Frontiers in Molecular Biosciences最新文献

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Review of cancer cell volatile organic compounds: their metabolism and evolution.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-07 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1499104
Takeshi Furuhashi, Kanako Toda, Wolfram Weckwerth
{"title":"Review of cancer cell volatile organic compounds: their metabolism and evolution.","authors":"Takeshi Furuhashi, Kanako Toda, Wolfram Weckwerth","doi":"10.3389/fmolb.2024.1499104","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1499104","url":null,"abstract":"<p><p>Cancer is ranked as the top cause of premature mortality. Volatile organic compounds (VOCs) are produced from catalytic peroxidation by reactive oxygen species (ROS) and have become a highly attractive non-invasive cancer screening approach. For future clinical applications, however, the correlation between cancer hallmarks and cancer-specific VOCs requires further study. This review discusses and compares cellular metabolism, signal transduction as well as mitochondrial metabolite translocation in view of cancer evolution and the basic biology of VOCs production. Certain cancerous characteristics as well as the origin of the ROS removal system date back to procaryotes and early eukaryotes and share commonalities with non-cancerous proliferative cells. This calls for future studies on metabolic cross talks and regulation of the VOCs production pathway.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1499104"},"PeriodicalIF":3.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Irisin reshapes bone metabolic homeostasis to delay age-related osteoporosis by regulating the multipotent differentiation of BMSCs via Wnt pathway.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-07 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1524978
Shangman Xing, Yifan Ma, Bing Song, Min Bai, Kexin Wang, Wenjing Song, Tingting Cao, Chao Guo, Yanying Zhang, Zhandong Wang, Yongfeng Wang
{"title":"Irisin reshapes bone metabolic homeostasis to delay age-related osteoporosis by regulating the multipotent differentiation of BMSCs via Wnt pathway.","authors":"Shangman Xing, Yifan Ma, Bing Song, Min Bai, Kexin Wang, Wenjing Song, Tingting Cao, Chao Guo, Yanying Zhang, Zhandong Wang, Yongfeng Wang","doi":"10.3389/fmolb.2024.1524978","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1524978","url":null,"abstract":"<p><strong>Introduction: </strong>Bone aging is linked to changes in the lineage differentiation of bone marrow stem cells (BMSCs), which show a heightened tendency to differentiate into adipocytes instead of osteoblasts. The therapeutic potential of irisin in addressing age-related diseases has garnered significant attention. More significantly, irisin has the capacity to enhance bone mass recovery and sustain overall bone health. Its mechanism of action in preventing osteoporosis has generated considerable interest within the research community. Nonetheless, the targeting effect of irisin on age-related osteoporosis and its underlying molecular biological mechanisms remain unclear.</p><p><strong>Methods: </strong>The specific role of irisin in osteogenic-adipogenic differentiation in young or aging BMSCs was evaluated by multiple cells staining and quantitative real-time PCR (RT-qPCR) analysis. RNA-seq and protein Western blotting excavated and validated the key pathway by which irisin influences the fate determination of aging BMSCs. The macroscopic and microscopic changes of bone tissue in aging mice were examined using Micro-computed tomography (Micro-CT) and morphological staining.</p><p><strong>Results: </strong>It was noted that irisin affected the multilineage differentiation of BMSCs in a manner dependent on the dosage. Simultaneously, the Wnt signaling pathway might be a crucial mechanism through which irisin sustains the bone-fat balance in aging BMSCs and mitigates the decline in pluripotency. <i>In vivo</i>, irisin reduced bone marrow fat deposition in aging mice and effectively alleviating the occurrence of bone loss.</p><p><strong>Conclusion: </strong>Irisin mediates the Wnt signaling pathway, thereby influencing the fate determination of BMSCs. In addition, it is essential for preserving metabolic equilibrium in the bone marrow microenvironment and significantly contributes to overall bone health. The findings provide new evidence for the use of iris extract in the treatment of age-related osteoporosis.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1524978"},"PeriodicalIF":3.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11746060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the shared gene signatures and mechanism among three autoimmune diseases by bulk RNA sequencing integrated with single-cell RNA sequencing analysis.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-07 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1520050
Xiaofang Liu, Bin Li, Yuxi Lin, Xueying Ma, Yingying Liu, Lili Ma, Xiaomeng Ma, Xia Wang, Nanjing Li, Xiaoyun Liu, Xiaohong Chen
{"title":"Exploring the shared gene signatures and mechanism among three autoimmune diseases by bulk RNA sequencing integrated with single-cell RNA sequencing analysis.","authors":"Xiaofang Liu, Bin Li, Yuxi Lin, Xueying Ma, Yingying Liu, Lili Ma, Xiaomeng Ma, Xia Wang, Nanjing Li, Xiaoyun Liu, Xiaohong Chen","doi":"10.3389/fmolb.2024.1520050","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1520050","url":null,"abstract":"<p><strong>Background: </strong>Emerging evidence underscores the comorbidity mechanisms among autoimmune diseases (AIDs), with innovative technologies such as single-cell RNA sequencing (scRNA-seq) significantly advancing the explorations in this field. This study aimed to investigate the shared genes among three AIDs-Multiple Sclerosis (MS), Systemic Lupus Erythematosus (SLE), and Rheumatoid Arthritis (RA) using bioinformatics databases, and to identify potential biomarkers for early diagnosis.</p><p><strong>Methods: </strong>We retrieved transcriptomic data of MS, SLE, and RA patients from public databases. Weighted Gene Co-Expression Network Analysis (WGCNA) was employed to construct gene co-expression networks and identify disease-associated modules. Functional enrichment analyses and Protein-Protein Interaction (PPI) network was constructed. We used machine learning algorithms to select candidate biomarkers and evaluate their diagnostic value. The Cibersort algorithm was and scRNA-seq analysis was performed to identify key gene expression patterns and assess the infiltration of immune cells in MS patients. Finally, the biomarkers' expression was validated in human and mice experiments.</p><p><strong>Results: </strong>Several shared genes among MS, SLE, and RA were identified, which play crucial roles in immune responses and inflammation regulation. PPI network analysis highlighted key hub genes, some of which were selected as candidate biomarkers through machine learning algorithms. Receiver Operating Characteristic (ROC) curve analysis indicated that some genes had high diagnostic value (Area Under the Curve, AUC >0.7). Immune cell infiltration pattern analysis showed significant differences in the expression of various immune cells in MS patients. scRNA-seq analysis revealed clusters of genes that were significantly upregulated in the single cells of cerebrospinal fluid in MS patients. The expression of shared genes was validated in the EAE mose model. Validation using clinical samples confirmed the expression of potential diagnostic biomarkers.</p><p><strong>Conclusion: </strong>This study identified shared genes among MS, SLE, and RA and proposed potential early diagnostic biomarkers. These genes are pivotal in regulating immune responses, providing new targets and theoretical basis for the early diagnosis and treatment of autoimmune diseases.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1520050"},"PeriodicalIF":3.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11746102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial: Modelling esophageal adenocarcinoma.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-07 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1550595
Hisham F Bahmad, Farah Ballout
{"title":"Editorial: Modelling esophageal adenocarcinoma.","authors":"Hisham F Bahmad, Farah Ballout","doi":"10.3389/fmolb.2024.1550595","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1550595","url":null,"abstract":"","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1550595"},"PeriodicalIF":3.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative analysis of anticoagulant influence on PMI estimation based on porcine blood metabolomics profile measured using GC-MS.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-07 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1400622
Patrycja Mojsak, Paulina Samczuk, Paulina Klimaszewska, Michal Burdukiewicz, Jaroslaw Chilimoniuk, Krystyna Grzesiak, Karolina Pietrowska, Justyna Ciborowska, Anna Niemcunowicz-Janica, Adam Kretowski, Michal Ciborowski, Michal Szeremeta
{"title":"Comparative analysis of anticoagulant influence on PMI estimation based on porcine blood metabolomics profile measured using GC-MS.","authors":"Patrycja Mojsak, Paulina Samczuk, Paulina Klimaszewska, Michal Burdukiewicz, Jaroslaw Chilimoniuk, Krystyna Grzesiak, Karolina Pietrowska, Justyna Ciborowska, Anna Niemcunowicz-Janica, Adam Kretowski, Michal Ciborowski, Michal Szeremeta","doi":"10.3389/fmolb.2024.1400622","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1400622","url":null,"abstract":"<p><strong>Introduction: </strong>Accurate post-mortem interval (PMI) estimation is essential in forensic investigations. Although various methods for PMI determination have been developed, only an approximate estimation is still achievable, and an accurate PMI indication is still challenging. Therefore, in this study, we employed gas chromatography-mass spectrometry (GC-MS)-based metabolomics to assess post-mortem changes in porcine blood samples collected with and without the addition of anticoagulant (EDTA). Our study aimed to identify metabolites dependent on the EDTA addition and time (taking into account the biodiversity of the studied organism) and those that are time-dependent but resistant to the addition of an anticoagulant.</p><p><strong>Methods: </strong>The experiment was performed on blood samples collected from 16 animals (domestic pig, breed: Polish Large White), 8 with and 8 without EDTA addition. The moment of death (time 0) and 15 additional time points (from 3 to 168 h after death) were selected to examine changes in metabolites' levels in specific time intervals. We employed linear mixed models to study the relationship between metabolite intensities, time and presence of EDTA while accounting for the effect of individual pigs.</p><p><strong>Results and discussion: </strong>We confirmed that the intensity of 16 metabolites (mainly amino acids) significantly depends on PMI and the presence of EDTA. However, the intensity of the ideal biomarker(s) for PMI estimation should be determined only by the time after death and not by external factors such as the presence of the anticoagulant agent. Thus, we identified 41 metabolites with time-dependent intensities that were not susceptible to EDTA presence. Finally, we assessed the performance of these metabolites in a PMI predictive model. Citraconic acid yielded one of the lowest errors in general PMI estimation (32.82 h). Moreover, similar errors were observed for samples with and without EDTA (33.32 h and 32.34 h, respectively). Although the small sample size and information leak in predictive modelling prevent drawing definite conclusions, citraconic acid shows potential as a robust PMI estimator.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1400622"},"PeriodicalIF":3.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11746058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The role of neutrophilia in hyperlactatemia, blood acidosis, impaired oxygen transport, and mortality outcome in critically ill COVID-19 patients.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-06 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1510592
Basma A Yasseen, Aya A Elkhodiry, Hajar El-Sayed, Mona Zidan, Azza G Kamel, Mohamed A Badawy, Marwa S Hamza, Riem M El-Messiery, Mohamed El Ansary, Engy A Abdel-Rahman, Sameh S Ali
{"title":"The role of neutrophilia in hyperlactatemia, blood acidosis, impaired oxygen transport, and mortality outcome in critically ill COVID-19 patients.","authors":"Basma A Yasseen, Aya A Elkhodiry, Hajar El-Sayed, Mona Zidan, Azza G Kamel, Mohamed A Badawy, Marwa S Hamza, Riem M El-Messiery, Mohamed El Ansary, Engy A Abdel-Rahman, Sameh S Ali","doi":"10.3389/fmolb.2024.1510592","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1510592","url":null,"abstract":"<p><strong>Introduction: </strong>COVID-19 severity and high in-hospital mortality are often associated with severe hypoxemia, hyperlactatemia, and acidosis, yet the key players driving this association remain unclear. It is generally assumed that organ damage causes toxic acidosis, but since neutrophil numbers in severe COVID-19 can exceed 80% of the total circulating leukocytes, we asked if metabolic acidosis mediated by the glycolytic neutrophils is associated with lung damage and impaired oxygen delivery in critically ill patients.</p><p><strong>Methods: </strong>Based on prospective mortality outcome, critically ill COVID-19 patients were divided into ICU- survivors and ICU-non-survivors. Samples were analyzed to explore if correlations exist between neutrophil counts, lung damage, glycolysis, blood lactate, blood pH, hemoglobin oxygen saturation, and mortality outcome. We also interrogated isolated neutrophils, platelets, and PBMCs for glycolytic activities.</p><p><strong>Results: </strong>Arterial blood gas analyses showed remarkable hypoxemia in non-survivors with no consistent differences in PCO<sub>2</sub> or [HCO<sub>3</sub> <sup>-</sup>]. The hemoglobin oxygen dissociation curve revealed a right-shift, consistent with lower blood-pH and elevated blood lactate in non-survivors. Metabolic analysis of different blood cells revealed increased glycolytic activity only when considering the total number of neutrophils.</p><p><strong>Conclusion: </strong>This indicates the role of neutrophilia in hyperlactatemia and lung damage, subsequently contributing to mortality outcomes in severe SARS-CoV-2 infection.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1510592"},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and validation of five ferroptosis-related molecular signatures in keloids based on multiple transcriptome data analysis.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-06 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1490745
Zhen Sun, Yonghong Qin, Xuanfen Zhang
{"title":"Identification and validation of five ferroptosis-related molecular signatures in keloids based on multiple transcriptome data analysis.","authors":"Zhen Sun, Yonghong Qin, Xuanfen Zhang","doi":"10.3389/fmolb.2024.1490745","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1490745","url":null,"abstract":"<p><strong>Introduction: </strong>Keloids are a common skin disorder characterized by excessive fibrous tissue proliferation, which can significantly impact patients' health. Ferroptosis, a form of regulated cell death, plays a crucial role in the development of fibrosis; however, its role in the mechanisms of keloid formation remains poorly understood.</p><p><strong>Methods: </strong>This study aimed to identify key genes associated with ferroptosis in keloid formation. Data from the NCBI GEO database, including GSE145725, GSE7890, and GSE44270, were analyzed, comprising a total of 24 keloid and 17 normal skin samples. Additionally, single-cell data from GSE181316, which included 8 samples with complete expression profiles, were also evaluated. Differentially expressed genes were identified, and ferroptosis-related genes were extracted from the GeneCards database. LASSO regression was used to select key genes associated with keloids. Validation was performed using qRT-PCR and Western blot (WB) analysis on tissue samples from five keloid and five normal skin biopsies.</p><p><strong>Results: </strong>A total of 471 differentially expressed genes were identified in the GSE145725 dataset, including 225 upregulated and 246 downregulated genes. Five ferroptosis-related genes were selected through gene intersection and LASSO regression. Two of these genes were upregulated, while three were downregulated in keloid tissue. Further analysis through GSEA pathway enrichment, GSVA gene set variation, immune cell infiltration analysis, and single-cell sequencing revealed that these genes were primarily involved in the fibrotic process. The qRT-PCR and WB results confirmed the expression patterns of these genes.</p><p><strong>Discussion: </strong>This study provides novel insights into the molecular mechanisms of ferroptosis in keloid formation. The identified ferroptosis-related genes could serve as potential biomarkers or therapeutic targets for treating keloids.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1490745"},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the causal role of plasma metabolites and metabolite ratios in prostate cancer: a two-sample Mendelian randomization study.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-06 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1406055
Changzhou Feng, Haining Li, Chu Zhang, Ying Zhou, Huanhuan Zhang, Ping Zheng, Shaolin Zhao, Lei Wang, Jin Yang
{"title":"Exploring the causal role of plasma metabolites and metabolite ratios in prostate cancer: a two-sample Mendelian randomization study.","authors":"Changzhou Feng, Haining Li, Chu Zhang, Ying Zhou, Huanhuan Zhang, Ping Zheng, Shaolin Zhao, Lei Wang, Jin Yang","doi":"10.3389/fmolb.2024.1406055","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1406055","url":null,"abstract":"<p><strong>Background: </strong>Prostate cancer (PCa), the most prevalent malignant neoplasm in males, involves complex biological mechanisms and risk factors, many of which remain unidentified. By employing a novel two-sample Mendelian randomization (MR) approach, this study aims to elucidate the causal relationships between the circulating metabolome and PCa risk, utilizing comprehensive data on genetically determined plasma metabolites and metabolite ratios.</p><p><strong>Methods: </strong>For the MR analysis, we utilized data from the GWAS Catalog database to analyze 1,091 plasma metabolites and 309 ratios in relation to PCa outcomes within two independent GWAS datasets. The inverse variance weighted (IVW) method was the primary approach for determining the existence of the causal relationship, supplemented by additional MR methods for heterogeneity, pleiotropy, and cross-validation. The false discovery rate (FDR) and Bonferroni correction were applied to identify the most significant causative associations. Additionally, reverse MR and Steiger filtering were conducted to ascertain whether PCa influenced the observed metabolite levels. Furthermore, metabolic pathway analysis was conducted with MetaboAnalyst 6.0 software.</p><p><strong>Results: </strong>In the MR analysis, our findings reveal three overlapped metabolite ratios (arginine to glutamate, phosphate to uridine, and glycerol to mannitol/sorbitol) inversely associated with PCa risk. Following FDR correction (FDR < 0.05), cysteinylglycine disulfide was identified as a potential reducer of PCa risk, whereas Uridine and N-acetyl-L-glutamine (NAG) were pinpointed as potential risk factors. Notably, NAG (OR 1.044; 95% CI 1.025-1.063) emerged as a metabolite with significant causal influence, as confirmed by stringent Bonferroni correction (<i>P</i> < 0.05/1400). Steiger's directionality test (<i>P</i> < 0.001) and reverse MR confirmed the proposed causal direction. Furthermore, metabolic pathway analysis revealed a significant association between the \"Glutathione Metabolism\" pathway and PCa development.</p><p><strong>Conclusion: </strong>This study provides novel insights into the potential causal effects of plasma metabolites and metabolite ratios on PCa. The identified metabolites and ratios could serve as candidate biomarkers, contributing to the elucidation of PCa's biological mechanisms.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1406055"},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and validation of reference genes for quantitative gene expression analysis under 409 and 415 nm antimicrobial blue light treatment.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-06 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1467726
Beata Kruszewska-Naczk, Mariusz Grinholc, Aleksandra Rapacka-Zdonczyk
{"title":"Identification and validation of reference genes for quantitative gene expression analysis under 409 and 415 nm antimicrobial blue light treatment.","authors":"Beata Kruszewska-Naczk, Mariusz Grinholc, Aleksandra Rapacka-Zdonczyk","doi":"10.3389/fmolb.2024.1467726","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1467726","url":null,"abstract":"<p><strong>Introduction: </strong>Reverse transcription quantitative real-time polymerase chain reaction Q7 (RT‒qPCR) is a commonly used tool for gene expression quantification. Because the qPCR method depends on several variables that can influence the analysis process, stably expressed genes should be selected for relative gene expression studies. To date, there is insufficient information on the selection of appropriate reference genes for antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) treatment. Therefore, the purpose of the present study was to determine the most stable reference gene under treatment with aBL under sublethal conditions and to evaluate differences in the expression of the selected gene after aBL treatment in comparison to the nontreated control.</p><p><strong>Methods: </strong>Selection of stable reference genes was performed using 4 programs: BestKeeper, geNorm, NormFinder and RefFinder under 409 and 415 nm aBL treatment.</p><p><strong>Results: </strong>The results revealed that the gene encoding the integration host factor β subunit (ihfB) in <i>Escherichia coli</i> was the most stably expressed gene after both 409 and 415 nm aBL treatment. Three programs, RefFinder, geNorm, and NormFinder, indicated that this gene had the most stable expression in comparison to the other reference gene candidates. The next best candidates were cysG, uidA, and gyrA. NormFinder revealed ihfB as the single gene and cysG - gyrA as the combination of reference genes with the best stability.</p><p><strong>Discussion: </strong>Universal reference genes are characterized by stable expression that remains consistent across various stress conditions. Consequently, it is essential to evaluate reference genes for each specific stress factor under investigation. In the case of aBL at different wavelengths, we identified genes that maintain stable expression following irradiation.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1467726"},"PeriodicalIF":3.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ProAD - A database of rotary ion-translocating ATPases in prokaryotic genomes.
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-01-03 eCollection Date: 2024-01-01 DOI: 10.3389/fmolb.2024.1471556
A V Litvin, A S Lapashina, A P Ermidis, M S Gelfand, B A Feniouk
{"title":"ProAD - A database of rotary ion-translocating ATPases in prokaryotic genomes.","authors":"A V Litvin, A S Lapashina, A P Ermidis, M S Gelfand, B A Feniouk","doi":"10.3389/fmolb.2024.1471556","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1471556","url":null,"abstract":"","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1471556"},"PeriodicalIF":3.9,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11738941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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