title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=204 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Diversity, antibacterial and phytotoxic activities of actinomycetes associated with Periplaneta fuliginosa link: https://peerj.com/articles/18575 last-modified: 2024-11-25 description: BackgroundInsect-associated actinomycetes represent a potentially rich source for discovering bioactive metabolites. However, the diversity, antibacterial and phytotoxic activities of symbiotic actinomycetes associated with Periplaneta fuliginosa have not yet been conducted.ResultsA total of 86 strains of actinomycetes were isolated from the cornicles and intestines of both nymphs and adults of P. fuliginosa. Diversity analysis revealed that the isolated strains were preliminarily identified as 17 species from two genera, and the dominant genus was Streptomyces. A total of 36 crude extracts (60%) obtained from the supernatant of the 60 fermented strains exhibited a potent antibacterial activity against at least one tested pathogenic bacterium. Among these active strains, 27 crude extracts (75%) exhibited phytotoxic activity against the radicle of Echinochloa crusgalli. Furthermore, seven known compounds, including methoxynicotine (1), (3Z,6Z)-3-(4-methoxybenzylidene)-6-(2-methylpropyl) piperazine-2,5-dione (2), XR334 (3), 1-hydroxy-4-methoxy-2-naphthoic acid (4), nocapyrone A (5), β-daucosterol (6), and β-sitosterol (7) were isolated from an active rare actinomycete Nocardiopsis sp. ZLC-87 which was isolated from the gut of adult P. fuliginosa. Among them, compound 4 exhibited moderate antibacterial activity against Micrococcus tetragenus, Staphylococcus aureus, Escherichia coli, and Pseudomonas syringae pv. actinidiae with the zone of inhibition (ZOI) of 14.5, 12.0, 12.5, and 13.0 mm at a concentration of 30 μg/disc, respectively, which was weaker than those of gentamicin sulfate (ZOI of 29.5, 19.0, 18.5, and 24.5 mm). In addition, the compound 4 had potent phytotoxic activity against the radicle of E. crusgalli and Abutilon theophrasti with the inhibition rate of 65.25% and 92.68% at the concentration of 100 μg/mL.ConclusionBased on these findings, this study showed that P. fuliginosa-associated actinomycetes held promise for the development of new antibiotic and herbicide resources. creator: Qihua Liu creator: Jian Tao creator: Longhui Kan creator: Yinglao Zhang creator: Shuxiang Zhang uri: https://doi.org/10.7717/peerj.18575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Feldspathic sandstone as an emerging soil stabilizer for aeolian sand in the Mu Us Sandy Land: insights into particle size distribution link: https://peerj.com/articles/18577 last-modified: 2024-11-25 description: Stabilization of aeolian sand is essential for achieving desertification control, soil and water conservation, and agricultural development in sandy lands. Feldspathic sandstone is a soft clay rock widely found in the Mu Us Sandy Land. The purpose of this study was to ascertain the mechanism for aeolian sand stabilization with feldspathic sandstone from the perspective of particle size distribution. Feldspathic sandstone was added to aeolian sand at different ratios (mf:ms = 1:0, 1:1, 1:2, 1:5, and 0:1, where mf is the mass of feldspathic sandstone and ms is the mass of aeolian sand). The results showed that the soil texture was modified upon addition of feldspathic sandstone. The content of particles <0.05 mm increased with increasing addition ratio of feldspathic sandstone, in contrast to the downward trend observed for particles >0.05 mm. Consequently, the soil texture changed from sand to sandy loam, then loam, and finally silty loam. The addition of feldspathic sandstone ameliorated aeolian sand, resulting in a broader particle size distribution and lower particle size uniformity. Continuously well-graded soil was obtained at mf:ms = 1:5 (coefficient of uniformity: 54.71; coefficient of curvature: 2.54) or 1:2 (coefficient of uniformity: 76.21; coefficient of curvature: 1.12). While the addition of feldspathic sandstone solved the problem of single particle size distribution in aeolian sand, the presence of aeolian sand prevented soil compaction caused by the high clay content of feldspathic sandstone. Findings of this study indicate that the addition of feldspathic sandstone to aeolian sand leads to the mixing of various sized particles and continuous gradation of the soil. Although a higher addition ratio of feldspathic sandstone is more favorable for soil texture improvement, mf:ms = 1:5 is recommended for practical application in terms of particle gradation and cost effectiveness. creator: Lu Zhang creator: Jichang Han creator: Juan Li creator: Shenglan Ye creator: Dan Wu uri: https://doi.org/10.7717/peerj.18577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Balance training in older adults enhances feedback control after perturbations link: https://peerj.com/articles/18588 last-modified: 2024-11-25 description: BackgroundAs we age, avoiding falls becomes increasingly challenging. While balance training can mitigate such challenges, the specific mechanisms through which balance control improves remains unclear.MethodsWe investigated the impact of balance training in older adults on feedback control after perturbations, focusing on kinematic balance recovery strategies and muscle synergy activation. Twenty older adults aged over 65 underwent short-term (one session) and long-term (3-weeks, 10 sessions) balance training, and their recovery from unpredictable mediolateral perturbations was assessed. Perturbations consisted of 8° rotations of a robot-controlled platform on which participants were balancing on one leg. We measured full-body 3D kinematics and activation of 15 leg and trunk muscles, from which linear and rotational kinematic balance recovery responses and muscle synergies were obtained.ResultsOur findings revealed improved balance performance after long-term training, characterized by reduced centre of mass acceleration and (rate of change of) angular momentum. Particularly during the later stage of balance recovery the use of angular momentum to correct centre of mass displacement was reduced after training, decreasing the overshoot in body orientation. Instead, more ankle torque was used to correct centre of mass displacement, but only for perturbations in medial direction. These situation and strategy specific changes indicate adaptations in feedback control. Activation of muscle synergies during balance recovery was also affected by training, specifically the synergies responsible for leg stiffness and ankle torques. Training effects on angular momentum and the leg stiffness synergy were already evident after short-term training.ConclusionWe conclude that balance training in older adults refines feedback control through the tuning of control strategies, ultimately enhancing the ability to recover balance. creator: Ruud A. J. Koster creator: Leila Alizadehsaravi creator: Wouter Muijres creator: Sjoerd M. Bruijn creator: Nadia Dominici creator: Jaap H. van Dieën uri: https://doi.org/10.7717/peerj.18588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Koster et al. title: Risk factors and prediction models for recurrent acute ischemic stroke: a retrospective analysis link: https://peerj.com/articles/18605 last-modified: 2024-11-25 description: BackgroundIschemic stroke is one of the leading causes of disability and death worldwide, with a high risk of recurrence that severely impacts the quality of life of patients. Therefore, identifying and analyzing the risk factors for recurrent ischemic stroke is crucial for the prevention and management of this disease.MethodsA total of 114 cases of recurrent acute ischemic stroke patients admitted from July 2017 to March 2021 were selected as the observation group, and another 409 cases of initial ischemic stroke patients from the same period as the control group. The clinical data of the observation group and the control group were compared to analyze the risk factors associated with the readmission of ischemic stroke. A single-factor analysis (Model 1), Least Absolute Shrinkage and Selection Operator (LASSO) regression, and machine learning methods (Model 2) were used to screen important variables, and a multi-factor COX Proportional Hazards Model regression stroke recurrence risk prediction model was constructed. The predictive performance of the model was evaluated by the consistency index (C-index).ResultsMultivariate COX regression analysis revealed that history of hypertension (Hazard Ratio [HR] = 2.549; 95% Confidence Interval (CI) [1.503–4.321]; P = 0.001), history of cerebral infarction (HR = 1.709; 95% CI [1.066–2.738]; P = 0.026), cerebral artery stenosis (HR = 0.534; 95% CI [0.306–0.931]; P = 0.027), carotid arteriosclerosis (HR = 1.823; 95% CI [1.137–2.924]; P = 0.013), systolic blood pressure (HR = 0.981; 95% CI [0.971–0.991]; P < 0.0001), red cell distribution width-coefficient of variation (RDW-CV) (HR = 1.251; 95% CI [1.019–1.536]; P = 0.033), mean platelet volume (MPV) (HR = 1.506; 95% CI [1.148–1.976]; P = 0.003), uric acid (UA) (HR = 0.995; 95% CI [0.991–1.000]; P = 0.049) were found significantly associated with acute ischemic stroke. The C-index of the full COX model was 0.777 (0.732~0.821), showing a good discrimination between Model 1 and Model 2.ConclusionsHistory of hypertension, history of cerebral infarction, cerebral artery stenosis, carotid atherosclerosis, systolic blood pressure, UA, RDW-CV, and MPV were identified as risk factors for acute ischemic stroke recurrence. The model can be used to predict the recurrence of acute ischemic stroke. creator: Liuhua Ke creator: Hongyu Zhang creator: Kang Long creator: Zheng Peng creator: Yongjun Huang creator: Xingxuan Ma creator: Wanjun Wu uri: https://doi.org/10.7717/peerj.18605 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Ke et al. title: Effect of the diet level of whole-plant corn silage on the colonic microflora of Hezuo pigs link: https://peerj.com/articles/18630 last-modified: 2024-11-25 description: BackgroundWhole-plant corn silage (WPCS) is an important roughage source for livestock, and have critical influences on rumen or intestinal microbiota, thus affecting the growth performance and feed efficiency. Our previous studies showed that adding WPCS to the diet of Hezuo pigs could promote the growth and fiber digestibility. While the aim of this study is to understand the effect of dietary WPCS on the colonic microflora in Hezuo pigs, which is essential for improving the roughage exploitation of pigs.MethodsThirty-two Hezuo pigs with similar body weight (7.88 ± 0.81) kg were selected and randomly divided into four groups with eight pigs in each group. Pigs in the control group were fed a basal diet, pigs in the experimental groups (Groups I, II, and III) were fed basal diet supplemented with 5%, 10%, and 15% WPCS, respectively, under 120 d experimental period. Six pigs from each group were picked for collecting colonic contents samples. 16S rRNA sequencing was performed to analyze the colonic microbiota of experimental pigs.ResultsThe results showed that community richness indexes Chao1 and Observed_species in group III of Hezuo pig were significantly lower than that of the other three groups, community diversity indexes Shannon and Simpson were significantly higher in group I and II in comparison to the control group, and significantly lower in group III in comparison to the control group, group I and II. Adding WPCS to the diet of Hezuo pigs has no influence on the colonic dominant phylum, Clostridium sensu stricto 1 and Rikenellaceae RC9 gut group were most prevalent in the colon of Hezuo pig. When compared with the control group, the relative abundance of Streptococcus was significantly decreased in three experimental groups, while p-251-o5, Parabacteroides, Prevotellaceae UCG-003, Prevotellaceae UCG-001, and F082 exhibited significantly higher relative abundances in at least two experimental groups. Fibrobacter, Rikenellaceae RC9 gut group in group I, UCG-010 in group II, Bacteroides in group III exhibited increased relative abundance as compared with the control group. PICRUSt functional annotation indicated that the functions of cellular process and signaling were significantly increased in all WPCS-rationed groups, cancers, nervous system, immune system and environmental adaptation were all differed from groups I and II; three predominant pathways of translation, nucleotide metabolism and signal were only differed from the group II.ConclusionsFeeding with 5% and 10% WPCS for Hezuo pigs could improve their colonic microflora diversity, and increase the relative abundance of fiber-digesting bacteria, which may potentially help to improve the fibre digestibility of Hezuo pigs by regulating the microbial function of cellular process and signaling, nucleotide metabolism, translation. creator: Qiaoli Yang creator: Longlong Wang creator: Pengfei Wang creator: Zunqiang Yan creator: Qiong Chen creator: Pengxia Zhang creator: Jie Li creator: Rui Jia creator: Yao Li creator: Xitong Yin creator: Shuangbao Gun uri: https://doi.org/10.7717/peerj.18630 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Climate change effect on the widely distributed Palearctic plant bug species (Insecta: Heteroptera: Miridae) link: https://peerj.com/articles/18377 last-modified: 2024-11-22 description: Insects are poikilothermic organisms and temperature increase usually accelerates their development rates, population and distribution area growth. Therefore, it is assumed that global warming can be beneficial for the pests and other widespread species at least in the relatively cool temperate zones. However, climate change’s effect on the widespread species in the Palearctic remains poorly studied. This work was performed on three plant bug species (Insecta: Heteroptera: Miridae), at present inhabiting Europe and Asia. Liocoris tripustulatus is known from the Western Palearctic, Lygocoris pabulinus occupies the territories from Western Europe to South Asia, Lygus punctatus is distributed from Northern Europe to the Far East. In this paper, it is tested whether temperature rise is positively connected with the area of preferred climatic conditions for those species, and explores the particular climatic variables which can be limiting for the distribution of those species. Maxent software was used for the environmental niche modeling and to find the variables with significant contribution to the climatic models for the studied species. Based on those models, areas with preferred climatic conditions over different periods were calculated in QGIS. Principal component analysis and logistic regression were performed to find the variables highly contributing to the differences between the species. The results contradict the assumption that temperature growth alone can be a predictor for the widespread species and pest distribution range change. All species differ in suitable climatic conditions and their area dynamics in time, and the temperature affects each species differently. Only Liocoris tripustulatus might significantly expand its distribution area by 2070 due to the climate change. The areas in Asia and above the polar circle will be more suitable by that time for all three species than now. However, conditions in Europe might be less suitable for Lygocoris pabulinus and Lygus punctatus in the future. Both, temperature and precipitation variables, can be important for shaping distribution of Liocoris tripustulatus and Lygocoris pabulinus. Mean annual temperature and temperature in winter, most probably, limit the distribution of at least Liocoris tripsutulatus and Lygus punctatus, but changes in this variable affect those two species differently. creator: Anna A. Namyatova creator: Polina A. Dzhelali creator: Veronica D. Tyts creator: Alexander A. Popkov uri: https://doi.org/10.7717/peerj.18377 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Namyatova et al. title: Fluctuations of continuous soil moisture evaporation under different rainfall conditions during the growing period of the non-monsoon season, the eastern Loess Plateau link: https://peerj.com/articles/18514 last-modified: 2024-11-22 description: Soil moisture is an important link between material and energy exchange between the land and atmosphere, and its evaporation loss is crucial to sustainable development of agriculture. Based on observations of long-term stable isotopes of soil moisture in the eastern Loess Plateau (ECLP) during the non-rainy season growing period, this study systematically explored soil water evaporation loss at different soil depths using the Craig–Gordon model and revealed the internal relationship between soil evaporation loss and environmental elements. Main findings included: (1) The soil moisture content showed a gradual decreasing trend, with a weak soil moisture δ18O fluctuation appearing in April, whereas a stronger fluctuation was observed in June. (2) A significant vertical spatial heterogeneity was observed in soil moisture δ18O of each soil layer. Enriched soil moisture δ18O values appeared in the 0–20 cm soil layer, and the minimum value appeared in the 40–60 cm soil layer. (3) A significant spatial and temporal heterogeneity was observed in the soil moisture evaporation loss fraction (f) (0–23.35%), with weaker values at the beginning of the study period and larger values between mid-late May and mid-June. The largest soil evaporation loss was observed in the 0–20 cm soil layer (average value of 8.97%), a fluctuating decreasing trend appeared with increasing soil depth. (4) Regional soil moisture evaporation loss was positively correlated with regional air temperature (T) and potential evapotranspiration (ET0) and negatively correlated with soil water content (SWC) and relative humidity (RH). The correlation between soil moisture evaporation loss and environmental elements gradually weakened with increasing soil depth. (5) The environmentally driven model of continuous evaporation of soil moisture was suitable for larger amounts, especially for the surface soil layers. The results of this study have important implications for water resource management, ecosystem stability, and sustainable regional agriculture in the ECLP. creator: Congjian Sun creator: Sitong Meng creator: Wei Chen uri: https://doi.org/10.7717/peerj.18514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Targeting squalene epoxidase in the treatment of metabolic-related diseases: current research and future directions link: https://peerj.com/articles/18522 last-modified: 2024-11-22 description: Metabolic-related diseases are chronic diseases caused by multiple factors, such as genetics and the environment. These diseases are difficult to cure and seriously affect human health. Squalene epoxidase (SQLE), the second rate-limiting enzyme in cholesterol synthesis, plays an important role in cholesterol synthesis and alters the gut microbiota and tumor immunity. Research has shown that SQLE is expressed in many tissues and organs and is involved in the occurrence and development of various metabolic-related diseases, such as cancer, nonalcoholic fatty liver disease, diabetes mellitus, and obesity. SQLE inhibitors, such as terbinafine, NB598, natural compounds, and their derivatives, can effectively ameliorate fungal infections, nonalcoholic fatty liver disease, and cancer. In this review, we provide an overview of recent research progress on the role of SQLE in metabolic-related diseases. Further research on the regulation of SQLE expression is highly important for developing drugs for the treatment of metabolic-related diseases with good pharmacological activity. creator: Mingzhu Chen creator: Yongqi Yang creator: Shiting Chen creator: Zhigang He creator: Lian Du uri: https://doi.org/10.7717/peerj.18522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses link: https://peerj.com/articles/18543 last-modified: 2024-11-22 description: BackgroundAutophagy plays a key role in the development of carotid atherosclerosis (CAS). This study aimed to identify key autophagy-related genes (ATGs) related with CAS using bioinformatics analysis, in vivo AS mouse model, and in vitro experiments.MethodsThe GSE100927 and GSE28829 datasets were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics analyses of differentially expressed ATGs (DE-ATGs) was conducted. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify the biological processes and pathways associated with DE-ATGs. Protein-protein interaction (PPI) network was constructed with the DE-ATGs to identify the key CAS-related DE-ATGs. Receiver operating characteristic (ROC) curve analysis was used to determine the diagnostic value of the key CAS-related DE-ATGs. CIBERSORT analysis was performed to determine the infiltration status of 22 immune cell types and their correlation with the expression levels of the key CAS-related DE-ATGs. Hematoxylin and eosin (HE) staining was used to estimate the plaque histology in the AS mouse model. Western blotting, quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) were performed to validate the protein and mRNA expression levels of the key CAS-related DE-ATGs in the in vitro and in vivo models.ResultsWe compared transcriptome profiles of 12 early CAS plaques and 29 advanced CAS plaques in the GSE100927 dataset and identified 41 DE-ATGs (33 up-regulated and eight down-regulated). Functional enrichment analysis showed that the DE-ATGs were closely related with apoptosis, autophagy, and immune activation. ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively. CIBERSORT analyses showed close association between the three key CAS-related DE-ATGs and the infiltration of immune cell types in the plaques. Finally, the western blot, qRT-PCR, and IHC staining confirmed that CCL2, LAMP2, and CTSB were highly expressed in the plaques of the AS model mice or ox-LDL-treated human umbilical vein endothelial cells (HUVECs) and human aorta vascular smooth muscle cells (HAoSMCs).ConclusionWe identified and validated three key CAS-associated ATGs, namely, CCL2, LAMP2, and CTSB with high diagnostic value. These three key CAS-associated ATGs are promising diagnostic markers and therapeutic targets for patients with CAS. creator: Tiegen Huang creator: Chen Su creator: Quanli Su creator: Yali Nie creator: Zhenni Xiao creator: Yao Tang creator: Jiahao Wang creator: Xiaotian Luo creator: Yixin Tang uri: https://doi.org/10.7717/peerj.18543 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Huang et al. title: Different sound exposures causes alterations in stress-related serum indicators, behaviors, and cecal microbiota of green-shell egg-laying chickens under different stocking densities link: https://peerj.com/articles/18544 last-modified: 2024-11-22 description: Sound and stocking density are two common factors which influence the performance and welfare of layers. Accumulated studies have been conducted on the impacts of the two factors on production performance, while knowledge regarding the impacts of the two factors and their interactions on stress-related serum indicators, behaviors, and cecal bacterial communities in laying hens is still limited. A 3 × 3 factorial design with three sound sources (natural sound (NS), instrumental music (IMS), or mixed road noise (MRS)) and three stocking densities (low density (LD), medium density (MD), and high density (HD)) was used in this 24-day experiment, in which 378 30-week-old Xiandao green-shell layers were randomly distributed into nine treatments with six replicates per treatment. At the 3rd, 12th, and 24th experimental day, we evaluated the serum levels of adrenocorticotropic hormone (ACTH) and corticosterone (CORT) and recorded stress-related animal behaviors. At the end of the experiment, 16S rRNA gene amplicon sequencing of the cecal bacterial communities was performed. Our results confirmed that MRS and HD induced significantly elevated serum ACTH and CORT levels, and were correlated with significantly increased feather pecking behavior. IMS and LD were associated with enhanced preening behavior and reduced feather pecking behavior. LD significantly increased the Firmicutes/Bacteriodetes ratio and IMS significantly enriched the beneficial Lactobacillus population. Based on the obtained results we proposed that music exposure and reduced stocking density were helpful in reducing stress and improving cecal bacterial profile, which were beneficial for improving layers’ health status and welfare. creator: Shiwen Cao creator: Manhong Ye creator: Wanhong Wei creator: Fengping Yang uri: https://doi.org/10.7717/peerj.18544 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cao et al.