Progress in Biophysics & Molecular Biology最新文献

From bench to Bone: Clinical promise of exosome-enhanced scaffolds in orthopedic regeneration 从工作台到骨骼：外泌体增强支架在骨科再生中的临床应用前景

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-10-01 DOI: 10.1016/j.pbiomolbio.2025.10.001

Asrin Emami , Iman Menbari Oskouie

{"title":"From bench to Bone: Clinical promise of exosome-enhanced scaffolds in orthopedic regeneration","authors":"Asrin Emami , Iman Menbari Oskouie","doi":"10.1016/j.pbiomolbio.2025.10.001","DOIUrl":"10.1016/j.pbiomolbio.2025.10.001","url":null,"abstract":"<div><div>Bone regeneration remains one of the greatest challenges in orthopedic medicine, particularly in cases of complex fractures, nonhealing bones, or large bone defects. Traditional treatments, such as autologous grafts, allogeneic grafts, synthetic materials, or drug therapies, often face limitations, including donor-site pain, immune rejection, and limited ability to stimulate true bone healing. A promising new approach involves the use of exosome-enhanced scaffolds, which combine the structural support of biomaterial scaffolds with the potent regenerative effects of exosomes. Exosomes are nanosized vesicles secreted by cells such as mesenchymal stem cells, osteoblasts, and macrophages. They carry proteins, lipids, and regulatory RNAs that play crucial roles in coordinating bone formation, angiogenesis, and immune modulation. When incorporated into scaffolds, exosomes promote osteogenesis, stimulate vascularization, and facilitate tissue remodeling, thereby creating an optimal microenvironment for bone repair. Preclinical studies have demonstrated accelerated healing, enhanced bone strength, and improved overall bone quality, while early clinical trials indicate that these therapies are both safe and effective. Current research efforts focus on optimizing exosome isolation, understanding their interactions with scaffolds, and developing controlled delivery systems. This strategy holds great promise for transforming orthopedic care by providing patient-specific, biologically active treatments for even the most challenging bone defects.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"198 ","pages":"Pages 32-38"},"PeriodicalIF":4.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219857","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

Exploring the parallels between nanoparticles and viruses with emphasis on environmental roles and remediation 探索纳米颗粒和病毒之间的相似之处，重点是环境作用和补救。

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-09-29 DOI: 10.1016/j.pbiomolbio.2025.09.003

Mahima Kaushik , Madhu Pruthi , Arpana Sharma , Radhey Shyam Sharma , Vandana Mishra , Swagata Karmakar , Niloy Sarkar

{"title":"Exploring the parallels between nanoparticles and viruses with emphasis on environmental roles and remediation","authors":"Mahima Kaushik , Madhu Pruthi , Arpana Sharma , Radhey Shyam Sharma , Vandana Mishra , Swagata Karmakar , Niloy Sarkar","doi":"10.1016/j.pbiomolbio.2025.09.003","DOIUrl":"10.1016/j.pbiomolbio.2025.09.003","url":null,"abstract":"<div><div>Nanoparticles and viruses share several similarities and link the fields of physical and biological sciences by covering and overlapping both realms. In this review we have discussed their commonalities based on classification of constituent material, mode of replication and origin, size, as well as function and application in cargo delivery. We have discussed the modulatory and characteristics of each subunit and how it contributes to cellular uptake and replication. We have also gone into their environmental roles in nutrient mobilization and cycling, being subject to and themselves exerting evolutionary pressures as well as their final environmental fates of immobilization and disintegration. Finally, we have explored their potential use in environmental remediation and energy generation. The novelty of this work is in signifying that both nanoparticles and viruses fall into the realm of macro-biomolecular or nano assemblies and are in many ways similar in origin, characteristics and can be often used synergistically to solve contemporary problems.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"198 ","pages":"Pages 39-54"},"PeriodicalIF":4.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208465","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

Delineation and functions of HCN channels in neurons 神经元中HCN通道的描绘和功能。

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-09-13 DOI: 10.1016/j.pbiomolbio.2025.09.002

Sodikdjon A. Kodirov

{"title":"Delineation and functions of HCN channels in neurons","authors":"Sodikdjon A. Kodirov","doi":"10.1016/j.pbiomolbio.2025.09.002","DOIUrl":"10.1016/j.pbiomolbio.2025.09.002","url":null,"abstract":"<div><div>The observation of non-linear current-voltage relationships of membrane potential responses in neurons led to the discovery of hyperpolarization-induced membrane conductance. The main underlying hallmark of this conductance was the presence of sag – spontaneous depolarization of membrane potential during constant hyperpolarization in current-clamp mode. Gradually, the presence of underling hyperpolarization-activated cyclic nucleotide-gated non-selective cation channels (HCN, <em>I</em><sub>h</sub>, or <em>I</em><sub>f</sub>, where <em>f</em> is for funny) was established. The earliest delineation of HCN-mediated sag in the hippocampus was documented by Purpura, Prelevic, and Santini with a short communication in 1968. The study was performed using classical electrophysiology by impaling the perikaryon of hippocampal neurons, but the outcomes are as insightful as with the patch-clamp technique, and the quality of traces exceeds some of the recent recordings. However, the latter authors were not convinced that the sag phenomenon could play a role under physiological conditions. It is logical since a depolarization and linked excitability are frequently observed in <em>vivo</em>, but not a hyperpolarization. At least a sudden, sharp hyperpolarization does not occur in the CNS. Besides, in order to activate the HCN channels, the amplitude and duration of hyperpolarization should be significant and sufficient. Nonetheless, those with skepticism conveyed pioneer observations were pivotal, since the presence of sag – activation of HCN channels – may also play a role in autism and epilepsy.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"198 ","pages":"Pages 21-31"},"PeriodicalIF":4.5,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071257","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

Cationic calcium channels activated by cyclic nucleotides in plants: A systematic review using the PRISMA method 植物中环核苷酸激活的阳离子钙通道：基于PRISMA方法的系统综述。

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-09-06 DOI: 10.1016/j.pbiomolbio.2025.09.001

Camilo Tayac , J. Torres-Osorio , José Mauricio Rodas-Rodríguez

{"title":"Cationic calcium channels activated by cyclic nucleotides in plants: A systematic review using the PRISMA method","authors":"Camilo Tayac , J. Torres-Osorio , José Mauricio Rodas-Rodríguez","doi":"10.1016/j.pbiomolbio.2025.09.001","DOIUrl":"10.1016/j.pbiomolbio.2025.09.001","url":null,"abstract":"<div><div>The primary objective of this review is to analyze primary research published over the past six years concerning cyclic nucleotide-gated calcium channels (CNGC) in plants. The aim is to structure this information to identify and organize existing knowledge regarding their tertiary and quaternary structures, as well as the activation mechanisms of CNGC. Studies on plant CNGC published between January 2018 and May 2025 were included, while research focused on animals, bacteria, or ions other than calcium was excluded. Articles were retrieved from Scopus, Web of Science, and PubMed databases through searches conducted between June 2024 and May 2025, as well as from additional personal sources. A total of 111 articles met the inclusion criteria. These were categorized into seven groups: phylogenetic analysis and classification of plant CNGC monomers, gene expression regulation, structural composition of monomers and tetramers, channel activation, selectivity mechanisms, cellular localization, and the plant species and structural types in which they are found. The findings revealed that CNGC can be activated by individual mechanisms or by the interplay of multiple pathways. However, uncertainties remain regarding certain activation processes. A lack of experimental studies specifically aimed at elucidating their crystallographic structure was evident, which limits a comprehensive understanding of these channels and represents one of the main constraints of the available evidence. This limitation highlights the need for further research to fully elucidate both the activation mechanisms and structural characteristics of CNGC. Despite these constraints, the findings indicate that CNGC play a pivotal role in plant physiology.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"198 ","pages":"Pages 8-20"},"PeriodicalIF":4.5,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145014478","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

A guide to transport-of-intensity equation (TIE) imaging for biologists 生物学家的强度传输方程（TIE）成像指南

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-08-18 DOI: 10.1016/j.pbiomolbio.2025.08.001

N.C. Ruppel, M.A. Model

{"title":"A guide to transport-of-intensity equation (TIE) imaging for biologists","authors":"N.C. Ruppel, M.A. Model","doi":"10.1016/j.pbiomolbio.2025.08.001","DOIUrl":"10.1016/j.pbiomolbio.2025.08.001","url":null,"abstract":"<div><div>The measurement of dry cell mass (often referred to as “protein”) under the microscope can be accomplished using a quantitative phase imaging technique known as Transport of Intensity Equation (TIE) microscopy. This method requires no specialized equipment, relying instead on two slightly defocused brightfield images acquired with a standard optical microscope. The images are processed by the TIE equation to convert the gradient of intensity into phase shifts and ultimately a distribution of protein mass. Beyond its simplicity, a major advantage of TIE over most other quantitative phase methods is its compatibility with fluorescence and with cell volume measurements. When paired with volume data, TIE enables the conversion of protein mass into the biologically significant parameters of protein concentration and intracellular water content.</div><div>This review emphasizes practical implementation, including calibration, focal plane selection, reproducibility, image size effects, strategies for artifact reduction, as well as the biological relevance of the recovered phase. We also describe an easy-to-use Fiji plugin for solving the TIE equation, eliminating the need for advanced computational tools.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"198 ","pages":"Pages 1-7"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144889890","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

Corrigendum to “The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures” [Prog. Biophys. Mol. Biol. 195 (2025) 167–191] “细胞中分子组织的主要来源”的勘误。自组织和自我调节的动态生物结构图谱”[Prog。Biophys。Mol. Biol. 195 (2025) 167-191]

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-08-01 DOI: 10.1016/j.pbiomolbio.2025.07.004

Ildefonso M. De la Fuente , Jesus M. Cortes , Iker Malaina , Gorka Pérez-Yarza , Luis Martinez , José I. López , Maria Fedetz , Jose Carrasco-Pujante

引用次数: 0

The microelectrode array technique - a crucial tool for studying excitable tissue disorders and drug testing: an update on recent advances 微电极阵列技术-研究兴奋性组织紊乱和药物测试的关键工具：最新进展。

IF 4.5 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-07-21 DOI: 10.1016/j.pbiomolbio.2025.07.005

Andrijana Angelovski , Markéta Bébarová

{"title":"The microelectrode array technique - a crucial tool for studying excitable tissue disorders and drug testing: an update on recent advances","authors":"Andrijana Angelovski , Markéta Bébarová","doi":"10.1016/j.pbiomolbio.2025.07.005","DOIUrl":"10.1016/j.pbiomolbio.2025.07.005","url":null,"abstract":"<div><div>The microelectrode array (MEA) is an electronic device composed of a varying number of microelectrodes used to detect the extracellular field potential generated by excitable tissues. This technology allows for the measurement of electrical activity without damaging the cell membrane during recording. MEA offers a better way of getting long-term recordings and observing different cellular activities than the invasive patch clamp technique. Recent research demonstrates that MEA technology enables scientists to detect both cellular and subcellular events, allowing them to study cellular properties and reactions across different experimental conditions and even to identify distinct ion currents and their impact on cellular electrophysiology. The paper reviews the historical development of MEA technology along with its modern applications for electrophysiological research. The future advancement of MEA technology will improve our knowledge about neuronal and cardiac excitability and expand its use to additional electrically active tissues, advancing research in pharmacology, neuroscience, cardiology, and other fields.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"197 ","pages":"Pages 97-107"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700292","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 protein design: Advancing biotechnology through in silico engineering 计算蛋白设计：通过计算机工程推进生物技术

IF 3.2 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-07-17 DOI: 10.1016/j.pbiomolbio.2025.07.003

Ranjit Ranbhor , Ruthvik Venkatesan , Amay Sanjay Redkar , Vibin Ramakrishnan

{"title":"Computational protein design: Advancing biotechnology through in silico engineering","authors":"Ranjit Ranbhor , Ruthvik Venkatesan , Amay Sanjay Redkar , Vibin Ramakrishnan","doi":"10.1016/j.pbiomolbio.2025.07.003","DOIUrl":"10.1016/j.pbiomolbio.2025.07.003","url":null,"abstract":"<div><div>Currently, computational protein design (CPD) is a disruptive force in biotechnology, changing the paradigm by which proteins are engineered for many applications. In this article, the evolution of CPD has been tracked from its initial forays in the late 1990s to the current advanced and sophisticated domain that it now occupies as one driven by artificial intelligence (AI). It highlights recent advancements that have extended its scope and into which broader elements including protein backbone modeling, energy functions, sampling algorithms, and techniques for sequence optimization were placed. Computer-aided protein design has thus become increasingly accurate and efficient through machine learning, quantum mechanics, and high-throughput virtual screening. In biotechnology, CPD finds applications in developing innovative therapeutics, industrial enzymes, and synthetic biomaterials. Such remarkable successes aside, however, CPD has various challenges, such as energy function, structural predictions, and computational resource requirements. Future predictions in areas such as programmable cellular systems and self-assembling protein-based materials could establish new avenues for growth. Finally, the review points out the need for multidisciplinarity and ethical considerations as well in utilizing CPD to reach its full potential for solving global issues of health, energy, and environmental sustainability. Having moved in that direction, CPD promises to open new avenues of biotechnological development that will enable the creation of proteins with functions and properties never before possible.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"197 ","pages":"Pages 75-83"},"PeriodicalIF":3.2,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144662684","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

Taurine up-regulated 1: A dual regulator in immune cell-mediated pathogenesis of human diseases 牛磺酸上调1：免疫细胞介导的人类疾病发病机制中的双重调节因子。

IF 3.2 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-07-15 DOI: 10.1016/j.pbiomolbio.2025.07.002

Xin Lan , Shuwen Zhang , Lu Yang

{"title":"Taurine up-regulated 1: A dual regulator in immune cell-mediated pathogenesis of human diseases","authors":"Xin Lan , Shuwen Zhang , Lu Yang","doi":"10.1016/j.pbiomolbio.2025.07.002","DOIUrl":"10.1016/j.pbiomolbio.2025.07.002","url":null,"abstract":"<div><div>Taurine up-regulated 1 (TUG1) is a long non-coding RNA (lncRNA) that plays a significant role in the pathogenesis of both cancer and non-cancer diseases. Recent studies have revealed its involvement in regulating the development of various diseases by modulating the activity of the body's immune cells. In non-cancer diseases, TUG1 primarily influences disease progression through the competing endogenous RNA (ceRNA) network, promoting the expression of pro-inflammatory cytokines via pathways such as the NF-κB inflammatory signaling pathway. Most research indicates that TUG1 exerts a positive regulatory effect on immune cells, including Th2 cells, M1 macrophages, and microglia. In cancer, TUG1 regulates disease progression predominantly through the ceRNA network and by modulating the activity of specific transcription factors. It fosters tumor development by promoting the establishment of immune tolerance within the tumor microenvironment. This immune tolerance is associated with TUG1's regulation of immune checkpoint molecules, which enhances the infiltration of pro-tumor immune cells (e.g., regulatory T cells, M2 macrophages, neutrophils, and dendritic cells) while suppressing the infiltration of anti-tumor immune cells, including CD8<sup>+</sup> T cells, NK cells, and M1 macrophages. In this study, we systematically evaluate the impact of abnormal TUG1 expression across various diseases, focusing on its mechanisms of action in regulating immune cell infiltration and disease progression in both cancer and non-cancer contexts. We also discuss potential targets for future research related to TUG1's role in these pathogenic processes.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"197 ","pages":"Pages 84-96"},"PeriodicalIF":3.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144661019","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

Advances and challenges in the treatment of osteosarcoma 骨肉瘤治疗的进展与挑战。

IF 3.2 3区生物学

Progress in Biophysics & Molecular Biology Pub Date : 2025-07-04 DOI: 10.1016/j.pbiomolbio.2025.07.001

Xingkai Wang , Kunpeng Zhu , Jianping Hu , Chunlin Zhang

{"title":"Advances and challenges in the treatment of osteosarcoma","authors":"Xingkai Wang , Kunpeng Zhu , Jianping Hu , Chunlin Zhang","doi":"10.1016/j.pbiomolbio.2025.07.001","DOIUrl":"10.1016/j.pbiomolbio.2025.07.001","url":null,"abstract":"<div><div>Osteosarcoma represents the greatest percentage of malignant tumors in the bone and is distinguished by its high incidence of aggressiveness, metastasis, and recurrence after therapy. At present, the treatment strategies for osteosarcoma typically encompass surgical resection, chemotherapy, targeted therapy, and radiotherapy. Even though there are now more extensive treatment options for osteosarcoma, the prognosis is still dismal, particularly for those who have metastatic osteosarcoma. Developing efficient treatment approaches therefore becomes crucial to turning things around. With the ongoing advancements in science and technology, together with the integration of research in diverse domains, more creative approaches to treating osteosarcoma have been explored in recent years. This article reviews the cutting-edge advances in osteosarcoma immunotherapy, biomedical materials, and gut microbiota in the field of osteosarcoma treatment. Ultimately, our goal is to increase the overall survival rate for patients with osteosarcoma by providing robust theoretical support for the development of innovative medications through an in-depth analysis and summary of the most recent advancements and obstacles facing osteosarcoma treatment.</div></div>","PeriodicalId":54554,"journal":{"name":"Progress in Biophysics & Molecular Biology","volume":"197 ","pages":"Pages 60-74"},"PeriodicalIF":3.2,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144576926","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