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Annual Review of Biophysics May 2022Biophysics is a way of approaching biological problems through numbers, physical laws, models, and quantitative logic. In a long scientific career, I have seen the... (Review)
Review
Biophysics is a way of approaching biological problems through numbers, physical laws, models, and quantitative logic. In a long scientific career, I have seen the formation and fruition of the ion channel concept through biophysical study. Marvelous discoveries were made as our instruments evolved from vacuum tubes to transistors; computers evolved from the size of an entire building to a few chips inside our instruments; and genome sequencing, gene expression, and atom-level structural biology became accessible to all laboratories. Science is rewarding and exhilarating.
Topics: Biophysical Phenomena; Biophysics; Ion Channels
PubMed: 34932910
DOI: 10.1146/annurev-biophys-120121-074034 -
Biophysical Journal Mar 2023The formation of biomolecular condensates has emerged as a new biophysical principle for subcellular compartmentalization within cells to facilitate the spatiotemporal...
The formation of biomolecular condensates has emerged as a new biophysical principle for subcellular compartmentalization within cells to facilitate the spatiotemporal regulation of a multitude of complex biomolecular reactions. In this Research Highlight, we summarize the findings that were published in Biophysical Journal during the past two years (2021 and 2022). These papers provided biophysical insights into the formation of biomolecular condensates via phase separation of proteins with or without nucleic acids.
Topics: Biomolecular Condensates; Biophysics; Nucleic Acids
PubMed: 36791720
DOI: 10.1016/j.bpj.2023.02.002 -
Biophysical Journal Apr 2023
Topics: Biophysics; Biophysical Phenomena
PubMed: 36990087
DOI: 10.1016/j.bpj.2023.03.025 -
Expert Opinion on Drug Discovery Sep 2017There are many challenges to the drug discovery process, including the complexity of the target, its interactions, and how these factors play a role in causing the... (Review)
Review
There are many challenges to the drug discovery process, including the complexity of the target, its interactions, and how these factors play a role in causing the disease. Traditionally, biophysics has been used for hit validation and chemical lead optimization. With its increased throughput and sensitivity, biophysics is now being applied earlier in this process to empower target characterization and hit finding. Areas covered: In this article, the authors provide an overview of how biophysics can be utilized to assess the quality of the reagents used in screening assays, to validate potential tool compounds, to test the integrity of screening assays, and to create follow-up strategies for compound characterization. They also briefly discuss the utilization of different biophysical methods in hit validation to help avoid the resource consuming pitfalls caused by the lack of hit overlap between biophysical methods. Expert opinion: The use of biophysics early on in the drug discovery process has proven crucial to identifying and characterizing targets of complex nature. It also has enabled the identification and classification of small molecules which interact in an allosteric or covalent manner with the target. By applying biophysics in this manner and at the early stages of this process, the chances of finding chemical leads with novel mechanisms of action are increased. In the future, focused screens with biophysics as a primary readout will become increasingly common.
Topics: Biophysics; Drug Design; Drug Discovery; High-Throughput Screening Assays; Humans; Pharmaceutical Preparations
PubMed: 28658992
DOI: 10.1080/17460441.2017.1349096 -
European Biophysics Journal : EBJ Jul 2019Recent decades brought a revolution to biology, driven mainly by exponentially increasing amounts of data coming from "'omics" sciences. To handle these data,... (Review)
Review
Recent decades brought a revolution to biology, driven mainly by exponentially increasing amounts of data coming from "'omics" sciences. To handle these data, bioinformatics often has to combine biologically heterogeneous signals, for which methods from statistics and engineering (e.g. machine learning) are often used. While such an approach is sometimes necessary, it effectively treats the underlying biological processes as a black box. Similarly, systems biology deals with inherently complex systems, characterized by a large number of degrees of freedom, and interactions that are highly non-linear. To deal with this complexity, the underlying physical interactions are often (over)simplified, such as in Boolean modelling of network dynamics. In this review, we argue for the utility of applying a biophysical approach in bioinformatics and systems biology, including discussion of two examples from our research which address sequence analysis and understanding intracellular gene expression dynamics.
Topics: Biophysics; Gene Expression Regulation; Proteomics; Sequence Analysis, DNA; Systems Biology
PubMed: 30972433
DOI: 10.1007/s00249-019-01366-3 -
Biophysical Journal Jul 2023
Topics: Computers; Biophysics; Biophysical Phenomena
PubMed: 37419113
DOI: 10.1016/j.bpj.2023.06.017 -
Biophysical Journal Oct 2020
Topics: Biophysical Phenomena; Biophysics; Calcium
PubMed: 33031740
DOI: 10.1016/j.bpj.2020.09.032 -
Biochimica Et Biophysica Acta. Proteins... Nov 2017
Topics: Animals; Biomedical Research; Biophysics; Canada; Humans
PubMed: 29031794
DOI: 10.1016/j.bbapap.2017.10.002 -
Psychological Bulletin May 1965
Review
Topics: Behavior; Biophysical Phenomena; Biophysics; Bradycardia; Central Nervous System; Cerebral Cortex; Conditioning, Psychological; Electrophysiology; Humans; Infrared Rays; Magnetic Phenomena; Magnetics; Parapsychology; Perception; Radiation; Touch
PubMed: 14298209
DOI: 10.1037/h0021698 -
Wiley Interdisciplinary Reviews.... 2010Stem cells are defined by their ability to self-renew and to differentiate into one or more mature lineages, and they reside within natural niches in many types of adult... (Review)
Review
Stem cells are defined by their ability to self-renew and to differentiate into one or more mature lineages, and they reside within natural niches in many types of adult and embryonic tissues that present them with complex signals to regulate these two hallmark properties. The diverse nature of these in vivo microenvironments raises important questions about the microenvironmental cues regulating stem cell plasticity, and the stem cell field has built a strong foundation of knowledge on the biochemical identities and regulatory effects of the soluble, cellular, and extracellular matrix factors surrounding stem cells through the isolation and culture of stem cells in vitro within microenvironments that, in effect, emulate the properties of the natural niche. Recent work, however, has expanded the field's perspective to include biophysical and dynamic characteristics of the microenvironment. These include biomechanical characteristics such as elastic modulus, shear force, and cyclic strain; architectural properties such as geometry, topography, and dimensionality; and dynamic structures and ligand profiles. We will review how these microenvironmental characteristics have been shown to regulate stem cell fate and discuss future research directions that may help expand our current understanding of stem cell biology and aid its application to regenerative medicine.
Topics: Adult; Animals; Biomechanical Phenomena; Biophysics; Cell Culture Techniques; Environment; Humans; Kinetics; Models, Biological; Stem Cells; Tissue Engineering
PubMed: 20836010
DOI: 10.1002/wsbm.46