Generalized Langevin equation for a tagged monomer in a Gaussian semiflexible polymer.

In this study, we present a comprehensive analysis of the motion of a tagged monomer within a Gaussian semiflexible polymer model. We carefully derived the generalized Langevin equation (GLE) that governs the motion of a tagged central monomer. This derivation involves integrating out all the other degrees of freedom within the polymer chain, thereby yielding an effective description of the viscoelastic motion of the tagged monomer.

Exploration of drug resistance mechanisms in triple negative breast cancer cells using a microfluidic device and patient tissues.

Chemoresistance is a major cause of treatment failure in many cancers. However, the life cycle of cancer cells as they respond to and survive environmental and therapeutic stress is understudied. In this study, we utilized a microfluidic device to induce the development of doxorubicin-resistant (DOXR) cells from triple negative breast cancer (TNBC) cells within 11 days by generating gradients of DOX and medium.

3D printed fluidic swab for COVID-19 testing with improved diagnostic yield and user comfort.

The current standard method of diagnosing coronavirus disease 2019 (COVID-19) involves uncomfortable and invasive nasopharyngeal (NP) sampling using cotton swabs (CS), which can be unsuitable for self-testing. Although mid-turbinate sampling is an alternative, it has a lower diagnostic yield than NP sampling. Nasal wash (NW) has a similar diagnostic yield to NP sampling, but is cumbersome to perform.

Statistical modeling of mRNP transport in dendrites: A comparative analysis of β-actin and Arc mRNP dynamics.

Localization of messenger RNA (mRNA) in dendrites is crucial for regulating gene expression during long-term memory formation. mRNA binds to RNA-binding proteins (RBPs) to form messenger ribonucleoprotein (mRNP) complexes that are transported by motor proteins along microtubules to their target synapses. However, the dynamics by which mRNPs find their target locations in the dendrite have not been well understood.

Nonequilibrium diffusion of active particles bound to a semiflexible polymer network: Simulations and fractional Langevin equation.

In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question concerns quantitatively explaining how self-propulsion particles with directional memory diffuse in such a medium. Based on simulations and analytic theory, we address this issue with active viscoelastic systems where an active particle is connected with multiple semiflexible filaments.

A machine learning approach to discover migration modes and transition dynamics of heterogeneous dendritic cells.

Dendritic cell (DC) migration is crucial for mounting immune responses. Immature DCs (imDCs) reportedly sense infections, while mature DCs (mDCs) move quickly to lymph nodes to deliver antigens to T cells. However, their highly heterogeneous and complex innate motility remains elusive.

Fractal and Knot-Free Chromosomes Facilitate Nucleoplasmic Transport.

Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular transport, yet its characteristics remain poorly understood. Using computer simulations and scaling analysis, we show that the 3D folding and macromolecular size of the chromosomes determine their transport characteristics.

Stochastic chromatin packing of 3D mitotic chromosomes revealed by coherent X-rays.

DNA molecules are atomic-scale information storage molecules that promote reliable information transfer via fault-free repetitions of replications and transcriptions. Remarkable accuracy of compacting a few-meters-long DNA into a micrometer-scale object, and the reverse, makes the chromosome one of the most intriguing structures from both physical and biological viewpoints. However, its three-dimensional (3D) structure remains elusive with challenges in observing native structures of specimens at tens-of-nanometers resolution.

Objective comparison of methods to decode anomalous diffusion.

Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.

Inducible Prmt1 ablation in adult vascular smooth muscle leads to contractile dysfunction and aortic dissection.

Vascular smooth muscle cells (VSMCs) have remarkable plasticity in response to diverse environmental cues. Although these cells are versatile, chronic stress can trigger VSMC dysfunction, which ultimately leads to vascular diseases such as aortic aneurysm and atherosclerosis. Protein arginine methyltransferase 1 (Prmt1) is a major enzyme catalyzing asymmetric arginine dimethylation of proteins that are sources of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide synthase.

Enhanced Sensing Behavior of Three-Dimensional Microfluidic Paper-Based Analytical Devices (3D-μPADs) with Evaporation-Free Enclosed Channels for Point-of-Care Testing.

Despite the potential in fabrication of microfluidic paper-based analytical devices (μPADs) for point-of-care testing (POCT) kits, the development of simple, accurate, and rapid devices with higher sensitivity remains challenging. Here, we report a novel method for 3D-μPAD fabrication with enclosed channels using vat photopolymerization to avoid fluid evaporation. In detail, height of the enclosed channels was adjusted from 0.

Three-Dimensional Paper-Based Microfluidic Analysis Device for Simultaneous Detection of Multiple Biomarkers with a Smartphone.

Paper-based microfluidic analysis devices (μPADs) have attracted attention as a cost-effective platform for point-of-care testing (POCT), food safety, and environmental monitoring. Recently, three-dimensional (3D)-μPADs have been developed to improve the performance of μPADs. For accurate diagnosis of diseases, however, 3D-μPADs need to be developed to simultaneously detect multiple biomarkers.

Cleavage of HSP90β induced by histone deacetylase inhibitor and proteasome inhibitor modulates cell growth and apoptosis.

HSP90, one of the molecular chaperones, contributes to protein stability in most living organisms. Previously, we found cleavage of HSP90 by caspase 10 in response to treatment with histone deacetylase inhibitor or proteasome inhibitor in leukemic cell lines. In this study, we investigated this phenomenon in various cell lines and found that HSP90 was cleaved by treatment with SAHA or MG132 in 6 out of 16 solid tumor cell lines.

Anomalous diffusion of active Brownian particles cross-linked to a networked polymer: Langevin dynamics simulation and theory.

Quantitatively understanding the dynamics of an active Brownian particle (ABP) interacting with a viscoelastic polymer environment is a scientific challenge. It is intimately related to several interdisciplinary topics such as the microrheology of active colloids in a polymer matrix and the athermal dynamics of the in vivo chromosomes or cytoskeletal networks. Based on Langevin dynamics simulation and analytic theory, here we explore such a viscoelastic active system in depth using a star polymer of functionality f with the center cross-linker particle being ABP.

Correction: Immature dendritic cells navigate microscopic mazes to find tumor cells.

Correction for 'Immature dendritic cells navigate microscopic mazes to find tumor cells' by Eujin Um et al., Lab Chip, 2019, 19, 1665-1675.

Traditional and Novel Mechanisms of Heat Shock Protein 90 (HSP90) Inhibition in Cancer Chemotherapy Including HSP90 Cleavage.

HSP90 is a molecular chaperone that increases the stability of client proteins. Cancer cells show higher HSP90 expression than normal cells because many client proteins play an important role in the growth and survival of cancer cells. HSP90 inhibitors mainly bind to the ATP binding site of HSP90 and inhibit HSP90 activity, and these inhibitors can be distinguished as ansamycin and non-ansamycin depending on the structure.

Mapping the spectrum of 3D communities in human chromosome conformation capture data.

Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales.

Immature dendritic cells navigate microscopic mazes to find tumor cells.

Dendritic cells (DCs) are potent antigen-presenting cells with high sentinel ability to scan their neighborhood and to initiate an adaptive immune response. Whereas chemotactic migration of mature DCs (mDCs) towards lymph nodes is relatively well documented, the migratory behavior of immature DCs (imDCs) in tumor microenvironments is still poorly understood. Here, microfluidic systems of various geometries, including mazes, are used to investigate how the physical and chemical microenvironment influences the migration pattern of imDCs.

Fluctuations of random walks in critical random environments.

Percolation networks have been widely used in the description of porous media but are now found to be relevant to understand the motion of particles in cellular membranes or the nucleus of biological cells. Random walks on the infinite cluster at criticality of a percolation network are asymptotically ergodic. On any finite size cluster of the network stationarity is reached at finite times, depending on the cluster's size.

Asymmetric polar localization dynamics of the serine chemoreceptor protein Tsr in Escherichia coli.

The spatial location of proteins in living cells can be critical for their function. For example, the E. coli chemotaxis machinery is localized to the cell poles.

Neuronal messenger ribonucleoprotein transport follows an aging Lévy walk.

Localization of messenger ribonucleoproteins (mRNPs) plays an essential role in the regulation of gene expression for long-term memory formation and neuronal development. Knowledge concerning the nature of neuronal mRNP transport is thus crucial for understanding how mRNPs are delivered to their target synapses. Here, we report experimental and theoretical evidence that the active transport dynamics of neuronal mRNPs, which is distinct from the previously reported motor-driven transport, follows an aging Lévy walk.

Geometry controlled anomalous diffusion in random fractal geometries: looking beyond the infinite cluster.

We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion.

Superdiffusion dominates intracellular particle motion in the supercrowded cytoplasm of pathogenic Acanthamoeba castellanii.

Acanthamoebae are free-living protists and human pathogens, whose cellular functions and pathogenicity strongly depend on the transport of intracellular vesicles and granules through the cytosol. Using high-speed live cell imaging in combination with single-particle tracking analysis, we show here that the motion of endogenous intracellular particles in the size range from a few hundred nanometers to several micrometers in Acanthamoeba castellanii is strongly superdiffusive and influenced by cell locomotion, cytoskeletal elements, and myosin II. We demonstrate that cell locomotion significantly contributes to intracellular particle motion, but is clearly not the only origin of superdiffusivity.

Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.

Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation.