title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=501
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Genetic polymorphism of the Dab2 gene and its association with Type 2 Diabetes Mellitus in the Chinese Uyghur population
link: https://peerj.com/articles/15536
last-modified: 2023-06-21
description: ObjectiveThe human Disabled-2 (Dab2) protein is an endocytic adaptor protein, which plays an essential role in endocytosis of transmembrane cargo, including low-density lipoprotein cholesterol (LDL-C). As a candidate gene for dyslipidemia, Dab2 is also involved in the development of type 2 diabetes mellitus(T2DM). The aim of this study was to investigate the effects of genetic variants of the Dab2 gene on the related risk of T2DM in the Uygur and Han populations of Xinjiang, China.MethodsA total of 2,157 age- and sex-matched individuals (528 T2DM patients and 1,629 controls) were included in this case-control study. Four high frequency SNPs (rs1050903, rs2255280, rs2855512 and rs11959928) of the Dab2 gene were genotyped using an improved multiplex ligation detection reaction (iMLDR) genotyping assay, and the forecast value of the SNP for T2DM was assessed by statistical analysis of clinical data profiles and gene frequencies.ResultsWe found that in the Uygur population studied, for both rs2255280 and rs2855512, there were significant differences in the distribution of genotypes (AA/CA/CC), and the recessive model (CC vs. CA + AA) between T2DM patients and the controls (P < 0.05). After adjusting for confounders, the recessive model (CC vs. CA + AA) of both rs2255280 and rs2855512 remained significantly associated with T2DM in this population (rs2255280: OR = 5.303, 95% CI [1.236 to −22.755], P = 0.025; rs2855512: OR = 4.892, 95% CI [1.136 to −21.013], P = 0.033). The genotypes (AA/CA/CC) and recessive models (CC vs. CA + AA) of rs2855512 and rs2255280 were also associated with the plasma glucose and HbA1c levels (all P < 0.05) in this population. There were no significant differences in genotypes, all genetic models, or allele frequencies between the T2DM and control group in the Han population group (all P > 0.05).ConclusionsThe present study suggests that the variation of the Dab2 gene loci rs2255280 and rs2855512 is related to the incidence of T2DM in the Uygur population, but not in the Han population. In this study, these variations in Dab2 were an independent predictor for T2DM in the Uygur population of Xinjiang, China.
creator: Yan-Peng Li
creator: Dilare Adi
creator: Ying-Hong Wang
creator: Yong-Tao Wang
creator: Xiao-Lei Li
creator: Zhen-Yan Fu
creator: Fen Liu
creator: Aibibanmu Aizezi
creator: Jialin Abuzhalihan
creator: Min-Tao Gai
creator: Xiang Ma
creator: Xiao-mei Li
creator: Xiang Xie
creator: Yi-Tong Ma
uri: https://doi.org/10.7717/peerj.15536
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Li et al.

title: Direct, indirect, and vicarious nature experiences collectively predict preadolescents’ self-reported nature connectedness and conservation behaviors
link: https://peerj.com/articles/15542
last-modified: 2023-06-21
description: BackgroundThe quantity and context of children’s nature experiences are undergoing significant changes, exacerbating a pervasive negative cycle that could impact future conservation efforts. Therefore, it is essential to conduct further studies on the potential impacts of these changes on children’s willingness to engage in conservation practices.MethodsWe surveyed 2,175 preadolescents (aged 9–12) from rural and city schools in Hangzhou, Kunming, and Xishuangbanna, China, regarding their nature experiences (direct, indirect, and vicarious) and self-reported nature connectedness and conservation behaviors.ResultsWe found that children in urban areas have higher frequencies of indirect and vicarious experiences than those in rural areas, with some direct nature experiences seldom reported among city respondents. Direct, indirect, and vicarious nature experiences significantly predicted children’s conservation behavior and collectively provided the highest predictive power for conservation behavior. Direct and vicarious experiences were strongly correlated with pro-nature behavior, and the latter with pro-environmental behavior. Emotional and cognitive connection with nature positively predicted conservation behavior, influenced by location and residence type.DiscussionThis study reveals that different types of nature experiences shape children’s current conservation behaviors in China.
creator: Zhihui Yue
creator: Jin Chen
uri: https://doi.org/10.7717/peerj.15542
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Yue and Chen

title: Cnidom in Ceriantharia (Cnidaria, Anthozoa): new findings in the composition and micrometric variations of cnidocysts
link: https://peerj.com/articles/15549
last-modified: 2023-06-21
description: BackgroundLike all cnidarians, the subclass Ceriantharia (Cnidaria, Anthozoa) is known for producing cnidocysts, which mainly serve for prey immobilization, predator defense, and locomotion.AimThe present study aimed to understand the variability of the cnidom, i.e., the inventory of all cnidocyst types, in the ceriantharians (tube anemones) Ceriantheomorphe brasiliensis (10 individuals) and Cerianthus sp. (seven individuals).MethodsIn each individual, 30 intact cnidocysts of each identified type were measured in the following parts of tube anemones: marginal tentacles (four from each individual), labial tentacles (four from each individual), column, actinopharynx and metamesenteries. Each of these structures was divided into three levels (high, middle, and low) and the cnidom was analyzed. Statistical descriptive parameters (mean, standard deviation, minimum and maximum) of the sizes of all types of cnidocysts were calculated. The normality of the data for cnidocyst length was assessed using a Shapiro-Wilk test (α = 0.05). Based on the acceptance or rejection of the normality, either linear models or generalized linear models were used to evaluate variations in cnidocyst lengths. The normality of the cnidocyst length was tested by Shapiro-Wilk, and due to its rejection, generalized linear mixed models were applied to test the cnidocyst lengths variations.ResultsThe analysis of Ceriantheomorphe brasiliensis revealed 23 categories of cnidocysts, thereby expanding the understanding of its cnidome. The cnidoms of Ceriantheomorphe brasiliensis and Cerianthus sp. presented intraspecific variations, both qualitatively and in the lengths of cnidocysts. The cnidoms of the two species studied also showed qualitative intra-individual variations between different levels (high, middle, low) within each structure of the tube anemone (tentacles, actinopharynx, column and metamesenteries). Some cnidocyst types, such as atrichs from the column of C. brasiliensis, presented a length gradient along the column, from larger lengths at the “low” level to smaller lengths at the “high” level.ConclusionsThe cnidom of a tube anemone could be better described if samples are taken at different levels of the structures, as observed in C. brasiliensis. In addition, we can conclude that the cnidocyst lengths of both C. brasiliensis and Cerianthus sp. present intraspecific variation, which is coincident with that observed in actiniarian sea anemones. Moreover, as main conclusion, this work also proved that individuals of tube anemone species could present qualitative intra-structure variations in both the cnidom and cnidocyst lengths. This characteristic appears as an exception in cnidom variations, and has so far not been recorded even in the most studied actiniarian sea anemones. Finally, the intra-structure cnidocyst variations could reveal different functions of the different levels of a particular body part of the organisms.
creator: Agustín Garese
creator: Fabiola Goes Correa
creator: Fabián H. Acuña
creator: Sérgio Nascimento Stampar
uri: https://doi.org/10.7717/peerj.15549
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Garese et al.

title: Response of in situ root phenotypes to potassium stress in cotton
link: https://peerj.com/articles/15587
last-modified: 2023-06-21
description: Potassium plays a significant role in the basic functions of plant growth and development. Potassium uptake is closely associated with morphological characteristics of the roots. However, the dynamic characteristics of phenotype and lifespan of cotton (Gossypium hirsutum L.) lateral roots and root hairs under low and high potassium stress remain unclear. In this study, potassium stress experiments (low and high potassium, medium potassium as control) were conducted using RhizoPot (an in situ root observation device) to determine the response characteristics of lateral roots and root hairs in cotton under potassium stress. The plant morphology, photosynthetic characteristics, root phenotypic changes, and lifespan of lateral roots and root hairs were measured. Potassium accumulation, aboveground phenotype, photosynthetic capacity, root length density, root dry weight, root diameter, lateral root lifespan, and root hair lifespan under low potassium stress were significantly decreased compared to medium potassium treatment. However, the root hair length of the former was significantly increased than that of the latter. Potassium accumulation and the lateral root lifespan were significantly increased under high potassium treatment, while root length density, root dry weight, root diameter, root hair length, and root hair lifespan were significantly decreased compared to the medium potassium treatment. Notably, there were no significant differences in aboveground morphology and photosynthetic characters. Principal component analysis revealed that lateral root lifespan, root hair lifespan of the first lateral root, and root hair length significantly correlated with potassium accumulation. The root had similar regularity responses to low and high potassium stress except for lifespan and root hair length. The findings of this study enhance the understanding of the phenotype and lifespan of cotton’s lateral roots and root hairs under low and high potassium stress.
creator: Heyang Tian
creator: Hongchun Sun
creator: Lingxiao Zhu
creator: Ke Zhang
creator: Yongjiang Zhang
creator: Haina Zhang
creator: Jijie Zhu
creator: Xiaoqing Liu
creator: Zhiying Bai
creator: Anchang Li
creator: Liwen Tian
creator: Liantao Liu
creator: Cundong Li
uri: https://doi.org/10.7717/peerj.15587
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Tian et al.

title: Identification of iron metabolism-related genes as prognostic indicators for papillary thyroid carcinoma: a retrospective study
link: https://peerj.com/articles/15592
last-modified: 2023-06-21
description: BackgroundThe thyroid cancer subtype that occurs more frequently is papillary thyroid carcinoma (PTC). Despite a good surgical outcome, treatment with traditional antitumor therapy does not offer ideal results for patients with radioiodine resistance, recurrence, and metastasis. The evidence for the connection between iron metabolism imbalance and cancer development and oncogenesis is growing. Nevertheless, the iron metabolism impact on PTC prognosis is still indefinite.MethodsHerein, we acquired the medical data and gene expression of individuals with PTC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. Typically, three predictive iron metabolism-related genes (IMRGs) were examined and employed to build a risk score (RS) model via the least absolute shrinkage and selection operator (LASSO) regression, univariate Cox, and differential gene expression analyses. Then we analyzed somatic mutation and immune cell infiltration among RS groups. We also validated the prognostic value of two IMRGs (SFXN3 and TFR2) by verifying their biological function through in vitro experiments.ResultsBased on RS, all patients with PTC were stratified into low- and high-risk groups, where Kaplan-Meier analysis indicated that disease-free survival (DFS) in the high-risk group was much lower than in the low-risk group (P < 0.0001). According to ROC analysis, the RS model successfully predicted the 1-, 3-, and 5-year DFS of individuals with PTC. Additionally, in the TCGA cohort, a nomogram model with RS was developed and exhibited a strong capability to anticipate PTC patients’ DFS. In the high-risk group, the enriched pathological processes and signaling mechanisms were detected utilizing the gene set enrichment analysis (GSEA). Moreover, the high-risk group had a significantly higher level of BRAF mutation frequency, tumor mutation burden, and immune cell infiltration than the low-risk group. In vitro experiments found that silencing SFXN3 or TFR2 significantly reduced cell viability.ConclusionCollectively, our predictive model depended on IMRGs in PTC, which could be potentially utilized to predict the PTC patients’ prognosis, schedule follow-up plans, and provide potential targets against PTC.
creator: Tiefeng Jin
creator: Luqi Ge
creator: Jianqiang Chen
creator: Wei Wang
creator: Lizhuo Zhang
creator: Minghua Ge
uri: https://doi.org/10.7717/peerj.15592
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Jin et al.

title: Genotypic characteristics of Uropathogenic Escherichia coli isolated from complicated urinary tract infection (cUTI) and asymptomatic bacteriuria—a relational analysis
link: https://peerj.com/articles/15305
last-modified: 2023-06-20
description: BackgroundUropathogenic Escherichia coli (UPEC) is the predominant agent causing various categories of complicated urinary tract infections (cUTI). Although existing data reveals that UPEC harboured numerous virulence determinants to aid its survival in the urinary tract, the reason behind the occurrence of differences in the clinical severity of uninary tract infections (UTI) demonstrated by the UPEC infection is poorly understood. Therefore, the present study aims to determine the distribution of virulence determinants and antimicrobial resistance among different phylogroups of UPEC isolated from various clinical categories of cUTI and asymptomatic bacteriuria (ASB) E. coli isolates. The study will also attempt a relational analysis of the genotypic characteristics of cUTI UPEC and ASB E. coli isolates.MethodsA total of 141 UPEC isolates from cUTI and 160 ASB E. coli isolates were obtained from Universiti Malaya Medical Centre (UMMC). Phylogrouping and the occurrence of virulence genes were investigated using polymerase chain reaction (PCR). Antimicrobial susceptibility of the isolates to different classes of antibiotics was determined using the Kirby Bauer Disc Diffusion method.ResultsThe cUTI isolates were distributed differentially among both Extraintestinal Pathogenic E. coli (ExPEC) and non-ExPEC phylogroups. Phylogroup B2 isolates were observed to possess the highest average aggregative virulence score (7.17), a probable representation of the capability to cause severe disease. Approximately 50% of the cUTI isolates tested in this study were multidrug resistant against common antibiotics used to treat UTI. Analysis of the occurrence of virulence genes among different cUTI categories demonstrated that UPEC isolates of pyelonephritis and urosepsis were highly virulent and had the highest average aggregative virulence scores of 7.80 and 6.89 respectively, compared to other clinical categories. Relational analysis of the occurrence of phylogroups and virulence determinants of UPEC and ASB E. coli isolates showed that 46.1% of UPEC and 34.3% of ASB E. coli from both categories were distributed in phylogroup B2 and had the highest average aggregative virulence score of 7.17 and 5.37, respectively. The data suggest that UPEC isolates which carry virulence genes from all four virulence genes groups studied (adhesions, iron uptake systems, toxins and capsule synthesis) and isolates from phylogroup B2 specifically could predispose to severe UTI involving the upper urinary tract. Therefore, specific analysis of the genotypic characteristics of UPEC could be further explored by incorporating the combination of virulence genes as a prognostic marker for predicting disease severity, in an attempt to propose a more evidence driven treatment decision-making for all UTI patients. This will go a long way in enhancing favourable therapeutic outcomes and reducing the antimicrobial resistance burden among UTI patients.
creator: Lalitha Maniam
creator: Kumutha Malar Vellasamy
creator: Teng Aik Ong
creator: Cindy Shuan Ju Teh
creator: Kartini Abdul Jabar
creator: Vanitha Mariappan
creator: Vallikkannu Narayanan
creator: Jamuna Vadivelu
creator: Vinod Pallath
uri: https://doi.org/10.7717/peerj.15305
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Maniam et al.

title: Spatial and temporal population genetic analysis of Semaprochilodus insignis (Prochilodontidae), an overexploited fish from the Amazon basin
link: https://peerj.com/articles/15503
last-modified: 2023-06-20
description: BackgroundSemaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks.MethodsThis study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin.ResultsResults for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon.DiscussionAlthough overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.
creator: Ingrid Nunes
creator: Kelmer Passos
creator: Aline Mourão Ximenes
creator: Tomas Hrbek
creator: Izeni Pires Farias
uri: https://doi.org/10.7717/peerj.15503
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Nunes et al.

title: The reliability and validity of repeat power ability assessments and measurement indices in loaded vertical jumps
link: https://peerj.com/articles/15553
last-modified: 2023-06-20
description: BackgroundRepeat power ability (RPA) assessments are a valuable evaluation of an athlete’s ability to repeatedly perform high intensity movements. Establishing the most reliable and valid loaded jump RPA assessment and method to quantify RPA has yet to be determined. This study aimed to compare the reliability and validity of an RPA assessment performed with loaded squat jumps (SJ) or countermovement jumps (CMJ) using force-time derived mean and peak power output.Materials and MethodsRPA was quantified using calculations of average power output, a fatigue index and a percent decrement score for all repetitions and with the first and last repetitions removed. Validity was established by comparing to a 30 second Bosco repeated jump test (30BJT). Eleven well-trained male field hockey players performed one set of 20 repetitions of both SJs (20SJ) and CMJs (20CMJ) on separate occasions using a 30% one repetition maximum half squat load. These assessments were repeated 7 days apart to establish inter-test reliability. On a separate occasion, each participant performed the 30BJT.ResultsThe reliability of average peak power for 20SJ and 20CMJ was acceptable (CV < 5%; ICC > 0.9), while average mean power reliability for 20CMJ (CV < 5%; ICC > 0.9) was better than 20SJ (CV > 5%; ICC > 0.8). Percent decrement of 20CMJ peak power, with the first and final jump removed from the percent decrement calculation (PD%CMJpeak18), was the most reliable measurement of power output decline (CV < 5 %; ICC > 0.8). Average mean and peak power for both RPA protocols had moderate to strong correlations with 30BJT average mean and peak power (r = 0.5–0.8; p< 0.05–0.01). No RPA measurements of power decline were significantly related to BJT measurements of power decline.ConclusionsThese findings indicate that PD%CMJpeak18 is the most reliable measure of RPA power decline. The lack of relationship between power decline in the loaded RPA and the 30BJT assessment suggest that each assessment may be measuring a different physical quality. These results provide sport science practitioners with additional methods to assess RPA and provide useful information on the reliability and validity of these outcome measures. Additional research needs to be performed to examine the reliability and validity of the novel RPA assessments in other athletic populations and to determine the sensitivity of these measurements to training and injury.
creator: Alex O. Natera
creator: Dale W. Chapman
creator: Neil D. Chapman
creator: Justin W.L. Keogh
uri: https://doi.org/10.7717/peerj.15553
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Natera et al.

title: Exploring the molecular basis of resistance to Botrytis cinerea in chickpea genotypes through biochemical and morphological markers
link: https://peerj.com/articles/15560
last-modified: 2023-06-20
description: Chickpea (Cicer arietinum L.) is an important pulse crop around the globe and a valuable source of protein in the human diet. However, it is highly susceptible to various plant pathogens such as fungi, bacteria, and viruses, which can cause significant damage from the seedling phase until harvest, leading to reduced yields and affecting its production. Botrytis cinerea can cause significant damage to chickpea crops, especially under high humidity and moisture conditions. This fungus can cause grey mould disease, which can lead to wilting, stem and pod rot, and reduced yields. Chickpea plants have developed specific barriers to counteract the harmful effects of this fungus. These barriers include biochemical and structural defences. In this study, the defence responses against B. cinerea were measured by the quantification of biochemical metabolites such as antioxidant enzymes, malondialdehyde (MDA), proline, glutathione (GSH), H2O2, ascorbic acid (AA) and total phenol in the leaf samples of chickpea genotypes (one accession of wild Cicer species, viz. Cicer pinnatifidum188 identified with high level of resistance to Botrytis grey mould (BGM) and a cultivar, Cicer arietinumPBG5 susceptible to BGM grown in the greenhouse). Seedlings of both the genotypes were inoculated with (1 × 104 spore mL−1) inoculum of isolate 24, race 510 of B. cinerea and samples were collected after 1, 3, 5, and 7 days post-inoculation (dpi). The enhanced enzymatic activity was observed in the pathogen-inoculated leaf samples as compared to uninoculated (healthy control). Among inoculated genotypes, the resistant one exhibited a significant change in enzymatic activity, total phenolic content, MDA, proline, GSH, H2O2, and AA, compared to the susceptible genotype. The study also examined the isozyme pattern of antioxidant enzymes at various stages of B. cinerea inoculation. Results from scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy revealed that BGM had a more significant impact on susceptible genotypes compared to resistant ones when compared to the control (un-inoculated). In addition, SEM and FTIR spectroscopy analyses confirmed the greater severity of BGM on susceptible genotypes compared to their resistant counterparts. Our results suggest the role of antioxidant enzymes and other metabolites as defence tools and biochemical markers to understand compatible and non-compatible plant-pathogen interactions better. The present investigation will assist future plant breeding programs aimed at developing resistant varieties.
creator: Richa Thakur
creator: Sucheta Sharma
creator: Rajni Devi
creator: Asmita Sirari
creator: Rahul Kumar Tiwari
creator: Milan Kumar Lal
creator: Ravinder Kumar
uri: https://doi.org/10.7717/peerj.15560
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Thakur et al.

title: Revisiting the evolutionary trend toward the mammalian lower jaw in non-mammalian synapsids in a phylogenetic context
link: https://peerj.com/articles/15575
last-modified: 2023-06-20
description: The mammalian lower jaw comprises a single bone, the dentary, which is a unique feature among vertebrates. The lower jaws of extinct non-mammalian synapsids were composed of the dentary and several postdentary bones. Synapsid fossils exhibit variation in the dentary size relative to the overall lower jaw. An evolutionary trend toward dentary enlargement and postdentary reduction in non-mammalian synapsids has long been documented but has not been established using modern phylogenetic comparative methods. In this study, we examine the evolutionary pattern of dentary size relative to the lower jaw through phylogenetic analyses of measurements in a broad range of non-mammalian synapsid taxa. Our analyses revealed an evolutionary trend toward dentary area enlargement relative to the overall lower jaw in the lateral view across all non-mammalian synapsids. This trend is likely due to vertical expansion of the dentary given that the same trend is not evident when looking at anterior to posterior measurements of the dentary relative to the lower jaw as a whole in lateral view. Ancestral character reconstructions revealed that the evolution of the measurements was not unidirectional in non-mammalian synapsids. Our results provide no evidence of an evolutionary trend toward the dentary enlargement at the expense of postdentary bones across non-mammalian synapsids. This implies that the evolutionary origin of the mammalian lower jaw is not adequately explained by the evolutionary trend of dentary enlargement throughout non-mammalian synapsids. Instead, selection that occurred during the transition from non-mammalian cynodonts to early mammals may have produced the mammalian lower jaw.
creator: Tomohiro Harano
creator: Masakazu Asahara
uri: https://doi.org/10.7717/peerj.15575
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Harano and Asahara