Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.

Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities.

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.

Phylogenetic Analyses of Microbial Hydrolytic Dehalogenases Reveal Polyphyletic Origin.

Hydrolytic dehalogenases form an important class of dehalogenases that include haloacid dehalogenase, haloalkane dehalogenase, haloacetate dehalogenase, and atrazine chlorohydrolase. These enzymes are involved in biodegradation of various environmental pollutants and therefore it is important to understand their phylogeny. In the present study, it was found that the enzymes haloalkane and haloacetate dehalogenases share a common ancestry with enzymes such as carboxyesterase, epoxide hydrolase, and lipases, which can be traced to ancestral α/ß hydrolase fold enzyme. Haloacid dehalogenases and atrazine chlorohydrolases have probabaly evolved from ancestral enzymes with phosphatase and deaminases activity, respectively. These findings were supported by the similarities in the secondary structure, key catalytic motifs and placement of catalytic residues. The phylogeny of haloalkane dehalogenases and haloacid dehalogenases differs from 16S rRNA gene phylogeny, suggesting spread through horizontal gene transfer. Hydrolytic dehalogenases are polyphyletic and do not share a common evolutionay history, the functional similarities are due to convergent evolution. The present study also identifies key functional residues, mutating which, can help in generating better enzymes for clean up of the persistent environmental pollutants using enzymatic bioremediation. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-022-01043-8.

Characteristics and Functions of the Yip1 Domain Family (YIPF), Multi-Span Transmembrane Proteins Mainly Localized to the Golgi Apparatus.

Yip1 domain family (YIPF) proteins are multi-span, transmembrane proteins mainly localized in the Golgi apparatus. YIPF proteins have been found in virtually all eukaryotes, suggesting that they have essential function(s). Saccharomyces cerevisiae contains four YIPFs: Yip1p, Yif1p, Yip4p, and Yip5p. Early analyses in S. cerevisiae indicated that Yip1p and Yif1p bind to each other and play a role in budding of transport vesicles and/or fusion of vesicles to target membranes. However, the molecular basis of their functions remains unclear. Analysis of YIPF proteins in mammalian cells has yielded significant clues about the function of these proteins. Human cells have nine family members that appear to have overlapping functions. These YIPF proteins are divided into two sub-families: YIPFα/Yip1p and YIPFß/Yif1p. A YIPFα molecule forms a complex with a specific partner YIPFß molecule. In the most broadly hypothesized scenario, a basic tetramer complex is formed from two molecules of each partner YIPF protein, and this tetramer forms a higher order oligomer. Three distinct YIPF protein complexes are formed from pairs of YIPFα and YIPFß proteins. These are differently localized in either the early, middle, or late compartments of the Golgi apparatus and are recycled between adjacent compartments. Because a YIPF protein is predicted to have five transmembrane segments, a YIPF tetramer complex is predicted to have 20 transmembrane segments. This high number of transmembrane segments suggests that YIPF complexes function as channels, transporters, or transmembrane receptors. Here, the evidence from functional studies of YIPF proteins obtained during the last two decades is summarized and discussed.

Connexin 26 (GJB2) Mutations Associated with Non-Syndromic Hearing Loss (NSHL).

OBJECTIVE: To determine the prevalence and spectrum of Connexin 26 (GJB2) mutations in pre-lingual non-syndromic hearing loss (NSHL) patients in authors' centre and to review the data of Indian patients from the literature. METHODS: Sanger sequencing of entire coding region contained in single exon (Exon 2) of GJB2 gene in 15 patients of NSHL. RESULTS: GJB2 mutations were found in 40% (6/15) of NSHL patients, out of which mono-allelic were 33.3% (2/6). Bi-allelic GJB2 mutations were identified in 4 of 6 patients. Most common GJB2 mutation identified was c.71G > A(p.W24X), comprising 30% of the total GJB2 mutant alleles. Six studies involving 1119 patients with NSHL were reviewed and 4 of them have reported c.71G > A(p.W24X) as the commonest mutation while 2 studies found c.35delG as the commonest. GJB2 mutations accounted for 10.9%-36% cases of NSHL. Sixteen other mutations in GJB2 gene were reported in Indian patients out of which 6 mutations other than c.71G > A(p.W24X) viz., c.35delG, c.1A > G(p.M1V), c.127G > A(p.V43 M), c.204C > G(p.Y86X), c.231G > A(p.W77X) and c.439G > A(p.E147K) were identified in the present study. CONCLUSIONS: Connexin 26 (GJB2) mutations are responsible for 19.4% of NSHL in Indian population. The c.71G > A(W24X) and c.35delG were the most prevalent GJB2 mutations accounting for 72.2% (234 of 324 total mutated alleles from 7 studies) and 15.4% (50 of 324 total mutated alleles from 7 studies) respectively. Thus, screening of these two common mutations in GJB2 gene by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) would greatly help in providing easy genetic diagnosis and help in genetic counseling of the families with NSHL.

Genetic interaction of DISC1 and Neurexin in the development of fruit fly glutamatergic synapses.

Originally identified at the breakpoint of a (1;11)(q42.1; q14.3) chromosomal translocation in a Scottish family with a wide range of mental disorders, the DISC1 gene has been a focus of intensive investigations as an entry point to study the molecular mechanisms of diverse mental dysfunctions. Perturbations of the DISC1 functions lead to behavioral changes in animal models, which are relevant to psychiatric conditions in patients. In this work, we have expressed the human DISC1 gene in the fruit fly (Drosophila melanogaster) and performed a genetic screening for the mutations of psychiatric risk genes that cause modifications of DISC1 synaptic phenotypes at the neuromuscular junction. We found that DISC1 interacts with dnrx1, the Drosophila homolog of the human Neurexin (NRXN1) gene, in the development of glutamatergic synapses. While overexpression of DISC1 suppressed the total bouton area on the target muscles and stimulated active zone density in wild-type background, a partial reduction of the dnrx1 activity negated the DISC1-mediated synaptic alterations. Likewise, overexpression of DISC1 stimulated the expression of a glutamate receptor component, DGLURIIA, in wild-type background but not in the dnrx1 heterozygous background. In addition, DISC1 caused mislocalization of Discs large, the Drosophila PSD-95 homolog, in the dnrx1 heterozygous background. Analyses with a series of domain deletions have revealed the importance of axonal localization of the DISC1 protein for efficient suppression of DNRX1 in synaptic boutons. These results thus suggest an intriguing converging mechanism controlled by the interaction of DISC1 and Neurexin in the developing glutamatergic synapses.

Hotspots in PTPN11 Gene Among Indian Children With Noonan Syndrome.

OBJECTIVE: To test for PTPN11 mutations in clinically diagnosed cases of Noonan syndrome. METHODS: 17 individuals with clinical diagnosis of Noonan syndrome were included in the study. Sanger sequencing of all the 15 exons of PTPN11 was done. A genotype-phenotype correlation was attempted. RESULTS: Mutation in PTPN11 was detected in 11 out of 17 (64.7%) patients with Noonan syndrome; 72% had mutation in exon 3 and 27 % had mutation in exon 13. CONCLUSION: PTPN11 mutation accounts for 64.7% of cases with clinical features of Noonan syndrome in India. Majority of the mutations are in exon 3 and exon 13 of PTPN11, making them the hotspots in Indian population.

Spondyloepiphyseal dysplasia Omani type: CHST3 mutation spectrum and phenotypes in three Indian families.

We describe three consanguineous Indian families with a distinct form of spondyloepiphyseal dysplasia (SED Omani type). It is an autosomal recessive disorder due to mutation in CHST3 gene. CHST3 gene encodes the enzyme chondroitin 6-O-sulfotransferase-1 (C6ST-1) which mediates the sulfation of proteoglycans, (chondroitin sulfate), in the extracellular matrix of cartilage. CHST3 gene was sequenced in probands from three different families with SED. In two families missense mutations (c.904G>C predicting the substitution D302H) and c.491C>T (P164L) were identified. A frameshift (insertion) mutation (c.533_534ins G predicting the substitution A179Rfs*) was found in the third family. SNP micrarray in the family 2 helped to localize the common areas of homozygosity and identified the candidate gene. The confirmation by molecular diagnosis will be useful in the management and in the counseling of affected patients and their families. The presence of sclerosis of cranial sutures adds to the phenotypic spectrum of the disorder. Severe cardiac valvular disease in a case and triangular epiphyses of knees are other features which are highlighted in this report. © 2016 Wiley Periodicals, Inc.

Phylogenetic relationship and molecular identification of five Indian Mahseer species using COIsequence.

This study examined the phylogenetic relationship and identification of five Mahseer species (Tor putitoro, Tor tor, Tor khudree, Tor chelynoides and Neolissochilus hexogonolopis) using partial sequencing of a Cytochrome Oxidase I (COl) DNA barcodes. The sequence analysis data showed that 134 (21.61%) sites out of 628 sites were variable without insertion or deletion. Rate of transition (70.5%) were higher than transversion (29.41%). There was a high inter-species divergence (range 4.1% to 12.2%) in Mahseer species as compared to intra-specific sequence divergence (1.7% for T. putitora, 1.2% for T tor, 1.4% for T. khudree, 3.0% for T chelynoides, 0.26 % for N. hexagonolopis). The phylogenetic tree, constructed by maximum parsimony, maximum likelihood and unweighted pair group average methods revealed similar results suggesting that T. putitoro, T. tor and T. khudree had a close relationship to each other while maximum divergence was observed in T. chelynoides, which was also confirmed by the genetic distance data. The results indicate that COl sequencing or bar-coding is useful in unravelling phylogenetic relationship and identification of Mahseer species.