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Open AccessJournal ArticleDOI

Zinc inhibits lethal inflammatory shock by preventing microbe-induced interferon signature in intestinal epithelium.

TLDR
Zinc modulates the gut microbiota, causing less induction of ISRE/IRF genes in crypt cells, less TNF‐induced necroptosis in Paneth cells, and less fatal evasion of gut bacteria into the system.
Abstract
The cytokine TNF drives inflammatory diseases, e.g., Crohn's disease. In a mouse model of TNF-induced systemic inflammatory response syndrome (SIRS), severe impact on intestinal epithelial cells (IECs) is observed. Zinc confers complete protection in this model. We found that zinc no longer protects in animals which lack glucocorticoids (GCs), or express mutant versions of their receptor GR in IECs, nor in mice which lack gut microbiota. RNA-seq studies in IECs showed that zinc caused reduction in expression of constitutive (STAT1-induced) interferon-stimulated response (ISRE) genes and interferon regulatory factor (IRF) genes. Since some of these genes are involved in TNF-induced cell death in intestinal crypt Paneth cells, and since zinc has direct effects on the composition of the gut microbiota (such as several Staphylococcus species) and on TNF-induced Paneth cell death, we postulate a new zinc-related anti-inflammatory mechanism. Zinc modulates the gut microbiota, causing less induction of ISRE/IRF genes in crypt cells, less TNF-induced necroptosis in Paneth cells, and less fatal evasion of gut bacteria into the system.

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Gut microbiota‐derived nicotinamide mononucleotide alleviates acute pancreatitis by activating pancreatic SIRT3 signalling

TL;DR: In this article , the effect of faecal microbiota transplantation on acute pancreatitis (AP) was investigated and the mechanisms associated with pancreatic damage and inflammation were further clarified.
Journal ArticleDOI

Differential Effects of Transition Metals on Growth and Metal Uptake for Two Distinct Lactobacillus Species

TL;DR: Investigation of metal uptake by quantifying total cellular metal contents and compared how transition metals affect the growth of two distinct Lactobacillus species highlights how distinct species can respond differently to varied metal availability and provide a foundation for future molecular and mechanistic studies.
Journal ArticleDOI

Metal ions and nanometallic materials in antitumor immunity: Function, application, and perspective

TL;DR: In this article , the authors focus on the physiopathology of metal ions in tumorigenesis and discuss several breakthroughs regarding the use of nanometallic materials in antitumor immunotherapeutics.
Journal ArticleDOI

Paneth cells as the cornerstones of intestinal and organismal health: a primer

TL;DR: Paneth cells are versatile secretory cells located in the crypts of Lieberkühn of the small intestine as discussed by the authors , and they function as the cornerstones of intestinal health by preserving homeostasis.
Journal ArticleDOI

Metallobiology of Lactobacillaceae in the gut microbiome.

TL;DR: In this article , a review provides a current overview of these mechanisms and covers how iron, zinc and manganese impact Lactobacillaceae in the gut microbiota with an emphasis on their biochemical roles, requirements, and homeostatic mechanisms in several species.
References
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Journal ArticleDOI

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Posted ContentDOI

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI

featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features

TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
Journal ArticleDOI

HISAT: a fast spliced aligner with low memory requirements

TL;DR: Tests showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method, and requires only 4.3 gigabytes of memory.
Journal ArticleDOI

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

TL;DR: It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.
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