title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1271 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs link: https://peerj.com/articles/7839 last-modified: 2019-10-01 description: Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha−1. Soil samples were collected at a 0–15 cm depth from 2016–2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health. creator: Yichao Yang creator: Amanda J. Ashworth creator: Jennifer M. DeBruyn creator: Cammy Willett creator: Lisa M. Durso creator: Kim Cook creator: Philip A. Moore, Jr. creator: Phillip R. Owens uri: https://doi.org/10.7717/peerj.7839 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: 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.