Enhancing Micropipette Aspiration with Artificial-Intelligence Analysis
Biophys J. 2024 Apr 10:S0006-3495(24)00250-9. doi: 10.1016/j.bpj.2024.04.006. Online ahead of print.ABSTRACTThe micropipette aspiration technique is commonly used in the field of mechanobiology, offering a variety of measurement types. To extract biophysical parameters from the experiments, numerical analysis is required. Although previous works have developed techniques for the partial automation of this analyses, these approaches are relatively time-consuming for the researchers. In this article we describe the development and application of an artificial-intelligence tool for the completely-automatic analysis of micropi...
Source: Biophysical Journal - April 11, 2024 Category: Physics Authors: Aldo Abarca-Ortega Blanca Gonz ález-Bermúdez Gustavo R Plaza Source Type: research
Solving stochastic gene expression models using queueing theory: a tutorial review
Biophys J. 2024 Apr 8:S0006-3495(24)00248-0. doi: 10.1016/j.bpj.2024.04.004. Online ahead of print.ABSTRACTStochastic models of gene expression are typically formulated using the chemical master equation, which can be solved exactly or approximately using a repertoire of analytical methods. Here, we provide a tutorial review of an alternative approach based on queueing theory that has rarely been used in the literature of gene expression. We discuss the interpretation of six types of infinite server queues from the angle of stochastic single-cell biology and provide analytical expressions for the stationary and non-station...
Source: Biophysical Journal - April 10, 2024 Category: Physics Authors: Juraj Szavits-Nossan Ramon Grima Source Type: research
Solving stochastic gene expression models using queueing theory: a tutorial review
Biophys J. 2024 Apr 8:S0006-3495(24)00248-0. doi: 10.1016/j.bpj.2024.04.004. Online ahead of print.ABSTRACTStochastic models of gene expression are typically formulated using the chemical master equation, which can be solved exactly or approximately using a repertoire of analytical methods. Here, we provide a tutorial review of an alternative approach based on queueing theory that has rarely been used in the literature of gene expression. We discuss the interpretation of six types of infinite server queues from the angle of stochastic single-cell biology and provide analytical expressions for the stationary and non-station...
Source: Biophysical Journal - April 10, 2024 Category: Physics Authors: Juraj Szavits-Nossan Ramon Grima Source Type: research
How Much Does TRPV1 Deviate from An Ideal MWC-Type Protein
Biophys J. 2024 Apr 6:S0006-3495(24)00249-2. doi: 10.1016/j.bpj.2024.04.005. Online ahead of print.ABSTRACTMany ion channels are known to behave as an allosteric protein, coupling environmental stimuli captured by specialized sensing domains to the opening of a central pore. The classic Monod-Wyman-Changeux (MWC) model, originally proposed to describe binding of gas molecules to hemoglobin, has been widely used as a framework for analyzing ion channel gating. Here we address the issue of how accurate the MWC model predicts activation of the capsaicin receptor TRPV1 by vanilloids. Taking advantage of a concatemeric design t...
Source: Biophysical Journal - April 7, 2024 Category: Physics Authors: Shisheng Li Jie Zheng Source Type: research
How Much Does TRPV1 Deviate from An Ideal MWC-Type Protein
Biophys J. 2024 Apr 6:S0006-3495(24)00249-2. doi: 10.1016/j.bpj.2024.04.005. Online ahead of print.ABSTRACTMany ion channels are known to behave as an allosteric protein, coupling environmental stimuli captured by specialized sensing domains to the opening of a central pore. The classic Monod-Wyman-Changeux (MWC) model, originally proposed to describe binding of gas molecules to hemoglobin, has been widely used as a framework for analyzing ion channel gating. Here we address the issue of how accurate the MWC model predicts activation of the capsaicin receptor TRPV1 by vanilloids. Taking advantage of a concatemeric design t...
Source: Biophysical Journal - April 7, 2024 Category: Physics Authors: Shisheng Li Jie Zheng Source Type: research
How Much Does TRPV1 Deviate from An Ideal MWC-Type Protein
Biophys J. 2024 Apr 6:S0006-3495(24)00249-2. doi: 10.1016/j.bpj.2024.04.005. Online ahead of print.ABSTRACTMany ion channels are known to behave as an allosteric protein, coupling environmental stimuli captured by specialized sensing domains to the opening of a central pore. The classic Monod-Wyman-Changeux (MWC) model, originally proposed to describe binding of gas molecules to hemoglobin, has been widely used as a framework for analyzing ion channel gating. Here we address the issue of how accurate the MWC model predicts activation of the capsaicin receptor TRPV1 by vanilloids. Taking advantage of a concatemeric design t...
Source: Biophysical Journal - April 7, 2024 Category: Physics Authors: Shisheng Li Jie Zheng Source Type: research
Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos
Biophys J. 2024 Apr 3:S0006-3495(24)00243-1. doi: 10.1016/j.bpj.2024.03.041. Online ahead of print.ABSTRACTEarly embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell division timing and the subsequent, mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo, without breaking its eggshell. Compressing embryos to about 2/3 of their unperturbed diameter only resulted in m...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Vincent Borne Matthias Weiss Source Type: research
Base Pair Dynamics, Electrostatics, and Thermodynamics at the LTR-III Quadruplex:Duplex Junction
Biophys J. 2024 Apr 3:S0006-3495(24)00244-3. doi: 10.1016/j.bpj.2024.03.042. Online ahead of print.ABSTRACTG-quadruplexes (GQs) play key regulatory roles within the human genome and have also been identified to play similar roles in other eukaryotes, bacteria, archaea, and viruses. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immunodeficiency syndrome (AIDS), can form two GQs in its long terminal repeat (LTR) promoter region, each of which act to regulate viral gene expression in opposing manners. The major LTR GQ, called LTR-III, is a distinct hybrid GQ containing a 12-nucleotide duplex loop a...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Haley M Michel Justin A Lemkul Source Type: research
AI in Cellular Engineering and Reprogramming
Biophys J. 2024 Apr 4:S0006-3495(24)00245-5. doi: 10.1016/j.bpj.2024.04.001. Online ahead of print.ABSTRACTDuring the last decade, Artificial Intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of ...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Sara Capponi Shangying Wang Source Type: research
Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos
Biophys J. 2024 Apr 3:S0006-3495(24)00243-1. doi: 10.1016/j.bpj.2024.03.041. Online ahead of print.ABSTRACTEarly embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell division timing and the subsequent, mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo, without breaking its eggshell. Compressing embryos to about 2/3 of their unperturbed diameter only resulted in m...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Vincent Borne Matthias Weiss Source Type: research
Base Pair Dynamics, Electrostatics, and Thermodynamics at the LTR-III Quadruplex:Duplex Junction
Biophys J. 2024 Apr 3:S0006-3495(24)00244-3. doi: 10.1016/j.bpj.2024.03.042. Online ahead of print.ABSTRACTG-quadruplexes (GQs) play key regulatory roles within the human genome and have also been identified to play similar roles in other eukaryotes, bacteria, archaea, and viruses. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immunodeficiency syndrome (AIDS), can form two GQs in its long terminal repeat (LTR) promoter region, each of which act to regulate viral gene expression in opposing manners. The major LTR GQ, called LTR-III, is a distinct hybrid GQ containing a 12-nucleotide duplex loop a...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Haley M Michel Justin A Lemkul Source Type: research
AI in Cellular Engineering and Reprogramming
Biophys J. 2024 Apr 4:S0006-3495(24)00245-5. doi: 10.1016/j.bpj.2024.04.001. Online ahead of print.ABSTRACTDuring the last decade, Artificial Intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of ...
Source: Biophysical Journal - April 5, 2024 Category: Physics Authors: Sara Capponi Shangying Wang Source Type: research
The rotamer of the second sphere histidine in AA9 Lytic polysaccharide monooxygenase is pH-dependent
Biophys J. 2024 Apr 2:S0006-3495(24)00246-7. doi: 10.1016/j.bpj.2024.04.002. Online ahead of print.ABSTRACTLytic polysaccharides monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH dependent conformation of a second sphere histidine (His) that we call the "stacking histidine", which is conserved in fungal AA9 LPMOs, and is speculated to assist catalysis in several of ...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Ingvild Isaksen Suvamay Jana Christina M Payne Bastien Bissaro Åsmund K Røhr Source Type: research
Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning
Biophys J. 2024 Apr 2:S0006-3495(24)00247-9. doi: 10.1016/j.bpj.2024.04.003. Online ahead of print.ABSTRACTConformational dynamics of RNA plays crucial for variety of cellular functions including acting as regulators of gene expression to being molecular scaffolds and sensors. The liquid-liquid phase separation of RNAs and the formation of stress granules partly relies on RNA's conformational plasticity and its ability to engage in multivalent interactions. Recent experiments with homopolymeric and low-complexity RNAs have revealed significant differences in phase separations due to differences in base chemistry of RNA uni...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Vysakh Ramachandran Davit A Potoyan Source Type: research
The rotamer of the second sphere histidine in AA9 Lytic polysaccharide monooxygenase is pH-dependent
Biophys J. 2024 Apr 2:S0006-3495(24)00246-7. doi: 10.1016/j.bpj.2024.04.002. Online ahead of print.ABSTRACTLytic polysaccharides monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH dependent conformation of a second sphere histidine (His) that we call the "stacking histidine", which is conserved in fungal AA9 LPMOs, and is speculated to assist catalysis in several of ...
Source: Biophysical Journal - April 4, 2024 Category: Physics Authors: Ingvild Isaksen Suvamay Jana Christina M Payne Bastien Bissaro Åsmund K Røhr Source Type: research
