title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=527 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity link: https://peerj.com/articles/14894 last-modified: 2023-04-24 description: BackgroundCashew (Anacardium occidentale L.) is a crop currently grown in several tropical countries because of the economic importance of cashew nuts. Despite its enormous economic worth, limited research has been conducted on the molecular diversity of cashew genetic resources. In this study, a wide comprehensive assessment of the genetic diversity of cashew trees in East Timor was performed using microsatellites (SSRs) to evaluate intraspecific diversity and population structuring.MethodsA total of 207 individual cashew trees, including trees from East Timor (11), and outgroup populations from Indonesia (one) and Mozambique (two), were analyzed with 16 cashew-specific SSRs. A comprehensive sampling of cashew trees within East Timor was performed, covering the distribution of cashew orchards in the country. Genetic diversity indices were calculated, and population structuring was determined using three different approaches: genetic distances (UPGMA and NJ), AMOVA, and individual-based clustering methods through Bayesian (STRUCTURE) and multivariate (DAPC) analyses.ResultsThe population structuring analysis revealed that the genetic diversity of cashew populations in East Timor was higher in this study than previously reported for cashew trees. A higher allelic richness was found within cashew populations in East Timor compared with the outgroup populations (Mozambique and Indonesia), reinforced by the presence of private alleles. Moreover, our study showed that cashew populations in East Timor are grouped into two dissimilar genetic groups, which may suggest multiple cashew introductions over time. These new cashew genetic resources could be explored for future crop improvement.ConclusionsCrop diversity underpins the productivity, resilience, and adaptive capacity of agriculture. Therefore, this study provides useful information regarding genetic diversity and population structure that can be harnessed to improve cashew production in East Timor. This data is also important to creating a country-specific genetic cashew signature to increase cashew market value. creator: Lara Guterres creator: João Barnabé creator: André Barros creator: Alberto Bento Charrua creator: Maria Cristina Duarte creator: Maria M. Romeiras creator: Filipa Monteiro uri: https://doi.org/10.7717/peerj.14894 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guterres et al. title: Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park link: https://peerj.com/articles/15083 last-modified: 2023-04-24 description: Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model’s predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities. creator: Alexander Weiss creator: Joseph T. Feldblum creator: Drew M. Altschul creator: David Anthony Collins creator: Shadrack Kamenya creator: Deus Mjungu creator: Steffen Foerster creator: Ian C. Gilby creator: Michael L. Wilson creator: Anne E. Pusey uri: https://doi.org/10.7717/peerj.15083 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Weiss et al. title: In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease link: https://peerj.com/articles/15086 last-modified: 2023-04-24 description: Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development. creator: Kanpong Boonthaworn creator: Kowit Hengphasatporn creator: Yasuteru Shigeta creator: Warinthorn Chavasiri creator: Thanyada Rungrotmongkol creator: Puey Ounjai uri: https://doi.org/10.7717/peerj.15086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Boonthaworn et al. title: Hidden diversity: comparative functional morphology of humans and other species link: https://peerj.com/articles/15148 last-modified: 2023-04-24 description: Gastrointestinal (GI) morphology plays an important role in nutrition, health, and epidemiology; yet limited data on GI variation have been collected since 1885. Here we demonstrate that students can collect reliable data sets on gut morphology; when they do, they reveal greater morphological variation for some structures in the GI tract than has been documented in the published literature. We discuss trait variability both within and among species, and the implications of that variability for evolution and epidemiology. Our results show that morphological variation in the GI tract is associated with each organ’s role in food processing. For example, the length of many structures was found to vary significantly with feeding strategy. Within species, the variability illustrated by the coefficients of variation suggests that selective constraints may vary with function. Within humans, we detected significant Pearson correlations between the volume of the liver and the length of the appendix (t-value = 2.5278, df = 28, p = 0.0174, corr = 0.4311) and colon (t-value = 2.0991, df = 19, p = 0.0494, corr = 0.4339), as well as between the lengths of the small intestine and colon (t-value = 2.1699, df = 17, p = 0.0445, corr = 0.4657), which are arguably the most vital organs in the gut for nutrient absorption. Notably, intraspecific variation in the small intestine can be associated with life history traits. In humans, females demonstrated consistently and significantly longer small intestines than males (t-value15 = 2.245, p = 0.0403). This finding supports the female canalization hypothesis, specifically, increased female investment in the digestion and absorption of lipids. creator: Erin A. McKenney creator: Amanda R. Hale creator: Janiaya Anderson creator: Roxanne Larsen creator: Colleen Grant creator: Robert R. Dunn uri: https://doi.org/10.7717/peerj.15148 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 McKenney et al. title: Effects of ambient temperature on atopic dermatitis and attributable health burden: a 6-year time-series study in Chengdu, China link: https://peerj.com/articles/15209 last-modified: 2023-04-24 description: BackgroundDespite increasing public concerns about the widespread health effects of climate change, the impacts of ambient temperature on atopic dermatitis (AD) remain poorly understood.ObjectivesWe aimed to explore the effect of ambient temperature on AD and to estimate the burdens of AD attributed to extreme temperature.MethodsData on outpatients with AD and climate conditions in Chengdu, China were collected. A distributed lag nonlinear model (DLNM) was adopted to explore the association between daily mean temperature and AD outpatient visits. Subgroup analysis was used to identify vulnerable populations. Attributable burden was estimated by the epidemiological attributable method.ResultsWe analyzed 10,747 outpatient visits from AD patients at West China Hospital in Chengdu between January 1, 2015, and December 31, 2020. Both low (<19.6 °C) and high temperatures (>25.3 °C) were associated with increased AD outpatient visits, with the increase being more pronounced at low temperature, as evidenced by a 160% increase in visits when the temperature dropped below zero from the minimum mortality temperature (22.8 °C). Children and males were the most susceptible populations. Approximately 25.4% of AD outpatient visits were associated with temperatures, causing an excessive 137161.5 US dollars of health care expenditures during this 6-year period.ConclusionsBoth high and low temperatures, particularly low temperatures, were significantly associated with an increased risk of AD, with children and males showing the strongest associations. Extreme environmental temperature has been identified as one of the major factors promoting the development of AD. However, individual patient-level exposures still needed to be investigated in future studies to confirm the causality between temperature and AD. creator: Zerong Chen creator: Mengmeng Li creator: Tianjiao Lan creator: Yiyi Wang creator: Xingli Zhou creator: Wei Dong creator: Gong Cheng creator: Wei Li creator: Liangliang Cheng uri: https://doi.org/10.7717/peerj.15209 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Chen et al. title: Mapping the global distribution of invasive pest Drosophila suzukii and parasitoid Leptopilina japonica: implications for biological control link: https://peerj.com/articles/15222 last-modified: 2023-04-24 description: Insect pest invasions cause significant damage to crop yields, and the resultant economic losses are truly alarming. Climate change and trade liberalization have opened new ways of pest invasions. Given the consumer preference towards organic agricultural products and environment-friendly nature of natural pest control strategies, biological control is considered to be one of the potential options for managing invasive insect pests. Drosophila suzukii (Drosophilidae) is an extremely damaging fruit pest, demanding development of effective and sustainable biological control strategies. In this study, we assessed the potential of the parasitoid Leptopilina japonica (Figitidae) as a biocontrol agent for D. suzukii using ecological niche modeling approaches. We developed global-scale models for both pest and parasitoid to identify four components necessary to derive a niche based, target oriented prioritization approach to plan biological control programs for D. suzukii: (i) potential distribution of pest D. suzukii, (ii) potential distribution of parasitoid L. japonica, (iii) the degree of overlap in potential distributions of pest and parasitoid, and (iv) biocontrol potential of this system for each country. Overlapping suitable areas of pest and parasitoid were identified at two different thresholds and at the most desirable threshold (E = 5%), potential for L. japonica mediated biocontrol management existed in 125 countries covering 1.87 × 107 km2, and at the maximum permitted threshold (E = 10%), land coverage was reduced to 1.44 × 107 km2 in 121 countries. Fly pest distributional information as a predictor variable was not found to be improving parasitoid model performance, and globally, only in half of the countries, >50% biocontrol coverage was estimated. We therefore suggest that niche specificities of both pest and parasitoid must be included in site-specific release planning of L. japonica for effective biocontrol management aimed at D. suzukii. This study can be extended to design cost-effective pre-assessment strategies for implementing any biological control management program. creator: Rahul R. Nair creator: A. Townsend Peterson uri: https://doi.org/10.7717/peerj.15222 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nair and Peterson title: Association of ApoE gene polymorphisms with serum lipid levels and the risk of type 2 diabetes mellitus in the Chinese Han population of central China link: https://peerj.com/articles/15226 last-modified: 2023-04-24 description: BackgroundApolipoprotein E (ApoE) is involved in lipid transformation and metabolism. Although some studies have examined the association between ApoE polymorphisms and the risk of type 2 diabetes mellitus (T2DM), the findings differ depending on the location and population.MethodsA total of 1,738 participants, including 743 patients with T2DM and 995 controls without T2DM, were enrolled from central China, and ApoE polymorphisms, 388T > C (rs429358) and 526C > T (rs7412), were genotyped. The association between ApoE alleles and T2DM and blood lipid levels was analyzed. Logistic regression analysis was performed to evaluate the interactions between ApoE polymorphisms and various factors, such as age, sex, and prevalence of hypertension in patients with T2DM.ResultsThe genotype ɛ3/ɛ4 and ɛ4 alleles of ApoE were associated with T2DM risk in the Chinese Han population in central China. Moreover, in patients with T2DM, participants in the E4 (ɛ3/ɛ4, ɛ4/ɛ4) group had significantly higher lipid profiles than those in the E3 (ɛ3/ɛ3) group, whereas participants in the E2 group (ɛ2/ɛ2, ɛ2/ɛ3) showed lower total cholesterol, low-density lipoprotein cholesterol, and ApoE-A1 levels than those in the E3 (ɛ3/ɛ3) group. The results from the current study may help in understanding ApoE polymorphisms and lipid profiles in the Chinese Han population. creator: Yali Zeng creator: Shuang Wen creator: Lijun Huan creator: Liang Xiong creator: Botao Zhong creator: Pengyun Wang uri: https://doi.org/10.7717/peerj.15226 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zeng et al. title: Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat link: https://peerj.com/articles/15231 last-modified: 2023-04-24 description: Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences. creator: Wenli Chen creator: Weiwei Zhou creator: Qianqian Li creator: Xiuguang Mao uri: https://doi.org/10.7717/peerj.15231 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Uncovering the potential functions of lymph node metastasis-associated aberrant methylation differentially expressed genes and their association with the immune infiltration and prognosis in bladder urothelial carcinoma link: https://peerj.com/articles/15284 last-modified: 2023-04-24 description: BackgroundBladder urothelial carcinoma (BLCA) is a malignant tumor of the urinary system. This study aimed to explore the potential role of lymph node metastasis-associated aberrant methylation differentially expressed genes (DEGs) in BLCA.MethodsCHAMP and limma packages were used to identify lymph node metastasis-associated aberrant methylation DEGs. Univariate Cox analysis and Lasso analysis were performed to identify the signature genes, and multivariate Cox analysis was used to construct the risk score. Subsequently, the molecular characteristics of the signature genes and the relationship between risk score and prognosis, clinical characteristics and immune cell infiltration were analyzed. The signature gene AKAP7 was selected for functional verification.ResultsA novel risk score model was constructed based on 12 signature genes. The risk score had a good ability to predict overall survival (OS). The nomogram constructed based on age, N stage and risk score had a higher value in predicting the prognosis of patients. It was also found that stromal activation in TIME may inhibit the antitumor effects of immune cells. Functional enrichment analysis revealed that ECM receptor interaction and focal adhesion were two important pathways involved in the regulation of BLCA. Immunohistochemistry showed that AKAP7 may be associated with the occurrence, clinical stages and grades, and lymph node metastasis of BLCA. In vitro cell experiments showed that the migration and invasion ability of EJ cells was significantly inhibited after AKAP7 overexpression, while the migration and invasion ability of T24 cells was significantly promoted after AKAP7 knockdown.ConclusionThe risk score model based on lymph node metastasis-associated aberrant methylation DEGs has a good ability to predict OS and is an independent prognostic factor for BLCA. It was also found that stromal activation in TIME may inhibit the antitumor effects of immune cells. This implicates aberrant methylation modifications as an important factor contributing to the heterogeneity and complexity of individual tumor microenvironments. Functional enrichment analysis revealed that ECM receptor interaction and focal adhesion were two important pathways involved in the regulation of BLCA, which contributed to the exploration of the pathological mechanism of BLCA. In addition, immunohistochemistry showed that AKAP7 may be associated with the occurrence, progression and lymph node metastasis of BLCA. In vitro cell experiments showed that AKAP7 could also inhibit the migration and invasion of cancer cells. creator: Wenzhi Gao creator: Jiafeng Zhang creator: Tai Tian creator: Zhixin Fu creator: Liangliang Bai creator: Yifei Yang creator: Qiangqiang Wu creator: Wei Wang creator: Yuexian Guo uri: https://doi.org/10.7717/peerj.15284 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gao et al. title: Effects of two different dual-task training protocols on gait, balance, and cognitive function in community-dwelling older adults: a 24-week randomized controlled trial link: https://peerj.com/articles/15030 last-modified: 2023-04-21 description: BackgroundAlthough alternating dual-task (ADT) training is functionally easier for older adults, a large part of the motor and cognitive tasks is simultaneously performed, especially during activities of daily living that require maintaining body balance.ObjectiveTo evaluate the effects of mixed dual-task training on mobility, cognitive function, and balance in community-dwelling older adults.MethodsSixty participants were randomly allocated at a 1:1 ratio into the experimental group—single motor task (SMT) and simultaneous dual task (SDT) interchangeably in stage 1 (for 12 weeks) and after strictly with SDT in stage 2 (the last 12 weeks)—or into the control group—only SMT and SDT interchangeably in stages 1 and 2. Gait parameters were acquired by two inertial sensors. Physical and cognitive performance were acquired by specific questionnaires. Generalized linear mixed models were used for analyzing interaction and main effects.ResultsNo between-group difference was observed for gait performance. Both protocols improved mobility (mean change ((MC) = 0.74)), dual-task effect (MC = −13.50), lower limb function (MC = 4.44), static (MC = −0.61), and dynamic balance (MC = −0.23), body sway (MC = 4.80), and cognitive function (MC = 41.69).ConclusionBoth dual-task training protocols improved these outcomes. creator: Francis Trombini-Souza creator: Vitória Thaysa Gomes de Moura creator: Lucas Willian Nunes da Silva creator: Iara dos Santos Leal creator: Cleber Anderson Nascimento creator: Paloma Sthefane Teles Silva creator: Monica Rodrigues Perracini creator: Isabel CN Sacco creator: Rodrigo Cappato de Araújo creator: Marcelo de Maio Nascimento uri: https://doi.org/10.7717/peerj.15030 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Trombini-Souza et al.