title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=382 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A multimodal prediction model for suicidal attempter in major depressive disorder link: https://peerj.com/articles/16362 last-modified: 2023-11-08 description: BackgroundSuicidal attempts in patients with major depressive disorder (MDD) have become an important challenge in global mental health affairs. To correctly distinguish MDD patients with and without suicidal attempts, a multimodal prediction model was developed in this study using multimodality data, including demographic, depressive symptoms, and brain structural imaging data. This model will be very helpful in the early intervention of MDD patients with suicidal attempts.MethodsTwo feature selection methods, support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) algorithms, were merged for feature selection in 208 MDD patients. SVM was then used as a classification model to distinguish MDD patients with suicidal attempts or not.ResultsThe multimodal predictive model was found to correctly distinguish MDD patients with and without suicidal attempts using integrated features derived from SVM-RFE and RF, with a balanced accuracy of 77.78%, sensitivity of 83.33%, specificity of 70.37%, positive predictive value of 78.95%, and negative predictive value of 76.00%. The strategy of merging the features from two selection methods outperformed traditional methods in the prediction of suicidal attempts in MDD patients, with hippocampal volume, cerebellar vermis volume, and supracalcarine volume being the top three features in the prediction model.ConclusionsThis study not only developed a new multimodal prediction model but also found three important brain structural phenotypes for the prediction of suicidal attempters in MDD patients. This prediction model is a powerful tool for early intervention in MDD patients, which offers neuroimaging biomarker targets for treatment in MDD patients with suicidal attempts. creator: Qiaojun Li creator: Kun Liao uri: https://doi.org/10.7717/peerj.16362 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li and Liao title: Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand link: https://peerj.com/articles/16401 last-modified: 2023-11-08 description: BackgroundEscherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern.ObjectivesTo characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS.MethodsAntimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms.ResultsST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6′)-Ib (57.28%) was found and the coexistence of aac(6′)-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6′)-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene.ConclusionsThis study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism. creator: Parichart Boueroy creator: Peechanika Chopjitt creator: Rujirat Hatrongjit creator: Masatomo Morita creator: Yo Sugawara creator: Yukihiro Akeda creator: Tetsuya Iida creator: Shigeyuki Hamada creator: Anusak Kerdsin uri: https://doi.org/10.7717/peerj.16401 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Boueroy et al. title: BIBR1532 inhibits proliferation and enhances apoptosis in multiple myeloma cells by reducing telomerase activity link: https://peerj.com/articles/16404 last-modified: 2023-11-08 description: BackgroundMultiple myeloma (MM) is a rare haematological disorder with few therapeutic options. BIBR1532, a telomerase inhibitor, is widely used in cancer treatment and has promising outcomes. In this study, we investigated the efficacy and mechanism of action of BIBR1532 in MM.MethodsK562 and MEG-01 cells were cultured with BIBR1532 at different concentrations. After 24 and 48 h, cell survival was analyzed. Next, these cells were cultured with 25 and 50 µM BIBR1532 for 48 h, then, cell proliferation, apoptosis, and the expression of the telomerase activity related markers were tested by 5-Ethynyl-2′-deoxyuridine (EdU) staining, flow cytometric analysis, western blot and quantitative real-time PCR (qRT-PCR), respectively. Expression of Bcl-xL, Bad, Survivin, phosphorylation of PI3K, AKT, mTOR, ERK1/2, and MAPK were tested via western blotting. Further experiments were conducted to evaluate the synergistic effects of BIBR1532 and doxorubicin (Dox) or bortezomib (Bor).ResultsBIBR1532 inhibited K562 and MEG-01 cell survival in a dose- and time-dependent manner. In addition, BIBR1532 hindered cell proliferation while promoting apoptosis, and this effect was enhanced by increasing the BIBR1532 concentration. Moreover, BIBR1532 inhibited TERT and c-MYC expression, PI3K, AKT, mTOR phosphorylation, and facilitated ERK1/2 and MAPK phosphorylation. Additionally, BIBR1532 combined with Dox or Bor showed synergistic effects in MM treatment.ConclusionBIBR1532 inhibits proliferation and promotes apoptosis in MM cells by inhibiting telomerase activity. Additionally, BIBR1532 combined with Dox or Bor exhibited synergistic effects, indicating that BIBR1532 may be a novel medicine for the treatment of MM. creator: Yuefeng Zhang creator: Xinxin Yang creator: Hangqun Zhou creator: Guoli Yao creator: Li Zhou creator: Chunyan Qian uri: https://doi.org/10.7717/peerj.16404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation link: https://peerj.com/articles/16415 last-modified: 2023-11-08 description: BackgroundGlycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and is experiencing population declines across its natural range. Understanding the patterns of genetic diversity in G. soja populations can help to inform conservation practices.MethodsIn this study, we analyzed the genetic diversity and differentiation of G. soja at different sites and investigated the gene flow within the species. We obtained 147 G. soja accessions collected from 16 locations across the natural range of the species from China, Korea and Japan. Samples were analyzed using SLAF-seq (Specific-Locus Amplified Fragment Sequencing).ResultsWe obtained a total of 56,489 highly consistent SNPs. Our results suggested that G. soja harbors relatively high diversity and that populations of this species are highly differentiated. The populations harboring high genetic diversity, especially KR, should be considered first when devising conservation plans for the protection of G. soja, and in situ protection should be adopted in KR. G. soja populations from the Yangtze River, the Korean peninsula and northeastern China have a close relationship, although these areas are geographically disconnected. Other populations from north China clustered together. Analysis of gene flow suggested that historical migrations of G. soja may have occurred from the south northwards across the East-Asia land-bridge, but not across north China. All G. soja populations could be divided into one of two lineages, and these two lineages should be treated separately when formulating protection policies. creator: Jing Meng creator: Guoqian Yang creator: Xuejiao Li creator: Yan Zhao creator: Shuilian He uri: https://doi.org/10.7717/peerj.16415 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Meng et al. title: A new pseudoscorpion genus (Garypinoidea: Garypinidae) from the Eocene supports extinction and range contraction in the European paleobiota link: https://peerj.com/articles/15989 last-modified: 2023-11-07 description: During the Paleogene, the Holarctic experienced drastic climatic oscillations, including periods of extensive glaciation. These changes had a severe impact on both the flora and fauna causing widespread extinction and range shifts with some taxa retreating to refugia in the Mediterranean Basin. Here we provide evidence for this hypothesis using fossils from the pseudoscorpion family Garypinidae Daday, 1889 (Arachnida: Pseudoscorpiones). This family comprises 21 extant genera from all continents except Antarctica but is restricted to low mid-latitudes (<44°N) in the Northern Hemisphere. We provide the second record of garypinids from the European succinite ambers of the Eocene by describing the first extinct genus in Garypinidae, Baltamblyolpium gen. nov., which includes two species: Baltamblyolpium gizmotum sp. nov. from Baltic amber and Baltamblyolpium grabenhorsti sp. nov. from Bitterfeld amber. The new genus exhibits a morphology that closely resembles Neoamblyolpium Hoff, 1956 from western North America and the genus Amblyolpium Simon, 1898, which is widespread but includes taxa restricted to Mediterranean refugia in Europe. The discovery of a new fossil genus of Garypinidae from Europe confirms that the family was found at more northerly latitudes during the Eocene, however, extinction and range contraction resulted in their present-day relictual distribution in southern Europe like many other lineages that once thrived in the European “Baltic amber forest” of the Eocene. creator: Nova Stanczak creator: Mark S. Harvey creator: Danilo Harms creator: Jörg U. Hammel creator: Ulrich Kotthoff creator: Stephanie F. Loria uri: https://doi.org/10.7717/peerj.15989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Stanczak et al. title: Participatory ethnobotany: comparison between two quilombos in the Atlantic Forest, Ubatuba, São Paulo, Brazil link: https://peerj.com/articles/16231 last-modified: 2023-11-07 description: Ethnobotanical studies that use the participatory research approach seek to involve the residents of a community in different stages of the study, promoting the registration, dissemination and strengthening of local knowledge, as well as the empowerment of decisions related to the sustainable use and management of resources. Using the participatory methodology, this study recorded and made a comparative analysis on the use of plants in two quilombola communities (Quilombo do Cambury-QC and Quilombo da Fazenda-QF) in the State of São Paulo. After a training on anthropological and botanical methods, local researchers selected and interviewed the local experts, recording their knowledge on plant uses and collecting the indicated plants, to be identified and deposited in herbariums. In addition, participant observation and field diaries were used by the academic researchers, helping to analyze the data. To test the differences in the composition of species known to local community, a Jaccard dissimilarity matrix was created, and a Permanova test was employed. During the 178 days of fieldwork, three local researchers from the QC and two from the QF, selected nine and eight experts on the uses of the plants in each quilombo, respectively, corresponding to 214 plant species, indicated for eight ethnobotanical categories. Our hypothesis has been confirmed, since the traditional knowledge found in both quilombos, regarding plant uses and the number of plant species by category, are distinct, since each community occupies particular plant areas and different phytophysiognomies. Most of the indicated species are native to the Atlantic forest, and no significant differences were observed in the proportion of native species vs. introduced among quilombos for any of the categories of use studied. Furthermore, the innovative methodology used, participatory ethnobotany, contributed to the empowerment of community members with regard to the use of their available resources in the environment in which they live, while retaining the intellectual property rights over their own knowledge. creator: Thamara Sauini creator: Paulo Henrique Gonçalves Santos creator: Ulysses Paulino Albuquerque creator: Priscila Yazbek creator: Cremilda da Cruz creator: Eduardo Hortal Pereira Barretto creator: Maria Alice dos Santos creator: Maria Angélica Silva Gomes creator: Ginacil dos Santos creator: Silvestre Braga creator: Ricardo José Francischetti Garcia creator: Sumiko Honda creator: Priscila Matta creator: Sonia Aragaki creator: Anderson Ueno creator: Eliana Rodrigues uri: https://doi.org/10.7717/peerj.16231 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sauini et al. title: circMSH3 is a potential biomarker for the diagnosis of colorectal cancer and affects the distant metastasis of colorectal cancer link: https://peerj.com/articles/16297 last-modified: 2023-11-07 description: ObjectivesTo identify the most significantly differentially expressed circular RNAs (circRNAs) in colorectal cancer (CRC) tissues in terms of their expression levels and circularity, and to analyze the relationship between their expression levels and the clinical characteristics of patients.MethodscircRNA RNA-seq technology was used to screen differentially expressed circRNAs in CRC. Sanger sequencing was used to identify circRNA back-splice junction sites. The relative expression levels of hsa_circ_0003761 (circMSH3) in CRC tissues and cell lines were detected by quantitative real-time fluorescence PCR technology. An RNA-protein pull-down assay was used to detect protein binding to circRNAs. Dual-luciferase reporter gene vectors were constructed to verify that circRNAs bind to microRNAs.ResultsFour hundred twenty circRNAs were found to be upregulated, and 616 circRNAs were downregulated. circMSH3 was derived from the MutS homolog 3 (MSH3) gene and was formed by a loop of exons 9, 10, 11, and 12. In 110 pairs of CRC and adjacent tissues, circMSH3 expression was 4.487-fold higher in CRC tissues. circMSH3 was also highly expressed in the HT-29 and LOVO CRC cell lines. The expression level of circMSH3 was associated with distant metastasis in CRC patients (P = 0.043); the area under the curve (AUC) of circMSH3 for CRC diagnosis was 0.75, with a sensitivity and specificity of 70.9% and 66.4%, respectively. circMSH3 could bind to a variety of proteins, mainly those involved in RNA transcription, splicing, cell cycle, and cell junctions. Furthermore, circMSH3 could bind to miR-1276, miR-942-5p, and miR-409-3p.ConclusioncircMSH3 is a potential biomarker for the diagnosis of CRC and affects the distant metastasis of CRC. Multiple RNA-binding protein binds to circMSH3, and circMSH3 binds to miR-1276, miR-942-5p, and miR-409-3p, thereby affecting the expression of circMSH3. creator: Jian Shen creator: Yu Min creator: Jingen Luo creator: Xingkui Tang creator: Zeping Han creator: Wenfeng Luo creator: Fangmei Xie creator: Mingrong Cao creator: Taicheng Zhou creator: Jinhua He uri: https://doi.org/10.7717/peerj.16297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shen et al. title: RBM25 binds to and regulates alternative splicing levels of Slc38a9, Csf1, and Coro6 to affect immune and inflammatory processes in H9c2 cells link: https://peerj.com/articles/16312 last-modified: 2023-11-07 description: BackgroundAlternative splicing (AS) is a biological process that allows genes to be translated into diverse proteins. However, aberrant AS can predispose cells to aberrations in biological mechanisms. RNA binding proteins (RBPs), closely affiliated with AS, have gained increased attention in recent years. Among these RBPs, RBM25 has been reported to participate in the cardiac pathological mechanism through regulating AS; however, the involvement of RBM25 as a splicing factor in heart failure remains unclarified.MethodsRBM25 was overexpressed in H9c2 cells to explore the target genes bound and regulated by RBM25 during heart failure. RNA sequencing (RNA-seq) was used to scrutinize the comprehensive transcriptional level before identifying AS events influenced by RBM25. Further, improved RNA immunoprecipitation sequencing (iRIP-seq) was employed to pinpoint RBM25-binding sites, and RT-qPCR was used to validate specific genes modulated by RBM25.ResultsRBM25 was found to upregulate the expression of genes pertinent to the inflammatory response and viral processes, as well as to mediate the AS of genes associated with cellular apoptosis and inflammation. Overlap analysis between RNA-seq and iRIP-seq suggested that RBM25 bound to and manipulated the AS of genes associated with inflammation in H9c2 cells. Moreover, qRT-PCR confirmed Slc38a9, Csf1, and Coro6 as the binding and AS regulatory targets of RBM25.ConclusionOur research implies that RBM25 plays a contributory role in cardiac inflammatory responses via its ability to bind to and regulate the AS of related genes. This study offers preliminary evidence of the influence of RBM25 on inflammation in H9c2 cells. creator: Xin Tian creator: Guangli Zhou creator: Hao Li creator: Xueting Zhang creator: Lingmin Zhao creator: Keyi Zhang creator: Luqiao Wang creator: Mingwei Liu creator: Chen Liu creator: Ping Yang uri: https://doi.org/10.7717/peerj.16312 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Tian et al. title: Association of triglyceride-glucose index with the risk of prostate cancer: a retrospective study link: https://peerj.com/articles/16313 last-modified: 2023-11-07 description: BackgroundProstate cancer is the most common malignancy in men, and its incidence is increasing year by year. Some studies have shown that risk factors for prostate cancer are related to insulin resistance. The triglyceride-glucose (TyG) index is a marker of insulin resistance. We investigated the validity of TyG index for predicting prostate cancer and the dose-response relationship in prostate cancer in relation to it.ObjectiveTo investigate the risk factors of TyG index and prostate cancer prevalence.MethodsThis study was screened from the First Affiliated Hospital of Xinjiang Medical University and included 767 people, including 136 prostate cancer patients in the case group and 631 healthy people in the control group. The relationship between TyG index and the risk of prostate cancer was analyzed by one-way logistic regression, adjusted for relevant factors, and multi-factor logistic regression analysis was performed to further investigate the risk factors affecting the prevalence of prostate cancer. ROC curves and Restricted Cubic Spline were established to determine the predictive value and dose-response relationship of TyG index in prostate cancer.ResultsBlood potassium (OR = 0.056, 95% CI [0.021–0.148]), total cholesterol (OR = 1.07, 95% CI [0.792–1.444]) and education level (OR = 0.842, 95% CI [0.418–1.697]) were protective factors for prostate cancer, alkaline phosphatase, age, LDL, increased the risk of prostate cancer (OR = 1.016, 95% CI [1.006–1.026]) (OR = 139.253, 95% CI [18.523–1,046.893] (OR = 0.318, 95% CI [0.169–0.596]); TyG index also was a risk factor for prostate cancer, the risk increased with TyG levels,and persons in the TyGQ3 group (8.373–8.854 mg/dL) was 6.918 times (95% CI [2.275–21.043]) higher than in the Q1 group,in the TyGQ4 group (≥8.854) was 28.867 times of those in the Q1 group (95% CI [9.499–87.727]).ConclusionTyG index may be a more accurate and efficient predictor of prostate cancer. creator: Tianqi Li creator: Yijie Zhou creator: Jinru Wang creator: Songtao Xiao creator: Yajun Duan creator: Caihong Li creator: Yi Gao creator: Hengqing An creator: Ning Tao uri: https://doi.org/10.7717/peerj.16313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Assessment of intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on omega, gamma and alpha-gliadin profiles link: https://peerj.com/articles/16330 last-modified: 2023-11-07 description: Durum and bread wheat are well adapted to the Mediterranean Basin. Twenty-three genotypes of each species were grown to evaluate the intra- and inter-genetic diversity based on omega (ω), gamma (γ) and alpha (α)-gliadin profiles. To achieve this purpose, the endosperm storage proteins (both gliadins and glutenins) were extracted from wheat grains and electrophoresed on sodium dodecyl sulfate (SDS)–polyacrylamide gels. The results of SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) revealed nine polymorphic loci out of 16 loci with durum wheat genotypes and nine polymorphic loci out of 18 loci with bead wheat genotypes. The polymorphisms revealed by the SDS-PAGE were 56% and 50% in durum and bread wheat genotypes, respectively. Using the cluster analysis, the durum wheat genotypes were clustered into five groups, while the bread wheat genotypes were grouped into six clusters using un-weighed pair group mean analyses based on ω, γ, and α-gliadins profiles. The 46 durum and bread wheat genotypes were grouped into seven clusters based on the combined ω, γ, and α-gliadins profiles revealed by the SDS-PAGE. The in silico analysis determined the intra-genetic diversity between bread and durum wheat based on the sequences of ω, γ, and α-gliadins. The alignment of ω-gliadin revealed the highest polymorphism (52.1%) between bread and durum wheat, meanwhile, the alignment of γ and α-gliadins revealed very low polymorphism 6.6% and 15.4%, respectively. According to computational studies, all gliadins contain a lot of glutamine and proline residues. The analysis revealed that the bread wheat possessed ω and γ -gliadins with a lower content of proline and a higher content of glutamine than durum wheat. In contrast, durum wheat possessed α-gliadin with a lower content of proline and a higher content of glutamine than bread wheat. In conclusion, the SDS-PAGE, in silico and computational analyses are effective tools to determine the intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on ω, γ, and α-gliadins profiles. creator: Jameel M. Al-Khayri creator: Khairiah M. Alwutayd creator: Fatmah A. Safhi creator: Mesfer M. Alqahtani creator: Rana M. Alshegaihi creator: Diaa Abd El-Moneim creator: Shri Mohan Jain creator: Ahmed S. Eldomiaty creator: Rahma Alshamrani creator: Amani Omar Abuzaid creator: Abdallah A. Hassanin uri: https://doi.org/10.7717/peerj.16330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Al-Khayri et al.