Use of Steered Molecular Dynamics to Explore the Conformational Changes of SNARE Proteins.

Steered Molecular Dynamics (SMD) simulation is a powerful computational simulation technique that enables the controlled manipulation of molecular systems by applying external forces. This method is frequently utilized to investigate the slow processes of biomolecular systems that occur within sub-second to second time scales, achieved through SMD simulations that only span nanoseconds. SMD simulation can be utilized to study the detailed mechanism of protein conformational changes, protein unfolding, and ligand dissociation, etc.

Inferring structure of cortical neuronal networks from activity data: A statistical physics approach.

Understanding the relation between cortical neuronal network structure and neuronal activity is a fundamental unresolved question in neuroscience, with implications to our understanding of the mechanism by which neuronal networks evolve over time, spontaneously or under stimulation. It requires a method for inferring the structure and composition of a network from neuronal activities. Tracking the evolution of networks and their changing functionality will provide invaluable insight into the occurrence of plasticity and the underlying learning process.

Molecular and cellular dynamics of the developing human neocortex.

The development of the human neocortex is highly dynamic, involving complex cellular trajectories controlled by gene regulation. Here we collected paired single-nucleus chromatin accessibility and transcriptome data from 38 human neocortical samples encompassing both the prefrontal cortex and the primary visual cortex. These samples span five main developmental stages, ranging from the first trimester to adolescence.

Osteoarthritis synovium as a nidus for monosodium urate crystal deposition inducing severe gout studied by label-free stimulated Raman scattering combined with synovial organoids.

Gout, a common chronic disease, is characterized by the formation and deposition of monosodium urate (MSU) crystal deposition in articular and nonarticular structures. Osteoarthritis (OA), the most prevalent type of arthritis, is a progressive degenerative joint disease. Previous clinical studies have reported that gout frequently affects OA joints; however, the underlying mechanism remains unidentified.

Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses.

All matter must obey the general laws of physics and living matter is not an exception. Viruses have not only learnt how to cope with them but have managed to use them for their own survival. In this chapter, we will review some of the exciting physics that are behind viruses and discuss simple physical models that can shed some light on different aspects of the viral life cycle and viral properties.

Mechanisms of alignment of lamellar-forming block copolymer under shear flow.

The potential applications of block copolymer thin films, utilising their self-assembly capabilities, are enhanced when achieving long-range ordering. In this study we explain the experimental alignment of lamellae under shear flow findings [S. Pujari , 2012, , 5258] and classify the alignment mechanisms based on shear rate and segregation, uncovering similarities to the systems subjected to electric fields, suggesting a common pathway of lamellae orientations.

Tile by tile: capturing the evolutionary mosaic of human conditions.

The collection of Homo sapiens anatomical hallmarks hypothesized to support the 'human condition' did not appear at one specific time and place, but gradually, creating a reticulate evolutionary trajectory. The recent reconstruction of migration patterns and gene flows across different hominin species and populations draws a mosaic that we contend can be illuminated by genomic comparisons and specific experiments. Here, we first review key discoveries that could allow this experimental endeavor by describing recent advances in a variety of fields, stressing the importance of charting the current human neurodiversity as an interpretive substrate for evolutionary changes.

Detection of germline CNVs from gene panel data: benchmarking the state of the art.

Germline copy number variants (CNVs) play a significant role in hereditary diseases. However, the accurate detection of CNVs from targeted next-generation sequencing (NGS) gene panel data remains a challenging task. Several tools for calling CNVs within this context have been published to date, but the available benchmarks suffer from limitations, including testing on simulated data, testing on small datasets, and testing a small subset of published tools.

Enhanced Imbibition in Liquid-Infused Coated Microchannels.

Spontaneous capillary imbibition has the potential to improve the performance of many micro and nanodevices since it does not require an external energy source to drive a fluid flow. Despite this advantage, controlling and reducing the friction exerted by the channel walls, which limits the speed of the liquid, remains a challenge. Here, we demonstrate experimentally that infusing the walls of a channel with a liquid lubricant substantially speeds up the imbibition process and reduces the overall viscous friction.

Crowding effects on the structure and rheology of ultrasoft PNIPAM-PEGMA copolymer microgels.

We investigate the link between the internal microstructure of poly(-isopropylacrylamide)-poly(ethylene glycol) methyl ether methacrylate (PNIPAM-PEGMA) microgels, their bulk moduli and the rheological response and structural arrangement in dense suspensions. The low degree of crosslinking combined with the increased hydrophilicity induced by the presence of PEGMA results in a diffuse, star-like density profile of the particle and very low values of the bulk modulus in dilute conditions, as determined by small angle neutron scattering (SANS). The ultrasoft nature of the particle is reflected in the changes of the structural arrangement in dense suspensions, which evidence a strong deswelling and a sharp rise of the bulk modulus at moderate packing fractions.

Collective motion of energy depot active disks.

In the present work we have studied collectives of active disks with an energy depot, moving in the two-dimensional plane and interacting an excluded volume. The energy depot accounts for the extraction of energy taking place at the level of each particle in order to perform self-propulsion, included in an underdamped Langevin dynamics. We show that this model undergoes a flocking transition, exhibiting some of the key features of the Vicsek model, namely, band formation and giant number fluctuations.

Body mass index at birth and early life and colorectal cancer: A two-sample Mendelian randomization analysis in European and East Asian genetic similarity populations.

Background: Varying obesogenic inherited predisposition in early to later life may differentially impact colorectal cancer (CRC) development. Previous Mendelian randomization (MR) studies, conducted in populations of European genetic similarity, have not observed any significant associations between early life body weight with CRC risk. However, it remains unclear whether body mass index (BMI) at different early lifetime points is causally related with CRC risk in both Europeans and East Asian populations.

Molecular insights into AGS3's role in spindle orientation: a biochemical perspective.

The intrinsic regulation of spindle orientation during asymmetric cell division depends on the evolutionarily conserved protein complex LGN (Pins)/NuMA (Mud)/Gα⋅GDP. While the role of LGN and its Drosophila orthologue Pins is well-established, the function of AGS3, the paralogue of LGN, in spindle orientation during cell division remains controversial. This study substantiates the contentious nature of AGS3's function through systematic biochemical characterizations.

The alveolar trill is perceived as jagged/rough by speakers of different languagesa).

Typological research shows that across languages, trilled [r] sounds are more common in adjectives describing rough as opposed to smooth surfaces. In this study, this lexical research is built on with an experiment with speakers of 28 different languages from 12 different families. Participants were presented with images of a jagged and a straight line and imagined running their finger along each.

Thermodynamics of the Fredrickson-Andersen model on the Bethe lattice.

The statics of the Fredrickson-Andersen model (FAM) of the liquid-glass transition is solved on the Bethe lattice (BL). The kinetic constraints of the FAM imply on the BL an ergodicity-breaking transition to a (glassy) phase where a fraction of spins of the system is permanently blocked, and the remaining "free" spins become nontrivially correlated. We compute several observables of the ergodicity-broken phase, such as the self-overlap, the configurational entropy, and the spin-glass susceptibility, and we compare the analytical predictions with numerical experiments.

Functional brain hubs are related to age: A primer study with rs-fMRI.

Background/objective: Research on the ontogenetic development of brain networks using resting state has shown to be useful for understanding age-associated changes in brain connectivity. This work aimed to analyze the relationship between brain connectivity, age and intelligence.

Methods: A sample of 26 children and adolescents between 6 and 18 years of both sexes underwent a resting-state functional magnetic resonance imaging study.

Photocatalytic Magnetic Microgyroscopes with Activity-Tunable Precessional Dynamics.

Magnetic nano/microrotors are passive elements spinning around an axis due to an external rotating field while remaining confined to a plane. They have been used to date in different applications related to fluid mixing, drug delivery, or biomedicine. Here we realize an active version of a magnetic microgyroscope which is simultaneously driven by a photoactivated catalytic reaction and a rotating magnetic field.

Exploring the Chemopreventive Effect of Medication on Gene Expression Linked to Colorectal Cancer: An Observational and Mendelian Randomization Analysis in Healthy Colon Mucosa.

Gene expression appears altered in apparently normal tissue surrounding tumor tissue. The observed biological alterations in the tumor microenvironment play a crucial role in cancer development and are named the cancer field effect (FE). A robust set of overexpressed FE genes in tissue surrounding colorectal cancer (CRC) tumor were identified in previous studies.

Enhancement of the Elastocaloric Performance of Natural Rubber by Forced Air Convection.

We study the enhancement of the elastocaloric effect in natural rubber by using forced air convection to favour heat extraction during the elongation stage of a stretching-unstretching cycle. Elastocaloric performance is quantified by means of the adiabatic undercooling that occurs after fast removal of the stress, measured by infrared thermography. To ensure accuracy, spatial averaging on thermal maps of the sample surface is performed since undercooled samples display heterogeneities caused by various factors.

AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg transporters.

The CNNM/CorC Mg transporters are widely conserved in eukaryotes (cyclin M [CNNM]) and prokaryotes (CorC) and participate in various biological processes. Previous structural analyses of the CorC transmembrane domain in the Mg-bound inward-facing conformation revealed the conserved Mg recognition mechanism in the CNNM/CorC family; however, the conformational dynamics in the Mg transport cycle remain unclear because structures in other conformations are unknown. Here, we used AlphaFold structure prediction to predict the occluded-like and outward-facing-like conformations of the CorC and CNNM proteins and identified conserved hydrophilic interactions close to the cytoplasmic side in these conformations.

Molecular mechanisms at the basis of the protective effect exerted by EPPS on neurodegeneration induced by prefibrillar amyloid oligomers.

It has been shown recently, without an explanation of the possible molecular mechanisms involved, that 4-(2-hydroxyethyl)-1-piperazinepropanesulphonic (EPPS) acid effectively protects from the neurotoxicity induced by oligomers and plaques formed by the protein amyloid-β protein. Here we report the same protective effect, obtained in vitro (HT22-diff cell line) and ex vivo (hippocampal slices) models, against amyloid neurotoxicity induced by oligomers of salmon Calcitonin (sCT), which has been shown to be a good model for the study of neurodegenerative diseases. Based on biophysical studies focusing on the protein aggregation kinetic and the interaction of the aggregates with model membranes, we propose a possible molecular mechanism underlying the protective effects.

Alien Rainbow Trout in the Balkhash Basin (Kazakhstan, Central Asia): 50 Years of Naturalization.

Rainbow trout, or mykiss (), is one of the most popular species used in aquaculture and has been naturalized worldwide, including in the Central Asian Balkhash basin, which has unique aboriginal fish fauna. Both rainbow trout from European farms and wild mykiss from Kamchatka were introduced to some mountain lakes and rivers of the Balkhash basin about 50 years ago. This study investigates the current distribution and life history traits of the alien species and its possible impact on the local fish fauna.