title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=524
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Dynamics of bacterial and archaeal communities during horse bedding and green waste composting
link: https://peerj.com/articles/15239
last-modified: 2023-05-03
description: Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.
creator: Vanessa Grenier
creator: Emmanuel Gonzalez
creator: Nicholas JB Brereton
creator: Frederic E. Pitre
uri: https://doi.org/10.7717/peerj.15239
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Grenier et al.

title: Impact of artificial waterholes on temporal partitioning in a carnivore guild: a comparison of activity patterns at artificial waterholes to roads and trails
link: https://peerj.com/articles/15253
last-modified: 2023-05-03
description: Temporal partitioning in large carnivores have previously been found to be one of the main factors enabling co-existence. While activity patterns have been investigated separately at artificial waterholes and e.g., game trails, simultaneous comparative analyses of activity patterns at artificial waterholes and game trails have not been attempted. In this study, camera trap data from Maremani Nature Reserve was used to investigate whether temporal partitioning existed in a carnivore guild of four species (spotted hyena, leopard, brown hyena and African wild dog). Specifically, we investigated temporal partitioning at artificial waterholes and on roads and trails an average of 1,412 m away from an artificial waterhole. Activity patterns for the same species at artificial waterholes and roads/game trails were also compared. We found no significant differences in temporal activity between species at artificial waterholes. Temporal partitioning on game trails and roads was only found between spotted hyena (nocturnal) and African wild dog (crepuscular). Between nocturnal species (spotted hyena and leopard) no temporal partitioning was exhibited. Only African wild dog exhibited significantly different activity patterns at waterholes and roads/game trails. This indicates artificial waterholes may be a location for conflict in a carnivore guild. Our study highlights the impact of anthropogenic landscape changes and management decisions on the temporal axis of carnivores. More data on activity patterns at natural water sources such as ephemeral pans are needed to properly assess the effect of artificial waterholes on temporal partitioning in a carnivore guild.
creator: Charlotte Krag
creator: Linnea Worsøe Havmøller
creator: Lourens Swanepoel
creator: Gigi Van Zyl
creator: Peter Rask Møller
creator: Rasmus Worsøe Havmøller
uri: https://doi.org/10.7717/peerj.15253
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Krag et al.

title: Genome-wide characterization of the xyloglucan endotransglucosylase/hydrolase gene family in Solanum lycopersicum L. and gene expression analysis in response to arbuscular mycorrhizal symbiosis
link: https://peerj.com/articles/15257
last-modified: 2023-05-03
description: Xyloglucan endotransglucosylase/hydrolases (XTHs) are a glycoside hydrolase protein family involved in the biosynthesis of xyloglucans, with essential roles in the regulation of plant cell wall extensibility. By taking advantage of the whole genome sequence in Solanum lycopersicum, 37 SlXTHs were identified in the present work. SlXTHs were classified into four subfamilies (ancestral, I/II, III-A, III-B) when aligned to XTHs of other plant species. Gene structure and conserved motifs showed similar compositions in each subfamily. Segmental duplication was the primary mechanism accounting for the expansion of SlXTH genes. In silico expression analysis showed that SlXTH genes exhibited differential expression in several tissues. GO analysis and 3D protein structure indicated that all 37 SlXTHs participate in cell wall biogenesis and xyloglucan metabolism. Promoter analysis revealed that some SlXTHs have MeJA- and stress-responsive elements. qRT-PCR expression analysis of nine SlXTHs in leaves and roots of mycorrhizal colonized vs. non-colonized plants showed that eight of these genes were differentially expressed in leaves and four in roots, suggesting that SlXTHs might play roles in plant defense induced by arbuscular mycorrhiza. Our results provide valuable insight into the function of XTHs in S. lycopersicum, in addition to the response of plants to mycorrhizal colonization.
creator: Luis G. Sarmiento-López
creator: Maury Yanitze López-Espinoza
creator:  Marco Adán Juárez-Verdayes
creator: Melina López-Meyer
uri: https://doi.org/10.7717/peerj.15257
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Sarmiento-López et al.

title: Analysis of QTL mapping for germination and seedling response to drought stress in sunflower (Helianthus annuus L.)
link: https://peerj.com/articles/15275
last-modified: 2023-05-03
description: Sunflower is an important oilseed crop across the world. It is considered as a moderately drought tolerant plant, however, its yield is still negatively affected by drought stress. Improving drought tolerance is of the outmost important for breeding. Although several studies have documented the relationship between the sunflower phenotype and genotype under drought stress, but relatively few studies have simultaneously investigated the molecular mechanisms of drought tolerance in the sunflower at different growth stages. In this study, we conducted quantitative trait locus (QTL) analysis for different sunflower traits during the germination and seedling stages. Eighteen phenotypic traits were evaluated under well-watered and drought stress conditions. We determined that the germination rate, germination potential, germination index, and root-to-shoot ratio can be used as effective indexes for drought tolerance selection and breeding. A total of 33 QTLs were identified on eight chromosomes (PVE: 0.016%–10.712% with LOD: 2.017–7.439). Within the confidence interval of the QTL, we identified 60 putative drought-related genes. Four genes located on chromosome 13 may function in both germination and seedling stages for drought response. Genes LOC110898128, LOC110898092, LOC110898071, and LOC110898072 were annotated as aquaporin SIP1-2-like, cytochrome P450 94C1, GABA transporter 1-like, and GABA transporter 1-like isoform X2, respectively. These genes will be used for further functional validation. This study provides insight into the molecular mechanisms of the sunflower’s in response to drought stress. At the same time, it lays a foundation for sunflower drought tolerance breeding and genetic improvement.
creator: Huimin Shi
creator: Yang Wu
creator: Liuxi Yi
creator: Haibo Hu
creator: Feiyan Su
creator: Yanxia Wang
creator: Dandan Li
creator: Jianhua Hou
uri: https://doi.org/10.7717/peerj.15275
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Shi et al.

title: Pathological mechanism of heart failure with preserved ejection fraction in rats based on iTRAQ technology
link: https://peerj.com/articles/15280
last-modified: 2023-05-03
description: ObjectiveHeart failure with preserved ejection fraction (HFpEF) is a public health problem worldwide. Treatments for the patients with HFpEF are not satisfactory because there is no unified understanding of the pathological mechanism of HFpEF. This study aims at investigating the potential pathological mechanism for the effective diagnosis and treatment of HFpEF.MethodsTen adult male Dahl salt sensitive rats (180–200 g) were divided into control and model groups. The rats in model group were fed with high salt diet (8% NaCl) to induce HFpEF for this comparative study. Behavioral changes, biochemical parameters, and histopathological changes of the rats were detected. iTRAQ technology combined with bioinformatics analysis was employed to study the differentially expressed proteins (DEPs) and their enrichment in signaling pathways.ResultsEchocardiography detection showed decreased LVEF, indicating impaired cardiac function (P < 0.01), increased LVPWd, indicating ventricular wall hypertrophy (P < 0.05), prolonged duration of IVRT and decreased E/A ratio, indicating diastolic dysfunction (P < 0.05) of the rats in model group. 563 DEPs were identified in the rats of both groups, with 243 up-regulated and 320 down-regulated. The expression of PPAR signaling pathway in the rats of model group was down-regulated, with PPARα most significantly decreased (91.2%) (P < 0.01), PPARγ obviously decreased (63.60%) (P < 0.05), and PPARβ/δ decreased (45.33%) (P < 0.05). The DEPs enriched in PPAR signaling pathway were mainly related to such biological processes as fatty acid beta-oxidation, such cellular components as peroxisome, and such molecular functions as lipid binding.ConclusionsNaCl high salt diet is one of the factors to increase the incidence of HFpEF in rats. PPARα, PPARγ and PPAR β/δ might be the targets of HFpEF. The findings may provide a theoretical basis for the treatment of HFpEF in clinical practice.
creator: Hang Xu
creator: Kai Gao
creator: Chao Liu
creator: Tian Li
creator: Yi Ding
creator: Jing Ma
uri: https://doi.org/10.7717/peerj.15280
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Xu et al.

title: The influence of pet ownership on self-compassion among nurses: a cross-sectional study
link: https://peerj.com/articles/15288
last-modified: 2023-05-03
description: BackgroundThe modern lifestyle trend of pet ownership is undoubtedly beneficial for both physical and mental health. Research has shown a connection between pet ownership and staff self-compassion. However, there has not been any evidence linking pet ownership to self-compassion in the nurse population.AimsTo investigate the current status of pet ownership among nurses and explore the influence of pet ownership on self-compassion among nurses.MethodsAn online survey was conducted in July 2022 with 1,308 nurses in China. Data were collected using a general information questionnaire and a self-compassion scale. To compare categorical variables, the independent t test, one-way ANOVA, and multiple linear regression analysis were utilized. SPSS software was used for the statistical analysis.ResultsWe found that 16.9% of nurses owned at least one pet, and dogs and cats were the primary pets. The t test for independent samples showed that pet owners and non-pet owners scored differently on self-compassion (t = 3.286, p = 0.001), self-kindness (t = 3.378, p = 0.001), common humanity (t = 2.419, p = 0.016), and mindfulness (t = 2.246, p = 0.025). One-way ANOVA revealed that the highest degree was an influencing factor of self-compassion (χ2 = 1.386, p = 0.019). Multiple linear regression showed that average monthly income, pet ownership, and highest degree were the factors that influenced self-compassion most significantly (F = 8.335, p < 0.001).ConclusionThe results revealed that nurses actually own pets as part of their modern lifestyle, which provides them with social support and potentially enhances their self-compassion. More efforts should be focused on the impact of pet ownership on nurses’ physical and mental health, and pet-based interventions should also be developed.
creator: Hu Jiang
creator: Yongxia Mei
creator: Xiaoxuan Wang
creator: Wenna Wang
creator: Beilei Lin
creator: Zhixin Zhao
creator: Zhenxiang Zhang
uri: https://doi.org/10.7717/peerj.15288
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Jiang et al.

title: Semantic plausibility preferentially affects the semantic preview benefit in Chinese reading: evidence from an eye-movement study
link: https://peerj.com/articles/15291
last-modified: 2023-05-03
description: BackgroundNumerous studies have confirmed that skilled readers can benefit from a semantically related preview word (i.e., semantic preview benefit, SPB), suggesting that readers can extract semantic information from the parafovea to achieve efficient reading. It is still under debate whether the occurrence of this benefit is because of the semantic association between the preview and target words or because of the contextual fit of the preview word in the sentence context.MethodsTwo independent factors, preview plausibility (preview plausible/implausible) and semantic relatedness (semantically related/unrelated), were manipulated, and we further strictly controlled for syntactic plausibility in the present study.ResultsThe results showed that the first-pass reading times of the target words were significantly shorter in the plausible preview condition than in the implausible preview condition. However, the main effect of semantic relatedness was found only in the gaze duration measure.DiscussionThe pattern of results revealed that semantic plausibility affects the semantic preview benefit preferentially in Chinese reading, supporting the contextual fit account. Our findings have implications for a better understanding of parafoveal processing and provide empirical support for the eye-movement control model.
creator: Lijuan Zhang
creator: Zhiwei Liu
creator: Sainan Zhao
creator: Jingxin Wang
uri: https://doi.org/10.7717/peerj.15291
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Zhang et al.

title: Molecular basis of a high Hb A2/Hb Fβ-thalassemia trait: a retrospective analysis, genotype-phenotype interaction, diagnostic implication, and identification of a novel interaction with α-globin gene triplication
link: https://peerj.com/articles/15308
last-modified: 2023-05-03
description: Backgroundβ0-thalassemia deletion removing 5´β-globin promoter usually presents phenotype with high hemoglobin (Hb) A2 and Hb F levels. We report the molecular characteristics and phenotype-genotype correlation in a large cohort of the β0-thalassemia with 3.4 kb deletion.MethodsA total of 148 subjects, including 127 heterozygotes, 20 Hb E-β-thalassemia patients, and a double heterozygote with α-globin gene triplication, were recruited. Hb and DNA analysis were performed to identify thalassemia mutations and four high Hb F single nucleotide polymorphisms (SNPs) including four base pair deletion (-AGCA) at Aγ-globin promoter, rs5006884 on OR51B6 gene, −158 Gγ-XmnI, BCL11A binding motifs (TGGTCA) between 3´Aγ-globin gene and 5´δ-globin gene.ResultsIt was found that heterozygous β0-thalassemia and Hb E-β0-thalassemia with 3.4 kb deletion had significantly higher Hb, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin and Hb F values as compared with those with other mutations. Co-inheritance of heterozygous β0-thalassemia with 3.4 kb deletion and α-thalassemia was associated with even higher MCV and MCH values. The Hb E-β0-thalassemia patients carried a non-transfusion-dependent thalassemia phenotype with an average Hb of around 10 g/dL without blood transfusion. A hitherto undescribed double heterozygous β0-thalassemia with 3.4 kb deletion and α-globin gene triplication presented as a plain β-thalassemia trait. Most of the subjects had wild-type sequences for the four high Hb F SNPs examined. No significant difference in Hb F was observed between those of subjects with and without these SNPs. Removal of the 5´β-globin promoter may likely be responsible for this unusual phenotype.ConclusionsThe results indicate that β0-thalassemia with 3.4 kb deletion is a mild β-thalassemia allele. This information should be provided at genetic counseling and prenatal thalassemia diagnosis.
creator: Chayada Soontornpanawet
creator: Kritsada Singha
creator: Hataichanok Srivorakun
creator: Wanicha Tepakhan
creator: Goonnapa Fucharoen
creator: Supan Fucharoen
uri: https://doi.org/10.7717/peerj.15308
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Soontornpanawet et al.

title: Building consensus around the assessment and interpretation of Symbiodiniaceae diversity
link: https://peerj.com/articles/15023
last-modified: 2023-05-02
description: Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
creator: Sarah W. Davies
creator: Matthew H. Gamache
creator: Lauren I. Howe-Kerr
creator: Nicola G. Kriefall
creator: Andrew C. Baker
creator: Anastazia T. Banaszak
creator: Line Kolind Bay
creator: Anthony J. Bellantuono
creator: Debashish Bhattacharya
creator: Cheong Xin Chan
creator: Danielle C. Claar
creator: Mary Alice Coffroth
creator: Ross Cunning
creator: Simon K. Davy
creator: Javier del Campo
creator: Erika M. Díaz-Almeyda
creator: Jörg C. Frommlet
creator: Lauren E. Fuess
creator: Raúl A. González-Pech
creator: Tamar L. Goulet
creator: Kenneth D. Hoadley
creator: Emily J. Howells
creator: Benjamin C. C. Hume
creator: Dustin W. Kemp
creator: Carly D. Kenkel
creator: Sheila A. Kitchen
creator: Todd C. LaJeunesse
creator: Senjie Lin
creator: Shelby E. McIlroy
creator: Ryan McMinds
creator: Matthew R. Nitschke
creator: Clinton A. Oakley
creator: Raquel S. Peixoto
creator: Carlos Prada
creator: Hollie M. Putnam
creator: Kate Quigley
creator: Hannah G. Reich
creator: James Davis Reimer
creator: Mauricio Rodriguez-Lanetty
creator: Stephanie M. Rosales
creator: Osama S. Saad
creator: Eugenia M. Sampayo
creator: Scott R. Santos
creator: Eiichi Shoguchi
creator: Edward G. Smith
creator: Michael Stat
creator: Timothy G. Stephens
creator: Marie E. Strader
creator: David J. Suggett
creator: Timothy D. Swain
creator: Cawa Tran
creator: Nikki Traylor-Knowles
creator: Christian R. Voolstra
creator: Mark E. Warner
creator: Virginia M. Weis
creator: Rachel M. Wright
creator: Tingting Xiang
creator: Hiroshi Yamashita
creator: Maren Ziegler
creator: Adrienne M. S. Correa
creator: John Everett Parkinson
uri: https://doi.org/10.7717/peerj.15023
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Davies et al.

title: Spatial orientation, postural control and the vestibular system in healthy elderly and Alzheimer’s dementia
link: https://peerj.com/articles/15040
last-modified: 2023-05-02
description: BackgroundWhile extensive research has been advancing our understanding of the spatial and postural decline in healthy elderly (HE) and Alzheimer’s disease (AD), much less is known about how the vestibular system contributes to the spatial and postural processing in these two populations. This is especially relevant during turning movements in the dark, such as while walking in our garden or at home at night, where the vestibular signal becomes central. As the prevention of falls and disorientation are of serious concern for the medical service, more vestibular-driven knowledge is necessary to decrease the burden for HE and AD patients with vestibular disabilities.Overview of the articleThe review briefly presents the current “non-vestibular based” knowledge (i.e. knowledge based on research that does not mention the “vestibular system” as a contributor or does not investigate its effects) about spatial navigation and postural control during normal healthy ageing and AD pathology. Then, it concentrates on the critical sense of the vestibular system and explores the current expertise about the aspects of spatial orientation and postural control from a vestibular system point of view. The norm is set by first looking at how healthy elderly change with age with respect to their vestibular-guided navigation and balance, followed by the AD patients and the difficulties they experience in maintaining their balance or during navigation.ConclusionVestibular spatial and vestibular postural deficits present a considerable disadvantage and are felt not only on a physical but also on a psychological level by all those affected. Still, there is a clear need for more (central) vestibular-driven spatial and postural knowledge in healthy and pathological ageing, which can better facilitate our understanding of the aetiology of these dysfunctions. A possible change can start with the more frequent implementation of the “vestibular system examination/rehabilitation/therapy” in the clinic, which can then lead to an improvement of future prognostication and disease outcome for the patients.
creator: Mariya K. Chepisheva
uri: https://doi.org/10.7717/peerj.15040
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Chepisheva