title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=693 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The DNA methylation landscape of five pediatric-tumor types link: https://peerj.com/articles/13516 last-modified: 2022-06-10 description: Fewer DNA mutations have been identified in pediatric tumors than in adult tumors, suggesting that alternative tumorigenic mechanisms, including aberrant DNA methylation, may play a prominent role. In one epigenetic process of regulating gene expression, methyl groups are attached at the 5-carbon of the cytosine ring, leading to 5-methylcytosine (5mC). In somatic cells, 5mC occurs mostly in CpG islands, which are often within promoter regions. In Wilms tumors and acute myeloid leukemias, increased levels of epigenetic silencing have been associated with worse patient outcomes. However, to date, researchers have studied methylation primarily in adult tumors and for specific genes—but not on a pan-pediatric cancer scale. We addressed these gaps first by aggregating methylation data from 309 noncancerous samples, establishing baseline expectations for each probe and gene. Even though these samples represent diverse, noncancerous tissue types and population ancestral groups, methylation levels were consistent for most genes. Second, we compared tumor methylation levels against the baseline values for 489 pediatric tumors representing five cancer types: Wilms tumors, clear cell sarcomas of the kidney, rhabdoid tumors, neuroblastomas, and osteosarcomas. Tumor hypomethylation was more common than hypermethylation, and as many as 41.7% of genes were hypomethylated in a given tumor, compared to a maximum of 34.2% for hypermethylated genes. However, in known oncogenes, hypermethylation was more than twice as common as in other genes. We identified 139 probes (31 genes) that were differentially methylated between at least one tumor type and baseline levels, and 32 genes that were differentially methylated across the pediatric tumor types. We evaluated whether genomic events and aberrant methylation were mutually exclusive but did not find evidence of this phenomenon. creator: Alyssa C. Parker creator: Badí I. Quinteros creator: Stephen R. Piccolo uri: https://doi.org/10.7717/peerj.13516 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Parker et al. title: Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia link: https://peerj.com/articles/13522 last-modified: 2022-06-10 description: IntroductionA global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health.MethodsData were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia.ResultsPhylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein).ConclusionOur findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health. creator: Muhammad Nasrum Massi creator: Rufika Shari Abidin creator: Abd-ElAziem Farouk creator: Handayani Halik creator: Gita Vita Soraya creator: Najdah Hidayah creator: Rizalinda Sjahril creator: Irda Handayani creator: Mohamad Saifudin Hakim creator: Faris Muhammad Gazali creator: Vivi Setiawaty creator: Tri Wibawa uri: https://doi.org/10.7717/peerj.13522 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Massi et al. title: Genome-wide analysis of the strigolactone biosynthetic and signaling genes in grapevine and their response to salt and drought stresses link: https://peerj.com/articles/13551 last-modified: 2022-06-10 description: Strigolactones (SLs) are a novel class of plant hormones that play critical roles in regulating various developmental processes and stress tolerance. Although the SL biosynthetic and signaling genes were already determined in some plants such as Arabidopsis and rice, the information of SL-related genes in grapevine (Vitis vinifera L.) remains largely unknown. In this study, the SL-related genes were identified from the whole grapevine genome, and their expression patterns under salt and drought stresses were determined. The results indicated that the five genes that involved in the SL biosynthesis included one each of the D27, CCD7, CCD8, MAX1 and LBO genes, as well as the three genes that involved in the SL signaling included one each of the D14, MAX2, D53 genes. Phylogenetic analysis suggested that these SL-related proteins are highly conserved among different plant species. Promoter analysis showed that the prevalence of a variety of cis-acting elements associated with hormones and abiotic stress existed in the promoter regions of these SL-related genes. Furthermore, the transcription expression analysis demonstrated that most SL-related genes are involved in the salt and drought stresses response in grapevine. These findings provided valuable information for further investigation and functional analysis of SL biosynthetic and signaling genes in response to salt and drought stresses in grapevine. creator: Yanyan Yu creator: Jinghao Xu creator: Chuanyin Wang creator: Yunning Pang creator: Lijian Li creator: Xinjie Tang creator: Bo Li creator: Qinghua Sun uri: https://doi.org/10.7717/peerj.13551 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yu et al. title: Antibiotic perturbation of gut bacteria does not significantly alter host responses to ocular disease in a songbird species link: https://peerj.com/articles/13559 last-modified: 2022-06-10 description: Bacterial communities in and on wild hosts are increasingly appreciated for their importance in host health. Through both direct and indirect interactions, bacteria lining vertebrate gut mucosa provide hosts protection against infectious pathogens, sometimes even in distal body regions through immune regulation. In house finches (Haemorhous mexicanus), the bacterial pathogen Mycoplasma gallisepticum (MG) causes conjunctivitis, with ocular inflammation mediated by pro- and anti-inflammatory cytokines and infection triggering MG-specific antibodies. Here, we tested the role of gut bacteria in host responses to MG by using oral antibiotics to perturb bacteria in the gut of captive house finches prior to experimental inoculation with MG. We found no clear support for an impact of gut bacterial disruption on conjunctival pathology, MG load, or plasma antibody levels. However, there was a non-significant trend for birds with intact gut communities to have greater conjunctival pathology, suggesting a possible impact of gut bacteria on pro-inflammatory cytokine stimulation. Using 16S bacterial rRNA amplicon sequencing, we found dramatic differences in cloacal bacterial community composition between captive, wild-caught house finches in our experiment and free-living finches from the same population, with lower bacterial richness and core communities composed of fewer genera in captive finches. We hypothesize that captivity may have affected the strength of results in this experiment, necessitating further study with this consideration. The abundance of anthropogenic impacts on wildlife and their bacterial communities, alongside the emergence and spread of infectious diseases, highlights the importance of studies addressing the role of commensal bacteria in health and disease, and the consequences of gut bacterial shifts on wild hosts. creator: Chava L. Weitzman creator: Lisa K. Belden creator: Meghan May creator: Marissa M. Langager creator: Rami A. Dalloul creator: Dana M. Hawley uri: https://doi.org/10.7717/peerj.13559 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Weitzman et al. title: A European giant: a large spinosaurid (Dinosauria: Theropoda) from the Vectis Formation (Wealden Group, Early Cretaceous), UK link: https://peerj.com/articles/13543 last-modified: 2022-06-09 description: Postcranial elements (cervical, sacral and caudal vertebrae, as well as ilium, rib and limb bone fragments) belonging to a gigantic tetanuran theropod were recovered from the basal unit (the White Rock Sandstone equivalent) of the Vectis Formation near Compton Chine, on the southwest coast of the Isle of Wight. These remains appear to pertain to the same individual, with enormous dimensions similar to those of the Spinosaurus holotype and exceeding those of the largest European theropods previously reported. A combination of features—including the presence of spinodiapophyseal webbing on an anterior caudal vertebra—suggest that this is a member of Spinosauridae, though a lack of convincing autapomorphies precludes the identification of a new taxon. Phylogenetic analysis supports spinosaurid affinities but we were unable to determine a more precise position within the clade weak support for a position within Spinosaurinae or an early-diverging position within Spinosauridae were found in some data runs. Bioerosion in the form of curved tubes is evident on several pieces, potentially related to harvesting behaviour by coleopteran bioeroders. This is the first spinosaurid reported from the Vectis Formation and the youngest British material referred to the clade. This Vectis Formation spinosaurid is unusual in that the majority of dinosaurs from the Lower Cretaceous units of the Wealden Supergroup are from the fluviolacustrine deposits of the underlying Barremian Wessex Formation. In contrast, the lagoonal facies of the upper Barremian–lower Aptian Vectis Formation only rarely yield dinosaur material. Our conclusions are in keeping with previous studies that emphasise western Europe as a pivotal region within spinosaurid origination and diversification. creator: Chris T. Barker creator: Jeremy A.F. Lockwood creator: Darren Naish creator: Sophie Brown creator: Amy Hart creator: Ethan Tulloch creator: Neil J. Gostling uri: https://doi.org/10.7717/peerj.13543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Barker et al. title: The LINC00261/MiR105-5p/SELL axis is involved in dysfunction of B cell and is associated with overall survival in hepatocellular carcinoma link: https://peerj.com/articles/12588 last-modified: 2022-06-09 description: BackgroundPrevious studies have been reported the immune dysfunction of various live tissues. However, the potential molecular mechanism of post-transcriptional regulation of immune related genes in hepatocellular carcinoma (HCC) is still not clear. We tried to identify crucial immune related biomarkers associated with HCC patients’ outcomes and to reveal the transcriptional regulation.MethodThe fractions of 22 immune cells in tumor and adjacent tissues were estimated by CIBERSORT. Kruskal-Wallis test and differentially expressed analyzes were used for comparative studies. Cox proportional hazard regression model, Kaplan-Meier estimates and Log-rank test were used for survival analyses.ResultsFrom The Cancer Genome Atlas (TCGA), the gene, lncRNA and miRNA expression profiles of 379 HCC samples with clinical information were used for comparative studies. Eleven adaptive and innate immune cell types were significantly altered in HCC samples, including B cell memory, regulatory T cells and follicular helper T cells. Differentially expressed competing endogenous RNA (ceRNA) network associated with patients’ overall survival was identified. Then, the novel pathway, including LINC00261, MiR105-5p and selectin L(SELL) was found and may be potential novel biomarkers for patients’ outcomes and immunotherapy. Furthermore, SELL was significantly positively correlated (correlation coefficients: 0.47–0.69) with 12 known gene signatures of immunotherapy except for programmed cell death 1 (PDCD1).ConclusionsOur findings could provide insights into the selection of novel LINC00261/MiR105-5p/SELL pathway which is associated with overall survival and may impact on efficacy of immunotherapy in HCC. creator: Hao Song creator: Xing-Feng Huang creator: Shu-yang Hu creator: Lei-Lei Lu creator: Xiao-Yu Yang uri: https://doi.org/10.7717/peerj.12588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Song et al. title: Pollinator identity and behavior affect pollination in kiwifruit (Actinidia chinensis Planch.) link: https://peerj.com/articles/12963 last-modified: 2022-06-09 description: Many crop plants rely on insect pollination, particularly insect-pollinated crops which are functionally dioecious. These crops require insects to move pollen between separate plants which are functionally male or female. While honey bees are typically considered the most important crop pollinator species, many other insects are known to visit crops but the pollination contribution of the full diversity of these flower visitors is poorly understood. In this study, we examine the role of diverse insect pollinators for two kiwifruit cultivars as model systems for dioecious crops: Actinidia chinensis var. deliciosa ‘Hayward’ (a green-fleshed variety) and A. chinensis var. chinensis ‘Zesy002’ (a gold-fleshed variety). In our round-the-clock insect surveys, we identified that psychodid flies and mosquitoes were the second and third most frequent floral visitors after honey bees (Apis mellifera L), but further work is required to investigate their pollination efficiency. Measures of single-visit pollen deposition identified that several insects, including the bees Leioproctus spp. and Bombus spp. and the flies Helophilus hochstetteri and Eristalis tenax, deposited a similar amount of pollen on flowers as honey bees (Apis mellifera). Due to their long foraging period and high pollen deposition, we recommend the development of strategies to boost populations of Bombus spp., Eristalis tenax and other hover flies, and unmanaged bees for use as synergistic pollinators alongside honey bees. creator: Melissa A. Broussard creator: Brad G. Howlett creator: Lisa J. Evans creator: Heather McBrydie creator: Brian T. Cutting creator: Samantha F.J. Read creator: David E. Pattemore uri: https://doi.org/10.7717/peerj.12963 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Broussard et al. title: Long noncoding RNA Gm31629 promotes bone regeneration by maintaining bone marrow mesenchymal stem cells activity link: https://peerj.com/articles/13475 last-modified: 2022-06-09 description: BackgroundLong noncoding RNA Gm31629 can regulate hypothalamic neural stem cells (htNSCs) senescence and the aging process. However, the effect of Gm31629 on the senescence of bone marrow mesenchymal stem cells (BMSCs) and bone regeneration is unclear. In the present study, we investigated the effects of Gm31629 on the senescence of BMSCs and bone regeneration.MethodsGm31629 knockout (Gm31629-KO) and wild-type (WT) mice were used to establish a bone regeneration model. The Brdu labelling, CCK8 assay, wound healing assay, β-gal staining and osteogenic differentiation assay were used to assess the effects of Gm31629 on the functions of BMSCs. Micro-computed tomography (CT), histochemical and immunohistochemical staining were used to evaluate the ability of bone regeneration. The mimic of Gm31629, theaflavin 3-gallate, was used to investigate its role on the senescence of BMSCs and bone regeneration.ResultsThe expression of Gm31629 reduced in BMSCs of middle-aged mice was compared with that of young mice. The deletion of Gm31629 was sufficient to drive the senescence of BMSCs, resulting in impaired bone regeneration in mice. Mechanistically, Gm31629 could interact with Y-box protein 1(YB-1) and delay its degradation, decreasing the transcription of p16INK4A of BMSCs. We also found that theaflavin 3-gallate could alleviate the senescence of BMSCs and promote bone regeneration in middle-aged mice.ConclusionThese results indicated that Gm31629 played an important role on BMSCs senescence and bone regeneration and provided a therapeutic target to promote bone regeneration. creator: Guangping Cai creator: Ye Xiao creator: Mi Yang creator: Qi Guo creator: Tian Su creator: Yalin Liu creator: Tiejian Jiang creator: Chun Li uri: https://doi.org/10.7717/peerj.13475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cai et al. title: Use of semantic segmentation for mapping Sargassum on beaches link: https://peerj.com/articles/13537 last-modified: 2022-06-09 description: The unusual arrival of Sargassum on Caribbean beaches is an emerging problem that has generated numerous challenges. The monitoring, visualization, and estimation of Sargassum coverage on the beaches remain a constant complication. This study proposes a new mapping methodology to estimate Sargassum coverage on the beaches. Semantic segmentation of geotagged photographs allows the generation of accurate maps showing the percent coverage of Sargassum. The first dataset of segmented Sargassum images was built for this study and used to train the proposed model. The results demonstrate that the currently proposed method has an accuracy of 91%, improving on the results reported in the state-of-the-art method where data was also collected through a crowdsourcing scheme, in which only information on the presence and absence of Sargassum is displayed. creator: Javier Arellano-Verdejo creator: Martin Santos-Romero creator: Hugo E. Lazcano-Hernandez uri: https://doi.org/10.7717/peerj.13537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Arellano-Verdejo et al. title: Role of active joint position sense on the upper extremity functional performance tests in college volleyball players link: https://peerj.com/articles/13564 last-modified: 2022-06-09 description: BackgroundIt has been well established that proprioception plays a decisive role in shoulder stability and sport performance. Notwithstanding, there is a lack of clear association between active joint position sense (AJPS) and the performance of upper-extremity functional performance tests. The aim of this study was to determine whether the AJPS of the shoulder complex is associated with the performance of college volleyball players with the following functional tests: Y-Balance Test-Upper Quarter (YBT-UQ), Closed Kinetic Chain Upper-Extremity Stability Test (CKCUEST), and Seated Medicine Ball Throw (SMBT). The secondary aim was to investigate whether the magnitude of the proprioception error through the AJPS had the ability to act as a predictor for functional test scores.MethodsCross-sectional study with a convenience sampling. Healthy college volleyball players (≥12 h of training/week), 30 males and 22 females, between 18 and 26 years of age were included. AJPS of the shoulder (90° of flexion (90°Flex), 90° of internal rotation at 90° of abduction (90°IR/ABD), 90° of external rotation at 90° of abduction (90°ER/ABD)) and three upper-extremity functional performance tests (YBT-UQ, CKCUEST and SMBT) were assessed. A Pearson’s test and a stepwise multiple linear regression analysis were used to determine possible associations and relationships between outcome measures, respectively.ResultsThe analysis revealed that AJPS at 90°IR/ABD and 90°ER/ABD were the only proprioceptive variables with an association to the YBT-UQ and SMBT. Despite these relationships, only the AJPS at 90°IR/ABD was associated with the performance of the YBT-UQ in; superolateral direction (β = −0.7; 95% CI [−1.3 to 0.1]; p = 0.025); inferolateral direction (β = −1.5; 95% CI [−2.1 to −0.8]; p = 0.001); and composite score (β = −0.8; 95% CI [−1.3 to −0.3]; p = 0.002). From these, AJPS at 90°IR/ABD mainly explained the variability of YBT-UQ (inferolateral direction) performance (R2 = 0.32; %R2 = 0.32). Our findings allow for a possible expanded role for proprioception as a contributing factor in upper limb motor control during functional movements. Further research is required to explore and distinguish the associations between proprioception, motor control and sport performance involving the upper limbs. creator: Guillermo Mendez-Rebolledo creator: Amanda L. Ager creator: Diana Ledezma creator: Julieta Montanez creator: Juan Guerrero-Henriquez creator: Carlos Cruz-Montecinos uri: https://doi.org/10.7717/peerj.13564 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mendez-Rebolledo et al.