Biophysical reviews最新文献

Biophysical Reviews: the IUPAB journal promoting biophysics on an international stage. 《生物物理评论》：IUPAB在国际舞台上推广生物物理学的期刊。

IF 4.9

Biophysical reviews Pub Date : 2025-01-03 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01266-7

Wilma K Olson

引用次数: 0

Probing living cell dynamics and molecular interactions using atomic force microscopy. 利用原子力显微镜探测活细胞动力学和分子相互作用。

IF 4.9

Biophysical reviews Pub Date : 2024-12-28 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01258-7

David Alsteens

引用次数: 0

Biophysical assays to test cellular mechanosensing: moving towards high throughput. 测试细胞机械传感的生物物理分析：迈向高通量。

IF 4.9

Biophysical reviews Pub Date : 2024-12-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01263-w

Marta Cubero-Sarabia, Anna Maria Kapetanaki, Massimo Vassalli

引用次数: 0

Hydrogel models of pancreatic adenocarcinoma to study cell mechanosensing. 胰腺癌水凝胶模型研究细胞力学传感。

IF 4.9

Biophysical reviews Pub Date : 2024-12-18 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01265-8

M Walker, J P Morton

{"title":"Hydrogel models of pancreatic adenocarcinoma to study cell mechanosensing.","authors":"M Walker, J P Morton","doi":"10.1007/s12551-024-01265-8","DOIUrl":"10.1007/s12551-024-01265-8","url":null,"abstract":"Pancreatic adenocarcinoma (PDAC) is the predominant form of pancreatic cancer and one of the leading causes of cancer-related death worldwide, with an extremely poor prognosis after diagnosis. High mortality from PDAC arises partly due to late diagnosis resulting from a lack of early-stage biomarkers and due to chemotherapeutic drug resistance, which arises from a highly fibrotic stromal response known as desmoplasia. Desmoplasia alters tissue mechanics, which triggers changes in cell mechanosensing and leads to dysregulated transcriptional activity and disease phenotypes. Hydrogels are effective in vitro models to mimic mechanical changes in tissue mechanics during PDAC progression and to study the influence of these changes on mechanosensitive cell responses. Despite the complex biophysical changes that occur within the PDAC microenvironment, carefully designed hydrogels can very closely recapitulate these properties during PDAC progression. Hydrogels are relatively inexpensive, highly reproducible and can be designed in a humanised manner to increase their relevance for human PDAC studies. In vivo models have some limitations, including species-species differences, high variability, expense and legal/ethical considerations, which make hydrogel models a promising alternative. Here, we comprehensively review recent advancements in hydrogel bioengineering for developing our fundamental understanding of mechanobiology in PDAC, which is critical for informing advanced therapeutics.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"851-870"},"PeriodicalIF":4.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Editorial to the topical issue: the 7th Nanoengineering for Mechanobiology Symposium 2024 Camogli, Genoa, Italy. 时事社论：第七届机械生物学纳米工程研讨会2024卡莫格利，热那亚，意大利。

IF 4.9

Biophysical reviews Pub Date : 2024-12-13 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01262-x

Costanza Giampietro, Aldo Ferrari, Massimo Vassalli

引用次数: 0

Correction to: Dimensional reduction and adaptation-development-evolution relation in evolved biological systems. 修正：进化生物系统中的降维与适应-发展-进化关系。

IF 4.9

Biophysical reviews Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01255-w

Kunihiko Kaneko

引用次数: 0

Tracing the birth and intrinsic disorder of loops and domains in protein evolution. 追踪蛋白质进化中环和结构域的诞生和内在紊乱。

IF 4.9

Biophysical reviews Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01251-0

Gustavo Caetano-Anollés, Fizza Mughal, M Fayez Aziz, Kelsey Caetano-Anollés

{"title":"Tracing the birth and intrinsic disorder of loops and domains in protein evolution.","authors":"Gustavo Caetano-Anollés, Fizza Mughal, M Fayez Aziz, Kelsey Caetano-Anollés","doi":"10.1007/s12551-024-01251-0","DOIUrl":"10.1007/s12551-024-01251-0","url":null,"abstract":"Protein loops and structural domains are building blocks of molecular structure. They hold evolutionary memory and are largely responsible for the many functions and processes that drive the living world. Here, we briefly review two decades of phylogenomic data-driven research focusing on the emergence and evolution of these elemental architects of protein structure. Phylogenetic trees of domains reconstructed from the proteomes of organisms belonging to all three superkingdoms and viruses were used to build chronological timelines describing the origin of each domain and its embedded loops at different levels of structural abstraction. These timelines consistently recovered six distinct evolutionary phases and a most parsimonious evolutionary progression of cellular life. The timelines also traced the birth of domain structures from loops, which allowed to model their growth ab initio with AlphaFold2. Accretion decreased the disorder of the growing molecules, suggesting disorder is molecular size-dependent. A phylogenomic survey of disorder revealed that loops and domains evolved differently. Loops were highly disordered, disorder increased early in evolution, and ordered and moderate disordered structures were derived. Gradual replacement of loops with α-helix and β-strand bracing structures over time paved the way for the dominance of more disordered loop types. In contrast, ancient domains were ordered, with disorder evolving as a benefit acquired later in evolution. These evolutionary patterns explain inverse correlations between disorder and sequence length of loops and domains. Our findings provide a deep evolutionary view of the link between structure, disorder, flexibility, and function.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"723-735"},"PeriodicalIF":4.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analyzing aptamer structure and interactions: in silico modelling and instrumental methods. 分析适体结构和相互作用：在硅建模和仪器方法。

IF 4.9

Biophysical reviews Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01252-z

Daria O Malysheva, Maya A Dymova, Vladimir A Richter

{"title":"Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.","authors":"Daria O Malysheva, Maya A Dymova, Vladimir A Richter","doi":"10.1007/s12551-024-01252-z","DOIUrl":"10.1007/s12551-024-01252-z","url":null,"abstract":"Aptamers are short oligonucleotides that bind specifically to various ligands and are characterized by their low immunogenicity, thermostability, and ease of labeling. Many biomedical applications of aptamers as biosensors and drug delivery agents are currently being actively researched. Selective affinity selection with exponential ligand enrichment (SELEX) allows to discover aptamers for a specific target, but it only provides information about the sequence of aptamers; hence other approaches are used for determining aptamer structure, aptamer-ligand interactions and the mechanism of action. The first one is in silico modelling that allows to infer likely secondary and tertiary structures and model their interactions with a ligand. The second approach is to use instrumental methods to study structure and aptamer-ligand interaction. In silico modelling and instrumental methods are complimentary and their combined use allows to eliminate some ambiguity in their respective results. This review examines both the advantages and limitations of in silico modelling and instrumental approaches currently used to study aptamers, which will allow researchers to develop optimal study designs for analyzing aptamer structure and ligand interactions.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"685-700"},"PeriodicalIF":4.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Survey of the Aβ-peptide structural diversity: molecular dynamics approaches. a - β肽结构多样性的研究：分子动力学方法。

IF 4.9

Biophysical reviews Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01253-y

Anna P Tolstova, Alexei A Adzhubei, Maria A Strelkova, Alexander A Makarov, Vladimir A Mitkevich

引用次数: 0

The dry lab microscopist or prompt microscopist: do we need them? 干式实验室显微镜师或即时显微镜师：我们需要他们吗？

IF 4.9

Biophysical reviews Pub Date : 2024-10-30 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01250-1

Filip Braet, Weidong Cai

引用次数: 0