title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1050 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Interpreting character variation in turtles: Araripemys barretoi (Pleurodira: Pelomedusoides) from the Araripe Basin, Early Cretaceous of Northeastern Brazil link: https://peerj.com/articles/9840 last-modified: 2020-09-29 description: The Araripe Basin (Northeastern Brazil) has yielded a rich Cretaceous fossil fauna of both vertebrates and invertebrates found mainly in the Crato and Romualdo Formations, of Aptian and Albian ages respectively. Among the vertebrates, the turtles were found to be quite diverse, with several specimens retrieved and five valid species described to this date for the Romualdo Formation. There were also records of turtles from Ipubi and Crato Formations, mainly fragmentary material which precluded proper specific identification; however, Araripemys barretoi is supposed to occur on both Crato and Romualdo Formations. Here we describe thirteen specimens of A. barretoi-including the first description of an almost complete individual, bearing a skull, from the Crato Formation. We report a great amount of morphological variation, interpreted as being essentially of intraspecific nature, including individual, sexual and ontogenetic variation. creator: Saulo Limaverde creator: Rodrigo Vargas Pêgas creator: Rafael Damasceno creator: Chiara Villa creator: Gustavo R. Oliveira creator: Niels Bonde creator: Maria E.C. Leal uri: https://doi.org/10.7717/peerj.9840 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Limaverde et al. title: Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2) link: https://peerj.com/articles/9855 last-modified: 2020-09-29 description: BackgroundThe present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required.MethodsIn this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2.0, AllergenFP 1.0 and ElliPro.ResultsThe predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59−HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS−105, 227−LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK−266, 3−DNGPQNQRNAPRITFGGP−20, 29−GERSGARSKQRRPQGL−45. Two other prime vaccine targets, 370−NSASFSTFKCYGVSPTKLNDLCFTNV−395 and 260−AGAAAYYVGYLQPRT−274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins.ConclusionsTaken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2. creator: Rajesh Anand creator: Subham Biswal creator: Renu Bhatt creator: Bhupendra N. Tiwary uri: https://doi.org/10.7717/peerj.9855 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Anand et al. title: Bigfin reef squid demonstrate capacity for conditional discrimination and projected future carbon dioxide levels have no effect on learning capabilities link: https://peerj.com/articles/9865 last-modified: 2020-09-29 description: Anthropogenic carbon dioxide (CO2) emissions are being absorbed by the oceans, a process known as ocean acidification, and risks adversely affecting a variety of behaviours in a range of marine species, including inhibited learning in some fishes. However, the effects of elevated CO2 on learning in advanced invertebrates such as cephalopods are unknown. Any impacts to the learning abilities of cephalopods could have far-reaching consequences for their populations and the communities they inhabit. Cephalopods have some of the most advanced cognitive abilities among invertebrates and are one of the few invertebrate taxa in which conditional discrimination has been demonstrated, though the trait has not been demonstrated in any species of squid. Here, we tested for the first time the capacity for conditional discrimination in a squid species (Sepioteuthis lessoniana). Furthermore, we investigated the effects of projected future CO2 levels (1,084 µatm) on conditional discrimination and learning more generally. A three-task experiment within a two-choice arena was used to test learning and conditional discrimination. Learning was measured by improvements in task completion in repeated trials over time and the number of trials required to pass each task. Squid exhibited significant learning capabilities, with an increase in correct choices over successive trials and a decrease in the number of trials needed to complete the successive tasks. Six of the 12 squid tested successfully passed all three tasks indicating a capacity for conditional discrimination in the species. Elevated CO2 had no effect on learning or on the capacity for conditional discrimination in squid. This study highlights the remarkable cognitive abilities of S. lessoniana, demonstrated by their capacity for conditional discrimination, and suggests that ocean acidification will not compromise learning abilities. However, other behavioural traits in the species have been shown to be altered at comparable elevated CO2 conditions. It is not clear why some ecologically important behaviours are altered by elevated CO2 whereas others are unaffected. Future research should focus on the physiological mechanism responsible for altered behaviours in squid at elevated CO2. creator: Blake L. Spady creator: Sue-Ann Watson uri: https://doi.org/10.7717/peerj.9865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Spady and Watson title: The increasing prevalence of CPV-2c in domestic dogs in China link: https://peerj.com/articles/9869 last-modified: 2020-09-29 description: BackgroundCanine parvovirus type 2 (CPV-2), a serious pathogen, leads to high morbidity and mortality in dogs and several wild carnivore species. Although it is a DNA virus, it evolves particularly rapidly, with a genomic substitution rate of approximately 10−4 substitutions/site/year, close to that of some RNA viruses. Tracing the prevalence of CPV-2 in dogs is significant.MethodsIn this study, an aetiological survey was carried out from 2016 to 2019 in Guangdong Province, China, involving Guangzhou, Shenzhen and Dongguan. Furthermore, to systematically analyse the prevalence of CPV-2 in China, the VP2 gene sequences of all Chinese isolates were downloaded from the NCBI nucleotide database in December 2019, and changes in CPV-2 variants were examined.ResultsA total of 55.7% (34/61) of samples were CPV-2 positive by PCR detection and virus isolation. In addition to different variants circulating in dogs, coinfection with multiple variants was identified, as was coinfection with other canine enteric pathogens in some cases. Two previously reported amino acid sites, A5G and Q370R of CPV-2c mutants, reported in variants in China were assessed, and several CPV-2 isolates with P13S and K582N mutations were detected in this study. Finally, we speculate on the prevalence of different CPV-2 variants in China. According to the VP2 gene sequence obtained from the NCBI nucleotide database, the proportion of different variants in China has changed, and CPV-2c appears to be growing rapidly. In conclusion, this aetiology survey suggests that CPV-2 continues to be common in China and that the prevalence of CPV-2c is increasing. creator: Xiangqi Hao creator: Yuwei He creator: Chuhan Wang creator: Weiqi Xiao creator: Ruohan Liu creator: Xiangyu Xiao creator: Pei Zhou creator: Shoujun Li uri: https://doi.org/10.7717/peerj.9869 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hao et al. title: The relationship between individual phenotype and the division of labour in naked mole-rats: it’s complicated link: https://peerj.com/articles/9891 last-modified: 2020-09-29 description: BackgroundThe naked mole-rat (Heterocephalus glaber) is among the most social mammals on the planet, living in eusocial groups of up to 300 individuals that contain a single reproductive female and up to three reproductive males. A critical aspect of their complex social system is the division of labour that allows non-breeders to form an effective workforce. Age- or weight-based polyethisms are widely cited as explanations for how labour is divided, but evidence in support of these hypotheses has been equivocal.MethodsTo assess the extent to which individual working behaviour is determined by sex, age, weight and social rank, we studied the behaviours of 103 animals from eight captive colonies. We performed focal sampling and ran mixed-effects models to assess which factors explained variation in working behaviour during six ten-minute observation periods per individual.ResultsContrary to widely-held beliefs, we found that working behaviour did not decrease linearly with weight, although polynomial regressions indicated younger and medium-sized individuals worked most frequently, while high-ranking individuals worked for the shortest periods of time. Working behaviour and its relationship with individual characteristics also varied between colonies.ConclusionsWhile age- or size-based polyethisms may have some influence on working behaviour, we argue that other characteristics of the individual and colony are also important. In particular, the interactions of individual, social and environmental factors must be considered in order to understand the emergence and effectiveness of the division of labour that is so critical to many social organisms. creator: James D. Gilbert creator: Stephen J. Rossiter creator: Chris G. Faulkes uri: https://doi.org/10.7717/peerj.9891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gilbert et al. title: Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies link: https://peerj.com/articles/9902 last-modified: 2020-09-29 description: BackgroundThe blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system.MethodsBy reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages.ResultsWhile the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our mutant models revealed an abnormal delay in the BCR assembly upon NFkB activation, concomitant to sustained Flt3 signaling, down-regulation of Ebf1, Irf4 and Pax5 genes transcription, and reduced Ig recombination, pointing to a potential lineage commitment blockage.DiscussionFor the first time, an inducible CXCR7hi B cell precursor endowed with the potential capability of shifting central lymphoid niches, is inferred by computational modeling. Its phenotype is compatible with that of leukemia-initiating cells and might be the foundation that bridges inflammation with blockage-related malignancies and a wide range of immunological diseases. Besides the predicted differentiation impairment, inflammation-inducible phenotypes open the possibility of newly formed niches colonized by the reported precursor. Thus, emergent bone marrow ecosystems are predicted following a pro-inflammatory induction, that may lead to hematopoietic instability associated to blockage pathologies. creator: Jennifer Enciso creator: Luis Mendoza creator: Elena R. Álvarez-Buylla creator: Rosana Pelayo uri: https://doi.org/10.7717/peerj.9902 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Enciso et al. title: Study of marsh wetland landscape pattern evolution on the Zoigê Plateau due to natural/human dual-effects link: https://peerj.com/articles/9904 last-modified: 2020-09-29 description: Zoigê Plateau, China’s largest plateau marsh wetland, has experienced large-scale degradation of the marsh wetland and evolution of the wetland landscape pattern over the past 40 years due to climate warming and human activities. How exactly do the wetland landscape pattern characteristics change? How do climatic change and human activities affect the wetland evolution? These questions are yet to be systematically investigated. In order to investigate changes to the marsh wetland on the Zoigê Plateau, field investigations, spatial and statistical analysis were undertaken. Findings from our study indicate that from 1977–2016, the area of marsh wetland on the Plateau reduced by 56.54%, approximately 66,700 hm2 of marsh wetland has been lost. The centroids of both marsh and marshy meadow migrated and the landscape centroid migration behaviors were also correlated with the distribution and variation of the marsh wetland on different slopes. In addition, the number of marsh landscape patches initially increased before decreasing; the number of marshy meadow landscape patches also recorded an initial increase, followed by a decline before a final increase. As the effects of human activities weakened, the aggregation degrees of both marsh and marshy meadow increased. Overall, the fragmentation degree, diversity and fractal dimension of the marsh wetland all declined. An investigation into the driving factors affecting the Plateau area shows that the increase of annual average temperature was the natural factor while trenching and overgrazing were the main human factors resulting in wetland degradation. Results from this study provide basic data and theoretical foundation for the protection and restoration of marsh wetland in alpine regions. creator: Liqin Dong creator: Wen Yang creator: Kun Zhang creator: Shuo Zhen creator: Xiping Cheng creator: Lihua Wu uri: https://doi.org/10.7717/peerj.9904 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Dong et al. title: A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma link: https://peerj.com/articles/9944 last-modified: 2020-09-29 description: BackgroundHepatocellular carcinoma (HCC) is one of the most universal malignant liver tumors worldwide. However, there were no systematic studies to establish glycolysis‑related gene pairs (GRGPs) signatures for the patients with HCC. Therefore, the study aimed to establish novel GRGPs signatures to better predict the prognosis of HCC.MethodsBased on the data from Gene Expression Omnibus, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium databases, glycolysis-related mRNAs were used to construct GRGPs. Cox regression was applied to establish a seventeen GRGPs signature in TCGA dataset, which was verified in two validation (European and American, and Asian) datasets.ResultsSeventeen prognostic GRGPs (HMMR_PFKFB1, CHST1_GYS2, MERTK_GYS2, GPC1_GYS2, LDHA_GOT2, IDUA_GNPDA1, IDUA_ME2, IDUA_G6PD, IDUA_GPC1, MPI_GPC1, SDC2_LDHA, PRPS1_PLOD2, GALK1_IER3, MET_PLOD2, GUSB_IGFBP3, IL13RA1_IGFBP3 and CYB5A_IGFBP3) were identified to be significantly progressive factors for the patients with HCC in the TCGA dataset, which constituted a GRGPs signature. The patients with HCC were classified into low-risk group and high-risk group based on the GRGPs signature. The GRGPs signature was a significantly independent prognostic indicator for the patients with HCC in TCGA (log-rank P = 2.898e−14). Consistent with the TCGA dataset, the patients in low-risk group had a longer OS in two validation datasets (European and American: P = 1.143e−02, and Asian: P = 6.342e−08). Additionally, the GRGPs signature was also validated as a significantly independent prognostic indicator in two validation datasets.ConclusionThe seventeen GRGPs and their signature might be molecular biomarkers and therapeutic targets for the patients with HCC. creator: Weige Zhou creator: Shijing Zhang creator: Zheyou Cai creator: Fei Gao creator: Wenhui Deng creator: Yi Wen creator: Zhen-wen Qiu creator: Zheng-kun Hou creator: Xin-Lin Chen uri: https://doi.org/10.7717/peerj.9944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhou et al. title: Identification of hub genes and small molecule therapeutic drugs related to breast cancer with comprehensive bioinformatics analysis link: https://peerj.com/articles/9946 last-modified: 2020-09-29 description: Breast cancer is one of the most common malignant tumors among women worldwide and has a high morbidity and mortality. This research aimed to identify hub genes and small molecule drugs for breast cancer by integrated bioinformatics analysis. After downloading multiple gene expression datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, 283 overlapping differentially expressed genes (DEGs) significantly enriched in different cancer-related functions and pathways were obtained using LIMMA, VennDiagram and ClusterProfiler packages of R. We then analyzed the topology of protein–protein interaction (PPI) network with overlapping DEGs and further obtained six hub genes (RRM2, CDC20, CCNB2, BUB1B, CDK1, and CCNA2) from the network via STRING and Cytoscape. Subsequently, we conducted genes expression verification, genetic alterations evaluation, immune infiltration prediction, clinicopathological parameters analysis, identification of transcriptional and post-transcriptional regulatory molecules, and survival analysis for these hub genes. Meanwhile, 29 possible drug candidates (e.g., Cladribine, Gallium nitrate, Alvocidib, 1β-hydroxyalantolactone, Berberine hydrochloride, Nitidine chloride) were identified from the DGIdb database and the GSE85871 dataset. In addition, some transcription factors and miRNAs (e.g., E2F1, PTTG1, TP53, ZBTB16, hsa-miR-130a-3p, hsa-miR-204-5p) targeting hub genes were identified as key regulators in the progression of breast cancer. In conclusion, our study identified six hub genes and 29 potential drug candidates for breast cancer. These findings may advance understanding regarding the diagnosis, prognosis and treatment of breast cancer. creator: Mingqian Hao creator: Wencong Liu creator: Chuanbo Ding creator: Xiaojuan Peng creator: Yue Zhang creator: Huiying Chen creator: Ling Dong creator: Xinglong Liu creator: Yingchun Zhao creator: Xueyan Chen creator: Sadia Khatoon creator: Yinan Zheng uri: https://doi.org/10.7717/peerj.9946 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hao et al. title: Clostridioides difficile infection after cardiac surgery: Assessment of prevalence, risk factors and clinical outcomes—retrospective study link: https://peerj.com/articles/9972 last-modified: 2020-09-29 description: BackgroundClostridioides difficile infection (CDI) is the most common cause of hospital-acquired diarrhea. There is little available data regarding risk factors of CDI for patients who undergo cardiac surgery. The study evaluated the course of CDI in patients after cardiac surgery.MethodsOf 6,198 patients studied, 70 (1.1%) developed CDI. The control group consisted of 73 patients in whom CDI was excluded. Perioperative data and clinical outcomes were analyzed.ResultsPatients with CDI were significantly older in comparison to the control group (median age 73.0 vs 67.0, P = 0.005) and more frequently received proton pump inhibitors, statins, β-blockers and acetylsalicylic acid before surgery (P = 0.008, P = 0.012, P = 0.004, and P = 0.001, respectively). In addition, the presence of atherosclerosis, coronary disease and history of malignant neoplasms correlated positively with the development of CDI (P = 0.012, P = 0.036 and P = 0.05, respectively). There were no differences in the type or timing of surgery, aortic cross-clamp and cardiopulmonary bypass time, volume of postoperative drainage and administration of blood products between the studied groups. Relapse was more common among overweight patients with high postoperative plasma glucose or patients with higher C-reactive protein during the first episode of CDI, as well as those with a history of coronary disease or diabetes mellitus (P = 0.005, P = 0.030, P = 0.009, P = 0.049, and P = 0.025, respectively). Fifteen patients died (21.4%) from the CDI group and 7 (9.6%) from the control group (P = 0.050). Emergent procedures, prolonged stay in the intensive care unit, longer mechanical ventilation and high white blood cell count during the diarrhea were associated with higher mortality among patients with CDI (P = 0.05, P = 0.041, P = 0.004 and P = 0.007, respectively).ConclusionsThe study did not reveal any specific cardiac surgery-related risk factors for development of CDI. creator: Anna Rzucidło-Hymczak creator: Hubert Hymczak creator: Aldona Olechowska-Jarząb creator: Anna Gorczyca creator: Boguslaw Kapelak creator: Rafał Drwiła creator: Dariusz Plicner uri: https://doi.org/10.7717/peerj.9972 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rzucidło-Hymczak et al.