title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=742 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Inhibition of Connexin 43 reverses ox-LDL-mediated inhibition of autophagy in VSMC by inhibiting the PI3K/Akt/mTOR signaling pathway link: https://peerj.com/articles/12969 last-modified: 2022-03-16 description: BackgroundOxidized low-density lipoproteins (ox-LDL) may induce foam cell formation from the vascular smooth muscle cell (VSMC) by inhibiting VSMC autophagy. This process accelerates the formation of atherosclerosis (AS). Connexin 43 (Cx43), which is the most widely distributed connexin in VSMC is associated with autophagy. However, the mechanism of action and the involvement of Cx43 in ox-LDL-inhibited VSMC autophagy remain unclear.MethodsThe primary VSMC were obtained and identified, before primary VSMC were pretreated with an inhibitor (Cx43-specific inhibitor Gap26 and PI3K inhibitor LY294002) and stimulated with ox-LDL.ResultsOx-LDL not only inhibited autophagy in VSMC via downregulation of autophagy-related proteins (such as Beclin 1, LC3B, p62), but also increased Cx43 protein levels. Then we added Gap26 to VSMC in the ox-LDL+Gap26 group, in which autophagy-related proteins were increased and the accumulation of lipid droplets was reduced. These result suggested that an enhanced level of autophagy and an alleviation of lipid accumulation might be caused by inhibiting Cx43 in VSMC. The phosphorylation levels of PI3K, AKT, mTOR were increased by ox-LDL, thus down-regulating autophagy-related proteins. However, this situation was partially reversed by the Gap26. Moreover, Cx43 expression were decreased by LY294002 in ox-LDL-induced VSMCs.ConclusionInhibiting Cx43 may activate VSMC autophagy to inhibit foam cell formation by inhibiting the PI3K/AKT/mTOR signaling pathway. creator: Xuqing Qin creator: Wenjun He creator: Rui Yang creator: Luqian Liu creator: Yingying Zhang creator: Li Li creator: Junqiang Si creator: Xinzhi Li creator: Ketao Ma uri: https://doi.org/10.7717/peerj.12969 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qin et al. title: Onyx disparamphis sp. n. (Nematoda, Desmodorida) from South Korea with a taxonomic review of the genus link: https://peerj.com/articles/13010 last-modified: 2022-03-16 description: A new free-living marine nematode Onyx disparamphis sp. n. (Nematoda, Desmodorida) is described from sandy littoral of Jeju Island, South Korea. The new species differs from all other Onyx species by the unusual amphideal fovea morphology in males (elongated loop). O. disparamphis relates to O. balochinensis, and O. brevispiculatum by having simple non-double terminal pharyngeal bulb and relatively small and straight, non-sigmoid supplementary organs, but differs from them by smaller body length, shorter cephalic setae, smaller terminal pharyngeal bulb, smaller spicules, number of supplementary organs and tail shape expressed as ratio tail length/anal diameter. The genus Onyx is revised with updated genus diagnosis, and an annotated list of 23 valid species is presented. Onyx ferox is considered species inquirenda because the species is known only from a sole immature female specimen, while within Onyx, the males provide the most important distinguishing characters such as enlarged and complicated amphids, supplementary organs and copulatory spicules. For species identification, a pictorial key consisting of illustrations of simplified icons of male heads and posterior body sections, as well as a table of the most important morphometric and numerical characters are provided. Geographical distribution and habitat specifity of Onyx species is analysed briefly. creator: Alexei V. Tchesunov creator: Raehyuk Jeong creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.13010 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tchesunov et al. title: A SNP variation in an expansin (EgExp4) gene affects height in oil palm link: https://peerj.com/articles/13046 last-modified: 2022-03-16 description: Oil palm (Elaeis guineensis Jacq.), an Aracaceae family plant, is utilized for both consumable and non-consumable products, including cooking oil, cosmetics and biodiesel production. Oil palm is a perennial tree with 25 years of optimal harvesting time and a height of up to 18 m. However, harvesting of oil palm fruit bunches with heights of more than 2–3 meters is challenging for oil palm farmers. Thus, understanding the genetic control of height would be beneficial for using gene-based markers to speed up oil palm breeding programs to select semi-dwarf oil palm varieties. This study aims to identify Insertion/Deletions (InDels) and single nucleotide polymorphisms (SNPs) of five height-related genes, including EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4, in short and tall oil palm groups by PacBio SMRT sequencing technology. Then, the SNP variation’s association with height was validated in the Golden Tenera (GT) population. All targeted genes were successfully amplified by two rounds of PCR amplification with expected sizes that ranged from 2,516 to 3,015 base pair (bp), covering 5′ UTR, gene sequences and 3′ UTR from 20 short and 20 tall oil palm trees. As a result, 1,166, 909, 1,494, 387 and 5,384 full-length genomic DNA sequences were revealed by PacBio SMRT sequencing technology, from EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4 genes, respectively. Twelve variations, including eight InDels and four SNPs, were identified from EgDELLA1, EgGRF1, EgGA20ox1 and EgExp4. No variation was found for EgAPG1. After SNP through-put genotyping of 4 targeted SNP markers was done by PACE™ SNP genotyping, the association with height was determined in the GT population. Only the mEgExp4_SNP118 marker, designed from EgExp4 gene, was found to associate with height in 2 of 4 height-recordings, with p values of 0.0383 for height (HT)-1 and 0.0263 for HT-4. In conclusion, this marker is a potential gene-based marker that may be used in oil palm breeding programs for selecting semi-dwarf oil palm varieties in the near future. creator: Suthasinee Somyong creator: Phakamas Phetchawang creator: Abdulloh Kafa Bihi creator: Chutima Sonthirod creator: Wasitthee Kongkachana creator: Duangjai Sangsrakru creator: Nukoon Jomchai creator: Wirulda Pootakham creator: Sithichoke Tangphatsornruang uri: https://doi.org/10.7717/peerj.13046 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Somyong et al. title: Skin microbiota diversity among genetically unrelated individuals of Indian origin link: https://peerj.com/articles/13075 last-modified: 2022-03-16 description: BackgroundHuman skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography.MethodsAxillary sweat samples from genetically unrelated individuals (N = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3–V4) of the 16S rRNA gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location.ResultsOur study indicated the prevalence of phyla- Firmicutes, Proteobacteria, and Actinobacteria, consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal–Wallis test, p = 0.02), but not with geography (p = 0.62) or diet (p = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R2 = 0.07, p = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of Staphylococcus and Corynebacterium among individuals of the Pune district. Pseudomonas and Anaerococcus were abundant in individuals from Ahmednagar whereas, Paenibacillus, Geobacillus, Virgibacillus, Jeotgalicoccus, Pullulanibacillus, Delsulfosporomusa, Citinovibrio, and Calditerricola were abundant in individuals from Nashik district.ConclusionOur work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals. creator: Renuka Potbhare creator: Ameeta RaviKumar creator: Eveliina Munukka creator: Leo Lahti creator: Richa Ashma uri: https://doi.org/10.7717/peerj.13075 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Potbhare et al. title: Whole-genome analysis of CGS, SAHH, SAMS gene families in five Rosaceae species and their expression analysis in Pyrus bretschneideri link: https://peerj.com/articles/13086 last-modified: 2022-03-16 description: Cystathionine γ-synthase (CGS), S-adenosyl-L-homocysteine hydrolase (SAHH), and S-adenosy-L-methionine synthetase (SAMS) play an important role in the regulation of plant growth, development, and secondary metabolism. In this study, a total of 6 CGS, 6 SAHH, and 28 SAMS genes were identified from five Rosaceae species (Pyrus bretschneideri, Prunus persica, Prunus mume, Fragaria vesca, and Malus domestica). The evolutionary relationship and microsynteny analysis in five Rosaceae species revealed that duplicated regions were conserved between three gene families (CGS, SAHH, SAMS). Moreover, the chromosomal locations, gene structures, conserved motifs, cis-elements, physicochemical properties, and Ka/Ks analysis were performed by using numerous bioinformatics tools. The expression of different organs showed that the CGS, SAHH and SAMS genes of pear have relatively high expression patterns in flowers and stems, except for PbCGS1. RNA-seq and qRT-PCR combined analysis showed that PbSAMS1 may be involved in the regulation of pear stone cell development. In summary, this study provides the basic information of CGS, SAHH and SAMS genes in five Rosaceae species, further revealing the expression patterns in the pear fruit, which provides the theoretical basis for the regulation of pear stone cells. creator: Yang Zhang creator: Decong Li creator: Xiaofeng Feng creator: Xinya Wang creator: Mengna Wang creator: Wenlong Han creator: Muhammad Aamir Manzoor creator: Guohui Li creator: Tianzhe Chen creator: Han Wang creator: Yongping Cai uri: https://doi.org/10.7717/peerj.13086 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Identification of potential biomarkers of vascular calcification using bioinformatics analysis and validation in vivo link: https://peerj.com/articles/13138 last-modified: 2022-03-16 description: BackgroundVascular calcification (VC) is the most widespread pathological change in diseases of the vascular system. However, we know poorly about the molecular mechanisms and effective therapeutic approaches of VC.MethodsThe VC dataset, GSE146638, was downloaded from the Gene Expression Omnibus (GEO) database. Using the edgeR package to screen Differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to find pathways affecting VC. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the DEGs. Meanwhile, using the String database and Cytoscape software to construct protein-protein interaction (PPI) networks and identify hub genes with the highest module scores. Correlation analysis was performed for hub genes. Receiver operating characteristic (ROC) curves, expression level analysis, GSEA, and subcellular localization were performed for each hub gene. Expression of hub genes in normal and calcified vascular tissues was verified by quantitative reverse transcription PCR (RT-qPCR) and immunohistochemistry (IHC) experiments. The hub gene-related miRNA-mRNA and TF-mRNA networks were constructed and functionally enriched for analysis. Finally, the DGIdb database was utilized to search for alternative drugs targeting VC hub genes.ResultsBy comparing the genes with normal vessels, there were 64 DEGs in mildly calcified vessels and 650 DEGs in severely calcified vessels. Spp1, Sost, Col1a1, Fn1, and Ibsp were central in the progression of the entire VC by the MCODE plug-in. These hub genes are primarily enriched in ossification, extracellular matrix, and ECM-receptor interactions. Expression level results showed that Spp1, Sost, Ibsp, and Fn1 were significantly highly expressed in VC, and Col1a1 was incredibly low. RT-qPCR and IHC validation results were consistent with bioinformatic analysis. We found multiple pathways of hub genes acting in VC and identified 16 targeting drugs.ConclusionsThis study perfected the molecular regulatory mechanism of VC. Our results indicated that Spp1, Sost, Col1a1, Fn1, and Ibsp could be potential novel biomarkers for VC and promising therapeutic targets. creator: Chuanzhen Chen creator: Yinteng Wu creator: Hai-lin Lu creator: Kai Liu creator: Xiao Qin uri: https://doi.org/10.7717/peerj.13138 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Study on the differences of phyllosphere microorganisms between poplar hybrid offspring and their parents link: https://peerj.com/articles/12915 last-modified: 2022-03-15 description: The females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microorganism of dioecious plants between parents and hybrid offspring remain largely unexplored. Here, the phyllosphere bacterial and fungal community diversity and composition of female (Populus nigra ‘DH5’ (PNDH5)), male (P. simonii ‘DH4’ (PSDH4)), and the hybrid offspring (P. simonii × P. nigra ‘DH1’ (PSPNDH1), P. simonii × P. nigra ‘DH2’ (PSPNDH2), P. simonii × P. nigra ‘DH3’ (PSPNDH3)) were investigated using 16S rDNA/ITS rDNA gene-based Illumina NovaSeq 6000 sequencing. There was considerable variation of plant height, diameter at breast height, leaf area, length of petioles, leaf moisture content, and starch among different samples, and PSDH2 owned the highest plant height, diameter at breast height, and length of petioles. No distinct differences of phyllosphere bacterial community diversity were observed among PSDH4, PNDH5, PSPNDH1, PSPNDH2, and PSPNDH3; while, PSPNDH2 owned the highest fungal Pielou_e index, Shannon index, and Simpson index. Firmicutes and Ascomycota were the predominant phyllosphere bacterial and fungal community at the phylum level, respectively. Bacilli and Gammaproteobacteria were the two most dominant bacterial classes regardless of parent and the hybrid offspring. The predominant phyllosphere fungal community was Dothideomycetes at the class level. The NMDS demonstrated that phyllosphere microbial community obviously differed between parents and offspring, while the phyllosphere microbial community presented some similarities under different hybrid progeny. Also, leaf characteristics contributed to the differentiation of phyllosphere bacterial and fungal communities between parents and hybrid offspring. These results highlighted the discrimination of phyllosphere microorganisms on parent and hybrid offspring, which provided clues to potential host-related species in the phyllosphere environment. creator: Changjun Ding creator: Weixi Zhang creator: Yanbo Wang creator: Mi Ding creator: Xiaojiang Wang creator: Aiping Li creator: Dejun Liang creator: Xiaohua Su uri: https://doi.org/10.7717/peerj.12915 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ding et al. title: CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments link: https://peerj.com/articles/12983 last-modified: 2022-03-15 description: BackgroundThroughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce.ResultsWe present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is designed with an emphasis on solving specific and common alignment problems and on providing transparency to the user.ConclusionCIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options. This tool can be used to fine-tune alignments for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs. creator: Charlotte Tumescheit creator: Andrew E. Firth creator: Katherine Brown uri: https://doi.org/10.7717/peerj.12983 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tumescheit et al. title: Diegoaelurus, a new machaeroidine (Oxyaenidae) from the Santiago Formation (late Uintan) of southern California and the relationships of Machaeroidinae, the oldest group of sabertooth mammals link: https://peerj.com/articles/13032 last-modified: 2022-03-15 description: Machaeroidinae is a taxonomically small clade of early and middle Eocene carnivorous mammals that includes the earliest known saber-toothed mammalian carnivores. Machaeroidine diversity is low, with only a handful of species described from North America and Asia. Here we report a new genus and species of machaeroidine, Diegoaelurus vanvalkenburghae, established on the basis of a nearly complete dentary with most of the dentition from the late Uintan (middle Eocene) portion of the Santiago Formation of southern California. The new taxon is the youngest known machaeroidine and provides the first evidence for the presence of multiple machaeroidine lineages, as it differs substantially from Apataelurus kayi, the only near-contemporaneous member of the group. Phylogenetic analysis indicates that Diegoaelurus is the sister taxon of Apataelurus, while older species are recovered as a monophyletic Machaeroides. Both phylogenetic results are relatively weakly supported. The new taxon extends the record of machaeroidines to the end of the Uintan, potentially tying machaeroidine extinction to the faunal turnover spanning the middle to late Eocene transition in North America. creator: Shawn P. Zack creator: Ashley W. Poust creator: Hugh Wagner uri: https://doi.org/10.7717/peerj.13032 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zack et al. title: Spinal-pelvic sagittal parameters in patients with gluteal muscle contracture: an imaging study link: https://peerj.com/articles/13093 last-modified: 2022-03-15 description: BackgroundGluteal muscle contracture (GMC) may cause abnormal spinal alignment as well as hip and pelvic deformities. The spine-pelvis alignment of GMC patients is unclear. This study aimed to describe the spine-pelvis sagittal alignment in patients with GMC and to explore the impact of GMC on the pathogenesis of low back pain (LBP).MethodsRadiological analysis was performed in 100 patients with GMC and 100 asymptomatic volunteers who acted as the control group. Sagittal parameters were measured by two independent raters and their averages were presented on lateral radiographs of the whole spine, including pelvic incidence (PI), sagittal vertical axis (SVA), pelvic tilt (PT), lumbar lordosis (LL), sacral slope (SS), thoracic kyphosis (TK), and the relationship between PI and LL (expressed as PI-LL). All cases were categorized into one of three classes based on the apex position of lumbar lordosis and were further divided into three groups by the PI value. The GMC and control parameters were compared and the correlations between the parameters in the GMC group were analysed.ResultsThe PI value of the GMC group was significantly less than that of the control group (42.38 ± 10.90° vs 45.68 ± 7.49°, P < 0.05). There was no difference found between the key parameters (SVA, PT, and PI-LL), which correlated with outcomes in adult deformity. No differences of SS were found between the two groups (P > 0.05). The GMC group showed lower average LL (42.77 ± 10.97° vs 46.41 ± 9.07°) and TK (17.34 ± 9.50° vs 20.45 ± 8.02°) compared with the control group (P < 0.05). LL was correlated with PI, SS, PT, TK (P < 0.01) and SVA (P < 0.05). TK and SVA were not correlated with any parameters except LL and pairwise correlations were found among PI, SS, and PT. There were no differences found between the distributions of the lumbar lordosis apex of GMC and the control but the range of SS in apex groups 3 and 4 did differ. GMC patients had the most small-PI value (44%) while approximately 64% of asymptomatic individuals had a normal PI. Interobserver variability was sufficient for all parameters calculated by the intraclass correlation coefficient (ICC).ConclusionsGluteal muscle contracture causes a low PI which may contribute to low back pain. Patients with GMC present the same global sagittal spinal-pelvic balance as asymptomatic individuals due to a compensatory mechanism through excessive flat lumbar and thoracic curves. Future studies on the relationship between spinal-pelvic sagittal and coronal alignment and low back pain are needed to understand the mechanical forces involved in the onset of GMC. creator: Jiyi Liu creator: Pengzhou Huang creator: Guanwei Jiang creator: Liang Gao creator: Mengdi Zhang creator: Xueping Dong creator: Wentao Zhang creator: Xintao Zhang uri: https://doi.org/10.7717/peerj.13093 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al.