Alignment and Nonlinear Elasticity in Biopolymer Gels

We present a Landau type theory for the non-linear elasticity of biopolymer gels with a part of the order parameter describing induced nematic order of fibers in the gel. We attribute the non-linear elastic behavior of these materials to fiber alignment induced by strain. We suggest an application to contact guidance of cell motility in tissue. We compare our theory to simulation of a disordered lattice model for biopolymers. We treat homogeneous deformations such as simple shear, hydrostatic expansion, and simple extension, and obtain good agreement between theory and simulation. We also consider a localized perturbation which is a simple model for a contracting cell in a medium.Comment: 5 pages, 4 Figure

Normal stress anisotropy and marginal stability in athermal elastic networks

Hydrogels of semiflexible biopolymers such as collagen have been shown to contract axially under shear strain, in contrast to the axial dilation observed for most elastic materials. Recent work has shown that this behavior can be understood in terms of the porous, two-component nature and consequent time-dependent compressibility of hydrogels. The apparent normal stress measured by a torsional rheometer reflects only the tensile contribution of the axial component $\sigma_{zz}$ on long (compressible) timescales, crossing over to the first normal stress difference, $N_1 = \sigma_{xx}-\sigma_{zz}$ at short (incompressible) times. While the behavior of $N_1$ is well understood for isotropic viscoelastic materials undergoing affine shear deformation, biopolymer networks are often anisotropic and deform nonaffinely. Here, we numerically study the normal stresses that arise under shear in subisostatic, athermal semiflexible polymer networks. We show that such systems exhibit strong deviations from affine behavior and that these anomalies are controlled by a rigidity transition as a function of strain

Modeling delayed processes in biological systems

Delayed processes are ubiquitous in biological systems and are often characterized by delay differential equations (DDEs) and their extension to include stochastic effects. DDEs do not explicitly incorporate intermediate states associated with a delayed process but instead use an estimated average delay time. In an effort to examine the validity of this approach, we study systems with significant delays by explicitly incorporating intermediate steps. We show by that such explicit models often yield significantly different equilibrium distributions and transition times as compared to DDEs with deterministic delay values. Additionally, different explicit models with qualitatively different dynamics can give rise to the same DDEs revealing important ambiguities. We also show that DDE-based predictions of oscillatory behavior may fail for the corresponding explicit model

Alchemical and structural distribution based representation for improved QML

We introduce a representation of any atom in any chemical environment for the generation of efficient quantum machine learning (QML) models of common electronic ground-state properties. The representation is based on scaled distribution functions explicitly accounting for elemental and structural degrees of freedom. Resulting QML models afford very favorable learning curves for properties of out-of-sample systems including organic molecules, non-covalently bonded protein side-chains, (H$_2$O)$_{40}$-clusters, as well as diverse crystals. The elemental components help to lower the learning curves, and, through interpolation across the periodic table, even enable "alchemical extrapolation" to covalent bonding between elements not part of training, as evinced for single, double, and triple bonds among main-group elements

RACIPE: a computational tool for modeling gene regulatory circuits using randomization.

BACKGROUND: One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental data and/or educated guesses, which can be time-consuming and error-prone, especially for large networks. RESULTS: We present a user-friendly computational tool for the community to use our newly developed method named random circuit perturbation (RACIPE), to explore the robust dynamical features of gene regulatory circuits without the requirement of detailed kinetic parameters. Taking the network topology as the only input, RACIPE generates an ensemble of circuit models with distinct randomized parameters and uniquely identifies robust dynamical properties by statistical analysis. Here, we discuss the implementation of the software and the statistical analysis methods of RACIPE-generated data to identify robust gene expression patterns and the functions of genes and regulatory links. Finally, we apply the tool on coupled toggle-switch circuits and a published circuit of B-lymphopoiesis. CONCLUSIONS: We expect our new computational tool to contribute to a more comprehensive and unbiased understanding of mechanisms underlying gene regulatory networks. RACIPE is a free open source software distributed under (Apache 2.0) license and can be downloaded from GitHub ( https://github.com/simonhb1990/RACIPE-1.0 )

Prevalence and risk factors of hepatitis C among former blood donors in rural China

SummaryBackgroundIllegal commercial plasma and blood donation activities in the late 1980s and early 1990s caused a large number of hepatitis C virus (HCV) infections in rural areas of China.MethodsA cross-sectional survey was carried out in 2008, in which all residents in a former blood donation village in rural Hebei Province were invited for a questionnaire interview and testing for HCV antibodies. Questionnaires were administered to collect information about their personal status and commercial blood donation history, and HCV antibodies were tested by enzyme immunoassay.ResultsOf 520 villagers who participated in the interviews, 236 (45.4%) reported a history of selling whole blood or plasma. HCV seropositivity was confirmed in 148/520 (28.5%) interviewees and 101/236 (42.8%) former commercial plasma and blood donors. Selling plasma was the strongest independent predictor of HCV seropositivity (p=0.0037). Past history of an operation was also independently associated with HCV infection (p=0.0270).ConclusionsUnsafe practices during illegal plasma donation led to a high risk of HCV seropositivity for donors during the late 1980s and early 1990s. Many infected people suffered chronic hepatitis from that time onwards and urgently needed treatment and care

Insights into midgut cell types and their crucial role in antiviral immunity in the lepidopteran model Bombyx mori

The midgut, a vital component of the digestive system in arthropods, serves as an interface between ingested food and the insect’s physiology, playing a pivotal role in nutrient absorption and immune defense mechanisms. Distinct cell types, including columnar, enteroendocrine, goblet and regenerative cells, comprise the midgut in insects and contribute to its robust immune response. Enterocytes/columnar cells, the primary absorptive cells, facilitate the immune response through enzyme secretions, while regenerative cells play a crucial role in maintaining midgut integrity by continuously replenishing damaged cells and maintaining the continuity of the immune defense. The peritrophic membrane is vital to the insect’s innate immunity, shielding the midgut from pathogens and abrasive food particles. Midgut juice, a mixture of digestive enzymes and antimicrobial factors, further contributes to the insect’s immune defense, helping the insect to combat invading pathogens and regulate the midgut microbial community. The cutting-edge single-cell transcriptomics also unveiled previously unrecognized subpopulations within the insect midgut cells and elucidated the striking similarities between the gastrointestinal tracts of insects and higher mammals. Understanding the intricate interplay between midgut cell types provides valuable insights into insect immunity. This review provides a solid foundation for unraveling the complex roles of the midgut, not only in digestion but also in immunity. Moreover, this review will discuss the novel immune strategies led by the midgut employed by insects to combat invading pathogens, ultimately contributing to the broader understanding of insect physiology and defense mechanisms

Genome-Wide Characterization of Endogenous Retroviruses in Bombyx mori Reveals the Relatives and Activity of env Genes

Endogenous retroviruses (ERVs) are retroviral sequences that remain fixed in the host genome, where they could play an important role. Some ERVs have been identified in insects and proven to have infectious properties. However, no information is available regarding Bombyx mori ERVs (BmERVs) to date. Here, we systematically identified 256 potential BmERVs in the silkworm genome via a whole-genome approach. BmERVs were relatively evenly distributed across each of the chromosomes and accounted for about 25% of the silkworm genome. All BmERVs were classified as young ERVs, with insertion times estimated to be less than 10 million years. Seven BmERVs possessing the env genes were identified. With the exception of the Orf133 Helicoverpa armigera nuclear polyhedrosis virus, the env sequences of BmERVs were distantly related to genes encoding F (Fa and Fb) and GP64 proteins from Group I and Group II NPVs. In addition, only the amino acid sequence of the BmERV-21 envelope protein shared a similar putative furin-like cleavage site and fusion peptide with Group II baculoviruses. All of the env genes in the seven BmERVs were verified to exist in the genome and be expressed in the midgut and fat bodies, which suggest that BmERVs might play an important role in the host biology