title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Protein expression profile changes of lung tissue in patients with pulmonary hypertension link: https://peerj.com/articles/8153 last-modified: 2020-01-31 description: BackgroundPulmonary hypertension occurs in approximately 1% of the global population, and the prognosis for such patients may be poor. However, the mechanisms underlying the development of this disease remain unclear. Thus, understanding the development of pulmonary hypertension and finding new therapeutic targets and approaches are important for improved clinical outcomes.MethodsLung tissue specimens were collected from six patients with atrial septal defect and pulmonary hypertension (all women, with a mean age of 46.5 ± 4.7 years, and their condition could not be corrected with an internal medical occlusion device) and from nine control patients with lung cancer who underwent lobectomy (six men and three women, with a mean age of 56.7 ± 1.7 years). Isobaric tags for relative and absolute quantitation and liquid chromatography tandem mass spectrometry analyses were used to detect protein expression levels.ResultsWe found 74 significantly upregulated and 88 significantly downregulated differentially expressed proteins between control and pulmonary hypertensive lung tissue specimens. Gene ontology analyses identified the top 20 terms in all three categories, that is, biological process, cellular component, and molecular function. Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction analyses determined the top 10 signaling pathways and found that the six hub proteins associated with the differentially expressed upregulated proteins (PRKAA1, DHPR, ACTB, desmin, ACTG1, and ITGA1) were all involved in hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy, and dilated cardiomyopathy.ConclusionOur results identified protein expression profile changes in lung tissue derived from patients with pulmonary hypertension, providing potential new biomarkers for clinical diagnosis and prognosis for patients with pulmonary hypertension and offering candidate protein targets for future therapeutic drug development. creator: Min Wu creator: Yijin Wu creator: Jinsong Huang creator: Yueheng Wu creator: Hongmei Wu creator: Benyuan Jiang creator: Jian Zhuang uri: https://doi.org/10.7717/peerj.8153 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Spatial analysis, local people’s perception and economic valuation of wetland ecosystem services in the Usumacinta floodplain, Southern Mexico link: https://peerj.com/articles/8395 last-modified: 2020-01-31 description: The Usumacinta floodplain is an exceptional area for biodiversity with important ecosystem services for local people. The main objective of this paper was to estimate reference values and define local perceptions of ecosystem services provided by wetlands and overlapping them with spatially explicit socioeconomic and biodiversity indicators. We used the Usumacinta floodplain as an example of a territory where high dependence of rural people on ecosystem services is confronted with development projects that threat the flow of ecosystem services, thus affecting rural people well-being. With a combination of data from remote sensing, global databases of ecosystem service values, local perception of ecosystem services and socioeconomic and biodiversity richness indicators in a spatially explicit framework, we develop a policy-oriented approach for rapid assessment to manage wetlands and maintain people’s livelihoods. Regulating and provisioning services are identified as the most relevant ecosystem services in terms of their monetary value and local perceived importance. In a spatially explicit manner, this approach highlights the most valuable wetlands and identifies rural societies that are highly dependent on ecosystem services. Our approach can be replicated elsewhere and could provide valuable information for policymakers to design policies that can contribute to conserve wetland ecosystems where under threat of development. creator: Vera Camacho-Valdez creator: Andrea Saenz-Arroyo creator: Andrea Ghermandi creator: Dario A. Navarrete-Gutiérrez creator: Rocío Rodiles-Hernández uri: https://doi.org/10.7717/peerj.8395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Camacho-Valdez et al. title: Novel insights into the effect of drought stress on the development of root and caryopsis in barley link: https://peerj.com/articles/8469 last-modified: 2020-01-31 description: Drought is a common natural disaster in barley production, which restricts the growth and development of barley roots and caryopses seriously, thereby decreasing yield and debasing grain quality. However, mechanisms for how drought stress affects barley caryopses and roots development under drought stress are unclear. In this paper, Suluomai1 was treated with drought from flowering to caryopses mature stage. The morphological and structural changes in roots growth and caryopses development of barley were investigated. Drought stress increased root/shoot ratio and eventually led to the 20.16% reduction of ear weight and 7.75% reduction of 1,000-grain weight by affecting the biomass accumulation of roots and caryopses. The barley roots under drought had more lateral roots while the vessel number and volume of roots decreased. Meanwhile, drought stress accelerated the maturation of caryopses, resulting in a decrease in the accumulation of starch but a significant increase of protein accumulation in barley endosperm. There was a significantly positive correlation (0.76) between the area of root vessel and the relative area of protein in endosperm cells under normal condition and drought increased the correlation coefficient (0.81). Transcriptome analysis indicated that drought induced differential expressions of genes in caryopses were mainly involved in encoding storage proteins and protein synthesis pathways. In general, drought caused changes in the morphology and structure of barley roots, and the roots conveyed stress signals to caryopses, inducing differential expression of genes related to protein biosynthesis, ultimately leading to the increase in the accumulation of endosperm protein. The results not only deepen the study on drought mechanism of barley, but also provide theoretical basis for molecular breeding, high-yield cultivation and quality improvement in barley. creator: Fali Li creator: Xinyu Chen creator: Xurun Yu creator: Mingxin Chen creator: Wenyi Lu creator: Yunfei Wu creator: Fei Xiong uri: https://doi.org/10.7717/peerj.8469 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Effects of chronic prazosin, an alpha-1 adrenergic antagonist, on anxiety-like behavior and cortisol levels in a chronic unpredictable stress model in zebrafish (Danio rerio) link: https://peerj.com/articles/8472 last-modified: 2020-01-31 description: Post-traumatic stress disorder (PTSD) is often associated with significant neuroendocrine dysfunction and a variety of other symptoms. Today, there are limited efficacious treatment options for PTSD, none of which directly target the dysfunction observed with the hypothalamic-pituitary-adrenal (HPA) axis. The development of new pharmacological treatments is expensive and time consuming; thus, there is utility in repurposing compounds already approved for use in other conditions. One medication in particular that has shown promise for the alleviation of PTSD symptoms is prazosin, an alpha-1 adrenergic receptor antagonist used to treat hypertension. While there have been many studies indicating the efficacy of prazosin in the treatment of PTSD symptoms, no studies fully elucidate mechanisms elicited by this treatment, nor is it clear if prazosin normalizes neuroendocrine dysfunction associated with trauma exposure. The use of zebrafish (Danio rerio) has been growing in popularity, in part, due to the homology of the stress response system with mammals. In this study, the zebrafish model was utilized to determine behavioral and biological changes induced by chronic unpredictable stress (CUS) and how these effects could be modulated by chronic prazosin treatment. The results indicated that 7d of CUS increased anxiety-like behavior in the novel tank test and decreased basal levels of cortisol. Chronic (7d) prazosin treatment decreased anxiety-like behaviors overall but did not appear to affect CUS-induced changes in behavior and basal cortisol levels. This suggests that the clinical effectiveness of prazosin may not normalize dysregulated stress responses prevalent in many patients with PTSD, but that prazosin-induced relief from anxiety in stress-related conditions may involve an alternative mechanism other than by normalizing neuroendocrine dysfunction. creator: Michael P. O’Daniel creator: Maureen L. Petrunich-Rutherford uri: https://doi.org/10.7717/peerj.8472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 O’Daniel and Petrunich-Rutherford title: Assessment of crusting effects on interrill erosion by laser scanning link: https://peerj.com/articles/8487 last-modified: 2020-01-31 description: BackgroundCrust formation affects soil erosion by raindrop impacted flow through changing particle size and cohesion between particles on the soil surface, as well as surface microtopography. Therefore, changes in soil microtopography can, in theory, be employed as a proxy to reflect the complex and dynamic interactions between crust formation and erosion caused by raindrop-impacted flow. However, it is unclear whether minor variations of soil microtopography can actually be detected with tools mapping the crust surface, often leaving the interpretation of interrill runoff and erosion dynamics qualitative or even speculative.MethodsIn this study, we used a laser scanner to measure the changes of the microtopography of two soils placed under simulated rainfall in experimental flumes and crusting at different rates. The two soils were of the same texture, but under different land management, and thus organic matter content and aggregate stability. To limit the amount of scanning and data analysis in this exploratory study, two transects and four subplots on each experimental flume were scanned with a laser in one-millimeter interval before and after rainfall simulations.ResultsWhile both soils experienced a flattening, they displayed different temporal patterns of crust development and associated erosional responses. The laser scanning data also allowed to distinguish the different rates of developments of surface features for replicates with extreme erosional responses. The use of the laser data improved the understanding of crusting effects on soil erosional responses, illustrating that even limited laser scanning provides essential information for quantitatively exploring interrill erosion processes. creator: Yaxian Hu creator: Wolfgang Fister creator: Yao He creator: Nikolaus J. Kuhn uri: https://doi.org/10.7717/peerj.8487 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hu et al. title: Analysis of the genetic diversity of the coastal and island endangered plant species Elaeagnus macrophylla via conserved DNA-derived polymorphism marker link: https://peerj.com/articles/8498 last-modified: 2020-01-31 description: The genetic diversity and genetic structure of five natural populations of the island and coastal endangered plant species Elaeagnus macrophylla were analyzed via conserved DNA-derived polymorphism molecular markers. A total of 289 discernible loci were obtained from 102 individuals via fifteen primers, and 100% of the loci were polymorphic. The observed number of alleles was 1.9654, and the effective number of alleles was 1.2604. Nei’s genetic diversity index was 0.1724 on average, and Shannon’s information index was 0.2869, indicating that Elaeagnus macrophylla had lower levels of genetic diversity than those reported for its continental relatives and other continental species. The average percentage of polymorphic loci was 42.1%, and the maximum and minimum were 80.97% and 14.88%, respectively, which were associated with the Nanji Island and Liugong Island populations, respectively. The populations of Elaeagnus macrophylla were highly differentiated. Cluster analysis revealed that the similarity between the tested samples was related to their geographical location, that the samples from the same island tended to cluster together, and that there was no cross-clustering between samples. The Nanji Island and Da Rushan populations differentiated into two subpopulations. Last, we detected no correlation between genetic distance and geographic distance between populations (Pearson’s correlation coefficient r = 0.256579, p-value = 0.8309). creator: Yi Wang creator: Yan Ma creator: Bingyu Jia creator: Qichao Wu creator: Dekui Zang creator: Xiaoyan Yu uri: https://doi.org/10.7717/peerj.8498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Potential use of human hair shaft keratin peptide signatures to distinguish gender and ethnicity link: https://peerj.com/articles/8248 last-modified: 2020-01-30 description: BackgroundMost human hairs collected at old crime scenes do not contain nuclear DNA and are therefore of less value for forensic investigations. In the present study, hair shaft proteins were extracted from 40 healthy subjects between the ages of 21 to 40 years and profiled using gel electrophoresis-based proteomics to determine if they can be used to distinguish gender and ethnicity.MethodsExtraction of the human hair shaft proteins was performed using a newly developed alkaline solubilisation method. The extracts were profiled by 2-dimensional electrophoresis and resolved protein spots were identified by mass spectrometry and queried against the human hair database. The study was then followed-up by immunoblotting of the identified hair shaft keratin of interest using commercially available antibodies.ResultsSeparation of the human hair shaft proteins by 2-dimensional electrophoresis generated improved and highly resolved profiles. Comparing the hair shaft protein profiles of 10 female with 10 male subjects and their identification by mass spectrometry and query of the human hair database showed significant altered abundance of truncated/processed type-II keratin peptides K81 (two spots), K83 (one spot) and K86 (three spots). The 2-dimensional electrophoresis profiling of 30 hair shaft samples taken from women of similar age range but from three distinctive ethnic subpopulations in Malaysia further showed significant altered abundance of one type-I and four type-II truncated/processed keratin peptides including K33b, K81, K83 and K86 (2 spots) between at least two of the ethnic groups. When a followed-up immunoblotting experiment was performed to detect the relative expression of the K86 peptides using commercialised antibodies, similar trends of expression were obtained. The present data, when taken together, demonstrated the potential use of keratin peptide signatures of the human hair shaft to distinguish gender and ethnicity although this needs to be further substantiated in a larger scale study. creator: Nurdiena Mohamed Nasir creator: Jumriah Hiji creator: Jaime Jacqueline Jayapalan creator: Onn Haji Hashim uri: https://doi.org/10.7717/peerj.8248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mohamed Nasir et al. title: Morpho-physiological traits, biochemical response and phytoextraction potential of short-term copper stress on kenaf (Hibiscus cannabinus L.) seedlings link: https://peerj.com/articles/8321 last-modified: 2020-01-30 description: Kenaf (Hibiscus cannabinus L.) is a fibrous crop, grown in tropical climate having huge biomass and can be a good candidate for the phytoremediation of different heavy metals. Consequently, the present study was conducted to explore morpho-physiological traits, photosynthetic pigments, gaseous exchange attributes, antioxidative response and phytoextraction of copper (Cu) in H. cannabinus grown under different levels of Cu i.e. 0 (control), 60, 120 and 180 µmol L−1 in Hoagland nutrient solution (pH 6.2). The results from the present study revealed that Cu toxicity reduced plant height, plant diameter, plant fresh weight, plant dry weight, photosynthetic pigments and gaseous exchange attributes compared to control. Moreover, excess Cu in the nutrient solution ameliorates contents of malondialdehyde (MDA), hydrogen peroxide (H2O2) and electrolyte leakage (EL) which showed that Cu induced oxidative damage in the roots and leaves of H. cannabinus. The oxidative stress which was induced by a high concentration of Cu in the nutrient solution is overcome by enzymatic activities of antioxidants which increased with the increase in Cu concentration, i.e. 60 and 120 µmol L−1, while the addition of Cu (180 µmol L−1) caused a reduction in the activities of superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in the roots and leaves of H. cannabinus. The results also demonstrated that an increase in Cu concentration in the nutrient solution causes an increase in Cu accumulation through roots, leaves and stems of H. cannabinus, although the highest Cu concentration was accumulated in roots while only a little transported to the above ground parts (leaves and stems) of the plants. All the values of bioaccumulation factor (BAF) and translocation factor (TF) were less than 1, which also indicated that a small quantity of Cu concentration is transported to the aboveground part of the plants. These findings suggested that phytotoxicity of Cu affected plant growth and biomass and increased ROS production while accumulation of Cu in different parts of plant proved that H. cannabinus is an ideal specie for phytoremediation of Cu when grown under Cu contaminated sites. creator: Muhammad Hamzah Saleem creator: Shah Fahad creator: Muzammal Rehman creator: Shah Saud creator: Yousaf Jamal creator: Sajjad Khan creator: Lijun Liu uri: https://doi.org/10.7717/peerj.8321 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Saleem et al. title: Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns link: https://peerj.com/articles/8349 last-modified: 2020-01-30 description: BackgroundWhen considering therapies for lung adenocarcinoma (LUAD) patients, the carcinogenic mechanisms of smokers are believed to differ from those who have never smoked. The rising trend in the proportion of nonsmokers in LUAD urgently requires the understanding of such differences at a molecular level for the development of precision medicine.MethodsThree independent LUAD tumor sample sets—TCGA, SPORE and EDRN—were used. Genome patterns of expression (GE), copy number variation (CNV) and methylation (ME) were reviewed to discover the differences between them for both smokers and nonsmokers. Tobacco-related signature genes distinguishing these two groups of LUAD were identified using the GE, ME and CNV values of the whole genome. To do this, a novel iterative multi-step selection method based on the partial least squares (PLS) algorithm was proposed to overcome the high variable dimension and high noise inherent in the data. This method can thoroughly evaluate the importance of genes according to their statistical differences, biological functions and contributions to the tobacco exposure classification model. The kernel partial least squares (KPLS) method was used to further optimize the accuracies of the classification models.ResultsForty-three, forty-eight and seventy-five genes were identified as GE, ME and CNV signatures, respectively, to distinguish smokers from nonsmokers. Using only the gene expression values of these 43 GE signature genes, ME values of the 48 ME signature genes or copy numbers of the 75 CNV signature genes, the accuracies of TCGA training and SPORE/EDRN independent validation datasets all exceed 76%. More importantly, the focal amplicon in Telomerase Reverse Transcriptase in nonsmokers, the broad deletion in ChrY in male nonsmokers and the greater amplification of MDM2 in female nonsmokers may explain why nonsmokers of both genders tend to suffer LUAD. These pattern analysis results may have clear biological interpretation in the molecular mechanism of tumorigenesis. Meanwhile, the identified signature genes may serve as potential drug targets for the precision medicine of LUAD. creator: Yan-mei Dong creator: Li-da Qin creator: Yi-fan Tong creator: Qi-en He creator: Ling Wang creator: Kai Song uri: https://doi.org/10.7717/peerj.8349 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dong et al. title: A retrospective assessment of different endodontic treatment protocols link: https://peerj.com/articles/8495 last-modified: 2020-01-30 description: BackgroundThe aim of this study was to assess the clinical impact of non-surgical root canal treatments (NSRCT) performed with different treatment protocols on the probability of tooth survival without untoward events and to identify predictors influencing the outcome.MethodsDuring the period from July 1999 to October 2016, 5,858 patients were identified in which 9,967 NSRCTs were performed. The treatments were followed up and divided into three groups. In Group 1 root canal treatment was performed with hand instruments, in Group 2 with multiple file rotary instruments and passive ultrasonic irrigation (PUI), and Group 3 was treated with Reciproc instruments and PUI. Untoward events were defined as orthograde retreatment, apicoectomy or extraction of the tooth after initial treatment. Weibull regression was used to analyse the data.ResultsA total of 9,938 cases could be included into the analyses. The results showed 5-years predicted survival rates without untoward events of 73.9% (95% CI [71.7%–76.1%]), 75.1% (95% CI [71.7%–78.0%]) and 78.4% (95% CI [75.1%–81.4%]) for study group 1 (N = 5,580), 2 (N = 1,700) and 3 (N = 2,658), respectively. The differences between Group 1 and 3 were statistically significant (p < 0.006). Higher age of the patient (per year increase) and number of earlier NSRCTs (per unit increase) reduce the survival without untoward events statistically significant (both p < 0.02), while treatment of premolars had a statistically significant lower hazard ratio [0.89 (95% CI [0.79–0.99]; p = 0.030)] compared to treatment of molars and anterior teeth. A higher number of supportive periodontal treatments (per unit increase) improved tooth survival without untoward events highly significant (p < 0.0001).DiscussionMore recent endodontic treatment protocols involving reciprocating instruments and PUI appear to be associated with higher tooth survival rates without untoward events compared to hand instruments. creator: Andreas Bartols creator: Carsten Bormann creator: Luisa Werner creator: Melanie Schienle creator: Winfried Walther creator: Christof E. Dörfer uri: https://doi.org/10.7717/peerj.8495 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bartols et al. title: Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses link: https://peerj.com/articles/8258 last-modified: 2020-01-29 description: Drought and heat stresses can influence the expressions of genes, and thereby affect the growth and development of plants. Alternative splicing (AS) of genes plays crucial roles through increasing transcriptome diversity in plant stress responses. Tea plants, widely cultivated in the tropics and subtropics, are often simultaneously exposed to drought and heat stresses. In the present study, we performed a global transcriptome of tea leaves treated with drought, heat or their combination. In total, 19,019, 20,025 and 20,253 genes underwent AS in response to drought (DT), heat (HT) and their combined stress (HD), respectively, of which 12,178, 11,912 and 14,413 genes differentially spliced in response to DT, HT and HD, respectively. Also, 2,447 specific differentially spliced genes (DSGs) were found only in response to HD. All DSGs accounted for  48% of the annotated genes in tea tree genome. Comparison of DSGs and differentially expressive genes (DEGs) showed that the proportions of HT and HD-induced DSGs were 13.4% and 9.2%, while the proportion of DT increased to 28.1%. Moreover, the DEG-DSG overlapped genes tended to be enriched in a wide large of pathways in response to DT. The results indicated that the AS of genes in tea leaves was extensively triggered by drought, heat and their combined stresses. In addition, the AS enhanced the transcriptome adaption in response to drought and heat stresses, and the AS also provoked specific molecular functions in response to drought and heat synergy stress. The study might have practical significance for molecular genetic breeding of tea plants with stress resistance. creator: Yiqian Ding creator: Yu Wang creator: Chen Qiu creator: Wenjun Qian creator: Hui Xie creator: Zhaotang Ding uri: https://doi.org/10.7717/peerj.8258 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ding et al. title: The immunostimulatory activity of polysaccharides from Glycyrrhiza uralensis link: https://peerj.com/articles/8294 last-modified: 2020-01-29 description: BackgroundThe enhancement of immunity is very important for immunocompromised patients such as cancer patients with radiotherapy or chemotherapy. Glycyrrhiza uralensis has been used as food and medicine for a long history. G. uralensis polysaccharides (GUPS) were prepared and its immunostimulatory effects were investigated.MethodsHuman monocyte-derived dendritic cells (DCs) and murine bone marrow-derived DCs were treated with different concentrations of GUPS. The DCs maturation and cytokine production were analyzed by flow cytometry and ELISA, respectively. Inhibitors and Western blot were used to study the mechanism of GUPS. The immunostimulatory effects of GUPS were further evaluated by naïve mouse model and immunosuppressive mouse model induced by cyclophosphamide. ResultsGUPS significantly promoted the maturation and cytokine secretion of human monocyte-derived DCs and murine bone marrow-derived DCs through TLR4 and down-stream p38, JNK and NF-κB signaling pathways. Interestingly, the migration of GUPS treated-DCs to lymph node was increased. In the mouse model, GUPS increased IL-12 production in sera but not for TNF-α. Moreover, GUPS ameliorated the side effect of cyclophosphamide and improved the immunity of immunosuppressive mice induced by cyclophosphamide. These results suggested that GUPS might be used for cancer therapy to ameliorate the side effect of chemotherapy and enhance the immunity. creator: Adila Aipire creator: Mahepali Mahabati creator: Shanshan Cai creator: Xianxian Wei creator: Pengfei Yuan creator: Alimu Aimaier creator: Xinhui Wang creator: Jinyao Li uri: https://doi.org/10.7717/peerj.8294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Aipire et al. title: Post-treatment of hyaluronan to decrease the apoptotic effects of carprofen in canine articular chondrocyte culture link: https://peerj.com/articles/8355 last-modified: 2020-01-29 description: A major concern associated with the use of drugs is their adverse side effects. Specific examples of the drugs of concern include antibiotic agents and non-steroidal anti-inflammatory drugs. Despite the presence of a high degree of efficacy for specific conditions, these drugs may deteriorate the surrounding tissues that are exposed to them. Often, carprofen is used for joint inflammation; however, it may stimulate cartilage degradation which can then lead to osteoarthritis progression. In this study, hyaluronan was combined with carprofen treatment in three different applications (pre-treatment, co-treatment and post-treatment) on normal canine chondrocytes to determine whether Hyaluronan (HA) is capable of mitigating the degree of chondrotoxicity of carprofen. Our findings revealed that carprofen at IC20 (0.16 mg/mL) decreased viability and increased nitric oxide (NO) production. Importantly, carprofen induced the apoptosis of canine chondrocytes via the up-regulation of Bax, Casp3, Casp8, Casp9 and NOS2 as compared to the control group. Although the co-treatment of HA and carprofen appeared not to further alleviate the chondrotoxicity of carprofen due to the presence of a high number of apoptotic chondrocytes, post-treatment with HA (carprofen treatment for 24 h and then changed to HA for 24 h) resulted in a decrease in chondrocyte apoptosis by the down-regulation of Bax, Casp3, Casp8, Casp9, NOS2, along with NO production when compared with the treatment of carprofen for 48 h (P < 0.05). These results suggest that HA can be used as a therapeutic agent to mitigate the degree of chondrotoxicity of carprofen. creator: Korakot Nganvongpanit creator: Thippaporn Euppayo creator: Puntita Siengdee creator: Kittisak Buddhachat creator: Siriwadee Chomdej creator: Siriwan Ongchai uri: https://doi.org/10.7717/peerj.8355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nganvongpanit et al. title: Remarks on Mastigodiaptomus (Calanoida: Diaptomidae) from Mexico using integrative taxonomy, with a key of identification and three new species link: https://peerj.com/articles/8416 last-modified: 2020-01-29 description: BackgroundIn Mexico, species of four families of free-living calanoid copepods have been recorded as inhabitants of several freshwater systems. These families are Centropagidae, Temoridae, Pseudodiaptomidae and Diaptomidae. The genera Leptodiaptomus and Mastigodiaptomus are the most speciose diaptomid genera in Mexico, and they inhabit natural and artificial lakes, ephemeral ponds, springs, and caverns. Leptodiaptomus is considered as an endemic Nearctic genus, whereas Mastigodiaptomus is a widely distributed Neotropical genus in the southern USA, Mexico, the Caribbean Islands and Central America. Based on new and recent evidence, Mastigodiaptomus diversity has been underestimated: six species of the genus were known before 2000. In this work three new Mastigodiaptomus species have been described from different regions of Mexico by using integrative taxonomy. We also gave amended diagnosis of M. nesus Bowman (1986) and M. patzcuarensis s. str. (Kiefer, 1938).MethodsIn this work, the taxonomic status of the species was clarified using modern, integrative method based on the COI gene as a DNA marker, plus micro-structural analysis (based on SEM and ligth microscopy).ResultsThree new species of Mastigodiaptomus were described based on genetic and morphological analyses: M. alexei sp. n., M. ha sp. n. and M. cihuatlan sp. n. Also amended description of M. nesus, morphological variation of M. patzcuarensis s. str., and a comparison of them with all known sequences within the genus are provided. These new findings show that in Mastigodiaptomus differences in several cuticular microstructures of several appendages (such as the antennules, the fifth legs, or the urosomites of these copepods) agree with the interspecific genetic divergence >3% observed in sequences of the COI gene, and the integration of this information is a powerful tool in species delineation. creator: Martha A. Gutiérrez-Aguirre creator: Adrián Cervantes-Martínez creator: Manuel Elías-Gutiérrez creator: Alfonso Lugo-Vázquez uri: https://doi.org/10.7717/peerj.8416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gutiérrez-Aguirre et al. title: Candidal carriage in saliva and subgingival plaque among smokers and non-smokers with chronic periodontitis—a cross-sectional study link: https://peerj.com/articles/8441 last-modified: 2020-01-29 description: Background and ObjectivesStudies of gum or periodontal disease have focused mainly on bacterial pathogens. However, information related to fungal species in the saliva and subgingival mileu is particularly lacking in smokers with periodontitis. This cross-sectional study compared the prevalence of various Candida species in saliva and subgingival plaque samples of smokers and non-smokers with periodontal disease.MethodologyStudy subjects were recruited into three group—Group 1: Smokers with chronic periodontitis (N = 30), Group 2: Non-smokers with chronic periodontitis (N = 30) and Group 3: Healthy controls (N = 30). Clinical parameters recorded included plaque index (PI), gingival index (GI), periodontal probing depth (PPD) and clinical attachment loss (CAL). Saliva and subgingival plaque samples were collected from subjects from the above groups. The collected samples were processed for isolation and identification of various Candida species using CHROMagar chromogenic media. Additionally, antifungal susceptibility tests were performed for the isolated Candida species in order to assess antifungal drug resistance to fluconazole and voriconazole.ResultsPrevalence of Candida species in saliva samples was quantified as 76.6% in Group 1, 73.3% in Group 2 and 36.6% in Group 3 and statistically significant differences were observed between groups 1 & 3. Prevalence of Candida species in subgingival plaque samples was quantified as 73.3% in Group 1, 66.6% in Group 2 and 60% in Group 3 and no statistically significant differences were observed between groups. Candida albicans was the most frequently isolated species followed by Candida krusei and Candida tropicalis. A positive correlation was observed for smoking exposure, pack years and Candida colonization. A marginally significant positive correlation was observed between Candida colonization and increasing pocket depth and attachment loss. Antifungal drug resistance was mainly observed for Candida krusei in both saliva and subgingival plaque samples.ConclusionBased on the results we can conclude that oral candidal carriage is significantly increased in smokers with periodontal disease. Mechanistic studies are needed to understand the importance of Candida species in periodontal disease. creator: Gayathri Santhana Krishnan creator: Dilip Naik creator: Ashita Uppoor creator: Sangeeta Nayak creator: Shrikala Baliga creator: Abhiram Maddi uri: https://doi.org/10.7717/peerj.8441 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Santhana Krishnan et al. title: A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice link: https://peerj.com/articles/8491 last-modified: 2020-01-29 description: Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing. creator: Xiaoli Liu creator: Xiujuan Zhou creator: Kang Li creator: Dehong Wang creator: Yuanhao Ding creator: Xianqing Liu creator: Jie Luo creator: Chuanying Fang uri: https://doi.org/10.7717/peerj.8491 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu et al. title: Long non-coding RNA ERICH3-AS1 is an unfavorable prognostic factor for gastric cancer link: https://peerj.com/articles/8050 last-modified: 2020-01-28 description: Long non-coding RNAs (lncRNAs) play important roles in gastric cancer (GC), but the mechanism is not fully clear. ERICH3-AS1 (ERICH3 antisense RNA1) is affiliated with the non-coding RNA class which has proven to be involved in the prognostic of GC, but the function of ERICH3-AS1 is still unclear. In this study, we aim to explore the potential function of ERICH3-AS1 in the development of GC and analyze the prognostic role of ERICH3-AS1 in GC. We found that the lncRNA ERICH3-AS1 was significantly up-regulated in GC tissues in the analysis of The Cancer Genome Atlas (TCGA) data; the Kaplan-Meier analysis showed that the higher the expression of ERICH3-AS1 was, the earlier the recurrence and the poorer the prognosis would be in patients. Cox univariate and multivariate analyses revealed that ERICH3-AS1 was a risk factor of disease-free survival (DFS) (p < 0.05) and overall survival (OS) (p < 0.05) of patients. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, it demonstrated that the ERBB pathways, the mitogen-activated protein kinase (MAPK) pathways, the MTOR pathways, p53 pathways and Wnt pathways were differentially enriched in ERICH3-AS1 high expression phenotype. Furthermore, the correlation analysis showed that ERICH3-AS1 had significant correlations with apoptosis-related proteins such as BCL2L10 and CASP14; cell cycle-associated proteins CDK14 and invasion and migration-associated proteins such as MMP20, MMP26 and MMP27. In summary, we identified that increased ERICH3-AS1 might be a potential biomarker for diagnosis and independent prognostic factor of GC. Moreover, ERICH3-AS1 might participate in the oncogenesis and development of tumors via cell cycle and apoptosis pathway mediated by ERBB, MAPK, MTOR, p53 and Wnt pathways. creator: Qiongyun Chen creator: Xiaoqing Huang creator: Xuan Dong creator: Jingtong Wu creator: Fei Teng creator: Hongzhi Xu uri: https://doi.org/10.7717/peerj.8050 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: The Global Museum: natural history collections and the future of evolutionary science and public education link: https://peerj.com/articles/8225 last-modified: 2020-01-28 description: Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums. creator: Freek T. Bakker creator: Alexandre Antonelli creator: Julia A. Clarke creator: Joseph A. Cook creator: Scott V. Edwards creator: Per G.P. Ericson creator: Søren Faurby creator: Nuno Ferrand creator: Magnus Gelang creator: Rosemary G. Gillespie creator: Martin Irestedt creator: Kennet Lundin creator: Ellen Larsson creator: Pável Matos-Maraví creator: Johannes Müller creator: Ted von Proschwitz creator: George K. Roderick creator: Alexander Schliep creator: Niklas Wahlberg creator: John Wiedenhoeft creator: Mari Källersjö uri: https://doi.org/10.7717/peerj.8225 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bakker et al. title: ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae) link: https://peerj.com/articles/8392 last-modified: 2020-01-28 description: Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group. creator: Janice Valencia-D creator: José Murillo-A creator: Clara Inés Orozco creator: Carlos Parra-O creator: Kurt M. Neubig uri: https://doi.org/10.7717/peerj.8392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Valencia-D et al. title: LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression link: https://peerj.com/articles/8394 last-modified: 2020-01-28 description: BackgroundAberrant expression of long noncoding RNAs are implicated in the pathogenesis of human malignancies. LINC00844 expression is dramatically downregulated in prostate cancer, and functional studies have revealed the association between the aberrant expression of LINC00844 and prostate cancer cell invasion and metastasis. However, the function and mechanism of action of LINC00844 in the pathogenesis of hepatocellular carcinoma (HCC) are poorly understood.MethodsLINC00844 and N-Myc downstream-regulated 1 (NDRG1) expression in HCC tissues and cell lines was detected with real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. Correlations between LINC00844 expression level and clinicopathological features were investigated using the original data from The Cancer Genome Atlas (TCGA) database. HepG2 and HCCLM9 cell lines were transfected with Lv-LIN00844 virus to obtain LINC00844-overexpressing cell lines. Cell proliferation and cell invasion and migration were examined with the cell counting kit-8 (CCK-8) and transwell assay, respectively. Furthermore, the correlation between LINC00844 and NDRG1 expression was analysed using Pearson’s correlation analysis.ResultsLINC00844 expression was significantly downregulatedin HCC tissues and cell lines, and a statistical correlation was detected between low LINC00844 expression and sex (Female), advanced American Joint Committee on Cancer (AJCC) stage (III + IV), histological grade (G3 + G4), and vascular invasion (Micro and Macro). In vitro experiments showed that LINC00844 overexpression significantly repressed the proliferation, migration, and invasion of HCC cells. NDRG1 expression was higher in HCC tissues and LINC00844 could partly inhibit the expression of NDRG1. creator: Wei Zhou creator: Kang Huang creator: Qiuyan Zhang creator: Shaojun Ye creator: Zibiao Zhong creator: Cheng Zeng creator: Guizhu Peng creator: Ling Li creator: Qifa Ye uri: https://doi.org/10.7717/peerj.8394 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: Teenage sleep and technology engagement across the week link: https://peerj.com/articles/8427 last-modified: 2020-01-28 description: BackgroundThroughout the developed world, adolescents are growing up with increased access to and engagement with a range of screen-based technologies, allowing them to encounter ideas and people on a global scale from the intimacy of their bedroom. The concerns about digital technologies negatively influencing sleep are therefore especially noteworthy, as sleep has been proven to greatly affect both cognitive and emotional well-being. The associations between digital engagement and adolescent sleep should therefore be carefully investigated in research adhering to the highest methodological standards. This understood, studies published to date have not often done so and have instead focused mainly on data derived from general retrospective self-report questionnaires. The value of this work has been called into question by recent research showing that retrospective questionnaires might fail to accurately measure these variables of interest. Novel and diverse approaches to measurement are therefore necessary for academic study to progress.MethodsThis study analyses data from 11,884 adolescents included in the UK Millennium Cohort Study to examine the association between digital engagement and adolescent sleep, comparing the relative effects of retrospective self-report vs. time-use diary measures of technology use. By doing so, it provides an empirical lens to understand the effects of digital engagement both throughout the day and before bedtime and adds nuance to a research area primarily relying on retrospective self-report.ResultsThe study finds that there is a small negative association relating digital engagement to adolescent sleep both on weekdays and weekend days (median standardized association βweekday = −0.06 and βweekend = −0.03). There is a more negative association between digital engagement and total sleep time on weekdays compared to weekend days (median standardized βweekday = −0.08, median standardized βweekend = −0.02), while there is no such difference when examining adolescents’ bedtime. Surprisingly, and contrary to our expectations, digital technology use before bedtime is not substantively associated with the amount of sleep and the tardiness of bedtime in adolescents.ConclusionsResults derived from the use of transparent Specification Curve Analysis methods show that the negative associations in evidence are mainly driven by retrospective technology use measures and measures of total time spent on digital devices during the day. The effects are overall very small: for example, an additional hour of digital screen time per day was only related to a 9 min decrease in total time spent sleeping on weekdays and a 3 min decrease on weekends. Using digital screens 30 min before bed led to a 1 min decrease in total time spent sleeping on weekdays and weekends. The study shows that more work should be done examining how to measure digital screen time before interventions are designed. creator: Amy Orben creator: Andrew K. Przybylski uri: https://doi.org/10.7717/peerj.8427 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Orben and Przybylski title: Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics link: https://peerj.com/articles/8445 last-modified: 2020-01-28 description: Marine mollusks are commonly subjected to heat stress. To evaluate the effects of heat stress on the physiological metabolism of the ark shell Scapharca subcrenata, clams were exposed to different high temperatures (24, 28 and 32 °C) for 72 h. The oxygen consumption and ammonia excretion rates were measured at 2, 12, 24, 48 and 72 h. The results indicated that the metabolic rates of the ark shell significantly increased with increasing heat stress, accompanied by mortalities in response to prolonged exposure. A metabolomics approach based on gas chromatography coupled with mass spectrometry was further applied to assess the changes of metabolites in the mantle of the ark shell at 32 °C. Moreover, multivariate and pathway analyses were conducted for the different metabolites. The results showed that the heat stress caused changes in energy metabolism, amino acid metabolism, osmotic regulation, carbohydrate metabolism and lipid metabolism through different metabolic pathways. These results are consistent with the significant changes of oxygen consumption rate and ammonia excretion rate. The present study contributes to the understanding of the impacts of heat stress on intertidal bivalves and elucidates the relationship between individual-level responses and underlying molecular metabolic dynamics. creator: Yazhou Jiang creator: Haifeng Jiao creator: Peng Sun creator: Fei Yin creator: Baojun Tang uri: https://doi.org/10.7717/peerj.8445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jiang et al. title: Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue link: https://peerj.com/articles/8461 last-modified: 2020-01-28 description: BackgroundThe Schlafen (Slfn) family proteins are important for regulation of cell growth, cell differentiation and cell cycle progression. We sought to distinguish Slfn family expression in Slfn3 knockout (KO) mice after RNA sequencing analysis of Slfn3KO vs. wildtype (WT) mice revealed varying expressions of Slfn family in ileal mucosa.MethodsQuantitative PCR analysis of Slfn members was evaluated in ileal mucosa, thymus and spleen tissue since Slfn family members have roles in differentiating intestinal and immune cells.ResultsIleal mucosa of Slfn3KO mice displayed a decrease in Slfn3, 4, 8 and 9 while Slfn1 and 5 increased in mRNA expression vs. WT mice. Thymic tissue had a Slfn9 increase and a Slfn4 decrease while splenic tissue had a Slfn8 and Slfn9 increase in Slfn3KO mice vs. WT mice. These differential expressions of Slfn members could indicate a feedback regulatory mechanism within the Slfn family. Indeed, MATCH™ tool from geneXplain predicted that all Slfn members have regions in their promoters for the Kruppel-like factor-6 transcription factor. In addition, NFAT related factors, ING4, ZNF333 and KLF4 are also predicted to bind in up to 6 of the 8 Slfn promoters. This study further describes a possible autoregulatory mechanism amongst the Slfn family members which could be important in how they regulate the differentiation of various cell types. creator: Emilie E. Vomhof-DeKrey creator: Josey Umthun creator: Marc D. Basson uri: https://doi.org/10.7717/peerj.8461 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vomhof-DeKrey et al. title: Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis link: https://peerj.com/articles/8465 last-modified: 2020-01-28 description: The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha. creator: Yongguo Zhao creator: Hua Kong creator: Yunling Guo creator: Zhi Zou uri: https://doi.org/10.7717/peerj.8465 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients link: https://peerj.com/articles/8481 last-modified: 2020-01-28 description: BackgroundOur previous study demonstrated that the composition of the urinary microbiota in female patients with type 2 diabetes mellitus (T2DM) was correlated with the concentration of urinary interleukin (IL)-8. As the composition of urine is mainly determined by diet, diet might mediate the correlation.MethodsSeventy female T2DM patients and 70 healthy controls (HCs) were recruited. Midstream urine was used for the urine specimens. Urinary IL-8 was determined by enzyme-linked immunosorbent assay. A Chinese Food Frequency Questionnaire was used to collect food intake data. The independent variables in the hierarchical regression analysis were the relative abundances of the bacterial genera and species that were significantly different between the T2DM and HCs and between the T2DM patients with and without detectable urinary IL-8, and the bacterial genera associated with IL-8 concentration in the multiple regression model reported in our previous research. IL-8 concentration was the dependent variable, and nutrient intakes were moderator variables.ResultsFiber and vitamin B3 and E intake exerted enhancing effects, and water intake exerted a buffering effect, on the positive relationship between the relative abundance of Ruminococcus and IL-8 concentration (p < 0.05). Cholesterol and magnesium intake exerted enhancing effects on the positive relationship between the relative abundance of Comamonas and IL-8 concentration (p < 0.05).ConclusionModulating T2DM patients’ dietary patterns may prevent bladder inflammation. creator: Fengping Liu creator: Zongxin Ling creator: Chulei Tang creator: Fendi Yi creator: Yong Q. Chen uri: https://doi.org/10.7717/peerj.8481 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu et al. title: Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia link: https://peerj.com/articles/7971 last-modified: 2020-01-27 description: For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries. creator: Paul M. Oliver creator: Audrey Miranda Prasetya creator: Leonardo G. Tedeschi creator: Jessica Fenker creator: Ryan J. Ellis creator: Paul Doughty creator: Craig Moritz uri: https://doi.org/10.7717/peerj.7971 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oliver et al. title: Investigating the effects of management practice on mammalian co-occurrence along the West Coast of South Africa link: https://peerj.com/articles/8184 last-modified: 2020-01-27 description: The subtle and cascading effects (e.g., altered interspecific interactions) that anthropogenic stressors have on local ecological assemblages often go unnoticed but are concerning given their importance in ecosystem function. For example, elimination of buffalo from the Serengeti National Park is suggested to have driven increased abundance of smaller antelope as a result of release from competition. The perceived low abundance of small antelope in the contractual Postberg section of the West Coast National Park (the park) has been an ongoing management concern which has been anecdotally attributed to predation by a mesopredator (the caracal, Caracal caracal). However, we hypothesized that the historical overstocking, and consequent overgrazing by larger-bodied managed ungulates would influence small antelope abundance. Using camera traps, we investigated species co-occurrence and temporal activity between small antelope, managed ungulates and caracals in Postberg as well as another part of the park (Langebaan) and a farm outside of the park. Results suggest that small antelope and managed ungulates have a high degree of temporal overlap (Δ = 0.74, 0.79 and 0.86 for the farm, Langebaan and Postberg respectively), while temporal partitioning between small antelope and caracal is apparent (Δ = 0.59). Further, small antelope and managed ungulates appear to occur independently of one another (SIF = 0.91–1 across areas). Managed ungulates were detected almost three times more frequently on fallow lands when compared to the more vegetated sites within the park suggesting that segregated food/cover resources allow for independent occurrence. Small antelope had a much higher probability of occurrence outside of the protected area (e.g., ψ = 0.192 and 0.486 for steenbok at Postberg, Langebaan compared to 0.841 on the farm), likely due to less variable (more intact) habitat outside of the protected area. There is not sufficient evidence to currently warrant management intervention for predators. The small size of the protected area provides limited scope for spatial replication thus reducing possibilities to infer the cause and effect for complex interactions (which would historically have taken place over much larger areas) with negative implications for adaptive management. We recommend continued monitoring over multiple seasons and a wider area to determine the spatial information requirements to inform management of small protected areas. creator: Deborah Jean Winterton creator: Nicola J. van Wilgen creator: Jan A. Venter uri: https://doi.org/10.7717/peerj.8184 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Winterton et al. title: Bacterial inoculations can perturb the growth trajectory of diatoms with an existing microbiome link: https://peerj.com/articles/8352 last-modified: 2020-01-27 description: Inoculation of axenic diatom monocultures with individual bacterial strains has been used effectively to examine the relationship between bacteria and a diatom host. Both beneficial and harmful effects on diatom fitness have been observed. Yet, diatoms commonly host a consortium of bacteria that could influence their response to perturbation by bacterial inoculations. In this study, diatom cultures with an existing microbiome were inoculated with individual bacterial strains. Strains of two genera of bacteria commonly found associated with diatoms (Alteromonas and Marinobacter) were isolated from a culture of the diatom Chaetoceros sp. KBDT20. To evaluate whether bacterial inoculations can impact the growth, peak abundance, or decline of diatoms with an intact microbiome, individual bacterial strains were inoculated into batch cultures of the original host as well as two non-origin diatom hosts (Chaetoceros sp. KBDT32 and Amphiprora sp. KBDT35). Inoculations were repeated under vitamin-replete and vitamin-deficient conditions to assess whether vitamin concentration modulates the impact of bacterial inoculations on the host. The origin Chaetoceros culture was largely unperturbed by bacterial inoculations. In contrast, non-origin hosts experienced long-term impacts on their growth trajectory, and those impacts were found to be dependent on the concentration of vitamins in the growth medium. For the non-origin Chaetoceros, all positive impacts were observed in vitamin-replete conditions and all negative impacts were observed in vitamin-deficient conditions. Amphiprora was only impacted by inoculation with Marinobacter strains in vitamin-deficient conditions, and the effect was negative. Neither individual bacterial strains nor genera resulted in exclusively beneficial nor detrimental impacts, and the magnitude of effect varied among bacterial strains. This study demonstrates that bacterial inoculations can have long-lasting impacts on the growth trajectory of diatoms with an existing microbiome, that this impact can differ even between congeneric diatoms, and that the impact can be significantly modulated by vitamin concentration. creator: Lydia J. Baker creator: Paul F. Kemp uri: https://doi.org/10.7717/peerj.8352 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Baker and Kemp title: Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii link: https://peerj.com/articles/8356 last-modified: 2020-01-27 description: To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria. creator: Darrin T. Schultz creator: Jordan M. Eizenga creator: Russell B. Corbett-Detig creator: Warren R. Francis creator: Lynne M. Christianson creator: Steven H.D. Haddock uri: https://doi.org/10.7717/peerj.8356 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Schultz et al. title: A cross-sectional study on interference control: age affects reactive control but not proactive control link: https://peerj.com/articles/8365 last-modified: 2020-01-27 description: BackgroundWorking memory updating (WMU), a controlled process to continuously adapt to the changing task demand and environment, is crucial for cognitive executive function. Although previous studies have shown that the elderly were more susceptible to cognitive interference than the youngsters, the picture of age-related deterioration of WMU is incomplete due to lack of study on people at their middle ages. Thus, the present study investigated the impact of age on the WMU among adults by a cross-sectional design to verify whether inefficiency interference control accounts for the aging of WMU.MethodsIn total, 112 healthy adults were recruited for this study; 28 old adults (21 female) ranging from 60 to 78 years of age; 28 middle-age adults (25 female) ranging from 45 to 59 years of age; 28 adults (11 female) ranging from 26 to 44 years of age; and 28 young adults (26 female) ranging from 18 to 25 years of age. Each participant completed a 1-back task. The inverse efficiency score was calculated in various sequences of three trials in a row to quantify the performance of WMU for adults of various ages.ResultsInverse efficiency score of both young groups (young adult and adult) were significantly shorter than the old group in both Repeat-Alternate (RA, including □□○ and ○○□) and Alternate-Alternate (AA, including ○□○ and □○□) sequential patterns and they were additionally better than the middle-age group in AA sequential pattern.ConclusionWith the increase of difficulty in the task, the difference in reactive interference control between young and middle age was gradually revealed, while the difference between young and old remained to apparent. The degradation of WMU aging may begin from middle-age and presents selective impairment in that only reactive interference control, but not proactive interference control, shows pronounced age-related decline. The preliminary results can inform future studies to further explore the whole lifespan trajectories of cognitive functions. creator: Yanfang Peng creator: Qin Zhu creator: Biye Wang creator: Jie Ren uri: https://doi.org/10.7717/peerj.8365 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Peng et al. title: Effects of silver-graphene oxide on seed germination and early growth of crop species link: https://peerj.com/articles/8387 last-modified: 2020-01-27 description: Due to its excellent material properties, silver-graphene oxide (Ag-GO) is being studied for diverse applications, such as antimicrobial agents, catalysts and absorbents. Such use of Ag-GO may lead to its release into terrestrial ecosystems, but little is known about the impact of Ag-GO on plants. In the present study, we determined the effects of Ag-GO on seed germination and early growth of crop species by analyzing the germination rate, growth of roots and shoots, hydrogen peroxide (H2O2) accumulation, and the uptake of Ag in alfalfa, radish and cucumber treated with 0.2–1.6 mg mL−1 of Ag-GO. Ag-GO treatment increased the shoot growth of radish at 0.2–1.6 mg mL−1 but decreased that of cucumber at 0.8 mg mL−1. In addition, Ag-GO enhanced the root elongation of radish at 0.2 mg mL−1 but inhibited that of alfalfa at 0.2, 0.8 and 1.6 mg mL−1. Ag-GO treatment induced H2O2 production in alfalfa, radish and cucumber in a concentration-dependent manner. Larger amounts of Ag accumulated in the seedlings as the concentration of Ag-GO increased, and such accumulation suggests that Ag may be transferred to higher trophic levels when plants are exposed to Ag-GO in ecosystems. Our study can, thus, serve as an important basis for setting guidelines for the release of nanomaterials into the environment. creator: Min-Ji Kim creator: Woong Kim creator: Haegeun Chung uri: https://doi.org/10.7717/peerj.8387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kim et al. title: Resection vs. ablation for lesions characterized as resectable-ablative within the colorectal liver oligometastases criteria: a propensity score matching from retrospective study link: https://peerj.com/articles/8398 last-modified: 2020-01-27 description: BackgroundThere has been no prospective or retrospective studies reporting the comparison outcome between surgery and ablation for resectable-ablative (lesions could be treated by resection or complete ablation) colorectal liver oligometastases (CLOM). The purpose of this study was to compare the efficacy and prognostic difference in patients who underwent R0 resection vs. complete ablation within the resectable-ablative CLOM criteria.MethodsFrom January 2008 to May 2018, a total of 2,367 patients diagnosed with colorectal liver metastases were included in this observational study. The metastasis was characterized by only limited to liver with number ≤5, size ≤5 cm, and resectable-ablative (lesions could be treated by resection or complete ablation). The evaluated indications, including liver progression-free survival (LPFS), overall survival (OS), survival rates, pattern and number of recurrences, and complications, were compared by using propensity score matching (PSM). The Kaplan−Meier curves were generated, and a log-rank test was performed. The Cox regression model was used for univariate and multivariate analyses to identify predictors of outcomes.ResultsA total of 421 consecutive patients were eligible for this study, with 250 and 171 undergoing R0 resection and complete ablation, respectively. PSM identified 145 patients from each group. The 1-, 3-, 5- and 8-year OS rates in the resection group and the ablation group were 95.8% vs. 95.0%, 69.8% vs. 60.1%, 53.6% vs. 42.5%, and 45.1% vs. 32.9% (p = 0.075), respectively. The median LPFS in the resection group was significantly longer than that in the ablation group (35 months vs. 15 months, p = 0.011). No statistical difference was found in LPFS between the two groups when comparing ≤3 cm liver metastases. For liver metastasis >3 cm, the median LPFS in the resection group and ablation group was 11 months and 5 months, respectively (p = 0.001). In terms of high risk of clinical risk score (CRS), the resection group showed longer LPFS than the ablation group (median 18 months vs. 10 months, p = 0.043).ConclusionFor patients within the CLOM criteria suggesting that liver metastases were resectable as well as ablative, resection could result in longer liver recurrence-free survival than ablation in cases with size >3 cm or high risk of CRS. But for ≤3 cm liver metastases, their treatment efficacies were comparable. creator: Ma Luo creator: Si-Liang Chen creator: Jiawen Chen creator: Huzheng Yan creator: Zhenkang Qiu creator: Guanyu Chen creator: Ligong Lu creator: Fujun Zhang uri: https://doi.org/10.7717/peerj.8398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Luo et al. title: Speeding up training of automated bird recognizers by data reduction of audio features link: https://peerj.com/articles/8407 last-modified: 2020-01-27 description: Automated acoustic recognition of birds is considered an important technology in support of biodiversity monitoring and biodiversity conservation activities. These activities require processing large amounts of soundscape recordings. Typically, recordings are transformed to a number of acoustic features, and a machine learning method is used to build models and recognize the sound events of interest. The main problem is the scalability of data processing, either for developing models or for processing recordings made over long time periods. In those cases, the processing time and resources required might become prohibitive for the average user. To address this problem, we evaluated the applicability of three data reduction methods. These methods were applied to a series of acoustic feature vectors as an additional postprocessing step, which aims to reduce the computational demand during training. The experimental results obtained using Mel-frequency cepstral coefficients (MFCCs) and hidden Markov models (HMMs) support the finding that a reduction in training data by a factor of 10 does not significantly affect the recognition performance. creator: Allan G. de Oliveira creator: Thiago M. Ventura creator: Todor D. Ganchev creator: Lucas N.S. Silva creator: Marinêz I. Marques creator: Karl-L. Schuchmann uri: https://doi.org/10.7717/peerj.8407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 de Oliveira et al. title: Airborne microbial biodiversity and seasonality in Northern and Southern Sweden link: https://peerj.com/articles/8424 last-modified: 2020-01-27 description: Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by artificial and agricultural surroundings. Our results further indicate that local landscape, as well as seasonal variation, shapes microbial communities in air. creator: Edvin Karlsson creator: Anna-Mia Johansson creator: Jon Ahlinder creator: Moa J. Lundkvist creator: Navinder J. Singh creator: Tomas Brodin creator: Mats Forsman creator: Per Stenberg uri: https://doi.org/10.7717/peerj.8424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Karlsson et al. title: Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China link: https://peerj.com/articles/8433 last-modified: 2020-01-27 description: Variation in precipitation can markedly affect the structure and function of soil microbial communities, especially in arid areas which are limited by water resources. Therefore, it is critical to understand how soil bacterial community composition and diversity will respond to variation in precipitation. In this study, we examined the soil bacterial community structure and diversity between five precipitation treatments (60% decrease, 30% decrease, control, 30% increase and 60% increase in precipitation) in the same arid site, in the Junggar desert of Xinjiang, northern China. The dominant bacterial phyla, present at similar frequencies in plots with different precipitation levels, were Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria and Chloroflexi. The Shannon-Wiener and Chao1 indices of soil bacterial α-diversity were both positively correlated with plant diversity. Our results indicated that (1) extreme drought significantly decreased bacterial abundance and diversity compared with increased precipitation; (2) variation in precipitation did not change the dominant components of the bacterial communities; and (3) soil pH and total nitrogen concentration were the key factors affecting soil bacterial composition in the Junggar desert. creator: Ke Wu creator: Wenxuan Xu creator: Weikang Yang uri: https://doi.org/10.7717/peerj.8433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Association of IGF1 single-nucleotide polymorphisms with myopia in Chinese children link: https://peerj.com/articles/8436 last-modified: 2020-01-27 description: PurposeTo investigate the association between insulin-like growth factor 1 (IGF1) single-nucleotide polymorphisms (SNPs) and myopia in a young Chinese population.MethodsA total of 654 Chinese children aged 6–13 years from one primary school participated in our study and underwent a series of comprehensive ocular examinations, including cycloplegic refraction and measurements of axial length. Myopia was defined as a spherical equivalence (SE) ≤ −0.5 D in the worse eye. In total, six tagging SNPs of IGF1 were genotyped using the PCR-LDR (Polymerase Chain Reaction-Ligation Detection Reaction) method. We tested four different genetic modes (the allele, dominant, recessive, and additive models) of these SNPs and used multivariate logistic regression to calculate the effect of SNPs on myopia. In addition, we conducted a haplotype analysis with a variable-sized slide-window strategy.ResultsOverall, 281 myopic children and 373 non-myopic controls were included in the analysis. The SNP rs2162679 showed a statistical difference between the two groups in both the allele (p = 0.0474) and additive (p = 0.0497) models. After adjusting for age and gender, children with the genotype AA in the SNP rs2162679 had a higher risk of myopia than those with the genotype GG (OR = 2.219, 95% CI [1.218–4.039], p = 0.009). All haplotypes that varied significantly between the two groups contained the SNP rs2162679, and the four-SNP window rs5742653–rs2162679 had the lowest p value (Chi square = 5.768, p = 0.0163). However, after permutation tests, none of the associations remained statistically significant.ConclusionThe SNP rs2162679 in IGF1 was associated with myopia in a young Chinese population. The G allele in the SNP rs2162679 may protect against myopia. creator: Tianyu Cheng creator: Jingjing Wang creator: Shuyu Xiong creator: Bo Zhang creator: Qiangqiang Li creator: Xun Xu creator: Xiangui He uri: https://doi.org/10.7717/peerj.8436 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cheng et al. title: The diagnostic and prognostic value of UBE2T in intrahepatic cholangiocarcinoma link: https://peerj.com/articles/8454 last-modified: 2020-01-27 description: BackgroundUbiquitin-conjugating enzyme E2T (UBE2T) is overexpressed in several types of malignancies. However, little is known about its diagnostic significance in intrahepatic cholangiocarcinoma (ICC) and other bile duct diseases or its prognostic value in ICC.MethodsThe expression levels of UBE2T in the intrahepatic bile duct (IHBD, N = 13), biliary intraepithelial neoplasia (BilIN; BilIN-1/2, N = 23; BilIN-3, N = 11), and ICC (N = 401) were examined by immunohistochemistry. The differential diagnostic and prognostic values were also assessed.ResultsThe number of UBE2T-positive cells was significantly higher in ICC tissues than in nonmalignant tissues, including the IHBD, BilIN-1/2, and BilIN-3 tissues. Kaplan–Meier analysis showed that overexpression of UBE2T was correlated with a shorter time to recurrence (TTR) and overall survival (OS). The 5-year TTR rates in the high UBE2T and low UBE2T groups were 100% and 86.2%, respectively. The corresponding OS rates were 1.9% and 22.2%, respectively. High expression of UBE2T was an independent risk factor for both TTR (hazard ratio: 1.345; 95% confidence interval: 1.047,1.728) and OS (hazard ratio: 1.420; 95% confidence interval: 1.098,1.837).ConclusionsUBE2T can assist in differentiating benign bile duct diseases from ICC, and high expression of UBE2T suggests a poor prognosis for ICC. creator: Hua Yu creator: Han Wang creator: Wei Dong creator: Zhen-Ying Cao creator: Rong Li creator: Chao Yang creator: Wen-Ming Cong creator: Hui Dong creator: Guang-Zhi Jin uri: https://doi.org/10.7717/peerj.8454 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yu et al. title: The complete genome of Banana streak GF virus Yunnan isolate infecting Cavendish Musa AAA group in China link: https://peerj.com/articles/8459 last-modified: 2020-01-27 description: Banana streak virus (BSV) belongs to the members of the genus Badnavirus, family Caulimoviridae. At present, BSV contains nine species in the International Committee on Taxonomy of Viruses (ICTV) classification report (2018b release). Previous study indicated that the viral particles of Banana streak virus Acuminata Yunnan (BSV-Acum) were purified from banana (Cavendish Musa AAA group) leaves in Yunnan Province, China, and its complete genome was obtained. To further determine whether this sample infecting with Banana streak GF virus (BSGFV), the polymerase chain reaction (PCR) cloning and complete genome analysis of the Banana streak GF virus Yunnan isolate (BSGFV-YN) isolate were carried out in this study. The result showed that BSGFV-YN infecting Cavendish Musa AAA group was co-infecting this sample. Its genome contains a total of 7,325 bp in length with 42% GC content. This complete genome sequence was deposited in GenBank under accession number MN296502. Sequence analysis showed that the complete genome of BSGFV-YN was 98.14% sequence similarity to BSGFV Goldfinger, while it was 49.10–57.09% to other BSV species. Two phylogenetic trees based on the complete genome and ORFIII polyprotein indicated that BSGFV-YN and other BSV species clustered into a group, while it was the highest homology with BSGFV Goldfinger. Although BSGFV-YN and BSGFV Goldfinger were highly homologous, their cultivating bananas are different. The former cultivating banana was from Cavendish Musa AAA group, while the latter cultivating banana was from Goldfinger Musa AAAB group. Compared with BSGFV Goldfinger, the genome of BSGFV-YN has an extra multiple repetitive sequences in the intergenetic region between ORFIII and ORFI, suggesting that this region might be related to host selection. In summary, a BSGFV-YN distant from BSV-Acum was identified from the same sample, and its complete genome sequence was determined and analyzed. The study extends the polymorphism of BSVs in China and provides scientific clue for the evolutionary relationship with host selection of badnaviruses. creator: Wei-li Li creator: Nai-tong Yu creator: Jian-hua Wang creator: Jun-cheng Li creator: Zhi-xin Liu uri: https://doi.org/10.7717/peerj.8459 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Evaluation of three wheat (Triticum aestivum L.) cultivars as sensitive Cd biomarkers during the seedling stage link: https://peerj.com/articles/8478 last-modified: 2020-01-27 description: Sensitive seedling crops have been developed to monitor Cadmium (Cd) contamination in agricultural soil. In the present study, 18 parameters involving growth conditions and physiological performances were assessed to evaluate Cd-responses of three wheat (Triticum aestivum L.) cultivars, Xihan1 (XH), Longzhong1 (LZ) and Dingfeng16 (DF). Principle component analysis illustrated that Factor 1, representing growth performance, soluble sugar content and catalase activity, responded to the Cd treatments in a dose dependent manner, while Factor 2 represented by chlorophyll content and germinating root growth was mainly dependent on cultivar differences. Higher inhibition rates were observed in growth performance than in physiological responses, with the highest inhibition rates of shoot biomasses (39.6%), root length (58.7%), root tip number (57.8%) and bifurcation number (83.2%), even under the lowest Cd treatment (2.5 mg·L−1). According to the Cd toxicity sensitivity evaluation, DF exerted highest tolerance to Cd stress in root growth while LZ was more sensitive to Cd stress, suggesting LZ as an ideal Cd contaminant biomarker. This study will provide novel insight into the cultivar-dependent response during using wheat seedlings as Cd biomarkers. creator: Chuntao He creator: Zhihai Ding creator: Samavia Mubeen creator: Xuying Guo creator: Huiling Fu creator: Guorong Xin uri: https://doi.org/10.7717/peerj.8478 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 He et al. title: Cranial anatomy of Allosaurus jimmadseni, a new species from the lower part of the Morrison Formation (Upper Jurassic) of Western North America link: https://peerj.com/articles/7803 last-modified: 2020-01-24 description: Allosaurus is one of the best known theropod dinosaurs from the Jurassic and a crucial taxon in phylogenetic analyses. On the basis of an in-depth, firsthand study of the bulk of Allosaurus specimens housed in North American institutions, we describe here a new theropod dinosaur from the Upper Jurassic Morrison Formation of Western North America, Allosaurus jimmadseni sp. nov., based upon a remarkably complete articulated skeleton and skull and a second specimen with an articulated skull and associated skeleton. The present study also assigns several other specimens to this new species, Allosaurus jimmadseni, which is characterized by a number of autapomorphies present on the dermal skull roof and additional characters present in the postcrania. In particular, whereas the ventral margin of the jugal of Allosaurus fragilis has pronounced sigmoidal convexity, the ventral margin is virtually straight in Allosaurus jimmadseni. The paired nasals of Allosaurus jimmadseni possess bilateral, blade-like crests along the lateral margin, forming a pronounced nasolacrimal crest that is absent in Allosaurus fragilis. creator: Daniel J. Chure creator: Mark A. Loewen uri: https://doi.org/10.7717/peerj.7803 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chure and Loewen title: Viability and management of the Asian elephant (Elephas maximus) population in the Endau Rompin landscape, Peninsular Malaysia link: https://peerj.com/articles/8209 last-modified: 2020-01-24 description: The need for conservation scientists to produce research of greater relevance to practitioners is now increasingly recognized. This study provides an example of scientists working alongside practitioners and policy makers to address a question of immediate relevance to elephant conservation in Malaysia and using the results to inform wildlife management policy and practice including the National Elephant Conservation Action Plan for Peninsular Malaysia. Since ensuring effective conservation of elephants in the Endau Rompin Landscape (ERL) in Peninsular Malaysia is difficult without data on population parameters we (1) conducted a survey to assess the size of the elephant population, (2) used that information to assess the viability of the population under different management scenarios including translocation of elephants out of the ERL (a technique long used in Malaysia to mitigate human–elephant conflict (HEC)), and (3) assessed a number of options for managing the elephant population and HEC in the future. Our dung-count based survey in the ERL produced an estimate of 135 (95% CI [80–225]) elephants in the 2,500 km2 area. The population is thus of national significance, containing possibly the second largest elephant population in Peninsular Malaysia, and with effective management elephant numbers could probably double. We used the data from our survey plus other sources to conduct a population viability analysis to assess relative extinction risk under different management scenarios. Our results demonstrate that the population cannot sustain even very low levels of removal for translocation or anything other than occasional poaching. We describe, therefore, an alternative approach, informed by this analysis, which focuses on in situ management and non-translocation-based methods for preventing or mitigating HEC. The recommended approach includes an increase in law enforcement to protect the elephants and their habitat, maintenance of habitat connectivity between the ERL and other elephant habitat, and a new focus on adaptive management. creator: Salman Saaban creator: Mohd Nawayai Yasak creator: Melvin Gumal creator: Aris Oziar creator: Francis Cheong creator: Zaleha Shaari creator: Martin Tyson creator: Simon Hedges uri: https://doi.org/10.7717/peerj.8209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Saaban et al. title: Within-person coupling of estradiol, testosterone, and cortisol in women athletes link: https://peerj.com/articles/8402 last-modified: 2020-01-24 description: PurposeIn variety of settings cortisol and testosterone are positively “coupled.” That is, within-person fluctuations of cortisol and testosterone levels occur in parallel—increases and decreases in one hormone are associated with corresponding increases and decreases in the other. The present report explored hormone coupling in women athletes in two studies selected because they included measurements of salivary levels of cortisol, testosterone, and estradiol—a hormone that has been only infrequently studied in the context of competitive athletics.MethodsConsenting members of Emory University’s varsity volleyball and soccer teams gave saliva samples on multiple occasions in the run-up to and over the course of two different intercollegiate contests.ResultsVolleyball and soccer players showed remarkably similar hormone-specific patterns of increase in relationship to the different stages of competition—before warm-up, after warm-up, and after competition. For both the volleyball and soccer team, Hierarchical Linear Model (HLM) analyses showed estradiol as being significantly coupled with testosterone which was also coupled with cortisol.ConclusionsThis is, apparently, the first report of significant within-person coupling between estradiol and testosterone in the context of competitive athletic stress. These two hormones may be coupled in a wide variety of circumstances not limited to ones involving sport competition, and results reported here should encourage exploration of the extent to which coordinated fluctuations in estradiol, testosterone, and cortisol levels are present in other, more neutral settings and the ways in which the coordination of these fluctuating hormone levels may benefit human performance. creator: David A. Edwards creator: Bulent Turan uri: https://doi.org/10.7717/peerj.8402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Edwards and Turan title: New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes link: https://peerj.com/articles/8406 last-modified: 2020-01-24 description: Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation. creator: Paulina Janik creator: Michał Ronikier creator: Anna Ronikier uri: https://doi.org/10.7717/peerj.8406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Janik et al. title: Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics link: https://peerj.com/articles/8455 last-modified: 2020-01-24 description: Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera. creator: Wentao Niu creator: Jiaguang Xiao creator: Peng Tian creator: Shuangen Yu creator: Feng Guo creator: Jianjia Wang creator: Dingyong Huang uri: https://doi.org/10.7717/peerj.8455 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Niu et al. title: Developing and assessing a density surface model in a Bayesian hierarchical framework with a focus on uncertainty: insights from simulations and an application to fin whales (Balaenoptera physalus) link: https://peerj.com/articles/8226 last-modified: 2020-01-23 description: Density surface models (DSMs) are an important tool in the conservation and management of cetaceans. Most previous applications of DSMs have adopted a two-step approach to model fitting (hereafter referred to as the Two-Stage Method), whereby detection probabilities are first estimated using distance sampling detection functions and subsequently used as an offset when fitting a density-habitat model. Although variance propagation techniques have recently become available for the Two-Stage Method, most previous applications have not propagated detection probability uncertainty into final density estimates. In this paper, we describe an alternative approach for fitting DSMs based on Bayesian hierarchical inference (hereafter referred to as the Bayesian Method), which is a natural framework for simultaneously propagating multiple sources of uncertainty into final estimates. Our framework includes (1) a mark-recapture distance sampling observation model that can accommodate two team line transect data, (2) an informed prior for the probability a group of animals is at the surface and available for detection (i.e. surface availability) (3) a density-habitat model incorporating spatial smoothers and (4) a flexible compound Poisson-gamma model for count data that incorporates overdispersion and zero-inflation. We evaluate our method and compare its performance to the Two-Stage Method with simulations and an application to line transect data of fin whales (Balaenoptera physalus) off the east coast of the USA. Simulations showed that both methods had low bias (<1.5%) and confidence interval coverage close to the nominal 95% rate when variance was propagated from the first step. Results from the fin whale analysis showed that density estimates and predicted distribution patterns were largely similar among methods; however, the coefficient of variation of the final abundance estimate more than doubled (0.14 vs 0.31) when detection variance was correctly propagated into final estimates. An analysis of the variance components demonstrated that overall detectability as well as surface availability contributed substantial amounts of variance in the final abundance estimates whereas uncertainty in mean group size contributed a negligible amount. Our method provides a Bayesian alternative to DSMs that incorporates much of the flexibility available in the Two-Stage Method. In addition, these results demonstrate the degree to which uncertainty can be underestimated if certain components of a DSM are assumed fixed. creator: Douglas B. Sigourney creator: Samuel Chavez-Rosales creator: Paul B. Conn creator: Lance Garrison creator: Elizabeth Josephson creator: Debra Palka uri: https://doi.org/10.7717/peerj.8226 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Sigourney et al. title: Life history traits and reproductive performance of the caridean shrimp Lysmata boggessi, a heavily traded invertebrate in the marine aquarium industry link: https://peerj.com/articles/8231 last-modified: 2020-01-23 description: The most intense commercial harvest of marine aquarium species in North America occurs in the coastal waters surrounding Florida, yet very often little information exists on the life histories, population dynamics, or reproductive characteristics of these organisms. The peppermint shrimp Lysmata boggessi is one such species and is heavily targeted along the west coast of Florida. It is known primarily among aquarists for its ability to control pest anemones and in the scientific community for its unique sexual system, protandric simultaneous hermaphroditism. However, no study has addressed fishery interactions or long-term population dynamics for L. boggessi. We used monthly fisheries-dependent sampling, with a trained observer present, for a full year to assess seasonality in sex phase ratio (males to males + hermaphrodites), size at sex change, fecundity, embryo volume and reproductive output of an exploited L. boggessi population. L. boggessi exhibited distinct seasonality in size distribution, sex phase ratio, size at sex phase change and reproductive activity. The peak reproductive season was in spring, when the population was dominated by small but fecund hermaphrodites. Reproduction decreased during fall and winter and sex phase ratios favored male phase shrimp that exhibited delayed sex change. This population and individual level information is the first of its kind for L. boggessi and fills a much needed data gap for the informed management of this fishery. creator: Michael D. Dickson creator: Donald C. Behringer creator: J. Antonio Baeza uri: https://doi.org/10.7717/peerj.8231 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dickson et al. title: Analysis and prediction of vegetation dynamics under the background of climate change in Xinjiang, China link: https://peerj.com/articles/8282 last-modified: 2020-01-23 description: BackgroundVegetation dynamics is defined as a significant indictor in regulating terrestrial carbon balance and climate change, and this issue is important for the evaluation of climate change. Though much work has been done concerning the correlations among vegetation dynamics, precipitation and temperature, the related questions about relationships between vegetation dynamics and other climatic factors (e.g., specific humidity, net radiation, soil moisture) have not been thoroughly considered. Understanding these questions is of primary importance in developing policies to address climate change.MethodsIn this study, the least squares regression analysis method was used to simulate the trend of vegetation dynamics based on the normalized difference vegetation index (NDVI) from 1981 to 2018. A partial correlation analysis method was used to explore the relationship between vegetation dynamics and climate change; and further,the revised greyscale model was applied to predict the future growth trend of natural vegetation.ResultsThe Mann-Kendall test results showed that th e air temperature rose sharply in 1997 and had been in a state of high fluctuations since then. Strong changes in hydrothermal conditions had major impact on vegetation dynamics in the area. Specifically, the NDVI value of natural vegetation showed an increasing trend from 1981 to 2018, and the same changes occurred in the precipitation. From 1981 to 1997, the values of natural vegetation increased at a rate of 0.0016 per year. From 1999 to 2009, the NDVI value decreased by an average rate of 0.0025 per year. From 2010 to 2018, the values began an increasing trend and reached a peak in 2017, with an average annual rate of 0.0033. The high vegetation dynamics areas were mainly concentrated in the north and south slopes of the Tianshan Mountains, the Ili River Valley and the Altay area. The greyscale prediction results showed that the annual average NDVI values of natural vegetation may present a fluctuating increasing trend. The NDVI value in 2030 is 0.0196 higher than that in 2018, with an increase of 6.18%.ConclusionsOur results indicate that: (i) the variations of climatic factors have caused a huge change in the hydrothermal conditions in Xinjiang; (ii) the vegetation dynamics in Xinjiang showed obvious volatility, and then in the end stage of the study were higher than the initial stage the vegetation dynamics in Xinjiang showed a staged increasing trend; (iii) the vegetation dynamics were affected by many factors,of which precipitation was the main reason; (iv) in the next decade, the vegetation dynamics in Xinjiang will show an increasing trend. creator: Qingwei Zhuang creator: Shixin Wu creator: Xiaoyu Feng creator: Yaxuan Niu uri: https://doi.org/10.7717/peerj.8282 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhuang et al. title: Occurrence, ecological function and medical importance of dermestid beetle hastisetae link: https://peerj.com/articles/8340 last-modified: 2020-01-23 description: Hastisetae are a specific group of detachable setae characterizing the larvae of Megatominae (Coleoptera: Dermestidae), commonly known as carpet and khapra beetles. These setae are located on both thoracic and abdominal tergites and they are the primary defense of the larva against invertebrate predators. According to previous studies, the main purpose of hastisetae is to work as a mechanical obstacle, but they are also capable to block and kill a predator. Hastisetae, single or aggregate, function as an extremely efficient mechanical trap, based on an entangling mechanism of cuticular structures (spines and hairs) and body appendages (antennae, legs and mouthparts). It is believed that this defensive system evolved primarily to contrast predation by invertebrates, however it has been observed that hastisetae may affect vertebrates as well. Although information on the impacts of vertebrate predators of the beetles is lacking, hastisetae have been shown to be a possible threat for human health as an important contaminant of stored products (food and fabric), work and living environment. Review of past and recent literature on dermestid larvae has revealed that despite these structures indicated as one of the distinctive characters in species identification, very little is known about their ultrastructure, evolution and mechanism of action. In the present work, we will provide the state of knowledge on hastisetae in Dermestidae and we will present and discuss future research perspectives intended to bridge the existing knowledge gaps. creator: Enrico Ruzzier creator: Marcin Kadej creator: Andrea Battisti uri: https://doi.org/10.7717/peerj.8340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ruzzier et al. title: Growth rate and locomotor performance tradeoff is not universal in birds link: https://peerj.com/articles/8423 last-modified: 2020-01-23 description: Though a tradeoff between growth rate and locomotor performance has been proposed, empirical data on this relationship are still limited. Here we statistically analyze the associations of growth rate and flight ability in birds by assessing how growth rate is correlated with three wing parameters of birds: flight muscle ratio, wing aspect ratio, and wing loading. We find that fast-growing birds tended to have higher flight muscle ratios and higher wing loadings than slow-growing birds, which suggests that fast-growing birds may have better takeoff performance, but lower efficiency in maneuvering flight. Accordingly, our findings suggest that the relationship between growth rate and flight ability is more complex than a simple tradeoff. Since the hindlimbs also contribute greatly to the locomotion of birds, future investigations on the relationship between growth rate and hindlimb performance will provide more insights into the evolution of birds. creator: Tao Zhao creator: Zhiheng Li uri: https://doi.org/10.7717/peerj.8423 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhao and Li title: Permutation-based methods for mediation analysis in studies with small sample sizes link: https://peerj.com/articles/8246 last-modified: 2020-01-22 description: BackgroundMediation analysis can be used to evaluate the effect of an exposure on an outcome acting through an intermediate variable or mediator. For studies with small sample sizes, permutation testing may be useful in evaluating the indirect effect (i.e., the effect of exposure on the outcome through the mediator) while maintaining the appropriate type I error rate. For mediation analysis in studies with small sample sizes, existing permutation testing methods permute the residuals under the full or alternative model, but have not been evaluated under situations where covariates are included. In this article, we consider and evaluate two additional permutation approaches for testing the indirect effect in mediation analysis based on permutating the residuals under the reduced or null model which allows for the inclusion of covariates.MethodsSimulation studies were used to empirically evaluate the behavior of these two additional approaches: (1) the permutation test of the Indirect Effect under Reduced Models (IERM) and (2) the Permutation Supremum test under Reduced Models (PSRM). The performance of these methods was compared to the standard permutation approach for mediation analysis, the permutation test of the Indirect Effect under Full Models (IEFM). We evaluated the type 1 error rates and power of these methods in the presence of covariates since mediation analysis assumes no unmeasured confounders of the exposure–mediator–outcome relationships.ResultsThe proposed PSRM approach maintained type I error rates below nominal levels under all conditions, while the proposed IERM approach exhibited grossly inflated type I rates in many conditions and the standard IEFM exhibited inflated type I error rates under a small number of conditions. Power did not differ substantially between the proposed PSRM approach and the standard IEFM approach.ConclusionsThe proposed PSRM approach is recommended over the existing IEFM approach for mediation analysis in studies with small sample sizes. creator: Miranda E. Kroehl creator: Sharon Lutz creator: Brandie D. Wagner uri: https://doi.org/10.7717/peerj.8246 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kroehl et al. title: Rapid digitization to reclaim thematic maps of white-tailed deer density from 1982 and 2003 in the conterminous US link: https://peerj.com/articles/8262 last-modified: 2020-01-22 description: BackgroundDespite availability of valuable ecological data in published thematic maps, manual methods to transfer published maps to a more accessible digital format are time-intensive. Application of object-based image analysis makes digitization faster.MethodsUsing object-based image analysis followed by random forests classification, we rapidly digitized choropleth maps of white-tailed deer (Odocoileus virginianus) densities in the conterminous US during 1982 and 2001 to 2005 (hereafter, 2003), allowing access to deer density information stored in images.ResultsThe digitization process took about one day each per deer density map, of which about two hours was computer processing time, which will differ due to factors such as resolution and number of objects. Deer were present in 4.75 million km2 (60% of the area) and 5.56 million km2 (70%) during 1982 and 2003, respectively. Population and density in areas with deer presence were 17.15 million and 3.6 deer/km2 during 1982 and 29.93 million and 5.4 deer/km2 during 2003. Greatest densities were 7.2 deer/km2 in Georgia during 1982 and 14.6 deer/km2 in Wisconsin during 2003. Six states had deer densities ≥9.8 deer/km2 during 2003. Colorado, Idaho, and Oregon had greatest increases in population and area of deer presence, and deer expansion is likely to continue into western states. Error in these estimates may be similar to error resulting from differential reporting by state agencies. Deer densities likely are within historical levels in most of the US.DiscussionThis method rapidly reclaimed informational value of deer density maps, enabling greater analysis, and similarly may be applied to digitize a variety of published maps to geographic information system layers, which permit greater analysis. creator: Brice Hanberry creator: Phillip Hanberry uri: https://doi.org/10.7717/peerj.8262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hanberry and Hanberry title: Social rank overrides environmental and community fluctuations in determining meat access by female chimpanzees in the Taï National Park, Côte d’Ivoire link: https://peerj.com/articles/8283 last-modified: 2020-01-22 description: Meat, long hypothesized as an important food source in human evolution, is still a substantial component of the modern human diet, with some humans relying entirely on meat during certain times of the year. Understanding the socio-ecological context leading to the successful acquisition and consumption of meat by chimpanzees (Pan troglodytes), our closest living relative, can provide insight into the emergence of this trait because humans and chimpanzees are unusual among primates in that they both (i) hunt mammalian prey, (ii) share meat with community members, and (iii) form long-term relationships and complex social hierarchies within their communities. However, females in both human hunter-gatherer societies as well as chimpanzee groups rarely hunt, instead typically accessing meat via males that share meat with group members. In general, female chimpanzee dominance rank affects feeding competition, but so far, the effect of female dominance rank on meat access found different results within and across studied chimpanzee groups. Here we contribute to the debate on how female rank influences meat access while controlling for several socio-ecological variables. Multivariate analyses of 773 separate meat-eating events collected over more than 25 years from two chimpanzee communities located in the Taï National Park, Côte d’Ivoire, were used to test the importance of female dominance rank for being present at, and for acquiring meat, during meat-eating events. We found that high-ranking females were more likely to be present during a meat-eating event and, in addition, were more likely to eat meat compared to the subordinates. These findings were robust to both large demographic changes (decrease of community size) and seasonal ecological changes (fruit abundance dynamics). In addition to social rank, we found that other female properties had a positive influence on presence to meat-eating events and access to meat given presence, including oestrus status, nursing of a small infant, and age. Similar to findings in other chimpanzee populations, our results suggest that females reliably acquire meat over their lifetime despite rarely being active hunters. The implication of this study supports the hypothesis that dominance rank is an important female chimpanzee property conferring benefits for the high-ranking females. creator: Julia Riedel creator: Leo Polansky creator: Roman M. Wittig creator: Christophe Boesch uri: https://doi.org/10.7717/peerj.8283 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Riedel et al. title: High variability within pet foods prevents the identification of native species in pet cats’ diets using isotopic evaluation link: https://peerj.com/articles/8337 last-modified: 2020-01-22 description: Domestic cats preying on wildlife is a frequent conservation concern but typical approaches for assessing impacts rely on owner reports of prey returned home, which can be biased by inaccurate reporting or by cats consuming prey instead of bringing it home. Isotopes offer an alternative way to quantify broad differences in animal diets. By obtaining samples of pet food from cat owners we predicted that we would have high power to identify cats feeding on wild birds or mammals, given that pet food is thought to have higher C isotope values, due to the pervasive use of corn and/or corn by-products as food ingredients, than native prey. We worked with citizen scientists to quantify the isotopes of 202 cat hair samples and 239 pet food samples from the US and UK. We also characterized the isotopes of 11 likely native prey species from the southeastern US and used mixing models to assess the diet of 47 cats from the same region. Variation in C and N isotope values for cat food was very high, even within the same brand/flavor, suggesting that pet food manufacturers use a wide range of ingredients, and that these may change over time. Cat food and cat hair from the UK had lower C values than the US, presumably reflecting differences in the amount of corn used in the food chains of the two countries. This high variation in pet food reduced our ability to classify cats as hunters of native prey, such that only 43% of the animals could be confidently assigned. If feral or free ranging cats were considered, this uncertainty would be even higher as pet food types would be unknown. Our results question the general assumption that anthropogenic foods always have high C isotope values, because of the high variability we documented within one product type (cat food) and between countries (US vs. UK), and emphasize the need to test a variety of standards before making conclusions from isotope ecology studies. creator: Brandon W. McDonald creator: Troi Perkins creator: Robert R. Dunn creator: Jennifer McDonald creator: Holly Cole creator: Robert S. Feranec creator: Roland Kays uri: https://doi.org/10.7717/peerj.8337 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 McDonald et al. title: Prehaustorial local resistance to coffee leaf rust in a Mexican cultivar involves expression of salicylic acid-responsive genes link: https://peerj.com/articles/8345 last-modified: 2020-01-22 description: BackgroundIn Mexico, coffee leaf rust (CLR) is the main disease that affects the Arabica coffee crop. In this study, the local response of two Mexican cultivars of Coffea arabica (Oro Azteca and Garnica) in the early stages of Hemileia vastatrix infection was evaluated.MethodsWe quantified the development of fungal structures in locally-infected leaf disks from both cultivars, using qRT-PCR to measure the relative expression of two pathogenesis recognition genes (CaNDR1 and CaNBS-LRR) and three genes associated with the salicylic acid (SA)-related pathway (CaNPR1, CaPR1, and CaPR5).ResultsResistance of the cv. Oro Azteca was significantly higher than that of the cv. Garnica, with 8.2% and 53.3% haustorial detection, respectively. In addition, the non-race specific disease resistance gene (CaNDR1), a key gene for the pathogen recognition, as well as the genes associated with SA, CaNPR1, CaPR1, and CaPR5, presented an increased expression in response to infection by H. vastatrix in cv. Oro Azteca if comparing with cv. Garnica. Our results suggest that Oro Azteca’s defense mechanisms could involve early recognition of CLR by NDR1 and the subsequent activation of the SA signaling pathway. creator: Edgar Couttolenc-Brenis creator: Gloria L. Carrión creator: Luc Villain creator: Fernando Ortega-Escalona creator: Daniel Ramírez-Martínez creator: Martín Mata-Rosas creator: Alfonso Méndez-Bravo uri: https://doi.org/10.7717/peerj.8345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Couttolenc-Brenis et al. title: The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells link: https://peerj.com/articles/8371 last-modified: 2020-01-22 description: Background2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical, adversely affecting reproductive processes. The well-characterized canonical mechanism of TCDD action involves the activation of aryl hydrocarbon receptor (AhR) pathway, but AhR-independent mechanisms were also suggested. By applying RNA interference technology and Next Generation Sequencing (NGS) we aimed to identify genes involved in the mechanism of TCDD action in AhR knock-down porcine granulosa cells.MethodsPorcine granulosa cells were transfected with small interfering RNAs targeting mRNA of AhR. After transfection, medium was exchanged and the AhR knock-down cells were treated with TCDD (100 nM) for 3, 12 or 24 h, total cellular RNA was isolated and designated for NGS. Following sequencing, differentially expressed genes (DEGs) were identified. To analyze functions and establish possible interactions of DEGs, the Gene Ontology (GO) database and the Search Tool for the Retrieval of Interacting Genes (STRING) database were used, respectively.ResultsThe AhR gene expression level and protein abundance were significantly decreased after AhR-targeted siRNAs transfection of the cells. In TCDD-treated AhR knock-down cells we identified 360 differentially expressed genes (DEGs; P-adjusted < 0.05 and log2 fold change [log2FC] ≥ 1.0). The functional enrichment analysis of DEGs revealed that TCDD influenced the expression of genes involved, among other, in the metabolism of vitamin A, follicular development and oocyte maturation, proliferation and differentiation as well as inflammation, stress response, apoptosis and oncogenesis. The three-time point study demonstrated that TCDD-induced changes in the transcriptome of AhR knock-down porcine granulosa cells were especially pronounced during the early stages of the treatment (3 h).ConclusionsTCDD affected the transcriptome of AhR knock-down porcine granulosa cells. The molecules involved in the AhR-independent action of TCDD were indicated in the study. The obtained data contribute to better understanding of molecular processes induced by xenobiotics in the ovary. creator: Monika Ruszkowska creator: Agnieszka Sadowska creator: Anna Nynca creator: Karina Orlowska creator: Sylwia Swigonska creator: Tomasz Molcan creator: Lukasz Paukszto creator: Jan P. Jastrzebski creator: Renata E. Ciereszko uri: https://doi.org/10.7717/peerj.8371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ruszkowska et al. title: Shifts in soil nutrient concentrations and C:N:P stoichiometry during long-term natural vegetation restoration link: https://peerj.com/articles/8382 last-modified: 2020-01-22 description: BackgroundEcological stoichiometry (C:N:P ratios) in soil is an important indicator of the elemental balance in ecological interactions and processes. Long-term natural vegetation plays an important role in the accumulation and distribution of soil stoichiometry. However, information about the effects of long-term secondary forest succession on soil stoichiometry along a deep soil profile is still limited.MethodsWe selected Ziwuling secondary succession forest developed from farmland as the study area, investigated the concentrations and stoichiometry of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) at a depth of 0–100 cm along a 90-year succession chronosequence, including farmland (control), grassland, shrub, early forest, and climax forest.ResultsSOC and TN concentrations significantly increased with increasing restoration age, whereas soil P concentration remained relatively stable across various successional stages. SOC and TN concentrations decreased with an increase in soil depth, exhibiting distinct soil nutrient “surface-aggregation” (high nutrients concentration in the top soil layer). The soil C:P and N:P ratios increased with an increase in restoration age, whereas the variation of the C:N ratio was small and relatively stable across vegetation succession. The nutrient limitation changed along with vegetation succession, transitioning from limited N in the earlier successional stages to limited P in the later successional stages.ConclusionOur results suggest that more nitrogen input should be applied to earlier succession stages, and more phosphorus input should be utilized in later succession stages in order to address limited availability of these elements. In general, natural vegetation restoration was an ecologically beneficial practice for the recovery of degraded soils in this area. The findings of this study strengthen our understanding of the changes of soil nutrient concentration and nutrient limitation after vegetation restoration, and provide a simple guideline for future vegetation restoration and reconstruction efforts on the Loess Plateau. creator: Rentian Ma creator: Feinan Hu creator: Jingfang Liu creator: Chunli Wang creator: Zilong Wang creator: Gang Liu creator: Shiwei Zhao uri: https://doi.org/10.7717/peerj.8382 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ma et al. title: First record of Gyrosteus mirabilis (Actinopterygii, Chondrosteidae) from the Toarcian (Lower Jurassic) of the Baltic region link: https://peerj.com/articles/8400 last-modified: 2020-01-22 description: An isolated hyomandibula from a lower Toarcian carbonate concretion of the Ahrensburg erratics assemblage (Schleswig-Holstein, northern Germany) represents the first record of a chondrosteid fish from the Lower Jurassic of the southwestern Baltic realm. Except for its smaller size, the specimen is morphologically indistinguishable from corresponding elements of Gyrosteus mirabilis from the Toarcian of Yorkshire, England. This find, which probably originates from the western Baltic basin between Bornholm Island (Denmark) and northeastern Germany, markedly expands the known range of this chondrosteid taxon across the northern part of the strait connecting the Boreal Sea with the Tethys Ocean during the Early Jurassic. For the first time the extension of the paleogeographic range of a chondrosteid species beyond its type area is documented, which can contribute to future studies of vertebrate faunal provincialism during the Lower Jurassic in Europe. creator: Jahn J. Hornung creator: Sven Sachs uri: https://doi.org/10.7717/peerj.8400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hornung and Sachs title: Florida manatees Trichechus manatus latirostris actively consume the sponge Chondrilla caribensis link: https://peerj.com/articles/8443 last-modified: 2020-01-22 description: The Florida manatee (Trichechus manatus latirostris Linnaeus 1758) actively selects and consumes the “chicken-liver” sponge Chondrilla caribensis. Manatees ate over 10% of C. caribensis on a sample dock, mostly from pylons that received no direct sunlight. Since manatees reportedly eat mostly seagrasses and algae, it was thought that the chlorophyll-a content of the symbiotic cyanobacteria in C. caribensis might be correlated to the amount eaten; however the correlation was not significant (P > 0.05). C. caribensis has variable chemical defenses and round spherasters (spicules), but these do not appear to be effective deterrents to predation by manatees. This is the first direct evidence that manatees actively seek out and consume a sponge. creator: William Fitt uri: https://doi.org/10.7717/peerj.8443 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fitt title: CD86+/CD206+ tumor-associated macrophages predict prognosis of patients with intrahepatic cholangiocarcinoma link: https://peerj.com/articles/8458 last-modified: 2020-01-22 description: BackgroundAs the main cellular ingredients of tumor microenvironment, tumor-associated macrophages (TAMs) play a vital role in tumor development and progression. Recent studies have suggested that TAMs are sensitive and specific prognostic factors in numerous cancers. The primary purpose of this study is to determine the prognostic significance of TAMs in intrahepatic cholangiocarcinoma (ICC).MethodsImmunohistochemical staining of CD68, CD86 and CD206 were performed in tissue microarrays containing 322 patients, who underwent surgical resection and were pathologically diagnosed with ICC. The prognostic value of CD68, CD86 and CD206 were evaluated by Kaplan–Meier analysis (log-rank test) and nomogram models.ResultsWe demonstrated that the CD86+/CD206+ TAMs model was an independent prognostic index for ICC patients. Patients with low CD86+ TAMs and high CD206+ TAMs infiltration had a markedly worse prognosis and increased risk of post-operative recurrence when compared to high CD86+ TAMs and low CD206+ TAMs intratumoral infiltration. Furthermore, subgroup analysis indicated that the CD86+/CD206+ TAMs model predicted prognosis of ICC patients more powerfully than single macrophage immunomarker. Interestingly, the CD86+/CD206+ TAMs model could further distinguish prognosis of CA-199 negative ICC patients, who were generally presumed to have a more favorable outcome. In order to further perfect the prognostic value of the CD86+/CD206+ TAMs model, we constructed and validated a postoperative nomogram to predict overall survival and recurrence-free survival time in ICC patients.ConclusionsThese findings indicate that the CD86+/CD206+ TAMs model possess potential value as a novel prognostic indicator for ICC patients. creator: Dalong Sun creator: Tiancheng Luo creator: Pingping Dong creator: Ningping Zhang creator: Jing Chen creator: Shuncai Zhang creator: Longzi Liu creator: Ling Dong creator: Si Zhang uri: https://doi.org/10.7717/peerj.8458 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sun et al. title: Predicting hedgehog mortality risks on British roads using habitat suitability modelling link: https://peerj.com/articles/8154 last-modified: 2020-01-21 description: Road vehicle collisions are likely to be an important contributory factor in the decline of the European hedgehog (Erinaceus europaeus) in Britain. Here, a collaborative roadkill dataset collected from multiple projects across Britain was used to assess when, where and why hedgehog roadkill are more likely to occur. Seasonal trends were assessed using a Generalized Additive Model. There were few casualties in winter—the hibernation season for hedgehogs—with a gradual increase from February that reached a peak in July before declining thereafter. A sequential multi-level Habitat Suitability Modelling (HSM) framework was then used to identify areas showing a high probability of hedgehog roadkill occurrence throughout the entire British road network (∼400,000 km) based on multi-scale environmental determinants. The HSM predicted that grassland and urban habitat coverage were important in predicting the probability of roadkill at a national scale. Probabilities peaked at approximately 50% urban cover at a one km scale and increased linearly with grassland cover (improved and rough grassland). Areas predicted to experience high probabilities of hedgehog roadkill occurrence were therefore in urban and suburban environments, that is, where a mix of urban and grassland habitats occur. These areas covered 9% of the total British road network. In combination with information on the frequency with which particular locations have hedgehog road casualties, the framework can help to identify priority areas for mitigation measures. creator: Patrick G.R. Wright creator: Frazer G. Coomber creator: Chloe C. Bellamy creator: Sarah E. Perkins creator: Fiona Mathews uri: https://doi.org/10.7717/peerj.8154 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wright et al. title: Pseudolebinthus lunipterus sp. nov.: a striking deaf and mute new cricket from Malawi (Orthoptera, Gryllidae, Eneopterinae) link: https://peerj.com/articles/8204 last-modified: 2020-01-21 description: This article presents an intriguing new cricket species of the tribe Xenogryllini discovered in Northern Malawi. This is the first case of mute and deaf species in the subfamily Eneopterinae; it shows no stridulatory apparatus on short male forewings and no tympana on either side of fore tibiae in both sexes. We introduce the new species and its complete mitogenome and assess phylogenetic relationships based on molecular data obtained from next-generation sequencing genome skimming method. Phylogenetic analyses place the new species within the genus Pseudolebinthus in Xenogryllini, as the sister species of Pseudolebinthus gorochovi Robillard. We describe Pseudolebinthus lunipterus sp. nov., provide illustrations of main morphology, male and female genitalia, photographs of living specimens and information about habitat and update the identification key for species of genus Pseudolebinthus. We discuss the differences between the new species and related taxa and the striking loss of acoustic communication in this cricket. creator: Karen Salazar creator: Raymond J. Murphy creator: Marion Guillaume creator: Romain Nattier creator: Tony Robillard uri: https://doi.org/10.7717/peerj.8204 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Salazar et al. title: Clinical characteristics and prognostic value of MEX3A mRNA in liver cancer link: https://peerj.com/articles/8252 last-modified: 2020-01-21 description: BackgroundMEX3A is an RNA-binding proteins (RBPs) that promotes the proliferation, invasion, migration and viability of cancer cells. The aim of this study was to explore the clinicopathological characteristics and prognostic significance of MEX3A mRNA expression in liver cancer.MethodsRNA-Seq and clinical data were collected from The Cancer Genome Atlas (TCGA). Boxplots were used to represent discrete variables of MEX3A. Chi-square tests were used to analyze the correlation between clinical features and MEX3A expression. Receiver operating characteristic (ROC) curves were used to confirm diagnostic ability. Independent prognostic ability and values were assessed using Kaplan–Meier curves and Cox analysis.ResultsWe acquired MEX3A RNA-Seq from 50 normal liver tissues and 373 liver cancer patients along with clinical data. We found that MEX3A was up-regulated in liver cancer which increased according to histological grade (p < 0.001). MEX3A showed moderate diagnostic ability for liver cancer (AUC = 0.837). Kaplan–Meier curves and Cox analysis revealed that the high expression of MEX3A was significantly associated with poor survival (OS and RFS) (p < 0.001). Moreover, MEX3A was identified as an independent prognostic factor of liver cancer (p < 0.001).ConclusionsMEX3A expression shows promise as an independent predictor of liver cancer prognosis. creator: Dingquan Yang creator: Yan Jiao creator: Yanqing Li creator: Xuedong Fang uri: https://doi.org/10.7717/peerj.8252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Inhibiting SLC26A4 reverses cardiac hypertrophy in H9C2 cells and in rats link: https://peerj.com/articles/8253 last-modified: 2020-01-21 description: BackgroundIt has been confirmed that mutations in solute carrier family 26 member 4 (SLC26A4) contribute to pendred syndrome. However, the role of SLC26A4 in cardiac hypertrophy and the signaling pathways remain unclear.MethodsCardiomyocytes were treated by 200 µM phenylephrine (PE) to induce cardiac hypertrophy. Also, the expression of SLC26A4, GSK3, cardiac hypertrophy markers including atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) was detected through real-time quantitative polymerase chain reaction (RT-qPCR). Flow cytometry assay was used to test the apoptosis of PE-induced cardiomyocytes transfected by small interfere RNA (siRNA)-SLC26A4. Furthermore, we detected the expression of autophagy-related markers including light chain 3 (LC3) and P62. Finally, we established a rat model of abdominal aortic constriction (AAC)-induced cardiac hypertrophy in vivo.ResultsRT-qPCR results showed that the mRNA expression of SLC26A4 was significantly up-regulated in PE-induced cardiac hypertrophy. After inhibiting SLC26A4, the release of ANP and BNP was significantly decreased and GSK3β was elevated in vivo and in vitro. Furthermore, inhibiting SLC26A4 promoted apoptosis of cardiac hypertrophy cells. In addition, LC3 was down-regulated and P62 was enhanced after transfection of siRNA-SLC26A4.ConclusionOur findings revealed that SLC26A4 increases cardiac hypertrophy, and inhibiting SLC26A4 could decrease the release of ANP/BNP and promote the expression of GSK-3β in vitro and in vivo. Moreover, SLC26A4 silencing inhibits autophagy of cardiomyocytes and induces apoptosis of cardiomyocytes. Therefore, SLC26A4 possesses potential value to be a therapeutic target of cardiac hypertrophy, and our study provides new insights into the mechanisms of cardiac hypertrophy. creator: Liqun Tang creator: Xiaoqin Yu creator: Yangyang Zheng creator: Ning Zhou uri: https://doi.org/10.7717/peerj.8253 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tang et al. title: Variability of soil carbon and nitrogen stocks after conversion of natural forest to plantations in Eastern China link: https://peerj.com/articles/8377 last-modified: 2020-01-21 description: Forest plantation, either through afforestation or reforestation, has been suggested to reverse and mitigate the process of deforestation. However, uncertainties remain in the potential of plantation forest (PF) to sequestrate carbon (C) and nitrogen (N) compared to natural forest (NF). Soil C and N stocks require a critical and updated look at what is happening especially in the context of increasing rate of land use change and climate change. The current study was conducted in China’s Eastern forest to estimate soil C and N stocks in six depth layers (0–10, 10–20, 20–40, 40–60, 60–80 and 80–100 cm) and two forest types (NF and PF) at four sites along climate factors gradient. The results showed that the overall mean soil C and N amounts to a depth of 20 cm ranged from 2.6 ± 1.1 Mg ha−1 to 38.6 ± 23.1 Mg ha−1, and soil nitrogen stock ranged from 0.2 ± 0.1 Mg ha−1 to 3.3 ± 1.5 Mg ha−1. Moreover, a loss of C stock was observed at Qingyuan (QY) by −7%, Dinghushan (DH) by −26%, Jianfengling (JF) by −13% while that of N stock was observed at QY (−8%), DH (−19%) and JF (−12%) at both depth layers. These results indicate that NFs have a better capacity to accumulate soil C and N. The soil C and N decreased from the southeast to the northeast and increased from tropical to temperate mixed forests zone in the eastern part of the study area. The C and N stock mainly occurred in the topsoil and decreased significantly with depth. Moreover, soil C and N stocks increased with age of plantation. This study provides an overview of the current spatial distribution and soil stocks of C and N, as well as the effects of environmental factors on soil C and N stocks. It also indicated that, although mean annual temperature and mean annual precipitation are the key factors affecting the variations in soil C and N, their vertical and horizontal distribution differed in various aspects. creator: Mbezele Junior Yannick Ngaba creator: Xiang-Qing Ma creator: Ya-Lin Hu uri: https://doi.org/10.7717/peerj.8377 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Ngaba et al. title: Soil temperatures and active carbon components as key drivers of C stock dynamics between two different stand ages of Larix principis-rupprechtii plantation link: https://peerj.com/articles/8384 last-modified: 2020-01-21 description: Forest soils sequester a large amount of carbon (C) and have a significant effect on the global C balance. Forests are commonly managed to maintain certain age structures but the effects of this management on soil C pools (kg C m−2) is still uncertain. We compared 40-year-old (1GF) and 24-year-old (2GF) plantations of Larix principis-rupprechtii in North China. Specifically, we measured environmental factors (e.g., soil temperature, moisture, and pH), the active C and nitrogen (N) pools (e.g., soil organic C, soil total N, dissolved organic C and N, microbial biomass C and N), and soil processes (e.g., C mineralization and microbial activity in different seasons) in five soil layers (0–50 cm, 10 cm for each soil layer) across the growing seasons in three 25 m × 25 m plots in each age class (1GF and 2GF). Findings indicated that the soil organic C pool in the older 1GF forest (12.43 kg C m−2) was significantly higher than 2GF forests (9.56 kg C m−2), and that soil temperature in 1GF forests was 9.8 °C, on average, 2.9% warmer than temperature in 2GF forests. The C lost as carbon dioxide (CO2) as a result of mineralization in the 2GF plots may partly explain the lower soil organic C pool in these younger forests; microorganisms likely drive this process. creator: Junyong Ma creator: Hairong Han creator: Xiaoqin Cheng uri: https://doi.org/10.7717/peerj.8384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ma et al. title: Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses link: https://peerj.com/articles/8403 last-modified: 2020-01-21 description: BackgroundBRCA1 and BRCA2 genes are currently proven to be closely related to high lifetime risks of breast cancer. To date, the closely related genes to BRCA1/2 mutations in breast cancer remains to be fully elucidated. This study aims to identify the gene expression profiles and interaction networks influenced by BRCA1/2 mutations, so as to reflect underlying disease mechanisms and provide new biomarkers for breast cancer diagnosis or prognosis.MethodsGene expression profiles from The Cancer Genome Atlas (TCGA) database were downloaded and combined with cBioPortal website to identify exact breast cancer patients with BRCA1/2 mutations. Gene set enrichment analysis (GSEA) was used to analyze some enriched pathways and biological processes associated BRCA mutations. For BRCA1/2-mutant breast cancer, wild-type breast cancer and corresponding normal tissues, three independent differentially expressed genes (DEGs) analysis were performed to validate potential hub genes with each other. Protein–protein interaction (PPI) networks, survival analysis and diagnostic value assessment helped identify key genes associated with BRCA1/2 mutations.ResultsThe regulation process of cell cycle was significantly enriched in mutant group compared with wild-type group. A total of 294 genes were identified after analysis of DEGs between mutant patients and wild-type patients. Interestingly, by the other two comparisons, we identified 43 overlapping genes that not only significantly expressed in wild-type breast cancer patients relative to normal tissues, but more significantly expressed in BRCA1/2-mutant breast patients. Based on the STRING database and cytoscape software, we constructed a PPI network using 294 DEGs. Through topological analysis scores of the PPI network and 43 overlapping genes, we sought to select some genes, thereby using survival analysis and diagnostic value assessment to identify key genes pertaining to BRCA1/2-mutant breast cancer. CCNE1, NPBWR1, A2ML1, EXO1 and TTK displayed good prognostic/diagnostic value for breast cancer and BRCA1/2-mutant breast cancer.ConclusionOur research provides comprehensive and new insights for the identification of biomarkers connected with BRCA mutations, availing diagnosis and treatment of breast cancer and BRCA1/2-mutant breast cancer patients. creator: Yue Li creator: Xiaoyan Zhou creator: Jiali Liu creator: Yang Yin creator: Xiaohong Yuan creator: Ruihua Yang creator: Qi Wang creator: Jing Ji creator: Qian He uri: https://doi.org/10.7717/peerj.8403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights link: https://peerj.com/articles/8415 last-modified: 2020-01-21 description: The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish. creator: Huaxing Zhou creator: Yuting Hu creator: He Jiang creator: Guoqing Duan creator: Jun Ling creator: Tingshuang Pan creator: Xiaolei Chen creator: Huan Wang creator: Ye Zhang uri: https://doi.org/10.7717/peerj.8415 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves link: https://peerj.com/articles/8426 last-modified: 2020-01-21 description: Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa. creator: Jianbo Yuan creator: Xinbo Sun creator: Tao Guo creator: Yuehui Chao creator: Liebao Han uri: https://doi.org/10.7717/peerj.8426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yuan et al. title: Toward a clinical real time tissue ablation technology: combining electroporation and electrolysis (E2) link: https://peerj.com/articles/7985 last-modified: 2020-01-20 description: BackgroundPercutaneous image-guided tissue ablation (IGA) plays a growing role in the clinical management of solid malignancies. Electroporation is used for IGA in several modalities: irreversible electroporation (IRE), and reversible electroporation with chemotoxic drugs, called electrochemotherapy (ECT). It was shown that the combination of electrolysis and electroporation—E2—affords tissue ablation with greater efficiency, that is, lower voltages, lower energy and shorter procedure times than IRE and without the need for chemotoxic additives as in ECT.MethodsA new E2 waveform was designed that delivers optimal doses of electroporation and electrolysis in a single waveform. A series of experiments were performed in the liver of pigs to evaluate E2 in the context of clinical applications. The goal was to find initial parameter boundaries in terms of electrical field, pulse duration and charge as well as tissue behavior to enable real time tissue ablation of clinically relevant volumes.ResultsHistological results show that a single several hundred millisecond long E2 waveform can ablate large volume of tissue at relatively low voltages while preserving the integrity of large blood vessels and lumen structures in the ablation zone without the use of chemotoxic drugs or paralyzing drugs during anesthesia. This could translate clinically into much shorter treatment times and ease of use compared to other techniques that are currently applied. creator: Enric Guenther creator: Nina Klein creator: Paul Mikus creator: Florin Botea creator: Mihail Pautov creator: Franco Lugnani creator: Matteo Macchioro creator: Irinel Popescu creator: Michael K. Stehling creator: Boris Rubinsky uri: https://doi.org/10.7717/peerj.7985 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gunther et al. title: Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano link: https://peerj.com/articles/8141 last-modified: 2020-01-20 description: Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer roosts as well as movement from maternity colonies fall swarms. We detected Pd DNA in guano 56 and 70 days after inoculation with 1 million and 100,000 fg respectively, while the lowest quantity (1,000 fg) was detected until 42 days. Detection probability was variable among sites and lower where samples were left exposed without overhead cover. If Pd is shed as extracellular DNA in guano at quantities above 1,000 fg, then guano collection is likely to provide an effective tool for environmental screening of Pd that can be employed in an early detection and rapid response framework throughout Washington and other regions where this disease is rapidly emerging. creator: Jenny Urbina creator: Tara Chestnut creator: Donelle Schwalm creator: Jenn Allen creator: Taal Levi uri: https://doi.org/10.7717/peerj.8141 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Urbina et al. title: TRANSPARENT TESTA GLABRA 1 participates in flowering time regulation in Arabidopsis thaliana link: https://peerj.com/articles/8303 last-modified: 2020-01-20 description: Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is such a factor that has been predominantly described as a regulator of early developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 affect photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported. Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcript levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92. Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation. creator: Barbara A.M. Paffendorf creator: Rawan Qassrawi creator: Andrea M. Meys creator: Laura Trimborn creator: Andrea Schrader uri: https://doi.org/10.7717/peerj.8303 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Paffendorf et al. title: A revised Holocene coral sea-level database from the Florida reef tract, USA link: https://peerj.com/articles/8350 last-modified: 2020-01-20 description: The coral reefs and mangrove habitats of the south Florida region have long been used in sea-level studies for the western Atlantic because of their broad geographic extent and composition of sea-level tracking biota. The data from this region have been used to support several very different Holocene sea-level reconstructions (SLRs) over the years. However, many of these SLRs did not incorporate all available coral-based data, in part because detailed characterizations necessary for inclusion into sea-level databases were lacking. Here, we present an updated database comprised of 303 coral samples from published sources that we extensively characterized for the first time. The data were carefully screened by evaluating and ranking the visual taphonomic characteristics of every dated sample within the database, which resulted in the identification of 134 high-quality coral samples for consideration as suitable sea-level indicators. We show that our database largely agrees with the most recent SLR for south Florida over the last ∼7,000 years; however, the early Holocene remains poorly characterized because there are few high-quality data spanning this period. Suggestions to refine future Holocene SLRs in the region are provided including filling spatial and temporal data gaps of coral samples, particularly from the early Holocene, as well as constructing a more robust peat database to better constrain sea-level variability during the middle to late Holocene. Our database and taphonomic-ranking protocol provide a framework for researchers to evaluate data-selection criteria depending on the robustness of their sea-level models. creator: Anastasios Stathakopoulos creator: Bernhard M. Riegl creator: Lauren T. Toth uri: https://doi.org/10.7717/peerj.8350 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Stathakopoulos et al. title: Flavonoids from Epimedium pubescens: extraction and mechanism, antioxidant capacity and effects on CAT and GSH-Px of Drosophila melanogaster link: https://peerj.com/articles/8361 last-modified: 2020-01-20 description: BackgroundEpimedium is a famous medicinal plant in China, Southeast Asian and some other regions. Flavonoids are regarded as its supremely important active constituents used in phytomedicines and/or functional foods. It is of theoretical and applied significance to optimize the procedure for extraction of flavonoids with high bioactivity from Epimedium, to unveil extraction mechanism, to identify chemical composition of flavonoids, to analyze free radical-scavenging ability of flavonoids, and to investigate their effects on the model organism Drosophila melanogaster.MethodsBox-Behnken design was applied to optimization of extraction procedure. Laser diffraction particle size analysis was used to clarify extraction mechanism. Chemical composition of flavonoids was analyzed using high-performance liquid chromatography. Antiradical capacities of flavonoids were determined by chemical-based assay. Then, effects of flavonoids on catalase (CAT) and glutathione peroxidase (GSH-Px) in D. melanogaster were investigated for the first time.ResultsThe optimal condition for ultrasonic extraction of antioxidant flavonoids from Epimedium pubescens was achieved and extraction mechanism was discussed. Epimedium flavonoids contained icariin, epimedin A, epimedin B and epimedin C. Epimedium flavonoids exhibited the ability to scavenge ABTS+ and DPPH⋅ radicals with EC50 values of 55.8 and 52.1 µg/ml, respectively. Moreover, Epimedium flavonoids were able to increase activities of CAT and GSH-Px in D. melanogaster. For females, oral administration of flavonoids improved CAT and GSH-Px activities by 13.58% and 5.18%, respectively. For males, oral administration of flavonoids increased CAT and GSH-Px activities by 13.90% and 5.65%, respectively.ConclusionFlavonoids ultrasonically extracted from E. pubescens considerably affected antioxidant defense system in D. melanogaster. Flavonoids of E. pubescens showed great potential for becoming a natural antioxidant because of their antiradical ability and effects on CAT and GSH-Px of the model organism. creator: Xiao-Hua Yang creator: Lu Li creator: Yao-Bi Xue creator: Xue-Xue Zhou creator: Jie-Hua Tang uri: https://doi.org/10.7717/peerj.8361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids link: https://peerj.com/articles/8375 last-modified: 2020-01-20 description: Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two appetite-regulating genes (anorexigenic genes), cart and npy2r, in the brain of carnivorous species in all the three lakes. This supports the notion that appetite gene regulation might play a part in determining trophic niche specialization in divergent cichlid species, already prior to exposure to different diets. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations in cichlids and other teleosts. creator: Ehsan P. Ahi creator: Anna Duenser creator: Pooja Singh creator: Wolfgang Gessl creator: Christian Sturmbauer uri: https://doi.org/10.7717/peerj.8375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ahi et al. title: A comprehensive analysis for associations between multiple microRNAs and prognosis of osteosarcoma patients link: https://peerj.com/articles/8389 last-modified: 2020-01-20 description: BackgroundOsteosarcoma (OS) is the most common malignant primary bone tumor occurring in children and young adults, which occupies the second important cause of tumor-associated deaths among children and young adults. Recent studies have demonstrated that many microRNAs (miRNAs) have abnormal expression in OS, and can function as prognostic factors of OS patients. However, no previous studies have comprehensively analyzed the relationship between multiple miRNAs and prognosis of OS patients.MethodsA total of 63 OS patients were retrospectively enrolled. The clinical characteristics were collected, and the expression levels of miRNA-21, miRNA-30c, miRNA-34a, miRNA-101, miRNA-133a, miRNA-214, miRNA-218, miRNA-433 and miRNA-539 in tumor tissues were measured through quantitative real-time polymerasechain reaction. Kaplan–Meier analysis was used to perform univariate survival analysis, and Cox regression model was used to perform multivariate survival analysis which included the variables with P < 0.1 in univariate survival analysis.ResultsThe cumulative survival for 1, 2 and 5 years was 90.48%, 68.25% and 38.10%, respectively, and mean survival time was (45.39 ± 3.60) months (95% CI [38.34–52.45]). Kaplan–Meier analysis demonstrated that TNM stage, metastasis or recurrence, miRNA-21, miRNA-214, miRNA-34a, miRNA-133a and miRNA-539 were correlated with cum survival, but gender, age, tumor diameter, differentiation, miRNA-30c, miRNA-433, miRNA-101 and miRNA-218 were not. Multivariate survival analysis demonstrated that miRNA-21 (hazard ratio (HR): 3.457, 95% CI [2.165–11.518]), miRNA (HR: 3.138, 95% CI [2.014–10.259]), miRNA-34a (HR: 0.452, 95% CI [0.202–0.915]), miRNA-133a (HR: 0.307, 95% CI [0.113–0.874]) and miRNA-539 (HR: 0.358, 95% CI [0.155–0.896]) were independent prognostic markers of OS patients after adjusting for TNM stage (HR: 2.893, 95% CI [1.496–8.125]), metastasis or recurrence (HR: 3.628, 95% CI [2.217–12.316]) and miRNA-30c (HR: 0.689, 95% CI [0.445–1.828]).ConclusionsHigh expression of miRNA-21 and miRNA-214 and low expression of miRNA-34a, miRNA-133a and miRNA-539 were associated with poor prognosis of OS patients after adjusting for TNM stage, metastasis or recurrence and miRNA-30c. creator: Wen Yang creator: Yu-bin Qi creator: Meng Si creator: Yong Hou creator: Lin Nie uri: https://doi.org/10.7717/peerj.8389 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi link: https://peerj.com/articles/8410 last-modified: 2020-01-20 description: BackgroundSalmonella Typhi (S. Typhi), the causative agent of typhoid fever, causes serious systemic disease in humans. Antibiotic treatment is required for the S. Typhi infection, while the inappropriate use of antibiotics causes increased drug-resistant S. Typhi. Hence, alternative therapies through non-antibiotic approaches are urgently needed. The use of beneficial lactic acid bacterium and/or its metabolites to control typhoid fever represent a promising approach, as it may exert protective actions through various mechanisms.MethodIn this study, the cell-free culture supernatant (CFCS) of Weissella confusa WM36 was evaluated via the antibacterial activity, and its metabolites were identified. In addition, the effects of CFCS on Salmonella virulence behaviors were also investigated.ResultBased on strong inhibition the growth of S. Typhi DMST 22842, organic acids (lactic acid and acetic acid) and 2,4-Di-tert-butylphenol (2,4 DTBP), were the main antibacterial metabolites presented in CFCS of strain WM36. Minimum inhibitory concentration (MIC) at 40% WM36–CFCS dramatically reduced the S. Typhi population to more than 99.99% at 4 h and completely inhibited biofilm formation, while sub-MIC at 20% (v/v) and MIC could reduce 100% of motility. Additionally, sub-MIC at only 10% (v/v) WM36–CFCS did down-regulate the expression of virulence genes which are responsible for the type-III secretion system, effector proteins, and quorum sensing system in this pathogen.ConclusionW. confusa WM36 and its metabolites are shown to be a promising candidates, and an effective approach against typhoid Salmonella burden. creator: Wattana Pelyuntha creator: Chaiyavat Chaiyasut creator: Duangporn Kantachote creator: Sasithorn Sirilun uri: https://doi.org/10.7717/peerj.8410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pelyuntha et al. title: Ecology of an ocelot population at the northern edge of the species’ distribution in northern Sonora, Mexico link: https://peerj.com/articles/8414 last-modified: 2020-01-20 description: We used data from eight years of camera trapping at Rancho El Aribabi, a cattle ranch and conservation property in northern Sonora, Mexico, to examine the ecology of the northern-most known breeding population of ocelots (Leopardus pardalis). Ocelots were found mostly in two discrete and disjunct areas: a riverine riparian canyon at just less than 1,000 masl elevation and along arroyos in an oak-mesquite savanna in the Sierra Azul at 1,266–1,406 masl. An ocelot was also detected at a site between those two areas, in an area of a Sonoran desertscrub-foothills thornscrub ecotone at 1,300 masl. At least 18 ocelots, both males and females, were detected during the 2007–2011 and 2014–2018 sampling periods. A female with a kitten was documented in 2011. No individual ocelots were photographed in both areas, which are separated by a minimum of 11.29 km, and no individuals were photographed in both time periods. In a binary logistic regression, key environmental variables predicting ocelot presence were, in order of importance, distance to a paved road, distance to human habitation, proximity to water, and an anthropogenic influences index that was dominated by cattle. Another analysis corroborated the finding regarding ocelot presence and cattle. Contrary to previous studies, ocelot presence was not tied to vegetation cover close to the ground. We present information about the types of habitats and sites ocelots used, short-term movements, daily and seasonal activity patterns, and behavior, including occurrence of different individuals at or near the same site over short periods of time. We discuss ocelot home range, density, and movements, but small sample sizes and study design problems limit the value of estimates derived from our work. Rancho El Aribabi is a private, conservation ranch for which the owners have made voluntary conservation commitments that provide habitat and protection for ocelots and other animals and plants. This northern-most known breeding population is a likely source of ocelots that are periodically detected in southeastern Arizona. Our results should help facilitate conservation of the ocelot in other semi-arid areas of northwestern Mexico and adjacent USA. creator: James C. Rorabaugh creator: Jan Schipper creator: Sergio Avila-Villegas creator: Jessica A. Lamberton-Moreno creator: Timothy Flood uri: https://doi.org/10.7717/peerj.8414 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rorabaugh et al. title: Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot link: https://peerj.com/articles/8422 last-modified: 2020-01-20 description: BackgroundAs one of the most common major congenital distal skeletal abnormalities, congenital talipes equinovarus (clubfoot) affects approximately one in one thousandth newborns. Although several etiologies of clubfoot have been proposed and several genes have been identified as susceptible genes, previous studies did not further explore signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore abnormal pathways and their interactions in clubfoot using integrated bioinformatics analyses.MethodsKEGG, gene ontology (GO), Reactome (REAC), WikiPathways (WP) or human phenotype ontology (HP) enrichment analysis were performed using WebGestalt, g:Profiler and NetworkAnalyst.ResultsA large number of signaling pathways were enriched e.g. signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM. Protein-protein interactions (PPIs) and gene regulatory networks (GRNs) analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, regulated these candidate proteins.ConclusionThe results of the present study supported previously proposed hypotheses, such as ECM, genetic, muscle, neurological, skeletal, and vascular abnormalities. More importantly, the enrichment results also indicated cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism may be new potential etiological mechanisms of clubfoot. creator: Guiquan Cai creator: Xuan Yang creator: Ting Chen creator: Fangchun Jin creator: Jing Ding creator: Zhenkai Wu uri: https://doi.org/10.7717/peerj.8422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cai et al. title: Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath link: https://peerj.com/articles/8430 last-modified: 2020-01-20 description: IntroductionPathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study.Materials & MethodsThe V3–V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity.ResultsA total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected.Discussion & ConclusionsThe effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding. creator: Jia Bie creator: Qing Tong creator: Xiaoning Liu creator: Xianhao Zhang creator: Hongbin Wang uri: https://doi.org/10.7717/peerj.8430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bie et al. title: Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity link: https://peerj.com/articles/8434 last-modified: 2020-01-20 description: ObjectivesGini coefficients have been used to describe the distribution of Chlamydia trachomatis (CT) infections among individuals with different levels of sexual activity. The objectives of this study were to investigate Gini coefficients for different sexually transmitted infections (STIs), and to determine how STI control interventions might affect the Gini coefficient over time.MethodsWe used population-based data for sexually experienced women from two British National Surveys of Sexual Attitudes and Lifestyles (Natsal-2: 1999–2001; Natsal-3: 2010–2012) to calculate Gini coefficients for CT, Mycoplasma genitalium (MG), and human papillomavirus (HPV) types 6, 11, 16 and 18. We applied bootstrap methods to assess uncertainty and to compare Gini coefficients for different STIs. We then used a mathematical model of STI transmission to study how control interventions affect Gini coefficients.ResultsGini coefficients for CT and MG were 0.33 (95% CI [0.18–0.49]) and 0.16 (95% CI [0.02–0.36]), respectively. The relatively small coefficient for MG suggests a longer infectious duration compared with CT. The coefficients for HPV types 6, 11, 16 and 18 ranged from 0.15 to 0.38. During the decade between Natsal-2 and Natsal-3, the Gini coefficient for CT did not change. The transmission model shows that higher STI treatment rates are expected to reduce prevalence and increase the Gini coefficient of STIs. In contrast, increased condom use reduces STI prevalence but does not affect the Gini coefficient.ConclusionsGini coefficients for STIs can help us to understand the distribution of STIs in the population, according to level of sexual activity, and could be used to inform STI prevention and treatment strategies. creator: Sandro Gsteiger creator: Nicola Low creator: Pam Sonnenberg creator: Catherine H. Mercer creator: Christian L. Althaus uri: https://doi.org/10.7717/peerj.8434 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gsteiger et al. title: Comparative analysis of the demographic parameters of seven spotted ladybird beetle (Coleoptera: Coccinellidae) reared on various host aphid species link: https://peerj.com/articles/8313 last-modified: 2020-01-17 description: BackgroundThe demographic parameters of the predacious seven spotted ladybird beetle Coccinella septempunctata Linnaeus (Coleoptera: Coccinellidae) reared on the following four host aphid species were compared: Rhopalosiphum padi Linnaeus (Hemiptera: Aphididae), Rhopalosiphum maidis Fitch (Hemiptera: Aphididae), Sitobion avenae Fabricius (Hemiptera: Aphididae), and Schizaphis graminum Rondani (Hemiptera: Aphididae).MethodsThe developmental period, fecundity, adult preoviposition period, total preoviposition period and population parameters were evaluated based on the two-sex age-stage life table. The duration of the developmental stages and the population parameters were calculated with the TWOSEX-MSChart program, whereas population size was projected based on the two-sex age-stage life table data with the TIMING-MSChart program.ResultsThe intrinsic rate of increase (r) was the highest in the R. padi predators (0.1946 per day), followed by the S. graminum (0.1435 per day), S. avenae (0.1400 per day), and R. maidis (0.1180 per day) predators. The differences in the net reproductive rate (R0) and the finite rate of increase (λ) when C. septempunctata was reared on the four aphid species were consistent with the r values. This trend was reversed for the mean generation time (T), which ranged from 29.02 days for the lady beetles reared on R. padi to 39.75 days for the lady beetles reared on R. maidis. Interestingly, R. padi was the most suitable host, while the congeneric R. maidis was the least suitable. The results of this study may be useful for future investigations regarding the ecological effects of predatory species and the mass-production of C. septempunctata in the laboratory for an augmentative release of an aphid predator. creator: Muhammad Farooq creator: Xun Zhu creator: Muhammad Shakeel creator: Ayesha Iftikhar creator: Muhammad Rafiq Shahid creator: Nadia Saeed creator: Muhammad Shahid Arain uri: https://doi.org/10.7717/peerj.8313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Farooq et al. title: Evolution of sexual size dimorphism in the wing musculature of Drosophila link: https://peerj.com/articles/8360 last-modified: 2020-01-17 description: Male courtship songs in Drosophila are exceedingly diverse across species. While much of this variation is understood to have evolved from changes in the central nervous system, evolutionary transitions in the wing muscles that control the song may have also contributed to song diversity. Here, focusing on a group of four wing muscles that are known to influence courtship song in Drosophila melanogaster, we investigate the evolutionary history of wing muscle anatomy of males and females from 19 Drosophila species. We find that three of the wing muscles have evolved sexual dimorphisms in size multiple independent times, whereas one has remained monomorphic in the phylogeny. These data suggest that evolutionary changes in wing muscle anatomy may have contributed to species variation in sexually dimorphic wing-based behaviors, such as courtship song. Moreover, wing muscles appear to differ in their propensity to evolve size dimorphisms, which may reflect variation in the functional constraints acting upon different wing muscles. creator: Claire B. Tracy creator: Janet Nguyen creator: Rayna Abraham creator: Troy R. Shirangi uri: https://doi.org/10.7717/peerj.8360 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tracy et al. title: Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis link: https://peerj.com/articles/8390 last-modified: 2020-01-17 description: BackgroundOsteoarthritis (OA) is the most common chronic degenerative joint disease and is mainly characterized by cartilage degeneration, subcartilage bone hyperplasia, osteophyte formation and joint space stenosis. Recent studies showed that synovitis might also be an important pathological change of OA. However, the molecular mechanisms of synovitis in OA are still not well understood.ObjectiveThis study was designed to identify key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis.Materials and MethodsThe gene expression profiles of GSE12021, GSE55235 and GSE55457 were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by the LIMMA package in Bioconductor, and functional enrichment analyses were performed. A protein-protein interaction network (PPI) was constructed, and module analysis was performed using STRING and Cytoscape. The CIBERSORT algorithm was used to analyze the immune infiltration of synovial tissue between OA and normal controls.ResultsA total of 106 differentially expressed genes, including 68 downregulated genes and 38 upregulated genes, were detected. The PPI network was assessed, and the most significant module containing 14 hub genes was identified. Gene Ontology analysis revealed that the hub genes were significantly enriched in immune cell chemotaxis and cytokine activity. KEGG pathway analysis showed that the hub genes were significantly enriched in the rheumatoid arthritis signaling pathway, IL-17 signaling pathway and cytokine-cytokine receptor interaction signaling pathway. The immune infiltration profiles varied significantly between osteoarthritis and normal controls. Compared with normal tissue, OA synovial tissue contained a higher proportion of memory B cells, naive CD4+ T cells, regulatory T cells, resting dendritic cells and resting mast cells, while naive CD4+ T cells, activated NK cells, activated mast cells and eosinophils contributed to a relatively lower portion (P > 0.05). Finally, the expression levels of 11 hub genes were confirmed by RT-PCR.ConclusionThe hub genes and the difference in immune infiltration in synovial tissue between osteoarthritis and normal controls might provide new insight for understanding OA development. creator: Weisong Cai creator: Haohuan Li creator: Yubiao Zhang creator: Guangtao Han uri: https://doi.org/10.7717/peerj.8390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cai et al. title: Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple link: https://peerj.com/articles/8391 last-modified: 2020-01-17 description: BackgroundAP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple.MethodsThirty full-length cDNA sequences of apple AP2/ERF genes were isolated from ‘Zihong Fuji’ apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR.ResultsThe sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members of the apple ERF and DREB subfamilies were induced by Alternaria alternate apple pathotype (AAAP) infection. Under salt treatment, many members in the apple ERF and DREB subfamilies were transcriptionally up or down-regulated. Under mannitol treatment, many members of the apple ERF, DREB, and AP2 subfamilies were induced at the transcriptional level. Taken together, the results indicated that the cloned apple AP2/ERF genes were expressed in all examined tissues. These genes were up-regulated or down-regulated in response to AAAP infection and to salt or mannitol treatment, which suggested they may be involved in regulating growth, development, and stress response in apple. creator: Huifeng Li creator: Qinglong Dong creator: Qiang Zhao creator: Song Shi creator: Kun Ran uri: https://doi.org/10.7717/peerj.8391 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma link: https://peerj.com/articles/8383 last-modified: 2020-01-17 description: Autophagy-related genes (ATGs) depress tumorigenesis. However, in tumor tissue, it promotes tumor progression. Here, we demonstrated that 63 ATGs were differentially expressed in normal tissues and tumor tissues of hepatocellular carcinoma (HCC), and seven prognostic-related genes were chosen to establish prognostic risk signatures. It is not just an independent prognostic factor for HCC, but also closely related to the degree of malignancy of HCC. Further, the hallmarks of PI3K–AKT–mTOR signaling was significantly enriched in the high-risk group. Moreover, AKT–pS473 and mTOR–pS2448 expression was down-regulated and correlated with patient prognosis in high-risk group. Finally, we demonstrate that the prognosis signature of ATGs is closely related to immune cell infiltration and PD-L1 expression. In conclusion, ATGs are a crucial factor in the malignant progression of HCC and will be a new prognostic marker for diagnosis and treatment. ATGs prognostic signatures are potentially useful for predicting PD-L1 therapeutic effects. creator: Deli Mao creator: Zhe Zhang creator: Xin Zhao creator: Xiaoqiang Dong uri: https://doi.org/10.7717/peerj.8383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mao et al. title: Genome-wide identification and expression analysis of NADPH oxidase genes in response to ABA and abiotic stresses, and in fibre formation in Gossypium link: https://peerj.com/articles/8404 last-modified: 2020-01-17 description: Plasma membrane NADPH oxidases, also named respiratory burst oxidase homologues (Rbohs), play pivotal roles in many aspects of growth and development, as well as in responses to hormone signalings and various biotic and abiotic stresses. Although Rbohs family members have been identified in several plants, little is known about Rbohs in Gossypium. In this report, we characterized 13, 13, 26 and 19 Rbohs in G. arboretum, G. raimondii, G. hirsutum and G. barbadense, respectively. These Rbohs were conservative in physical properties, structures of genes and motifs. The expansion and evolution of the Rbohs dominantly depended on segmental duplication, and were under the purifying selection. Transcription analyses showed that GhRbohs were expressed in various tissues, and most GhRbohs were highly expressed in flowers. Moreover, different GhRbohs had very diverse expression patterns in response to ABA, high salinity, osmotic stress and heat stress. Some GhRbohs were preferentially and specifically expressed during ovule growth and fiber formation. These results suggest that GhRbohs may serve highly differential roles in mediating ABA signaling, in acclimation to environmental stimuli, and in fiber growth and development. Our findings are valuable for further elucidating the functions and regulation mechanisms of the Rbohs in adaptation to diverse stresses, and in growth and development in Gossypium. creator: Gaofeng Zhang creator: Caimeng Yue creator: Tingting Lu creator: Lirong Sun creator: Fushun Hao uri: https://doi.org/10.7717/peerj.8404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Effects of the mycorrhizal fungus Ceratobasidium sp. AR2 on growth and flavonoid accumulation in Anoectochilus roxburghii link: https://peerj.com/articles/8346 last-modified: 2020-01-16 description: BackgroundAnoectochilus roxburghii is a traditional Chinese medicine with potent medicinal activity owing to the presence of secondary metabolites, particularly flavonoids. A. roxburghii also maintains a symbiotic relationship with mycorrhizal fungi. Moreover, mycorrhizal fungi can induce metabolite synthesis in host plants. However, little is known about the role of mycorrhizal fungi in promoting the accumulation of flavonoid metabolites in A. roxburghii.MethodsA. roxburghii and the isolated fungus Ceratobasidium sp. AR2 were cocultured. The portion of A. roxburghii above the medium treated with or without AR2 was studied by transcriptome and target metabolome analyses.ResultsAR2 promoted the growth and development of A. roxburghii. The contents of total flavonoid, rutin, isorhamnetin, and cyanidin-3-glucoside chloride were increased compared with those in uninoculated cultures. Transcriptome analysis suggested that 109 unigenes encoding key enzymes were potentially associated with changes in flavonoids. Quantitative real-time polymerase chain reaction of fourteen flavonoid-related unigenes showed that most flavonoid biosynthetic genes were significantly differentially expressed between inoculated and uninoculated plantlets.ConclusionThe isolate AR2 could significantly promote the growth and development of A. roxburghii and the accumulation of flavonoids. Overall, our findings highlighted the molecular basis of the effects of mycorrhizal fungi on flavonoid biosynthesis in A. roxburghii and provided novel insights into methods to improve the yield and quality of A. roxburghii. creator: Ying Zhang creator: Yuanyuan Li creator: Shunxing Guo uri: https://doi.org/10.7717/peerj.8346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Application of problem-based learning and case-based learning integrated method in the teaching of maxillary sinus floor augmentation in implant dentistry link: https://peerj.com/articles/8353 last-modified: 2020-01-16 description: BackgroundTeaching of maxillary sinus floor augmentation (MSFA) is challenging for dental educators due to the varied sinus anatomy and high rate of complications. The method integrating problem-based learning and case-based learning (PBL-CBL method) may be more effective than the traditional teacher-centered method. The aim is to evaluate the efficacy of the PBL-CBL method in teaching MSFA.Materials & MethodsNinety-two students who received training between 2015 and 2017 at the Department of Implant Dentistry were divided randomly into an experimental group and a control group. Students in the experimental group were trained using the PBL-CBL method, while those in the control group were trained using the traditional teacher-centered method. After three months of training, a survey of the students’ opinions about the corresponding teaching method was carried out through a feedback questionnaire. A theory test was used to investigate the level of MSFA knowledge among the students. A case analysis was designed to test whether the students can apply the knowledge in solving new problems.ResultsCompared with the control method, the PBL-CBL method resulted in higher scores in both the theory test and the case analysis, and obtained a higher rate of satisfaction among the students. The difference in scores between the two methods were statistically significant (P < 0.01),ConclusionThe PBL-CBL method resulted in better results regarding acquisition of academic knowledge, ability in case analysis and student satisfaction compared with the teacher-centered method. It may be a promising mode for teaching complex surgical techniques in implant dentistry and other dental fields. creator: Yunfei Liu creator: Yamei Xu creator: Yueheng Li creator: Qingqing Wu uri: https://doi.org/10.7717/peerj.8353 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis link: https://peerj.com/articles/8379 last-modified: 2020-01-16 description: Ophiocordyceps sinensis is a highly valued fungus that has been used as traditional Asian medicine. This fungus is one of the most important sources of income for the nomadic populations of the Tibetan Plateau. With global warming and excessive collection, the wild O. sinensis resources declined dramatically. The cultivation of O. sinensis hasn’t been fully operational due to the unclear genetic basis of the fruiting body development. Here, our study conducted pairwise comparisons between transcriptomes acquired from different growth stages of O. sinensis including asexual mycelium (CM), developing fruiting body (DF) and mature fruiting body (FB). All RNA-Seq reads were aligned to the genome of O. sinensis CO18 prior to comparative analyses. Cluster analysis showed that the expression profiles of FB and DF were highly similar compared to CM. Alternative splicing analysis (AS) revealed that the stage-specific splicing genes may have important functions in the development of fruiting body. Functional enrichment analyses showed that differentially expressed genes (DEGs) were enriched in protein synthesis and baseline metabolism during fruiting body development, indicating that more protein and energy might be required for fruiting body development. In addition, some fruiting body development-associated genes impacted by ecological factors were up-regulated in FB samples, such as the nucleoside diphosphate kinase gene (ndk), β subunit of the fatty acid synthase gene (cel-2) and the superoxide dismutase gene (sod). Moreover, the expression levels of several cytoskeletons genes were significantly altered during all these growth stages, suggesting that these genes play crucial roles in both vegetative growth and the fruiting body development. Quantitative PCR (qPCR) was used to validate the gene expression profile and the results supported the accuracy of the RNA-Seq and DEGs analysis. Our study offers a novel perspective to understand the underlying growth stage-specific molecular differences and the biology of O. sinensis fruiting body development. creator: Xinxin Tong creator: Han Zhang creator: Fang Wang creator: Zhengyao Xue creator: Jing Cao creator: Cheng Peng creator: Jinlin Guo uri: https://doi.org/10.7717/peerj.8379 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tong et al. title: Genetic architecture study of rheumatoid arthritis and juvenile idiopathic arthritis link: https://peerj.com/articles/8234 last-modified: 2020-01-15 description: BackgroundRheumatoid arthritis and juvenile idiopathic arthritis are two types of autoimmune diseases with inflammation at the joints, occurring to adults and children respectively. There are phenotypic overlaps between these two types of diseases, despite the age difference in patient groups.MethodsTo systematically compare the genetic architecture of them, we conducted analyses at gene and pathway levels and constructed protein-protein-interaction network based on summary statistics of genome-wide association studies of these two diseases. We examined their difference and similarity at each level.ResultsWe observed extensive overlap in significant SNPs and genes at the human leukocyte antigen region. In addition, several SNPs in other regions of the human genome were also significantly associated with both diseases. We found significantly associated genes enriched in 32 pathways shared by both diseases. Excluding genes in the human leukocyte antigen region, significant enrichment is present for pathways like interleukin-27 pathway and NO2-dependent interleukin-12 pathway in natural killer cells.DiscussionThe identification of commonly associated genes and pathways may help in finding population at risk for both diseases, as well as shed light on repositioning and designing drugs for both diseases. creator: Jun Jia creator: Junyi Li creator: Xueming Yao creator: YuHang Zhang creator: Xiaohao Yang creator: Ping Wang creator: Qianghua Xia creator: Hakon Hakonarson creator: Jin Li uri: https://doi.org/10.7717/peerj.8234 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jia et al. title: Bayesian estimation of diagnostic accuracy of fecal culture and PCR-based tests for the detection of Salmonella enterica in California cull dairy cattle link: https://peerj.com/articles/8310 last-modified: 2020-01-15 description: Epidemiological studies of low prevalence disease problems are often hindered by the high cost of diagnostic testing. The objective of this study was to evaluate PCR screening of both individual and pooled fecal samples from culled dairy cows for the invA gene of Salmonella followed by culture to determine if the sensitivity and specificity were comparable to the results from traditional culture methods applied to individual samples. Cows from six different dairies were sampled in all four seasons. A total of 240 individual cow fecal samples, 24 fecal pools and 24 pools of 24-hour tetrathionate enrichment broth were tested. Diagnostic sensitivity of PCR screening followed by culture of PCR positive or indeterminate samples (i.e PCR-CUL method) was lower than that of culture (CUL) when applied to individual fecal samples (94.8%, 99.5%), however the specificity was comparable (99.6% and 97.7% respectively). For pools of five fecal samples and pools of five, 24 h tetrathionate broth samples, the specificity of both tests were comparable (∼98%); however, their sensitivity was only comparable in pooled fecal samples (∼93%) but greater for culture compared to PCR-CUL in pooled broth samples (∼99% versus ∼93%). Compared to culture results from testing of individual fecal samples, testing pooled fecal samples by culture had a relative sensitivity of 74% and relative specificity of 96%, testing pooled fecal samples by PCR-CUL resulted in relative sensitivity of 90% and relative specificity of 96%. Testing of pooled 24-hour enrichment broth by PCR-CUL increased the relative sensitivity and specificity to 100%. PCR testing followed by culture of positive or indeterminate samples is a time saving alternative to traditional methods. In addition, pooling of samples may be a useful method for decreasing cost if study aims can accommodate a moderate loss of relative sensitivity. creator: John M. Adaska creator: Pius S. Ekong creator: Kristin A. Clothier creator: Deniece R. Williams creator: Paul V. Rossitto creator: Terry W. Lehenbauer creator: Edward R. Atwill creator: Xunde Li creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.8310 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Adaska et al. title: Comparison of bacterial diversity and abundance between sexes of Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) from China link: https://peerj.com/articles/8411 last-modified: 2020-01-15 description: BackgroundInsects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and the thelytokous parthenogenesis, low temperature resistance, protection in galls, generation overlap and small body of L. invasa contribute to its rapid invasion and population growth. However, the endosymbiotic bacterial composition, abundance and sex differences of L. invasa remain unclear. Therefore, this research aimed to identify the bacterial communities in L. invasa adults and compare them between the sexes of L. invasa lineage B.ResultsThe Illumina MiSeq platform was used to compare bacterial community composition between females and males of L. invasa by sequencing the V3–V4 region of the 16S ribosomal RNA gene. A total of 1,320 operational taxonomic units (OTUs) were obtained. These OTUs were subdivided into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males were Rickettsia and Rhizobium, respectively.ConclusionThe endosymbiotic bacteria of L. invasa females and males were highly diverse. There were differences in the bacterial community of L. invasa between sexes, and the bacterial diversity in male specimens was greater than that in female specimens. This study presents a comprehensive comparison of bacterial communities in L. invasa and these data will provide an overall view of the bacterial community in both sexes of L. invasa with special attention on sex-related bacteria. creator: Chunhui Guo creator: Xin Peng creator: Xialin Zheng creator: Xiaoyun Wang creator: Ruirui Wang creator: Zongyou Huang creator: Zhende Yang uri: https://doi.org/10.7717/peerj.8411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Effects of indium exposure on respiratory symptoms: a retrospective cohort study in Japanese workers using health checkup data link: https://peerj.com/articles/8413 last-modified: 2020-01-15 description: BackgroundIndium compounds are known health hazards for lung cancer and interstitial pneumonia. Furthermore, they are related to emphysema, alveolar proteinosis, and cholesterol granuloma. In Japan, laws were revised in 2013 to tighten regulations on indium exposure in workplaces. However, its impact on the health of workers who handle indium has not been evaluated. This study aimed to investigate whether subjective respiratory symptoms in these workers have reduced after the 2013 amendment in the regulations.MethodsThe subjects were workers from certain areas of Japan who had undergone health checkups between January 1, 2013, and June 30, 2015. Indium-handling and non-handling workers were categorized into the exposed and less-exposed groups, respectively. Based on the findings of health checkups during this period, the hazard ratio of subjective respiratory symptoms (cough, sputum production, shortness of breath, and palpitation) and its 95% confidence intervals (CIs) were calculated with the less-exposed group as the reference. The Prentice-Williams-Peterson model was used for calculation, and a model that adjusted for coarse analysis and potential confounding factors was adopted.ResultsOverall, 2,561 workers (from 22 companies) who underwent 6,033 health checkups were included. The total person-years were 2,562.8 years, and 162 outcome events occurred. The hazard ratios of the exposed group were 1.65 (95% CI [1.14–2.39]: p = 0.008) and 1.61 (95% CI [1.04–2.50]: p = 0.032) in the crude and adjusted models, respectively.ConclusionIndium-handling workers had a high hazard of the subjective respiratory symptoms than non-indium -handling workers despite stricter regulations on indium exposure in workplaces. This indicates the need for further changes to the legislation to protect the health of workers exposed to harmful substances in workplaces. Further studies including larger diverse cohorts are needed to validate our findings. creator: Toshiharu Mitsuhashi uri: https://doi.org/10.7717/peerj.8413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mitsuhashi title: Isolation and identification of L-asparaginase-producing endophytic fungi from the Asteraceae family plant species of Iran link: https://peerj.com/articles/8309 last-modified: 2020-01-14 description: L-asparaginase is an important anticancer enzyme that is used in the first line treatment of acute lymphoblastic leukemia. This study was conducted to isolate L-asparaginase-producing endophytic fungi from medicinal plants of family Asteraceae. Seven healthy medicinal plants from family Asteraceae were selected for the isolation of endophytic fungi using standard surface sterilization techniques. A total of 837 isolates belonging to 84 species were comprised of the stem (55.6%), leaf (31.1%), root (10.6%) and flower (2.7%). Initial screening of L-asparaginase-producing endophytes was performed by qualitative plate assay on modified Czapex dox’s agar medium. L-asparaginase activity of fungal endophytes was quantified by the nesslerization method. Identification of endophytic fungi was performed using both morphological characteristics and phylogenetic analyses of DNA sequence data including ribosomal DNA regions of ITS (Internal transcribed spacer) and LSU (partial large subunit rDNA), TEF1 (Translation Elongation Factor) and TUB (β-tubulin). Of the 84 isolates, 38 were able to produce L-asparaginase and their L-asparaginase activities were between 0.019 and 0.492 unit/mL with Fusarium proliferatum being the most potent. L-asparaginase-producing endophytes were identified as species of Plectosphaerella, Fusarium, Stemphylium, Septoria, Alternaria, Didymella, Phoma, Chaetosphaeronema, Sarocladium, Nemania, Epicoccum, Ulocladium and Cladosporium. This study showed that endophytic fungi from Asteraceae members have a high L-asparaginase-producing potential and they can be used as an alternative source for production of anticancer enzymes. creator: Sareh Hatamzadeh creator: Kamran Rahnama creator: Saeed Nasrollahnejad creator: Khalil Berdi Fotouhifar creator: Khodayar Hemmati creator: James F. White creator: Fakhtak Taliei uri: https://doi.org/10.7717/peerj.8309 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hatamzadeh et al. title: Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing link: https://peerj.com/articles/8317 last-modified: 2020-01-14 description: BackgroundObesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota.MethodsAccording to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform.ResultsThe number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P = 0.008). Principal coordinate analysis (PCoA) and Nonmetric multidimensional scaling (NMDS) revealed significant differences in gut microbial community structure between the normal weight group and the obese group. The liner discriminant analysis (LDA) effect size (LEfSe) analysis showed that fifty-five species of bacteria were abundant in the fecal samples of the normal weight group and forty-five species of bacteria were abundant in the obese group. In regard to phyla, the gut microbiota in the obese group had lower proportions of Bacteroidetes (51.35%) compared to the normal weight group (55.48%) (P = 0.030). There was no statistical difference in Firmicutes between the two groups (P = 0.436), and the Firmicutes/Bacteroidetes between the two groups had no statistical difference (P = 0.983). At the genus level, Faecalibacterium, Phascolarctobacterium, Lachnospira, Megamonas, and Haemophilus were significantly more abundant in the obese group than in the normal weight group (P = 0.048, P = 0.018, P < 0.001, P = 0.040, and P = 0.003, respectively). The fecal microbiota of children in the obese group had lower proportions of Oscillospira and Dialister compared to the normal weight group (P = 0.002 and P = 0.002, respectively).ConclusionsOur results showed a decrease in gut microbiota abundance and diversity as the BMI increased. Variations in the bacterial community structure were associated with obesity. Gut microbiota dysbiosis might play a crucial part in the development of obesity in Chinese children. creator: Xiaowei Chen creator: Haixiang Sun creator: Fei Jiang creator: Yan Shen creator: Xin Li creator: Xueju Hu creator: Xiaobing Shen creator: Pingmin Wei uri: https://doi.org/10.7717/peerj.8317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: An analysis of abnormalities in the B cell receptor repertoire in patients with systemic sclerosis using high-throughput sequencing link: https://peerj.com/articles/8370 last-modified: 2020-01-14 description: Systemic sclerosis is a chronic multisystem autoimmune disease that is associated with polyclonal B cell hyperreactivity. The CDR3 of BCRs is the major site of antigen recognition. Therefore, we analyzed the BCR repertoire of patients with SSc. The BCR repertoires in 12 subjects including eight SSc patients and four healthy controls were characterized by high-throughput sequencing, and bioinformatics analysis were studied. The average CDR3 length in the SSc group was significantly shorter. The SSc patient displayed more diverse BCR. Moreover, SSc patients with mild skin sclerosis, anti-Scl70, interstitial lung disease or female sex were more diversified. B cells from the SSc patients showed a differential V and J gene usage. SSc patients had distinct BCR repertoires.These findings reflected the differences of BCR repertoires between SSc patients and controls. The higher-usage genes for the BCR sequence might be potential biomarkers of B cell-targeted therapies or diagnosis for SSc. creator: Xiaodong Shi creator: Tihong Shao creator: Feifei Huo creator: Chenqing Zheng creator: Wanyu Li creator: Zhenyu Jiang uri: https://doi.org/10.7717/peerj.8370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al. title: New insights into human hair: SAXS, SEM, TEM and EDX for Alopecia Areata investigations link: https://peerj.com/articles/8376 last-modified: 2020-01-14 description: BackgroundAlopecia areata (AA) is a T-cell-mediated autoimmune disease and affects up to 2% of the population. There is a need for a more profound and rigorous understanding of the structure and composition of human hair affected by AA in order to manage this disease. The aim of this article is to understand the effects of AA on the structure and composition of human hair.MethodsSeveral physico-chemical investigation methods, such as Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Energy-Dispersive X-ray Spectroscopy (EDX), and microbeam Small Angle X-ray Scattering (SAXS), were used to analyze human hair samples obtained from healthy donors and patients with AA.ResultsSEM revealed more severe hair surface defects for the white regrown hair (W-AA) samples. TEM showed the presence of air-like vesicles located in the endocuticle of regrown hair. Analysis of ultrathin sections of W-AA showed the existence of empty vesicles and smaller melanin granules compared to control samples. SAXS demonstrated that unaffected hair of patients with AA (B-AA) and W-AA melanin aggregates are different in their sizes and shapes compared to the control samples. EDX data showed that W-AA elemental composition was significantly different from the other sample groups. Our study showcases promising non-invasive techniques for a better and more accurate understanding of changes in the internal structure and composition of hair affected by AA. creator: Adina Coroaba creator: Anca E. Chiriac creator: Liviu Sacarescu creator: Tudor Pinteala creator: Bogdan Minea creator: Sorin-Alexandru Ibanescu creator: Mihaela Pertea creator: Aurelian Moraru creator: Irina Esanu creator: Stelian S. Maier creator: Anca Chiriac creator: Mariana Pinteala uri: https://doi.org/10.7717/peerj.8376 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Coroaba et al. title: Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant (Camellia sinensis) under abiotic stress and withering processing link: https://peerj.com/articles/8432 last-modified: 2020-01-14 description: DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants (Camellia sinensis) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET, CsCMT, CsDRM and CsDNMT2. The CsdMTase genes can be classified into CsROS, CsDME and CsDML. Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase. Furthermore, multiple cis-acting elements were observed in the CsC5-MTase and CsdMTase, including light responsiveness, phytohormone responsiveness, stress responsiveness, and plant growth and development-related elements. Then, we investigated the transcript abundance of CsC5-MTase and CsdMTase under abiotic stress (cold and drought) and withering processing (white tea and oolong tea). Notably, most CsC5-MTases, except for CsCMT1 and CsCMT2, were significantly downregulated under abiotic stress, while the transcript abundance of all four CsdMTase genes was significantly induced. Similarly, the same transcript abundance of CsC5-MTase and CsdMTase was found during withering processing of white tea and oolong tea, respectively. In total, our findings will provide a basis for the roles of CsC5-MTase and CsdMTase in response to abiotic stress and the potential functions of these two gene families in affecting tea flavor during tea withering processing. creator: Chen Zhu creator: Shuting Zhang creator: Chengzhe Zhou creator: Lan Chen creator: Haifeng Fu creator: Xiaozhen Li creator: Yuling Lin creator: Zhongxiong Lai creator: Yuqiong Guo uri: https://doi.org/10.7717/peerj.8432 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhu et al. title: Structure and pigment make the eyed elater’s eyespots black link: https://peerj.com/articles/8161 last-modified: 2020-01-13 description: Surface structures that trap light leading to near complete structural absorption creates an appearance of “super black.” Well known in the natural world from bird feathers and butterfly scales, super black has evolved independently from various anatomical structures. Due to an exceptional ability to reduce specular reflection, these biological materials have garnered interest from optical industries. Here we describe the false eyes of the eyed elater click beetle, which, while not classified as super black, still attains near complete absorption of light partly due to an array of vertically-aligned microtubules. These cone-shaped microtubules are modified hairs (setae) that are localized to eyespots on the dorsum of the beetle, and absorb 96.1% of incident light (at a 24.8° collection angle) in the spectrum between 300–700 nm. Filled with melanin, the setae combine structure and pigment to generate multiple reflections and refractions causing light to travel a greater distance. This light-capturing architecture leaves little light available to receivers and the false eyes appear as deep black making them appear more conspicuous to predators. creator: Victoria L. Wong creator: Paul E. Marek uri: https://doi.org/10.7717/peerj.8161 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Declines in skeletal muscle quality vs. size following two weeks of knee joint immobilization link: https://peerj.com/articles/8224 last-modified: 2020-01-13 description: BackgroundDisuse of a muscle group, which occurs during bedrest, spaceflight, and limb immobilization, results in atrophy. It is unclear, however, if the magnitude of decline in skeletal muscle quality is similar to that for muscle size. The purpose of this study was to examine the effects of two weeks of knee joint immobilization on vastus lateralis and rectus femoris echo intensity and cross-sectional area.MethodsThirteen females (mean ± SD age = 21 ± 2 years) underwent two weeks of left knee joint immobilization via ambulating on crutches and use of a brace. B-mode ultrasonography was utilized to obtain transverse plane images of the immobilized and control vastus lateralis and rectus femoris at pretest and following immobilization. Effect size statistics and two-way repeated measures analyses of variance were used to interpret the data.ResultsNo meaningful changes were demonstrated for the control limb and the rectus femoris of the immobilized limb. Analyses showed a large increase in vastus lateralis echo intensity (i.e., decreased muscle quality) for the immobilized limb (p = .006, Cohen’s d = .918). For vastus lateralis cross-sectional area, no time × limb interaction was observed (p = .103), but the effect size was moderate (d = .570). There was a significant association between the increase in vastus lateralis echo intensity and the decrease in cross-sectional area (r =  − .649, p = .016).ConclusionIn female participants, two weeks of knee joint immobilization resulted in greater deterioration of muscle quality than muscle size. Echo intensity appears to be an attractive clinical tool for monitoring muscle quality during disuse. creator: Rob J. MacLennan creator: Michael Sahebi creator: Nathan Becker creator: Ethan Davis creator: Jeanette M. Garcia creator: Matt S. Stock uri: https://doi.org/10.7717/peerj.8224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 MacLennan et al. title: Investigating Los Angeles’ urban roadway network from a biologically-formed perspective link: https://peerj.com/articles/8238 last-modified: 2020-01-13 description: The evolution of networks is constrained by spatial properties of the environment; a characterization that is true in both biological and built networks. Hence built networks such as urban streets can be compared to biological networks to reveal differences in efficiency and complexity. This study assessed foraging networks created by the slime-mold Physarium polycephalum on proportional 3D-printed topographic maps of metropolitan city of Los Angeles, California. Rapidly-generated isomorphic solutions were found to be consistently and statistically shorter than existing roadways in system length. Slime mold also allocated resources to supporting key nodes, analogous to how heavy traffic flows through major intersections. Further, chemical deterrents inhibited exploration of slime mold in selected areas and allows for testing of network redundancy and system resilience, such as after an earthquake or wildfire. creator: Sophia Deen creator: Tatiana Kuzmenko creator: Hossein Asghari creator: Demian A. Willette uri: https://doi.org/10.7717/peerj.8238 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Deen et al. title: The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales link: https://peerj.com/articles/8305 last-modified: 2020-01-13 description: Cycadales is an extant group of seed plants occurring in subtropical and tropical regions comprising putatively three families and 10 genera. At least one complete plastid genome sequence has been reported for all of the 10 genera except Microcycas, making it an ideal plant group to conduct comprehensive plastome comparisons at the genus level. This article reports for the first time the plastid genome of Microcycas calocoma. The plastid genome has a length of 165,688 bp with 134 annotated genes including 86 protein-coding genes, 47 non-coding RNA genes (39 tRNA and eight rRNA) and one pseudogene. Using global sequence variation analysis, the results showed that all cycad genomes share highly similar genomic profiles indicating significant slow evolution and little variation. However, identity matrices coinciding with the inverted repeat regions showed fewer similarities indicating that higher polymorphic events occur at those sites. Conserved non-coding regions also appear to be more divergent whereas variations in the exons were less discernible indicating that the latter comprises more conserved sequences. Phylogenetic analysis using 81 concatenated protein-coding genes of chloroplast (cp) genomes, obtained using maximum likelihood and Bayesian inference with high support values (>70% ML and = 1.0 BPP), confirms that Microcycas is closest to Zamia and forms a monophyletic clade with Ceratozamia and Stangeria. While Stangeria joined the Neotropical cycads Ceratozamia, Zamia and Microcyas, Bowenia grouped with the Southern Hemisphere cycads Encephalartos, Lepidozamia and Macrozamia. All Cycas species formed a distinct clade separated from the other genera. Dioon, on the other hand, was outlying from the rest of Zamiaceae encompassing two major clades—the Southern Hemisphere cycads and the Neotropical cycads. Analysis of the whole cp genomes in phylogeny also supports that the previously recognized family—Stangeriaceae—which contained Bowenia and Stangeria, is not monophyletic. Thus, the cp genome topology obtained in our study is congruent with other molecular phylogenies recognizing only a two-family classification (Cycadaceae and Zamiaceae) within extant Cycadales. creator: Aimee Caye G. Chang creator: Qiang Lai creator: Tao Chen creator: Tieyao Tu creator: Yunhua Wang creator: Esperanza Maribel G. Agoo creator: Jun Duan creator: Nan Li uri: https://doi.org/10.7717/peerj.8305 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chang et al. title: A new species of rorqual whale (Cetacea, Mysticeti, Balaenopteridae) from the Late Miocene of the Southern North Sea Basin and the role of the North Atlantic in the paleobiogeography of Archaebalaenoptera link: https://peerj.com/articles/8315 last-modified: 2020-01-13 description: BackgroundThe rich fossil record of rorqual and humpback whales (Cetacea, Mysticeti, Balaenopteridae) is mainly characterized by monotypic genera since genera including more than one species are extremely rare. The discovery of new species belonging to known genera would be of great importance in order to better understand ancestor-descendant relationships and paleobiogeographic patterns in this diverse group. Recent discoveries in the southern North Sea Basin yielded a number of reasonably well preserved fossil balaenopterids from the Late Miocene; this sample includes a balaenopterid skull from Liessel, The Netherlands, which shares key characters with Archaebalaenoptera castriarquati from the Pliocene of Mediterranean. This skull is permanently held by Oertijdmuseum, Boxtel, The Netherlands, with the number MAB002286 and is investigated here.MethodsA detailed comparative anatomical analysis of the skull MAB002286 is performed in order to understand its relationships. The age of the skull is determined by dinocyst analysis of the associated sediment. A paleobiogeographic analysis is performed to understand paleobiogeographic patterns within the balaenopterid clade the new skull belongs to.ResultsOur work resulted in the description of Archaebalaenoptera liesselensis new species. The geological age of the holotype skull is between 8.1 and 7.5 Ma. The phylogenetic relationships of this species reveals that it is monophyletic with Archaebalaenoptera castriarquati from the Italian Pliocene. Moreover, in combination with a more basal species of Archaebalaenoptera from the late Miocene of Peru, our paleobiogeographic analysis suggests that the North Atlantic ocean played a major role as a center of origin of a number of balaenopterid clades including Protororqualus, Archaebalaenoptera and more advanced balaenopterid taxa. From a North Atlantic center of origin, two dispersal events are inferred that led to the origins of Archaebalaenoptera species in the South Pacific and Mediterranean. The distribution of Archaebalaenoptera was antitropical in the late Miocene. The role played by the Mediterranean salinity crisis is also investigated and discussed. creator: Michelangelo Bisconti creator: Dirk K. Munsterman creator: René H.B. Fraaije creator: Mark E.J. Bosselaers creator: Klaas Post uri: https://doi.org/10.7717/peerj.8315 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bisconti et al. title: Risk-sensitive foraging does not explain condition-dependent choices in settling reef fish larvae link: https://peerj.com/articles/8333 last-modified: 2020-01-13 description: The transition from the planktonic larval to the benthic adult stage in reef fishes is perilous, and involves decisions about habitat selection and group membership. These decisions are consequential because they are essentially permanent (many fish rarely leave their initial settlement habitat, at least for the first several days or weeks). In one common Caribbean reef fish, the bluehead wrasse (Thalassoma bifasciatum), settling larvae either join groups or remain solitary. Grouped fish have lower mortality rates but slightly slower growth rates, and fish that are smaller at the time of settlement are less likely to join groups. We hypothesized that the decision of smaller (i.e., lower condition) fish to remain solitary could be explained by risk-sensitive foraging: with less competition, solitary fish may have higher variance in foraging success, so that there is a chance of a high payoff (outweighing the increased mortality risk) despite the lack of a large difference in the average outcome. We tested this by comparing the mean, standard deviation, and maximum number of (a) prey items in stomach contents and (b) post-settlement growth rates (from otolith measurements) of solitary and grouped fish during two settlement pulses on St. Croix, US Virgin Islands. However, we did not find evidence to support our hypothesis, nor any evidence to support the earlier finding that fish in groups have lower average growth rates. Thus we must consider alternative explanations for the tendency of smaller fish to remain solitary, such as the likely costs of searching for and joining groups at the time of settlement. This study reinforces the value of larval and juvenile fish as a testbed for behavioral decisionmaking, because their recent growth history is recorded in their otoliths. creator: Emma E. Bogdan creator: Andrea L. Dingeldein creator: Deirdre Bertrand creator: Will White uri: https://doi.org/10.7717/peerj.8333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bogdan et al. title: Response of total phenols, flavonoids, minerals, and amino acids of four edible fern species to four shading treatments link: https://peerj.com/articles/8354 last-modified: 2020-01-13 description: Total phenols, flavonoids, minerals and amino acids content were investigated in leaves of four fern species grown under four shading treatments with different sunlight transmittance in 35% full sunlight (FS), 13% FS, 8% FS and 4% FS. The leaves of four fern species contain high levels of total phenols and flavonoids, abundant minerals and amino acids, and these all were strongly affected by transmittance. Total phenols and flavonoids content were significantly positively correlated with transmittance, while minerals and total amino acids content were significantly negatively correlated with transmittance, a finding that supports research into how higher light intensity can stimulate the synthesis of phenols and flavonoids, and proper shading can stimulate the accumulation of minerals and amino acids. Matteuccia struthiopteris (L.) Todaro (MS) had the highest total phenols content, Athyrium multidentatum (Doll.) Ching (AM) showed the highest total amino acids, total essential amino acids content, Osmunda cinnamomea (L) var. asiatica Fernald (OCA) exhibited the highest total non-essential amino acids and flavonoids content. Pteridium aquilinum (L.) Kuhn var. latiusculum (Desy.) Underw. ex Heller (PAL) exhibited the highest minerals content. This research can provide a scientific basis for the cultivation and management of those four fern species. creator: Yanlin Wang creator: Shanshan Gao creator: Xingyuan He creator: Yan Li creator: Yue Zhang creator: Wei Chen uri: https://doi.org/10.7717/peerj.8354 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.) link: https://peerj.com/articles/8359 last-modified: 2020-01-13 description: Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. Sugarcane bacilliform viruses (SCBVs) are one of the main species that infect sugarcane. During the last 30 years, significant genetic changes in SCBV strains have been observed with a high risk of disease incidence associated with crop damage. SCBV infection may lead to significant losses in biomass production in susceptible sugarcane cultivars. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORFs) on the positive strand that replicate by a reverse transcriptase. SCBGAV can infect sugarcane in a semipersistent manner via the insect vectors sugarcane mealybug species. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. Mature miRNA target sequences were retrieved from the miRBase (miRNA database) and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments—were considered by all algorithms. Among them, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. The predicted sugarcane miRNAs against viral mRNA targets possess antiviral activities, leading to translational inhibition by mRNA cleavage. Interaction network of sugarcane-encoded miRNAs with SCBGAV genes, created using Circos, allow analyze new targets. The finding of the present study acts as a first step towards the creation of SCBGAV-resistant sugarcane through the expression of the identified miRNAs. creator: Fakiha Ashraf creator: Muhammad Aleem Ashraf creator: Xiaowen Hu creator: Shuzhen Zhang uri: https://doi.org/10.7717/peerj.8359 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ashraf et al. title: The mitochondrial genome of Apion squamigerum (Coleoptera, Curculionoidea, Brentidae) and the phylogenetic implications link: https://peerj.com/articles/8386 last-modified: 2020-01-13 description: In this article, we present the nearly complete mitochondrial genome (mitogenome) of the weevil beetle Apion squamigerum (Curculionoidea, Brentidae), assembled using data from Illumina next generation sequencing (NGS). This mitogenome was found to be very large, with the total length of 18,562 bp. Two trnM genes were identified. A large non-coding intergenic spacer spanning 1,949 bp occurred between trnI and trnM2. Combined with 111 existing weevil mitogenomes, we conducted phylogenetic reconstructions based on various datasets under maximum likelihood and Bayesian inference. Firstly, phylogenetic analyses robustly supported a sister group of A. squamigerum and Rhopalapion longirostre, namely, that two species of Apioninae (Brentidae) formed a clade. Within the entire Curculionoidea, the Nemonychidae diverged firstly, following the families Anthribidae and Attelabidae. In addition, a large clade comprising the sister families Brentidae and Curculionidae was strongly supported in all trees. creator: Nan Song creator: Xinxin Li creator: Xinming Yin creator: Xinghao Li creator: Shengjun Yin creator: Mingsheng Yang uri: https://doi.org/10.7717/peerj.8386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. title: The influence of ecological infrastructures adjacent to crops on their carabid assemblages in intensive agroecosystems link: https://peerj.com/articles/8094 last-modified: 2020-01-10 description: BackgroundConserving biodiversity and enhancing ecosystem services of interest in intensive agroecosystems is a major challenge. Perennial ecological infrastructures (EIs), such as hedges and grassy strips, and annual EI under Agri-Environment Schemes appear to be good candidates to promote both. Our study focused on carabids, an indicator group responding both at the species and functional trait level to disturbances and supporting pest control and weed seed consumption services.MethodsWe compared carabid assemblages at the species and functional traits levels, sampled via pitfall trapping, in three types of EIs (hedges, grassy strips and annual flower strips) and crops. We also tested via GLMs the effect of (1) the type of EI at the crops’ border and (2) the distance from the crops’ border (two meters or 30 meters) on carabid assemblages of crops. Tested variables comprised: activity-density, species richness, functional dispersion metrics (FDis) and proportions of carabids by functional categories (Diet: generalist predators/specialist predators/seed-eaters; Size: small/medium/large/very large; Breeding period: spring/autumn).Results and DiscussionCarabid assemblages on the Principal Coordinate Analysis split in two groups: crops and EIs. Assemblages from all sampled EIs were dominated by mobile generalist predator species from open-land, reproducing in spring. Assemblages of hedges were poor in activity-density and species richness, contrarily to grassy and annual flower strips. Differences in carabid assemblages in crops were mainly driven by the presence of hedges. The presence of hedges diminished the Community Weighted Mean size of carabids in crops, due to an increased proportion of small (<5 mm) individuals, while distance from crops’ border favoured large (between 10–15 mm) carabids. Moreover, even if they were attracted by EIs, granivorous carabid species were rare in crops. Our results underlie the importance of local heterogeneity when adapting crops’ borders to enhance carabid diversity and question the relevance of hedge implantation in intensive agrolandscapes, disconnected from any coherent ecological network. Moreover, this study emphasizes the difficulty to modify functional assemblages of crops for purposes of ecosystem services development, especially for weed seed consumption, as well as the role of distance from the crops’ border in the shaping of crop carabid assemblages. creator: Emilie Pecheur creator: Julien Piqueray creator: Arnaud Monty creator: Marc Dufrêne creator: Grégory Mahy uri: https://doi.org/10.7717/peerj.8094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pecheur et al. title: Haplopelma hainanum venom induces inflammatory skin lesions link: https://peerj.com/articles/8264 last-modified: 2020-01-10 description: The Haplopelma hainanum is a species of theraphosid spider from China. Its large size and charming appearance make this species a popular pet. According to a previous study, theraphosid spider bites can induce pain, erythema, and edema in humans and can present more severely in domestic animals. The pathological consequences of envenomation by H. hainanum remain unclear. In this study, we investigated the effects and mechanisms of H. hainanum envenomation in mice. We showed that the venom induced slight swelling, intense inflammatory response, and increased the microvascular density in mice skin. Moreover, we found that 50 µg/ml of the spider’s venom induced IL-1β expression in both HaCaT cells and fibroblast cells, but repressed CXCL10 expression in fibroblasts. The venom significantly induced cell senescence and repressed cell proliferation and migration in both HaCaT cells and fibroblast cells. Finally, we examined the expression of Nav channel in HaCaT and fibroblast cells and found that H. hainanum venom effectively inhibited Na+ currents in HaCaT cells. Our study calls for further investigation of the pathological consequences and potential mechanisms of H. hainanum envenomation. This information might assist in the development of suitable therapy. creator: Zhili Deng creator: Yaling Wang creator: Wei Shi creator: Lei Zhou creator: San Xu creator: Ji Li creator: Yiya Zhang uri: https://doi.org/10.7717/peerj.8264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Deng et al. title: Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP link: https://peerj.com/articles/8271 last-modified: 2020-01-10 description: Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials. creator: Drew J. Duckett creator: Tara A. Pelletier creator: Bryan C. Carstens uri: https://doi.org/10.7717/peerj.8271 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Duckett et al. title: Morphological variation of leaf traits in the Ternstroemia lineata species complex (Ericales: Penthaphylacaceae) in response to geographic and climatic variation link: https://peerj.com/articles/8307 last-modified: 2020-01-10 description: Variation in leaf morphology is correlated with environmental variables, such as precipitation, temperature and soil composition. Several studies have pointed out that individual plasticity can largely explain the foliar phenotypic differences observed in populations due to climatic change and have suggested that the environment plays an important role in the evolution of plant species by selecting for phenotypic variation. Thus, the study of foliar morphology in plant populations can help us identify the environmental factors that have potentially influenced the process of species diversification. In this study, we analyzed morphological variation in the leaf traits of the Ternstroemia lineata species complex (Penthaphylacaceae) and its relation to climatic variables across the species distribution area to identify the patterns of morphological differentiation within this species complex. Based on the collected leaves of 270 individuals from 32 populations, we analyzed nine foliar traits using spatial interpolation models and multivariate statistics. A principal component analysis identified three main morphological traits (leaf length and two leaf shape variables) that were used to generate interpolated surface maps to detect discrete areas delimited by zones of rapid change in the values of the morphological traits. We identified a mosaic coarse-grain pattern of geographical distribution in the variation of foliar traits. According to the interpolation maps, we could define nine morphological groups and their geographic distributions. Longer leaves, spatulate leaves and the largest foliar area were located in sites with lower precipitation and higher seasonality of precipitation following a northwest–southeast direction and following significant latitudinal and longitudinal gradients. According to the phenogram of the relationships of the nine morphological groups based on morphological similarity, the putative species and subspecies of the T. lineata species complex did not show a clear pattern of differentiation. In this study, we found a complex pattern of differentiation with some isolated populations and some other contiguous populations differentiated by different traits. Further genetic and systematic studies are needed to clarify the evolutionary relationships in this species complex. creator: Othón Alcántara-Ayala creator: Ken Oyama creator: César A. Ríos-Muñoz creator: Gerardo Rivas creator: Santiago Ramirez-Barahona creator: Isolda Luna-Vega uri: https://doi.org/10.7717/peerj.8307 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alcántara-Ayala et al. title: 16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates link: https://peerj.com/articles/8417 last-modified: 2020-01-10 description: Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth. creator: Qiang Chen creator: William A. Meyer creator: Qiuwei Zhang creator: James F. White uri: https://doi.org/10.7717/peerj.8417 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chen et al. title: Effects of plant growth-promoting rhizobacteria on co-inoculation with Bradyrhizobium in soybean crop: a meta-analysis of studies from 1987 to 2018 link: https://peerj.com/articles/7905 last-modified: 2020-01-09 description: BackgroundThe co-inoculation of soybean with Bradyrhizobium and other plant growth-promoting rhizobacteria (PGPR) is considered a promising technology. However, there has been little quantitative analysis of the effects of this technique on yield variables. In this context, the present study aiming to provide a quantification of the effects of the co-inoculation of Bradyrhizobium and PGPR on the soybean crop using a meta-analysis approach.MethodsA total of 42 published articles were examined, all of which considered the effects of co-inoculation of PGPR and Bradyrhizobium on the number of nodules, nodule biomass, root biomass, shoot biomass, shoot nitrogen content, and grain yield of soybean. We also determined whether the genus of the PGPR used as co-inoculant, as well as the experimental conditions, altered the effect size of the PGPR.ResultsThe co-inoculation technology resulted in a significant increase in nodule number (11.40%), nodule biomass (6.47%), root biomass (12.84%), and shoot biomass (6.53%). Despite these positive results, no significant increase was observed in shoot nitrogen content and grain yield. The response of the co-inoculation varied according to the PGPR genus used as co-inoculant, as well as with the experimental conditions. In general, the genera Azospirillum, Bacillus, and Pseudomonas were more effective than Serratia. Overall, the observed increments were more pronounced under pot than that of field conditions. Collectively, this study summarize that co-inoculation improves plant development and increases nodulation, which may be important in overcoming nutritional limitations and potential stresses during the plant growth cycle, even though significant increases in grain yield have not been evidenced by this data meta-analysis. creator: Douglas M. Zeffa creator: Lucas H. Fantin creator: Alessandra Koltun creator: André L.M. de Oliveira creator: Maria P.B.A. Nunes creator: Marcelo G. Canteri creator: Leandro S.A. Gonçalves uri: https://doi.org/10.7717/peerj.7905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zeffa et al. title: Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude link: https://peerj.com/articles/8139 last-modified: 2020-01-09 description: Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams. creator: Sharmeen Rahman creator: Daniel Schmidt creator: Jane M. Hughes uri: https://doi.org/10.7717/peerj.8139 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rahman et al. title: Dendritic complexity change in the triple transgenic mouse model of Alzheimer’s disease link: https://peerj.com/articles/8178 last-modified: 2020-01-09 description: Alzheimer’s disease (AD) is an irreversible, neurodegenerative disease that is characterized by memory impairment and executive dysfunction. However, the change of fine structure of neuronal morphology remains unclear in the AD model mouse. In this study, high-resolution mouse brain sectional images were scanned by Micro-Optical Sectioning Tomography (MOST) technology and reconstructed three-dimensionally to obtain the pyramidal neurons. The method of Sholl analysis was performed to analyze the neurons in the brains of 6- and 12-month-old AD mice. The results showed that dendritic complexity was not affected in the entorhinal cortex between 6-month-old mice and 12-month-old mice. The dendritic complexity had increased in the primary motor cortex and CA1 region of hippocampus of 12- month-old mice compared with 6-month-old mice. On the contrary, dendritic complexity in the prefrontal cortex was decreased significantly between 6-month-old and 12-month-old mice. To our knowledge, this is the first study to provide high-resolution brain images of triple transgenic AD mice for statistically analyzing neuronal dendrite complexity by MOST technology to reveal the morphological changes of neurons during AD progression. creator: Yu Zhang creator: Zhenlong Xiao creator: Zhijun He creator: Junyu Chen creator: Xin Wang creator: Liang Jiang uri: https://doi.org/10.7717/peerj.8178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Spraying 6-BA could alleviate the harmful impacts of waterlogging on dry matter accumulation and grain yield of wheat link: https://peerj.com/articles/8193 last-modified: 2020-01-09 description: BackgroundThe middle and lower reaches of the Yangtze River plain produce the second highest amount of wheat in China; however, waterlogging is an important environmental factor that substantially affects the yield production of wheat (Triticum aestivum L.) in this region.MethodsIn this study, seven treatments were implemented, including no waterlogging and exogenous 6-benzylaminopurine (6-BA) as a control (CK); waterlogging at booting (BW), anthesis (AW) and 15 days after anthesis (DAA, FW); and spraying 6-BA before waterlogging at booting (BW-6BA), anthesis (AW-6BA) and 15 DAA (FW-6BA), to determine the ability of 6-BA to alleviate the harmful impact of waterlogging on aboveground biomass production and grain yield. The widely cultivated wheat cultivar “Zhengmai 9023” was used.ResultsThe results showed that more than 190.0 mm of rainfall, which accounted for approximately 45.0% of the precipitation over the whole wheat growing season, was distributed after the booting stage (April and May). In all waterlogged treatments, the photosynthetic rate, aboveground biomass and grain yield decreased, but the differences between the CK and the FW treatment were not significant. The grain yield decreased by 18.38%, 41.79% and 5.67% in the BW, AW and FW treatments, respectively. Spraying 6-BA before waterlogging enhanced the root activities after anthesis and then decreased the malondialdehyde concentrations of the flag leaves and the third leaf, increased the photosynthetic rate of the flag leaves and enhanced aboveground biomass and grain yield. Among the increments between the treatments, the increments between the BW and BW-6BA treatments were the largest, but between the FW and FW-6BA were smallest. In comparison to the other waterlogging treatments, the grain yields from the FW and FW-6BA treatments were significantly higher because of the higher kernel numbers per spike. The results indicated that waterlogging after the booting stage restrained the dry matter production of winter wheat, but spraying 6-BA before waterlogging slowed the plant senescence rate and reduced grain yield loss. creator: Xiaoyan Wang creator: Daoming Liu creator: Mingmei Wei creator: Jianguo Man uri: https://doi.org/10.7717/peerj.8193 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Elucidating physiological and biochemical alterations in giant duckweed (Spirodela polyrhiza L. Schleiden) under diethyl phthalate stress: insights into antioxidant defence system link: https://peerj.com/articles/8267 last-modified: 2020-01-09 description: BackgroundThe emollient properties of phthalates have led to their extensive production and intense use in plastic products. Owing to their weak covalent bonding with the plastic polymers, phthalates enter into the environment during their manufacturing, processing, disposal, consequently found their way directly into water sources, soil, and sediments.MethodsThe present study envisaged the toxic effects of diethyl phthalate (DEP) on physiological and biochemical attributes of Spirodela polyrhiza, when exposed to various concentrations of DEP (0, 10, 20, 40, 80, 100, 200, and 400 ppm) for short term exposure period of seven days.ResultsPlants of S. polyrhiza accumulated significant amount of DEP (112 mg kg−1 fw) when exposed to various concentrations of DEP for seven days. Results depicted that DEP toxicity significantly (p ≤ 0.05) affected growth parameters and pigments in treated S. polyrhiza as compared to control. Further, high doses of DEP (400 ppm) caused significant decrement in carbohydrate (86%), protein (76%) and elevation in MDA content (42%). Meanwhile, DEP altered the activities of antioxidant enzymes (SOD, CAT, APX, GPX and GR) along with the induction of enhanced levels of proline, electrolyte leakage and phenolic content. Scanning electron microscopic and confocal studies also confirmed oxidative stress in plants under DEP stress.ConclusionsPresent findings will help understand the accumulation, tolerance, and detoxification mechanisms of DEP by S. polyrhiza to counteract the effects of reactive oxygen species (ROS), along with the evaluation of environmental threat for aquatic plants in aquatic ecosystems. creator: Ritika Sharma creator: Rajinder Kaur uri: https://doi.org/10.7717/peerj.8267 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sharma and Kaur title: New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica link: https://peerj.com/articles/8268 last-modified: 2020-01-09 description: The middle–late Eocene of Antarctica was characterized by dramatic change as the continent became isolated from the other southern landmasses and the Antarctic Circumpolar Current formed. These events were crucial to the formation of the permanent Antarctic ice cap, affecting both regional and global climate change. Our best insight into how life in the high latitudes responded to this climatic shift is provided by the fossil record from Seymour Island, near the eastern coast of the Antarctic Peninsula. While extensive collections have been made from the La Meseta and Submeseta formations of this island, few avian taxa other than penguins have been described and mammalian postcranial remains have been scarce. Here, we report new fossils from Seymour Island collected by the Antarctic Peninsula Paleontology Project. These include a mammalian metapodial referred to Xenarthra and avian material including a partial tarsometatarsus referred to Gruiformes (cranes, rails, and allies). Penguin fossils (Sphenisciformes) continue to be most abundant in new collections from these deposits. We report several penguin remains including a large spear-like mandible preserving the symphysis, a nearly complete tarsometatarsus with similarities to the large penguin clade Palaeeudyptes but possibly representing a new species, and two small partial tarsometatarsi belonging to the genus Delphinornis. These findings expand our view of Eocene vertebrate faunas on Antarctica. Specifically, the new remains referred to Gruiformes and Xenarthra provide support for previously proposed, but contentious, earliest occurrence records of these clades on the continent. creator: Sarah N. Davis creator: Christopher R. Torres creator: Grace M. Musser creator: James V. Proffitt creator: Nicholas M.A. Crouch creator: Ernest L. Lundelius creator: Matthew C. Lamanna creator: Julia A. Clarke uri: https://doi.org/10.7717/peerj.8268 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Davis et al. title: Analysis of the RNA virome of basal hexapods link: https://peerj.com/articles/8336 last-modified: 2020-01-09 description: The diversity and evolution of RNA viruses has been well studied in arthropods and especially in insects. However, the diversity of RNA viruses in the basal hexapods has not been analysed yet. To better understand their diversity, evolutionary histories and genome organizations, we searched for RNA viruses in transcriptome and genome databases of basal hexapods. We discovered  40 novel RNA viruses, some of which are also present as endogenous viral elements derived from RNA viruses. Here, we demonstrated that basal hexapods host 14 RNA viral clades that have been recently identified in invertebrates. The following RNA viral clades are associated with basal hexapods: Reo, Partiti-Picobirna, Toti-Chryso, Mono-Chu, Bunya-Arena, Orthomyxo, Qinvirus, Picorna-Calici, Hepe-Virga, Narna-Levi, Tombus-Noda, Luteo-Sobemo, Permutotetra and Flavi. We have found representatives of the nine RNA viral clades that are present as endogenous genomic copies in the genomes of Machilis (Monocondylia) and Catajapyx (Diplura). Our study provided a first insight into the diversity of RNA viruses in basal hexapods and demonstrated that the basal hexapods possess quite high diversity of RNA viral clades. creator: Sabina Ott Rutar creator: Dusan Kordis uri: https://doi.org/10.7717/peerj.8336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ott Rutar and Kordis title: Temporal dynamics of the hummingbird-plant interaction network of a dry forest in Chamela, Mexico: a 30-year follow-up after two hurricanes link: https://peerj.com/articles/8338 last-modified: 2020-01-09 description: BackgroundInteractions among species are a driving force of community structure. The species composition of animal-plant interaction networks can be highly dynamic on a temporal scale, even though the general network structure is usually not altered. However, few studies have examined how interaction networks change over long periods of time, particularly after extreme natural events. We analyzed herein the structure of the hummingbird-plant interaction network in a dry forest of Chamela, Mexico, comparing the structure in 1985–1986 with that in 2016–2017 following the passage of two hurricanes (category 2 Jova in 2011 and category 4 Patricia in 2015).MethodsThe fieldwork was carried out in the Chamela-Cuixmala Biosphere Reserve in Jalisco, Mexico. In the last 30 years, three severe drought events and two hurricanes have affected this region. Previously, from 1985–1986, hummingbird-plant interactions were recorded monthly for one year in the study area. Then, from 2016–2017, we replicated the sampling in the same localities. We compared the network parameters describing the plant-hummingbird interactions of each period using adjacency matrices.ResultsWe found differences in the number and identity of interacting species, especially plants. The plant species missing in 2016–2017 were either the least connected in the original network (1985–1986) or belonged to groups such as cacti, epiphytes, or trees. The new plant species incorporated in the 2016–2017 network were herbs, vines, and shrubs, or other species barely connected. These changes in the composition are consistent with reports on vegetation damage after strong hurricanes at other study sites. Conversely, all hummingbird species remained in the network, with the exception of Heliomaster constantii, which was primarily connected to a plant species absent in the 2016–2017 network. Migratory and habitat generalist species (i.e., Archilochus spp.) showed higher abundances following the disturbance events.ConclusionsMost of the parameters describing the hummingbird-plant network structure remained unchanged after 30 years, with the exception of an increase in plant robustness and hummingbird niche overlap. However, the network’s generalist core was affected by the loss of some species. Also, core plant species such as Ipomoea bracteata, Combretum farinosum, and Justicia candicans were found to be important for maintaining the hummingbird-plant interaction network. The temporal perspective of this study provides unique insights into the conservation of plant-hummingbird networks across time and extreme natural events. creator: Sergio Díaz Infante creator: Carlos Lara creator: Maria del Coro Arizmendi uri: https://doi.org/10.7717/peerj.8338 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Díaz Infante et al. title: A multiomics comparison between endometrial cancer and serous ovarian cancer link: https://peerj.com/articles/8347 last-modified: 2020-01-09 description: BackgroundEndometrial carcinoma (EC) and serous ovarian carcinoma (OvCa) are both among the common cancer types in women. EC can be divided into two subtypes, endometroid EC and serous-like EC, with distinct histological characterizations and molecular phenotypes. There is an increasing awareness that serous-like EC resembles serous OvCa in genetic landscape, but a clear relationship between them is still lacking.MethodsHere, we took advantage of the large-scale molecular profiling of The Cancer Genome Atlas(TCGA) to compare the two EC subtypes and serous OvCa. We used bioinformatics data analytic methods to systematically examine the somatic mutation (SM) and copy number alteration (SCNA), gene expression, pathway activities, survival gene signatures and immune infiltration. Based on these quantifiable molecular characterizations, we asked whether serous-like EC should be grouped more closely to serous OvCa, based on the context of being serous-like; or if should be grouped more closely to endometroid EC, based on the same organ origin.ResultsWe found that although serous-like EC and serous OvCa share some common genotypes, including mutation and copy number alteration, they differ in molecular phenotypes such as gene expression and signaling pathway activity. Moreover, no shared prognostic gene signature was found, indicating that they use unique genes governing tumor progression. Finally, although the endometrioid EC and serous OvCa are both highly immune infiltrated, the immune cell composition in serous OvCa is mostly immune suppressive, whereas endometrioid EC has a higher level of cytotoxic immune cells. Overall, our genetic aberration and molecular phenotype characterizations indicated that serous-like EC and serous OvCa cannot be simply treated as a simple “serous” cancer type. In particular, additional attention should be paid to their unique gene activities and tumor microenvironments for novel targeted therapy development. creator: Hui Zhong creator: Huiyu Chen creator: Huahong Qiu creator: Chen Huang creator: Zhihui Wu uri: https://doi.org/10.7717/peerj.8347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhong et al. title: Age-related alterations in inhibitory control investigated using the minimally delayed oculomotor response task link: https://peerj.com/articles/8401 last-modified: 2020-01-09 description: Healthy, older adults are widely reported to experience cognitive decline, including impairments in inhibitory control. However, this general proposition has recently come under scrutiny because ageing effects are highly variable between individuals, are task dependent, and are sometimes not distinguished from general age-related slowing. We recently developed the minimally delayed oculomotor response (MDOR) task in which participants are presented with a simple visual target step, and instructed to saccade not to the target when it appears (a prosaccade response), but when it disappears (i.e. on target offset). Varying the target display duration (TDD) prevents offset timing being predictable from the time of target onset, and saccades prior to the offset are counted as errors. A comparison of MDOR task performance in a group of 22 older adults (mean age 62 years, range 50–72 years) with that in a group of 39 younger adults (22 years, range 19–27 years) demonstrated that MDOR latency was significantly increased in the older group by 34–68 ms depending on TDD. However, when MDOR latencies were corrected by subtracting the latency observed in a standard prosaccade task, the latency difference between groups was abolished. There was a larger latency modulation with TDD in the older group which was observed even when their generally longer latencies were taken into account. Error rates were significantly increased in the older group. An analysis of the timing distribution of errors demonstrated that most errors were failures to inhibit responses to target onsets. When error distributions were used to isolate clear inhibition failures from other types of error, the older group still exhibited significantly higher error rates as well as a higher residual error rate. Although MDOR latency in older participants may largely reflect a general slowing in the oculomotor system with age, both the latency modulation and error rate results are consistent with an age-related inhibitory control deficit. How this relates to performance on other inhibitory control tasks remains to be investigated. creator: Paul C. Knox creator: Nikitha Pasunuru uri: https://doi.org/10.7717/peerj.8401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Knox and Pasunuru title: Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study link: https://peerj.com/articles/8366 last-modified: 2020-01-08 description: PurposeThe iPro Cube is a small portable point-of-care device designed to analyse salivary markers of stress in a user-friendly manner (e.g., fast, convenient). Our aim was to test the reliability and validity of the iPro Cube to measure salivary cortisol and α-amylase as compared to the common laboratory standard method (ELISA immunoassay) prior to and after moderate intensity exercise.MethodsThe study was a repeated measures, pre-registered design, and statistical framework that incorporated prior knowledge directly into the estimation process. Twenty-nine individuals (age = 27.4 ± 6.6 y; body-mass = 70.8 ± 11.3 kg; height = 1.74 ± 0.92 m; 18 males) completed a single PWC75%HRmax, with repeated measures of salivary cortisol and -amylase pre, immediately post, and 30 min post-exercise.ResultsCorrelation between the iPro Cube and laboratory-based assessments of salivary cortisol was moderate-to-large (0.53 > r < 0.81) across all three testing points. In contrast, correlation between the iPro Cube and laboratory-based assessments of -amylase was small-to-moderate (0.25 > r < 0.46). We found a large correlation between duplicate samples of iPro Cube cortisol assessment (0.75 > r < 0.82), and a moderate-to-large correlation for -amylase (0.51> r < 0.77).ConclusionsThe iPro Cube is capable of taking measures of salivary cortisol that are moderately correlated to values obtained via ELISA immunoassay, however the unit underestimates salivary cortisol and overestimates salivary -amylase at rest and post-moderate intensity exercise. It is recommended that researchers continue using standard laboratory techniques to assess these salivary stress markers. creator: Kagan J. Ducker creator: Robin L.J. Lines creator: Michael T. Chapman creator: Peter Peeling creator: Alannah K.A. McKay creator: Daniel F. Gucciardi uri: https://doi.org/10.7717/peerj.8366 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ducker et al. title: Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics link: https://peerj.com/articles/8374 last-modified: 2020-01-08 description: The use of zebrafish larvae has aroused wide interest in the medical field for its potential role in the development of new therapies. The larvae grow extremely quickly and the embryos are nearly transparent which allows easy examination of its internal structures using fluorescent imaging techniques. Medical treatment of zebrafish larvae can directly influence its swimming behaviours. These behaviour changes are related to functional changes of central nervous system and transformations of the zebrafish body such as muscle mechanical power and force variation, which cannot be measured directly by pure experiment observation. To quantify the influence of drugs on zebrafish larvae swimming behaviours and energetics, we have developed a novel methodology to exploit intravital changes based on observed zebrafish locomotion. Specifically, by using an in-house MATLAB code to process the recorded live zebrafish swimming video, the kinematic locomotion equation of a 3D zebrafish larvae was obtained, and a customised Computational Fluid Dynamics tool was used to solve the fluid flow around the fish model which was geometrically the same as experimentally tested zebrafish. The developed methodology was firstly verified against experiment, and further applied to quantify the fish internal body force, torque and power consumption associated with a group of normal zebrafish larvae vs. those immersed in acetic acid and two neuroactive drugs. As indicated by our results, zebrafish larvae immersed in 0.01% acetic acid display approximately 30% higher hydrodynamic power and 10% higher cost of transport than control group. In addition, 500 μM diphenylhydantoin significantly decreases the locomotion activity for approximately 50% lower hydrodynamic power, whereas 100 mg/L yohimbine has not caused any significant influences on 5 dpf zebrafish larvae locomotion. The approach has potential to evaluate the influence of drugs on the aquatic animal’s behaviour changes and thus support the development of new analgesic and neuroactive drugs. creator: Zhenkai Zhao creator: Gen Li creator: Qing Xiao creator: Hui-Rong Jiang creator: Gabriel Mbuta Tchivelekete creator: Xinhua Shu creator: Hao Liu uri: https://doi.org/10.7717/peerj.8374 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhao et al. title: DNA methylation profiling in recurrent miscarriage link: https://peerj.com/articles/8196 last-modified: 2020-01-07 description: Recurrent miscarriage (RM) is a complex clinical problem. However, specific diagnostic biomarkers and candidate regulatory targets have not yet been identified. To explore RM-related biological markers and processes, we performed a genome-wide DNA methylation analysis using the Illumina Infinium HumanMethylation450 array platform. Methylation variable positions and differentially methylated regions (DMRs) were selected using the Limma package in R language. Thereafter, gene ontology (GO) enrichment analysis and pathway enrichment analysis were performed on these DMRs. A total of 1,799 DMRs were filtered out between patients with RM and healthy pregnant women. The GO terms were mainly related to system development, plasma membrane part, and sequence-specific DNA binding, while the enriched pathways included cell adhesion molecules, type I diabetes mellitus, and ECM–receptor interactions. In addition, genes, including ABR, ALCAM, HLA-E, HLA-G, and ISG15, were obtained. These genes may be potential candidates for diagnostic biomarkers and possible regulatory targets in RM. We then detected the mRNA expression levels of the candidate genes. The mRNA expression levels of the candidate genes in the RM group were significantly higher than those in the control group. However, additional research is still required to confirm their potential roles in the occurrence of RM. creator: Li Pi creator: Zhaofeng Zhang creator: Yan Gu creator: Xinyue Wang creator: Jianmei Wang creator: Jianhua Xu creator: Junwei Liu creator: Xuan Zhang creator: Jing Du uri: https://doi.org/10.7717/peerj.8196 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pi et al. title: Soil aggregate size influences the impact of inorganic nitrogen deposition on soil nitrification in an alpine meadow of the Qinghai–Tibet Plateau link: https://peerj.com/articles/8230 last-modified: 2020-01-07 description: BackgroundAmmonium (NH4+) and nitrate (NO3−) are two inorganic forms of nitrogen (N) that are deposited from the atmosphere into soil systems. As the substrate and product of soil nitrification, these two forms of inorganic nitrogen will affect or be affected by the soil net nitrification rate (Nr). Our knowledge regarding soil nitrification is mainly derived from studies with bulk soil. However, soil is composed of different aggregate fractions, which may have an important impact on Nr.MethodsIn 2017, we collected soil samples from an alpine meadow of the Qinghai–Tibet Plateau and separated them into four soil aggregates (2–4, 1–2, 0.25–1, and <0.25 mm) using the dry sieving method. The four soil aggregate sizes amended with the 2 N deposition forms (NH4+-N and NO3−-N) were then incubated at 25 °C for 28 days, and the soil aggregates for each treatment were collected on day 0, 7, 14, 21, and 28 to determine the NO3−-N concentration. The soil Nr and contribution of soil aggregates to the nitrification rate in the bulk soil were calculated.ResultsThere were differences in the physicochemical properties of the soil aggregates. The addition of N and aggregate size had strong effects on soil Nr, which were significantly increased under high levels of NH4+ addition across all soil aggregates. The Nr during the 4 week incubation period differed among aggregate sizes. Nr in the 2–4 mm aggregates was higher than in the other aggregates, which was correlated with the maximum values of the soil porosity observed in the 2–4 mm aggregates. Furthermore, almost half of the soil was composed of aggregates of <0.25 mm, indicating that the <0.25 mm aggregates made a higher contribution to the nitrification rate in the bulk soil than the other aggregates, even though these aggregates had a lower nitrification ability. Overall, our study revealed that the soil nitrification rate was influenced by both the N addition and soil aggregates, and that the 2–4 mm aggregates had a dominant effect on the response of soil N transformation processes to future nitrogen deposition in the alpine meadow. creator: Jingjing Li creator: Chao Yang creator: Xiaoli Liu creator: Hanzhong Ji creator: Xinqing Shao uri: https://doi.org/10.7717/peerj.8230 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: A pilot study on searching for peri-nuclear NeuN-positive cells link: https://peerj.com/articles/8254 last-modified: 2020-01-07 description: The aim of this study was to find out neuron (-like) cells in peripheral organs by cell markers in rats. Adult male Sprague-Dawley rats were anaesthetized. Their organs including brain, heart, lung, liver, kidney, stomach, duodenum, and ileum were harvested. The mRNA and protein in these organs were extracted. RNA sequencing (RNA-Seq) was carried out, and NeuN, a “specific” marker for neuronal soma, was assayed with Western blotting. The sections of the aforementioned organs were obtained after a routine fixation (4% methanal)-dehydration (ethanol)-embedding (paraffin) process. NeuN in the sections and seven non-neuronal cell lines was analyzed by immunofluorescence (IF) or immunohistochemistry (IHC). Neuronal markers, such as Eno2, NeuN (Rbfox3), choline acetyltransferase (Chat), as well as tyrosine hydroxylase (Th), and neuronal-glial markers, e.g., glial fibrillary acidic protein (Gfap), S100b, 2′, 3′-cyclic nucleotide 3′-phosphodiesterase (Cnp), and other related markers, were positively expressed in all the organs at mRNA level. NeuN was further analyzed by Western blotting. The IF and IHC assays showed that NeuN-positive cells were distributed in all the peripheral tissues (mainly peri-nuclear NeuN-positive cells) though with different patterns from that in brain (nuclear NeuN-positive cells), and a NeuN-negative tissue could not be found. Especially, NeuN and Myl3 co-expressed in the cytoplasm of myocardial cells, suggesting that NeuN could possess other functions than neuronal differentiation. Also, the protein was positively expressed in seven non-neuronal cell lines. Our findings suggested that NeuN-positive cells exist widely, and without identification of its distribution pattern, the specificity of NeuN for neurons could be limited. creator: Yun Yu creator: Meiyu Wu creator: Nan Zhang creator: Hua Yin creator: Bin Shu creator: Weigang Duan uri: https://doi.org/10.7717/peerj.8254 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yu et al. title: Development of an autophagy-related gene prognostic signature in lung adenocarcinoma and lung squamous cell carcinoma link: https://peerj.com/articles/8288 last-modified: 2020-01-07 description: PurposeThere is plenty of evidence showing that autophagy plays an important role in the biological process of cancer. The purpose of this study was to establish a novel autophagy-related prognostic marker for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC).MethodsThe mRNA microarray and clinical data in The Cancer Genome Atlas (TCGA) were analyzed by using a univariate Cox proportional regression model to select candidate autophagy-related prognostic genes. Bioinformatics analysis of gene function using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) platforms was performed. A multivariate Cox proportional regression model helped to develop a prognostic signature from the pool of candidate genes. On the basis of this prognostic signature, we could divide LUAD and LUSC patients into high-risk and low-risk groups. Further survival analysis demonstrated that high-risk patients had significantly shorter disease-free survival (DFS) than low-risk patients. The signature which contains six autophagy-related genes (EIF4EBP1, TP63, BNIP3, ATIC, ERO1A and FADD) showed good performance for predicting the survival of LUAD and LUSC patients by having a better Area Under Curves (AUC) than other clinical parameters. Its efficacy was also validated by data from the Gene Expression Omnibus (GEO) database.ConclusionCollectively, the prognostic signature we proposed is a promising biomarker for monitoring the outcomes of LUAD and LUSC. creator: Jie Zhu creator: Min Wang creator: Daixing Hu uri: https://doi.org/10.7717/peerj.8288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhu et al. title: EEG alpha activity increased in response to transcutaneous electrical nervous stimulation in young healthy subjects but not in the healthy elderly link: https://peerj.com/articles/8330 last-modified: 2020-01-07 description: Transcutaneous Electrical Nerve Stimulation (TENS) is used not only in the treatment of pain but also in the examination of sensory functions. With aging, there is decreased sensitivity to somatosensory stimuli. It is essential to examine the effect of TENS application on the sensory functions in the brain by recording the spontaneous electroencephalogram (EEG) activity and the effect of aging on the sensory functions of the brain during the application. The present study aimed to investigate the effect of the application of TENS on the brain’s electrical activity and the effect of aging on the sensory functions of the brain during application of TENS. A total of 15 young (24.2 ± 3.59) and 14 elderly (65.64 ± 4.92) subjects were included in the study. Spontaneous EEG was recorded from 32 channels during TENS application. Power spectrum analysis was performed by Fast Fourier Transform in the alpha frequency band (8–13 Hz) for all subjects. Repeated measures of analysis of variance was used for statistical analysis (p < 0.05). Young subjects had increased alpha power during the TENS application and had gradually increased alpha power by increasing the current intensity of TENS (p = 0.035). Young subjects had higher alpha power than elderly subjects in the occipital and parietal locations (p = 0.073). We can, therefore, conclude that TENS indicated increased alpha activity in young subjects. Young subjects had higher alpha activity than elderly subjects in the occipital and somatosensory areas. To our knowledge, the present study is one of the first studies examining the effect of TENS on spontaneous EEG in healthy subjects. Based on the results of the present study, TENS may be used as an objective method for the examination of sensory impairments, and in the evaluative efficiency of the treatment of pain conditions. creator: Ebru Yıldırım creator: Bahar Güntekin creator: Lütfü Hanoğlu creator: Candan Algun uri: https://doi.org/10.7717/peerj.8330 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yıldırım et al. title: Feasibility of assessing ultra-short-term pulse rate variability from video recordings link: https://peerj.com/articles/8342 last-modified: 2020-01-07 description: ObjectivesRemote photoplethysmography (rPPG) is a promising non-contact measurement technique for assessing numerous physiological parameters: pulse rate, pulse rate variability (PRV), respiratory rate, pulse wave velocity, blood saturation, blood pressure, etc. To justify its use in ultra-short-term (UST) PRV analysis, which is of great benefit for several healthcare applications, the agreement between rPPG- and PPG-derived UST-PRV metrics was studied.ApproachThree time-domain metrics—standard deviation of normal-to-normal (NN) intervals (SDNN), root mean square of successive NN interval differences (RMSSD), and the percentage of adjacent NN intervals that differ from each other by more than 50 ms (pNN50)—were extracted from 56 video recordings in a publicly available data set. The selected metrics were calculated on the basis of three groups of 10 s recordings and their average, two groups of 30 s recordings and their average, and a group of 60 s recordings taken from the full-length recordings and then compared with metrics derived from the corresponding reference (PPG) pulse waveform signals by using correlation and effect size parameters, and Bland–Altman plots.Main resultsThe results show there is stronger agreement as the recording length increases for SDNN and RMSSD, yet there is no significant change for pNN50. The agreement parameters reach r = 0.841 (p < 0.001), r = 0.529 (p < 0.001), and r = 0.657 (p < 0.001), estimated median bias −1.52, −2.28 ms and −1.95% and a small effect size for SDNN, RMSSD, and pNN50 derived from the 60 s recordings, respectively.SignificanceRemote photoplethysmography-derived UST-PRV metrics manage to capture UST-PRV metrics derived from reference (PPG) recordings well. This feature is highly desirable in numerous applications for the assessment of one’s health and well-being. In future research, the validity of rPPG-derived UST-PRV metrics compared to the gold standard electrocardiography recordings is to be assessed. creator: Miha Finžgar creator: Primož Podržaj uri: https://doi.org/10.7717/peerj.8342 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Finžgar and Podržaj title: Exercise mode and attentional networks in older adults: a cross-sectional study link: https://peerj.com/articles/8364 last-modified: 2020-01-07 description: BackgroundPrevious studies have indicated that physical exercise enhances attentional function; however, the relationship between exercise mode and attentional networks has not been clarified for older adults (>60 years old). This study aimed to investigate the relationship between attentional networks and different exercise modes in older adults.MethodsTwo hundred and fifty-nine participants aged between 60 to 81 years were enrolled and classified into three groups (closed-skill group, open-skill group, or sedentary control group) using an exercise-related questionnaire. All participants completed an attention network test (ANT), which measured executive control, orienting, and alerting networks.ResultsThe open-skill group had significantly higher executive network efficiency compared to the closed-skill (p < 0.01) and sedentary (p < 0.01) groups. The closed-skill group had significantly higher values compared to the sedentary control group (p < 0.05). Differences were not detected among groups for alerting and orienting networks (p > 0.05). The open-skill group had significantly higher values compared to the sedentary control group regarding proportion score of executive network (p < 0.01). In comparison, no significant differences were detected among groups for proportion scores of alerting and orienting networks.ConclusionThis study extends current knowledge by demonstrating that open-skill exercises selectively enhance the executive control of attentional networks in older adults. Open-skill exercises combines physical exercise and cognitive training, potentially representing a more effective exercise mode to maintain or enhance attentional function in older adults. creator: Biye Wang creator: Wei Guo uri: https://doi.org/10.7717/peerj.8364 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang and Guo title: Risk of phosphorus losses in surface runoff from agricultural land in the Baltic Commune of Puck in the light of assessment performed on the basis of DPS indicator link: https://peerj.com/articles/8396 last-modified: 2020-01-07 description: BackgroundIn order to counteract the eutrophication of waterways and reservoirs, a basic risk assessment of phosphorus (P) losses in the surface runoff from agricultural land should be included in water management plans. A new method has been developed to assess the risk of P losses by estimating the degree of P saturation (DPS) based on the P concentration of the water extract water-soluble P.MethodsThe risk of P losses in surface runoff from agricultural land in the Puck Commune on the Baltic Sea Coast was assessed with the DPS method. The results were compared to an agronomic interpretation of the soil test P concentration (STP). Research was conducted on mineral and organic soils from 50 and 11 separate agricultural plots with a total area of 133.82 and 37.23 ha, respectively. Phosphorus was extracted from the collected samples using distilled water on all soil samples, acid ammonium lactate on mineral soils, and an extract of 0.5 mol HCl·dm−3 on organic soils. The organic matter content and pH values were also determined. The results of the P content in the water extracted from the soils were converted into DPS values, which were then classified by appropriate limit intervals.Results and discussionThere was a high risk of P losses from the soil via surface runoff in 96.7% of the agricultural parcels tested (96% of plots with mineral soils and 100% of plots with organic soils). Simultaneously, a large deficiency of plant-available P was found in soils from 62% of agricultural plots. These data indicate that the assessment of P concentration in soils made on the basis of an environmental soil P test conflicts with the assessment made based on STP and create a cognitive dissonance. The risk level of P losses through surface runoff from the analyzed plots as determined by the DPS indicator is uncertain. This uncertainty is increased as the DPS index is not correlated with other significant factors in P runoff losses, such as the type of crop and area inclination. creator: Stefan Pietrzak creator: Grażyna Pazikowska-Sapota creator: Grażyna Dembska creator: Lidia Anita Dzierzbicka-Glowacka creator: Dominika Juszkowska creator: Zuzanna Majewska creator: Marek Urbaniak creator: Dominika Ostrowska creator: Agnieszka Cichowska creator: Katarzyna Galer-Tatarowicz uri: https://doi.org/10.7717/peerj.8396 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pietrzak et al. title: The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico link: https://peerj.com/articles/8102 last-modified: 2020-01-06 description: BackgroundStenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents.MethodStenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed.ResultsAnthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil. creator: Temidayo O. Elufisan creator: Isabel C. Rodríguez-Luna creator: Omotayo Opemipo Oyedara creator: Alejandro Sánchez-Varela creator: Armando Hernández-Mendoza creator: Edgar Dantán Gonzalez creator: Alma D. Paz-González creator: Kashif Muhammad creator: Gildardo Rivera creator: Miguel Angel Villalobos-Lopez creator: Xianwu Guo uri: https://doi.org/10.7717/peerj.8102 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Elufisan et al. title: Assessment of a Takagi–Sugeno-Kang fuzzy model assembly for examination of polyphasic loglinear allometry link: https://peerj.com/articles/8173 last-modified: 2020-01-06 description: BackgroundThe traditional allometric analysis relies on log- transformation to contemplate linear regression in geometrical space then retransforming to get Huxley’s model of simple allometry. Views assert this induces bias endorsing multi-parameter complex allometry forms and nonlinear regression in arithmetical scales. Defenders of traditional approach deem it necessary since generally organismal growth is essentially multiplicative. Then keeping allometry as originally envisioned by Huxley requires a paradigm of polyphasic loglinear allometry. A Takagi-Sugeno-Kang fuzzy model assembles a mixture of weighted sub models. This allows direct identification of break points for transition between phases. Then, this paradigm is seamlessly appropriate for efficient allometric examination of polyphasic loglinear allometry patterns. Here, we explore its suitability.MethodsPresent fuzzy model embraces firing strength weights from Gaussian membership functions and linear consequents. Weights are identified by subtractive clustering and consequents through recursive least squares or maximum likelihood. Intersection of firing strength factors set criterion to estimate breakpoints. A multi-parameter complex allometry model follows by adapting firing strengths by composite membership functions and linear consequents in arithmetical space.ResultsTakagi-Sugeno-Kang surrogates adapted complexity depending on analyzed data set. Retransformation results conveyed reproducibility strength of similar proxies identified in arithmetical space. Breakpoints were straightforwardly identified. Retransformed form implies complex allometry as a generalization of Huxley’s power model involving covariate depending parameters. Huxley reported a breakpoint in the log–log plot of chela mass vs. body mass of fiddler crabs (Uca pugnax), attributed to a sudden change in relative growth of the chela approximately when crabs reach sexual maturity. G.C. Packard implied this breakpoint as putative. However, according to present fuzzy methods existence of a break point in Huxley’s data could be validated.ConclusionsOffered scheme bears reliable analysis of zero intercept allometries based on geometrical space protocols. Endorsed affine structure accommodates either polyphasic or simple allometry if whatever turns required. Interpretation of break points characterizing heterogeneity is intuitive. Analysis can be achieved in an interactive way. This could not have been obtained by relying on customary approaches. Besides, identification of break points in arithmetical scale is straightforward. Present Takagi-Sugeno-Kang arrangement offers a way to overcome the controversy between a school considering a log-transformation necessary and their critics claiming that consistent results can be only obtained through complex allometry models fitted by direct nonlinear regression in the original scales. creator: Hector A. Echavarria-Heras creator: Juan R. Castro-Rodriguez creator: Cecilia Leal-Ramirez creator: Enrique Villa-Diharce uri: https://doi.org/10.7717/peerj.8173 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Echavarria-Heras et al. title: The Rametrix™ PRO Toolbox v1.0 for MATLAB® link: https://peerj.com/articles/8179 last-modified: 2020-01-06 description: BackgroundExisting tools for chemometric analysis of vibrational spectroscopy data have enabled characterization of materials and biologicals by their broad molecular composition. The Rametrix™ LITE Toolbox v1.0 for MATLAB® is one such tool available publicly. It applies discriminant analysis of principal components (DAPC) to spectral data to classify spectra into user-defined groups. However, additional functionality is needed to better evaluate the predictive capabilities of these models when “unknown” samples are introduced. Here, the Rametrix™ PRO Toolbox v1.0 is introduced to provide this capability.MethodsThe Rametrix™ PRO Toolbox v1.0 was constructed for MATLAB® and works with the Rametrix™ LITE Toolbox v1.0. It performs leave-one-out analysis of chemometric DAPC models and reports predictive capabilities in terms of accuracy, sensitivity (true-positives), and specificity (true-negatives). Rametrix™PRO is available publicly through GitHub under license agreement at: https://github.com/SengerLab/RametrixPROToolbox. Rametrix™ PRO was used to validate Rametrix™ LITE models used to detect chronic kidney disease (CKD) in spectra of urine obtained by Raman spectroscopy. The dataset included Raman spectra of urine from 20 healthy individuals and 31 patients undergoing peritoneal dialysis treatment for CKD.ResultsThe number of spectral principal components (PCs) used in building the DAPC model impacted the model accuracy, sensitivity, and specificity in leave-one-out analyses. For the dataset in this study, using 35 PCs in the DAPC model resulted in 100% accuracy, sensitivity, and specificity in classifying an unknown Raman spectrum of urine as belonging to a CKD patient or a healthy volunteer. Models built with fewer or greater number of PCs showed inferior performance, which demonstrated the value of Rametrix™ PRO in evaluating chemometric models constructed with Rametrix™ LITE. creator: Ryan S. Senger creator: John L. Robertson uri: https://doi.org/10.7717/peerj.8179 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Senger and Robertson title: sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data link: https://peerj.com/articles/8214 last-modified: 2020-01-06 description: Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems. creator: Arnold Kuzniar creator: Jason Maassen creator: Stefan Verhoeven creator: Luca Santuari creator: Carl Shneider creator: Wigard P. Kloosterman creator: Jeroen de Ridder uri: https://doi.org/10.7717/peerj.8214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kuzniar et al. title: Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species link: https://peerj.com/articles/8251 last-modified: 2020-01-06 description: Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species. creator: Zhanjun Wang creator: Beibei Xu creator: Bao Li creator: Qingqing Zhou creator: Guiyi Wang creator: Xingzhou Jiang creator: Chenchen Wang creator: Zhongdong Xu uri: https://doi.org/10.7717/peerj.8251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China link: https://peerj.com/articles/8256 last-modified: 2020-01-06 description: Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 108 gene copies (g-soil−1) to 2.23 × 108 gene copies (g-soil−1) and 5.45 × 108 gene copies (g-soil−1) to 3.30 × 107 gene copies (g-soil−1), respectively. Five environmental variables, namely, ORP, DO, NO${}_{3}^{-}$3−, Temp, and NH${}_{4}^{+}$4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment. creator: Amjed Ginawi creator: Lixiao Wang creator: Huading Wang creator: Bingbing Yu creator: Yan Yunjun uri: https://doi.org/10.7717/peerj.8256 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ginawi et al. title: Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development link: https://peerj.com/articles/8259 last-modified: 2020-01-06 description: Grafting has been reported as a factor that influences fruit quality. However, a comprehensive study of the metabolic profile related to fruit quality and the underlying molecular mechanism in grafted watermelon has not been carried out. Metabolomics and transcriptome analysis were performed on both pumpkin-grafted watermelon and ungrafted watermelon at different developmental stages. In total, 56 primary metabolites were identified with either high or low abundance between ungrafted and pumpkin-grafted watermelon. The results indicated that ornithine, arginine, lysine (amino acids), glucose, sucrose, glucosamine (sugars), malic acid, fumaric acid and succinic acid (organic acids) were among the dominant metabolites influencing fruit quality. Additionally, comparative RNA sequence analysis on grafted and ungrafted watermelon yielded 729, 174, 128 and 356 differentially expressed genes at 10, 18, 26 and 34 days after pollination (DAP), respectively. Functional annotations of these genes indicated that grafting significantly altered the biological and metabolic processes related to fruit quality. Our comparative metabolomics and transcriptome analysis revealed that FBA2, FK, SuSy, SPS, IAI, AI and sugar transporter gene (SWT3b) might play a central role in the accumulation of glucose and sucrose, whereas higher malic acid content was attributed to high down regulation of ALMT13 and ALMT8 in pumpkin-grafted watermelon. Changes in the ornithine, glutamine, alanine, tyrosine, valine, asparagine, phenylalanine, arginine and tryptophan contents were consistent with the transcript level of their metabolic genes such as NAOD, GS, AGT, TaT, aDH1, OGDH, aDC, 4CL 1, PaL, CaT and two nitrate transporter genes (NRT1) in pumpkin-grafted watermelon. This study provides the basis for understanding the graft-responsive changes in the metabolic profile and regulatory mechanism related to fruit quality. creator: Ali Aslam creator: Shengjie Zhao creator: Muhammad Azam creator: Xuqiang Lu creator: Nan He creator: Bingbing Li creator: Junling Dou creator: Hongju Zhu creator: Wenge Liu uri: https://doi.org/10.7717/peerj.8259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Aslam et al. title: Diagnosis and treatment of epididymal tuberculosis: a review of 47 cases link: https://peerj.com/articles/8291 last-modified: 2020-01-06 description: ObjectiveTo analyze the clinical manifestations, diagnosis and treatment outcomes in a series of patients with epididymal tuberculosis.MethodsThis study is a retrospective data analysis of 47 cases of histologically-confirmed epididymal tuberculosis in patients treated at our hospital from November 2012 to December 2018.ResultsThe average age of the patients was approximately 42 years. The epididymal lesion location was left-sided in 15 patients (31.9%), right-sided in 22 patients (46.8%) and bilateral in 10 patients (21.3%). The main symptoms were painless swelling of the scrotum in 21 cases (44.7%) and scrotal drop pain in 21 cases (44.7%). Scrotal physical examination revealed epididymal beaded enlargement in 12 patients (25.5%), testicular mass in one patient (2.1%), scrotal tenderness alone in seven patients (14.9%), ill-defined epididymal-testicular border in 21 patients (44.7%) and sinus formation in six patients (12.8%). After 2–4 weeks of anti-tuberculosis chemotherapy, the patients underwent a surgical procedure. We found that 10 (83.3%) of the 12 patients whose main symptom was epididymal beaded enlargement underwent simple epididymal surgery. Of the 21 patients whose main clinical manifestation was ill-defined testis-epididymis demarcation, 16 (72.2%) underwent epididymis-testicular surgery. All patients underwent postoperative chemotherapy for 3–6 months. Postoperative follow-up showed good response to treatment.ConclusionIt is difficult to diagnose early-stage epididymal tuberculosis. Epididymal tuberculosis is likely to have invaded surrounding tissues when signs such as epididymal beaded changes and ill-defined epididymis-testis border are present. Surgical treatment combined with preoperative and postoperative chemotherapy is an effective approach to treating this condition. creator: Jiangwei Man creator: Lei Cao creator: Zhilong Dong creator: Junqiang Tian creator: Zhiping Wang creator: Li Yang uri: https://doi.org/10.7717/peerj.8291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Man et al. title: The first pterosaur basihyal, shedding light on the evolution and function of pterosaur hyoid apparatuses link: https://peerj.com/articles/8292 last-modified: 2020-01-06 description: The pterosaur is the first known vertebrate clade to achieve powered flight. Its hyoid apparatus shows a simplification similar to that of birds, although samples of the apparatus are rare, limiting the ability to make an accurate determination. In this study we reveal a new pterosaur specimen, including the first definite basihyal. Through the comparison of pterosaur hyoids, a trend has been discovered for the shortened hyoid relative to the length of the skull, indicating a diminished role of lingual retraction during the evolution of the pterosaur. The new material, possibly from a gallodactylid Gladocephaloideus, represents one of the least effective lingual retractions in all pterosaurs. Based on the structure of an elongated ceratobranchial and retroarticular process on mandibles, the function of the Y-shaped istiodactylid tongue bone is similar to those of scavenger crows rather than chameleons, which is consistent with the interpretation of the scavenging behavior of this taxon. More fossil samples are needed for further study on the function of other pterosaur hyoids. creator: Shunxing Jiang creator: Zhiheng Li creator: Xin Cheng creator: Xiaolin Wang uri: https://doi.org/10.7717/peerj.8292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: Changes in long non-coding RNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord link: https://peerj.com/articles/8293 last-modified: 2020-01-06 description: With the aim of exploring expression profiles and biological functions of long non-coding RNA (lncRNA) and mRNAs after spinal cord ischemia-reperfusion injury (SCII), differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in rat spinal cords were identified following SCII through high-throughput RNA sequencing. In total, 1,455 lncRNAs and 6,707 mRNAs were observed to be differentially expressed (—Fold Change— ≥ 2 and P < 0.05) after SCII, including 761 up-regulated and 694 down-regulated lncRNAs, 3,772 up-regulated and 2,935 down-regulated mRNAs. Gene ontology and KEGG pathway analysis showed that the DElncRNAs and DEmRNAs were implicated in many different biological processes and pathways. Further, lncRNA-mRNA co-expression networks were built to explore the potential roles of these DElncRNAs. Our results demonstrate genome-wide lncRNA and mRNA expression patterns in spinal cords after SCII, which may play vital roles in post-SCII pathophysiological processes. These findings are important for future functional research on the lncRNAs involved in SCII and might be critical for providing new insight into identification of potential targets for SCII therapy. creator: Zhibin Zhou creator: Bin Han creator: Hai Jin creator: Aimin Chen creator: Lei Zhu uri: https://doi.org/10.7717/peerj.8293 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: The effect on twinning rate of transferring double vitrified-warmed embryos in women of advanced reproductive age: a retrospective study link: https://peerj.com/articles/8308 last-modified: 2020-01-06 description: Twin pregnancies are associated with greater risk of neonatal morbidity and mortality than a singleton. This study was performed to investigate the twin pregnancy rate when two vitrified-warmed embryos are transferred in women of advanced reproductive age (≥35 years at the time of oocyte retrieval) and to evaluate the implications of findings in selecting candidates for elective single embryo transfer (eSET). A retrospective analysis of data which included 2,038 women aged 35–45 years, who underwent vitrified-warmed double embryo transfer (DET), from January 2013 to December 2016 was undertaken. Pregnancy and twin rates were estimated after stratifying by prognostic profile. The twin pregnancy rate was lower in women with poor prognosis (12/96, 12.5%) as compared with that in women with favorable prognosis (102/374, 27.3%) and average prognosis (78/346, 22.5%) with significant differences (P < 0.05). The twin rate for women with favorable prognosis was 29.2% (70/240) in the cycles of women aged 35–37 years, 26.8% (26/97) in the cycles of women aged 38–40 years and 16.2% (6/37) in the cycles of women >40 years. The twin rate for women with average prognosis was 25.8% (51/198) in the cycles of women aged 35–37 years, 22.0% (22/100) in the cycles of women aged 38–40 years and 10.4% (5/48) in the cycles of women >40 years. The twin rate for women with poor prognosis was 15.3% (9/59) in the cycles of women aged 35–37 years, 10.3% (3/29) in the cycles of women aged 38–40 years and 0% (0/8) in the cycles of women >40 years. From these results, it was concluded that women with a favorable or average prognosis have a high risk of twin pregnancies. The finding can be used to guide future practice: that is, performing eSET in women with favorable or average prognosis and DET in women with poor prognosis. creator: Yamei Xue creator: Kun Li creator: Songying Zhang uri: https://doi.org/10.7717/peerj.8308 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xue et al. title: Gene co-expression network for analysis of plasma exosomal miRNAs in the elderly as markers of aging and cognitive decline link: https://peerj.com/articles/8318 last-modified: 2020-01-06 description: BackgroundEvidence has shown that microRNA (miRNAs) are involved in molecular pathways responsible for aging and age-related cognitive decline. However, there is a lack of research linked plasma exosome-derived miRNAs changes with cognitive function in older people and aging, which might prove a new insight on the transformation of miRNAs on clinical applications for cognitive decline for older people.MethodsWe applied weighted gene co-expression network analysis to investigated miRNAs within plasma exosomes of older people for a better understanding of the relationship of exosome-derived miRNAs with cognitive decline in elderly adults. We identified network modules of co-expressed miRNAs in the elderly exosomal miRNAs dataset. In each module, we selected vital miRNAs and carried out functional enrichment analyses of their experimentally known target genes and their function.ResultsWe found that plasma exosomal miRNAs hsa-mir-376a-3p, miR-10a-5p, miR-125-5p, miR-15a-5p have critical regulatory roles in the development of aging and cognitive dysfunction in the elderly and may serve as biomarkers and putative novel therapeutic targets for aging and cognitive decline. creator: Zheng Ye creator: Bo Sun creator: Xue Mi creator: Zhongdang Xiao uri: https://doi.org/10.7717/peerj.8318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ye et al. title: Blood lactate dynamics in awake and anaesthetized mice after intraperitoneal and subcutaneous injections of lactate—sex matters link: https://peerj.com/articles/8328 last-modified: 2020-01-06 description: Lactate treatment has shown a therapeutic potential for several neurological diseases, including Alzheimer’s disease. In order to optimize the administration of lactate for studies in mouse models, we compared blood lactate dynamics after intraperitoneal (IP) and subcutaneous (SC) injections. We used the 5xFAD mouse model for familial Alzheimer’s disease and performed the experiments in both awake and anaesthetized mice. Blood glucose was used as an indication of the hepatic conversion of lactate. In awake mice, both injection routes resulted in high blood lactate levels, mimicking levels reached during high-intensity training. In anaesthetized mice, SC injections resulted in significantly lower lactate levels compared to IP injections. Interestingly, we observed that awake males had significantly higher lactate levels than awake females, while the opposite sex difference was observed during anaesthesia. We did not find any significant difference between transgenic and wild-type mice and therefore believe that our results can be generalized to other mouse models. These results should be considered when planning experiments using lactate treatment in mice. creator: Øyvind P. Haugen creator: Evan M. Vallenari creator: Imen Belhaj creator: Milada Cvancarova Småstuen creator: Jon Storm-Mathisen creator: Linda H. Bergersen creator: Ingrid Åmellem uri: https://doi.org/10.7717/peerj.8328 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Haugen et al. title: A new species of Oligodon Fitzinger, 1826 from the Langbian Plateau, southern Vietnam, with additional information on Oligodon annamensis Leviton, 1953 (Squamata: Colubridae) link: https://peerj.com/articles/8332 last-modified: 2020-01-06 description: We describe a new species of Oligodon from the highlands of the Langbian Plateau, southern Truong Son Mountains, Vietnam, based on morphological and molecular phylogenetic analyses. The new species, Oligodon rostralissp. nov is distinguished from its congeners by the following morphological characters: medium size in adults (male TL = 582 mm); small and broad head with long protruding snout; dorsal scale row formula 15-15-13; 167 ventrals, 47 subcaudals; single preocular, single postocular; loreal and presubocular absent; six supralabials, third and fourth entering orbit; six infralabials, anterior four contacting first pair of chin shields; internasals separate from prefrontals; nasal divided; single anterior and two posterior temporals; cloacal plate undivided; hemipenes short, bilobed, bifurcating in anterior one third of their length, extending to 8th subcaudal, lacking spines and papillae, with a prominent transverse flounces and distal calyces; six maxillary teeth, the posterior three enlarged; dorsal pattern consisting of 14+4 large dark-brown blotches and a bright-orange vertebral stripe on tail and dorsum; and ventral surfaces in life cream laterally with dark quadrangular spots; dark temporal streak present, edged with white. We also provide additional information on O. annamensis, including a morphological dataset of all specimens known from natural history collections and confirmation of an earlier record of O. annamensis from Cambodia. We also provide the first record of O. annamensis for Dak Lak Province. Phylogenetic analyses of mtDNA genes (3,131 bp of 12S rRNA, 16S rRNA and cyt b) suggest sister relationships of Oligodon rostralissp. nov. and O. annamensis and place them in one clade with the O. cyclurus and O. taeniatus species groups, which is concordant with previous studies on the phylogenetic relationships of Oligodon. Our study demonstrates high level of herpetofaunal diversity and endemism of Langbian Plateau and further supports the importance of this area for conservation herpetofaunal diversity in Indochina. creator: Hung Ngoc Nguyen creator: Bang Van Tran creator: Linh Hoang Nguyen creator: Thy Neang creator: Platon V. Yushchenko creator: Nikolay A. Poyarkov uri: https://doi.org/10.7717/peerj.8332 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nguyen et al. title: Effective governance for management of invasive alien plants: evidence from the perspective of forest and wildlife officers in Sri Lanka link: https://peerj.com/articles/8343 last-modified: 2020-01-06 description: Invasive alien plants (IAPs) are a significant cause of socio-ecological change in Sri Lanka. Many studies have focused on the ecological dimensions of this problem, but few have addressed sociological factors such as the knowledge and perceptions of individuals and groups tasked with addressing IAPs. This study investigates how IAP issues are understood and perceived by professional forest and wildlife officers in Sri Lanka. The data analyzed were gathered using a questionnaire that covered three themes: the respondents’ ability to identify IAPs, the impacts of IAPs and the threats they pose, and knowledge regarding control and mitigation. The questionnaire was completed by 186 field officers, and the resulting descriptive statistics and a probit regression analysis were used to analyze the data. The results show that almost all of the participating forest and wildlife officers were aware of the problems associated with IAPs but more than 75% of them lacked an accurate understanding of scientific means for controlling them and control policies established by the government of Sri Lanka. Generally, wildlife officers had a better understanding than forest officers. In addition, the analysis shows that officers’ knowledge and perceptions of IAPs were positively correlated with their level of education and position within the organization. The analysis points to several recommendations for Sri Lankan officials when designing and implementing comprehensive policies and professional programs, particularly for lower-level field officers. creator: E.M.B.P. Ekanayake creator: Yi Xie creator: Abubakar Sadiq Ibrahim creator: N.T.P. Karunaratne creator: Shahzad Ahmad uri: https://doi.org/10.7717/peerj.8343 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ekanayake et al. title: Prognostic value of CLIC3 mRNA overexpression in bladder cancer link: https://peerj.com/articles/8348 last-modified: 2020-01-06 description: BackgroundHuman intracellular chloride channel 3 (CLIC3) is involved in the development of various cancers, but the expression and prognostic value of CLIC3 mRNA in bladder cancer (BC) remain unclear.MethodsThe gene expression data and clinical information of CLIC3 were obtained from the Gene Expression Omnibus (GEO) database and verified in the Oncomine and The Cancer Genome Atlas (TCGA) database. The expression of CLIC3 mRNA in BC tissues and adjacent normal tissues was detected by quantitative real-time polymerase chain reaction (qRT-PCR). The Kaplan-Meier method was used to analyze the relationship between the expression of CLIC3 mRNA and the prognosis of BC. Cox univariate and multivariate analyses were performed on the overall survival and tumor-specific survival of BC patients. The genes coexpressed with CLIC3 were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). CLIC3-related signal transduction pathways in BC were explored with gene set enrichment analysis (GSEA).ResultsThe expression of CLIC3 mRNA in BC tissues was higher than that in normal tissues (P < 0.01). High CLIC3 mRNA expression was associated with age (P = 0.021) and grade (P = 0.045) in BC patients. High CLIC3 mRNA expression predicted a poor prognosis in BC patients (P < 0.05). Cox univariate and multivariate analyses showed that high CLIC3 mRNA expression was associated with tumor-specific survival in BC patients (P < 0.05). Functional enrichment analyses indicated that CLIC3 may be significantly associated with the cell cycle, focal adhesion, the extracellular matrix (ECM) receptor interaction and the P53 signaling pathway.ConclusionsCLIC3 mRNA is highly expressed in BC, and its high expression is related to the adverse clinicopathological factors and prognosis of BC patients. CLIC3 can be used as a biomarker for the prognosis of BC patients. creator: Mei Chen creator: Shufang Zhang creator: Xiaohong Wen creator: Hui Cao creator: Yuanhui Gao uri: https://doi.org/10.7717/peerj.8348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts link: https://peerj.com/articles/8362 last-modified: 2020-01-06 description: We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated “Edit Plasmids,” were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ repair system in most bacteria, which are believed to be ancestors of organelles. This is the first demonstration of CRISPR-mediated genome editing in both mitochondria and chloroplasts in two distantly related organisms. The Edit Plasmid approach is expected to open the door to engineer organelle genomes of a wide range of organisms in a precise fashion. creator: Byung-Chun Yoo creator: Narendra S. Yadav creator: Emil M. Orozco creator: Hajime Sakai uri: https://doi.org/10.7717/peerj.8362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yoo et al. title: Morphological descriptions and morphometric discriminant function analysis reveal an additional four groups of Scylla spp link: https://peerj.com/articles/8066 last-modified: 2020-01-03 description: There are four species of mud crabs within the genus Scylla, and most of them live sympatrically in the equatorial region. Apart from a report in Japan about the finding of a natural Scylla hybrid more than a decade ago after the division of genus Scylla into four species by Keenan, Davie & Mann (1998), no subsequent sighting was found. Thus, this study investigates the possible natural occurrence of potential hybridization among Scylla species in the wild. A total of 76,211 individuals from mud crab landing sites around the Malacca Straits, South China Sea and Sulu Sea were screened. In addition to the four-purebred species, four groups (SH 1, n = 2, 627; SH 2, n = 136; SH 3, n = 1; SH 4, n = 2) with intermediate characteristics were found, mostly at Sulu Sea. Discriminant Function Analysis revealed that all Scylla species, including SH 1 - 4, are distinguishable via their morphometric ratios. The most powerful discriminant ratios for each character and the top five discriminant ratios of males and females were suggested. The carapace width of SH 1 males and females were significantly smaller than pure species. Based on the discriminant ratios and the description of morphological characters, we hypothesize that the additional four groups of Scylla with intermediate characteristics could be presumed hybrids. Future work at the molecular level is urgently needed to validate this postulate. creator: Hanafiah Fazhan creator: Khor Waiho creator: Emilia Quinitio creator: Juliana C. Baylon creator: Yushinta Fujaya creator: Nita Rukminasari creator: Mohammad Farhan Darin Azri creator: Md. Sheriff Shahreza creator: Hongyu Ma creator: Mhd Ikhwanuddin uri: https://doi.org/10.7717/peerj.8066 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fazhan et al. title: OLA1 is responsible for normal spindle assembly and SAC activation in mouse oocytes link: https://peerj.com/articles/8180 last-modified: 2020-01-03 description: BackgroundOLA1 is a member of the GTPase protein family; unlike other members, it possess both GTPase and ATPase activities, and can bind and hydrolyze ATP more efficiently than GTP. OLA1 participates in cell proliferation, oxidative response, protein synthesis and tumorigenesis. However, whether OLA1 is also required for oocyte meiosis is still unknown.MethodsIn this study, the localization, expression, and functions of OLA1 in the mouse oocyte meiosis were examined. Immunofluorescent and confocal microscopy were used to explore the location pattern of OLA1 in the mouse oocyte. Moreover, nocodazole treatment was used to confirm the spindle-like location of OLA1 during mouse meiosis. Western blot was used to explore the expression pattern of OLA1 in the mouse oocyte. Microinjection of siRNA was used to explore the OLA1 functions in the mouse oocyte meiosis. In addition, chromosome spreading was used to investigate the spindle assembly checkpoint (SAC) activity.ResultsImmunofluorescent staining showed that OLA1 evenly distributed in the cytoplasm at germinal vesicle (GV) stage. After meiosis resumption (GVBD), OLA1 co-localized with spindles, which was further identified by nocodazole treatment experiments. Knockdown of OLA1 impaired the germinal vesicle breakdown progression and finally resulted in a lower polar body extrusion rate. Immunofluorescence analysis indicated that knockdown of OLA1 led to abnormal spindle assembly, which was evidenced by multipolar spindles in OLA1-RNAi-oocytes. After 6 h post-GVBD in culture, an increased proportion of oocyte which has precociously entered into anaphase/telephase I (A/TI) was observed in OLA1-knockdown oocytes, suggesting that loss of OLA1 resulted in the premature segregation of homologous chromosomes. In addition, the chromosome spread analysis suggested that OLA1 knockdown induced premature anaphase onset was due to the precocious inactivation of SAC. Taken together, we concluded that OLA1 plays important role in GVBD, spindle assembly and SAC activation maintenance in oocyte meiosis. creator: Di Xie creator: Juan Zhang creator: JinLi Ding creator: Jing Yang creator: Yan Zhang uri: https://doi.org/10.7717/peerj.8180 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xie et al. title: Estimation of regional irrigation water requirements and water balance in Xinjiang, China during 1995–2017 link: https://peerj.com/articles/8243 last-modified: 2020-01-03 description: Estimating water requirements and water balance for irrigated agricultural areas are important and will facilitate the efficient allocation of water resources for agriculture while minimizing the impact on natural ecosystems in arid regions. Based on the Penman-Monteith formula and GIS technology, the irrigation water requirements (IWR) of three main crops (cotton, corn and wheat) during the growing season were estimated and their spatio-temporal changes over the past 23 years (1995–2017) were analyzed in Xinjiang province, China. Our results indicated a dramatic increase in IWR from 14.12 billion m3 in 1995 to 38.99 billion m3 in 2017 due to the rapid cropland expansion of approximately 2.58 × 104 km2 in this period. Monthly IWR usually peaked in summer from May to July and varied in different basins. From the perspective of crops, cotton was identified to have consumed the largest amount of water, reaching 26.39 billion m3 in 2017, accounting for 67.68% of total water consumption. Spatially, the fastest increasing rate of IWR was Tarim Basin, which was attributable to the increase in water requirement of cotton. By comparing IWR and actual irrigation of Xinjiang in 2014, the amount of water scarcity had reached −15.01 billion m3 (−9.80 billion m3 in Tarim Basin and −6.58 billion m3 in Junggar Basin). The planting areas of three main crops (wheat, corn and cotton) were more sensitive to IWR than rising temperature indicated by our model. This study is of great significance for the scientific allocation of water resources in the irrigated areas of the different prefectures of Xinjiang. creator: Yinbo Li creator: Hongwei Wang creator: Yun Chen creator: Mingjiang Deng creator: Qian Li creator: Adiliai Wufu creator: Dan Wang creator: Ligang Ma uri: https://doi.org/10.7717/peerj.8243 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Phylogeography of the rare and endangered lycophyte Isoetes yunguiensis link: https://peerj.com/articles/8270 last-modified: 2020-01-03 description: BackgroundIsoetes yunguiensis Q. F. Wang & W. C. Taylor is a lycophyte of an ancient genus, and it is endemic to China. It is a first-class protected plant in China. This living fossil is used in paleoecology and studies on the evolution of Lycophytes in the Yunnan-Guizhou Plateau. In recent years, human activities have caused the disappearance of several wild populations, and the number of plants in the existing populations is low. Study of the genetic structure, distribution pattern, and historical dynamics of I. yunguiensis in all areas of its distribution is of guiding significance for its rational and effective protection.MethodsExpressed sequence tag-simple sequence repeat (EST-SSR) markers were used to study the genetic diversity and structure of I. yunguiensis, and noncoding chloroplast DNA (cpDNA) sequences were used to study the pedigree, population dynamics history, and glacial shelter of I. yunguiensis. A maximum entropy model was used to predict the past, present, and future distribution patterns of I. yunguiensis.ResultsAnalysis with EST-SSR markers revealed that I. yunguiensis showed high genetic diversity and that genetic variation was significantly higher within populations than between populations. Based on cpDNA data, it was concluded that there was no significant geographic pedigree in the whole area of I. yunguiensis distribution (NST = 0.344 >  GST = 0.183, p > 0.05); 21 haplotypes were detected using DnaSP v5. Neutral test and LAMARC simulation showed that I. yunguiensis has experienced rapid expansion in recent years. The maximum entropy model predicted that the potential distribution area of I. yunguiensis in the last glacial maximum period has increased significantly compared with the present distribution area, but the future distribution area did not show substantial changes. creator: Tao Zheng creator: Xuanze He creator: Honghuan Ye creator: Wei Fu creator: Maimai Peng creator: Guangqian Gou uri: https://doi.org/10.7717/peerj.8270 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zheng et al. title: The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns link: https://peerj.com/articles/8273 last-modified: 2020-01-03 description: Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes. creator: Sonja I. Repetti creator: Christopher J. Jackson creator: Louise M. Judd creator: Ryan R. Wick creator: Kathryn E. Holt creator: Heroen Verbruggen uri: https://doi.org/10.7717/peerj.8273 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Repetti et al. title: Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining link: https://peerj.com/articles/8276 last-modified: 2020-01-03 description: BackgroundNeurogenic heterotopic ossification is a disorder of aberrant bone formation affecting one in five patients sustaining a spinal cord injury or traumatic brain injury (SCI-TBI-HO). However, the underlying mechanisms of SCI-TBI-HO have proven difficult to elucidate. The aim of the present study is to identify the most promising candidate genes and biological pathways for SCI-TBI-HO.MethodsIn this study, we used text mining to generate potential explanations for SCI-TBI-HO. Moreover, we employed several additional datasets, including gene expression profile data, drug data and tissue-specific gene expression data, to explore promising genes that associated with SCI-TBI-HO.ResultsWe identified four SCI-TBI-HO-associated genes, including GDF15, LDLR, CCL2, and CLU. Finally, using enrichment analysis, we identified several pathways, including integrin signaling, insulin pathway, internalization of ErbB1, urokinase-type plasminogen activator and uPAR-mediated signaling, PDGFR-beta signaling pathway, EGF receptor (ErbB1) signaling pathway, and class I PI3K signaling events, which may be associated with SCI-TBI-HO.ConclusionsThese results enhance our understanding of the molecular mechanisms of SCI-TBI-HO and offer new leads for researchers and innovative therapeutic strategies. creator: Yichong Zhang creator: Yuanbo Zhan creator: Yuhui Kou creator: Xiaofeng Yin creator: Yanhua Wang creator: Dianying Zhang uri: https://doi.org/10.7717/peerj.8276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Genetic diversity and population structure of two subspecies of western honey bees (Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping link: https://peerj.com/articles/8280 last-modified: 2020-01-03 description: Apis mellifera scutellata and Apis mellifera capensis, two native subspecies of western honey bees in the Republic of South Africa (RSA), are important to beekeepers in their native region because beekeepers use these bees for honey production and pollination purposes. Additionally, both bees are important invasive pests outside of their native ranges. Recently, whole mitogenome sequencing and single nucleotide polymorphisms were used to study their genetic diversity. To add to our knowledge of the molecular ecology of both bees, we tested the ability of microsatellites to be used as a tool to discriminate between A.m. capensis and A.m. scutellata. We analyzed the genetic variability and overall population structure of both bee subspecies and hybrids of the two by genotyping individuals collected from RSA (N = 813 bees from 75 apiaries) at 19 microsatellite DNA loci. Overall, populations averaged between 9.2 and 11.3 alleles per locus, with unbiased heterozygosity values ranging from 0.81 to 0.86 per population. Bayesian clustering analyses revealed two distinct evolutionary units, though the results did not match those of earlier morphometric and molecular analyses. This suggests that the microsatellites we tested were not sufficient for subspecies identification purposes, especially for Cape and hybrid bees. Nevertheless, the microsatellite data highlight the considerable genetic diversity within both populations and a larger-than-expected hybridization zone between the natural distributions of A.m. capensis and A.m. scutellata. creator: Amin Eimanifar creator: Johanna T. Pieplow creator: Alireza Asem creator: James D. Ellis uri: https://doi.org/10.7717/peerj.8280 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Eimanifar et al. title: Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on communities link: https://peerj.com/articles/8296 last-modified: 2020-01-03 description: Diatoms are generally regarded as inhabitants of water bodies. However, numerous taxa are able to survive and reproduce in a variety of non-aquatic ecosystems. Although terrestrial diatoms are discussed extensively in the literature, most of those studies covered floristic aspects and few information exists on their ecology. This lack of knowledge thwarts their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal patterns and the role of different disturbances on the community composition. We collected soil diatom samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 14 months. Our results indicate that forests create a stable microhabitat for diatoms and that temporal variation of the diatom communities is mainly controlled by farming practices rather than seasonal changes in environmental variables. We also found out that communities need one to 2 months to reestablish a new, stable community after a significant change in the environment. We were able to confirm the applicability of the Pollution-Sensitivity Index (IPS) to identify anthropic disturbances. creator: Jasper Foets creator: Carlos E. Wetzel creator: Adriaan J. Teuling creator: Laurent Pfister uri: https://doi.org/10.7717/peerj.8296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Foets et al. title: Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China link: https://peerj.com/articles/8304 last-modified: 2020-01-03 description: Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca. creator: Biao Xiong creator: Limei Zhang creator: Shubin Dong creator: Zhixiang Zhang uri: https://doi.org/10.7717/peerj.8304 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xiong et al. title: Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma link: https://peerj.com/articles/8312 last-modified: 2020-01-03 description: BackgroundLower grade glioma (LGG) are a heterogeneous tumor that may develop into high-grade malignant glioma seriously shortens patient survival time. The clinical prognostic biomarker of lower-grade glioma is still lacking. The aim of our study is to explore novel biomarkers for LGG that contribute to distinguish potential malignancy in low-grade glioma, to guide clinical adoption of more rational and effective treatments.MethodsThe RNA-seq data for LGG was downloaded from UCSC Xena and the Chinese Glioma Genome Atlas (CGGA). By a robust likelihood-based survival model, least absolute shrinkage and selection operator regression and multivariate Cox regression analysis, we developed a three-gene signature and established a risk score to predict the prognosis of patient with LGG. The three-gene signature was an independent survival predictor compared to other clinical parameters. Based on the signature related risk score system, stratified survival analysis was performed in patients with different age group, gender and pathologic grade. The prognostic signature was validated in the CGGA dataset. Finally, weighted gene co-expression network analysis (WGCNA) was carried out to find the co-expression genes related to the member of the signature and enrichment analysis of the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were conducted for those co-expression network. To prove the efficiency of the model, time-dependent receiver operating characteristic curves of our model and other models are constructed.ResultsIn this study, a three-gene signature (WEE1, CRTAC1, SEMA4G) was constructed. Based on the model, the risk score of each patient was calculated with LGG (low-risk vs. high-risk, hazard ratio (HR) = 0.198 (95% CI [0.120–0.325])) and patients in the high-risk group had significantly poorer survival results than those in the low-risk group. Furthermore, the model was validated in the CGGA dataset. Lastly, by WGCNA, we constructed the co-expression network of the three genes and conducted the enrichment of GO and KEGG. Our study identified a three-gene model that showed satisfactory performance in predicting the 1-, 3- and 5-year survival of LGG patients compared to other models and may be a promising independent biomarker of LGG. creator: Kai Xiao creator: Qing Liu creator: Gang Peng creator: Jun Su creator: Chao-Ying Qin creator: Xiang-Yu Wang uri: https://doi.org/10.7717/peerj.8312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xiao et al. title: Survival between synchronous and non-synchronous multiple primary cutaneous melanomas—a SEER database analysis link: https://peerj.com/articles/8316 last-modified: 2020-01-03 description: BackgroundThere is no criterion to distinguish synchronous and non-synchronous multiple primary cutaneous melanomas (MPMs). This study aimed to distinguish synchronous and non-synchronous MPMs and compare the survivals of them using the Surveillance, Epidemiology, and End Results database.MethodsSynchronous and non-synchronous MPMs were distinguished by fitting the double log transformed distribution of the time interval between the first and second primary cutaneous melanomas (TIFtS) through a piecewise linear regression. The overall and melanoma-specific survivals were compared by the Kaplan–Meier method and Cox proportional hazard model through modeling the occurrence of synchronous MPMs as a time-dependent variable.ResultsThe distribution of TIFtS was composed by three power-law distributions. According to its first inflection point, synchronous MPMs were defined as tumors that occurred within 2 months. The Kaplain–Meier plot revealed a significant inferior survival for synchronous MPMs than non-synchronous MPMs (P < 0.0001), and the occurrence of synchronous MPM was a risk factor for overall survival of cutaneous melanoma (CM) (hazard ratio: 2.213; (95% CI [2.087–2.346]); P < 0.0001).ConclusionsThis study provided data analysis evidences for using 2 months to distinguish synchronous MPMs and non-synchronous MPMs. Furthermore, the occurrence of synchronous MPM was a risk factor for prognosis of patients with CM. creator: Jie Xiong creator: Yanlin Su creator: Zhitong Bing creator: Bihai Zhao uri: https://doi.org/10.7717/peerj.8316 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xiong et al. title: Transcriptional patterns of Coffea arabica L. nitrate reductase, glutamine and asparagine synthetase genes are modulated under nitrogen suppression and coffee leaf rust link: https://peerj.com/articles/8320 last-modified: 2020-01-03 description: This study evaluated the transcriptional profile of genes related to nitrogen (N) assimilation in coffee plants susceptible and resistant to rust fungi under N sufficiency and N suppression. For this purpose, we inoculated young coffee leaves with Hemileia vastatrix uredospores and collected them at 0, 12, 24 and 48 hours post-inoculation (HPI) to evaluate the relative expressions of genes encoding cytosolic glutamine synthetase (CaGS1), plastid glutamine synthetase (CaGS2), nitrate reductase (CaNR), and asparagine synthetase (CaAS). The genes exhibited distinct patterns of transcriptional modulation for the different genotypes and N nutritional regimes. The resistant genotype (I59) presented high levels of transcription in response to pathogen inoculation for CaNR and CaGS1 genes, evaluated under N sufficiency in the initial moments of infection (12 HPI). The gene CaGS1 also showed a peak at 48 HPI. The susceptible genotype (CV99) showed increased transcript rates of CaNR at 12 and 24 HPI in response to rust inoculation. The transcriptional patterns observed for CV99, under N suppression, were high levels for CaAS and CaGS2 at all post-inoculation times in response to coffee leaf rust disease. In addition, CaGS1 was up-regulated at 48 HPI for CV99. Cultivar I59 showed high transcript levels at 12 HPI for CaAS and peaks at 24 and 48 HPI for CaGS2 in inoculated samples. Consequently, total chlorophyl concentration was influenced by N suppression and by rust infection. Regarding enzyme activities in vitro for glutamine synthetase and CaNR, there was an increase in infected coffee leaves (I59) and under N sufficiency. Moreover, CV99 was modulated in both N nutritional regimes for GS activity in response to rust. Our results indicate that N transport genes trigger a differential modulation between genotypes through the action of rust disease. creator: Viviane Yumi Baba creator: Masako Toma Braghini creator: Tiago Benedito dos Santos creator: Kenia de Carvalho creator: João Danillo Moura Soares creator: Suzana Tiemi Ivamoto-Suzuki creator: Mirian P. Maluf creator: Lilian Padilha creator: Luzia D. Paccola-Meirelles creator: Luiz Filipe Pereira creator: Douglas S. Domingues uri: https://doi.org/10.7717/peerj.8320 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baba et al. title: Obesity in the Balinese is associated with FTO rs9939609 and rs1421085 single nucleotide polymorphisms link: https://peerj.com/articles/8327 last-modified: 2020-01-03 description: Obesity prevalence is increasing worldwide, including in the Bali Province, Indonesia, a popular tourism destination area. The common single nucleotide polymorphisms (SNPs) rs9939609 and rs1421085 of the fat mass and obesity-associated (FTO) gene have been repeatedly reported as one of the important obesity genetic risk factors. We have examined the associations of FTO rs9939609 and rs1421085 SNPs with obesity in the 612 unrelated Balinese subjects living in urban and rural areas. Linear and logistic regression analyses with adjustment for age and gender were employed to investigate the association between FTO genotypes, haplotypes and obesity parameters. We found that the FTO SNPs genotypes increased BMI by 1.25 kg/m2 (p = 0.012) for rs9939609 AA and 1.12 kg/m2 (p = 0.022) for rs1421085 CC, particularly in females and in rural population. Subjects carrying these genotypes also showed a tendency to maintain high BMI, regardless of their age. Our result showed that the FTO rs9939609 and rs1421085 risk alleles were associated with increased BMI and obesity in the Balinese. creator: Lidwina Priliani creator: Sukma Oktavianthi creator: Ria Hasnita creator: Hazrina T. Nussa creator: Rut C. Inggriani creator: Clarissa A. Febinia creator: Anom Bowolaksono creator: Rini Puspitaningrum creator: Rully A. Nugroho creator: Ketut Suastika creator: Safarina G. Malik uri: https://doi.org/10.7717/peerj.8327 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Priliani et al. title: Clinical outcome of endonasal endoscopic prelacrimal approach in managing different maxillary pathologies link: https://peerj.com/articles/8331 last-modified: 2020-01-03 description: BackgroundThe aim of the study was to evaluate the treatment outcomes of endoscopic prelacrimal recess approaches (EPLAs) in managing different sinus pathologies, analyzing associated adverse events and post-treatment quality-of-life.MethodsWe enrolled 21 consecutive patients (22 lesions) who received endoscopic sinus surgical procedures with EPLAs in two tertiary medical institutes between 2015 and 2018. Quality-of-life and self-rated symptom severity data were collected using the 22-item Sino-Nasal Outcomes Test (SNOT-22) and 10-point visual analog scales (VAS), respectively.ResultsA total of 21 patients (mean age (standard deviation) 51.7 (14.5) years; 16(76.2%) male) were followed up for 12.7 months. The most common symptoms were nasal discharge and nasal airway obstructions. Nine lesions (40.9%) were sinonasal papilloma’s, seven lesions were other types of neoplasms (31.8%; five benign and two malignant), two were trauma-related (9.1%), and four inflammatory diseases (18.2%). Patients with non-papilloma lesions had higher presurgical SNOT-22 than those with papillomas (P-value = 0.021). After EPLAs, non-papilloma patients had significant improvements in SNOT-22 and VAS (P-values = 0.012 and 0.012, respectively), while those with papillomas had only marginally significant improvements in VAS (P-value = 0.061). The most common adverse events was temporary cheek/tooth numbness (n = 11), and patients with sinonasal papillomas were more likely to have post-treatment complications than those with other disease entities.ConclusionsEPLAs were found to effectively manage various sinus diseases. Short-term life-quality improvements were promising. Future large-scale studies with longer follow-up periods are recommended. creator: Yu Hsuan Lin creator: Wei-Chih Chen uri: https://doi.org/10.7717/peerj.8331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lin and Chen title: Identification of a genome-specific repetitive element in the Gossypium D genome link: https://peerj.com/articles/8344 last-modified: 2020-01-03 description: The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling. creator: Hejun Lu creator: Xinglei Cui creator: Yanyan Zhao creator: Richard Odongo Magwanga creator: Pengcheng Li creator: Xiaoyan Cai creator: Zhongli Zhou creator: Xingxing Wang creator: Yuling Liu creator: Yanchao Xu creator: Yuqing Hou creator: Renhai Peng creator: Kunbo Wang creator: Fang Liu uri: https://doi.org/10.7717/peerj.8344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lu et al. title: Osmotrophic glucose and leucine assimilation and its impact on EPA and DHA content in algae link: https://peerj.com/articles/8363 last-modified: 2020-01-03 description: The uptake of dissolved organic compounds, that is, osmotrophy, has been shown to be an efficient nutritional strategy for algae. However, this mode of nutrition may affect the biochemical composition, for example, the fatty acid (FA) contents, of algal cells. This study focused on the osmotrophic assimilation of glucose and leucine by selected seven algal strains belonging to chlorophytes, chrysophytes, cryptophytes, dinoflagellates and euglenoids. Our laboratory experiments with stable isotope labeling showed that osmotrophy occurred in four of the selected seven strains. However, only three of these produced long chain omega-3 FAs eicosapentaenoic acid (EPA; 20:5ω3) and docosahexaenoic acid (DHA; 22:6ω3). High glucose content (5 mg L−1) affected negatively on the total FAs of Mallomonas kalinae and the total omega-3 FAs of Cryptomonas sp. Further, glucose assimilation explained 35% (negative effect) and leucine assimilation 48% (positive effect) of the variation of EPA, DHA and the FAs related to their synthesis in Cryptomonas sp. Moderate glucose concentration (2 mg L−1) was found to enhance the growth of Cryptomonas ozolinii, whereas low leucine (20 µg L−1) enhanced the growth of M. kalinae. However, no systematic effect of osmotrophy on growth rates was detected. Our study shows that osmotrophic assimilation of algae is species and compound specific, and that the effects of the assimilated compounds on algal metabolism also varies depending on the species. creator: Elina T. Peltomaa creator: Sami Taipale uri: https://doi.org/10.7717/peerj.8363 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Peltomaa and Taipale title: A transcriptomic study of probenecid on injured spinal cords in mice link: https://peerj.com/articles/8367 last-modified: 2020-01-03 description: BackgroundRecent studies have found that probenecid has neuroprotective and reparative effects on central nervous system injuries. However, its effect on genome-wide transcription in acute spinal cord injury (SCI) remains unknown. In the present study, RNA sequencing (RNA-Seq) is used to analyze the effect of probenecid on the local expression of gene transcription 8 h after spinal injury.MethodsAn Infinite Horizon impactor was used to perform contusive SCI in mice. The SCI model was made by using a rod (1.3 mm diameter) with a force of 50 Kdynes. Sham-operated mice only received a laminectomy without contusive injury. The injured mice were randomly assigned into either the control (SCI_C) or probenecid injection (SCI_P) group. In the latter group, the probenecid drug was intraperitoneally injected (0.5 mg/kg) immediately following injury. Eight hours after the injury or laminectomy, the spinal cords were removed from the mice in both groups. The total RNAs were extracted and purified for library preparation and transcriptome sequencing. Differential gene expressions (DEGs) of the three groups—sham, SCI_C and SCI_P—were analyzed using a DESeq software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed using a GOseq R package and KOBAS software. Real-time quantitative reverse-transcriptase polymerase chain reaction was used to validate RNA-Seq results.ResultsRNA-Seq showed that, compared to the SCI_C group, the number of DEGs was 641 in the SCI_P group (286 upregulated and 355 downregulated). According to GO analysis, DEGs were most enriched in extracellular matrix (ECM), collagen trimer, protein bounding and sequence specific DNA binding. KEGG analysis showed that the most enriched pathways included: cell adhesion molecules, Leukocyte transendothelial migration, ECM-receptor interactions, PI3K-Akt signaling pathways, hematopoietic cell lineages, focal adhesions, the Rap1 signaling pathway, etc. The sequence data have been deposited into the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra/PRJNA554464). creator: Yu-Xin Zhang creator: Sai-Nan Wang creator: Jing Chen creator: Jian-Guo Hu creator: He-Zuo Lü uri: https://doi.org/10.7717/peerj.8367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Questioning the proverb ‘more haste, less speed’: classic versus metabarcoding approaches for the diet study of a remote island endemic gecko link: https://peerj.com/articles/8084 last-modified: 2020-01-02 description: Dietary studies can reveal valuable information on how species exploit their habitats and are of particular importance for insular endemics conservation as these species present higher risk of extinction. Reptiles are often neglected in island systems, principally the ones inhabiting remote areas, therefore little is known on their ecological networks. The Selvagens gecko Tarentola (boettgeri) bischoffi, endemic to the remote and integral reserve of Selvagens Archipelago, is classified as Vulnerable by the Portuguese Red Data Book. Little is known about this gecko’s ecology and dietary habits, but it is assumed to be exclusively insectivorous. The diet of the continental Tarentola species was already studied using classical methods. Only two studies have used next-generation sequencing (NGS) techniques for this genus thus far, and very few NGS studies have been employed for reptiles in general. Considering the lack of information on its diet and the conservation interest of the Selvagens gecko, we used morphological and DNA metabarcoding approaches to characterize its diet. The traditional method of morphological identification of prey remains in faecal pellets collected over a longer period was compared with metabarcoding of samples collected during rapid surveys. Molecular results revealed that this species is a generalist, feeding on invertebrate, plant and vertebrate items, whereas the morphological approaches were unable to detect the latter two. These results opened up new questions on the ecological role of the Selvagens gecko that deserves to be further explored, such as the possible predation on seabirds, plant services or trophic competition with the sympatric Madeira lizard Teira dugesii. Metabarcoding identified a greater diversity of dietary items at higher taxonomic resolution, but morphological identification enabled calculation of relative abundances and biomasses of ingested arthropods, and detected a dietary shift on invertebrate preys between seasons. Results of this study highlight the global applicability of rapid metabarcoding surveys for understudied taxa on remote islands that are difficult to access. We recommend using the metabarcoding approach, even if ‘speedy’ sampling only is possible, but we must highlight that disregarding long-term ecological data may lead to ‘hasty’ conclusion. creator: Vanessa Gil creator: Catarina J. Pinho creator: Carlos A.S. Aguiar creator: Carolina Jardim creator: Rui Rebelo creator: Raquel Vasconcelos uri: https://doi.org/10.7717/peerj.8084 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gil et al. title: Bioactivity of compounds secreted by symbiont bacteria of Nudibranchs from Indonesia link: https://peerj.com/articles/8093 last-modified: 2020-01-02 description: The aims of this work are to isolate bacterial symbionts from nudibranchs and subsequently to determine anti-Methicillin resistant Staphylococcus aureus (MRSA), cytotoxicity and anti-Herpes simplex virus type 1 (HSV-1) activities of bio compounds. A total of 15 species of nudibranchs were collected from Karimunjawa and five species from Bali, respectively. A total of 245 bacteria isolates were obtained. The anti-MRSA activity screening activity indicated two active bacteria. Ethyl acetate extracts from supernatants, indicating extracelullar compounds, showed an inhibition zone against MRSA at concentrations of 500–1,000 µg/ml. DNA sequence analysis showed that the strain KJB-07 from Phyllidia coelestis was closely related to Pseudoalteromonas rubra, whereas the strain NP31-01 isolated from Phyllidia varicosa was closely related to Virgibacillus salarius. The extract of Pseudoalteromonas rubra was cytotoxic to Vero cells at a concentration of 75 µg/ml. The extract of V. salarius presented no cytotoxicity at concentrations of 5–1,000 µg/ml. No anti HSV-1 was observed for both isolated bacteria. This is the first study describing research on anti-MRSA, cytotoxicity and anti HSV-1 activity of bacterial symbionts from the viscera of nudibranch. Compounds produced by Pseudoalteromonas rubra and V. salarius, had potential anti-MRSA activity. However, only extracts from Pseudoalteromonas rubra showed cytotoxic effects on Vero cells. Three compounds were identified by LC/MS after purification from culture supernatant. creator: Rhesi Kristiana creator: Gilles Bedoux creator: Gerard Pals creator: I. Wayan Mudianta creator: Laure Taupin creator: Christel Marty creator: Meezan Ardhanu Asagabaldan creator: Diah Ayuningrum creator: Agus Trianto creator: Nathalie Bourgougnon creator: Ocky Karna Radjasa creator: Agus Sabdono creator: Muhammad Hanafi uri: https://doi.org/10.7717/peerj.8093 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kristiana et al. title: A new p-terphenyl derivative from the insect-derived fungus Aspergillus candidus Bdf-2 and the synergistic effects of terphenyllin link: https://peerj.com/articles/8221 last-modified: 2020-01-02 description: A new p-terphenyl derivative 4″-deoxy-2′-methoxyterphenyllin (1), along with six known p-terphenyl derivatives (2–7), a known flavonoid derivative dechlorochlorflavonin (8) and a known fellutanine A (9), were isolated from the insect-derived strain of the fungus Aspergillus candidus Bdf-2, associated with Blaptica dubia. The structure of 1 was established by the analysis of the 1D and 2D NMR and HR-ESI-MS spectra. Compounds 1–9 were evaluated for antibacterial activities against Staphylococcus aureus ATCC29213, Escherichia coli ATCC25922 and Ralstonia solanacearum, and for antioxidant activities. Synergistic effects of compound 2 with the other compounds were also investigated. As a result, compound 6 displayed the best antibacterial activities in all single compound with MIC value of 32 µg/mL against S. aureus ATCC29213 and R. solanacearum, respectively. However, no antibacterial effect against E. coli ATCC25922 was detected from any single compound. The combination of 2 + 6 exhibited obvious synergistic effect against S. aureus ATCC29213 and the MIC value was 4 µg/mL. Compound 6 also showed the best antioxidant activity as a single compound with an IC50 value of 17.62 µg/mL. Combinations of 5 + 6, 2 + 4 + 5 and 2 + 4 + 5 + 6 displayed synergistic effect and their antioxidant activities were better than that of any single compound. creator: Tijiang Shan creator: Yuyang Wang creator: Song Wang creator: Yunying Xie creator: Zehua Cui creator: Chunyin Wu creator: Jian Sun creator: Jun Wang creator: Ziling Mao uri: https://doi.org/10.7717/peerj.8221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shan et al. title: Testing marine regional-scale hypotheses along the Yucatan continental shelf using soft-bottom macrofauna link: https://peerj.com/articles/8227 last-modified: 2020-01-02 description: Different hypotheses related to the regional-scale configuration of the Yucatan Continental Shelf (YCS) between the Gulf of Mexico (GoM) and the Caribbean Sea have been proposed. Hypotheses regarding its regional boundaries include: (i) an ecoregional boundary at Catoche Cape, dividing the Western Caribbean and the Southern GoM ecoregions; and (ii) a boundary within the Southern GoM ecoregion at 89°W, separating the West and Mid-Yucatan areas. We tested the hypothesis of no variation in benthic macrofaunal assemblages between regions delimited by the former boundaries using the species and functional traits of soft-bottom macrofauna. We considered that the depth and temporal environmental dynamics might interact with regional variations, generating complex benthic community patterns. The data were collected over five years (2010–2012, 2015–2016) at 86 stations (N = 1, 017 samples, 10–270 m depth), comprising 1,327 species with 45 combinations of functional traits. The variation in species composition and functional trait assemblages were both consistent with the occurrence of three separate regions in the Yucatan Peninsula (West Yucatan, Mid-Yucatan and Western Caribbean). This regional configuration was consistent with changes in assemblage structure and depth zonation as well as temporal variation. Along with spatial and temporal variation, diversity diminished with depth and different regions exhibited contrasting patterns in this regard. Our results suggest that the spatial and temporal variation of soft-bottom macrofauna at YCS demonstrate the complex organization of a carbonate shelf encompassing different regions, which may represent transitional regions between the Caribbean and the GoM. creator: Ivan Hernandez-Avila creator: Frank A. Ocaña creator: Daniel Pech uri: https://doi.org/10.7717/peerj.8227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hernandez-Avila et al. title: Sagittal spinal morphotype assessment in 8 to 15 years old Inline Hockey players link: https://peerj.com/articles/8229 last-modified: 2020-01-02 description: BackgroundPhysiological sagittal spinal curvatures play an important role in health and performance in sports. For that reason, several scientific studies have assessed spinal morphology in young athletes. However, to our knowledge, no study has assessed the implications of Inline Hockey (IH) practice on sagittal integrative spinal morphotype in adolescent players.ObjectivesThe aims of the present study were to describe habitual sagittal spinal posture in young federated IH players and its relationship with training load and to determine the sagittal integrative spinal morphotype in these players.MethodsAn observational analysis was developed to describe the sagittal spinal morphotype in young federated IH players. A total of 74 IH players from the Technification Plan organized by the Skating Federation of the Valencian Community (aged from 8 to 15 years) participated in the study. Thoracic and lumbar curvatures of the spine were measured in a relaxed standing position (SP), in a slump sitting position (SSP) and in maximum flexion of the trunk (MFT) to determine the “Sagittal Integrative Morphotype” of all players. An unilevel inclinometer was used to quantify the sagittal spinal curvatures. The Hip Joint Angle test was used to quantify the Lumbo-Horizontal angle in flexion (L-H fx) of all participants with a goniometer.ResultsWhen thoracic curvature was analyzed according to normality references, it was found that 64.9% of IH players had thoracic hyperkyphosis in a SSP, while 60.8% and 74.3% of players were classified as normal in a SP and in MFT, respectively. As for the lumbar curve, 89.2% in a SP and 55.4% in MFT were normal, whereas 68.9% of IH players presented lumbar hyperkyphosis in a SSP. Regarding the “Sagittal Integrative Morphotype,” only 17.6% of players were classified as “Normal” in the three measured positions for the thoracic curve, while 37.8% had “Thoracic Hyperkyphosis” and 41.8% presented “Functional Thoracic Hyperkyphosis.” As for the “Sagittal Integrative Lumbar Morphotype,” only 23% of athletes had a normal curve in the three positions, whereas 66.2% presented “Functional Lumbar Hyperkyphosis.” When the L-H fx was evaluated, the results showed that only 16.2% of the athletes were classified as normal.ConclusionsFederative IH practice seems to cause specific adaptations in spinal sagittal morphotype. Taking into account the “Sagittal Integrative Morphotype” only 17.6% IH players presented “Normal Morphotype” with a normal thoracic kyphosis in the three measured positions, while only 23% IH players presented “Normal Morphotype” with a normal lumbar curvature in the three assessed positions. Furthermore, only 16.2% of IH players showed normal pelvic tilt. Exercise programs to prevent or rehabilitate these imbalances in young IH players are needed. creator: Pilar Sainz de Baranda creator: Antonio Cejudo creator: Victor Jesus Moreno-Alcaraz creator: Maria Teresa Martinez-Romero creator: Alba Aparicio-Sarmiento creator: Fernando Santonja-Medina uri: https://doi.org/10.7717/peerj.8229 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sainz de Baranda et al. title: Effects of low pH and feeding on calcification rates of the cold-water coral Desmophyllum dianthus link: https://peerj.com/articles/8236 last-modified: 2020-01-02 description: Cold-Water Corals (CWCs), and most marine calcifiers, are especially threatened by ocean acidification (OA) and the decrease in the carbonate saturation state of seawater. The vulnerability of these organisms, however, also involves other global stressors like warming, deoxygenation or changes in sea surface productivity and, hence, food supply via the downward transport of organic matter to the deep ocean. This study examined the response of the CWC Desmophyllum dianthus to low pH under different feeding regimes through a long-term incubation experiment. For this experiment, 152 polyps were incubated at pH 8.1, 7.8, 7.5 and 7.2 and two feeding regimes for 14 months. Mean calcification rates over the entire duration of the experiment ranged between −0.3 and 0.3 mg CaCO3 g−1d−1. Polyps incubated at pH 7.2 were the most affected and 30% mortality was observed in this treatment. In addition, many of the surviving polyps at pH 7.2 showed negative calcification rates indicating that, in the long term, CWCs may have difficulty thriving in such aragonite undersaturated waters. The feeding regime had a significant effect on skeletal growth of corals, with high feeding frequency resulting in more positive and variable calcification rates. This was especially evident in corals reared at pH 7.5 (ΩA = 0.8) compared to the low frequency feeding treatment. Early life-stages, which are essential for the recruitment and maintenance of coral communities and their associated biodiversity, were revealed to be at highest risk. Overall, this study demonstrates the vulnerability of D. dianthus corals to low pH and low food availability. Future projected pH decreases and related changes in zooplankton communities may potentially compromise the viability of CWC populations. creator: Ariadna Martínez-Dios creator: Carles Pelejero creator: Àngel López-Sanz creator: Robert M. Sherrell creator: Stanley Ko creator: Verena Häussermann creator: Günter Försterra creator: Eva Calvo uri: https://doi.org/10.7717/peerj.8236 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Martínez-Dios et al. title: Symmetry systems on the wings of Dichromodes Guenée (Lepidoptera: Geometridae) are unconstrained by venation link: https://peerj.com/articles/8263 last-modified: 2020-01-02 description: The nymphalid groundplan, an idealized schematic illustrating the essential elements of butterfly wing patterns, predicts a consistent relationship between color pattern and wing venation. Moths in the family Geometridae have wing shapes and patterns that often resemble those of butterflies, and until recently, this family was believed to be among butterflies’ closest relatives. However, an examination of the geometrid genus Dichromodes Guenée, 1858 shows no consistent relationship between the central symmetry system and wing venation. Whereas the distal edge of the central symmetry system is predicted to reach the costal margin proximal to the Subcostal vein in butterflies and acronictine moths, it has no consistent relationship with the Subcostal, Radius, or Radial Sector 1 veins in Dichromodes. This finding highlights developmental diversity that was previously overlooked due to the overwhelming preference for butterflies in studies of lepidopteran wing patterns. creator: Sandra R. Schachat uri: https://doi.org/10.7717/peerj.8263 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Schachat title: Interspecific differences of stridulatory signals in three species of bark beetles from the genus Polygraphus Er. (Coleoptera: Curculionidae, Scolytinae) inhabiting the island of Sakhalin link: https://peerj.com/articles/8281 last-modified: 2020-01-02 description: Stridulatory signals are involved in conspecific interactions between bark beetles (Coleoptera: Curculionidae, Scolytinae). In this study, we compared the qualitative profiles of acoustic signals in three species from the genus Polygraphus Er. Sympatry can be periodically observed in two of them –P. proximus and P. subopacus. Sporadically they occur on the same plants. P. nigrielytris colonize distinctly different host plant species; however, on the island of Sakhalin it inhabits the same biotopes. The purpose of the study is to identify species-specific parameters and the extent of differences in stridulatory signals of these species. Airborne signals produced during the contact of males of the same species were experimentally recorded. Among tested parameters of stridulatory signals, as the most species-specific were noted: chirp duration, number of tooth-strikes per chirp, and intertooth-strike interval. creator: Ivan Andreevich Kerchev uri: https://doi.org/10.7717/peerj.8281 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kerchev title: Ambulatory sleep scoring using accelerometers—distinguishing between nonwear and sleep/wake states link: https://peerj.com/articles/8284 last-modified: 2020-01-02 description: BackgroundDifferentiating nonwear time from sleep and wake times is essential for the estimation of sleep duration based on actigraphy data. To efficiently analyze large-scale data sets, an automatic method of identifying these three different states is required. Therefore, we developed a classification algorithm to determine nonwear, sleep and wake periods from accelerometer data. Our work aimed to (I) develop a new pattern recognition algorithm for identifying nonwear periods from actigraphy data based on the influence of respiration rate on the power spectrum of the acceleration signal and implement it in an automatic classification algorithm for nonwear/sleep/wake states; (II) address motion artifacts that occur during nonwear periods and are known to cause misclassification of these periods; (III) adjust the algorithm depending on the sensor position (wrist, chest); and (IV) validate the algorithm on both healthy individuals and patients with sleep disorders.MethodsThe study involved 98 participants who wore wrist and chest acceleration sensors for one day of measurements. They spent one night in the sleep laboratory and continued to wear the sensors outside of the laboratory for the remainder of the day. The results of the classification algorithm were compared to those of the reference source: polysomnography for wake/sleep and manual annotations for nonwear/wear classification.ResultsThe median kappa values for the two locations were 0.83 (wrist) and 0.84 (chest). The level of agreement did not vary significantly by sleep health (good sleepers vs. subjects with sleep disorders) (p = 0.348, p = 0.118) or by sex (p = 0.442, p = 0.456). The intraclass correlation coefficients of nonwear total time between the reference and the algorithm were 0.92 and 0.97 with the outliers and 0.95 and 0.98 after the outliers were removed for the wrist and chest, respectively. There was no evidence of an association between the mean difference (and 95% limits of agreement) and the mean of the two methods for either sensor position (wrist p = 0.110, chest p = 0.164), and the mean differences (algorithm minus reference) were 5.11 [95% LoA −15.4–25.7] and 1.32 [95% LoA −9.59–12.24] min/day, respectively, after the outliers were removed.DiscussionWe studied the influence of the respiration wave on the power spectrum of the acceleration signal for the differentiation of nonwear periods from sleep and wake periods. The algorithm combined both spectral analysis of the acceleration signal and rescoring. Based on the Bland-Altman analysis, the chest-worn accelerometer showed better results than the wrist-worn accelerometer. creator: Amna Barouni creator: Jörg Ottenbacher creator: Johannes Schneider creator: Bernd Feige creator: Dieter Riemann creator: Anne Herlan creator: Driss El Hardouz creator: Darren McLennan uri: https://doi.org/10.7717/peerj.8284 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Barouni et al. title: Basic and target eco-environment water requirements of a dry inland river under typical flow frequencies in China link: https://peerj.com/articles/8285 last-modified: 2020-01-02 description: Analysis of eco-environmental water requirements (EEWRs) and water resource allocation strategies for arid, inland river basins can provide the theoretical basis for sustainable water utilization and management. In this paper, an optimal water resource allocation strategy is proposed for Yarkand River Basin in Xinjiang, China, on the basis of a comprehensive analysis of runoff data collected between 1970 and 2016, three ecological environmental protection goals, basic eco-environmental water requirement (BEEWR) aimed at sustaining aquatic ecosystems within the river, and target eco-environmental water requirements (TEEWR) aimed at protecting various types of riparian vegetation along the river. The results showed that: (1) after the runoff in Kaqun reach subtracting the BEEWR, the annual average river loss (recharge), and the amount of water diversion for irrigation (51.43 × 108 m3) from flows along the Kaqun reach, the remaining water volume during wet years was able to meet all three TEEWRs; (2) during moderately wet years, the remaining water was capable of meeting the second and third TEEWRs; and (3) during dry and extremely dry years, there was little or no residual water available to meet TEEWRs. The proposed optimal water resource allocation strategy, based on the above findings, states that the water diversion requirement for irrigation and domestic use allocated from the total amount of runoff should not exceed the National Water Policy (Three Red Lines) standard first. Then, the BEEWR allocated from the runoff should be met second, and the annual average river loss, third. Depending on the amount of remaining water, the second and third TEEWRs can be fulfilled during wet years, but during moderately wet years, only the third TEEWR can be met. During dry and extremely dry years, only the BEEWR of the river can be met and only during the flood season. creator: Aihong Fu creator: Weihong Li creator: Yi Wang creator: Yifei Bai uri: https://doi.org/10.7717/peerj.8285 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fu et al. title: Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa) link: https://peerj.com/articles/8287 last-modified: 2020-01-02 description: Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β =  − 0.21, 95% CI [−0.35 to −0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States. creator: Amberly N. Hauger creator: Karmen M. Hollis-Etter creator: Dwayne R. Etter creator: Gary J. Roloff creator: Andrew R. Mahon uri: https://doi.org/10.7717/peerj.8287 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hauger et al. title: The fossil record of the genus Varanus from the Southern Caucasus (Armenia, Georgia) link: https://peerj.com/articles/8322 last-modified: 2020-01-02 description: The Southern Caucasus, with its special geographic position and complex topography, is a well-known biodiversity hotspot. However, the formation of this hotspot remains largely unstudied. To reveal this, a thorough study of the fossil record of the region is necessary. In the present paper, we describe for the first time fossil monitor lizards (Varanus sp.) from two late Miocene localities from the Southern Caucasus (Jradzor, Armenia and Tetri Udabno, Georgia). We suggest that both fossils belong to a small-sized monitor lizard, comparable to the present-day species found in Iran and the Middle East (e.g., Iraq, Saudi Arabian)—the most western part of the extant monitor lizards’ Eurasian distribution range. Our finds show that the genus had a broad distribution in the Eastern Paratethyan region during the late Miocene. In addition, we provide the probable temperature ranges for fossil localities. creator: Davit Vasilyan creator: Maia Bukhsianidze uri: https://doi.org/10.7717/peerj.8322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Vasilyan and Bukhsianidze