title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1255 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology link: https://peerj.com/articles/8079 last-modified: 2019-11-26 description: BackgroundThere are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep.MethodsIndigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis.ResultsWe identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (GenBank ID: 443299, g. 75320741G>A site), GUCY1A1 (GenBank ID: 101110000, g. 43266624C>T site), and COIL (GenBank ID: 101123134, g. 7321466C>G site) were found to be significantly or extremely significantly associated with litter size. These three loci are expected to be used as molecular markers to determine differences in litter size in sheep. creator: Haiyu Ma creator: Chao Fang creator: Lingling Liu creator: Qiong Wang creator: Jueken Aniwashi creator: Yiming Sulaiman creator: Kezierkailedi Abudilaheman creator: Wujun Liu uri: https://doi.org/10.7717/peerj.8079 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma link: https://peerj.com/articles/8096 last-modified: 2019-11-26 description: Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us understand the molecular mechanisms underlying the carcinogenesis and progression of ccRCC, and provide potential diagnostic, therapeutic and prognostic biomarkers. creator: Haiping Zhang creator: Jian Zou creator: Ying Yin creator: Bo Zhang creator: Yaling Hu creator: Jingjing Wang creator: Huijun Mu uri: https://doi.org/10.7717/peerj.8096 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Oxidative stress and antioxidants in the trabecular meshwork link: https://peerj.com/articles/8121 last-modified: 2019-11-26 description: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention. creator: Mingxuan Wang creator: Yajuan Zheng uri: https://doi.org/10.7717/peerj.8121 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang and Zheng title: Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia link: https://peerj.com/articles/8144 last-modified: 2019-11-26 description: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress. creator: Kyle K. Biggar creator: Jing Zhang creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.8144 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Biggar et al. title: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) link: https://peerj.com/articles/7929 last-modified: 2019-11-25 description: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species. creator: Xin Hu creator: Lili Zhu creator: Yi Zhang creator: Li Xu creator: Na Li creator: Xingguo Zhang creator: Yu Pan uri: https://doi.org/10.7717/peerj.7929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hu et al. title: Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications link: https://peerj.com/articles/8033 last-modified: 2019-11-25 description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong. creator: Siuli Mitra creator: Vaishnavi Kunteepuram creator: Klaus-Peter Koepfli creator: Neha Mehra creator: Wajeeda Tabasum creator: Ara Sreenivas creator: Ajay Gaur uri: https://doi.org/10.7717/peerj.8033 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mitra et al. title: Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research link: https://peerj.com/articles/8086 last-modified: 2019-11-25 description: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research. creator: Neil S. Cobb creator: Lawrence F. Gall creator: Jennifer M. Zaspel creator: Nicolas J. Dowdy creator: Lindsie M. McCabe creator: Akito Y. Kawahara uri: https://doi.org/10.7717/peerj.8086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cobb et al. title: Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference link: https://peerj.com/articles/8104 last-modified: 2019-11-25 description: BackgroundThe exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences.MethodsOnthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton.ResultsBoth species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to suspect that an unconsidered elytron characteristic may also be affecting these differences.DiscussionThe results of the involvement of the exoskeleton thickness and spots in the thermoregulation of insects opens new research lines to obtain a better understanding of the function of the exoskeleton as a passive thermoregulation mechanism in Coleoptera. creator: Eva Cuesta creator: Jorge M. Lobo uri: https://doi.org/10.7717/peerj.8104 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cuesta and Lobo title: Familiarity with visual stimuli boosts recency bias in macaques link: https://peerj.com/articles/8105 last-modified: 2019-11-25 description: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect. creator: Nicolas Brunet creator: Bharathi Jagadeesh uri: https://doi.org/10.7717/peerj.8105 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Brunet and Jagadeesh title: Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry link: https://peerj.com/articles/8113 last-modified: 2019-11-25 description: BackgroundThe production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns.MethodsIn this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view.ResultsThe production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints. creator: Samir Meramo-Hurtado creator: Kariana Moreno-Sader creator: Ángel D. González-Delgado uri: https://doi.org/10.7717/peerj.8113 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Meramo-Hurtado et al.