title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=355 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Characterization of PYL gene family and identification of HaPYL genes response to drought and salt stress in sunflower link: https://peerj.com/articles/16831 last-modified: 2024-03-07 description: In the context of global climate change, drought and soil salinity are some of the most devastating abiotic stresses affecting agriculture today. PYL proteins are essential components of abscisic acid (ABA) signaling and play critical roles in responding to abiotic stressors, including drought and salt stress. Although PYL genes have been studied in many species, their roles in responding to abiotic stress are still unclear in the sunflower. In this study, 19 HaPYL genes, distributed on 15 of 17 chromosomes, were identified in the sunflower. Fragment duplication is the main cause of the expansion of PYL genes in the sunflower genome. Based on phylogenetic analysis, HaPYL genes were divided into three subfamilies. Members in the same subfamily share similar protein motifs and gene exon-intron structures, except for the second subfamily. Tissue expression patterns suggested that HaPYLs serve different functions when responding to developmental and environmental signals in the sunflower. Exogenous ABA treatment showed that most HaPYLs respond to an increase in the ABA level. Among these HaPYLs, HaPYL2a, HaPYL4d, HaPYL4g, HaPYL8a, HaPYL8b, HaPYL8c, HaPYL9b, and HaPYL9c were up-regulated with PEG6000 treatment and NaCl treatment. This indicates that they may play a role in resisting drought and salt stress in the sunflower by mediating ABA signaling. Our findings provide some clues to further explore the functions of PYL genes in the sunflower, especially with regards to drought and salt stress resistance. creator: Zhaoping Wang creator: Jiayan Zhou creator: Jian Zou creator: Jun Yang creator: Weiying Chen uri: https://doi.org/10.7717/peerj.16831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Identification and transcriptomic profiling of salinity stress response genes in colored wheat mutant link: https://peerj.com/articles/17043 last-modified: 2024-03-06 description: BackgroundSalinity is a major abiotic stress that prevents normal plant growth and development, ultimately reducing crop productivity. This study investigated the effects of salinity stress on two wheat lines: PL1 (wild type) and PL6 (mutant line generated through gamma irradiation of PL1).ResultsThe salinity treatment was carried out with a solution consisting of a total volume of 200 mL containing 150 mM NaCl. Salinity stress negatively impacted germination and plant growth in both lines, but PL6 exhibited higher tolerance. PL6 showed lower Na+ accumulation and higher K+ levels, indicating better ion homeostasis. Genome-wide transcriptomic analysis revealed distinct gene expression patterns between PL1 and PL6 under salt stress, resulting in notable phenotypic differences. Gene ontology analysis revealed positive correlations between salt stress and defense response, glutathione metabolism, peroxidase activity, and reactive oxygen species metabolic processes, highlighting the importance of antioxidant activities in salt tolerance. Additionally, hormone-related genes, transcription factors, and protein kinases showed differential expression, suggesting their roles in the differential salt stress response. Enrichment of pathways related to flavonoid biosynthesis and secondary metabolite biosynthesis in PL6 may contribute to its enhanced antioxidant activities. Furthermore, differentially expressed genes associated with the circadian clock system, cytoskeleton organization, and cell wall organization shed light on the plant’s response to salt stress.ConclusionsUnderstanding these mechanisms is crucial for developing stress-tolerant crop varieties, improving agricultural practices, and breeding salt-resistant crops to enhance global food production and address food security challenges. creator: Min Jeong Hong creator: Chan Seop Ko creator: Jin-Baek Kim creator: Dae Yeon Kim uri: https://doi.org/10.7717/peerj.17043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hong et al. title: Heavy grazing reduces soil bacterial diversity by increasing soil pH in a semi-arid steppe link: https://peerj.com/articles/17031 last-modified: 2024-03-07 description: BackgroundIn a context of long-term highly intensive grazing in grassland ecosystems, a better understanding of how quickly belowground biodiversity responds to grazing is required, especially for soil microbial diversity.MethodsIn this study, we conducted a grazing experiment which included the CK (no grazing with a fenced enclosure undisturbed by livestock), light and heavy grazing treatments in a desert steppe in Inner Mongolia, China. Microbial diversity and soil chemical properties (i.e., pH value, organic carbon, inorganic nitrogen (IN, ${\mathrm{NH}}_{4}^{+}$NH4+-N and ${\mathrm{NO}}_{3}^{-}$NO3−-N), total carbon, nitrogen, phosphorus, and available phosphorus content) both in rhizosphere and non-rhizosphere soils were analyzed to explore the responses of microbial diversity to grazing intensity and the underlying mechanisms.ResultsThe results showed that heavy grazing only deceased bacterial diversity in the non-rhizosphere soil, but had no any significant effects on fungal diversity regardless of rhizosphere or non-rhizosphere soils. Bacterial diversity in the rhizosphere soil was higher than that of non-rhizosphere soil only in the heavy grazing treatment. Also, heavy grazing significantly increased soil pH value but deceased NH4+-N and available phosphorus in the non-rhizosphere soil. Spearman correlation analysis showed that soil pH value was significantly negatively correlated with the bacterial diversity in the non-rhizosphere soil. Combined, our results suggest that heavy grazing decreased soil bacterial diversity in the non-rhizosphere soil by increasing soil pH value, which may be due to the accumulation of dung and urine from livestock. Our results highlight that soil pH value may be the main factor driving soil microbial diversity in grazing ecosystems, and these results can provide scientific basis for grassland management and ecological restoration in arid and semi-arid area. creator: Xiaonan Wang creator: Chengyang Zhou creator: Shining Zuo creator: Yixin Ji creator: Wenxin Liu creator: Ding Huang uri: https://doi.org/10.7717/peerj.17031 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Research overview on the genetic mechanism underlying the biosynthesis of polysaccharide in tuber plants link: https://peerj.com/articles/17052 last-modified: 2024-03-07 description: Tuber plants are of great significance in the world as human food crops. Polysaccharides, important metabolites in tuber plants, also serve as a source of innovative drugs with significant pharmacological effects. These drugs are particularly known for their immunomodulation and antitumor properties. To fully exploit the potential value of tuber plant polysaccharides and establish a synthetic system for their targeted synthesis, it is crucial to dissect their metabolic processes and genetic regulatory mechanisms. In this article, we provide a comprehensive summary of the basic pathways involved in the synthesis of various types of tuber plant polysaccharides. We also outline the key research progress that has been made in this area in recent years. We classify the main types and functions of tuber plant polysaccharides and analyze the biosynthetic processes and genetic regulation mechanisms of key enzymes involved in the metabolic pathways of starch, cellulose, pectin, and fructan in tuber plants. We have identified hexokinase and glycosyltransferase as the key enzymes involved in the polysaccharide synthesis process. By elucidating the synthesis pathway of polysaccharides in tuber plants and understanding the underlying mechanism of action of key enzymes in the metabolic pathway, we can provide a theoretical framework for enhancing the yield of polysaccharides and other metabolites in plant culture cells. This will ultimately lead to increased production efficiency. creator: Mengwei Xu creator: Jiao Hu creator: Hongwei Li creator: Kunqian Li creator: Delin Xu uri: https://doi.org/10.7717/peerj.17052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xu et al. title: High-resolution density assessment assisted by deep learning of Dendrophyllia cornigera (Lamarck, 1816) and Phakellia ventilabrum (Linnaeus, 1767) in rocky circalittoral shelf of Bay of Biscay link: https://peerj.com/articles/17080 last-modified: 2024-03-07 description: This study presents a novel approach to high-resolution density distribution mapping of two key species of the 1170 “Reefs” habitat, Dendrophyllia cornigera and Phakellia ventilabrum, in the Bay of Biscay using deep learning models. The main objective of this study was to establish a pipeline based on deep learning models to extract species density data from raw images obtained by a remotely operated towed vehicle (ROTV). Different object detection models were evaluated and compared in various shelf zones at the head of submarine canyon systems using metrics such as precision, recall, and F1 score. The best-performing model, YOLOv8, was selected for generating density maps of the two species at a high spatial resolution. The study also generated synthetic images to augment the training data and assess the generalization capacity of the models. The proposed approach provides a cost-effective and non-invasive method for monitoring and assessing the status of these important reef-building species and their habitats. The results have important implications for the management and protection of the 1170 habitat in Spain and other marine ecosystems worldwide. These results highlight the potential of deep learning to improve efficiency and accuracy in monitoring vulnerable marine ecosystems, allowing informed decisions to be made that can have a positive impact on marine conservation. creator: Alberto Gayá-Vilar creator: Adolfo Cobo creator: Alberto Abad-Uribarren creator: Augusto Rodríguez creator: Sergio Sierra creator: Sabrina Clemente creator: Elena Prado uri: https://doi.org/10.7717/peerj.17080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gayá-Vilar et al. title: Reliability and validity of an app-assisted tissue compliance meter in measuring tissue stiffness on a phantom model link: https://peerj.com/articles/17122 last-modified: 2024-03-07 description: BackgroundMost methods for soft tissue stiffness assessment require high financial resources, significant technical effort, or extensive therapist training. The PACT Sense device was developed to be used in a wide range of applications and user groups. However, to date, there are no data on its validity and reliability. The aim of this study was to investigate the validity and reliability of the PACT device.MethodsA polyurethane phantom tissue model (PTM) mimicking the mechanical properties of the fascia profunda and the erector spinae muscle was used. Stiffness measurements with PACT were conducted by two independent investigators. For construct validity, correlations were calculated between the known stiffness of the PTM and values obtained with PACT. For concurrent validity, we determined the association between the PACT values and additional measurements with the established MyotonPRO device. To estimate interrater and intrarater (two measurements with an interval of 7 days) reliability, we used the intraclass correlation coefficient (ICC).ResultsCorrelation analysis (PTM/PACT) revealed very high concurrent validity (r = 0.99; p < 0.001), construct validity (PACT/MyotonPRO) was 0.87, p < 0.001. Both, interrater reliability (ICC = 0.85; p = 0.036) and intrarater reliability were good (ICC = 0.89; p < 0.001).ConclusionsThe PACT provides valid and reliable stiffness measurements in tissue phantoms. Further studies in humans are needed to confirm its physiometric properties under in vivo conditions. creator: Andreas Brandl creator: Eda Acikalin creator: Katja Bartsch creator: Jan Wilke creator: Robert Schleip uri: https://doi.org/10.7717/peerj.17122 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Brandl et al. title: Scalable neighbour search and alignment with uvaia link: https://peerj.com/articles/16890 last-modified: 2024-03-06 description: Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop. creator: Leonardo de Oliveira Martins creator: Alison E. Mather creator: Andrew J. Page uri: https://doi.org/10.7717/peerj.16890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 de Oliveira Martins et al. title: A new sports garment with elastomeric technology optimizes physiological, mechanical, and psychological acute responses to pushing upper-limb resistance exercises link: https://peerj.com/articles/17008 last-modified: 2024-03-06 description: This study aimed to compare the mechanical (lifting velocity and maximum number of repetitions), physiological (muscular activation, lactate, heart rate, and blood pressure), and psychological (rating of perceived exertion) responses to upper-body pushing exercises performed wearing a sports elastomeric garment or a placebo garment. Nineteen physically active young adults randomly completed two training sessions that differed only in the sports garment used (elastomeric technology or placebo). In each session, subjects performed one set of seated shoulder presses and another set of push-ups until muscular failure. The dependent variables were measured immediately after finishing the set of each exercise. Compared to the placebo garment, the elastomeric garment allowed participants to obtain greater muscular activation in the pectoralis major (push-ups: p = 0.04, d = 0.49; seated shoulder press: p < 0.01, d = 0.64), triceps brachialis (push-ups, p < 0.01, d = 0.77; seated shoulder press: p < 0.01, d = 0.65), and anterior deltoid (push-ups: p < 0.01, d = 0.72; seated shoulder press: p < 0.01, d = 0.83) muscles. Similarly, participants performed more repetitions (push-ups: p < 0.01; d = 0.94; seated shoulder press: p = 0.03, d = 0.23), with higher movement velocity (all p ≤ 0.04, all d ≥ 0.47), and lower perceived exertion in the first repetition (push-ups: p < 0.01, d = 0.61; seated shoulder press: p = 0.05; d = 0.76) wearing the elastomeric garment compared to placebo. There were no between-garment differences in most cardiovascular variables (all p ≥ 0.10). Higher diastolic blood pressure was only found after the seated shoulder press wearing the elastomeric garment compared to the placebo (p = 0.04; d = 0.49). Finally, significantly lower blood lactate levels were achieved in the push-ups performed wearing the elastomeric garment (p < 0.01; d = 0.91), but no significant differences were observed in the seated shoulder press (p = 0.08). Overall, the findings of this study suggest that elastomeric technology integrated into a sports garment provides an ergogenic effect on mechanical, physiological, and psychological variables during the execution of pushing upper-limb resistance exercises. creator: Angel Saez-Berlanga creator: Carlos Babiloni-Lopez creator: Ana Ferri-Caruana creator: Pablo Jiménez-Martínez creator: Amador García-Ramos creator: Jorge Flandez creator: Javier Gene-Morales creator: Juan C. Colado uri: https://doi.org/10.7717/peerj.17008 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Saez-Berlanga et al. title: Unsupervised AI reveals insect species-specific genome signatures link: https://peerj.com/articles/17025 last-modified: 2024-03-06 description: Insects are a highly diverse phylogeny and possess a wide variety of traits, including the presence or absence of wings and metamorphosis. These diverse traits are of great interest for studying genome evolution, and numerous comparative genomic studies have examined a wide phylogenetic range of insects. Here, we analyzed 22 insects belonging to a wide phylogenetic range (Endopterygota, Paraneoptera, Polyneoptera, Palaeoptera, and other insects) by using a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions in their genomic fragments (100-kb or 1-Mb sequences), which is an unsupervised machine learning algorithm that can extract species-specific characteristics of the oligonucleotide compositions (genome signatures). The genome signature is of particular interest in terms of the mechanisms and biological significance that have caused the species-specific difference, and can be used as a powerful search needle to explore the various roles of genome sequences other than protein coding, and can be used to unveil mysteries hidden in the genome sequence. Since BLSOM is an unsupervised clustering method, the clustering of sequences was performed based on the oligonucleotide composition alone, without providing information about the species from which each fragment sequence was derived. Therefore, not only the interspecies separation, but also the intraspecies separation can be achieved. Here, we have revealed the specific genomic regions with oligonucleotide compositions distinct from the usual sequences of each insect genome, e.g., Mb-level structures found for a grasshopper Schistocerca americana. One aim of this study was to compare the genome characteristics of insects with those of vertebrates, especially humans, which are phylogenetically distant from insects. Recently, humans seem to be the “model organism” for which a large amount of information has been accumulated using a variety of cutting-edge and high-throughput technologies. Therefore, it is reasonable to use the abundant information from humans to study insect lineages. The specific regions of Mb length with distinct oligonucleotide compositions have also been previously observed in the human genome. These regions were enriched by transcription factor binding motifs (TFBSs) and hypothesized to be involved in the three-dimensional arrangement of chromosomal DNA in interphase nuclei. The present study characterized the species-specific oligonucleotide compositions (i.e., genome signatures) in insect genomes and identified specific genomic regions with distinct oligonucleotide compositions. creator: Yui Sawada creator: Ryuhei Minei creator: Hiromasa Tabata creator: Toshimichi Ikemura creator: Kennosuke Wada creator: Yoshiko Wada creator: Hiroshi Nagata creator: Yuki Iwasaki uri: https://doi.org/10.7717/peerj.17025 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sawada et al. title: Collaborative clinical reasoning: a scoping review link: https://peerj.com/articles/17042 last-modified: 2024-03-06 description: BackgroundCollaborative clinical reasoning (CCR) among healthcare professionals is crucial for maximizing clinical outcomes and patient safety. This scoping review explores CCR to address the gap in understanding its definition, structure, and implications.MethodsA scoping review was undertaken to examine CCR related studies in healthcare. Medline, PsychInfo, SciVerse Scopus, and Web of Science were searched. Inclusion criteria included full-text articles published between 2011 to 2020. Search terms included cooperative, collaborative, shared, team, collective, reasoning, problem solving, decision making, combined with clinical or medicine or medical, but excluded shared decision making.ResultsA total of 24 articles were identified in the review. The review reveals a growing interest in CCR, with 14 articles emphasizing the decision-making process, five using Multidisciplinary Team-Metric for the Observation of Decision Making (MDTs-MODe), three exploring CCR theory, and two focusing on the problem-solving process. Communication, trust, and team dynamics emerge as key influencers in healthcare decision-making. Notably, only two articles provide specific CCR definitions.ConclusionsWhile decision-making processes dominate CCR studies, a notable gap exists in defining and structuring CCR. Explicit theoretical frameworks, such as those proposed by Blondon et al. and Kiesewetter et al., are crucial for advancing research and understanding CCR dynamics within collaborative teams. This scoping review provides a comprehensive overview of CCR research, revealing a growing interest and diversity in the field. The review emphasizes the need for explicit theoretical frameworks, citing Blondon et al. and Kiesewetter et al. The broader landscape of interprofessional collaboration and clinical reasoning requires exploration. creator: Ching-Yi Lee creator: Hung-Yi Lai creator: Ching-Hsin Lee creator: Mi-Mi Chen creator: Sze-Yuen Yau uri: https://doi.org/10.7717/peerj.17042 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lee et al.