title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=349 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of WRKY gene family in Dioscorea opposita Thunb. reveals that DoWRKY71 enhanced the tolerance to cold and ABA stress link: https://peerj.com/articles/17016 last-modified: 2024-03-28 description: WRKY transcription factors constitute one of the largest plant-specific gene families, regulating various aspects of plant growth, development, physiological processes, and responses to abiotic stresses. This study aimed to comprehensively analyze the WRKY gene family of yam (Dioscorea opposita Thunb.), to understand their expression patterns during the growth and development process and their response to different treatments of yam and analyze the function of DoWRKY71 in detail. A total of 25 DoWRKY genes were identified from the transcriptome of yam, which were divided into six clades (I, IIa, IIc, IId, IIe, III) based on phylogenetic analysis. The analysis of conserved motifs revealed 10 motifs, varying in length from 16 to 50 amino acids. Based on real-time quantitative PCR (qRT-PCR) analysis, DoWRKY genes were expressed at different stages of growth and development and responded differentially to various abiotic stresses. The expression level of DoWRKY71 genes was up-regulated in the early stage and then down-regulated in tuber enlargement. This gene showed responsiveness to cold and abiotic stresses, such as abscisic acid (ABA) and methyl jasmonate (MeJA). Therefore, further study was conducted on this gene. Subcellular localization analysis revealed that the DoWRKY71 protein was localized in the nucleus. Moreover, the overexpression of DoWRKY71 enhanced the cold tolerance of transgenic tobacco and promoted ABA mediated stomatal closure. This study presents the first systematic analysis of the WRKY gene family in yam, offering new insights for studying WRKY transcription factors in yam. The functional study of DoWRKY71 lays theoretical foundation for further exploring the regulatory function of the DoWRKY71 gene in the growth and development related signaling pathway of yam. creator: Linan Xing creator: Yanfang Zhang creator: Mingran Ge creator: Lingmin Zhao creator: Xiuwen Huo uri: https://doi.org/10.7717/peerj.17016 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xing et al. title: Accuracy of augmented reality-guided needle placement for pulsed radiofrequency treatment of pudendal neuralgia: a pilot study on a phantom model link: https://peerj.com/articles/17127 last-modified: 2024-03-28 description: BackgroundPudendal neuralgia (PN) is a chronic neuropathy that causes pain, numbness, and dysfunction in the pelvic region. The current state-of-the-art treatment is pulsed radiofrequency (PRF) in which a needle is supposed to be placed close to the pudendal nerve for neuromodulation. Given the effective range of PRF of 5 mm, the accuracy of needle placement is important. This study aimed to investigate the potential of augmented reality guidance for improving the accuracy of needle placement in pulsed radiofrequency treatment for pudendal neuralgia.MethodsIn this pilot study, eight subjects performed needle placements onto an in-house developed phantom model of the pelvis using AR guidance. AR guidance is provided using an in-house developed application on the HoloLens 2. The accuracy of needle placement was calculated based on the virtual 3D models of the needle and targeted phantom nerve, derived from CBCT scans.ResultsThe median Euclidean distance between the tip of the needle and the target is found to be 4.37 (IQR 5.16) mm, the median lateral distance is 3.25 (IQR 4.62) mm and the median depth distance is 1.94 (IQR 7.07) mm.ConclusionIn this study, the first method is described in which the accuracy of patient-specific needle placement using AR guidance is determined. This method could potentially improve the accuracy of PRF needle placement for pudendal neuralgia, resulting in improved treatment outcomes. creator: Lars L. Boogaard creator: Kim Notten creator: Kirsten Kluivers creator: Selina Van der Wal creator: Thomas J. J. Maal creator: Luc Verhamme uri: https://doi.org/10.7717/peerj.17127 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Boogaard et al. title: The behavior and welfare of neglected species: some examples from fish and mammals link: https://peerj.com/articles/17149 last-modified: 2024-03-28 description: Animal welfare is the state of an animal’s body and mind and the level to which its requirements are satisfied. Animal welfare is affected by human decisions and actions. Numerous decisions concerning animals are driven by human desires to enhance their own lives, and some of these decisions may be influenced by self-interest or a strong emphasis on economic factors. How to assess the welfare state of animals is a central issue in animal welfare science. Two critical questions can be used to address animal welfare: first, is the animal healthy, and second, does the animal have what it needs? Both of these questions can potentially be answered using the study of animal behavior. The development of behavioral methodologies is crucial for evaluating welfare in contexts where concern for animal welfare is often highest, such as on intensive modern farms and sites where working animals are used. Herein, we discuss animal welfare by focusing on some of its major concepts and explanations. Later, to illustrate key aspects of animal welfare, we chose to examine the information that is available for some ‘neglected’ livestock species, which are commercially important on a global basis and found in large numbers: buffaloes (Bubalus bubalis), camels (Camelus dromedarius), donkeys (Equus asinus), mules (Equus asinus × Equus caballus), and lumpfish (Cyclopterus lumpus). We chose these species because there are major ongoing concerns about their welfare, and more research is required to help solve the various problems. Overall, there are strong imbalances in terms of the species that are usually studied in terms of animal welfare research, and we call for greater attention to those that have traditionally been neglected. creator: Syed S. U. H. Bukhari creator: Rebecca S. V. Parkes creator: Lynne U. Sneddon creator: Alan G. McElligott uri: https://doi.org/10.7717/peerj.17149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bukhari et al. title: The first occurrence of machimosaurid crocodylomorphs from the Oxfordian of south-central Poland provides new insights into the distribution of macrophagous teleosauroids link: https://peerj.com/articles/17153 last-modified: 2024-03-28 description: Teleosauroid thalattosuchians were a clade of semi-aquatic crocodylomorphs that achieved a broad geographic distribution during the Mesozoic. While their fossils are well documented in Western European strata, our understanding of teleosauroids (and thalattosuchians in general) is notably poorer in Central-Eastern Europe, and from Poland in particular. Herein, we redescribe a teleosauroid rostrum (MZ VIII Vr-72) from middle Oxfordian strata of Załęcze Wielkie, in south-central Poland. Until now, the specimen has been largely encased in a block of limestone. After preparation, its rostral and dental morphology could be evaluated, showing the specimen to be a non-machimosaurin machimosaurid, similar in morphology to taxa Neosteneosaurus edwardsi and Proexochokefalos heberti. The well-preserved teeth enable us to study the specimen feeding ecology through the means of comparing its teeth to other teleosauroids through PCoA analysis. Comparisons with inferred closely related taxa suggest that the referred specimen was a macrophagous generalist. Notably, MZ VIII Vr-72 displays a prominent pathological distortion of the anterior rostrum, in the form of lateral bending. The pathology affects the nasal passage and tooth size and position, and is fully healed, indicating that, despite its macrophagous diet, it did not prevent the individual from food acquisition. creator: Łukasz Weryński creator: Błazej Błażejowski creator: Tomasz Szczygielski creator: Mark T. Young uri: https://doi.org/10.7717/peerj.17153 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Weryński et al. title: Genome-wide identification of the CYP82 gene family in cucumber and functional characterization of CsCYP82D102 in regulating resistance to powdery mildew link: https://peerj.com/articles/17162 last-modified: 2024-03-28 description: The cytochrome P450 (CYP450) gene family plays a vital role in basic metabolism, hormone signaling, and enhances plant resistance to stress. Among them, the CYP82 gene family is primarily found in dicots, and they are typically activated in response to various specific environmental stresses. Nevertheless, their roles remain considerably obscure, particularly within the context of cucumber. In the present study, 12 CYP82 subfamily genes were identified in the cucumber genome. Bioinformatics analysis included gene structure, conserved motif, cis-acting promoter element, and so on. Subcellular localization predicted that all CYP82 genes were located in the endoplasmic reticulum. The results of cis element analysis showed that CYP82s may significantly affect the response to stress, hormones, and light exposure. Expression patterns of the CYP82 genes were characterized by mining available RNA-seq data followed by qRT-PCR (quantitative real-time polymerase chain reaction) analysis. Members of CYP82 genes display specific expression profiles in different tissues, and in response to PM and abiotic stresses in this study, the role of CsCYP82D102, a member of the CYP82 gene family, was investigated. The upregulation of CsCYP82D102 expression in response to powdery mildew (PM) infection and treatment with methyl jasmonate (MeJA) or salicylic acid (SA) was demonstrated. Further research found that transgenic cucumber plants overexpressing CsCYP82D102 display heightened resistance against PM. Wild-type (WT) leaves exhibited average lesion areas of approximately 29.7% at 7 dpi upon powdery mildew inoculation. In contrast, the two independent CsCYP82D102 overexpression lines (OE#1 and OE#3) displayed significantly reduced necrotic areas, with average lesion areas of approximately 13.4% and 5.7%. Additionally, this enhanced resistance is associated with elevated expression of genes related to the SA/MeJA signaling pathway in transgenic cucumber plants. This study provides a theoretical basis for further research on the biological functions of the P450 gene in cucumber plants. creator: Hongyu Wang creator: Pengfei Li creator: Yu Wang creator: Chunyu Chi creator: Guohua Ding uri: https://doi.org/10.7717/peerj.17162 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: scAnnoX: an R package integrating multiple public tools for single-cell annotation link: https://peerj.com/articles/17184 last-modified: 2024-03-28 description: BackgroundSingle-cell annotation plays a crucial role in the analysis of single-cell genomics data. Despite the existence of numerous single-cell annotation algorithms, a comprehensive tool for integrating and comparing these algorithms is also lacking.MethodsThis study meticulously investigated a plethora of widely adopted single-cell annotation algorithms. Ten single-cell annotation algorithms were selected based on the classification of either reference dataset-dependent or marker gene-dependent approaches. These algorithms included SingleR, Seurat, sciBet, scmap, CHETAH, scSorter, sc.type, cellID, scCATCH, and SCINA. Building upon these algorithms, we developed an R package named scAnnoX for the integration and comparative analysis of single-cell annotation algorithms.ResultsThe development of the scAnnoX software package provides a cohesive framework for annotating cells in scRNA-seq data, enabling researchers to more efficiently perform comparative analyses among the cell type annotations contained in scRNA-seq datasets. The integrated environment of scAnnoX streamlines the testing, evaluation, and comparison processes among various algorithms. Among the ten annotation tools evaluated, SingleR, Seurat, sciBet, and scSorter emerged as top-performing algorithms in terms of prediction accuracy, with SingleR and sciBet demonstrating particularly superior performance, offering guidance for users. Interested parties can access the scAnnoX package at https://github.com/XQ-hub/scAnnoX. creator: Xiaoqian Huang creator: Ruiqi Liu creator: Shiwei Yang creator: Xiaozhou Chen creator: Huamei Li uri: https://doi.org/10.7717/peerj.17184 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Huang et al. title: Association between visfatin and periodontitis: a systematic review and meta-analysis link: https://peerj.com/articles/17187 last-modified: 2024-03-28 description: BackgroundPeriodontitis is a chronic inflammatory disease caused by bacterial infection in the periodontal support tissue. Visfatin, a hormone secreted mainly by adipocytes and macrophages, plays an important role in immune regulation and defense. Although studies have indicated that patients with periodontitis have significantly high serum and gingival crevicular fluid levels of visfatin, the relationship between this adipocytokine and periodontal disease remains unclear.AimThe aim of this study was to systematically evaluate the association between visfatin levels and periodontitis.MethodsThe PubMed, Web of Science, ScienceDirect, EBSCO, and Wiley Online Library databases were searched for potential studies, using “periodontitis” and “visfatin” as the keywords in the title and abstract search fields. Standardized mean difference (SMD) values with corresponding 95% confidence intervals (CIs) were determined from the results of this meta-analysis.ResultsIn total, 22 articles involving 456 patients with periodontitis and 394 healthy individuals (controls) were included in the meta-analysis. Visfatin levels were significantly higher in the patients with periodontitis than in the healthy individuals (SMD: 3.82, 95% CI [3.01–4.63]). Moreover, the visfatin levels were significantly lowered after periodontitis treatment (SMD: −2.29, 95% CI [−3.33 to −1.26]).ConclusionThis first-ever meta-analysis comparing visfatin levels between patients with periodontitis and healthy individuals suggests that this adipocytokine can be a diagnostic and therapeutic biomarker for periodontal disease. creator: Yaoqin Li creator: Caihong Xin creator: Jing Xie creator: Xin Sun uri: https://doi.org/10.7717/peerj.17187 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Antibiotic susceptibility and resistance genes profiles of Vagococcus salmoninarum in a rainbow trout (Oncorhyncus mykiss, Walbaum) farm link: https://peerj.com/articles/17194 last-modified: 2024-03-28 description: Disease outbreaks negatively affect fish production. Antimicrobial agents used in the treatment of diseases become ineffective over time because of antibiotic resistance developed by bacteria distributed in the aquaculture environment. This study was conducted for 4 months (cold period) in a fish farm to detect the fish disease, cold water streptococcosis. In the study, four brood stock showing disease signs were detected. Bacteria isolates were obtained and identified as Vagococcus salmoninarum. Antimicrobial susceptibility of V. salmoninarum was tested and antibiotic resistance gene profiles of V. salmoninarum isolates were screened. The phylogenetic relation of the isolates with the previously reported strains was evaluated. Antibiotic resistance developed by pathogenic bacteria is distributed in the aquaculture environment. The transfer of resistance genes from one bacterium to another is very common. This situation causes the antimicrobial agents used in the treatment of diseases to become ineffective over time. The disc diffusion test showed that all four isolates developed resistance to 13 (FFC30, AX25, C30, E15, CF30, L2, OX1, S10, T30, CRO30, CC2, PT15 and TY15) of the evaluated antibiotics and were about to develop resistance to six others (AM 10, FM 300, CFP75, SXT25, APR15 and TE30). Furthermore, antibiotic resistance genes tetA, sul1, sul2, sul3, dhfr1, ereB and floR were detected in the isolated strain. Moreover, the phylogenetic analysis showed that isolated V. salmoninarum strain (ESN1) was closely related to the bacterial strains isolated from USA and Jura. creator: Mesut Yilmaz creator: Tulin Arslan creator: Mükerrem Atalay Oral creator: Aysegul Kubilay uri: https://doi.org/10.7717/peerj.17194 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yilmaz et al. title: Mathematical model explains differences in Omicron and Delta SARS-CoV-2 dynamics in Caco-2 and Calu-3 cells link: https://peerj.com/articles/16964 last-modified: 2024-03-27 description: Within-host infection dynamics of Omicron dramatically differs from previous variants of SARS-CoV-2. However, little is still known about which parameters of virus-cell interplay contribute to the observed attenuated replication and pathogenicity of Omicron. Mathematical models, often expressed as systems of differential equations, are frequently employed to study the infection dynamics of various viruses. Adopting such models for results of in vitro experiments can be beneficial in a number of aspects, such as model simplification (e.g., the absence of adaptive immune response and innate immunity cells), better measurement accuracy, and the possibility to measure additional data types in comparison with in vivo case. In this study, we consider a refinement of our previously developed and validated model based on a system of integro-differential equations. We fit the model to the experimental data of Omicron and Delta infections in Caco-2 (human intestinal epithelium model) and Calu-3 (lung epithelium model) cell lines. The data include known information on initial conditions, infectious virus titers, and intracellular viral RNA measurements at several time points post-infection. The model accurately explains the experimental data for both variants in both cell lines using only three variant- and cell-line-specific parameters. Namely, the cell entry rate is significantly lower for Omicron, and Omicron triggers a stronger cytokine production rate (i.e., innate immune response) in infected cells, ultimately making uninfected cells resistant to the virus. Notably, differences in only a single parameter (e.g., cell entry rate) are insufficient to obtain a reliable model fit for the experimental data. creator: Vladimir Staroverov creator: Alexei Galatenko creator: Evgeny Knyazev creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.16964 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Staroverov et al. title: The clinical association of programmed death-1/PD-L1 axis, myeloid derived suppressor cells subsets and regulatory T cells in peripheral blood of stable COPD patients link: https://peerj.com/articles/16988 last-modified: 2024-03-27 description: BackgroundMyeloid-derived suppressor cells (MDSCs) have crucial immunosuppressive role in T cell dysfunction in various disease processes. However, the role of MDSCs and their impact on Tregs in COPD have not been fully understood. The aim of the present study is to investigate the immunomodulatory role of MDSCs and their potential impact on the expansion and function of Tregs in COPD patients.MethodsPeripheral blood samples were collected to analyze circulating MDSCs, Tregs, PD-1/PD-L1 expression to assess the immunomodulatory role of MDSC and their potential impact on the expansion and function of Treg in COPD. A total of 54 COPD patients and 24 healthy individuals were enrolled in our study. Flow cytometric analyses were performed to identify granulocytic MDSCs (G-MDSCs), monocytic MDSCs (M-MDSCs), Tregs, and the expression of PD-1/PD-L1(L2) on MDSCs and Tregs in peripheral blood.ResultsOur results revealed a significantly higher percentage of G-MDSCs and M-MDSCs (p < 0.001) in COPD patients compared to the healthy controls. Additionally, a significantly higher proportion of peripheral blood Tregs was observed in COPD patients. Furthermore, an increased expression of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) on Tregs (p < 0.01) was detected in COPD patients. The expression of PD-1 on CD4+ Tcells and Tregs, but not CD8+Tcells, was found to be increased in patients with COPD compared to controls. Furthermore, an elevated expression of PD-L1 on M-MDSCs (p < 0.01) was also observed in COPD patients. A positive correlation was observed between the accumulation of M-MDSCs and Tregs in COPD patients. Additionally, the percentage of circulating M-MDSCs is positively associated with the level of PD-1 (r = 0.51, p < 0.0001) and CTLA-4 (r = 0.42, p = 0.0014) on Tregs in COPD.ConclusionThe recruitment of MDSCs, accumulation of Tregs, and up-regulation of CTLA-4 on Treg in COPD, accompanied by an increased level of PD-1/PD-L1, suggest PD-1/PD-L1 axis may be potentially involved in MDSCs-induced the expansion and activation of Treg at least partially in COPD. creator: Mingqiang Zhang creator: Yinghua Wan creator: Jie Han creator: Jun Li creator: Haihong Gong creator: Xiangdong Mu uri: https://doi.org/10.7717/peerj.16988 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al.