title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=286 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures link: https://peerj.com/articles/17710 last-modified: 2024-07-09 description: As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds. creator: Jundie Zhai creator: You Wang creator: Boyu Tang creator: Sisi Zheng creator: Shunfu He creator: Wenxin Zhao creator: Jun Lin creator: Feng Li creator: Yuzi Bao creator: Zhuoma Lancuo creator: Chuanfa Liu creator: Wen Wang uri: https://doi.org/10.7717/peerj.17710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhai et al. title: Green nanobiocatalysts: enhancing enzyme immobilization for industrial and biomedical applications link: https://peerj.com/articles/17589 last-modified: 2024-07-08 description: Nanobiocatalysts (NBCs), which merge enzymes with nanomaterials, provide a potent method for improving enzyme durability, efficiency, and recyclability. This review highlights the use of eco-friendly synthesis methods to create sustainable nanomaterials for enzyme transport. We investigate different methods of immobilization, such as adsorption, ionic and covalent bonding, entrapment, and cross-linking, examining their pros and cons. The decreased environmental impact of green-synthesized nanomaterials from plants, bacteria, and fungi is emphasized. The review exhibits the various uses of NBCs in food industry, biofuel production, and bioremediation, showing how they can enhance effectiveness and eco-friendliness. Furthermore, we explore the potential impact of NBCs in biomedicine. In general, green nanobiocatalysts are a notable progression in enzyme technology, leading to environmentally-friendly and effective biocatalytic methods that have important impacts on industrial and biomedical fields. creator: Doaa S. R. Khafaga creator: Ghazala Muteeb creator: Abdullrahman Elgarawany creator: Mohammad Aatif creator: Mohd Farhan creator: Salma Allam creator: Batool Abdulhadi Almatar creator: Mohamed G. Radwan uri: https://doi.org/10.7717/peerj.17589 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Khafaga et al. title: Morphology and vocalization comparison of the Houston Toad and the Dwarf American Toad: implications for their historic range link: https://peerj.com/articles/17635 last-modified: 2024-07-08 description: Documenting changes in the distribution and abundance of a given taxon requires historical data. In the absence of long-term monitoring data collected throughout the range of a taxon, conservation biologists often rely on preserved museum specimens to determine the past or present, putative geographic distribution. Distributional data for the Houston Toad (Anaxyrus houstonensis) has consistently been confounded by similarities with a sympatric congener, the Dwarf American Toad (A. americanus charlesmithi), both in monitoring data derived from chorusing surveys, and in historical data via museum specimens. In this case, misidentification can have unintended impacts on conservation efforts, where the Houston Toad is federally endangered, and the Dwarf American Toad is of least concern. Previously published reports have compared these two taxon on the basis of their male advertisement call and morphological appearance, often with the goal of using these characters to substantiate their taxonomic status prior to the advent of DNA sequencing technology. However, numerous studies report findings that contradict one another, and no consensus on the true differences or similarities can be drawn. Here, we use contemporary recordings of wild populations of each taxon to test for quantifiable differences in male advertisement call. Additionally, we quantitatively examine a subset of vouchered museum specimens representing each taxon to test previously reported differentiating morphometric characters used to distinguish among other Bufonids of East-Central Texas, USA. Finally, we assemble and qualitatively evaluate a database of photographs representing catalogued museum vouchers for each taxon to determine if their previously documented historic ranges may be larger than are currently accepted. Our findings reveal quantifiable differences between two allopatric congeners with respect to their male advertisement call, whereas we found similarities among their detailed morphology. Additionally, we report on the existence of additional, historically overlooked, museum records for the Houston Toad in the context of its putative historic range, and discuss errors associated with the curation of these specimens whose identity and nomenclature have not been consistent through time. These results bookend decades of disagreement regarding the morphology, voice, and historic distribution of these taxa, and alert practitioners of conservation efforts for the Houston Toad to previously unreported locations of occurrence. creator: Andrew R. MacLaren creator: Toby J. Hibbitts creator: Michael R.J. Forstner creator: Shawn F. McCracken uri: https://doi.org/10.7717/peerj.17635 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 MacLaren et al. title: Establishing Silphids in the invertebrate DNA toolbox: a proof of concept link: https://peerj.com/articles/17636 last-modified: 2024-07-08 description: Environmental DNA (eDNA) analyses are an increasingly popular tool for assessing biodiversity. eDNA sampling that uses invertebrates, or invertebrate DNA (iDNA), has become a more common method in mammal biodiversity studies where biodiversity is assessed via diet analysis of different coprophagous or hematophagous invertebrates. The carrion feeding family of beetles (Silphidae: Coleoptera, Latreille (1807)), have not yet been established as a viable iDNA source in primary scientific literature, yet could be useful indicators for tracking biodiversity in forested ecosystems. Silphids find carcasses of varying size for both food and reproduction, with some species having host preference for small mammals; therefore, iDNA Silphid studies could potentially target small mammal communities. To establish the first valid use of iDNA methods to detect Silphid diets, we conducted a study with the objective of testing the validity of iDNA methods applied to Silphids using both Sanger sequencing and high throughput Illumina sequencing. Beetles were collected using inexpensive pitfall traps in Alberta, Michigan in 2019 and 2022. We successfully sequenced diet DNA and environmental DNA from externally swabbed Silphid samples and diet DNA from gut dissections, confirming their potential as an iDNA tool in mammalian studies. Our results demonstrate the usefulness of Silphids for iDNA research where we detected species from the genera Anaxyrus, Blarina, Procyon, Condylura, Peromyscus, Canis, and Bos. Our results highlight the potential for Silphid iDNA to be used in future wildlife surveys. creator: Katherine E. Higdon creator: Kristin E. Brzeski creator: Melanie A. Ottino creator: Tara L. Bal uri: https://doi.org/10.7717/peerj.17636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Higdon et al. title: Unraveling genomic features and phylogenomics through the analysis of three Mexican endemic Myotis genomes link: https://peerj.com/articles/17651 last-modified: 2024-07-08 description: BackgroundGenomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data for bat species hinder insights into their evolutionary processes, particularly within the diverse Myotis genus of the Vespertilionidae family. In Mexico, 15 Myotis species exist, with three—M. vivesi, M. findleyi, and M. planiceps—being endemic and of conservation concern.MethodsWe obtained samples of Myotis vivesi, M. findleyi, and M. planiceps for genomic analysis. Each of three genomic DNA was extracted, sequenced, and assembled. The scaffolding was carried out utilizing the M. yumanensis genome via a genome-referenced approach within the ntJoin program. GapCloser was employed to fill gaps. Repeat elements were characterized, and gene prediction was done via ab initio and homology methods with MAKER pipeline. Functional annotation involved InterproScan, BLASTp, and KEGG. Non-coding RNAs were annotated with INFERNAL, and tRNAscan-SE. Orthologous genes were clustered using Orthofinder, and a phylogenomic tree was reconstructed using IQ-TREE.ResultsWe present genome assemblies of these endemic species using Illumina NovaSeq 6000, each exceeding 2.0 Gb, with over 90% representing single-copy genes according to BUSCO analyses. Transposable elements, including LINEs and SINEs, constitute over 30% of each genome. Helitrons, consistent with Vespertilionids, were identified. Values around 20,000 genes from each of the three assemblies were derived from gene annotation and their correlation with specific functions. Comparative analysis of orthologs among eight Myotis species revealed 20,820 groups, with 4,789 being single copy orthogroups. Non-coding RNA elements were annotated. Phylogenomic tree analysis supported evolutionary chiropterans’ relationships. These resources contribute significantly to understanding gene evolution, diversification patterns, and aiding conservation efforts for these endangered bat species. creator: Edgar G. Gutiérrez creator: Jesus E. Maldonado creator: Gabriela Castellanos-Morales creator: Luis E. Eguiarte creator: Norberto Martínez-Méndez creator: Jorge Ortega uri: https://doi.org/10.7717/peerj.17651 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gutiérrez et al. title: Mechanism of action of miR-15a-5p and miR-152-3p in paraquat-induced pulmonary fibrosis through Wnt/β-catenin signaling mediation link: https://peerj.com/articles/17662 last-modified: 2024-07-08 description: BackgroundmiRNAs are small, conserved, single-stranded non-coding RNA that are typically transported by exosomes for their functional roles. The therapeutic potential of exosomal miRNAs has been explored in various diseases including breast cancer, pancreatic cancer, cholangiocarcinoma, skin diseases, Alzheimer’s disease, stroke, and glioma. Pathophysiological processes such as cellular inflammation, apoptosis, necrosis, immune dysfunction, and oxidative stress are closely associated with miRNAs. Internal and external factors such as tissue ischemia, hypoxia, pathogen infection, and endotoxin exposure can trigger these reactions and are linked to miRNAs. Paraquat-induced fibrosis is a protracted process that may not manifest immediately after injury but develops during bodily recovery, providing insights into potential miRNA intervention treatments.RationaleThese findings could potentially be applied for further pharmaceutical research and clinical therapy of paraquat-induced pulmonary fibrosis, and are likely to be of great interest to clinicians involved in lung fibrosis research.MethodologyThrough a literature review, we identified an association between miR-15a-5p and miR-152-3p and their involvement in the Wnt signaling pathway. This allowed us to deduce the molecular mechanisms underlying regulatory interactions involved in paraquat-induced lung fibrosis.ResultsmiR-15a-5p and miR-152-3p play roles in body repair processes, and pulmonary fibrosis can be considered a form of reparative response by the body. Although the initial purpose of fibrotic repair is to restore normal body function, excessive tissue fibrosis, unlike scar formation following external skin trauma, can significantly and adversely affect the body. Modulating the Wnt/β-catenin signaling pathway is beneficial in alleviating tissue fibrosis in various diseases.ConclusionsIn this study, we delineate the association between miR-15a-5p and miR-152-3p and the Wnt/β-catenin signaling pathway, presenting a novel concept for addressing paraquat-induced pulmonary fibrosis. creator: Dong Liu creator: Yan Guan uri: https://doi.org/10.7717/peerj.17662 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu and Guan title: Response of growth and physiological enzyme activities in Eriogyna pyretorum to various host plants link: https://peerj.com/articles/17680 last-modified: 2024-07-08 description: Morphological attributes and chemical composition of host plants shape growth and development of phytophagous insects via influences on their behavior and physiological processes. This research delves into the relationship between Eriogyna pyretorum and various host plants through studuying how feeding on different host tree species affect growth, development, and physiological enzyme activities. We examined E. pyretorum response to three distinct host plants: Camphora officinarum, Liquidambar formosana and Pterocarya stenoptera. Notably, larvae feeding on C. officinarum and L. formosana displayed accelerated development, increased pupal length, and higher survival rates compared to those on P. stenoptera. This underlines the pivotal role of host plant selection in shaping the E. pyretorum’s life cycle. The activities of a-amylase, lipase and protective enzymes were the highest in larvae fed on the most suitable host L. formosana which indicated that the increase of these enzyme activities was closely related to growth and development. Furthermore, our investigation revealed a relationship between enzymatic activities and host plants. Digestive enzymes, protective enzymes, and detoxifying enzymes exhibited substantial variations contingent upon the ingested host plant. Moreover, the total phenolics content in the host plant leaves manifested a noteworthy positive correlation with catalase and lipase activities. In contrast, a marked negative correlation emerged with glutathione S-transferase and α-amylase activities. The total developmental duration of larvae exhibited a significant positive correlation with the activities of GST and CarE. The survival rate of larvae showed a significant positive correlation with CYP450. These observations underscore the insect’s remarkable adaptability in orchestrating metabolic processes in accordance with available nutritional resources. This study highlights the interplay between E. pyretorum and its host plants, offering novel insights into how different vegetation types influence growth, development, and physiological responses. These findings contribute to a deeper comprehension of insect-plant interactions, with potential applications in pest management and ecological conservation. creator: Haoyu Lin creator: Songkai Liao creator: Hongjian Wei creator: Qi Wang creator: Xinjie Mao creator: Jiajin Wang creator: Shouping Cai creator: Hui Chen uri: https://doi.org/10.7717/peerj.17680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Expression profile analysis of cotton fiber secondary cell wall thickening stage link: https://peerj.com/articles/17682 last-modified: 2024-07-08 description: To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17–24, with long fibers labeled as L, and 62–33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17–24 (L) and 62–33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17–24 (L) and 62–33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton. creator: Li Liu creator: Corrinne E. Grover creator: Xianhui Kong creator: Josef Jareczek creator: Xuwen Wang creator: Aijun Si creator: Juan Wang creator: Yu Yu creator: Zhiwen Chen uri: https://doi.org/10.7717/peerj.17682 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Changes in the composition of invertebrate assemblages from wave-exposed intertidal mussel stands along the Nova Scotia coast, Canada link: https://peerj.com/articles/17697 last-modified: 2024-07-08 description: Rocky intertidal habitats occur worldwide and are mainly characterized by primary space holders such as seaweeds and sessile invertebrates. Some of these organisms are foundation species, as they can form structurally complex stands that host many small invertebrates. The abundance of primary space holders is known to vary along coastlines driven directly or indirectly by environmental variation. However, it is less clear if the invertebrate assemblages associated to a foundation species may remain relatively unchanged along coastlines, as similar stands of a foundation species can generate similar microclimates. We examined this question using abundance data for invertebrate species found in mussel stands of a similar structure in wave-exposed rocky habitats at mid-intertidal elevations along the Atlantic coast of Nova Scotia (Canada). While the most abundant invertebrate species were found at three locations spanning 315 km of coastline, species composition (a combined measure of species identity and their relative abundance) differed significantly among the locations. One of the species explaining the highest amount of variation among locations (a barnacle) exhibited potential signs of bottom-up regulation involving pelagic food supply, suggesting benthic–pelagic coupling. The abundance of the species that explained the highest amount of variation (an oligochaete) was positively related to the abundance of their predators (mites), further suggesting bottom-up forcing in these communities. Overall, we conclude that species assemblages associated to structurally similar stands of a foundation species can show clear changes in species composition at a regional scale. creator: Ricardo A. Scrosati creator: Julius A. Ellrich uri: https://doi.org/10.7717/peerj.17697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Scrosati and Ellrich title: Lysyl oxidase-like 1 predicts the prognosis of patients with primary glioblastoma and promotes tumor invasion via EMT pathway link: https://peerj.com/articles/17579 last-modified: 2024-07-05 description: BackgroundLysyl oxidase enzymes (LOXs), as extracellular matrix (ECM) protein regulators, play vital roles in tumor progression by remodeling the tumor microenvironment. However, their roles in glioblastoma (GBM) have not been fully elucidated.MethodsThe genetic alterations and prognostic value of LOXs were investigated via cBioPortal. The correlations between LOXs and biological functions/molecular tumor subtypes were explored in The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). After Kaplan‒Meier and Cox survival analyses, a Loxl1-based nomogram and prognostic risk score model (PRSM) were constructed and evaluated by time-dependent receiver operating characteristic curves, calibration curves, and decision curve analyses. Tumor enrichment pathways and immune infiltrates were explored by single-cell RNA sequencing and TIMER. Loxl1-related changes in tumor viability/proliferation and invasion were further validated by CCK-8, western blot, wound healing, and Transwell invasion assays.ResultsGBM patients with altered LOXs had poor survival. Upregulated LOXs were found in IDH1-wildtype and mesenchymal (not Loxl1) GBM subtypes, promoting ECM receptor interactions in GBM. The Loxl1-based nomogram and the PRSM showed high accuracy, reliability, and net clinical benefits. Loxl1 expression was related to tumor invasion and immune infiltration (B cells, neutrophils, and dendritic cells). Loxl1 knockdown suppressed GBM cell proliferation and invasion by inhibiting the EMT pathway (through the downregulation of N-cadherin/Vimentin/Snai1 and the upregulation of E-cadherin).ConclusionThe Loxl1-based nomogram and PRSM were stable and individualized for assessing GBM patient prognosis, and the invasive role of Loxl1 could provide a promising therapeutic strategy. creator: Gui-Qiang Yuan creator: Guoguo Zhang creator: Qianqian Nie creator: Zhong Wang creator: Hong-Zhi Gao creator: Gui-Shan Jin creator: Zong-Qing Zheng uri: https://doi.org/10.7717/peerj.17579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yuan et al.