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Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N–H stretch of DNA base pairs and the O–H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration. [ABSTRACT FROM AUTHOR]

The ability to distinguish between stochastic systems based on their trajectories is crucial in thermodynamics, chemistry, and biophysics. The Kullback–Leibler (KL) divergence, D KL A B (0 , τ) , quantifies the distinguishability between the two ensembles of length-τ trajectories from Markov processes A and B. However, evaluating D KL A B (0 , τ) from histograms of trajectories faces sufficient sampling difficulties, and no theory explicitly reveals what dynamical features contribute to the distinguishability. This work provides a general formula that decomposes D KL A B (0 , τ) in space and time for any Markov processes, arbitrarily far from equilibrium or steady state. It circumvents the sampling difficulty of evaluating D KL A B (0 , τ). Furthermore, it explicitly connects trajectory KL divergence with individual transition events and their waiting time statistics. The results provide insights into understanding distinguishability between Markov processes, leading to new theoretical frameworks for designing biological sensors and optimizing signal transduction. [ABSTRACT FROM AUTHOR]

The study of electrolytic solutions is of relevance in many research fields, ranging from biophysics, materials, and colloid science to catalysis and electrochemistry. The dependence of solution dynamics on the nature of electrolytes and their concentrations has been the subject of many experimental and computational studies, yet it remains challenging to obtain a full understanding of the factors that govern solution behavior. Here, we provide additional insights into the behavior of aqueous solutions of alkali chlorides by combining 17O relaxation data with diffusion and viscosity data and contrast their behavior with 1H nuclear magnetic resonance relaxation data. The main findings are that 17O relaxation correlates well with viscosity data but not with diffusion data, while 1H relaxation correlates with neither. Certain ionic trends match known ion-specific series behavior, especially at high concentrations. Notably, we also examine the ranges of the interactions and conclude that the majority of the effects are tied to local water reorientation dynamics. [ABSTRACT FROM AUTHOR]

Intragenic translational heterogeneity describes the variation in translation at the level of transcripts for an individual gene. A factor that contributes to this source of variation is the mRNA structure. Both the composition of the thermodynamic ensemble, i.e., the stationary distribution of mRNA structures, and the switching dynamics between those play a role. The effect of the switching dynamics on intragenic translational heterogeneity remains poorly understood. We present a stochastic translation model that accounts for mRNA structure switching and is derived from a Markov model via approximate stochastic filtering. We assess the approximation on various timescales and provide a method to quantify how mRNA structure dynamics contributes to translational heterogeneity. With our approach, we allow quantitative information on mRNA switching from biophysical experiments or coarse-grain molecular dynamics simulations of mRNA structures to be included in gene regulatory chemical reaction network models without an increase in the number of species. Thereby, our model bridges a gap between mRNA structure kinetics and gene expression models, which we hope will further improve our understanding of gene regulatory networks and facilitate genetic circuit design. [ABSTRACT FROM AUTHOR]

This document, published in the Journal of Applied Physics, discusses the importance of multiscale modeling and analysis in the field of biophysics. The authors emphasize the need for tools and analyses that integrate across physical scales and time scales in order to advance medical science. The document includes a collection of studies on various topics such as cardiac biomechanics, tissue mechanics, cerebral fluid flow, cell mechanics, protein modeling, and molecular fluorescence microscopy. The authors hope that readers will find these studies informative and inspiring. [Extracted from the article]

Spontaneous locomotion is a common feature of most metazoan cells, generally attributed to the properties of actomyosin networks. This force-producing machinery has been studied down to the most minute molecular details, especially in lamellipodium-driven migration. Nevertheless, how actomyosin networks work inside contraction-driven amoeboid cells still lacks unifying principles. Here, using stable motile blebs from HeLa cells as a model amoeboid motile system, we imaged the dynamics of the actin cortex at the single filament level and revealed the co-existence of three distinct rheological phases. We introduce "advected percolation," a process where rigidity percolation and active advection synergize, spatially organizing the actin network's mechanical properties into a minimal and generic locomotion mechanism. Expanding from our observations on simplified systems, we speculate that this model could explain, down to the single actin filament level, how amoeboid cells, such as cancer or immune cells, can propel efficiently through complex 3D environments. [Display omitted] • Actin filament density at the cell front controls bleb protrusion • A solid-like actomyosin cortex in the cell middle sterically enables cell propulsion • The material properties of amoeboid cells organize spatially by advected percolation • Stable blebs in adhesive environments can fragment into cytoplasts García-Arcos et al. propose a universal framework for amoeboid migration: actin filaments and myosin motors spatially self-organize and give rise to different material properties in different parts of the cell. A solid-like state in the actin network found in the middle of the cell enables efficient cell propulsion. [ABSTRACT FROM AUTHOR]

Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these networks can and do consume biochemical energy. How does this dissipation enable cellular behaviors forbidden in equilibrium? This open question demands quantitative models that transcend thermodynamic equilibrium. Here, we study the control of simple, ubiquitous gene regulatory networks to explore the consequences of departing equilibrium in transcription. Employing graph theory to model a set of especially common regulatory motifs, we find that dissipation unlocks nonmonotonicity and enhanced sensitivity of gene expression with respect to a transcription factor's concentration. These features allow a single transcription factor to act as both a repressor and activator at different concentrations or achieve outputs with multiple concentration regimes of locally enhanced sensitivity. We systematically dissect how energetically driving individual transitions within regulatory networks, or pairs of transitions, generates a wide range of more adjustable and sensitive phenotypic responses than in equilibrium. These results generalize to more complex regulatory scenarios, including combinatorial control by multiple transcription factors, which we relate and often find collapse to simple mathematical behaviors. Our findings quantify necessary conditions and detectable consequences of energy expenditure. These richer mathematical behaviors--feasibly accessed using biological energy budgets and rates--may empower cells to accomplish sophisticated regulation with simpler architectures than those required at equilibrium. [ABSTRACT FROM AUTHOR]

Formation of fluid-filled lumina by epithelial tissues is essential for organ development. How cells control the hydraulic and cortical forces to control lumen morphology is not well understood. Here, we quantified the mechanical role of tight junctions in lumen formation using MDCK-II cysts. We found that the paracellular ion barrier formed by claudin receptors is not required for the hydraulic inflation of a lumen. However, the depletion of the zonula occludens scaffold resulted in lumen collapse and folding of apical membranes. Combining quantitative measurements of hydrostatic lumen pressure and junctional tension with modeling enabled us to explain lumen morphologies from the pressure-tension force balance. Tight junctions promote lumen inflation by decreasing cortical tension via the inhibition of myosin. In addition, our results suggest that excess apical area contributes to lumen opening. Overall, we provide a mechanical understanding of how epithelial cells use tight junctions to modulate tissue and lumen shape. [Display omitted] • Depletion of ZO scaffold causes lumen collapse and apical membrane folding • The claudin permeability barrier is not necessary for hydraulic lumen inflation • Tight junctions promote lumen inflation by decreasing cortical tension • Lumen shape controlled by pressure-tension force balance and apical area constraints Mukenhirn et al. show that epithelial cells use tight junctions to control lumen shape, and the depletion of the tight junction scaffold leads to lumen collapse and increased cortical tension. Claudin-depleted MDCK-II cysts maintain lumen pressure and shape despite high ion permeability. [ABSTRACT FROM AUTHOR]

Objective: Anterior disc displacement (ADD) has been used to establish temporomandibular joint disorder (TMD) models. Based on whether preserve of the retrodiscal attachment, the modelling methodologies include ADD with dissecting the retrodiscal attachment (ADDwd) and ADD without dissecting the retrodiscal attachment (ADDwod). This article aims to determine which model better matches the micromechanical and microstructural progression of TMD. Methods: Through meticulous microscopic observations, the microstructure and micromechanical deformation of the TMJ discs in ADDwd and ADDwod rabbit models were compared at 2 and 20 weeks. Result: Scanning electron microscopy and transmission electron microscopy showed that collagen fibres became slenderized and straightened, collagen fibrils lost diameter and arrangement in the ADDwd group at 2 weeks. Meanwhile, nanoindentation and atomic electron microscopy showed that the micro‐ and nano‐ mechanical properties decreased dramatically. However, the ADDwod group exhibited no significant microstructure and micromechanical deformations at 2 weeks. Dissection of the retrodiscal attachment contribute in the acceleration of disease progression at the early stage, the devastating discal phenotype remained fundamentally the same within the two models at 20 weeks. Conclusion: ADDwod models, induced stable and persistent disc deformation, therefore, can better match the progression of TMD. While ADDwd models can be considered for experiments which aim to obtain advanced phenotype in a short time. [ABSTRACT FROM AUTHOR]

Colloidal matter undergoing Brownian motion serves as a model system to study various physical phenomena. Understanding the effect of external perturbation on the assembly and dynamics of "Brownian colloids" has emerged as a relevant research issue in soft matter and biological physics. Optical perturbation in the form of photonic forces and torques has added impetus to this exploration. In recent years, optothermal effects arising due to optical excitation of mesoscale matter have expanded the toolbox of light–colloidal matter interactions. In this perspective, we present an experimental viewpoint on some of the developments related to the assembly and dynamics of Brownian colloids driven by the optothermal field. Furthermore, we discuss some interesting prospects on driven colloidal matter that can have implications on soft matter physics and soft photonics. [ABSTRACT FROM AUTHOR]

Protists, an umbrella term first coined by Ernst Haeckel in 1866, are a vast collection of (primarily unicellular) eukaryotes that are "neither animals nor plants". This basic definition by exclusion has been exercised for centuries, even though recent advances have led to more rigorous taxonomic assignment of various protist groups. Pioneering comparative phylogenetic approaches have been applied to these organisms to reconstruct the deep branches of the eukaryotic tree, revealing essential clues about early eukaryotic evolution. Protists, including amoebae, flagellates, ciliates, and algae, are also vital constituents of global ecosystems, where they appear at the base of food chains, control the relative abundance of other microbes, and participate in global biogeochemical recycling. Due to their typically small size and lack of nervous systems, protists are often associated with the unfortunate label 'primitive'. Yet they exhibit remarkable behavioural sophistication and are able to feed, predate, navigate and interact with their surroundings. Unlike macroscopic animals, many protists reside in a non-intuitive physical regime where viscous forces dominate over inertia, and where they use diverse propulsion and navigation strategies. Interdisciplinary research into these cell-scale phenomena, characterised by a complex interplay of physical forces and mechanical constraints, has significantly advanced the emerging fields of active matter, microhydrodynamics, and non-equilibrium statistical physics. This primer discusses the biophysics of protist behaviour, with a focus on locomotion and feeding. I will highlight the most extensively studied principles and describe some more esoteric behaviours that have not yet been systematically explored. Kirsty Wan discusses the biophysics of protist behaviour, with a focus on locomotion and feeding, highlighting the most extensively studied principles and describing some more esoteric behaviours that have not yet been systematically explored. [ABSTRACT FROM AUTHOR]

The cytoskeleton is essential for spatial and temporal organisation of a wide range of cellular and tissue‐level processes, such as proliferation, signalling, cargo transport, migration, morphogenesis, and neuronal development. Cytoskeleton research aims to study these processes by imaging, or by locally manipulating, the dynamics and organisation of cytoskeletal proteins with high spatiotemporal resolution: which matches the capabilities of optical methods. To date, no photoresponsive microtubule‐stabilising tool has united all the features needed for a practical high‐precision reagent: a low potency and biochemically stable non‐illuminated state; then an efficient, rapid, and clean photoresponse that generates a high potency illuminated state; plus good solubility at suitable working concentrations; and efficient synthetic access. We now present CouEpo, a photocaged epothilone microtubule‐stabilising reagent that combines these needs. Its potency increases approximately 100‐fold upon irradiation by violet/blue light to reach low‐nanomolar values, allowing efficient photocontrol of microtubule dynamics in live cells, and even the generation of cellular asymmetries in microtubule architecture and cell dynamics. CouEpo is thus a high‐performance tool compound that can support high‐precision research into many microtubule‐associated processes, from biophysics to transport, cell motility, and neuronal physiology. [ABSTRACT FROM AUTHOR]

The cytoskeleton is essential for spatial and temporal organisation of a wide range of cellular and tissue‐level processes, such as proliferation, signalling, cargo transport, migration, morphogenesis, and neuronal development. Cytoskeleton research aims to study these processes by imaging, or by locally manipulating, the dynamics and organisation of cytoskeletal proteins with high spatiotemporal resolution: which matches the capabilities of optical methods. To date, no photoresponsive microtubule‐stabilising tool has united all the features needed for a practical high‐precision reagent: a low potency and biochemically stable non‐illuminated state; then an efficient, rapid, and clean photoresponse that generates a high potency illuminated state; plus good solubility at suitable working concentrations; and efficient synthetic access. We now present CouEpo, a photocaged epothilone microtubule‐stabilising reagent that combines these needs. Its potency increases approximately 100‐fold upon irradiation by violet/blue light to reach low‐nanomolar values, allowing efficient photocontrol of microtubule dynamics in live cells, and even the generation of cellular asymmetries in microtubule architecture and cell dynamics. CouEpo is thus a high‐performance tool compound that can support high‐precision research into many microtubule‐associated processes, from biophysics to transport, cell motility, and neuronal physiology. [ABSTRACT FROM AUTHOR]

Environment-sensitive probes are frequently used in spectral and multi-channel microscopy to study alterations in cell homeostasis. However, the few open-source packages available for processing of spectral images are limited in scope. Here, we present VISION, a stand-alone software based on Python for spectral analysis with improved applicability. In addition to classical intensity-based analysis, our software can batch-process multidimensional images with an advanced single-cell segmentation capability and apply userdefined mathematical operations on spectra to calculate biophysical and metabolic parameters of single cells. VISION allows for 3D and temporal mapping of properties such as membrane fluidity and mitochondrial potential. We demonstrate the broad applicability of VISION by applying it to study the effect of various drugs on cellular biophysical properties. the correlation between membrane fluidity and mitochondrial potential, protein distribution in cell--cell contacts and properties of nanodomains in cell-derived vesicles. Together with the code, we provide a graphical user interface for easy adoption. [ABSTRACT FROM AUTHOR]

Consciousness, defined as being aware of and responsive to one's surroundings, is characteristic of normal waking life and typically is lost during sleep and general anaesthesia. The traditional view of consciousness as a global brain state has evolved toward a more sophisticated interplay between global and local states, with the presence of local sleep in the awake brain and local wakefulness in the sleeping brain. However, this interplay is not clear for general anaesthesia, where loss of consciousness was recently suggested to be associated with a global state of brain‐wide synchrony that selectively involves layer 5 cortical pyramidal neurons across sensory, motor and associative areas. According to this global view, local wakefulness of layer 5 cortex should be incompatible with deep anaesthesia, a hypothesis that deserves to be scrutinised with causal manipulations. Here, we show that unilateral chemogenetic activation of layer 5 pyramidal neurons in the sensorimotor cortex of isoflurane‐anaesthetised mice induces a local state transition from slow‐wave activity to tonic firing in the transfected hemisphere. This wakefulness‐like activity dramatically disrupts layer 5 interhemispheric synchrony with mirror‐image locations in the contralateral hemisphere, but does not reduce the level of unconsciousness under deep anaesthesia, nor in the transitions to/from anaesthesia. Global layer 5 synchrony may thus be a sufficient condition for anaesthesia‐induced unconsciousness, but is not a necessary one, at least under isoflurane anaesthesia. Local wakefulness‐like activity of layer 5 cortex can be induced and maintained under deep anaesthesia, encouraging further investigation into the local vs. global aspects of anaesthesia‐induced unconsciousness. Key points: The neural correlates of consciousness have evolved from global brain states to a nuanced interplay between global and local states, evident in terms of local sleep in awake brains and local wakefulness in sleeping brains.The concept of local wakefulness remains unclear for general anaesthesia, where the loss of consciousness has been recently suggested to involve brain‐wide synchrony of layer 5 cortical neurons.We found that local wakefulness‐like activity of layer 5 cortical can be chemogenetically induced in anaesthetised mice without affecting the depth of anaesthesia or the transitions to and from unconsciousness.Global layer 5 synchrony may thus be a sufficient but not necessary feature for the unconsciousness induced by general anaesthesia.Local wakefulness‐like activity of layer 5 neurons is compatible with general anaesthesia, thus promoting further investigation into the local vs. global aspects of anaesthesia‐induced unconsciousness. [ABSTRACT FROM AUTHOR]

Understanding the mechanisms of assembly and disassembly of macromolecular structures in cells relies on solving biomolecular interactions. However, those interactions often remain unclear because tools to track molecular dynamics are not sufficiently resolved in time or space. In this study, we present a straightforward method for resolving inter‐ and intra‐molecular interactions in cell adhesive machinery, using quantum dot (QD) based Förster resonance energy transfer (FRET) nanosensors. Using a mechanosensitive protein, talin, one of the major components of focal adhesions, we are investigating the mechanosensing ability of proteins to sense and respond to mechanical stimuli. First, we quantified the distances separating talin and a giant unilamellar vesicle membrane for three talin variants. These variants differ in molecular length. Second, we investigated the mechanosensing capabilities of talin, i.e., its conformational changes due to mechanical stretching initiated by cytoskeleton contraction. Our results suggest that in early focal adhesion, talin undergoes stretching, corresponding to a decrease in the talin‐membrane distance of 2.5 nm. We demonstrate that QD‐FRET nanosensors can be applied for the sensitive quantification of mechanosensing with a sub‐nanometer accuracy. [ABSTRACT FROM AUTHOR]

Understanding the mechanisms of assembly and disassembly of macromolecular structures in cells relies on solving biomolecular interactions. However, those interactions often remain unclear because tools to track molecular dynamics are not sufficiently resolved in time or space. In this study, we present a straightforward method for resolving inter‐ and intra‐molecular interactions in cell adhesive machinery, using quantum dot (QD) based Förster resonance energy transfer (FRET) nanosensors. Using a mechanosensitive protein, talin, one of the major components of focal adhesions, we are investigating the mechanosensing ability of proteins to sense and respond to mechanical stimuli. First, we quantified the distances separating talin and a giant unilamellar vesicle membrane for three talin variants. These variants differ in molecular length. Second, we investigated the mechanosensing capabilities of talin, i.e., its conformational changes due to mechanical stretching initiated by cytoskeleton contraction. Our results suggest that in early focal adhesion, talin undergoes stretching, corresponding to a decrease in the talin‐membrane distance of 2.5 nm. We demonstrate that QD‐FRET nanosensors can be applied for the sensitive quantification of mechanosensing with a sub‐nanometer accuracy. [ABSTRACT FROM AUTHOR]

RG1 is a quadruplex‐forming sequence in the SARS‐CoV‐2 genome proposed as possible therapeutic target for COVID‐19. We demonstrate that the dominant conformation of RG1 under physiological conditions differs from the parallel quadruplex previously assumed. Through comprehensive investigations employing CD, UV, NMR, DSC, gel electrophoresis, MD simulations, in silico spectroscopy and the use of truncated RG1 sequences, we have identified this stable conformation as an RNA G‐triplex composed of two G‐triads. We believe this previously unreported RNA structure could serve as a novel therapeutic target. Our findings open new avenues for further studies on the presence and biological role of RNA G‐triplexes in vivo. [ABSTRACT FROM AUTHOR]

Much of the complexity and diversity found in nature is driven by nonlinear phenomena, and this holds true for the brain. Nonlinear dynamics theory has been successfully utilized in explaining brain functions from a biophysics standpoint, and the field of statistical physics continues to make substantial progress in understanding brain connectivity and function. This study delves into complex brain functional connectivity using biophysical nonlinear dynamics approaches. We aim to uncover hidden information in high-dimensional and nonlinear neural signals, with the hope of providing a useful tool for analyzing information transitions in functionally complex networks. By utilizing phase portraits and fuzzy recurrence plots, we investigated the latent information in the functional connectivity of complex brain networks. Our numerical experiments, which include synthetic linear dynamics neural time series and a biophysically realistic neural mass model, showed that phase portraits and fuzzy recurrence plots are highly sensitive to changes in neural dynamics and can also be used to predict functional connectivity based on structural connectivity. Furthermore, the results showed that phase trajectories of neuronal activity encode low-dimensional dynamics, and the geometric properties of the limit-cycle attractor formed by the phase portraits can be used to explain the neurodynamics. Additionally, our results showed that the phase portrait and fuzzy recurrence plots can be used as functional connectivity descriptors, and both metrics were able to capture and explain nonlinear dynamics behavior during specific cognitive tasks. In conclusion, our findings suggest that phase portraits and fuzzy recurrence plots could be highly effective as functional connectivity descriptors, providing valuable insights into nonlinear dynamics in the brain. [ABSTRACT FROM AUTHOR]

PIEZO2 is a trimeric mechanically-gated ion channel expressed by most sensory neurons in the dorsal root ganglia. Mechanosensitive PIEZO2 channels are also genetically required for normal touch sensation in both mice and humans. We previously showed that PIEZO2 channels are also strongly modulated by membrane voltage. Specifically, it is only at very positive voltages that all channels are available for opening by mechanical force. Conversely, most PIEZO2 channels are blocked at normal negative resting membrane potentials. The physiological function of this unusual biophysical property of PIEZO2 channels, however, remained unknown. We characterized the biophysical properties of three PIEZO2 ion channel mutations at an evolutionarily conserved arginine (R2756). Using genome engineering in mice we generated Piezo2 R2756H/R2756H and Piezo2 R2756K/R2756K knock-in mice to characterize the physiological consequences of altering PIEZO2 voltage sensitivity in vivo. We measured endogenous mechanosensitive currents in sensory neurons isolated from the dorsal root ganglia and characterized mechanoreceptor and nociceptor function using electrophysiology. Mice were also assessed behaviourally and morphologically. Mutations at the conserved Arginine (R2756) dramatically changed the biophysical properties of the channel relieving voltage block and lowering mechanical thresholds for channel activation. Piezo2R2756H/R2756H and Piezo2R2756K/R2756K knock-in mice that were homozygous for gain-of-function mutations were viable and were tested for sensory changes. Surprisingly, mechanosensitive currents in nociceptors, neurons that detect noxious mechanical stimuli, were substantially sensitized in Piezo2 knock-in mice, but mechanosensitive currents in most mechanoreceptors that underlie touch sensation were only mildly affected by the same mutations. Single-unit electrophysiological recordings from sensory neurons innervating the glabrous skin revealed that rapidly-adapting mechanoreceptors that innervate Meissner's corpuscles exhibited slightly decreased mechanical thresholds in Piezo2 knock-in mice. Consistent with measurements of mechanically activated currents in isolated sensory neurons essentially all cutaneous nociceptors, both fast conducting Aδ-mechanonociceptors and unmyelinated C-fibre nociceptors were substantially more sensitive to mechanical stimuli and indeed acquired receptor properties similar to ultrasensitive touch receptors in Piezo2 knock-in mice. Mechanical stimuli also induced enhanced ongoing activity in cutaneous nociceptors in Piezo2 knock-in mice and hyper-sensitive PIEZO2 channels were sufficient alone to drive ongoing activity, even in isolated nociceptive neurons. Consistently, Piezo2 knock-in mice showed substantial behavioural hypersensitivity to noxious mechanical stimuli. Our data indicate that ongoing activity and sensitization of nociceptors, phenomena commonly found in human chronic pain syndromes, can be driven by relieving the voltage-block of PIEZO2 ion channels. Indeed, membrane depolarization caused by multiple noxious stimuli may sensitize nociceptors by relieving voltage-block of PIEZO2 channels. [ABSTRACT FROM AUTHOR]

Nuclear magnetic resonance (NMR) is recognized as the gold standard method in fragment‐based drug design for screening, hit validation, and affinity determination. However, its deployment at a large scale is limited by the cost and expertise needed to implement NMR as a routine drug discovery method. The increase in the adoption of fragment‐based drug design created a need for biophysics to provide high‐quality data for weak ligand‐target interactions that can be implemented at scale. NMR must adapt its position in drug design operations to enter this new era. The recent development of commercially available benchtop NMR spectrometers in combination with hyperpolarization methods represents an opportunity for highly deployable and scalable systems. [ABSTRACT FROM AUTHOR]

Astrophysics to physical oceanography. String theory to machine learning. High energy theory to biophysics. Such leaps in research focus can be challenging—and rewarding. [ABSTRACT FROM AUTHOR]

Objective: Most individuals with lower extremity peripheral artery disease (PAD) experience symptoms other than claudication and live with undiagnosed PAD yet no tools exist to detect atypical PAD symptoms. The purpose of this study was to identify discriminating PAD symptom descriptors from a community-based sample of patients with no current diagnosis of PAD. Methods: Symptoms descriptors were obtained in a sample of 22 participants with persistent lower extremity symptoms pre/post exercise. An ankle brachial index with exercise was used to classify participants as "PAD" or "No PAD." Results: Thirteen (59%) participants had a positive ankle brachial index (<0.9, ≥20% drop postexercise, or 30 mmHg drop postexercise). Symptoms do not disappear while walking, trouble keeping up with friends/family, positive response to pain or discomfort while sitting, and pain outside of the calves and thighs were associated with a positive ankle brachial index. Conclusion: Atypical symptoms were common among study participants. Symptoms while sitting and symptoms outside of the calf and thigh were negatively associated with a positive ankle brachial index. More precise descriptions of symptom characteristics are needed to improve PAD symptom recognition. [ABSTRACT FROM AUTHOR]

Achilles tendinopathy is prevalent among Irish dancers, believed to be due to aesthetic technical requirements and high-impact landing tasks. However, the peak Achilles tendon force during Irish dancing-specific landing tasks has not been quantified. Furthermore, the influence of fatigue is unclear. This study aimed to quantify the peak Achilles tendon force during three common Irish dancing landing tasks and investigate the effects of fatigue on this force. Twelve nationally competitive Irish dancers completed the landing tasks prior to and following a fatigue protocol. A Vicon motion analysis system and AMTI force plates were used to calculate sagittal plane ankle joint kinematics during landing to estimate peak Achilles tendon force. Three independent measures (Rating-of-Fatigue scale, Flight time: Contraction during a counter movement jump and jump height during the landing trials) were used to evaluate participant fatigue between conditions. Results revealed a significant difference in peak Achilles tendon force between the three landing tasks, however, no significant difference was observed between pre- and post-fatigue. Further research is required to investigate the effects of the landing technique used in Irish Dancing on peak Achilles tendon force with the aim to reduce peak Achilles tendon force and the risk of developing Achilles tendinopathy. [ABSTRACT FROM AUTHOR]

Summary: The plant cuticle is located at the interface of the plant with the environment, thus acting as a protective barrier against biotic and abiotic external stress factors, and regulating water loss. Additionally, it modulates mechanical stresses derived from internal tissues and also from the environment. Recent advances in the understanding of the hydric, mechanical, thermal, and, to a lower extent, optical and electric properties of the cuticle, as well as their phenomenological connections and relationships are reviewed. An equilibrium based on the interaction among the different biophysical properties is essential to ensure plant growth and development. The notable variability reported in cuticle geometry, surface topography, and microchemistry affects the analysis of some biophysical properties of the cuticle. This review aimed to provide an updated view of the plant cuticle, understood as a modification of the cell wall, in order to establish the state‐of‐the‐art biophysics of the plant cuticle, and to serve as an inspiration for future research in the field. [ABSTRACT FROM AUTHOR]

AbstractNonstationary count time series characterized by features such as abrupt changes and fluctuations about the trend arise in many scientific domains including biophysics, ecology, energy, epidemiology, and social science domains. Current approaches for integer-valued time series lack the flexibility to capture local transient features while more flexible models for continuous data types are inadequate for universal applications to integer-valued responses such as settings with small counts. We present a modeling framework, the negative binomial Bayesian trend filter (NB-BTF), that offers an adaptive model-based solution to capturing multiscale features with valid integer-valued inference for trend filtering. The framework is a hierarchical Bayesian model with a dynamic global-local shrinkage process. The flexibility of the global-local process allows for the necessary local regularization while the temporal dependence induces a locally smooth trend. In simulation, the NB-BTF outperforms a number of alternative trend filtering methods. Then, we demonstrate the method on weekly power outage frequency in Massachusetts townships. Power outage frequency is characterized by a persistent low level trend with occasional spikes. These illustrations show the estimation of a smooth, nonstationary trend with adequate uncertainty quantification. [ABSTRACT FROM AUTHOR]

Biofilm formation by Staphylococcus aureus is a major challenge in clinical settings due to its role in persistent infections. The AgrA protein, a key regulator in biofilm development, is a promising target for therapeutic intervention. This study investigates the antibiofilm potential of halogenated phenazine compounds by targeting AgrA and explores their molecular interactions to provide insights for drug development. We employed molecular docking, molecular dynamics simulations, and computational mutagenesis to evaluate the binding of halogenated phenazine compounds (C1 to C7, HP, and HP‐14) to AgrA. Binding free energy analysis was performed to assess the affinity of these compounds for the AgrA‐DNA complex. Additionally, the impact of these compounds on AgrA's structural conformation and salt bridge interactions was examined. The binding‐free energy analysis revealed that all compounds enhance binding affinity compared to the Apo form of AgrA, which has a ΔGbind of −80.75 kcal/mol. The strongest binding affinities were observed with compounds C7 (−113.84 kcal/mol), HP‐14 (−115.23 kcal/mol), and HP (−112.28 kcal/mol), highlighting their effectiveness. Molecular dynamics simulations demonstrated that these compounds bind at the hydrophobic cleft of AgrA, disrupting essential salt bridge interactions between His174‐Glu163 and His174‐Glu226. This disruption led to structural conformational changes and reduced DNA binding affinity, aligning with experimental findings on biofilm inhibition. The halogenated phenazine compounds effectively inhibit biofilm formation by targeting AgrA, disrupting its DNA‐binding function. The study supports the potential of these compounds as antibiofilm agents and provides a foundation for rational drug design targeting the AgrA‐DNA interaction. Future research should focus on further optimizing these lead compounds and exploring additional active sites on AgrA to develop novel treatments for biofilm‐associated infections. [ABSTRACT FROM AUTHOR]

In this Voices article, we introduce seven impressive young group leaders that presented their work at the recent Gordon Research Conference "Biophysics and biology of intrinsically disordered proteins" in Les Diablerets, Switzerland. We asked them to tell us more about their careers and their fascinating research on proteins that do not adopt a single-folded structure. [Display omitted] [ABSTRACT FROM AUTHOR]

Quantum sensors find applications ranging from material science to biophysics. Nitrogen‐vacancy (NV) center in diamond has been successfully implemented for measuring various types of signals. Optical NV center readout, routinely used in confocal microscopes, allows achieving high spatial resolution down to the diffraction limit. This work describes in detail the combined confocal‐atomic‐force microscope (confocal‐AFM), which takes advantage of sharp AFM cantilevers, and shows its possible applications for nanoscale resolution. It demonstrates the sub‐diffractional localization of NV centers with platinum‐coated cantilevers and the ability to separately address optically unresolved sensors using cantilevers with ferromagnetic coating. The presented setup exhibits a lateral resolution of 13 nm, providing a tool for nanoscale quantum sensing. [ABSTRACT FROM AUTHOR]

Precise measurement of magnetic fields is essential for various applications, such as fundamental physics, space exploration, and biophysics. Although recent progress in quantum engineering has assisted in creating advanced quantum magnetometers, there are still ongoing challenges in improving their efficiency and noise resistance. This study focuses on using symmetric graph state resources for quantum magnetometry to enhance measurement precision by analyzing the estimation theory under time-homogeneous and time-inhomogeneous noise models. The results show a significant improvement in estimating both single and multiple Larmor frequencies. In single Larmor frequency estimation, the quantum Fisher information spans a spectrum from the standard quantum limit to the Heisenberg limit within a periodic range of the Larmor frequency, and in the case of multiple Larmor frequencies, it can exceed the standard quantum limit for both noisy cases. This study highlights the potential of graph state-based methods for improving magnetic field measurements under noisy environments. [ABSTRACT FROM AUTHOR]

Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shapes, relative locations, movement, and interactions of cells in space. Spatial technologies that collect genomic or epigenomic data while preserving spatial information have begun to overcome these limitations. These new data promise a deeper understanding of the factors that affect cellular behavior, and in particular the ability to directly test existing theories about cell state and variation in the context of morphology, location, motility, and signaling that could not be tested before. Rapid advancements in resolution, ease-of-use, and scale of spatial genomics technologies to address these questions also require an updated toolkit of statistical methods with which to interrogate these data. We present a framework to respond to this new avenue of research: four open biological questions that can now be answered using spatial genomics data paired with methods for analysis. We outline spatial data modalities for each open question that may yield specific insights, discuss how conflicting theories may be tested by comparing the data to conceptual models of biological behavior, and highlight statistical and machine learning-based tools that may prove particularly helpful to recover biological understanding. [ABSTRACT FROM AUTHOR]

The origin of life, being one of the most fascinating questions in science, is increasingly addressed by interdisciplinary research. In addition to developing plausible chemical models for synthesizing the first biomolecules from prebiotic building blocks, searching for suitable and plausible non‐equilibrium boundary conditions that drive such reactions is thus a central task in this endeavor. This perspective highlights the remarkably simple yet versatile scenario of heat flows in geologically plausible crack‐like compartments as a habitat for prebiotic chemistry. Based on our recent findings, it is discussed how thermophoretically driven systems offer insights into solving key milestones in the origin of life research, such as the template inhibition problem, prebiotic symmetry breaking, and the promotion of prebiotic chemistry by selective enrichment of biochemical precursors. Our results on molecular‐selective thermogravitational accumulation, heat flow‐induced pH gradients, and environmental cycles are put in the context of other approaches to non‐equilibrium systems and prebiotic chemistry. The coupling of heat flows to chemical and physical boundary conditions thus opens up numerous future experimental research avenues, such as the extraction of phosphate from geomaterials or the integration of chemical reaction networks into thermal non‐equilibrium systems, offering a promising framework for advancing the field of prebiotic chemistry. [ABSTRACT FROM AUTHOR]

Synthetic cells can advance immunotherapy, offering innovative approaches to understanding and enhancing immune responses. This review article delves into the advancements and potential of synthetic cell technologies in immunology, emphasizing their role in understanding and manipulating immune functions. Recent progress in understanding vertebrate immune systems and the challenges posed by diseases highlight the need for innovative research methods, complementing the analysis of multidimensional datasets and genetic engineering. Synthetic immune cell engineering aims to simplify the complexity of immunological systems by reconstructing them in a controlled setting. This approach, alongside high‐throughput strategies, facilitates systematic investigations into immunity and the development of novel treatments. The article reviews synthetic cell technologies, focusing on their alignment with the three laws of immunity: universality, tolerance, and appropriateness. It explores the integration of synthetic cell modules to mimic processes such as controlled T‐cell activation, bacteria engulfment and elimination, or cellular maturation into desirable phenotypes. Together, such advancements expand the toolbox for understanding and manipulating immune functions. Synthetic cell technologies stand at the innovation crossroads in immunology, promising to illuminate fundamental immune system principles and open new avenues for research and therapy. [ABSTRACT FROM AUTHOR]

The migrasome, an organelle recently discovered in migrating cells, facilitates intercellular communication and plays crucial roles in various physiological and pathological conditions. The formation of migrasomes is governed by a tightly regulated process that progresses through three distinct stages: nucleation, maturation, and expansion. This process is regulated by essential molecules such as sphingomyelin lsynthase 2 (SMS2), phosphatidylinositol-4-phosphate 5-kinase type I α (PIP5K1α), integrins, and tetraspanins. The formation of migrasomes is propelled by the assembly of membrane microdomains, driven by the dynamic interaction between biochemical reactions and the physical properties of the membrane at migrasome formation sites. Migrasomes, newly identified organelles, play crucial roles in intercellular communication, contributing to organ development and angiogenesis. These vesicles, forming on retraction fibers of migrating cells, showcase a sophisticated architecture. Recent research reveals that migrasome biogenesis is a complicated and highly regulated process. This review summarizes the mechanisms governing migrasome formation, proposing a model in which biogenesis is understood through the lens of membrane microdomain assembly. It underscores the critical interplay between biochemistry and biophysics. The biogenesis unfolds in three distinct stages: nucleation, maturation, and expansion, each characterized by unique morphological, biochemical, and biophysical features. We also explore the broader implications of migrasome research in membrane biology and outline key unanswered questions that represent important directions for future investigation. [ABSTRACT FROM AUTHOR]

Mechanotransduction, which is the integration of mechanical signals from the external environment of a cell to changes in intracellular signaling, governs many cellular functions. Recent studies have shown that the mechanical state of the cell is also coupled to the cellular circadian clock. To investigate possible interactions between circadian rhythms and cellular mechanotransduction, we have developed a computational model that integrates the two pathways. We postulated that translocation of the transcriptional regulators MRTF (herein referring to both MRTF-A and MRTF-B), YAP and TAZ (also known as YAP1 and WWTR1, respectively; collectively denoted YAP/TAZ) into the nucleus leads to altered expression of circadian proteins. Simulations from our model predict that lower levels of cytoskeletal activity are associated with longer circadian oscillation periods and higher oscillation amplitudes, which is consistent with recent experimental observations. Furthermore, accumulation of YAP/TAZ and MRTF in the nucleus causes circadian oscillations to decay in our model. These effects hold both at the single-cell level and within a population-level framework. Finally, we investigated the effects of mutations in YAP or lamin A, the latter of which result in a class of diseases known as laminopathies. In silico, oscillations in circadian proteins are substantially weaker in populations of cells with mutations in YAP or lamin A, suggesting that defects in mechanotransduction can disrupt the circadian clock in certain disease states; however, reducing substrate stiffness in the model restores normal oscillatory behavior, suggesting a possible compensatory mechanism. Thus, our study identifies that mechanotransduction could be a potent modulatory cue for cellular clocks and that this crosstalk can be leveraged to rescue the circadian clock in disease states. [ABSTRACT FROM AUTHOR]

Objective: This study was planned to determine the reliability, validity, and applicability of the isolated hamstring flexibility test (IHFT). Design: A cohort study (diagnosis); level of evidence, 2. Setting: It was performed in the research and application laboratory. Participants: Seventy-five individuals aged 18 to 25 years, selected through simple probability random sampling, with a normal Beighton Horan and Joint Mobility Index scores, and who volunteered to participate, were included for evaluation. Interventions: On then first and third days, participants underwent muscle strength, sit-and-reach test, active knee extension test, IHFT for validity and reliability. Stretching exercises were prescribed as a home program for 31 patients with limited knee extension, and measurements were repeated at the end of the eighth week. Main outcomemeasures: Sit-and-reach test, active knee extension test, IHFT. Results: The test-retest reliability was high (intraclass correlation coefficient, 0.993). Our test demonstrated validity when compared in terms of flexibility gained. A significant difference was found between pre-post stretching exercise training in all 3 tests (P, 0.05). Conclusion: It was observed that the IHFT is reliable and applicable in determining hamstring flexibility. Given the absence of another test specifically measuring hamstring flexibility in isolation, its indirect validity was established through analysis with other tests using the gold standard for assessing gains in hamstring flexibility. [ABSTRACT FROM AUTHOR]

To compare the changes in outcomes of balance and postural control after balance training exercise and gaze stability exercise in the elderly population with fall risk. After the screening process, 44 subjects were randomized into three groups: Experimental Group A (Balance training exercises, BTE); Experimental Group B (Gaze stability exercises, GSE), and Control Group C (Fall prevention education only). The outcome measures were center of pressure (COP) range, COP sway, reaction time, proprioception, static balance, Clinical Test for Sensory Interaction in Balance (CTSIB), and Short Falls Efficacy Scale (SFES). The pre and post-data were recorded at baseline and after 8 weeks. The normality of the distribution was assessed using the Shapiro-Wilk test. Demographic data and baseline measures were compared using one-way ANOVA considering group as between factor and mixed model ANOVA was used to find out the group effect and time effect and time × group interaction effect. Statistical significance was indicated if p ≤ 0.05. GSE had significant changes only in CTSIB 4 whereas BTE had significant changes in CTSIB 4, 5, and 6. COP range showed a significant time effect in the front direction (p = 0.02). For proprioception, there was a significant time effect in the left (p = 0.018) and right direction (p = 0.005), whereas changes in front and back directions were found to be insignificant. SFES showed a significant time effect (p < 0.001), group effect (p = 0.21), and time × group interaction effect (p < 0.001). Balance training exercises may be a more effective form of intervention to improve balance and postural control in the elderly population. [ABSTRACT FROM AUTHOR]

BACKGROUND: People with forward head posture (FHP) and rounded shoulder posture (RSP) may experience shifts in scapular position and alterations in the strength of the muscles surrounding the scapula. Therefore, a reliable scapula position and scapula muscle strength test are required to identified scapula problem and provided appropriate intervention programs. OBJECTIVE: This study aimed to determine the reliability of scapular position measurements obtained using a modified digital inclinometer and palpation meter, as well as muscle strength using a hand-held dynamometer (HHD) in individuals with FHP and RSP. METHODS: Thirty healthy subjects underwent scapular position tests (upward rotation, anterior tilt, depression, and protraction) and strength tests of periscapular muscles (serratus anterior, upper trapezius, middle trapezius, and lower trapezius) on both the dominant and non-dominant sides. The reliability of the measurements was confirmed by computing the intraclass correlation coefficient (ICC), standard error of measurement (SEM), and minimal clinically important difference (MCID). Test and re-tests were conducted over a period of one week and actual values for each measurement were also obtained and assessed. RESULTS: The ICC ranged from 0.802 to 0.935 for the scapular position tests and from 0.808 to 0.949 for muscle strength tests on the dominant and non-dominant sides. For scapular position tests, SEM values ranged from 0.3 cm to 0.6 cm (protraction and depression), from 1.0∘ to 1.7∘ (upward rotation and anterior tilt) and MCID values ranged from 0.7 cm to 1.6 cm (protraction and depression), from 2.8∘ to 4.7∘ (upward rotation and anterior tilt). Regarding muscle strength tests, SEM and MCID values were in the range 14.4N–27.3N and 39.9N–75.7N, respectively. CONCLUSIONS: Scapular position and periscapular muscle strength can be reproducibly measured in healthy subjects individuals with FHP and RSP. These instruments can hence be recommended for evaluating these functional traits in subjects with FHP and RSP. [ABSTRACT FROM AUTHOR]

Context: Excessive hip adduction and internal rotation are abnormal movements that may lead to the onset and progression of patellofemoral pain. Previous studies have reported that lower dynamic frontal plane hip joint stiffness in the gait of women is associated with the magnitude of hip adduction and internal rotation angles. However, the factors contributing to the lack of dynamic frontal plane hip joint stiffness in the gait of young women are unclear. This study aims to investigate the factors affecting dynamic frontal plane hip joint stiffness during the weight-acceptance phase of the gait of healthy young women. Design: Cross-sectional study. Methods: This study included 30 healthy women between the ages of 18 and 30 years. The pelvic width/femur length ratio was calculated by dividing the pelvic width by the femur length. Data on hip kinematics and kinetics and activation of the gluteus maximus and medius, tensor fasciae latae, and adductor longus muscles during gait were collected using a motion capture system, force plates, and surface electromyography. Stepwise multiple regression analysis was conducted to determine the extent to which each independent factor affected dynamic frontal plane hip joint stiffness. Results: In healthy young women, decreased dynamic frontal plane hip joint stiffness was associated with decreased muscle activity of the gluteus maximus during the gait, as well as greater pelvic width/femur length ratio. Conclusions: Women with a relatively great pelvic width relative to femur length may have more difficulty in producing dynamic frontal plane hip joint stiffness. However, increasing the muscle activity of the gluteus maximus may contribute to increased dynamic frontal plane hip joint stiffness. [ABSTRACT FROM AUTHOR]

Trapping diffusive particles at surfaces is a key step in many systems in chemical and biological physics. Trapping often occurs via reactive patches on the surface and/or the particle. The theory of boundary homogenization has been used in many prior works to estimate the effective trapping rate for such a system in the case that either (i) the surface is patchy and the particle is uniformly reactive or (ii) the particle is patchy and the surface is uniformly reactive. In this paper, we estimate the trapping rate for the case that the surface and the particle are both patchy. In particular, the particle diffuses translationally and rotationally and reacts with the surface when a patch on the particle contacts a patch on the surface. We first formulate a stochastic model and derive a five-dimensional partial differential equation describing the reaction time. We then use matched asymptotic analysis to derive the effective trapping rate, assuming that the patches are roughly evenly distributed and occupy a small fraction of the surface and the particle. This trapping rate involves the electrostatic capacitance of a four-dimensional duocylinder, which we compute using a kinetic Monte Carlo algorithm. We further use Brownian local time theory to derive a simple heuristic estimate of the trapping rate and show that it is remarkably close to the asymptotic estimate. Finally, we develop a kinetic Monte Carlo algorithm to simulate the full stochastic system and then use these simulations to confirm the accuracy of our trapping rate estimates and homogenization theory. [ABSTRACT FROM AUTHOR]

G protein‐coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, photons, food tastants and odorants, and are renowned drug targets. Advancements in structural biology techniques, including X‐ray crystallography and cryo‐electron microscopy (cryo‐EM), have driven the elucidation of an increasing number of GPCR structures. These structures reveal novel features that shed light on receptor activation, dimerization and oligomerization, dichotomy between orthosteric and allosteric modulation, and the intricate interactions underlying signal transduction, providing insights into diverse ligand‐binding modes and signalling pathways. However, a substantial portion of the GPCR repertoire and their activation states remain structurally unexplored. Future efforts should prioritize capturing the full structural diversity of GPCRs across multiple dimensions. To do so, the integration of structural biology with biophysical and computational techniques will be essential. We describe in this review the progress of nuclear magnetic resonance (NMR) to examine GPCR plasticity and conformational dynamics, of atomic force microscopy (AFM) to explore the spatial–temporal dynamics and kinetic aspects of GPCRs, and the recent breakthroughs in artificial intelligence for protein structure prediction to characterize the structures of the entire GPCRome. In summary, the journey through GPCR structural biology provided in this review illustrates how far we have come in decoding these essential proteins architecture and function. Looking ahead, integrating cutting‐edge biophysics and computational tools offers a path to navigating the GPCR structural landscape, ultimately advancing GPCR‐based applications. [ABSTRACT FROM AUTHOR]

Proper vertebrae formation relies on a tissue-wide oscillator called the segmentation clock. Individual cellular oscillators in the presomitic mesoderm are modulated by intercellular coupling and external signals, leading to the propagation of oscillatory waves of genetic expression eventually stabilizing into a static pattern. Here, we review 4 decades of biophysical models of this process, starting from the pioneering Clock and Wavefront model by Cooke and Zeeman, and the reaction–diffusion model by Meinhardt. We discuss how modern descriptions followed advances in molecular description and visualization of the process, reviewing phase models, delayed models, systems-level, and finally geometric models. We connect models to high-level aspects of embryonic development from embryonic scaling to wave propagation, up to reconstructed stem cell systems. We provide new analytical calculations and insights into classical and recent models, leading us to propose a geometric description of somitogenesis organized along two primary waves of differentiation. [ABSTRACT FROM AUTHOR]

How complex 3D tissue shape emerges during animal development remains an important open question in biology and biophysics. Here, we discover a mechanism for 3D epithelial shape change based on active, in-plane cellular events that is analogous to inanimate "shape programmable" materials, which undergo blueprinted 3D shape transformations from in-plane gradients of spontaneous strains. We study eversion of the Drosophila wing disc pouch, when the epithelium transforms from a dome into a curved fold, quantifying 3D tissue shape changes and mapping spatial patterns of cellular behaviors on the evolving geometry using cellular topology. Using a physical model inspired by shape programming, we find that active cell rearrangements are the major contributor to pouch eversion and validate this conclusion using a knockdown of MyoVI, which reduces rearrangements and disrupts morphogenesis. This work shows that shape programming is a mechanism for animal tissue morphogenesis and suggests that patterns in nature could present design strategies for shape-programmable materials. [ABSTRACT FROM AUTHOR]

Infections that are acquired due to a prolonged hospital stay and manifest 2 days following the admission of a patient to a health-care institution can be classified as hospital-acquired infections. Klebsiella pneumoniae (K. pneumoniae) has become a critical pathogen, posing serious concern globally due to the rising incidences of hypervirulent and carbapenem-resistant strains. Glutaredoxin is a redox protein that protects cells from oxidative stress as it associates with glutathione to reduce mixed disulfides. Protein adenylyltransferase (PrAT) is a pseudokinase with a proposed mechanism of transferring an AMP group from ATP to glutaredoxin. Inducing oxidative stress to the bacterium by inhibiting the activity of PrAT is a promising approach to combating its contribution to hospital-acquired infections. Thus, this study aims to overexpress, purify, and analyse the effects of ATP and Mg2+ binding to Klebsiella pneumoniae PrAT (KpPrAT). The pET expression system and nickel affinity chromatography were effective in expressing and purifying KpPrAT. Far-UV CD spectroscopy demonstrates that the protein is predominantly α-helical, even in the presence of Mg2+. Extrinsic fluorescence spectroscopy with ANS indicates the presence of a hydrophobic pocket in the presence of ATP and Mg2+, while mant-ATP studies allude to the potential nucleotide binding ability of KpPrAT. The presence of Mg2+ increases the thermostability of the protein. Isothermal titration calorimetry provides insight into the binding affinity and thermodynamic parameters associated with the binding of ATP to KpPrAT, with or without Mg2+. Conclusively, the presence of Mg2+ induces a conformation in KpPrAT that favours nucleotide binding. [ABSTRACT FROM AUTHOR]

The Arrhenius energy of activation of unfolding Ea unfolding and Gibbs free energy of unfolding ΔG unfolding have been calculated utilizing DSC differential scanning calorimetry for 4 mAbs (1 biosimilar) in 3 formulations. DSC derived ΔTm melting temperature changes for each mAb domain (CH2, Fab, CH3) at calorimetric scan rates at 60 °C, 90 °C, 150 °C and 200 °C / hr. were utilized to calculate the kinetic Ea unfolding. The DSC derived Ea trend with observed aggregate formation and can be used to predict%HMW formation post 9-month storage at 5 °C and 40 °C for all formulations analyzed. Additionally, thermodynamic ΔG unfolding energies were also derived (Tm, ΔCp and ΔH measurements) for each mAb at every scan rate to observe scan rate dependence of ΔG and for extrapolation to 0 °C/hr. (to report ΔG at true equilibrium conditions). Both derived thermodynamic ΔG and kinetic Ea energies were combined to build full energetic landscapes for mAb unfolding and aggregation. Statistical multivariate analysis of kinetic (Ea CH2, Ea Fab, Ea CH3) energies, thermodynamic (ΔG 5 ° C and ΔG 40 ° C) energies and in-silico modeled surface properties was also performed. Analysis revealed key significant parameters contributing to aggregation. These parameters were utilized to build predictive aggregation models for 25 mg/mL mAb formulations stored 9-months at 5 °C and 40 °C. [ABSTRACT FROM AUTHOR]

Purpose: Tear fluid gained attention as a representative biological fluid. Its simple and non-invasive collection methods as well as richness of candidate biomarkers made it a potential diagnostic tool for different diseases such as dry eye. Synchronous fluorescence spectroscopy is a highly sensitive analytical tool that results in narrowing and enhanced peak resolution, and has a potential role in disease diagnosis, biomarker identification, and therapeutic monitoring. We applied synchronous fluorescence spectroscopy to monitor variations of tear fluid composition during the development of dry eye disease and to evaluate the potential effects of phytotherapy. Methods: Dry eye model was induced in Chinchilla rabbits by instillation of 1% atropine sulfate ophthalmic solution. Then, the tear fluid was collected at 3, 7, and 14 days and subjected to synchronous fluorescence spectroscopy. Phytotherapy was achieved by topical instillation of 20 µl of water extracts of pomegranate peel or green tea powders. Results: The fluorescence results revealed changes in the structure of tear fluid over time and the eye is subjected to toxification due to oxidative stress. In addition, dry eye disease was found to affect the metabolic/energetic state of the eye. On the other hand, phytotherapy led to enhancement of the metabolic/biosynthesis state due to activation of flavin adenine dinucleotide-associated proteins. Conclusion: There was change in the electrical conductivity of tear fluid proteins. In the case of dry eyes, they became electrical insulators, while in the case of treatment with extracts, their electrical conductivity properties improved. The effects of phytotherapy can be related to the high content of ellagic acid and anthocyanin of pomegranate extract, while in green tea, they are related to catechins and phenolic compounds. [ABSTRACT FROM AUTHOR]

Molecular docking has become an essential part of a structural biologist's and medicinal chemist's toolkits. Given a chemical compound and the three-dimensional structure of a molecular target—for example, a protein—docking methods fit the compound into the target, predicting the compound's bound structure and binding energy. Docking can be used to discover novel ligands for a target by screening large virtual compound libraries. Docking can also provide a useful starting point for structure-based ligand optimization or for investigating a ligand's mechanism of action. Advances in computational methods, including both physics-based and machine learning approaches, as well as in complementary experimental techniques, are making docking an even more powerful tool. We review how docking works and how it can drive drug discovery and biological research. We also describe its current limitations and ongoing efforts to overcome them. [ABSTRACT FROM AUTHOR]

Background: There is growing interest in the development of objective methods for assessing lip‐closing function in children. Objective: To obtain normative data for healthy children in the developmental stages of lip closure function, we quantitatively evaluated oral movements associated with lip closure in children and adults using a composite sensor (CS). Methods: Twenty‐five normal children (11 boys, 14 girls) aged 8.8 ± 1.6 years and 25 young adults (13 men, 12 women) aged 27.4 ± 3.9 years were asked to perform test movements, maximal lip closure and swallowing of 3 mL of water. Lip‐closing pressure (LP), intraoral baro‐pressure (IP) and electromyographic (EMG) activity of the upper orbicularis oris muscle were simultaneously recorded using the CS. Results: EMG activity of the upper orbicularis oris muscle during closure was significantly greater in adults than in children. There were significant positive correlations between integral values of LP and EMG for closure in adults (r =.527, p =.008) but not in children, and significant positive correlations between integral values of LP and IP for swallowing in children (r =.508, p =.010) but not in adults. Conclusions: The CS may provide an effective tool for evaluating lip function in children acquiring oral function. For the combination of maxillary orbicularis oculus contraction and formation of intraoral negative pressure, EMG activity of the upper orbicularis oris muscle involvement in LP and IP involvement in LP may differ between children and adults. [ABSTRACT FROM AUTHOR]

Large cells often rely on cytoplasmic flows for intracellular transport, maintaining homeostasis, and positioning cellular components. Understanding the mechanisms of these flows is essential for gaining insights into cell function, developmental processes, and evolutionary adaptability. Here, we focus on a class of self-organized cytoplasmic stirring mechanisms that result from fluid--structure interactions between cytoskeletal elements at the cell cortex. Drawing inspiration from streaming flows in late-stage fruit fly oocytes, we propose an analytically tractable active carpet theory. This model deciphers the origins and three-dimensional spatiotemporal organization of such flows. Through a combination of simulations and weakly nonlinear theory, we establish the pathway of the streaming flow to its global attractor: a cell-spanning vortical twister. Our study reveals the inherent symmetries of this emergent flow, its low-dimensional structure, and illustrates how complex fluid--structure interaction aligns with classical solutions in Stokes flow. This framework can be easily adapted to elucidate a broad spectrum of self-organized, cortex-driven intracellular flows. [ABSTRACT FROM AUTHOR]

Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has lagged behind. Active particle-based methods, which typically excel at this, suffer from large density fluctuations that affect the dynamics of inclusions. To this end, we advance the Active-Nematic Multi-Particle Collision Dynamics algorithm, a particle-based method for simulating active nematics, by addressing the large density fluctuations that arise from activity. This paper introduces three activity formulations that mitigate the coupling between activity and local density. Local density fluctuations are decreased to a level comparable to the passive limit while retaining active nematic phenomenology and increasing the active turbulence regime four-fold in two dimensions. These developments extend the technique into a flexible tool for modeling active systems, including solutes and inclusions, with broad applications for the study of biophysical systems. Particle-based models of soft active matter are known to exhibit large density fluctuations, which may be problematic for considering homogeneous systems. Through considering the coupling of activity to local density, we reduce density fluctuations while retaining active turbulent dynamics. [ABSTRACT FROM AUTHOR]