title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=297 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max link: https://peerj.com/articles/17590 last-modified: 2024-06-24 description: BackgroundGlutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide.MethodsIn this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions.ResultsWe identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding. creator: Hind Abdelmonim Elsanosi creator: Tiantian Zhu creator: Guisheng Zhou creator: Li Song uri: https://doi.org/10.7717/peerj.17590 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Elsanosi et al. title: Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.) link: https://peerj.com/articles/17601 last-modified: 2024-06-24 description: BackgroundTungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination.MethodsIn this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened.ResultsThe results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination. creator: Qi Li creator: Xiaojun Zheng creator: Ming Chen uri: https://doi.org/10.7717/peerj.17601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: The emerging roles of circHECTD1 in human diseases and the specific underlying regulatory mechanisms link: https://peerj.com/articles/17612 last-modified: 2024-06-24 description: Circular RNAs (circRNAs) are a class of single-stranded closed-loop RNAs that have become a popular research subject in biology. Compared to linear RNAs, they are more stable, more conserved, and more widely distributed, and they play crucial biological functions in many diseases. CircHECTD1, a newly identified member of the circRNA family, is widely distributed in humans. Recent studies have shown that circHECTD1 is abnormally expressed in various human diseases, including glioma, hepatocellular carcinoma, gastric cancer, acute ischaemic stroke, silicosis, acute lung injury, ulcerative colitis, atherosclerosis, and hypertrophic scarring. In malignant tumours, circHECTD1 is thought to be an oncogene that promotes malignant tumour behaviours and influences tumour prognosis. In nontumour diseases, it plays a dual role, promoting disease in silicosis, stroke, and other diseases, while alleviating the disease process in ulcerative colitis, acute lung injury, and atherosclerosis. This article provides a review of the regulatory roles and mechanisms of action of circHECTD1 in different diseases. We also discuss and prospectively evaluate the clinical potential of circHECTD1 as a diagnostic biomarker and a therapeutic target for related diseases, providing new insights for developing new therapeutic strategies. creator: Yiran Yuan creator: Xiaomin Zhang creator: Xiaoxiao Wang creator: Lei Zhang creator: Jiefeng He uri: https://doi.org/10.7717/peerj.17612 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Yuan et al. title: Evaluation of alanine aminotransferase/aspartate aminotransferase ratio and high-density lipoprotein for predicting neonatal adverse outcomes associated with intrahepatic cholestasis of pregnancy link: https://peerj.com/articles/17613 last-modified: 2024-06-24 description: BackgroundTo determine the association between lipid metabolism and intrahepatic cholestasis of pregnancy (ICP), and explore the value of maternal alanine aminotransferase/aspartate aminotransferase (ALT/AST) and high-density lipoprotein (HDL) in predicting adverse neonatal outcomes in women with ICP.MethodsA total of 147 pregnant women with ICP admitted to The Fourth Hospital of Shijiazhuang and 120 normal pregnant women in the same period were selected in this study. The Mann-Whitney U test and Chi-square tests were used to compare the differences in clinical data. Multivariate logistic regression was used to analyze the relationship between ALT/AST and the occurrence of adverse pregnancy outcomes in patients with ICP. The combined predictive value of ALT/AST and HDL was determined by receiver operating characteristic (ROC) curve analysis.ResultsAmong 147 women with ICP, 122 women had total bile acid (TBA) levels of 10–39.9 µmol/L, and 25 had TBA ≥ 40 µmol/L. There was significantly lower gestational age in patients with severe ICP than in those with mild and control groups (all p < 0.05), and the weight of newborns in the maternal ICP group was significantly lower than in the control group (p < 0.05). Increasing TBA levels was associated with higher AST, ALT, ALT/AST, and lower HDL level (all p < 0.05). Meanwhile, higher levels of ALT/AST was positively associated with neonatal hyperbilirubinemia [adjusted odds ratio (AOR) = 4.019, 95% CI [1.757–9.194, p = 0.001] and cardiac injury [AOR = 3.500, 95% CI [1.535–7.987], p = 0.003]. HDL was a significant protective factor for neonatal hyperbilirubinemia and cardiac injury [AOR = 0.315, 95% CI [0.126–0.788], p = 0.014; AOR = 0.134 (0.039–0.461), p = 0.001]. The area under the ROC curve (AUC) for prediction of neonatal hyperbilirubinemia by ALT/AST combined with HDL was 0.668 [95% CI [56.3–77.3%], p = 0.002], and the sensitivity and specificity were 47.1% and 84.0%, respectively. To predict neonatal cardiac injury, the AUC value was 0.668 [95% CI [56.4–77.1%], p = 0.002], with sensitivity and specificity were 41.2% and 87.1%, respectively.ConclusionsThe levels of higher ALT/AST and lower HDL were significantly associated with the risk of ICP-related adverse neonatal outcomes. Moreover, ALT/AST combined with HDL has moderate clinical value in predicting the adverse outcomes of neonatal hyperbilirubinemia and cardiac injury. creator: Xizhenzi Fan creator: Xia Li creator: Tianxiao Yu creator: Ruifen Jiao creator: Wenhui Song creator: Achou Su creator: Mingwei Li creator: Qing Guo uri: https://doi.org/10.7717/peerj.17613 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Fan et al. title: Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling link: https://peerj.com/articles/17629 last-modified: 2024-06-24 description: While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model’s accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a “hot” immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment. creator: Jinglu Yu creator: Yabin Gong creator: Zhenye Xu creator: Lei Chen creator: Shuang Li creator: Yongkang Cui uri: https://doi.org/10.7717/peerj.17629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: Towards the development of cost-effective point-of-care diagnostic tools for poverty-related infectious diseases in sub-Saharan Africa link: https://peerj.com/articles/17198 last-modified: 2024-06-21 description: In this review, we examine the current landscape of point-of-care testing (POCT) diagnostic tools designed for poverty-related infectious diseases (PRIDs) in sub-Saharan Africa (sSA) while delineating key avenues for future advancements. Our analysis encompasses both established and emerging diagnostic methods for PRIDs, addressing the persistent challenges in POCT tool development and deployment, such as cost, accessibility, and reliability. We emphasize recent advancements in POCT diagnostic tools as well as platforms poised to enhance diagnostic testing in sSA. Recognizing the urgency for affordable and widely accessible POCT diagnostic tools to detect PRIDs in sSA, we advocate for a multidisciplinary approach. This approach integrates current and emerging diagnostic methods, explicitly addressing challenges hindering point-of-care (POC) tool development. Furthermore, it recognizes the profound impact of misdiagnosis on public and global health, emphasizing the need for effective tools. To facilitate the successful development and implementation of POCT diagnostic tools in sSA, we propose strategies including the creation of multi-analyte detection POCT tools, the implementation of education and training programs, community engagement initiatives, fostering public-private collaborations, and the establishment of reliable supply chains. Through these concerted efforts, we aim to accelerate the development of POCT in the sSA region, ensuring its effectiveness and accessibility in addressing the diagnostic challenges associated with PRIDs. creator: Benedict Ofori creator: Seth Twum creator: Silas Nkansah Yeboah creator: Felix Ansah creator: Kwabena Amofa Nketia Sarpong uri: https://doi.org/10.7717/peerj.17198 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ofori et al. title: Path for recovery: an ecological overview of the Jambato Harlequin Toad (Bufonidae: Atelopus ignescens) in its last known locality, Angamarca Valley, Ecuador link: https://peerj.com/articles/17344 last-modified: 2024-06-21 description: The Jambato Harlequin toad (Atelopus ignescens), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in 1988. The species was considered Extinct by the IUCN until 2016, when a fortuitous discovery of one Jambato by a local boy reignited hope. In this study, we present findings from an investigation conducted in the Angamarca parish, focusing on distribution, abundance, habitat preferences, ecology, disease susceptibility, and dietary habits of the species. In one year we identified 71 individuals at different stages of development in various habitats, with a significant presence in agricultural mosaic areas and locations near water sources used for crop irrigation, demonstrating the persistence of the species in a complex landscape, with considerable human intervention. The dietary analysis based on fecal samples indicated a diverse prey selection, primarily comprising arthropods such as Acari, Coleoptera, and ants. Amphibian declines have been associated with diseases and climate change; notably, our study confirmed the presence of the pathogen Batrachochytrium dendrobatidis (Bd), but, surprisingly, none of the infected Jambatos displayed visible signs of illness. When analyzing climatic patterns, we found that there are climatic differences between historical localities and Angamarca; the temporal analysis also exposes a generalized warming trend. Finally, in collaboration with the local community, we developed a series of management recommendations for terrestrial and aquatic environments occupied by the Jambato. creator: Mateo A. Vega-Yánez creator: Amanda B. Quezada-Riera creator: Blanca Rios-Touma creator: María del Carmen Vizcaíno-Barba creator: William Millingalli creator: Orlando Ganzino creator: Luis A. Coloma creator: Elicio E. Tapia creator: Nadine Dupérré creator: Mónica Páez-Vacas creator: David Parra-Puente creator: Daniela Franco-Mena creator: Gabriela Gavilanes creator: David Salazar-Valenzuela creator: Carlos A. Valle creator: Juan M. Guayasamin uri: https://doi.org/10.7717/peerj.17344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vega-Yánez et al. title: Taxon-dependent diversity response along a temperate elevation gradient covered by grassland link: https://peerj.com/articles/17375 last-modified: 2024-06-21 description: Elevational gradients constitute excellent systems for understanding the mechanisms that generate and maintain global biodiversity patterns. Climatic gradients associated with elevation show strong influence on species distribution in mountains. The study of mountains covered by the same habitat type is an ideal scenario to compare alternatives to the energy hypotheses. Our aim was to investigate how changes in climatic conditions along the elevational gradient drive α- and β-diversity of four taxa in a mountain system located within a grassland biome. We sampled ants, spiders, birds and plants, and measured climatic variables at six elevational bands (with 10 sampling sites each) established between 470 and 1,000 masl on a mountain from the Ventania Mountain System, Argentina. Species richness per site and β-diversity (turnover and nestedness) between the lowest band and upper sites were estimated. For most taxa, species richness declined at high elevations and energy, through temperature, was the major driver of species richness for ants, plants and birds, prevailing over productivity and water availability. The major β-diversity component was turnover for plants, spiders and birds, and nestedness for ants. The unique environmental conditions of the upper bands could favour the occurrence of specialist and endemic species. creator: Santiago Santoandré creator: Carolina Samanta Ramos creator: Pablo Picca creator: Julieta Filloy uri: https://doi.org/10.7717/peerj.17375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Santoandré et al. title: Interlimb and trunk asymmetry in the frontal plane of table tennis female players link: https://peerj.com/articles/17526 last-modified: 2024-06-21 description: BackgroundAn interesting and little-reported problem in the literature is the scale of asymmetry in table tennis players, the magnitude of which should perhaps be treated as a risk for injury. Determining the degree of asymmetry in table tennis players can indicate the need to appropriately manage the training process, including compensatory or corrective exercises in the training program, especially since recent studies confirm that training interventions can reduce sporting asymmetries and improve performance. This study aimed to assess the amount of asymmetry in the trunk regarding the frontal plane and the difference between limb circumferences in female table tennis players compared to the control group (non-athletes).MethodsTwenty-two women took part in the study. Ten of them were table tennis professionals with an average training experience of 7 ± 4.3 years (the exclusion criterion of the study was a minimum of 3 years of training experience). As a comparison group, the study included 12 female students who did not participate in competitive sports. Body posture was assessed in all subjects using equipment for computer analysis of asymmetry in the torso using the photogrammetric method. Additionally, all the subjects had their upper and lower limb circumferences measured.ResultsThe results of the conducted research showed asymmetry in the frontal plane in the table tennis player group. As many as six parameters—regarding the pelvic rotation angle, angle of trunk inclination, the height of the angles of the lower shoulder blades and their distance from the spine, as well as the waist triangles, difference in the width and height of the waist triangles and the angle of trunk inclination—indicated asymmetry in this group but significantly differed from the control group (p ≤ 0.05) only in the first parameter given above. The calculated differences in circumference between the right and left sides in the individual groups were statistically different in several cases (p ≤ 0.05). This concerned the circumferences of the arms, forearms, elbows, and knees of table tennis players.ConclusionsThe research carried out in this study allowed us to determine the occurrence of asymmetry in the frontal plane of the trunk and between the limbs of table tennis players. According to some studies, this may be a risk factor for injury. However, despite the lack of uniform views in the literature on the importance and threats resulting from asymmetries, it appears that, if only for aesthetic reasons, table tennis would require compensatory or corrective training aimed at developing symmetry of the body structure. creator: Ziemowit Bańkosz creator: Arletta Hawrylak creator: Małgorzata Kołodziej creator: Lenka Murinova creator: Katarzyna Barczyk-Pawelec uri: https://doi.org/10.7717/peerj.17526 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bańkosz et al. title: Decrease in the usual walking speed and body fat percentage associated with a deterioration in long-term care insurance certification levels link: https://peerj.com/articles/17529 last-modified: 2024-06-21 description: BackgroundIn Japan, the number of older adults requiring long-term care insurance (LTCI) is increasing and the cost is becoming a social problem. In these fields, the role of geriatric rehabilitation includes maintaining the physical function and LTCI certification levels. The prevalence of sarcopenia is high among older adults requiring LTCI certification, and there are many opportunities to assess the handgrip strength, walking speed, and muscle mass. This study aimed to identify sarcopenia-related assessments sensitive to transitions in LTCI certification levels and determine cut-off values to predict them.MethodsThis prospective cohort study analyzed 98 daycare users (mean age ± standard error: 78.5 ± 0.8 years) between March 2019 and 2023. The participants received LTCI certification before the study, and their levels were renewed between baseline and follow-up (six months later). The measurements included handgrip strength, usual walking speed, body composition, and SARC-F score. Participants were classified into maintenance, deterioration, and improvement groups according to the changes in their LTCI certification levels. We identified factors contributing to the deterioration of LTCI certification levels using baseline and before and after comparisons, multivariate analyses, and receiver operating characteristic analyses.ResultsNo significant differences were observed in the baseline data among the groups. Only the deterioration group showed significant changes in the usual walking speed (baseline: 0.64 ± 0.25 m/s, follow-up: 0.53 ± 0.21 m/s, P = 0.008) and body fat percentage (baseline: 29.2 ± 9.9%, follow-up: 27.7 ± 10.3%, P = 0.047). Binomial logistic regression showed that changes in usual walking speed (P = 0.042) and body fat percentage (P = 0.011) were significantly associated with the deterioration of LTCI certification levels, even after adjustment. The cutoff values of change to discriminate the deterioration of LTCI certification levels were −0.14 m/s at the usual walking speed (P = 0.047) and −1.0% for body fat percentage (P = 0.029).ConclusionsDecreases in usual walking speed and body fat percentage may predict worse certification levels in older adults requiring LTCI. creator: Yohei Sawaya creator: Tamaki Hirose creator: Takahiro Shiba creator: Ryo Sato creator: Lu Yin creator: Akira Kubo creator: Tomohiko Urano uri: https://doi.org/10.7717/peerj.17529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sawaya et al.