Progress in Biophysics & Molecular Biology最新文献_第8页

Cold snapshots of DNA repair: Cryo-EM structures of DNA-PKcs and NHEJ machinery DNA修复的冷快照:DNA- pkcs和NHEJ机制的低温电镜结构。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-11-28 DOI: 10.1016/j.pbiomolbio.2023.11.007

Himani Amin , Sayma Zahid , Chloe Hall , Amanda K. Chaplin

{"title":"Cold snapshots of DNA repair: Cryo-EM structures of DNA-PKcs and NHEJ machinery","authors":"Himani Amin , Sayma Zahid , Chloe Hall , Amanda K. Chaplin","doi":"10.1016/j.pbiomolbio.2023.11.007","DOIUrl":"10.1016/j.pbiomolbio.2023.11.007","url":null,"abstract":"<div><p>The proteins and protein assemblies involved in DNA repair have been the focus of a multitude of structural studies for the past few decades. Historically, the structures of these protein complexes have been resolved by X-ray crystallography. However, more recently with the advancements in cryo-electron microscopy (cryo-EM) ranging from optimising the methodology for sample preparation to the development of improved electron detectors, the focus has shifted from X-ray crystallography to cryo-EM. This methodological transition has allowed for the structural determination of larger, more complex protein assemblies involved in DNA repair pathways and has subsequently led to a deeper understanding of the mechanisms utilised by these fascinating molecular machines. Here, we review some of the key structural advancements that have been gained in the study of non-homologous end joining (NHEJ) by the use of cryo-EM, with a focus on assemblies composed of DNA-PKcs and Ku70/80 (Ku) and the various methodologies utilised to obtain these structures.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"186 ","pages":"Pages 1-13"},"PeriodicalIF":3.8,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0079610723001001/pdfft?md5=82993d4cb25614e14dc6c19e75a17d9e&pid=1-s2.0-S0079610723001001-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138464451","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

Cells and sounds 细胞和声音。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-11-23 DOI: 10.1016/j.pbiomolbio.2023.11.004

Michael Spitzer

引用次数: 0

Shannon's (informational) dissipation as the major engine leading to living dynamic and the origin of self. 香农(信息)耗散作为生命动力和自我起源的主要引擎。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-11-13 DOI: 10.1016/j.pbiomolbio.2023.11.003

Salvatore Chirumbolo, Antonio Vella

引用次数: 0

Growth or death? Control of cell destiny by mTOR and autophagy pathways 成长还是死亡？mTOR和自噬途径对细胞命运的控制。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-11-08 DOI: 10.1016/j.pbiomolbio.2023.10.002

Mahmoud I. Khalil , Mohamad M. Ali , Jasmine Holail , Marwa Houssein

{"title":"Growth or death? Control of cell destiny by mTOR and autophagy pathways","authors":"Mahmoud I. Khalil , Mohamad M. Ali , Jasmine Holail , Marwa Houssein","doi":"10.1016/j.pbiomolbio.2023.10.002","DOIUrl":"10.1016/j.pbiomolbio.2023.10.002","url":null,"abstract":"<div><p><span>One of the central regulators of cell growth, proliferation, and metabolism is the mammalian target of rapamycin<span><span>, mTOR, which exists in two structurally and functionally different complexes: mTORC1 and mTORC2; unlike m TORC2, mTORC1 is activated in response to the sufficiency of nutrients and is inhibited by rapamycin. mTOR complexes have critical roles not only in protein synthesis<span>, gene transcription regulation, proliferation, tumor metabolism, but also in the regulation of the programmed cell death mechanisms such as autophagy and apoptosis. Autophagy is a conserved catabolic mechanism in which damaged molecules are recycled in response to nutrient starvation. Emerging evidence indicates that the mTOR </span></span>signaling pathway<span> is frequently activated in tumors. In addition, dysregulation of autophagy was associated with the development of a variety of human diseases, such as cancer and aging. Since mTOR can inhibit the induction of the autophagic process from the early stages of autophagosome formation to the late stage of </span></span></span>lysosome degradation, the use of mTOR inhibitors to regulate autophagy could be considered a potential therapeutic option. The present review sheds light on the mTOR and autophagy signaling pathways and the mechanisms of regulation of mTOR-autophagy.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"185 ","pages":"Pages 39-55"},"PeriodicalIF":3.8,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72016183","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

How an emergent cosmology of a nonlocally unified, meaningfully in-formed and holographically manifested Universe can underpin and frame the biological embodiment of quantum entanglement 一个非局部统一、有意义地形成和全息显示的宇宙的新兴宇宙学如何支撑和构建量子纠缠的生物学体现。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-21 DOI: 10.1016/j.pbiomolbio.2023.10.001

Jude Currivan

{"title":"How an emergent cosmology of a nonlocally unified, meaningfully in-formed and holographically manifested Universe can underpin and frame the biological embodiment of quantum entanglement","authors":"Jude Currivan","doi":"10.1016/j.pbiomolbio.2023.10.001","DOIUrl":"10.1016/j.pbiomolbio.2023.10.001","url":null,"abstract":"<div><p>With a Nobel Prize for Physics widely viewed as only given for ‘settled’ science, the award then essentially accepts the validity of universal nonlocality. Other key discoveries and insights in recent years are also progressively pointing to the appearance of our Universe, its energy-matter and space-time, as not being foundational but emerging from deeper, discarnate realms of causation. as digitized and meaningful, in-formation, its manifestation pixelated at the so-named Planck scale of existence. Extending from studies of black holes to the entire Universe, a growing number of cosmologists have also developed the so-named holographic principle, to model the four-dimensional appearance of our Universe (three dimensions of space and one of time) as a holographic projection of its two- dimensional boundary. In framing the emergent cosmology of a nonlocally unified, meaningfully in-formed and holographically manifested Universe, an expansion of the three universal Laws of Thermodynamics to three Laws of Information, or Infodynamics also points the way to reconciling Quantum Theory<span> that describes energy-matter and Relativity Theory that describes space-time and offers too an understanding of how the lifecycle of our Universe flows from its first moment until its last. Treating gravity as an emergent consequence of the in-formational and holographic structure of space- time and describing it as the consequence of the intropy associated with the positions in space-time of massive bodies, also points to the findings of the loss of phenotype identity in zero gravity and the role between gravity and cellular identity and the emergence of symbiogenesis.</span></p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"185 ","pages":"Pages 33-36"},"PeriodicalIF":3.8,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694035","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

Computational approaches for modeling and structural design of biological systems: A comprehensive review 生物系统建模和结构设计的计算方法：综述。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-09 DOI: 10.1016/j.pbiomolbio.2023.08.002

Ekambaram Gayathiri , Palanisamy Prakash , Priya Kumaravel , Jayanthi Jayaprakash , Manikkavalli Gurunathan Ragunathan , Sharmila Sankar , Saravanan Pandiaraj , Natesan Thirumalaivasan , Muthu Thiruvengadam , Rajakumar Govindasamy

{"title":"Computational approaches for modeling and structural design of biological systems: A comprehensive review","authors":"Ekambaram Gayathiri , Palanisamy Prakash , Priya Kumaravel , Jayanthi Jayaprakash , Manikkavalli Gurunathan Ragunathan , Sharmila Sankar , Saravanan Pandiaraj , Natesan Thirumalaivasan , Muthu Thiruvengadam , Rajakumar Govindasamy","doi":"10.1016/j.pbiomolbio.2023.08.002","DOIUrl":"10.1016/j.pbiomolbio.2023.08.002","url":null,"abstract":"<div><p>The convergence of biology and computational science has ushered in a revolutionary era, revolutionizing our understanding of biological systems and providing novel solutions to global problems. The field of genetic engineering has facilitated the manipulation of genetic codes, thus providing opportunities for the advancement of innovative disease therapies and environmental enhancements. The emergence of bio-molecular simulation represents a significant advancement in this particular field, as it offers the ability to gain microscopic insights into molecular-level biological processes<span> over extended periods. Biomolecular simulation plays a crucial role in advancing our comprehension of organismal mechanisms by establishing connections between molecular structures, interactions, and biological functions. The field of computational biology has demonstrated its significance in deciphering intricate biological enigmas through the utilization of mathematical models and algorithms. The process of decoding the human genome has resulted in the advancement of therapies for a wide range of genetic disorders, while the simulation of biological systems contributes to the identification of novel pharmaceutical compounds. The potential of biomolecular simulation and computational biology is vast and limitless. As the exploration of the underlying principles that govern living organisms progresses, the potential impact of this understanding on cancer treatment, environmental restoration, and other domains is anticipated to be transformative. This review examines the notable advancements achieved in the field of computational biology, emphasizing its potential to revolutionize the comprehension and enhancement of biological systems.</span></p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"185 ","pages":"Pages 17-32"},"PeriodicalIF":3.8,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220333","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

Recent progress of mechanosensitive mechanism on breast cancer 乳腺癌症机械敏感性机制的最新进展。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-02 DOI: 10.1016/j.pbiomolbio.2023.09.003

Xiao-Xia Chai , Jie Liu , Tong-Yao Yu , Ge Zhang , Wen-Jun Sun , Yan Zhou , Li Ren , Hui-Ling Cao , Da-Chuan Yin , Chen-Yan Zhang

{"title":"Recent progress of mechanosensitive mechanism on breast cancer","authors":"Xiao-Xia Chai , Jie Liu , Tong-Yao Yu , Ge Zhang , Wen-Jun Sun , Yan Zhou , Li Ren , Hui-Ling Cao , Da-Chuan Yin , Chen-Yan Zhang","doi":"10.1016/j.pbiomolbio.2023.09.003","DOIUrl":"10.1016/j.pbiomolbio.2023.09.003","url":null,"abstract":"<div><p><span><span><span>The mechanical environment is important for tumorigenesis and progression. Tumor cells can sense mechanical signals by mechanosensitive receptors, and these mechanical signals can be converted to biochemical signals to regulate cell behaviors, such as cell differentiation, proliferation, migration, apoptosis, and drug resistance. Here, we summarized the effects of the mechanical microenvironment on breast cancer cell activity, and </span>mechanotransduction mechanism from cellular microenvironment to cell membrane, and finally to the nucleus, and also relative mechanosensitive proteins, ion channels, and </span>signaling pathways were elaborated, therefore the mechanical signal could be transduced to biochemical or molecular signal. Meanwhile, the mechanical models commonly used for biomechanics study </span><em>in vitro</em> and some quantitative descriptions were listed. It provided an essential theoretical basis for the occurrence and development of mechanosensitive breast cancer, and also some potential drug targets were proposed to treat such disease.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"185 ","pages":"Pages 1-16"},"PeriodicalIF":3.8,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41174861","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

Commentary on “A systematic review on machine learning and deep learning techniques in cancer survival prediction”: Validation of survival methods 评论“癌症生存预测中的机器学习和深度学习技术的系统综述”：生存方法的验证。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-01 DOI: 10.1016/j.pbiomolbio.2023.08.001

J. Sidorova, J.J. Lozano

引用次数: 0

A systematic review on intracranial aneurysm and hemorrhage detection using machine learning and deep learning techniques 利用机器学习和深度学习技术检测颅内动脉瘤和出血的系统综述。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-10-01 DOI: 10.1016/j.pbiomolbio.2023.07.001

S. Nafees Ahmed, P. Prakasam

{"title":"A systematic review on intracranial aneurysm and hemorrhage detection using machine learning and deep learning techniques","authors":"S. Nafees Ahmed, P. Prakasam","doi":"10.1016/j.pbiomolbio.2023.07.001","DOIUrl":"10.1016/j.pbiomolbio.2023.07.001","url":null,"abstract":"<div><p>The risk of discovering an intracranial aneurysm during the initial screening and follow-up screening are reported as around 11%, and 7% respectively (Zuurbie et al., 2023) to these mass effects, unruptured aneurysms frequently generate symptoms, however, the real hazard occurs when an aneurysm ruptures and results in a cerebral hemorrhage known as a subarachnoid hemorrhage. The objective is to study the multiple kinds of hemorrhage and aneurysm detection problems and develop machine and deep learning models to recognise them. Due to its early stage, subarachnoid hemorrhage, the most typical symptom after aneurysm rupture, is an important medical condition. It frequently results in severe neurological emergencies or even death. Although most aneurysms are asymptomatic and won't burst, because of their unpredictable growth, even small aneurysms are susceptible. A timely diagnosis is essential to prevent early mortality because a large percentage of hemorrhage cases present can be fatal. Physiological/imaging markers and the degree of the subarachnoid hemorrhage can be used as indicators for potential early treatments in hemorrhage. The hemodynamic pathomechanisms and microcellular environment should remain a priority for academics and medical professionals. There is still disagreement about how and when to care for aneurysms that have not ruptured despite studies reporting on the risk of rupture and outcomes. We are optimistic that with the progress in our understanding of the pathophysiology of hemorrhages and aneurysms and the advancement of artificial intelligence has made it feasible to conduct analyses with a high degree of precision, effectiveness and reliability.</p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"183 ","pages":"Pages 1-16"},"PeriodicalIF":3.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10273805","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: 1

HIF-1α and periodontitis: Novel insights linking host-environment interplay to periodontal phenotypes HIF-1α与牙周炎：将宿主环境相互作用与牙周表型联系起来的新见解。

IF 3.8 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2023-09-26 DOI: 10.1016/j.pbiomolbio.2023.09.002

Chao Shan , YuNing Xia , Zeyu Wu , Jin Zhao

{"title":"HIF-1α and periodontitis: Novel insights linking host-environment interplay to periodontal phenotypes","authors":"Chao Shan , YuNing Xia , Zeyu Wu , Jin Zhao","doi":"10.1016/j.pbiomolbio.2023.09.002","DOIUrl":"10.1016/j.pbiomolbio.2023.09.002","url":null,"abstract":"<div><p><span>Periodontitis, the sixth most prevalent epidemic disease globally, profoundly impacts oral aesthetics and masticatory functionality. Hypoxia-inducible factor-1α (HIF-1α), an oxygen-dependent transcriptional activator<span>, has emerged as a pivotal regulator in periodontal tissue and alveolar bone metabolism, exerts critical functions in angiogenesis, </span></span>erythropoiesis<span><span>, energy metabolism, and cell fate determination. Numerous essential phenotypes regulated by HIF are intricately associated with bone metabolism in periodontal tissues. Extensive investigations have highlighted the central role of HIF and its downstream target genes and pathways in the coupling of angiogenesis and osteogenesis. Within this concise perspective, we comprehensively review the cellular phenotypic alterations and microenvironmental dynamics linking HIF to periodontitis. We analyze current research on the HIF pathway, elucidating its impact on bone repair and regeneration, while unraveling the involved cellular and molecular mechanisms. Furthermore, we briefly discuss the potential application of targeted interventions aimed at HIF in the field of bone </span>tissue regeneration engineering. This review expands our biological understanding of the intricate relationship between the HIF gene and bone angiogenesis in periodontitis and offers valuable insights for the development of innovative therapies to expedite bone repair and regeneration.</span></p></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"184 ","pages":"Pages 50-78"},"PeriodicalIF":3.8,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41158378","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