title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=420 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides link: https://peerj.com/articles/16056 last-modified: 2023-09-18 description: BackgroundGardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough.MethodsIn this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides.ResultsAfter data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future. creator: Xinyu Xu creator: Bihua Chen creator: Juan Zhang creator: Siren Lan creator: Shasha Wu uri: https://doi.org/10.7717/peerj.16056 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: In vitro and ex vitro propagation of Turkish myrtles through conventional and plantform bioreactor systems link: https://peerj.com/articles/16061 last-modified: 2023-09-18 description: The myrtle (Myrtus communis) plant naturally grows in the temperate Mediterranean and subtropical regions and is used for various purposes; thus, it is among the promising species of horticultural crops. This study aimed to evaluate and compare the performance of different propagation systems, including rooting, solid media propagation, rooting, and with the Plantform bioreactor system, in achieving healthy and rapid growth of four myrtle genotypes with diverse genetic origins and well-regional adaptation. The selection of myrtle genotypes with distinct genetic backgrounds and proven adaptability to specific regions allowed for a comprehensive assessment of the propagation systems under investigation. Present findings proved that the Plantform system, the new-generation tissue culture system, was quite successful in micropropagation and rooting myrtle genotypes. We succeeded in vitro micropropagation and rooting of diverse wild myrtle genotypes, enabling year-round propagation without reliance on specific seasons or environmental conditions. The process involved initiating cultures from explants and multiplying them through shoot proliferation in a controlled environment. This contributes to sustainable plant propagation, preserving and utilizing genetic resources for conservation and agriculture. creator: Özhan Şimşek creator: Dicle Dönmez creator: Mehmet Ali Sarıdaş creator: Emine Acar creator: Yıldız Aka Kaçar creator: Sevgi Paydaş Kargı creator: Tolga İzgü uri: https://doi.org/10.7717/peerj.16061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Şimşek et al. title: The mediating roles of coping styles and academic burnout in the relationship between stressors and depressive symptoms among Chinese postgraduates link: https://peerj.com/articles/16064 last-modified: 2023-09-18 description: BackgroundSince few studies have incorporated factors like stressors, coping styles, and academic burnout into the same model to analyze their impacts on depressive symptoms, this research attempts to establish an optimal structural model to explore the direct and indirect effects of these factors on depressive symptoms.MethodsA total of 266 postgraduates completed questionnaires regarding coping styles, academic burnout, stressors, and depressive symptoms. The path analysis was applied for investigating the roles of coping styles and academic burnout in mediating the relationship between stressors and depressive symptoms.ResultsThe total and direct effects of stressors on depressive symptoms were 0.53 and 0.31, respectively. The proportion of the direct effect of stressors on depressive symptoms to its total effect amounted to 58.50%. The indirect effects of academic burnout, positive coping style, and negative coping style on the association between stressors and depressive symptoms were 0.11, 0.04, and 0.03, taking up 20.75%, 7.55%, and 5.66% of the total effect, respectively. The serial indirect effect of positive coping style and academic burnout was 0.02, accounting for 3.77% of the total effect, while that of negative coping style and academic burnout was 0.02, taking up 3.77% of the total effect.ConclusionsCoping styles and academic burnout chain jointly mediate the relationship between stressors and depressive symptoms among postgraduates. Thus, encouraging postgraduates to tackle stress positively may reduce the likelihood of the development of academic burnout and further reduce depressive symptoms. creator: Hong Shi creator: Hanfang Zhao creator: Minfu He creator: Zheng Ren creator: Shixun Wang creator: Li Cui creator: Jieyu Zhao creator: Wenjun Li creator: Yachen Wei creator: Wenjing Zhang creator: Ziqiang Chen creator: Hongjian Liu creator: Xiumin Zhang uri: https://doi.org/10.7717/peerj.16064 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shi et al. title: Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study link: https://peerj.com/articles/16072 last-modified: 2023-09-18 description: BackgroundCOVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group.MethodsLithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19).ResultsPlasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the “WHO clinical progression scale”. D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels.ConclusionThe results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomarker of disease severity in COVID-19. creator: Katharina Hoeter creator: Elmo Neuberger creator: Susanne Fischer creator: Manuel Herbst creator: Ema Juškevičiūtė creator: Kira Enders creator: Heidi Rossmann creator: Martin F. Sprinzl creator: Perikles Simon creator: Marc Bodenstein creator: Michael Schaefer uri: https://doi.org/10.7717/peerj.16072 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hoeter et al. title: Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators link: https://peerj.com/articles/16103 last-modified: 2023-09-18 description: BackgroundSerine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9.MethodsIn this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed.ResultsSplicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1.ConclusionThe insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies. creator: Tao Jiang creator: Li Wang creator: Liang Tang creator: Azhar Zeb creator: Yanjun Hou uri: https://doi.org/10.7717/peerj.16103 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jiang et al. title: Lower-limb sagittal joint angles during gait can be predicted based on foot acceleration and angular velocity link: https://peerj.com/articles/16131 last-modified: 2023-09-18 description: Background and purposeContinuous monitoring of lower-limb movement may help in the early detection and control/reduction of diseases (such as the progression of orthopedic diseases) by applying suitable interventions. Therefore, it is invaluable to calculate the lower-limb movement (sagittal joint angles) while walking daily for continuous evaluation of such risks. Although cameras in a motion capture system are necessary for calculating lower-limb sagittal joint angles during gait, the method is unrealistic considering the setting is difficult to achieve in daily life. Therefore, the estimation of lower-limb sagittal joint angles during walking based on variables, which can be measured using wearable sensors (e.g., foot acceleration and angular velocity), is important. This study estimates the lower-limb sagittal joint angles during gait from the norms of foot acceleration and angular velocity using machine learning and validates the accuracy of the estimated joint angles with those obtained using a motion capture system.MethodsHealthy adults (n = 200) were asked to walk at a comfortable speed (10 trials), and their lower-limb sagittal joint angles, foot accelerations, and angular velocities were obtained. Using these variables, we established a feedforward neural network and estimated the lower-limb sagittal joint angles.ResultsThe average root mean squared errors of the lower-limb sagittal joint angles during gait ranged between 2.5°–7.0° (hip: 7.0°; knee: 4.0°; and ankle: 2.5°).ConclusionThese results show that we can estimate the lower-limb sagittal joint angles during gait using only the norms of foot acceleration and angular velocity, which can help calculate the lower-limb sagittal joint angles during daily walking. creator: Takuma Inai creator: Tomoya Takabayashi uri: https://doi.org/10.7717/peerj.16131 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Inai and Takabayashi title: miR-200a-3p overexpression alleviates diabetic cardiomyopathy injury in mice by regulating autophagy through the FOXO3/Mst1/Sirt3/AMPK axis link: https://peerj.com/articles/15840 last-modified: 2023-09-15 description: ObjectiveHyperglycemia and insulin resistance or deficiency are characteristic features of diabetes. Diabetes is accompanied by cardiomyocyte hypertrophy, fibrosis and ventricular remodeling, and eventually heart failure. In this study, we established a diabetic cardiomyopathy (DCM) mouse model to explore the role and mechanism of miR-200a-3p in DCM.MethodsWe used db/db mice to simulate the animal model of DCM and the expression of miR-200a-3p was then examined by RT-qPCR. Tail vein injection of mice was done with rAAV-miR-200a-3p for 8 weeks, and cardiac function was assessed by cardiac ultrasound. The levels of myocardial tissue injury, fibrosis, inflammation, apoptosis and autophagy in mice were detected by histological staining, TUNEL and other molecular biological experiments.ResultsmiR-200a-3p expression levels were significantly decreased in the myocardium of DCM mice. Diabetic mice developed cardiac dysfunction and presented pathological changes such as myocardial injury, myocardial interstitial fibrosis, cardiomyocyte apoptosis, autophagy, and inflammation. Overexpression of miR-200a-3p expression significantly ameliorated diabetes induced-cardiac dysfunction and myocardial injury, myocardial interstitial fibrosis, cardiomyocyte apoptosis, and inflammation, and enhanced autophagy. Mechanistically, miR-200a-3p interacted with FOXO3 to promote Mst1 expression and reduce Sirt3 and p-AMPK expression.ConclusionIn type 2 diabetes, increased miR-200a-3p expression enhanced autophagy and participated in the pathogenic process of cardiomyopathy throug7 Mst1/Sirt3/AMPK axis regulation by its target gene FOXO3. This conclusion provides clues for the search of new gene targeted therapeutic approaches for diabetic cardiomyopathy. creator: Penghua You creator: Haichao Chen creator: Wenqi Han creator: Jizhao Deng uri: https://doi.org/10.7717/peerj.15840 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 You et al. title: Tibial cortex transverse transport potentiates diabetic wound healing via activation of SDF-1/CXCR4 signaling link: https://peerj.com/articles/15894 last-modified: 2023-09-15 description: BackgroundThe current treatments for diabetic foot ulcers have disadvantages of slow action and numerous complications. Tibial cortex transverse transport (TTT) surgery is an extension of the Ilizarov technique used to treat diabetic foot ulcers, and can shorten the repair time of diabetic foot ulcers. This study assessed the TTT technique for its effectiveness in healing diabetic foot ulcer skin lesions and its related molecular mechanisms.MethodsDiabetic rat models were established by injecting healthy Sprague-Dawley rats with streptozotocin (STZ). The effects of TTT surgery on the model rats were assessed by recording changes in body weight, analyzing skin wound pictures, and performing H&E staining to assess the recovery of wounded skin. The numbers of endothelial progenitor cells (EPCs) in peripheral blood were analyzed by flow cytometry, and levels of CXCR4 and SDF-1 expression were qualitatively analyzed by immunofluorescence, immunohistochemistry, qRT-PCR, and western blotting.ResultsBoth the histological results and foot wound pictures indicated that TTT promoted diabetic wound healing. Flow cytometry results showed that TTT increased the numbers of EPCs in peripheral blood as determined by CD34 and CD133 expression. In addition, activation of the SDF-1/CXCR4 signaling pathway and an accumulation of EPCs were observed in skin ulcers sites after TTT surgery. Finally, the levels of SDF-1 and CXCR4 mRNA and protein expression in the TTT group were higher than those in a blank or fixator group.ConclusionTTT promoted skin wound healing in diabetic foot ulcers possibly by activating the SDF-1/CXCR4 signaling pathway. creator: Shuanji Ou creator: Xiaodong Wu creator: Yang Yang creator: Changliang Xia creator: Wei Zhang creator: Yudun Qu creator: Jiaxuan Li creator: Bo Chen creator: Lilin Zhu creator: Changpeng Xu creator: Yong Qi uri: https://doi.org/10.7717/peerj.15894 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ou et al. title: AP003352.1/miR-141-3p axis enhances the proliferation of osteosarcoma by LPAR3 link: https://peerj.com/articles/15937 last-modified: 2023-09-15 description: Osteosarcoma (OS) is a highly malignant tumor with a poor prognosis and a growing incidence. LncRNAs and microRNAs control the occurrence and development process of osteosarcoma through ceRNA patterns. The LPAR3 gene is important in cancer cell proliferation, apoptosis and disease development. However, the regulatory mechanism of the ceRNA network through which LPAR3 participates in osteosarcoma has not been clarified. Herein, our study demonstrated that the AP003352.1/miR-141-3p axis drives LPAR3 expression to induce the malignant progression of osteosarcoma. First, the expression of LPAR3 is regulated by the changes in AP003352.1 and miR-141-3p. Similar to the ceRNA of miR-141-3p, AP003352.1 regulates the expression of LPAR3 through this mechanism. In addition, the regulation of AP003352.1 in malignant osteosarcoma progression depends to a certain degree on miR-141-3p. Importantly, the AP003352.1/miR-141-3p/LPAR3 axis can better serve as a multi-gene diagnostic marker for osteosarcoma. In conclusion, our research reveals a new ceRNA regulatory network, which provides a novel potential target for the diagnosis and treatment of osteosarcoma. creator: Hongde Yu creator: Bolun Zhang creator: Lin Qi creator: Jian Han creator: Mingyang Guan creator: Jiaze Li creator: Qingtao Meng uri: https://doi.org/10.7717/peerj.15937 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yu et al. title: Predictive value of liver and spleen stiffness measurement based on two-dimensional shear wave elastography for the portal vein pressure in patients with compensatory viral cirrhosis link: https://peerj.com/articles/15956 last-modified: 2023-09-15 description: ObjectiveThis study aimed to explore the predictive value of liver and spleen stiffness measurement based on two-dimensional shear wave elastography for the portal vein pressure in patients with compensatory viral cirrhosis.MethodsFrom January 2017 to August 2019, 107 patients with compensatory viral cirrhosis and 76 patients with viral hepatitis were enrolled as cirrhosis group and hepatitis group, respectively. Patient data were obtained during admission, and this study was a review and analysis of patient data. Liver stiffness measurement (LSM), spleen stiffness measurement (SSM), portal vein diameter and spleen thickness were compared between the two groups, and their diagnostic value for compensatory viral cirrhosis was analyzed. According to the hepatic vein pressure, the cirrhosis group patients were divided into non-hypertensive group (no portal hypertension, hepatic venous pressure gradient (HVPG) < 5 mmHg), mild group (mild portal hypertension, 5 mmHg ≤ HVPG ≤ 10 mmHg) and severe group (clinically significant portal hypertension group, HVPG > 10 mmHg). LSM, SSM, portal vein diameter and spleen thickness of the three groups were compared, and the correlation between SSM and hepatic vein pressure was analyzed.ResultsLSM, SSM, portal vein diameter and spleen thickness in the cirrhosis group were higher than those in hepatitis group (all P < 0.05). The area under the curve (AUC) of combined detection was larger than that of LSM, SSM and spleen thickness detection alone in liver cirrhosis diagnosis (all P < 0.05). LSM, SSM, portal vein diameter and spleen thickness increased with the increase of hepatic vein pressure in patients with liver cirrhosis (all P < 0.05). LSM, SSM, portal vein diameter and spleen thickness were all positively correlated with hepatic vein pressure (P < 0.05). ROC curve showed that AUC of combined detection was greater than that of LSM, SSM, portal vein diameter and spleen thickness alone detection in the diagnosis of clinically significant portal hypertension (all P < 0.05). The increase of LSM, SSM, portal vein diameter and spleen thickness were the influencing factors for hepatic vein pressure rising (all P < 0.05).ConclusionThere was an increase of LSM and SSM in patients with compensatory viral cirrhosis, which were positively correlated with hepatic venous pressure, and combined index detection has diagnostic and predictive value for the change of portal venous pressure. creator: Peng Wang creator: Xinhong Hu creator: Feng Xie uri: https://doi.org/10.7717/peerj.15956 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al.