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Lecithin:retinol acyltransferase and retinol-binding protein enable vitamin A (VA) storage and transport, respectively, maintaining tissue homeostasis of retinoids (VA derivatives). The precarious VA status of the lecithin:retinol acyltransferase-deficient (Lrat -/- ) retinol-binding protein-deficient (Rbp -/- ) mice rapidly deteriorates upon dietary VA restriction, leading to signs of severe vitamin A deficiency (VAD). As retinoids impact gut morphology and functions, VAD is often linked to intestinal pathological conditions and microbial dysbiosis. Thus, we investigated the contribution of VA storage and transport to intestinal retinoid homeostasis and functionalities. We showed the occurrence of intestinal VAD in Lrat -/- Rbp -/- mice, demonstrating the critical role of both pathways in preserving gut retinoid homeostasis. Moreover, in the mutant colon, VAD resulted in a compromised intestinal barrier as manifested by reduced mucins and antimicrobial defense, leaky gut, increased inflammation and oxidative stress, and altered mucosal immunocytokine profiles. These perturbations were accompanied by fecal dysbiosis, revealing that the VA status (sufficient vs. deficient), rather than the amount of dietary VA per se, is likely a major initial discriminant of the intestinal microbiome. Our data also pointed to a specific fecal taxonomic profile and distinct microbial functionalities associated with VAD. Overall, our findings revealed the suitability of the Lrat -/- Rbp -/- mice as a model to study intestinal dysfunctions and dysbiosis promoted by changes in tissue retinoid homeostasis induced by the host VA status and/or intake., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Reduced costs and increased speed and accuracy of sequencing can bring the genome-based evaluation of individual disease risk to the bedside. While past efforts have identified a number of actionable mutations, the bulk of genetic risk remains hidden in sequence data. The biggest challenge facing genomic medicine today is the development of new techniques to predict the specifics of a given human phenome (set of all expressed phenotypes) encoded by each individual variome (full set of genome variants) in the context of the given environment. Numerous tools exist for the computational identification of the functional effects of a single variant. However, the pipelines taking advantage of full genomic, exomic, transcriptomic (and other) sequences have only recently become a reality. This review looks at the building of methodologies for predicting "variome"-defined disease risk. It also discusses some of the challenges for incorporating such a pipeline into everyday medical practice., (© 2013. Published by Elsevier Ltd. All rights reserved.)

Some mutations of protein residues matter more than others, and these are often conserved evolutionarily. The explosion of deep sequencing and genotyping increasingly requires the distinction between effect and neutral variants. The simplest approach predicts all mutations of conserved residues to have an effect; however, this works poorly, at best. Many computational tools that are optimized to predict the impact of point mutations provide more detail. Here, we expand the perspective from the view of single variants to the level of sketching the entire mutability landscape. This landscape is defined by the impact of substituting every residue at each position in a protein by each of the 19 non-native amino acids. We review some of the powerful conclusions about protein function, stability and their robustness to mutation that can be drawn from such an analysis. Large-scale experimental and computational mutagenesis experiments are increasingly furthering our understanding of protein function and of the genotype-phenotype associations. We also discuss how these can be used to improve predictions of protein function and pathogenicity of missense variants., (Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The metabolism of adenine nucleotides (AdRN) has been studied previously in whole brains, brain slices and brain extracts, containing mixed populations of neurons and glia. The availability of primary neuronal cultures enables us to study these pathways in almost pure neuronal preparations. The aim of the present study was to characterize the relative importance of the pathways of AdRN metabolism in the neurons. The metabolic fate of (8-14C) adenine and of AdRN prelabeled with (8-14C)adenine were studied in immature and mature primary rat neuronal cultures. Specific inhibitors were used to clarify the various metabolic fluxes, which were evaluated based on the time-related changes in the distribution of label (the cellular nucleotide content did not change during incubation). The turnover rate of AdRN was found to reflect mainly conversion of label to acid insoluble derivatives (AID) and partly degradation to hypoxanthine. The turnover was faster in the immature neurons. The combined addition of 2'-deoxycoformycin (2'-dCF) and of 5'-amino-5'-deoxyadenosine, inhibiting adenosine metabolism, resulted in both cultures in enhanced loss of label from AdRN, mainly to adenosine and adenine. This finding indicates the activity of the futile cycle AMP-->adenosine-->AMP. In both cultures, in the presence of these inhibitors, the ratio (hypoxanthine + inosine)/(adenine + adenosine) was 1.1, indicating that the fluxes through AMP deamination and AMP dephosphorylation are about equal. Addition of L-alanosine, inhibiting the conversion of IMP to AMP, resulted in both cultures, but especially in the mature neurons, in enhanced loss of label from AdRN to hypoxanthine and inosine. This finding indicates the functioning of the adenine nucleotide cycle (AMP-->IMP-->adenylosuccinic acid-->AMP). Under conditions of enhanced degradation of ATP (induced by iodoacetate and antimycin A), addition of 2'-dCF resulted in the immature cultures in lowering the ratio (hypoxanthine + inosine + IMP)/(adenine + adenosine) to 0.62, indicating a shift in favor of AMP dephosphorylation.

Chemically elicited guinea pig peritoneal exudate macrophages respond by superoxide (O2-) production to a large number of unrelated stimulants. It has been found that 8 out of 10 stimulants also induce arachidonic acid (20:4) liberation and thromboxane synthesis. The elicitation of O2- production by most stimulants was reduced or totally suppressed by three procedures that inhibit the activity of endogenous phospholipases: the use of drug p-bromophenacyl bromide, elevation of the cellular cyclic AMP level, and the removal of extracellular Ca2+. O2- production in response to concanavalin A, wheat germ agglutinin, and fMet-Leu-Phe were exquisitely sensitive to inhibition of phospholipase activity. Exogenously applied 20:4 as well as other unsaturated fatty acids (linolenic, linoleic, and oleic) induced massive and instantaneous O2- production in a dose-dependent manner. Saturated fatty acids (stearic) and methyl esters of unsaturated acids were inactive. Lysophosphoglycerides were also inactive. Incubation of macrophages with inhibitors of cyclooxygenase or lipoxygenase did not prevent the elicitation of O2- production by stimulants or fatty acids. On the contrary, O2- formation was enhanced by indomethacin and indomethacin by itself was capable of evoking O2- generation. Treatment of 20:4 with soybean lipoxygenase did not abolish its capacity to induce O2- production; native and lipoxygenase-treated 20:4 exhibited similar dose-response ratios. Purified 15-hydroxyeicosatetraenoic acid also elicited O2- production by macrophages with a potency comparable to but not exceeding that of 20:4. Equimolar amounts of prostaglandin E2 were inactive. These findings suggest that liberation of unsaturated fatty acid (principally, 20:4) from membrane phospholipids, as a consequence of phospholipase activation, is a necessary step in the elicitation of an oxidative burst in macrophages. O2- generation is stimulated by unesterified 20:4 and, possibly, by certain metabolites of 20:4. It appears that the lipoxygenase pathway may generate metabolites with stimulating capacity while the cyclooxygenase pathway is abortive.

Arachidonic acid (C20:4) and other unsaturated fatty acids are shown to activate superoxide (O2-) production in a cell-free system represented by sonically disrupted guinea pig peritoneal macrophages. The reaction requires a heat-sensitive cellular component and NADPH, is enhanced by flavin adenine dinucleotide (FAD), and is not linked to enzymatic oxidation of the fatty acid. C20:4-elicited O2- formation is dependent on the cooperation between a subcellular component sedimentable at 48,000g (probably containing the O2- -forming enzyme) and a cytosolic factor. This appears to be the first report of O2- generation being elicited in a cell-free system derived from unstimulated cells and supports the idea that unesterified unsaturated fatty acids act as second messengers of O2- formation in intact phagocytes.