Molecular Biology Reports最新文献

{"title":"Correction: Exome sequencing identified mutations in the WNT1 and COL1A2 genes in osteogenesis imperfecta cases.","authors":"Poonam Mehta, Rahul Vishvkarma, Sushil Gupta, Naibedya Chattopadhyay, Singh Rajender","doi":"10.1007/s11033-024-10023-8","DOIUrl":"https://doi.org/10.1007/s11033-024-10023-8","url":null,"abstract":"","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1117"},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical significance and potential mechanism of hsa_circ_0006892 in acute respiratory distress syndrome complicated with pulmonary fibrosis.","authors":"Shuping Zhang, Lingbo Rong, Guangwen Long, Feihong Huang, Qian Zhang, Xiulin Yang, Hongpeng Sun, Chunling Ji, Rui-Hai Ye","doi":"10.1007/s11033-024-10047-0","DOIUrl":"https://doi.org/10.1007/s11033-024-10047-0","url":null,"abstract":"<p><strong>Background: </strong>Acute respiratory distress syndrome (ARDS) is a serious acute lung injury, and can develop into pulmonary fibrosis (PLF). Circular RNAs (circRNAs) regulatory network in ARDS is important. The study explored the role of hsa_circ_0006892 in the occurrence of ARDS and the development of PLF.</p><p><strong>Methods: </strong>Hsa_circ_0006892 levels were verified in serum samples of 203 ARDS patients with or without PLF, and the diagnostic value was evaluated through ROC. Cox regression analysis was performed to identify PLF-related factors. The downstream target genes were predicted online. The function and pathway of key genes were annotated through GO and KEGG pathway analysis. Protein-protein interaction (PPI) analysis was performed for the examination of protein interactions.</p><p><strong>Results: </strong>qRT-PCR determined the downregulation of hsa_circ_0006892 in the serum of both ARDS and PLF patients. Hsa_circ_0006892 can differentiate ARDS from controls, and independently related to the development of PLF. Nine targeted related miRNAs were integrated with dysregulated miRNAs from GSE27430 dataset. Clinically, miR-486-3p was the only miRNA that was significantly different in both ARDS and PLF groups, and was determined to be the target of hsa_circ_0006892. 180 target genes of miR-486-3p were predicted, which were integrated with ARDS and PLF-related GSE84439 and GSE38958 datasets. Go and KEGG pathway analysis identified Ras signaling pathway as the most commonly enriched pathway in the overlapped genes.</p><p><strong>Conclusions: </strong>The present results identified the differentially expressed hsa_circ_0006892 in ARDS and PLF, and suggested a possible molecular mechanism of hsa_circ_0006892/miR-486-3p axis.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1120"},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The implication of TET1, miR-200, and miR-494 expression with tumor formation in colorectal cancer: through targeting Wnt signaling.","authors":"Raziye Tajali, Neda Zali, Fatemeh Naderi Noukabadi, Meysam Jalili, Morteza Valinezhad, Farnaz Ghasemian, Makan Cheraghpour, Sanaz Savabkar, Ehsan Nazemalhosseini Mojarad","doi":"10.1007/s11033-024-10060-3","DOIUrl":"10.1007/s11033-024-10060-3","url":null,"abstract":"<p><strong>Objective: </strong>Colorectal cancer (CRC) is a diverse and multifaceted disease characterized by genetic and epigenetic changes that contribute to tumor initiation and progression. CRC pathophysiology has been linked to the deregulation of the Wnt signaling pathway and the ten-eleven translocation (TET) DNA demethylases. This study aimed to evaluate the expression level of selective miRNAs (miR-200 and miR-494), TET1, and Wnt1 in colorectal polyps, actual colorectal tumors, and normal adjacent tissues. We also evaluated the effect of 5-aza cytidine on the expression level of TET1 and wnt1 in the HT29 cell line.</p><p><strong>Materials and methods: </strong>In this study, we assessed TET1 and Wnt1 expression in 5-azacytidine-treated HT29 cells, a demethylating agent commonly used in cancer therapy. Additionally, we enrolled 114 individuals who underwent radical surgical colon resection, including 47 with cancerous tissues and 67 with polyps. We utilized qRT-PCR to measure miR-200, miR-494, TET1, and Wnt1 mRNA levels in colorectal polyps, actual colorectal tumors, and normal adjacent tissues.</p><p><strong>Results: </strong>Our study revealed that TET1 expression was notably lower in both polyps and CRC tissue compared to adjacent normal tissue, with higher TET1 expression in tumors than polyps. We also observed significant differences in miR-200 and miR-494 expression in tumor samples compared to adjacent normal tissue. Our in vitro experiments revealed that 5-azacytidine administration increased TET1 and decreased Wnt1 expression in CRC cell lines. This suggests that DNA-demethylating drugs may have a therapeutic role in modifying TET1 and Wnt signaling in the development of CRC.</p><p><strong>Conclusions: </strong>Overall, our findings shed light on the intricate interactions between TET1, Wnt1, and specific miRNAs in colorectal cancer (CRC) and their potential implications for diagnosis and treatment.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1119"},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synergistic effects of curcumin and stem cells on spinal cord injury: a comprehensive review.","authors":"Reza Arefnezhad, Arian Jahandideh, Mahdi Rezaei, Mohamad Salehi Khatouni, Hooman Zarei, Saleheh Jahani, Ali Molavi, Mohammadhossein Hefzosseheh, Parisa Ghasempour, Hadis Moazen Movahedi, Romina Jahandideh, Fatemeh Rezaei-Tazangi","doi":"10.1007/s11033-024-10057-y","DOIUrl":"https://doi.org/10.1007/s11033-024-10057-y","url":null,"abstract":"<p><p>Spinal cord injury (SCI) is damage to the spinal cord that permanently or temporarily disrupts its function, causing considerable autonomic, sensory, and motor disorders, and involves between 10 and 83 cases per million yearly. Traumatic SCI happens following primary acute mechanical damage, leading to injury to the spinal cord tissue and worsening clinical outcomes. The present therapeutic strategies for this complex disease fundamentally rely on surgical approaches and conservative remedies. However, these modalities are not effective enough for neurological recovery. Therefore, it is necessary to discover more efficient methods to treat patients with SCI. Today, considerable attention has been drawn to bioactive compounds-based remedies and stem cell therapy for curing various ailments and disorders, such as neurological diseases. Some researchers have recommended that harnessing curcumin, a polyphenol obtained from turmeric, in combination with stem cells, like mesenchymal stem cells, neural stem cells, and ependymal stem cells, can remarkably improve neurological recovery-related parameters more effective than the treatment with these two methods separately in experimental models. Hereby, this literature review delves into the functionality of curcumin combined with stem cells in treating SCI with a focus on cellular and molecular mechanisms.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1113"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Geniposide attenuates early brain injury by inhibiting oxidative stress and neurocyte apoptosis after subarachnoid hemorrhage in rats.","authors":"Xiaolan Xiao, Shuangxi Sun, Yingbin Li, Xuecheng Cen, Shibiao Wu, Aili Lu, Jun Cai, Junjie Zhao, Shaoxue Li","doi":"10.1007/s11033-024-09972-x","DOIUrl":"https://doi.org/10.1007/s11033-024-09972-x","url":null,"abstract":"","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1110"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of water-insoluble wheat bran-fraction powder on disease activity and caecal microbiota in dextran sodium sulphate-induced inflammatory bowel disease mouse model.","authors":"Kazuya Koga, Mizuki Sato, Nanase Okamoto, Hikaru Ogura, Ayaka Nakamura, Hajime Takahashi, Takashi Kuda","doi":"10.1007/s11033-024-10045-2","DOIUrl":"https://doi.org/10.1007/s11033-024-10045-2","url":null,"abstract":"<p><strong>Background: </strong>Water-soluble arabinoxylan exerts anti-colitic effect and exhibits ameliorative activity in an inflammatory bowel disease (IBD) mouse model. Water soluble fibre from wheat bran (WB) also exhibits anti-colitic effect. However, arabinoxylan is a primary compound of insoluble polysaccharide (hemicellulose) in WB. This study aimed to clarify the anti-IBD effects of the WB water-soluble (WBS) and water-insoluble (WBI) fractions.</p><p><strong>Methods and results: </strong>WB suspension was autoclaved and fractionated to WBS and WBI. C57BL/6 mice were divided into control (CT), dextran sodium sulphate (DSS), WBI, and WBS groups. They were fed as follows from day 1: CT, standard diet and distilled water; DSS and WBI, 3% (w/v) DSS in drinking water; WBI, 8% (w/w) WBI diet; and WBS, 50% (v/v) WBS and 3% (w/v) DSS in water. DSS group mice showed diarrhoea, body weight reduction, and blood in faeces by day 5 and colon tissue damage by day 6. These inflammatory indices were significantly inhibited by treatment with WBI. Amplicon sequencing of the 16S rDNA (V4) gene of the caecal contents of the CT, DSS, and WBI groups showed that the abundances of Escherichia, Allobaculum, and Bacteroidaceae increased and that of Faecalibaculum decreased in the DSS group. KEGG pathway prediction showed that amino acid metabolism and lipopolysaccharide biosynthesis decreased and increased, respectively, in the DSS group. However, WBI treatment tended to suppress these effects.</p><p><strong>Conclusion: </strong>WBI, rather than WBS, reduces inflammation and maintains the gut microbiota. However, further studies are warranted to elucidate the properties of the WBI active components and efficacy of WBI metabolites on gut microbiota, particularly on Faecalibaculum.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1112"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring transcriptomic mechanisms underlying pulmonary adaptation to diverse environments in Indian rams.","authors":"Ritika Gera, Reena Arora, Pooja Chhabra, Upasna Sharma, Ram Parsad, Sonika Ahlawat, Mohsin Ayoub Mir, Manoj Kumar Singh, Rajesh Kumar","doi":"10.1007/s11033-024-10067-w","DOIUrl":"https://doi.org/10.1007/s11033-024-10067-w","url":null,"abstract":"<p><strong>Background: </strong>The Changthangi sheep thrive at high altitudes in the cold desert regions of Ladakh, India while Muzaffarnagri sheep are well-suited to the low altitude plains of northern India. This study investigates the molecular mechanisms of pulmonary adaptation to diverse environments by analyzing gene expression profiles of lung tissues through RNA sequencing.</p><p><strong>Methods and results: </strong>Four biological replicates of lung tissue from each breed were utilized to generate the transcriptomic data. Differences in gene expression analysis revealed discrete expression profiles in lungs of each breed. In Changthangi sheep, genes related to immune responses, particularly cytokine signaling, were significantly enriched. Pathway analysis highlighted the activation of NF-kB signaling, a key mediator of inflammation and immune response. Additionally, the gene network analysis indicated a strong association between cytokine signaling, hypoxia-inducible factor (HIF) and NF-kB activation, suggesting a coordinated response to hypoxic stress in lungs of Changthangi sheep. In Muzaffarnagri sheep, the gene expression profiles were enriched for pathways related to energy metabolism, homeostasis and lung physiology. Key pathways identified include collagen formation and carbohydrate metabolism, both of which are crucial for maintaining lung function and structural integrity. Gene network analysis further reinforced this by revealing a strong connection between genes associated with lung structure and function.</p><p><strong>Conclusions: </strong>Our findings shed light on the valuable insights into gene expression mechanisms that enable these sheep breeds to adapt to their respective environments and contribute to a better understanding of high altitude adaptation in livestock.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1111"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Menthol as an effective inhibitor of quorum sensing and biofilm formation in Candida albicans and Candida glabrata by targeting the transcriptional repressor TUP1.","authors":"Pouria Khodavandi, Maryam Miri Soogh, Fahimeh Alizadeh, Alireza Khodavandi, Sadegh Nouripour-Sisakht","doi":"10.1007/s11033-024-10054-1","DOIUrl":"https://doi.org/10.1007/s11033-024-10054-1","url":null,"abstract":"<p><strong>Background: </strong>Menthol, a natural quorum sensing molecule, is derived from the Mentha species. Combating pathogenicity by inactivating quorum sensing is an emerging approach. Therefore, our objective was to investigate anti-quorum sensing and anti-biofilm potentials of menthol in Candida albicans and Candida glabrata.</p><p><strong>Methods: </strong>The antifungal properties of menthol were evaluated using a broth microdilution assay and a time-kill assay, and its effects on quorum sensing-mediated virulence factors, cellular reactive oxygen species (ROS), and biofilm formation were tested by evaluating TUP1 expression levels in both C. albicans and C. glabrata.</p><p><strong>Results: </strong>Quorum sensing-mediated virulence factors and biofilm formation were inhibited by menthol in both C. albicans and C. glabrata. Furthermore, coinciding with elevated ROS levels, mRNAs of the quorum sensing-related gene TUP1 were upregulated in both C. albicans and C. glabrata.</p><p><strong>Conclusions: </strong>This study highlights the anti-quorum sensing potential of menthol through the inhibition of quorum sensing-mediated virulence factors, ROS generation, and biofilm development by targeting TUP1, which could have potential in the treatment of Candida infections.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1114"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis of calmodulin binding Protein60 candidates in the important crop plants.","authors":"Diksha Kumari, Bishun Deo Prasad, Padmanabh Dwivedi","doi":"10.1007/s11033-024-10032-7","DOIUrl":"10.1007/s11033-024-10032-7","url":null,"abstract":"<p><strong>Background: </strong>Efficient management of environmental stresses is essential for sustainable crop production. Calcium (Ca²⁺) signaling plays a crucial role in regulating responses to both biotic and abiotic stresses, particularly during host-pathogen interactions. In Arabidopsis thaliana, calmodulin-binding protein 60 (CBP60) family members, such as AtCBP60g, AtCBP60a, and AtSARD1, have been well characterized for their involvement in immune regulation. However, a comprehensive understanding of CBP60 genes in major crops remains limited.</p><p><strong>Methods: </strong>In this study, we utilized the Phytozome v12.1 database to identify and analyze CBP60 genes in agriculturally important crops. Expression patterns of a Oryza sativa (rice) CBP60 gene, OsCBP60bcd-1, were assessed in resistant and susceptible rice genotypes in response to infection by the bacterial pathogen Xanthomonas oryzae. Localization of CBP60 proteins was analyzed to predict their functional roles, and computational promoter analysis was performed to identify stress-responsive cis-regulatory elements.</p><p><strong>Results: </strong>Phylogenetic analysis revealed that most CBP60 genes in crops belong to the immune-related clade. Expression analysis showed that OsCBP60bcd-1 was significantly upregulated in the resistant rice genotype upon pathogen infection. Subcellular localization studies suggested that the majority of CBP60 proteins are nuclear-localized, indicating a potential role as transcription factors. Promoter analysis identified diverse stress-responsive cis-regulatory elements in the promoters of CBP60 genes, highlighting their regulatory potential under stress conditions.</p><p><strong>Conclusion: </strong>The upregulation of OsCBP60bcd-1 in response to Xanthomonas oryzae and the presence of stress-responsive elements in its promoter underscore the importance of CBP60 genes in pathogen defense. These findings provide a basis for further investigation into the functional roles of CBP60 genes in crop disease resistance, with implications for enhancing stress resilience in agricultural species.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1105"},"PeriodicalIF":2.6,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic study reveals alteration in the expression of long non-coding RNAs (lncRNAs) during reversal of HIV-1 latency in monocytic cell line.","authors":"Ankita Rai, Aradhana Singh, Ritu Gaur, Tannu Bhagchandani, Anjali Verma, Nikita, Hemant Ritturaj Kushwaha, Rupali Malik, Himanshu Dandu, Abhishek Kumar, Ravi Tandon","doi":"10.1007/s11033-024-10037-2","DOIUrl":"https://doi.org/10.1007/s11033-024-10037-2","url":null,"abstract":"<p><strong>Background: </strong>The presence of latent HIV reservoirs continues to be the biggest obstacle to achieving an HIV cure. Thus, long non-coding RNAs (lncRNAs) may serve as the preferred targets for HIV latency reversal. The goal of the study was to identify prospective lncRNAs for subsequent in vitro molecular and functional characterization.</p><p><strong>Methods and results: </strong>RNA-sequencing was performed in latently HIV-infected monocytic cell line (U1) under stimulated and unstimulated condition using Illumina-HiSeqX platform, followed by its validation using qRT-PCR assay. Gene ontology (GO), KEGG pathway, and co-expression analyses were performed to identify the enriched biological processes and pathways in U1 cells post-stimulation with the latency reversal agent SAHA. A total of 3,576 and 1,467 significantly altered lncRNAs and protein-coding genes respectively, were identified in SAHA-stimulated U1 cells compared to unstimulated ones. The GO and KEGG pathway analyses of the differentially expressed protein-coding genes showed the enrichment of diverse biological processes and pathways respectively, in SAHA-stimulated U1 cells. Co-expression analysis between lncRNAs and protein-coding gene pairs, helped predict potential pathways with which these lncRNAs are associated. Further in vitro validation in HIV-infected monocytes showed that the expression of the top two candidate lncRNAs, LINC01231 and LINC00560, are specific to HIV infection.</p><p><strong>Conclusion: </strong>Transcriptome analysis revealed changes in the expression of numerous lncRNAs and protein-coding genes following stimulation with SAHA. Co-expression analysis identified candidate lncRNAs and their associated biological pathways. However, additional in vitro experimental exploration using gene knockdown strategies is needed to ascertain the specific role of LINC01231 and LINC00560 lncRNAs in latently infected monocytes.</p>","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"51 1","pages":"1102"},"PeriodicalIF":2.6,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}