Assessing Extracellular Vesicle-Host Interaction Using a Microfluidic Platform with Caco-2 Spheroides-on-Chip.

is a foodborne pathogen that adheres to and invades the epithelial cells of the human intestinal tract. The extracellular vesicles (EVs) of have an important impact during pathogenicity, but their role in invasion of host intestinal epithelial cells remains largely unknown. models lack the complexity of tissue and fail to accurately replicate the dynamic interactions between EVs and human intestinal epithelial cells, while animal infection models have species-specific differences that limit their translational relevance and are associated with ethical concerns.

The Microbial Anti-Inflammatory Molecule (MAM) is a key protein processed and exported to envelope.

MAM (Microbial-Anti-Inflammatory Molecule) is a key effector protein with anti-inflammatory properties in , a critical human gut microbiota species. Despite its importance, MAM function and molecular features remain poorly understood. This study elucidates MAM's physiological importance by examining its cellular localization, secretion dynamics, and structural organization.

The microbiologist's guide to metaproteomics.

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics.

High-Throughput Analysis of the Flagella FliK-Dependent Surfaceome and Secretome in .

Bacterial pathogens employ multiple strategies to invade and damage host tissues while evading immune defenses. Recent studies highlight flagella as crucial contributors to bacterial virulence, not only by facilitating motility, but also by regulating the secretion of virulence factors. However, the role of the flagella-dependent secretome remains largely unexplored.

Isolation of derivatives from the food-grade probiotic CNCM I-4884 with enhanced anti- activity.

Giardiasis, a widespread intestinal parasitosis affecting humans and animals, is a growing concern due to the emergence of drug-resistant strains of . Probiotics offer a promising alternative for preventing and treating giardiasis. Recent studies have shown that the probiotic CNCM I-4884 inhibits growth both and .

Regulation of respiratory syncytial virus nucleoprotein oligomerization by phosphorylation.

The negative-sense RNA genome of respiratory syncytial virus (RSV) is encapsidated by the viral nucleoprotein N, forming a left-handed helical nucleocapsid which serves as template for the viral polymerase. Specific oligomerization of N along the viral genome necessitates a switch of conformation of N, from the neosynthesized monomeric and RNA-free N protein, named N, to N-RNA oligomers. Although the binding of the N-terminal part of RSV phosphoprotein P plays the role of chaperone to impair RNA binding to N, N-P interaction alone is not sufficient to prevent N oligomerization.

A widespread family of ribosomal peptide metallophores involved in bacterial adaptation to metal stress.

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a structurally diverse group of natural products that bacteria employ in their survival strategies. Herein, we characterized the structure, the biosynthetic pathway, and the mode of action of a RiPP family called bufferins. With thousands of homologous biosynthetic gene clusters throughout the bacterial phylogenetic tree, bufferins form by far the largest family of RiPPs modified by multinuclear nonheme iron-dependent oxidases (MNIO, DUF692 family).

Dual Fractions Proteomic Analysis of Silica Nanoparticle Interactions with Protein Extracts.

Unlabelled: Dual-fraction proteomics reveals a novel class of proteins impacted by nanoparticle exposure.

Background: Nanoparticles (NPs) interact with cellular proteomes, altering biological processes. Understanding these interactions requires comprehensive analyses beyond solely characterizing the NP corona.

The effect of obesity on uterine receptivity is mediated by endometrial extracellular vesicles that control human endometrial stromal cell decidualization and trophoblast invasion.

The objectives of the present study were to determine whether obesity impacts human decidualization and the endometrial control of trophoblast invasion (both of which are required for embryo implantation) and evaluate the potential involvement of endometrial extracellular vesicles (EVs) in the regulation of these physiological processes. Using primary human cell cultures, we first demonstrated that obesity is associated with significantly lower in vitro decidualization of endometrial stromal cells (ESCs). We then showed that a trophoblastic cell line's invasive ability was greater in the presence of conditioned media from cultures of ESCs from obese women.

Oxidative stress is intrinsic to staphylococcal adaptation to fatty acid synthesis antibiotics.

Antibiotics inhibiting the fatty acid synthesis pathway (FASII) of the major pathogen reach their enzyme targets, but bacteria continue growth by using environmental fatty acids (eFAs) to produce phospholipids. We assessed the consequences and effectors of FASII-antibiotic (anti-FASII) adaptation. Anti-FASII induced lasting expression changes without genomic rearrangements.

Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption.

The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium's gene expression strategies. Here, we investigated the effect of acetate on temporal changes in the transcriptome of F.

Wood Degradation by M. Fischer: Exploring Fungal Adaptation Using Metabolomic Networking.

M. Fischer (Fmed) is a white-rot wood-decaying fungus associated with one of the most important and challenging diseases in vineyards: Esca. To relieve microbial degradation, woody plants, including , use structural and chemical weapons.

Peripheral proteomic changes after electroconvulsive seizures in a rodent model of non-response to chronic fluoxetine.

Major depressive disorder (MDD) is the psychiatric disorder with the highest prevalence in the world. Pharmacological antidepressant treatment (AD), such as selective serotonin reuptake inhibitors [SSRI, i.e.

A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica.

Background: Yarrowia lipolytica, a nonconventional oleaginous yeast species, has attracted attention due to its high lipid degradation and accumulation capacities. Y. lipolytica is used as a chassis for the production of usual and unusual lipids and lipid derivatives.

Top-Down proteomics based on LC-MS combined with cDNA sequencing to characterize multiple proteoforms of Amiata donkey milk proteins.

An in-depth molecular characterization of the main milk proteins, caseins (CNs) and whey proteins, from Amiata donkey combining top-down proteomic analysis (LC-MS) and cDNA sequencing revealed multiple proteoforms arising from complex splicing patterns, including cryptic splice site usage and exon skipping events. Post-translational modifications, in particular phosphorylation, increased the variety and complexity of proteoforms. α-CN perfectly exemplifies such a complexity.

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.

Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction.

Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers-Example of Crohn's Disease and Ulcerative Colitis Flare-Ups.

Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs).

Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance.

In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the "gold standard" for carrying out global assessments of biological samples containing thousands of proteins.

Insights into the Structure and Protein Composition of Spores Formed at Different Temperatures.

The bacterium produces the most heat-resistant spores of any spoilage-causing microorganism known in the food industry. Previous work by our group revealed that the resistance of these spores to wet heat and biocides was lower when spores were produced at a lower temperature than the optimal temperature. Here, we used electron microcopy to characterize the ultrastructure of the coat of the spores formed at different sporulation temperatures; we found that spores produced at 55 °C mainly exhibited a lamellar inner coat tightly associated with a diffuse outer coat, while spores produced at 45 °C showed an inner and an outer coat separated by a less electron-dense zone.

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.

Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.

An Immunomodulatory Transcriptional Signature Associated With Persistent Infection in Hepatocytes.

causes severe foodborne illness in pregnant women and immunocompromised individuals. After the intestinal phase of infection, the liver plays a central role in the clearance of this pathogen through its important functions in immunity. However, recent evidence suggests that during long-term infection of hepatocytes, a subpopulation of may escape eradication by entering a persistence phase in intracellular vacuoles.