Biological Procedures Online最新文献

{"title":"Impact of different mating and surgical protocols on the establishment of a mouse model for fetal scarless skin healing.","authors":"Lu Huang, Xinran Ye, Yifan Zhang, Chia-Kang Ho, Qingfeng Li","doi":"10.1186/s12575-025-00290-5","DOIUrl":"10.1186/s12575-025-00290-5","url":null,"abstract":"<p><strong>Background: </strong>The mouse fetal intrauterine wound healing model is crucial and commonly used for investigating mechanisms and evaluating potential therapies for scarless skin regeneration compared to fibrotic healing. However, traditional intrauterine surgery remains technically challenging and understudied, which is associated with high maternal mortality and pregnancy loss, prompting us to refine the surgical protocol. Here, we report how the choice of surgical and mating procedure impact outcomes obtained.</p><p><strong>Methods: </strong>Pregnant mice underwent fetal surgery at embryonic days 15.5, 16.5 (E15.5, E16.5, scarless) and 18.5 (e18.5, fibrotic). Two surgical protocols were used: traditional method involved purse-string sutures, microsurgical scissors, amniotic fluid supplementation, and suture closure (Traditional); and our modified method omitting purse-string sutures, replacing scissors with needle puncture for uterine and fetal incisions, eliminating amniotic fluid supplementation, and employing skin staples for abdominal closure (Modified).</p><p><strong>Results: </strong>The modified protocol significantly increased the likelihood of successful pregnancy, reduced operative time, decreased abortion rates, and enabled earlier modeling compared to the traditional method. At 48 h, 7 days, and 9 days post-surgery, E15.5 wounds healed scarlessly, displaying regenerated hair follicles and organized collagen. Conversely, E18.5 wounds formed typical fibrotic scars, characterized by dense, disorganized collagen without hair follicles.</p><p><strong>Conclusion: </strong>The optimized surgical protocol presented here provides a simplified, reliable fetal mouse model with improved pregnancy success, reduced fetal loss, earlier implementation, and consistent phenotypic outcomes. This refined model enhances experimental efficiency, reproducibility, and animal welfare, having a major impact on mechanistic studies and therapeutic exploration for scarless skin regeneration.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"38"},"PeriodicalIF":4.3,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12466002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145172437","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}

{"title":"Sheet Protector Strategy for Western Blot to Reduce Antibody Consumption and Incubation Time.","authors":"Sunmin Kwon, So Yeong Lee, Gun Kim","doi":"10.1186/s12575-025-00300-6","DOIUrl":"10.1186/s12575-025-00300-6","url":null,"abstract":"<p><strong>Background: </strong>Western blot is one of the most routinely conducted biochemical assays due to its technical ease and relatively low cost. The use of antibody is at the center of Western blot assay, providing great sensitivity and specificity. However, challenges can be posed when using a rare antibody stock. There have been efforts to improve the Western blot procedure to minimize the use of antibody, but these methods require specialized devices.</p><p><strong>Results: </strong>In this study, we hypothesized that the conventional large pool of antibody is not essential for detection and attempted applying only a small volume of antibody. We used sheet protector (SP), a common stationery material that protects office documents, to effectively distribute the antibody solution over the nitrocellulose (NC) membrane. This way, 20-150 µL antibody solution was sufficient for mini-sized membrane, which was adjustable depending on the size of the membrane. We confirmed that the sensitivity and specificity of this SP strategy was comparable to conventional (CV) method. The SP strategy brought a few additional advantages including: (1) antibody incubation without agitation (2), incubation at room temperature, and (3) faster detection on the order of minutes. Finally, we examined 15-min incubation SP protocol using time-series apoptosis samples.</p><p><strong>Conclusions: </strong>We propose that SP strategy is a universally accessible approach using a common consumable, greatly enhancing the efficiency of antibody consumption and incubation time in Western blot assays.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"37"},"PeriodicalIF":4.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136360","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}

{"title":"SOCS3: An Immunological Biomarker Offering Potential Therapeutic Targets for Malignant Tumors.","authors":"Yan Zhang, Meiling Chu, Meina Ye, Yulian Yin, Hongfeng Chen","doi":"10.1186/s12575-025-00296-z","DOIUrl":"10.1186/s12575-025-00296-z","url":null,"abstract":"<p><p>Suppressor of Cytokine Signaling 3 (SOCS3) is a critical regulator of cytokine signaling, primarily acting through the Janus Kinase (JAK)/Signal Transducer and Activator of Transcription (STAT) pathway. It plays a significant role in the development and progression of various malignancies. Abnormal expression of SOCS3 in cancer cells is linked to dysregulated cell growth, migration, and apoptosis, driven by cytokines and hormones. This aberrant expression makes SOCS3 a potential biomarker for tumor diagnosis, prognosis, and gene therapy. Targeting SOCS3 may offer innovative strategies for cancer treatment. This review provides a comprehensive overview of SOCS3's molecular structure, its biological functions in tumors, underlying molecular mechanisms, and therapeutic strategies targeting SOCS3.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"36"},"PeriodicalIF":4.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124082","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}

{"title":"Organotypic Culture of Adult Vascularized Porcine Retina Explants In Vitro on Nanotube Scaffolds.","authors":"Sabrina Friebe, Solveig Weigel, Mike Francke, Stefan G Mayr","doi":"10.1186/s12575-025-00301-5","DOIUrl":"10.1186/s12575-025-00301-5","url":null,"abstract":"<p><strong>Background: </strong>Organotypic long-term cultivation of vascularized retina explants is a major challenge for application in drug development, drug screening, diagnostics and future personalized medicine. With this background, an assay and protocol for organotypic culture of vascularized retina explants in vitro with optimum tissue integrity preservation is developed and demonstrated.</p><p><strong>Methods: </strong>Morphological, histologic and biochemical integrity as well as viability of vascularized retina explants are compared as function of cultivation time for differently structured nanotube scaffolds. In doing so, porcine retina explants obtained from a local slaughterhouse are employed as paradigm for vascularized retina.</p><p><strong>Conclusions: </strong>We demonstrate that titania nanotube arrays are highly promising as culturing scaffold of vascularized retina explants in vitro due to highly tunable surface properties regarding biomedical signaling. The unprecedented maintenance of tissue integrity allows for screening of pharmacological drugs and disease mechanisms in an ex-vivo test-based culture system with reduced need for animal experiments.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"35"},"PeriodicalIF":4.3,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028865","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}

{"title":"Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples.","authors":"Brando Poggiali, Mikkel Eriksen Dupont, Marie-Louise Kampmann, Athina Vidaki, Vania Pereira, Claus Børsting, Jacob Tfelt-Hansen, Jeppe Dyrberg Andersen","doi":"10.1186/s12575-025-00292-3","DOIUrl":"10.1186/s12575-025-00292-3","url":null,"abstract":"<p><strong>Background: </strong>The HumanMethylationEPIC v2.0 BeadChip (EPIC v2.0) microarray is a widely used tool for genome-wide DNA methylation (DNAm) analysis, designed for high-quality human DNA with a recommended input of 250 ng. However, in clinical and forensic settings, DNA samples may be of low quality and/or quantity (highly fragmented and/or available in low amounts). This study assessed the performance of the EPIC v2.0 on DNA samples with various combinations of average DNA fragment size (350, 230, 165, and 95 bp) and DNA input amount (100, 50, 20, and 10 ng), compared to a paired control sample analyzed under optimal conditions (high-quality DNA and 250 ng DNA input).</p><p><strong>Results: </strong>The best performance was obtained for samples with average DNA fragment size of 350 bp and 100 ng DNA input (~ 90% probe detection rate, r = 0.995, and median absolute beta value differences|Δβ| = 0.012 when compared with the control sample). Samples with lower average DNA fragment sizes and DNA input amount performed worse, with the lowest probe detection rate (~ 43%), r = 0.946, and the highest|Δβ| (0.038). Samples with average DNA fragment sizes of 95 bp and those with 165 bp at 10 ng DNA input failed to pass sample quality control (QC). CpG sites with intermediate DNAm values (β = 0.1-0.9) showed higher|Δβ| than the extreme DNAm values (β = 0-0.1, and β = 0.9-1). Finally, we assessed an application of DNAm by performing epigenetic age analysis, and observed mean absolute errors (MAEs) below 10 years for 350 bp samples across four epigenetic clocks.</p><p><strong>Conclusions: </strong>Both DNA fragment size and DNA input amounts affect DNAm analysis on the EPIC v2.0, with the investigated DNA fragment size having a greater impact than the investigated DNA input amount. DNAm measurements were achieved with the EPIC v2.0 microarray down to an average DNA fragment size of 165 bp and a 20 ng DNA input. Highly fragmented DNA (95 bp) did not result in usable DNAm analysis as all samples failed QC. Overall, our study demonstrates the potential and limitations of EPIC v2.0 microarray with low quality and quantity DNA samples.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"34"},"PeriodicalIF":4.3,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941447","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}

{"title":"c-MET Inhibition Reverses the Osimertinib Resistance in Lung Circulating Tumor Cell Clusters and Suppresses Metastasis.","authors":"Zhipeng Zhang, Xinyi Lu, Jianhui Tian, Jiaxuan Li, Shihui Liu, Jiajun Liu, Bin Luo, Jialiang Yao, Yao Liu, Yanhong Wang, Wang Yao, Yun Yang, Wenji Shangguan, Zujun Que","doi":"10.1186/s12575-025-00295-0","DOIUrl":"10.1186/s12575-025-00295-0","url":null,"abstract":"","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"32"},"PeriodicalIF":4.3,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941460","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}

{"title":"Refining Flow Cytometry-based Sorting of Plasma-derived Extracellular Vesicles.","authors":"Daniele Reverberi, Maria Chiara Ciferri, Nicole Rosenwasser, Alessandro Catino, Giuseppina Poppa, Ilaria Giusti, Vincenza Dolo, Rodolfo Quarto, Sara Santamaria, Monica Colombo, Simona Coco, Roberta Tasso","doi":"10.1186/s12575-025-00293-2","DOIUrl":"10.1186/s12575-025-00293-2","url":null,"abstract":"","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"33"},"PeriodicalIF":4.3,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941387","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}

{"title":"The Role of the TIMP1/LINC01615 Axis as a Regulator of the EMT Pathway in Gastric Cancer.","authors":"Jiying Liu, Yeganeh Olyaee, Khatere Mokhtari, Chaoxiang Lv, Niloufar Salimian, Maliheh Entezari, Afshin Taheriazam, Mehrdad Hashemi, Mazaher Maghsoudloo, Ling Yuan","doi":"10.1186/s12575-025-00297-y","DOIUrl":"10.1186/s12575-025-00297-y","url":null,"abstract":"<p><strong>Objective: </strong>Gastric cancer (GCa) is a common malignancy where the epithelial-to-mesenchymal transition (EMT) pathway and lncRNAs are key to proliferation and metastasis. This study aimed to identify lncRNAs regulating the EMT pathway as therapeutic and diagnostic targets in GCa.</p><p><strong>Methods: </strong>We utilized the TCGA-STAD dataset and differential expression gene (DEG) analysis was performed to identify overlapping genes between DEGs and the EMT pathway. The LASSO feature reduction algorithm and ROC curve analysis were applied to prioritize candidate biomarkers. Additionally, immunological and immunotherapy analyses were conducted to evaluate the significance of TIMP1 in GCa. Pearson correlation analysis was performed between TIMP1 and all differentially expressed lncRNAs, and the most strongly correlated candidates were selected. Experimental validation of the results was carried out using RT-qPCR with 25 cancerous and 25 adjacent normal tissue samples in GCa.</p><p><strong>Results: </strong>DEG analysis identified 2,926 DEGs, among which 87 were associated with the EMT pathway. The LASSO algorithm reduced this list to 11 genes, and ROC curve analysis identified TIMP1 as a candidate biomarker in GCa. Higher TIMP1 expression was associated with improved response rates. Correlation analysis revealed that LINC01615 was most strongly co-regulated with TIMP1 in GCa. RT-qPCR confirmed that both TIMP1 and LINC01615 were significantly upregulated in tumor tissues compared to adjacent normal tissues, highlighting their potential as diagnostic biomarkers.</p><p><strong>Conclusion: </strong>A strong correlation between TIMP1 and LINC01615 suggests their role in promoting GCa proliferation, invasion, and metastasis. TIMP1/LINC01615 axis regulates the EMT pathway and is a potential biomarker and therapeutic target in GCa.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"31"},"PeriodicalIF":4.3,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12363065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871268","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}

{"title":"A Rare Case of Long-Term Survival in Stage IIIB Lung Adenocarcinoma: an 9-Year Follow-Up.","authors":"Jianing Chen, Li Liu, Qi Wang, Yan Wu, Jing Zhao, Li Wang, Lei Cheng, Huiming Zhu, Chunxia Su","doi":"10.1186/s12575-025-00291-4","DOIUrl":"10.1186/s12575-025-00291-4","url":null,"abstract":"<p><p>We report a rare case of long-term survival in a 59-year-old male patient diagnosed with stage IIIB lung adenocarcinoma. Despite disease progression following initial chemotherapy, the patient achieved prolonged survival through a combination of chemotherapy and radiotherapy. This case highlights the potential for extended survival in advanced lung cancer with multimodal treatment approaches.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"30"},"PeriodicalIF":4.3,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811680","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}

{"title":"Machine learning-driven multi-omics analysis identifies a prognostic gene signature associated with programmed cell death and metabolism in hepatocellular carcinoma.","authors":"Xiang Li, Donghao Yin, Jiahao Geng, Yanyu Xu, Zijing Xu, Xuemeng Yang, Quanwei Li, Zimeng Shang, Zhiyun Yang, Zhong Xu, Jiabo Wang, Enxiang Zhang, Xinhua Song","doi":"10.1186/s12575-025-00286-1","DOIUrl":"10.1186/s12575-025-00286-1","url":null,"abstract":"","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"29"},"PeriodicalIF":4.3,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811681","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}