title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=343
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

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.

title: Changes in red blood cell parameters during incremental exercise in highly trained athletes of different sport specializations
link: https://peerj.com/articles/17040
last-modified: 2024-03-27
description: BackgroundDuring physical exercise, the level of hematological parameters change depending on the intensity and duration of exercise and the individual’s physical fitness. Research results, based on samples taken before and after exercise, suggest that hematological parameters increase during incremental exercise. However, there is no data confirming this beyond any doubt. This study examined how red blood cell (RBC) parameters change during the same standard physical exertion in athletes representing different physiological training profiles determined by sport discipline.MethodsThe study included 39 highly trained male members of national teams: 13 futsal players, 12 sprinters, and 14 triathletes. We used multiple blood sampling to determine RBC, hemoglobin (Hb), hematocrit value (Hct), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and red blood cell distribution width (RDW) before, during (every 3 min), and after (5, 10, 15, 20, and 30 min) an incremental treadmill exercise test until exhaustion.ResultsThere were no significant exercise-induced differences in RBC parameters between athletic groups. No significant changes were recorded in RBC parameters during the low-intensity phase of exercise. RBC, Hb, and Hct increased significantly during incremental physical exercise, and rapidly returned to resting values upon test termination.ConclusionsThe general pattern of exercise-induced changes in RBC parameters is universal regardless of the athlete’s physiological profile. The changes in RBC parameters are proportional to the intensity of exercise during the progressive test. The increase in hemoglobin concentration associated with the intensity of exercise is most likely an adaptation to the greater demand of tissues, mainly skeletal muscles, for oxygen.
creator: Monika Ciekot-Sołtysiak
creator: Krzysztof Kusy
creator: Tomasz Podgórski
creator:  Barbara Pospieszna
creator: Jacek Zieliński
uri: https://doi.org/10.7717/peerj.17040
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Ciekot-Sołtysiak et al.

title: Interwoven processes in fish development: microbial community succession and immune maturation
link: https://peerj.com/articles/17051
last-modified: 2024-03-27
description: Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer’s investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish’s life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.
creator: Lisa Zoé Auclert
creator: Mousumi Sarker Chhanda
creator: Nicolas Derome
uri: https://doi.org/10.7717/peerj.17051
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2024 Auclert et al.

title: The contribution of estimated dead space fraction to mortality prediction in patients with chronic obstructive pulmonary disease—a new proposal
link: https://peerj.com/articles/17081
last-modified: 2024-03-27
description: BackgroundMortality due to chronic obstructive pulmonary disease (COPD) is increasing. However, dead space fractions at rest (VD/VTrest) and peak exercise (VD/VTpeak) and variables affecting survival have not been evaluated. This study aimed to investigate these issues.MethodsThis retrospective observational cohort study was conducted from 2010–2020. Patients with COPD who smoked, met the Global Initiatives for Chronic Lung Diseases (GOLD) criteria, had available demographic, complete lung function test (CLFT), medication, acute exacerbation of COPD (AECOPD), Charlson Comorbidity Index, and survival data were enrolled. VD/VTrest and VD/VTpeak were estimated (estVD/VTrest and estVD/VTpeak). Univariate and multivariable Cox regression with stepwise variable selection were performed to estimate hazard ratios of all-cause mortality.ResultsOverall, 14,910 patients with COPD were obtained from the hospital database, and 456 were analyzed after excluding those without CLFT or meeting the lung function criteria during the follow-up period (median (IQR) 597 (331–934.5) days). Of the 456 subjects, 81% had GOLD stages 2 and 3, highly elevated dead space fractions, mild air-trapping and diffusion impairment. The hospitalized AECOPD rate was 0.60 ± 2.84/person/year. Forty-eight subjects (10.5%) died, including 30 with advanced cancer. The incidence density of death was 6.03 per 100 person-years. The crude risk factors for mortality were elevated estVD/VTrest, estVD/VTpeak, ≥2 hospitalizations for AECOPD, advanced age, body mass index (BMI) <18.5 kg/m2, and cancer (hazard ratios (95% C.I.) from 1.03 [1.00–1.06] to 5.45 [3.04–9.79]). The protective factors were high peak expiratory flow%, adjusted diffusing capacity%, alveolar volume%, and BMI 24–26.9 kg/m2. In stepwise Cox regression analysis, after adjusting for all selected factors except cancer, estVD/VTrest and BMI <18.5 kg/m2 were risk factors, whereas BMI 24–26.9 kg/m2 was protective. Cancer was the main cause of all-cause mortality in this study; however, estVD/VTrest and BMI were independent prognostic factors for COPD after excluding cancer.ConclusionsThe predictive formula for dead space fraction enables the estimation of VD/VTrest, and the mortality probability formula facilitates the estimation of COPD mortality. However, the clinical implications should be approached with caution until these formulas have been validated.
creator: Ming-Lung Chuang
creator: Yu Hsun Wang
creator: I-Feng Lin
uri: https://doi.org/10.7717/peerj.17081
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2024 Chuang et al.