Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis.

Recent advances in synthetic biology have enabled the design of genetic feedback control circuits that could be implemented to build resilient plants against pathogen attacks. To facilitate the proper design of these genetic feedback control circuits, an accurate model that is able to capture the vital dynamical behaviour of the pathogen-infected plant is required. In this study, using a data-driven modelling approach, we develop and compare four dynamical models (i.

Heterogeneous Development of β-Cell Populations in Diabetes-Resistant and -Susceptible Mice.

Progressive dysfunction and failure of insulin-releasing β-cells are a hallmark of type 2 diabetes (T2D). To study mechanisms of β-cell loss in T2D, we performed islet single-cell RNA sequencing of two obese mouse strains differing in their diabetes susceptibility. With mice on a control diet, we identified six β-cell clusters with similar abundance in both strains.

Structures and mechanism of the plant PIN-FORMED auxin transporter.

Auxins are hormones that have central roles and control nearly all aspects of growth and development in plants. The proteins in the PIN-FORMED (PIN) family (also known as the auxin efflux carrier family) are key participants in this process and control auxin export from the cytosol to the extracellular space. Owing to a lack of structural and biochemical data, the molecular mechanism of PIN-mediated auxin transport is not understood.

Edible Polymers and Secondary Bioactive Compounds for Food Packaging Applications: Antimicrobial, Mechanical, and Gas Barrier Properties.

Edible polymers such as polysaccharides, proteins, and lipids are biodegradable and biocompatible materials applied as a thin layer to the surface of food or inside the package. They enhance food quality by prolonging its shelf-life and avoiding the deterioration phenomena caused by oxidation, humidity, and microbial activity. In order to improve the biopolymer performance, antimicrobial agents and plasticizers are also included in the formulation of the main compounds utilized for edible coating packages.

Advantages and Challenges of Differential Immune Cell Count Determination in Blood and Milk for Monitoring the Health and Well-Being of Dairy Cows.

A key challenge of the 21st century will be to provide the growing world population with a sustainable and secure supply of food. Consequently, the dairy farming's primary task is to lower milk losses and other inefficiencies associated with diseased cows. Moreover, a shift from curative to preventive health management would be desirable for mastitis and a wide variety of other infectious and non-infectious cattle diseases, some of which are known to have profound negative effects on the performance and well-being of cows.

Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19.

Disease recovery dynamics are often difficult to assess, as patients display heterogeneous recovery courses. To model recovery dynamics, exemplified by severe COVID-19, we apply a computational scheme on longitudinally sampled blood transcriptomes, generating recovery states, which we then link to cellular and molecular mechanisms, presenting a framework for studying the kinetics of recovery compared with non-recovery over time and long-term effects of the disease. Specifically, a decrease in mature neutrophils is the strongest cellular effect during recovery, with direct implications on disease outcome.

How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids.

Glucocorticoids (GCs) are widely used therapeutic agents to treat a broad range of inflammatory conditions. Their functional effects are elicited by binding to the glucocorticoid receptor (GR), which regulates transcription of distinct gene networks in response to ligand. However, the mechanisms governing various aspects of undesired side effects versus beneficial immunomodulation upon GR activation remain complex and incompletely understood.

Protein language-model embeddings for fast, accurate, and alignment-free protein structure prediction.

Advanced protein structure prediction requires evolutionary information from multiple sequence alignments (MSAs) from evolutionary couplings that are not always available. Artificial intelligence (AI)-based predictions inputting only single sequences are faster but so inaccurate as to render speed irrelevant. Here, we described a competitive prediction of inter-residue distances (2D structure) exclusively inputting embeddings from pre-trained protein language models (pLMs), namely ProtT5, from single sequences into a convolutional neural network (CNN) with relatively few layers.

The mosaic oat genome gives insights into a uniquely healthy cereal crop.

Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products.

Tumour cell budding and spread through air spaces in squamous cell carcinoma of the lung - Determination and validation of optimal prognostic cut-offs.

Purpose: Prognostic stratification of patients with squamous cell carcinomas of the lung (SCC-L) is challenging. Therefore, we investigated several histomorphological parameters (tumour cell budding (TCB), spread through air spaces (STAS), tumour-stroma-ratio, immune cell infiltration) which could potentially serve as prognostic parameters in SCC-L. We aimed to systematically determine optimal cut-off-values and assess the prognostic capability of these patterns.

Fluorescence Labeling of Cellulose Nanocrystals-A Facile and Green Synthesis Route.

Efficient chemical modification of cellulose nanocrystals (CNCs) by grafting commonly involves aprotic solvents, toxic reactants, harsh reaction conditions, or catalysts, which have negative effects on the particle character, reduced dispersibility and requires further purification, if products are intended for biomedical applications. This work, in contrast, presents a robust, facile, and green synthesis protocol for the grafting of an amino-reactive fluorophore like fluorescein isothiocyanate (FITC) on aqueous CNCs, combining and modifying existent approaches in a two-step procedure. Comparably high grafting yields were achieved, which were confirmed by thermogravimetry, FTIR, and photometry.

Nutritional Composition of Beach-Cast Marine Algae from the Brazilian Coast: Added Value for Algal Biomass Considered as Waste.

In some coastal areas, large quantities of beach-cast macroalgae can accumulate and are usually considered waste and disposed of. However, due to their biofunctional and nutritional properties, they have great potential as a new source of raw materials. Increasing population growth has made the search for alternative raw materials with valuable nutritional properties urgent; here, beach-cast macroalgae could provide great potential.

Earthworms as catalysts in the formation and stabilization of soil microbial necromass.

Microbial necromass is a central component of soil organic matter (SOM), whose management may be essential in mitigating atmospheric CO concentrations and climate change. Current consensus regards the magnitude of microbial necromass production to be heavily dependent on the carbon use efficiency of microorganisms, which is strongly influenced by the quality of the organic matter inputs these organisms feed on. However, recent concepts neglect agents relevant in many soils: earthworms.

Splenic Dendritic Cells and Macrophages Drive B Cells to Adopt a Plasmablast Cell Fate.

Upon encountering cognate antigen, B cells can differentiate into short-lived plasmablasts, early memory B cells or germinal center B cells. The factors that determine this fate decision are unclear. Past studies have addressed the role of B cell receptor affinity in this process, but the interplay with other cellular compartments for fate determination is less well understood.

Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer.

KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin structure alteration and transcriptional defects that could promote malignancy. Despite that KDM4 proteins are promising drug targets in cancer therapy, only a few drugs have been described as inhibitors of these enzymes, while studies on natural compounds as possible inhibitors are still needed.

From spores to fungal pellets: A new high-throughput image analysis highlights the structural development of Aspergillus niger.

Many filamentous fungi are exploited as cell factories in biotechnology. Cultivated under industrially relevant submerged conditions, filamentous fungi can adopt different macromorphologies ranging from dispersed mycelia over loose clumps to pellets. Central to the development of a pellet morphology is the agglomeration of spores after inoculation followed by spore germination and outgrowth into a pellet population, which is usually very heterogeneous.

Description and optimization of a multiplex bead-based flow cytometry method (MBFCM) to characterize extracellular vesicles in serum samples from patients with hematological malignancies.

Extracellular Vesicles (EVs) are membranous vesicles produced by all cells under physiological and pathological conditions. In hematological malignancies, tumor-derived EVs might reprogram the bone marrow environment, suppress antileukemic immunity, mediate drug resistance and interfere with immunotherapies. EVs collected from the serum of leukemic samples might correlate with disease stage, drug-/immunological resistance, or might correlate with antileukemic immunity/immune response.

T cell receptor and IL-2 signaling strength control memory CD8 T cell functional fitness via chromatin remodeling.

Cognate antigen signal controls CD8 T cell priming, expansion size and effector versus memory cell fates, but it is not known if and how it modulates the functional features of memory CD8 T cells. Here we show that the strength of T cell receptor (TCR) signaling controls the requirement for interleukin-2 (IL-2) signals to form a pool of memory CD8 T cells that competitively re-expand upon secondary antigen encounter. Combining strong TCR and intact IL-2 signaling during priming synergistically induces genome-wide chromatin accessibility in regions targeting a wide breadth of biological processes, consistent with greater T cell functional fitness.

The distribution of carbon stocks between tree woody biomass and soil differs between Scots pine and broadleaved species (beech, oak) in European forests.

Unlabelled: While the impacts of forest management options on carbon (C) storage are well documented, the way they affect C distribution among ecosystem components remains poorly investigated. Yet, partitioning of total forest C stocks, particularly between aboveground woody biomass and the soil, greatly impacts the stability of C stocks against disturbances in forest ecosystems. This study assessed the impact of species composition and stand density on C storage in aboveground woody biomass (stem + branches), coarse roots, and soil, and their partitioning in pure and mixed forests in Europe.

Isolation and Characterization of Urinary Extracellular Vesicles for MicroRNA Biomarker Signature Development with Reference to MISEV Compliance.

Urine bears high potential for serving as biomarker repository for renal and urinary tract associated disorders. Besides various metabolites and salts, urine carries extracellular vesicles (EVs)-a heterogeneous group of cell-derived mediators comprising proteins, lipids, and nucleic acids such as microRNAs (miRNAs). Particularly, EV-derived miRNA biomarkers have already been identified for numerous disorders such as sepsis, various blood and solid cancer entities, respiratory and renal diseases.

Radical Scavenging Mechanisms of Phenolic Compounds: A Quantitative Structure-Property Relationship (QSPR) Study.

Due to their antioxidant properties, secondary plant metabolites can scavenge free radicals such as reactive oxygen species and protect foods from oxidation processes. Our aim was to study structural influences, like basic structure, number of hydroxyl groups and number of Bors criteria on the outcome of the oxygen radical absorbance capacity (ORAC) assay. Furthermore, similarities and differences to other antioxidant assays were analyzed by principal component analysis.

When fat meets the gut-focus on intestinal lipid handling in metabolic health and disease.

The regular overconsumption of energy-dense foods (rich in lipids and sugars) results in elevated intestinal nutrient absorption and consequently excessive accumulation of lipids in the liver, adipose tissue, skeletal muscles, and other organs. This can eventually lead to obesity and obesity-associated diseases such as type 2 diabetes (T2D), non-alcoholic fatty liver disease (NAFLD), cardiovascular disease, and certain types of cancer, as well as aggravate inflammatory bowel disease (IBD). Therefore, targeting the pathways that regulate intestinal nutrient absorption holds significant therapeutic potential.

Epithelial Membrane Protein 1 Promotes Sensitivity to RSL3-Induced Ferroptosis and Intensifies Gefitinib Resistance in Head and Neck Cancer.

Epithelial membrane protein (EMP1), a member of the peripheral myelin protein (PMP22) family, is involved in the development of various human malignancies. However, the expression level of EMP1 and its functional role in head and neck squamous cell carcinoma (HNSCC) remain unclear to date. Ferroptosis, a newly characterized form of regulated cell death, plays an essential role in tumorigenesis.