BMB Reports最新文献_第3页

Role of histone modification in chromatin-mediated transcriptional repression in protozoan parasite Trichomonas vaginalis. 组蛋白修饰在原生寄生虫阴道毛滴虫染色质介导的转录抑制中的作用。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-02-01

Min-Ji Song, Mikyoung Kim, Jieun Seo, Heon-Woo Kwon, Chang Hoon Yang, Jung-Sik Joo, Yong-Joon Cho, Hyoung-Pyo Kim

{"title":"Role of histone modification in chromatin-mediated transcriptional repression in protozoan parasite Trichomonas vaginalis.","authors":"Min-Ji Song, Mikyoung Kim, Jieun Seo, Heon-Woo Kwon, Chang Hoon Yang, Jung-Sik Joo, Yong-Joon Cho, Hyoung-Pyo Kim","doi":"","DOIUrl":"","url":null,"abstract":"Trichomonas vaginalis is an extracellular flagellated protozoan responsible for trichomoniasis, one of the most prevalent nonviral sexually transmitted infections. To persist in its host, T. vaginalis employs sophisticated gene regulation mechanisms to adapt to hostile environmental conditions. Although transcriptional regulation is crucial for this adaptation, the underlying molecular mechanisms remain poorly understood. Epigenetic regulation, particularly histone modifications, has emerged as a key modulator of gene expression. A previous study demonstrated that histone modifications, H3K4me3 and H3K27ac, promote active transcription. However, the complete extent of epigenetic regulation in T. vaginalis remains unclear. The present study extended these findings by exploring the repressive role of two additional histone H3 modifications, H3K9me3 and H3K27me3. Genome-wide analysis revealed that these modifications negatively correlated with gene expression, affecting protein-coding and transposable element genes (TEGs). These findings offer new insights into the dual role of histone modifications in activating and repressing gene expression and provide a more comprehensive understanding of epigenetic regulation in T. vaginalis. This expanded knowledge may inform the development of novel therapeutic strategies targeting the epigenetic machinery of T. vaginalis. [BMB Reports 2025; 58(2): 82-88].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"82-88"},"PeriodicalIF":2.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11875748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833882","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

Quantum molecular resonance ameliorates atopic dermatitis through suppression of IL36G and SPRR2B. 量子分子共振通过抑制IL36G和SPRR2B改善特应性皮炎。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-06

Jinyoung Kim, Barsha Deshar, Min Hwang, Chandani Shrestha, Eunhye Ju, Bum-Ho Bin, Jiyoon Kim

{"title":"Quantum molecular resonance ameliorates atopic dermatitis through suppression of IL36G and SPRR2B.","authors":"Jinyoung Kim, Barsha Deshar, Min Hwang, Chandani Shrestha, Eunhye Ju, Bum-Ho Bin, Jiyoon Kim","doi":"","DOIUrl":"","url":null,"abstract":"Atopic dermatitis (AD) is a chronic, pruritic skin disease characterized by inflammation and skin lesion cornification. While the use of corticosteroids like dexamethasone (DXM), an antiinflammatory drug, improves symptoms temporarily and quickly, this use is not a cure. Thus, we aimed to identify a new therapeutic strategy for AD using quantum molecular resonance (QMR), a novel non-invasive technique with an electromagnetic field-based therapeutic approach as an alternative to pain killers. An AD mouse model presenting AD-like skin lesions was generated by treating BALB/c mice with dinitrochlorobenzene (DNCB), and then DNCB-induced AD mice were administered DXM or QMR, and the change of AD-like skin lesions was observed. QMR ameliorated AD-like skin lesions in DNCB-induced AD mice and reduced the numbers of infiltrated mast cells and macrophages in mouse skin. QMR also alleviated thickening of the epidermis and restored integrity of the epidermal basement membrane. Several genes regulated by DNCB and counterregulated by QMR were identified through transcriptome analysis in mouse skin, and RNA silencing experiments on these genes in TNF-α/IFN-γ- or DNCB-treated human keratinocytes revealed that IL36G and SPRR2B play important roles in inflammation and keratinization. The expression of IL36G and SPRR2B was significantly reduced by QMR in skin of DNCB-induced AD mice. These results underscore the promising role of QMR in ameliorating AD characterized by inflammation and skin lesion hyperkeratosis via targeting IL36G and SPRR2B.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tau reduction impairs nephrocyte function in Drosophila. Tau蛋白减少损害果蝇肾细胞功能。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-06

Jiyoung Lee, Dayoung Kim, Sun Joo Cha, Jang-Won Lee, Eun-Young Lee, Hyung-Jun Kim, Kiyoung Kim

引用次数: 0

Single-molecule perspectives of CRISPR/Cas systems: target search, recognition, and cleavage. CRISPR/Cas 系统的单分子视角：目标搜索、识别和切割。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Jeongmin Lee, Cherlhyun Jeong

引用次数: 0

Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements. 单分子测量揭示核小体和染色质纤维的动力学。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Sihyeong Nho, Hajin Kim

{"title":"Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.","authors":"Sihyeong Nho, Hajin Kim","doi":"","DOIUrl":"","url":null,"abstract":"The nucleosome is the fundamental structural unit of chromosome fibers. DNA wraps around a histone octamer to form a nucleosome while neighboring nucleosomes interact to form higher-order structures and fit gigabase-long DNAs into a small volume of the nucleus. Nucleosomes interrupt the access of transcription factors to a genomic region and provide regulatory controls of gene expression. Biochemical and physical cues stimulate wrapping-unwrapping and condensation-decondensation dynamics of nucleosomes and nucleosome arrays. Nucleosome dynamics and chromatin fiber organization are influenced by changes in the ionic background within the nucleus, post-translational modifications of histone proteins, and DNA sequence characteristics, such as histone-binding motifs and nucleosome spacing. Biochemical and biophysical measurements, along with in silico simulations, have been extensively used to study the regulatory effects on chromatin dynamics. In particular, single-molecule measurements have revealed novel mechanistic details of nucleosome and chromatin dynamics. This minireview elucidates recent findings on chromatin dynamics from these approaches. [BMB Reports 2025; 58(1): 24-32].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"24-32"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930673","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

Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions. 单分子dna流动拉伸试验是研究dna -蛋白质相互作用的多功能杂交工具。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Sadaf Shehzad, HyeongJun Kim

{"title":"Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions.","authors":"Sadaf Shehzad, HyeongJun Kim","doi":"","DOIUrl":"","url":null,"abstract":"Single-molecule techniques allow researchers to investigate individual molecules and obtain unprecedented details of the heterogeneous nature of biological entities. They play instrumental roles in studying DNA-protein interactions due to the ability to visualize DNA or proteins and to manipulate individual DNA molecules by applying force or torque. Here, we describe single-molecule DNA-flow stretching assays as hybrid tools that combine forces with fluorescence. We also review how widely these assays are utilized in elucidating working mechanisms of DNA-binding proteins. Additionally, we provide a brief explanation of various efforts to prepare DNA substrates with desired internal protein-binding sequences. More complicated needs for DNA-protein interaction research have led to improvements in single-molecule DNA flow-stretching techniques. Several DNA flow-stretching variants such as DNA curtain, DNA motion capture assays, and protein-induced fluorescence enhancement (PIFE) are introduced in this mini review. Singlemolecule DNA flow-stretching assays will keep contributing to our understanding of how DNA-binding proteins function due to their multiplexed, versatile, and robust capabilities. [BMB Reports 2025; 58(1): 41-51].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"41-51"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862971","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

Advancing membrane biology: single-molecule approaches meet model membrane systems. 推进膜生物学：单分子方法满足模型膜系统。

IF 2.9 3区生物学

BMB Reports Pub Date : 2025-01-01

Jaehyeon Shin, Sang Hyeok Jeong, Min Ju Shon

{"title":"Advancing membrane biology: single-molecule approaches meet model membrane systems.","authors":"Jaehyeon Shin, Sang Hyeok Jeong, Min Ju Shon","doi":"","DOIUrl":"","url":null,"abstract":"Model membrane systems have emerged as essential platforms for investigating membrane-associated processes in controlled environments, mimicking biological membranes without the complexity of cellular systems. However, integrating these model systems with single-molecule techniques remains challenging due to the fluidity of lipid membranes, including undulations and the lateral mobility of lipids and proteins. This mini-review explores the evolution of various model membranes ranging from black lipid membranes to nanodiscs and giant unilamellar vesicles as they adapt to accommodate electrophysiology, force spectroscopy, and fluorescence microscopy. We highlight recent advancements, including innovations in force spectroscopy and single-molecule imaging using free-standing lipid bilayers, and the development of membrane platforms with tunable composition and curvature for improving fluorescence-based studies of protein dynamics. These integrated approaches have provided deep insights into ion channel function, membrane fusion, protein mechanics, and protein dynamics. We highlight how the synergy between single-molecule techniques and model membranes enhances our understanding of complex cellular processes, paving the way for future discoveries in membrane biology and biophysics. [BMB Reports 2025; 58(1): 33-40].","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":"33-40"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862969","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

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