title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=381 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Bacterial diversity of herbal rhizospheric soils in Ordos desert steppes under different degradation gradients link: https://peerj.com/articles/16289 last-modified: 2023-11-01 description: ObjectivesThis study explored the effects of different degradation gradients on bacterial diversity in the rhizospheric soils of herb plants.MethodsThe alpha diversity, species composition and correlations of bacterial communities in the rhizospheric soils of herb plants were studied using metagenomics 16SrDNA gene high-throughput sequencing.ResultsThe diversity of bacterial communities in the rhizospheric soils of herb plants differed during the degradation of desert steppes. An analysis of bacterial community alpha diversity indices showed the bacterial diversity and species evenness of rhizospheric soils were best in moderately degraded desert steppes. Among all samples, a total of 43 phyla, 133 classes, 261 orders, 421 families, 802 genera and 1,129 species were detected. At the phylum level, the predominant bacterial phyla were: Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Bacteroidetes. At the genus level, the predominant bacterial genera were: RB41, Sphingomonas, WD2101_soil_group_unclassified, Pseudomonas and Actinomyces. The relative abundance of unknown genera was very large, which deserves further research. At the phylum and genus levels, the species abundance levels under slight and moderate degradation were significantly higher than those under extreme degradation. Correlation network diagrams showed there were many nodes in both slightly deteriorated and moderately deteriorated soils, and the node proportions were large and mostly positively correlated. These results indicate the bacterial communities in rhizospheric soils under slight or moderate deterioration are relatively stable. The rhizospheric soil microbes of desert steppes can form a stable network structure, allowing them to adequately respond to environmental conditions.ConclusionsThe bacterial communities in the rhizospheric soils of herb plants differ between different degradation gradients. The species number, abundance and diversity of bacterial communities in rhizospheric soils are not directly correlated with degree of degradation. The abundance, species diversity and species abundance of bacterial communities in the rhizospheric soils of moderately degraded desert steppes are the highest and most stable. The soil bacterial diversity is lowest in severely degraded desert steppes. creator: Yuefeng Guo creator: Dan Zhang creator: Wei Qi uri: https://doi.org/10.7717/peerj.16289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: A benzochalcone derivative synchronously induces apoptosis and ferroptosis in pancreatic cancer cells link: https://peerj.com/articles/16291 last-modified: 2023-11-01 description: BackgroundPancreatic cancer is a highly aggressive and lethal disease with limited treatment options. In this study, we investigated the potential therapeutic effects of compound KL-6 on pancreatic cancer cells.MethodsThe study involved assessing the inhibitory effects of KL-6 on cell proliferation, clonogenic potential, cell cycle progression, apoptosis, migration, and invasion. Additionally, we examined the action mechanism of KL-6 by RNA-seq and bioinformatic analysis and validated by qRT-PCR and western blot in pancreatic cancer cells.ResultsOur results demonstrated that KL-6 effectively inhibited the growth of pancreatic cancer cells in a dose-dependent manner. It induced G2/M phase cell cycle arrest and apoptosis, disrupting the cell cycle progression and promoting cell death. KL-6 also exhibited inhibitory effects on cell migration and invasion, suggesting its potential to suppress the metastatic properties of pancreatic cancer cells. Furthermore, KL-6 modulated the expression of genes involved in various cancer-related pathways including apoptosis and ferroptosis.ConclusionThese findings collectively support the potential of KL-6 as a promising therapeutic option for pancreatic cancer treatment. Further research is needed to fully understand the underlying mechanisms and evaluate the clinical efficacy of KL-6 in pancreatic cancer patients. creator: Xiaoqing Guan creator: Bing Zhao creator: Xiaodan Guan creator: Jinyun Dong creator: Jieer Ying uri: https://doi.org/10.7717/peerj.16291 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guan et al. title: Genome-wide identification of CaARR-Bs transcription factor gene family in pepper and their expression patterns under salinity stress link: https://peerj.com/articles/16332 last-modified: 2023-11-01 description: In plants, ARRs-B transcription factors play a crucial role in regulating cytokinin signal transduction, abiotic stress resistance, and plant development. A number of adverse environmental conditions have caused severe losses for the pepper (Capsicum annuum L.)—a significant and economically important vegetable. Among the transcription factors of the type B-ARRs family, multiple members have different functions. In pepper, only a few members of the ARRs-B family have been reported and characterized. The current study aimed to characterize ARRs-B transcription factors in C. annuum, including phylogenetic relationships, gene structures, protein motif arrangement, and RT-qPCR expression analyses and their role in salinity stress. In total, ten genes encode CaARRs-B transcription factors (CaARR1 to CaARR10) from the largest subfamily of type-B ARRs were identified in C. annum. The genome-wide analyses of the CaARRs-B family in C. annuum were performed based on the reported ARRs-B genes in Arabidopsis. An analysis of homologous alignments of candidate genes, including their phylogenetic relationships, gene structures, conserved domains, and qPCR expression profiles, was conducted. In comparison with other plant ARRs-B proteins, CaARRs-B proteins showed gene conservation and potentially specialized functions. In addition, tissue-specific expression profiles showed that CaARRs-B genes were differentially expressed, suggesting functionally divergent. CaARRs-B proteins had a typical conserved domain, including AAR-like (pfam: PF00072) and Myb DNA binding (pfam: PF00249) domains. Ten of the CaARRs-B genes were asymmetrically mapped on seven chromosomes in Pepper. Additionally, the phylogenetic tree of CaARRs-B genes from C. annuum and other plant species revealed that CaARRs-B genes were classified into four clusters, which may have evolved conservatively. Further, using quantitative real-time qRT-PCR, the study assessed the expression patterns of CaARRs-B genes in Capsicum annuum seedlings subjected to salt stress. The study used quantitative real-time qRT-PCR to examine CaARRs-B gene expression in Capsicum annuum seedlings under salt stress. Roots exhibited elevated expression of CaARR2 and CaARR9, while leaves showed decreased expression for CaARR3, CaARR4, CaARR7, and CaARR8. Notably, no amplification was observed for CaARR10. This research sheds light on the roles of CaARRs-B genes in pepper’s response to salinity stress. These findings enrich our comprehension of the functional implications of CaARRs-B genes in pepper, especially in responding to salinity stress, laying a solid groundwork for subsequent in-depth studies and applications in the growth and development of Capsicum annuum. creator: Rana M. Alshegaihi creator: Salha Mesfer Alshamrani uri: https://doi.org/10.7717/peerj.16332 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Alshegaihi and Alshamrani title: Trends in soil organic matter and topsoil thickness under regenerative practices at the University of Washington student farm link: https://peerj.com/articles/16336 last-modified: 2023-11-01 description: Conventional methods of agriculture, especially tillage, are often accompanied by soil degradation in the form of erosion and organic matter depletion. Regenerative agricultural methods seek to repair soil ecosystems by building topsoil and soil organic matter (SOM), decreasing reliance on chemical fertilizers and increasing both water retention capacity and the diversity and quantity of soil microbial and fungal communities. The University of Washington (UW) student farm is an organic and regeneratively managed site on the UW Seattle campus. Over the past 20 years the farm gradually expanded so locations on the farm encompass both unimproved topsoil and soils managed regeneratively for periods of 5 to 20 years. This arrangement allows a time-trend analysis of soil development under regenerative methods. Measurements of topsoil thickness (defined as the distance from the ground surface to the base of the soil A horizon) and organic matter content were collected across 14 distinct plots on the farm to quantify trends over time and estimate net change in SOM (and soil organic carbon, or SOC). While SOM content weakly increased by 0.5% per year, topsoil thickness exhibited a significant linear increase of 0.86 cm per year. Over a twenty-year period under the management practices of the UW Farm total organic carbon storage in soils, determined using topsoil thickness, density, and SOC content, increased by between 4 and 14 t ha−1 yr−1. The general increases in topsoil thickness, SOM content, and total soil carbon demonstrate the potential of soil-health-focused practices to help maintain a productive and efficient urban growing space. creator: Julia E. Macray creator: David R. Montgomery uri: https://doi.org/10.7717/peerj.16336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Macray and Montgomery title: Two new species of Parahesione (Annelida: Hesionidae) associated with ghost shrimps (Crustacea: Decapoda) and their phylogenetic relationships link: https://peerj.com/articles/16346 last-modified: 2023-11-01 description: Two new species of Hesionidae, Parahesione pulvinata sp. nov. and Parahesione apiculata sp. nov. are described based on materials collected at tidal flats in Okinawa (Japan) from burrows of the ghost shrimps Neocallichirus jousseaumei and Glypturus armatus. The two new species are characterized by having eight enlarged cirri, dorsal cirrophores with dorsal foliose lobe and biramous parapodia, and by lacking median antenna. Parahesione apiculata sp. nov. has digitate lobes on the posterior margin of the dorsal foliose lobe (absent in P. pulvinata sp. nov.). The two new species were never found outside the ghost shrimp burrows, suggesting they are obligate symbionts. Phylogenetic analyses based on four concatenated genes suggest that the symbiotic lifestyle has evolved several times in Hesionidae. creator: Naoto Jimi creator: Hiroki Nakajima creator: Taigi Sato creator: Brett C. Gonzalez creator: Sau Pinn Woo creator: Greg W. Rouse creator: Temir Britayev uri: https://doi.org/10.7717/peerj.16346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jimi et al. title: Shining a light on duckweed: exploring the effects of artificial light at night (ALAN) on growth and pigmentation link: https://peerj.com/articles/16371 last-modified: 2023-11-01 description: BackgroundArtificial light at night (ALAN) is a novel environmental stressor of global concern. Various sources of artificial light are now common in urbanized areas and have diverse negative effects on many species of animals and plants. However, ALAN has also been shown to have no effect or a positive effect on some organisms. This study investigates the impact of ALAN on the growth and leaf pigmentation of a common floating freshwater plant species.MethodsWe exposed wild-derived dotted duckweed (Landoltia punctata) to either darkness during the night (Control group) or to artificial light at night (ALAN group) for 49 days. We set up two large boxes of eighty samples each with 2–3 leaves of duckweed in each sample at the start of the experiment. The ALAN box had an opaque lid with a small lamp that was turned on at night. The Control box was also covered at night with an opaque lid but without a lamp. During the day, plants in both boxes were exposed to natural light. We counted the number of leaves in each sample weekly. We took photos of the samples on day 28 to measure the total leaf surface area per sample. On day 49, we took photos of the underside of the leaves for analyses of the relative levels of dark pigmentation across all samples.ResultsWe found that ALAN-exposed plant samples had, on average, more leaves than control plants after a few weeks of exposure. They also had a more variable number of leaves per sample. The total leaf area per sample on day 28 was larger in the ALAN samples. The underside of the leaves on day 49 was, on average, darker in the ALAN plants than in the control plants.ConclusionThere is a significant growth-enhancing effect from exposure to artificial light at night on Landolita punctata. However, higher variability induced by ALAN exposure indicates that ALAN is also a stressful condition for these plants. This is in line with our finding of the presence of larger amounts of dark pigments in the leaves of ALAN-exposed plants. Dark pigmentation in duckweed species could be a defence mechanism protecting tissues from stress-induced oxidative damage. Overall, both positive and negative effects of ALAN can be observed simultaneously in different traits of the same organism. Increased individual variation can facilitate population-level adaptation to stressful conditions. As such, this work contributes to our knowledge of the effects of light pollution in urban environments on common plants. creator: Totoro Nakagawa-Lagisz creator: Malgorzata Lagisz uri: https://doi.org/10.7717/peerj.16371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nakagawa-Lagisz and Lagisz title: The impact of core self-evaluation on school adaptation of high school students after their return to school during the COVID-19 pandemic: the parallel mediation of positive and negative coping styles link: https://peerj.com/articles/15871 last-modified: 2023-10-31 description: BackgroundTo explore the direct effect of core self-evaluation and the indirect effects of positive and negative coping styles on school adaptation of high school students after their return to school during the COVID-19 pandemic.MethodsThe Core Self-Evaluation Scale, Simple Coping Style Scale, and School Adaptation Questionnaire were used for the psychometric analysis of 500 high school students (229 males and 271 females) one month after their return to school. The bootstrap method was applied for mediation analysis.ResultsA positive correlation was noted between core self-evaluation and school adaptation (r = 0.56), and the predictive effect was significant (β = 0.43). Core self-evaluation positively predicted positive coping styles, which positively predicted school adaptation, while core self-evaluation negatively predicted negative coping styles, which negatively predicted school adaptation. Positive and negative coping styles played a significant mediating role between core self-evaluation and school adaptation. The mediating effect included the indirect effects generated by two pathways: core self-evaluation → positive coping style → school adaptation (95% CI [0.08–0.19]) and core self-evaluation → negative coping style → school adaptation (95% CI [0.03–0.11]).ConclusionThere is a positive association between the core self-evaluation and school adaptation of high school students after their return to school during the COVID-19 pandemic. It may directly or indirectly affect the school adaptation of high school students after their return to school through positive or negative coping styles. After returning to school, educators should guide students to view themselves positively, cultivate healthy core self-evaluation, and enable them to have good school adaptation. creator: Qinglin Wang creator: Ruirui Duan creator: Fulei Han creator: Beibei Huang creator: Wei Wang creator: Qiulin Wang uri: https://doi.org/10.7717/peerj.15871 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: The efficacy of digital cognitive behavioral therapy for insomnia and depression: a systematic review and meta-analysis of randomized controlled trials link: https://peerj.com/articles/16137 last-modified: 2023-10-31 description: BackgroundInsomnia and depression often co-occur. Cognitive behavioral therapy for insomnia (CBT-I) seems to be effective and safe for mitigating insomnia and depression. However, the efficacy of digitally-delivered CBT-I (dCBT-I) remains unclear. Therefore, this meta-analysis of randomized controlled trials (RCTs) was to systematically review and evaluate the efficacy of dCBT-I in adults with insomnia and depression.MethodsA systematic search in PubMed, Cochrane, Embase, and Web of Science databases (as of June 5, 2022) was conducted for RCTs on dCBT-I. Statistical analyses were performed using Revan Manager. The effects of dCBT-I on insomnia and depression were expressed as standardized mean difference (SMD) with 95% confidence intervals (CIs).ResultsSeven studies involving 3,597 participants were included. This meta-analysis showed that dCBT-I reduced the severity of insomnia (SMD = −0.85, 95% CI [−1.00 to −0.69], p < 0.001) and depression (SMD = −0.47, 95% CI [−0.55 to −0.38], p < 0.001) in short terms, and also mitigated the severity of insomnia (SMD = −0.71, 95% CI [−1.00 to −0.44], p < 0.001) and depression (SMD = −0.42, 95% CI [−0.68 to −0.15], p = 0.002) in long terms. The effect of dCBT-I was comparable to that of traditional face-to-face CBT-I, and was generally maintained at follow-ups of 6 weeks to 6 months.ConclusiondCBT-I seems to be effective in alleviating insomnia and depression and might be considered as a viable treatment option for depression. creator: Wenyao Lin creator: Na Li creator: Lili Yang creator: Yuqing Zhang uri: https://doi.org/10.7717/peerj.16137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lin et al. title: Murine models of colorectal cancer: the azoxymethane (AOM)/dextran sulfate sodium (DSS) model of colitis-associated cancer link: https://peerj.com/articles/16159 last-modified: 2023-10-31 description: BackgroundColorectal cancer (CRC) is the third most common cancer. It is a heterogeneous disease, including both hereditary and sporadic types of tumors. CRC results from complex interactions between various genetic and environmental factors. Inflammatory bowel disease is an important risk factor for developing CRC. Despite growing understanding of the CRC biology, preclinical models are still needed to investigate the etiology and pathogenesis of the disease, as well as to find new methods of treatment and prevention.ObjectivesThe purpose of this review is to describe existing murine models of CRC with a focus on the models of colitis-associated CRC. This manuscript could be relevant for experimental biologists and oncologists.MethodologyWe checked PubMed and Google from 01/2018 to 05/2023 for reviews of CRC models. In addition, we searched PubMed from 01/2022 to 01/2023 for articles using the azoxymethane (AOM)/dextran sulfate sodium (DSS) CRC model.ResultsExisting murine models of CRC include spontaneous, genetically engineered, transplantation, and chemically induced models. For the study of colitis-associated cancer (CAC), the AOM/DSS model is predominantly used. This model is very similar in histological and molecular characteristics to the human CAC, and is highly reproducible, inexpensive, and easy to use. Despite its popularity, the AOM/DSS model is not standardized, which makes it difficult to analyze and compare data from different studies.ConclusionsEach model demonstrates particular advantages and disadvantages, and allows to reproduce different subtypes or aspects of the pathogenesis of CRC. creator: Dzhuliia Dzhalilova creator: Natalia Zolotova creator: Nikolai Fokichev creator: Olga Makarova uri: https://doi.org/10.7717/peerj.16159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dzhalilova et al. title: RUNX1 facilitates heart failure progression through regulating TGF-β-induced cardiac remodeling link: https://peerj.com/articles/16202 last-modified: 2023-10-31 description: BackgroundHeart failure is caused by acute or chronic cardiovascular diseases with limited treatments and unclear pathogenesis. Therefore, it is urgent to explore new therapeutic targets and reveal new pathogenesis for heart failure.MethodsWe carried out heart failure animal model by transverse aortic arch constriction (TAC) in mice. The left ventricular internal diameter diastole (LVIDd), left ventricular internal diameter systole (LVIDs), and ejection fraction (EF) value were detected using ultrasound and myocardial fibrosis was evaluated by Masson stain assay. Cell apoptosis in myocardial tissues were detected by TUNEL immunofluorescence stain. Signal pathway analysis was performed by dual-luciferase reporter assay and western blot.ResultsOur results showed that inhibition of RUNX1 led to remission of cardiac enlargement induced by TAC in mice. Inhibition of RUNX1 also caused raise of EF and FS value under TAC-induced condition. Besides, RUNX1 inhibition mice showed decreased myocardial fibrosis area under TAC-induced condition. RUNX1 inhibition caused decrease of apoptotic cell rate in myocardial tissues under TAC. Interestingly, we found that RUNX1 could promote the activation of TGF-β/Smads in dual-luciferase reporter assay.InterpretationWe illustrated that RUNX1 could be considered as a new regulator of myocardial remodeling by activating TGF-β/Smads signaling. Based on this, we concluded that RUNX1 may be developed as a new therapeutic target against heart failure in the future. In addition, this study also provide a new insight for the etiological study on heart failure. creator: Peng Qi creator: Qian Zhai creator: Xiquan Zhang uri: https://doi.org/10.7717/peerj.16202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Qi et al.