title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=549 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Adherence to the Mediterranean diet, kinanthropometric characteristics and physical performance of young male handball players link: https://peerj.com/articles/14329 last-modified: 2022-12-01 description: IntroductionHandball is a team sport whose performance depends on a large number of factors. The objectives of the present study were to analyze the differences in physical performance, kinanthropometric variables, and adherence to the Mediterranean diet (MD), in handball players according to sports category, as well as the possible relationships between these variables.MethodsOne hundred and thirty-three male handball players (35 infant; 46 cadets; 26 juniors and 26 seniors players) underwent a kinanthropometric analysis following the ISAK protocol, self-completed the KIDMED questionnaire, and their physical condition was evaluated with different physical tests.ResultsSignificant differences (p < 0.001–0.007) were found between the sports categories in most of the physical condition variables and anthropometric characteristics, but not in the degree of adherence to the MD. The predominant level of adherence to the MD was medium (47.4%), followed by good (42.1%), and correlated with the body mass, the height, the BMI, the muscle mass and the ∑3-girths sum corrected, but not with physical test results. A multiple linear regression analysis showed that the fat mass and muscle mass variables had a more specific weight in the results of the physical fitness tests.ConclusionsThere are differences according to sports category in kinanthropometric characteristics and physical fitness tests in adolescent handball players. The predominant degrees of adherence to the MD were medium and good. A relationship was found between anthropometric characteristics and physical performance in handball players. creator: David Romero-García creator: Francisco Esparza-Ros creator: María Picó García creator: José Miguel Martínez-Sanz creator: Raquel Vaquero-Cristóbal uri: https://doi.org/10.7717/peerj.14329 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Romero-García et al. title: METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner link: https://peerj.com/articles/14379 last-modified: 2022-12-01 description: BackgroundAs the most prevalent chemical modifications on eukaryotic mRNAs, N6-methyladenosine (m6A) methylation was reported to participate in the regulation of various metabolic diseases. This study aimed to investigate the roles of m6A methylation and methyltransferase-like16 (METTL16) in non-alcoholic fatty liver disease (NAFLD).MethodsIn this study, we used a model of diet-induced NAFLD, maintaining six male C57BL/6J mice on high-fat diet (HFD) to generate hepatic steatosis. The high-throughput sequencing and RNA sequencing were performed to identify the m6A methylation patterns and differentially expressed mRNAs in HFD mice livers. Furthermore, we detected the expression levels of m6A modify enzymes by qRT-PCR in liver tissues, and further investigated the potential role of METTL16 in NAFLD through constructing overexpression and a knockdown model of METTL16 in HepG2 cells.ResultsIn total, we confirmed 15,999 m6A recurrent peaks in HFD mice and 12,322 in the control. Genes with differentially methylated m6A peaks were significantly associated with the dysregulated glucolipid metabolism and aggravated hepatic inflammatory response. In addition, we identified five genes (CIDEA, THRSP, OSBPL3, GDF15 and LGALS1) that played important roles in NAFLD progression after analyzing the differentially expressed genes containing differentially methylated m6A peaks. Intriguingly, we found that the expression levels of METTL16 were substantially increased in the NAFLD model in vivo and in vitro, and further confirmed that METTL16 upregulated the expression level of lipogenic genes CIDEA in HepG2 cells.ConclusionsThese results indicate the critical roles of m6A methylation and METTL16 in HFD-induced mice and cell NAFLD models, which broaden people’s perspectives on potential m6A-related treatments and biomarkers for NAFLD. creator: Jinhong Tang creator: Xiangyun Zhao creator: Wei Wei creator: Weiwei Liu creator: Huining Fan creator: Xiu ping Liu creator: Yungai Li creator: Long Wang creator: Jinghui Guo uri: https://doi.org/10.7717/peerj.14379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tang et al. title: Effects of land use types on soil erodibility in a small karst watershed in western Hubei link: https://peerj.com/articles/14423 last-modified: 2022-12-01 description: BackgroundSoil erosion is a severe problem in the karst watershed, and analysis of soil erosion at the watershed scale is urgently needed.MethodsThis study tried to estimate the soil erodibility factor (K-factor) using the Erosion Productivity Impact Calculator (EPIC) nomograph and evaluate the spatial distribution of the predicted K-factor in a karst watershed. Soil properties and K-factors of five land use types (NF: natural mixed forest, CF: cypress forest, EF: economic forest, ST: stone dike terrace, VF: vegetable land) in the Xialaoxi small watershed were compared and key factors affecting erodibility were analyzed.ResultsResults showed that (1) The erodibility K-factor was unevenly distributed within different site types and strongly influenced by anthropogenic activities. The soil K-factors of sample sites subjected to frequent human disturbance (ST, VF) were high, ranging from 0.0480-0.0520 t hm2 h/(MJ mm hm2), while the soil K-factors of natural site types (NF, CF, and EF) were low, ranging from 0.0436-0.0448 t hm2 h/(MJ mm hm2). (2) The soil texture in the Xialaoxi watershed was mostly loamy, and that of the agricultural areas frequently disturbed by agricultural practices (ST, VF) was silty loam. (3) Soil carbon fractions were affected by land use types. Soil organic carbon storage of NF and CF had strong spatial heterogeneity. The soil organic carbon (SOC) and labile organic carbon (LOC) of the two were significantly higher than those of the disturbed EF and cultivated land soil. (4) There was a synergistic effect between the soil properties and the K-factor. K was significantly negatively related to sand fractions (2-0.05 mm) and non-capillary porosity, while positively related to silt content (0.05–0.002 mm). Overall, changes in bulk density (BD), total porosity (TP), non-capillary porosity (NCP), texture, and organic matter content caused by natural restoration or anthropogenic disturbance were the main reasons for soil erodibility. Natural care (sealing) and construction of stone dike planting practices were effective ways to reduce soil erosion in small karst watershed areas of western Hubei. creator: Ting Luo creator: Wenjing Liu creator: Dong Xia creator: Lu Xia creator: Ting Guo creator: Yueyang Ma creator: Wennian Xu creator: Yue Hu uri: https://doi.org/10.7717/peerj.14423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Luo et al. title: Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L link: https://peerj.com/articles/14452 last-modified: 2022-12-01 description: Foxtail millet is commonly used as a food and forage grass. ERECTA (ER) is a receptor-like kinase that can improve plant biomass and stress resistance. The sorghum SbER10_X1 gene was used as a probe to identify ER family genes on the Setaria italica genomes (SiERs), and determine the characteristics of the SiERs family. Herein, the structural features, expression patterns, and thermotolerance of SiERs function were identified by bioinformatics analysis, real-time PCR and transgenesis estimation. Results showed that SiERs had four members: two members were located on chromosome 1 with a total of six copies (SiER1_X1, SiER1_X2, SiER1_X3, SiER1_X4, SiER1_X5, and SiER1_X6), and two were on chromosome 4, namely, SiER4 (SiER4_X1 and SiER4_X2) and SiERL1. Among them, SiER1_X4 and SiER4_X1 were expressed highest in above-ground organs of foxtail millet, and actively responded to treatments with abscisic acid, brassinolide, gibberellin, and indole acetic acid. After overexpression of SiER1_X4 and SiER4_X1 in Arabidopsis, the plant height and biomass of the transgenic Arabidopsis significantly increased. Following high-temperature treatment, transgenic seedlings survived better compared to wild type. Transgenic lines showed higher SOD and POD activities, and expression level of AtHSF1 and AtBl1 genes significantly increased. These results indicated that SiER1_X4 and SiER4_X1 played important regulatory roles in plant growth and thermotolerance. The two genes provide potential targets for conventional breeding or biotechnological intervention to improve the biomass of forage grass and thermotolerance of field crops. creator: Jiacheng Zheng creator: Xiaoyi Huang creator: Jieqin Li creator: Qingyuan He creator: Wan Zhao creator: Chaowu Zeng creator: Haizhou Chen creator: Qiuwen Zhan creator: Zhaoshi Xu uri: https://doi.org/10.7717/peerj.14452 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zheng et al. title: A systematic review of effects of daytime napping strategies on sports performance in physically active individuals with and without partial-sleep deprivation link: https://peerj.com/articles/14460 last-modified: 2022-12-01 description: BackgroundSleep is the body’s natural recovery process, restoring routine metabolic and regulatory functions. Various sleep interventions have been developed to facilitate recovery, and athletic performance, and daytime napping are among them. However, due to inconsistencies in studies, it remains unclear whether daytime napping affects sports performance. This article aims to review the effects of daytime napping on various variables of sports performance in physically active individuals with and without partial-sleep deprivation.MethodsA systematic search in three clinical databases, namely Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and Web of Science, was conducted. To be included in the current review, the study should be a randomized controlled trial that evaluated the influence of daytime napping on one or more components of sports performance in healthy adults, 18 years old or older.ResultsIn the accessible data available until December 2021, 1,094 records were found, of which 12 relevant randomized controlled trials were selected for qualitative synthesis. The majority of studies reported favourable effects of daytime napping on sports performance. However, only one study reported no significant impact, possibly due to a different methodological approach and a shorter nap duration.ConclusionNapping strategies optimize sports performance in physically active, athletic populations, benefitting partially sleep-deprived and well-slept individuals, with longer nap durations (~90 min) having more significant advantages. Daytime naps can be considered as cost-efficient, self-administered methods promoting recovery of body functions. creator: Priya Sirohi creator: Moazzam Hussain Khan creator: Saurabh Sharma creator: Shibili Nuhmani creator: Wafa Hashem Al Muslem creator: Turki Abualait uri: https://doi.org/10.7717/peerj.14460 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sirohi et al. title: Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication link: https://peerj.com/articles/14471 last-modified: 2022-12-01 description: Humans and other mammalian species communicate emotions in ways that reflect evolutionary conservation and continuity, an observation first made by Darwin. One approach to testing this hypothesis has been to assess the capacity to perceive the emotional content of the vocalizations of other species. Using a binary forced choice task, we tested perception of the emotional intensity represented in coos and screams of infant and juvenile female rhesus macaques (Macaca mulatta) by 113 human listeners without, and 12 listeners with, experience (as researchers or care technicians) with this species. Each stimulus pair contained one high- and one low-arousal vocalization, as measured at the time of recording by stress hormone levels for coos and the degree of intensity of aggression for screams. For coos as well as screams, both inexperienced and experienced participants accurately identified the high-arousal vocalization at significantly above-chance rates. Experience was associated with significantly greater accuracy with scream stimuli but not coo stimuli, and with a tendency to indicate screams as reflecting greater emotional intensity than coos. Neither measures of empathy, human emotion recognition, nor attitudes toward animal welfare showed any relationship with responses. Participants were sensitive to the fundamental frequency, noisiness, and duration of vocalizations; some of these tendencies likely facilitated accurate perceptions, perhaps due to evolutionary homologies in the physiology of arousal and vocal production between humans and macaques. Overall, our findings support a view of evolutionary continuity in emotional vocal communication. We discuss hypotheses about how distinctive dimensions of human nonverbal communication, like the expansion of scream usage across a range of contexts, might influence perceptions of other species’ vocalizations. creator: Jay W. Schwartz creator: Harold Gouzoules uri: https://doi.org/10.7717/peerj.14471 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Schwartz and Gouzoules title: Differential responses of the seed germination of three functional groups to low temperature and darkness in a typical steppe, Northern China link: https://peerj.com/articles/14485 last-modified: 2022-12-01 description: Seed germination is a key stage in the life history of plants, which has a crucial effect on plant community structure. Climate change has substantially altered the surface soil temperature and light availability, which can affect seed germination. However, whether the seed germination of different functional groups is affected by the interactions of light and temperature remains unclear. Under laboratory conditions, we examined the effects of low temperature and darkness, as well as their interaction, on the seed germination of 16 species belonging to three plant functional groups (annual and biennials, perennial grasses, and perennial forbs) in a typical steppe, Northern China. We found that low temperature had a significant negative effect on seed germination of all species. Low temperature significantly decreased the final germination percentage and germinative force of the three plant functional groups, and the germination duration of perennial grasses. Darkness significantly decreased the germinative force of perennial forbs and total seeds, and the germination duration of perennial grasses. The interactive effects of light and temperature on the seed final germination percentage and germinative force of perennial grass indicated that darkness strengthened the inhibitory effect of low temperature on the seed germination of the grass functional group. Our study indicate that the seed germination of different plant functional groups varied greatly in response to changing environmental conditions. Our results suggest that future climate change could alter the regeneration and species composition of plant communities through changing seed germination. creator: Mengzhou Liu creator: Ning Qiao creator: Bing Zhang creator: Fengying Liu creator: Yuan Miao creator: Ji Chen creator: Yanfeng Sun creator: Peng Wang creator: Dong Wang uri: https://doi.org/10.7717/peerj.14485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach link: https://peerj.com/articles/14132 last-modified: 2022-11-30 description: BackgroundPrimary congenital glaucoma (PCG) is the most common subtype of glaucoma caused by defects in the cytochrome P450 1B1 (CYP1B1) gene. It is developing among infants in more than 80% of cases who exhibit impairments in the anterior chamber angle and the trabecular meshwork. Thus, a comprehensive in silico approach was performed to evaluate the effect of high-risk deleterious missense variations in the CYP1B1 gene.Material and methodsAll the information for CYP1B1 missense variants was retrieved from the dbSNP database. Seven different tools, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, PhD-SNP, and Predict-SNP, were used for functional annotation, and two packages, which were I-Mutant 2.0 and MUpro, were used to predict the effect of the variants on protein stability. A phylogenetic conservation analysis using deleterious variants was performed by the ConSurf server. The 3D structures of the wild-type and mutants were generated using the I-TASSER tool, and a 50 ns molecular dynamic simulation (MDS) was executed using the GROMACS webserver to determine the stability of mutants compared to the native protein. Co-expression, protein-protein interaction (PPI), gene ontology (GO), and pathway analyses were additionally performed for the CYP1B1 in-depth study.ResultsAll the retrieved data from the dbSNP database was subjected to functional, structural, and phylogenetic analysis. From the conducted analyses, a total of 19 high-risk variants (P52L, G61E, G90R, P118L, E173K, D291G, Y349D, G365W, G365R, R368H, R368C, D374N, N423Y, D430E, P442A, R444Q, F445L, R469W, and C470Y) were screened out that were considered to be deleterious to the CYP1B1 gene. The phylogenetic analysis revealed that the majority of the variants occurred in highly conserved regions. The MD simulation analysis exhibited that all mutants’ average root mean square deviation (RMSD) values were higher compared to the wild-type protein, which could potentially cause CYP1B1 protein dysfunction, leading to the severity of the disease. Moreover, it has been discovered that CYP1A1, VCAN, HSD17B1, HSD17B2, and AKR1C3 are highly co-expressed and interact with CYP1B1. Besides, the CYP1B1 protein is primarily involved in the metabolism of xenobiotics, chemical carcinogenesis, the retinal metabolic process, and steroid hormone biosynthesis pathways, demonstrating its multifaceted and important roles.DiscussionThis is the first comprehensive study that adds essential information to the ongoing efforts to understand the crucial role of genetic signatures in the development of PCG and will be useful for more targeted gene-disease association studies. creator: Muhammad Shahid creator: Ahmad Azfaralariff creator: Muhammad Tufail creator: Nazeer Hussain Khan creator: Ahmed Abdulkareem Najm creator: Sabika Firasat creator: Muhammad Zubair creator: Shazrul Fazry creator: Douglas Law uri: https://doi.org/10.7717/peerj.14132 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Shahid et al. title: PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2 link: https://peerj.com/articles/14425 last-modified: 2022-11-30 description: The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was −0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/. creator: David E. Valencia-Valencia creator: Diana Lopez-Alvarez creator: Nelson Rivera-Franco creator: Andres Castillo creator: Johan S. Piña creator: Carlos A. Pardo creator: Beatriz Parra uri: https://doi.org/10.7717/peerj.14425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Valencia-Valencia et al. title: Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand link: https://peerj.com/articles/14419 last-modified: 2022-11-30 description: BackgroundOngoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses.MethodsFull-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4.ResultsML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4.ConclusionH5N1 viruses existed, and were presumably introduced and circulated in avian species in Thailand, before they were officially reported in 2004. HA and NA genes continuously evolved during circulation between 2004 and 2010. This study provides a better understanding of genetic evolution with respect to molecular epidemiology. Monitoring and surveillance of emerging variants/reassortants should be continued. creator: Pirom Noisumdaeng creator: Juthamas Phadungsombat creator: Sasrinakarn Weerated creator: Witthawat Wiriyarat creator: Pilaipan Puthavathana uri: https://doi.org/10.7717/peerj.14419 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Noisumdaeng et al.