IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-20

Jeongmin Lee, Cherlhyun Jeong

引用次数: 0

Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-20

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. Single-molecule DNA flow-stretching assays will keep contributing to our understanding of how DNA-binding proteins function due to their multiplexed, versatile, and robust capabilities.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 : 2024-12-20

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.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 : 2024-12-20

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 cryo-fluorescence 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-to-noise 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.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-molecule studies of repair proteins in base excision repair.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-20

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.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a prime editor with improved editing efficiency in Arabidopsis.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-17

Yeong Yeop Jeong, Cheljong Hong, Jun Hee Han, Sangsu Bae, Pil Joon Seo

引用次数: 0

Establishment and Characterization of Endometrial Organoids from Different Placental Types.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-17

Dong-Hyeok Kwon, Byeonghwi Lim, Sung-Yeon Lee, Sung-Ho Won, Goo Jang

{"title":"Establishment and Characterization of Endometrial Organoids from Different Placental Types.","authors":"Dong-Hyeok Kwon, Byeonghwi Lim, Sung-Yeon Lee, Sung-Ho Won, Goo Jang","doi":"","DOIUrl":"","url":null,"abstract":"Understanding the molecular characteristics and metabolic processes of the mammalian endometrium is crucial for advancing biological research, particularly in veterinary obstetrics and pathology. This study established and analyzed organoids from the endometrial epithelial stem cells of five mammals with different placental types: cows (cotyledonary), dogs and cats (zonary), pigs (diffuse), and rats (discoid). The organoids from these five species were maintained for over 13 passages, successfully frozen-thawed, and confirmed by pathological analysis to retain the characteristics of the original tissues. Furthermore, integrative transcriptome analysis of the organoids and tissues from the five species highlighted key pathways, such as PI3K-Akt signaling and extracellular matrix-receptor interaction, which are crucial in cancer research. Despite the downregulation of genes associated with vascular smooth muscle contraction, the organoids exhibited significant activity of genes involved in hormone metabolism. In conclusion, our study achieves stable establishment of endometrial organoids from five mammals with different placental types and offers foundational data for organoid research. In the future, these organoids are suitable models for investigating uterine physiology, diseases, and assessing potential therapies.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833799","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

PGC1α is a key regulator of erastin-induced mitochondrial dysfunction during ferroptotic cell death.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-17

Byeong Geun Seok, Eunhee Park, Young-Jun Park, Young-Jun Park, Hyuk Nam Kwon, Su Wol Chung

{"title":"PGC1α is a key regulator of erastin-induced mitochondrial dysfunction during ferroptotic cell death.","authors":"Byeong Geun Seok, Eunhee Park, Young-Jun Park, Young-Jun Park, Hyuk Nam Kwon, Su Wol Chung","doi":"","DOIUrl":"","url":null,"abstract":"A type of programmed cell death called ferroptosis is defined by increased iron-dependent lipid peroxidation. Mitochondria play a central role in iron metabolism. Mitochondrial defects include decreased cristae density, membrane rupture, and decreased mitochondrial membrane density, which occur as a result of ferroptosis. One of the important regulator of mitochondrial biogenesis is PGC1α. While recent studies have begun to explore the association between PGC1α and ferroptosis, the specific role of PGC1α in erastin-induced mitochondrial dysfunction during ferroptotic cell death has not been fully elucidated. In this study, we demonstrate for the first time that PGC1α is a key regulator of erastin-induced mitochondrial-dependent lipid peroxidation and dysfunction during ferroptosis in HT1080 fibrosarcoma cells. In this study, we examined PGC1α function in ferroptosis. Erastin, an inducer of ferroptosis, boosted the expression of PGC1α. Moreover, PGC1α down-regulation reduced erastin-induced ferroptosis. The most important biochemical feature of ferroptosis is the increase in iron ion (Fe2+)-dependent lipid peroxide (LOOH) concentration. Mitochondrial-dependent lipid peroxidation was abolished by PGC1α downregulation. In addition, PGC1α was induced during mitochondrial dysfunction in erastin-induced ferroptosis. Mitochondrial membrane potential loss and mitochondrial ROS production associated with erastin-induced mitochondrial dysfunction were blocked by PGC1α inhibition. In addition, erastin-induced lipid peroxidation in HT1080 fibrosarcoma cells was regulated by PGC1α inhibitor. This phenomenon was also consistent in HT1080 cells transfected with PGC1α shRNA transfected cells. Taken together, these results suggest that PGC1α is a key factor in erastin-induced mitochondrial-dependent lipid peroxidation and dysfunction during ferroptosis cell death.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833826","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

Wnt5a exacerbates pathological bone features and trabecular bone loss in curdlan-injected SKG mice via osteoclast activation.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-17

Min Whangbo, Eunae Ko, Dongju Kim, Chanhyeok Jeon, Hye-Ryeong Jo, Hye-Ryeong Jo, Seung Hoon Lee, Jeehee Youn, Sungsin Jo, Tae-Hwan Kim

{"title":"Wnt5a exacerbates pathological bone features and trabecular bone loss in curdlan-injected SKG mice via osteoclast activation.","authors":"Min Whangbo, Eunae Ko, Dongju Kim, Chanhyeok Jeon, Hye-Ryeong Jo, Hye-Ryeong Jo, Seung Hoon Lee, Jeehee Youn, Sungsin Jo, Tae-Hwan Kim","doi":"","DOIUrl":"","url":null,"abstract":"Many studies on osteoblasts have suggested that Wnt5a plays a crucial role in excessive osteoblast activity, which is responsible for ectopic new bone formation, but research on osteoclasts in ankylosing spondylitis (AS) remains relatively limited. This study aimed to explore whether Wnt5a influences osteoclast-mediated bone resorption in curdlan-injected SKG mice, a model that mimics AS. Compared to the Vehicle group, the Wnt5a treatment group exhibited statistically higher clinical arthritis scores and increased hindpaw thickness values. Micro-computed tomography (microCT) analysis of hindpaws revealed a significant increase in inflamed and ectopic bone density in the Wnt5a-treated group compared to the Vehicle group. Histological examination also showed pronounced inflammation and structural bone damage in the bone marrow of ankles in the Wnt5a-treated group. Intriguingly, microCT analysis of the femur revealed that trabecular bone loss was markedly observed in the Wnt5a-treated group. Both the number of TRAP-positive osteoclasts and their activity were statistically greater in the Wnt5a-treated group compared to the Vehicle group. Serum markers of bone resorption, but not bone formation, were also significantly elevated in the Wnt5a-treated group. Notably, promotion of osteoclast differentiation by Wnt5a was inhibited following treatment with anti-Wnt5a. These findings suggest that targeting Wnt5a could be a promising strategy for mitigating pathological bone features in AS by modulating osteoclast activity.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833883","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

Role of histone modification in chromatin-mediated transcriptional repression in protozoan parasite Trichomonas vaginalis.

IF 2.9 3区生物学

BMB Reports Pub Date : 2024-12-17

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.","PeriodicalId":9010,"journal":{"name":"BMB Reports","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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