title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=787 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Rediscovery of Laura’s glassfrog Nymphargus laurae (Anura: Centrolenidae) with new data on its morphology, colouration, phylogenetic position and conservation in Ecuador link: https://peerj.com/articles/12644 last-modified: 2021-12-23 description: We report the rediscovery of Laura’s Glassfrog, Nymphargus laurae Cisneros-Heredia & McDiarmid, 2007, based on two specimens collected at the Colonso-Chalupas Biological Reserve, province of Napo, Ecuador. The species was described and known from a single male specimen collected in 1955 at Loreto, north-eastern Andean foothills of Ecuador. Limited information was available about the colouration, systematics, ecology, and biogeography of N. laurae. We provide new data on the external morphology, colouration, distribution and comment on its conservation status and extinction risk. We discuss the phylogenetic relationships of N. laurae, which forms a clade together with N. siren and N. humboldti. The importance of research in unexplored areas must be a national priority to document the biodiversity associated, especially in protected areas. creator: María José Sánchez-Carvajal creator: Grace C. Reyes-Ortega creator: Diego F. Cisneros-Heredia creator: H. Mauricio Ortega-Andrade uri: https://doi.org/10.7717/peerj.12644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sánchez-Carvajal et al. title: Identification and molecular characterization of the alternative spliced variants of beta carbonic anhydrase 1 (βCA1) from Arabidopsis thaliana link: https://peerj.com/articles/12673 last-modified: 2021-12-23 description: Carbonic anhydrases (CAs) are ubiquitous zinc metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Higher plants mainly contain the three evolutionarily distinct CA families αCA, βCA, and γCA, with each represented by multiple isoforms. Alternative splicing (AS) of the CA transcripts is common. However, there is little information on the spliced variants of individual CA isoforms. In this study, we focused on the characterization of spliced variants of βCA1 from Arabidopsis. The expression patterns and subcellular localization of the individual spliced variants of βCA1 were examined. The results showed that the spliced variants of βCA1 possessed different subcellular and tissue distributions and responded differently to environmental stimuli. Additionally, we addressed the physiological role of βCA1 in heat stress response and its protein-protein interaction (PPI) network. Our results showed that βCA1 was regulated by heat stresses, and βca1 mutant was hypersensitive to heat stress, indicating a role for βCA1 in heat stress response. Furthermore, PPI network analysis revealed that βCA1 interacts with multiple proteins involved in several processes, including photosynthesis, metabolism, and the stress response, and these will provide new avenues for future investigations of βCA1. creator: Jinyu Shen creator: Zhiyong Li creator: Yajuan Fu creator: Jiansheng Liang uri: https://doi.org/10.7717/peerj.12673 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Shen et al. title: Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance link: https://peerj.com/articles/12683 last-modified: 2021-12-23 description: BackgroundSoil salinity is a major environmental stress that restricts crop growth and yield.MethodsHere, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum ‘Y1805’ using the data-independent acquisition proteomics techniques to explore its salt-tolerance mechanism.ResultsIn total, 44 and 102 differentially expressed proteins (DEPs) were identified in ‘Y1805’ under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. ‘Response to stimulus’, ‘antioxidant activity’, ‘carbohydrate metabolism’, ‘amino acid metabolism’, ‘signal transduction’, ‘transport and catabolism’ and ‘biosynthesis of other secondary metabolites’ were present under both conditions in ‘Y1805’. In addition, ‘energy metabolism’ and ‘lipid metabolism’ were recovery-specific pathways, while ‘antioxidant activity’, and ‘molecular function regulator’ under salt-stress conditions, and ‘virion’ and ‘virion part’ during recovery, were ‘Y1805’-specific compared with the salt-sensitive wheat ‘Chinese Spring’. ‘Y1805’ contained eight specific DEPs related to salt-stress responses. The strong salt tolerance of ‘Y1805’ could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat. creator: Rui Yang creator: Zhifen Yang creator: Ze Peng creator: Fang He creator: Luxi Shi creator: Yabing Dong creator: Mingjian Ren creator: Qingqin Zhang creator: Guangdong Geng creator: Suqin Zhang uri: https://doi.org/10.7717/peerj.12683 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective link: https://peerj.com/articles/12691 last-modified: 2021-12-23 description: BackgroundThere have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships.MethodsBuilding on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs.ResultsFrom the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests. creator: Jiajia Wang creator: Yu Bai creator: Haifeng Zhao creator: Ruinan Mu creator: Yan Dong uri: https://doi.org/10.7717/peerj.12691 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences link: https://peerj.com/articles/12707 last-modified: 2021-12-23 description: The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp. creator: Girum Fitihamlak Ejigu creator: Gangman Yi creator: Jong Im Kim creator: Jaehee Jung uri: https://doi.org/10.7717/peerj.12707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ejigu et al. title: Identifying biomarkers for evaluating wound extent and age in the contused muscle of rats using microarray analysis: a pilot study link: https://peerj.com/articles/12709 last-modified: 2021-12-23 description: Wound age estimation is still one of the most important and significant challenges in forensic practice. The extent of wound damage greatly affects the accuracy and reliability of wound age estimation, so it is important to find effective biomarkers to help diagnose wound degree and wound age. In the present study, the gene expression profiles of both mild and severe injuries in 33 rats were assayed at 0, 1, 3, 24, 48, and 168 hours using the Affymetrix microarray system to provide biomarkers for the evaluation of wound age and the extent of the wound. After obtaining thousands of differentially expressed genes, a principal component analysis, the least absolute shrinkage and selection operator, and a time-series analysis were used to select the most predictive prognostic genes. Finally, 15 genes were screened for evaluating the extent of wound damage, and the top 60 genes were also screened for wound age estimation in mild and severe injury. Selected indicators showed good diagnostic performance for identifying the extent of the wound and wound age in a Fisher discriminant analysis. A function analysis showed that the candidate genes were mainly related to cell proliferation and the inflammatory response, primarily IL-17 and the Hematopoietic cell lineage signalling pathway. The results revealed that these genes play an essential role in wound-healing and yield helpful and valuable potential biomarkers for further targeted studies. creator: Na Li creator: Chun Li creator: Dan Li creator: Li-hong Dang creator: Kang Ren creator: Qiu-xiang Du creator: Jie Cao creator: Qian-qian Jin creator: Ying-yuan Wang creator: Ru-feng Bai creator: Jun-hong Sun uri: https://doi.org/10.7717/peerj.12709 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea link: https://peerj.com/articles/12515 last-modified: 2021-12-22 description: Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other “typical” spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision. creator: Andreu Santín creator: María-Jesús Uriz creator: Javier Cristobo creator: Joana R. Xavier creator: Pilar Ríos uri: https://doi.org/10.7717/peerj.12515 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Santín et al. title: Development of a T-cell activation-related module with predictive value for the prognosis and immune checkpoint blockade therapy response in glioblastoma link: https://peerj.com/articles/12547 last-modified: 2021-12-22 description: BackgroundDespite the rise in the use of immune checkpoint blockade drugs (ICBs) in recent years, there are no ICB drugs that are currently approved or under large-scale clinical trials for glioblastoma (GBM). T-cells, which mainly mediate adaptive immunity, are an important part of the tumor immune microenvironment. The activation of T-cells in tumors plays a key role in evaluating the sensitivity of patients to immunotherapy. Therefore, we applied bioinformatics approaches to construct a T-cell activation related risk score to study the effect of the activation of T-cells on the prognosis and ICB response of patients with GBM.Materials and MethodsThis study collected TCGA, CGGA, and GSE16011 glioma cohorts, as well as the IMvigor210 immunotherapy dataset, with complete mRNA expression profiles and clinical information. GraphPad Prism 8 and R 3.6.3 were used for bioinformatics analysis and plotting.ResultsThe activation of T-cells in patients with GBM is characterized by obvious heterogeneity. We established a T-cell activation-related risk score based on five univariate Cox regression prognostic genes (CD276, IL15, SLC11A1, TNFSF4, and TREML2) in GBM. The risk score was an independent risk factor for poor prognosis. The overall survival time of patients in the high-risk group was significantly lower than in the low-risk group. Moreover, the high-risk score was accompanied by a stronger immune response and a more complex tumor immune microenvironment. “Hot tumors” were mainly enriched in the high-risk group, and high-risk group patients highly expressed inhibitory immune checkpoints (PD1, PD-L1, TIM3 etc.). By combining the risk and priming scores we obtained the immunotherapy score, which was shown to be a good evaluation index for sensitivity to GBM immunotherapy.ConclusionsAs an independent risk factor for poor prognosis, the T-cell activation-related risk score, combined with other clinical characteristics, could efficiently evaluate the survival of patients with GBM. The immunotherapy score obtained by combining the risk and priming scores could evaluate the ICB response of patients with GBM, providing treatment opportunities. creator: Zihao Yan creator: Siwen Chu creator: Chen Zhu creator: Yunhe Han creator: Qingyu Liang creator: Shuai Shen creator: Wen Cheng creator: Anhua Wu uri: https://doi.org/10.7717/peerj.12547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yan et al. title: The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance link: https://peerj.com/articles/12563 last-modified: 2021-12-22 description: Insects are the most widespread group of organisms and more than one million species have been described. These animals have significant ecological functions, for example they are pollinators of many types of plants. However, they also have direct influence on human life in different manners. They have high medical and veterinary significance, stemming from their role as vectors of disease and infection of wounds and necrotic tissue; they are also plant pests, parasitoids and predators whose activities can influence agriculture. In addition, their use in medical treatments, such as maggot therapy of gangrene and wounds, has grown considerably. They also have many uses in forensic science to determine the minimum post-mortem interval and provide valuable information about the movement of the body, cause of the death, drug use, or poisoning. It has also been proposed that they may be used as model organisms to replace mammal systems in research. The present review describes the role of free fatty acids (FFAs) in key physiological processes in insects. By focusing on insects of medical, veterinary significance, we have limited our description of the physiological processes to those most important from the point of view of insect control; the study examines their effects on insect reproduction and resistance to the adverse effects of abiotic (low temperature) and biotic (pathogens) factors. creator: Agata Kaczmarek creator: Mieczysława Boguś uri: https://doi.org/10.7717/peerj.12563 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kaczmarek and Boguś title: Wearable technology to inform the prediction and diagnosis of cardiorespiratory events: a scoping review link: https://peerj.com/articles/12598 last-modified: 2021-12-22 description: BackgroundThe need for health systems that allow for continuous monitoring and early adverse event detection in individuals outside of the acute care setting has been highlighted by the global rise in chronic cardiorespiratory diseases and the recent COVID-19 pandemic. Currently, it is unclear what type of evidence exists concerning the use of physiological data collected from commercially available wrist and textile wearables to assist in clinical decision making. The aim of this review was therefore to systematically map and summarize the scientific literature surrounding the use of these wearables in clinical decision making as well as identify knowledge gaps to inform further research.MethodologySix electronic bibliographic databases were systematically searched (Ovid MEDLINE, EMBASE, CINAHL, PubMed, Scopus, and SportsDiscus). Publications from database inception to May 6, 2020 were reviewed for inclusion. Non-indexed literature relevant to this review was also searched systematically. Results were then collated, summarized and reported.ResultsA total of 107 citations were retrieved and assessed for eligibility with 31 citations included in the final analysis. A review of the 31 papers revealed three major study designs which included (1) observational studies (n = 19), (2) case control series and reports (n = 8), and (3) reviews (n = 2). All papers examined the use of wearable monitoring devices for clinical decisions in the cardiovascular domain, with cardiac arrhythmias being the most studied. When compared to electrocardiogram (ECG) the performance of the wearables in facilitating clinical decisions varied depending upon the type of wearable, user’s activity levels and setting in which they were employed. Observational studies collecting data in the inpatient and outpatient settings were equally represented. Eight case control series and reports were identified which reported on the use of wrist wearables in patients presenting to an emergency department or clinic to aid in the clinical diagnosis of a cardiovascular event. Two narrative reviews were identified which examined the impact of wearable devices in monitoring cardiovascular disease as well as potential challenges they may pose in the future.ConclusionsTo date, studies employing wearables to facilitate clinical decisions have largely focused upon the cardiovascular domain. Despite the ability of some wearables to collect physiological data accurately, there remains a need for a specialist physician to retrospectively review the raw data to make a definitive diagnosis. Analysis of the results has also highlighted gaps in the literature such as the absence of studies employing wearables to facilitate clinical decisions in the respiratory domain. The disproportionate study of wearables in atrial fibrillation detection in comparison to other cardiac arrhythmias and conditions, as well as the lack of diversity in the sample populations used prevents the generalizability of results. creator: Hamzeh Khundaqji creator: Wayne Hing creator: James Furness creator: Mike Climstein uri: https://doi.org/10.7717/peerj.12598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Khundaqji et al.