Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink.

Analyzing host-microbe interactions is essential for understanding how microbiota changes disrupt host homeostasis. Here, we present a protocol for predicting host-microbe protein-protein interactions and their downstream effects using MicrobioLink. We describe steps for setting up the environment, installing software, and preparing human transcriptomic and bacterial proteomic data.

mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate.

Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies.

Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease.

The gut microbiome is crucial for nutrient metabolism, immune regulation, and intestinal homeostasis with changes in its composition linked to complex diseases like inflammatory bowel disease (IBD). Although the precise host-microbial mechanisms in disease pathogenesis remain unclear, high-throughput sequencing have opened new ways to unravel the role of interspecies interactions in IBD. Systems biology-a holistic computational framework for modeling complex biological systems-is critical for leveraging multi-omics datasets to identify disease mechanisms.

'Monkeypox 2.0': Case series on a reconditioned virus causing sexually transmissible disease in urban population.

Background: MPOX (Monkeypox) viral infection, a zoonotic disease previously confined to the African sub-continent, has caught attention worldwide recently due to its resurgence in a new 'avatar' among urban communities. Dermatologists in the U. A.

Effect of oleaster ( L.) flour addition combined with high-pressure homogenization on the acidification kinetics, physicochemical, functional, and rheological properties of kefir.

In this study, the effects of peeled oleaster flour (OF) addition (0.5% and 1%) with high-pressure homogenization (HPH) at 100 MPa on acidification kinetics, physicochemical, functional, and rheological properties of kefir made from bovine whole milk were investigated. The fermentation kinetic parameters such as and decreased by 23.

AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation.

Macroautophagy/autophagy is a highly-conserved catabolic procss eliminating dysfunctional cellular components and invading pathogens. Autophagy malfunction contributes to disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy regulation in health and disease has been the focus of the last decades.

Influence of pH and ionic strength on the bulk and interfacial rheology and technofunctional properties of hazelnut meal protein isolate.

The functional, bulk, and interfacial shear rheological properties of hazelnut protein isolate were studied at different pH values between 3.0 and 8.0 and ionic strength levels between 0.

Structural Characterization, Technofunctional and Rheological Properties of Sesame Proteins Treated by High-Intensity Ultrasound.

Plant-derived proteins, such as those from sesame seeds, have the potential to be used as versatile food ingredients. End-use functionality can be further improved by high-intensity ultrasound treatments. The effects of high-intensity ultrasound on the properties of sesame protein isolates from cold-pressed sesame cake were evaluated.

Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy.

The function of interleukin-22 (IL-22) in intestinal barrier homeostasis remains controversial. Here, we map the transcriptional landscape regulated by IL-22 in human colonic epithelial organoids and evaluate the biological, functional and clinical significance of the IL-22 mediated pathways in ulcerative colitis (UC). We show that IL-22 regulated pro-inflammatory pathways are involved in microbial recognition, cancer and immune cell chemotaxis; most prominently those involving CXCR2 neutrophils.

Computational prediction and experimental validation of Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells.

Macroautophagy is a ubiquitous homeostasis and health-promoting recycling process of eukaryotic cells, targeting misfolded proteins, damaged organelles and intracellular infectious agents. Some intracellular pathogens such as serovar Typhimurium hijack this process during pathogenesis. Here we investigate potential protein-protein interactions between host transcription factors and secreted effector proteins of and their effect on host gene transcription.

Flaviviruses hijack the host microbiota to facilitate their transmission.

Flaviviruses, such as Dengue and Zika viruses, infect millions of people worldwide using mosquitos as vectors. In this issue of Cell, Zhang et al. reveal how these viruses manipulate the skin microbiome of infected hosts in a way that increases vector recruitment and viral spread.

Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways.

Increasing evidence points towards the key role of the epithelium in the systemic and over-activated immune response to viral infection, including SARS-CoV-2 infection. Yet, how viral infection alters epithelial-immune cell interactions regulating inflammatory responses, is not well known. Available experimental approaches are insufficient to properly analyse this complex system, and computational predictions and targeted data integration are needed as an alternative approach.

Characterization and Selection of Potential Antifungal Lactic Acid Bacteria Isolated From Turkish Spontaneous Sourdough.

The aim of this research was to investigate the antifungal potential of lactic acid bacteria (LAB) isolated from Turkish spontaneous sourdough collected in summer and winter seasons from 25 different small bakeries in Trabzon, Giresun, Ordu, and Samsun. Lactic acid bacteria (933 isolates) were screened for inhibition of three common food spoilage molds (Aspergillus flavus, Aspergillus niger, and Penicillium expansum). Eight LAB isolates identified as Weissella cibaria 908, Lactiplantibacillus plantarum subsp.

Potential Use of High Pressure Homogenized Hazelnut Beverage for a Functional Yoghurt-Like Product.

Hazelnut beverage is a plant-based beverage produced from hazelnut cake as a by-product obtained after cold press extraction. It has high nutritional value and a significant percentage of consumers show interest in it due to its health benefits. In this study, hazelnut beverage manufactured from by-products of hazelnut oil industry was incorporated into functional yoghurt production.

Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease.

The gastrointestinal (GI) tract harbours a complex microbial community, which contributes to its homeostasis. A disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease (IBD), therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), released into the gut lumen, can cross the mucus layer and access underlying immune cells.

CytokineLink: A Cytokine Communication Map to Analyse Immune Responses-Case Studies in Inflammatory Bowel Disease and COVID-19.

Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines downstream. However, there are no readily available bioinformatic resources that can model cytokine-cytokine interactions.

Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.

Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes.

SARS-CoV-2 Causes a Different Cytokine Response Compared to Other Cytokine Storm-Causing Respiratory Viruses in Severely Ill Patients.

Hyper-induction of pro-inflammatory cytokines, also known as a cytokine storm or cytokine release syndrome (CRS), is one of the key aspects of the currently ongoing SARS-CoV-2 pandemic. This process occurs when a large number of innate and adaptive immune cells activate and start producing pro-inflammatory cytokines, establishing an exacerbated feedback loop of inflammation. It is one of the factors contributing to the mortality observed with coronavirus 2019 (COVID-19) for a subgroup of patients.

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.

The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling.

Storage stability and sourdough acidification kinetic of freeze-dried Lactobacillus curvatus N19 under optimized cryoprotectant formulation.

In this study, the response surface methodology was used to optimize the cryoprotective agent (skimmed milk powder, lactose and sucrose) formulation for enhancing the viability of Lactobacillus curvatus N19 during freeze-drying and storage stability of cells freeze-dried by using optimum formulation was evaluated. Our results showed that the most significant cryoprotective agent influencing the viability of L. curvatus N19 to freezing and freeze-drying was sucrose and skim milk, respectively.

Effect of different encapsulating agent combinations on viability of Shirota during storage, in simulated gastrointestinal conditions and dairy dessert.

In this study, the effects of various matrices consisting of maltodextrin and reconstitute skim milk and their binary and ternary mixtures with gum Arabic in the microencapsulation of Shirota by freeze-drying technique were assessed. Microcapsules produced with reconstitute skim milk showed high viability (>99%) after freeze drying. While the free cells were completely inactivated after exposure to simulated gastrointestinal conditions, the survival rates of microencapsulated Shirota were found high for all microcapsules except for maltodextrin and maltodextrin:gum Arabic formulas.

Influence of thermosonication (TS) process on the quality parameters of high pressure homogenized hazelnut milk from hazelnut oil by-products.

Hazelnut, an important source of nutrition, is reasonably expensive for hazelnut milk production. Hazelnut cake, a by-product from hazelnut oil production by cold press extraction technique, does not contain any chemical residue and can be used for hazelnut beverage production. This study investigates the effects of thermosonication process on the quality parameters of hazelnut milks and also compares the observed results with the conventional thermal process.

Targeted interplay between bacterial pathogens and host autophagy.

Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert it. Despite previous key findings of bacteria-autophagy interplay, asystems-level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between human autophagy proteins and effector proteins from 56 pathogenic bacterial species by identifying bacterial proteins predicted to have recognition motifs for selective autophagy receptors SQSTM1/p62, CALCOCO2/NDP52 and MAP1LC3/LC3.

Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy.

Paneth cells are key epithelial cells that provide an antimicrobial barrier and maintain integrity of the small-intestinal stem cell niche. Paneth cell abnormalities are unfortunately detrimental to gut health and are often associated with digestive pathologies such as Crohn's disease or infections. Similar alterations are observed in individuals with impaired autophagy, a process that recycles cellular components.