title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1349 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Serum heparan sulfate and chondroitin sulfate concentrations in patients with newly diagnosed exfoliative glaucoma link: https://peerj.com/articles/6920 last-modified: 2019-05-23 description: BackgroundExfoliative glaucoma (XFG) is typically classified as a high-pressure type of secondary open-angle glaucoma that develops as a consequence of exfoliation syndrome (XFS). Exfoliation syndrome is an age-related, generalized disorder of the extracellular matrix characterized by production and progressive accumulation of a fibrillar exfoliation material (XFM) in intra- and extraocular tissues. Exfoliation material represents complex glycoprotein/proteoglycan structure composed of a protein core surrounded by glycosaminoglycans such as heparan sulfate (HS) and chondroitin sulfate (CS). The purpose of the present study was to investigate HS and CS concentrations in serum samples of patients with newly diagnosed XFG and compare the obtained values with those pertaining to newly diagnosed primary open-angle glaucoma (POAG), normal controls (NC) and subjects with XFS.MethodsThis case–control study involved 165 subjects, including patients with newly diagnosed XFG, patients with newly diagnosed POAG, subjects with XFS and age- and sex-matched NC. The study was conducted at the Glaucoma Department of Clinic for Eye Diseases, Clinical Centre of Serbia, as the referral center for glaucoma in Serbia.ResultsThe mean age in the XFG, POAG, XFS and NC groups was 73.3 ± 9.0, 66.3 ± 7.8, 75.5 ± 7.0 and 73.5 ± 9.5 years, respectively, XFG vs. POAG, p < 0.001. Mean serum HS concentrations in the XFG, POAG, NC and XFS groups were 3,189.0 ± 1,473.8 ng/mL, 2,091.5 ± 940.9 ng/mL, 2,543.1 ± 1,397.3 ng/mL and 2,658.2 ± 1,426.8 ng/mL respectively, XFG vs. POAG, p = 0.001 and XFG vs. NC, p = 0.032. Mean serum CS concentrations in the XFG, POAG, NC and XFS group were 43.9 ± 20.7 ng/mL, 38.5 ± 22.0 ng/mL, 35.8 ± 16.4 ng/mL and 43.3 ± 21.8 ng/mL, respectively, XFG vs. NC, p = 0.041.ConclusionsOur findings revealed greater HS and CS concentrations in XFG patients and XFS subjects compared to those without XFM. Implications of HS and CS in the pathophysiology of XFS and glaucoma should be studied further. Serum is easily accessible and should thus be explored as rich sources of potential biomarkers. Further research should aim to identify XFG biomarkers that could be utilized in routine blood analysis tests, aiding in timely disease diagnosis. creator: Vesna D. Maric creator: Marija M. Bozic creator: Andja M. Cirkovic creator: Sanja Dj Stankovic creator: Ivan S. Marjanovic creator: Anita D. Grgurevic uri: https://doi.org/10.7717/peerj.6920 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Maric et al. title: Identification and characterization of mRNAs and lncRNAs in the uterus of polytocous and monotocous Small Tail Han sheep (Ovis aries) link: https://peerj.com/articles/6938 last-modified: 2019-05-23 description: BackgroundLong non-coding RNAs (lncRNAs) regulate endometrial secretion and uterine volume. However, there is little research on the role of lncRNAs in the uterus of Small Tail Han sheep (FecB++). Herein, RNA-seq was used to comparatively analyze gene expression profiles of uterine tissue between polytocous and monotocous sheep (FecB++) in follicular and luteal phases.MethodsTo identify lncRNA and mRNA expressed in the uterus, the expression of lncRNA and mRNA in the uterus of Small Tail Han sheep (FecB++) from the polytocous group (n = 6) and the monotocous group (n = 6) using RNA-sequencing and real-time polymerase chain reaction (RT-PCR). Identification of differentially expressed lncRNAs and mRNAs were performed between the two groups and two phases . Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA co-expression network was constructed to further analyses the function of related genes.ResultsIn the follicular phase, 473 lncRNAs and 166 mRNAs were differentially expressed in polytocous and monotocous sheep; in the luteal phase, 967 lncRNAs and 505 mRNAs were differentially expressed in polytocous and monotocous sheep. GO and KEGG enrichment analysis showed that the differentially expressed lncRNAs and their target genes are mainly involved in ovarian steroidogenesis, retinol metabolism, the oxytocin signaling pathway, steroid hormone biosynthesis, and the Foxo signaling pathway. Key lncRNAs may regulate reproduction by regulating genes involved in these signaling pathways and biological processes. Specifically, UGT1A1, LHB, TGFB1, TAB1, and RHOA, which are targeted by MSTRG.134747, MSTRG.82376, MSTRG.134749, MSTRG.134751, and MSTRG.134746, may play key regulatory roles. These results offer insight into molecular mechanisms underlying sheep prolificacy. creator: Yongfu La creator: Jishun Tang creator: Xiaoyun He creator: Ran Di creator: Xiangyu Wang creator: Qiuyue Liu creator: Liping Zhang creator: Xiaosheng Zhang creator: Jinlong Zhang creator: Wenping Hu creator: Mingxing Chu uri: https://doi.org/10.7717/peerj.6938 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 La et al. title: Gene expression in Tribolium castaneum life stages: Identifying a species-specific target for pest control applications link: https://peerj.com/articles/6946 last-modified: 2019-05-23 description: The red flour beetle, Tribolium castaneum, is a major agricultural pest of post-harvest products and stored grain. Control of T. castaneum in stored products and grain is primarily by fumigants and sprays, but insecticide resistance is a major problem, and new control strategies are needed. T. castaneum is a genetic model for coleopterans, and the reference genome can be used for discovery of candidate gene targets for molecular-based control, such as RNA interference. Gene targets need to be pest specific, and ideally, they are expressed at low levels for successful control. Therefore, we sequenced the transcriptome of four major life stages of T. castaneum, sorted data into groups based on high or low expression levels, and compared relative gene expression among all life stages. We narrowed our candidate gene list to a cuticle protein gene (CPG) for further analysis. We found that the CPG sequence was unique to T. castaneum and expressed only in the larval stage. RNA interference targeting CPG in newly-emerged larvae caused a significant (p < 0.05) decrease in CPG expression (1,491-fold) compared to control larvae and 64% mortality over 18 d. RNA-Seq of survivors after 18 d identified changes in the expression of other genes as well, including 52 long noncoding RNAs. Expression of three additional cuticle protein genes were increased and two chitinase genes were decreased in response to injection of CPG dsRNA. The data demonstrate that RNA-Seq can identify genes important for insect survival and thus may be used to develop novel biologically-based insect control products. creator: Lindsey C. Perkin creator: Brenda Oppert uri: https://doi.org/10.7717/peerj.6946 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Perkin and Oppert title: Transcriptomic study of the mechanism of anoikis resistance in head and neck squamous carcinoma link: https://peerj.com/articles/6978 last-modified: 2019-05-23 description: BackgroundNormal epithelial cells rapidly undergo apoptosis as soon as they lose contact with the extracellular matrix (ECM), which is termed as anoikis. However, cancer cells tend to develop a resistance mechanism to anoikis. This acquired ability is termed as anoikis resistance. Cancer cells, with anoikis resistance, can spread to distant tissues or organs via the peripheral circulatory system and cause cancer metastasis. Thus, inhibition of anoikis resistance blocks the metastatic ability of cancer cells.MethodsAnoikis-resistant CAL27 (CAL27AR) cells were induced from CAL27 cells using the suspension culture approach. Transcriptome analysis was performed using RNA-Seq to study the differentially expressed genes (DEGs) between the CAL27ARcells and the parental CAL27 cells. Gene function annotation and Gene Ontology (GO) enrichment analysis were performed using DAVID database. Signaling pathways involved in DEGs were analyzed using Gene Set Enrichment Analysis (GSEA) software. Analysis results were confirmed by reverse transcription PCR (RT-PCR), western blotting, and gene correlation analysis based on the TCGA database.ResultsGO enrichment analysis indicated that the biological process (BP) of the DEGs was associated with epidermal development, DNA replication, and G1/S transition of the mitotic cell cycle. The analysis of cellular component (CC) showed that the most significant up-regulated genes were related to extracellular exosome. KEGG Pathway analysis revealed that 23 signaling pathways were activated (p-value ≤ 0.05, FDR q-value ≤ 0.05) and 22 signaling pathways were suppressed (p-value ≤ 0.05, FDR q-value ≤ 0.05). The results from the GSEA indicated that in contrast to the inhibition of EGFR signaling pathway, the VEGF signaling pathway was activated. The VEGF signaling pathway possibly activates STAT3 though induction of STAT3 phosphorylation. Gene correlation analysis revealed that the VEGFA- STAT3-KLF4-CDKN1A signal axis was not only present in head and neck squamous carcinoma (HNSCC) but also two other epithelial-derived carcinomas that highly express VEGFA, including kidney renal clear cell carcinoma (KIRC) and ovarian serous cystadenocarcinoma (OV). creator: Chen Guo creator: Ling-feng Xu creator: Hui-min Li creator: Wei Wang creator: Ji-hua Guo creator: Meng-qi Jia creator: Rong Jia creator: Jun Jia uri: https://doi.org/10.7717/peerj.6978 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al. title: Simphony: simulating large-scale, rhythmic data link: https://peerj.com/articles/6985 last-modified: 2019-05-23 description: Simulated data are invaluable for assessing a computational method’s ability to distinguish signal from noise. Although many biological systems show rhythmicity, there is no general-purpose tool to simulate large-scale, rhythmic data. Here we present Simphony, an R package for simulating data from experiments in which the abundances of rhythmic and non-rhythmic features (e.g., genes) are measured at multiple time points in multiple conditions. Simphony has parameters for specifying experimental design and each feature’s rhythmic properties (e.g., amplitude and phase). In addition, Simphony can sample measurements from Gaussian and negative binomial distributions, the latter of which approximates read counts from RNA-seq data. We show an example of using Simphony to evaluate the accuracy of rhythm detection. Our results suggest that Simphony will aid experimental design and computational method development. Simphony is thoroughly documented and freely available at https://github.com/hugheylab/simphony. creator: Jordan M. Singer creator: Darwin Y. Fu creator: Jacob J. Hughey uri: https://doi.org/10.7717/peerj.6985 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Singer et al. title: A mathematical landmark-based method for measuring worn molars in hominoid systematics link: https://peerj.com/articles/6990 last-modified: 2019-05-23 description: Worn teeth pose a major limitation to researchers in the fields of extinct and extant hominoid systematics because they lack clearly identifiable anatomical landmarks needed to take measurements on the crown enamel surface and are typically discarded from a study. This is particularly detrimental when sample sizes for some groups are already characteristically low, if there is an imbalance between samples representing populations, sexes or dietary strategies, or if the worn teeth in question are type specimens of fossil species or other key specimens. This study proposes a methodology based predominantly on mathematically-derived landmarks for measuring size and shape features of molars, irrespective of wear. With 110 specimens of lower second molars from five species of extant hominoids (Pan troglodytes, P. paniscus, Gorilla gorilla, G. beringei, Homo sapiens), n ≥ 20 per species, n ≥ 10 per subspecies, good species separation in morphospace is achieved in a principal components analysis. Classification accuracy in a discriminant function analysis is 96.4% at the species level and 88.2% at the subspecies level (92.7% and 79.1%, respectively, on cross-validation). The classification accuracy compares favorably to that achieved by anatomically-derived measurements based on published research (94% and 84% at the species and subspecies level respectively; 91% and 76% on cross-validation). The mathematical landmarking methodology is rapid and uncomplicated. The results support the use of mathematical landmarks to enable the inclusion of worn molar teeth in dental studies so as to maximize sample sizes and restore balance between populations and/or sexes in hominoid systematic studies. creator: Susan J. Dykes creator: Varsha C. Pilbrow uri: https://doi.org/10.7717/peerj.6990 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dykes and Pilbrow title: Effect of GARP on osteogenic differentiation of bone marrow mesenchymal stem cells via the regulation of TGFβ1 in vitro link: https://peerj.com/articles/6993 last-modified: 2019-05-23 description: Mesenchymal stem cells (MSCs), which have multipotential differentiation and self-renewal potential, are possible cells for tissue engineering. Transforming growth factor β1 (TGFβ1) can be produced by MSCs in an inactive form, and the activation of TGFβ1 functions as an important regulator of osteogenic differentiation in MSCs. Recently, studies showed that Glycoprotein A repetitions predominant (GARP) participated in the activation of latent TGFβ1, but the interaction between GARP and TGFβ1 is still undefined. In our study, we successfully isolated the MSCs from bone marrow of rats, and showed that GARP was detected in bone mesenchymal stem cells (BMSCs). During the osteogenic differentiation of BMSCs, GARP expression was increased over time. To elucidate the interaction between GARP and TGFβ1, we downregulated GARP expression in BMSCs to examine the level of active TGFβ1. We then verified that the downregulation of GARP decreased the secretion of active TGFβ1. Furthermore, osteogenic differentiation experiments, alkaline phosphatase (ALP) activity analyses and Alizarin Red S staining experiments were performed to evaluate the osteogenic capacity. After the downregulation of GARP, ALP activity and Alizarin Red S staining significantly declined and the osteogenic indicators, ALP, Runx2, and OPN, also decreased, both at the mRNA and protein levels. These results demonstrated that downregulated GARP expression resulted in the reduction of TGFβ1 and the attenuation of osteoblast differentiation of BMSCs in vitro. creator: Ruixue Li creator: Jian Sun creator: Fei Yang creator: Yang Sun creator: Xingwen Wu creator: Qianrong Zhou creator: Youcheng Yu creator: Wei Bi uri: https://doi.org/10.7717/peerj.6993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Boat anchoring contributes substantially to coral reef degradation in the British Virgin Islands link: https://peerj.com/articles/7010 last-modified: 2019-05-23 description: Community decline is often linked to anthropogenic activities. Coral reef declines, for example, have been linked to overfishing and climate change, but impacts of coastal development, pollution, and tourism have received increasing attention. Here, we isolated the impact of one little-studied aspect of recreational activity on coral reefs—damage from boat anchoring—by performing a survey of 24 sites in the British Virgin Islands (BVI) subject to varying levels of anchoring activity. The percent cover of hard corals and sea fans was reduced by a factor of ∼1.7 and ∼2.6 respectively at highly anchored sites. Hard coral colonies were  40% smaller in surface area and ∼60% less dense at sites experiencing high anchoring frequency. In addition, highly anchored sites supported only ∼60% of the species richness of little anchored sites. Frequently anchored sites were ∼60% as structurally complex and supported less than half as many fish as those rarely anchored, with 5 of 7 fish functional groups affected. Roughly 24% of BVI coral reef by area appears suitable for anchoring, suggesting that impacts associated with boat anchoring may be both locally severe and more pervasive than previously appreciated. creator: Rebecca L. Flynn creator: Graham E. Forrester uri: https://doi.org/10.7717/peerj.7010 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Flynn and Forrester title: The braincase of Mesosuchus browni (Reptilia, Archosauromorpha) with information on the inner ear and description of a pneumatic sinus link: https://peerj.com/articles/6798 last-modified: 2019-05-22 description: Rhynchosauria is a group of archosauromorph reptiles abundant in terrestrial ecosystems of the Middle Triassic. Mesosuchus is one of the earliest and basalmost rhynchosaurs, playing an important role not only for the understanding of the evolution of the group as a whole, but also of archosauromorphs in general. The braincase of Mesosuchus has been previously described, albeit not in detail, and the middle and inner ears were missing. Here, we provide new information based on micro-computed tomography scanning of the best-preserved specimen of Mesosuchus, SAM-PK-6536. Contrary to what has been stated previously, the braincase of Mesosuchus is dorso-ventrally tall. The trigeminal foramen lies in a deep recess on the prootic whose flat ventral rim could indicate the articulation surface to the laterosphenoid, although no such element was found. The middle ear of Mesosuchus shows a small and deeply recessed fenestra ovalis, with the right stapes preserved in situ. It has a rather stout, imperforated and posteriorly directed shaft with a small footplate. These features suggest that the ear of Mesosuchus was well-suited for the detection of low-frequency sounds. The semicircular canals are slender and elongate and the floccular fossa is well-developed. This is indicative of a refined mechanism for gaze stabilization, which is usually related to non-sprawling postures. The most striking feature of the Mesosuchus braincase is, however, the presence of a pneumatic sinus in the basal tubera. The sinus is identified as originating from the pharyngotympanic system, implying ossified Eustachian tubes. Braincase pneumatization has not yet been a recognized feature of stem-archosaurs, but the potential presence of pneumatic foramina in an array of taxa, recognized here as such for the first time, suggests braincase sinuses could be present in many other archosauromorphs. creator: Gabriela Sobral creator: Johannes Müller uri: https://doi.org/10.7717/peerj.6798 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sobral and Müller title: FunPred 3.0: improved protein function prediction using protein interaction network link: https://peerj.com/articles/6830 last-modified: 2019-05-22 description: Proteins are the most versatile macromolecules in living systems and perform crucial biological functions. In the advent of the post-genomic era, the next generation sequencing is done routinely at the population scale for a variety of species. The challenging problem is to massively determine the functions of proteins that are yet not characterized by detailed experimental studies. Identification of protein functions experimentally is a laborious and time-consuming task involving many resources. We therefore propose the automated protein function prediction methodology using in silico algorithms trained on carefully curated experimental datasets. We present the improved protein function prediction tool FunPred 3.0, an extended version of our previous methodology FunPred 2, which exploits neighborhood properties in protein–protein interaction network (PPIN) and physicochemical properties of amino acids. Our method is validated using the available functional annotations in the PPIN network of Saccharomyces cerevisiae in the latest Munich information center for protein (MIPS) dataset. The PPIN data of S. cerevisiae in MIPS dataset includes 4,554 unique proteins in 13,528 protein–protein interactions after the elimination of the self-replicating and the self-interacting protein pairs. Using the developed FunPred 3.0 tool, we are able to achieve the mean precision, the recall and the F-score values of 0.55, 0.82 and 0.66, respectively. FunPred 3.0 is then used to predict the functions of unpredicted protein pairs (incomplete and missing functional annotations) in MIPS dataset of S. cerevisiae. The method is also capable of predicting the subcellular localization of proteins along with its corresponding functions. The code and the complete prediction results are available freely at: https://github.com/SovanSaha/FunPred-3.0.git. creator: Sovan Saha creator: Piyali Chatterjee creator: Subhadip Basu creator: Mita Nasipuri creator: Dariusz Plewczynski uri: https://doi.org/10.7717/peerj.6830 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Saha et al.