title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2019-06 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome sequencing and analysis of Salmonella enterica subsp. enterica serovar Stanley UPM 517: Insights on its virulence-associated elements and their potentials as vaccine candidates link: https://peerj.com/articles/6948 last-modified: 2019-06-28 description: Salmonella enterica subsp. enterica serovar Stanley (S. Stanley) is a pathogen that contaminates food, and is related to Salmonella outbreaks in a variety of hosts such as humans and farm animals through products like dairy items and vegetables. Despite the fact that several vaccines of Salmonella strains had been constructed, none of them were developed according to serovar Stanley up to this day. This study presents results of genome sequencing and analysis on our S. Stanley UPM 517 strain taken from fecal swabs of 21-day-old healthy commercial chickens in Perak, Malaysia and used Salmonella enterica subsp. enterica serovar Typhimurium LT2 (S. Typhimurium LT2) as a reference to be compared with. First, sequencing and assembling of the Salmonella Stanley UPM 517 genome into a contiguous form were done. The work was then continued with scaffolding and gap filling. Annotation and alignment of the draft genome was performed with S. Typhimurium LT2. The other elements of virulence estimated in this study included Salmonella pathogenicity islands, resistance genes, prophages, virulence factors, plasmid regions, restriction-modification sites and the CRISPR-Cas system. The S. Stanley UPM 517 draft genome had a length of 4,736,817 bp with 4,730 coding sequence and 58 RNAs. It was discovered via genomic analysis on this strain that there were antimicrobial resistance properties toward a wide variety of antibiotics. Tcf and ste, the two fimbrial virulence clusters related with human and broiler intestinal colonizations which were not found in S. Typhimurium LT2, were atypically discovered in the S. Stanley UPM 517 genome. These clusters are involved in the intestinal colonization of human and broilers, respectively. There were seven Salmonella pathogenicity islands (SPIs) within the draft genome, which contained the virulence factors associated with Salmonella infection (except SPI-14). Five intact prophage regions, mostly comprising of the protein encoding Gifsy-1, Fels-1, RE-2010 and SEN34 prophages, were also encoded in the draft genome. Also identified were Type I–III restriction-modification sites and the CRISPR-Cas system of the Type I–E subtype. As this strain exhibited resistance toward numerous antibiotics, we distinguished several genes that had the potential for removal in the construction of a possible vaccine candidate to restrain and lessen the pervasiveness of salmonellosis and to function as an alternative to antibiotics. creator: Khalidah Syahirah Ashari creator: Najwa Syahirah Roslan creator: Abdul Rahman Omar creator: Mohd Hair Bejo creator: Aini Ideris creator: Nurulfiza Mat Isa uri: https://doi.org/10.7717/peerj.6948 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ashari et al. title: Estrogen receptor 1 gene polymorphisms (PvuII and XbaI) are associated with type 2 diabetes in Palestinian women link: https://peerj.com/articles/7164 last-modified: 2019-06-28 description: BackgroundType 2 diabetes mellitus (T2DM) is a multifactorial disease where both genetic and environmental factors contribute to its pathogenesis. The PvuII and XbaI polymorphisms of the estrogen receptor 1 (ESR1) gene have been variably associated with T2DM in several populations. This association has not been studied in the Palestinian population. Therefore, the aim of this study was to investigate the association between the PvuII and XbaI variants in the ESR1 and T2DM and its related metabolic traits among Palestinian women.MethodsThis case–control study included 102 T2DM and 112 controls in which PvuII and XbaI variants of the ESR1 gene were genotyped using amplicon based next generation sequencing (NGS).ResultsAllele frequencies of both PvuII and XbaI variants were not significantly different between patients and control subjects (P > 0.05). In logestic regression analysis adjusted for age and BMI, the ESR1 PvuII variant was associated with risk of T2DM in three genotypic models (P < 0.025) but the strongest association was observed under over-dominant model (TT+CC vs. TC) (OR = 2.32, CI [1.18–4.55] adjusted P = 0.013). A similar but non-significant trend was also observed for the ESR1 XbaI variant under the over-dominant model (AA+GG vs. AG) (OR = 2.03, CI [1.05–3.95]; adjusted P = 0.035). The frequencies of the four haplotypes (TA, CG, CA, TG) were not significantly different in the T2DM patients compared with control group (P > 0.025). Among diabetic group, an inverse trend with risk of cardio vascular diseases was shown in carriers of CG haplotype compared to those with TA haplotype (OR = 0.28, CI [0.09–0.90]; adjusted P = 0.035). Further, stratified analyses based on ESR1 PvuII and XbaI genotypes revealed no evidence for association with lipid levels (TC, TG, HDL, LDL).ConclusionsThis is the first Palestinian study to conclude that ESR1 PuvII and XbaI variants may contribute to diabetes susceptibility in Palestinian women. Identification of genetic risk markers can be used in defining high risk subjects and in prevention trials. creator: Suheir Ereqat creator: Stéphane Cauchi creator: Khaled Eweidat creator: Muawiyah Elqadi creator: Abedelmajeed Nasereddin uri: https://doi.org/10.7717/peerj.7164 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ereqat et al. title: Transcriptomic analysis of gills provides insights into the molecular basis of molting in Chinese mitten crab (Eriocheir sinensis) link: https://peerj.com/articles/7182 last-modified: 2019-06-28 description: Chinese mitten crab (Eriocheir sinensis) is an economically important freshwater aquaculture species and is a model species for research on the mechanism of molting. This study aimed to identify important candidate genes associated with the molting process and to determine the role of gills in the regulation of molting with the help of transcriptomic analysis. The transcriptomes of crabs at different molting stages—postmolt (PoM), intermolt (InM), premolt (PrM) and ecdysis (E)—were de novo assembled to generate 246,232 unigenes with a mean length of 851 bp. A total of 86,634 unigenes (35.18% of the total unigenes) were annotated against reference databases. Significantly upregulated genes were identified in postmolt compared to intermolt (1,475), intermolt compared to premolt (65), premolt compared to ecdysis (1,352), and ecdysis compared to postmolt (153), and the corresponding numbers of downregulated genes were 1,276, 32, 1,573 and 171, respectively. Chitin synthase, endochitinase, chitinase A, chitinase 3, chitinase 6 and chitin deacetylase 1 were upregulated during the postmolt and ecdysis stages, while phosphoglucomutase 3 (PGM3), glucosamine 6-phosphate deaminase (GNPDA) and glucosamine glycoside hydrolase (nagZ) were upregulated during the intermolt and premolt stages compared to the other stages. The upregulated genes were enriched in several lipid-related metabolic pathways, such as “fatty acid elongation”, “glycerophospholipid metabolism” and “sulfur metabolism”. Meanwhile, three signaling pathways, including the “phosphatidylinositol signaling system”, the “calcium signaling pathway” and the “GnRH signaling pathway” were also enriched. Tetraspanin-18, an important effector gene in the lysosomal pathway involved in cell apoptosis, up-regulate with the beginning of molting (in premolt stage) and reach the top in the ecdysis stage, and barely expressed in the intermolt stage. The expression variations in the tetraspanin-18 gene indicated that it may play an important role in the beginning of molting cycle, which might be regulated by the stress of salinity. This study revealed that the gills could participate in chitin degradation, in reestablishment of the exoskeleton and the signaling process. Based on transcriptomic analysis of the gills, we not only explored novel molecular mechanisms of molting in E. sinensis but also acquired foundational genetic data for E. sinensis. creator: Jingjing Li creator: Jinsheng Sun creator: Xuewang Dong creator: Xuyun Geng creator: Gaofeng Qiu uri: https://doi.org/10.7717/peerj.7182 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: TOXIFY: a deep learning approach to classify animal venom proteins link: https://peerj.com/articles/7200 last-modified: 2019-06-28 description: In the era of Next-Generation Sequencing and shotgun proteomics, the sequences of animal toxigenic proteins are being generated at rates exceeding the pace of traditional means for empirical toxicity verification. To facilitate the automation of toxin identification from protein sequences, we trained Recurrent Neural Networks with Gated Recurrent Units on publicly available datasets. The resulting models are available via the novel software package TOXIFY, allowing users to infer the probability of a given protein sequence being a venom protein. TOXIFY is more than 20X faster and uses over an order of magnitude less memory than previously published methods. Additionally, TOXIFY is more accurate, precise, and sensitive at classifying venom proteins. creator: T. Jeffrey Cole creator: Michael S. Brewer uri: https://doi.org/10.7717/peerj.7200 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cole and Brewer title: Covariations between personality behaviors and metabolic/performance traits in an Asian agamid lizard (Phrynocephalus vlangalii) link: https://peerj.com/articles/7205 last-modified: 2019-06-28 description: Ecological factors related to predation risks and foraging play major roles in determining which behavioral traits may mediate life history trade-offs and, therefore, the pace-of-life syndrome (POLS) structure among behavioral, physiological, and life-history traits. It has been proposed that activity/exploration or risk-taking behaviors are more likely to impact resource acquisition for organisms (individuals, populations, and species) foraging on clumped and ephemeral food sources than for organisms foraging on abundant and evenly distributed resources. In contrast, vigilance or freezing behavior would be expected to covary with the pace of life when organisms rely on food items requiring long bouts of handling. Nevertheless, it remains unclear how general this pattern is. We tested this hypothesis by examining the associations between exploration/risk-taking behaviors and metabolic/performance traits for the viviparous agamid lizard, Phrynocephalus vlangalii. This species forages on sparse and patchy food sources. The results showed positive correlations between exploration and endurance capacity, and between bite force and risk-taking willingness. Our current findings, in conjunction with our previous work showed no correlations between freezing behavior and performance in this species, support the idea that behaviors in life-history trade-offs are natural history-dependent in P. vlangalii, and provide evidence that behavioral types play functional roles in life history trade-offs to supporting POLS hypothesis. creator: Jingfeng Chen creator: Yin Qi creator: Yayong Wu creator: Xiaocui Wang creator: Yezhong Tang uri: https://doi.org/10.7717/peerj.7205 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chen et al. title: Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China link: https://peerj.com/articles/7214 last-modified: 2019-06-28 description: BackgroundDeformed wing virus (DWV) is one of many viruses that infect honeybees and has been extensively studied because of its close association with honeybee colony collapse that is induced by Varroa destructor. However, virus genotypes, sequence characteristics, and genetic variations of DWV remain unknown in China.MethodsTwo DWV strains were isolated from Jinzhou and Qinhuangdao cities in China, and were named China1-2017 (accession number: MF770715) and China2-2018 (accession number: MH165180), respectively, and their complete genome sequences were analyzed. To investigate the phylogenetic relationships of the DWV isolates, a phylogenetic tree of the complete open reading frame (ORF), structural protein VP1, and non-structural protein 3C+RdRp of the DWV sequences was constructed using the MEGA 5.0 software program. Then, the similarity and recombinant events of the DWV isolated strains were analyzed using recombination detection program (RDP4) software and genetic algorithm for recombination detection (GARD).ResultsThe complete genomic analysis showed that the genomes of the China1-2017 and China2-2018 DWV strains consisted of 10,141 base pairs (bp) and 10,105 bp, respectively, and contained a single, large ORF (China1-2017: 1,146–9,827 bp; China2-2018: 1,351–9,816 bp) that encoded 2,894 amino acids. The sequences were compared with 20 previously reported DWV sequences from different countries and with sequences of two closely related viruses, Kakugo virus (KV) and V. destructor virus-1. Multiple sequence comparisons revealed a nucleotide identity of 84.3–96.7%, and identity of 94.7–98.6% in amino acids between the two isolate strains and 20 reference strains. The two novel isolates showed 96.7% nucleotide identity and 98.1% amino acid identity. The phylogenetic analyses showed that the two isolates belonged to DWV Type A and were closely related to the KV-2001 strain from Japan. Based on the RDP4 and GARD analyses, the recombination of the China2-2018 strain was located at the 4,266–7,507 nt region, with Korea I-2012 as an infer unknown parent and China-2017 as a minor parent, which spanned the entire helicase ORF. To the best of our knowledge, this is the first study to the complete sequence of DWV isolated from Apis cerana and the possible DWV recombination events in China. Our findings are important for further research of the phylogenetic relationship of DWVs in China with DWV strains from other countries and also contribute to the understanding of virological properties of these complex DWV recombinants. creator: Dongliang Fei creator: Yaxi Guo creator: Qiong Fan creator: Haoqi Wang creator: Jiadi Wu creator: Ming Li creator: Mingxiao Ma uri: https://doi.org/10.7717/peerj.7214 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fei et al. title: Automatic optic disc detection in colour fundus images by means of multispectral analysis and information content link: https://peerj.com/articles/7119 last-modified: 2019-06-27 description: The optic disc (OD) in retinal fundus images is widely used as a reference in computer-based systems for the measurement of the severity of retinal disease. A number of algorithms have been published in the past 5 years to locate and measure the OD in digital fundus images. Our proposed algorithm, automatically: (i) uses the three channels (RGB) of the digital colour image to locate the region of interest (ROI) where the OD lies, (ii) measures the Shannon information content per channel in the ROI, to decide which channel is most appropriate for searching for the OD centre using the circular Hough transform. A series of evaluations were undertaken to test our hypothesis that using the three channels gives a better performance than a single channel. Three different databases were used for evaluation purposes with a total of 2,371 colour images giving a misdetection error of 3% in the localisation of the centre of the OD. We find that the area determined by our algorithm which assumes that the OD is circular, is similar to that found by other algorithms that detected the shape of the OD. Five metrics were measured for comparison with other recent studies. Combining the two databases where expert delineation of the OD is available (1,240 images), the average results for our multispectral algorithm are: TPR = 0.879, FPR = 0.003, Accuracy = 0.994, Overlap = 80.6% and Dice index = 0.878. creator: M. Elena Martinez-Perez creator: Nicholas Witt creator: Kim H. Parker creator: Alun D. Hughes creator: Simon A.M. Thom uri: https://doi.org/10.7717/peerj.7119 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Martinez-Perez et al. title: Identification of microRNA-21 target genes associated with hair follicle development in sheep link: https://peerj.com/articles/7167 last-modified: 2019-06-27 description: AimThe target molecule regulatory function of microRNA-21 (miR-21) in multiple signalling pathways has become a main focus of genetic and pharmacological regulatory studies of various diseases. The identification of target genes for miRNA-21 in the development of hair follicles can provide new research pathways for the regulation of cell development.MethodsIn the present study, eight six-month-old ewes from Super Merino (SM) and Small Tailed Han (STH) sheep breeds were selected. Target prediction and dual-luciferase wild-type and mutant vectors were used to identify the target genes of miR-21. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and bioinformatics analysis were conducted to analyze the effects of miR-21.ResultsThe results show that the expressions of CNKSR2, KLF3 and TNPO1 were downregulated by miRNA-21 at rates of 36%, 26% and 48%, respectively. Moreover, there was a significant negative correlation between the expression of miR-21 and the three target genes in sheep with two extreme phenotypes. The expression of microRNA-21in October was significantly lower than that in January and February; while the expression of CNKSR2, KLF3 and TNPO1 in October was higher than that in January and February. Conclusions: These results suggest that CNKSR2, KLF3 and TNPO1 are three newly discovered target genes of miR-21 and might be involved in the effects of miR-21 on hair follicle development. creator: Bo Zhai creator: Lichun Zhang creator: Chunxin Wang creator: Zhuo Zhao creator: Mingxin Zhang creator: Xu Li uri: https://doi.org/10.7717/peerj.7167 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhai et al. title: Population-, sex- and individual level divergence in life-history and activity patterns in an annual killifish link: https://peerj.com/articles/7177 last-modified: 2019-06-27 description: Variation in life-history strategies along a slow-fast continuum is largely governed by life-history trade-offs. The pace-of-life syndrome hypothesis (POLS) expands on this idea and suggests coevolution of these traits with personality and physiology at different levels of biological organization. However, it remains unclear to what extent covariation at different levels aligns and if also behavioral patterns such as diurnal activity changes should be incorporated. Here, we investigate variation in life-history traits as well as behavioral variation at the individual, sex and population level in the Turquoise killifish Nothobranchius furzeri. We performed a common garden laboratory experiment with four populations that differ in pond permanence and scored life-history and behavioral (co-) variation at the individual and population level for both males and females. In addition, we focused on diurnal activity change as a behavioral trait that remains understudied in ecology. Our results demonstrate sex-specific variation in adult body size and diurnal activity change among populations that originate from ponds with differences in permanence. However, there was no pond permanence-dependent divergence in maturation time, juvenile growth rate, fecundity and average activity level. With regard to behavior, individuals differed consistently in locomotor activity and diurnal activity change while, in contrast with POLS predictions, we found no indications for life-history and behavioral covariation at any level. Overall, this study illustrates that diurnal activity change differs consistently between individuals, sexes and populations although this variation does not appear to match POLS predictions. creator: Eli S.J. Thoré creator: Arnout F. Grégoir creator: Bart Adriaenssens creator: Charlotte Philippe creator: Robby Stoks creator: Luc Brendonck creator: Tom Pinceel uri: https://doi.org/10.7717/peerj.7177 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Thoré et al. title: Nutritional condition and physiological stress levels of elk in the Black Hills, South Dakota link: https://peerj.com/articles/7185 last-modified: 2019-06-27 description: Percent of body fat and physiological stress are important correlates to wildlife demographics. We studied winter percent of body fat and physiological stress levels for a declining elk (Cervus canadensis nelsoni) population in South Dakota, 2011–2013. We obtained percent of winter body fat, pregnancy status, lactation status, and physiological stress data from 58 adult females (2+ years old). We compared physiological stress level data from 2011 with data collected from this same herd when elk densities were much higher (1995–1997). Our objectives were to determine percent of body fat during winter, examine if winter body fat was correlated with pregnancy and lactation status, and quantify and compare physiological stress hormone values from elk in the mid-1990s. Probability of being pregnant increased with higher winter nutritional condition, or percent of body fat; whereas females with a higher probability of previously lactating were lower in winter body fat. Mean fecal glucocorticoid metabolite (FGM) levels in 2011 (mean = 47.78 ng/g, SE = 2.37) were higher during summer compared to data collected in 1995–1997 (mean = 34.21 ng/g, SE = 3.71); however, mean FGM levels during winter did not differ between the two time periods. Although summer levels of FGM have significantly increased since the mid-1990s, we caution against any interpretation of increased FGM levels on elk fitness, as it may not infer biological significance. Mean winter percent of body fat of elk was lower when compared to other populations in the west but this difference does not appear to be limiting vital rates and population growth for this elk herd. We recommend future research focus on summer/autumn data collection to provide a more comprehensive understanding of percent of body fat for elk in our region. creator: Chadwick P. Lehman creator: Christopher T. Rota creator: Joshua J. Millspaugh uri: https://doi.org/10.7717/peerj.7185 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lehman et al. title: Screening of immunosuppressive factors for biomarkers of breast cancer malignancy phenotypes and subtype-specific targeted therapy link: https://peerj.com/articles/7197 last-modified: 2019-06-27 description: We aimed to screen and validate immunosuppressive factors in luminal- and basal-like breast cancer cell lines and tissue samples associated with malignant phenotypes. The mRNA microarray datasets, GSE40057 and GSE1561, were downloaded and remodeled, and differentially expressed genes were identified. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) and KEGG pathway enrichment analysis were performed to explore the immune-related events related to the basal-like breast cancer. The online resources, GOBO, Kaplan–Meier Plotter and UALCAN, were employed to screen for immunosuppressive factors associated with breast cancer malignant phenotypes. Immunohistochemistry was used to evaluate VEGFA and MIF levels in breast tumors and normal breast tissues; qPCRs and western blots were used to validate the expression of clinical immuno-oncology (IO) therapeutic targets CD274 (PD-L1) and IL8 in cell lines. The results showed that various immune-related events contribute to basal-like breast cancer. First, TGFβ1 and IL8 had higher average expression levels in more malignant cell lines; second, MIF and VEGFA had higher average expression levels in more malignant breast cancer tissues, and the high expression levels were associated with poor survival rate. Third, IO targets CD274 and IL8 which were confirmed to be more suitable for the treatment of basal-like breast cancer. In view of the above, during the formation and development of breast cancer, immune-related genes are always activated, and immunosuppressive factors, IL8, TGFβ1, MIF, and VEGFA are up-regulated. Such molecules could be used as biomarkers for breast cancer prognosis. However, because individual immune-related factors can play several biological roles, the mechanistic relationship between immunosuppressive factors and breast cancer malignant phenotypes and the feasibility of their application as drug targets require further investigation. creator: Ping Wang creator: Jiaxuan Liu creator: Yunlei Song creator: Qiang Liu creator: Chao Wang creator: Caiyun Qian creator: Shuhua Zhang creator: Weifeng Zhu creator: Xiaohong Yang creator: Fusheng Wan creator: Zhuoqi Liu creator: Daya Luo uri: https://doi.org/10.7717/peerj.7197 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Marshland restoration benefits Collembola recruitment: a long-term chronosequence study in Sanjiang mire marshland, China link: https://peerj.com/articles/7198 last-modified: 2019-06-27 description: To examine the biodiversity restoration of marshlands after human-induced disturbances, a long-term chronosequence study of Collembola communities was completed that included cultivated treatment (marshes with 15 years of soybean cultivation; CU15), two restored treatments (with 6 and 12 years of agricultural abandonment; RE06 and RE12, respectively), and an intact marshland (IM) as a reference in the Sanjiang Plain, Northeastern China. Changes in the soil properties and Collembola communities under different treatments were analyzed. Soil parameters (i.e., soil organic carbon, available N, P and K, soil moisture) significantly increased from the cultivated treatment to the 6-year agricultural abandoned, and then 12-year agricultural abandoned treatment, indicating that the degraded soil began to recover after agricultural abandonment. The density, species richness and diversity of Collembola in RE12 were significantly higher than in RE06 and CU15, and even surpass the IM, indicating marshland restoration (after 12 years of agricultural abandonment) benefited recruitment and reconstruction of Collembola community. We found soil surface-dwelling Collembola recovered faster than eu-edaphic species, that is probably due to some common traits (i.e., parthenogenesis and fast dispersal) between epi- and hemi-edaphic species. The changes in the vegetation and soil properties during long-term soybean cultivation and agricultural abandonment were the key factors affecting the composition, density, and species richness of soil Collembola. creator: Yongjing Dou creator: Bing Zhang creator: Xin Sun creator: Liang Chang creator: Donghui Wu uri: https://doi.org/10.7717/peerj.7198 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dou et al. title: Automatic generation of objective footprint outlines link: https://peerj.com/articles/7203 last-modified: 2019-06-27 description: The objective definition of footprint margins poses a central problem in ichnology. The transition from the footprint to the surrounding sediment is often continuous, and the footprint wall complex, requiring interpolation, approximation, and a priori assumptions about trackmaker anatomy to arrive at feasible interpretations of footprint shapes. The degree of subjectivity of such interpretations is substantial, and outlines produced by separate researchers can differ greatly. As a consequence, statistical shape analysis, regardless if based on linear and angular measurements or on the shape as a whole, are neither fully repeatable nor objective. Here I present an algorithm implemented in the programming environment R that is able to generate continuous footprint outlines based on three-dimensional models—fully automatically, objectively, and repeatable. The approach, which is based on contour lines extracted from the model, traces the outline at the point where the slope of the track wall is steepest. An option for automatic landmark placement is implemented for tridactyl footprints. A case study was carried out on 13 footprints of a single trackway of a theropod trackmaker from the Lower Cretaceous of Münchehagen, Germany. Analysis of the landmark coordinates returned by the script did reproduce statistical results published in an earlier study that was based on human-made interpretative drawings, demonstrating the applicability of the present method for the objective and quantitative shape analysis of tracks. Although faint anatomical details are not always recorded and features not related to the foot anatomy may be included, the generated outlines tend to correspond with human-made interpretative drawings regarding the overall shape. While not suited as a full replacement of interpretative drawings, these generated outlines may be used as an objective basis for such interpretations. creator: Jens N. Lallensack uri: https://doi.org/10.7717/peerj.7203 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lallensack title: Biochemical and molecular characterization of N66 from the shell of Pinctada mazatlanica link: https://peerj.com/articles/7212 last-modified: 2019-06-27 description: Mollusk shell mineralization is a tightly controlled process made by shell matrix proteins (SMPs). However, the study of SMPs has been limited to a few model species. In this study, the N66 mRNA of the pearl oyster Pinctada mazatlanica was cloned and functionally characterized. The full sequence of the N66 mRNA comprises 1,766 base pairs, and encodes one N66 protein. A sequence analysis revealed that N66 contained two carbonic anhydrase (CA) domains, a NG domain and several glycosylation sites. The sequence showed similarity to the CA VII but also with its homolog protein nacrein. The native N66 protein was isolated from the shell and identified by mass spectrometry, the peptide sequence matched to the nucleotide sequence obtained. Native N66 is a glycoprotein with a molecular mass of 60–66 kDa which displays CA activity and calcium carbonate precipitation ability in presence of different salts. Also, a recombinant form of N66 was produced in Escherichia coli, and functionally characterized. The recombinant N66 displayed higher CA activity and crystallization capability than the native N66, suggesting that the lack of posttranslational modifications in the recombinant N66 might modulate its activity. creator: Crisalejandra Rivera-Perez creator: Catalina Magallanes-Dominguez creator: Rosa Virginia Dominguez-Beltran creator: Josafat Jehu Ojeda-Ramirez de Areyano creator: Norma Y. Hernandez-Saavedra uri: https://doi.org/10.7717/peerj.7212 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rivera-Perez et al. title: The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae link: https://peerj.com/articles/7216 last-modified: 2019-06-27 description: Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches. creator: Lucile Vigué creator: Adam Eyre-Walker uri: https://doi.org/10.7717/peerj.7216 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Vigué and Eyre-Walker title: Impact of metal oxide nanoparticles on in vitro DNA amplification link: https://peerj.com/articles/7228 last-modified: 2019-06-27 description: Polymerase chain reaction (PCR) is used as an in vitro model system of DNA replication to assess the genotoxicity of nanoparticles (NPs). Prior results showed that several types of NPs inhibited PCR efficiency and increased amplicon error frequency. In this study, we examined the effects of various metal oxide NPs on inhibiting PCR, using high- vs. low-fidelity DNA polymerases; we also examined NP-induced DNA mutation bias at the single nucleotide level. The effects of seven major types of metal oxide NPs (Fe2O3, ZnO, CeO2, Fe3O4, Al2O3, CuO, and TiO2) on PCR replication via a low-fidelity DNA polymerase (Ex Taq) and a high-fidelity DNA polymerase (Phusion) were tested. The successfully amplified PCR products were subsequently sequenced using high-throughput amplicon sequencing. Using consistent proportions of NPs and DNA, we found that the effects of NPs on PCR yield differed depending on the DNA polymerase. Specifically, the efficiency of the high-fidelity DNA polymerase (Phusion) was significantly inhibited by NPs during PCR; such inhibition was not evident in reactions with Ex Taq. Amplicon sequencing showed that the overall error rate of NP-amended PCR was not significantly different from that of PCR without NPs (p > 0.05), and NPs did not introduce single nucleotide polymorphisms during PCR. Thus, overall, NPs inhibited PCR amplification in a DNA polymerase-specific manner, but mutations were not introduced in the process. creator: Chun-Hui Gao creator: Monika Mortimer creator: Ming Zhang creator: Patricia A. Holden creator: Peng Cai creator: Shan Wu creator: Yuexing Xin creator: Yichao Wu creator: Qiaoyun Huang uri: https://doi.org/10.7717/peerj.7228 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gao et al. title: Evaluation of energy balances and greenhouse gas emissions from different agricultural production systems in Minqin Oasis, China link: https://peerj.com/articles/6890 last-modified: 2019-06-26 description: Agricultural production in Minqin Oasis, China, is commonly categorized as intensive crop production (ICP), integrated crop–livestock production (ICLP), intensive livestock production (confined feeding) (IFLP), and extensive livestock production (grazing) (EGLP). The objectives of the present study were to use a life cycle assessment technique to evaluate on-farm energy balances and greenhouse gas (GHG) emissions of agricultural production, and to compare the differences among the four systems. Data used in the present study were collected from published literature and face-to face questionnaires from 529 farms in eight towns (two towns per production system) within Minqin county. The ANOVA of averaged data from 2014 to 2015 indicated that the net energy ratio (Output/Input) for the EGLP system was significantly higher than that for any other system (P < 0.01), whereas the difference among other three systems were not significant. The EGLP system generated lower CO2-eq emissions per hectare of farmland than other systems (P < 0.01). Relating carbon economic efficiency to market values (US$) of agricultural products, indicated that the carbon economic efficiency (US$/kg CO2-eq) of the IFLP system was significantly greater than that of other systems (P < 0.01). The major GHG emission sources varied across the systems, that is, soil respiration is the dominant source in EGLP, while the main sources in IFLP are enteric methane and manure management; in ICLP major sources are enteric methane, soil respiration and fertilizer; and in ICP are soil respiration and fertilizer. The structural equation modelling analysis showed that livestock category was strongly linked to net income. The direct effects and total effects of water use efficiency, via its positive influence on energy balances and GHG emissions were much stronger than those of other dependent variables. The study provides important benchmark information to help develop sustainable agricultural production systems on energy balances and GHG emissions in northwestern China. creator: Zhengang Yan creator: Wei Li creator: Tianhai Yan creator: Shenghua Chang creator: Fujiang Hou uri: https://doi.org/10.7717/peerj.6890 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yan et al. title: Optical microscopic study of surface morphology and filtering efficiency of face masks link: https://peerj.com/articles/7142 last-modified: 2019-06-26 description: BackgroundLow-cost face masks made from different cloth materials are very common in developing countries. The cloth masks (CM) are usually double layered with stretchable ear loops. It is common practice to use such masks for months after multiple washing and drying cycles. If a CM is used for long time, the ear loops become stretched. The loop needs to be knotted to make the mask loop fit better on the face. It is not clear how washing and drying and stretching practices change the quality of a CM. The particulate matter (PM) filtering efficiency of a mask depends on multiple parameters, such as pore size, shape, clearance, and pore number density. It is important to understand the effect of these parameters on the filtering efficiency.MethodsWe characterized the surface of twenty different types of CMs using optical image analysis method. The filtering efficiency of selected cloth face masks was measured using the particle counting method. We also studied the effects of washing and drying and stretching on the quality of a mask.ResultsThe pore size of masks ranged from 80 to 500 μm, which was much bigger than particular matter having diameter of 2.5 μm or less (PM2.5) and 10 μm or less (PM10) size. The PM10 filtering efficiency of four of the selected masks ranged from 63% to 84%. The poor filtering efficiency may have arisen from larger and open pores present in the masks. Interestingly, we found that efficiency dropped by 20% after the 4th washing and drying cycle. We observed a change in pore size and shape and a decrease in microfibers within the pores after washing. Stretching of CM surface also altered the pore size and potentially decreased the filtering efficiency. As compared to CMs, the less frequently used surgical/paper masks had complicated networks of fibers and much smaller pores in multiple layers in comparison to CMs, and therefore had better filtering efficiency. This study showed that the filtering efficiency of cloth face masks were relatively lower, and washing and drying practices deteriorated the efficiency. We believe that the findings of this study will be very helpful for increasing public awareness and help governmental agencies to make proper guidelines and policies for use of face mask. creator: Bhanu Bhakta Neupane creator: Sangita Mainali creator: Amita Sharma creator: Basant Giri uri: https://doi.org/10.7717/peerj.7142 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Neupane et al. title: Validation of endogenous reference genes in rat cerebral cortex for RT-qPCR analyses in developmental toxicity studies link: https://peerj.com/articles/7181 last-modified: 2019-06-26 description: Relative gene expression data obtained from quantitative RT-PCR (RT-qPCR) experiments are dependent on appropriate normalization to represent true values. It is common to use constitutively expressed endogenous reference genes (RGs) for normalization, but for this strategy to be valid the RGs must be stably expressed across all the tested samples. Here, we have tested 10 common RGs for their expression stability in cerebral cortex from young rats after in utero exposure to thyroid hormone (TH) disrupting compounds. We found that all 10 RGs were stable according to the three algorithms geNorm, NormFinder and BestKeeper. The downstream target gene Pvalb was significantly downregulated in brains from young rats after in utero exposure to propylthiouracil (PTU), a medicinal drug inhibiting TH synthesis. Similar results were obtained regardless of which of the 10 RGs was used for normalization. Another potential gene affected by developmental TH disruption, Dio2, was either not affected, or significantly upregulated about 1.4-fold, depending on which RG was used for normalization. This highlights the importance of carefully selecting correct RGs for normalization and to take into account the sensitivity of the RT-qPCR method when reporting on changes to gene expression that are less than 1.5-fold. For future studies examining relative gene expression in rat cerebral cortex under toxicological conditions, we recommend using a combination of either Rps18/Rpl13a or Rps18/Ubc for normalization, but also continuously monitor any potential regulation of the RGs themselves following alterations to study protocols. creator: Louise Ramhøj creator: Marta Axelstad creator: Terje Svingen uri: https://doi.org/10.7717/peerj.7181 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ramhøj et al. title: Recruitment of cyanobacteria by reverse transcription quantitative real-time PCR based on expression of Microcystis gene link: https://peerj.com/articles/7188 last-modified: 2019-06-26 description: In this study, a SYBR Green quantitative real-time PCR method was established and applied. Relative expression of the synthetic genes from Microcystis gas vesicles (gvpC), algal toxin genes (mcyA), and polysaccharides (espL) from water and sediments of Meiliang Bay and from the center of Lake Taihu were tested from January to June, 2017. Indoor Microcystis aeruginosa was used as the control group. The kit for total RNA extraction in Microcystis was optimized. Results showed that the optimized kit extracted high-concentrations and high-quality total RNA from Microcystis. The extraction purity and concentration were significantly higher than those extracted by the original kit. The transcription level of gvpC increased gradually until a peak was reached in March. However, expression of gvpC decreased continuously at the proliferating and floating stages of Cyanobacterial biomass. The maximum level of expression of gvpC in April in comparison to expression of mcyA in March occurred first. We found that the SYBR Green qRT-PCR method, which is characterized by high specificity, repeatability, is rapid, and can be used for quantitative detection of expression of gvpC, mcyA, and espL. The recruitment of cyanobacteria is the process in which cyanobacteria in the sediment began to regain their activity, started to grow and migrated to the water column. creator: Long Yu creator: Xiaofei Wu creator: Yang Yu creator: Limei Shi creator: Min Zhang uri: https://doi.org/10.7717/peerj.7188 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yu et al. title: Evaluation of extracellular polymeric substances extracted from waste activated sludge as a renewable corrosion inhibitor link: https://peerj.com/articles/7193 last-modified: 2019-06-26 description: BackgroundWaste activated sludge (WAS) has recently gained attention as a feedstock for resource recovery. The aim of this study is to investigate the corrosion inhibition efficiencies of extracellular polymeric substances (EPS) extracted from WAS.MethodsThe studied corrosion inhibitors were tested with carbon steel in 3.64% NaCl saturated with CO2 at 25 °C, which is the typical oilfield environment. They were first prepared by EPS extraction (heating at 80 °C), followed by centrifugation for solid and liquid separation, then the supernatant was freeze-thawed five times for sterilization of microorganisms in WAS to terminate metabolic activities in the test inhibitors to ensure consistency in corrosion inhibition. The EPS mixture (supernatant) was then deemed as the test corrosion inhibitor. The inhibition performance was determined using potentiodynamic polarization scans.ResultsWaste activated sludge alone showed unsatisfactory inhibition. However, EPS extracted from WAS showed an optimum inhibition of approximately 80% with 1,000 mg/L of inhibitor. The average total solid (TS) and EPS contents of the WAS were 7,330 mg TS/L WAS and 110 mg EPS/g TS, respectively. Three sets of extracted EPS were scanned with fourier-transform infrared spectroscopy (FTIR) and showed almost overlapping curves, yielding the consistent inhibition performance.DiscussionThe potentiodynamic polarization results indicated that EPS acts as a mixed-type inhibitor which inhibits corrosion on both anode and cathode sites of metal surfaces. Based on the FTIR results, it was assumed that major chemical groups O–H, N–H, C–N, C=O, and C–H contributed to the inhibition by adsorbing on the metal surface, forming a biofilm that acts as a protective barrier to isolate the metal from its corrosive environment. Results show that WAS EPS corrosion inhibitors have inhibition performance comparable to commercial products, signifying their potential in commercialization. This corrosion inhibitor is renewable, biodegradable, non-toxic, and free from heavy metal, making it a superior green corrosion inhibitor candidate. Additionally, turning biomass into value-added product can be beneficial to the environment and, in this case, deriving new materials from WAS could also transform the economics of wastewater treatment operations. creator: Liew Chien Go creator: William Holmes creator: Dilip Depan creator: Rafael Hernandez uri: https://doi.org/10.7717/peerj.7193 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Go et al. title: Determination of the evolutionary pressure on Camellia oleifera on Hainan Island using the complete chloroplast genome sequence link: https://peerj.com/articles/7210 last-modified: 2019-06-26 description: Camellia oleifera is one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study used C. oleifera that was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies of Camellia plants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of Hainan C. oleifera. The results showed that the whole chloroplast genome of C. oleifera in Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of Hainan C. oleifera’s chloroplast genome was 37.29%. The chloroplast genome structure characteristics of Hainan C. oleifera were compared with mainland C. oleifera and those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of Hainan C. oleifera, and all Camellia plants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that Hainan C. oleifera had a similar evolutionary relationship with C. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family. creator: Wan Zhang creator: Yunlin Zhao creator: Guiyan Yang creator: Jiao Peng creator: Shuwen Chen creator: Zhenggang Xu uri: https://doi.org/10.7717/peerj.7210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Cancer driver genes: a guilty by resemblance doctrine link: https://peerj.com/articles/6979 last-modified: 2019-06-25 description: A major benefit of expansive cancer genome projects is the discovery of new targets for drug treatment and development. To date, cancer driver genes have been primarily identified by methods based on gene mutation frequency. This approach fails to identify culpable genes that are not mutated, rarely mutated, or contribute to the development of rare forms of cancer. Due to the complexity of the disease and the sheer volume of data, computational methods may encounter a NP-complete problem. We have developed a novel pathway and reach (PAR) method that employs a guilty by resemblance approach to identify cancer driver genes that avoids the above problems. Essentially PAR sifts through a list of genes of biological pathways to find those that are common to the same pathways and possess a similar 2-reach topology metric as a reference set of recognized driver genes. This approach leads to faster processing times and eliminates any dependency on gene mutation frequency. Out of the three pathways, signal transduction, immune system, and gene expression, a set of 50 candidate driver genes were identified, 30 of which were new. The top five were HGF, E2F1, C6, MIF, and CDK2. creator: Emilie Ramsahai creator: Vrijesh Tripathi creator: Melford John uri: https://doi.org/10.7717/peerj.6979 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ramsahai et al. title: Comparison of soil bacterial community and functional characteristics following afforestation in the semi-arid areas link: https://peerj.com/articles/7141 last-modified: 2019-06-25 description: Changes in soil bacterial communities, which are crucial for the assessment of ecological restoration in Chinese plantations, have never been studied in the “Three North Shelterbelt” project in the semi-arid areas. We used high-throughput sequencing of the 16S rDNA gene to investigate the soil bacterial community diversity, structure, and functional characteristics in three plantation forests, including Populus × canadensis Moench (PC), Pinus sylvestris var. mongolica (PS), and Pinus tabuliformis (PT). In addition, soil environment factors were measured. There were distinct differences in soil characteristics among different plantation forests. Compared to PS and PT, PC had a higher soil pH, dissolved organic carbon (DOC), and available P, as well as a lower C/N ratio. Furthermore, afforestation with different tree species significantly altered the abundance of Proteobacteria, and Chloroflexi in the soil, and its influence on the bacterial diversity indices. The bacterial community compositions and functional groups related to C and N cycling from PS, and PT were grouped tightly, indicating that the soil bacterial phylogenetic distance of PS and PT were closer than that between PS plus PT and PC. Our results implied that the soil characteristics, as well as the diversity, compositions and functions related to C and N cycling of soil bacterial community obviously differed from the following afforestation, especially between PC and PS plus PT, which in turn enormously established the correlation between the soil microbial community characteristics and the afforestation tree species. creator: Jiaojiao Deng creator: Yan Zhang creator: You Yin creator: Xu Zhu creator: Wenxu Zhu creator: Yongbin Zhou uri: https://doi.org/10.7717/peerj.7141 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Deng et al. title: False head complexity and evidence of predator attacks in male and female hairstreak butterflies (Lepidoptera: Theclinae: Eumaeini) from Mexico link: https://peerj.com/articles/7143 last-modified: 2019-06-25 description: In many butterfly species, the posterior end of the hindwings of individuals perching with their wings closed resembles a butterfly head. This “false head” pattern is considered an adaptation to deflect predator attacks to less vulnerable parts of the body. The presence of symmetrical damage in left and right wings is considered evidence of failed predator attacks to perching butterflies. In this research, we tested the prediction derived from the deflection hypothesis that the degree of resemblance of the false head area (FH) to a real head, as measured by the number of FH “components” (eyespots, “false antennae”, modified outline of the FH area and lines converging on the FH area) present in the hindwings, is positively correlated to the frequency of symmetrical damage in the FH area. We studied specimens from two scientific collections of butterflies of the subfamily Theclinae (Lycaenidae) belonging to the Universidad Nacional Autónoma de México (Colección Nacional de Insectos [CNIN] and Museo de Zoología, Facultad de Ciencias [MZFC]). We scored the presence of symmetrical damage in a sample of 20,709 specimens (CNIN: 3,722; MZFC: 16,987) from 126 species (CNIN: 78 species; MZFC: 117 species; 71 species shared by both collections) whose hindwings vary in the number of FH components, and found that, as predicted, the proportion of specimens with symmetrical damage increases as the number of FH components increases. We also tested the hypothesis that behavioural differences between the sexes makes males more prone to receive predator attacks and, thus, we predicted a higher frequency of symmetrical damage in the FH of males than in that of females. We found that the frequency of symmetrical damage was not significantly different between males and females, suggesting that behavioural differences between the sexes produce no differences in the risk of being attacked. Overall, our results provide support to the idea that the FH of butterflies is an adaptation that deflects predator attacks to less vulnerable parts of the body in both sexes. creator: Eric Novelo Galicia creator: Moisés Armando Luis Martínez creator: Carlos Cordero uri: https://doi.org/10.7717/peerj.7143 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Novelo Galicia et al. title: Freshwater reservoir offsets on radiocarbon-dated dog bone from the headwaters of the St. Lawrence River, USA link: https://peerj.com/articles/7174 last-modified: 2019-06-25 description: Isotopic analysis of dog (Canis lupus familiaris) bone recovered from archaeological sites as proxies for human bone is becoming common in North America. Chronological placement of the dogs is often determined through radiocarbon dating of dog bone. The Great Lakes, their tributaries, and nearby lakes and streams were important fisheries for Native Americans prior to and after sustained European presence in the region. Carbon entering the food web in freshwater systems is often not in full isotopic equilibrium with the atmosphere, giving rise to spuriously old radiocarbon ages in fish, other aquatic organisms, and their consumers. These freshwater reservoir offsets (FROs) have been noted on human and dog bone in several areas of the world. Here we report the results of multi-tracer Bayesian dietary modeling using δ15N and δ13C values on dog bone collagen from mid-fifteenth to mid-sixteenth-century Iroquoian village sites at the headwaters of the St. Lawrence River, New York, USA. Results indicate that fish was an important component of dog diets. A comparison of radiocarbon dates on dog bone with dates on deer bone or maize from the same sites indicate FROs ranging from 97 ± 24 to 220 ± 39 14Cyr with a weighted mean of 132 ± 8 14Cyr. These results suggest that dog bone should not be used for radiocarbon dating in the absence of modeling to determine fish consumption and that previously reported radiocarbon dates on human bone from the larger region are likely to have FROs given the known importance of fish in regional human diets. creator: John P. Hart creator: Robert S. Feranec creator: Timothy J. Abel creator: Jessica L. Vavrasek uri: https://doi.org/10.7717/peerj.7174 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hart et al. title: Influence of adiposity and fatigue on the scapular muscle recruitment order link: https://peerj.com/articles/7175 last-modified: 2019-06-25 description: BackgroundSeveral authors have indicated that excess body weight can modify the electromyographic (EMG) amplitude due to the accumulation of subcutaneous fat. This accumulation of adipose tissue around the muscle would affect the metabolic capacity during functional activities. On the other hand, some authors have not observed differences in the myoelectric manifestations of fatigue between normal weight and obese people. Furthermore, these manifestations have not been investigated regarding EMG onset latency, which indicates a pattern of muscle activation between different muscles. The objective of this study was to determine whether an increase in body weight, skinfolds, and muscle fatigue modify the trapezius and serratus anterior (SA) onset latencies and to determine the scapular muscle recruitment order in fatigue and excess body weight conditions.MethodsThis cross-sectional study was carried out in a university laboratory. The participants were randomly assigned to the no-fatigue group (17 participants) or the fatigue (17 participants) group. The body mass index, skinfold thickness (axillary, pectoral, and subscapular), and percentage of body fat were measured. In addition, the onset latency of the scapular muscles [lower trapezius (LT), middle trapezius (MT), upper trapezius (UT), and SA] was assessed by surface EMG during the performance of a voluntary arm raise task. A multiple linear regression model was adjusted and analyzed for the additive combination of the variables, percentage body fat, skinfold thickness, and fatigue. The differences in onset latency between the scapular muscles were analyzed using a three-way repeated measure analysis of variance. In all the tests, an alpha level <0.05 was considered statistically significant.ResultsFor the MT, LT, and SA onset latencies, the body mass index was associated with a delayed onset latency when it was adjusted for the additive combination of percentage of body fat, skinfold thickness, and fatigue. Of these adjustment factors, the subscapular skinfold thickness (R2 = 0.51; β = 10.7; p = 0.001) and fatigue (R2 = 0.86; β = 95.4; p = 0.001) primarily contributed to the increase in SA onset latency. A significant muscle ×body mass index ×fatigue interaction (F = 4.182; p = 0.008) was observed. In the fatigue/excess body weight condition, the UT was activated significantly earlier than the other three scapular muscles (p < 0.001) and SA activation was significantly delayed compared to LT (p < 0.001).DiscussionExcess body weight, adjusted for skinfold thickness (axillary and subscapular) and fatigue, increases the onset latency of the MT, LT, and SA muscles and modifies the recruitment order of scapular muscles. In fact, the scapular stabilizing muscles (MT, LT, and SA) increase their onset latency in comparison to the UT muscle. These results were not observed when excess body weight was considered as an individual variable or when adjusted by the percentage body fat. creator: Guillermo Mendez-Rebolledo creator: Eduardo Guzman-Muñoz creator: Rodrigo Ramírez-Campillo creator: Pablo Valdés-Badilla creator: Carlos Cruz-Montecinos creator: Juan Morales-Verdugo creator: Francisco Jose Berral de la Rosa uri: https://doi.org/10.7717/peerj.7175 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mendez-Rebolledo et al. title: Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts link: https://peerj.com/articles/7178 last-modified: 2019-06-25 description: Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae. creator: Joshua I. Brian creator: Simon K. Davy creator: Shaun P. Wilkinson uri: https://doi.org/10.7717/peerj.7178 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Brian et al. title: Updated advances of linking psychosocial factors and sex hormones with systemic lupus erythematosus susceptibility and development link: https://peerj.com/articles/7179 last-modified: 2019-06-25 description: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that primarily affects women, especially those of reproductive age. Genetics, environment, and gene-environment interactions play key roles in the development of SLE. Despite the numerous susceptibility genes of SLE identified to date, gene therapy is far from a clinical reality. Thus, more attention should be paid to the risk factors and underlying mechanisms of SLE. Currently, it is reported that psychosocial factors and sex hormones play vital roles in patients with SLE, which still need further investigated. The purpose of this review is to update the roles and mechanisms of psychosocial factors and sex hormones in the susceptibility and development of SLE. Based on review articles and reports in reputable peer-reviewed journals and government websites, this paper summarized psychosocial factors (e.g., alexithymia, depression, anxiety, negative emotions, and perceived stress) and sex hormones (e.g., estrogens, progesterone, androgens, and prolactin) involved in SLE. We further explore the mechanisms linking these factors with SLE susceptibility and development, which can guide the establishment of practical measures to benefit SLE patients and offer new ideas for therapeutic strategies. creator: Qingjun Pan creator: Xiaoqun Chen creator: Shuzhen Liao creator: Xiaocui Chen creator: Chunfei Zhao creator: Yong-zhi Xu creator: Hua-feng Liu uri: https://doi.org/10.7717/peerj.7179 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pan et al. title: Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend link: https://peerj.com/articles/7204 last-modified: 2019-06-25 description: It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution. creator: Kai Wei creator: Lei Ma creator: Tingting Zhang uri: https://doi.org/10.7717/peerj.7204 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wei et al. title: Performance of Modified Early Warning Score (MEWS) and Circulation, Respiration, Abdomen, Motor, and Speech (CRAMS) score in trauma severity and in-hospital mortality prediction in multiple trauma patients: a comparison study link: https://peerj.com/articles/7227 last-modified: 2019-06-25 description: BackgroundWith an increasing number of motor vehicle crashes, there is an urgent need in emergency departments (EDs) to assess patients with multiple trauma quickly, easily, and reliably. Trauma severity can range from a minor to major threats to life or bodily function. In-hospital mortality and trauma severity prediction in such cases is crucial in the ED for the management of multiple trauma and improvement of the outcome of these patients. Previous studies have examined the performance of Modified Early Warning Score (MEWS) or Circulation, Respiration, Abdomen, Motor, and Speech (CRAMS) score based solely on mortality prediction or injury severity prediction. However, to the best of our knowledge, the performances of both scoring systems on in-hospital mortality and trauma severity prediction have not been compared previously. This retrospective study evaluated the value of MEWS and CRAMS score to predict in-hospital mortality and trauma severity in patients presenting to the ED with multiple traumatic injuries.MethodsAll study subjects were multiple trauma patients. Medical data of 1,127 patients were analyzed between January 2014 and April 2018. The MEWS and CRAMS score were calculated, and logistic regression and receiver operating characteristic curve analysis were conducted to investigate their performances regarding in-hospital mortality and trauma severity prediction.ResultsFor in-hospital mortality prediction, the areas under the receiver operating characteristic curve (AUROCs) for MEWS and CRAMS score were 0.90 and 0.91, respectively, indicating that both of them were good in-hospital mortality predictors. Further, our study indicated that the CRAMS score performed better in trauma severity prediction, with an AUROC value of 0.84, which was higher than that of MEWS (AUROC = 0.77). For trauma severity prediction, the optimal cut-off value for MEWS was 2, while that of the CRAMS score was 8.ConclusionsWe found that both MEWS and CRAMS score can be used as predictors for trauma severity and in-hospital mortality for multiple trauma patients, but that CRAMS score was superior to MEWS for trauma severity prediction. CRAMS score should be prioritized in the prediction of trauma severity due to its excellence as a multiple trauma triage tool and potential contribution to rapid emergency rescue decisions. creator: Xiaobin Jiang creator: Ping Jiang creator: Yuanshen Mao uri: https://doi.org/10.7717/peerj.7227 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jiang et al. title: Expression of osteopontin, matrix metalloproteinase-2 and -9 proteins in vascular instability in brain arteriovenous malformation link: https://peerj.com/articles/7058 last-modified: 2019-06-24 description: BackgroundMatrix metalloproteinase (MMP)-2 and -9 are Osteopontin (OPN) dependent molecules implicated in the destabilization of blood vessels. OPN and MMPs have been studied in brain arteriovenous malformation (BAVM) patients’ tissues and blood samples before intervention. In this study, we compared the serum level of these markers before and after treatment, as well as assessed their protein expressions in BAVM tissues to evaluate their roles in this disease.MethodologySerum samples from six BAVM patients and three control subjects were analyzed using enzyme-linked immunoabsorbent assay (ELISA) for OPN. A total of 10 BAVM patients and five control subjects were analyzed using Multiplex ELISA for MMPs. A total of 16 BAVM tissue samples and two normal brain tissue samples were analyzed using immunohistochemistry.ResultMMP-2 and -9 were significantly higher in the serum of BAVM patients before and after treatment than in control patients. There were no significant differences of OPN and MMP-9 serum level in BAVM patients before and after treatment. MMP-2 showed a significant elevation after the treatment. Expression of OPN, MMP-2 and -9 proteins were seen in endothelial cells, perivascular cells and brain parenchyma of BAVM tissues.ConclusionFindings revealed that the level of MMP-2 and -9 in the serum correlated well with the expression in BAVM tissues in several cases. Knockdown studies will be required to determine the relationships and mechanisms of action of these markers in the near future. In addition, studies will be required to investigate the expression of these markers’ potential applications as primary medical therapy targets for BAVM patients. creator: Lalita Anbarasen creator: Jasmine Lim creator: Retnagowri Rajandram creator: Kein Seong Mun creator: Sheau Fung Sia uri: https://doi.org/10.7717/peerj.7058 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Anbarasen et al. title: Do human screams permit individual recognition? link: https://peerj.com/articles/7087 last-modified: 2019-06-24 description: The recognition of individuals through vocalizations is a highly adaptive ability in the social behavior of many species, including humans. However, the extent to which nonlinguistic vocalizations such as screams permit individual recognition in humans remains unclear. Using a same-different vocalizer discrimination task, we investigated participants’ ability to correctly identify whether pairs of screams were produced by the same person or two different people, a critical prerequisite to individual recognition. Despite prior theory-based contentions that screams are not acoustically well-suited to conveying identity cues, listeners discriminated individuals at above-chance levels by their screams, including both acoustically modified and unmodified exemplars. We found that vocalizer gender explained some variation in participants’ discrimination abilities and response times, but participant attributes (gender, experience, empathy) did not. Our findings are consistent with abundant evidence from nonhuman primates, suggesting that both human and nonhuman screams convey cues to caller identity, thus supporting the thesis of evolutionary continuity in at least some aspects of scream function across primate species. creator: Jonathan W. M. Engelberg creator: Jay W. Schwartz creator: Harold Gouzoules uri: https://doi.org/10.7717/peerj.7087 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Engelberg et al. title: Sevoflurane postconditioning alleviates hypoxia-reoxygenation injury of cardiomyocytes by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway link: https://peerj.com/articles/7165 last-modified: 2019-06-24 description: BackgroundSevoflurane postconditioning (SpostC) can alleviate hypoxia-reoxygenation injury of cardiomyocytes; however, the specific mechanism remains unclear. This study aimed to investigate whether SpostC promotes mitochondrial autophagy through the hypoxia-inducible factor-1 (HIF-1)/BCL2/adenovirus E1B 19-kDa-interacting protein 3 (BNIP3) signaling pathway to attenuate hypoxia-reoxygenation injury in cardiomyocytes.MethodsThe H9C2 cardiomyocyte hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the beginning of reoxygenation. Cell damage was determined by measuring cell viability, lactate dehydrogenase activity, and apoptosis. Mitochondrial ultrastructural and autophagosomes were observed by transmission electron microscope. Western blotting was used to examine the expression of HIF-1, BNIP3, and Beclin-1 proteins. The effects of BNIP3 on promoting autophagy were determined using interfering RNA technology to silence BNIP3.ResultsHypoxia-reoxygenation injury led to accumulation of autophagosomes in cardiomyocytes, and cell viability was significantly reduced, which seriously damaged cells. Sevoflurane postconditioning could upregulate HIF-1α and BNIP3 protein expression, promote autophagosome clearance, and reduce cell damage. However, these protective effects were inhibited by 2-methoxyestradiol or sinBNIP3.ConclusionSevoflurane postconditioning can alleviate hypoxia-reoxygenation injury in cardiomyocytes, and this effect may be achieved by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway. creator: Long Yang creator: Jianjiang Wu creator: Peng Xie creator: Jin Yu creator: Xin Li creator: Jiang Wang creator: Hong Zheng uri: https://doi.org/10.7717/peerj.7165 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: Osteology and phylogeny of Robustichthys luopingensis, the largest holostean fish in the Middle Triassic link: https://peerj.com/articles/7184 last-modified: 2019-06-24 description: The extinct ray-finned fish taxon Robustichthys luopingensis from Luoping, eastern Yunnan, China represents the largest holostean known in the Middle Triassic. Despite its potential significance for investigating the holostean phylogeny and reconstructing the Triassic marine ecosystems, Robustichthys has so far not been described in detail and its phylogenetic position within the Holostei was controversy. This study provides a redescription and revision of Robustichthys based upon a comparative study of eight type specimens and nine new specimens. Newly recognized information includes a toothed parasphenoid, a pair of premaxillae not pierced by the olfactory nerve, a splint-like quadratojugal, a hatchet-shaped hyomandibula, an hourglass-shaped symplectic, anterior and posterior ceratohyals, a complete series of branchiostegal rays, and sclerotic bones. A revised reconstruction of Robustichthys is presented. Results of a cladistic analysis confirmed Robustichthys as an ionoscopiform within the Halecomorphi; the previous placements of Robustichthys as a basal ginglymodian and Ionoscopidae as a basal amiiform clade are not supported. The sister group relationship between Sinamiinae (Sinamia and Ikechaoamia) and Amiinae (Amia and Cyclurus) within the Amiidae is newly recognized. This revised topology provides new insights into the evolution and historical paleoecology of halecomorph fishes. creator: Guang-Hui Xu uri: https://doi.org/10.7717/peerj.7184 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xu title: Isolation and identification of a halophilic and alkaliphilic microalgal strain link: https://peerj.com/articles/7189 last-modified: 2019-06-24 description: Halophilic and alkaliphilic microalgal strain SAE1 was isolated from the saline–alkaline soil of Songnen Plain of Northeast China. Morphological observation revealed that SAE1 has a simple cellular structure, single cell, spherical, diameter of four to six μm, cell wall of about 0.22 μm thick, two chloroplasts and one nucleus. Analysis of the phylogenetic tree constructed by 18S sequence homology suggests that SAE1 is highly homologous to Nannochloris sp. BLD-15, with only four base substitutions in the homologous region. SAE1 was initially considered as Nannochloris sp. Analysis of the halophilic and alkaliphilic characteristics of SAE1 indicates that it can grow under one M NaHCO3 and NaCl concentrations, with optimal growth under 400 mM NaHCO3 and 200 mM NaCl. The intracellular ultrastructure of SAE1 significantly changed after NaCl and NaHCO3 treatments. A large number of starch grains accumulated after treatment with 400 mM NaHCO3 in cells, but few were found after treatment with 200 mM NaCl and none in the living condition without treatment. We conjectured that one of the metabolic characteristics of alkaliphilic (NaHCO3) microalga SAE1 is the formation of massive starch grains, which induce glycerol anabolism and increase osmotic pressure, thereby enhancing its ability to resist saline–sodic conditions. This feature of alkaliphilic (NaHCO3) microalga SAE1 contributes to its growth in the carbonate soil of Songnen Plain. creator: Chenxi Liu creator: Jiali Liu creator: Songmiao Hu creator: Xin Wang creator: Xuhui Wang creator: Qingjie Guan uri: https://doi.org/10.7717/peerj.7189 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Decoupled recovery of ecological communities after reclamation link: https://peerj.com/articles/7038 last-modified: 2019-06-21 description: Grassland restoration is largely focused on creating plant communities that match reference conditions. However, these communities reflect only a subset of the biodiversity of grassland systems. We conducted a multi-trophic study to assess ecosystem recovery following energy development for oil and gas extraction in northern US Great Plains rangelands. We compared soil factors, plant species composition and cover, and nematode trophic structuring between reclaimed oil and gas well sites (“reclaims”) that comprise a chronosequence of two—33 years since reclamation and adjacent, undeveloped rangeland at distances of 50 m and 150 m from reclaim edges. Soils and plant communities in reclaims did not match those on undeveloped rangeland even after 33 years. Reclaimed soils had higher salt concentrations and pH than undeveloped soils. Reclaims had lower overall plant cover, a greater proportion of exotic and ruderal plant cover and lower native plant species richness than undeveloped rangeland. However, nematode communities appear to have recovered following reclamation. Although total and omni-carnivorous nematode abundances differed between reclaimed well sites and undeveloped rangeland, community composition and structure did not. These findings suggest that current reclamation practices recover the functional composition of nematode communities, but not soil conditions or plant communities. Our results show that plant communities have failed to recover through reclamation: high soil salinity may create a persistent impediment to native plant growth and ecosystem recovery. creator: Zachary A. Sylvain creator: David H. Branson creator: Tatyana A. Rand creator: Natalie M. West creator: Erin K. Espeland uri: https://doi.org/10.7717/peerj.7038 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling link: https://peerj.com/articles/7044 last-modified: 2019-06-21 description: The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts. creator: Angie Estrada creator: Myra C. Hughey creator: Daniel Medina creator: Eria A. Rebollar creator: Jenifer B. Walke creator: Reid N. Harris creator: Lisa K. Belden uri: https://doi.org/10.7717/peerj.7044 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Estrada et al. title: Description and classification of bivalve mollusks hemocytes: a computational approach link: https://peerj.com/articles/7056 last-modified: 2019-06-21 description: The fractal formalism in combination with linear image analysis enables statistically significant description and classification of “irregular” (in terms of Euclidean geometry) shapes, such as, outlines of in vitro flattened cells. We developed an optimal model for classifying bivalve Spisula sachalinensis and Callista brevisiphonata immune cells, based on evaluating their linear and non-linear morphological features: size characteristics (area, perimeter), various parameters of cell bounding circle, convex hull, cell symmetry, roundness, and a number of fractal dimensions and lacunarities evaluating the spatial complexity of cells. Proposed classification model is based on Ward’s clustering method, loaded with highest multimodality index factors. This classification scheme groups cells into three morphological types, which can be distinguished both visually and by several linear and quasi-fractal parameters. creator: Yuriy A. Karetin creator: Aleksandra A. Kalitnik creator: Alina E. Safonova creator: Eduardas Cicinskas uri: https://doi.org/10.7717/peerj.7056 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Karetin et al. title: SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus link: https://peerj.com/articles/7062 last-modified: 2019-06-21 description: BackgroundAnanas comosus var. bracteatus is an herbaceous perennial monocot cultivated as an ornamental plant for its chimeric leaves. Because of its genomic complexity, and because no genomic information is available in the public GenBank database, the complete structure of the mRNA transcript is unclear and there are limited molecular mechanism studies for Ananas comosus var. bracteatus.MethodsThree size fractionated full-length cDNA libraries (1–2 kb, 2–3 kb, and 3–6 kb) were constructed and subsequently sequenced in five single-molecule real-time (SMRT) cells (2 cells, 2 cells, and 1 cell, respectively).ResultsIn total, 19,838 transcripts were identified for alternative splicing (AS) analysis. Among them, 19,185 (96.7%) transcripts were functionally annotated. A total of 9,921 genes were identified by mapping the non-redundant isoforms to the reference genome. A total of 10,649 AS events were identified, the majority of which were intron retention events. The alternatively spliced genes had functions in the basic metabolism processes of the plant such as carbon metabolism, amino acid biosynthesis, and glycolysis. Fourteen genes related to chlorophyll biosynthesis were identified as having AS events. The distribution of the splicing sites and the percentage of conventional and non-canonical AS sites of the genes categorized in pathways related to the albino leaf phenotype (ko00860, ko00195, ko00196, and ko00710) varied greatly. The present results showed that there were 8,316 genes carrying at least one poly (A) site, which generated 21,873 poly (A) sites. These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. bracteatus. creator: Jun Ma creator: Yixuan Xiang creator: Yingyuan Xiong creator: Zhen Lin creator: Yanbin Xue creator: Meiqin Mao creator: Lingxia Sun creator: Yujue Zhou creator: Xi Li creator: Zhuo Huang uri: https://doi.org/10.7717/peerj.7062 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Isolation and functional characterization of two dioxygenases putatively involved in bixin biosynthesis in annatto (Bixa orellana L.) link: https://peerj.com/articles/7064 last-modified: 2019-06-21 description: Carotenoid cleavage dioxygenases (CCDs) are enzymes that have been implicated in the biosynthesis of a wide diversity of secondary metabolites with important economic value, including bixin. Bixin is the second most used pigment in the world’s food industry worldwide, and its main source is the aril of achiote (Bixa orellana L.) seeds. A recent transcriptome analysis of B. orellana identified a new set of eight CCD members (BoCCD4s and BoCCD1s) potentially involved in bixin synthesis. We used several approaches in order to discriminate the best candidates with CCDs genes. A reverse transcription-PCR (RT-qPCR) expression analysis was carried out in five developmental stages of two accessions of B. orellana seeds with different bixin contents: (P13W, low bixin producer and N4P, high bixin producer). The results showed that three BoCCDs (BoCCD4-1, BoCCD4-3, and BoCCD1-1) had an expression pattern consistent with bixin accumulation during seed development. Additionally, an alignment of the CCD enzyme family and homology models of proteins were generated to verify whether the newly proposed CCD enzymes were bona fide CCDs. The study confirmed that these three enzymes were well-preserved and belonged to the CCD family. In a second selection round, the three CCD genes were analyzed by in situ RT-qPCR in seed tissue. Results indicated that BoCCD4-3 and BoCCD1-1 exhibited tissue-specific expressions in the seed aril. To test whether the two selected CCDs had enzymatic activity, they were expressed in Escherichia coli; activity was determined by identifying their products in the crude extract using UHPLC-ESI-QTOF-MS/MS. The cleavage product (bixin aldehyde) was also analyzed by Fourier transform infrared. The results indicated that both BoCCD4-3 and BoCCD1-1 cleave lycopene in vitro at 5,6-5′,6′. creator: Victor Manuel Carballo-Uicab creator: Yair Cárdenas-Conejo creator: Alba Adriana Vallejo-Cardona creator: Margarita Aguilar-Espinosa creator: Jacobo Rodríguez-Campos creator: Hugo Serrano-Posada creator: José Alberto Narváez-Zapata creator: Felipe Vázquez-Flota creator: Renata Rivera-Madrid uri: https://doi.org/10.7717/peerj.7064 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Carballo-Uicab et al. title: Wnt signaling in liver disease: emerging trends from a bibliometric perspective link: https://peerj.com/articles/7073 last-modified: 2019-06-21 description: BackgroundThe Wnt signaling pathway, an evolutionarily conserved molecular transduction cascade, has been identified as playing a pivotal role in various physiological and pathological processes of the liver, including homeostasis, regeneration, cirrhosis, and hepatocellular carcinoma (HCC). In this study, we aimed to use a bibliometric method to evaluate the emerging trends on Wnt signaling in liver diseases.MethodsArticles were retrieved from the Web of Science Core Collection. We used a bibliometric software, CiteSpace V 5.3.R4, to analyze the active countries or institutions in the research field, the landmark manuscripts, important subtopics, and evolution of scientific ideas.ResultsIn total, 1,768 manuscripts were published, and each was cited 33.12 times on average. The U.S. published most of the articles, and the most active center was the University of Pittsburgh. The top 5 landmark papers were identified by four bibliometric indexes including citation, burstness, centrality, and usage 2013. The clustering process divided the whole area into nine research subtopics, and the two major important subtopics were “liver zonation” and “HCC.” Using the “Part-of-Speech” technique, 1,743 terms representing scientific ideas were identified. After 2008, the bursting phrases were “liver development,” “progenitor cells,” “hepatic stellate cells,” “liver regeneration,” “liver fibrosis,” “epithelial-mesenchymal transition,” and etc.ConclusionUsing bibliometric methods, we quantitatively summarized the advancements and emerging trends in Wnt signaling in liver diseases. These bibliometric findings may pioneer the future direction of this field in the next few years, and further studies are needed. creator: Guangyi Jiang creator: Chiung-Kuei Huang creator: Xinjie Zhang creator: Xingyu Lv creator: Yifan Wang creator: Tunan Yu creator: Xiujun Cai uri: https://doi.org/10.7717/peerj.7073 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jiang et al. title: Metabolomic and biochemical characterization of a new model of the transition of acute kidney injury to chronic kidney disease induced by folic acid link: https://peerj.com/articles/7113 last-modified: 2019-06-21 description: BackgroundRenal diseases represent a major public health problem. The demonstration that maladaptive repair of acute kidney injury (AKI) can lead to the development of chronic kidney disease (CKD) and end-stage renal disease has generated interest in studying the pathophysiological pathways involved. Animal models of AKI–CKD transition represent important tools to study this pathology. We hypothesized that the administration of multiple doses of folic acid (FA) would lead to a progressive loss of renal function that could be characterized through biochemical parameters, histological classification and nuclear magnetic resonance (NMR) profiling.MethodsWistar rats were divided into groups: the control group received a daily intraperitoneal (I.P.) injection of double-distilled water, the experimental group received a daily I.P. injection of FA (250 mg kg body weight−1). Disease was classified according to blood urea nitrogen level: mild (40–80 mg dL−1), moderate (100–200 mg dL−1) and severe (>200 mg dL−1). We analyzed through biochemical parameters, histological classification and NMR profiling.ResultsBiochemical markers, pro-inflammatory cytokines and kidney injury biomarkers differed significantly (P < 0.05) between control and experimental groups. Histology revealed that as damage progressed, the degree of tubular injury increased, and the inflammatory infiltrate was more evident. NMR metabolomics and chemometrics revealed differences in urinary metabolites associated with CKD progression. The main physiological pathways affected were those involved in energy production and amino-acid metabolism, together with organic osmolytes. These data suggest that multiple administrations of FA induce a reproducible model of the induction of CKD. This model could help to evaluate new strategies for nephroprotection that could be applied in the clinic. creator: Marlene Marisol Perales-Quintana creator: Alma L. Saucedo creator: Juan Ricardo Lucio-Gutiérrez creator: Noemí Waksman creator: Gabriela Alarcon-Galvan creator: Gustavo Govea-Torres creator: Concepcion Sanchez-Martinez creator: Edelmiro Pérez-Rodríguez creator: Francisco J. Guzman-de la Garza creator: Paula Cordero-Pérez uri: https://doi.org/10.7717/peerj.7113 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Perales-Quintana et al. title: A functional magnetic resonance imaging investigation of the autonomous sensory meridian response link: https://peerj.com/articles/7122 last-modified: 2019-06-21 description: BackgroundAutonomous Sensory Meridian Response (ASMR) is a sensory-emotional experience in which specific stimuli (ASMR “triggers”) elicit tingling sensations on the scalp, neck, and shoulders; these sensations are accompanied by a positive affective state. In the current research, functional magnetic resonance imaging (fMRI) was used in order to delineate the neural substrates of these responses.MethodsA total of 17 individuals with ASMR and 17 age- and sex-matched control participants underwent fMRI scanning while watching six 4-minute videos. Three of the videos were designed to elicit ASMR tingling and three videos were not.ResultsThe results demonstrated that ASMR videos have a distinct effect on the neural activity of individuals with ASMR. The contrast of ASMR participants’ responses to ASMR videos showed greater activity in the cingulate gyrus as well as in cortical regions related to audition, movement, and vision. This activity was not observed in control participants. The contrast of ASMR and control participants’ responses to ASMR-eliciting videos detected greater activity in right cingulate gyrus, right paracentral lobule, and bilateral thalamus in ASMR participants; control participants showed greater activity in the lingula and culmen of the cerebellum.ConclusionsTogether, these results highlight the fact that ASMR videos elicit activity in brain areas related to sensation, emotion, and attention in individuals with ASMR, but not in matched control participants. creator: Stephen D. Smith creator: Beverley K. Fredborg creator: Jennifer Kornelsen uri: https://doi.org/10.7717/peerj.7122 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Smith et al. title: Molecular mechanisms linking peri-implantitis and type 2 diabetes mellitus revealed by transcriptomic analysis link: https://peerj.com/articles/7124 last-modified: 2019-06-21 description: AimsTo explore molecular mechanisms that link peri-implantitis and type 2 diabetes mellitus (T2DM) by bioinformatic analysis of publicly available experimental transcriptomic data.Materials and methodsGene expression data from peri-implantitis were downloaded from the Gene Expression Omnibus database, integrated and differentially expressed genes (DEGs) in peri-implantitis were identified. Next, experimentally validated and computationally predicted genes related to T2DM were downloaded from the DisGeNET database. Protein–protein interaction network (PPI) pairs of DEGs related to peri-implantitis and T2DM related genes were constructed, “hub” genes and overlapping DEG were determined. Functional enrichment analysis was used to identify significant shared biological processes and signaling pathways. The PPI networks were subjected to cluster and specific class analysis for identifying “leader” genes. Module network analysis of the merged PPI network identified common or cross-talk genes connecting the two networks.ResultsA total of 92 DEGs overlapped between peri-implantitis and T2DM datasets. Three hub genes (IL-6, NFKB1, and PIK3CG) had the highest degree in PPI networks of both peri-implantitis and T2DM. Three leader genes (PSMD10, SOS1, WASF3), eight cross-talk genes (PSMD10, PSMD6, EIF2S1, GSTP1, DNAJC3, SEC61A1, MAPT, and NME1), and one signaling pathway (IL-17 signaling) emerged as peri-implantitis and T2DM linkage mechanisms.ConclusionsExploration of available transcriptomic datasets revealed IL-6, NFKB1, and PIK3CG expression along with the IL-17 signaling pathway as top candidate molecular linkage mechanisms between peri-implantitis and T2DM. creator: Tianliang Yu creator: Aneesha Acharya creator: Nikos Mattheos creator: Simin Li creator: Dirk Ziebolz creator: Gerhard Schmalz creator: Rainer Haak creator: Jana Schmidt creator: Yu Sun uri: https://doi.org/10.7717/peerj.7124 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yu et al. title: Response patterns of routinely measured inflammatory and coagulatory parameters in sepsis link: https://peerj.com/articles/7147 last-modified: 2019-06-21 description: BackgroundSepsis is characterized by a pro-inflammatory and pro-coagulatory shift which can induce life-threatening complications. Close monitoring and risk stratification of sepsis patients is crucial for proper treatment and consequently patient outcome. Therefore, this study focuses on the response patterns of inflammatory and coagulatory parameters used in clinical routines to estimate the course of sepsis.MethodsA total of 1,110 patients diagnosed with sepsis were retrospectively analyzed to identify response patterns for risk stratification of routine parameters measured at the peak level of C-reactive protein. Cluster analysis was used and the differences in the patient characteristics and 28-day survival were assessed. Cox proportional hazards regression model for survival stratified by the clusters was performed.ResultsThe analyses revealed the parameters to have five distinct response patterns. These clusters reflect the etiology as well as the course of sepsis associated with different mortalities. Here, impairment of the liver plays a crucial role in the ability to appropriately respond to sepsis. Of the routinely measured parameters, C-reactive protein and antithrombin seem to be unspecific for stratification of septic patients. Adjusted for the individual clusters, survival was associated with an increase in fibrinogen (p = 0.0042), platelets (p = 0.0003) and PT (p = 0.001) as well as a decrease in leukocytes (p = 0.034).ConclusionsThis study reveals that patients have distinct response patterns of inflammatory and coagulatory parameters depending on disease etiology. These patterns are associated with different mortalities although the patients have similar levels of C-reactive protein. Independently of the type of response, good coagulatory capacity seems to be crucial for patient survival. creator: Mirjam Bachler creator: Tobias Hell creator: Lukas Schausberger creator: Christine Schlömmer creator: Volker Schäfer creator: Marlies Liebensteiner creator: Katharina Schäffler creator: Bettina Schenk creator: Dietmar Fries creator: Petra Innerhofer creator: Christian Niederwanger uri: https://doi.org/10.7717/peerj.7147 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bachler et al. title: Diagnostic performance of clinical properties and conventional magnetic resonance imaging for determining the IDH1 mutation status in glioblastoma: a retrospective study link: https://peerj.com/articles/7154 last-modified: 2019-06-21 description: BackgroundGlioblastoma (GBM), the most malignant form of gliomas, is a relatively common primary brain tumor in adults. Preoperative identification of isocitrate dehydrogenase 1 (IDH1) mutations in GBM is of critical prognostic importance. The aim of the present study was to explore the feasibility and diagnostic performance of basic patient information combined with conventional magnetic resonance imaging (MRI) findings for determination of the IDH1 status (mutant vs wild type) in patients with GBM.MethodsFrom January 1, 2016 to December 31, 2017, a consecutive series of 50 patients with GBM was retrospectively collected. The patients were divided into two group according to their IDH1 mutation status. Basic information and MRI features were analyzed for the establishment of a diagnostic prediction model using logistic regression. A receiver operating characteristic curve was used to evaluate the diagnostic performance.ResultsPatients with IDH1-mutant tumors were younger than those with IDH1-wild type tumors, and exhibited a larger tumor volume. The diagnostic predictive model established by combining age and the tumor size exhibited a sensitivity and specificity of 70% and 93%, respectively. The area under the curve was 0.88, which indicated high diagnostic performance.ConclusionPatient age and tumor volume can be used as indicators of IDH1 mutation status in patients with GBM, with high diagnostic performance for simple evaluations in clinical practice. The combined use of these two indicators can further enhance the diagnostic specificity. creator: Qun Wang creator: Jiashu Zhang creator: Fangye Li creator: Xinghua Xu creator: Bainan Xu uri: https://doi.org/10.7717/peerj.7154 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Initial decomposition of floating leaf blades of waterlilies: causes, damage types and impacts link: https://peerj.com/articles/7158 last-modified: 2019-06-21 description: The initial decomposition of large floating-leaved macrophytes, such as waterlilies, can be studied by following changes in leaf damage and area loss of leaf blades tagged in their natural environment. This approach was taken in the present study to examine the initial decomposition patterns of floating leaf blades of Nuphar lutea (L.) Sm., Nymphaea alba L. and Nymphaea candida C. Presl at three freshwater sites differing in nutrient status, alkalinity and pH. Floating leaf blades of the three plant species were tagged and numbered within established replicate plots and the leaf length, percentages and types of damage and decay of all tagged leaves were recorded weekly during the growing season. Microbial decay, infection by phytopathogenic fungi (Colletotrichum nymphaeae) and oomycetes (Pythium sp.), consumption by pond snails, and mechanical factors were the most important causes of leaf damage. Several types of succession comprising different causes of damage were distinguished during the season. For example, young floating leaves are affected by more or less specialized invertebrate species consuming leaf tissue, followed by non-specialized invertebrate species feeding on the damaged floating leaves. In the two investigated hardwater lakes the seasonal patterns of initial decomposition differed between Nymphaea and Nuphar. creator: Peter F. Klok creator: Gerard van der Velde uri: https://doi.org/10.7717/peerj.7158 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Klok and van der Velde title: Isisfordia molnari sp. nov., a new basal eusuchian from the mid-Cretaceous of Lightning Ridge, Australia link: https://peerj.com/articles/7166 last-modified: 2019-06-21 description: The Australian Mesozoic crocodyliform record is sparse in comparison to other Gondwanan localities. A single formally-named taxon is known from this interval; Isisfordia duncani (Winton Formation, Albian–Turonian, Queensland). We present a previously undescribed crocodyliform braincase from the Griman Creek Formation (Cenomanian), New South Wales, which we assign to Isisfordia molnari sp. nov. Assignment to the genus is based on the possession of a newly-defined autapomorphy of Isisfordia: a broadly exposed prootic within the supratemporal foramen. A second autapomorphy of I. duncani (maximum diameter of the caudal aperture of the cranioquadrate siphonium approximately one-third the mediolateral width of the foramen magnum, with the lateral wall of the caudal aperture formed exclusively by the quadrate) may also be present in I. molnari; however, definitive recognition of this feature is marred by incomplete preservation. The new taxon is differentiated from I. duncani based on the absence of a median ridge on the parietal, and the lack of characteristic ridges on the parietal that form the medial margin of the supratemporal foramina. Reanalysis of a second specimen (the former holotype of the nomen dubium,‘Crocodylus (Bottosaurus) selaslophensis’) allows for its referral to the genus Isisfordia. Crucial to this reappraisal is the reinterpretation of the specimen as a partial maxilla, not the dentary as previously thought. This maxillary fragment possesses specific characteristics shared only with I. duncani; namely an alveolar groove. However, several key features differentiate the maxillary fragment from I. duncani, specifically the presence of continuous alveolar septa, the thickening of the medial alveolar rim, and the alveolar and crown base morphology. These findings constitute the first evidence of Isisfordia outside of the type locality and indicate its widespread occurrence on the freshwater floodplains along the eastern margin of the epeiric Eromanga Sea during the Albian–Cenomanian. creator: Lachlan J. Hart creator: Phil R. Bell creator: Elizabeth T. Smith creator: Steven W. Salisbury uri: https://doi.org/10.7717/peerj.7166 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hart et al. title: Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples link: https://peerj.com/articles/7171 last-modified: 2019-06-21 description: BackgroundMajor depressive disorder (MDD) is a severe disease characterized by multiple pathological changes. However, there are no reliable diagnostic biomarkers for MDD. The aim of the current study was to investigate the gene network and biomarkers underlying the pathophysiology of MDD.MethodsIn this study, we conducted a comprehensive analysis of the mRNA expression profile of MDD using data from Gene Expression Omnibus (GEO). The MDD dataset (GSE98793) with 128 MDD and 64 control whole blood samples was divided randomly into two non-overlapping groups for cross-validated differential gene expression analysis. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) were performed for annotation, visualization, and integrated discovery. Protein–protein interaction (PPI) network was constructed by STRING database and hub genes were identified by the CytoHubba plugin. The gene expression difference and the functional similarity of hub genes were investigated for further gene expression and function exploration. Moreover, the receiver operating characteristic curve was performed to verify the diagnostic value of the hub genes.ResultsWe identified 761 differentially expressed genes closely related to MDD. The Venn diagram and GO analyses indicated that changes in MDD are mainly enriched in ribonucleoprotein complex biogenesis, antigen receptor-mediated signaling pathway, catalytic activity (acting on RNA), structural constituent of ribosome, mitochondrial matrix, and mitochondrial protein complex. The GSEA suggested that tumor necrosis factor signaling pathway, Toll-like receptor signaling pathway, apoptosis pathway, and NF-kappa B signaling pathway are all crucial in the development of MDD. A total of 20 hub genes were selected via the PPI network. Additionally, the identified hub genes were downregulated and show high functional similarity and diagnostic value in MDD.ConclusionsOur findings may provide novel insight into the functional characteristics of MDD through integrative analysis of GEO data, and suggest potential biomarkers and therapeutic targets for MDD. creator: Huimei Wang creator: Mingwei Zhang creator: Qiqi Xie creator: Jin Yu creator: Yan Qi creator: Qiuyuan Yue uri: https://doi.org/10.7717/peerj.7171 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers link: https://peerj.com/articles/7173 last-modified: 2019-06-21 description: BackgroundMallotus oblongifolius, an evergreen shrub endemic to Hainan Island, China, is important both medicinally and economically. Due to its special medicinal significance and the continuing rise of market demand, its populations in the wild have been subject to long-term illegal and unrestrained collection. Hence, an evaluation of genetic variability is essential for the conservation and genetic reserve development of this species.MethodsSequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and genetic structure of 20 natural populations of M. oblongifolius growing in different eco-geographical regions of Hainan Island, China.ResultsWe revealed a considerable genetic diversity (h = 0.336, I = 0.5057, SRAP markers; h = 0.3068, I = 0.4657, ISSR markers) and weak genetic differentiation (Gst = 0.2764 for SRAP, Gst = 0.2709 for ISSR) with the same gene flow (Nm = 1.3092 for SRAP, Nm = 1.346 for ISSR) among the M. oblongifolius populations. The Mantel Test showed that the distribution of genetic variation among populations could not be explained by the pronounced geographical distances (r = 0.01255, p = 0.5538). All results of the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), Neighbor-joining (NJ), Principal Coordinate Analysis (PCoA) and Bayesian analyses supported a habitat-specific genetic clustering model for M. oblongifolius, indicating a local adaptive divergence for the studied populations.DiscussionWe suggested that the habitat fragmentation and specificity for M. oblongifolius populations weakened the natural gene flow and promoted an adaptation to special habitats, which was the main reason for local adaptive divergence among M. oblongifolius. creator: Wuping Yan creator: Juanling Li creator: Daojun Zheng creator: Cynthia Friedman creator: Huafeng Wang uri: https://doi.org/10.7717/peerj.7173 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yan et al. title: Clinical outcomes and risk factors of secondary extraintestinal manifestation in ulcerative colitis: results of a multicenter and long-term follow-up retrospective study link: https://peerj.com/articles/7194 last-modified: 2019-06-21 description: BackgroundExtraintestinal manifestations (EIM) are common in ulcerative colitis (UC). In Shanghai, China, data on the incidence rate and risk factors of EIM in UC patients remain scarce.MethodsThe study population consisted of UC patients who were identified from a prospectively maintained, institutional review board-approved database at our institutes from June 1986 to December 2018. The demographic and clinical characteristics of the study participants were analyzed. The study included secondary EIM in UC patients and follow-up, while primary EIM was excluded. The diagnosis of EIM was based on clinical, radiological, endoscopic, and immunologic examination and histological findings.ResultsIn total, 271 eligible patients were included in the current study, with a median follow-up time of 13.0 years (interquartile range, 9.0–17.0), and including 31 cases (11.4%) that developed EIM. EIM was associated with clinical outcomes in UC patients and the following factors were identified as contributing factors for the development of EIM: a disease duration of >5 years (odds ratio (OR), 3.721; 95% confidence interval (CI) [1.209–11.456]), age at diagnosis >40 years (OR, 2.924, 95% CI [1.165–7.340]), refractory clinical symptoms (OR, 4.119; 95% CI [1.758–9.650]), and moderate or severe anemia (OR, 2.592; 95% CI [1.047–6.413]).ConclusionIn this study, approximately 11.4% UC patients go on to develop at least one EIM. Clinicians should prioritize early control of the disease and treatment of anemia in UC in order to prevent the development of EIM and improve disease prognosis. creator: Weimin Xu creator: Weijun Ou creator: Yuegui Guo creator: Yubei Gu creator: Long Cui creator: Jie Zhong creator: Peng Du uri: https://doi.org/10.7717/peerj.7194 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xu et al. title: Pleistocene epilithic foraminifera from the Arctic Ocean link: https://peerj.com/articles/7207 last-modified: 2019-06-21 description: Attached epilithic foraminifera constitute an important but overlooked component of the benthic foraminiferal assemblage in the Pleistocene sediment of the central Arctic Ocean. We report 12 types of epilithic foraminifera that have colonised lithic and biogenic grains found in glacial sediments, including representatives of the genera Rhizammina, Hemisphaerammina, Ammopemphix, Diffusilina, Subreophax, Placopsilina, Placopsilinella, Hormosinelloides and Tholosina, accompanied by mat-like and ribbon-like forms of uncertain taxonomic affinity. The attached agglutinated forms appear to be colonisers, adapted to extremely oligotrophic conditions. creator: Anna Waśkowska creator: Michael A. Kaminski uri: https://doi.org/10.7717/peerj.7207 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Waśkowska and Kaminski title: Antioxidant activity, α-glucosidase inhibition and phytochemical profiling of Hyophorbe lagenicaulis leaf extracts link: https://peerj.com/articles/7022 last-modified: 2019-06-20 description: BackgroundDiabetes mellitus type II (DMT-2) is a widely spread metabolic disorder both in developed and developing countries. The role of oxidative stress is well established in DMT-2 pathogenesis. The synthetic drugs for DMT-2 are associated with serious side complications. Antioxidant and α-glucosidase inhibitory actions of phytochemicals from various plant species are considered as an alternative to synthetic drugs for DMT-2 management. The present study aimed to evaluate the antioxidant activity, α-glucosidase inhibitory potential and phytochemical profiling of Hyophorbe lagenicaulis.MethodsThe total phenolic and flavonoid contents, in vitro antioxidant activity (α, α-diphenyl-β-picrylhydrazyl (DPPH) free radical scavenging and phosphomolybdenum method) and α-glucosidase inhibition of ultrasonicated hydroethanolic H. lagenicaulis leaf extracts were determined spectrophotometrically. The results of DPPH assay and α-glucosidase inhibition were reported in terms of IC50 value. The phytochemical profiling was accomplished by UHPLC-Q-TOF/MS/MS technique.Results and DiscussionFindings leaped 60% ethanolic extract as rich fraction regarding total phenolic and flavonoid contents. The 60% ethanolic fraction was a promising source of natural antioxidants and α-glucosidase inhibitory agents as indicated by anti-radical and enzyme inibitory activities. Kaempferol, rutin, hesperetin 5-O-glucoside, kaempferol-coumaroyl-glucoside, luteolin 3-glucoside, Isorhamnetin-3-O-rutinoside, trimethoxyflavone derivatives and citric acid were identified by UHPLC-Q-TOF-MS/MS. These compounds were believed to be responsible for the strong antioxidant and enzyme inhibitory activity of plant extracts. The extensive metabolite profiling of H. lagenicaulis was carried out the first time as never reported previously. The H. lagenicaulis might be an appropriate choice to manage diabetes mellitus in an alternate way. The findings may be further exploited extensively for toxicity evaluation to proceed with functional food development having antidiabetic attributes. creator: James William creator: Peter John creator: Muhammad Waseem Mumtaz creator: Ayoub Rashid Ch creator: Ahmad Adnan creator: Hamid Mukhtar creator: Shahzad Sharif creator: Syed Ali Raza creator: Muhammad Tayyab Akhtar uri: https://doi.org/10.7717/peerj.7022 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 William et al. title: Proteomic identification of membrane-associated placental protein 4 (MP4) as perlecan and characterization of its placental expression in normal and pathologic pregnancies link: https://peerj.com/articles/6982 last-modified: 2019-06-20 description: BackgroundMore than 50 human placental proteins were isolated and physico-chemically characterized in the 70–80s by Hans Bohn and co-workers. Many of these proteins turned to have important role in placental functions and diagnostic significance in pregnancy complications. Among these proteins was membrane-associated placental protein 4 (MP4), for which identity or function has not been identified yet. Our aim was to analyze the sequence and placental expression of this protein in normal and complicated pregnancies including miscarriage, preeclampsia and HELLP syndrome.MethodsLyophilized MP4 protein and frozen healthy placental tissue were analyzed using HPLC-MS/MS. Placental tissue samples were obtained from women with elective termination of pregnancy (first trimester controls, n = 31), early pregnancy loss (EPL) (n = 13), early preeclampsia without HELLP syndrome (n = 7) and with HELLP syndrome (n = 8), late preeclampsia (n = 8), third trimester early controls (n = 5) and third trimester late controls (n = 9). Tissue microarrays were constructed from paraffin-embedded placentas (n = 81). Slides were immunostained with monoclonal perlecan antibody and evaluated using light microscopy and virtual microscopy. Perlecan was also analyzed for its expression in placentas from normal pregnancies using microarray data.ResultsMass spectrometry-based proteomics of MP4 resulted in the identification of basement membrane-specific heparan sulfate proteoglycan core protein also known as perlecan. Immunohistochemistry showed cytoplasmic perlecan localization in syncytiotrophoblast and cytotrophoblasts of the villi. Perlecan immunoscore decreased with gestational age in the placenta. Perlecan immunoscores were higher in EPL compared to controls. Perlecan immunoscores were higher in early preeclampsia without and with HELLP syndrome and lower in late preeclampsia than in respective controls. Among patients with preeclampsia, placental perlecan expression positively correlated with maternal vascular malperfusion and negatively correlated with placental weight.ConclusionOur findings suggest that an increased placental perlecan expression may be associated with hypoxic ischaemic injury of the placenta in miscarriages and in early preeclampsia with or without HELLP syndrome. creator: Nikolett Lilla Szenasi creator: Eszter Toth creator: Andrea Balogh creator: Kata Juhasz creator: Katalin Karaszi creator: Oliver Ozohanics creator: Zsolt Gelencser creator: Peter Kiraly creator: Beata Hargitai creator: Laszlo Drahos creator: Petronella Hupuczi creator: Ilona Kovalszky creator: Zoltan Papp creator: Nandor Gabor Than uri: https://doi.org/10.7717/peerj.6982 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Szenasi et al. title: The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes link: https://peerj.com/articles/7031 last-modified: 2019-06-20 description: We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5′ end of nad4 overlapped with the 3′ end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu. These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies. creator: Thanh Hoa Le creator: Khue Thi Nguyen creator: Nga Thi Bich Nguyen creator: Huong Thi Thanh Doan creator: Takeshi Agatsuma creator: David Blair uri: https://doi.org/10.7717/peerj.7031 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Le et al. title: Compression shorts reduce prenatal pelvic and low back pain: a prospective quasi-experimental controlled study link: https://peerj.com/articles/7080 last-modified: 2019-06-20 description: BackgroundCommon prenatal ailments negatively impact performance of activities of daily living and it has been proposed that the use of dynamic elastomeric fabric orthoses, more commonly referred to as compression garments, during pregnancy might aid in the reduction of pain from these ailments, allowing for improved functional capacity. However, the effectiveness of such garments in this context has not been established. This study aims to determine whether compression shorts are effective and thermally safe in the prevention and management of prenatal pelvic and low back pain (LBP).MethodA prospective quasi-experimental controlled study using parallel groups without random allocation was conducted, involving 55 childbearing women (gestational weeks 16–31) recruited from hospital and community-based maternity care providers. The compression shorts group (SG) wore SRC Pregnancy Shorts in addition to receiving usual care. The comparison group (CG) received usual care alone. Primary outcome measures—Numeric Pain Rating Scale (NPRS) and Roland Morris Disability Questionnaire (RMDQ) and secondary measures Pelvic Floor Impact Questionnaire - 7 (PFIQ-7) and SF-36 Short Form Health Survey—were assessed fortnightly over 6-weeks for both groups. The compression SG self-assessed daily their body temperatures to monitor thermal impact. Data analysis involved descriptive analyses of the primary and secondary outcome measures scores by group and time-point, and multivariable linear regressions to assess between-group differences in change scores at 6-weeks from baseline while controlling for baseline factors.ResultsAfter controlling for baseline scores, gestational weeks and parity, statistically significant differences in NPRS and RMDQ change scores between groups were in favour of the compression SG. At 6-weeks, mean (SD) NPRS change scores in the compression SG and CG were significantly different, at −0.38 (2.21) and 2.82 (2.68), respectively, p = 0.003. Mean (SD) RMDQ change scores in the compression SG and CG were also significantly different, at 0.46 (3.05) and 3.64 (3.32), respectively, p = 0.009. A total of 883 (99.7%) of the reported daily self-assessed body temperatures ranged between 35.4 and 38.0 °C when wearing the compression shorts. At 6-weeks, mean (SD) PFIQ-7 and SF-36 change scores in the compression SG and CG were not significantly different.ConclusionCompression shorts are effective and thermally safe for prenatal management of pelvic and LBP.RegistrationTrial registration was not required (Australian Government Department of Health Therapeutic Goods Administration (TGA), 2018). creator: Jaclyn M. Szkwara creator: Wayne Hing creator: Rodney Pope creator: Evelyne Rathbone uri: https://doi.org/10.7717/peerj.7080 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Szkwara et al. title: Quantifying morphological variation in the Castilleja pilosa species complex (Orobanchaceae) link: https://peerj.com/articles/7090 last-modified: 2019-06-20 description: Robustly delimited species are of paramount importance, the identification of which relies on our ability to discern boundaries between one species and the next. This is not difficult to do when species are very distinct from one another. However, in recently evolved lineages where putative species may have relatively few diagnostic features (e.g., species complexes composed of very similar species, the boundaries between which are often unclear), defining species boundaries can be more challenging. Hence, the field of species delimitation has widely advocated the use of multiple lines of evidence to delimit species, particularly in species complexes. Excessive taxonomic confusion, often the result of species descriptions that shift through time (e.g., during revisionary work and regional treatments), can further complicate the search for diagnostic features in species complexes. Here, as a first step in robustly delimiting species boundaries, we quantify and describe morphological variation in the Castilleja pilosa species complex. We first infer the morphospace of the species complex and use fuzzy-clustering techniques to explore the morphological variation in the system. Next, we hypothesize the position of type specimens within that morphospace. In so doing, we aim to visualize the impact that regional treatments have had on the conceptualization of taxa through time. We find that there is limited morphological variation among members of this complex, and we determine that the morphological concept of these species have shifted through time and are no longer accurately represented by species descriptions. creator: Sarah J. Jacobs creator: Sarah Herzog creator: David C. Tank uri: https://doi.org/10.7717/peerj.7090 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jacobs et al. title: The lacewing Ceraeochrysa caligata as a potential biological agent for controlling the red palm mite Raoiella indica link: https://peerj.com/articles/7123 last-modified: 2019-06-20 description: BackgroundCompared to chemical control, the use of naturally occurring biological agents to control invasive pests is less threatening to the environment and human health.ObjectivesHere, we assessed the ability of immature stages of the lacewing Ceraeochrysa caligata (Neuroptera: Chrysopidae) to prey upon different developmental stages of the red palm mite Raoiella indica (Acari: Tenuipalpidae), one of the most destructive invasive pests of palm trees in Neotropical regions.MethodsIncreasing densities of three stages of R. indica (eggs, immature stages, and adult females) were offered to C. caligata in coconut leaf arenas. The immature stages of C. caligata were less than 24 h old and were starved before being transferring to the arenas. The amount of prey consumed was recorded 6 h after releasing the C. caligata.ResultsOur results indicated that the ability of C. caligata to feed upon R. indica increased with the larval development of the predator. Higher feeding levels and shorter handling times were recorded for the first and second instars of C. caligata when preying upon the eggs and immature stages of R. indica. Furthermore, C. caligata individuals of different stages exhibited differential functional responses according to prey type (i.e., eggs, immatures, or adult females of R. indica). Ceraeochrysa caligata second instar individuals exhibited a sigmoid increase in consumption rate with increasing prey availability (i.e., a type III functional response) when preying upon immature stages of R. indica. However, when preying upon R. indica adult females, C. caligata second instar individuals exhibited a type II functional response (i.e., an increase in consumption rate with increasing prey availability, before reaching a plateau). Predator individuals of the first and third instar stages exhibited a type II functional response for all prey types.ConclusionsCollectively, our findings demonstrate that C. caligata, especially at the second instar stage, has potential as a tool for ecological management of the red palm mite. creator: Luis O. Viteri Jumbo creator: Adenir V. Teodoro creator: Adriano S. Rêgo creator: Khalid Haddi creator: Andréia S. Galvão creator: Eugênio Eduardo de Oliveira uri: https://doi.org/10.7717/peerj.7123 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Viteri Jumbo et al. title: Reference genes for qRT-PCR normalisation in different tissues, developmental stages, and stress conditions of Hypericum perforatum link: https://peerj.com/articles/7133 last-modified: 2019-06-20 description: Hypericum perforatum L. is a widely known medicinal herb used mostly as a remedy for depression because it contains high levels of naphthodianthrones, phloroglucinols, alkaloids, and some other secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is essential for the interpretation of qRT-PCR data. In this study, we investigated the expression of 14 candidate genes, including nine housekeeping genes (HKGs) (ACT2, ACT3, ACT7, CYP1, EF1-α, GAPDH, TUB-α, TUB-β, and UBC2) and five potential candidate genes (GSA, PKS1, PP2A, RPL13, and SAND). Three programs—GeNorm, NormFinder, and BestKeeper—were applied to evaluate the gene expression stability across four different plant tissues, four developmental stages and a set of abiotic stress and hormonal treatments. Integrating all of the algorithms and evaluations revealed that ACT2 and TUB-β were the most stable combination in different developmental stages samples and all of the experimental samples. ACT2, TUB-β, and EF1-α were identified as the three most applicable reference genes in different tissues and stress-treated samples. The majority of the conventional HKGs performed better than the potential reference genes. The obtained results will aid in improving the credibility of the standardization and quantification of transcription levels in future expression studies on H. perforatum. creator: Wen Zhou creator: Shiqiang Wang creator: Lei Yang creator: Yan Sun creator: Qian Zhang creator: Bin Li creator: Bin Wang creator: Lin Li creator: Donghao Wang creator: Zhezhi Wang uri: https://doi.org/10.7717/peerj.7133 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhou et al. title: Effects of obesity on the lipid and metabolite profiles of young adults by serum 1H-NMR spectroscopy link: https://peerj.com/articles/7137 last-modified: 2019-06-20 description: BackgroundOverweight (OW) is considered a risk for various metabolic diseases. However, its effects as a mechanism that alters the metabolite profiles remain unclear. The purpose of this study is to investigate the effects that OW has on the lipid and metabolite profiles in young adults.MethodsThe serum metabolite profiles of 46 young adults of normal weight and those considered OW were studied by Proton nuclear magnetic resonance spectroscopy (1H NMR) technique.Results1H NMR metabolite analysis shows the alteration of metabolic levels and increased levels of CH2 lipids and CH3 lipids, which are used as unique biomarkers to identify OW subjects from the normal weight groups.ConclusionThis present study reveals that OW contributes to the systemic metabolism and the metabolite alteration among young adults. The alteration in serum lipids level could shed the light on metabolic syndrome pathogenesis in young adults and needs further elucidation. creator: Duanghathai Pasanta creator: Sirirat Chancharunee creator: Montree Tungjai creator: Hong Joo Kim creator: Suchart Kothan uri: https://doi.org/10.7717/peerj.7137 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pasanta et al. title: Fishing for vaccines against Vibrio cholerae using in silico pan-proteomic reverse vaccinology approach link: https://peerj.com/articles/6223 last-modified: 2019-06-19 description: BackgroundCholera, an acute enteric infection, is a serious health challenge in both the underdeveloped and the developing world. It is caused by Vibrio cholerae after ingestion of fecal contaminated food or water. Cholera outbreaks have recently been observed in regions facing natural calamities (i.e., earthquake in Haiti 2010) or war (i.e., ongoing civil war in Yemen 2016) where healthcare and sanitary setups have been disrupted as a consequence. Whole-cell oral cholera vaccines (OCVs) have been in market but their regimen efficacy has been questioned. A reverse vaccinology (RV) approach has been applied as a successful anti-microbial measure for many infectious diseases.MethodologyWith the aim of finding new protective antigens for vaccine development, the V. cholerae O1 (biovar eltr str. N16961) proteome was computationally screened in a sequential prioritization approach that focused on determining the antigenicity of potential vaccine candidates. Essential, accessible, virulent and immunogenic proteins were selected as potential candidates. The predicted epitopes were filtered for effective binding with MHC alleles and epitopes binding with greater MHC alleles were selected.ResultsIn this study, we report lipoprotein NlpD, outer membrane protein OmpU, accessory colonization factor AcfA, Porin, putative and outer membrane protein OmpW as potential candidates qualifying all the set criteria. These predicted epitopes can offer a potential for development of a reliable peptide or subunit vaccine for V. cholerae. creator: Muhammad I. Rashid creator: Sammia Rehman creator: Amjad Ali creator: Saadia Andleeb uri: https://doi.org/10.7717/peerj.6223 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rashid et al. title: Linked within-host and between-host models and data for infectious diseases: a systematic review link: https://peerj.com/articles/7057 last-modified: 2019-06-19 description: The observed dynamics of infectious diseases are driven by processes across multiple scales. Here we focus on two: within-host, that is, how an infection progresses inside a single individual (for instance viral and immune dynamics), and between-host, that is, how the infection is transmitted between multiple individuals of a host population. The dynamics of each of these may be influenced by the other, particularly across evolutionary time. Thus understanding each of these scales, and the links between them, is necessary for a holistic understanding of the spread of infectious diseases. One approach to combining these scales is through mathematical modeling. We conducted a systematic review of the published literature on multi-scale mathematical models of disease transmission (as defined by combining within-host and between-host scales) to determine the extent to which mathematical models are being used to understand across-scale transmission, and the extent to which these models are being confronted with data. Following the PRISMA guidelines for systematic reviews, we identified 24 of 197 qualifying papers across 30 years that include both linked models at the within and between host scales and that used data to parameterize/calibrate models. We find that the approach that incorporates both modeling with data is under-utilized, if increasing. This highlights the need for better communication and collaboration between modelers and empiricists to build well-calibrated models that both improve understanding and may be used for prediction. creator: Lauren M. Childs creator: Fadoua El Moustaid creator: Zachary Gajewski creator: Sarah Kadelka creator: Ryan Nikin-Beers creator: John W. Smith, Jr creator: Melody Walker creator: Leah R. Johnson uri: https://doi.org/10.7717/peerj.7057 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Childs et al. title: How glyphosate and its associated acidity affect early development in zebrafish (Danio rerio) link: https://peerj.com/articles/7094 last-modified: 2019-06-19 description: BackgroundGlyphosate is among the most extensively used pesticides worldwide. Following the ongoing highly controversial debate on this compound, its potential impact on non-target organisms is a fundamental scientific issue. In its pure compound form, glyphosate is known for its acidic properties.MethodsWe exposed zebrafish (Danio rerio) embryos to concentrations between 10 μM and 10 mM glyphosate in an unbuffered aqueous medium, as well as at pH 7, for 96 hours post fertilization (hpf). Furthermore, we investigated the effects of aqueous media in the range of pH 3 to 8, in comparison with 1 mM glyphosate treatment at the respective pH levels. Additionally, we exposed zebrafish to 7-deoxy-sedoheptulose (7dSh), another substance that interferes with the shikimate pathway by a mechanism analogous to that of glyphosate, at a concentration of one mM. The observed endpoints included mortality, the hatching rate, developmental delays at 24 hpf, the heart rate at 48 hpf and the malformation rate at 96 hpf. LC10/50, EC10 and, if reasonable, EC50 values were determined for unbuffered glyphosate.ResultsThe results revealed high mortalities in all treatments associated with low pH, including high concentrations of unbuffered glyphosate (>500 μM), low pH controls and glyphosate treatments with pH < 3.4. Sublethal endpoints like developmental delays and malformations occurred mainly at higher concentrations of unbuffered glyphosate. In contrast, effects on the hatching rate became particularly prominent in treatments at pH 7, showing that glyphosate significantly accelerates hatching compared with the control and 7dSh, even at the lowest tested concentration. Glyphosate also affected the heart rate, resulting in alterations both at pH 7 and, even more pronounced, in the unbuffered system. In higher concentrations, glyphosate tended to accelerate the heart rate in zebrafish embryos, again, when not masked by the decelerating influence of its low pH. At pH > 4, no mortality occurred, neither in the control nor in glyphosate treatments. At 1 mM, 7dSh did not induce any mortality, developmental delays or malformations; only slightly accelerated hatching and a decelerated heart rate were observed. Our results demonstrate that lethal impacts in zebrafish embryos can be attributed mainly to low pH, but we could also show a pH-independent effect of glyphosate on the development of zebrafish embryos on a sublethal level. creator: Mona Schweizer creator: Klaus Brilisauer creator: Rita Triebskorn creator: Karl Forchhammer creator: Heinz-R. Köhler uri: https://doi.org/10.7717/peerj.7094 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schweizer et al. title: Effect of insecticide formulation and adjuvant combination on agricultural spray drift link: https://peerj.com/articles/7136 last-modified: 2019-06-19 description: Loss of crop protection products when agricultural spray applications drift has economic and ecological consequences. Modification of the spray solution through tank additives and product formulation is an important drift reduction strategy that could mitigate these effects, but has been studied less than most other strategies. Therefore, an experimental field study was conducted to evaluate spray drift resulting from agricultural ground applications of an insecticide formulated as a suspension concentrate (SC) and as a wettable powder (WP), with and without two adjuvants. Droplet sizes were also measured in a wind tunnel to determine if indirect methods could be substituted for field experimentation to quantify spray drift from these technologies. Results suggest that spray drift was reduced by 37% when comparing the SC to the WP formulation. As much as 63% drift reduction was achieved by incorporating certain spray adjuvants, but this depended on the formulation/adjuvant combination. The wind tunnel data for droplet spectra showed strong agreement with field deposition trends, suggesting that droplet statistics could be used to estimate drift reduction of spray solutions. These findings can be used to develop a classification scheme for formulated products and tank additives based on their potential for reducing spray drift. creator: Collin J. Preftakes creator: Jerome J. Schleier creator: Greg R. Kruger creator: David K. Weaver creator: Robert K.D. Peterson uri: https://doi.org/10.7717/peerj.7136 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Preftakes et al. title: Fuzzysplit: demultiplexing and trimming sequenced DNA with a declarative language link: https://peerj.com/articles/7170 last-modified: 2019-06-19 description: Next-generation sequencing technologies create large, multiplexed DNA sequences that require preprocessing before any further analysis. Part of this preprocessing includes demultiplexing and trimming sequences. Although there are many existing tools that can handle these preprocessing steps, they cannot be easily extended to new sequence schematics when new pipelines are developed. We present Fuzzysplit, a tool that relies on a simple declarative language to describe the schematics of sequences, which makes it incredibly adaptable to different use cases. In this paper, we explain the matching algorithms behind Fuzzysplit and we provide a preliminary comparison of its performance with other well-established tools. Overall, we find that its matching accuracy is comparable to previous tools. creator: Daniel Liu uri: https://doi.org/10.7717/peerj.7170 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu title: Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale link: https://peerj.com/articles/6127 last-modified: 2019-06-18 description: BackgroundA great number of studies have shown that the distribution of microorganisms in the soil is not random, but that their abundance changes along environmental gradients (spatial patterns). The present study examined the spatial variability of the physicochemical characteristics of an extreme alkaline saline soil and how they controlled the archaeal and bacterial communities so as to determine the main spatial community drivers.MethodsThe archaeal and bacterial community structure, and soil characteristics were determined at 13 points along a 211 m transect in the former lake Texcoco. Geostatistical techniques were used to describe spatial patterns of the microbial community and soil characteristics and determine soil properties that defined the prokaryotic community structure.ResultsA high variability in electrolytic conductivity (EC) and water content (WC) was found. Euryarchaeota dominated Archaea, except when the EC was low. Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacterial phyla independent of large variations in certain soil characteristics. Multivariate analysis showed that soil WC affected the archaeal community structure and a geostatistical analysis found that variation in the relative abundance of Euryarchaeota was controlled by EC. The bacterial alpha diversity was less controlled by soil characteristics at the scale of this study than the archaeal alpha diversity.DiscussionResults indicated that WC and EC played a major role in driving the microbial communities distribution and scale and sampling strategies were important to define spatial patterns. creator: Martha Adriana Martínez-Olivas creator: Norma G. Jiménez-Bueno creator: Juan Alfredo Hernández-García creator: Carmine Fusaro creator: Marco Luna-Guido creator: Yendi E. Navarro-Noya creator: Luc Dendooven uri: https://doi.org/10.7717/peerj.6127 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Martínez-Olivas et al. title: Rosmarinic acid treatment during porcine oocyte maturation attenuates oxidative stress and improves subsequent embryo development in vitro link: https://peerj.com/articles/6930 last-modified: 2019-06-18 description: BackgroundIn vitro maturation (IVM) of oocytes has been widely used in the field of assisted reproductive technology. However, oocytes can be injured by oxidative stress during the process of IVM.MethodsThe present study was designed to evaluate the influences of rosmarinic acid (RA) on the IVM of porcine oocytes and the subsequent development of early-stage embryos as well as its underlying mechanisms. Various concentrations of RA (5 µM, 10 µM, and 25 µM) were treated with porcine oocyte maturation medium during the period of IVM.Results and DiscussionThe results showed that 5 µM RA treatment during the period of porcine oocyte IVM improves blastocyst quality and hatching ability after parthenogenetic activation. Furthermore, the presence of RA during the period of IVM dramatically improved the total number of cells after somatic cell nuclear transfer compared to the number of cells in the control group. Notably, RA treatment during the period of porcine oocyte IVM decreased intracellular reactive oxygen species generation not only in oocytes but also in cumulus cells. Further analysis showed that the intracellular free thiols levels in the oocytes were enhanced by treatment with RA during the period of porcine oocyte IVM compared to the free thiols levels in the control groups. These results indicate that RA improves the developmental competence of porcine oocytes during the IVM period by attenuating oxidative stress. creator: Yan Zhang creator: Jing Guo creator: Xiao Wei Nie creator: Zi Yue Li creator: Yu Meng Wang creator: Shuang Liang creator: Suo Li uri: https://doi.org/10.7717/peerj.6930 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Discovery of plasma messenger RNA as novel biomarker for gastric cancer identified through bioinformatics analysis and clinical validation link: https://peerj.com/articles/7025 last-modified: 2019-06-18 description: BackgroundGastric cancer (GC) is the third leading cause of cancer-related death worldwide, partially due to the lack of effective screening strategies. Thus, there is a stringent need for non-invasive biomarkers to improve patient diagnostic efficiency in GC.MethodsThis study initially filtered messenger RNAs (mRNAs) as prospective biomarkers through bioinformatics analysis. Clinical validation was conducted using circulating mRNA in plasma from patients with GC. Relationships between expression levels of target genes and clinicopathological characteristics were calculated. Then, associations of these selected biomarkers with overall survival (OS) were analyzed using the Kaplan-Meier plotter online tool.ResultsBased on a comprehensive analysis of transcriptional expression profiles across 5 microarrays, top 3 over- and underexpressed mRNAs in GC were generated. Compared with normal controls, expression levels of collagen type VI alpha 3 chain (COL6A3), serpin family H member 1 (SERPINH1) and pleckstrin homology and RhoGEF domain containing G1 (PLEKHG1) were significantly upregulated in GC plasmas. Receiver-operating characteristic (ROC) curves on the diagnostic efficacy of plasma COL6A3, SERPINH1 and PLEKHG1 mRNAs in GC showed that the area under the ROC (AUC) was 0.720, 0.698 and 0.833, respectively. Combined, these three biomarkers showed an elevated AUC of 0.907. Interestingly, the higher COL6A3 level was significantly correlated with lymph node metastasis and poor prognosis in GC patients. High level of SERPINH1 mRNA expression was correlated with advanced age, poor differentiation, lower OS, and PLEKHG1 was also associated with poor OS in GC patients.ConclusionOur results suggested that circulating COL6A3, SERPINH1 and PLEKHG1 mRNAs could be putative noninvasive biomarkers for GC diagnosis and prognosis. creator: Wei Cao creator: Dan Zhou creator: Weiwei Tang creator: Hanxiang An creator: Yun Zhang uri: https://doi.org/10.7717/peerj.7025 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cao et al. title: Photoprotection practices, knowledge and sun-related skin damage in Spanish beach handball players link: https://peerj.com/articles/7030 last-modified: 2019-06-18 description: BackgroundOutdoor sports are a risk activity for skin cancer, especially if adequate sun protection measures are not used. The aim of this study is to examine the photoprotection habits of outdoor (beach) handball players, and to determine the relation between duration of sports practice, photoprotection behaviour and sun-related damage to the skin.MethodsThis cross-sectional study is based on a health survey of sun exposure and protection habits and practices conducted among beach handball players in southern Spain. This survey provided data for a descriptive and comparative analysis, by groups and gender, of photoprotection and skin self-examination practices.ResultsAmong the whole sample, 76.9% had suffered at least one sunburn event during the last year. By groups, 73.97% of the older participants (Group I, University students) and 81.25% of the younger ones (Group II, youngers players) reported this outcome, and the difference was statistically significant (p = 0.003). With respect to photoprotection, 68.5% of the players in group I and 66.7% of those in group II used sun cream with a protection factor of 30 or higher, although 52.1% of group I and 35.4% of group II did not reapply it. As concerns self-examination, 94.5% of group I and 87.5% of group II had not examined their body for skin damage during the previous year. Medical examination revealed the presence of lentigines and freckles among many players, with no significant differences between the two groups.ConclusionsBeach handball players are highly exposed to the effects of ultraviolet radiation and often take insufficient measures of sun protection. Programmes should be designed and implemented to raise awareness among adolescent and young adult sport competitors of the risks of skin cancer associated with their sports activity and to encourage them to improve their photoprotection and skin monitoring practices. creator: Guillermo De Castro-Maqueda creator: Jose Vicente Gutierrez-Manzanedo creator: Carolina Lagares-Franco creator: Mario Linares-Barrios creator: Magdalena de Troya-Martin uri: https://doi.org/10.7717/peerj.7030 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 De Castro-Maqueda et al. title: Effect of assisted walking-movement in patients with genetic and acquired neuromuscular disorders with the motorised Innowalk device: an international case study meta-analysis link: https://peerj.com/articles/7098 last-modified: 2019-06-18 description: People with physical disabilities (PD) suffer from consequences due to lack of physical activity and consequently, are at increased risk of chronic diseases. We aimed to evaluate the ability of a motorised assistive device for dynamic standing with weight-bearing in addition to standard state-of-the-art therapy to improve clinical outcome in a meta-analysis of available studies. A total of 11 studies were identified from different European countries analysing the effect of the dynamic device Innowalk. Raw data of nine studies were pooled including a total of 31 patients observed between 2009 and 2017. Standardised questionnaires and physical outcomes were examined in this exploratory meta-analysis. We recorded patients’ characteristics, duration, intensity, and location of usage as well as general clinical outcomes and improvement of passive range of motion (PROM). The analysed population consisted in 90% cases of patients younger than 18 years of age. Patients were severely disabled individuals (aged 8 (6–10) years; 58% male; 67% non-ambulatory, 86% cerebral palsy). A total of 94% used the Innowalk in a home-based or day-care setting. For nearly all individuals (94%), improvements were recorded for: walking or weight-bearing transfer (n = 13), control/strength of the trunk or head (n = 6), joint mobility (n = 14), sleep (n = 4 out of 6/67%), or muscle strength (n = 17), vital functions (n = 16), bowel function (n = 10), attention/orientation (n = 2). PROM of the hip (flexion, abduction, and adduction) significantly (p < 0.001 for multiple comparisons) increased after 1 month (p < 0.05 flexion, adduction) and further after 5 months (p < 0.05 each) in contrast (p < 0.05 each) to a control group with state-of-the-art therapy. Similarly, PROM showed a trend towards improvement in dorsal extension of the ankle (p = 0.07). In summary, this is the first report of a novel device with additional benefit to standard therapy for severe PD. These intriguing results warrant the planned prospective randomised controlled trial to prove the concept and mechanism of action of this device. creator: Caroline Schmidt-Lucke creator: Jana Käferle creator: Britt-Marie Rydh Berner creator: Lotta Ahlborg creator: Hege Marie Hansen creator: Ulrika Skjellvik Tollefsen creator: Tonje Thon creator: Rikke Damkjær Moen creator: Ana Pekanovic creator: Åsa B. Tornberg creator: Katarina Lauruschkus uri: https://doi.org/10.7717/peerj.7098 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schmidt-Lucke et al. title: Expanding global commodities trade and consumption place the world’s primates at risk of extinction link: https://peerj.com/articles/7068 last-modified: 2019-06-17 description: As a consequence of recent human activities. populations of approximately 75% of the world’s primates are in decline, and more than 60% of species (n = 512) are threatened with extinction. Major anthropogenic pressures on primate persistence include the widespread loss and degradation of natural habitats caused by the expansion of industrial agriculture, pastureland for cattle, logging, mining, and fossil fuel extraction. This is the result of growing global market demands for agricultural and nonagricultural commodities. Here, we profile the effects of international trade of forest-risk agricultural and nonagricultural commodities, namely soybean, oil palm, natural rubber, beef, forestry products, fossil fuels, metals, minerals, and gemstones on habitat conversion in the Neotropics, Africa, and South and Southeast Asia. Total estimated forest loss for these regions between 2001 and 2017 was ca 179 million ha. The average percent of commodity-driven permanent deforestation for the period 2001–2015 was highest in Southeast Asia (47%) followed by the Neotropics (26%), South Asia (26%), and Africa (7%). Commodities exports increased significantly between 2000 and 2016 in all primate range regions leading to the widespread conversion of forested land to agricultural fields and an increase in natural resource extraction. In 2016, US $1.1 trillion of natural-resource commodities were traded by countries in primate range regions. The Neotropics accounted for 41% of the total value of these exports, Southeast Asia for 27%, Africa 21%, and South Asia 11%. Major commodity exporters in 2016 were Brazil, India, Indonesia, Malaysia and South Africa, countries of high primate diversity and endemism. Among the top 10 importers were China, the US, Japan, and Switzerland. Primate range countries lag far behind importer nations in food security and gross domestic product per capita, suggesting that trade and commodity-driven land-use have done little to generate wealth and well-being in primate habitat countries. Modeling of land-use and projected extinction of primate species by 2050 and 2100 under a business as usual scenario for 61 primate range countries indicate that each country is expected to see a significant increase in the number of species threatened with extinction. To mitigate this impending crisis, we advocate the “greening” of trade, a global shift toward a low-meat diet, reduced consumption of oil seed, diminished use of tropical timber, fossil fuels, metals, minerals, and gemstones from the tropics, accompanied by a stronger and sustained global resolve to regulate and reverse the negative impacts of growing unsustainable global demands and commodity trade on income inequality, and the destruction of primates and their habitats. creator: Alejandro Estrada creator: Paul A. Garber creator: Abhishek Chaudhary uri: https://doi.org/10.7717/peerj.7068 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Estrada et al. title: Repeatedly adopting power postures does not affect hormonal correlates of dominance and affiliative behavior link: https://peerj.com/articles/6726 last-modified: 2019-06-17 description: BackgroundAdopting expansive vs. constrictive postures related to high vs. low levels of social power has been suggested to induce changes in testosterone and cortisol levels, and thereby to mimic hormonal correlates of dominance behavior. However, these findings have been challenged by several non-replications recently. Despite this growing body of evidence that does not support posture effects on hormone levels, the question remains as to whether repeatedly holding postures over time and/or assessing hormonal responses at different time points would yield different outcomes. The current study assesses these methodological characteristics as possible reasons for previous null-findings. Additionally, it investigates for the first time whether expansive and constrictive postures impact progesterone levels, a suggested correlate of affiliative motives and behavior. By testing the effects of repeated but short posture manipulations in between the blocks of a social task while using a cover story, it further fulfills the conditions previously raised as potentially necessary for the effects to occur.MethodsA total of 82 male participants repeatedly adopted an expansive or constrictive posture for 2 min in between blocks of a task that consisted in categorizing faces based on first impressions. Saliva samples were taken at two different time points in a time window in which hormonal responses to stress, competition and other manipulations are known to be strongest.ResultsNeither testosterone and cortisol levels linked to dominance behaviors, nor progesterone levels related to affiliative tendencies, responded differently to adopting expansive as opposed to constrictive postures. The present results suggest that even repeated power posing in a context where social stimuli are task-relevant does not elicit changes in hormone levels. creator: Hannah Metzler creator: Julie Grèzes uri: https://doi.org/10.7717/peerj.6726 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Metzler and Grèzes title: Mir-421 in plasma as a potential diagnostic biomarker for precancerous gastric lesions and early gastric cancer link: https://peerj.com/articles/7002 last-modified: 2019-06-17 description: ObjectiveMicroRNA (miR)-421 plays a key role in cancer progression. It has been reported that circulating miR-421may be a potential tumor marker for the diagnosis of several cancers. However, the role of miR-421 in plasma as a potential biomarker in the diagnosis of precancerous gastric lesions (Pre) and early-stage gastric cancer (GC) remains poorly understood. In this study, we investigated miR-421 in plasma as a novel potential biomarker for the detection of precancerous gastric lesions and early-stage (GC).Materials & MethodsThe miRNA content was determined by quantitative real-time polymerase chain reaction (qRT-PCR). MiR-421 content in all subjects was normalized by endogenous miRNA (miR-16). The diagnostic value of miR-421 for Pre and GC was assessed by comparing receiver operating characteristic (ROC) analysis with traditional tumor markers, including CEA, CA125, CA153, CA211 and CA50. The correlation between the expression of miR-421 and the pathological characteristics of Pre and GC was analyzed.ResultsElevated expression of miR-421 in plasma can robustly distinguish the normal population from Pre and GC cases, especially in the early stages of gastric cancer cases (all p < 0.05). The ROC analyses showed that the area under the ROC curve (AUC), sensitivity, accuracy and Youden index of miR-421 were superior to traditional tumor markers (CEA, CA125, CA153, CA211, and CA50) in GC diagnosis, while its specificity was higher than CEA, CA153 and CA50 (all p < 0.05). MiR-421 in plasma had higher AUC value than AFP, CA153, CA211 and CA50 in the diagnosis of Pre (all p < 0.05), while specificity, accuracy and Youden index of miR-421 was only lower than CA211. The efficiency of miR-421 in the diagnosis of GC was significantly higher than that of CA211 and CA50, and it was significantly higher than CA153, CA211 and CA50 in the diagnosis of Pre (all p < 0.05). In addition, up-regulation of miR-421 occurred initially in precancerous gastric lesions as well as in the early stage of GC. ConclusionsOverexpression of plasma miR-421 is a novel biomarker for the detection of precancerous lesions and early gastric cancer. creator: Jianlin Chen creator: Lihua Wu creator: Yifan Sun creator: Qi Yin creator: Xianhua Chen creator: Siqun Liang creator: Qingyan Meng creator: Haihua Long creator: Fangying Li creator: Changjun Luo creator: Xiaorong Xiao uri: https://doi.org/10.7717/peerj.7002 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Influence of nonylphenol exposure on basic growth, development, and thyroid tissue structure in F1 male rats link: https://peerj.com/articles/7039 last-modified: 2019-06-17 description: ObjectiveEnvironmental endocrine disruptors (EEDs) with a weak ability to mimic estrogen have been associated with thyroid dysfunction. However, little is known about the effect of nonylphenol (NP), a well-known EED, on thyroid structure. The present study evaluates whether gestational and lactational exposure to NP impacts growth and thyroid structure in F1 male rats.MethodsA total of 60 rats were gavaged with NP (25, 50, and 100 mg/kg), estradiol (E2, 30 μg/kg/day), and corn oil alone (vehicle control) from gestational day 6 to postnatal day (PND) 21. Serum thyroid hormones free triiodothyronine (FT3), free thyroxine (FT4) and thyroid stimulating hormone levels were detected by automated chemiluminescence immunoassay analyzer. The NP level in the thyroid was measured using high-performance liquid chromatography. The ultrastructure of follicular epithelial cells was examined using transmission electron microscopy. Histopathology was conducted using hematoxylin and eosin staining.ResultsOn PND 0, exposure to 50 and 100 mg/kg/day NP led to a significant decrease in the average litter size, litter weight and number of live pups per litter compared to the control group (P < 0.05). Dams exposed to NP during perinatal period demonstrated decreased serum levels of FT3 and FT4 in F1 male rats, when compared to the control group (P < 0.05). The NP level in the control group was 3.39 ± 0.08 ng/mg, while NP levels in the low, middle, and high dose groups ranged from 5.20 to 11.00 ng/mg. Exposure caused a dose-related increase in NP level in the thyroid of male pups (P < 0.01). The thicknesses of the thyroid follicular epithelium were 2.06 ± 0.37 μm in the control group and 3.97 ± 1.61 μm in the high-dose group. The thickness of the thyroid follicular epithelium increased with an increase in treatment dose in a dose-dependent manner (P < 0.05). The sizes of the thyroid follicles were 1,405.53 ± 866.62 μm2 in the control group and 317.49 ± 231.15 μm2 in the high-dose group. With increasing NP dosages, animals showed a decreased size of the thyroid follicle (P < 0.01). Thyroid follicular cells of NP-treated rats showed mildly swollen mitochondria and dilated rough endoplasmic reticulum in the cytoplasm.ConclusionNonylphenol can cross the placental barrier and accumulate in the thyroid of F1 male rats. Gestational and lactational exposure to NP in dams impacted both development and growth of pups and damaged the ultrastructure of their thyroid tissue, which may further negatively influence normal thyroid function. creator: Lin Wang creator: Jie Xu creator: Feng Zeng creator: Xiangjun Fu creator: Weihong Xu creator: Jie Yu uri: https://doi.org/10.7717/peerj.7039 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Symmetry preference in shapes, faces, flowers and landscapes link: https://peerj.com/articles/7078 last-modified: 2019-06-17 description: Most people like symmetry, and symmetry has been extensively used in visual art and architecture. In this study, we compared preference for images of abstract and familiar objects in the original format or when containing perfect bilateral symmetry. We created pairs of images for different categories: male faces, female faces, polygons, smoothed version of the polygons, flowers, and landscapes. This design allows us to compare symmetry preference in different domains. Each observer saw all categories randomly interleaved but saw only one of the two images in a pair. After recording preference, we recorded a rating of how salient the symmetry was for each image, and measured how quickly observers could decide which of the two images in a pair was symmetrical. Results reveal a general preference for symmetry in the case of shapes and faces. For landscapes, natural (no perfect symmetry) images were preferred. Correlations with judgments of saliency were present but generally low, and for landscapes the salience of symmetry was negatively related to preference. However, even within the category where symmetry was not liked (landscapes), the separate analysis of original and modified stimuli showed an interesting pattern: Salience of symmetry was correlated positively (artificial) or negatively (original) with preference, suggesting different effects of symmetry within the same class of stimuli based on context and categorization. creator: Marco Bertamini creator: Giulia Rampone creator: Alexis D.J. Makin creator: Andrew Jessop uri: https://doi.org/10.7717/peerj.7078 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bertamini et al. title: Identification and characterization of Gypsophila paniculata color morphs in Sleeping Bear Dunes National Lakeshore, MI, USA link: https://peerj.com/articles/7100 last-modified: 2019-06-17 description: BackgroundGypsophila paniculata (baby’s breath) is an invasive species found throughout much of the northwest United States and western Canada. Recently, plants exhibiting a different color morphology were identified within the coastal dunes along eastern Lake Michigan. The common baby’s breath (G. paniculata) typically produces stems that are purple in color (purple morph), while the atypical morph has stems that are green-yellow (green-yellow morph). The purpose of this study was to characterize these newly identified morphs and determine if they are genetically distinct species from the common baby’s breath in order to assess whether alternative management strategies should be employed to control these populations.MethodsWe sequenced two chloroplast regions, ribulose-bisphosphate carboxylase gene (rbcL), and maturase K (matK), and one nuclear region, internal transcribed spacer 2 (ITS2), from the purple morphs and green-yellow morphs collected from Sleeping Bear Dunes National Lakeshore, MI, USA (SBDNL). Sequences were aligned to reference sequences from other Gypsophila species obtained from the Barcode of Life Database and GenBank databases. We also collected seeds from wild purple morph and wild green-yellow morph plants in SBDNL. We grew the seeds in a common garden setting and characterized the proportion of green-yellow individuals produced from the two color morphs after 5-months of growth.ResultsPhylogenetic analyses based upon rbcL, matK, and ITS2 regions suggest that the two color morphs are not distinct species and they both belong to G. paniculata. Seeds collected from wild green-yellow morphs produced a significantly higher proportion of green-yellow individuals compared to the number produced by seeds collected from wild purple morphs. However, seeds collected from both color morphs produced more purple morphs than green-yellow morphs.DiscussionBased upon these results, we propose that the two color morphs are variants of G. paniculata. Given the significant difference in the number of green-yellow morphs produced from the seeds of each morph type, we also suggest that this color difference has some genetic basis. We propose that current management continue to treat the two color morphs in a similar manner in terms of removal to prevent the further spread of this species. creator: Marisa L. Yang creator: Emma Rice creator: Hailee Leimbach-Maus creator: Charlyn G. Partridge uri: https://doi.org/10.7717/peerj.7100 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart link: https://peerj.com/articles/7104 last-modified: 2019-06-17 description: BackgroundWheat is one of the most important staple crops worldwide. Fusarium head blight (FHB) severely affects wheat yield and quality. A novel bread wheat mutant, ZK001, characterized as cleistogamic was isolated from a non-cleistogamous variety Yumai 18 (YM18) through static magnetic field mutagenesis. Cleistogamy is a promising strategy for controlling FHB. However, little is known about the mechanism of cleistogamy in wheat.MethodsWe performed a FHB resistance test to identify the FHB infection rate of ZK001. We also measured the agronomic traits of ZK001 and the starch and total soluble sugar contents of lodicules in YM18 and ZK001. Finally, we performed comparative studies at the proteome level between YM18 and ZK001 based on the proteomic technique of isobaric tags for relative and absolute quantification.ResultsThe infection rate of ZK001 was lower than that of its wild-type and Aikang 58. The abnormal lodicules of ZK001 lost the ability to push the lemma and palea apart during the flowering stage. Proteome analysis showed that the main differentially abundant proteins (DAPs) were related to carbohydrate metabolism, protein transport, and calcium ion binding. These DAPs may work together to regulate cellular homeostasis, osmotic pressure and the development of lodicules. This hypothesis is supported by the analysis of starch, soluble sugar content in the lodicules as well as the results of Quantitative reverse transcription polymerase chain reaction.ConclusionsProteomic analysis has provided comprehensive information that should be useful for further research on the lodicule development mechanism in wheat. The ZK001 mutant is optimal for studying flower development in wheat and could be very important for FHB resistant projects via conventional crossing. creator: Caiguo Tang creator: Huilan Zhang creator: Pingping Zhang creator: Yuhan Ma creator: Minghui Cao creator: Hao Hu creator: Faheem Afzal Shah creator: Weiwei Zhao creator: Minghao Li creator: Lifang Wu uri: https://doi.org/10.7717/peerj.7104 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tang et al. title: Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset link: https://peerj.com/articles/7107 last-modified: 2019-06-17 description: The “bidirectional gene pair” indicates a particular head-to-head gene organization in which transcription start sites of two genes are located on opposite strands of genomic DNA within a region of one kb. Despite bidirectional gene pairs are well characterized, little is known about their expression profiles and regulation features in tumorigenesis. We used RNA-seq data from The Cancer Genome Atlas (TCGA) dataset for a systematic analysis of the expression profiles of bidirectional gene pairs in 13 cancer datasets. Gene pairs on the opposite strand with transcription end site distance within one kb or on the same strand with the distance of two genes between 1–10 kb and gene pairs comprising two randomly chosen genes were used as control gene pairs (CG1, CG2, and random). We identified and characterized up-/down-regulated genes by comparing the expression level between tumors and adjacent normal tissues in 13 TCGA datasets. There were no consistently significant difference in the percentage of up-/down-regulated genes between bidirectional and control/random genes in most of TCGA datasets. However, the percentage of bidirectional gene pairs comprising two up- or two down-regulated genes was significantly higher than gene pairs from CG1/2 in 12/11 analyzed TCGA datasets and the random gene pairs in all 13 TCGA datasets. Then we identified the methylation correlated bidirectional genes to explore the regulatory mechanism of bidirectional genes. Like the differentially expressed gene pairs, the bidirectional genes in a pair were significantly prone to be both hypo- or hyper-methylation correlated genes in 12/13 TCGA datasets when comparing to the CG2/random gene pairs despite no significant difference between the percentages of hypo-/hyper-methylation correlated genes in bidirectional and CG2/random genes in most of TCGA datasets. Finally, we explored the correlation between bidirectional genes and patient’s survival, identifying prognostic bidirectional genes and prognostic bidirectional gene pairs in each TCGA dataset. Remarkably, we found a group of prognostic bidirectional gene pairs in which the combination of two protein coding genes with different expression level correlated with different survival prognosis in survival analysis for OS. The percentage of these gene pairs in bidirectional gene pair were significantly higher than the gene pairs in controls in COAD datasets and lower in none of 13 TCGA datasets. creator: Juchuanli Tu creator: Xiaolu Li creator: Jianjun Wang uri: https://doi.org/10.7717/peerj.7107 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tu et al. title: Worldwide scientific productions with immunotherapy of sepsis: a bibliometric analysis link: https://peerj.com/articles/7116 last-modified: 2019-06-17 description: BackgroundSepsis represents a significant healthcare problem worldwide and causes a high number of deaths every year but remains to be fully understood. During and after sepsis, the host immune response is complex and involves an initial excessive host inflammatory response to infection that is closely related to tissue damage and leads to organ failure. Over the past three decades, immunotherapy for sepsis has vastly improved, but in this area, the most influential articles, journals, authors, and countries have not yet been completely summarized and analyzed.ObjectivePerformed a bibliometric analysis on all the articles concerning immunotherapy for sepsis from 1962 to 2019 was our objective, and we also explored the potential correlations between publications of different countries and their gross domestic product (GDP).MethodsAll articles about immunotherapy for sepsis were extracted from the Scopus database and analyzed. We also retrieved GDP data from all the countries that have published information from the World Bank.ResultsIn summary, we have retrieved 1,483 related articles from the Scopus database starting from the first publication on immunotherapy for sepsis in 1962 through March 16, 2019. Over the past decade, the number of the articles published has increased year by year to reach 866 in total, which accounts for about 58% of all publications, with 2017 being the most prolific year when 179 articles were published. The US published 604 articles (41%), followed by China (n = 163, 11%), and Germany (n = 158, 11%). In terms of publishing media, the journal that published the highest number of the articles was Journal of Critical Care Medicine with 65 articles (4%), followed by Shock with 55 articles (4%), and Critical Care with 35 articles (2%). There was a strong correlation between the GDP of the different countries and their publication numbers (r = 0.811, P < 0.001).ConclusionsOur present study analyzed all types of articles concerning immunotherapy for sepsis over the past 57 years and countries with high GDP tends to make more contributions to the medical field of this field. In the meantime, these studies highlight the importance of immunotherapy in the treatment of sepsis patients. The recognition of the historical status and development trend of this field can promote inter-agency cooperation, guide future research, and ultimately provide the basis for clinical practice guidelines. creator: Ronghao Wan creator: Lei Li creator: Chenwei Xing creator: Ronggang Peng creator: Liang Gao uri: https://doi.org/10.7717/peerj.7116 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wan et al. title: A tropomyosin receptor kinase family protein, NTRK2 is a potential predictive biomarker for lung adenocarcinoma link: https://peerj.com/articles/7125 last-modified: 2019-06-17 description: Neurotrophic receptor tyrosine kinase 2 (NTRK2) is a member of the tropomyosin receptor kinase family associated with the tumor development. However, the detailed function of NTRK2 in lung cancer, especially in lung adenocarcinoma (LUAD), is still not fully understood. Here, we investigated the effects of NTRK2 on LUAD biology. Through analyzing bioinformatics data derived from several databases, such as Oncomine, Gene Expression Profiling Interactive Analysis and UALCAN, we found that NTRK2 expression was significantly decreased in LUAD tissues. Clinical data acquired from Wanderer database, which is linked to The Cancer Genome Atlas database, demonstrated that the expression and methylation site of NTRK2 were significantly related to the clinical characteristics and prognosis of LUAD. Furthermore, NTRK2 expression was increased remarkably after treatment with the protein kinase B (AKT) inhibitor MK2206 and the anticancer agent actinomycin D. Functional enrichment analysis of NTRK2-associated coexpression genes was further conducted. Together, our results suggested that downregulated NTRK2 might be used in the diagnostic and prognostic evaluation of LUAD patients, or as a potential therapeutic target for the treatment of LUAD. creator: Xiang Wang creator: Zhijie Xu creator: Xi Chen creator: Xinxin Ren creator: Jie Wei creator: Shuyi Zhou creator: Xue Yang creator: Shuangshuang Zeng creator: Long Qian creator: Geting Wu creator: Zhicheng Gong creator: Yuanliang Yan uri: https://doi.org/10.7717/peerj.7125 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: An integration of deep learning with feature embedding for protein–protein interaction prediction link: https://peerj.com/articles/7126 last-modified: 2019-06-17 description: Protein–protein interactions are closely relevant to protein function and drug discovery. Hence, accurately identifying protein–protein interactions will help us to understand the underlying molecular mechanisms and significantly facilitate the drug discovery. However, the majority of existing computational methods for protein–protein interactions prediction are focused on the feature extraction and combination of features and there have been limited gains from the state-of-the-art models. In this work, a new residue representation method named Res2vec is designed for protein sequence representation. Residue representations obtained by Res2vec describe more precisely residue-residue interactions from raw sequence and supply more effective inputs for the downstream deep learning model. Combining effective feature embedding with powerful deep learning techniques, our method provides a general computational pipeline to infer protein–protein interactions, even when protein structure knowledge is entirely unknown. The proposed method DeepFE-PPI is evaluated on the S. Cerevisiae and human datasets. The experimental results show that DeepFE-PPI achieves 94.78% (accuracy), 92.99% (recall), 96.45% (precision), 89.62% (Matthew’s correlation coefficient, MCC) and 98.71% (accuracy), 98.54% (recall), 98.77% (precision), 97.43% (MCC), respectively. In addition, we also evaluate the performance of DeepFE-PPI on five independent species datasets and all the results are superior to the existing methods. The comparisons show that DeepFE-PPI is capable of predicting protein–protein interactions by a novel residue representation method and a deep learning classification framework in an acceptable level of accuracy. The codes along with instructions to reproduce this work are available from https://github.com/xal2019/DeepFE-PPI. creator: Yu Yao creator: Xiuquan Du creator: Yanyu Diao creator: Huaixu Zhu uri: https://doi.org/10.7717/peerj.7126 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yao et al. title: PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition link: https://peerj.com/articles/7131 last-modified: 2019-06-17 description: Selection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present PhD7Faster 2.0 for predicting fast-propagating clones from the Ph.D.-7 phage display library, which was developed based on the support vector machine. Feature selection was performed against PseAAC and tripeptide composition using the incremental feature selection method. Ten-fold cross-validation results show that PhD7Faster 2.0 succeeds a decent performance with the accuracy of 81.84%, the Matthews correlation coefficient of 0.64 and the area under the ROC curve of 0.90. The permutation test with 1,000 shuffles resulted in p < 0.001. We implemented PhD7Faster 2.0 into a publicly accessible web tool (http://i.uestc.edu.cn/sarotup3/cgi-bin/PhD7Faster.pl) and constructed standalone graphical user interface and command-line versions for different systems. The standalone PhD7Faster 2.0 is able to detect PrTUPs within small datasets as well as large-scale datasets. This makes PhD7Faster 2.0 an enhanced and powerful tool for scanning and reporting faster-growing clones from the Ph.D.-7 phage display library. creator: Bifang He creator: Heng Chen creator: Jian Huang uri: https://doi.org/10.7717/peerj.7131 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 He et al. title: Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis link: https://peerj.com/articles/7135 last-modified: 2019-06-17 description: BackgroundPulpitis is a common inflammatory disease that affects dental pulp. It is important to understand the molecular signals of inflammation and repair associated with this process. Increasing evidence has revealed that long noncoding RNAs (lncRNAs), via competitively sponging microRNAs (miRNAs), can act as competing endogenous RNAs (ceRNAs) to regulate inflammation and reparative responses. The aim of this study was to elucidate the potential roles of lncRNA, miRNA and messenger RNA (mRNA) ceRNA networks in pulpitis tissues compared to normal control tissues.MethodsThe oligo and limma packages were used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs, respectively) based on expression profiles in two datasets, GSE92681 and GSE77459, from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were further analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Protein–protein interaction (PPI) networks and modules were established to screen hub genes using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the Molecular Complex Detection (MCODE) plugin for Cytoscape, respectively. Furthermore, an lncRNA-miRNA-mRNA-hub genes regulatory network was constructed to investigate mechanisms related to the progression and prognosis of pulpitis. Then, quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify critical lncRNAs that may significantly affect the pathogenesis in inflamed and normal human dental pulp.ResultsA total of 644 upregulated and 264 downregulated differentially expressed genes (DEGs) in pulpitis samples were identified from the GSE77459 dataset, while 8 up- and 19 downregulated probes associated with lncRNA were identified from the GSE92681 dataset. Protein–protein interaction (PPI) based on STRING analysis revealed a network of DEGs containing 4,929 edges and 623 nodes. Upon combined analysis of the constructed PPI network and the MCODE results, 10 hub genes, including IL6, IL8, PTPRC, IL1B, TLR2, ITGAM, CCL2, PIK3CG, ICAM1, and PIK3CD, were detected in the network. Next, a ceRNA regulatory relationship consisting of one lncRNA (PVT1), one miRNA (hsa-miR-455-5p) and two mRNAs (SOCS3 and PLXNC1) was established. Then, we constructed the network in which the regulatory relationship between ceRNA and hub genes was summarized. Finally, our qRT-PCR results confirmed significantly higher levels of PVT1 transcript in inflamed pulp than in normal pulp tissues (p = 0.03).ConclusionOur study identified a novel lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of pulpitis. creator: Fangcao Lei creator: Han Zhang creator: Xiaoli Xie uri: https://doi.org/10.7717/peerj.7135 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lei et al. title: Coleoptera genome and transcriptome sequences reveal numerous differences in neuropeptide signaling between species link: https://peerj.com/articles/7144 last-modified: 2019-06-17 description: BackgroundInsect neuropeptides are interesting for the potential their receptors hold as plausible targets for a novel generation of pesticides. Neuropeptide genes have been identified in a number of different species belonging to a variety of insects. Results suggest significant neuropeptide variation between different orders, but much less is known of neuropeptidome variability within an insect order. I therefore compared the neuropeptidomes of a number of Coleoptera.MethodologyPublicly available genome sequences, transcriptomes and the original sequence data in the form of short sequence read archives were analyzed for the presence or absence of genes coding neuropeptides as well as some neuropeptide receptors in seventeen beetle species.ResultsSignificant differences exist between the Coleoptera analyzed here, while many neuropeptides that were previously characterized from Tribolium castaneum appear very similar in all species, some are not and others are lacking in one or more species. On the other hand, leucokinin, which was presumed to be universally absent from Coleoptera, is still present in non-Polyphaga beetles.ConclusionThe variability in neuropeptidome composition between species from the same insect order may be as large as the one that exists between species from different orders. creator: Jan A. Veenstra uri: https://doi.org/10.7717/peerj.7144 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Veenstra title: Targeted metabolomics study of serum bile acid profile in patients with end-stage renal disease undergoing hemodialysis link: https://peerj.com/articles/7145 last-modified: 2019-06-17 description: BackgroundBile acids are important metabolites of intestinal microbiota, which have profound effects on host health. However, whether metabolism of bile acids is involved in the metabolic complications of end-stage renal disease (ESRD), and the effects of bile acids on the prognosis of ESRD remain obscure. Therefore, this study investigated the relationship between altered bile acid profile and the prognosis of ESRD patients.MethodsA targeted metabolomics approach based on ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to determine the changes in serum bile acids between ESRD patients (n = 77) and healthy controls (n = 30). Univariate and multivariate statistical analyses were performed to screen the differential proportions of bile acids between the two groups.ResultsSix differentially expressed bile acids were identified as potential biomarkers for differentiating ESRD patients from healthy subjects. The decreased concentrations of chenodeoxycholic acid, deoxycholic acid and cholic acid were significantly associated with dyslipidemia in ESRD patients. Subgroup analyses revealed that the significantly increased concentrations of taurocholic acid, taurochenodeoxycholic acid, taurohyocholic acid and tauro α-muricholic acid were correlated to the poor prognosis of ESRD patients.ConclusionsThe serum bile acid profile of ESRD patients differed significantly from that of healthy controls. In addition, the altered serum bile acid profile might contribute to the poor prognosis and metabolic complications of ESRD patients. creator: Rong Li creator: Li Zeng creator: Shuqin Xie creator: Jianwei Chen creator: Yuan Yu creator: Ling Zhong uri: https://doi.org/10.7717/peerj.7145 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Importance of active layer freeze-thaw cycles on the riverine dissolved carbon export on the Qinghai-Tibet Plateau permafrost region link: https://peerj.com/articles/7146 last-modified: 2019-06-17 description: The Qinghai-Tibet Plateau (QTP) is experiencing severe permafrost degradation, which can affect the hydrological and biogeochemical processes. Yet how the permafrost change affects riverine carbon export remains uncertain. Here, we investigated the seasonal variations of dissolved inorganic and organic carbon (DIC and DOC) during flow seasons in a watershed located in the central QTP permafrost region. The results showed that riverine DIC concentrations (27.81 ± 9.75 mg L−1) were much higher than DOC concentrations (6.57 ± 2.24 mg L−1). DIC and DOC fluxes were 3.95 and 0.94 g C m−2 year−1, respectively. DIC concentrations increased from initial thaw (May) to freeze period (October), while DOC concentrations remained relatively steady. Daily dissolved carbon concentrations were more closely correlated with baseflow than that with total runoff. Spatially, average DIC and DOC concentrations were positively correlated with vegetation coverage but negatively correlated with bare land coverage. DIC concentrations increased with the thawed and frozen depths due to increased soil interflow, more thaw-released carbon, more groundwater contribution, and possibly more carbonate weathering by soil CO2 formed carbonic acid. The DIC and DOC fluxes increased with thawed depth and decreased with frozen layer thickness. The seasonality of riverine dissolved carbon export was highly dependent on active layer thawing and freezing processes, which highlights the importance of changing permafrost for riverine carbon export. Future warming in the QTP permafrost region may alter the quantity and mechanisms of riverine carbon export. creator: Chunlin Song creator: Genxu Wang creator: Tianxu Mao creator: Xiaopeng Chen creator: Kewei Huang creator: Xiangyang Sun creator: Zhaoyong Hu uri: https://doi.org/10.7717/peerj.7146 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Song et al. title: Could do better! A high school market survey of fish labelling in Sydney, Australia, using DNA barcodes link: https://peerj.com/articles/7138 last-modified: 2019-06-14 description: BackgroundProcessed seafood products are not readily identifiable based on physical characteristics, which leaves the industry vulnerable to high levels of product mislabelling (globally estimated at 5–30% mislabelled). This is both a food safety issue and a consumer protection issue as cheaper species could be substituted for more expensive species. DNA barcoding is proving to be a valuable tool for authentication of fish products. We worked with high school students to perform a market survey and subsequent species assessment via DNA barcoding to investigate the accuracy of fish product names used by retailers in Sydney, Australia.MethodsSixty-eight fish samples, sold under 50 different common names, were purchased anonymously from two retailers in Sydney. Each product name was recorded and reconciled with the Australian Fish Names Standard (AFNS). Samples were DNA barcoded and resulting sequences were deposited in the online Barcode of Life Data system using the simplified Student Data Portal interface.ResultsForty percent of the fish names did not comply with the AFNS, however, half of these were either spelling errors or vendors supplied more information than the standard requires. The other half of the non-compliant samples were given common names not listed on the AFNS. Despite this lack of standardization, DNA barcode data confirmed the retailers’ identifications for 93% of samples and 90% of species sampled.DiscussionThe level of mislabelling we report for Sydney retailers (7% of samples or 10% of species) compares favorably with the global rates of 5–30%, but unfavorably with the only previous DNA barcode fish authentication study for Australia, which found no confirmed mislabelling in Hobart. Our study sampled mostly Australian produce, only two retailers and no restaurants. Results of our limited sample suggest that although many Sydney fish retailers attempt to implement the voluntary fish name standards, the standards are inadequate. As Australia imports 75% of its seafood, and in other countries restaurants generally show lower levels of compliance than retailers, broader surveys are needed before generalizing these results. DNA barcoding is a powerful yet simple method supported by accessible online analytical tools. Incorporation of fish barcoding into high school science classes provided students with valuable firsthand experience in scientific research and drew together different strands of the NSW curriculum relating to genetics and sustainability. Given the techniques, equipment, and reagents are now readily accessible, we expect to see greater uptake of DNA barcoding technology by high schools, citizen scientists and consumer groups in Australia in future. However, there remains much scope for further development of DNA barcode diagnostics (both data and analytical methods) for commercial fish species. creator: Andrew Mitchell creator: Anna Rothbart creator: Greta Frankham creator: Rebecca N. Johnson creator: Linda E. Neaves uri: https://doi.org/10.7717/peerj.7138 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mitchell et al. title: Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph Methylococcus capsulatus str. Bath link: https://peerj.com/articles/6685 last-modified: 2019-06-14 description: The increase in greenhouse gases with high global warming potential such as methane is a matter of concern and requires multifaceted efforts to reduce its emission and increase its mitigation from the environment. Microbes such as methanotrophs can assist in methane mitigation. To understand the metabolic capabilities of methanotrophs, a complete genome-scale metabolic model (GSMM) of an obligate methanotroph, Methylococcus capsulatus str. Bath was reconstructed. The model contains 535 genes, 899 reactions and 865 metabolites and is named iMC535. The predictive potential of the model was validated using previously-reported experimental data. The model predicted the Entner–Duodoroff pathway to be essential for the growth of this bacterium, whereas the Embden–Meyerhof–Parnas pathway was found non-essential. The performance of the model was simulated on various carbon and nitrogen sources and found that M. capsulatus can grow on amino acids. The analysis of network topology of the model identified that six amino acids were in the top-ranked metabolic hubs. Using flux balance analysis, 29% of the metabolic genes were predicted to be essential, and 76 double knockout combinations involving 92 unique genes were predicted to be lethal. In conclusion, we have reconstructed a GSMM of a methanotroph Methylococcus capsulatus str. Bath. This is the first high quality GSMM of a Methylococcus strain which can serve as an important resource for further strain-specific models of the Methylococcus genus, as well as identifying the biotechnological potential of M. capsulatus Bath. creator: Ankit Gupta creator: Ahmad Ahmad creator: Dipesh Chothwe creator: Midhun K. Madhu creator: Shireesh Srivastava creator: Vineet K. Sharma uri: https://doi.org/10.7717/peerj.6685 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gupta et al. title: Stochastic and deterministic drivers of seasonal variation of fungal community in tobacco field soil link: https://peerj.com/articles/6962 last-modified: 2019-06-14 description: BackgroundThe soil fungal community plays an important role in global carbon cycling and shows obvious seasonal variations, however, drivers, particularly stochastic drivers, of the seasonal variation in the fungal community have never been addressed in sufficient detail.MethodsWe investigated the soil fungal community variation between summer growing (SG) and winter fallow (WF) stage, through high throughput sequencing of internal transcribed spacer (ITS) amplicons. Subsequently, we assessed the contribution of different ecological processes to community assembly using null-model-based statistical framework.ResultsThe results showed that the fungal community diversity decreased significantly after tobacco cropping in the SG stage and the composition showed a clear turnover between the WF and SG stages. The variation in community composition was largely attributable to the presence of a small portion of Dothideomycetes in the WF stage that dominated the soil fungal community in the SG stage. The organic matter, temperature, and water content were the main deterministic factors that regulated the fungal community; these factors explained 34.02% of the fungal community variation. Together with the result that the fungal community was mainly assembled by the dispersal process, our results suggested that the stochastic factors played important roles in driving the seasonal variation of fungal community. The dispersal limitation dominated the fungal community assembly during the WF stage when homogenizing dispersal was the main assembly process of the fungal community in the SG stage. Thus, we proposed that the dispersal processes are important drivers for seasonal variation of fungal community in tobacco planted soil. creator: Xing Li creator: Tianming Li creator: Delong Meng creator: Tianbo Liu creator: Yongjun Liu creator: Huaqun Yin creator: Jie Deng creator: Songrong Zeng creator: Li Shen uri: https://doi.org/10.7717/peerj.6962 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Reservoir frogs: seasonality of Batrachochytrium dendrobatidis infection in robber frogs in Dominica and Montserrat link: https://peerj.com/articles/7021 last-modified: 2019-06-14 description: Emerging infectious diseases are an increasingly important threat to wildlife conservation, with amphibian chytridiomycosis, caused by Batrachochytrium dendrobatidis, the disease most commonly associated with species declines and extinctions. However, some amphibians can be infected with B. dendrobatidis in the absence of disease and can act as reservoirs of the pathogen. We surveyed robber frogs (Eleutherodactylus spp.), potential B. dendrobatidis reservoir species, at three sites on Montserrat, 2011–2013, and on Dominica in 2014, to identify seasonal patterns in B. dendrobatidis infection prevalence and load (B. dendrobatidis genomic equivalents). On Montserrat there was significant seasonality in B. dendrobatidis prevalence and B. dendrobatidis load, both of which were correlated with temperature but not rainfall. B. dendrobatidis prevalence reached 35% in the cooler, drier months but was repeatedly undetectable during the warmer, wetter months. Also, B. dendrobatidis prevalence significantly decreased from 53.2% when the pathogen emerged on Montserrat in 2009 to a maximum 34.8% by 2011, after which it remained stable. On Dominica, where B. dendrobatidis emerged seven years prior to Montserrat, the same seasonal pattern was recorded but at lower prevalence, possibly indicating long-term decline. Understanding the dynamics of disease threats such as chytridiomycosis is key to planning conservation measures. For example, reintroductions of chytridiomycosis-threatened species could be timed to coincide with periods of low B. dendrobatidis infection risk, increasing potential for reintroduction success. creator: Michael A. Hudson creator: Richard A. Griffiths creator: Lloyd Martin creator: Calvin Fenton creator: Sarah-Louise Adams creator: Alex Blackman creator: Machel Sulton creator: Matthew W. Perkins creator: Javier Lopez creator: Gerardo Garcia creator: Benjamin Tapley creator: Richard P. Young creator: Andrew A. Cunningham uri: https://doi.org/10.7717/peerj.7021 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hudson et al. title: Genome-wide characterization and expression analysis of PP2CA family members in response to ABA and osmotic stress in Gossypium link: https://peerj.com/articles/7105 last-modified: 2019-06-14 description: Clade A type 2C protein phosphatases (PP2CAs), as central regulators of abscisic acid (ABA) signaling, negative control growth, development and responses to multiple stresses in plants. PP2CA gene families have been characterized at genome-wide levels in several diploid plants like Arabidopsis and rice. However, the information about genome organization, phylogenesis and putative functions of PP2CAs in Gossypium is lacking. Here, PP2CA family members were comprehensively analyzed in four Gossypium species including the diploid progenitor Gossypium arboreum, G. raimondii and the tetraploid G. hirsutum and G. barbadense, and 14, 13, 27, and 23 PP2CA genes were identified in the genomic sequences of these plants, respectively. Analysis results showed that most Gossypium PP2CAs were highly conserved in chromosomal locations, structures, and phylogeny among the four cotton species. Segmental duplication might play important roles in the formation of the PP2CAs, and most PP2CAs may be under purifying selection in Gossypium during evolution. The majority of the PP2CAs were expressed specifically in diverse tissues, and highly expressed in flowers in G. hirsutum. The GhPP2CAs displayed diverse expression patterns in responding to ABA and osmotic stress. Yeast-two hybrid assays revealed that many GhPP2CAs were capable of interaction with the cotton ABA receptors pyrabactin resistance1/PYR1-like/regulatory components of ABA receptors (PYR1/PYL/RCAR) GhPYL2-2D (Gh_D08G2587), GhPYL6-2A (Gh_A06G1418), and GhPYL9-2A (Gh_A11G0870) in the presence and/or absence of ABA. These results gave a comprehensive view of the Gossypium PP2CAs and are valuable for further studying the functions of PP2CAs in Gossypium. creator: Tingting Lu creator: Gaofeng Zhang creator: Yibin Wang creator: Shibin He creator: Lirong Sun creator: Fushun Hao uri: https://doi.org/10.7717/peerj.7105 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lu et al. title: Deconstructing the Polymerase Chain Reaction II: an improved workflow and effects on artifact formation and primer degeneracy link: https://peerj.com/articles/7121 last-modified: 2019-06-14 description: Polymerase chain reaction (PCR) amplification of complex microbial genomic DNA templates with degenerate primers can lead to distortion of the underlying community structure due to inefficient primer-template interactions leading to bias. We previously described a method of deconstructed PCR (“PEX PCR”) to separate linear copying and exponential amplification stages of PCR to reduce PCR bias. In this manuscript, we describe an improved deconstructed PCR (“DePCR”) protocol separating linear and exponential stages of PCR and allowing higher throughput of sample processing. We demonstrate that the new protocol shares the same benefits of the original and show that the protocol dramatically and significantly decreases the formation of chimeric sequences during PCR. By employing PCR with annealing temperature gradients, we further show that there is a strong negative correlation between annealing temperature and the evenness of primer utilization in a complex pool of degenerate primers. Shifting primer utilization patterns mirrored shifts in observed microbial community structure in a complex microbial DNA template. We further employed the DePCR method to amplify the same microbial DNA template independently with each primer variant from a degenerate primer pool. The non-degenerate primers generated a broad range of observed microbial communities, but some were highly similar to communities observed with degenerate primer pools. The same experiment conducted with standard PCR led to consistently divergent observed microbial community structure. The DePCR method is simple to perform, is limited to PCR mixes and cleanup steps, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible. creator: Ankur Naqib creator: Silvana Poggi creator: Stefan J. Green uri: https://doi.org/10.7717/peerj.7121 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Naqib et al. title: Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera link: https://peerj.com/articles/7153 last-modified: 2019-06-14 description: Lotus (Nelumbo nucifera Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115 NnbHLHs were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115 NnbHLHs were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted. NnbHLHs were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15 NnbHLHs were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of NnbHLHs in four tissues indicated that many NnbHLHs showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of NnbHLHs, and identifies candidate genes for stress resistance in lotus. creator: Tian-Yu Mao creator: Yao-Yao Liu creator: Huan-Huan Zhu creator: Jie Zhang creator: Ju-Xiang Yang creator: Qiang Fu creator: Nian Wang creator: Ze Wang uri: https://doi.org/10.7717/peerj.7153 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mao et al. title: Association between complementary and alternative medicine use and prolonged time to conventional treatment among Thai cancer patients in a tertiary-care hospital link: https://peerj.com/articles/7159 last-modified: 2019-06-14 description: ObjectivesThe purpose of this study is to investigate the patterns of complementary and alternative medicine use and its association with time to conventional treatment.DesignA cross-sectional study design was designed.Setting and participantsThe study was performed at the Chonburi Cancer Hospital, with chart reviews and interviews performed for 426 patients with various cancers between May and December 2018.ResultsThe results indicated that 192 of the 426 patients (45.1%) reported using complementary and alternative medicines; herbal products were the most common type. Approximately 34.3% of these medicines involved unlabeled herbal products with unidentifiable components. The rates of complementary and alternative medicine use were significantly elevated for men and patients with stage IV cancer. The multivariable linear regression analysis of the relationship between factors and the time until conventional treatment was received revealed that the regression coefficient of the use of complementary and alternative medicine was 56.3 (95% confidence interval [27.9–84.6]). This coefficient reflected an additional 56.3 days of time until conventional treatment, relative to patients who did not use complementary and alternative medicine.ConclusionsThe present study revealed that complementary and alternative medicine use was fairly common among Thai patients with cancer and was associated with a prolonged time to receiving conventional treatment. creator: Adit Chotipanich creator: Chulaporn Sooksrisawat creator: Benjamabhon Jittiworapan uri: https://doi.org/10.7717/peerj.7159 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chotipanich et al. title: Age-related late-onset disease heritability patterns and implications for genome-wide association studies link: https://peerj.com/articles/7168 last-modified: 2019-06-14 description: Genome-wide association studies (GWASs) and other computational biology techniques are gradually discovering the causal gene variants that contribute to late-onset human diseases. After more than a decade of genome-wide association study efforts, these can account for only a fraction of the heritability implied by familial studies, the so-called “missing heritability” problem. Computer simulations of polygenic late-onset diseases (LODs) in an aging population have quantified the risk allele frequency decrease at older ages caused by individuals with higher polygenic risk scores (PRSs) becoming ill proportionately earlier. This effect is most prominent for diseases characterized by high cumulative incidence and high heritability, examples of which include Alzheimer’s disease, coronary artery disease, cerebral stroke, and type 2 diabetes. The incidence rate for LODs grows exponentially for decades after early onset ages, guaranteeing that the cohorts used for GWASs overrepresent older individuals with lower PRSs, whose disease cases are disproportionately due to environmental causes such as old age itself. This mechanism explains the decline in clinical predictive power with age and the lower discovery power of familial studies of heritability and GWASs. It also explains the relatively constant-with-age heritability found for LODs of lower prevalence, exemplified by cancers. creator: Roman Teo Oliynyk uri: https://doi.org/10.7717/peerj.7168 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Oliynyk title: A proposed terminology for the dentition of gomphodont cynodonts and dental morphology in Diademodontidae and Trirachodontidae link: https://peerj.com/articles/6752 last-modified: 2019-06-13 description: Gomphodont cynodonts were close relatives of mammals and one of the Mesozoic lineages of cynodont therapsids that became extinct at the end of the Triassic. Gomphodonts were omnivorous to herbivorous animals characterized by labiolingually expanded postcanines, which allowed tooth-to-tooth occlusion. The morphology of the upper and lower postcanines presents important means of distinguishing among major lineages within Gomphodontia, that is, Diademodontidae, Trirachodontidae, and Traversodontidae, but the dentition of most Diademodontidae and Trirachodontidae remain poorly documented. Here, we present a comprehensive description of the dentition of each diademodontid and trirachodontid species, as well as detailed illustrations of each dental unit, after firsthand examination of material and 3D reconstructions of postcanine teeth. Based on dental morphology, Trirachodon berryi and “Trirachodon kannemeyeri,” considered as separate taxa by some authors are here interpreted as representing different ontogenetic stages of the same species. Likewise, Sinognathus and Beishanodon, thought to belong to non-cynognathian cynodonts and traversodontids by some authors, are referred to Trirachodontidae and Gomphodontia based on dental characters, respectively. Finally, we propose a standardized list of terms and abbreviations for incisors, canines, and postcanines anatomical entities, with the goal of facilitating future descriptions and communication between researchers studying the gomphodont dentition. creator: Christophe Hendrickx creator: Fernando Abdala creator: Jonah N. Choiniere uri: https://doi.org/10.7717/peerj.6752 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hendrickx et al. title: Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots link: https://peerj.com/articles/7102 last-modified: 2019-06-13 description: BackgroundThere have been few studies on the partial defoliation response of grass. It has been unclear how partial defoliation may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular impacts of partial defoliation by using a model grass species, Brachypodium distachyon.ResultsOur Inductively Coupled Plasma Mass Spectrometry analyses of B. distachyon revealed shoot- and root-specific accumulation patterns of a group of macronutrients including potassium (K), Phosphorus (P), Calcium (Ca), Magnesium (Mg), and micronutrients including Sodium (Na), iron (Fe), and Manganese (Mn). Meanwhile, our genome-wide profiling of gene expression patterns depicts transcriptional impacts on B. distachyon roots by cutting the aerial portion. The RNAseq analyses identified a total of 1,268 differentially expressed genes in B. distachyon with partial defoliation treatment. Our comprehensive analyses by means of multiple approaches, including Gene Ontology, InterPro and Pfam protein classification, KEGG pathways, and Plant TFDB, jointly highlight the involvement of hormone-mediated wounding response, primary and secondary metabolites, and ion homeostasis, in B. distachyon after the partial defoliation treatment. In addition, evidence is provided that roots respond to partial defoliation by modifying nutrient uptake and rhizosphere acidification rate, indicating that an alteration of the root/soil interaction occurs in response to this practice.ConclusionsThis study reveals how partial defoliation alters ion accumulation levels in shoots and roots, as well as partial defoliation-induced transcriptional reprogramming on a whole-genome scale, thereby providing insight into the molecular mechanisms underlying the recovery process of grass after partial defoliation. creator: Wei Wang creator: Sunil Kumar Singh creator: Xiwen Li creator: Hui Sun creator: Yu Yang creator: Min Jiang creator: Hailing Zi creator: Renyi Liu creator: Huiming Zhang creator: Zhaoqing Chu uri: https://doi.org/10.7717/peerj.7102 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Temperament and character profiles of medical students associated with tolerance of ambiguity and perfectionism link: https://peerj.com/articles/7109 last-modified: 2019-06-13 description: BackgroundCertain personal attributes, such as perfectionism and tolerance of ambiguity, have been identified as influential in high achieving students. Medical students have been identified as high achievers and perfectionistic, and as such may be challenged by ambiguity. Medical students undertake a long and challenging degree. Personality has been shown to influence the well-being and coping and may equip some students to better cope with challenges. This paper examines the association between temperament and character personality profiles with measures of tolerance of ambiguity and with both adaptive and maladaptive constructs of perfectionism.MethodsA self-report questionnaire collected data on a sample of 808 Australian medical students in 2014 and 2015. Personality was measured using the Temperament and Character Inventory (TCIR-140) and classified traits as profiles using a latent class analysis. Two profiles were found. Profile 1 was characterized by low-average levels of Harm Avoidance, and high to very high levels of Persistence, Self-Directedness and Cooperativeness. Moderately-high levels of Harm Avoidance and high levels of Persistence, Self-Directedness and Cooperativeness characterized Profile 2. Moderation regression analyses were conducted to examine the association between the personality profiles with levels of Tolerance of Ambiguity (MSAT-II), Perfectionism-Concern over Mistakes and Perfectionism-High Standards (FMPS), considering demographic characteristics.ResultsStudents with Profile 1 were higher in levels of Tolerance of Ambiguity, and Perfectionism-High Standards, and lower levels of Perfectionism-Concern over Mistakes compared to Profile 2. These findings remained statistically significant after adjusting for age and gender. A significant personality by age interaction on Tolerance of Ambiguity was found. While higher levels of Tolerance of Ambiguity were associated with older age overall, it remained low across age for students with a personality Profile 2.ConclusionsA particular combination of personality traits was identified to be associated with low Tolerance of Ambiguity and high levels of maladaptive Perfectionism. An intolerance of ambiguity and over concern about mistakes may be maladaptive and underlie vulnerability to stress and poor coping. The psychobiological model of personality provides insight into traits that are stable and those that can be self-regulated through education and training. The interaction between biological mechanisms and socio-cultural learning is relevant to a sample of medical students because it accounts for interaction of the biological or innate aspects of their personal development within an intense and competitive learning environment of medical school. creator: Janni Leung creator: C. Robert Cloninger creator: Barry A. Hong creator: Kevin M. Cloninger creator: Diann S. Eley uri: https://doi.org/10.7717/peerj.7109 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Leung et al. title: Capsazepine prolongation of the duration of lidocaine block of sensory transmission in mice may be mediated by modulation of HCN channel currents link: https://peerj.com/articles/7111 last-modified: 2019-06-13 description: Background and objectivesHyperpolarization-activation cyclic nucleotide-gated (HCN) channels contribute to the effects of lidocaine. Capsazepine (CPZ), a competitive inhibitor of capsaicin of transient receptor potential vanilloid-1 channel, has also been found to inhibit HCN channel currents (Ih). This study was designed to investigate whether CPZ could prolong durations of lidocaine in regional anesthesia.MethodsMouse HCN1 and HCN2 channels were expressed in human embryonic kidney 293 (HEK 293) cells. The effect of CPZ on Ih was measured by whole-cell patch-clamping recording. Sciatic nerve block model in mice was used for the study in vivo. The mice were randomly divided into seven groups, respectively, receiving lidocaine, CPZ, ZD7288 (HCN channel blocker), CPZ + lidocaine, ZD7288 + lidocaine, ZD7288 + CPZ + lidocaine, forskolin (an activator of adenylyl cyclase) + CPZ + lidocaine. Regional anesthetic durations of lidocaine were determined. Voltage-gated sodium channel currents (INa) and Ih were recorded in dorsal root ganglion neurons of mice. The effects of CPZ on INa and Ih with or without Cyclic adenosine monophosphate (cAMP) were assessed. Isolated mice sciatic nerve was prepared to evaluate the effect of CPZ on the compound action potentials (CAP).ResultsCapsazepine non-selectively inhibited transfected mHCN1 and mHCN2 channel currents in HEK 293 cells. In sciatic nerve block in vivo, compared to lidocaine alone, adding CPZ extended the durations of lidocaine for noxious sensory block (35.1 ± 3.3 vs. 20.3 ± 1.7 min), tactile sensory block (25.5 ± 4.4 vs. 20.0 ± 3.7 min), thermal sensory block (39.6 ± 6.6 vs. 26.8 ± 5.5 min), and motor function block (28.6 ± 4.1 vs. 20.9 ± 4.2 min). Duration of thermal sensory block was longer in CPZ + lidocaine group than that of ZD7288 + lidocaine group (39.6 ± 6.6 vs. 33.4 ± 4.5 min). Forskolin reversed the prolongation by CPZ on lidocaine durations. CPZ or ZD7288 alone did not produce typical regional anesthetic effects. Increased intracellular concentration of cAMP reversed the inhibition of CPZ on Ih. Although CPZ alone inhibited INa at the concentration more than 30 μM, it did not inhibit the CAP amplitudes in isolated sciatic nerves. CPZ dose-dependently enhanced the inhibitory effect of 1% lidocaine on the CAP amplitudes.ConclusionsCapsazepine may prolong durations of lidocaine in peripheral nerve block by modulation of HCN channel currents. creator: Wenling Zhao creator: Peng Liang creator: Jin Liu creator: Huan Li creator: Daqing Liao creator: Xiangdong Chen creator: Qian Li creator: Cheng Zhou uri: https://doi.org/10.7717/peerj.7111 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhao et al. title: Soil respiration and its Q10 response to various grazing systems of a typical steppe in Inner Mongolia, China link: https://peerj.com/articles/7112 last-modified: 2019-06-13 description: BackgroundAs one of the important management practices of grassland ecosystems, grazing has fundamental effects on soil properties, vegetation, and soil microbes. Grazing can thus alter soil respiration (Rs) and the soil carbon cycle, yet its impacts and mechanisms remain unclear.MethodsTo explore the response of soil carbon flux and temperature sensitivity to different grazing systems, Rs, soil temperature (ST), and soil moisture (SM) were observed from December 2014 to September 2015 in a typical steppe of Inner Mongolia under three grazing systems: year-long grazing, rest-rotation grazing, and grazing exclusion. In addition, plant aboveground and root biomass, soil microbial biomass and community composition, and soil nutrients were measured during the pilot period.ResultsSoil respiration was significantly different among the three grazing systems. The average Rs was highest under rest-rotation grazing (1.26 μmol·m−2·s−1), followed by grazing exclusion (0.98 μmol·m−2·s−1) and year-long grazing (0.94 μmol·m−2·s−1). Rs was closely associated with ST, SM, potential substrate and root, and soil microbe activity. The effects of grazing among two grazing systems had generality, but were different due to grazing intensity. The root biomass was stimulated by grazing, and the rest-rotation grazing system resulted in the highest Rs. Grazing led to decreases in aboveground and microbial biomass as well as the loss of soil total nitrogen and total phosphorus from the steppe ecosystem, which explained the negative effect of grazing on Rs in the year-long grazing system compared to the grazing exclusion system. The temperature sensitivity of Rs (Q10) was higher in the rest-rotation and year-long grazing systems, likely due to the higher temperature sensitivity of rhizosphere respiration and higher “rhizosphere priming effect” in the promoted root biomass. The structural equation model analysis showed that while grazing inhibited Rs by reducing soil aeration porosity, ground biomass and SM, it increased Q10 but had a lower effect than other factors. A better understanding of the effects of grazing on soil respiration has important practical implications. creator: Cheng Nie creator: Yue Li creator: Lei Niu creator: Yinghui Liu creator: Rui Shao creator: Xia Xu creator: Yuqiang Tian uri: https://doi.org/10.7717/peerj.7112 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Nie et al. title: Effect of heat-killed Streptococcus thermophilus on type 2 diabetes rats link: https://peerj.com/articles/7117 last-modified: 2019-06-13 description: Background and AimsThe link between gut microbiota and type 2 diabetes (T2D) has been addressed by numerous studies. Streptococcus thermophilus from fermented milk products, has been used as a probiotic in previous research. However, whether heat-killed S. thermophilus can improve the glycemic parameters of diabetic rats remains unanswered. In this study, we evaluated the effect of heat-killed S. thermophilus on T2D model rats and the potential mechanisms of the effect.MethodsZucker diabetic fatty (ZDF) rats were used to generate a diabetic rat model induced by feeding a high-fat diet. Heat-killed S. thermophilus were orally administered to normal and diabetic rats for 12 weeks. Intestinal microbiota analysis, histology analysis, oral glucose tolerance test and measurement of inflammatory factors were performed.ResultsWe found that heat-killed S. thermophilus treatment reduced fasting blood glucose levels and alleviated glucose intolerance and total cholesterol in diabetic ZDF rats. Additionally, heat-killed S. thermophilus increased the interleukin 10 while reducing the levels of lipopolysaccharide, interleukin 6, and tumor necrosis factor-α in diabetic ZDF rats. The heat-killed S. thermophilus treatment can normalize the structure of the intestinal and colon mucosal layer of diabetic rats. The characteristics of the gut microbiota in heat-killed S. thermophilus-treated and control rats were similar. At the genus level, the abundances of beneficial bacteria, including Ruminococcaceae, Veillonella, Coprococcus, and Bamesiella, were all significantly elevated by heat-killed S. thermophilus treatment in ZDF diabetic rats.ConclusionOur study supports the hypothesis that treatment with heat-killed S. thermophilus could effectively improve glycemic parameters in T2D model rats. In addition, the potential mechanisms underlying the protection maybe include changing the composition of gut microbiota, reinforcing the intestinal epithelial barrier and the immunity of the intestinal mucosa, decreasing the level of inflammation, and then reducing the insulin resistance. creator: Xiangyang Gao creator: Fei Wang creator: Peng Zhao creator: Rong Zhang creator: Qiang Zeng uri: https://doi.org/10.7717/peerj.7117 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gao et al. title: Dynamics of soil properties and fungal community structure in continuous-cropped alfalfa fields in Northeast China link: https://peerj.com/articles/7127 last-modified: 2019-06-13 description: To compensate for the seasonal imbalance between livestock and forage yield in the cold region of Northeast China, alfalfa (Medicago sativa L.) continuous cropping has been widely employed in animal husbandry. However, the effects of continuous cropping of alfalfa on soil properties, including physical, chemical and biological properties, are poorly understood. In this study, we investigated the soil properties and fungal community composition of alfalfa fields under continuous cropping for different time periods (i.e., 1, 2, 6, 9, 12, 13 and 35 years). The results showed that soil moisture, total C, total N, NO3−-N and available K content decreased at less than 10 years of continuous cropping and then increased at more than 10 years of continuous cropping, but soil total P and available P content showed the opposite tendency. The soil fungal community composition determined using Illumina Miseq sequencing showed that continuous cropping increased the fungal alpha diversity and changed the fungal community structure. The relative abundances of Guehomyces and Chaetomium decreased, but the relative abundances of Phaeomycocentrospora and Paecilomyces increased with continuous cropping time. In addition, continuous cropping of alfalfa increased the relative abundances of some plant pathogens, such as Haematonectria haematococca and Cyphellophora sp. Soil total P and available P content were important soil factors affecting the soil fungal community diversity, fungal community structure and the relative abundances of specific fungi in this alfalfa continuous cropping system. creator: Qin Yao creator: Yanxia Xu creator: Xuefeng Liu creator: Junjie Liu creator: Xinyu Huang creator: Weiguang Yang creator: Zhao Yang creator: Lan Lan creator: Jingming Zhou creator: Guanghua Wang uri: https://doi.org/10.7717/peerj.7127 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yao et al. title: Development of the cephalopod-specific universal primer set and its application for the metabarcoding analysis of planktonic cephalopods in Korean waters link: https://peerj.com/articles/7140 last-modified: 2019-06-13 description: Although spatiotemporal analysis of the cephalopod larvae provides the useful information for the effective management of their resources, it has been difficult mainly due to their low numbers in the mixed zooplankton net samples and difficulty in morphological identification. In order to analyze the planktonic cephalopods using next-generation sequencing (NGS), we have designed a cephalopod-specific universal (CPD) primer set targeting a region covering mitochondrial cytochrome b and ND6 genes based on the currently identified 36 complete cephalopod mitochondrial genome sequences in the GenBank database. The expected amplicon sizes by CPD primers were between 465 and 471 bp, which was applicable to the MiSeq system (Illumina, San Diego, CA, USA). NGS results of pooled DNAs from 8 months (including 739 zooplankton net samples) collected from Korean waters in 2016 showed the exclusive cephalopod sequences with little contaminant sequences supporting the specificity of CPD primer set. Total 47 representative cephalopod haplotypes (seven families and 10 genera) were obtained from 1,439,414 merged reads. Among the total analyzed haplotypes, Watasenia scintillans, Todarodes pacificus, and Sepiola birostrata were the most abundant species in Korean waters. Two “unidentified” clades in order Oegopsida were identified, which was showed less than 90% sequence identity but closely related to Enoploteuthidae and Idiosepiidae, respectively. Monthly changes in proportions of each haplotype were also identified, which may reflect its reproduction and spawning period. The larvae of W. scintillans was dominant from February to June, while high proportions of other cephalopod taxa were also identified from August to November. Only single haplotype was dominant in W. scintillans (Type 2) throughout the year, while two distinct haplotypes showed seasonal differences in T. pacificus. creator: Eun-Bi Kim creator: Soo Rin Lee creator: Chung Il Lee creator: Hyun Park creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.7140 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kim et al. title: Extraction of polysaccharides from Amaranthus hybridus L. by hot water and analysis of their antioxidant activity link: https://peerj.com/articles/7149 last-modified: 2019-06-13 description: BackgroundAmaranthus hybridus L. is an annual herb that belongs to the Amaranthceae family, a type of multi-purpose grain, vegetable and feed crop that has received considerable attention due to its great economic value. However, the composition of polysaccharides from A. hybridus has rarely been previously reported.MethodsIn this study, the aboveground part of A. hybridus was used as material and polysaccharides were isolated by the hot water extraction method. Two acidic polysaccharides were isolated and purified by the Sevage method and diethylaminoethyl cellulose-32 column chromatography.ResultsTwo acidic polysaccharides were obtained from A. hybridus: AHP-H-1 and AHP-H-2. There were significant differences between the monosaccharide content from each sample according to gas chromatography-mass spectrometer. AHP-H-2 had higher antioxidant activity in vitro than AHP-H-1. The 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate of two mg/mL AHP-H-2 was 80%, its hydroxyl radical scavenging rate was approximately 48.5%, its superoxide anion radical scavenging rate was 85.3% and its reduction ability of Fe3+ was approximately 0.92. The total antioxidant capacity of each milligram of AHP-H-2 was 6.5, which was higher than ascorbic acid.ConclusionThe results of the study promote the effective use of A. hybridus and provide a theoretical basis for its development. creator: Yujia Tang creator: Yirong Xiao creator: Zizhong Tang creator: Weiqiong Jin creator: Yinsheng Wang creator: Hui Chen creator: Huipeng Yao creator: Zhi Shan creator: Tongliang Bu creator: Xiaoli Wang uri: https://doi.org/10.7717/peerj.7149 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tang et al. title: Age at menarche and depression: results from the NHANES 2005–2016 link: https://peerj.com/articles/7150 last-modified: 2019-06-13 description: ObjectiveThe association between early age at menarche and depression among adolescent girls and adult women has been examined in many studies. However, inconsistent results and limitations such as small sample size, low generalizability, and measurement error exist. We aimed to address these issues to assess the association between age at menarche and depressive symptoms in a nationally representative sample of US women aged 18 years and older.MethodsWe used the 2005–2016 National Health and Nutrition Examination Survey (NHANES) data with a total of 15,674 women aged 18 years and older included in our study. Logistic regression models were used after adjusting for sociodemographic and health-related factors.ResultsThe crude-adjusted model suggests that women with early age of menarche had 1.36 (95% CI [1.16–1.61]) times the odds of current depressive symptoms compared with the normal menarche group, after controlling for age, race/ethnicity, education, poverty income ratio (PIR) and marital status. In the fully-adjusted model, women with early menarche had 1.25 (95% CI [1.05–1.48]) times the odds of current depressive symptoms, after additionally adjusting for smoking status and body mass index (BMI). However, no significant difference was observed between the normal and late menarche groups.ConclusionFurther studies are warranted to determine the causal relationship and mechanisms between early menarche and increased risk of depression. creator: Yun Shen creator: Deepthi S. Varma creator: Yi Zheng creator: Jenny Boc creator: Hui Hu uri: https://doi.org/10.7717/peerj.7150 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Shen et al. title: Investigation of the protein profile of silkworm (Bombyx mori) pupae reared on a well-calibrated artificial diet compared to mulberry leaf diet link: https://peerj.com/articles/6723 last-modified: 2019-06-12 description: BackgroundSilkworm pupae is the main by-product of the sericulture industry with an interesting nutritional profile, especially in terms of proteins. In consideration of its possible use as a food or food ingredient in Western countries, a comparative proteomic experiment has been performed to investigate the differences of the protein profile of male and female silkworm pupae reared on mulberry leaves or on an artificial diet.MethodsThe nutritional profile of lyophilized silkworm pupae in terms of dry matter and ash was evaluated according to the AOAC procedures, the total nitrogen content was determined by a nitrogen analyzer and the silkworm pupae gross energy value was measured using an adiabatic calorimetric bomb. The comparative proteomic analysis was performed on male and female silkworm pupae reared on mulberry leaves or on the artificial diet. Proteins were separated by two-dimensional electrophoresis and, after a multivariate statistical analysis, the differentially expressed proteins were identified by LC-MS/MS.ResultsThe comparative proteomic approach highlighted 47 silkworm pupae proteins differentially expressed comparing diet and gender. PCA analysis showed that seven proteins were more effective in discriminating the sex and five were more effective in discriminating the diet type. In spite of the above-mentioned differences in the silkworm pupae protein profile, no strong alteration of the pupa physiological traits have been demonstrated, suggesting a general silkworm pupae flexibility to adapt to a well-balanced artificial diet. Differences in lipid transport and metabolism were found among the experimental groups, that might have a relevant effect on the timing and on hormone secretion. This aspect may also affect silk production, as univoltine strains are the most productive. The proteomic data provided in this work, may offer a contribution in understanding also the influence of gender and farming strategy on the allergen profile of Bombyx mori, when used as food or as a food ingredient. Female silkworm pupae reared on mulberry leaves seemed to contain lower levels of known allergens than those reared in the other experimental conditions; these findings will have to be taken into account when farming B. mori for food production purposes. However, our results need to be supported by further characterization of the allergenic potential of B. mori. creator: Cristina Lamberti creator: Francesco Gai creator: Simona Cirrincione creator: Marzia Giribaldi creator: Micol Purrotti creator: Marcello Manfredi creator: Emilio Marengo creator: Benedetto Sicuro creator: Alessio Saviane creator: Silvia Cappellozza creator: Maria Gabriella Giuffrida creator: Laura Cavallarin uri: https://doi.org/10.7717/peerj.6723 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lamberti et al. title: Analysis of microbiota in elderly patients with Acute Cerebral Infarction link: https://peerj.com/articles/6928 last-modified: 2019-06-12 description: Background and AimsRecent evidence suggest that microbiota is associated with almost all major types of diseases, including cardiovascular diseases. However, its role in Acute Cerebral Infarction remains unexplored. It is important to understand the diversity and distribution of gut microbiota (GM) in patients with Acute Cerebral Infarction and the role that GM plays in this type of disease.MethodsWe performed pyrosequencing on the gut microbiota of 40 individuals in order to elucidate whether the composition of the microbiota differs between patients with Acute Cerebral Infarction and healthy controls: Of these individuals, there were 31 with Acute Cerebral Infarction and nine controls. We applied linear regression to calculate the correlation between the gut flora and disease risk factors. Finally, KEGG functional enrichment analysis was conducted to examine the correlation between the gut flora and Acute Cerebral Infarction.ResultsThe overall microbial structure was similar in both the controls and the patients, but the control group had higher relative presence of Blautia obeum while the presence of Streptococcus infantis and Prevotella copri were relatively higher in the patient group. Using linear regression, we found that Blautia obeum was negatively associated with white blood cell count and Streptococcus infantis was positively correlated with creatinine and lipoprotein. The KEGG pathway analysis indicated that the bio-pathways including methane metabolism, lipopolysaccharide synthesis, bacterial secretion, and flagellar assembly of the gut microbiota in the patient group was expressed differently than that of the controls. We identified three differentially expressed gut microbial functions in Acute Cerebral Infarction and found four bacterial pathways that might be related to the development of this disease.ConclusionsOur study identified three abnormally-expressed bacteria—Blautia obeum, Streptococcus infantis, and Prevotella copri—in patients with Acute Cerebral Infarction compared with healthy controls. It reveals a correlation of these bacterial species with Acute Cerebral Infarction as they relate to disease factors and functional pathways. These findings may shed light on the treatment of cerebral infarction because gut microbiota could serve as a potential therapeutic approach for the treatment of cardiovascular and metabolic diseases. creator: Lin Huang creator: Teng Wang creator: Qian Wu creator: Xin Dong creator: Feifei Shen creator: Dong Liu creator: Xiaoxuan Qin creator: Lanyun Yan creator: Qi Wan uri: https://doi.org/10.7717/peerj.6928 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huang et al. title: Coastal fish assemblages and predation pressure in northern-central Chilean Lessonia trabeculata kelp forests and barren grounds link: https://peerj.com/articles/6964 last-modified: 2019-06-12 description: Kelp forests are declining in many parts of the globe, which can lead to the spreading of barren grounds. Increased abundances of grazers, mainly due to reduction of their predators, are among the causes of this development. Here, we compared the species richness (SR), frequency of occurrence (FO), and maximum abundance (MaxN) of predatory fish and their predation pressure between kelp forest and barren ground habitats of northern-central Chile. Sampling was done using baited underwater cameras with vertical and horizontal orientation. Two prey organisms were used as tethered baits, the black sea urchin Tetrapygus niger and the porcelanid crab Petrolisthes laevigatus. SR did not show major differences between habitats, while FO and MaxN were higher on barren grounds in vertical videos, with no major differences between habitats in horizontal videos. Predation pressure did not differ between habitats, but after 24 h consumption of porcelanid crabs was significantly higher than that of sea urchins. Scartichthys viridis/gigas was the main predator, accounting for 82% of the observed predation events on Petrolisthes laevigatus. Most of these attacks occurred on barren grounds. Scartichthys viridis/gigas was the only fish observed attacking (but not consuming) tethered sea urchins. High abundances of opportunistic predators (Scartichthys viridis/gigas) are probably related to low abundances of large predatory fishes. These results suggest that intense fishing activity on large predators, and their resulting low abundances, could result in low predation pressure on sea urchins, thereby contributing to the increase of T. niger abundances in subtidal rocky habitats. creator: Nicolás Riquelme-Pérez creator: Catalina A. Musrri creator: Wolfgang B. Stotz creator: Osvaldo Cerda creator: Oscar Pino-Olivares creator: Martin Thiel uri: https://doi.org/10.7717/peerj.6964 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Riquelme-Pérez et al. title: Relative and absolute within-session reliability of the modified Star Excursion Balance Test in healthy elite athletes link: https://peerj.com/articles/6999 last-modified: 2019-06-12 description: BackgroundThe Star Excursion Balance Test (SEBT) is commonly used to assess dynamic postural balance both in clinical practice and research. The aim of our study was to assess the within-session relative and absolute reliability of participants’ performance of the modified SEBT (mSEBT) using a single practice trial in healthy elite athletes who were familiar with the test.MethodsAn intra-session repeated-measures design was used to investigate the relative and absolute reliability of participants’ (healthy athletes partaking in sports at a high-risk of ankle sprain injury) performance of the mSEBT. A total of 122 healthy elite athletes from soccer (n = 73), basketball (n = 15), and volleyball (n = 34) performed one practice trial and three test trials within one session, in three directions (anterior, postero-medial, and postero-lateral), for both legs. Intraclass correlation coefficient (ICC), standard error of measurement (SEM), and smallest detectable change at a 95% confidence were calculated.ResultsWe found a good to excellent relative within-session intra-rater reliability between the three trials on specified directions, with an ICC (3,1) from 0.90 to 0.95. SEM and SDC95 for normalized and composite scores, for both legs ranged from 0.91 to 2.86, and 2.54 to 7.94, respectively.ConclusionsIn conclusion, we report good to excellent within-session reliability for the mSEBT. Our results confirm that the test can be reliably used with only one practice trial in healthy elite athletes familiar with the test. creator: Roxana R. Onofrei creator: Elena Amaricai creator: Radu Petroman creator: Oana Suciu uri: https://doi.org/10.7717/peerj.6999 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Onofrei et al. title: Fine-root traits of allelopathic rice at the seedling stage and their relationship with allelopathic potential link: https://peerj.com/articles/7006 last-modified: 2019-06-12 description: BackgroundAllelopathic rice releases allelochemicals through its root systems, thereby exerting a negative effect on paddy weeds. This research aimed to evaluate the relationship between fine-root traits and the rice allelopathic potential at the seedling stage.MethodsTwo allelopathic rice cultivars, ‘PI312777’ and ‘Taichung Native1,’ and one non-allelopathic rice cultivar, ‘Lemont,’ were grown to the 3–6 leaf stage in a hydroponic system. Their fine roots were collected for morphological trait (root length, root surface area, root volume, and root tips number) in smaller diameter cutoffs and proliferative trait (root biomass) analysis. Their root-exudates were used for quantitative analysis of phenolic acids contents and an evaluation of allelopathic potential. Correlation analysis was also used to assess whether any linear relationships existed.ResultsOur results showed that allelopathic rice cultivars had significantly higher fine-root length having diameters <0.2 mm, more root tips number, and greater root biomass, coupled with higher allelopathic potential and phenolic acid contents of their root exudates, comparing with non-allelopathic rice cultivar. These fine-root traits were significantly-positively correlated to allelopathic inhibition and total phenolic contents in rice root-exudates. However, there were not significant correlations among the rice allelopathic potential and total phenolic acid contents of rice root-exudates with the root length, root surface area, and root volume of fine root in diameter >0.2 mm.DiscussionOur results implied that fine-root traits appears to be important in understanding rice allelopathy at the seedling stage. The high allelopathic potential of rice cultivars might be attributed to their higher length of fine roots <0.2 mm in diameter and more number of root tips of fine root, which could accumulate and release more allelochemicals to solutions, thereby resulting in high inhibition on target plants. The mechanisms regulating this process need to be further studied. creator: Jiayu Li creator: Shunxian Lin creator: Qingxu Zhang creator: Qi Zhang creator: Wenwen Hu creator: Haibin He uri: https://doi.org/10.7717/peerj.7006 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Water regime and osmotic adjustment under warming conditions on wheat in the Yaqui Valley, Mexico link: https://peerj.com/articles/7029 last-modified: 2019-06-12 description: An experiment was carried out to evaluate the effect of increased temperature on roots and leaf water and osmotic potential, osmotic adjustment (OA) and transpiration on Triticum durum L. (CIRNO C2008 variety) during growth (seedling growth), tillering and heading phenophases. Wheat was sown under field conditions at the Experimental Technology Transfer Center (CETT-910), as a representative wheat crop area from the Yaqui Valley, Sonora México. Thermal radiators were placed at 1.20 m from the crop canopy. Treatments included warmed plots (2 °C) and ambient canopy temperature with five replicates. Temperature treatment was controlled using a (proportional, integrative, derivative) feedback control system on plots covering a circular area of r = 1.5 m. Results indicated a significant decrease in the osmotic potential of roots and leaves for the warmed plots. Water potential, under warming treatment, also experienced a significant reduction and a potential gradient was observed in both, roots and leaves, while the phenophases were delayed. Such results demonstrate that, under warmer conditions, plants increase water absorption for cooling. Hence, transpiration experienced a significant increase under warming in all phenophases that was related to the low root and leaf water potential. CIRNO C2008 also experienced OA in all phenophases with glycine betaine as the osmolyte with major contribution. creator: Leandris Argentel-Martínez creator: Jaime Garatuza-Payan creator: Enrico A. Yepez creator: Tulio Arredondo creator: Sergio de los Santos-Villalobos uri: https://doi.org/10.7717/peerj.7029 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Argentel-Martínez et al. title: Identification and characterization of PsDREB2 promoter involved in tissue-specific expression and abiotic stress response from Paeonia suffruticosa link: https://peerj.com/articles/7052 last-modified: 2019-06-12 description: Dehydration-responsive element-binding factor 2 (DREB2) belongs to the C-repeat-binding factor (CBF)/DREB subfamily of proteins. In this study, a 2,245 bp PsDREB2 promoter fragment was isolated from the genome of Paeonia suffruticosa. The fragment was rich in A/T bases and contained TATA box sequences, abscisic acid (ABA)-response elements, and other cis-elements, such as MYB and CAAT box. The promoter was fused with the β-glucuronidase (GUS) reporter gene to generate an expression vector. Arabidopsis thaliana was transformed with a flower dipping method. Gus activity in different tissues and organs of transgenic plants was determined via histochemical staining and quantified via GUS fluorescence. The activity of promoter regulatory elements in transgenic plants under drought, low-temperature, high-salt, and ABA stresses was analyzed. The results showed that the PsDREB2 gene promoter was expressed in the roots, stems, leaves, flowers, and silique pods but not in the seeds of transgenic Arabidopsis. Furthermore, the promoter was induced by drought, low temperature, high salt, and ABA. Hence, the PsDREB2 promoter is tissue- and stress-specific and can be used in the genetic engineering of novel peony cultivars in the future. creator: Huichun Liu creator: Kaiyuan Zhu creator: Chen Tan creator: Jiaqiang Zhang creator: Jianghua Zhou creator: Liang Jin creator: Guangying Ma creator: Qingcheng Zou uri: https://doi.org/10.7717/peerj.7052 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Sex- and tissue-specific expression of odorant-binding proteins and chemosensory proteins in adults of the scarab beetle Hylamorpha elegans (Burmeister) (Coleoptera: Scarabaeidae) link: https://peerj.com/articles/7054 last-modified: 2019-06-12 description: In this study, we addressed the sex- and tissue-specific expression patterns of odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) in Hylamorpha elegans (Burmeister), an important native scarab beetle pest species from Chile. Similar to other members of its family, this scarab beetle exhibit habits that make difficult to control the pest by conventional methods. Hence, alternative ways to manage the pest populations based on chemical communication and signaling (such as disrupting mating or host finding process) are highly desirable. However, developing pest-control methods based on chemical communication requires to understand the molecular basis for pheromone recognition/chemical perception in this species. Thus, with the aim of discovering olfaction-related genes, we obtained the first reference transcriptome assembly of H. elegans. We used different tissues of adult beetles from males and females: antennae and maxillary palps, which are well known for embedded sensory organs. Then, the expression of predicted odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) was analyzed by qRT-PCR. In total, 165 transcripts related to chemoperception were predicted. Of these, 16 OBPs, including one pheromone-binding protein (PBP), and four CSPs were successfully amplified by qRT-PCR. All of these genes were differentially expressed in the sensory tissues with respect to the tibial tissue that was used as a control. The single predicted PBP found was highly expressed in the antennal tissues, particularly in males, while several OBPs and one CSP showed male-biased expression patterns, suggesting that these proteins may participate in sexual recognition process. In addition, a single CSP was expressed at higher levels in female palps than in any other studied condition, suggesting that this CSP would participate in oviposition process. Finally, all four CSPs exhibited palp-biased expression while mixed results were obtained for the expression of the OBPs, which were more abundant in the palps than in the antennae. These results suggest that these chemoperception proteins would be interesting novel targets for control of H. elegans, thus providing a theoretical basis for further studies involving new pest control methods. creator: Angélica González-González creator: María E. Rubio-Meléndez creator: Gabriel I. Ballesteros creator: Claudio C. Ramírez creator: Rubén Palma-Millanao uri: https://doi.org/10.7717/peerj.7054 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 González-González et al. title: Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants link: https://peerj.com/articles/7071 last-modified: 2019-06-12 description: BackgroundExtensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic analysis of transcriptomic data, especially in cases with cSVs, is a complex and challenging task, and the development of proper bioinformatic tools for transcriptome studies is necessary.MethodsWe designed a bioinformatic workflow for the analysis of total RNA-Seq data consisting of two separate parts (pipelines): The first pipeline incorporates a statistical solution for differential gene expression analysis in a biologically heterogeneous sample set. We utilized results from transcriptomic arrays which were carried out in parallel to increase the precision of the analysis. The second pipeline is used for the identification of de novo fusion genes. Special attention was given to the filtering of false positives (FPs), which was achieved through consensus fusion calling with several fusion gene callers. We applied the workflow to the data obtained from ten patients with chronic lymphocytic leukemia (CLL) to describe the consequences of their cSVs in detail. The fusion genes identified by our pipeline were correlated with genomic break-points detected by genomic arrays.ResultsWe set up a novel solution for differential gene expression analysis of individual samples and de novo fusion gene detection from total RNA-Seq data. The results of the differential gene expression analysis were concordant with results obtained by transcriptomic arrays, which demonstrates the analytical capabilities of our method. We also showed that the consensus fusion gene detection approach was able to identify true positives (TPs) efficiently. Detected coordinates of fusion gene junctions were in concordance with genomic breakpoints assessed using genomic arrays.DiscussionByapplying our methods to real clinical samples, we proved that our approach for total RNA-Seq data analysis generates results consistent with other genomic analytical techniques. The data obtained by our analyses provided clues for the study of the biological consequences of cSVs with far-reaching implications for clinical outcome and management of cancer patients. The bioinformatic workflow is also widely applicable for addressing other research questions in different contexts, for which transcriptomic data are generated. creator: Jakub Hynst creator: Karla Plevova creator: Lenka Radova creator: Vojtech Bystry creator: Karol Pal creator: Sarka Pospisilova uri: https://doi.org/10.7717/peerj.7071 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hynst et al. title: Estimating biological accuracy of DSM for attention deficit/hyperactivity disorder based on multivariate analysis for small samples link: https://peerj.com/articles/7074 last-modified: 2019-06-12 description: ObjectiveTo estimate whether the “Diagnostic and Statistical Manual of Mental Disorders” (DSM) is biologically accurate for the diagnosis of Attention Deficit/ Hyperactivity Disorder (ADHD) using a biological-based classifier built by a special method of multivariate analysis of a large dataset of a small sample (much more variables than subjects), holding neurophysiological, behavioral, and psychological variables.MethodsTwenty typically developing boys and 19 boys diagnosed with ADHD, aged 10–13 years, were examined using the Attentional Network Test (ANT) with recordings of event-related potentials (ERPs). From 774 variables, a reduced number of latent variables (LVs) were extracted with a clustering of variables method (CLV), for further reclassification of subjects using the k-means method. This approach allowed a multivariate analysis to be applied to a significantly larger number of variables than the number of cases.ResultsFrom datasets including ERPs from the mid-frontal, mid-parietal, right frontal, and central scalp areas, we found 82% of agreement between DSM and biological-based classifications. The kappa index between DSM and behavioral/psychological/neurophysiological data was 0.75, which is regarded as a “substantial level of agreement”.DiscussionThe CLV is a useful method for multivariate analysis of datasets with much less subjects than variables. In this study, a correlation is found between the biological-based classifier and the DSM outputs for the classification of subjects as either ADHD or not. This result suggests that DSM clinically describes a biological condition, supporting its validity for ADHD diagnostics. creator: Dimitri M. Abramov creator: Vladimir V. Lazarev creator: Saint Clair Gomes Junior creator: Carlos Alberto Mourao-Junior creator: Monique Castro-Pontes creator: Carla Q. Cunha creator: Leonardo C. deAzevedo creator: Evelyne Vigneau uri: https://doi.org/10.7717/peerj.7074 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Abramov et al. title: Genetic diversity of gliadin-coding alleles in bread wheat (Triticum aestivum L.) from Northern Kazakhstan link: https://peerj.com/articles/7082 last-modified: 2019-06-12 description: BackgroundSpring bread wheat (Triticum aestivum L.) represents the main cereal crop in Northern Kazakhstan. The quality of wheat grain and flour strongly depends on the structure of gluten, comprised of gliadin and glutenin proteins. Electrophoresis spectra of gliadins are not altered by environmental conditions or plant growth, are easily reproducible and very useful for wheat germplasm identification in addition to DNA markers. Genetic polymorphism of two Gli loci encoding gliadins can be used for selection of preferable genotypes of wheat with high grain quality.MethodsPolyacrylamide gel electrophoresis was used to analyse genetic diversity of gliadins in a germplasm collection of spring bread wheat from Northern Kazakhstan.ResultsThe highest frequencies of gliadin alleles were found as follows, in Gli1: -A1f (39.3%), -B1e (71.9%), and -D1a (41.0%); and in Gli-2: -A2q (17.8%), -B2t (13.5%), and -D2q (20.4%). The combination of these alleles in a single genotype may be associated with higher quality of grain as well as better adaptation to the dry environment of Northern Kazakhstan; preferable for wheat breeding in locations with similar conditions. creator: Maral Utebayev creator: Svetlana Dashkevich creator: Nina Bome creator: Kulpash Bulatova creator: Yuri Shavrukov uri: https://doi.org/10.7717/peerj.7082 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Utebayev et al. title: T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection link: https://peerj.com/articles/7089 last-modified: 2019-06-12 description: BackgroundRespiratory syncytial virus (RSV) is the main cause of respiratory tract infection, which seriously threatens the health and life of children. This study is conducted to reveal the rehabilitation mechanisms of RSV infection.MethodsE-MTAB-5195 dataset was downloaded from EBI ArrayExpress database, including 39 acute phase samples in the acute phase of infection and 21 samples in the recovery period. Using the limma package, differentially expressed RNAs (DE-RNAs) were analyzed. The significant modules were identified using WGCNA package, and the mRNAs in them were conducted with enrichment analysis using DAVID tool. Afterwards, co-expression network for the RNAs involved in the significant modules was built by Cytoscape software. Additionally, RSV-correlated pathways were searched from Comparative Toxicogenomics Database, and then the pathway network was constructed.ResultsThere were 2,489 DE-RNAs between the two groups, including 2,386 DE-mRNAs and 103 DE-lncRNAs. The RNAs in the black, salmon, blue, tan and turquoise modules correlated with stage were taken as RNA set1. Meanwhile, the RNAs in brown, blue, magenta and pink modules related to disease severity were defined as RNA set2. In the pathway networks, CD40LG and RASGRP1 co-expressed with LINC00891/LINC00526/LINC01215 were involved in the T cell receptor signaling pathway, and IL1B, IL1R2, IL18, and IL18R1 co-expressed with BAIAP2-AS1/CRNDE/LINC01503/SMIM25 were implicated in cytokine-cytokine receptor interaction.ConclusionLINC00891/LINC00526/LINC01215 co-expressed with CD40LG and RASGRP1 might affect the rehabilitation process of RSV infection through the T cell receptor signaling pathway. Besides, BAIAP2-AS1/CRNDE/LINC01503/SMIM25 co-expressed with IL1 and IL18 families might function in the clearance process after RSV infection via cytokine-cytokine receptor interaction. creator: Zuanhao Qian creator: Zhenglei Zhang creator: Yingying Wang uri: https://doi.org/10.7717/peerj.7089 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qian et al. title: Growth-promoting characteristics of potential nitrogen-fixing bacteria in the root of an invasive plant Ageratina adenophora link: https://peerj.com/articles/7099 last-modified: 2019-06-12 description: Root endophytic nitrogen-fixing bacteria (reNFB) have been proposed as important contributors to the invasiveness of exotic legumes; however, the reNFB of invasive nonlegumes has received less attention. In particular, the growth-promoting effect of reNFB on invasive plants remains unknown. In this study, 131 strains of potential nitrogen-fixing bacteria were isolated and purified from the roots of the invasive plant, Ageratina adenophora, in Southwest China. Phylogenetically, these reNFB were categorized into three phyla at 97% sequence identity that included Proteobacteria (92.4%), Actinobacteria (4.6%), and Firmicutes (3.1%). The dominant isolates ranked by number were Pseudomonas (80 isolates, 61.1%), Rhizobium (12 isolates, 9.2%), and Duganella (11 isolates, 8.4%). The community composition and diversity of A. adenophora reNFB were markedly different across study regions. The capacity of these reNFB to accumulate indolyl-3-acetic acid (IAA), solubilize phosphate, and produce siderophores was determined. All 131 isolates of reNFB accumulated IAA, 67 isolates solubilized phosphate, and 108 isolates produced siderophores. Among the three dominant genera of reNFB, Pseudomonas had the highest phosphorus solubilization and siderophore production, while the accumulation of IAA in the genus Duganella was the lowest. Interestingly, the calculated reNFB Shannon diversity index of each A. adenophora individual was negatively correlated with the capacity of reNFB to produce growth-promoting products. Six randomly selected isolates from three dominant genera were further used to conduct inoculation experiments, and all isolates showed significant positive growth-promoting effects on A. adenophora seedlings. The contribution of reNFB to the root biomass was higher than that to the shoot biomass. Our results suggest that reNFB, similar to soil or nodular nitrogen-fixing bacteria, can potentially promote plant growth and may play an important role in the invasion of nonleguminous plants. More detailed studies on the correlation between reNFB and invasive plants are necessary. creator: Kai Fang creator: Zhu-Shou-Neng Bao creator: Lin Chen creator: Jie Zhou creator: Zhi-Ping Yang creator: Xing-Fan Dong creator: Han-Bo Zhang uri: https://doi.org/10.7717/peerj.7099 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fang et al. title: Engagement in physical activity, suicidal thoughts and suicide attempts among older people in five developing countries link: https://peerj.com/articles/7108 last-modified: 2019-06-12 description: BackgroundSuicide causes rising economic costs and public health risks for communities in the worldwide. Physical activity (PA) is considered a potentially feasible approach to reduce risk of suicide with low cost and high accessibility, and therefore attracting increasing attention. However, current literature on the association between PA and suicidal behavior amongst elderly people in low- and middle-income countries (LMICs) are scarce. Therefore, in this study we aimed to examine the relationship between suicidal thoughts (ST) and suicidal attempts (SA) with PA among elderly people in five LMICs.MethodsCross-sectional data were collected from WHO’s Study of Global Ageing and Adult Health (SAGE) with 2,861 participants aged 50 years or above. Variables included: self-reported occurrence of ST and SA during past 12 months and four types of PA (vigorous physical activity (VPA), moderate physical activity (MPA), walking/bike riding, moderate leisure time physical activity (MLPA)).ResultsThe overall prevalence of taking >75 min of VPA/week, >150 min/week, MLPA and walking/bike riding were, respectively, 85.4% (95% CI [81.3–88.7]), 61.6% (95% CI [52.9–69.6]), 9.6% (95% CI [7.2–12.6]) and 75.1% (95% CI [68.7–80.6]). Respectively, 31.0% (95% CI [24.3–38.7]) and 5.5% (95% CI [3.9–7.5]) of the respondents reported having morbid thoughts and SA during last 12 months. In adjusted multivariable regression analysis, not engaging in PA revealed positive association with higher odds of having morbid thoughts and SA, however, with varying degrees for different types of PA among men and women and across countries. The adjusted odds ratio among elderly who encountered ST increased significantly with PA levels (1.265 in male and 1.509 in female with VPA, 1.292 in male and 1.449 in female with MPA, 1.669 in female with LMPA and 3.039 in women with walk/bike); similarly, with SA (1.526, 1.532, 1.474 and 1.392 in women with VPA, MPA, LMPA and Walk/bike, respectively). The degree of adjusted odds ratio varied between genders and among countries.ConclusionAlthough the data were cross-sectional, and no linear dose-response relationship was observed between PA and morbid thought and suicide ideation, the findings provide important indications of potential harmful effects of no/inadequate PA on psychological morbidities among older individuals. Promoting adequate PA among older individuals through community-based suicide prevention programs can potentially contribute to reduction in the burden of PA in LMICs. creator: Bishwajit Ghose creator: Ruoxi Wang creator: Shangfeng Tang creator: Sanni Yaya uri: https://doi.org/10.7717/peerj.7108 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ghose et al. title: Spotting the “small eyes”: using photo-ID methodology to study a wild population of smalleye stingrays (Megatrygon microps) in southern Mozambique link: https://peerj.com/articles/7110 last-modified: 2019-06-11 description: BackgroundThe smalleye stingray (Megatrygon microps) is a large and rare dasyatid ray, patchily distributed across the Indo-West Pacific. Free-swimming individuals have regularly been recorded in Southern Mozambican coastal waters utilizing different inshore environments. Distinctive features of the species include latitudinal rows of white spots on the dorsal surface of their pectoral disc.MethodsThis study aimed to determine if the natural spot patterns on M. microps are sufficiently unique and stable to use in photo-identification studies of wild populations. Research dive logs were combined with opportunistic photographs from local dive centers and recreational divers to create a photographic database from the Inhambane Province coastline.ResultsSeventy different individuals were identified over a 15-year period, all exhibiting uniquely identifiable patterns. Stingrays were easily identifiable over a period of six years with multiple re-sightings of the same individuals recorded. Analysis of encounters across the Inhambane coastline revealed that individual rays regularly use inshore reefs along a 350 km stretch of coastline. Fifteen stingrays were re-sighted during the study period, including one showing a 400 km return movement between Tofo Beach and the Bazaruto Archipelago, which is the longest distance traveled by a dasyatid ray on record. Several presumably pregnant females have also been recorded in the Bazaruto Archipelago National Park. creator: Atlantine Boggio-Pasqua creator: Anna L. Flam creator: Andrea D. Marshall uri: https://doi.org/10.7717/peerj.7110 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Boggio-Pasqua et al. title: A new species of Micryletta frog (Microhylidae) from Northeast India link: https://peerj.com/articles/7012 last-modified: 2019-06-11 description: We describe a new species of frog in the microhylid genus MicrylettaDubois, 1987 from Northeast India based on molecular and morphological evidence. The new species, formally described as Micryletta aishani sp. nov., is phenotypically distinct from other congeners by a suite of morphological characters such as brown to reddish-brown dorsum; dorsal skin shagreened with minute spinules; snout shape nearly truncate in dorsal and ventral view; a prominent dark streak extending from tip of the snout up to the lower abdomen; ash-grey mottling along the margins of upper and lower lip extending up to the flanks, limb margins and dorsal surfaces of hand and foot; tibiotarsal articulation reaching up to the level of armpits; absence of outer metatarsal tubercles; and absence of webbing between toes. Phylogenetic relationships within the genus are inferred based on mitochondrial data and the new taxon is found to differ from all the recognised Micryletta species by 3.5–5.9% divergence in the mitochondrial 16S rRNA. The new species was found in the states of Assam, Manipur, and Tripura, from low to moderate elevation (30–800 m asl) regions lying south of River Brahmaputra and encompassing the Indo-Burma Biodiversity Hotspot. The discovery validates the presence of genus Micryletta in Northeast India based on genetic evidence, consequently confirming the extension of its geographical range, westwards from Southeast Asia up to Northeast India. Further, for nomenclatural stability of two previously known species, Microhyla inornata (= Micryletta inornata) and Microhyla steinegeri (= Micryletta steinegeri), lectotypes are designated along with detailed descriptions. creator: Abhijit Das creator: Sonali Garg creator: Amir Hamidy creator: Eric N. Smith creator: S. D. Biju uri: https://doi.org/10.7717/peerj.7012 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Das et al. title: Conservation and diversity in expression of candidate genes regulating socially-induced female-male sex change in wrasses link: https://peerj.com/articles/7032 last-modified: 2019-06-11 description: Fishes exhibit remarkably diverse, and plastic, patterns of sexual development, most striking of which is sequential hermaphroditism, where individuals readily reverse sex in adulthood. How this stunning example of phenotypic plasticity is controlled at a genetic level remains poorly understood. Several genes have been implicated in regulating sex change, yet the degree to which a conserved genetic machinery orchestrates this process has not yet been addressed. Using captive and in-the-field social manipulations to initiate sex change, combined with a comparative qPCR approach, we compared expression patterns of four candidate regulatory genes among three species of wrasses (Labridae)—a large and diverse teleost family where female-to-male sex change is pervasive, socially-cued, and likely ancestral. Expression in brain and gonadal tissues were compared among the iconic tropical bluehead wrasse (Thalassoma bifasciatum) and the temperate spotty (Notolabrus celidotus) and kyusen (Parajulus poecilepterus) wrasses. In all three species, gonadal sex change was preceded by downregulation of cyp19a1a (encoding gonadal aromatase that converts androgens to oestrogens) and accompanied by upregulation of amh (encoding anti-müllerian hormone that primarily regulates male germ cell development), and these genes may act concurrently to orchestrate ovary-testis transformation. In the brain, our data argue against a role for brain aromatase (cyp19a1b) in initiating behavioural sex change, as its expression trailed behavioural changes. However, we find that isotocin (it, that regulates teleost socio-sexual behaviours) expression correlated with dominant male-specific behaviours in the bluehead wrasse, suggesting it upregulation mediates the rapid behavioural sex change characteristic of blueheads and other tropical wrasses. However, it expression was not sex-biased in temperate spotty and kyusen wrasses, where sex change is more protracted and social groups may be less tightly-structured. Together, these findings suggest that while key components of the molecular machinery controlling gonadal sex change are phylogenetically conserved among wrasses, neural pathways governing behavioural sex change may be more variable. creator: Jodi T. Thomas creator: Erica V. Todd creator: Simon Muncaster creator: P Mark Lokman creator: Erin L. Damsteegt creator: Hui Liu creator: Kiyoshi Soyano creator: Florence Gléonnec creator: Melissa S. Lamm creator: John R. Godwin creator: Neil J. Gemmell uri: https://doi.org/10.7717/peerj.7032 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Thomas et al. title: The role of acetyl-coA carboxylase2 in head and neck squamous cell carcinoma link: https://peerj.com/articles/7037 last-modified: 2019-06-11 description: BackgroundAcetyl-CoA carboxylase (ACC) plays an important role in the metabolism of various cancer cells, but its role in head and neck squamous cell carcinoma (HNSCC) is uncertain. Therefore, in the present study, we explored the role of ACC2 in HNSCC.MethodsWestern blot and immunohistochemistry assays were used to determine ACC2 protein expression levels in laryngocarcinoma and adjacent normal tissues derived from patients with laryngocarcinoma. ACC2 expression was knocked down in the hypopharyngeal cancer cell line FaDu to determine its effect on apoptosis. Lipid oil red staining was used to test the change of intracellular lipid.ResultsThe results showed that the ACC2 protein was highly expressed in laryngocarcinoma and that the ACC2 expression level was positively associated with the clinical cancer stage and negatively associated with the degree of laryngocarcinoma cell differentiation. Kaplan–Meier analyses indicated that compared with patients having low levels of ACC2, those with high ACC2 levels had a decreased 5-year survival rate. The results of western blot and terminal deoxynucleotidyl transferase dUTP nick-end labeling assays showed that knockdown of ACC2 accelerated apoptosis in FaDu cells. Furthermore, knockdown of ACC2 significantly reduced the intracellular lipid levels in FaDu cells.ConclusionThese findings suggest that ACC2 may be an important prognostic marker for patients with HNSCC and that ACC2 may be a potential target in the treatment of HNSCC. creator: Kun Li creator: Chengcheng Zhang creator: Lei Chen creator: Pingping Wang creator: Yang Fang creator: Junwei Zhu creator: Shuo Chen creator: Juan Du creator: Bing Shen creator: Kaile Wu creator: Yehai Liu uri: https://doi.org/10.7717/peerj.7037 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Elaborated pollen packaging and dispensing mechanism induced by petal architecture from a Papaveraceae species link: https://peerj.com/articles/7066 last-modified: 2019-06-11 description: Secondary pollen presentation (SPP) is a reproductive strategy that enhances the efficiency of pollen transfer, which has been explored for more than 200 years, resulting in 10 identified types of SPP. The ephemeral plant Hypecoum erectum L. (Papaveraceae) has an elaborate petal structure. The middle lobe is a key functional organ in SPP. To explore the importance of the middle lobe structure, we measured the flowering process, the curling movement and growth of the middle lobe, pollination characteristics, pollination efficiency, and the mating system in H. erectum in the field. The yellow middle lobe structure had an important role in attracting pollinators. The middle lobes on the inner petals function as a redundant cucullate structure and wrapped about 84% of the total pollen grains as soon as the anthers dehisced. These then grew upward and gradually presented pollen to pollinators via the roll out of the middle lobes. One bee species, Colletes vestitus from Colletidae, was the only effective pollinator of H. erectum. The SPP mechanism increased the efficiency of pollen transfer by C. vestitus. The middle lobes, which wrapped pollen and grew upward, contacted the stigma and provided an advantage for self-pollination and outcrossing by growing upward higher than the corolla. Hypecoum erectum L. has a mixed mating system with selfing and outcrossing. Thus, the SPP mechanism plays a key role during the pollination process and is necessary for improving pollination efficiency and promoting reproductive success. creator: Shanlin Yang creator: Guangming Chu creator: Xiang Shi creator: Shaoming Wang uri: https://doi.org/10.7717/peerj.7066 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: PGM5: a novel diagnostic and prognostic biomarker for liver cancer link: https://peerj.com/articles/7070 last-modified: 2019-06-11 description: BackgroundLiver cancer is a common malignancy and a significant public health problem worldwide, but diagnosis and prognostic evaluation remain challenging for clinicians. Metabolic reprogramming is a hallmark of cancer, and we therefore examined the diagnostic and prognostic value of a metabolic enzyme, phosphoglucomutase-like protein 5 (PGM5), in liver cancer.MethodsAll data were from The Cancer Genome Atlas database. R and related statistical packages were used for data analysis. Hepatic PGM5 expression was determined in different groups, and the chi-squared test and Fisher’s exact test were used to determine the significance of differences. The pROC package was used to determine receiver operating characteristic (ROC) curves, the survival package was used to for survival analysis and development of a Cox multivariable model, and the ggplot2 package was used for data visualization.ResultsPGM5 expression was significantly lower in cancerous than adjacent normal liver tissues, and had modest diagnostic value based on ROC analysis and calculations of area under the curve (AUC). Hepatic PGM5 expression had positive associations with male sex and survival, but negative associations with advanced histologic type, advanced histologic grade, advanced stage, and advanced T classification. Patents with low PGM5 levels had poorer overall survival and relapse-free survival. PGM5 was independently associated with patient prognosis.ConclusionPGM5 has potential use as a diagnostic and prognostic biomarker for liver cancer. creator: Yan Jiao creator: Yanqing Li creator: Peiqiang Jiang creator: Wei Han creator: Yahui Liu uri: https://doi.org/10.7717/peerj.7070 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jiao et al. title: The role of serum and urinary biomarkers in the diagnosis of early diabetic nephropathy in patients with type 2 diabetes link: https://peerj.com/articles/7079 last-modified: 2019-06-11 description: BackgroundPrevious studies have shown that a variety of biomarkers are closely related to the occurrence and development of early-stage diabetic nephropathy (DN) in patients. The aim of this study was to evaluate the role of multiple sera and urinary biomarkers in the diagnosis of early-stage DN in patients with type 2 diabetes.MethodsWe enrolled 287 patients with type 2 diabetes, who were classified into normoalbuminuria (n = 144), microalbuminuria (n = 94), or macroalbuminuria (n = 49) groups based on their urine albumin to creatinine ratios (UACR), along with 42 healthy controls. We assessed 13 biomarkers, including transferrin (Tf), immunoglobulin G (IgG), podocalyxin, neutrophil gelatinase-associated lipocalin (NGAL), N-acetyl-beta-glucosaminidase, α-1-microglobulin, 8-hydroxy-deoxyguanosine, tumor necrosis factor-alpha (TNF-α), and interleukin-18 in urine samples, along with cystatin C, total bilirubin, and uric acid in sera samples, to evaluate their diagnostic roles. From the measurements, the blood neutrophil to lymphocyte ratio was also calculated.ResultsUrinary Tf, IgG, NGAL, and TNF-α were significantly related to the UACR. We calculated the area under the receiver operating characteristic curves (area under the curve) and found that urinary IgG (0.894), NGAL (0.875), Tf (0.861), TNF-α (0.763), and the combination of urinary Tf + IgG + TNF-α + NGAL (0.922) showed good diagnostic value for early-stage DN.ConclusionsUrinary Tf, IgG, NGAL, TNF-α, and the combination of all four biomarkers demonstrated excellent diagnostic value for early-stage DN in patients with type 2 diabetes. creator: Deyuan Zhang creator: Shandong Ye creator: Tianrong Pan uri: https://doi.org/10.7717/peerj.7079 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Hydroclimatic variations reveal differences in carbon capture in two sympatric conifers in northern Mexico link: https://peerj.com/articles/7085 last-modified: 2019-06-11 description: BackgroundForest ecosystems are considered among the largest terrestrial carbon sinks. The dynamics of forest carbon depend on where the carbon is stored and its responses to environmental factors, as well as the physiology of the trees. Thus, threatened forest regions with high biodiversity have great scientific importance, such as the Sierra Madre Occidental in Mexico. A comparative analysis of tree species can expand the knowledge of the carbon cycle dynamics and ecological processes in this region. Here, we examined the growth, wood density, and carbon accumulation of two threatened species (Pseudotsuga menziesii and Cupressus lusitanica) to evaluate their hydroclimatic responsiveness.MethodsThe temporal variations in the carbon accumulation patterns of two co-occurring species (P. menziesii and C. lusitanica) and their sensitivity to the local climate were studied using dendroecological techniques, X-ray densitometry, and allometric equations.ResultsThe results show that the annual carbon accumulation in C. lusitanica is positively associated with the temperature during the current fall, while the carbon accumulation in P. menziesii is correlated with the rainfall during the winter of the previous year. The climatic responses are associated with the intra-annual variations of wood density and ring widths for each species. The ring width was strongly correlated with carbon accumulation in C. lusitanica, while the mean wood density was linked to carbon accumulation in P. menziesii.DiscussionThis study has implications for the carbon accumulation rates of both species, revealing differences in the carbon capture patterns in response to climatic variations. Although the species coexist, there are variation in the hydroclimatic sensitivity of the annual carbon sequestered by trunks of trees, which would be associated with tree-ring width and/or wood density, i.e., directly by anatomical features. The results are relevant to analyze the response to the variability of climatic conditions expected in the near future of the tree communities of Sierra Madre Occidental. Therefore, this study provides a basis for modeling the long-term carbon budget projections in terrestrial ecosystems in northern Mexico. creator: Marcos González-Cásares creator: Marín Pompa-García creator: Alejandro Venegas-González creator: Pedro Domínguez-Calleros creator: José Hernández-Díaz creator: Artemio Carrillo-Parra creator: Marco González-Tagle uri: https://doi.org/10.7717/peerj.7085 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 González-Cásares et al. title: Analyzing moisture-heat coupling in a wheat-soil system using data-driven vector autoregression model link: https://peerj.com/articles/7101 last-modified: 2019-06-11 description: Soil temperature and moisture have a close relationship, the accurate controlling of which is important for crop growth. Mechanistic models built by previous studies need exhaustive parameters and seldom consider time stochasticity and lagging effect. To circumvent these problems, this study designed a data-driven stochastic model analyzing soil moisture-heat coupling. Firstly, three vector autoregression models are built using hourly data on soil moisture and temperature at the depth of 10, 30, and 90 cm. Secondly, from impulse response functions, the time lag and intensity of two variables’ response to one unit of positive shock can be obtained, which describe the time length and strength at which temperature and moisture affect each other, indicating the degree of coupling. Thirdly, Granger causality tests unfold whether one variable’s past value helps predict the other’s future value. Analyzing data obtained from Shangqiu Experiment Station in Central China, we obtained three conclusions. Firstly, moisture’s response time lag is 25, 50, and 120 h, while temperature’s response time lag is 50, 120, and 120 h at 10, 30, and 90 cm. Secondly, temperature’s response intensity is 0.2004, 0.0163, and 0.0035 °C for 1% variation in moisture, and moisture’s response intensity is 0.0638%, 0.0163%, and 0.0050% for 1 °C variation in temperature at 10, 30, and 90 cm. Thirdly, the past value of soil moisture helps predict soil temperature at 10, 30, and 90 cm. Besides, the past value of soil temperature helps predict soil moisture at 10 and 30 cm, but not at 90 cm. We verified this model by using data from a different year and linking it to soil plant atmospheric continuum model. creator: Xiaohang Feng creator: Xia Zhang creator: Zhenqi Feng creator: Yichang Wei uri: https://doi.org/10.7717/peerj.7101 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Feng et al. title: A comparison of impact and risk assessment methods based on the IMO Guidelines and EU invasive alien species risk assessment frameworks link: https://peerj.com/articles/6965 last-modified: 2019-06-10 description: A comparative analysis of two risk assessment (RA) frameworks developed to support the implementation of the international Ballast Water Management Convention (BWMC) and European Regulation on Invasive Alien Species (IAS) was performed. This analysis revealed both differences and similarities between the IMO Risk Assessment Guidelines (IMO, 2007) and EU Regulation supplement on RA of IAS (EU, 2018) in RA approaches, key principles, RA components and categories of IAS impacts recommended for assessment. The results of this analysis were used to produce a common procedure for the evaluation of the bioinvasion risk and impact assessment methods intended to support international, regional and/or national policy on IAS. The procedure includes a scoring scheme to assess compliance with the key principles, RA components and categories of bioinvasion impacts taken into account by the methods. In these methods the categories of impacts on human health and economy are underrepresented comparing with impacts on environment. creator: Greta Srėbalienė creator: Sergej Olenin creator: Dan Minchin creator: Aleksas Narščius uri: https://doi.org/10.7717/peerj.6965 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Srėbalienė et al. title: In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation link: https://peerj.com/articles/7017 last-modified: 2019-06-10 description: One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation. creator: Alejandra Hernández-Terán creator: Ana Wegier creator: Mariana Benítez creator: Rafael Lira creator: Tania Gabriela Sosa Fuentes creator: Ana E. Escalante uri: https://doi.org/10.7717/peerj.7017 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hernández-Terán et al. title: Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales link: https://peerj.com/articles/7045 last-modified: 2019-06-10 description: BackgroundMicrobes have been recognized as important symbionts to regulate host life. The animal gut harbors abundance and diverse bacteria. Numerous internal and external factors influence intestinal bacterial communities, including diet, seasonal fluctuations and habitat sites. However, the factors that influence the gut bacterial communities of wild bird is poorly characterized.MethodsBy high-throughput sequencing and statistical analysis, we investigated the variations in gut bacterial communities of the hooded cranes at three wintering stages in Caizi (CZL) and Shengjin Lake (SJL), which are two shallow lakes in the middle and lower Yangtze River floodplain.ResultsOur results revealed significant differences in gut bacterial community structure and diversity among different sampling sites and wintering stages. Seasonal changes have a significant impact on the gut microbe composition of hooded cranes in the two lakes. ANOSIM analysis demonstrated that the samples in CZL had greater differences in the gut bacterial composition than that in SJL. Our data showed strong evidence that the host’s gut filtering might be an important factor in shaping bacterial community according to mean nearest taxon distance (MNTD). The PICRUSt analysis showed that the predicted metagenomes associated with the gut microbiome were carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes.ConclusionsThe results demonstrated that both seasonal changes and habitat sites have significant impact on the gut bacterial communities of hooded cranes. In addition, predictive function of gut microbes in hooded cranes varied over time. These results provide new insights into the gut microbial community of the cranes, which serves as a foundation for future studies. creator: Yuanqiu Dong creator: Xingjia Xiang creator: Guanghong Zhao creator: Yunwei Song creator: Lizhi Zhou uri: https://doi.org/10.7717/peerj.7045 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dong et al. title: Stoichiometric ratios support plant adaption to grazing moderated by soil nutrients and root enzymes link: https://peerj.com/articles/7047 last-modified: 2019-06-10 description: BackgroundVegetation succession is one of the major driving processes of grassland degradation. Stoichiometry significantly contributes to vegetation dynamics. However, a knowledge gap exists in how soil nutrients and root enzymes influence the stoichiometric ratio to affect vegetation dynamics.MethodsTo address these questions, we selected a dominant species (Leymus chinensis (Trin.) Tzvel.) and a degraded-dominant species (Artemisia frigida Willd.) under different management regimes (enclosure and grazing) on the Inner Mongolia steppe. We measured (i) plant nutrient concentrations, (ii) root enzymes and (iii) soil nutrients to investigate how the selected plant species responded to grazing.ResultsThe results show that: (i) N and P concentrations and the C:N:P ratio in different organs are significantly affected by grazing, and there is variation in the plant species’ response. Grazing significantly increased N and P in the leaves and stems of L. chinensis and the stems and roots of A. frigida. (ii) Grazing significantly increased the activities of glutamine synthase but decreased the activities of acid phosphatase in L. chinensis. The nitrate reductase and acid phosphatase activities significantly increased in A. frigida under grazing conditions. (iii) Grazing decreased the total nitrogen, total phosphorus, and available nitrogen, but increased the available phosphorus in the soil.ConclusionWe conclude that A. frigida is better adapted to grazing than L. chinensis, possibly because of its relatively increased stem and root growth, which enhance population expansion following grazing. Conversely, L. chinensis showed increased leaf and stem growth, but suffered nutrient and biomass loss as a result of excessive foraging by livestock, which severely affected its ability to colonize. Root enzymes coupled with soil nutrients can regulate plant nutrients and stoichiometric ratios as an adaptive response to grazing. Thus, we demonstrated that stoichiometric ratios allow species to better withstand grazing disturbances. This study provides a new understanding of the mechanisms involved in grazing-resistance within a plant-soil system. creator: Wenjing Ma creator: Jin Li creator: Saheed Olaide Jimoh creator: Yujuan Zhang creator: Fenghui Guo creator: Yong Ding creator: Xiliang Li creator: Xiangyang Hou uri: https://doi.org/10.7717/peerj.7047 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Genome-wide analysis of the WRKY gene family in drumstick (Moringa oleifera Lam.) link: https://peerj.com/articles/7063 last-modified: 2019-06-10 description: WRKY proteins belong to one of the largest families of transcription factors. They have important functions in plant growth and development, signal transduction and stress responses. However, little information is available regarding the WRKY family in drumstick (Moringa oleifera Lam.). In the present study, we identified 54 MoWRKY genes in this species using genomic data. On the basis of structural features of the proteins they encode, the MoWRKY genes were classified into three main groups, with the second group being further divided into five subgroups. Phylogenetic trees constructed from the sequences of WRKY domains and overall amino acid compositions derived from drumstick and Arabidopsis were similar; the results indicated that the WRKY domain was the main evolutionary unit of WRKY genes. Gene structure and conserved motif analysis showed that genes with similar structures and proteins with similar motif compositions were usually clustered in the same class. Selective pressure analysis indicated that although neutral evolution and positive selection have happened in several MoWRKY genes, most have evolved under strong purifying selection. Moreover, different subgroups had evolved at different rates. The levels of expression of MoWRKY genes in response to five different abiotic stresses (salt, heat, drought, H2O2, cold) were evaluated by reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR), with the results indicating that these genes had different expression levels and that some may be involved in abiotic stress responses. Our results will provide a foundation for cloning genes with specific functions for use in further research and applications. creator: Junjie Zhang creator: Endian Yang creator: Qian He creator: Mengfei Lin creator: Wei Zhou creator: Ruiqi Pian creator: Xiaoyang Chen uri: https://doi.org/10.7717/peerj.7063 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Prognosis predictive value of the Oxford Acute Severity of Illness Score for sepsis: a retrospective cohort study link: https://peerj.com/articles/7083 last-modified: 2019-06-10 description: BackgroundThe Oxford Acute Severity of Illness Score (OASIS) has shown fair prognosis predictive value in critically ill patients, but its predictive value has not been assessed in septic patients.ObjectiveThe aim of this study was to evaluate the performance of the OASIS for the assessment of mortality in septic patients, especially when compared with the Sepsis-related Organ Failure Assessment (SOFA) score.MethodsA retrospective cohort study was conducted using data from a public database and septic patients were identified using the Sepsis-3 criteria. The primary outcome was hospital mortality. Data were mainly analyzed using multivariable logistic regression and receiver operating characteristic (ROC) curves. Sensitive analyses were performed in patients with an ICD-9-CM code for sepsis and ROC curves analyses were also conducted in septic patients stratified by the Simplified Acute Physiology Score (SAPS) II as subgroup analyses.ResultsA total of 10,305 septic patients were included. The OASIS was found to be significantly associated with hospital mortality (odds ratio 1.07 per one-point increase, 95% confidence interval [1.06–1.08]), while ROC curves analyses showed the discriminatory power of the OASIS for hospital mortality was statistically significantly lower than that of the SOFA score (area under the ROC curve: 0.652 vs 0.682, p < 0.001). Results of sensitive analyses were consistent, but the significant difference existed only when the SAPS II was higher than 50 according to results of the subgroup analyses.ConclusionsThe OASIS might serve as an initial predictor of clinical outcomes for septic patients, but one should be circumspect when it is applied to severer patients. creator: Qingui Chen creator: Lishan Zhang creator: Shanhui Ge creator: Wanmei He creator: Mian Zeng uri: https://doi.org/10.7717/peerj.7083 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chen et al. title: Global transcriptomic analysis identifies SERPINE1 as a prognostic biomarker associated with epithelial-to-mesenchymal transition in gastric cancer link: https://peerj.com/articles/7091 last-modified: 2019-06-10 description: BackgroundThe plasminogen activation system plays a pivotal role in regulating tumorigenesis. In this work, we aim to identify key regulators of plasminogen activation associated with tumorigenesis and explore potential mechanisms in gastric cancer (GC).MethodsGene profiling datasets were extracted from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened for and obtained by the GEO2R tool. The Database for Annotation, Visualization and Integrated Discovery was used for GO and KEGG enrichment analysis. Gene set enrichment analysis (GSEA) was performed to verify molecular signatures and pathways among The Cancer Genome Atlas or GEO datasets. Correlations between SERPINE1 and markers of epithelial-to-mesenchymal transition (EMT) were analyzed using the GEPIA database and quantitative real-time PCR (qRT-PCR). Interactive networks of selected genes were built by STRING and Cytoscape software. Finally, selected genes were verified with the Kaplan–Meier (KM) plotter database.ResultsA total of 104 overlapped upregulated and 61 downregulated DEGs were obtained. Multiple GO and KEGG terms associated with the extracellular matrix were enriched among the DEGs. SERPINE1 was identified as the only regulator of angiogenesis and the plasminogen activator system among the DEGs. A high level of SERPINE1 was associated with a poor prognosis in GC. GSEA analysis showed a strong correlation between SERPINE1 and EMT, which was also confirmed with the GEPIA database and qRT-PCR validation. FN1, TIMP1, MMP2, and SPARC were correlated with SERPINE1.The KM plotter database showed that an overexpression of these genes correlated with a shorter survival time in GC patients.ConclusionsIn conclusion, SERPINE1 is a potent biomarker associated with EMT and a poor prognosis in GC. Furthermore, FN1, TIMP1, MMP2, and SPARC are correlated with SERPINE1 and may serve as therapeutic targets in reversing EMT in GC. creator: Bodong Xu creator: Zhigang Bai creator: Jie Yin creator: Zhongtao Zhang uri: https://doi.org/10.7717/peerj.7091 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xu et al. title: Association between VDR gene FokI polymorphism and renal function in patients with IgA nephropathy link: https://peerj.com/articles/7092 last-modified: 2019-06-10 description: BackgroundStudies have shown that the occurrence and development of IgA nephropathy (IgAN) are genetically susceptible, but the relationship between vitamin D receptor (VDR) gene polymorphisms and renal function in IgAN patients is unclear.MethodsWe investigated the relationship between VDR FokI (rs2228570) single nucleotide polymorphism (SNP) and renal function and related clinicopathologic parameters in IgAN patients. Clinical and pathological data of 282 IgAN patients treated at the First Affiliated Hospital of Guangxi Medical University were collected, and FokI genotypes were determined by PCR and direct sequencing. Patients were divided into the renal dysfunction group and normal renal function (control) group by estimated glomerular filtration rate (eGFR) and serum creatinine level.ResultsFrequencies of TT genotype and T allele in the renal dysfunction group were higher than those of the control group. Blood urea nitrogen, serum phosphorus (P), proportions of mesangial cell proliferation, interstitial fibrosis/tubular atrophy and crescents in T allele carriers were higher than those in non-T allele carriers, while eGFR and 25-Hydroxyvitamin D3 were lower in T allele carriers than non-T allele carriers. Multiple linear regression analysis showed that eGFR was affected by FokI genotypes in IgAN patients. Logistics regression analysis showed that middle and elderly age, elevated P, intact parathyroid hormone and TT genotype were independent risk factors for renal dysfunction in IgAN patients; the odds ratio of carrying the TT genotype was as high as 84.77 (P < 0.05 for all).ConclusionsIgA nephropathy patients carrying the VDR FokI TT genotype have an increased risk of renal dysfunction. VDR FokI SNP is closely related to renal function, calcium-phosphate metabolism, and related pathological damage in IgAN patients. creator: Man-Qiu Mo creator: Ling Pan creator: Lin Tan creator: Ling Jiang creator: Yong-Qing Pan creator: Fu-Ji Li creator: Zhen-Hua Yang creator: Yun-Hua Liao uri: https://doi.org/10.7717/peerj.7092 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Mo et al. title: Age-related kinematic performance should be considered during fast head-neck rotation target task in individuals aged from 8 to 85 years old link: https://peerj.com/articles/7095 last-modified: 2019-06-10 description: Kinematic behavior during fast cervical rotations is a useful parameter for assessing sensorimotor control performances in neck-pain patients. However, the influence of age in asymptomatic individuals from children to older people still needs to be explored. Our aim was to assess the impact of age on sensorimotor control performance of the head-neck with execution time and kinematic variables (time of task, mean speed/acceleration/deceleration, overshoots (OSs), minimum/maximum speed) during standardized fast rotation target task using the DidRen Laser test. A total of 80 volunteers were stratified in four different age-groups: Children (8–14 years): n = 16; Young Adults (18–35 years): n = 29; Old Adults (36–64 years): n = 18; Seniors (65–85 years): n = 17. Results showed that to perform the test, Children were slower (69.0 (60.6–87.3)s) compared to Young Adults (49.6 (45.6–55.6)s) with p < 0.001, and Old Adults (51.7 (48.4–55.8)s) with p < 0.001. It was also slower in Seniors (57 (52.3–67.6)s) compared to Young Adults with p < 0.013. Mean speed was slower in Children (9.4 ± 2.3 °s−1) and Seniors (10.6 ± 2.4 °s−1) compared to Young Adults (13.7 ± 1.9 °s−1) with p < 0.001 and Old Adults (13.3 ± 2.4 °s−1) with p < 0.001. Mean acceleration was slower for Children (8.4(7.6–10.2) °s−2) compared to Young Adults (11.1 (8.8–15.3) °s−2) with p < 0.016, and Old Adults (12.0(8.4–15.3) °s−2) with p < 0.015. Mean deceleration was slower for Children (−1.9(−2.6–1.4) °s−2) compared to Young Adults (−2.9(−3.7–2.5) °s−2) with p < 0.001 and Old Adults (−3.2(−3.7–2.3) °s−2) with p < 0.003. The DidRen Laser test allows us to discriminate age-specific performances for mean speed, acceleration and deceleration. Seniors and Children needed to be slower to become as precise as Young Adults and Old Adults. No difference was observed for OSs which assesses accuracy of movement. Age should therefore be considered as a key parameter when analyzing execution time and kinematic results during DidRen Laser test. These normative data can therefore guide clinicians in the assessment of subjects with neck pain. creator: Renaud Hage creator: Frédéric Dierick creator: Nathalie Roussel creator: Laurent Pitance creator: Christine Detrembleur uri: https://doi.org/10.7717/peerj.7095 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hage et al. title: Timing and ecological priority shaped the diversification of sedges in the Himalayas link: https://peerj.com/articles/6792 last-modified: 2019-06-07 description: BackgroundDiversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone—Carex L. (Cyperaceae), with ca. 2100 species worldwide—has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex.MethodsPhylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model.ResultsThe Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan Carex flora comprises a heterogeneous sample of diversifications drawn from throughout the cosmopolitan, but mostly temperate, Carex radiation. Most radiations are relatively recent, but the widespread and diverse Himalayan Kobresia radiation arose at the early Miocene. The timing and predominance of Kobresia in high-elevation Himalayan meadows suggests that Kobresia may have excluded other Carex lineages: the success of Kobresia in the Himalayas, in other words, appears to be a consequence largely of priority, competitive exclusion and historical contingency. creator: Uzma creator: Pedro Jiménez-Mejías creator: Rabia Amir creator: Muhammad Qasim Hayat creator: Andrew L. Hipp uri: https://doi.org/10.7717/peerj.6792 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Uzma et al. title: A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri link: https://peerj.com/articles/6927 last-modified: 2019-06-07 description: Octopus oliveri is a widespread and common rocky intertidal cephalopod that mates readily in the laboratory, but for which mating behavior has not been reported previously. Four sets of behavioral experiments were recorded wherein three males, small, medium & large in varying order, were introduced to each of six females, for a total of 24 individual females and 12 individual males utilized in the experiments. Video analysis shows that successful mating occurred in each of the mount, reach and beak-to-beak positions. Mating was observed for all males, regardless of size relative to the female, or order of introduction. Females showed preference for the first male to which they were introduced in experimental pairings rather than any specific male trait, and mating time increased significantly with increasing female size. Five novel microsatellite markers were developed and used to test paternity in the eleven broods resulting from these experimental pairings. We found skewed paternity in each brood, with early male precedence and male size being the best predictors of parentage. Multiple paternity was observed in every experimental cross but was estimated to be comparatively low in the field, suggesting that sperm limitation might be common in this species. We saw no evidence of direct sperm competition in Octopus oliveri, but larger males produced significantly more offspring. This study contributes to the growing research on cephalopod mating systems and indicates that octopus mating dynamics might be more variable and complex than thought previously. creator: Heather Ylitalo creator: Thomas A. Oliver creator: Iria Fernandez-Silva creator: James B. Wood creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.6927 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ylitalo et al. title: The cutting-edge morphology of the mole snake’s dental apparatus link: https://peerj.com/articles/6943 last-modified: 2019-06-07 description: The mole snake (Pseudaspis cana) is capable of inflicting unusual bites in defence and during male combat that present as two parallel lacerations. We investigated the dental morphology of the mole snake by making SEM images, and by CT-scanning and digitally reconstructing the skulls of 14 specimens comprising both sexes. The lengths, volumes, shapes and positions of maxillary and dentary teeth were compared within individuals, between individuals, and between sexes. CT reconstructions show the occurrence of large, flat triangular teeth at the posterior end of the maxilla that are angled to point towards the posterior of the skull. SEM imagery highlights the presence of sharp ridges (carinae) on the posterior edges of the posterior dentary and maxillary teeth. Males have greater dental specialization, maxillary tooth variation, enlargement of the posterior-most maxillary teeth, and dentary teeth with posterior carinae. We hypothesize that mole snake dental specializations are adaptations for their particular form of male combat and possibly for subduing prey in the confines of underground burrows. Our findings reveal a complex dental morphology in mole snakes and provide impetus for further studies on the functional morphology of snake teeth. creator: Alexandra M. Evans creator: Jonah N. Choiniere creator: Graham J. Alexander uri: https://doi.org/10.7717/peerj.6943 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Evans et al. title: Move it or lose it: interspecific variation in risk response of pond-breeding anurans link: https://peerj.com/articles/6956 last-modified: 2019-06-07 description: Changes in behavior are often the proximate response of animals to human disturbance, with variability in tolerance levels leading some species to exhibit striking shifts in life history, fitness, and/or survival. Thus, elucidating the effects of disturbance on animal behavior, and how this varies among taxonomically similar species with inherently different behaviors and life histories is of value for management and conservation. We evaluated the risk response of three anuran species—southern leopard frog (Lithobates sphenocephalus), Blanchard’s cricket frog (Acris blanchardi), and green tree frog (Hyla cinerea)—to determine how differences in microhabitat use (arboreal vs ground-dwelling) and body size (small vs medium) may play a role in response to a potential threat within a human-altered subtropical forest. Each species responded to risk with both flight and freeze behaviors, however, behaviors were species- and context-specific. As distance to cover increased, southern leopard frogs increased freezing behavior, green tree frogs decreased freezing behavior, and Blanchard’s cricket frogs increased flight response. The propensity of green tree frogs to use the canopy of vegetation as refugia, and the small body size of Blanchard’s cricket frogs likely led to greater flight response as distance to cover increased, whereas innate reliance on camouflage among southern leopard frogs may place them at greater risk to landscaping, agricultural, and transportation practices in open terrain. As such, arboreal and small-bodied species may inherently be better suited in human altered-landscapes compared to larger, ground-dwelling species. As land-use change continues to modify habitats, understanding how species respond to changes in their environment continues to be of importance, particularly in ecosystems where human-wildlife interactions are expected to increase in frequency. creator: Philip Matich creator: Christopher M. Schalk uri: https://doi.org/10.7717/peerj.6956 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Matich and Schalk title: Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats link: https://peerj.com/articles/6989 last-modified: 2019-06-07 description: Excessive alcohol consumption is a risk factor for liver diseases. Enhancement of alcohol metabolism could be an effective strategy to prevent these adverse effects since it promotes the clearance of ethanol and acetaldehyde from the serum. Polyphenol-rich products have shown to protect against alcohol-related liver damage. Blueberry leaves have attracted attention as they are rich polyphenols such as proantocyanidins and chlorogenic acid. In this study, we investigated the effects of a high dose of blueberry leaf extract (BLEx) on alcohol metabolism during chronic intake of ethanol. Seven-week old Sprague-Dawley (SD) rats were divided into four groups: normal liquid diet group (NLD), normal liquid diet + BLEx group (NLD + BLEx), alcohol liquid diet group (ALD), and alcohol liquid diet + BLEx (ALD + BLEx). Then, rats were fed experimental diet for 5 weeks and at the end of feeding period, body weight, food intake, liver weight, indices of liver injury, expression and activity of alcohol metabolism-related and anti-oxidative enzymes, and levels of carbonyl protein, triglyceride (TG), and total cholesterol (T-Chol) were measured. Body weight and food intake decreased, whereas liver aldehyde dehydrogenase (ALDH) activity, liver microsomal cytochrome P450 2E1 (CYP2E1) protein and mRNA expression, and heme oxygenase 1 (HO-1) mRNA expression were upregulated by ethanol intake. Dietary BLEx, however, did not affect any of these ethanol-related changes. Indices of liver injury, expression and activity of other alcohol metabolism-related enzymes, liver carbonyl protein, TG, and T-Chol levels were not altered by ethanol and BLEx. Thus, chronic BLEx intake does not ameliorate the harmful effects of ethanol. creator: Kaede Yamasaki creator: Kazuhiro Sugamoto creator: Teruaki Arakawa creator: Kazuo Nishiyama creator: Masao Yamasaki uri: https://doi.org/10.7717/peerj.6989 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yamasaki et al. title: Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT) link: https://peerj.com/articles/7003 last-modified: 2019-06-07 description: BackgroundThe current study applies both traditional and Diffusible Iodine Contrast Enhanced computed microtomography (DICE µCT) techniques to reveal the musculoskeletal anatomy of Phlyctimantis maculatus. DICE µCT has emerged as a powerful tool to visualise intricate musculoskeletal anatomy. By generating 3D digital models, anatomical analyses can be conducted non-destructively, preserving the in situ 3D topography of the system, therefore eliminating some of the drawbacks associated with traditional methods. We aim to describe the musculature of the spine, pelvis, and hindlimb, compare the musculoskeletal anatomy and pelvic morphology of P. maculatus with functionally diverse frogs, and produce 3D digital anatomy reference data.MethodAn adult frog was stained using an aqueous Lugol’s solution and scanned in a SkyScan1176 in vivo µCT scanner. Scan images were reconstructed, resampled, and digitally segmented to produce a 3D model. A further adult female frog was dissected traditionally for visualisation of tendinous insertions.ResultsOur work revealed three main findings: (1) P. maculatus has similar gross muscular anatomy to Rana catesbeiana (bullfrog) but is distinct from those species that exhibit ancestral traits (leopelmids) and those that are highly specialised (pipids), (2) P. maculatus’s pelvic anatomy best fits the description of Emerson’s walking/hopping pelvic morphotype IIA, and (3) a split in the semimembranosus and gracilis major muscles is consistent with the reported myology in other anuran species.DiscussionWhile DICE µCT methods were instrumental in characterising the 3D anatomy, traditional dissection was still required to visualise important structures such as the knee aponeurosis, tendinous insertions, and fasciae. Nonetheless, the anatomical data presented here marks the first detailed digital description of an arboreal and terrestrial frog. Further, our digital model presents P. maculatus as a good frog model system and as such has formed a crucial platform for further functional analysis within the anuran pelvis and hindlimb. creator: Amber J. Collings creator: Christopher T. Richards uri: https://doi.org/10.7717/peerj.7003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Collings and Richards title: Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach link: https://peerj.com/articles/7015 last-modified: 2019-06-07 description: The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance. creator: Nattapat Isarankura Na Ayudhya creator: Kobkul Laoteng creator: Yuanda Song creator: Asawin Meechai creator: Wanwipa Vongsangnak uri: https://doi.org/10.7717/peerj.7015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Isarankura Na Ayudhya et al. title: Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis link: https://peerj.com/articles/7020 last-modified: 2019-06-07 description: The impacts of continued degradation of watersheds on coastal coral reefs world-wide is alarming, and action addressing anthropogenic stressors and subsequent rehabilitation of watersheds and adjacent reefs is an urgent priority. The aim of this study is to develop and improve the use of antioxidant enzymes as bioindicators of stress in coral species. In order to fully develop such tools, it is necessary to first understand baseline cycling of these enzymes within coral tissues. Due to inherent links between reproduction and oxidative stress, these aims may be facilitated by sampling coral tissues over reproductively-linked lunar cycles to determine variations from baseline. By developing a greater understanding of biochemical markers of stress in corals, specifically antioxidant defense enzymes catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx), and superoxide dismutase (SOD) in Hawaiian Pocillopora damicornis, we have provided molecular tools that identify thresholds of stress on coral reefs. Our results suggest that the coral reproductive state is a significant factor affecting the activity of antioxidant enzymes. Specifically, CAT and GR display maximum activity during peak reproductive state. Whereas significant maximal Se-independent GPx and SOD activity was measured during off-peak reproductive cycles. Such insight into the cyclical variation of the activity of these enzymes should be applied towards differentiating the influence of natural biological activity cycling in diagnostic tests identifying the effects of different physical environmental factors and chemical pollutants on coral health. Through the development and application of these molecular biomarkers of stress, we look to improve our ability to identify problems at the sub-lethal level, when action can be taken to mitigate a/biotic impacts. creator: James W.A. Murphy creator: Abby C. Collier creator: Robert H. Richmond uri: https://doi.org/10.7717/peerj.7020 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Murphy et al. title: The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana) link: https://peerj.com/articles/7026 last-modified: 2019-06-07 description: This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus. creator: James R. P. Worth creator: Luxian Liu creator: Fu-Jin Wei creator: Nobuhiro Tomaru uri: https://doi.org/10.7717/peerj.7026 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Worth et al. title: The influence of pharmacologically-induced affective states on attention bias in sheep link: https://peerj.com/articles/7033 last-modified: 2019-06-07 description: When an individual attends to certain types of information more than others, the behavior is termed an attention bias. The occurrence of attention biases in humans and animals can depend on their affective states. Based on evidence from the human literature and prior studies in sheep, we hypothesized that an attention bias test could discriminate between pharmacologically-induced positive and negative affective states in sheep. The test measured allocation of attention between a threat and a positive stimulus using key measures of looking time and vigilance. Eighty 7-year-old Merino ewes were allocated to one of four treatment groups; Anxious (m-chlorophenylpiperazine), Calm (diazepam), Happy (morphine) and Control (saline). Drugs were administered 30 min prior to attention bias testing. The test was conducted in a 4 × 4.2 m arena with high opaque walls. An approximately life-size photograph of a sheep was positioned on one wall of the arena (positive stimulus). A small window with a retractable opaque cover was positioned on the opposite wall, behind which a dog was standing quietly (threat). The dog was visible for 3 s after a single sheep entered the arena, then the window was covered and the dog was removed. Sheep then remained in the arena for 3 min while behaviors were recorded. Key behaviors included time looking toward the dog wall or photo wall, duration of vigilance behavior and latency to become non-vigilant. In contrast with our hypothesis, no significant differences were found between treatment groups for duration of vigilance or looking behaviors, although Anxious sheep tended to be more vigilant than Control animals (P < 0.1) and had a longer latency to become non-vigilant (P < 0.001). A total of 24 of 80 animals were vigilant for the entire test duration. This censoring of data may explain why no differences were detected between groups for vigilance duration. Overall, a lack of difference between groups may suggest the test cannot discriminate positive and negative states in sheep. We suggest that the censoring of vigilance duration data, the use of insufficient drug doses, the potential influence of background noise and the age of the sheep may explain a lack of difference between groups. Due to these potential effects, it remains unclear whether the attention bias test can detect positive states in sheep. creator: Jessica E. Monk creator: Caroline Lee creator: Sue Belson creator: Ian G. Colditz creator: Dana L.M. Campbell uri: https://doi.org/10.7717/peerj.7033 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Monk et al. title: Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting link: https://peerj.com/articles/7055 last-modified: 2019-06-07 description: BackgroundAlthough pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases.MethodsTo allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences.ResultsWe found that 14mer peptides with amino acids represented as simply either hydrophobic or hydrophilic provided the best models for discrimination of E3 ligases from other effector proteins with a receiver-operator characteristic area under the curve (AUC) of 0.90. When considering a subset of E3 ubiquitin ligase effectors that do not fall into known sequence based families we found that the AUC was 0.82, demonstrating the effectiveness of our method at identifying novel functional family members. Feature selection was used to identify a parsimonious set of 10 RED peptides that provided good discrimination, and these peptides were found to be located in functionally important regions of the proteins involved in E2 and host target protein binding. Our general approach enables construction of models based on other effector functions. We used SIEVE-Ub to predict nine potential novel E3 ligases from a large set of bacterial genomes. SIEVE-Ub is available for download at https://doi.org/10.6084/m9.figshare.7766984.v1 or https://github.com/biodataganache/SIEVE-Ub for the most current version. creator: Jason E. McDermott creator: John R. Cort creator: Ernesto S. Nakayasu creator: Jonathan N. Pruneda creator: Christopher Overall creator: Joshua N. Adkins uri: https://doi.org/10.7717/peerj.7055 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 McDermott et al. title: Reduced thermal variability in cities and its impact on honey bee thermal tolerance link: https://peerj.com/articles/7060 last-modified: 2019-06-07 description: Urbanization is one of the most significant land cover transformations, and while climate alteration is one of its most cited ecological consequences we have very limited knowledge on its effect on species’ thermal responses. We investigated whether changes in environmental thermal variability caused by urbanization influence thermal tolerance in honey bees (Apis mellifera) in a semi-arid city in central Mexico. Ambient environmental temperature and honey bee thermal tolerance were compared in urban and rural sites. Ambient temperature variability decreased with urbanization due to significantly higher nighttime temperatures in urban compared to rural sites and not from differences in maximum daily temperatures. Honey bee thermal tolerance breadth [critical thermal maxima (CTmax)—critical thermal minima (CTmin)] was narrower for urban bees as a result of differences in cold tolerance, with urban individuals having significantly higher CTmin than rural individuals, and CTmax not differing among urban and rural individuals. Honey bee body size was not correlated to thermal tolerance, and body size did not differ between urban and rural individuals. We found that honey bees’ cold tolerance is modified through acclimation. Our results show that differences in thermal variability along small spatial scales such as urban-rural gradients can influence species’ thermal tolerance breadths. creator: Karina Sánchez-Echeverría creator: Ignacio Castellanos creator: Luis Mendoza-Cuenca creator: Iriana Zuria creator: Gerardo Sánchez-Rojas uri: https://doi.org/10.7717/peerj.7060 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sánchez-Echeverría et al. title: Impact of body weight gain on hepatic metabolism and hepatic inflammatory cytokines in comparison of Shetland pony geldings and Warmblood horse geldings link: https://peerj.com/articles/7069 last-modified: 2019-06-07 description: BackgroundNon-alcoholic fatty liver disease is known as determining part of human obesity. The impact of body weight (BW) gain on liver metabolism has not been extensively investigated yet.ObjectivesTo investigate hepatic alterations caused by increasing BW in ponies and horses.AnimalsA total of 19 non-obese equines (10 Shetland ponies, geldings; nine Warmblood horses, geldings).MethodsAnimals received 200% of their metabolizable maintenance energy requirements for 2 years. Serum alkaline phosphatase, glutamate dehydrogenase (GLDH), aspartate aminotransferase (AST), and gamma-glutamyl transferase activities and bile acids were analyzed several times during 2 years of hypercaloric diet. Hepatic lipid content and hepatic levels of the interleukin (IL)-6, tumor necrosis factor α (TNFα), cluster of differentiation (CD) 68, IL-1β, lipoprotein lipase (LPL), fatty acid-binding protein 1, chemerin and nuclear factor-κB mRNAs were assessed at the start of the study and after 1 and 2 years of excess energy intake.ResultsThe mean (±SD) BW gain recorded during 2 years of excess energy intake was 29.9 ± 19.4% for ponies and 17 ± 6.74% for horses. The hepatic lipid content was not profoundly affected by increasing BW. Levels of the IL-6, TNFα, CD68 and IL-1β mRNAs did not change during BW gain. Levels of the chemerin mRNA increased significantly in both breeds (ponies: P = 0.02; horses: P = 0.02) in response to BW gain. Significant differences in serum GLDH and AST activities, serum bile acid concentrations and hepatic levels of the LPL mRNA were observed between ponies and horses at the end of the study.ConclusionsChemerin might represent an interesting marker for future equine obesity research. Interestingly, steatosis caused by increasing BW may occur later in the development of obesity in equines than in humans. Additionally, the hepatic metabolism exhibits differences between ponies and horses, which may explain in part the greater susceptibility of ponies to obesity-associated metabolic dysregulations. creator: Carola Schedlbauer creator: Dominique Blaue creator: Martin Gericke creator: Matthias Blüher creator: Janine Starzonek creator: Claudia Gittel creator: Walter Brehm creator: Ingrid Vervuert uri: https://doi.org/10.7717/peerj.7069 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schedlbauer et al. title: Sprint interval exercise versus continuous moderate intensity exercise: acute effects on tissue oxygenation, blood pressure and enjoyment in 18–30 year old inactive men link: https://peerj.com/articles/7077 last-modified: 2019-06-07 description: BackgroundSprint interval training (SIT) can be as effective, or more effective, than continuous moderate intensity exercise (CMIE) for improving a primary risk factor for cardiometabolic disease, low cardiorespiratory fitness (CRF). However, there has been no direct comparison in inactive individuals, of the acute effects of a session of SIT with a work-matched session of CMIE on local oxygen utilisation, which is a primary stimulus for increasing CRF. Furthermore, post-exercise blood pressure (BP) and enjoyment, if symptomatic and low, respectively, have implications for safety and adherence to exercise and have not been compared between these specific conditions. It was hypothesised that in young inactive men, local oxygen utilisation would be higher, while post-exercise BP and enjoyment would be lower for SIT, when compared to CMIE.MethodsA total of 11 inactive men (mean ± SD; age 23 ± 4 years) completed a maximal ramp-incremental exercise test followed by two experiment conditions: (1) SIT and (2) work-matched CMIE on a cycle ergometer on separate days. Deoxygenated haemoglobin (∆HHb) in the pre-frontal cortex (FH), gastrocnemius (GN), left vastus lateralis (LVL) and the right vastus lateralis (RVL) muscles, systemic oxygen utilisation (VO2), systolic (SBP) and diastolic (DBP) blood pressure and physical activity enjoyment scale (PACES) were measured during the experiment conditions.ResultsDuring SIT, compared to CMIE, ∆HHb in FH (p = 0.016) and GN (p = 0.001) was higher, while PACES (p = 0.032) and DBP (p = 0.043) were lower. No differences in SBP and ∆HHb in LVL and RVL were found between conditions.ConclusionsIn young inactive men, higher levels of physiological stress occurred during SIT, which potentially contributed to lower levels of post-exercise DBP and enjoyment, when compared to CMIE. creator: Yuri Kriel creator: Christopher D. Askew creator: Colin Solomon uri: https://doi.org/10.7717/peerj.7077 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kriel et al. title: A “modified Obel” method for the severity scoring of (endocrinopathic) equine laminitis link: https://peerj.com/articles/7084 last-modified: 2019-06-07 description: BackgroundLaminitis is a common equine disease characterized by foot pain, and is commonly diagnosed using a five-grade Obel system developed in 1948 using sepsis-related cases. However, endocrinopathic laminitis is now the most common form of the disease and clinical signs may be mild, or spread across two Obel grades. This paper describes a modified method which assigns scores to discreet clinical signs, providing a wider scale suitable for use in a research setting.MethodsThe “modified Obel” method was developed using an iterative process. First, a prototype method was developed during the detailed observation of 37 ponies undergoing a laminitis induction experiment. The final method was refined and validated using video footage taken during the induction study and from a clinical trial of naturally occurring endocrinopathic laminitis cases. The Obel method was deconstructed and key laminitis signs were evaluated to develop a three-stage, five criteria method that employs a severity scale of 0–12. Veterinarians (n = 28) were recruited to watch and assess 15 video recordings of cases of varying severity, using the Obel and “modified Obel” methods. The inter-observer agreement (reproducibility) was determined using Kendall’s coefficient of concordance (Kendall W) and Krippendorf’s alpha reliability coefficient. A total of 14 veterinarians repeated the exercise 2–4 weeks after their original assessment, to determine intra-observer agreement (repeatability), assessed using a weighted kappa statistic (kw). Agreement between methods was calculated by converting all “modified Obel” scores to Obel grades and calculating the mean and distribution of the differences.ResultsThe “modified Obel” and Obel methods showed excellent and similar inter-observer agreement based on the Kendall W value (0.87, P < 0.001 vs. 0.85, P < 0.001) and Krippendorf’s alpha (95% CI) value (0.83 [0.53–0.90] vs. 0.77 [0.55–0.85]). Based on the kw value, the “modified Obel” method also had substantial repeatability, although slightly less than the Obel method, (0.80 vs. 0.91). Excellent agreement between the methods was found, with the mean difference (95% CI), comparing the Obel grade, with the “modified Obel” score converted to an Obel grade, being −0.12 (−0.19 to −0.06) grades. The Obel and converted “modified Obel” grades were identical 62% of the time (259/420) and a difference of one grade (higher or lower) occurred in 35% of cases (148/420).ConclusionBoth methods show excellent agreement, reproducibility and repeatability when used to diagnose endocrinopathic laminitis. The “modified Obel” method is a three-step examination process for severity-scoring of endocrinopathic laminitis, initially proposed for use within a research setting. When using the modified method a diagnosis of laminitis also requires clinical acumen. The allocation of scores for specific clinical signs should be particularly useful in research trials monitoring laminitis recovery. creator: Alexandra Meier creator: Melody de Laat creator: Christopher Pollitt creator: Donald Walsh creator: James McGree creator: Dania B. Reiche creator: Marcella von Salis-Soglio creator: Luke Wells-Smith creator: Ulrich Mengeler creator: Daniel Mesa Salas creator: Susanne Droegemueller creator: Martin N. Sillence uri: https://doi.org/10.7717/peerj.7084 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Meier et al. title: Garden centre customer attitudes to pollinators and pollinator-friendly planting link: https://peerj.com/articles/7088 last-modified: 2019-06-07 description: Growing nectar- and pollen-rich flowering plant varieties in domestic gardens and other greenspace is an important pro-environmental behaviour that supports pollinating insects. Wildlife gardening is popular in the UK; however, public attitudes and behaviour relating to planting for pollinators are currently not well understood. We investigated these through questionnaires and interviews with customers in five garden centres in Sussex, southeast England, a relevant and useful consumer group representing horticulturally-engaged members of the public. Garden centre customers had strongly positive attitudes and were motivated to plant for bees and other pollinators: most (77%) grew pollinator-friendly varieties, while 64% would be more likely to buy a plant with a pollinator-friendly logo. Personal motivation to support pollinators was linked to a recent increase in personal and public awareness of their declines through (often negativistic) information from mass media sources. Practical implications of these findings in relation to the horticultural retail industry are discussed. creator: Veronica R. Wignall creator: Karin Alton creator: Francis L.W. Ratnieks uri: https://doi.org/10.7717/peerj.7088 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wignall et al. title: Opposite asymmetries of face and trunk and of kissing and hugging, as predicted by the axial twist hypothesis link: https://peerj.com/articles/7096 last-modified: 2019-06-07 description: The contralateral organization of the forebrain and the crossing of the optic nerves in the optic chiasm represent a long-standing conundrum. According to the Axial Twist Hypothesis (ATH) the rostral head and the rest of the body are twisted with respect to each other to form a left-handed half turn. This twist is the result, mainly, of asymmetric, twisted growth in the early embryo. Evolutionary selection tends to restore bilateral symmetry. Since selective pressure will decrease as the organism approaches symmetry, we expected a small control error in the form of a small, residual right-handed twist. We found that the mouth-eyes-nose (rostral head) region shows a left-offset with respect to the ears (posterior head) by up to 0.8° (P < 0.01, Bonferroni-corrected). Moreover, this systematic aurofacial asymmetry was larger in young children (on average up to 3°) and reduced with age. Finally, we predicted and found a right-sided bias for hugging (78%) and a left-sided bias for kissing (69%). Thus, all predictions were confirmed by the data. These results are all in support of the ATH, whereas the pattern of results is not (or only partly) explained by existing alternative theories. As of the present results, the ATH is the first theory for the contralateral forebrain and the optic chiasm whose predictions have been tested empirically. We conclude that humans (and all other vertebrates) are fundamentally asymmetric, both in their anatomy and their behavior. This supports the thesis that the approximate bilateral symmetry of vertebrates is a secondary feature, despite their being bilaterians. creator: Marc H.E. de Lussanet uri: https://doi.org/10.7717/peerj.7096 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 de Lussanet title: Emerging trends and knowledge structure of epilepsy during pregnancy research for 2000–2018: a bibliometric analysis link: https://peerj.com/articles/7115 last-modified: 2019-06-07 description: BackgroundEpilepsy during pregnancy presents a unique set of challenges for pregnant women, the fetus, and the health care community. As research in this area advances rapidly, it is critical to keep up with the emerging trends and key turning points of the development of the domain knowledge. This study aimed to construct a series of science maps to quantitatively and qualitatively evaluate the intellectual landscape and research frontiers in the field of epilepsy during pregnancy research.MethodsAll publications were extracted from the Web of Science Core Collection database. Bibliometric analysis was used to analyze the scientific research outputs, including journals, countries/regions, institutions, authors (cited authors), intellectual base and research hotspots.ResultsA total of 2,225 publications related to epilepsy during pregnancy were identified as published between 2000 and 2018. The overall trend of the number of publications showed a fluctuating growth from 59 articles in 2000 to 198 in 2018. Neurology was the leading journal in the field of epilepsy and pregnancy research both in terms of impact factor score (8.055) and H-index value (77). The US retained its leading position and exerted a pivotal influence in this area. The University of Melbourne was identified as a good research institution for research collaboration. Prof. Pennell and Tomson have made great achievements in this area, and Prof. Tomson laid a foundation for the development of this domain. The keyword “neonatal seizures” ranked first in research hotspots, and the keyword “autism spectrum disorders (ASD)” ranked first in research frontiers.ConclusionsEpilepsy during pregnancy is a fascinating and rapid development of subject matter. A more recent emerging trend focused on comprehensive management of pregnant and lactating women, evaluation of the safety and efficacy of newer antiepileptic drugs. The keywords “management issue,” “brain injury,” “meta-analysis,” “in utero exposure,” and “ASD” were the latest research frontiers and should be closely observed. creator: Minglu Wang creator: Weitao Li creator: Yuying Tao creator: Limei Zhao uri: https://doi.org/10.7717/peerj.7115 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Integrative analysis of common genes and driver mutations implicated in hormone stimulation for four cancers in women link: https://peerj.com/articles/6872 last-modified: 2019-06-06 description: Cancer is one of the leading cause of death of women worldwide, and breast, ovarian, endometrial and cervical cancers contribute significantly to this every year. Developing early genetic-based diagnostic tools may be an effective approach to increase the chances of survival and provide more treatment opportunities. However, the current cancer genetic studies are mainly conducted independently and, hence lack of common driver genes involved in cancers in women. To explore the potential common molecular mechanism, we integrated four comprehensive literature-based databases to explore the shared implicated genetic effects. Using a total of 460 endometrial, 2,068 ovarian, 2,308 breast and 537 cervical cancer-implicated genes, we identified 52 genes which are common in all four types of cancers in women. Furthermore, we defined their potential functional role in endogenous hormonal regulation pathways within the context of four cancers in women. For example, these genes are strongly associated with hormonal stimulation, which may facilitate rapid diagnosis and treatment management decision making. Additional mutational analyses on combined the cancer genome atlas datasets consisting of 5,919 gynaecological and breast tumor samples were conducted to identify the frequently mutated genes across cancer types. For those common implicated genes for hormonal stimulants, we found that three quarter of 5,919 samples had genomic alteration with the highest frequency in MYC (22%), followed by NDRG1 (19%), ERBB2 (14%), PTEN (13%), PTGS2 (13%) and CDH1 (11%). We also identified 38 hormone related genes, eight of which are associated with the ovulation cycle. Further systems biology approach of the shared genes identified 20 novel genes, of which 12 were involved in the hormone regulation in these four cancers in women. Identification of common driver genes for hormone stimulation provided an unique angle of involving the potential of the hormone stimulants-related genes for cancer diagnosis and prognosis. creator: Salma Begum Bhyan creator: YongKiat Wee creator: Yining Liu creator: Scott Cummins creator: Min Zhao uri: https://doi.org/10.7717/peerj.6872 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bhyan et al. title: Interaction of mindfulness disposition and instructional self-talk on motor performance: a laboratory exploration link: https://peerj.com/articles/7034 last-modified: 2019-06-06 description: In considering that high mindfulness disposition individuals possess a unique ability to maintain attention and awareness, and attention is one of the key mechanisms of instructional self-talk, the purpose of this study was to examine the interaction of mindfulness disposition and instructional self-talk on motor performance. Forty-nine college students (M age = 18.96 ± 1.08) with high/low mindfulness disposition (high n = 23; low n = 26) selected out of 126 college students performed a discrete motor task (standing long jump) and a continuous motor task (line tracking task) under instructional and unrelated self-talk conditions. Two separate 2 (self-talk type) X 2 (high/low mindfulness) mixed design ANOVA statistical analyses indicated that mindfulness disposition interacted with unrelated self-talk in the line tracking task. Specifically, low mindfulness participants performed poorer than high mindfulness participants in line tracking task under unrelated self-talk. Further, participants performed better in both standing long jump and line tracking under instructional self-talk than unrelated self-talk. Results not only revealed the triangular relationships among mindfulness, self-talk, and motor performance but also indirectly support the role of attention in self-talk effectiveness. Limitations, future research directions, and practical implications were discussed. creator: Yi-Hsiang Chiu creator: Frank J.H. Lu creator: Diane L. Gill creator: Tzu-Wen Lin creator: Chiu-Chen Chang creator: Shu-Ching Wu uri: https://doi.org/10.7717/peerj.7034 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chiu et al. title: The relationship between vigilance capacity and physical exercise: a mixed-effects multistudy analysis link: https://peerj.com/articles/7118 last-modified: 2019-06-06 description: A substantial body of work has depicted a positive association between physical exercise and cognition, although the key factors driving that link are still a matter of scientific debate. Here, we aimed to contribute further to that topic by pooling the data from seven studies (N = 361) conducted by our research group to examine whether cardiovascular fitness (VO2), sport type participation (externally-paced (e.g., football or basketball) and self-paced (e.g., triathlon or track and field athletes) vs. sedentary), or both, are crucial factors to explain the association between the regular practice of exercise and vigilance capacity. We controlled for relevant variables such as age and the method of VO2 estimation. The Psychomotor Vigilance Task was used to measure vigilance performance by means of reaction time (RT). The results showed that externally-paced sport practice (e.g., football) resulted in significantly shorter RT compared to self-paced sport (e.g., triathlon) and sedentary condition, depicting larger effects in children and adolescents than in adults. Further analyses revealed no significant effect of cardiovascular fitness and self-paced sport practice, in comparison to the sedentary condition, on RT. Our data point to the relevance of considering the type of sport practice over and above the level of cardiovascular fitness as crucial factor to explain the positive association between the regular practice of exercise and vigilance capacity. creator: Daniel Sanabria creator: Antonio Luque-Casado creator: José C. Perales creator: Rafael Ballester creator: Luis F. Ciria creator: Florentino Huertas creator: Pandelis Perakakis uri: https://doi.org/10.7717/peerj.7118 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sanabria et al. title: Effects of stream grazers with different functional traits on the spatial heterogeneity of periphyton mats link: https://peerj.com/articles/6747 last-modified: 2019-06-05 description: BackgroundGrazing activity on periphytic mats determines mat structure and spatial heterogeneity. Spatial complexity in stream periphyton is highly divergent and may depend on the functional traits of the different primary consumers species (i.e., grazers) such as mouthpart morphology, feeding behavior, and feeding activity. We evaluated the effect of grazing by three species having different functional traits on periphytic mat structure with a focus on mohthpart morphology.MethodsAn enclosure experiment was conducted in a stream located in the Nara Prefecture of Japan using two caddisflies with scraping mouthparts, Micrasema quadriloba and Glossosoma, and one mayfly, Epeorus, with brushing mouthparts. The spatial heterogeneity of chlorophyll a(Chl a) was evaluated, and the periphytic mat was analyzed using scanning electron microscopy (SEM) after a 12-d feeding experiment.ResultsOur results showed the differences in the spatial heterogeneity of the periphytic mats, such as differences in Chl a levels, grazed by the different grazing species. The strongest effect on the spatial heterogeneity and periphytic abundance was observed for Micrasema quadriloba, a caddisfly species with scraping mouthparts. Epeorus mayfly, with brushing mouthparts and high-mobility behavior, produced the weakest effect on spatial heterogeneity. Glossosoma caddisflies had moderate effects on periphytic spatial heterogeneity and abundance. Our results suggest that differences in grazing effects are largely dependent on grazer mouthparts and behavior. creator: Izumi Katano creator: Hideyuki Doi uri: https://doi.org/10.7717/peerj.6747 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Katano and Doi title: High resistance to climatic variability in a dominant tundra shrub species link: https://peerj.com/articles/6967 last-modified: 2019-06-05 description: Climate change is modifying temperature and precipitation regimes across all seasons in northern ecosystems. Summer temperatures are higher, growing seasons extend into spring and fall and snow cover conditions are more variable during winter. The resistance of dominant tundra species to these season-specific changes, with each season potentially having contrasting effects on their growth and survival, can determine the future of tundra plant communities under climate change. In our study, we evaluated the effects of several spring/summer and winter climatic variables (i.e., summer temperature, growing season length, growing degree days, and number of winter freezing days) on the resistance of the dwarf shrub Empetrum nigrum. We measured over six years the ability of E. nigrum to keep a stable shoot growth, berry production, and vegetative cover in five E. nigrum dominated tundra heathlands, in a total of 144 plots covering a 200-km gradient from oceanic to continental climate. Overall, E. nigrum displayed high resistance to climatic variation along the gradient, with positive growth and reproductive output during all years and sites. Climatic conditions varied sharply among sites, especially during the winter months, finding that exposure to freezing temperatures during winter was correlated with reduced shoot length and berry production. These negative effects however, could be compensated if the following growing season was warm and long. Our study demonstrates that E. nigrum is a species resistant to fluctuating climatic conditions during the growing season and winter months in both oceanic and continental areas. Overall, E. nigrum appeared frost hardy and its resistance was determined by interactions among different season-specific climatic conditions with contrasting effects. creator: Victoria T. González creator: Mikel Moriana-Armendariz creator: Snorre B. Hagen creator: Bente Lindgård creator: Rigmor Reiersen creator: Kari Anne Bråthen uri: https://doi.org/10.7717/peerj.6967 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 González et al. title: Characterization of genes encoding small heat shock proteins from Bemisia tabaci and expression under thermal stress link: https://peerj.com/articles/6992 last-modified: 2019-06-05 description: Small heat shock proteins (sHSPs) are probably the most diverse in structure and function among the various super-families of stress proteins, and they play essential roles in various biological processes. The sweet potato whitefly, Bemisia tabaci (Gennadius), feeds in the phloem, transmits several plant viruses, and is an important pest on cotton, vegetables and ornamentals. In this research, we isolated and characterized three α-crystallin/sHSP family genes (Bthsp19.5, Bthsp19.2, and Bthsp21.3) from Bemisia tabaci. The three cDNAs encoded proteins of 171, 169, and 189 amino acids with calculated molecular weights of 19.5, 19.2, and 21.3 kDa and isoelectric points of 6.1, 6.2, and 6.0, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in Hemiptera and Thysanoptera insects species. All three sHSPs genes from Bemisia tabaci lacked introns. Quantitative real-time PCR analyses revealed that the three BtsHSPs genes were significantly up-regulated in Bemisia tabaci adults and pupae during high temperature stress (39, 41, 43, and 45 °C) but not in response to cold temperature stress (−6, −8, −10, and −12 °C). The expression levels of Bthsp19.2 and Bthsp21.3 in pupae was higher than adults in response to heat stress, while the expression level of Bthsp19.5 in adults was higher than pupae. In conclusion, this research results show that the sHSP genes of Bemisia tabaci had shown differential expression changes under thermal stress. creator: Jing Bai creator: Xiao-Na Liu creator: Ming-Xing Lu creator: Yu-Zhou Du uri: https://doi.org/10.7717/peerj.6992 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bai et al. title: Bibliometric analysis of research on the trends in autophagy link: https://peerj.com/articles/7103 last-modified: 2019-06-05 description: BackgroundAutophagy is an important mechanism to maintain homeostasis in cells. It has been linked with ageing and many currently incurable diseases, including heart disease, cancer, myopathies, neurodegeneration, and diabetes. Autophagy research is very important for identifying better treatments. This study aimed to explore the hotspots of autophagy research published from different countries, organizations, and authors.MethodsBetween 1962 and 2018, articles published about autophagy were identified in the Web of Science database. The total and annual number of articles, citations, impact factor, Hirsch (H)-index, number of article citations, productive authors, and involved journals were collected for quantitative and qualitative comparisons.ResultsFrom 1962 to 2018, 18,811 autophagy-related articles written in English were published. Most were from China (6,731). The United States dominated in citation frequency (391,030) and h-index (264). Among related journals, Autophagy published the most articles (1,388), followed by Plos One (585) and Oncotarget (392). Daniel Klionsky was the most productive author, with 171 publications. The article “LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing” was cited most frequently. The top-ranked keyword was “degradation” of macroautophagy.ConclusionsPublication of articles about autophagy has increased notably from 1962 to 2018, and has increased annually. The general quality of publications from China is still in need of improvement. Autophagy research has shifted gradually from basic studies to clinical studies in recent years. creator: Ting Hong creator: Xinzhe Feng creator: Wenwen Tong creator: Weidong Xu uri: https://doi.org/10.7717/peerj.7103 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hong et al. title: Exploring the feasibility, sustainability and the benefits of the GrACE + GAIT exercise programme in the residential aged care setting link: https://peerj.com/articles/6973 last-modified: 2019-06-04 description: BackgroundThe feasibility and benefits of a 24-week targeted progressive supervised resistance and weight-bearing exercise programme (Group Aged Care Exercise + GAIT (GrACE + GAIT)) in the residential aged care (RAC) setting was investigated as very little peer-reviewed research has been conducted in relation to exercise programmes of this duration in this cohort.MethodsA quasi-experimental study design consisting of two groups (control and exercise) explored a 24-week targeted progressive supervised resistance and weight-bearing exercise programme (GrACE + GAIT) in two RAC facilities in Northern New South Wales, Australia. A total of 42 adults consented to participate from a total of 68 eligible residents (61.7%). The primary outcome measures were feasibility and sustainability of the exercise programme via intervention uptake, session adherence, attrition, acceptability and adverse events. Secondary measures included gait speed and the spatio-temporal parameters of gait, handgrip muscle strength and sit to stand performance.ResultsTwenty-three residents participated in the exercise intervention (mean (SD) 85.4 (8.1) years, 15 females) and 19 in the control group (87.4 (6.6) years 13 females). Exercise adherence was 79.3%, with 65% of exercise participants attending ≥70% of the sessions; 100% of those originally enrolled completed the programme and strongly agreed with the programme acceptability. Zero exercise-related adverse events were reported. ANCOVA results indicated that post-intervention gait speed significantly increased (p < 0.001) with an 18.8% increase in gait speed (m/s).DiscussionThe GrACE + GAIT programme was shown to be feasible and significantly improve adults living in RAC facilities gait speed, handgrip strength and sit to stand performance. These results suggest that the GrACE + GAIT programme is suitable for use in the RAC sector and that it has the potential to reduce disability and improve function and quality of life of the residents. creator: Samantha Fien creator: Tim Henwood creator: Mike Climstein creator: Evelyne Rathbone creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.6973 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fien et al. title: CAM: an alignment-free method to recover phylogenies using codon aversion motifs link: https://peerj.com/articles/6984 last-modified: 2019-06-04 description: BackgroundCommon phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an approach to quickly calculate distances between species based on codon aversion.MethodsUtilizing a novel alignment-free character state, we present CAM, an alignment-free approach to recover phylogenies by comparing differences in codon aversion motifs (i.e., the set of unused codons within each gene) across all genes within a species. Synonymous codon usage is non-random and differs between organisms, between genes, and even within a single gene, and many genes do not use all possible codons. We report a comprehensive analysis of codon aversion within 229,742,339 genes from 23,428 species across all kingdoms of life, and we provide an alignment-free framework for its use in a phylogenetic construct. For each species, we first construct a set of codon aversion motifs spanning all genes within that species. We define the pairwise distance between two species, A and B, as one minus the number of shared codon aversion motifs divided by the total codon aversion motifs of the species, A or B, containing the fewest motifs. This approach allows us to calculate pairwise distances even when substantial differences in the number of genes or a high rate of divergence between species exists. Finally, we use neighbor-joining to recover phylogenies.ResultsUsing the Open Tree of Life and NCBI Taxonomy Database as expected phylogenies, our approach compares well, recovering phylogenies that largely match expected trees and are comparable to trees recovered using maximum likelihood and other alignment-free approaches. Our technique is much faster than maximum likelihood and similar in accuracy to other alignment-free approaches. Therefore, we propose that codon aversion be considered a phylogenetically conserved character that may be used in future phylogenomic studies.AvailabilityCAM, documentation, and test files are freely available on GitHub at https://github.com/ridgelab/cam. creator: Justin B. Miller creator: Lauren M. McKinnon creator: Michael F. Whiting creator: Perry G. Ridge uri: https://doi.org/10.7717/peerj.6984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Miller et al. title: Biochar prepared at different pyrolysis temperatures affects urea-nitrogen immobilization and N2O emissions in paddy fields link: https://peerj.com/articles/7027 last-modified: 2019-06-04 description: BackgroundFood safety has become a major issue, with serious environmental pollution resulting from losses of nitrogen (N) fertilizers. N is a key element for plant growth and is often one of the most important yield-limiting nutrients in paddy soil. Urea-N immobilization is an important process for restoring the levels of soil nutrient depleted by rice production and sustaining productivity. The benefits of biochar application include improved soil fertility, altered N dynamics, and reduced nutrient leaching. However, due to high variability in the quality of biochar, the responses of N loss and rice productivity to biochar amendments, especially those prepared at different pyrolysis temperatures, are still unclear. The main objectives of the present study were to examine the effects of biochar prepared at different pyrolysis temperatures on fertilizer N immobilization in paddy soil and explore the underlying mechanisms.MethodsTwo biochar samples were prepared by pyrolysis of maize straw at 400 °C (B400) and 700 °C (B700), respectively. The biochar was applied to paddy soil at three rates (0, 0.7, and 2.1%, w/w), with or without N fertilization (0, 168, and 210 kg N ha–1). Pot experiments were performed to determine nitrous oxide (N2O) emissions and 15N recovery from paddy soil using a 15N tracer across the rice growing season.ResultsCompared with the non-biochar control, biochar significantly decreased soil bulk density while increasing soil porosity, irrespective of pyrolysis temperature and N fertilizer level. Under B400 and B700, a high biochar rate decreased N loss rate to 66.42 and 68.90%, whereas a high N level increased it to 77.21 and 76.99%, respectively. Biochar also markedly decreased N2O emissions to 1.06 (B400) and 0.75 kg ha−1 (B700); low-N treatment caused a decrease in N2O emissions under B400, but this decrease was not observed under B700. An application rate of biochar of 2.1% plus 210 kg ha−1 N fertilizer substantially decreased the N fertilizer-induced N2O emission factor under B400, whereas under B700 no significant difference was observed. Biochar combined with N fertilizer treatment decreased rice biomass and grain yield by an average of 51.55 and 23.90 g pot–1, respectively, but the yield reduction under B700 was lower than under B400.ConclusionIrrespective of pyrolysis temperature, biochar had a positive effect on residual soil 15N content, while it negatively affected the 15N recovery of rice, N2O emissions from soil, rice biomass, and grain yield in the first year. Generally, a high application rate of biochar prepared at high or low pyrolysis temperature reduced the N fertilizer-induced N2O emission factor considerably. These biochar effects were dependent on N fertilizer level, biochar application rate, and their interactions. creator: Jiping Gao creator: Yanze Zhao creator: Wenzhong Zhang creator: Yanghui Sui creator: Dandan Jin creator: Wei Xin creator: Jun Yi creator: Dawei He uri: https://doi.org/10.7717/peerj.7027 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gao et al. title: Composition and dynamics of the bacterial communities present in the post-slaughter environment of farmed Atlantic salmon (Salmo salar L.) and correlations to gelatin degrading activity link: https://peerj.com/articles/7040 last-modified: 2019-06-04 description: BackgroundMicrobial analyses performed in connection with the post-slaughter environment of farmed Atlantic salmon (Salmo salar L.) have mostly focused on specific bacteria that may have negative effects on the health of consumers. However, bacteria may also affect other quality variables. The objective of this study was to provide general knowledge about composition and dynamics of the bacterial communities present at slaughter and cold storage of farmed Atlantic salmon, as well as reveal any possible correlations to gelatinase activity, which may affect fillet quality. Thus, these data may provide a basis for optimization opportunities in the aquaculture industry.MethodsSamples were taken from the digestive system harvested from 15 salmon immediately after slaughter. Another 17 salmon were taken from the processing line just before the final cleaning stage; of these eight were distributed in three iced storage boxes while the other nine were rinsed an extra time with industrial water before being distributed into another three storage boxes. In the following 6 days, samples were taken of skin mucus, liquids in the abdominal cavity and the storage ice. The compositions of the bacterial communities were analyzed by next-generation sequencing and gelatinase activity was measured in all samples except the storage ice.ResultsThe bacterial communities in the digestive tract samples were dominated by the family Mycoplasmataceae. The genus Aliivibrio was also relatively abundant. Bacterial communities in the abdominal cavity were generally more diverse than the intestinal samples. However, all of the abdominal samples from storage box no. 3 had a high relative abundance of Mycoplasmataceae, and could not be distinguished from the intestinal samples (Q = 1.27, p = 0.633) while being significantly different from the other abdominal samples (Q = 9.02, p = 0.01). In addition, the abdominal samples from storage box no. 3 had a significantly higher gelatin degrading activity (Q = 9.43, p = 0.001) than those from the other storage boxes and similar to the high gelatinase activity in the intestinal samples. This indicated that in storage box no. 3 there was a transfer of intestinal fluids to the abdominal cavities, which was not removed by the cleaning procedure. There was a significant difference of the major phyla detected in the skin mucus of salmon rinsed an additional time, as these salmon had a higher relative amount of Firmicutes (F = 4.76, p = 0.04) and lower amount of Proteobacteria (F = 4.41, p = 0.047).ConclusionsThe study showed a correlation between intestinal fluids and bacteria left in the abdominal cavity and gelatinase activity. This suggested that intestinal fluids and/or bacteria could enhance the degradation of connective tissue in the abdominal cavity and hence negatively affect the fillet quality. In addition, the study provided general knowledge of the composition and dynamics of bacterial communities present. creator: Ása Jacobsen creator: Svein-Ole Mikalsen creator: Hóraldur Joensen creator: Jonhard Eysturskarð uri: https://doi.org/10.7717/peerj.7040 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jacobsen et al. title: Systematic review and meta-analysis of 50 years of coral disease research visualized through the scope of network theory link: https://peerj.com/articles/7041 last-modified: 2019-06-04 description: Coral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. In order to gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: (1) studied disease(s); (2) host genus; (3) marine ecoregion(s) associated with the study site; and (4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g., bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research. creator: Luis M. Montilla creator: Alfredo Ascanio creator: Alejandra Verde creator: Aldo Croquer uri: https://doi.org/10.7717/peerj.7041 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Montilla et al. title: PTMphinder: an R package for PTM site localization and motif extraction from proteomic datasets link: https://peerj.com/articles/7046 last-modified: 2019-06-04 description: BackgroundMass-spectrometry-based proteomics is a prominent field of study that allows for the unbiased quantification of thousands of proteins from a particular sample. A key advantage of these techniques is the ability to detect protein post-translational modifications (PTMs) and localize them to specific amino acid residues. These approaches have led to many significant findings in a wide range of biological disciplines, from developmental biology to cancer and infectious diseases. However, there is a current lack of tools available to connect raw PTM site information to biologically meaningful results in a high-throughput manner. Furthermore, many of the available tools require significant programming knowledge to implement.ResultsThe R package PTMphinder was designed to enable researchers, particularly those with minimal programming background, to thoroughly analyze PTMs in proteomic data sets. The package contains three functions: parseDB, phindPTMs and extractBackground. Together, these functions allow users to reformat proteome databases for easier analysis, localize PTMs within full proteins, extract motifs surrounding the identified sites and create proteome-specific motif backgrounds for statistical purposes. Beta-testing of this R package has demonstrated its simplicity and ease of integration with existing tools.ConclusionPTMphinder empowers researchers to fully analyze and interpret PTMs derived from proteomic data. This package is simple enough for researchers with limited programming experience to understand and implement. The data produced from this package can inform subsequent research by itself and also be used in conjunction with other tools, such as motif-x, for further analysis. creator: Jacob M. Wozniak creator: David J. Gonzalez uri: https://doi.org/10.7717/peerj.7046 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wozniak and Gonzalez title: Future CO2-induced seawater acidification mediates the physiological performance of a green alga Ulva linza in different photoperiods link: https://peerj.com/articles/7048 last-modified: 2019-06-04 description: Photoperiods have an important impact on macroalgae living in the intertidal zone. Ocean acidification also influences the physiology of macroalgae. However, little is known about the interaction between ocean acidification and photoperiod on macroalgae. In this study, a green alga Ulva linza was cultured under three different photoperiods (L: D = 8:16, 12:12, 16:8) and two different CO2 levels (LC, 400 ppm; HC, 1,000 ppm) to investigate their responses. The results showed that relative growth rate of U. linza increased with extended light periods under LC but decreased at HC when exposed to the longest light period of 16 h compared to 12 h. Higher CO2 levels enhanced the relative growth rate at a L: D of 8:16, had no effect at 12:12 but reduced RGR at 16:8. At LC, the L: D of 16:8 significantly stimulated maximum quantum yield (Yield). Higher CO2 levels enhanced Yield at L: D of 12:12 and 8:16, had negative effect at 16:8. Non-photochemical quenching (NPQ) increased with increasing light period. High CO2 levels did not affect respiration rate during shorter light periods but enhanced it at a light period of 16 h. Longer light periods had negative effects on Chl a and Chl b content, and high CO2 level also inhibited the synthesis of these pigments. Our data demonstrate the interactive effects of CO2 and photoperiod on the physiological characteristics of the green tide macroalga Ulva linza and indicate that future ocean acidification may hinder the stimulatory effect of long light periods on growth of Ulva species. creator: Furong Yue creator: Guang Gao creator: Jing Ma creator: Hailong Wu creator: Xinshu Li creator: Juntian Xu uri: https://doi.org/10.7717/peerj.7048 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yue et al. title: Effects of prolonged continuous computer gaming on physical and ocular symptoms and binocular vision functions in young healthy individuals link: https://peerj.com/articles/7050 last-modified: 2019-06-04 description: Background and ObjectiveAddiction to computer gaming has become a social problem in Korea and elsewhere, and it has been enlisted as a mental health disorder by the World Health Organization. Most studies related to computer use and vision have individually assessed physical and ocular symptoms and binocular vision. Accordingly, the present study comprehensively assessed subjective physical and ocular symptoms and functions related to binocular vision after prolonged continuous computer gaming. This study aimed to investigate the effects of prolonged continuous computer gaming on physical and ocular health and visual functions in young healthy individuals.MethodsFifty healthy college students (35 male/15 female), aged 19–35 years old, were enrolled in this study. The inclusion criteria were no binocular vision problems and no reported history of ocular disease. Participants played continuously for 4 h from 6:00 to 10:00 p.m. Physical and ocular symptoms and visual functions such as convergence, accommodation, phoria, and the blink rate were assessed before and after continuous computer gaming for 4 h.ResultsContinuous computer gaming for 4 h resulted in convergence and accommodation disturbances and increased physical and ocular discomfort. Near phoria showed an exophoric shift, whereas distance phoria showed no change. Moreover, the accommodative and vergence facilities and blink rate were significantly decreased. All visual functions recovered to the baseline levels by the following morning.DiscussionOur findings suggest that excessive and continuous computer gaming impairs visual functions and causes ocular and physical fatigue. Our findings further the understanding of the adverse effects of excessive computer use on physical and ocular health, and adequate breaks are necessary to reduce physical and visual discomfort during computer gaming. creator: Ji-Woo Lee creator: Hyun Gug Cho creator: Byeong-Yeon Moon creator: Sang-Yeob Kim creator: Dong-Sik Yu uri: https://doi.org/10.7717/peerj.7050 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lee et al. title: Assessing the performance of a suite of machine learning models for daily river water temperature prediction link: https://peerj.com/articles/7065 last-modified: 2019-06-04 description: In this study, different versions of feedforward neural network (FFNN), Gaussian process regression (GPR), and decision tree (DT) models were developed to estimate daily river water temperature using air temperature (Ta), flow discharge (Q), and the day of year (DOY) as predictors. The proposed models were assessed using observed data from eight river stations, and modelling results were compared with the air2stream model. Model performances were evaluated using four indicators in this study: the coefficient of correlation (R), the Willmott index of agreement (d), the root mean squared error (RMSE), and the mean absolute error (MAE). Results indicated that the three machine learning models had similar performance when only Ta was used as the predictor. When the day of year was included as model input, the performances of the three machine learning models dramatically improved. Including flow discharge instead of day of year, as an additional predictor, provided a lower gain in model accuracy, thereby showing the relatively minor role of flow discharge in river water temperature prediction. However, an increase in the relative importance of flow discharge was noticed for stations with high altitude catchments (Rhône, Dischmabach and Cedar) which are influenced by cold water releases from hydropower or snow melting, suggesting the dependence of the role of flow discharge on the hydrological characteristics of such rivers. The air2stream model outperformed the three machine learning models for most of the studied rivers except for the cases where including flow discharge as a predictor provided the highest benefits. The DT model outperformed the FFNN and GPR models in the calibration phase, however in the validation phase, its performance slightly decreased. In general, the FFNN model performed slightly better than GPR model. In summary, the overall modelling results showed that the three machine learning models performed well for river water temperature modelling. creator: Senlin Zhu creator: Emmanuel Karlo Nyarko creator: Marijana Hadzima-Nyarko creator: Salim Heddam creator: Shiqiang Wu uri: https://doi.org/10.7717/peerj.7065 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhu et al. title: Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae) link: https://peerj.com/articles/6959 last-modified: 2019-06-03 description: A phylogenomic analysis of 42 complete plastid genomes (plastomes), including 16 that were newly sequenced, was conducted. Plastomes were sampled from 19 subtribes of Pooideae, to investigate relationships within and between Chloroplast Group 1 (Aveneae) and Group 2 (Poeae) species. Two data partitions: complete plastomes, and a combined plastome and rare genomic change (RGC) data matrix, were analyzed. Overall, 156 non-ambiguous RGC were identified, of which homology was inferred for 38 RGC. Among the 38 RGC identified, six were synapomorphic among the Group 1 subtribes: Aveninae, Agrostidinae, and Anthoxanthinae, (Phalaridinae + Torreyochloinae), and 27 were synapomorphic among the Group 2 subtribes: Loliinae, (Ammochloinae + Parapholiinae + Dactylidinae), Parapholiinae, Dactylidinae, Poinae, and Coleanthinae. Four RGC were determined to be homoplasious in Groups 1 and 2. Two other RGC originated through intrastrand deletion events. The remaining RGC events likely originated through recombination given their size and lack of sequence evidence for other types of mutations. This study also determined that relationships between taxa, even those only weakly supported in previous studies, could be inferred with strong support when utilizing complete plastomes. creator: Lauren M. Orton creator: Sean V. Burke creator: Melvin R. Duvall uri: https://doi.org/10.7717/peerj.6959 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Orton et al. title: Dietary supplementation with probiotics regulates gut microbiota structure and function in Nile tilapia exposed to aluminum link: https://peerj.com/articles/6963 last-modified: 2019-06-03 description: Backgrounds and aimsAluminum contamination of water is becoming increasingly serious and threatens the health status of fish. Lactobacillus plantarum CCFM639 was previously shown to be a potential probiotic for alleviation aluminum toxicity in Nile tilapia. Considering the significant role of the gut microbiota on fish health, it seems appropriate to explore the relationships among aluminum exposure, probiotic supplementation, and the gut microbiota in Nile tilapia and to determine whether regulation of the gut microbiota is related to alleviation of aluminum toxicity by a probiotic in Nile tilapia.Methods and resultsThe tilapia were assigned into four groups, control, CCFM639 only, aluminum only, and aluminum + CCFM639 groups for an experimental period of 4 weeks. The tilapia in the aluminum only group were grown in water with an aluminum ion concentration of 2.73 mg/L. The final concentration of CCFM639 in the diet was 108 CFU/g. The results show that environmental aluminum exposure reduced the numbers of L. plantarum in tilapia feces and altered the gut microbiota. As the predominant bacterial phyla in the gut, the abundances of Bacteroidetes and Proteobacteria in aluminum-exposed fish were significantly elevated and lowered, respectively. At the genus level, fish exposed to aluminum had a significantly lower abundance of Deefgea, Plesiomonas, and Pseudomonas and a greater abundance of Flavobacterium, Enterovibrio, Porphyromonadaceae uncultured, and Comamonadaceae. When tilapia were exposed to aluminum, the administration of a probiotic promoted aluminum excretion through the feces and led to a decrease in the abundance of Comamonadaceae, Enterovibrio and Porphyromonadaceae. Notably, supplementation with a probiotic only greatly decreased the abundance of Aeromonas and Pseudomonas.ConclusionAluminum exposure altered the diversity of the gut microbiota in Nile tilapia, and probiotic supplementation allowed the recovery of some of the diversity. Therefore, regulation of gut microbiota with a probiotic is a possible mechanism for the alleviation of aluminum toxicity in Nile tilapia. creator: Leilei Yu creator: Nanzhen Qiao creator: Tianqi Li creator: Ruipeng Yu creator: Qixiao Zhai creator: Fengwei Tian creator: Jianxin Zhao creator: Hao Zhang creator: Wei Chen uri: https://doi.org/10.7717/peerj.6963 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yu et al. title: Large-scale gene expression analysis reveals robust gene signatures for prognosis prediction in lung adenocarcinoma link: https://peerj.com/articles/6980 last-modified: 2019-06-03 description: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide. High mortality in LUAD motivates us to stratify the patients into high- and low-risk groups, which is beneficial for the clinicians to design a personalized therapeutic regimen. To robustly predict the risk, we identified a set of robust prognostic gene signatures and critical pathways based on ten gene expression datasets by the meta-analysis-based Cox regression model, 25 of which were selected as predictors of multivariable Cox regression model by MMPC algorithm. Gene set enrichment analysis (GSEA) identified the Aurora-A pathway, the Aurora-B pathway, and the FOXM1 transcription factor network as prognostic pathways in LUAD. Moreover, the three prognostic pathways were also the biological processes of G2-M transition, suggesting that hyperactive G2-M transition in cell cycle was an indicator of poor prognosis in LUAD. The validation in the independent datasets suggested that overall survival differences were observed not only in all LUAD patients, but also in those with a specific TNM stage, gender, and age group. The comprehensive analysis demonstrated that prognostic signatures and the prognostic model by the large-scale gene expression analysis were more robust than models built by single data based gene signatures in LUAD overall survival prediction. creator: Yiyan Songyang creator: Wei Zhu creator: Cong Liu creator: Lin-lin Li creator: Wei Hu creator: Qun Zhou creator: Han Zhang creator: Wen Li creator: Dejia Li uri: https://doi.org/10.7717/peerj.6980 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Songyang et al. title: Comparison of therapeutic effects of different mesenchymal stem cells on rheumatoid arthritis in mice link: https://peerj.com/articles/7023 last-modified: 2019-06-03 description: BackgroundRheumatoid arthritis (RA) is a chronic and nonspecific autoimmune disease, which leads to joint destruction and deformity. To investigate the potential of human mesenchymal stem cells (MSCs) as a new therapeutic strategy for patients with RA, we compared the therapeutic effects of bone marrow derived MSCs (BMSCs), umbilical cord derived MSCs (UCs), and stem cells derived from human exfoliated deciduous teeth (SHED) on collagen-induced arthritis (CIA) in mice.MethodsA total of 24 DBA/1 mice were infused with type II collagen to induce RA in the experimental model. MSC-treated mice were infused with UCs, BMSCs, and SHED, respectively. Bone erosion and joint destruction were measured by micro-computed tomographic (micro-CT) analysis and hematoxylin and eosin staining. The levels of tumor necrosis factor α (TNF-α) and interleukin-1β (IL-1β) were measured by immunohistochemistry and Enzyme-Linked Immunosorbent Assay (ELISA).ResultsSystemic delivery of MSCs significantly improved the severity of the symptoms related to CIA to greater extent compared with the untreated control group. Micro-CT revealed reduced bone erosions in the metatarsophalangeal joints upon treatment with MSCs. Additionally, according to histologic evaluation, reduced synovitis and articular destruction were observed in MSC-treated groups. The levels of TNF-α and IL-1β in the serum and joints decreased with treatment by MSCs.ConclusionOur findings suggest that systemic infusion of UCs, BMSCs, and SHED may significantly alleviate the effects of RA. The therapeutic effect of BMSCs was greater than that of SHED, while the UCs were shown to have the best therapeutic effect on CIA mice. In conclusion, compared with BMSCs and SHED, UCs may be a more suitable source of MSCs for the treatment of patients with RA. creator: Qing Zhang creator: Qihong Li creator: Jun Zhu creator: Hao Guo creator: Qiming Zhai creator: Bei Li creator: Yan Jin creator: Xiaoning He creator: Fang Jin uri: https://doi.org/10.7717/peerj.7023 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Associations between cortisol awakening response and resting electroencephalograph asymmetry link: https://peerj.com/articles/7059 last-modified: 2019-06-03 description: The cortisol awakening response (CAR), a rapid cortisol rise in the morning after awakening, has been proposed to provide energy to cope with daily demands and suggested to be associated with brain functions. Electroencephalogram (EEG) asymmetry studies have implicated asymmetric cortical activation, especially in frontal cortex, in approach-withdrawal motivation. In this study, we examined the relationship between the CAR and lateralized cortical activity under rest in 55 university male students. Saliva samples were collected at 0, 15, 30 and 60 min after awakening on the two consecutive workdays. The lateralized cortical activity at frontocentral sites was examined by alpha asymmetry score. The results showed that a higher CAR was positively associated with alpha asymmetry score, which indicated that the higher CAR is linked with more left-sided cortical activity at frontocentral sites under resting state. This association still existed even after controlling psychological and sleep quality variables. These results suggested that appropriately mobilizing energy resource storage after awakening revealed as CAR might be associated with goal-directed approach tendencies before any eventual stressful situation, characteristic of more left than right resting-state frontocentral cortical activity. creator: Hongxia Duan creator: Huihua Fang creator: Yuling Zhang creator: Xia Shi creator: Liang Zhang uri: https://doi.org/10.7717/peerj.7059 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Duan et al.