differences in 30-day dialysis risks with the aHR of 1.12 (95% CI [0.38–3.33], p = 0.83) and 0.95 (95% CI [0.44–2.05], p = 0.90), respectively.ConclusionsWithin 30 days of receiving contrast-enhanced CT scans, 4.1% of CKD coded patients required dialysis, which appear to be lower compared with subjects who received non-contrast CT scans. However, no statistically significant difference is observed after adjustments are made for other baseline conditions. Thereby, the application of administrative data to identify patients with CKD cannot be viewed as a risk factor for the necessity to undergo dialysis within 30 days of receiving contrast-enhanced CT scans. creator: Yun-Ju Shih creator: Yu-Ting Kuo creator: Chung-Han Ho creator: Chia-Chun Wu creator: Ching-Chung Ko uri: https://doi.org/10.7717/peerj.7757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Shih et al. title: qPCR and loop mediated isothermal amplification for rapid detection of Ustilago tritici link: https://peerj.com/articles/7766 last-modified: 2019-09-30 description: Loose smut of wheat caused by the basidiomycete fungus Ustilago tritici, a seed-borne disease, is difficult to control because of the expanse of wheat planting area and difficulty in pathogen detection. In this study, real-time fluorescence quantitative PCR (qPCR) and loop-mediated isothermal amplification (LAMP) assays are used to rapidly amplify the DNA of U. tritici. Five pairs of primers for qPCR and two series primers for LAMP were designed. Primarily, the specificity of the primer was assessed by using genomic DNA of U. tritici, Fusarium graminearum, Blumeria graminis, Rhizoctonia cerealis, Puccinia striiformis, Bipolaris sorokiniana, and Alternaria solani as templates. Further, the amplification systems were optimized. Finally, the sensitivity of qPCR and LAMP assays were evaluated. The results showed that the primer Y-430 F/R, Y-307 F/R, Y-755 F/R, and Y-139 F/R for qPCR and primers L-139 and L-988 for LAMP could be used for U. tritici detection. In the sensitivity test, the detection limit of qPCR assay was identified as 10 pg μL−1 of genomic DNA, the detection limit for LAMP assay was 100 fg μL−1. We successfully performed qPCR and LAMP assays on wheat loose smut wheat samples. This paper establishes two methods for U. tritici detection, which can be used for diagnosis of wheat loose smut in the laboratory and in the field. creator: Hanwen Yan creator: Jian Zhang creator: Dongfang Ma creator: Junliang Yin uri: https://doi.org/10.7717/peerj.7766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yan et al. title: Physiological and anatomical investigation of the auditory brainstem in the Fat-tailed dunnart (Sminthopsis crassicaudata) link: https://peerj.com/articles/7773 last-modified: 2019-09-30 description: The fat-tailed dunnart (Sminthopsis crassicaudata) is a small (10–20 g) native marsupial endemic to the south west of Western Australia. Currently little is known about the auditory capabilities of the dunnart, and of marsupials in general. Consequently, this study sought to investigate several electrophysiological and anatomical properties of the dunnart auditory system. Auditory brainstem responses (ABR) were recorded to brief (5 ms) tone pips at a range of frequencies (4–47.5 kHz) and intensities to determine auditory brainstem thresholds. The dunnart ABR displayed multiple distinct peaks at all test frequencies, similar to other mammalian species. ABR showed the dunnart is most sensitive to higher frequencies increasing up to 47.5 kHz. Morphological observations (Nissl stain) revealed that the auditory structures thought to contribute to the first peaks of the ABR were all distinguishable in the dunnart. Structures identified include the dorsal and ventral subdivisions of the cochlear nucleus, including a cochlear nerve root nucleus as well as several distinct nuclei in the superior olivary complex, such as the medial nucleus of the trapezoid body, lateral superior olive and medial superior olive. This study is the first to show functional and anatomical aspects of the lower part of the auditory system in the Fat-tailed dunnart. creator: Andrew Garrett creator: Virginia Lannigan creator: Nathanael J. Yates creator: Jennifer Rodger creator: Wilhelmina Mulders uri: https://doi.org/10.7717/peerj.7773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Garrett et al. title: Long-term studies reveal major environmental factors driving zooplankton dynamics and periodicities in the Black Sea coastal zooplankton link: https://peerj.com/articles/7588 last-modified: 2019-09-27 description: BackgroundThe development and management of shelf-sea ecosystems require a holistic understanding of the factors that influence the zooplankton structure and ecosystem functions. The Black Sea is an example of such areas influenced by eutrophication, overfishing, climate variability, invasions of the ctenophores Mnemiopsis leidyi followed by Beroe ovata. Thus, there is a set of principal factors which may influence and explain periodicities in the Black Sea ecosystem.MethodsWe analysed a total of 918 samples taken from 1991 to 2017 with intervals of 10 days. Taxa were identified to species, their abundance and biomass were calculated. We tested 12 environmental factors, which may explain zooplankton distribution: temperature, productivity-linked factors (surface chlorophyll as a proxi), wind, turbidity, lowest winter temperature, and concentration of the ctenophore M. leidyi. We used canonical correspondence analyses to find the dominant environmental factors and further regression analyses to retrieve dependences of plankton biomass on the major factors. Periodicities were assessed with the use of the Continuous wavelet transform and tested with use of One-way ANOSIM and PERMANOVA. The distances between ecosystem states in different years were assessed using non-metric multidimensional scaling.ResultsCurrently, temperature and productivity are the major environmental factors driving zooplankton dynamics. Not long ago, before 1999, abundance of M. leidyi was one of the major factors explaining the zooplankton variance. Spectral analysis of species abundances revealed a 4-year transitional period in 1999–2002 (not reported before) when ecosystem adapted to a new invader B. ovata. Statistically robust 2- and 3-year periodicities were retrieved for most plankton taxa and some benthic larvae. We found robust correlations between temperature and surface chlorophyll concentration on one side and plankton abundances and biomass on the other, and retrieved multivariate regressions, which may have a prognostic value. creator: Alexander L. Vereshchaka creator: Liudmila L. Anokhina creator: Taisiya A. Lukasheva creator: Anastasiia A. Lunina uri: https://doi.org/10.7717/peerj.7588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Vereshchaka et al. title: FoxO1 is a critical regulator of hepatocyte lipid deposition in chronic stress mice link: https://peerj.com/articles/7668 last-modified: 2019-09-27 description: Forkhead box O1 (FoxO1) is involved in lipid metabolisms. However, its role in chronic stress-related nonalcoholic fatty liver disease (NAFLD) is unclear. The scientific premise of our study was based on the finding that FoxO1 expression is increased in the liver of mice after chronic stress. It is important to understand the mechanisms involved in the activation of FoxO1 and how its function affects the liver lipid deposition. We employed a murine chronic stress model, in which mice were treated by plantar electrical stimulation and restraint for 6 weeks, and a cellular model, in which Hepa1–6 cells were treated with corticosterone. We also used a pharmacologic approach as1842856, a highly specific FoxO1 inhibitor. Lipid metabolism related genes levels were measured by qRT-PCR and the lipid levels by biochemical detection. We show that the level of FoxO1 is significantly elevated in the liver of chronic stress mice. Transcription factor FoxO1 regulates a lipid synthesis phenotype of hepatocyte that is involved in the development and progression of NAFLD. We have shown that inhibition of FoxO1 induced phenotypic conversion of hepatocytes and down-regulates lipid synthesis genes expression by hepatocytes, which contribute to lipid deposition in NAFLD. At the cellular level, the inhibitor of FoxO1 as1842856 can also attenuate the lipid deposition of Hepa1–6 cells induced by corticosterone. Targeting FoxO1 is a novel therapeutic target for chronic stress-related NAFLD. creator: Yun-zi Liu creator: Wei Peng creator: Ji-kuai Chen creator: Wen-jun Su creator: Wen-jie Yan creator: Yun-xia Wang creator: Chun-lei Jiang uri: https://doi.org/10.7717/peerj.7668 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Comparison of injury pattern and clinical outcomes between young adults and elderly patients with alcohol-related injury in South Korea 2011–2016 link: https://peerj.com/articles/7704 last-modified: 2019-09-27 description: BackgroundAlcohol is an important factor that contributes to emergency department (ED) visits due to injury. However, the role of alcohol in elderly patients visiting ED due to injury has not been clearly defined. This study aims to examine age and alcohol as risk factors of injury severity and clinical outcomes.MethodsThis study included patients who visited EDs between January 2011 and December 2016. Data was obtained from the Emergency Department-Based Injury In-depth Surveillance of the Korea Centers for Disease Control and Prevention, South Korea. Injury patients aged ≥18 years were included, but those who visited the ED more than 48 hours after injury, with unknown clinical outcomes (admission, mortality, and excess mortality ratio-adjusted injury severity score [EMR-ISS]) were excluded.ResultsWe analyzed 887,712 patients, of whom 131,708 (17.7%) non-elderly and 9,906 (7.0%) elderly had alcohol-related injury. Falls and slips are the most common injury mechanism (37.9%) in patients consuming alcohol (36.3% non-elderly/58.40% elderly). The injury occurred on roads (40.6%), houses (33.8%), and commercial facilities (11.9%) in elderly patients consuming alcohol. Suicide rate was 12.0% in elderly and 9.7% in non-elderly patients. According to the time of day of injury, evening (60.8%) was the most common in elderly and night (62.6%) in non-elderly patients. Admission rate (odds ratio [OR] 2.512 confidence interval [CI] 2.407–2.621), intensive care unit (ICU) care rate (OR 5.507 [CI] 5.178–5.858), mortality rate (OR 4.593 [CI] 4.086–5.162), and EMR-ISS >25 (OR 5.498 [CI] 5.262–5.745) were compared between patients with alcohol-related injury and non-elderly with non-alcohol-related injury patients. Alcohol consumption in elderly patients results in significant impairment and increases EMR-ISS, ICU care rate, and mortality rate. To reduce injury in elderly patients, alcohol screening, appropriate counseling, and intervention are needed. creator: Jae Hee Lee creator: Duk Hee Lee uri: https://doi.org/10.7717/peerj.7704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lee and Lee title: Cytotoxic activity of IMMUNEPOTENT CRP against non-small cell lung cancer cell lines link: https://peerj.com/articles/7759 last-modified: 2019-09-27 description: BackgroundIMMUNEPOTENT-CRP® (I-CRP) is a bovine dialyzable leukocyte extract containing transfer factor. It is a cost-effective, unspecific active immunotherapy that has been used in patients with non-small cell lung cancer (NSCLC) as an adjuvant to reduce the side-effects of chemotherapy and radiotherapy, and has shown cytotoxic activity in vitro on different cancer cell lines. However, its mechanism of action against lung cancer cells has not been assessed. Therefore, the objective of this work was to assess the cytotoxic mechanism of I-CRP on lung cancer cell lines.MethodsWe assessed cell viability through MTT assay on the NSCLC cell lines A549, A427, Calu-1, and INER-51 after treatment with I-CRP. To further understand the mechanisms of cell viability diminution we used fluorescence-activated cell sorting to evaluate cell death (annexin-V and propidium iodide [PI] staining), cell cycle and DNA degradation (PI staining), mitochondrial alterations (TMRE staining), and reactive oxygen species (ROS) production (DCFDA staining). Additionally, we evaluated caspase and ROS dependence of cell death by pretreating the cells with the pan-caspase inhibitor Q-VD-OPH and the antioxidant N-acetylcysteine (NAC), respectively.ResultsOur data shows that I-CRP is cytotoxic to NSCLC cell lines in a dose and time dependent manner, without substantial differences between the four cell lines tested (A549, A427, Calu-1, and INER-51). Cytotoxicity is induced through regulated cell death and cell cycle arrest induction. I-CRP-induced cell death in NSCLC cell lines is characterized by DNA degradation, mitochondrial damage, and ROS production. Moreover, cell death is independent of caspases but relies on ROS production, as it is abrogated with NAC.ConclusionAltogether, these results improve the knowledge about the cytotoxic activity of I-CRP on NSCLC cells, indicating that cell death, cell cycle arrest, DNA degradation and mitochondrial damage are important features, while ROS play the main role for I-CRP mediated cytotoxicity in lung cancer cells. creator: Ana Carolina Martinez-Torres creator: Luis Gomez-Morales creator: Alan B. Martinez-Loria creator: Ashanti Concepcion Uscanga-Palomeque creator: Jose Manuel Vazquez-Guillen creator: Cristina Rodriguez-Padilla uri: https://doi.org/10.7717/peerj.7759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Martinez-Torres et al. title: Dinosaur paleohistology: review, trends and new avenues of investigation link: https://peerj.com/articles/7764 last-modified: 2019-09-27 description: In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the “growth age” of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from “sluggish” reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., “metaplastic” tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry—recently developed branches of paleohistology—and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions. creator: Alida M. Bailleul creator: Jingmai O’Connor creator: Mary H. Schweitzer uri: https://doi.org/10.7717/peerj.7764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bailleul et al. title: The host range of Aphis gossypii is dependent on aphid genetic background and feeding experience link: https://peerj.com/articles/7774 last-modified: 2019-09-27 description: BackgroundA polyphagous insect herbivore has a wide range of host plants. However, it has been found that many polyphagous herbivores commonly exhibit a strong preference for a subset of species in their broad host range, and various host biotypes exist in herbivore populations. Nutrition and secondary metabolites in plants affect herbivore preference and performance, but it is still not clear which factors determine the host range and host preference of polyphagous herbivores.MethodCotton-melon aphids, Aphis gossypii Glover, collected from cotton and cucumber crops, were used in this study. The genetic backgrounds of these aphids were detected using microsatellite PCR and six genotypes were evaluated. Performance of these six aphid genotypes on excised leaves and plants of cotton and cucumber seedlings were examined through a reciprocal transplant experiment. In order to detect whether the feeding experience on artificial diet would alter aphid host range, the six genotypes of aphids fed on artificial diet for seven days were transferred onto cotton and cucumber leaves, and then their population growth on these two host plants was surveyed.ResultsAphids from cotton and cucumber plants could not colonize the excised leaves and intact plants of cucumber and cotton seedlings, respectively. All six genotypes of aphids collected from cotton and cucumber plants could survive and produce offspring on artificial diet, which lacked plant secondary metabolites. The feeding experience on the artificial diet did not alter the ability of all six genotypes to use their native host plants. However, after feeding on this artificial diet for seven days, two aphid genotypes from cotton and one from cucumber acquired the ability to use both of the excised leaves from cucumber and cotton plants. The two aphid genotypes from cotton conditioned by the feeding experience on artificial diet and then reared on excised cucumber leaves for >12 generations still maintained the ability to use intact cotton plants but did not establish a population on cucumber plants. However, one cucumber genotype conditioned by artificial diet and then reared on excised cotton leaves could use both the intact cotton and cucumber plants, showing that the expansion of host range was mediated by feeding experience.ConclusionFeeding experience on artificial diet induced the expansion of host range of the cucurbit-specialized A. gossypii, and this expansion was genotype-specific. We speculated that feeding on a constant set of host plants in the life cycle of aphids may contribute to the formation of host specialization. creator: Lin Ma creator: Meng-Yue Li creator: Chun-Yan Chang creator: Fang-Fang Chen creator: Yang Hu creator: Xiang-Dong Liu uri: https://doi.org/10.7717/peerj.7774 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Warm seawater temperature promotes substrate colonization by the blue coral, Heliopora coerulea link: https://peerj.com/articles/7785 last-modified: 2019-09-27 description: BackgroundHeliopora coerulea, the blue coral, is a reef building octocoral that is reported to have a higher optimum temperature for growth compared to most scleractinian corals. This octocoral has been observed to grow over both live and dead scleractinians and to dominate certain reefs in the Indo-Pacific region. The molecular mechanisms underlying the ability of H. coerulea to tolerate warmer seawater temperatures and to effectively compete for space on the substrate remain to be elucidated.MethodsIn this study, we subjected H. coerulea colonies to various temperatures for up to 3 weeks. The growth and photosynthetic efficiency rates of the coral colonies were measured. We then conducted pairwise comparisons of gene expression among the different coral tissue regions to identify genes and pathways that are expressed under different temperature conditions.ResultsA horizontal growth rate of 1.13 ± 0.25 mm per week was observed for corals subjected to 28 or 31 °C. This growth rate was significantly higher compared to corals exposed at 26 °C. This new growth was characterized by the extension of whitish tissue at the edges of the colony and was enriched for a matrix metallopeptidase, a calcium and integrin binding protein, and other transcripts with unknown function. Tissues at the growth margin and the adjacent calcified encrusting region were enriched for transcripts related to proline and riboflavin metabolism, nitrogen utilization, and organic cation transport. The calcified digitate regions, on the other hand, were enriched for transcripts encoding proteins involved in cell-matrix adhesion, translation, receptor-mediated endocytosis, photosynthesis, and ion transport. Functions related to lipid biosynthesis, extracellular matrix formation, cell migration, and oxidation-reduction processes were enriched at the growth margin in corals subjected for 3 weeks to 28 or 31 °C relative to corals at 26 °C. In the digitate region of the coral, transcripts encoding proteins that protect against oxidative stress, modify cell membrane composition, and mediate intercellular signaling pathways were enriched after just 24 h of exposure to 31 °C compared to corals at 28 °C. The overall downregulation of gene expression observed after 3 weeks of sustained exposure to 31 °C is likely compensated by symbiont metabolism.DiscussionThese findings reveal that the different regions of H. coerulea have variable gene expression profiles and responses to temperature variation. Under warmer conditions, the blue coral invests cellular resources toward extracellular matrix formation and cellular migration at the colony margins, which may promote rapid tissue growth and extension. This mechanism enables the coral to colonize adjacent reef substrates and successfully overgrow slower growing scleractinian corals that may already be more vulnerable to warming ocean waters. creator: Christine Guzman creator: Michael Atrigenio creator: Chuya Shinzato creator: Porfirio Aliño creator: Cecilia Conaco uri: https://doi.org/10.7717/peerj.7785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guzman et al. title: An update on anatomy and function of the teleost olfactory system link: https://peerj.com/articles/7808 last-modified: 2019-09-27 description: About half of all extant vertebrates are teleost fishes. Although our knowledge about anatomy and function of their olfactory systems still lags behind that of mammals, recent advances in cellular and molecular biology have provided us with a wealth of novel information about the sense of smell in this important animal group. Its paired olfactory organs contain up to five types of olfactory receptor neurons expressing OR, TAAR, VR1- and VR2-class odorant receptors associated with individual transduction machineries. The different types of receptor neurons are preferentially tuned towards particular classes of odorants, that are associated with specific behaviors, such as feeding, mating or migration. We discuss the connections of the receptor neurons in the olfactory bulb, the differences in bulbar circuitry compared to mammals, and the characteristics of second order projections to telencephalic olfactory areas, considering the everted ontogeny of the teleost telencephalon. The review concludes with a brief overview of current theories about odor coding and the prominent neural oscillations observed in the teleost olfactory system. creator: Jesús Olivares creator: Oliver Schmachtenberg uri: https://doi.org/10.7717/peerj.7808 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Olivares and Schmachtenberg title: Perspectives on the utilization of resistance mechanisms from host and nonhost plants for durable protection of Brassica crops against Alternaria blight link: https://peerj.com/articles/7486 last-modified: 2019-09-26 description: BackgroundAlternaria brassicae, the causal organism of Alternaria blight, is a necrotroph infecting crops of the Brassicaceae family at all growth stages. To circumvent this problem, several disease management strategies are being used in the field, and disease-resistant varieties have also been developed. However, no strategy has proven completely successful, owing to the high variability in virulence among A. brassicae isolates, which causes a diverse spectrum of symptoms. Nonhost resistance (NHR) is a robust and broad-spectrum defense mechanism available in plants, and the exploitation of gene pools from plant species that are nonhost to A. brassicae could serve as novel sources of resistance.MethodologyWe searched the literature using key words relevant to this study in various search engines, such as PubMed, Web of Science, and Google Scholar, as well as certain journal websites. The literature was retrieved, sorted, and mined to extract data pertinent to the present review.ResultsIn this review, we have comprehensively covered the recent progress made in developing Alternaria blight resistance in Brassica crops by exploiting host germplasm. We also enumerate the potential NHR sources available for A. brassicae and the NHR layers possibly operating against this pathogen. In addition, we propose different strategies for identifying NHR-related genes from nonhost plants and testing their relevance in imparting broad-spectrum resistance when transferred to host plants.ConclusionThis review will help broaden the current knowledge base pertaining to the resistance sources available in host germplasm, the exploitation of NHR mechanisms, and their applications in protecting Brassica crops from Alternaria blight. The insights might also be applicable to a wider repertoire of plant pathogens. creator: Urooj Fatima creator: Priyadarshini Bhorali creator: Sudarshana Borah creator: Muthappa Senthil-Kumar uri: https://doi.org/10.7717/peerj.7486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fatima et al. title: Exploring the expression and preliminary function of chicken Gimap5 gene link: https://peerj.com/articles/7618 last-modified: 2019-09-26 description: GTPase immune-associated protein 5 (Gimap5) plays a key role in maintaining T cell homeostasis, immunological tolerance and inflammatory processes. However, there are no reports on the chicken Gimap5 gene. In this study, the Gimap5 gene was first cloned from chicken and characterized its tissue expression characteristics in different developmental stages. The transcriptional activities of the Gimap5 gene in immune response were identified. The results showed that full-length cDNA sequence of Gimap5 contained 771 bp and encoded a 256-amino acid protein. The Gimap5 gene was transcribed in various tissues and different development stages. The transcriptional activities of Gimap5 gene in the most tissues increased with the development of chicken, but significantly up to peak in liver and large intestine of 10-month-old chicken. The Gimap5 gene exhibited differential transcriptional activities in immune-related tissues in immune responses, with down-regulated in liver (P < 0.01), spleen (P < 0.05) and bursa of Fabricius (P < 0.05), and up-regulated in thymus (P < 0.01). The results show that Gimap5 may be a multifunctional gene involved in tissue function, development and immune response in chicken. These data can provide the foundation for further study of Gimap5. creator: Wanting Zhang creator: Sifan Xu creator: Guanxian Wu creator: Yang Liu creator: Qiuyuan Wang creator: Chaolai Man uri: https://doi.org/10.7717/peerj.7618 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers link: https://peerj.com/articles/7647 last-modified: 2019-09-26 description: Among amniotes, numerous lineages are subject to an evolutionary trend toward body mass and size increases. Large terrestrial species may face important constraints linked to weight bearing, and the limb segments are particularly affected by such constraints due to their role in body support and locomotion. Such groups showing important limb modifications related to high body mass have been called “graviportal.” Often considered graviportal, rhinoceroses are among the heaviest terrestrial mammals and are thus of particular interest to understand the limb modifications related to body mass and size increase. Here, we present a morphofunctional study of the shape variation of the limb long bones among the five living rhinos to understand how the shape may vary between these species in relation with body size, body mass and phylogeny. We used three dimensional geometric morphometrics and comparative analyses to quantify the shape variation. Our results indicate that the five species display important morphological differences depending on the considered bones. The humerus and the femur exhibit noticeable interspecific differences between African and Asiatic rhinos, associated with a significant effect of body mass. The radius and ulna are more strongly correlated with body mass. While the tibia exhibits shape variation both linked with phylogeny and body mass, the fibula displays the greatest intraspecific variation. We highlight three distinct morphotypes of bone shape, which appear in accordance with the phylogeny. The influence of body mass also appears unequally expressed on the different bones. Body mass increase among the five extant species is marked by an increase of the general robustness, more pronounced attachments for muscles and a development of medial parts of the bones. Our study underlines that the morphological features linked to body mass increase are not similar between rhinos and other heavy mammals such as elephants and hippos, suggesting that the weight bearing constraint can lead to different morphological responses. creator: Christophe Mallet creator: Raphaël Cornette creator: Guillaume Billet creator: Alexandra Houssaye uri: https://doi.org/10.7717/peerj.7647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mallet et al. title: Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy link: https://peerj.com/articles/7691 last-modified: 2019-09-26 description: Abyssal plains are among the most biodiverse yet least explored marine ecosystems on our planet, and they are increasingly threatened by human impacts, including future deep seafloor mining. Recovery of abyssal populations from the impacts of polymetallic nodule mining will be partially determined by the availability and dispersal of pelagic larvae leading to benthic recolonization of disturbed areas of the seafloor. Here we use a tree-of-life (TOL) metabarcoding approach to investigate the species richness, diversity, and spatial variability of the larval assemblage at mesoscales across the abyssal seafloor in two mining-claim areas in the eastern Clarion Clipperton Fracture Zone (CCZ; abyssal Pacific). Our approach revealed a previously unknown taxonomic richness within the meroplankton assemblage, detecting larvae from 12 phyla, 23 Classes, 46 Orders, and 65 Families, including a number of taxa not previously reported at abyssal depths or within the Pacific Ocean. A novel suite of parasitic copepods and worms were sampled, from families that are known to associate with other benthic invertebrates or demersal fishes as hosts. Larval assemblages were patchily distributed at the mesoscale, with little similarity in OTUs detected among deployments even within the same 30 × 30 km study area. Our results provide baseline observations on larval diversity prior to polymetallic nodule mining in this region, and emphasize our overwhelming lack of knowledge regarding larvae of the benthic boundary layer in abyssal plain ecosystems. creator: Oliver Kersten creator: Eric W. Vetter creator: Michelle J. Jungbluth creator: Craig R. Smith creator: Erica Goetze uri: https://doi.org/10.7717/peerj.7691 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kersten et al. title: Effect of orienteering experience on walking and running in the absence of vision and hearing link: https://peerj.com/articles/7736 last-modified: 2019-09-26 description: PurposeThis study aimed to examine differences between track and field (T&F) runners and foot-orienteers (Foot-O) in the walking and running tests in the absence of vision and hearing. We attempted to determine whether experienced foot orienteers show better ability to maintain the indicated direction compared to track and field runners.MethodsThis study examined 11 Foot-O and 11 T&F runners. The study consisted of an interview, a field experiment of walking and running in a straight line in the absence of vision and hearing, and coordination skills tests.ResultsParticipants moved straight min. 20 m and max. 40 m during the walking test and min. 20 m and max. 125 m during the running test and then they moved around in a circle. Significant differences between groups were found for the distance covered by walking. Differences between sexes were documented for the distance covered by running and angular deviations. Relationship between lateralization and tendencies to veer were not found. Differences were observed between Foot-O and T&F groups in terms of coordination abilities.ConclusionsParticipants moved in circles irrespective of the type of movement and experience in practicing the sport. Orienteers may use information about their tendencies to turning more often left or right to correct it during their races in dense forests with limited visibility or during night orienteering competition. creator: Weronika Machowska creator: Piotr Cych creator: Adam Siemieński creator: Juliusz Migasiewicz uri: https://doi.org/10.7717/peerj.7736 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Machowska et al. title: Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses link: https://peerj.com/articles/7744 last-modified: 2019-09-26 description: Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production. creator: Gian Maria Niccolò Benucci creator: Reid Longley creator: Peng Zhang creator: Qi Zhao creator: Gregory Bonito creator: Fuqiang Yu uri: https://doi.org/10.7717/peerj.7744 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Benucci et al. title: Kinematics of male Eupalaestrus weijenberghi (Araneae, Theraphosidae) locomotion on different substrates and inclines link: https://peerj.com/articles/7748 last-modified: 2019-09-26 description: BackgroundThe mechanics and energetics of spider locomotion have not been deeply investigated, despite their importance in the life of a spider. For example, the reproductive success of males of several species is dependent upon their ability to move from one area to another. The aim of this work was to describe gait patterns and analyze the gait parameters of Eupalaestrus weijenberghi (Araneae, Theraphosidae) in order to investigate the mechanics of their locomotion and the mechanisms by which they conserve energy while traversing different inclinations and surfaces.MethodsTarantulas were collected and marked for kinematic analysis. Free displacements, both level and on an incline, were recorded using glass and Teflon as experimental surfaces. Body segments of the experimental animals were measured, weighed, and their center of mass was experimentally determined. Through reconstruction of the trajectories of the body segments, we were able to estimate their internal and external mechanical work and analyze their gait patterns.ResultsSpiders mainly employed a walk-trot gait. Significant differences between the first two pairs and the second two pairs were detected. No significant differences were detected regarding the different planes or surfaces with respect to duty factor, time lags, stride frequency, and stride length. However, postural changes were observed on slippery surfaces. The mechanical work required for traversing a level plane was lower than expected. In all conditions, the external work, and within it the vertical work, accounted for almost all of the total mechanical work. The internal work was extremely low and did not rise as the gradient increased.DiscussionOur results support the idea of considering the eight limbs functionally divided into two quadrupeds in series. The anterior was composed of the first two pairs of limbs, which have an explorative and steering purpose and the posterior was more involved in supporting the weight of the body. The mechanical work to move one unit of mass a unit distance is almost constant among the different species tested. However, spiders showed lower values than expected. Minimizing the mechanical work could help to limit metabolic energy expenditure that, in small animals, is relatively very high. However, energy recovery due to inverted pendulum mechanics only accounts for only a small fraction of the energy saved. Adhesive setae present in the tarsal, scopulae, and claw tufts could contribute in different ways during different moments of the step cycle, compensating for part of the energetic cost on gradients which could also help to maintain constant gait parameters. creator: Valentina Silva-Pereyra creator: C Gabriel Fábrica creator: Carlo M. Biancardi creator: Fernando Pérez-Miles uri: https://doi.org/10.7717/peerj.7748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Silva-Pereyra et al. title: Physiological responses of hydroponically-grown Japanese mint under nutrient deficiency link: https://peerj.com/articles/7751 last-modified: 2019-09-26 description: This research aims to determine growth and deficiency patterns as well as antioxidative potentials of Japanese mint (Mentha arvensis) hydroponically grown under limited macronutrients and micronutrients. The experiment was conducted for 60 days after transplanting in an evaporative greenhouse (avg temp = 28–30 °C, 60–65 %RH), using deep water culture technique. Plants were grown in nutrient solution consisting of complete Hoagland’s solution (CTRL), and nutrient solutions lacking one of the following macronutrients and micronutrients: nitrogen (-N), phosphorus (-P), potassium (-K), iron (-Fe), manganese (-Mn), and copper (-Cu). The deficiency symptoms, growth patterns, and stress response mechanism were followed. All treatments except for the CTRL induced deficiency symptoms and physiological changes. Macronutrient deprivation reduced growth determined by the morphological parameters while micronutrient omission had no effect except for no iron treatment. The result showed that potassium and iron deficiencies had foremost adversely effect on growth of Japanese mint. Under nutrient stress conditions, plant only gave antioxidative responses to phosphorus and potassium deficiencies. However, the negative plant-stress relationship was found for no iron treatment indicating the detoxification mode of plant for lacking of micronutrient. creator: Chananchida Janpen creator: Naruemon Kanthawang creator: Chaiartid Inkham creator: Fui Ying Tsan creator: Sarana Rose Sommano uri: https://doi.org/10.7717/peerj.7751 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Janpen et al. title: Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system link: https://peerj.com/articles/7762 last-modified: 2019-09-26 description: BackgroundChanges in gut microbiome are closely related to dietary and environment variations, and diurnal circle interventions impact on human metabolism and the microbiome. Changes in human gut microbiome and serum biochemical parameters during long-term isolation in a controlled ecological life support system (CELSS) are of great significance for maintaining the health of crewmembers. The Green Star 180 project performed an integrated study involving a four-person, 180-day duration assessment in a CELSS, during which variations in gut microbiome and the concentration of serum 25-hydroxyvitamin D, α-tocopherol, retinol and folic acid from the crewmembers were determined.ResultsEnergy intake and body mass index decreased during the experiment. A trade-off between Firmicutes and Bacteroidetes during the study period was observed. Dynamic variations in the two dominant genus Bacteroides and Prevotella indicated a variation of enterotypes. Both the evenness and richness of the fecal microbiome decreased during the isolation in the CELSS. Transition of diurnal circle from Earth to Mars increased the abundance of Fusobacteria phylum and decreased alpha diversity of the fecal microbiome. The levels of serum 25-hydroxyvitamin D in the CELSS were significantly lower than those outside the CELSS.ConclusionsThe unique isolation process in the CELSS led to a loss of alpha diversity and a transition of enterotypes between Bacteroides and Prevotella. Attention should therefore be paid to the transition of the diurnal circle and its effects on the gut microbiome during manned Mars explorations. In particular, serum 25-hydroxyvitamin D levels require monitoring under artificial light environments and during long-term space flight. Large-scale studies are required to further consolidate our findings. creator: Hai-Sheng Dong creator: Pu Chen creator: Yan-Bo Yu creator: Peng Zang creator: Zhao Wei uri: https://doi.org/10.7717/peerj.7762 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dong et al. title: The relationships between bilingual learning, willingness to study abroad and convergent creativity link: https://peerj.com/articles/7776 last-modified: 2019-09-26 description: Convergent creativity is a form of creative thinking that uses existing knowledge or traditional methods to analyze available information and generate an appropriate solution. The differences in the performance of participants in convergent creativity caused by bilingual learning is a popular research area in creativity. A final sample of 68 participants was asked to complete the remote associates test (RAT). The results indicate that a moderate positive correlation exists between bilingual learning and convergent creativity. Students who want to study abroad perform better on the RAT than those who do not, and this effect is mediated by second language proficiency. These findings suggest that improving students’ English proficiency and increasing their opportunities to study abroad may be effective ways to promoting convergent creativity. creator: Yuan Zhao creator: Yuan Yuan creator: Wangbing Shen creator: Chuanlin Zhu creator: Dianzhi Liu uri: https://doi.org/10.7717/peerj.7776 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Transcriptome association studies of neuropsychiatric traits in African Americans implicate PRMT7 in schizophrenia link: https://peerj.com/articles/7778 last-modified: 2019-09-26 description: In the past 15 years, genome-wide association studies (GWAS) have provided novel insight into the genetic architecture of various complex traits; however, this insight has been primarily focused on populations of European descent. This emphasis on European populations has led to individuals of recent African descent being grossly underrepresented in the study of genetics. With African Americans making up less than 2% of participants in neuropsychiatric GWAS, this discrepancy is magnified in diseases such as schizophrenia and bipolar disorder. In this study, we performed GWAS and the gene-based association method PrediXcan for schizophrenia (n = 2,256) and bipolar disorder (n = 1,019) in African American cohorts. In our PrediXcan analyses, we identified PRMT7 (P = 5.5 × 10−6, local false sign rate = 0.12) as significantly associated with schizophrenia following an adaptive shrinkage multiple testing adjustment. This association with schizophrenia was confirmed in the much larger, predominantly European, Psychiatric Genomics Consortium. In addition to the PRMT7 association with schizophrenia, we identified rs10168049 (P = 1.0 × 10−6) as a potential candidate locus for bipolar disorder with highly divergent allele frequencies across populations, highlighting the need for diversity in genetic studies. creator: Peter N. Fiorica creator: Heather E. Wheeler uri: https://doi.org/10.7717/peerj.7778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fiorica and Wheeler title: Comprehensive evaluation of fluroxypyr herbicide on physiological parameters of spring hybrid millet link: https://peerj.com/articles/7794 last-modified: 2019-09-26 description: Foxtail millet (Setaria italic L.) is an important food and fodder crop that is cultivated worldwide. Quantifying the effects of herbicides on foxtail millet is critical for safe herbicide application. In this study, we analyzed the effects of different fluroxypyr dosages on the growth parameters and physiological parametric of foxtail millet, that is, peroxidation characteristics, photosynthetic characteristics, and endogenous hormone production, by using multivariate statistical analysis. Indicators were screened via Fisher discriminant analysis, and the growth parameters, peroxidation characteristics, photosynthesis characteristics and endogenous hormones of foxtail millet at different fluroxypyr dosages were comprehensively evaluated by principal component analysis. On the basis of the results of principal component analysis, the cumulative contribution rate of the first two principal component factors was 93.72%. The first principal component, which explained 59.23% of total variance, was selected to represent the photosynthetic characteristics and endogenous hormones of foxtail millet. The second principal component, which explained 34.49% of total variance, represented the growth parameters of foxtail millet. According to the principal component analysis, the indexes were simplified into comprehensive index Z, and the mathematical model of comprehensive index Z was set as F = 0.592Z1 + 0.345Z2. The results showed that the comprehensive evaluation score of fluroxypyr at moderate concentrations was higher than at high concentrations. Consequently, one L (active ingredient, ai) ha−1 fluroxypyr exerted minimal effects on growth parameters, oxidase activity, photosynthetic activity, and endogenous hormones, and had highest value of comprehensive evaluation, which had efficient and safe benefits in foxtail millet field. creator: Meijun Guo creator: Jie Shen creator: Xi-e Song creator: Shuqi Dong creator: Yinyuan Wen creator: Xiangyang Yuan creator: Pingyi Guo uri: https://doi.org/10.7717/peerj.7794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: The rediscovery of the rare Vietnamese endemic Eriophorum scabriculme redefines generic limits in the Scirpo-Caricoid Clade (Cyperaceae) link: https://peerj.com/articles/7538 last-modified: 2019-09-25 description: For those familiar with boreal bogs and wet tundra, species of Eriophorum (“the cotton grasses”) will undoubtedly represent some of the most striking and memorable taxa they have encountered. This small genus of 20 Holarctic sedge species (Cyperaceae) is remarkable because its inflorescences produce large, brilliantly white to rusty-red cottony masses when its flowers develop a perianth of highly elongated bristles after anthesis. In this study, we document the rediscovery of Eriophorum scabriculme, a narrow Vietnamese endemic known from only two collections made approximately 7 km apart near Sa Pa in Lào Cai Province over 75 years ago. Using plastid DNA sequences (matK, ndhF), embryology, and morphology, we test whether E. scabriculme is aligned within the Scirpo-Caricoid Clade (genus Khaosokia and tribes Cariceae, Dulichieae, Scirpeae, and Sumatroscirpeae) or the Ficinia Clade (Cypereae), and we determine whether its unique character combinations (≥10 elongated bristles, reduced sheathing basal leaves, 1–4 spikelets) could be evidence for a new genus or simply mark it as an unusual species within currently recognised genera. In addition, we document the discovery of seven new populations, and we extend its range westward to Lai Châu Province and southward in Lào Cai Province by more than 47 km. Our results demonstrate that Eriophorum scabriculme is best treated in the genus Trichophorum, thus re-circumscribing both genera and their limits with Scirpus s.str. In addition, we emend the description of Trichophorum scabriculme (Beetle) J.R.Starr, Lév.-Bourret & B.A. Ford, provide the first pictures and accurate illustration of the species, and assess its conservation status in Vietnam (VU, Vulnerable). Our study corroborates the fact that in such a diverse and taxonomically difficult family like the sedges, conspicuous characters like highly elongated bristles may be useful for dividing diversity, but they are no guarantee that the groups they mark are natural. creator: Julian R. Starr creator: Étienne Léveillé-Bourret creator: Vũ Anh Tài creator: Nguyê˜n Thị Kim Thanh creator: Bruce A. Ford uri: https://doi.org/10.7717/peerj.7538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Starr et al. title: Cellular accumulation and cytotoxic effects of zinc oxide nanoparticles in microalga Haematococcus pluvialis link: https://peerj.com/articles/7582 last-modified: 2019-09-25 description: BackgroundZinc oxide nanoparticles (ZnO NPs) are widely used in household and cosmetic products which imply an increased releasing of these particles into the environment, especially aquatic ecosystems, resulting in the need of assessing the potential toxic effects of ZnO NPS on the aquatic organisms, particularly on microalgae which form the base for food chain of aquatic biota. The present study has investigated the dose- and time-dependent cellular accumulation and the corresponding cytotoxic effects of increasing concentrations of ZnO NPs from 10–200 μg/mL on microalga Haematococcus pluvialis at an interval of 24 h for 96 h.MethodsThe scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX) was used to qualitatively detect the cellular accumulation of ZnO NPs in algal cells, while inductively coupled plasma optical emission spectrometry (ICP OES) was performed to quantify the cell associated-zinc in algal cells. The percentage of cell death, reduction in algal biomass, and loss in photosynthetic pigments were measured to investigate the cytotoxic effects of ZnO NPs on H. pluvialis. Extracellular and intracellular changes in algal cells resulted from the treatment of ZnO NPs were demonstrated through optical, scanning, and transmission electron microscopic studies.ResultsSEM-EDX spectrum evidenced the accumulation of ZnO NPs in algal biomass and ICP OES results reported a significant (p < 0.05) dose- and time-dependent accumulation of zinc in algal cells from 24 h for all the tested concentrations of ZnO NPs (10–200 μg/mL). Further, the study showed a significant (p < 0.05) dose- and time-dependent growth inhibition of H. pluvialis from 72 h at 10–200 μg/mL of ZnO NPs. The morphological examinations revealed substantial surface and intracellular damages in algal cells due to the treatment of ZnO NPs.DiscussionThe present study reported the significant cellular accumulation of ZnO NPs in algal cells and the corresponding cytotoxic effects of ZnO NPs on H. pluvialis through the considerable reduction in algal cell viability, biomass, and photosynthetic pigments together with surface and intracellular damages. creator: Sinouvassane Djearamane creator: Yang Mooi Lim creator: Ling Shing Wong creator: Poh Foong Lee uri: https://doi.org/10.7717/peerj.7582 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Djearamane et al. title: The effects of growth rate and biomechanical loading on bone laminarity within the emu skeleton link: https://peerj.com/articles/7616 last-modified: 2019-09-25 description: The orientation of vascular canals in primary bone may reflect differences in growth rate and/or adaptation to biomechanical loads. Previous studies link specific canal orientations to bone growth rates, but results between different taxa are contradictory. Circumferential vascular canals (forming laminar bone) have been hypothesized to reflect either (or both) rapid growth rate or locomotion-induced torsional loading. Previous work on the hindlimb biomechanics in the emu shows that the femur and tibiotarsus experience large shear strains, likely resulting from torsional loads that increase through ontogeny. Here, we test how growth rate and biomechanical loading affect bone laminarity in wing and hindlimb elements from growing emu (2–60 wks). If laminar bone is an adaptation to torsion-induced shear strains, it should increase from juveniles to adults. Alternatively, if bone laminarity reflects rapid growth, as has been shown previously in emu, it should be abundant in fast-growing juveniles and decrease with age. Transverse mid-shaft histological sections from the limb bones (femur, tibiotarsus, humerus, ulna, and radius) were prepared and imaged. Growth rates were measured using fluorescent bone labels. Vascular canal orientation was quantified using laminarity index (proportion of circumferential canals). Principal components analysis was performed to convert highly correlated variables (i.e., mass, age, growth rate, and shear strain) into principal components. Random-intercept beta regression modeling determined which principal components best explained laminarity. The fastest growth rates were found in young individuals for all five skeletal elements. Maximum growth rate did not coincide with peak laminarity. Instead, in the femur and tibiotarsus, elevated laminarity is strongly correlated with adult features such as large size, old age, and modest growth rate. This result is contrary to predictions made based on a previous study of emu but is consistent with results observed in some other avian species (penguin, chicken). Shear strain in the caudal octant of the femur and tibiotarsus is positively correlated with laminarity but has a weaker effect on laminarity relative to mass, age, and growth rate. Laminarity in the wing elements is variable and does not correlate with ontogenetic factors (including mass, age, and growth rate). Its presence may relate to relaxed developmental canalization or a retained ancestral feature. In conclusion, ontogeny (including growth rate) is the dominant influence on vascular canal orientation at least in the hindlimb of the emu. creator: Amanda L. Kuehn creator: Andrew H. Lee creator: Russell P. Main creator: Erin L.R. Simons uri: https://doi.org/10.7717/peerj.7616 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kuehn et al. title: Bar-HRM: a reliable and fast method for species identification of ginseng (Panax ginseng, Panax notoginseng, Talinum paniculatum and Phytolacca Americana) link: https://peerj.com/articles/7660 last-modified: 2019-09-25 description: BackgroundKorean ginseng has long been famous and is one of the most well known forms of ginseng. The root of plants in the genus Panax is commonly recognized as ginseng. Different Panax species of ginseng root have been used as treatments. Although many other herbs are called ginseng, they do not contain the active compounds of ginsenosides. In Thailand, we have Thai ginseng which is of course not one of Panax species. Thai ginseng is the root from Talinum paniculatum and, due to its morphological root similarity, it is almost impossible to differentiate between them. Also, another plant species, Phytollacca americana, has significantly similar root morphology to real ginseng but its seeds and root are poisonous. Misunderstanding what true ginseng is compared to others could endanger lives and cause financial loss by buying inferior products.MethodsDNA barcoding combination with High Resolution Melting (called Bar-HRM) was used for species discrimination of the Panax ginseng and others. Five regions included ITS2, matK, psbA-trnH and rbcL were evaluated in the analyses.ResultsThe ITS2 region was found to be the most suitable primers for the analysis. The melting profile from the HRM analyses using the chosen ITS2 primers showed that Korean ginseng (Panax ginseng) could be discriminated from other Penax species. Also, other ginseng species with morphological similarity could be easily distinguished from the true ginseng. The developed Bar-HRM method poses a great potential in ginseng species discrimination and thus could be also useful in ginseng authentication. creator: Maslin Osathanunkul creator: Panagiotis Madesis uri: https://doi.org/10.7717/peerj.7660 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Osathanunkul and Madesis title: Effect of reduced pH on physiology and shell integrity of juvenile Haliotis iris (pāua) from New Zealand link: https://peerj.com/articles/7670 last-modified: 2019-09-25 description: The New Zealand pāua or black footed abalone, Haliotis iris, is one of many mollusc species at potential risk from ocean acidification and warming. To investigate possible impacts, juvenile pāua (~24 mm shell length) were grown for 4 months in seawater pH/pCO2 conditions projected for 2100. End of century seawater projections (pHT 7.66/pCO2 ~1,000 μatm) were contrasted with local ambient conditions (pHT 8.00/pCO2 ~400 μatm) at two typical temperatures (13 and 15 °C). We used a combination of methods (morphometric, scanning electron microscopy, X-ray diffraction) to investigate effects on juvenile survival and growth, as well as shell mineralogy and integrity. Lowered pH did not affect survival, growth rate or condition, but animals grew significantly faster at the higher temperature. Juvenile pāua were able to biomineralise their inner nacreous aragonite layer and their outer prismatic calcite layer under end-of-century pH conditions, at both temperatures, and carbonate composition was not affected. There was some thickening of the nacre layer in the newly deposited shell with reduced pH and also at the higher temperature. Most obvious was post-depositional alteration of the shell under lowered pH: the prismatic calcite layer was thinner, and there was greater etching of the external shell surface; this dissolution was greater at the higher temperature. These results demonstrate the importance of even a small (2 °C) difference in temperature on growth and shell characteristics, and on modifying the effects at lowered pH. Projected CO2-related changes may affect shell quality of this iconic New Zealand mollusc through etching (dissolution) and thinning, with potential implications for resilience to physical stresses such as predation and wave action. creator: Vonda J. Cummings creator: Abigail M. Smith creator: Peter M. Marriott creator: Bryce A. Peebles creator: N. Jane Halliday uri: https://doi.org/10.7717/peerj.7670 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cummings et al. title: Cloning of a new HSP70 gene from western flowerthrips, Frankliniella occidentalis, and expression patterns during thermal stress link: https://peerj.com/articles/7687 last-modified: 2019-09-25 description: Frankliniella occidentalis (Pergande) is an invasive pest that endangers a wide variety of horticultural and agronomic crops. HSP70 is the most important member of the heat shock protein (HSP) family and plays an important role in insect thermal tolerance. In this study, a new gene encoding HSP70 from F. occidentalis, Fohsp706, was selected from the F. occidentalis transcriptome exposed to thermal stress (40 °C) and cloned by RT-PCR and RACE. Further characterization indicated that Fohsp706 localizes to the cytoplasm and does not contain introns. Quantitative real-time reverse transcriptase PCR indicated that Fohsp706 expression was significantly up-regulated by thermal stress; furthermore, there were significant differences in Fohsp706 expression in adults and second instar nymphs after heat stress. Our results indicated that Fohsp706 contributes to thermotolerance in F. occidentalis and provides another example of how this pest adapts to unfavorable environmental conditions. creator: Xiao-xiang Zhang creator: Jing Qin creator: Jia-Wen Yuan creator: Ming-Xing Lu creator: Yu-Zhou Du uri: https://doi.org/10.7717/peerj.7687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: The interplay between cognitive tasks and vision for upright posture balance in adolescents link: https://peerj.com/articles/7693 last-modified: 2019-09-25 description: BackgroundThe control of an upright stance in humans is important in medicine, psychology, and physiology. The maintenance of upright stance balance depends not only on sensory information from proprioceptive, vestibular, cutaneous, and visual sources but also on cognitive resources. The present study investigated the effects of cognitive tasks while standing with eyes open on upright stance balance in adolescents. We hypothesized that performing a cognitive task while standing with eyes open would increase body sway among these adolescents and that the upright posture would thus become less stable.MethodsA static balance assessment system comprising a force platform connected to a computer was used to evaluate the stability of the upright stance among 21 healthy adolescents under six conditions: no cognitive task, a relatively easy cognitive task, or the same cognitive task made more difficult, with each task being performed while the eyes were open and again while the eyes were closed. The participants performed mental calculations as fast as possible by subtracting either 3 or 18 from a random three-digit number continuously, for the simple cognitive task or the difficult cognitive task, respectively. Each calculation was completed within 10 s. The evaluation indexes used to measure upright posture stability were the root mean square (RMS) of the total body sway in the mediolateral and anteroposterior directions, the mean velocity (MV) value of the total body sway, and the Romberg quotient (RQ) of these values.ResultsThe RMS (p < 0.01) and MV (p < 0.01) values of the upright posture sway were lower when participants performed no cognitive task and their eyes were open than when their eyes were closed. When their eyes were open, compared with no cognitive task, the values of the measures evaluating upright posture sway were higher, meaning the stance was less stable, while performing either the simple or the more difficult cognitive task (RMS: simple task, p < 0.01; difficult task, p < 0.05; MV: simple task, p < 0.01; difficult task, p < 0.01) although no significant differences were detected for the RMS or MV values between the simple and more difficult cognitive tasks. The RQs for both the RMS and the total MV values of the upright posture sway during performance of the difficult cognitive task were significantly lower than when the participants performed no task.ConclusionPerformance of a cognitive task significantly reduced the upright posture balance in adolescents during eyes open although increased task difficulty did not show a greater effect. The interference between the performance of a cognitive task and the visual control of an upright stance may be attributable in part to cognitive and visual processing streams competing for common central resources, consistent with the Multiple Resource Theory of information processing. creator: Hai-Jiang Meng creator: Shan-Shan Luo creator: Yuan-Gang Wang uri: https://doi.org/10.7717/peerj.7693 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Meng et al. title: Soil warming increases soil temperature sensitivity in subtropical Forests of SW China link: https://peerj.com/articles/7721 last-modified: 2019-09-25 description: BackgroundSoil respiration (RS) plays an important role in the concentration of atmospheric CO2 and thus in global climate patterns. Due to the feedback between RS and climate, it is important to investigate RS responses to climate warming.MethodsA soil warming experiment was conducted to explore RS responses and temperature sensitivity (Q10) to climate warming in subtropical forests in Southwestern China, and infrared radiators were used to simulate climate warming.ResultsWarming treatment increased the soil temperature and RS value by 1.4 °C and 7.3%, respectively, and decreased the soil water level by 4.2% (%/%). Both one- and two-factor regressions showed that warming increased the Q10 values by 89.1% and 67.4%, respectively. The effects of water on Q10show a parabolic relationship to the soil water sensitivity coefficient. Both RS and Q10 show no acclimation to climate warming, suggesting that global warming will accelerate soil carbon release. creator: Chaoxiang Yuan creator: Guiqing Zhu creator: Shuangna Yang creator: Gang Xu creator: Yingyun Li creator: Hede Gong creator: Chuansheng Wu uri: https://doi.org/10.7717/peerj.7721 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yuan et al. title: Brodifacoum does not modulate human cannabinoid receptor-mediated hyperpolarization of AtT20 cells or inhibition of adenylyl cyclase in HEK 293 cells link: https://peerj.com/articles/7733 last-modified: 2019-09-25 description: BackgroundSynthetic cannabinoids are a commonly used class of recreational drugs that can have significant adverse effects. There have been sporadic reports of co-consumption of illicit drugs with rodenticides such as warfarin and brodifacoum (BFC) over the past 20 years but recently, hundreds of people have been reported to have been poisoned with a mixture of synthetic cannabinoids and BFC. We have sought to establish whether BFC directly affects cannabinoid receptors, or their activation by the synthetic cannabinoid CP55940 or the phytocannabinoid Δ9-tetrahydrocannabinol (Δ9-THC).MethodsThe effects of BFC on the hyperpolarization of wild type AtT20 cells, or AtT20 cells stably expressing human CB1- or CB2- receptors, were studied using a fluorescent assay of membrane potential. The effect of BFC on CB1- and CB2-mediated inhibition of forskolin-stimulated adenylyl cyclase (AC) activation was measured using a BRET assay of cAMP levels in HEK 293 cells stably expressing human CB1 or CB2.ResultsBFC did not activate CB1 or CB2 receptors, or affect the hyperpolarization of wild type AtT20 cells produced by somatostatin. BFC (1 µM) did not affect the hyperpolarization of AtT20-CB1 or AtT20-CB2 cells produced by CP55940 or Δ9-THC. BFC (1 µM) did not affect the inhibition of forskolin-stimulated AC activity by CP55940 in HEK 293 cells expressing CB1 or CB2. BFC (1 µM) also failed to affect the desensitization of CB1 and CB2 signaling produced by prolonged (30 min) application of CP55940 or Δ9-THC to AtT20 cells.DiscussionBFC is not a cannabinoid receptor agonist, and appeared not to affect cannabinoid receptor activation. Our data suggests there is no pharmacodynamic rationale for mixing BFC with synthetic cannabinoids; however, it does not speak to whether BFC may affect synthetic cannabinoid metabolism or biodistribution. The reasons underlying the mixing of BFC with synthetic cannabinoids are unknown, and it remains to be established whether the “contamination” was deliberate or accidental. However, the consequences for people who ingested the mixture were often serious, and sometimes fatal, but this seems unlikely to be due to BFC action at cannabinoid receptors. creator: Shivani Sachdev creator: Rochelle Boyd creator: Natasha L. Grimsey creator: Marina Santiago creator: Mark Connor uri: https://doi.org/10.7717/peerj.7733 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sachdev et al. title: Identification of genes encoding ALMT and MATE transporters as candidate aluminum tolerance genes from a typical acid soil plant, Psychotria rubra (Rubiaceae) link: https://peerj.com/articles/7739 last-modified: 2019-09-25 description: To understand how tropical plants have adapted to acid soils, we analyzed the transcriptome of seedlings of Psychotria rubra, a typical species found on acid soils. Using RNA-seq, we identified 22,798 genes, including several encoding proteins of the Al3+-activated malate transporter (ALMT) and multidrug and toxic compound extrusion (MATE) families. Molecular phylogenetic analysis of ALMTs and MATEs revealed the grouping of those from P. rubra, which may be useful to select targets for elucidating the molecular basis of P. rubra adaptation to acid soils in the future. The transcriptome datasets obtained in this study would help us to further understand the physiological and ecological aspects of soil adaptation of Psychotria species. creator: Akira Iguchi creator: Kazutsuka Sanmiya creator: Kenta Watanabe uri: https://doi.org/10.7717/peerj.7739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Iguchi et al. title: Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.) link: https://peerj.com/articles/7750 last-modified: 2019-09-25 description: BackgroundStarch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism, determining amylopectin structure.MethodsFull length coding sequences (CDS) of SBE genes were cloned using reverse transcription PCR (RT-PCR) technology, and neighbor-joining (NJ) tree was used for phylogenetic analysis. Single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyze the spatial and temporal expression of NnSBE genes. The effect of NnSBE genes on amylopectin’s fine structures was explored using affinity and the enzyme activity analysis of two isoforms in amylopectin and amylose.ResultsIn this study, two SBE family genes, NnSBEI and NnSBEIII, were identified in lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis sorted NnSBEI into SBE family B and NnSBEIII into SBE family A. UPGMA phylogenetic tree divided 45 individuals of lotus into three classes. The homozygous haplotype (A G G A G) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in the middle of the development stage, while NnSBEI increased in the mid-late developmental stage. The different affinity activity of the two isozymes binding amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity.DiscussionGenetic diversity showed that NnSBE genes received artificial selection during the process of cultivation and domestication in lotus seeds. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes were related to the chain length of amylopectin. creator: Fenglin Zhu creator: Han Sun creator: Ying Diao creator: Xingwen Zheng creator: Keqiang Xie creator: Zhongli Hu uri: https://doi.org/10.7717/peerj.7750 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhu et al. title: Cloning expression and immunogenicity analysis of inhibin gene in Ye Mule Aries sheep link: https://peerj.com/articles/7761 last-modified: 2019-09-25 description: BackgroundYe Mule Aries sheep is one of the most important sheep breeds in Xinjiang, China. This breed is well adapted to harsh environmental conditions and displays strong disease resistance, fast growth, and high cold tolerance. To analyze the clonal expression and immunogenicity of the Ye Mule Aries sheep inhibin gene, total RNA was extracted from sheep ovarian tissue and used as a template to generate a eukaryotic expression vector and study inhibin immunogenicity.MethodsPrimers were designed to amplify the inhibin A gene via polymerase chain reaction and the amplified product was cloned between the ScalI and EcoRI restriction sites of the expression vector pEGFP-N1 to construct a recombinant plasmid, pEGFP-INHα. Following the validation of successful cloning, the pEGFP-INHα plasmid was transfected into BHK cells to verify expression in eukaryotes and subsequently utilized as an antigen in rabbits. Rabbits were tested for anti-inhibin antibodies and serum follicle-stimulating hormone (FSH) concentrations.ResultsThe analysis of the INHα gene sequence revealed that INHα is 1109 bp long and is translated to an approximately 40 KDa protein. Bioinformatics approach indicated that the INHα gene is highly conserved between organisms. Immunization with the eukaryotic expression vector, pEGFP-INHα, which expresses the INHα gene elicited immune response and generatigeneration on of anti-INHα antibody. The antibody had a significant regulatory effect on the serum concentration of FSH in rabbits and led to higher levels of FSH, indicating increased ovary function.ConclusionsThe present work resulted in a successful construction of eukaryotic expression plasmid pEGFP-INHα and verified the immunogenicity of this highly conserved protein. Further, the expression of pEGFP-INHα was shown to have a significant impact on the secretion of FSH, indicating a potential regulatory role in ovarian function. In conclusion, our current findings can serve as a working model for studying the effect of INHα on the breeding performance of Ye Mule Aries sheep, providing a novel strategy to improve their reproduction rates. creator: Zengwen Huang creator: Juan Zhang creator: WuReliHazi Hazihan creator: Zhengyun Cai creator: Guosheng Xin creator: Xiaofang Feng creator: Yaling Gu uri: https://doi.org/10.7717/peerj.7761 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huang et al. title: Human disturbance caused stronger influences on global vegetation change than climate change link: https://peerj.com/articles/7763 last-modified: 2019-09-25 description: Global vegetation distribution has been influenced by human disturbance and climate change. The past vegetation changes were studied in numerous studies while few studies had addressed the relative contributions of human disturbance and climate change on vegetation change. To separate the influences of human disturbance and climate change on the vegetation changes, we compared the existing vegetation which indicates the vegetation distribution under human influences with the potential vegetation which reflects the vegetation distribution without human influences. The results showed that climate-induced vegetation changes only occurred in a few grid cells from the period 1982–1996 to the period 1997–2013. Human-induced vegetation changes occurred worldwide, except in the polar and desert regions. About 3% of total vegetation distribution was transformed by human activities from the period 1982–1996 to the period 1997–2013. Human disturbances caused stronger damage to global vegetation change than climate change. Our results indicated that the regions where vegetation experienced both human disturbance and climate change are eco-fragile regions. creator: Xianliang Zhang creator: Xuanrui Huang uri: https://doi.org/10.7717/peerj.7763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang and Huang title: Development of a highly sensitive magneto-enzyme lateral flow immunoassay for dengue NS1 detection link: https://peerj.com/articles/7779 last-modified: 2019-09-25 description: BackgroundDengue infection represents a global health issue of growing importance. Dengue non-structural protein 1 (NS1) plays a central role in the early detection of the disease. The most common method for NS1 detection is testing by lateral flow immunoassays (LFIAs) with varying sensitivity. In this study, we present a highly sensitive magneto-enzyme LFIA for prompt diagnosis of dengue.MethodsWe have demonstrated the development of a magneto-enzyme LFIA combining super-paramagnetic nanoparticles as labels and Biotin–Streptavidin signal amplification strategy to detect dengue NS1. Factors affecting the test performance including antibody pair, super-paramagnetic nanoparticle size, nitrocellulose membrane type, amounts of detection and capture antibodies, and amounts of Streptavidin-polyHRP were optimized. Analytical sensitivity and cross-reactivity were determined. Clinical performance of the novel assay was evaluated using a panel of 120 clinical sera.ResultsThis newly developed assay could detect NS1 of all four serotypes of dengue virus (DENV). The limit of detection (LOD) was found to be as low as 0.25 ng ml−1 for DENV-1 and DENV-3, 0.1 ng ml−1 for DENV-2, and 1.0 ng ml−1 for DENV-4. The LOD for DENV-2 was a 50-fold improvement over the best values previously reported. There was an absence of cross-reactivity with Zika NS1, Hepatitis B virus, Hepatitis C virus, and Japanese encephalitis virus. The sensitivity and specificity of the novel assay were 100% when tested on clinical samples.ConclusionsWe have successfully developed a magneto-enzyme LFIA, allowing rapid and highly sensitive detection of dengue NS1, which is essential for proper management of patients infected with DENV. creator: Tien V. Tran creator: Ba V. Nguyen creator: Thao T.P. Nguyen creator: Tung T. Tran creator: Khanh G. Pham creator: Quang B. Le creator: Binh N. Do creator: Hung N. Pham creator: Chuyen V. Nguyen creator: Duong P.H. Dinh creator: Van T. Ha creator: Trang H.T. Doan creator: Hoa Q. Le uri: https://doi.org/10.7717/peerj.7779 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tran et al. title: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics link: https://peerj.com/articles/7558 last-modified: 2019-09-24 description: BackgroundChloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.MethodsMitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.ResultsThe sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane’s female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed.ConclusionTranscript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars. creator: Dyfed Lloyd Evans creator: Thandekile Thandiwe Hlongwane creator: Shailesh V. Joshi creator: Diego M. Riaño Pachón uri: https://doi.org/10.7717/peerj.7558 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lloyd Evans et al. title: Tanaella quintanai, a new deep-water tanaellid (Crustacea: Peracarida: Tanaidacea) from the Colombian Caribbean Coast, with a key to the species of the genus Tanaella Norman & Stebbing, 1886 link: https://peerj.com/articles/7571 last-modified: 2019-09-24 description: A new tanaidacean, Tanaella quintanai sp. nov., is described based on specimens collected from depths of 1,598 to 2,853 m during 2014–2015. The new species appears to be most closely related to the western Atlantic species, T. kroyeri and T. mclellandi. Tanaella quintanai can be separated from the two former, as well as from the other members of the genus by a combination of characters, including (1) a labium with apical lobe bearing one blunt seta (2) a cheliped with the inner margin of the dactylus bearing a sub-proximal bipinnate seta, (3) pereopods 1−3 with basis having sub-dorsoproximal and sub-ventroproximal margins setulose, (4) pereopods 4−6 with basis having ventroproximal margin setulose, (5) pereopods 4−6 with unguis bearing two parallel rows of small setules, and (6) a pleotelson as long as pleonites 1–5 combined. A key separating the currently recognized species of Tanaella is presented. creator: Andrés G. Morales-Núñez creator: Néstor E. Ardila uri: https://doi.org/10.7717/peerj.7571 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Morales-Núñez and Ardila title: In situ growth and bioerosion rates of Lophelia pertusa in a Norwegian fjord and open shelf cold-water coral habitat link: https://peerj.com/articles/7586 last-modified: 2019-09-24 description: Coral reef resilience depends on the balance between carbonate precipitation, leading to reef growth, and carbonate degradation, for example, through bioerosion. Changes in environmental conditions are likely to affect the two processes differently, thereby shifting the balance between reef growth and degradation. In cold-water corals estimates of accretion-erosion processes in their natural habitat are scarce and solely live coral growth rates were studied with regard to future environmental changes in the laboratory so far, limiting our ability to assess the potential of cold-water coral reef ecosystems to cope with environmental changes. In the present study, growth rates of the two predominant colour morphotypes of live Lophelia pertusa as well as bioerosion rates of dead coral framework were assessed in different environmental settings in Norwegian cold-water coral reefs in a 1-year in situ experiment. Net growth (in weight gain and linear extension) of live L. pertusa was in the lower range of previous estimates and did not significantly differ between inshore (fjord) and offshore (open shelf) habitats. However, slightly higher net growth rates were obtained inshore. Bioerosion rates were significantly higher on-reef in the fjord compared to off-reef deployments in- and offshore. Besides, on-reef coral fragments yielded a broader range of individual growth and bioerosion rates, indicating higher turnover in live reef structures than off-reef with regard to accretion–bioerosion processes. Moreover, if the higher variation in growth rates represents a greater variance in (genetic) adaptations to natural environmental variability in the fjord, inshore reefs could possibly benefit under future ocean change compared to offshore reefs. Although not significantly different due to high variances between replicates, growth rates of orange branches were consistently higher at all sites, while mortality was statistically significantly lower, potentially indicating higher stress-resistance than the less pigmented white phenotype. Comparing the here measured rates of net accretion of live corals (regardless of colour morphotype) with net erosion of dead coral framework gives a first estimate of the dimensions of both processes in natural cold-water coral habitats, indicating that calcium carbonate loss through bioerosion amounts to one fifth to one sixth of the production rates by coral calcification (disregarding accretion processes of other organisms and proportion of live and dead coral framework in a reef). With regard to likely accelerating bioerosion and diminishing growth rates of corals under ocean acidification, the balance of reef accretion and degradation may be shifted towards higher biogenic dissolution in the future. creator: Janina V. Büscher creator: Max Wisshak creator: Armin U. Form creator: Jürgen Titschack creator: Kerstin Nachtigall creator: Ulf Riebesell uri: https://doi.org/10.7717/peerj.7586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Büscher et al. title: Estimating flowering transition dates from status-based phenological observations: a test of methods link: https://peerj.com/articles/7720 last-modified: 2019-09-24 description: The scale of phenological research has expanded due to the digitization of herbarium specimens and volunteer based contributions. These data are status-based, representing the presence or absence of a specific phenophase. Modelling the progress of plant dormancy to growth and reproduction and back to dormancy requires estimating the transition dates from these status-based observations. There are several methods available for this ranging from statistical moments using the day of year to newly introduced methods using concepts from other fields. Comparing the proficiency of different estimators is difficult since true transition dates are rarely known. Here I use a recently released dataset of in-situ flowering observations of the perennial forb Echinacea angustifolia. In this dataset, due to high sampling frequency and unique physiology, the transition dates of onset, peak, and end of flowering are known to within 3 days. I used a Monte Carlo analysis to test eight different estimators across two scales using a range of sample sizes and proportion of flowering presence observations. I evaluated the estimators accuracy in predicting the onset, peak, and end of flowering at the population level, and predicting onset and end of flowering for individual plants. Overall, a method using a Weibull distribution performed the best for population level onset and end estimates, but other estimators may be more appropriate when there is a large amount of absence observations relative to presence observations. For individual estimates a method using the midway point between the first flower presence and most prior flower absence, within 7 days, is the best option as long as the restriction does not limit the final sample size. Otherwise, the Weibull method is adequate for individual estimates as well. These methods allow practitioners to effectively utilize the large amount of status-based phenological observations currently available. creator: Shawn D. Taylor uri: https://doi.org/10.7717/peerj.7720 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Taylor title: ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics link: https://peerj.com/articles/7729 last-modified: 2019-09-24 description: Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed. creator: Marco Cacciabue creator: Anabella Currá creator: Maria I. Gismondi uri: https://doi.org/10.7717/peerj.7729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cacciabue et al. title: Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats link: https://peerj.com/articles/7743 last-modified: 2019-09-24 description: The hypothalamus has an integral role in energy homeostasis regulation, and its dysfunctions lead to the development of type 2 diabetes (T2D). Physical activity positively affects the prevention and treatment of T2D. However, there is not much information on the adaptive mechanisms of the hypothalamus. In this study, RNA sequencing was used to determine how acute exercise affects hypothalamic transcriptome from both type 2 diabetic Goto-Kakizaki (GK) and control Wistar rats with or without a single session of running (15 m/min for 60 min). Through pairwise comparisons, we identified 957 differentially expressed genes (DEGs), of which 726, 197, and 98 genes were found between GK and Wistar, exercised GK and GK, and exercised Wistar and Wistar, respectively. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that lipid metabolism-related terms and pathways were enriched in GK and exercised GK rats, and nervous system related terms and pathways were enriched in exercised GK and Wistar rats. Furthermore, 45 DEGs were associated with T2D and related phenotypes according to the annotations in the Rat Genome Database. Among these 45 DEGs, several genes (Plin2, Cd36, Lpl, Wfs1, Cck) related to lipid metabolism or the nervous system are associated with the exercise-induced benefits in the hypothalamus of GK rats. Our findings might assist in identifying potential therapeutic targets for T2D prevention and treatment. creator: Shuying Fu creator: Yuhuan Meng creator: Shudai Lin creator: Wenlu Zhang creator: Yuting He creator: Lizhen Huang creator: Hongli Du uri: https://doi.org/10.7717/peerj.7743 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fu et al. title: Characterizing gene tree conflict in plastome-inferred phylogenies link: https://peerj.com/articles/7747 last-modified: 2019-09-24 description: Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes. creator: Joseph F. Walker creator: Nathanael Walker-Hale creator: Oscar M. Vargas creator: Drew A. Larson creator: Gregory W. Stull uri: https://doi.org/10.7717/peerj.7747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Walker et al. title: Efficacy of Paclitaxel plus TS1 against previously treated EGFR mutated non-small cell lung cancer link: https://peerj.com/articles/7767 last-modified: 2019-09-24 description: BackgroundLater line chemotherapy (≥2nd lines) such as Docetaxel or immunotherapy is frequently used. As the life expectancy of lung cancer patients is getting longer, we need to provide more treatment options. Other treatment options are not well documented except for Doxetaxel and immunotherapy. Therefore, the efficacy of paclitaxel plus TS1 (TTS1) is warranted.MethodsWe retrospectively reviewed the chart records of our non-small cell lung cancer patients who were treated between 2010 and 2013. Clinical characteristics, type of tumor, EGFR mutation status, and treatment response to first-line EGFR-TKI therapy and efficacy of TTS1, were collected.ResultsTwenty eight patients were enrolled in this study. No patients archived complete response and seven patients had partial response (ORR: 25%). The disease control rate was 60.7% (17/28). The progression free survival (PFS) was 4.0 months and overall survival (OS) was 15.8 months. Of them, 17 had EGFR mutations, eight EGFR wild type, and three were unknown EGFR status. After TTS1 treatment, patients with EGFR mutations had better PFS (4.9 months vs. 1.8 months) and OS (15.5 months vs. 7.2 months) compared with those of EGFR wild type.ConclusionsTTS1 are effective later line chemotherapy, especially in tumor EGFR mutated patients. Paclitaxel plus TS1 is another treatment of choice for NSCLC patients before a more effective treatment strategy is found. creator: Yen-Han Tseng creator: Jen-Fu Shih creator: Heng-Sheng Chao creator: Yuh-Min Chen uri: https://doi.org/10.7717/peerj.7767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tseng et al. title: Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth link: https://peerj.com/articles/7445 last-modified: 2019-09-23 description: Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N2-fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N2-fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N2-fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis, Fusarium graminearum, Gibberella zeae, Fusarium solani, Colletotrichum gossypii and Alternaria longipes. 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture. creator: Xiaomeng Liu creator: Qin Li creator: Yongbin Li creator: Guohua Guan creator: Sanfeng Chen uri: https://doi.org/10.7717/peerj.7445 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Evaluation of the effects of the green nanoparticles zinc oxide on monosodium glutamate-induced toxicity in the brain of rats link: https://peerj.com/articles/7460 last-modified: 2019-09-23 description: BackgroundMonosodium glutamate (MSG) is used extensively as a food additive in the diets of many countries around the world.Aim of the studyOur aim was to determine the effects of green zinc oxide nanoparticles on MSG-induced oxidative damage, neurotransmitter changes, and histopathological alternation in the cerebral cortexes of rats.MethodsMSG was administered orally at two doses of 6 and 17.5 mg/kg body weight. The higher dose was associated with a significant decline in the activities of superoxide dismutase, catalase, and glutathione peroxidase, as well as the levels of brain-derived neurotrophic factor (BDNF) and glutathione (GSH) in the cerebral cortex of rats.ResultsThe administration of zinc oxide nanoparticles/green tea extract (ZnO NPs/GTE) to 17.5 mg/kg MSG-treated rats was associated with significant improvements in all parameters previously shown to be altered by MSG. The higher dose of MSG induced significant histopathological variation in brain tissue. Co-treatment of rats with ZnO NPs/GTE and MSG-HD inhibited the reduction of neurotransmitters and acetylcholinesterase by MSG.ConclusionsZnO NPs/GTE have the potential to protect against oxidative stress and neuronal necrosis induced by MSG-HD. ZnO NPs/GTE conferred a greater benefit than the control treatment or ZnO NPs or GTE administered separately. creator: Reham Z. Hamza creator: Fawziah A. Al-Salmi creator: Nahla S. El-Shenawy uri: https://doi.org/10.7717/peerj.7460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hamza et al. title: California air resources board forest carbon protocol invalidates offsets link: https://peerj.com/articles/7606 last-modified: 2019-09-23 description: The commercial asset value of sequestered forest carbon is based on protocols employed globally; however, their scientific basis has not been validated. We review and analyze commercial forest carbon protocols, claimed to have reduced net greenhouse gas emissions, issued by the California Air Resources Board and validated by the Climate Action Reserve (CARB-CAR). CARB-CAR forest carbon offsets, based on forest mensuration and model simulation, are compared to a global database of directly measured forest carbon sequestration, or net ecosystem exchange (NEE) of forest CO2. NEE is a meteorologically based method integrating CO2 fluxes between the atmosphere, forest and soils and is independent of the CARB-CAR methodology. Annual carbon accounting results for CAR681 are compared with NEE for the Ameriflux site, Howland Forest Maine, USA, (Ho-1), the only site where both methods were applied contemporaneously, invalidating CARB-CAR protocol offsets. We then test the null hypothesis that CARB-CAR project population data fall within global NEE population values for natural and managed forests measured in the field; net annual gC m−2yr−1 are compared for both protocols. Irrespective of geography, biome and project type, the CARB-CAR population mean is significantly different from the NEE population mean at the 95% confidence interval, rejecting the null hypothesis. The CARB-CAR population exhibits standard deviation ∼5× that of known interannual NEE ranges, is overcrediting biased, incapable of detecting forest transition to net positive CO2 emissions, and exceeds the 5% CARB compliance limit for invalidation. Exclusion of CO2 efflux via soil and ecosystem respiration precludes a valid net carbon accounting result for CARB-CAR and related protocols, consistent with our findings. Protocol invalidation risk extends to vendors and policy platforms such as the United Nations Program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) and the Paris Agreement. We suggest that CARB-CAR and related protocols include NEE methodology for commercial forest carbon offsets to standardize methods, ensure in situ molecular specificity, verify claims of carbon emission reduction and harmonize carbon protocols for voluntary and compliance markets worldwide. creator: Bruno D.V. Marino creator: Martina Mincheva creator: Aaron Doucett uri: https://doi.org/10.7717/peerj.7606 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Marino et al. title: Effect of radiotherapy on the gut microbiome in pediatric cancer patients: a pilot study link: https://peerj.com/articles/7683 last-modified: 2019-09-23 description: The incidence of pediatric cancer is lower than that of adult cancer worldwide. However, the former has detrimental side effects on the health of individuals, even after the cancer is cured, due to the impact of treatment on development. Recently, correlations have been made between the gut microbiome and cancer in several studies but only on adult participants. There is always a complication of dealing with pediatric cancer treatment protocols because they usually include a combination of chemotherapy, radiotherapy, and intensive prophylactic antibiotics. In the current study, a pilot study was conducted to analyze ten fecal samples from three pediatric cancer patients, suffering from rhabdomyosarcoma near their pelvic region, and two healthy individuals. A correlation between microbial composition and response to treatment was reported, in which the responders had generally a lower microbial diversity compared to non-responders. In addition, nucleotide changes and deletions in the tested 16S rRNA sequences post radiotherapy were detected. Despite the small sample size used in the experiments due to the uncommon rhabdomyosarcoma in children, the results can help in understanding the influence of radiotherapy on the gut microbiome in pediatric cancer patients. More work with larger sample size and different cancer types need to be conducted to understand the influence of radiotherapy on gut microbiome to mitigate the deleterious impact of radiation on treated children. creator: Nourhan Sahly creator: Ahmed Moustafa creator: Mohamed Zaghloul creator: Tamer Z. Salem uri: https://doi.org/10.7717/peerj.7683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sahly et al. title: Chemical profile and pancreatic lipase inhibitory activity of Sinobambusa tootsik (Sieb.) Makino leaves link: https://peerj.com/articles/7765 last-modified: 2019-09-23 description: BackgroundSinobambusa tootsik (Sieb.) Makino (S. tootsik) is one species of bamboo distributed in China, Japan and Vietnam. The chemical profile of its leaves and its potential application was unknown yet.MethodsThe chemical profile of S. tootsik was studied by HPLC and UPLC-DAD-QTOF-MS. The S. tootsik extract was prepared by extraction with 50% aqueous ethanol, followed by H103 macroporous resins adsorption and desorption processes. Pancreatic lipase inhibitory activity was determined using p-nitrophenyl palmitate as the substance, which was hydrolyzed by lipase to form coloured p-nitrophenol.ResultsEighteen compounds were identified in S. tootsik. Most of them were the C-glycosylated derivatives of luteolin and apigenin, such as isoorientin, isoorientin-2″-O-rhamnoside and isovitexin. Isoorientin-2″-O-rhamnoside was the most dominant flavonoid in the sample. S. tootsik extract was prepared through resin adsorption/desorption with yield of 1.12 ± 015% and total flavonoids content of 82 ± 2 mg/g (in term of isoorientin). The extract exhibited pancreatic lipase inhibitory activity with IC50 value of 0.93 mg/mL.ConclusionThe chemical profile of S. tootsik leaves was uncovered for the first time. C-glycosyl flavonoids were the main constituents in the plant. The extract exhibited pancreatic lipase inhibitory activity and may have potential for use as a food supplement for controlling obesity. creator: Xiao-Lin Qiu creator: Qing-Feng Zhang uri: https://doi.org/10.7717/peerj.7765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qiu and Zhang title: A comparison of inducible, ontogenetic, and interspecific sources of variation in the foliar metabolome in tropical trees link: https://peerj.com/articles/7536 last-modified: 2019-09-20 description: Plant interactions with other organisms are mediated by chemistry, yet chemistry varies among conspecific and within individual plants. The foliar metabolome—the suite of small-molecule metabolites found in the leaf—changes during leaf ontogeny and is influenced by the signaling molecule jasmonic acid. Species differences in secondary metabolites are thought to play an important ecological role by limiting the host ranges of herbivores and pathogens, and hence facilitating competitive coexistence among plant species in species-rich plant communities such as tropical forests. Yet it remains unclear how inducible and ontogenetic variation compare with interspecific variation, particularly in tropical trees. Here, we take advantage of novel methods to assemble mass spectra of all compounds in leaf extracts into molecular networks that quantify their chemical structural similarity in order to compare inducible and ontogenetic chemical variation to among-species variation in species-rich tropical tree genera. We ask (i) whether young and mature leaves differ chemically, (ii) whether jasmonic acid-inducible chemical variation differs between young and mature leaves, and (iii) whether interspecific exceeds intraspecific chemical variation for four species from four hyperdiverse tropical tree genera. We observed significant effects of the jasmonic acid treatment for three of eight combinations of species and ontogenetic stage evaluated. Three of the four species also exhibited large metabolomic differences with leaf ontogenetic stage. The profound effect of leaf ontogenetic stage on the foliar metabolome suggests a qualitative turnover in secondary chemistry with leaf ontogeny. We also quantified foliar metabolomes for 45 congeners of the four focal species. Chemical similarity was much greater within than between species for all four genera, even when within-species comparisons included leaves that differed in age and jasmonic acid treatment. Despite ontogenetic and inducible variation within species, chemical differences among congeneric species may be sufficient to partition niche space with respect to chemical defense. creator: Brian E. Sedio creator: Armando Durant Archibold creator: Juan Camilo Rojas Echeverri creator: Chloé Debyser creator: Cristopher A. Boya P creator: S. Joseph Wright uri: https://doi.org/10.7717/peerj.7536 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Effects of Trichophyton mentagrophytes infection on the immune response of rabbits link: https://peerj.com/articles/7632 last-modified: 2019-09-20 description: BackgroundRabbit breeding has developed into a large-scale industry, and as such, the incidence of dermatophytosis in rabbits has become increasingly common. A rabbit model with Trichophyton mentagrophytes infection was established to study the changes within the immune responses after fungal infection.MethodsAfter the T. mentagrophytes challenge on skin, pathogens on the skin were isolated from the rabbits in the fungal infection (FI) groups 20 days. Fungal observation under microscope were carried out. Identification of strains was achieved by polymerase chain reaction (PCR) using the CDR1 gene. The collected anticoagulant blood samples were analyzed for various blood cell parameters. The levels of antibodies, including IgM and IgA, cytokines, including IL-2, IL-6, and macrophage colony-stimulating factor (M-CSF), and soluble CD4 and CD8 in the serum of the FI group vs. the control group were determined independently. RNA isolation from blood samples and fluorescence-based quantitative PCR were carried out for the mRNA level of M-csf 20 days after fungal challenge.ResultsOur model resulted in typical symptoms of dermatophytosis on rabbit skin after challenged with fungus. Pathogens isolated from the infected rabbit skin were confirmed to be T. mentagrophytes by microscopic examination and PCR. The number of lymphocytes in the blood of the FI group was significantly decreased in comparison to the control group 2 days after the fungal challenge, but was significantly increased in comparison the control group 10 days after the fungal challenge (P < 0.01). Platelet counts of the FI group were significantly higher than in the control group at 2 (P < 0.05), 10 (P < 0.05), and 20 (P < 0.01) days after fungal challenge. The red blood cell distribution width of the FI group was significantly increased in comparison to that of the control group at 2, 10, and 20 days after fungal challenge (P < 0.01 for all days). The levels of antibodies (immunoglobulin (Ig) M and IgA (P < 0.01)), cytokines (interleukin (IL)-6 (P < 0.01), macrophage colony-stimulating factor (M-CSF) (P < 0.05)), and soluble CD4 (P < 0.01) and CD8 (P < 0.01) in the serum were significantly different between the FI and control groups. Serum M-csf mRNA level of the FI group was significantly higher than the control group 20 days after fungal challenge (P < 0.01).ConclusionsThis study demonstrates how the immune system responds to infection with T. mentagrophytes and provides potential targets for the prevention and treatment of dermatophytosis. creator: Chenwen Xiao creator: Guolian Bao creator: Qiang Wei creator: Yan Liu creator: Jiaoyu Wang creator: Quanan Ji creator: Yee Huang uri: https://doi.org/10.7717/peerj.7632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xiao et al. title: A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae link: https://peerj.com/articles/7649 last-modified: 2019-09-20 description: Milkweeds (Asclepias) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, Asclepias syriaca. This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in Asclepias relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family. creator: Kevin Weitemier creator: Shannon C.K. Straub creator: Mark Fishbein creator: C. Donovan Bailey creator: Richard C. Cronn creator: Aaron Liston uri: https://doi.org/10.7717/peerj.7649 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Transposon mutagenesis reveals Pseudomonas cannabina pv. alisalensis optimizes its virulence factors for pathogenicity on different hosts link: https://peerj.com/articles/7698 last-modified: 2019-09-20 description: Pseudomonas cannabina pv. alisalensis (Pcal), which causes bacterial blight disease of Brassicaceae, is an economically important pathogen worldwide. To identify Pcal genes involved in pathogenesis, we conducted a screen for 1,040 individual Pcal KB211 Tn5 mutants with reduced virulence on cabbage plants using a dip-inoculation method. We isolated 53 reduced virulence mutants and identified several potential virulence factors involved in Pcal virulence mechanisms such as the type III secretion system, membrane transporters, transcription factors, and amino acid metabolism. Importantly, Pcal is pathogenic on a range of monocotyledonous and dicotyledonous plants. Therefore, we also carried out the inoculation test on oat plants, which are cultivated after cabbage cultivation as green manure crops. Interestingly among the 53 mutants, 31 mutants also exhibited reduced virulence on oat seedlings, indicating that Pcal optimizes its virulence factors for pathogenicity on different host plants. Our results highlight the importance of revealing the virulence factors for each plant host-bacterial interaction, and will provide new insights into Pcal virulence mechanisms. creator: Nanami Sakata creator: Takako Ishiga creator: Haruka Saito creator: Viet Tru Nguyen creator: Yasuhiro Ishiga uri: https://doi.org/10.7717/peerj.7698 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sakata et al. title: Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species link: https://peerj.com/articles/7713 last-modified: 2019-09-20 description: As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees. creator: Yong Yang creator: Ying Zhang creator: Yukai Chen creator: Juma Gul creator: Jingwen Zhang creator: Qiang Liu creator: Qing Chen uri: https://doi.org/10.7717/peerj.7713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: Role of miR-10b-5p in the prognosis of breast cancer link: https://peerj.com/articles/7728 last-modified: 2019-09-20 description: Breast cancer is the leading cause of cancer-related death in women worldwide. Aberrant expression levels of miR-10b-5p in breast cancer has been reported while the molecular mechanism of miR-10b-5p in tumorigenesis remains elusive. Therefore, this study was aimed to investigate the role of miR-10b-5p in breast cancer and the network of its target genes using bioinformatics analysis. In this study, the expression profiles and prognostic value of miR-10b-5p in breast cancer were analyzed from public databases. Association between miR-10b-5p and clinicopathological parameters were analyzed by non-parametric test. Moreover, the optimal target genes of miR-10b-5p were obtained and their expression patterns were examined using starBase and HPA database. Additionally, the role of these target genes in cancer development were explored via Cancer Hallmarks Analytics Tool (CHAT). The protein–protein interaction (PPI) networks were constructed to further investigate the interactive relationships among these genes. Furthermore, GO, KEGG pathway and Reactome pathway analyses were carried out to decipher functions of these target genes. Results demonstrated that miR-10b-5p was down-regulated in breast cancer and low expression of miR-10b-5p was significantly correlated to worse outcome. Five genes, BIRC5, E2F2, KIF2C, FOXM1, and MCM5, were considered as potential key target genes of miR-10b-5p. As expected, higher expression levels of these genes were observed in breast cancer tissues than in normal tissues. Moreover, analysis from CHAT revealed that these genes were mainly involved in sustaining proliferative signaling in cancer development. In addition, PPI networks analysis revealed strong interactions between target genes. GO, KEGG, and Reactome pathway analysis suggested that these target genes of miR-10b-5p in breast cancer were significantly involved in cell cycle. Predicted target genes were further validated by qRT-PCR analysis in human breast cancer cell line MDA-MB-231 transfected with miR-10b mimic or antisense inhibitors. Taken together, our data suggest that miR-10b-5p functions to impede breast carcinoma progression via regulation of its key target genes and hopefully serves as a potential diagnostic and prognostic marker for breast cancer. creator: Junmin Wang creator: Yanyun Yan creator: Zhiqi Zhang creator: Yali Li uri: https://doi.org/10.7717/peerj.7728 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Sleep apnea detection from a single-lead ECG signal with automatic feature-extraction through a modified LeNet-5 convolutional neural network link: https://peerj.com/articles/7731 last-modified: 2019-09-20 description: Sleep apnea (SA) is the most common respiratory sleep disorder, leading to some serious neurological and cardiovascular diseases if left untreated. The diagnosis of SA is traditionally made using Polysomnography (PSG). However, this method requires many electrodes and wires, as well as an expert to monitor the test. Several researchers have proposed instead using a single channel signal for SA diagnosis. Among these options, the ECG signal is one of the most physiologically relevant signals of SA occurrence, and one that can be easily recorded using a wearable device. However, existing ECG signal-based methods mainly use features (i.e. frequency domain, time domain, and other nonlinear features) acquired from ECG and its derived signals in order to construct the model. This requires researchers to have rich experience in ECG, which is not common. A convolutional neural network (CNN) is a kind of deep neural network that can automatically learn effective feature representation from training data and has been successfully applied in many fields. Meanwhile, most studies have not considered the impact of adjacent segments on SA detection. Therefore, in this study, we propose a modified LeNet-5 convolutional neural network with adjacent segments for SA detection. Our experimental results show that our proposed method is useful for SA detection, and achieves better or comparable results when compared with traditional machine learning methods. creator: Tao Wang creator: Changhua Lu creator: Guohao Shen creator: Feng Hong uri: https://doi.org/10.7717/peerj.7731 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers link: https://peerj.com/articles/7742 last-modified: 2019-09-20 description: Annual ryegrass (Lolium multiflorum) is a widely used cool-season turf and forage grass with high productivity and ornamental characteristics. However, the abundant intra-cultivar genetic variability usually hampers the application of conventional techniques for cultivar identification. The objectives of this study were to: (1) describe an efficient strategy for identification of six tetraploid annual ryegrass cultivars and (2) investigate the genetic diversity based on SSR markers. A total of 242 reliable bands were obtained from 29 SSR primer pairs with an average of 8.3 bands for each primer pair and the average value of polymorphic information content (PIC) was 0.304. The result of analysis of molecular variance (AMOVA) revealed that 81.99% of the genetic variation occurred in within-cultivars and 18.01% among-cultivars. The principal coordinate analysis (PCoA) showed that the first two principal axes explain 8.57% (PC1) and 6.05% (PC2) of total variation, respectively. By using multi-bulk strategy based on different filtering thresholds, the results suggested that bands frequency of 40% could be used as a reliable standard for cultivar identification in annual ryegrass. Under this threshold, 12 SSR primer pairs (00-04A, 02-06G, 02-08C, 03-05A, 04-05B, 10-09E, 12-01A, 13-02H, 13-12D, 14-06F, 15-01C and 17-10D) were detected for direct identification of six tetraploid annual ryegrass cultivars, which could be incorporated into conservation schemes to protect the intellectual property of breeders, ensure purity for consumers, as well as guarantee effective use of cultivars in future. creator: Gang Nie creator: Ting Huang creator: Xiao Ma creator: Linkai Huang creator: Yan Peng creator: Yanhong Yan creator: Zhou Li creator: Xia Wang creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.7742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nie et al. title: Curcumin plays a synergistic role in combination with HSV-TK/GCV in inhibiting growth of murine B16 melanoma cells and melanoma xenografts link: https://peerj.com/articles/7760 last-modified: 2019-09-20 description: Melanoma is a global concern and accounts for the major mortality of skin cancers. Herpes simplex virus thymidine kinase gene with ganciclovir (HSV-TK/GCV) is a promising gene therapy for melanoma. Despite its low efficiency, it is well known for its bystander effect which is mainly mediated by gap junction. In this study, we found that curcumin reduced B16 melanoma cell viability in both time- and dose-dependent manner. Further study showed that curcumin improved the gap junction intercellular communication (GJIC) function, and upregulated the proteins essential to gap junction, such as connexin 32 and connexin 43, indicating the potential role in enhancing the bystander effect of HSV-TK/GCV. By co-culturing the B16TK cells, which stably expressed TK gene, with wildtype B16 (B16WT) cells, we found that co-treatment of curcumin and GCV synergistically inhibited B16 cell proliferation, but the effect could be eliminated by the gap junction inhibitor AGA. Moreover, curcumin markedly increased apoptosis rate of B16WT cells, suggesting its effect in enhancing the bystander effect of HSV-TK/GCV. In the in-vivo study, we established the xenografted melanoma model in 14 days by injecting mixture of B16TK and B16WT cell in a ratio of 3:7. The result demonstrated that, co-administration of curcumin and GCV significantly inhibited the xenograft growth, as indicated by the smaller size and less weight. The combinational effect was further confirmed as a synergistic effect. In conclusion, the results demonstrated that curcumin could enhance the killing effect and the bystander effect of HSV-TK/GCV in treating melanoma, which might be mediated by improved gap junction. Our data suggested that combination of HSV-TK/GCV with curcumin could be a potential chemosensitization strategy for cancer treatment. creator: Hong Li creator: Haiyan Du creator: Guangxian Zhang creator: Yingya Wu creator: Pengxiang Qiu creator: Jingjing Liu creator: Jing Guo creator: Xijuan Liu creator: Lingling Sun creator: Biaoyan Du creator: Yuhui Tan uri: https://doi.org/10.7717/peerj.7760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Identification of pivotal lncRNAs in papillary thyroid cancer using lncRNA–mRNA–miRNA ceRNA network analysis link: https://peerj.com/articles/7441 last-modified: 2019-09-19 description: BackgroundTo identify pivotal lncRNAs in papillary thyroid cancer (PTC) using lncRNA–mRNA–miRNA ceRNA network analysis.MethodsWe obtained gene expression profiles from the gene expression omnibus database. Cancer specific lncRNA, cancer specific miRNA and cancer specific mRNA were identified. An integrated analysis was conducted to detect potential lncRNA–miRNA–mRNA ceRNA in regulating disease transformation. The lncRNA regulated gene ontology (GO) terms and regulated pathways were performed by function analysis. Survival analysis was performed for the pivotal lncRNAs.ResultsA total of four lncRNAs, 15 miRNAs and 375 mRNAs are identified as the key mediators in the pathophysiological processes of PTC. GO annotation enrichment analysis showed the most relevant GO terms are signal transduction, integral component of membrane and calcium ion binding. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed different changed genes mainly enriched in pathways in cancer, PI3K-Akt signaling pathway and focal adhesion. Among four lncRNAs, only SLC26A4-AS1 was significantly associated with PTC patient disease free survival.ConclusionThis study has constructed lncRNA–mRNA–miRNA ceRNA networks in PTC. The study provides a set of pivotal lncRNAs for future investigation into the molecular mechanisms. creator: Weiwei Liang creator: Fangfang Sun uri: https://doi.org/10.7717/peerj.7441 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liang and Sun title: Ankle and midtarsal joint quasi-stiffness during walking with added mass link: https://peerj.com/articles/7487 last-modified: 2019-09-19 description: Examination of how the ankle and midtarsal joints modulate stiffness in response to increased force demand will aid understanding of overall limb function and inform the development of bio-inspired assistive and robotic devices. The purpose of this study is to identify how ankle and midtarsal joint quasi-stiffness are affected by added body mass during over-ground walking. Healthy participants walked barefoot over-ground at 1.25 m/s wearing a weighted vest with 0%, 15% and 30% additional body mass. The effect of added mass was investigated on ankle and midtarsal joint range of motion (ROM), peak moment and quasi-stiffness. Joint quasi-stiffness was broken into two phases, dorsiflexion (DF) and plantarflexion (PF), representing approximately linear regions of their moment-angle curve. Added mass significantly increased ankle joint quasi-stiffness in DF (p < 0.001) and PF (p < 0.001), as well as midtarsal joint quasi-stiffness in DF (p < 0.006) and PF (p < 0.001). Notably, the midtarsal joint quasi-stiffness during DF was ~2.5 times higher than that of the ankle joint. The increase in midtarsal quasi-stiffness when walking with added mass could not be explained by the windlass mechanism, as the ROM of the metatarsophalangeal joints was not correlated with midtarsal joint quasi-stiffness (r = −0.142, p = 0.540). The likely source for the quasi-stiffness modulation may be from active foot muscles, however, future research is needed to confirm which anatomical structures (passive or active) contribute to the overall joint quasi-stiffness across locomotor tasks. creator: Andrew M. Kern creator: Nikolaos Papachatzis creator: Jeffrey M. Patterson creator: Dustin A. Bruening creator: Kota Z. Takahashi uri: https://doi.org/10.7717/peerj.7487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kern et al. title: Negative emotional state slows down movement speed: behavioral and neural evidence link: https://peerj.com/articles/7591 last-modified: 2019-09-19 description: BackgroundAthletic performance is affected by emotional state. Athletes may underperform in competition due to poor emotion regulation. Movement speed plays an important role in many competition events. Flexible control of movement speed is critical for effective athletic performance. Although behavioral evidence showed that negative emotion can influence movement speed, the nature of the relationship remains controversial. Thus, the present study investigated how negative emotion affects movement speed and the neural mechanism underlying the interaction between emotion processing and movement control.MethodsThe present study combined electroencephalography (EEG) technology with a cued-action task to investigate the effect of negative emotion on movement speed. In total, 21 undergraduate students were recruited for this study. Participants were asked to perform six consecutive action tasks after viewing an emotional picture. Pictures were presented in two blocks (one negative and one neutral). After the participants completed a set of tasks (neutral of negative), they were subjected to complete a 9-point self-assessment manikin scale. Participants underwent EEG while performing the tasks.ResultsAt the behavior level, there was a significant main effect of emotional valence on movement speed, with participants exhibiting significantly slower movements in the negative emotional condition than in the neutral condition. EEG data showed increased theta oscillation and larger P1 amplitude in response to negative than to neural images suggesting that more cognitive resources were required to process negative than neutral images. EEG data also showed a larger late CNV area in the neutral condition than in the negative condition, which suggested that there was a significant decrease in brain activation during action tasks in negative emotional condition than in the neural. While the early CNV did not reveal a significant main effect of emotional valence.ConclusionThe present results indicate that a negative emotion can slow movement, which is largely due to negative emotional processing consuming more resources than non-emotional processing and this interference effect mainly occurred in the late movement preparation phase. creator: Xiawen Li creator: Guanghui Zhang creator: Chenglin Zhou creator: Xiaochun Wang uri: https://doi.org/10.7717/peerj.7591 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer link: https://peerj.com/articles/7602 last-modified: 2019-09-19 description: BackgroundRecent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC).MethodsHere we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs.ResultsIn this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found.ConclusionsOur findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets. creator: Wenliang Yuan creator: Sihua Peng creator: Jingyu Wang creator: Cai Wei creator: Zhen Ye creator: Ye Wang creator: Meiliang Wang creator: Hao Xu creator: Shouwen Jiang creator: Dan Sun creator: Chaoxu Dai creator: Linhua Jiang creator: Xiaobo Li uri: https://doi.org/10.7717/peerj.7602 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yuan et al. title: A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast link: https://peerj.com/articles/7610 last-modified: 2019-09-19 description: The Katalalixar National Reserve (KNR) lies in an isolated marine protected area of Magellan Sub-Antarctic channels, which represent an important area for marine biodiversity and macroalgal conservation. The present study is the first report of the species Lessonia spicata, “huiro negro”, in the Magellan Sub-Antarctic channels. This finding has implications for macroalgal biogeography and conservation concerns in the Chilean coast. In the ecological assessments of the KNR in 2018 we found populations of L. spicata, specifically on rocky shores of Torpedo Island and Castillo Channel. The morphological identification and molecular phylogeny based on nuclear (ITS1) sequences revealed that these populations of Lessonia are within the lineage of L. spicata of central Chile. This report increases the species richness of kelps for the Magellan Sub-Antarctic Channels from two to three confirmed species (L. flavicans, L. searlesiana and L. spicata), and it also extends the southern distribution range of L. spicata. This species has high harvest demand and is moving towards southern Chile; thus, these populations should be considered as essential for macroalgal conservation in high latitudes of South America. creator: Sebastián Rosenfeld creator: Fabio Mendez creator: Martha S. Calderon creator: Francisco Bahamonde creator: Juan Pablo Rodríguez creator: Jaime Ojeda creator: Johanna Marambio creator: Matthias Gorny creator: Andrés Mansilla uri: https://doi.org/10.7717/peerj.7610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rosenfeld et al. title: Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau link: https://peerj.com/articles/7645 last-modified: 2019-09-19 description: The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP. creator: Li Ma creator: Shixiao Xu creator: Hongjin Liu creator: Tianwei Xu creator: Linyong Hu creator: Na Zhao creator: Xueping Han creator: Xiaoling Zhang uri: https://doi.org/10.7717/peerj.7645 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae link: https://peerj.com/articles/7688 last-modified: 2019-09-19 description: A new istiodactylid pterosaur, Nurhachius luei sp. nov., is here reported based on a complete skull with mandible and some cervical vertebrae from the lower part of the Jiufotang Formation of western Liaoning (China). This is the second species of Nurhachius, the type-species being N. ignaciobritoi from the upper part of the Jiufotang Formation. A revised diagnosis of the genus Nurhachius is provided, being this taxon characterized by the presence of a slight dorsal deflection of the palatal anterior tip, which is homoplastic with the Anhangueria and Cimoliopterus. N. luei sp. nov. shows an unusual pattern of tooth replacement, with respect to other pterodactyloid species. The relationships within the Istiodactylidae and with their closest taxa are investigated through a phylogenetic analysis by parsimony. creator: Xuanyu Zhou creator: Rodrigo V. Pêgas creator: Maria E.C. Leal creator: Niels Bonde uri: https://doi.org/10.7717/peerj.7688 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhou et al. title: LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population link: https://peerj.com/articles/7695 last-modified: 2019-09-19 description: A novel application of the liquid chromatography method combined with the triple quadrupole tandem mass spectrometry method was developed for the quantification of vitamin K1 and two forms of vitamin K2 (menaquinone-4, menaquinone-7) in human serum. Total chromatography time for each run was 9 min. Time required for the sample pretreatment procedures was approximately 4 h. The coefficients of variation (CVs) of intra-assay were 10.4%, 3.2 % and 2.3% for vitamin K1 in three levels of quality control samples; were 14.3%, 3.2% and 6.7% for menaquinone-4; and were 11.1%, 6.0% and 7.0% for menaquinone-7. The inter-assay CVs were 12.8%, 11.3% and 7.4% for vitamin K1; were 15.2%, 9.2% and 8.7% for menaquinone-4; and were 13.2%,11.1% and 7.2% for menaquinone-7. No interference was found between K1, menaquinone-4 and menaquinone-7, nor any deuterated internal standards. This method was then used to determine reference values for Caucasian populations of central European origin. Samples were measured from 191 healthy volunteers (51.2 ± 16.2 years (mean ± SD)) and the values concerning K1 were 0.044–1.357 ng/mL for women and 0.030–1.214 ng/mL for men. The values for menaquinone-4 and menaquinone-7 did not exhibit any differences between women and men, and were 0.050–1.598 and 0.074–0.759 ng/mL, respectively. creator: Katerina Dunovska creator: Eva Klapkova creator: Bruno Sopko creator: Jana Cepova creator: Richard Prusa uri: https://doi.org/10.7717/peerj.7695 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dunovska et al. title: Phylogeny of Microphthalminae Hartmann-Schröder, 1971, and revision of Hesionella Hartman, 1939, and Struwela Hartmann-Schröder, 1959 (Annelida, Errantia) link: https://peerj.com/articles/7723 last-modified: 2019-09-19 description: Microphthalminae Hartmann-Schröder, 1971 was proposed in Hesionidae to include Microphthalmus and Hesionides; however, the affinities of these genera to other members of Hesionidae have been debated, and some authors have concluded they do not belong in Hesionidae. Herein, based on morphological characters, a phylogenetic analysis of the subfamily and some other similar poorly-known genera, with an uncertain position in Hesionidae was performed to clarify their affinities. Our results indicate that Microphthalminae, as currently delimited, is paraphyletic. The inclusion of Struwela, Uncopodarke, and Westheideius, a new genus, as well as the recognition of Fridericiella are proposed to meet the requirement of monophyly; and as result of this, the elevation in rank to the family level is herein presented. Furthermore, the type species for Hesionella and Struwela are redescribed, and a new species in the latter is described. A key to identify microphthalmid genera is also included. creator: Sergio I. Salazar-Vallejo creator: Jesús Angel de León-González creator: Luis F. Carrera-Parra uri: https://doi.org/10.7717/peerj.7723 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Salazar-Vallejo et al. title: The secret life of deep-sea shrimps: ecological and evolutionary clues from the larval description of Systellaspis debilis (Caridea: Oplophoridae) link: https://peerj.com/articles/7334 last-modified: 2019-09-18 description: Currently there are 21 shrimp species in the northeastern Atlantic and Mediterranean Sea which are considered to belong to the superfamily Oplophoroidea, but the larval development is unknown for most of them. The complete larval development of Systellaspis debilis (Milne-Edwards, 1881), here described and illustrated, is the first one to have been successfully reared in the laboratory, consisting of four zoeal and one decapodid stages. The zoeae were found to be fully lecithotrophic, which together with the females’ lower fecundity, are probably evolutionary consequences of the species mesopelagic habitat. creator: Cátia Bartilotti creator: Antonina Dos Santos uri: https://doi.org/10.7717/peerj.7334 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bartilotti and Dos Santos title: Open ocean nocturnal insect migration in the Brazilian South Atlantic with comments on flight endurance link: https://peerj.com/articles/7583 last-modified: 2019-09-18 description: We observed a nocturnal insect swarm aboard the oceanographic ship Cruzeiro do Sul of the Brazilian Navy, while conducting a survey of the Montague guyot (seamount), 389 km distant from the nearest land in the South Atlantic. The insects came from open sea toward the ship from all directions, attracted by the powerful light of the deck. Most insects collided with the hull and fell into the ocean, but we managed to capture and determine 17 (13 Hemiptera of a single species, three Lepidoptera of three species and one Odonata). With one exception, we are certain that none of the specimens caught originated from the ship. The geographic origin, most likely the coast of Brazil, and flight endurance of these insects were inferred using data on wind speed and direction, provided by the crew of the ship, and were reconstructed using Hysplit modeling of air current trajectories. creator: Ruy J.V. Alves creator: Luíz A.A. Costa creator: Alexandre Soares creator: Nílber G. Silva creator: Ângelo P. Pinto uri: https://doi.org/10.7717/peerj.7583 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Alves et al. title: Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs link: https://peerj.com/articles/7630 last-modified: 2019-09-18 description: Measurement of body dimensions of carnivores usually requires the chemical immobilization of subjects. This process can be dangerous, costly and potentially harmful to the target individuals. Development of an alternative, inexpensive, and non-invasive method therefore warrants attention. The objective of this study was to test whether it is possible to obtain accurate measurements of body dimensions of leopards from camera trap photographs. A total of 10 leopards (Panthera pardus) were captured and collared at Malilangwe Wildlife Reserve, Zimbabwe from May 7 to June 20, 2017 and four body measurements namely shoulder height, head-to-tail, body, and tail length were recorded. The same measurements were taken from 101 scaled photographs of the leopards recorded during a baited-camera trapping (BCT) survey conducted from July 1 to October 22, 2017 and differences from the actual measurements calculated. Generalized Linear Mixed Effects Models were used to determine the effect of type of body measurement, photographic scale, posture, and sex on the accuracy of the photograph-based measurements. Type of body measurement and posture had a significant influence on accuracy. Least squares means of absolute differences between actual and photographic measurements showed that body length in the level back-straight forelimb-parallel tail posture was measured most accurately from photographs (2.0 cm, 95% CI [1.5–2.7 cm]), while head-to-tail dimensions in the arched back-bent forelimb-parallel tail posture were least accurate (8.3 cm, 95% CI [6.1–11.2 cm]). Using the BCT design, we conclude that it is possible to collect accurate morphometric data of leopards from camera trap photographs. Repeat measurements over time can provide researchers with vital body size and growth rate information which may help improve the monitoring and management of species of conservation concern, such as leopards. creator: Allan Tarugara creator: Bruce W. Clegg creator: Edson Gandiwa creator: Victor K. Muposhi creator: Colin M. Wenham uri: https://doi.org/10.7717/peerj.7630 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tarugara et al. title: 13C values of glycolytic amino acids as indicators of carbohydrate utilization in carnivorous fish link: https://peerj.com/articles/7701 last-modified: 2019-09-18 description: BackgroundStable isotope analysis of single amino acids (AA) is usually applied in food web studies for tracing biosynthetic origins of AA carbon backbones and establishing trophic positions of consumers, but the method is also showing promise for characterizing quantity and quality of dietary lipids and carbohydrates.MethodsTo investigate whether changes in high- and low-digestible carbohydrates affect δ13C values of glycolytic AA, i.e., AA carbon backbones sourced from the glycolytic pathway, we compared Atlantic salmon (Salmo salar) from a feeding experiment with and without dietary inclusion of the red macroalga Palmaria palmata. The Control and experimental diets had similar relative proportions of macronutrients, but their ingredients differed; in the experimental treatment, 15% Palmaria inclusion substituted proteins from fishmeal and carbohydrates from corn starch.ResultsWe found that 13C values of the glycolytic AA were highly sensitive to substitution of corn starch with Palmaria. The δ13C offsets of glycolytic AA between salmon and their diets were significantly greater in the Palmaria inclusion than Control treatment. This greater offset can be attributed to the different utilization of high- vs. low-digestible carbohydrate sources, i.e., corn starch vs. Palmaria, in the two treatments, and metabolic routing of dietary lipids. In addition, similar δ13C values of essential AA between treatments indicate similar nutrient assimilation efficiency for all terrestrial (pea protein concentrate and wheat gluten meal) and marine (fishmeal and red alga) derived protein sources. These results show that δ13CAA analysis is a promising tool for improving our understanding of how carnivorous fish utilize macronutrient and route metabolic intermediates to tissue. creator: Yiming V. Wang creator: Alex H.L. Wan creator: Åshild Krogdahl creator: Mark Johnson creator: Thomas Larsen uri: https://doi.org/10.7717/peerj.7701 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Dynamics of carbon and nitrogen storage in two typical plantation ecosystems of different stand ages on the Loess Plateau of China link: https://peerj.com/articles/7708 last-modified: 2019-09-18 description: In China’s Loess Plateau, afforestation and reforestation are considered the foremost practices for sequestering carbon and conserving soil and water. In order to evaluate the carbon storage changes of tree, soil, and litter, and the soil total nitrogen (STN) in two typical artificial forests in the region, we conducted plot surveys for different ages of both artificial forest types. Soil samples were collected at different depths from 0–100 cm. The results indicated that forest ecosystem carbon storage increased with tree development. The rates of mean annual carbon sequestration of Pinus tabulaeformis and Robinia pseudoacacia plantation ecosystems were 3.31 and 3.53 Mg ha−1 year−1, respectively. The rate of mean annual carbon sequestration of R. pseudoacacia plantation ecosystems was higher by 6.65% than that of P. tabulaeformis plantation ecosystems. The soil organic carbon (SOC) and STN decreased at deeper soil depths in both plantations at different stand ages, significantly decreasing in the 0–60 cm of soil (P < 0.05), and the highest SOC content and storage were in the top 0–20 cm of soil. The temporal patterns for SOC and STN changes at different soil sampling depths from 0 to 100 cm all showed an initial decrease during the early stage of restoration, and then an increase that coincided with the development of the two plantation forests. At 0–100 cm depth, the SOC storage was in the range of 40.95–106.79 and 45.13–113.61 Mg ha−1 for the P. tabulaeformis forest and R. pseudoacacia forest, respectively. The STN storage in the 0–100 cm soil layer with the stand age development ranged from 4.16 to 8.34 Mg ha−1 in the R. pseudoacacia plantation and 4.19–7.55 Mg ha−1 in the P. tabulaeformis forest. The results showed a significant positive correlation between SOC and STN. This study suggests that we should pay more attention to changes in soil carbon and nitrogen sequestration during long-term vegetation restoration. creator: Yanfang Wang creator: Ling Liu creator: Feixue Yue creator: Dong Li uri: https://doi.org/10.7717/peerj.7708 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus link: https://peerj.com/articles/7709 last-modified: 2019-09-18 description: Sex determination and sex chromosomes can be very diverse between teleost species. The group of tilapias shows a polymorphism in sex determination not only between closely related species but also between domestic strains within a species. In the Nile tilapia, the major effect genes and therefore the Y chromosome have been located on either linkage group 1 (LG1) or LG23 depending on the strains. In a Japanese strain, the sex determinant of LG23 (the amhY gene) has been identified as a duplicated amh (anti-Müllerian hormone) gene, with its gametolog found on the X chromosome (amhX). AmhY is located in tandem with the amhΔY gene (a truncated form) on the Y chromosome. X and Y chromosome markers based on the amh genes have been validated only on a few domestic strains but not in wild populations. Here, we used four of these markers in order to examine (1) the possible variation in sex determination of a wild population of Nile tilapia living in Lake Kou (Burkina Faso), (2) putative polymorphisms for these amh copies and (3) the existence of sex reversed individuals in the wild. Our genotyping of 91 wild Kou individuals with the amh sex-diagnostic markers of LG23 showed that while phenotypic females were all XX, phenotypic males were either XY or XX. Progeny testing of eight of these XX males revealed that one of these males consistently sired all-female progenies, suggesting that it is a wild sex reversed male (which could result from high temperature effects). The other XX males gave balanced sex ratios, suggesting that sex is controlled by another locus (possibly on another LG) which may be epistatically dominant over the LG23 locus. Finally, identification of unexpected amh genotypes was found for two individuals. They produced either balanced or female-biased sex ratios, depending on the breeder with whom they were crossed, suggesting possible recombination between the X and the Y chromosomes. creator: Rokyatou Sissao creator: Helena D’Cotta creator: Jean-François Baroiller creator: Aboubacar Toguyeni uri: https://doi.org/10.7717/peerj.7709 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sissao et al. title: Chemical characterisation of potential pheromones from the shoulder gland of the Northern yellow-shouldered-bat, Sturnira parvidens (Phyllostomidae: Stenodermatinae) link: https://peerj.com/articles/7734 last-modified: 2019-09-18 description: Bats of the genus Sturnira (Family Phyllostomidae) are characterised by shoulder glands that are more developed in reproductively mature adult males. The glands produce a waxy secretion that accumulates on the fur around the gland, dyeing the fur a dark colour and giving off a pungent odour. These shoulder glands are thought to play a role in their reproductive behaviour. Using gas chromatography–mass spectrometry, we analysed solvent extracts of fur surrounding the shoulder gland in the northern-shouldered bat, Sturnira parvidens to (i) characterise the chemical composition of shoulder gland secretions for the first time, and (ii) look for differences in chemical composition among and between adult males, sub-adult/juvenile males and adult females. Fur solvent extracts were analysed as liquids and also further extracted using headspace solid-phase microextraction to identify volatile components in the odour itself. Odour fingerprint analysis using non-metric multidimensional scaling plots and multivariate analysis revealed clear and significant differences (P < 0.001) between adult males vs both juvenile males and adult females. The chemical components of the shoulder gland secretion included terpenes and phenolics, together with alcohols and esters, most likely derived from the frugivorous diet of the bat. Many of the compounds identified were found exclusively or in elevated quantities among adult (reproductive) males compared with adult females and non-reproductive (juvenile) males. This strongly suggests a specific role in male–female attraction although a function in male–male competition and/or species recognition is also possible. creator: Chris G. Faulkes creator: J. Stephen Elmore creator: David A. Baines creator: Brock Fenton creator: Nancy B. Simmons creator: Elizabeth L. Clare uri: https://doi.org/10.7717/peerj.7734 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Faulkes et al. title: The effect of elevational gradient on alpine gingers (Roscoea alpina and R. purpurea) in the Himalayas link: https://peerj.com/articles/7503 last-modified: 2019-09-17 description: There is currently enormous interest in how morphological and physiological responses of herbaceous plants may be affected by changing elevational gradient. Mountain regions provide an excellent opportunity to understand how closely related species may adapt to the conditions that rapidly change with elevation. We investigated the morphological and physiological responses of two Himalayan alpine gingers (Roscoea alpina and R. purpurea) along two different vertical transects of 400 m, R. purpurea between 2,174–2,574 m a.s.l and R. alpina between 2,675–3,079 m a.s.l. We measured the variables of plant height, leaf length, leaf area, specific leaf area, and stomata density at five plots, along the vertical transect at an elevational gap of ca. 100 m. Results revealed that with increased elevation plant height, and leaf area decreased while stomata density increased, whereas changes in specific leaf area, were not correlated with the elevation. Our results reveal that these alpine gingers undergo local adaptation by modifying their plant height, leaf area and stomata density in response to the varying selection pressure associated with the elevational gradient. Thus, the findings of this research provide valuable information on how a narrow range of elevational gradient affects the herbaceous plants at the alpine habitat of the Himalayas. creator: Babu Ram Paudel creator: Adrian G. Dyer creator: Jair E. Garcia creator: Mani Shrestha uri: https://doi.org/10.7717/peerj.7503 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Paudel et al. title: A novel methodology for optimal land allocation for agricultural crops using Social Spider Algorithm link: https://peerj.com/articles/7559 last-modified: 2019-09-17 description: In the current agricultural scenario, availability of suitable land for cultivation is less and profitable allocation of the land for cultivating crops seems to be a cumbersome task. Crop planning optimization is a major research field in agriculture, in which land optimization is a significant challenge, which falls under the category of combinatorial optimization problems. The main objective of the present research is to maximize the net income from agriculture through optimal land allocation. Bio-inspired algorithms are quite popular in solving combinatorial optimization problems. Social Spider Algorithm (SSA), a new bio-inspired algorithm, is used to solve land optimization problem in this research based on the simulation of cooperative behaviour of social spiders. The agricultural area chosen for case study is the Coimbatore region, located in Tamilnadu state, India and the relevant data for the crops are collected from Tamilnadu Agricultural University Coimbatore, India. The optimal planting area, crop productivity for various land holdings and the water requirements are computed by SSA and the results have shown better directions for agricultural planning to improve the profit with constrained land area and water limitations. creator: N Thilagavathi creator: T Amudha uri: https://doi.org/10.7717/peerj.7559 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Thilagavathi and Amudha title: Estimation of maize above-ground biomass based on stem-leaf separation strategy integrated with LiDAR and optical remote sensing data link: https://peerj.com/articles/7593 last-modified: 2019-09-17 description: Above-ground biomass (AGB) is an important indicator for effectively assessing crop growth and yield and, in addition, is an important ecological indicator for assessing the efficiency with which crops use light and store carbon in ecosystems. However, most existing methods using optical remote sensing to estimate AGB cannot observe structures below the maize canopy, which may lead to poor estimation accuracy. This paper proposes to use the stem-leaf separation strategy integrated with unmanned aerial vehicle LiDAR and multispectral image data to estimate the AGB in maize. First, the correlation matrix was used to screen optimal the LiDAR structural parameters (LSPs) and the spectral vegetation indices (SVIs). According to the screened indicators, the SVIs and the LSPs were subjected to multivariable linear regression (MLR) with the above-ground leaf biomass (AGLB) and above-ground stem biomass (AGSB), respectively. At the same time, all SVIs derived from multispectral data and all LSPs derived from LiDAR data were subjected to partial least squares regression (PLSR) with the AGLB and AGSB, respectively. Finally, the AGB was computed by adding the AGLB and the AGSB, and each was estimated by using the MLR and the PLSR methods, respectively. The results indicate a strong correlation between the estimated and field-observed AGB using the MLR method (R2 = 0.82, RMSE = 79.80 g/m2, NRMSE = 11.12%) and the PLSR method (R2 = 0.86, RMSE = 72.28 g/m2, NRMSE = 10.07%). The results indicate that PLSR more accurately estimates AGB than MLR, with R2 increasing by 0.04, root mean square error (RMSE) decreasing by 7.52 g/m2, and normalized root mean square error (NRMSE) decreasing by 1.05%. In addition, the AGB is more accurately estimated by combining LiDAR with multispectral data than LiDAR and multispectral data alone, with R2 increasing by 0.13 and 0.30, respectively, RMSE decreasing by 22.89 and 54.92 g/m2, respectively, and NRMSE decreasing by 4.46% and 7.65%, respectively. This study improves the prediction accuracy of AGB and provides a new guideline for monitoring based on the fusion of multispectral and LiDAR data. creator: Yaohui Zhu creator: Chunjiang Zhao creator: Hao Yang creator: Guijun Yang creator: Liang Han creator: Zhenhai Li creator: Haikuan Feng creator: Bo Xu creator: Jintao Wu creator: Lei Lei uri: https://doi.org/10.7717/peerj.7593 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhu et al. title: Undesirable immigrants: hobbyist vivaria as a potential source of alien invertebrate species link: https://peerj.com/articles/7617 last-modified: 2019-09-17 description: BackgroundSmall size and large diversity of adaptations make invertebrates a group of animals which can be easily transported by different human activities. Many species can travel as “hitchhikers” with plant material (both on plant surfaces and in the soil), including plants used for decoration in vivaria. Vivaria are often tropical in nature environments, with high temperatures and humidity, suitable for invertebrates from tropical regions. Although many of such invertebrates cannot survive in temperate regions where harsh weather conditions are present, it is also known that some can successfully acclimatise. As a result, their negative impact on local flora and fauna cannot be excluded.Material and methodsTerrestrial invertebrates were collected in several cities of Poland from tropical vivaria where poison dart frogs (Dendrobatidae) and/or orchids (Orchidaceae) were kept by hobbyists. Collecting of the material was preceded by a simple questionnaire placed on the biggest Polish forum devoted to poison dart frogs. Moreover, we contacted some Polish wholesalers offering tropical invertebrates (Isopoda and Collembola), used as the food source for frogs, hoping to receive information about locations where those invertebrates were delivered, over the period of one year. We obtained mtDNA barcodes using the COI marker (cytochrome c oxidase subunit I gene) for seven potential morphospecies.ResultsIn total, 12 taxa classified as Turbellaria, Annelida, Gastropoda, Isopoda, Diplopoda, Chilopoda and Collembola were collected and preserved in pure ethanol. We collected material and/or information from 65 locations, including 56 cities to which exotic isopods and springtails were sold by wholesalers over the period of nine months (average number per month = 18 cities). We obtained 18 COI sequences which were assigned to seven BINs and thus confirmed identification of seven species. The results indicate that the number of species transported with exotic plants is not small and can be observed regularly. Species noted as “hitchhikers” on plant structures and/or as inhabitants of soil in plant pots, originally came from South and Central America, Africa, Asia and possibly from North America or Southern Europe. Three taxa were noted for the first time from Poland, including Rhynchodemus sylvaticus (Rhynchodemidae), Trichorhina sp.1 (Platharthridae), and Guppya gundlachi (Euconulidae).DiscussionThe presented study clearly shows that an exotic hobby such as keeping tropical poison dart frogs and/or orchids may promote fast and uncontrolled dispersion of a high number of invertebrates classified in different taxonomical groups. Plant material (green elements of plants and the soil in which they are planted) used in vivaria can be an important source of such animals. creator: Radomir Jaskuła creator: Anna Sulikowska-Drozd creator: Aleksandra Jabłońska creator: Krzysztof Banaś creator: Tomasz Rewicz uri: https://doi.org/10.7717/peerj.7617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jaskuła et al. title: From habitat use to social behavior: natural history of a voiceless poison frog, Dendrobates tinctorius link: https://peerj.com/articles/7648 last-modified: 2019-09-17 description: Descriptive studies of natural history have always been a source of knowledge on which experimental work and scientific progress rely. Poison frogs are a well-studied group of small Neotropical frogs with diverse parental behaviors, distinct calls, and bright colors that warn predators about their toxicity; and a showcase of advances in fundamental biology through natural history observations. The dyeing poison frog, Dendrobates tinctorius, is emblematic of the Guianas region, widespread in the pet trade, and increasingly popular in research. This species shows several unusual behaviors, such as the lack of advertisement calls and the aggregation around tree-fall gaps, which remain poorly described and understood. Here, we summarize our observations from a natural population of D. tinctorius in French Guiana collected over various field trips between 2009 and 2017; our aim is to provide groundwork for future fundamental and applied research spanning parental care, animal dispersal, disease spread, habitat use in relation to color patterns, and intra-specific communication, to name a few. We report sex differences in habitat use and the striking invasion of tree-fall gaps; describe their courtship and aggressive behaviors; document egg development and tadpole transport; and discuss how the knowledge generated by this study could set the grounds for further research on the behavior, ecology, and conservation of this species. creator: Bibiana Rojas creator: Andrius Pašukonis uri: https://doi.org/10.7717/peerj.7648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rojas and Pašukonis title: Collisional mechanics of the diagonal gaits of horses over a range of speeds link: https://peerj.com/articles/7689 last-modified: 2019-09-17 description: One of the goals of the neuromotor control system is to minimize the cost of locomotion by reducing mechanical energy losses. Collisional mechanics, which studies the redirection of the downwards motion of the center of mass (COM) by ground reaction forces (GRF) generated by the limbs, represents an important source of energy loss. The primary objective of this study was to compare collisional mechanics and the associated mechanical energy losses in horses performing diagonally-synchronized gaits over a range of speeds. It is to be expected that collisional energy losses will be high when the COM velocity vector is closely aligned with the GRF vector. This condition is achieved in piaffe, an artificial gait performed in dressage competitions that has a diagonal limb coordination pattern similar to trot but performed with little or no forward velocity. Therefore, we hypothesized that collisional energy losses would be higher in piaffe than in trot. Synchronized kinematic and GRF data were collected from three highly-trained horses performing piaffe, passage and trot at a range of speeds. Derived variables were vertical excursion and velocity of the trunk COM, fore and hind limb compression expressed as percentage reduction of standing limb lengths, range of limb pro-retraction, GRF vector magnitude and vector angle, collision angle (Φ), and mechanical cost of motion (CoMotmech). Linear regression was used to investigate the relationship between CoMotmech and speed for each gait. Partial correlation was used to seek relationships between COM excursion and limb mechanics for each gait. Piaffe, passage and trot were clearly separated on the basis of speed. In all gaits the trunk was high at contact and lift off and descended to its lowest point in midstance following the pattern typical of spring mass mechanics. Mechanical cost was significantly (p < .05) and inversely related to speed in trot and piaffe with the value increasing steeply as speed approached zero due to a near vertical orientation of both the COM velocity vector and the GRF vector. Limb compression during stance was significantly (p < .05) linked to trunk COM vertical excursion in all gaits, with a stronger relationship in the forelimb. Hindlimb compression was, however, large in piaffe where the force magnitudes are notably smaller. The study illustrates the potential value of studying artificial gaits to provide data encompassing the entire range of locomotor capabilities. The results supported the experimental hypothesis by showing a threefold increase in collisional energy losses in piaffe compared with trot. In all gaits, dissociation between diagonal limb contacts and lift offs was thought to be an important strategy in reducing in collisional losses. Piaffe, the most costly gait, has similar characteristics to hopping on the spot. It appears that greater hindlimb compliance and a lower step frequency are important energy conservation strategies for piaffe. creator: Sarah Jane Hobbs creator: Hilary M. Clayton uri: https://doi.org/10.7717/peerj.7689 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hobbs and Clayton title: The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers link: https://peerj.com/articles/7696 last-modified: 2019-09-17 description: BackgroundRNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation.ResultsHere, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types—CHOL and KICH—is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively.ConclusionsThese results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic targets for patients with cancers at the N and M stages in two cancer types CHOL and KICH. creator: Shuaibin Lian creator: Liansheng Li creator: Yongjie Zhou creator: Zixiao Liu creator: Lei Wang uri: https://doi.org/10.7717/peerj.7696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lian et al. title: Characteristics and prognosis of pelvic Ewing sarcoma: a SEER population-based study link: https://peerj.com/articles/7710 last-modified: 2019-09-17 description: BackgroundThe pelvis is one of the primary sites of Ewing sarcoma (ES) and is associated with poorer prognoses than the extremities. Due to the rarity of this disease and limited data available, the prognostic factors of pelvic ES remain controversial. Thus, this study aimed to identify independent prognostic factors, and develop a nomogram for predicting survival rates in patients with pelvic ES.MethodsUsing data provided by the Surveillance, Epidemiology, and End Results (SEER) database, variables including age, sex, race, tumor size, tumor stage, surgery, and radiotherapy were analyzed using the Kaplan–Meier method and Cox proportional hazards regression. Based on the results of multivariate analyses, a nomogram was built to predict the overall survival (OS) of patients with pelvic ES. The performance of the nomogram was evaluated by the concordance index (C-index).ResultsA total of 267 cases diagnosed between 2004 and 2016 were included in the study. Univariate and multivariate analyses showed that patients who were younger, white, had a localized tumor stage, or underwent surgery were associated with improved prognoses, while no significant differences were observed in OS based on sex, tumor size, or radiotherapy. A nomogram was developed and the C-index was 0.728, indicating adequate performance for survival prediction.ConclusionsAge, race, tumor stage, and surgery were identified as independent prognostic factors for the OS of pelvic ES. The nomogram developed in this study can individually predict 3- and 5-year OS in patients with pelvic ES. creator: Li Chen creator: Cheng Long creator: Jiaxin Liu creator: Fei Xing creator: Xin Duan uri: https://doi.org/10.7717/peerj.7710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chen et al. title: MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses link: https://peerj.com/articles/7714 last-modified: 2019-09-17 description: BackgroundAlfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa.MethodsTo identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the M. sativa proteome sequences provided by the Noble Research Institute.ResultsIn the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein–protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This work provides information on the MYB family in alfalfa that was previously lacking and might promote the cultivation of stress-resistant alfalfa. creator: Qiang Zhou creator: Chenglin Jia creator: Wenxue Ma creator: Yue Cui creator: Xiaoyu Jin creator: Dong Luo creator: Xueyang Min creator: Zhipeng Liu uri: https://doi.org/10.7717/peerj.7714 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhou et al. title: Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia link: https://peerj.com/articles/7715 last-modified: 2019-09-17 description: Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams. creator: Ze Ren creator: Hongkai Gao uri: https://doi.org/10.7717/peerj.7715 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ren and Gao title: Urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells link: https://peerj.com/articles/7717 last-modified: 2019-09-17 description: BackgroundBiomarkers are changes associated with the disease. Urine is not subject to homeostatic control and therefore accumulates very early changes, making it an ideal biomarker source. Usually, we have performed urinary biomarker studies involving at least thousands of tumor cells. However, no tumor starts from a thousand tumor cells. We therefore examined urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells.MethodsHere, we serially diluted Walker-256 carcinosarcoma cells to a concentration of 102/mL and subcutaneously inoculated 0.1 mL of these cells into nine rats. The urine proteomes on days 0, 13 and 21 were analyzed by liquid chromatography coupled with tandem mass spectrometry.ResultsHierarchical clustering analysis showed that the urine proteome of each sample at three time points were clustered into three clusters, indicating the good consistency of these nine rats when inoculated with the same limited tumor cells. Differential proteins on days 13 and 21 were mainly associated with cell adhesion, autophagic cell death, changes in extracellular matrix organization, angiogenesis, and the pentose phosphate pathway. All of these enriched functional processes were reported to contribute to tumor progression and could not be enriched through random allocation analysis.ConclusionsOur results indicated that (1) the urine proteome reflects changes associated with cancer even with only approximately ten tumor cells in the body and that (2) the urine proteome reflects pathophysiological changes in the body with extremely high sensitivity and provides potential for a very early screening process of clinical patients. creator: Jing Wei creator: Wenshu Meng creator: Youhe Gao uri: https://doi.org/10.7717/peerj.7717 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wei et al. title: Effects of shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) on prostaglandin E2 production in lipopolysaccharide-treated mouse macrophage RAW264.7 cells link: https://peerj.com/articles/7725 last-modified: 2019-09-17 description: We previously reported that shokyo and kankyo, which are water-extracted fractions of ginger, reduced LPS-induced PGE2 production in human gingival fibroblasts. In this study, we examined the effects of these herbs on LPS-treated mouse macrophage RAW264.7 cells. Both shokyo and kankyo reduced LPS-induced PGE2 production in a concentration-dependent manner. Shokyo and kankyo did not inhibit cyclooxygenase (COX) activity, nor did they alter the expression of molecules in the arachidonic acid cascade. In addition, these herbs did not alter NF-κB p65 translocation into nucleus, or phosphorylation of p65 or ERK. These results suggest that shokyo and kankyo inhibit cPLA2 activity. Although 6-shogaol produced similar results to those of shokyo and kankyo, the concentration of 6-shogaol required for the reduction of PGE2 production were higher than those of 6-shogaol in shokyo and kankyo. Therefore, several gingerols and shogaols other than 6-shogaol may play a role in the reduction of LPS-induced PGE2 production. Thus, 6-shogaol, and other gingerols and shogaols inhibit cPLA2 activity and reduce LPS-induced PGE2 production via a different mechanism from traditional anti-inflammatory drugs. Moreover, kampo medicines that contain shokyo or kankyo are considered to be effective for inflammatory diseases. creator: Toshiaki Ara creator: Masanori Koide creator: Hiroyuki Kitamura creator: Norio Sogawa uri: https://doi.org/10.7717/peerj.7725 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ara et al. title: Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network link: https://peerj.com/articles/7727 last-modified: 2019-09-17 description: BackgroundLong noncoding RNAs (lncRNAs) play a role in the formation, development, and prognosis of various cancers. Our study aimed to identify prognostic-related lncRNAs in lung squamous cell carcinoma (LUSC), which may provide new perspectives for individualized treatment of patients.Materials and MethodsThe RNA sequencing (lncRNA, microRNA (miRNA), mRNA) data and clinical information related to LUSC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA sequences were used to construct the competitive endogenous RNA (ceRNA) network. In present study, we mainly used two prognostic verification methods, Cox analysis and survival analysis, to identify the prognostic relevance of specific lncRNAs and construct prognostic model of lncRNA.ResultsDatasets on 551 samples of lncRNA and mRNA and 523 miRNA samples were retrieved from the TCGA database. Analysis of the normal and LUSC samples identified 170 DElncRNAs, 331 DEmiRNAs, and 417 DEmRNAs differentially expressed RNAs. The ceRNA network contained 27 lncRNAs, 43 miRNAs, and 11 mRNAs. Furthermore, we identified seven specific lncRNAs (ERVH48-1, HCG9, SEC62-AS1, AC022148.1, LINC00460, C5orf17, LINC00261) as potential prognostic factors after correlation analysis, and five of the seven lncRNAs (AC022148.1, HCG9, LINC00460, C5orf17, LINC00261) constructed a prognostic model of LUSC.ConclusionIn present study, we identified seven lncRNAs in the ceRNA network that are associated with potential prognosis in LUSC patients, and constructed a prognostic model of LUSC which can be used to assess the prognosis risk of clinical patients. Further biological experiments are needed to elucidate the specific molecular mechanisms underlying them. creator: Lingyu Qi creator: Tingting Zhang creator: Yan Yao creator: Jing Zhuang creator: Cun Liu creator: Ruijuan Liu creator: Changgang Sun uri: https://doi.org/10.7717/peerj.7727 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2019 Qi et al. title: Liver slice culture as a model for lipid metabolism in fish link: https://peerj.com/articles/7732 last-modified: 2019-09-17 description: Hepatic lipid metabolism is traditionally investigated in vitro using hepatocyte monocultures lacking the complex three-dimensional structure and interacting cell types essential liver function. Precision cut liver slice (PCLS) culture represents an alternative in vitro system, which benefits from retention of tissue architecture. Here, we present the first comprehensive evaluation of the PCLS method in fish (Atlantic salmon, Salmo salar L.) and validate it in the context of lipid metabolism using feeding trials, extensive transcriptomic data, and fatty acid measurements. We observe an initial period of post-slicing global transcriptome adjustment, which plateaued after 3 days in major metabolic pathways and stabilized through 9 days. PCLS fed alpha-linolenic acid (ALA) and insulin responded in a liver-like manner, increasing lipid biosynthesis gene expression. We identify interactions between insulin and ALA, where two PUFA biosynthesis genes that were induced by insulin or ALA alone, were highly down-regulated when insulin and ALA were combined. We also find that transcriptomic profiles of liver slices are exceedingly more similar to whole liver than hepatocyte monocultures, both for lipid metabolism and liver marker genes. PCLS culture opens new avenues for high throughput experimentation on the effect of “novel feed composition” and represent a promising new strategy for studying genotype-specific molecular features of metabolism. creator: Thomas N. Harvey creator: Simen R. Sandve creator: Yang Jin creator: Jon Olav Vik creator: Jacob S. Torgersen uri: https://doi.org/10.7717/peerj.7732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Harvey et al. title: Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma link: https://peerj.com/articles/7414 last-modified: 2019-09-16 description: BackgroundEngrailed 1 (EN1), as a member of homeobox-containing transcription factors, participates in the development of the brain. High expressions of EN1 exist in various tumors. However, the role of EN1 in lower grade glioma (LGG) is still unknown.MethodsCoefficients of Cox regression were examined by data mining among 13 cancer types using OncoLnc to validate EN1 expressions in LGG patients from The Cancer Genome Atlas database (TCGA). Bioinformatic analysis was performed by using R2 and the UCSC Xena browser based on the data from 273 glioma cases in GSE16011 from GEO datasets and 530 cases of LGG patients in TCGA. Cases in GSE16011 were divided into two groups according to IDH1 mutation status. Cases in TCGA-LGG were classified to subtypes according to histopathological results, IDH1 mutation status and 1p19q status. The Kaplan–Meier survival curves were performed to analyze the relationship between EN1 expressions and clinicopathological characteristics and survival time respectively.ResultsCox regression results showed that LGG was ranked statistically first among 13 different cancer types according to the false discovery rate (FDR) correction. Results from GSE16011 showed that: glioma, LGG and LGG with IDH1 mutation patients with high EN1 expressions had significantly shorter 5, 10, and 15-year overall survival time (OS) (p < 0.001). Similar results from TCGA-LGG showed that LGG patients with high EN1 expressions had significantly shorter 15-year OS, irrespective of IDH1 mutation and 1p19q co-deletion (p < 0.001). The astrocytoma subgroup showed highest levels of EN1 expression and shortest 5, 10 and 15-year OS compared with oligoastrocytoma and oligodendroglioma (p < 0.05).ConclusionEN1 can be used as a prognostic marker in LGG patients, combined with IDH1 mutation and 1p19q co-deletion. creator: Jin Zhu creator: Yu-Qi Zhang uri: https://doi.org/10.7717/peerj.7414 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhu and and Zhang title: Seasonal and inter-annual community structure characteristics of zooplankton driven by water environment factors in a sub-lake of Lake Poyang, China link: https://peerj.com/articles/7590 last-modified: 2019-09-16 description: BackgroundSub-lakes are important for the maintenance of the ecosystem integrity of Lake Poyang, and zooplankton play an important role in its substance and energy flow.MethodsA seasonal investigation of zooplankton was conducted in spring (April), summer (July), autumn (October) and winter (January of the following year) from 2012 to 2016 in a sub-lake of Lake Poyang. The aim of the present study was to understand the seasonal dynamics and interannual variation of zooplankton communities and their relationship to environmental factors.ResultsA total of 115 species were identified in all samples in the four years, which comprised of 87 Rotifera, 13 Cladocera and 15 Copepoda. Rotifera was the dominant group in terms of quantity, and its species richness and abundance were significantly higher when compared to Cladocera and Copepoda (P < 0.05), while Cladocera dominated in terms of biomass. The species richness of Rotifera exhibited a significant seasonal difference (P < 0.05). Both the density and biomass of zooplankton revealed significant seasonal differences (P < 0.05). In general, the density and biomass of zooplankton were higher in summer and autumn, when compared to winter and spring. Biodiversity indices were dramatically lower in spring than in the other seasons. The non-metric multidimensional scaling (NMDS) analysis suggested that these zooplankton communities can be divided into three groups: spring community, summer-autumn community, and winter community. The seasonal succession of zooplankton communities did not have interannual reproducibility. In high water level years, the dominant species of zooplankton (Cladocerans and Copepods) in the wet season had a lower density, and the result in low water level years was exactly the opposite. The redundancy analysis revealed that water temperature (WT), conductivity, pH and dissolved oxygen (DO) had significant effects on the zooplankton community.ConclusionsThe community structure of zooplankton has a significant seasonal pattern, but has no interannual repeatability. In high water level years, the dominant species of zooplankton (Cladocerans and Copepods) in the wet season had a lower density, and the result in low water level years was exactly the opposite. The density, biomass and diversity indices of zooplankton were significantly different in different seasons. The present study was helpful in the further understanding of the ecosystem stability of lakes connected with rivers, providing scientific guidance for the protection of lake wetlands. creator: Beijuan Hu creator: Xuren Hu creator: Xue Nie creator: Xiaoke Zhang creator: Naicheng Wu creator: Yijiang Hong creator: Hai Ming Qin uri: https://doi.org/10.7717/peerj.7590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hu et al. title: Nomogram for predicting cancer specific survival in inflammatory breast carcinoma: a SEER population-based study link: https://peerj.com/articles/7659 last-modified: 2019-09-16 description: The clinicopathological features of inflammatory breast carcinoma (IBC), the effect of therapeutic options on survival outcome and the identification of prognostic factors were investigated in this study. Information on IBC patients were extracted from the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2015. Cox proportional hazard regression was used to determine potential significant prognostic factors of IBC. A nomogram was then constructed to evaluate patient survival based on certain variables. Univariate and multivariate analyses revealed that race (p < 0.001), M stage (p < 0.001), surgery (p = 0.010), chemotherapy (CT) (p < 0.001), tumor size (p = 0.010), estrogen receptor (p < 0.001), progesterone receptor (p = 0.04), and human epidermal growth factor receptor 2 (p < 0.001) were all independent risk factors. The concordance index (C-index) of the nomogram was 0.735, which showed good predictive efficiency. Survival analysis indicated that IBC patients without CT had poorer survival than those with CT (p < 0.001). Stratified analyses showed that modified radical mastectomy (MRM) had significant survival advantages over non-MRM in patients with stage IV IBC (p = 0.031). Patients treated with or without CT stratified by stage III and stage IV showed better survival than those without stage III and IV (p < 0.001). Trimodality therapy resulted in better survival than surgery combined with CT or CT alone (p < 0.001). Competing risk analysis also showed the same results. The nomogram was effectively applied to predict the 1, 3 and 5-year survival of IBC. Our nomogram showed relatively good accuracy with a C-index of 0.735 and is a visualized individually predictive tool for prognosis. Treatment strategy greatly affected the survival of patients. Trimodality therapy was the preferable therapeutic strategy for IBC. Further prospective studies are needed to validate these findings. creator: Haige Zhang creator: Guifen Ma creator: Shisuo Du creator: Jing Sun creator: Qian Zhang creator: Baoying Yuan creator: Xiaoyong Luo uri: https://doi.org/10.7717/peerj.7659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Land use management based on multi-scenario allocation and trade-offs of ecosystem services in Wafangdian County, Liaoning Province, China link: https://peerj.com/articles/7673 last-modified: 2019-09-16 description: Developing effective methods to coordinate the trade-offs among ecosystem services (ES) is important for achieving inclusive growth and sustainable development, and has been the focus of scholars and ecosystem managers globally. Using remote sensing and geographic information system (GIS) data, our study examined Wafangdian County of Liaoning Province as a case study to reveal the spatiotemporal evolution of four ES (food supply [FS], net primary productivity [NPP], water yield [WY], and soil conservation [SC]) and changes among their interactions. Then, an ordered weighted averaging model was introduced to simulate the optimal scenario of ES allocation. Results showed that: (1) the spatial and temporal changes in ES were significant over 14 years. All ES presented an inverted U-shaped growth curve from 2000–2014. (2) Synergies were observed within provisioning services, and there were trade-offs between provisioning services and regulating services, as well as provisioning services and supporting services. (3) The optimal scenario for Wafangdian was scenario 5 (trade-off coefficient, 0.68). The allocation of FS, NPP, WY, and SC in scenario 5 were 0.187, 0.427, 0.131, and 0.063, respectively. Implementing each ES weight of optimal scenario in land use management contributed to achieving intercoordination of ES. We propose to coordinate land and sea management to restore natural habitats that were expanded into in the high ES area. It is our anticipation that this study could provide a scientific basis for optimizing the allocation of ES and improving land use structure of coastal zones in the future. creator: Wenzhen Zhao creator: Zenglin Han creator: Xiaolu Yan creator: Jingqiu Zhong uri: https://doi.org/10.7717/peerj.7673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Why the long face? Comparative shape analysis of miniature, pony, and other horse skulls reveals changes in ontogenetic growth link: https://peerj.com/articles/7678 last-modified: 2019-09-16 description: BackgroundMuch of the shape variation found in animals is based on allometry and heterochrony. Horses represent an excellent model to investigate patterns of size-shape variation among breeds that were intentionally bred for extreme small and large sizes.MethodsWe tested whether ponies (wither height < 148 cm) have a diverging size-shape relationship in skull shape as compared to regular-sized horse breeds (wither height > 148 cm, here-after called horses) during ontogenetic growth. We used a dataset of 194 specimens from 25 horse and 13 pony breeds, two of which are miniature breeds (wither height < 96.5 cm)—Falabella, Shetland. We applied three-dimensional geometric morphometrics, linear measurements, and multivariate analyses (Procrustes ANOVAs) to quantitatively examine and compare the ontogenetic trajectories between pony and horse breeds with an emphasis on the miniature breeds as an extreme case of artificial selection on size. Additionally, we tested for juvenile characteristics in adult horse and miniature breeds that could resemble “paedomorphosis”—retention of juvenile characteristics in adult stage; e.g. large eyes, large braincase-to-face-relationship, and large head-to-body relationship.ResultsAllometric regression of size on shape revealed that 42% of shape variation could be explained by variation in size in all breeds. The ontogenetic trajectories of ponies and horses vary in slope and therefore in rate of change per unit size, and length. The differences in trajectory lengths and slopes result in ponies having a similar skull shape in an older age stage than horses of the same size in a younger age stage. This pattern could cause the generally perceived “paedomorphic” appearance of ponies. Miniature breeds have larger heads in relation to wither height compared to horses, a non-paedomorphic feature in horses specifically. Also, rostra (faces) are longer in adult individuals than in juveniles across all kinds of breeds. This pattern can be explained by the long-face hypothesis for grazing ungulates and could possibly be caused by the mismatch of selection by humans for shorter rostra and the dentition of ruminants.ConclusionsMiniature breed specimens do not exhibit any of the classical mammalian “paedomorphic” features (large orbits, large heads), except for the adult Falabella that has enlarged orbits, possibly because they are herbivorous ungulates that are affected by functional and metabolic constraints related to low nutrient-food consumption. Instead ponies, including miniature breeds, have faster and shorter ontogenetic growth compared to horses, resulting in adult pony skulls looking in part like juvenile horse skulls. creator: Laura Heck creator: Marcelo R. Sanchez-Villagra creator: Madlen Stange uri: https://doi.org/10.7717/peerj.7678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Heck et al. title: Effects of Lecanicillium lecanii strain JMC-01 on the physiology, biochemistry, and mortality of Bemisia tabaci Q-biotype nymphs link: https://peerj.com/articles/7690 last-modified: 2019-09-16 description: BackgroundLecanicillium lecanii is an entomopathogenic fungi, which was isolated from insects suffering from disease. Now, it is an effective bio-control resource that can control agricultural pests such as whitefly and aphids. There are many studies on the control of various agricultural pests by L. lecanii, but no report on its control of Bemisia tabaci biotype-Q exists. In this work, we studied the susceptibility of B. tabaci Q-biotype (from Ningxia, China) to L. lecanii JMC-01 in terms of nymph mortality and the changes in detoxifying protective enzymes activities.MethodsB. tabaci nymphs were exposed to L. lecanii JMC-01 conidia by immersion with the host culture. Mortality was assessed daily for all nymph stages. The detoxifying and protective enzyme activity changes, weight changes, and fat, and water contents of the nymphs were determined spectrophotometrically.ResultsAll instars of B. tabaci died after being infested with 1 × 108 conidia/mL. The 2nd-instar nymphs were the most susceptible, followed by the 3rd-instar nymphs. The corrected cumulative mortality of the 2nd- and 3rd-instar nymphs was 82.22% and 75.55%, respectively. The levels of detoxifying and protective enzymes initially increased and then decreased. The highest activities of carboxylesterase, acetylcholinesterase, peroxidase, and catalase occurred on the 3rd day, reaching 10.5, 0.32, 20, and 6.3 U/mg prot, respectively. These levels were 2.2-, 4.3-, 2.4-, and 1.4-fold the control levels, respectively. The highest activities of glutathione-S transferase and superoxide dismutase on the 2nd day were, respectively, 64 and 43.5 U/mg prot. These levels were, respectively, 2.7 and 1.1-fold that of the control level. The water and fat content in the infected B. tabaci nymphs decreased and differed significantly from the control levels. The weight increased continuously in the first 24 h, decreasing thereafter. At 72 h, the infestation level was about 0.78-fold that of the control level.ConclusionsThe studied L. lecanii JMC-01 strain is pathogenic to the B. tabaci Q-biotype. This strain interferes with the normal functioning of detoxifying and protective enzymes, and is also involved in the disruption of normal physiological metabolism in B. tabaci. creator: Ting Xie creator: Ling Jiang creator: Jianshe Li creator: Bo Hong creator: Xinpu Wang creator: Yanxia Jia uri: https://doi.org/10.7717/peerj.7690 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xie et al. title: The mineralization characteristics of organic carbon and particle composition analysis in reconstructed soil with different proportions of soft rock and sand link: https://peerj.com/articles/7707 last-modified: 2019-09-16 description: The organic carbon mineralization process reflects the release intensity of soil CO2. Therefore, the study of organic carbon mineralization and particle composition analysis of soft rock and sand compound soil can provide technical support and a theoretical basis for soil organic reconstruction (soil structure, materials and biological nutrition). Based on previous research, four treatments were selected: CK (soft rock:sand=0:1), C1 (soft rock:sand=1:5), C2 (soft rock:sand=1:2) and C3 (soft rock:sand=1:1), respectively. Specifically, we analyzed the organic carbon mineralization process and soil particle composition by lye absorption, laser granulometer, and scanning electron microscope. The results showed that there was no significant difference in organic carbon content between C1, C2 , and C3 treatments, but they were significantly higher than in the CK treatment (P < 0.05). The organic carbon mineralization rate in each treatment accords with a logarithmic function throughout the incubation period (P < 0.01), which can be divided into a rapid decline phase in days 1 to 11 followed by a steady decline phase in days 11 to 30. The cumulative mineralization on the 11th day reached 54.96%–74.44% of the total mineralization amount. At the end of the incubation, the cumulative mineralization and potential mineralizable organic carbon content of the C1, C2 and C3 treatments were significantly higher than those of the CK treatment. The cumulative mineralization rate was also the lowest in the C1 and C2 treatment. The turnover rate constant of soil organic carbon in each treatment was significantly lower than that of the CK treatment, and the residence time increased. With the increase of volume fraction of soft rock, the content of silt and clay particles increased gradually, the texture of soil changed from sandy soil to sandy loam, loam , and silty loam, respectively. With the increase of small particles, the structure of soil appear ed to collapse when the volume ratio of soft rock was 50%. A comprehensive mineralization index and scanning electron microscopy analysis, when the ratio of soft rock to sand volume was 1:5–1:2, this can effectively increase the accumulation of soil organic carbon. Then, the distribution of soil particles was more uniform, the soil structure was stable (not collapsed), and the mineralization level of unit organic carbon was lower. Our research results have practical significance for the large area popularization of soft rock and sand compound technology. creator: Zhen Guo creator: Jichang Han creator: Yan Xu creator: Yangjie Lu creator: Chendi Shi creator: Lei Ge creator: Tingting Cao creator: Juan Li uri: https://doi.org/10.7717/peerj.7707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al. title: AURKB: a promising biomarker in clear cell renal cell carcinoma link: https://peerj.com/articles/7718 last-modified: 2019-09-16 description: BackgroundAurora kinase B (AURKB) is an important carcinogenic factor in various tumors, while its role in clear cell renal cell carcinoma (ccRCC) still remains unclear. This study aimed to investigate its prognostic value and mechanism of action in ccRCC.MethodsGene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. R software was utilized to analyze the expression and prognostic role of AURKB in ccRCC. Gene set enrichment analysis (GSEA) was used to analyze AURKB related signaling pathways in ccRCC.ResultsAURKB was expressed at higher levels in ccRCC tissues than normal kidney tissues. Increased AURKB expression in ccRCC correlated with high histological grade, pathological stage, T stage, N stage and distant metastasis (M stage). Kaplan-Meier survival analysis suggested that high AURKB expression patients had a worse prognosis than patients with low AURKB expression levels. Multivariate Cox analysis showed that AURKB expression is a prognostic factor of ccRCC. GSEA indicated that genes involved in autoimmune thyroid disease, intestinal immune network for IgA production, antigen processing and presentation, cytokine-cytokine receptor interaction, asthma, etc., were differentially enriched in the AURKB high expression phenotype.ConclusionsAURKB is a promising biomarker for predicting prognosis of ccRCC patients and a potential therapeutic target. In addition, AURKB might regulate progression of ccRCC through modulating intestinal immune network for IgA production and cytokine-cytokine receptor interaction, etc. signaling pathways. However, more research is necessary to validate the findings. creator: Bangbei Wan creator: Yuan Huang creator: Bo Liu creator: Likui Lu creator: Cai Lv uri: https://doi.org/10.7717/peerj.7718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wan et al. title: Prediction model for patients with acute respiratory distress syndrome: use of a genetic algorithm to develop a neural network model link: https://peerj.com/articles/7719 last-modified: 2019-09-16 description: BackgroundAcute respiratory distress syndrome (ARDS) is associated with significantly increased risk of death, and early risk stratification may help to choose the appropriate treatment. The study aimed to develop a neural network model by using a genetic algorithm (GA) for the prediction of mortality in patients with ARDS.MethodsThis was a secondary analysis of two multicenter randomized controlled trials conducted in forty-four hospitals that are members of the National Heart, Lung, and Blood Institute, founded to create an acute respiratory distress syndrome Clinical Trials Network. Model training and validation were performed using the SAILS and OMEGA studies, respectively. A GA was employed to screen variables in order to predict 90-day mortality, and a neural network model was trained for the prediction. This machine learning model was compared to the logistic regression model and APACHE III score in the validation cohort.ResultsA total number of 1,071 ARDS patients were included for analysis. The GA search identified seven important variables, which were age, AIDS, leukemia, metastatic tumor, hepatic failure, lowest albumin, and FiO2. A representative neural network model was constructed using the forward selection procedure. The area under the curve (AUC) of the neural network model evaluated with the validation cohort was 0.821 (95% CI [0.753–0.888]), which was greater than the APACHE III score (0.665; 95% CI [0.590–0.739]; p = 0.002 by Delong’s test) and logistic regression model, albeit not statistically significant (0.743; 95% CI [0.669–0.817], p = 0.130 by Delong’s test).ConclusionsThe study developed a neural network model using a GA, which outperformed conventional scoring systems for the prediction of mortality in ARDS patients. creator: Zhongheng Zhang uri: https://doi.org/10.7717/peerj.7719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang title: CeRNA network analysis and functional enrichment of salt sensitivity of blood pressure by weighted-gene co-expression analysis link: https://peerj.com/articles/7534 last-modified: 2019-09-13 description: BackgroundSalt sensitivity of blood pressure (SSBP) is an independent risk factor for cardiovascular disease. The pathogenic mechanisms of SSBP are still uncertain. This study aimed to construct the co-regulatory network of SSBP and data mining strategy based on the competitive endogenous RNA (ceRNA) theory.MethodsLncRNA and mRNA microarray was performed to screen for candidate RNAs. Four criteria were used to select the potential differently expressed RNAs. The weighted correlation network analysis (WGCNA) package of R software and target miRNA and mRNA prediction online databases were used to construct the ceRNA co-regulatory network and discover the pathways related to SSBP. Gene ontology enrichment, gene set enrichment analysis (GSEA) and KEGG pathway analysis were performed to explore the functions of hub genes in networks.ResultsThere were 274 lncRNAs and 36 mRNAs that differently expressed between salt-sensitive and salt-resistant groups (P < 0.05). Using WGCNA analysis, two modules were identified (blue and turquoise). The blue module had a positive relationship with salt-sensitivity (R = 0.7, P < 0.01), high-density lipoprotein (HDL) (R = 0.53, P = 0.02), and total cholesterol (TC) (R = 0.55, P = 0.01). The turquoise module was positively related with triglyceride (TG) (R = 0.8, P < 0.01) and low-density lipoprotein (LDL) (R = 0.54, P = 0.01). Furthermore, 84 ceRNA loops were identified and one loop may be of great importance for involving in pathogenesis of SSBP. KEGG analysis showed that differently expressed mRNAs were mostly enriched in the SSBP-related pathways. However, the enrichment results of GSEA were mainly focused on basic physical metabolic processes.ConclusionThe microarray data mining process based on WGCNA co-expression analysis had identified 84 ceRNA loops that closely related with known SSBP pathogenesis. The results of our study provide implications for further understanding of the pathogenesis of SSBP and facilitate the precise diagnosis and therapeutics. creator: Han Cao creator: Han Qi creator: Zheng Liu creator: Wen-Juan Peng creator: Chun-Yue Guo creator: Yan-Yan Sun creator: Christine Pao creator: Yu-Tao Xiang creator: Ling Zhang uri: https://doi.org/10.7717/peerj.7534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cao et al. title: Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies link: https://peerj.com/articles/7543 last-modified: 2019-09-13 description: Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation. creator: Bruna Trevisan creator: Daniel M.C. Alcantara creator: Denis Jacob Machado creator: Fernando P.L. Marques creator: Daniel J.G. Lahr uri: https://doi.org/10.7717/peerj.7543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Trevisan et al. title: Biochar application significantly affects the N pool and microbial community structure in purple and paddy soils link: https://peerj.com/articles/7576 last-modified: 2019-09-13 description: BackgroundThe increasing demand for food production has resulted in the use of large quantities of chemical fertilizers. This has created major environmental problems, such as increased ammonia volatilization, N2O emission, and nitrogen (N) leaching from agricultural soil. In particular, the utilization rate of N fertilizer is low in subtropical southern parts of China due to high rainfall. This causes not only large financial losses in agriculture, but also serious environmental pollution.MethodsIn this study, 16S rDNA-based analysis and static-chamber gas chromatography were used to elucidate the effects of continuous straw biochar application on the N pool and bacteria environment in two typical soil types, purple and paddy soils, in southern China.ResultsStraw biochar application (1) improved the soil N pool in both rhizosphere and non-rhizosphere soils; (2) significantly reduced the emission of N2O, with no difference in emission between 1 and 2 years of application; (3) increased the abundance of N-processing bacteria in the soil and altered the bacterial community structure; and (4) improved the tobacco yield and N use efficiency in paddy soil. These findings suggest that, in southern China, the application of straw biochar can promote N transformation in purple and paddy soils and reduce the emission of the greenhouse gas N2O. creator: Shen Yan creator: Zhengyang Niu creator: Haitao Yan creator: Fei Yun creator: Guixin Peng creator: Yongfeng Yang creator: Guoshun Liu uri: https://doi.org/10.7717/peerj.7576 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al. title: Notes on vocalizations of Brazilian amphibians IV: advertisement calls of 20 Atlantic Forest frog species link: https://peerj.com/articles/7612 last-modified: 2019-09-13 description: Bioacoustics is a powerful tool used for anuran species diagnoses, given that advertisement calls are signals related to specific recognition and mate attraction. Thus, call descriptions can support species taxonomy. In spite of that, call descriptions are lacking for many species, delaying advances in biodiversity research. Here, we describe the advertisement calls of 20 anuran species from the Brazilian Atlantic Forest. We accessed 50 digital recordings deposited in the Fonoteca Neotropical Jacques Vielliard. Acoustic analyses were carried out in the software Raven pro 1.5. We provide a general comparison of call structure among species inside taxonomic groups and genera. The vocalizations described here belong to poorly known species, which are representatives of six families: Brachycephalidae, Bufonidae, Ceratophryidae, Cycloramphidae, Hylidae, and Phyllomedusidae. Despite this, still there are 163 species of anurans from Atlantic Forest with calls not formally described. Our work represents an important step in providing data for a taxonomic perspective and improving the knowledge of the Atlantic Forest anuran diversity. creator: Lucas Rodriguez Forti creator: Célio Fernando Baptista Haddad creator: Felipe Leite creator: Leandro de Oliveira Drummond creator: Clodoaldo de Assis creator: Lucas Batista Crivellari creator: Caio Marinho Mello creator: Paulo Christiano Anchietta Garcia creator: Camila Zornosa-Torres creator: Luís Felipe Toledo uri: https://doi.org/10.7717/peerj.7612 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Forti et al. title: Analysis of small RNA changes in different Brassica napus synthetic allopolyploids link: https://peerj.com/articles/7621 last-modified: 2019-09-13 description: Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation. creator: Yunxiao Wei creator: Fei Li creator: Shujiang Zhang creator: Shifan Zhang creator: Hui Zhang creator: Rifei Sun uri: https://doi.org/10.7717/peerj.7621 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wei et al. title: EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model link: https://peerj.com/articles/7657 last-modified: 2019-09-13 description: Chromatin contacts between regulatory elements are of crucial importance for the interpretation of transcriptional regulation and the understanding of disease mechanisms. However, existing computational methods mainly focus on the prediction of interactions between enhancers and promoters, leaving enhancer-enhancer (E-E) interactions not well explored. In this work, we develop a novel deep learning approach, named Enhancer-enhancer contacts prediction (EnContact), to predict E-E contacts using genomic sequences as input. We statistically demonstrated the predicting ability of EnContact using training sets and testing sets derived from HiChIP data of seven cell lines. We also show that our model significantly outperforms other baseline methods. Besides, our model identifies finer-mapping E-E interactions from region-based chromatin contacts, where each region contains several enhancers. In addition, we identify a class of hub enhancers using the predicted E-E interactions and find that hub enhancers tend to be active across cell lines. We summarize that our EnContact model is capable of predicting E-E interactions using features automatically learned from genomic sequences. creator: Mingxin Gan creator: Wenran Li creator: Rui Jiang uri: https://doi.org/10.7717/peerj.7657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gan et al. title: Screening and identification of SipC-interacting proteins in Salmonella enteritidis using Gal4 yeast two-hybrid system in duck link: https://peerj.com/articles/7663 last-modified: 2019-09-13 description: The zoonotic pathogen Salmonella not only reduces the production performance in ducks, but also poses a serious threat to human health through eggs and pollutes water bodies through feces. SipC, an effector protein of type III secretion systems (T3SS) in Salmonella, mediates translocation of effectors into the eukaryotic host. However, the precise role of SipC effectors remains unknown in ducks. In this study, the SipC from duck granulosa cells (dGCs) was selected as bait, and the SipC-interacting proteins in Salmonella enteritidis (SE) were screened using Gal4 yeast two-hybrid system in duck. Twelve SipC-interacting proteins were identified. Among those, the p53-effector related to PMP-22 (PERP) and TGF-β activated kinase 1-binding protein 2 (TAB2) were selected to further confirm the function by GST pull-down in vitro. Over-expression of PERP resulted in not only increasing SE adhesion and invasion but also triggering the production of IL-1β and IFN-α in SE infected dGCs, while knock-down PERP showed the opposite tendency (P < 0.01). In addition, TAB2 significantly induced the production of IL-6, IL-1β, IFN-α, and INF-γ in SE infected dGCs (P < 0.05), but did not cause obvious changes in SE adhesion and invasion. When the sipC in SE was deleted, the activities of duck PERP and TAB2 were abolished because they could not bind to SipC. Taken together, although the protein of PERP and TAB2 can interact with SipC, their mechanisms were different in duck challenged by SE. Therefore, PERP was involved in SE invasion and inflammatory response of dGC ovaries, and TAB2 only contributed to dGCs inflammatory response, which provided critical insights about the mechanism in host- bacterium protein interactions during Salmonella invasion in duck. creator: Yu Zhang creator: Tiantian Gu creator: Yang Chen creator: Guoqiang Zhu creator: Wanwipa Vongsangnak creator: Qi Xu creator: Guohong Chen uri: https://doi.org/10.7717/peerj.7663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals link: https://peerj.com/articles/7669 last-modified: 2019-09-13 description: Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship. creator: Sébastien Leveque creator: Lutfi Afiq-Rosli creator: Yin Cheong Aden Ip creator: Sudhanshi S. Jain creator: Danwei Huang uri: https://doi.org/10.7717/peerj.7669 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Leveque et al. title: Red-crowned crane (Grus japonensis) prefers postharvest reed beds during winter period in Yancheng National Nature Reserve link: https://peerj.com/articles/7682 last-modified: 2019-09-13 description: Reed beds represent an important habitat for the survival of birds by providing favorable foraging and reproduction conditions. Reed management, as a traditional agricultural activity, primarily includes water level control and vegetation removal by cutting. Red-crowned crane (Grus japonensis) is one of the most endangered cranes, and their population continues to decline due to habitat loss caused by artificial activities. A lack of research relating to how reed management affects crane habitat distribution patterns throughout the wintering period hinders our ability to offer conservation recommendations. In the present study, we explored the effect of reed management on the habitat distribution patterns and analyzed the food resources of red-crowned crane in the Yancheng National Nature Reserve (YNNR). According to the reed management activities in December, we divided the wintering period into two phases: the preharvest period and the postharvest period. Throughout the wintering period, the number of cranes recorded in the common seepweed (Suaeda glauca) tidal flats remained stable, but cranes were rarely recorded in the smooth cordgrass (Spartina alterniflora) tidal flats and aquaculture fish ponds. The number of cranes, however, showed a noticeable fluctuation in the reed beds during the two periods. Before the reed harvest, only a small proportion of cranes were recorded in the reed beds (relative abundance = 2.9%). However, more cranes (relative abundance = 61.0%) were recorded after the reed harvest. Water was introduced from adjacent rivers and fish ponds to submerge the cut reed beds. Changes in potential animal food resources (items and biomass) might be one of the vital reasons for the preference of cranes to the postharvest reed beds. Our results suggest that traditional reed management in the YNNR could benefit this flagship crane species that winters in the wetland system. However, as reed harvest has been forbidden in the core zone for conservation purposes since 2016, further research is needed to verify whether forbidding the harvest of reeds is reasonable. creator: Peng Xu creator: Yalan Zhang creator: Xiaoran Zhang creator: Hao Chen creator: Changhu Lu uri: https://doi.org/10.7717/peerj.7682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu et al. title: Niches and climate-change refugia in hundreds of species from one of the most arid places on Earth link: https://peerj.com/articles/7409 last-modified: 2019-09-12 description: Background and AimsGlobal climate change is a major threat to biodiversity worldwide. Several arid areas might expand in the future, but it is not clear if this change would be positive or negative for arid-adapted lineages. Here, we explore whether climatic niche properties are involved in the configuration of climate refugia and thus in future species trends.MethodsTo estimate putative climate refugia and potential expansion areas, we used maximum entropy models and four climate-change models to generate current and future potential distributions of 142 plant species endemic to the Atacama and mediterranean Chilean ecosystems. We assessed the relationship between the similarity and breadth of thermal and precipitation niches with the size of climate refugia and areas of potential expansions.Key ResultsWe found a positive relationship between breadth and similarity for thermal niche with the size of climate refugia, but only niche similarity of the thermal niche was positively related with the size of expansion areas. Although all lineages would reduce their distributions in the future, few species are predicted to be at risk of extinction in their current distribution, and all of them presented potential expansion areas.ConclusionSpecies with a broad niche and niche dissimilarity will have larger refugia, and species with niche dissimilarity will have larger expansion areas. In addition, our prediction for arid lineages shows that these species will be moderately affected by climate change. creator: Milen Duarte creator: Pablo C. Guerrero creator: Mary T.K. Arroyo creator: Ramiro O. Bustamante uri: https://doi.org/10.7717/peerj.7409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Duarte et al. title: Antimicrobial photodynamic therapy on Staphylococcus aureus and Escherichia coli using malachite green encapsulated mesoporous silica nanoparticles: an in vitro study link: https://peerj.com/articles/7454 last-modified: 2019-09-12 description: BackgroundRise in the number of healthcare associated or hospital acquired infections is a major problem affecting the global healthcare sector. We evaluated superior antibacterial and antibiofilm photodynamic therapy (aPDT) using malachite green encapsulated mesoporous silica nanoparticles (MG-MSN) against Staphylococcus aureus and Escherichia coli, which are known to be major causative agents of nosocomial infections.MethodsMalachite green (MG) was encapsulated on mesoporous silica nanoparticles (MSN). Fourier-transform infrared spectroscopy, Transmission electron microscopy, and spectroscopic analysis were performed to characterize the MG-MSN. The antimicrobial efficacies of MSN, MG, and MG-MSN were investigated and the results were recorded.ResultsMG-MSN was effective against both the tested bacteria. S. aureus was more phototoxic to MG-MSN compared to E. coli. The antibiofilm efficacy of MG-MSN on E. coli and S. aureus was also studied. Biofilm inhibition was 65.68 ± 2.62% in E. coli and 79.66 ± 3.82% in S. aureus. Cell viability assay, exopolysaccharides quantification, and confocal laser scanning microscopy studies also revealed the enhanced antibiofilm activity of MG-MSN when used as a potential photosensitizer for aPDT. This study can be extended to eradicate these strains from localized superficial infections and medical appliances, preventing nosocomial infections. creator: Parasuraman Paramanantham creator: Busi Siddhardha creator: Sruthil Lal SB creator: Alok Sharan creator: Abdullah A. Alyousef creator: Mohammed Saeed Al Dosary creator: Mohammed Arshad creator: Asad Syed uri: https://doi.org/10.7717/peerj.7454 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Paramanantham et al. title: Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known link: https://peerj.com/articles/7500 last-modified: 2019-09-12 description: Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known. creator: Mikhail I. Schelkunov creator: Maxim S. Nuraliev creator: Maria D. Logacheva uri: https://doi.org/10.7717/peerj.7500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schelkunov et al. title: Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses link: https://peerj.com/articles/7510 last-modified: 2019-09-12 description: Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo. creator: Yanan Shi creator: Huanlong Liu creator: Yameng Gao creator: Yujiao Wang creator: Min Wu creator: Yan Xiang uri: https://doi.org/10.7717/peerj.7510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Shi et al. title: A stepping stone to compositionality in chimpanzee communication link: https://peerj.com/articles/7623 last-modified: 2019-09-12 description: Compositionality refers to a structural property of human language, according to which the meaning of a complex expression is a function of the meaning of its parts and the way they are combined. Compositionality is a defining characteristic of all human language, spoken and signed. Comparative research into the emergence of human language aims at identifying precursors to such key features of human language in the communication of other primates. While it is known that chimpanzees, our closest relatives, produce a variety of gestures, facial expressions and vocalizations in interactions with their group members, little is known about how these signals combine simultaneously. Therefore, the aim of the current study is to investigate whether there is evidence for compositional structures in the communication of chimpanzees. We investigated two semi-wild groups of chimpanzees, with focus on their manual gestures and their combinations with facial expressions across different social contexts. If there are compositional structures in chimpanzee communication, adding a facial expression to a gesture should convey a different message than the gesture alone, a difference that we expect to be measurable by the recipient’s response. Furthermore, we expect context-dependent usage of these combinations. Based on a form-based coding procedure of the collected video footage, we identified two frequently used manual gestures (stretched arm gesture and bent arm gesture) and two facial expression (bared teeth face and funneled lip face). We analyzed whether the recipients’ response varied depending on the signaler’s usage of a given gesture + face combination and the context in which these were used. Overall, our results suggest that, in positive contexts, such as play or grooming, specific combinations had an impact on the likelihood of the occurrence of particular responses. Specifically, adding a bared teeth face to a gesture either increased the likelihood of affiliative behavior (for stretched arm gesture) or eliminated the bias toward an affiliative response (for bent arm gesture). We show for the first time that the components under study are recombinable, and that different combinations elicit different responses, a property that we refer to as componentiality. Yet our data do not suggest that the components have consistent meanings in each combination—a defining property of compositionality. We propose that the componentiality exhibited in this study represents a necessary stepping stone toward a fully evolved compositional system. creator: Linda S. Oña creator: Wendy Sandler creator: Katja Liebal uri: https://doi.org/10.7717/peerj.7623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Oña et al. title: Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum) link: https://peerj.com/articles/7664 last-modified: 2019-09-12 description: Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237–323 amino acids, with a theoretical molecular weight (MW) of 24.31–31.80 kDa and an isoelectric point (pI) value of 4.73–10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies. creator: Weiguo Qian creator: Xiaomin Yang creator: Jiawen Li creator: Rui Luo creator: Xiufeng Yan creator: Qiuying Pang uri: https://doi.org/10.7717/peerj.7664 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qian et al. title: Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035 link: https://peerj.com/articles/7665 last-modified: 2019-09-12 description: Acute farmland expansion and rapid urbanization in Central Asia have accelerated land use/land cover changes, which have substantial effects on ecosystem services. However, the spatiotemporal variations in ecosystem service values (ESVs) in Central Asia are not well understood. Here, based on land use products with 300-m resolution for the years 1995, 2005 and 2015 and transfer methodology, we predicted land use and land cover (LULC) for 2025 and 2035 using CA-Markov, assessed changes in ESVs in response to LULC dynamics, and explored the elasticity of the response of ESV to LULC changes. We found significant expansions of cropland (+22.10%) and urban areas (+322.40%) and shrinking of water bodies (−38.43%) and bare land (−9.42%) during 1995–2035. The combined value of ecosystem services of water bodies, cropland, and grassland accounted for over 90% of the total ESVs. Our study showed that cropland ecosystem services value increased by 93.45 billion US$ from 1995 to 2035, which was mainly caused by the expansion of cropland area. However, the area of water bodies decreased sharply during 1995–2035, causing a loss of 64.38 billion US$. Biodiversity, food production and water regulation were major ecosystem service functions, accounting for 80.52% of the total ESVs. Our results demonstrated that effective land-use policies should be made to control farmland expansion and protect water bodies, grassland and forestland for more sustainable ecosystem services. creator: Jiangyue Li creator: Hongxing Chen creator: Chi Zhang creator: Tao Pan uri: https://doi.org/10.7717/peerj.7665 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Dietary fermented products using koji mold and sweet potato-shochu distillery by-product promotes hepatic and serum cholesterol levels and modulates gut microbiota in mice fed a high-cholesterol diet link: https://peerj.com/articles/7671 last-modified: 2019-09-12 description: It has been reported that fermented products (FPs) prepared from sweet potato-shochu distillery by-product suppressed weight gain and decreased serum cholesterol levels in mice under normal dietary conditions. Furthermore, from the information gained from the above data regarding health benefits of the FPs, the aim of this study was evaluating the effects of dietary FPs on lipid accumulation and gut microbiota in mice with or without cholesterol-load in the diet. C57BL/6N mice were fed normal (CO) diet, CO with 10% FPs (CO + FPs) diet, cholesterol loaded (HC) diet, or HC with 10% FPs (HC + FPs) diet for 8 weeks. The mice were then euthanized, and blood samples, tissue samples, and feces were collected. The adipose tissue weight and liver triglyceride levels in the HC + FPs diet groups were significantly reduced compared to that in the HC diet groups. However, FPs significantly increased the serum non-high-density lipoprotein cholesterol (HDL-C) levels, the ratio of non-HDL-C to HDL-C and hepatic total cholesterol levels in mice fed cholesterol-loaded diet compared with that of the HC diet group. Since dietary FPs significantly decreased the protein expression levels of cholesterol 7 alpha-hydroxylase 1 in the HC + FPs diet groups, the cholesterol accumulation in FPs group may be explained by insufficient catabolism from cholesterol to bile acid. In addition, the dietary FPs tended to increase Clostridium cluster IV and XIVa, which are butyrate-producing bacteria. Related to the result, n-butyrate was significantly increased in the CO + FPs and the HC + FPs diet groups compared to their respective control groups. These findings suggested that dietary FPs modulated the lipid pool and gut microbiota. creator: Toshiki Kosakai creator: Hirotaka Kato creator: Cho Sho creator: Kuniaki Kawano creator: Ken-ichi Iwai creator: Yoshikazu Takase creator: Kenjiro Ogawa creator: Kazuo Nishiyama creator: Masao Yamasaki uri: https://doi.org/10.7717/peerj.7671 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kosakai et al. title: Arbuscular mycorrhizal fungi alter the food utilization, growth, development and reproduction of armyworm (Mythimna separata) fed on Bacillus thuringiensis maize link: https://peerj.com/articles/7679 last-modified: 2019-09-12 description: BackgroundThe cultivation of Bt maize (maize genetically modified with Bacillus thuringiensis) continues to expand globally. Arbuscular mycorrhizal fungi (AMF), an important kind of microorganism closely related to soil fertility and plant nutrition, may influence the ecological risk of target lepidopteran pests in Bt crops.MethodsIn this study, transgenic Bt maize (Line IE09S034 with Cry1Ie vs. its parental line of non-Bt maize cv. Xianyu335) was inoculated with a species of AMF, Glomus caledonium (GC). Its effects on the food utilization, reproduction and development of armyworm, Mythimna separata, were studied in a potted experiment from 2017 to 2018.ResultsGC inoculation increased the AMF colonization of both modified and non-modified maize, and also increased the grain weight per plant and 1,000-grain weight of modified and non-modified maize. However, the cultivation of Bt maize did not significantly affect the AMF colonization. The feeding of M. separata with Bt maize resulted in a notable decrease in RCR (relative consumption rate), RGR (relative growth rate), AD (approximate digestibility), ECD (efficiency of conversion of digested food) and ECI (efficiency of conversion of ingested food) parameters in comparison to those observed in larvae fed with non-Bt maize in 2017 and 2018, regardless of GC inoculation. Furthermore, remarkable prolongation of larval life span and decreases in the rate of pupation, weight of pupa, rate of eclosion, fecundity and adult longevity of M. separata were observed in the Bt treatment regardless of GC inoculation during the two-year experiment. Also, when M. separata was fed with Bt maize, a significant prolongation of larval life and significant decreases in the pupal weight, fecundity and adult longevity of M. separata were observed when inoculated with GC. However, it was just the opposite for larvae fed with non-Bt maize that was inoculated with GC. The increased percentage of larval life-span, the decreased percentages of the food utilization, and the other indexes of reproduction, growth, and development of M. separata fed on Bt maize relative to non-Bt maize were all visibly lower when under GC inoculation in contrast to the CK.DiscussionIt is presumed that Bt maize has a marked adverse impact on M. separata development, reproduction and feeding, especially when in combination with the GC inoculation. Additionally, GC inoculation favors the effectiveness of Bt maize against M. separata larvae by reducing their food utilization ability, which negatively affects the development and reproduction of the armyworm. Thus, Bt maize inoculated with AMF (here, GC) can reduce the severe threats arising of armyworms, and hence the AMF inoculation may play an important ecological functions in the field of Bt maize ecosystem, with potentially high control efficiency for the target lepidopteran pests. creator: Long Wang creator: Sabin Saurav Pokharel creator: Fajun Chen uri: https://doi.org/10.7717/peerj.7679 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Mental practice in isolation improves cervical joint position sense in patients with chronic neck pain: a randomized single-blind placebo trial link: https://peerj.com/articles/7681 last-modified: 2019-09-12 description: ObjectiveThe main objective of this trial was to assess whether action observation (AO) training and motor imagery (MI) produced changes in the cervical joint position sense (CJPS) both at the end of the intervention and 10 min postintervention compared with a placebo intervention in patients with nonspecific chronic neck pain (NSCNP).MethodsA single-blind placebo clinical trial was designed. A total of 30 patients with NSCNP were randomly assigned to the AO group, MI group or placebo observation (PO) group. CJPS in flexion, extension and rotation movements in both planes were the main variables.ResultsThe results obtained in the vertical plane showed that the AO group obtained greater improvements than the PO group in the CJPS in terms of cervical extension movement both at the end of the intervention and 10 min postintervention (p = .001, d = 1.81 and p = .004, d = 1.74, respectively), and also in cervical flexion movement, although only at 10 min after the intervention (p = .035, d = 0.72). In addition, the AO group obtained greater improvements than the MI group in the CJPS only at the end of the intervention in cervical extension movement (p = .041, d = 1.17). Regarding the left rotation cervical movement, both the MI and AO groups were superior to the PO group in both planes at the end of the intervention (p < .05, d > 0.80).ConclusionsAlthough both AO and MI could be a useful strategy for CJPS improvement, the AO group showed the strongest results. The therapeutic potential of the application of mental practice in a clinical context in the early stages of rehabilitation of NSCNP should be considered. creator: Ferran Cuenca-Martínez creator: Roy La Touche creator: Jose Vicente León-Hernández creator: Luis Suso-Martí uri: https://doi.org/10.7717/peerj.7681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cuenca-Martínez et al. title: Simultaneous molecular docking of different ligands to His6-tagged organophosphorus hydrolase as an effective tool for assessing their effect on the enzyme link: https://peerj.com/articles/7684 last-modified: 2019-09-12 description: BackgroundEnzymatic hydrolysis of N-acyl homoserine lactones (AHLs), which are signaling molecules responsible for the development of antibiotic resistance in gram-negative bacteria, is a potential solution to overcoming antibiotic resistance problem. It has been established that hexahistidine-tagged organophosphorus hydrolase (His6-OPH) exhibits lactonase activity against a number of AHLs and that the combined application of His6-OPH with β-lactam antibiotics leads to an increase in the efficiency of the action of both the enzyme and antibiotics. The use of computational methods can be an effective way to search for and select from the known antibiotics to find the most rational “partners” for combining with this enzyme and creating effective antibacterial agents with a dual (lactonase and antibacterial) functional activity.MethodsIn this study, by using AutoDock Vina and Gromacs softwares the molecular docking and the molecular dynamics methods were adopted to simulate models of puromycin, ceftiofur, and/or AHLs docked to the surface of a dimer molecule of His6-OPH and to study their binding properties. GABEDIT and GAMESS-US packages were used to generate and simulate electron densities of docked AHLs.ResultsInteractions of N-butyryl-DL-homoserine lactone (C4-HSL), N-(3-oxooctanoyl)-L-homoserine lactone (C8-HSL) and N-(3-oxododecanoyl)-L-homoserine lactone (C12-HSL) with His6-OPH dimer active sites in the presence of puromycin and ceftiofur were simulated and studied. The possible intersection of long-chain AHLs with antibiotic molecules in the active sites of the enzyme was revealed. The binding energies of antibiotics and AHLs with the His6-OPH surface were estimated. Statistically significant differences (p = 0.003) were observed between the values calculated for both C4-HSL and C12-HSL, whereas there were no statistically significant differences between the values of the other groups (p ≥ 0.100). The binding energies of AHLs with His6-OPH were slightly higher as compared with the binding energies of antibiotics with the enzyme. The dynamics of the most probable models obtained from docking were investigated. RMSD and RMSF analysis of His6-OPH-AHL complexes in the absence and presence of antibiotics were performed. The interaction energy values of antibiotics and AHLs with the His6-OPH were assessed. Significant increase of the AHLs steadiness in enzyme-substrate complexes in the presence of antibiotics was revealed. The interaction between His6-OPH and C12-HSL was established as thermodynamically more favored.ConclusionsIt has been established that the studied antibiotics puromycin and ceftiofur steady the enzyme-substrate complexes, but at the same time lead to a decrease in the long-chain AHL-hydrolytic activity of His6-OPH in such a combination as compared to a native enzyme, and, therefore, it should be taken into account when creating a therapeutic composition based on combining antibiotics with His6-OPH. creator: Aysel Aslanli creator: Elena Efremenko uri: https://doi.org/10.7717/peerj.7684 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Aslanli and Efremenko title: Effect of biomimetic material on stress distribution in mandibular molars restored with inlays: a three-dimensional finite element analysis link: https://peerj.com/articles/7694 last-modified: 2019-09-12 description: BackgroundAlthough biomimetic material has become increasingly popular in dental cosmetology nowadays, it remains unclear how it would affect the restored teeth during chewing. It is necessary to study the influence of biomimetic material on stress distribution in the restored teeth.MethodsEight three-dimensional finite element (FE) models were constructed and divided into two groups. Group 1 included the FE model of intact molar, and the FE models of inlay-restored molars fabricated from IPS e.max CAD, Lava Ultimate and biomimetic materials individually. Enamel was considered a homogeneous material. Group 2 included the FE models of intact molar and molars restored with inlays using IPS e.max CAD, Lava Ultimate and biomimetic materials individually, considering enamel as an inhomogeneous material.ResultsIn Group 1, compared with that in the intact molar, the maximum tensile stress (MTS) in the occlusal grooves decreased in the inlay-restored molars fabricated from IPS e.max CAD and was concentrated on the cavity floor at the buccal side in the inner dentin around inlay. When Lava Ultimate was selected, MTS decreased in the occlusal grooves and on the cavity floor but increased in the lateral walls. In the restored molar using biomimetic material, the MTS on the cavity floor was distributed more evenly than that in the molar using IPS e.max CAD, and no obvious changes were noted in the lateral walls. The same changes were observed in Group 2. No differences in the stress distribution pattern were noted among the FE models in Groups 1 and 2.ConclusionsMolars restored with inlays fabricated from biomimetic material exhibit a more uniform stress distribution in the dentin around restoration. The consideration of enamel as a homogeneous tissue is acceptable for analyzing the maximum principal stress distribution in the inlay-restored molar. creator: Junxin Zhu creator: Danmei Luo creator: Qiguo Rong creator: Xiaoyan Wang uri: https://doi.org/10.7717/peerj.7694 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhu et al. title: Relationship between ROS production, MnSOD activation and periods of fasting and re-feeding in freshwater shrimp Neocaridina davidi (Crustacea, Malacostraca) link: https://peerj.com/articles/7399 last-modified: 2019-09-11 description: The middle region of the digestive system, the midgut of freshwater shrimp Neocaridina davidi is composed of a tube-shaped intestine and the hepatopancreas formed by numerous caeca. Two types of cells have been distinguished in the intestine, the digestive cells (D-cells) and regenerative cells (R-cells). The hepatopancreatic tubules have three distinct zones distinguished along the length of each tubule—the distal zone with R-cells, the medial zone with differentiating cells, and the proximal zone with F-cells (fibrillar cells) and B-cells (storage cells). Fasting causes activation of cell death, a reduction in the amount of reserve material, and changes in the mitochondrial membrane potential. However, here we present how the concentration of ROS changes according to different periods of fasting and whether re-feeding causes their decrease. In addition, the activation/deactivation of mitochondrial superoxide dismutase (MnSOD) was analyzed. The freshwater shrimps Neocaridina davidi (Crustacea, Malacostraca, Decapoda) were divided into experimental groups: animals starved for 14 days, animals re-fed for 4, 7, and 14 days. The material was examined using the confocal microscope and the flow cytometry. Our studies have shown that long-term starvation increases the concentration of free radicals and MnSOD concentration in the intestine and hepatopancreas, while return to feeding causes their decrease in both organs examined. Therefore, we concluded that a distinct relationship between MnSOD concentration, ROS activation, cell death activation and changes in the mitochondrial membrane potential occurred. creator: Agnieszka Włodarczyk creator: Grażyna Wilczek creator: Piotr Wilczek creator: Sebastian Student creator: Anna Ostróżka creator: Monika Tarnawska creator: Magdalena Rost-Roszkowska uri: https://doi.org/10.7717/peerj.7399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Włodarczyk et al. title: Plant host and drought shape the root associated fungal microbiota in rice link: https://peerj.com/articles/7463 last-modified: 2019-09-11 description: Background and AimWater is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought.MethodsFifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation.ResultsThere was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum.ConclusionThis study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice. creator: Beatriz Andreo-Jimenez creator: Philippe Vandenkoornhuyse creator: Amandine Lê Van creator: Arvid Heutinck creator: Marie Duhamel creator: Niteen Kadam creator: Krishna Jagadish creator: Carolien Ruyter-Spira creator: Harro Bouwmeester uri: https://doi.org/10.7717/peerj.7463 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Andreo-Jimenez et al. title: Monitoring public awareness about the endangered northern bald ibis: a case study involving primary school children as citizen scientists link: https://peerj.com/articles/7569 last-modified: 2019-09-11 description: BackgroundCitizen science has evolved over the past decades by motivating members of the public to interact with scientists and actively participate in scientific research and monitoring. For this purpose, a proficient communication is mandatory in order to efficiently convey messages and reduce the gap of knowledge between scientists and lay people. In the present study, we aimed at evaluating the multiplying effect of children, who were trained to communicate their knowledge on an endangered bird species in order to engage the local community in the long-term ornithological monitoring of the free flying and individually marked colony of northern bald ibis (NBI, Geronticus eremita), which was established at the research station in 1997.MethodsPupils of the local primary schools were in regular contact with researchers, enjoyed outdoor encounters with the birds, and were invited to talk about their experience with as many people as possible. Later on, they acted as surveyors to assess the knowledge of the public on (i) the general knowledge about the species, (ii) specific knowledge about the local colony, and (iii) attitudes towards science. In two different years of evaluation (2012 and 2016) a total number of 387 persons were surveyed. The questions were generated together with the pupils and their teachers and the questionnaires were similar for both years of evaluation. All queries were in a closed format.ResultsOur results show an increase in the proportion of correct answers provided by the surveyed persons between the two years of evaluation. Education-based activities may encourage children to effectively act as multipliers of information and attitudes. This has the potential to induce sustainable changes with respect to attitude towards science, at least among local communities. Furthermore, the study suggests caution with the quality of some information reported by citizen scientists, which might be solved by more careful training actions and more specific information about local particularities. Even though the study would have gained more informative power with some additional precautions than in its current form, our findings recommend the empowerment of pupils as multipliers of scientific knowledge. creator: Didone Frigerio creator: Verena Puehringer-Sturmayr creator: Brigitte Neuböck-Hubinger creator: Gudrun Gegendorfer creator: Kurt Kotrschal creator: Katharina Hirschenhauser uri: https://doi.org/10.7717/peerj.7569 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Frigerio et al. title: Genome-wide identification, characterization and expression pattern analysis of APYRASE family members in response to abiotic and biotic stresses in wheat link: https://peerj.com/articles/7622 last-modified: 2019-09-11 description: APYRASEs, which directly regulate intra- and extra-cellular ATP homeostasis, play a pivotal role in the regulation of various stress adaptations in mammals, bacteria and plants. In the present study, we identified and characterized wheat APYRASE family members at the genomic level in wheat. The results identified a total of nine APY homologs with conserved ACR domains. The sequence alignments, phylogenetic relations and conserved motifs of wheat APYs were bioinformatically analyzed. Although they share highly conserved secondary and tertiary structures, the wheat APYs could be mainly categorized into three groups, according to phylogenetic and structural analysis. Additionally, these APYs exhibited similar expression patterns in the root and shoot, among which TaAPY3-1, TaAPY3-3 and TaAPY3-4 had the highest expression levels. The time-course expression patterns of the eight APYs in response to biotic and abiotic stress in the wheat seedlings were also investigated. TaAPY3-2, TaAPY3-3, TaAPY3-4 and TaAPY6 exhibited strong sensitivity to all kinds of stresses in the leaves. Some APYs showed specific expression responses, such as TaAPY6 to heavy metal stress, and TaAPY7 to heat and salt stress. These results suggest that the stress-inducible APYs could have potential roles in the regulation of environmental stress adaptations. Moreover, the catalytic activity of TaAPY3-1 was further analyzed in the in vitro system. The results showed that TaAPY3-1 protein exhibited high catalytic activity in the degradation of ATP and ADP, but with low activity in degradation of TTP and GTP. It also has an extensive range of temperature adaptability, but preferred relatively acidic pH conditions. In this study, the genome-wide identification and characterization of APYs in wheat were suggested to be useful for further genetic modifications in the generation of high-stress-tolerant wheat cultivars. creator: Wenbo Liu creator: Jun Ni creator: Faheem Afzal Shah creator: Kaiqin Ye creator: Hao Hu creator: Qiaojian Wang creator: Dongdong Wang creator: Yuanyuan Yao creator: Shengwei Huang creator: Jinyan Hou creator: Chenghong Liu creator: Lifang Wu uri: https://doi.org/10.7717/peerj.7622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Prevalence of generalized joint hypermobility, musculoskeletal injuries, and chronic musculoskeletal pain among American university students link: https://peerj.com/articles/7625 last-modified: 2019-09-11 description: The objective of this study was to investigate the prevalence of generalized joint hypermobility (GJH) in a university-aged population, whether young adults (aged 18–25 years) with GJH are prone to sustain more musculoskeletal injuries, and are more likely to suffer from chronic musculoskeletal pain. The study used an interactive survey to gather data; GJH was assessed using a cut-off Beighton score of ≥5 in accordance with the 2017 International Classification of EDS criteria. The analyzed sample consisted of 482 female and 172 male participants from Florida Gulf Coast University (USA). The prevalence of GJH in a university-aged population can be estimated at 12.5%. Women did not have higher rates of GJH than men. However, female participants showed significantly higher rates of hypermobility of the spine as well as the right knee and elbow joints. The Beighton scores did not differ by ethnicity/race. Female participants had a lower rate of self-reported injuries than male participants, although this difference was not significant. There was no difference in the proportion of all participants classified within different categories (0; 1–4; 5–9) of Beighton scores and whether or not they reported having been injured. Male and female participants reported chronic pain of joints and neck or back at the same rates across the Beighton score categories. Female participants, however, reported higher pain intensity for chronic neck and back pain. This study increases knowledge about a correlation between GJH, musculoskeletal injuries, and chronic pain of joints, neck, and back in a university-aged population. creator: Peter R. Reuter creator: Kaylee R. Fichthorn uri: https://doi.org/10.7717/peerj.7625 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Reuter and Fichthorn title: Propagule pressure does not consistently predict the outcomes of exotic bird introductions link: https://peerj.com/articles/7637 last-modified: 2019-09-11 description: Some have argued that the role of propagule pressure in explaining the outcomes of bird introductions is well-supported by the historical record. Here, we show that the data from a large published database (including 832 records with propagule information) do not support the conclusion that propagule pressure is the primary determinant of introduction success in birds. A few compendia of historical reports have been widely used to evaluate introduction success, typically by combining data from numerous species and introduction locations. Very few taxa, other than birds, have usable spatially explicit records of introductions over time. This availability of data inflates the perceived importance of bird analyses for addressing factors related to invasion success. The available data allow limited testing of taxonomic and site-level factors of introduction outcomes. We did find significant differences in effort and success probabilities among avian orders and across highly aggregated spatial regions. As a test of a standard and logical expectation of the propagule pressure hypothesis, we concentrated on introductions with the smallest propagules, because it is for these the hypothesis is most likely to be correct. We analyzed the effect of numbers released in small propagules (two through 10) for 227 releases. Weighted linear regression indicated no significant effect of propagule size for this range of release size. In fact, the mean success rate of 28% for propagules of 2–10 isn’t significantly different than that of 34% for propagules of 11–100. Following the example of previous analyses, we expanded the statistical test of propagule pressure to include the full range of release numbers. No significant support for the propagule pressure hypothesis was found using logistic regression with either logit or complementary log-log link functions. creator: Michael P. Moulton creator: Wendell P. Cropper uri: https://doi.org/10.7717/peerj.7637 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Moulton and Cropper title: Genetic associations of vitamin D receptor polymorphisms with advanced liver fibrosis and response to pegylated interferon-based therapy in chronic hepatitis C link: https://peerj.com/articles/7666 last-modified: 2019-09-11 description: Vitamin D receptor (VDR) modulates host immune responses to infections such as hepatitis C virus (HCV) infection, including interferon signaling. This study aimed to investigate the associations of VDR polymorphisms with advanced liver fibrosis and response to pegylated interferon (PEG-IFN)-based therapy in patients with chronic HCV infection. In total, 554 Thai patients with chronic HCV infection treated with a PEG-IFN-based regimen were enrolled. Six single-nucleotide polymorphisms (SNPs) were genotyped: the IL28B C > T (rs12979860) SNP and five VDR SNPs, comprising FokI T > C (rs2228570), BsmI C > T (rs1544410), Tru9I G > A (rs757343), ApaI C > A (rs7975232), and TaqI A > G (rs731236). In total, 334 patients (60.3%) achieved sustained virological response (SVR), and 255 patients (46%) were infected with HCV genotype 1. The bAt (CCA) haplotype, consisting of the BsmI rs1544410 C, ApaI rs7975232 C, and TaqI rs731236 A alleles, was associated with poor response (in terms of lack of an SVR) to PEG-IFN-based therapy. The IL28B rs12979860 CT/TT genotypes (OR = 3.44, 95% CI [2.12–5.58], p < 0.001), bAt haplotype (OR = 2.02, 95% CI [1.04–3.91], p = 0.03), pre-treatment serum HCV RNA (logIU/mL; OR = 1.73, 95% CI [1.31–2.28], p < 0.001), advanced liver fibrosis (OR = 1.68, 95% CI [1.10–2.58], p = 0.02), and HCV genotype 1 (OR = 1.59, 95% CI [1.07–2.37], p = 0.02) independently predicted poor response. Patients with the bAt haplotype were more likely to have poor response compared to patients with other haplotypes (41.4% vs 21.9%, p = 0.03). The FokI rs2228570 TT/TC genotypes (OR = 1.63, 95% CI [1.06–2.51], p = 0.03) and age ≥55 years (OR = 2.25; 95% CI [1.54–3.32], p < 0.001) were independently associated with advanced liver fibrosis, assessed based on FIB-4 score >3.25. VDR polymorphisms were not associated with pre-treatment serum HCV RNA. In Thai patients with chronic HCV infection, the bAt haplotype is associated with poor response to PEG-IFN-based therapy, and the FokI rs2228570 TT/TC genotypes are risk factors for advanced liver fibrosis. creator: Kessarin Thanapirom creator: Sirinporn Suksawatamnuay creator: Wattana Sukeepaisarnjaroen creator: Pisit Tangkijvanich creator: Panarat Thaimai creator: Rujipat Wasitthankasem creator: Yong Poovorawan creator: Piyawat Komolmit uri: https://doi.org/10.7717/peerj.7666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thanapirom et al. title: Risk assessment of FLT3 and PAX5 variants in B-acute lymphoblastic leukemia: a case–control study in a Pakistani cohort link: https://peerj.com/articles/7195 last-modified: 2019-09-10 description: AIMSB-cell acute lymphoblastic leukemia (B-ALL) is amongst the most prevalent cancers of children in Pakistan. Genetic variations in FLT3 are associated with auto-phosphorylation of kinase domain that leads to increased proliferation of blast cells. Paired box family of transcription factor (PAX5) plays a critical role in commitment and differentiation of B-cells. Variations in PAX5 are associated with the risk of B-ALL. We aimed to analyze the association of FLT3 and PAX5 polymorphisms with B cell leukemia in Pakistani cohort.METHODSWe collected 155 B-ALL subject and 155 control blood samples. For analysis, genotyping was done by tetra ARMS-PCR. SPSS was used to check the association of demographic factors of SNPs present in the population with the risk of B-ALL.RESULTSRisk allele frequency A at locus 13q12.2 (rs35958982, FLT3) was conspicuous and showed positive association (OR = 2.30, CI [1.20–4.50], P = 0.005) but genotype frequency (OR = 3.67, CI [0.75–18.10], P = 0.088) failed to show any association with the disease. At locus 9p13.2 (rs3780135, PAX5), the risk allele frequency was significantly higher in B-ALL subjects than ancestral allele frequency (OR = 2.17, CI [1.37–3.43], P = 0.000). Genotype frequency analysis of rs3780135 polymorphism exhibited the protective effect (OR = 0.55, CI [0.72–1.83], P = 0.029). At locus 13q12.2 (rs12430881, FLT3), the minor allele frequency G (OR = 1.15, CI [1.37–3.43], P = 0.043) and genotype frequency (OR = 2.52, P = 0.006) reached significance as showed p < 0.05.CONCLUSIONIn the present study, a strong risk of B-cell acute lymphoblastic leukemia was associated with rs35958982 and rs12430881 polymorphisms. However, rs3780135 polymorphism showed the protective effect. Additionally, other demographic factors like family history, smoking and consanguinity were also found to be important in risk assessment. We anticipate that the information from genetic variations in this study can aid in therapeutic approach in the future. creator: Ammara Khalid creator: Sara Aslam creator: Mehboob Ahmed creator: Shahida Hasnain creator: Aimen Aslam uri: https://doi.org/10.7717/peerj.7195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Khalid et al. title: Abundance of arthropods as food for meadow bird chicks in response to short- and long-term soil wetting in Dutch dairy grasslands link: https://peerj.com/articles/7401 last-modified: 2019-09-10 description: BackgroundThroughout the world, intensive dairy farming has resulted in grasslands almost devoid of arthropods and birds. Meadow birds appear to be especially vulnerable during the chick-rearing period. So far, studies have focused mainly on describing population declines, but solutions to effectively stop these trends on the short-term are lacking. In this study at a single farm, we experimentally manipulated soil moisture through occasional irrigation, to mitigate against early season drainage and create favorable conditions for the emergence of above-ground arthropods during the meadow bird chick rearing phase.MethodsTo guarantee the presence of at least a sizeable arthropod community for the measurement of effects of wetting, we selected a farm with low intensity management. The land use and intensity of the study site and surroundings were categorized according to the national land use database and quantified using remote sensing imagery. From May 1 to June 18, 2017, we compared a control situation, with no water added, to two wetting treatments, a “short-term” (3 weeks) treatment based on wetting on warm days with a sprinkler system and a “long-term” treatment next to a water pond with a consistently raised water table from 2010. We measured soil temperature, soil moisture and resistance as well as the biomass of arthropods at 3-day intervals. Flying arthropods were sampled by sticky traps and crawling arthropods by pitfall traps. Individual arthropods were identified to Order and their length recorded, to assess their relevance to meadow bird chicks.ResultsThe land use analysis confirmed that the selected dairy farm had very low intensity management. This was different from most of the surrounding area (20 km radius), characterized by (very) high intensity land use. The experiments showed that irrigation contributed to cooler soils during midday, and that his happened already in the early part of the season; the differences with the control increased with time. In the short- and long-term treatments, soil moisture increased and soil resistance decreased from the mid-measurement period onward. Compared with the control, cumulative arthropod biomass was higher in the long-term treatment, but showed no change in the irrigation treatment. We conclude that small-scale interventions, such as occasional irrigation, favorably affected local soil properties. However, the effects on above-ground arthropod abundance currently appear limited or overridden by negative landscape-scale processes on arthropods. creator: Livia De Felici creator: Theunis Piersma creator: Ruth A. Howison uri: https://doi.org/10.7717/peerj.7401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 De Felici et al. title: lncRNA TMEM51-AS1 and RUSC1-AS1 function as ceRNAs for induction of laryngeal squamous cell carcinoma and prediction of prognosis link: https://peerj.com/articles/7456 last-modified: 2019-09-10 description: BackgroundLong non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to interact with miRNAs to regulate target genes and promote cancer initiation and progression. The expression of lncRNAs and miRNAs can be epigenetically regulated. The goal of this study was to construct an lncRNA-miRNA-mRNA ceRNA network in laryngeal squamous cell carcinoma (LSCC) and reveal their methylation patterns, which was not investigated previously.MethodsMicroarray datasets available from the Gene Expression Omnibus database were used to identify differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between LSCC and controls, which were then overlapped with differentially methylated regions (DMRs). The ceRNA network was established by screening the interaction relationships between miRNAs and lncRNAs/mRNAs by corresponding databases. TCGA database was used to identify prognostic biomarkers.ResultsFive DELs (downregulated: TMEM51-AS1, SND1-IT1; upregulated: HCP5, RUSC1-AS1, LINC00324) and no DEMs were overlapped with the DMRs, but only a negative relationship occurred in the expression and methylation level of TMEM51-AS1. Five DELs could interact with 11 DEMs to regulate 242 DEGs, which was used to construct the ceRNA network, including TMEM51-AS1-miR-106b-SNX21/ TRAPPC10, LINC00324/RUSC1-AS1-miR-16-SPRY4/MICAL2/ SLC39A14, RUSC1-AS1-miR-10-SCG5 and RUSC1-AS1-miR-7-ZFP1 ceRNAs axes. Univariate Cox regression analysis showed RUSC1-AS1 and SNX21 were associated with overall survival (OS); LINC00324, miR-7 and ZFP1 correlated with recurrence-free survival (RFS); miR-16, miR-10, SCG5, SPRY4, MICAL2 and SLC39A14 were both OS and RFS-related. Furthermore, TRAPPC10 and SLC39A14 were identified as independent OS prognostic factors by multivariate Cox regression analysis.ConclusionDNA methylation-mediated TMEM51-AS1 and non-methylation-mediated RUSC1-AS1 may function as ceRNAs for induction of LSCC. They and their ceRNA axis genes (particularly TMEM51-AS1-miR-106b-TRAPPC10; RUSC1-AS1-miR-16-SLC39A14) may be potentially important prognostic biomarkers for LSCC. creator: Lian Hui creator: Jing Wang creator: Jialiang Zhang creator: Jin Long uri: https://doi.org/10.7717/peerj.7456 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hui et al. title: Wedge resection is equal to segmental resection for pulmonary typical carcinoid patients at localized stage: a population-based analysis link: https://peerj.com/articles/7519 last-modified: 2019-09-10 description: BackgroundMedical institutions worldwide have not reached a consensus on what surgery is the most advisable for pulmonary typical carcinoid (TC) patients at the localized stage. This research focuses on exploring whether wedge resection or segmental resection is the superior option.MethodsThe demographic and clinical information of 1,887 TC patients diagnosed at the localized stage from 2004 to 2015 was collected from the Surveillance, Epidemiology, and End Results (SEER) Program. Patient prognosis was evaluated by KM curves. The chi-square test was used to examine the variation between different groups that would be eliminated by propensity score matching (PSM). Univariate and multivariate Cox proportional hazard model analyses were used to evaluate prognostic values of relative factors.ResultsThe prognosis of TC was the most favorable for patients suffering from pulmonary squamous cell carcinoma (SCC), adenocarcinoma (ADC), and pulmonary carcinoids (PCs). The choice to have surgery, not the type of surgery chosen, was the most significant independent prognostic factor correlated with overall survival (OS) and lung cancer-special survival (LCSS). The prognostic result of the comparison between wedge resection and segmental resection was not statistically significant before or after PSM. In subgroup analysis, the inference still held. creator: Tao Yan creator: Kai Wang creator: Jichang Liu creator: Yukai Zeng creator: Fenglong Bie creator: Guanghui Wang creator: Jiajun Du uri: https://doi.org/10.7717/peerj.7519 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al. title: Oceanographic habitat and the coral microbiomes of urban-impacted reefs link: https://peerj.com/articles/7552 last-modified: 2019-09-10 description: Coral reefs are in decline worldwide. In response to this habitat loss, there are efforts to grow, outplant, and restore corals in many regions. The physical oceanographic habitat of corals—such as sea temperature, waves, ocean currents, and available light—is spatially heterogeneous. We therefore hypothesize that outplant location may affect microbiomes, and ultimately, coral health and restoration success. We evaluated the influence of the physical oceanographic habitat on microbes in wild Porites astreoides and Siderastrea siderea. Tissue samples were collected at four Florida reefs in March, June, and September of 2015. We estimated oceanographic conditions from moored instruments, diver observations, remote sensing data, and numerical models. We analyzed microbiomes using amplicon 16S rRNA high-throughput sequencing data. We found microbial alpha-diversity negatively correlated with in situ sea temperature (which represented both the annual cycle and upwelling), as well as modeled alongshore currents, in situ sea-level, and modeled tide. Microbial beta-diversity correlated positively with significant wave height and alongshore currents from models, remotely-sensed relative turbidity, and in situ temperature. We found that archaea from the order Marine Group II decrease with increases in significant wave height, suggesting that this taxon may be influenced by waves. Also, during times of high wave activity, the relative abundance of bacteria from the order Flavobacteriales increases, which may be due to resuspension and cross-shelf transport of sediments. We also found that bacteria from the order SAR86 increase in relative abundance with increased temperature, which suggests that this taxon may play a role in the coral microbiome during periods of higher temperature. Overall, we find that physical oceanographic variability correlates with the structure of these coral microbiomes in ways that could be significant to coral health. creator: Stephanie M. Rosales creator: Christopher Sinigalliano creator: Maribeth Gidley creator: Paul R. Jones creator: Lewis J. Gramer uri: https://doi.org/10.7717/peerj.7552 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rosales et al. title: Plant density and life history traits of Aconitum spicatum in North-central Nepal: effects of elevation and anthropogenic disturbances link: https://peerj.com/articles/7574 last-modified: 2019-09-10 description: Increasing cross-border trade of medicinal and aromatic plants (MAPs) has put heavy pressure on a considerable number of species in the Himalayas. One of the threatened species in Nepal is Aconitum spicatum. Unfortunately for this species and for many others, our knowledge on population ecology and performance across the distribution range is insufficient, hindering the formulation of species-specific management plans. We therefore studied density and population structure of A. spicatum and assessed variation in its life history traits among three populations (subalpine, lower alpine and alpine) along an elevation gradient (3,000–4,200 m a.s.l.) in Annapurna Conservation Area, north-central Nepal. The results show that human disturbances and topographic factors contributed to the variation in density and life history traits. The overall density ranged between 0.56 ± 0.09 (Mean ± SE) and 2.48 ±  0.24 plants/m2 with highest mean density in the lower alpine and lowest in the subalpine population. The subalpine population was also characterized by lower investment in reproductive structures with lowest seed mass and low seed viability and fecundity. Among the environmental variables tested, harvesting, animal droppings and fire appeared to be the most important factors affecting density of different life stages of A. spicatum. The prevailing harvesting pattern is destructive as it involves uprooting of the whole plant and this appears to be a main reason for low recruitment and reduced density of the subalpine population. The level of disturbance decreased with increasing elevation. In terms of reproductive effort, the alpine population performed best. Our results indicate that the viability of A. spicatum populations depends on controlling over-harvesting and pre-mature harvesting of tubers and protecting younger life stages from grazing, trampling and fire. We therefore recommend that when formulating management guidelines, measures aiming to mitigate such anthropogenic disturbances should be considered. creator: Deep J. Chapagain creator: Henrik Meilby creator: Suresh K. Ghimire uri: https://doi.org/10.7717/peerj.7574 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chapagain et al. title: Technical emptiability of dairy product packaging and its environmental implications in Austria link: https://peerj.com/articles/7578 last-modified: 2019-09-10 description: BackgroundFood waste is a major ecological concern around the globe. While the main function of packaging is to contain and protect food, it may also lead to food waste if residues remain in a package after emptying. Such residues could be attributed to wasteful behavior of consumers, but also to properties of packaging (e.g., geometry, surface tension) and food (e.g., surface tension, viscosity).MethodsIn this study, the technical emptiability (ability of packaging to be emptied entirely) of 36 dairy products is analyzed. Firstly, the amount of food residues in packaging after emptying at room and refrigerator temperature was weighed and set in relation to the original filling quantity. Secondly, streamlined life cycle assessments (LCAs) based on the Product Environmental Footprint guidance with a functional unit of “one kg of consumed dairy product at room or refrigerator temperature in the home of the consumer” are conducted. Finally, technical emptiability was included in the streamlined LCA and attributed to the primary packaging in order to evaluate its environmental impact.ResultsTechnical emptiability for both temperatures combined was found to be between 0.25% (±0.11) and 5.79% (±0.43) for the analyzed dairy products. While there were differences in emptiability results of the same product and different temperatures, no significant trend (p = 0.94) between emptiability and temperature could be observed. Liquid yogurt, cream, and buttermilk in beverage cartons and plastic bottles yielded the highest amounts, while milk in beverage cartons and glass bottles yielded the lowest amounts regarding food residues. Looking at global warming potential, poor technical emptiability of cream in a beverage carton leads to even higher environmental impacts than the production and waste management of its packaging.DiscussionThe streamlined LCA results show that food residues can contribute substantially to the footprint of packaging and can have similar or even higher environmental impacts than packaging production and waste management. Yet, emptiability is remarkably under-researched to this day. Future studies should further develop the methods presented in this paper, while LCA analysts should include technical emptiability when assessing the sustainability of packaging, particularly for those containing resource-intensive goods. creator: Bernhard Wohner creator: Nicole Schwarzinger creator: Ulla Gürlich creator: Victoria Heinrich creator: Manfred Tacker uri: https://doi.org/10.7717/peerj.7578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wohner et al. title: Allergic rhinitis, rather than asthma, might be associated with dental caries, periodontitis, and other oral diseases in adults link: https://peerj.com/articles/7643 last-modified: 2019-09-10 description: BackgroundThe association between asthma (AS), allergic rhinitis (AR) and oral diseases remains inconclusive in adults. AS and AR often coexist. However, studies that investigate AS, AR together and their association with oral diseases are scarce.MethodsData from 22,898 men and 28,541 women, aged 21 to 25 years, were collected from a national database in Taiwan. Five common oral diseases: dental caries, periodontitis, pulpitis, gingivitis, and stomatitis/aphthae were studied. Differences in the incidence of the five oral diseases in AR vs. non-AR, and AS vs. non-AS groups were compared. The incidence of the five oral diseases in men/ women, urban/country citizen, and high/low income groups was studied. The frequencies of clinical visits and impact of topical steroid use between the groups were also studied. The confounding factors included sex, socioeconomic status, urbanization, dentofacial anomalies, disease of salivary flow, diabetes mellitus, and esophageal reflux.ResultsThe incidence and the frequencies of clinical visits for all five oral diseases were higher in those with AR than in the non-AR group after adjusting for confounding factors and AS. Similar observation was made for the AS group, without adjusting for AR. However, if AR was included for adjustment, no relationship was found between AS and oral diseases. In the AR group, those with higher incomes, and country residents had a high risk of developing oral disease. Intranasal steroids, rather than inhaled steroids, were also associated with oral diseases.ConclusionAR, rather than AS, may be associated with oral diseases in young adults. creator: Sai-Wai Ho creator: Ko-Huang Lue creator: Min-Sho Ku uri: https://doi.org/10.7717/peerj.7643 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ho et al. title: Histological changes of female reproductive organs subjected to different jumping exercise intensities and honey supplementation in rats link: https://peerj.com/articles/7646 last-modified: 2019-09-10 description: BackgroundWe assessed histopathological changes of ovaries and uterus in female rats subjected to different jumping exercise intensities combined with honey supplementation at one g/kg body weight/day.MethodsA total of 72 rats were divided into six groups, 12 rats in each: control (C), 20 and 80 jumps (20E, 80E), honey (H), and 20 and 80 jump with honey (20EH, 80EH).ResultsThe endometrium was significantly thicker in the rats in H, 20EH and 80EH groups compared to C, 20E, and 80E. The myometrium thickness was significantly lower in 80E and significantly higher in 80EH compared to C, respectively. There was significantly higher myometrium thickness in 20EH and 80EH compared to 20E and 80E and H. The number of glands of the uterus in 20E and 80E was significantly lower than C. However, there was a significantly higher number of glands in H, 20EH, and 80EH compared to 20E and 80E. The numbers of uterus vessels were significantly lower in 80E compared to 20E. However, the numbers of vessels were significantly higher in H, 20EH, and 80EH compared to 80E. The number of ovarian haemorregia was significantly lower in 20E, 80E, H, 20EH, and 80EH compared to C. The number of corpora lutea was significantly lower in 80EH, H, 80E, and 20E compared to C. However, the number of corpora lutea was significantly higher in 20EH compared to J20 and H.ConclusionThis study suggested that jumping exercises in particularly high-intensity exercise may induce histopathological changes in uterus and ovary in rats, and honey supplementation may ameliorate these effects. creator: Maryam Mosavat creator: Mahaneem Mohamed creator: Foong Kiew Ooi creator: Mitra Mirsanjari creator: Anani Aila Mat Zin creator: Aminah Che Romli uri: https://doi.org/10.7717/peerj.7646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mosavat et al. title: Rate and success of study replication in ecology and evolution link: https://peerj.com/articles/7654 last-modified: 2019-09-10 description: The recent replication crisis has caused several scientific disciplines to self-reflect on the frequency with which they replicate previously published studies and to assess their success in such endeavours. The rate of replication, however, has yet to be assessed for ecology and evolution. Here, I survey the open-access ecology and evolution literature to determine how often ecologists and evolutionary biologists replicate, or at least claim to replicate, previously published studies. I found that approximately 0.023% of ecology and evolution studies are described by their authors as replications. Two of the 11 original-replication study pairs provided sufficient statistical detail for three effects so as to permit a formal analysis of replication success. Replicating authors correctly concluded that they replicated an original effect in two cases; in the third case, my analysis suggests that the finding by the replicating authors was consistent with the original finding, contrary the conclusion of “replication failure” by the authors. creator: Clint D. Kelly uri: https://doi.org/10.7717/peerj.7654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kelly title: Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs link: https://peerj.com/articles/7661 last-modified: 2019-09-10 description: The gut microbiome plays an important role in the health of dogs. Both beneficial microbes and overall diversity can be modulated by diet. Fermentable sources of fiber in particular often increase the abundance of beneficial microbes. Banded crickets (Gryllodes sigillatus) contain the fermentable polysaccharides chitin and chitosan. In addition, crickets are an environmentally sustainable protein source. Considering crickets as a potential source of both novel protein and novel fiber for dogs, four diets ranging from 0% to 24% cricket content were fed to determine their effects on healthy dogs’ (n = 32) gut microbiomes. Fecal samples were collected serially at 0, 14, and 29 days, and processed using high-throughput sequencing of 16S rRNA gene PCR amplicons. Microbiomes were generally very similar across all diets at both the phylum and genus level, and alpha and beta diversities did not differ between the various diets at 29 days. A total of 12 ASVs (amplicon sequence variants) from nine genera significantly changed in abundance following the addition of cricket, often in a dose-response fashion with increasing amounts of cricket. A net increase was observed in Catenibacterium, Lachnospiraceae [Ruminococcus], and Faecalitalea, whereas Bacteroides, Faecalibacterium, Lachnospiracaeae NK4A136 group and others decreased in abundance. Similar changes in Catenibacterium and Bacteroides have been associated with gut health benefits in other studies. However, the total magnitude of all changes was small and only a few specific taxa changed in abundance. Overall, we found that diets containing cricket supported the same level of gut microbiome diversity as a standard healthy balanced diet. These results support crickets as a potential healthy, novel food ingredient for dogs. creator: Jessica K. Jarett creator: Anne Carlson creator: Mariana Rossoni Serao creator: Jessica Strickland creator: Laurie Serfilippi creator: Holly H. Ganz uri: https://doi.org/10.7717/peerj.7661 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jarett et al. title: Rituximab increases the risk of hepatitis B virus reactivation in non-Hodgkin lymphoma patients who are hepatitis B surface antigen-positive or have resolved hepatitis B virus infection in a real-world setting: a retrospective study link: https://peerj.com/articles/7481 last-modified: 2019-09-09 description: BackgroundHepatitis B virus (HBV) reactivation with a hepatitis flare is a common complication in lymphoma patients treated with immunotherapy and/or chemotherapy. Anti-HBV prophylaxis is suggested for non-Hodgkin lymphoma (NHL) patients undergoing rituximab therapy, even those with resolved HBV infection. Since anti-HBV prophylaxis for patients with resolved HBV infection is not covered by national health insurance in Taiwan, a proportion of these patients receive no prophylaxis. In addition, late HBV reactivation has emerged as a new issue in recent reports, and no consensus has been reached for the optimal duration of antiviral prophylaxis. Thus, the aim of our study was to investigate the incidence and outcomes of HBV reactivation in NHL patients in a real-world setting and to study the frequency of late HBV reactivation.MaterialsNon-Hodgkin lymphoma patients who received rituximab and/or chemotherapy at our institute between January 2011 and December 2015 and who were hepatitis B surface antigen (HBsAg)- or hepatitis B core antibody (HBcAb)-positive were reviewed retrospectively.ResultsA total of 388 patients were screened between January 2011 and December 2015. In total, 196 patients were excluded because HBsAg was not assessed, HBcAb was negative or not assessed, or they were not treated with immunosuppressive therapy. Finally, the retrospective study included 62 HBsAg-positive NHL patients and 130 NHL patients with resolved HBV infection (HBsAg-negative and HBcAb-positive). During a median 30.5-month follow-up period, seven patients experienced HBV reactivation, five of whom had a hepatitis flare. The incidence of HBV reactivation did not significantly differ between the HBsAg-positive patients and the resolved HBV infection population without anti-HBV prophylaxis (4.8% vs. 3.1%, P = 0.683). All patients with HBV reactivation were exposed to rituximab. Notably, late HBV reactivation was not uncommon (two of seven patients with HBV reactivation events, 28.6%). Hepatitis B virus reactivation did not influence the patients’ overall survival. An age ≥65 years and an advanced disease stage were independent risk factors for poorer overall survival.ConclusionThe incidence of HBV reactivation was similar between the HBsAg-positive patients with antiviral prophylaxis and the resolved HBV infection population without anti-HBV prophylaxis. All HBV reactivation events occurred in NHL patients exposed to rituximab. Late reactivation was not uncommon. The duration of regular liver function monitoring for more than 1 year after immunosuppressive therapy or after withdrawal of prophylactic antiviral therapy should be prolonged. Determining the exact optimal duration of anti-HBV prophylaxis is warranted in a future prospective study for NHL patients treated with rituximab-containing therapy. creator: Yu-Fen Tsai creator: Ching-I Yang creator: Jeng-Shiun Du creator: Ming-Hui Lin creator: Shih-Hao Tang creator: Hui-Ching Wang creator: Shih-Feng Cho creator: Yi-Chang Liu creator: Yu-Chieh Su creator: Chia-Yen Dai creator: Hui-Hua Hsiao uri: https://doi.org/10.7717/peerj.7481 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tsai et al. title: Characterization of ceRNA network to reveal potential prognostic biomarkers in triple-negative breast cancer link: https://peerj.com/articles/7522 last-modified: 2019-09-09 description: Triple-negative breast cancer (TNBC) is a particular subtype of breast malignant tumor with poorer prognosis than other molecular subtypes. Previous studies have demonstrated that some abnormal expression of non-coding RNAs including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) were closely related to tumor cell proliferation, apoptosis, invasion, migration and drug sensitivity. However, the role of non-coding RNAs in the pathogenesis of TNBC is still unclear. In order to characterize the molecular mechanism of non-coding RNAs in TNBC, we downloaded RNA data and miRNA data from the cancer genome atlas database. We successfully identified 686 message RNAs (mRNAs), 26 miRNAs and 50 lncRNAs as key molecules for high risk of TNBC. Then, we hypothesized that the lncRNA–miRNA–mRNA regulatory axis positively correlates with TNBC and constructed a competitive endogenous RNA (ceRNA) network of TNBC. Our series of analyses has shown that five molecules (TERT, TRIML2, PHBP4, mir-1-3p, mir-133a-3p) were significantly associated with the prognosis of TNBC, and there is a prognostic ceRNA sub-network between those molecules. We mapped the Kaplan–Meier curve of RNA on the sub-network and also suggested that the expression level of the selected RNA is related to the survival rate of breast cancer. Reverse transcription-quantitative polymerase chain reaction showed that the expression level of TRIML2 in TNBC cells was higher than normal. In general, our findings have implications for predicting metastasis, predicting prognosis and discovering new therapeutic targets for TNBC. creator: Xiang Song creator: Chao Zhang creator: Zhaoyun Liu creator: Qi Liu creator: Kewen He creator: Zhiyong Yu uri: https://doi.org/10.7717/peerj.7522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Song et al. title: The new ichthyosauriform Chaohusaurus brevifemoralis (Reptilia, Ichthyosauromorpha) from Majiashan, Chaohu, Anhui Province, China link: https://peerj.com/articles/7561 last-modified: 2019-09-09 description: A new species of ichthyosauriform is recognized based on 20 specimens, including nearly complete skeletons, and named Chaohusaurus brevifemoralis. A part of the specimens was previously identified as Chaohusaurus chaoxianensis and is herein reassigned to the new species. The new species differs from existing species of Chaohusaurus in a suite of features, such as the bifurcation of the caudal peak neural spine and a short femur relative to trunk length. The specimens include both complete and partially disarticulated skulls, allowing rigorous scrutiny of cranial sutures. For example, the squamosal does not participate in the margin of the upper temporal fenestra despite previous interpretations. Also, the frontal unequivocally forms a part of the anterior margin of the upper temporal fenestra, forming the most medial part of the anterior terrace. The skull of the holotype largely retains three-dimensionality with the scleral rings approximately in situ, revealing that the eyeball was uncovered in two different directions, that is, laterally and slightly dorsally through the main part of the orbit, and dorsally through the medial extension of the orbit into the skull roof. This skull construction is likely a basal feature of Ichthyosauromorpha. Phylogenetic analyses place the new species as a sister taxon of Chaohusaurus chaoxianensis. creator: Jian-dong Huang creator: Ryosuke Motani creator: Da-yong Jiang creator: Andrea Tintori creator: Olivier Rieppel creator: Min Zhou creator: Xin-Xin Ren creator: Rong Zhang uri: https://doi.org/10.7717/peerj.7561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Huang et al. title: Correlation between 18F-FDG maximum standardized uptake value with CD147 expression in lung adenocarcinomas: a retrospective study link: https://peerj.com/articles/7635 last-modified: 2019-09-09 description: BackgroundThe pro-tumoral action of the cluster of differentiation 147 (CD147), which is associated with the chemotherapy resistance of lung adenocarcinoma, is partly due to accelerated tumor cell glycolysis. 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) metabolic parameters included maximal standardized uptake value (SUVmax), mean standardized uptake value (SUVmean), metabolic tumor volume (MTV), and total lesion glycolysis (TLG), which are non-invasive markers of the glucose metabolism of tumor cells in vivo. This study aimed to clarify the correlation between PET metabolic parameters and CD147 expression, and to evaluate the prognostic value of CD147 expression in resectable lung adenocarcinoma patients.MethodsA total of 89 lung adenocarcinoma chemotherapy-naive patients who underwent 18F-fluorodeoxyglucose positron emission tomography and computerized tomography scan before pulmonary surgery were retrospectively analyzed. The PET metabolic parameters were calculated by 18F-FDG PET imaging, and CD147 expression was analyzed by immunohistochemistry. SUVmax, SUVmean, MTV, and TLG compared for their performance in predicting the expression of CD147 were illustrated with statistical analysis. All patients were then followed-up for survival analysis.ResultsThe SUVmax was significantly correlated with the CD147 expression and was the primary predictor for the CD147 expression of lung adenocarcinoma. A cut-off value of the SUVmax, 9.77 allowed 85.1% sensitivity and 64.3% specificity for predicting the CD147 positive lung adenocarcinoma. CD147 expression was correlated with tumor differentiation and metastasis. Univariate survival analysis showed that CD147 expression was significantly associated with a shorter overall survival (OS) time. Multivariate analysis revealed that CD147 was an independent prognostic factor of lung adenocarcinoma patients.ConclusionThe SUVmax of a primary tumor measured with 18F-FDG PET may be a simple and non-invasive marker for predicting CD147 expression in lung adenocarcinoma. CD147 is an independent prognostic factor related to OS of postoperative lung adenocarcinoma patients. creator: Fei Guo creator: Xueyan Li creator: Guodong Yao creator: Guangchun Zeng creator: Lijuan Yu uri: https://doi.org/10.7717/peerj.7635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: Expanding walls and shrinking beaches: loss of natural coastline in Okinawa Island, Japan link: https://peerj.com/articles/7520 last-modified: 2019-09-06 description: Okinawa is the largest and most populated island of the Ryukyu Archipelago in southern Japan and is renowned for its natural resources and beauty. Similar as to what has been happening in the rest of the country, Okinawa Island has been affected by an increasing amount of development and construction work. The trend has been particularly acute after reversion to Japanese sovereignty in 1972, following 27 years of post-war American administration. A coastline once characterized by extended sandy beaches surrounded by coral reefs now includes tracts delimited by seawalls, revetments, and other human-made hardening structures. Additionally, part of coastal Okinawa Island was obtained by land-filling shallow ocean areas (land reclamation). Nevertheless, the current extension of the artificial coastline, as well as the level of fragmentation of the natural coastline are unclear, due to the lack of both published studies and easily accessible and updated datasets. The aims of this research were to quantify the extension of coastline alterations in Okinawa Island, including the amount of land-filling performed over the last 41 years, and to describe the coastlines that have been altered the most as well as those that are still relatively pristine. The analyses were performed using a reference map of Okinawa Island based on GIS vector data extracted from the OpenStreetMap (OSM) coastline dataset (average node distance for Okinawa Island = 24 m), in addition to satellite and aerial photography from multiple providers. We measured 431.8 km of altered coastline, equal to about 63% of the total length of coastline in Okinawa Island. Habitat fragmentation is also an issue as the remaining natural coastline was broken into 239 distinct tracts (mean length = 1.05 km). Finally, 21.03 km2 of the island’s surface were of land reclaimed over the last 41 years. The west coast has been altered the most, while the east coast is in relatively more natural conditions, particularly the northern part, which has the largest amount of uninterrupted natural coastline. Given the importance of the ecosystem services that coastal and marine ecosystems provide to local populations of subtropical islands, including significant economic income from tourism, conservation of remaining natural coastlines should be given high priority. creator: Giovanni Diego Masucci creator: James D. Reimer uri: https://doi.org/10.7717/peerj.7520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Masucci and Reimer title: Crucial lncRNAs associated with adipocyte differentiation from human adipose-derived stem cells based on co-expression and ceRNA network analyses link: https://peerj.com/articles/7544 last-modified: 2019-09-06 description: BackgroundInjection of adipose-derived stem cells (ASCs) is a promising treatment for facial contour deformities. However, its treatment mechanisms remain largely unknown. The study aimed to explain the molecular mechanisms of adipogenic differentiation from ASCs based on the roles of long noncoding RNAs (lncRNAs).MethodsDatasets of mRNA–lncRNA (GSE113253) and miRNA (GSE72429) expression profiling were collected from Gene Expression Omnibus database. The differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs) between undifferentiated and adipocyte differentiated human ASCs were identified using the Linear Models for Microarray Data method. DELs related co-expression and competing endogenous RNA (ceRNA) networks were constructed. Protein–protein interaction (PPI) analysis was performed to screen crucial target genes.ResultsA total of 748 DEGs, 17 DELs and 51 DEMs were identified. A total of 13 DELs and 279 DEGs with Pearson correlation coefficients > 0.9 and p-value < 0.01 were selected to construct the co-expression network. A total of 151 interaction pairs among 112 nodes (10 DEMs; eight DELs; 94 DEGs) were obtained to construct the ceRNA network. By comparing the lncRNAs and mRNAs in two networks, five lncRNAs (SNHG9, LINC02202, UBAC2-AS1, PTCSC3 and myocardial infarction associated transcript (MIAT)) and 32 genes (i.e., such as phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), protein tyrosine phosphatase receptor type B (PTPRB)) were found to be shared. PPI analysis demonstrated PIK3R1 , forkhead box O1 (FOXO1; a transcription factor) and estrogen receptor 1 (ESR1) were hub genes, which could be regulated by the miRNAs that interacted with the above five lncRNAs, such as LINC02202-miR-136-5p-PIK3R1, LINC02202-miR-381-3p-FOXO1 and MIAT-miR-18a-5p-ESR1. LINC02202 also could directly co-express with PIK3R1. Furthermore, PTPRB was predicted to be modulated by co-expression with LINC01119.ConclusionMIAT, LINC02202 and LINC01119 may be potentially important, new lncRNAs associated with adipogenic differentiation of ASCs. They may be involved in adipogenesis by acting as a ceRNA or co-expressing with their targets. creator: Kana Chen creator: Shujie Xie creator: Wujun Jin uri: https://doi.org/10.7717/peerj.7544 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chen et al. title: Design, synthesis and antimicrobial activities of novel 1,3,5-thiadiazine-2-thione derivatives containing a 1,3,4-thiadiazole group link: https://peerj.com/articles/7581 last-modified: 2019-09-06 description: A series of novel 1,3,5-thiadiazine-2-thione derivatives containing a 1,3,4-thiadiazole group was designed and synthesized. The structures of all the compounds were well characterized using 1H NMR, 13C NMR and high-resolution mass spectrometer, and further confirmed by the X-ray diffraction analysis of 8d. The antimicrobial activities of all the target compounds against Xanthomonas oryzae pv. oryzicola, X. oryzae pv. oryzae, Rhizoctonia solani and Fusarium graminearum were evaluated. The in vitro antimicrobial bioassays indicated that some title compounds exhibited noteworthy antimicrobial effects against the above strains. Notably, the compound N-(5-(ethylthio)-1,3,4-thiadiazol-2-yl)-2-(5-methyl-6-thioxo-1,3,5-thiadiazinan-3-yl)acetamide (8a) displayed obvious antibacterial effects against X. oryzae pv. oryzicola and X. oryzae pv. oryzae at 100 μg/mL with the inhibition rates of 30% and 56%, respectively, which was better than the commercial bactericide thiodiazole-copper. In addition, the anti-R. solani EC50 value of 8a was 33.70 μg/mL, which was more effective than that of the commercial fungicide hymexazol (67.10 μg/mL). It was found that the substitutes in the 1,3,5-thiadiazine-2-thione and the 1,3,4-thiadiazole rings played a vital role in the antimicrobial activities of the title compounds. More active title compounds against phytopathogenic microorganisms might be obtained via further structural modification. creator: Jinghua Yan creator: Weijie Si creator: Haoran Hu creator: Xu Zhao creator: Min Chen creator: Xiaobin Wang uri: https://doi.org/10.7717/peerj.7581 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yan et al. title: Sensitive and rapid detection of Ortleppascaris sinensis (Nematoda: Ascaridoidea) by loop-mediated isothermal amplification link: https://peerj.com/articles/7607 last-modified: 2019-09-06 description: Ortleppascaris sinensis is the dominant nematode species infecting the gastrointestinal tract of the captive Chinese alligator, a critically endangered species. Gastrointestinal nematode infection may cause a loss of appetite, growth, a development disorder, and even mortality in alligators, especially young ones. This research first establishment a loop-mediated isothermal amplification (LAMP) assay in rapidly identifying O. sinensis, upon the basis of the complete internal transcribed spacers (ITS) gene. Eight sets of primers were designed for recognition of the unique conserved ITS gene sequences, and one set was selected to be the most suitable primer for rapid detection. The specific as well as the sensitive features of the most appropriate primer in LAMP reactions for O. sinensis, and feces specimens of Chinese alligators suffering from O. sinensis were determined. Turbidity monitoring and Te Visual Reagent methods were used for determining negative and positive consequences. According to this study, amplification and visualization of the target DNA could be realized through two detection approaches during 50 min at 65 °C isothermal temperature. The sensitivity of LAMP was a detecting limitation of 3.46 pg/µl DNA. No cross-reactions were found between O. sinensis and any other of the nine heterologous nematode parasites, which shows the outstanding specific features of the primers. The LAMP assay could also perform a detection of target DNA of O. sinensis in the feces samples of Chinese alligators. This LAMP assay is useful for directly detecting O. sinensis in the Chinese alligator breeding centers, particularly due to its rapidity, simplicity and low cost. creator: Jinhong Zhao creator: Wei Xu creator: Genjun Tu creator: Yongkang Zhou creator: Xiaobing Wu uri: https://doi.org/10.7717/peerj.7607 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhao et al. title: Identification of Flap endonuclease 1 as a potential core gene in hepatocellular carcinoma by integrated bioinformatics analysis link: https://peerj.com/articles/7619 last-modified: 2019-09-06 description: Hepatocellular carcinoma (HCC) is a common yet deadly form of malignant cancer. However, the specific mechanisms involved in HCC diagnosis have not yet fully elucidated. Herein, we screened four publically available Gene Expression Omnibus (GEO) expression profiles (GSE14520, GSE29721, GSE45267 and GSE60502), and used them to identify 409 differentially expressed genes (DEGs), including 142 and 267 up- and down-regulated genes, respectively. The DAVID database was used to look for functionally enriched pathways among DEGs, and the STRING database and Cytoscape platform were used to generate a protein-protein interaction (PPI) network for these DEGs. The cytoHubba plug-in was utilized to detect 185 hub genes, and three key clustering modules were constructed with the MCODE plug-in. Gene functional enrichment analyses of these three key clustering modules were further performed, and nine core genes including BIRC5, DLGAP5, DTL, FEN1, KIAA0101, KIF4A, MCM2, MKI67, and RFC4, were identified in the most critical cluster. Subsequently, the hierarchical clustering and expression of core genes in TCGA liver cancer tissues were analyzed using the UCSC Cancer Genomics Browser, and whether elevated core gene expression was linked to a poor prognosis in HCC patients was assessed using the GEPIA database. The PPI of the nine core genes revealed an interaction between FEN1, MCM2, RFC4, and BIRC5. Furthermore, the expression of FEN1 was positively correlated with that of three other core genes in TCGA liver cancer tissues. FEN1 expression in HCC and other tumor types was assessed with the FIREBROWSE and ONCOMINE databases, and results were verified in HCC samples and hepatoma cells. FEN1 levels were also positively correlated with tumor size, distant metastasis and vascular invasion. In conclusion, we identified nine core genes associated with HCC development, offering novel insight into HCC progression. In particular, the aberrantly elevated FEN1 may represent a potential biomarker for HCC diagnosis and treatment. creator: Chuanfei Li creator: Feng Qin creator: Hao Hong creator: Hui Tang creator: Xiaoling Jiang creator: Shuangyan Yang creator: Zhechuan Mei creator: Di Zhou uri: https://doi.org/10.7717/peerj.7619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Dendrobium alkaloids decrease Aβ by regulating α- and β-secretases in hippocampal neurons of SD rats link: https://peerj.com/articles/7627 last-modified: 2019-09-06 description: BackgroundAlzheimer’s disease (AD) is the primary cause of dementia in the elderly. The imbalance between production and clearance of amyloid β (Aβ) is a very early, often initiating factor in AD. Dendrobium nobile Lindl. alkaloids (DNLA) extracted from a Chinese medicinal herb, which have been shown to have anti-aging effects, protected against neuronal impairment in vivo and in vitro. Moreover, we confirmed that DNLA can improve learning and memory function in elderly normal mice, indicating that DNLA has potential health benefits. However, the underlying mechanism is unclear. Therefore, we further explored the effect of DNLA on neurons, which is closely related to learning and memory, based on Aβ.MethodsWe exposed cultured hippocampal neurons to DNLA to investigate the effect of DNLA on Aβ in vitro. Cell viability was evaluated by MTT assays. Proteins were analyzed by Western blot analysis.ResultsThe cell viability of hippocampal neurons was not changed significantly after treatment with DNLA. But DNLA reduced the protein expression of amyloid precursor protein (APP), disintegrin and metalloprotease 10 (ADAM10), β-site APP cleaving enzyme 1 (BACE1) and Aβ1–42 of hippocampal neurons in rats and increased the protein expression of ADAM17.ConclusionsDNLA decreases Aβ by regulating α- and β-secretase in hippocampal neurons of SD rats. creator: Juan Huang creator: Nanqu Huang creator: Minghui Zhang creator: Jing Nie creator: Yunyan Xu creator: Qin Wu creator: Jingshan Shi uri: https://doi.org/10.7717/peerj.7627 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huang et al. title: Differential mechanisms underlying responses of soil bacterial and fungal communities to nitrogen and phosphorus inputs in a subtropical forest link: https://peerj.com/articles/7631 last-modified: 2019-09-06 description: Atmospheric nitrogen (N) deposition and phosphorus (P) addition both can change soil bacterial and fungal community structure with a consequent impact on ecosystem functions. However, which factor plays an important role in regulating responses of bacterial and fungal community to N and P enrichments remains unclear. We conducted a manipulative experiment to simulate N and P inputs (10 g N · m−2 · yr−1 NH4NO3 or 10 g P · m−2 · yr−1 NaH2PO4) and compared their effects on soil bacterial and fungal species richness and community composition. The results showed that the addition of N significantly increased NH4+ and Al3+ by 99.6% and 57.4%, respectively, and consequently led to a decline in soil pH from 4.18 to 3.75 after a 5-year treatment. P addition increased Al3+ and available P by 27.0% and 10-fold, respectively, but had no effect on soil pH. N addition significantly decreased bacterial species richness and Shannon index and resulted in a substantial shift of bacterial community composition, whereas P addition did not. Neither N nor P addition changed fungal species richness, Shannon index, and fungal community composition. A structural equation model showed that the shift in bacterial community composition was related to an increase in soil acid cations. The principal component scores of soil nutrients showed a significantly positive relationship with fungal community composition. Our results suggest that N and P additions affect soil bacterial and fungal communities in different ways in subtropical forest. These findings highlight how the diversity of microbial communities of subtropical forest soil will depend on future scenarios of anthropogenic N deposition and P enrichment, with a particular sensitivity of bacterial community to N addition. creator: Yong Li creator: Dashuan Tian creator: Jinsong Wang creator: Shuli Niu creator: Jing Tian creator: Denglong Ha creator: Yuxi Qu creator: Guangwei Jing creator: Xiaoming Kang creator: Bing Song uri: https://doi.org/10.7717/peerj.7631 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Two new species of Notodasus Fauchald, 1972 (Annelida: Capitellidae) from the Central Indo-Pacific region link: https://peerj.com/articles/7638 last-modified: 2019-09-06 description: NotodasusFauchald, 1972 is a small genus of the polychaete family Capitellidae, including 10 described species worldwide. The genus is unusual in the Central Indo-Pacific, and there is no taxonomic record of Notodasus in this region. In this study, two new species of Notodasus are described and illustrated, namely Notodasus celebensis sp. nov. and N. chinensis sp. nov. The former species, collected from the mixed-species seagrass beds in the Indonesian island of Sulawesi, is mainly characterized by the longitudinally striated epithelium on thoracic segments and the completely separated notopodial lobes. The latter species, obtained from coastal waters off southern China, differs from its congeners with the following characters: tessellated epithelium present on anterior thorax as well as on the dorsum of chaetigers 11 and 12, notopodial lobes fused and chaetal fascicles almost touching each other on anterior abdomen, and branchial pores evident from anterior abdomen. Comparisons are made with closely related species in this paper, and a revised key is provided to all described Notodasus species. The descriptions of the two new species represent the first record of Notodasus in this region and expand the geographical distribution of the genus. creator: Junhui Lin creator: María Elena García-Garza creator: Ucu Yanu Arbi creator: Jianjun Wang uri: https://doi.org/10.7717/peerj.7638 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lin et al. title: Cloning, phylogenetic research, and prokaryotic expression study of the metabolic detoxification gene EoGSTs1 in Empoasca onukii Matsuda link: https://peerj.com/articles/7641 last-modified: 2019-09-06 description: Due to the misuse of chemical pesticides, small green leafhoppers (Empoasca onukii Matsuda) have developed resistance to pesticides, thereby posing a serious problem to the tea industry. Glutathione S-transferases (GSTs) are an important family of enzymes that are involved in pesticide resistance in Empoasca onukii Matsuda. Empoasca onukii GST sigma 1 (EoGSTs1, GenBank: MK443501) is a member of the GST family. In this study, the full-length cDNA of EoGSTs1 was cloned by reverse transcription polymerase chain reaction (qPCR), and its taxonomic identity was examined. Furthermore, we performed bioinformatics and phylogenetic analyses of the gene and structural and functional domain prediction of the protein. The results demonstrate that EoGSTS1 belongs to the Sigma family of GSTs; the full-length EoGSTs1 cDNA is 841 bp with a 624-bp coding region that encodes a 23.68932-kDa protein containing 207 amino acids. The theoretical isoelectric point (IEP) was calculated to be 6.00. Phylogenetic analysis indicates that EoGSTS1 is closely related to the Sub psaltriayangi subfamily of the Cicadoidea superfamily in order Hemiptera, whereas it is distantly related to Periplaneta americana of order Blattodea. Amino acid sequence alignment of EoGSTS1 and GSTs from four other insects of order Hemiptera revealed protein sequence conservation. Tertiary structure analysis and structural domain functional predictions of the protein revealed that EoGSTS1 contains nine α helices and two β sheets with one conserved GST domain. The results of enzyme activity assay showed that recombinant EoGSTs1 (rEoGSTs1) protein had catalytic activity for substrate 1-chloro-2,4-dinitrobenzene (CDNB) and exhibited the highest activity at pH 7 and 25 °C. The Michaelis constant Km of rEoGSTs1 protein was 0.07782 ± 0.01990 mmol/L, and the maximum reaction rate Vmax was 12.15 ± 1.673 µmol/min⋅mg. Our study clarified the taxonomic identity of small green leafhopper EoGSTs1 and revealed some properties of the gene and its encoded protein sequence. According to the catalytic activity of the rEoGSTs1 enzyme on the model substrate CDNB, we infer that it functions in the degradation of exogenous substances. creator: Yujie Zhang creator: Wenlong Chen creator: Ming Li creator: Lin Yang creator: Xiangsheng Chen uri: https://doi.org/10.7717/peerj.7641 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Responses of weed community, soil nutrients, and microbes to different weed management practices in a fallow field in Northern China link: https://peerj.com/articles/7650 last-modified: 2019-09-06 description: The long-term use of herbicides to remove weeds in fallow croplands can impair soil biodiversity, affect the quality of agricultural products, and threaten human health. Consequently, the identification of methods that can effectively limit the weed seed bank and maintain fallow soil fertility without causing soil pollution for the next planting is a critical task. In this study, four weeding treatments were established based on different degrees of disturbance to the topsoil: natural fallow (N), physical clearance (C), deep tillage (D), and sprayed herbicide (H). The changes in the soil weed seed banks, soil nutrients, and soil microbial biomass were carefully investigated. During the fallow period, the C treatment decreased the annual and biennial weed seed bank by 34% against pretreatment, whereas the H treatment did not effectively reduce the weed seed bank. The D treatment had positive effects on the soil fertility, increasing the available nitrogen 108% over that found in the N soil. In addition, a pre-winter deep tillage interfered with the rhizome propagation of perennial weeds. The total biomass of soil bacterial, fungal, and actinomycete in H treatment was the lowest among the four treatments. The biomass of arbuscular mycorrhizal fungi in the N treatment was respectively 42%, 35%, and 91%, higher than that in the C, D, and H treatments. An ecological weeding strategy was proposed based on our findings, which called for exhausting seed banks, blocking seed transmission, and taking advantage of natural opportunities to prevent weed growth for fallow lands. This study could provide a theoretical basis for weed management in fallow fields and organic farming systems. creator: Xian Gu creator: Yu Cen creator: Liyue Guo creator: Caihong Li creator: Han Yuan creator: Ziwen Xu creator: Gaoming Jiang uri: https://doi.org/10.7717/peerj.7650 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gu et al. title: The heart of a hibernator: EGFR and MAPK signaling in cardiac muscle during the hibernation of thirteen-lined ground squirrels, Ictidomys tridecemlineatus link: https://peerj.com/articles/7587 last-modified: 2019-09-05 description: BackgroundThirteen-lined ground squirrels (Ictidomys tridecemlineatus) experience dramatic changes in physiological and molecular parameters during winter hibernation. Notably, these animals experience reduced blood circulation during torpor, which can put numerous stresses on their hearts. The present study evaluates the role played by the epidermal growth factor receptor (EGFR) in signal transduction during hibernation at low body temperature to evaluate signaling mechanisms. By investigating the regulation of intracellular mitogen activated protein kinase (MAPK) pathway responses, anti-apoptosis signals, downstream transcription factors, and heat shock proteins in cardiac muscle we aim to determine the correlation between upstream tyrosine phosphorylation events and downstream outcomes.MethodsProtein abundance of phosphorylated EGFR, MAPKs and downstream effector proteins were quantified using immunoblotting and Luminex® multiplex assays.ResultsMonitoring five time points over the torpor/arousal cycle, EGFR phosphorylation on T654, Y1068, Y1086 was found to increase significantly compared with euthermic control values particularly during the arousal process from torpor, whereas phosphorylation at Y1045 was reduced during torpor. Phosphorylation of intracellular MAPK targets (p-ERK 1/2, p-JNK, p-p38) also increased strongly during the early arousal stage with p-p38 levels also rising during prolonged torpor. However, of downstream MAPK effector kinases that were measured, only p-Elk-1 levels changed showing a decrease during interbout arousal (IA). Apoptosis markers revealed a strong reduction of the pro-apoptotic p-BAD protein during entrance into torpor that remained suppressed through torpor and IA. However, active caspase-9 protein rose strongly during IA. Levels of p-AKT were suppressed during the transition phases into and out of torpor. Of four heat shock proteins assessed, only HSP27 protein levels changed significantly (a 40% decrease) during torpor.ConclusionWe show evidence of EGFR phosphorylation correlating to activation of MAPK signaling and downstream p-ELK1 suppression during hibernation. We also demonstrate a reduction in p-BAD mediated pro-apoptotic signaling during hibernation with active caspase-9 protein levels increasing only during IA. I. tridecemlineatus has natural mechanisms of tissue protection during hibernation that is largely due to cellular regulation through phosphorylation-mediated signaling cascade. We identify a possible link between EGFR and MAPK signaling via p-ERK, p-p38, and p-JNK in the cardiac muscle of these hibernating mammals that correlates with an apparent reduction in caspase-9 apoptotic signaling. This reveals a piece of the mechanism behind how these mammals are resilient to cardiac stresses during hibernation that would otherwise be damaging. creator: Christine L. Childers creator: Shannon N. Tessier creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.7587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Childers et al. title: The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae link: https://peerj.com/articles/7633 last-modified: 2019-09-05 description: Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic. creator: Jun Wang creator: Xin-Yi Dai creator: Xiao-Dong Xu creator: Zi-Yi Zhang creator: Dan-Na Yu creator: Kenneth B. Storey creator: Jia-Yong Zhang uri: https://doi.org/10.7717/peerj.7633 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Assessing blue orchard bee (Osmia lignaria) propagation and pollination services in the presence of honey bees (Apis mellifera) in Utah tart cherries link: https://peerj.com/articles/7639 last-modified: 2019-09-05 description: Osmia lignaria is a commercially available, native solitary bee species recognized for its propensity to forage upon and pollinate tree fruit crops such as apple, almond and cherry. This study evaluated the implementation of O. lignaria co-pollination with honey bees in central Utah commercial tart cherry orchards during 2017 and 2018 bloom. Three paired 1.2 ha sites were selected for evaluation of cherry fruit set and yield with and without managed O. lignaria releases alongside the standard honey bee hive stocking rate of 2.5 hives/ha. Osmia lignaria supplementation did not measurably increase cherry fruit set, fruit per limb cross-sectional area or fruit weight. The lack of differences in yield is likely a consequence of local saturation of pollinator services supplied by managed honey bees throughout experimental orchards, such that no additive benefit of managed O. lignaria releases were measurable. An increase in managed O. lignaria populations was achieved in 2017 but not 2018, possibly due to unknown changes to orchard management or environmental factors. While flying O. lignaria in Utah tart cherries may support sustainable in-field bee propagation, their subsequent impacts on tart cherry yield were not detected when paired with standard stocking densities of honey bees. creator: Natalie K. Boyle creator: Theresa L. Pitts-Singer uri: https://doi.org/10.7717/peerj.7639 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Pyriproxyfen, a juvenile hormone analog, damages midgut cells and interferes with behaviors of Aedes aegypti larvae link: https://peerj.com/articles/7489 last-modified: 2019-09-04 description: Juvenile hormone analogs (JHA) are known to interfere with growth and biosynthesis of insects with potential for insecticide action. However, there has been comparatively few data on morphological effects of JHA on insect organs. To determine pyriproxyfen effects on Aedes aegypti larvae, we conducted toxicity, behavioral bioassays and assessed ultrastructural effects of pyriproxyfen on midgut cells. A. aegypti larvae were exposed in aqueous solution of pyriproxyfen LC50 concentrations and evaluated for 24 h. This study fulfilled the toxic prevalence of pyriproxyfen to A. aegypti larvae (LC50 = 8.2 mg L−1). Behavioral observations confirmed that pyriproxyfen treatment significantly changes swimming behavior of larvae, limiting its displacement and speed. The pyriproxyfen causes remarkable histopathological and cytotoxic alterations in the midgut of larvae. Histopathological study reveals presence of cytoplasmic vacuolization and damage to brush border of the digestive cells. The main salient lesions of cytotoxic effects are occurrence of cell debris released into the midgut lumen, cytoplasm rich in lipid droplets, autophagosomes, disorganized microvilli and deformed mitochondria. Data suggest that pyriproxyfen can be used to help to control and eradicate this insect vector. creator: Muhammad Fiaz creator: Luis Carlos Martínez creator: Angelica Plata-Rueda creator: Wagner Gonzaga Gonçalves creator: Debora Linhares Lino de Souza creator: Jamile Fernanda Silva Cossolin creator: Paulo Eduardo Gomes Rodrigues Carvalho creator: Gustavo Ferreira Martins creator: José Eduardo Serrão uri: https://doi.org/10.7717/peerj.7489 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fiaz et al. title: The number of nephrons in different glomerular diseases link: https://peerj.com/articles/7640 last-modified: 2019-09-04 description: BackgroundThe total number of nephrons has been measured mainly from post-mortem studies and only in selected populations. Data from living subjects are scanty, and direct comparisons among different glomerular diseases are lacking. The present work exploits modern methodology to estimate the total nephron number in glomerulopathies with prevalent proteinuria/nephrotic syndrome versus glomerulopathies with nephritic syndrome (IgA nephropathy (IgAN), lupus nephritis), thus extending previous observations about the number and function of glomeruli in different physiological and pathological states.MethodsThis is a retrospective study based on one hundred and seven patients who have undergone renal biopsy. The glomerular density has been estimated from the biopsy specimens and the total cortical volume has been obtained from ultrasound recordings. Stereological methods have been applied to calculate the total number of nephrons and their volume. The correlation between clinical parameters and quantitative morphological data have studied using the Pearson correlation coefficient (r).ResultsThe total number of nephrons inversely correlated with the systolic blood pressure (r = −0.4, p < 0.05). In proteinuric diseases, such as focal segmental glomerulo-sclerosis (FSGS), membranous nephropathy (MN) and diabetes, the change in estimated GFR (eGFR) directly correlated with the total number of non-sclerotic glomeruli (NSG) (r = 0.62, p < 0.01), whereas in nephritic syndrome no significant correlation was observed. The alterations in eGFR occurring in nephritic syndromes such as IgAN cannot be explained on the basis of the number of NSG.DiscussionThe fusion of the podocyte foot-processes that typically occurs in purely proteinuric diseases does not modify the glomerular filtration rate: therefore in these situations, the change in eGFR depends mainly on the number of available glomeruli. On the other side, the eGFR decrease occurring in nephritic syndromes, such as IgAN, cannot be explained simply on the basis of the number of NSG and likely depends on the substantial involvement of the mesangial axis. Future studies should verify whether these changes are reversible with appropriate therapy, thus reversing eGFR decrease. creator: Davide Viggiano creator: Michelangelo Nigro creator: Francesco Sessa creator: Graziano Vignolini creator: Riccardo Campi creator: Sergio Serni creator: Rosa Maria Pollastro creator: Gianfranco Vallone creator: Giuseppe Gigliotti creator: Giovambattista Capasso uri: https://doi.org/10.7717/peerj.7640 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Viggiano et al. title: Reduced gray matter volume in male adolescent violent offenders link: https://peerj.com/articles/7349 last-modified: 2019-09-03 description: BackgroundPrevious studies reported that reduced gray matter volume (GMV) was associated with violent-related behaviors. However, the previous studies were conducted on adults and no study has studied the association between GMV and violent behaviors on adolescents. The purpose of the study was to investigate GMV’s effects in adolescent violent offenders based on a Chinese Han population, which can address the problem of possible confounding factors in adult studies.MethodsWe recruited 30 male adolescent violent offenders and 29 age- and sex-matched healthy controls (HCs). Differences in both whole-brain and GMV were evaluated using voxel-based morphometry (VBM). We assessed the accuracy of VBM using the receiver operating characteristic curve (ROC) and discriminant analysis.ResultsCompared with HCs, the male adolescent offenders showed significantly reduced GMV in five cortical and subcortical brain regions, including the olfactory cortex, amygdala, middle temporal gyrus and inferior parietal lobe in the left hemisphere, as well as the right superior temporal gyrus. Both ROC curve and discriminate analyses showed that these regions had relatively high sensitivities (58.6%–89.7%) and specificities (58.1%–74.2%) with 76.7% classification accuracy.ConclusionsOur results indicated that reduced volume in the frontal-temporal-parietal-subcortical circuit may be closely related to violent behaviors in male adolescents, which might be an important biomarker for detecting violent behaviors in male adolescents. creator: Ying-Dong Zhang creator: Jian-Song Zhou creator: Feng-Mei Lu creator: Xiao-Ping Wang uri: https://doi.org/10.7717/peerj.7349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Network-based approach to identify biomarkers predicting response and prognosis for HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy link: https://peerj.com/articles/7515 last-modified: 2019-09-03 description: ObjectiveThis study aims to identify effective gene networks and biomarkers to predict response and prognosis for HER2-negative breast cancer patients who received sequential taxane-anthracycline neoadjuvant chemotherapy.Materials and MethodsTranscriptome data of training dataset including 310 HER2-negative breast cancer who received taxane-anthracycline treatment and an independent validation set with 198 samples were analyzed by weighted gene co-expression network analysis (WGCNA) approach in R language. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were performed for the selected genes. Module-clinical trait relationships were analyzed to explore the genes and pathways that associated with clinicopathological parameters. Log-rank tests and COX regression were used to identify the prognosis-related genes.ResultsWe found a significant correlation of an expression module with distant relapse–free survival (HR = 0.213, 95% CI [0.131–0.347], P = 4.80E−9). This blue module contained genes enriched in biological process of hormone levels regulation, reproductive system, response to estradiol, cell growth and mammary gland development as well as pathways including estrogen, apelin, cAMP, the PPAR signaling pathway and fatty acid metabolism. From this module, we further screened and validated six hub genes (CA12, FOXA1, MLPH, XBP1, GATA3 and MAGED2), the expression of which were significantly associated with both better chemotherapeutic response and favorable survival for BC patients.ConclusionWe used WGCNA approach to reveal a gene network that regulate HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy, which enriched in pathways of estrogen signaling, apelin signaling, cAMP signaling, the PPAR signaling pathway and fatty acid metabolism. In addition, genes of CA12, FOXA1, MLPH, XBP1, GATA3 and MAGED2 might serve as novel biomarkers predicting chemotherapeutic response and prognosis for HER2-negative breast cancer. creator: Cui Jiang creator: Shuo Wu creator: Lei Jiang creator: Zhichao Gao creator: Xiaorui Li creator: Yangyang Duan creator: Na Li creator: Tao Sun uri: https://doi.org/10.7717/peerj.7515 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jiang et al. title: Non-dinosaurian dinosauromorphs from the Chinle Formation (Upper Triassic) of the Eagle Basin, northern Colorado: Dromomeron romeri (Lagerpetidae) and a new taxon, Kwanasaurus williamparkeri (Silesauridae) link: https://peerj.com/articles/7551 last-modified: 2019-09-03 description: The “red siltstone” member of the Upper Triassic Chinle Formation in the Eagle Basin of Colorado contains a diverse assemblage of dinosauromorphs falling outside of Dinosauria. This assemblage is the northernmost known occurrence of non-dinosaurian dinosauromorphs in North America, and probably falls within the Revueltian land vertebrate estimated biochronozone (215–207 Ma, middle to late Norian). Lagerpetids are represented by proximal femora and a humerus referable to Dromomeron romeri. Silesaurids (non-dinosaurian dinosauriforms) are the most commonly recovered dinosauromorph elements, consisting of dentaries, maxillae, isolated teeth, humeri, illia, femora, and possibly a scapula and tibiae. These elements represent a new silesaurid, Kwanasaurus williamparkeri, gen. et sp. nov., which possesses several autapomorphies: a short, very robust maxilla with a broad ascending process, a massive ventromedial process, a complex articular surface for the lacrimal and jugal, and 12 teeth; 14 dentary teeth; an ilium with an elongate and blade-like preacetabular process and concave acetabular margin; a femur with an extremely thin medial distal condyle and a depression on the distal end anterior to the crista tibiofibularis. The recognition of K. williamparkeri further demonstrates the predominantly Late Triassic diversity and widespread geographic distribution across Pangea of the sister clade to Asilisaurus, here named Sulcimentisauria. Silesaurid dentition suggests a variety of dietary specializations from faunivory and omnivory in the Middle Triassic and early Late Triassic (Carnian), to herbivory in the Late Triassic (Carnian and Norian), with the latter specialization possibly coinciding with the radiation of Sulcimentisauria across Pangea. The extremely robust maxilla and folidont teeth of K. williamparkei may represent a strong herbivorous dietary specialization among silesaurids. creator: Jeffrey W. Martz creator: Bryan J. Small uri: https://doi.org/10.7717/peerj.7551 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Martz and Small title: Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem link: https://peerj.com/articles/7565 last-modified: 2019-09-03 description: Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science. creator: Alexander May creator: Shrinath Narayanan creator: Joe Alcock creator: Arvind Varsani creator: Carlo Maley creator: Athena Aktipis uri: https://doi.org/10.7717/peerj.7565 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 May et al. title: Effects of reflective warning markers on wildlife link: https://peerj.com/articles/7614 last-modified: 2019-09-03 description: Light pollution has become one of the top issues in environmental pollution, especially concerning how secondary light pollution, such as from traffic reflective materials, influences animal distribution and behavior. In this study, 15 camera traps were set up at sites with or without reflective warning markers (RWM) in coniferous forests on Cangshan Mountain located in Dali Prefecture, China. The results showed that the number of independent photographs and species at sites without RWMs were significantly higher than those at sites with RWMs. Significant differences were found between daytime and nighttime composition of bird species and non-flying mammals between two sites. This study found that RWMs had negative effects on wildlife, with the avoidance response of birds to RWMs being more obvious than that of animals at daytime. It is recommended that the use of reflective materials be carefully considered, especially in protected areas. creator: Yi-Hao Fang creator: Ying Gao creator: Yin Yang creator: Kun Tan creator: Yan-Peng Li creator: Guo-Peng Ren creator: Zhi-Pang Huang creator: Liang-Wei Cui creator: Wen Xiao uri: https://doi.org/10.7717/peerj.7614 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fang et al. title: Identification and evaluation of Lonicera japonica flos introduced to the Hailuogou area based on ITS sequences and active compounds link: https://peerj.com/articles/7636 last-modified: 2019-09-03 description: Lonicera japonica flos (LJF), the dried flower buds of L. japonica Thunb., have been used in traditional Chinese herbal medicine for thousands of years. Recent studies have reported that LJF has many medicinal properties because of its antioxidative, hypoglycemic, hypolipidemic, anti-allergic, anti-inflammatory, and antibacterial effects. LJF is widely used in China in foods and healthcare products, and is contained in more than 30% of current traditional Chinese medicine prescriptions. Because of this, many Chinese villages cultivate LJF instead of traditional crops due to its high commercial value in the herbal medicine market. Since 2005, the flower buds of L. japonica are the only original LJF parts considered according to the Chinese Pharmacopoeia of the People’s Republic of China. However, for historical and commercial reasons, some closely related species of Lonicera Linn. continue to be mislabeled and used as LJF. Currently, there are hundreds of commercial varieties of LJF on the market and it is difficult to choose fine LJF varieties to cultivate. In this study, a total of 21 varieties labeled as LJF on the market were planted in the Hailuogou area. In order to choose the optimum variety, internal transcribed spacer (ITS) sequence alignment analysis was used to test whether the 21 varieties were genuine LJF or not. Cluster analysis of active components based on the content of chlorogenic acid and luteoloside in flower buds, stems and leaves was used to evaluate the quality of the varieties. Results demonstrated that four of the varieties were L. macranthoides Hand.-Mazz., while the other 17 varieties were L. japonica, and genuine LJF. The ITS sequence analysis was proven to be highly effective in identifying LJF and Lonicerae flos. Among the 17 L. japonica varieties, the amounts of chlorogenic acid and luteoloside in flower buds, stems and leaves were significantly different. Based on the cluster analysis method, the variety H11 was observed to have the highest level of active components, and is therefore recommended for large-scale planting in the Hailuogou area. creator: Haiyan He creator: Dan Zhang creator: Jianing Gao creator: Theis Raaschou Andersen creator: Zishen Mou uri: https://doi.org/10.7717/peerj.7636 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 He et al. title: Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791) link: https://peerj.com/articles/7644 last-modified: 2019-09-03 description: Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together. creator: Zhansheng Guo creator: Leng Han creator: Zhenlin Liang creator: Xuguang Hou uri: https://doi.org/10.7717/peerj.7644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells link: https://peerj.com/articles/7652 last-modified: 2019-09-03 description: ObjectiveAloperine (ALO), an alkaloid isolated from the leaves of Sophora alopecuroides, has been suggested to exhibit anti-inflammatory and anti-tumor properties and is traditionally used to treat various human diseases, including cancer. However, limited information is available about the mechanisms that determine the anti-tumor activities of ALO.MethodsHerein, through comprehensive bioinformatics methods and in vitro functional analyses, we evaluated the detailed anti-tumor mechanisms of ALO.ResultsUsing the databases Bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine and PubChem Project, we identified the potential targets of ALO. A protein–protein interaction network was constructed to determine the relationship among these probable targets. Functional enrichment analysis revealed that ALO is potentially involved in the induction of apoptosis. In addition, molecular docking demonstrated that ALO expectedly docks into the active pocket of the Bcl2 protein, suggesting Bcl2 as a direct target of ALO. Moreover, western blot and qPCR analysis showed that ALO downregulated Bcl2 expression in human glioma cell lines, SK-N-AS and U118. Using flow cytometry methods, we further confirmed that ALO significantly promotes apoptosis in SK-N-AS and U118 cell lines, similar to the effect induced by ABT-737, a well-known Bcl2 inhibitor. In addition, Bcl-2 overexpression could rescue ALO-induced Bcl-2 inhibition and suppress pro-apoptotic effects in glioma cells.ConclusionTaken together, these findings suggest that the natural agent ALO effectively enhances apoptosis by acting as a potential Bcl2 inhibitor in human glioma cells. creator: Zhijie Xu creator: Xiang Wang creator: Xi Chen creator: Shuangshuang Zeng creator: Long Qian creator: Jie Wei creator: Zhicheng Gong creator: Yuanliang Yan uri: https://doi.org/10.7717/peerj.7652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xu et al. title: Effects of mechanical and chemical control on invasive Spartina alterniflora in the Yellow River Delta, China link: https://peerj.com/articles/7655 last-modified: 2019-09-03 description: Spartina alterniflora is one of the most noxious invasive plants in China and many other regions. Exploring environmentally friendly, economic and effective techniques for controlling Spartina alterniflora is of great significance for the management of coastal wetlands. In the present study, different approaches, including mowing and waterlogging, mowing and tilling and herbicide application, were used to control Spartina alterniflora. The results suggest that the integrated approach of mowing and waterlogging could eradicate Spartina alterniflora, the herbicide haloxyfop-r-methyl could kill almost all the Spartina alterniflora, and the integrated approach of mowing and tilling at the end of the growing season was a perfect way to inhibit the germination of Spartina alterniflora in the following year. However, no matter which control approach is adopted, secondary invasion of Spartina alterniflora must be avoided. Otherwise, all the efforts will be wasted in a few years. creator: Baohua Xie creator: Guangxuan Han creator: Peiyang Qiao creator: Baoling Mei creator: Qing Wang creator: Yingfeng Zhou creator: Anfeng Zhang creator: Weimin Song creator: Bo Guan uri: https://doi.org/10.7717/peerj.7655 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xie et al. title: Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae link: https://peerj.com/articles/6904 last-modified: 2019-09-02 description: BackgroundEnterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed.MethodsNine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms.ResultsThe cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene by qRT-PCR revealed a 14-fold induction in the EC01. Regulation of the DUF326-like domain in EC01 was more pronounced to mediate rapid cadmium accumulation (in 6 h) and tolerance than the other resistance mechanisms found in the ATCC 13047 and the EC07 strains. The only one major responsive protein against toxic cadmium found in these three strains belonged to an antioxidative enzyme, namely catalase. The unique proteins found in the ATCC 13047 and EC07 were identified as two groups: (i) ATP synthase subunit alpha, putative hydrolase and superoxide dismutase and (ii) OmpX, protein YciF, OmpC porin, DNA protection during starvation protein, and TrpR binding protein WrbA, respectively.ConclusionAll these findings gain insights not only into the molecular mechanisms of cadmium tolerance in EC but also open up a high feasibility to apply the newly discovered DUF326-like domain as cadmium biosorbents for environmental remediation in the future. creator: Kitipong Chuanboon creator: Piyada Na Nakorn creator: Supitcha Pannengpetch creator: Vishuda Laengsri creator: Pornlada Nuchnoi creator: Chartchalerm Isarankura-Na-Ayudhya creator: Patcharee Isarankura-Na-Ayudhya uri: https://doi.org/10.7717/peerj.6904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chuanboon et al. title: Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus) link: https://peerj.com/articles/7453 last-modified: 2019-09-02 description: BackgroundThe Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India.ResultsWe tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples.ConclusionOur results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore. creator: Shrushti Modi creator: Bilal Habib creator: Pallavi Ghaskadbi creator: Parag Nigam creator: Samrat Mondol uri: https://doi.org/10.7717/peerj.7453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Modi et al. title: The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine link: https://peerj.com/articles/7457 last-modified: 2019-09-02 description: The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores. creator: Douglass S. Rovinsky creator: Alistair R. Evans creator: Justin W. Adams uri: https://doi.org/10.7717/peerj.7457 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rovinsky et al. title: lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes link: https://peerj.com/articles/7491 last-modified: 2019-09-02 description: Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA. creator: Haibin Zhang creator: Cheng Chen creator: Yinghong Cui creator: Yuqing Li creator: Zhaojun Wang creator: Xinzhan Mao creator: Pengcheng Dou creator: Yihan Li creator: Chi Ma uri: https://doi.org/10.7717/peerj.7491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744 link: https://peerj.com/articles/7542 last-modified: 2019-09-02 description: Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds. creator: Krisztina Pesti creator: Peter Lukacs creator: Arpad Mike uri: https://doi.org/10.7717/peerj.7542 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pesti et al. title: Revealing biases in the sampling of ecological interaction networks link: https://peerj.com/articles/7566 last-modified: 2019-09-02 description: The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling by degree may therefore be common but unintentional in empirical sampling of networks. Conversely, sampling according to module (representing different interaction types or taxa) results in a rather complete view of certain modules, but fails to provide a complete picture of the underlying network. To reduce biases introduced by sampling methods, we recommend that these findings be incorporated into field design considerations for projects aiming to characterize large species interaction networks. creator: Marcus A.M. de Aguiar creator: Erica A. Newman creator: Mathias M. Pires creator: Justin D. Yeakel creator: Carl Boettiger creator: Laura A. Burkle creator: Dominique Gravel creator: Paulo R. Guimarães creator: James L. O’Donnell creator: Timothée Poisot creator: Marie-Josée Fortin creator: David H. Hembry uri: https://doi.org/10.7717/peerj.7566 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 de Aguiar et al. title: Nutrient availability induces community shifts in seagrass meadows grazed by turtles link: https://peerj.com/articles/7570 last-modified: 2019-09-02 description: In the Caribbean, green turtles graze seagrass meadows dominated by Thalassia testudinum through rotational grazing, resulting in the creation of grazed and recovering (abandoned) patches surrounded by ungrazed seagrasses. We evaluated the seagrass community and its environment along a turtle grazing gradient; with the duration of (simulated) grazing as a proxy for the level of grazing pressure. The grazing levels consisted of Short-term (4 months clipping), Medium-term (8 months clipping), Long-term grazing (8 months of clipping in previously grazed areas), 8-months recovery of previously grazed patches, and ungrazed or unclipped patches as controls. We measured biomass and density of the seagrasses and rhizophytic algae, and changes in sediment parameters. Medium- and Long-term grazing promoted a shift in community species composition. At increasing grazing pressure, the total biomass of T. testudinum declined, whereas that of early-successional increased. Ammonium concentrations were highest in the patches of Medium-term (9.2 + 0.8 μM) and Long-term grazing levels (11.0 + 2.2 μM) and were lowest in the control areas (4.6 + 1.5 μM). T. testudinum is a late-successional species that maintains sediment nutrient concentrations at levels below the requirements of early-successional species when dominant. When the abundance of this species declines due to grazing, these resources become available, likely driving a shift in community composition toward a higher abundance of early-successional species. creator: Isis Gabriela Martínez López creator: Marloes van Den Akker creator: Liene Walk creator: Marieke M. van Katwijk creator: Tjisse van Der Heide creator: Brigitta I. van Tussenbroek uri: https://doi.org/10.7717/peerj.7570 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Martínez López et al. title: The reproductive system of the male and oviparous female of a model organism—the pea aphid, Acyrthosiphon pisum (Hemiptera, Aphididae) link: https://peerj.com/articles/7573 last-modified: 2019-09-02 description: The structure of the reproductive system of the sexual generation—males and oviparous females—of the pea aphid Acyrthosiphon pisum (Harris) (Hemiptera, Aphididae), a serious pest of cultivated plants of Fabaceae, was investigated. For the first time we describe the morphology, histology and ultrastructure of the reproductive system in both morphs of the sexual generation of aphids within one species, using light and fluorescent microscopy, as well as transmission and scanning electron microscopy. The results revealed that males have testes composed of three follicles fused by the upper ends of the vasa efferentia, the vasa deferentia run independently, the accessory glands are asymmetric and the ejaculatory duct shortened. Oviparous females have ovaries composed of seven ovarioles each. The lateral oviducts join to a short common oviduct connected with the unpaired spermatheca and paired accessory glands. Yolky eggs with an aggregation of symbiotic bacteria at the posterior pole are produced. Histologically, the components of genital tracts are broadly similar: the epithelial cells of the walls of the vasa deferentia and accessory glands of the male and oviparous female have secretory functions which correlate with the age of the studied morphs. We also found symbiotic bacteria within the vasa deferentia epithelial cells in males and within the cells of the lateral oviducts of females. Because the pea aphid is listed among the 14 species that are of the greatest economic importance, our results will be useful for managing aphid populations, protecting plants and ensuring global food security. creator: Karina Wieczorek creator: Mariusz Kanturski creator: Cezary Sempruch creator: Piotr Świątek uri: https://doi.org/10.7717/peerj.7573 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wieczorek et al. title: Community composition of zooplankton exported from a shallow polymictic reservoir linked to wind conditions link: https://peerj.com/articles/7611 last-modified: 2019-09-02 description: Zooplankton exported from lentic systems provision lotic systems with easily captured, consumed, and assimilated prey items. Previous studies have demonstrated that the community composition of zooplankton exports (CCZE) vary over time, which introduces temporal differences in lotic resource availability (zooplankton prey) in downstream habitats. In the study presented here, we monitored variation in CCZE from a polymictic reservoir outfall in response to physical–chemical and atmospheric conditions bi-hourly over three different 24-h periods. Community composition of zooplankton export varied over the course of the day, and exports were most closely associated with wind directionality. Future studies of temporal variation in CCZE should incorporate wind conditions, especially in shallow systems where holomixis occurs frequently. Polymictic reservoirs are becoming increasingly common as the global pace of small dam construction quickens, making both the identification of factors influencing CCZE and the impact of zooplankton exports on local biodiversity and ecosystem function increasingly important to understand. creator: Nathan Ruhl creator: Desireé Haban creator: Caitlyn Czajkowski creator: Michael Grove creator: Courtney E. Richmond uri: https://doi.org/10.7717/peerj.7611 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ruhl et al. title: Winter bird-window collisions: mitigation success, risk factors, and implementation challenges link: https://peerj.com/articles/7620 last-modified: 2019-09-02 description: Millions of birds die in bird-window collisions in the United States each year. In specialized test settings, researchers have developed methods to alter window designs to mitigate collisions. However, few published studies provide pretest and posttest evaluations of mitigation treatment areas and untreated control areas on existing buildings. We initially monitored bird-window collisions at a single building on the University of Utah campus in Salt Lake City, Utah, USA, during winter 1 (November 9, 2017–January 2, 2018). We found 15 bird-window collisions, most under a portion of the building with a mirrored façade. To test a mitigation treatment, we installed Feather Friendly® bird deterrent film on part of the mirrored façade after winter 1. The unmitigated areas of the same building served as a control area. We continued monitoring during the following winter 2 (November 15, 2018–January 12, 2019). The treated area collisions declined from seven before mitigation to two after mitigation, a 71% reduction. The control area had eight collisions at both times. Results of a generalized estimating equation yielded a significant area by season interaction effect (p = 0.03) and fewer collisions in the mitigated area than the control area at winter 2 (p = 0.03), supporting efficacy of the mitigation. In winter 2 we also expanded monitoring to eight total buildings to evaluate the risks of mirrored windows and proximity to fruiting pear trees (Prunus calleryana) and the benefits of bird-friendly glass. Bird-friendly glass, found on two buildings, included windows with permanent fritted dots or embedded ultraviolet patterns. We counted 22 collisions across the eight buildings. Mirrored windows and proximity to fruiting pear trees related to higher odds of bird-window collisions, based on separate generalized estimating equations. The best fit model included mirrored windows and pear trees. The two buildings with bird-friendly glass had only one collision, suggesting that these designs deter collisions, although the difference was not statistically significant. To publicize the study and to receive reports of additional bird collisions or fatalities on campus, we created a citizen science project on iNaturalist and engaged in additional outreach efforts that yielded 22 ad hoc reports. Many previous studies have documented Cedar Waxwing (Bombycilla cedrorum) collisions, but at relatively low numbers. Cedar Waxwings accounted for 31 of 34 identifiable collisions from the monitoring study and 4 of 21 identifiable collisions or fatalities from ad hoc reports. creator: Barbara B. Brown creator: Erika Kusakabe creator: Angelo Antonopoulos creator: Sarah Siddoway creator: Lisa Thompson uri: https://doi.org/10.7717/peerj.7620 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Brown et al.