title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=222 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil link: https://peerj.com/articles/18383 last-modified: 2024-10-30 description: Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices. creator: Nattanan Rueangmongkolrat creator: Pichahpuk Uthaipaisanwong creator: Kanthida Kusonmano creator: Sasipa Pruksangkul creator: Prinpida Sonthiphand uri: https://doi.org/10.7717/peerj.18383 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rueangmongkolrat et al. title: Using vessels of opportunity for determining important habitats of bottlenose dolphins in Port Phillip Bay, south-eastern Australia link: https://peerj.com/articles/18400 last-modified: 2024-10-30 description: Understanding species’ critical habitat requirements is crucial for effective conservation and management. However, such information can be challenging to obtain, particularly for highly mobile, wide-ranging species such as cetaceans. In the absence of systematic surveys, alternative economically viable methods are needed, such as the use of data collected from platforms of opportunity, and modelling techniques to predict species distribution in un-surveyed areas. The present study used data collected by ecotourism and other vessels of opportunity to investigate important habitats of a small, poorly studied population of bottlenose dolphins in Port Phillip Bay, south-eastern Australia. Using 16 years of dolphin sighting location data, an ensemble habitat suitability model was built from which physical factors influencing dolphin distribution were identified. Results indicated that important habitats were those areas close to shipping channels and coastlines with these factors primarily influencing the variation in the likelihood of dolphin presence. The relatively good performance of the ensemble model suggests that simple presence-background data may be sufficient for predicting the species distribution where sighting data are limited. However, additional data from the center of Port Phillip Bay is required to further support this contention. Important habitat features identified in the study are likely to relate to favorable foraging conditions for dolphins as they are known to provide feeding, breeding, and spawning habitat for a diverse range of fish and cephalopod prey species. The results of the present study highlight the importance of affordable community-based data collection, such as ecotourism vessels, for obtaining information critical for effective management. creator: Maddison J. Ledwidge creator: Jacquomo Monk creator: Suzanne J. Mason creator: John P. Y. Arnould uri: https://doi.org/10.7717/peerj.18400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ledwidge et al. title: Kinematic differences between female national and provincial athletes in the tennis serve link: https://peerj.com/articles/18410 last-modified: 2024-10-30 description: BackgroundTennis, the second-largest ball game in the world, has a particularly wide audience. To date, little research has been conducted on the biomechanics of female serves.PurposeThe purpose of this study was to capture the key moments by using 1,000 frames/s high-speed video analysis, to analyze the kinematics of the serving techniques of national athletes and provincial athletes, to determine the differences between the two levels of athletes, and to provide theoretical references for the improvement of scientific training level.MethodsTen female athletes were selected as participants for this study, five of whom are national athletes, and the other are provincial athletes. Three-dimensional filming techniques were employed to capture videos of the first and second serve techniques. Simi Motion was applied to obtain the 3D kinematic data. Statistical analyses were performed using IBM SPSS Statistics 27.0, and Mann–Whitney U tests were conducted to determine differences between groups.ResultsSignificant differences in kinematics were found between national and provincial athletes. At the moment of the left knee’s minimum flexion (T2), in the first serve, national athletes had a smaller shoulder-hip vertical plane angle (−18.281 ± 6.142° vs. −25.631 ± 3.497°; p = 0.047) and a larger hip vertical plane rotation angle (−9.378 ± 4.263° vs. −0.470 ± 4.724°; p = 0.047). In the second serve, national athletes had a smaller hip horizontal plane rotation angle (−1.720 ± 4.683° vs. 24.146 ± 24.014°; p = 0.047) but a larger hip vertical plane rotation angle (−11.553 ± 1.949° vs. −0.422 ± 4.958°; p = 0.009). At the moment of impact (T4), in the second serve, national athletes’ batting position (0.296 ± 0.088 m vs. 0.446 ± 0.094 m; p = 0.047) was further back. Additionally, in the second serve, national athletes consistently had their body center of gravity further back at T2 (−0.106 ± 0.052 m vs. −0.018 ± 0.048 m; p = 0.028), T3 (0.002 ± 0.038 m vs. 0.132 ± 0.039 m; p = 0.009), and T4 (0.073 ± 0.050 m vs. 0.217 ± 0.034 m; p = 0.009).ConclusionsThe results of this study indicated several significant kinematic differences between national and provincial athletes, these variations were noted in the shoulder, hip, and body center of gravity. In summary, for the overall first and second serves, it is recommended that national athletes increase the horizontal plane angle of the shoulders and hips at T2, whereas provincial athletes decrease the horizontal plane angle of the shoulder–hip. In addition, provincial athletes need to increase the vertical plane angle of the hip joint, so that the top of the hip can be increased more, and provincial athletes need to be careful not to have the center of gravity too far in front of the body at T2, T3, and T4, so that it can hit the ball at a higher position to increase the swing speed. creator: Yan Chen creator: Tianyang Wang creator: Yuyan Zhao creator: Genghao Zhan creator: Yinchao Tang creator: Zefeng Wang uri: https://doi.org/10.7717/peerj.18410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients link: https://peerj.com/articles/18416 last-modified: 2024-10-30 description: BackgroundIgA nephropathy (IgAN) is the most common primary glomerular disease in chronic kidney disease (CKD), exhibiting significant heterogeneity in both clinical and pathological presentations. We aimed to explore the risk factors influencing short-term prognosis (≥90 days) and to construct a nomogram model for evaluating the risk of CKD progression in IgAN patients.MethodsClinical and pathological data of patients diagnosed with IgAN through biopsy at two centers were retrospectively collected. Logistic regression was employed to analyze the training cohort dataset and identify the independent predictors to construct a nomogram model based on the final variables. The predictive model was validated both internally and externally, with its performance assessed using the area under the curve (AUC), calibration curves, and decision curve analysis.ResultsOut of the patients in the modeling group, 129 individuals (41.6%) did not achieve remission following 3 months of treatment, indicating a high risk of CKD progression. A multivariate logistic regression analysis demonstrated that body mass index, urinary protein excretion, and tubular atrophy/interstitial fibrosis were identified as independent predictors for risk stratification. A nomogram model was formulated utilizing the final variables. The AUCs for the training set, internal validation set, and external validation set were 0.746 (95% confidence intervals (CI) [0.691–0.8]), 0.764 (95% CI [0.68–0.85]), and 0.749 (95% CI [0.65–0.85]), respectively. The validation of the subgroup analysis also demonstrated a satisfactory AUC.ConclusionThis study developed and validated a practical nomogram that can individually predict short-term treatment outcomes (≥90 days) and the risk of CKD progression in IgAN patients. It provides reliable guidance for timely and personalized intervention and treatment strategies. creator: Ying Zhang creator: Zhixin Wang creator: Wenwu Tang creator: Xinzhu Yuan creator: Xisheng Xie uri: https://doi.org/10.7717/peerj.18416 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Identification of common and specific cold resistance pathways from cold tolerant and non-cold tolerant mango varieties link: https://peerj.com/articles/18431 last-modified: 2024-10-30 description: Mango has frequently encountered severe climate and environmental challenges such as low temperatures, seriously affecting the sustainable development of the industry. In the study, physiological measurements showed that the activities of superoxide dismutase (SOD) and peroxidase (POD) were found to be higher in Jinhuang (JH) mango plants than those of Tainong (TN) mango plants under cold stress, indicating cold tolerant (JH) and non-cold tolerant (TN) mango varieties were firstly determined. Subsequently, transcriptomics showed 8,337 and 7,996 differentially expressed genes (DEGs) were respectively identified in JH and TN mango varieties treated at 4 °C for 36 h, while more DEGs (10,683 and 10,723) were screened when treated at 4 °C for 72 h. Quantitative real-time PCR (qRT-PCR) of the selected DEGs confirmed their transcriptional levels displayed agreement to the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed two primary cold resistant regulation pathways, photosynthesis-antenna proteins pathway and photosynthesis pathway, were both significant annotated in the two mango varieties, indicating share the common regulation mechanism response to cold stress. However, five specific cold resistant pathways, such as amino acid and carbohydrate metabolisms, were identified in JH mango variety with cold stress for longer duration, indicating the specific regulation pathways in the cold tolerant mango varieties. Furthermore, 43 ethylene-responsive transcription factors (ERFs) were significantly annotated in JH mango after cold-treated for 72 h comparing with the control group, and three of them ERF109-1, ERF017-1 and ERF017-2 were highly expressed, which may play important regulatory roles in plant cold resistance. These results provided insights into the primary and specific molecular mechanisms of different mango varieties resistance to chill. creator: Jian-hua Wang creator: Xiaoyan Feng creator: Muhammad Aleem Ashraf creator: Yufeng Li creator: Yu Kong creator: Qiuliang Cai creator: Shuli Xian creator: Huixiang Yin creator: Nai-tong Yu uri: https://doi.org/10.7717/peerj.18431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Reliability and validity of My Jump 2® app to measure the vertical jump in visually impaired five-a-side soccer athletes link: https://peerj.com/articles/18170 last-modified: 2024-10-29 description: BackgroundAlthough My Jump 2® consistently presented excellent values of reliability and validity when compared to force platforms (FPs) and contact mats, to date no scientific investigation assessed the validity and reliability of My Jump 2® to measure jump height in visually impaired five-a-side soccer athletes. Thus, the study aimed at analyzing the validity and reliability of the My Jump 2® to measure the vertical jump of five-a-side soccer athletes.MethodsTwelve visually impaired five-a-side soccer athletes, volunteered for this study. Each player performed five countermovement jumps (CMJs) and squat jumps (SJs) on a contact platform (CP) while they were simultaneously recorded using MyJump 2®.ResultsThere was almost perfect agreement between the My Jump 2® and the contact platform measurements of CMJ (intraclass correlation coefficient = 0.99; p < 0.001) and SJ (intraclass correlation coefficient = 0.99; p < 0.001), heights for athletes during the first and second measurement days. Bland-Altman analysis showed a bias of 0.25 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.88 for CMJ, while that Bland-Altman analysis showed bias 0.18 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.96, for SJ.ConclusionWe can conclude that the My Jump 2® is a valid and reliable method to measure CMJ and SJ in visually impaired five-a-side soccer athletes. creator: Julio Cesar Silva creator: Kalinne Fernandes Silva creator: Vitor Bruno Torres creator: Maria Socorro Cirilo-Sousa creator: Alexandre Igor Araripe Medeiros creator: Jacques Eanes Esmeraldo Melo creator: Gilmário Ricarte Batista uri: https://doi.org/10.7717/peerj.18170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Silva et al. title: Risk factors for recovery from oculomotor nerve palsy after aneurysm surgery: a meta-analysis link: https://peerj.com/articles/18207 last-modified: 2024-10-29 description: BackgroundRisk factors for recovery from oculomotor nerve palsy (ONP) after aneurysm surgery explored by meta-analysis.MethodsThe PubMed, Embase, web of science, Cochrane library, China Knowledge, Wan fang, and VIP databases were searched for case-control or cohort studies on risk factors of oculomotor nerve palsy recovery after aneurysm surgery, with a cut-off date of 14 February 2024, and data were analyzed using Stata 15.ResultA total of 12 articles involving 866 individuals were included, meta-analysis results suggesting that gender (OR = 0.75, 95% CI [0.51–1.10]), age (OR = 1.00, 95% CI [0.93–1.07]), aneurysm size (OR = 0.85, 95% CI [−0.71 to 1.01]), treatment time (OR = 1.01, 95% CI [0.91–1.13]) is not a risk factor for recovery of motor nerve palsy after aneurysm surgery. Preoperative complete ONP (OR = 2.27, 95% CI [1.07–4.81]), surgery (OR = 9.88, 95% CI [2.53–38.57]), subarachnoid hemorrhage (OR = 1.29, 95% CI [1.06–1.56]) is a risk factor for recovery of motor nerve palsy after aneurysm surgery.ConclusionBased on the results of the studies we included, we found that complete ONP before surgery led to poorer recovery, but patients with post-operative and subarachnoid hemorrhage had better recovery. creator: Yuan Li creator: Ming Zhao creator: Xuemei Li creator: Tiejuan Liu creator: Lin Zheng creator: Deyu Hu creator: Tongyan Liu creator: Lingyun Zhou uri: https://doi.org/10.7717/peerj.18207 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Clocks at a snail pace: biological rhythms in terrestrial gastropods link: https://peerj.com/articles/18318 last-modified: 2024-10-29 description: Biological rhythms are ubiquitous across the tree of life. Organisms must allocate their activities into moments of the day and of the season that will increase their probability of surviving and reproducing, which is done in the form of daily and annual rhythms. So far, the vast majority of studies on biological rhythms have focused on classical laboratory model species. Still, the use of non-model species is gaining traction, as part of an effort to achieve a more holistic understanding of clock/calendar mechanisms in the “real world” but this requires species that can be studied in both the lab and in nature. Terrestrial gastropods, i.e., land snails and slugs, have the potential to be exciting models for the study of biological rhythms in nature. Therefore, we provide a review of the research on biological rhythms in terrestrial gastropods, with a focus on ecology and evolution. We present the state of the art in the field while giving a historical perspective of the studies, exploring each of the main lineages of terrestrial gastropods. We also point out some interesting directions that future studies could take to fill some of the more urgent gaps in current knowledge. We hope that our contribution will renew interest in this area and spark novel projects. creator: Rodrigo Brincalepe Salvador creator: Barbara Mizumo Tomotani uri: https://doi.org/10.7717/peerj.18318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Salvador and Tomotani title: Cordyceps cateniannulata, a new potential strain for controlling Allantus luctifer from China link: https://peerj.com/articles/18345 last-modified: 2024-10-29 description: Allantus luctifer is one of the most serious pests of buckwheat, with its larvae mainly damaging leaves during the seedling and flowering stages. Entomogenous fungi play a crucial role as biological regulators of arthropod populations in nature. In this paper, a newly isolated strain 19GZAl-1, was identified as Cordyceps. cateniannulata through the observetions of macroscopic and microscopic morphological features, and the results of rDNA- ITS sequence alignment and phylogenetic analysis. By comparing the efficacy of ten entomopathogenic fungal strains, including six strains of C. cateniannulata and four other Cordyceps species, against A. luctifer larvae, the new strain 19GZAl-1 exhibited the highest mortality rate. Mortality rates of A. luctifer larvae treated by spraying with the strain 19GZAl-1 increased as larval stage decreased, with first instar larvae showing the highest mortality rate of 85%. The appressorium from conidia invaded the larval body through areas with thin cuticle, such as larva pod base and internode folds, after which the hyphae grew rapidly, filling the haemocoel, and finally protruding from the integument upon melanization and decomposition of the intestinal wall cells. The results suggest that the strain 19GZAL-1 of C. cateniannulata has potential against A. luctifer larvae, which is significant for further study on the infection mechanism of C. cateniannulata on insects. creator: Xiaona Zhang creator: Yu Wu creator: Xue Peng creator: Can Liu creator: Guimin Yang creator: Qingfu Chen creator: Daochao Jin uri: https://doi.org/10.7717/peerj.18345 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhang et al. title: In-depth study of pyroptosis-related genes and immune infiltration in colon cancer link: https://peerj.com/articles/18374 last-modified: 2024-10-29 description: BackgroundPyroptosis is a form of regulated necrosis that occurs in many cell and tissue types and plays a critical role in tumor progression. The diagnostic value of pyroptosis-related genes (PRGs) in colon cancer has been widely investigated. In the present study, we explored the relationship between PRG expression and colon cancer.MethodsWe retrieved genomic and clinical data pertaining to The Cancer Genome Atlas-Colon Adenocarcinoma from the UCSC Xena database, along with the corresponding genome annotation information from the GENCODE data portal. Utilising these data and a list of 33 pyrogenic genes, we performed principal component analysis and unsupervised clustering analysis to assess the pyroptosis subtypes. We analysed the differential expression between these subtypes to obtain PRGs, ultimately selecting 10 PRGs. We conducted Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set variation analysis, protein–protein interaction, and immune infiltration analyses of these PRGs. We validated the expression of TNNC1 via immunohistochemistry (IHC) and real-time quantitative PCR.ResultsAfter rigorous screening, excluding patients with incomplete survival data and unmatched transcriptomes, we refined our study cohort to 431 patients. We performed differential mRNA analysis and identified 445 PRGs, 10 of which were selected as hub genes. These genes were associated with various immune cell types. Specifically, TNNC1 expression was positively associated with immature dendritic cells and NK CD56+ cells. IHC staining indicated higher TNNC1 expression levels in tumor samples. Notably, TNNC1 expression levels were high in all the colon cancer cell lines, particularly in SW480 cells.ConclusionIn this study, we explored the characteristics of PRGs in colon cancer and identified novel biological targets for early individualised treatment and accurate diagnosis of colon cancer, thus contributing to the advancement of clinical oncology. creator: Bingbing Shang creator: Haiyan Qiao creator: Liang Wang creator: Jingyu Wang uri: https://doi.org/10.7717/peerj.18374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Shang et al.