BMB Reports最新文献_第5页

Cryogenic single-molecule fluorescence imaging. 低温单分子荧光成像。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Phil Sang Yu, Chae Un Kim, Jong-Bong Lee

{"title":"Cryogenic single-molecule fluorescence imaging.","authors":"Phil Sang Yu, Chae Un Kim, Jong-Bong Lee","doi":"","DOIUrl":"","url":null,"abstract":"Cryo-fixation techniques, including cryo-electron and cryofluorescence microscopy, enable the preservation of biological samples in a near-native state by rapidly freezing them into an amorphous ice phase. These methods prevent the structural distortions often caused by chemical fixation, allowing for high-resolution imaging. At low temperatures, fluorophores exhibit improved properties, such as extended fluorescence lifetimes, reduced photobleaching, and enhanced signal-tonoise ratios, making single-molecule imaging more accurate and insightful. Despite these advantages, challenges remain, including limitations in numerical aperture of objectives and cryo-stage for single-molecule imaging, which can affect photon detection and spatial resolution. Recent advancements at low temperatures have mitigated these issues, achieving resolutions at the nanometer scale. Looking forward, innovations in super-resolution techniques, optimized fluorophores, and Artificial Intelligence (AI)-based data analysis promise to further advance the field, providing deeper insights into biomolecular dynamics and interactions. In this mini-review, we will introduce low-temperature single-molecule fluorescence imaging techniques and discuss future perspectives in this field. [BMB Reports 2025; 58(1): 2-7].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"2-7"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862970","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

Attacking biological problems through single-molecule approaches. 社论：通过单分子方法解决生物学问题。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Jong-Bong Lee

引用次数: 0

Single-molecule studies of repair proteins in base excision repair. 碱基切除修复中的单分子修复蛋白研究。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Donghun Lee, Gwangrog Lee

{"title":"Single-molecule studies of repair proteins in base excision repair.","authors":"Donghun Lee, Gwangrog Lee","doi":"","DOIUrl":"","url":null,"abstract":"Base excision repair (BER) is an essential cellular mechanism that repairs small, non-helix-distorting base lesions in DNA, resulting from oxidative damage, alkylation, deamination, or hydrolysis. This review highlights recent advances in understanding the molecular mechanisms of BER enzymes through single-molecule studies. We discuss the roles of DNA glycosylases in lesion recognition and excision, with a focus on facilitated diffusion mechanisms such as sliding and hopping that enable efficient genome scanning. The dynamics of apurinic/apyrimidinic endonucleases, especially the coordination between APE1 and DNA polymerase β (Pol β), are explored to demonstrate their crucial roles in processing abasic sites. The review further explores the short-patch and long-patch BER pathways, emphasizing the activities of Pol β, XRCC1, PARP1, FEN1, and PCNA in supporting repair synthesis and ligation. Additionally, we highlight the emerging role of UV-DDB as a general damage sensor in BER, extending its recognized function beyond nucleotide excision repair. Single-molecule techniques have been instrumental in uncovering the complex interactions and mechanisms of BER proteins, offering unprecedented insights that could guide future therapeutic strategies for maintaining genomic stability. [BMB Reports 2025; 58(1): 17-23].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"17-23"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862973","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

Multi-omics analysis sandbox toolkit for swift derivations of clinically relevant genesets and biomarkers. 多组学分析沙盒工具包，用于快速推导临床相关基因组和生物标记物。

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Jin-Young Lee, Won Park, Hyunjoong Kim, Hong Seok Lee, Tae-Wook Kang, Dong-Hun Shin, Kyung Su Kim, Yoon Kyeong Lee, Seon-Young Kim, Ji Hwan Park, Young-Joon Kim

{"title":"Multi-omics analysis sandbox toolkit for swift derivations of clinically relevant genesets and biomarkers.","authors":"Jin-Young Lee, Won Park, Hyunjoong Kim, Hong Seok Lee, Tae-Wook Kang, Dong-Hun Shin, Kyung Su Kim, Yoon Kyeong Lee, Seon-Young Kim, Ji Hwan Park, Young-Joon Kim","doi":"","DOIUrl":"","url":null,"abstract":"The utilization of multi-omics research has gained popularity in clinical investigations. However, effectively managing and merging extensive and diverse datasets presents a challenge due to its intricacy. This research introduces a Multi-Omics Analysis Sandbox Toolkit, an online platform designed to facilitate the exploration, integration, and visualization of datasets ranging from single-omics to multi-omics. This platform establishes connections between clinical data and omics information, allowing for versatile analysis and storage of both single and multi-omics data. Additionally, users can repeatedly utilize and exchange their findings within the platform. This toolkit offers diverse alternatives for data selection and gene set analysis. It also presents visualization outputs, potential candidates, and annotations. Furthermore, this platform empowers users to collaborate by sharing their datasets, analyses, and conclusions with others, thus enhancing its utility as a collaborative research tool. This Multi-Omics Analysis Sandbox Toolkit stands as a valuable asset in comprehensively grasping the influence of diverse factors in diseases and pinpointing potential biomarkers. [BMB Reports 2024; 57(12): 521-526].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"521-526"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449592","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

Transmembrane E3 ligase RNF128 regulates N-glycosylation by promoting ribophorin I ubiquitination and degradation. 跨膜 E3 连接酶 RNF128 通过促进核糖蛋白 I 泛素化和降解来调节 N-糖基化。

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Eun-Bee Cho, Van Anh Vu, Sang-Hee Park, Lan Thi Trinh, Jong-Bok Yoon, Sungjoo Kim

{"title":"Transmembrane E3 ligase RNF128 regulates N-glycosylation by promoting ribophorin I ubiquitination and degradation.","authors":"Eun-Bee Cho, Van Anh Vu, Sang-Hee Park, Lan Thi Trinh, Jong-Bok Yoon, Sungjoo Kim","doi":"","DOIUrl":"","url":null,"abstract":"Ring finger protein 128 (RNF128) is a transmembrane E3 ubiquitin ligase mainly localized in the endoplasmic reticulum that is involved in various processes, including T cell anergy and tumor progression. However, the biological function of RNF128 in N-glycosylation remains unexplored. To investigate the functional role of RNF128, we used the proximity-directed biotin labeling method, and identified ribophorin I (RPN1) as a novel RNF128 substrate, demonstrating that RNF128 ubiquitinated RPN1 and promoted its degradation. RPN1 is a subunit of oligosaccharyltransferase complexes that facilitate N-glycosylation by binding substrates, and presenting them to the catalytic core. RPN1 also functions as an N-glycosylation-dependent chaperone that helps export a subset of newly synthesized glycoproteins to the plasma membrane. We found that RNF128 affects the N-glycosylation of model glycoproteins, such as sex hormone- binding globulin and asialoglycoprotein receptor 1. Furthermore, RNF128 inhibits the export of the opioid receptor mu 1 (OPRM1) to the plasma membrane, while expressing ubiquitination-incompetent RPN1 mutant, rescues the defect of OPRM1 export caused by RNF128 overexpression. Additionally, RNF128 influences colorectal cancer cell migration. The RNF128-dependent degradation of RPN1 likely inhibits the cell surface expression of specific glycoproteins, thereby affecting distinct cellular functions. This study contributes to understanding of the biological and functional roles of RNF128- and RPN1-dependent N-glycosylation. [BMB Reports 2024; 57(12): 546-552].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"546-552"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680082","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

DNA regulatory element cooperation and competition in transcription. DNA 调控元件在转录中的合作与竞争。

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Haram Lee, Meyer Joseph Friedman, Sang Bum Kim, Soohwan Oh

引用次数: 0

Identification of CD109 in the extracellular vesicles derived from ovarian cancer stem-like cells. 鉴定卵巢癌干样细胞胞外囊泡中的 CD109。

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Ye Eun Kim, Jun Se Kim, Min Joo Shin, Seo Yul Lee, Dae Kyoung Kim, Nam-Kyung Lee, Yang Woo Kwon, Kyung-Un Choi, Dong-Soo Suh, Byoung Soo Kim, Sanghwa Jeong, Jae Ho Kim

{"title":"Identification of CD109 in the extracellular vesicles derived from ovarian cancer stem-like cells.","authors":"Ye Eun Kim, Jun Se Kim, Min Joo Shin, Seo Yul Lee, Dae Kyoung Kim, Nam-Kyung Lee, Yang Woo Kwon, Kyung-Un Choi, Dong-Soo Suh, Byoung Soo Kim, Sanghwa Jeong, Jae Ho Kim","doi":"","DOIUrl":"","url":null,"abstract":"Ovarian cancer is the deadliest gynecological cancer because it has few early symptoms and metastasizes to the surrounding organs at advanced stages. Cancer stem cells (CSCs), a subpopulation of cells with acquired drug resistance, contribute to the recurrence and poor prognosis of ovarian cancer. CD109, a cell surface glycoprotein, has been reported to be a marker of CSCs; however, it remains unclear whether CD109 is secreted by CSCs. In this study, we investigated the amount of CD109 in conditioned media (CM) of CSC populations from ovarian cancer cell lines and patients with ovarian cancer. The CM of sphere-forming CSCs isolated from ovarian cancer cell lines (A2780 and SKOV3) had higher levels of CD109 than those isolated from their adherent cultured parental cells. Furthermore, higher levels of CD109 were detected on the cell surface and in the CM of sphere-forming CSC populations isolated from patient-derived primary ovarian cancer cells. To clarify whether CD109 is localized to the exosomal fraction secreted from CSCs, extracellular vesicles were isolated from the CM by ultracentrifugation. In addition to the CM, the exosomal fraction of ovarian CSCs contained greater levels of CD109 than the parental cells. These results suggest that CD109 is secreted in a soluble or exosomal form from CSCs, and that the measurement of secreted CD109 may be used as a diagnostic or prognostic marker for ovarian cancer. [BMB Reports 2024; 57(12): 527-532].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"527-532"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680669","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

Cereblon regulates the production of hepatic fibroblast growth factor 23 in diabetes. 脑龙调节糖尿病患者肝成纤维细胞生长因子 23 的产生。

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Seungwon An, Balachandar Nedumaran, Hangaram Oh, Taehyun Park, Chul-Seung Park, Ali R Djalilian, Sooyong Shin, Taehoon Chung, Yong Deuk Kim

{"title":"Cereblon regulates the production of hepatic fibroblast growth factor 23 in diabetes.","authors":"Seungwon An, Balachandar Nedumaran, Hangaram Oh, Taehyun Park, Chul-Seung Park, Ali R Djalilian, Sooyong Shin, Taehoon Chung, Yong Deuk Kim","doi":"","DOIUrl":"","url":null,"abstract":"Cereblon (CRBN) is an extensively expressed protein involved in crucial physiological processes. This study reveals CRBN's role in governing hepatic fibroblast growth factor 23 (FGF23) expression and production via the cyclic adenosine monophosphate (cAMP) pathway in diabetic conditions. The expressions of hepatic Crbn, Yin Yang 1 (Yy1), and Fgf23 genes were significantly increased in diabetic mice and forskolin (FSK)-treated primary hepatocytes, correlating with elevated FGF23 production. Overexpression of Crbn and Yy1 increased hepatic FGF23 and cytokines by upregulating YY1 gene expression, which was reduced in Crbn- and Yy1-silenced mice and primary hepatocytes. Besides, we also found that CRBN-mediated regulation of hepatic FGF23 involved YY1 recruitment to the Fgf23 gene promoters, evidenced by reporter assays, deletion studies, and mutant analyses. These findings identify CRBN and YY1 as key contributors to gluconeogenic signaling-driven FGF23 production and inflammation in diabetes, highlighting their potential as therapeutic targets for addressing metabolic disorders like diabetes. [BMB Reports 2024; 57(12): 533-538].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"533-538"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387639","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

Recombinant ADAMTS1 promotes muscle cell differentiation and alleviates muscle atrophy by repressing NOTCH1. 重组 ADAMTS1 通过抑制 NOTCH1 促进肌肉细胞分化并缓解肌肉萎缩。

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Sang Hyup Lee, Sang Yoon Kim, Yun Gu Gwon, Chanwoo Lee, Changhwan Kim, Ick Hyun Cho, Tae-Won Kim, Bong-Keun Choi

{"title":"Recombinant ADAMTS1 promotes muscle cell differentiation and alleviates muscle atrophy by repressing NOTCH1.","authors":"Sang Hyup Lee, Sang Yoon Kim, Yun Gu Gwon, Chanwoo Lee, Changhwan Kim, Ick Hyun Cho, Tae-Won Kim, Bong-Keun Choi","doi":"","DOIUrl":"","url":null,"abstract":"A disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1) plays crucial roles in various biological processes, including myogenesis, by modulating the neurogenic locus notch homolog protein 1 (NOTCH1) signaling pathway. However, the mechanisms through which ADAMTS1 regulates myogenesis remain unclear. In this study, we generated recombinant ADAMTS1 mutants and determined their effects on muscle cell differentiation, focusing on the regulation of NOTCH1 signaling. Treatment of C2C12 cells with recombinant ADAMTS1 protein enhanced muscle cell differentiation. Meanwhile, ADAM10 treatment inhibited muscle differentiation through the activation of NOTCH1 cleavage. Recombinant ADAMTS1 reversed ADAM10-induced muscle cell atrophy by suppressing NOTCH1 activation and downregulating its target gene. Recombinant ADAMTS1 also alleviated dexamethasoneinduced muscle atrophy in a mouse model. In summary, our findings suggest that recombinant ADAMTS1 promotes muscle regeneration by suppressing NOTCH1 and highlight the potential of recombinant ADAMTS1 proteins in the treatment of muscle wasting disease. [BMB Reports 2024; 57(12): 539-545].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"539-545"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680671","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

Targeting proprotein convertase subtilisin/kexin type 7 in macrophages as a therapeutic strategy to mitigate myocardial infarction-induced inflammation. 巨噬细胞中靶向蛋白转化酶枯草素/kexin 7作为缓解心肌梗死诱导炎症的治疗策略

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-01

Shin Hye Moon, Inyoung Chung, Na Hyeon Yoon, Jing Jin, Hyae Yon Kweon, Won Kee Yoon, Nabil G Seidah, Goo Taeg Oh

{"title":"Targeting proprotein convertase subtilisin/kexin type 7 in macrophages as a therapeutic strategy to mitigate myocardial infarction-induced inflammation.","authors":"Shin Hye Moon, Inyoung Chung, Na Hyeon Yoon, Jing Jin, Hyae Yon Kweon, Won Kee Yoon, Nabil G Seidah, Goo Taeg Oh","doi":"","DOIUrl":"","url":null,"abstract":"Myocardial infarction (MI), a major form of coronary artery disease (CAD), triggers a severe inflammatory response in the heart, resulting in increased cell death and adverse ventricular remodeling. Despite treatment advancements, MI remains a significant risk factor for heart failure, underscoring the necessity for a more in-depth exploration of immune cell mechanisms. Proprotein convertase subtilisin/kexin type 7 (PCSK7), expressed in various tissues and immune cells, has been implicated in cardiovascular disease, yet its specific role in cardiac immune cells remains poorly understood. This study aimed to elucidate the role of PCSK7 in MI-related inflammation. Our findings indicate that PCSK7 deficiency reduces circulating cholesterol levels, potentially mitigating infarct injury and improving cardiac function by modulating immune cells. Additionally, PCSK7 promotes macrophage activation and lipid uptake at the ischemic site, intensifying the pathology. We also observed that PCSK7 activates the TNF-α/JNK signaling pathway in macrophages intracellularly, amplifying the inflammatory response. Therefore, targeting PCSK7 in macrophages could help mitigate post-MI inflammation, alleviate disease severity, and offer novel therapeutic strategies for patients with CAD. [BMB Reports 2024; 57(12): 553-558].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"553-558"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765884","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