Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification

The fruit-bearing medicinal tree, Garcinia morella, grows in the tropical rain forests of India’s Western Ghats, Indo-Chinese Himalayan regions and Sri Lanka. Its fruit rinds are used as a garnish and in seasoning during food preparation. In order to genetically exploit it and assess diversity, development of microsatellite markers was attempted. We partially sequenced genomic DNA using the Illumina Hiseq 2000 platform and examined sequence data for microsatellite loci. We obtained high-quality 10653 Mbp data and was assembled into 1613263 contigs. A total of 121199 SSRs were discovered, Di nucleotide repeats were predominant (42.5%), followed by mono and tri nucleotide repeats (30.4 and 7.9%, respectively). We were able to design primers for 52901 microsatellites. Genetic analysis of 48 SSR loci, showed PIC values ranging from 0.067 to 0.939 with a mean value of 0.7547. The allele per locus ranged from 2 to 24 with a mean of 13. These microsatellite markers can be employed for genetic diversity analysis, molecular characterization and mapping different traits

GWAS of thyroid stimulating hormone highlights pleiotropic effects and inverse association with thyroid cancer

Correction: Volume12, Issue1 Article Number7354 DOI10.1038/s41467-021-27675-w PublishedDEC 16 2021Thyroid stimulating hormone (TSH) is critical for normal development and metabolism. To better understand the genetic contribution to TSH levels, we conduct a GWAS meta-analysis at 22.4 million genetic markers in up to 119,715 individuals and identify 74 genome-wide significant loci for TSH, of which 28 are previously unreported. Functional experiments show that the thyroglobulin protein-altering variants P118L and G67S impact thyroglobulin secretion. Phenome-wide association analysis in the UK Biobank demonstrates the pleiotropic effects of TSH-associated variants and a polygenic score for higher TSH levels is associated with a reduced risk of thyroid cancer in the UK Biobank and three other independent studies. Two-sample Mendelian randomization using TSH index variants as instrumental variables suggests a protective effect of higher TSH levels (indicating lower thyroid function) on risk of thyroid cancer and goiter. Our findings highlight the pleiotropic effects of TSH-associated variants on thyroid function and growth of malignant and benign thyroid tumors. Thyroid stimulating hormone (TSH) is critical for normal development and metabolism. Here, the authors conduct a GWAS and suggest protective effect of higher TSH on risk of thyroid cancer and goitre.Peer reviewe

Author Correction:GWAS of thyroid stimulating hormone highlights the pleiotropic effects and inverse association with thyroid cancer

The original version of this article contained an error in the results, in the second paragraph of the subsection entitled “Fine-mapping for potentially causal variants among TSH loci”, in which effect sizes for two variants were incorrectly reported

GWAS of thyroid stimulating hormone highlights pleiotropic effects and inverse association with thyroid cancer

Thyroid stimulating hormone (TSH) is critical for normal development and metabolism. To better understand the genetic contribution to TSH levels, we conduct a GWAS meta-analysis at 22.4 million genetic markers in up to 119,715 individuals and identify 74 genome-wide significant loci for TSH, of which 28 are previously unreported. Functional experiments show that the thyroglobulin protein-altering variants P118L and G67S impact thyroglobulin secretion. Phenome-wide association analysis in the UK Biobank demonstrates the pleiotropic effects of TSH-associated variants and a polygenic score for higher TSH levels is associated with a reduced risk of thyroid cancer in the UK Biobank and three other independent studies. Two-sample Mendelian randomization using TSH index variants as instrumental variables suggests a protective effect of higher TSH levels (indicating lower thyroid function) on risk of thyroid cancer and goiter. Our findings highlight the pleiotropic effects of TSH-associated variants on thyroid function and growth of malignant and benign thyroid tumors

Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease

Peer reviewe

Faecal microbiota of healthy adults in south India: Comparison of a tribal & a rural population

Background & objectives: The relevance of the gut microbiota to human health is increasingly appreciated. The objective of this study was to compare the gut microbiota of a group of adult tribals with that of healthy adult villagers in Tamil Nadu, India. Methods: Faeces were collected from 10 healthy tribal adults (TAs) in the Jawadhi hills and from 10 healthy villagers [rural adults (RAs)] in Vellore district, Tamil Nadu. DNA was extracted, and 456 bp segments comprising hypervariable regions 3 and 4 of the 16S rRNA gene were amplified, barcoded and 454 sequenced. Results: Totally 227,710 good-quality reads were analyzed. TAs consumed a millets-based diet, ate pork every day, and did not consume milk or milk products. RAs consumed a rice-based diet with meat intake once a week. In both groups, Firmicutes was the most abundant phylum, followed by Proteobacteria, Bacteroidetes and Actinobacteria. The median Firmicutes-to-Bacteroidetes ratio was 34.0 in TA and 92.9 in RA groups. Actinobacteria were significantly low in TA, possibly due to non-consumption of milk. Clostridium constituted the most abundant genus in both groups, but was significantly more abundant in TAs than RAs, while Streptococcus was significantly more abundant in RA (P<0.05). Analyses of genetic distance revealed that the microbiota were distinctly different between TA and RA, and principal component analysis using 550 distinct taxonomically identifiable sequences revealed a clear separation of microbiota composition in the two groups. Phylogenetic analysis of major microbiota indicated clustering of microbial groups at different major branch points for TAs and RAs. Interpretation & conclusions: Phylum Firmicutes and genus Clostridium constituted the bulk of the faecal microbiota, while significant differences in composition between the groups were probably due to differences in diet and lifestyle

Anti-inflammatory effect of a novel formulation of coconut inflorescence sap against ox-LDL induced inflammatory responses in human peripheral blood mononuclear cells by modulating TLR-NF-kappa B signaling pathway

Oxidized low density lipoprotein (ox LDL) induced inflammatory response was reported to play an important role in the pathogenesis of atherosclerosis. The purpose of this study was to explore the anti-inflammatory effect of a novel formulation of coconut inflorescence sap (CSP); COCOZENTM against ox-LDL induced inflammatory responses in human peripheral blood mononuclear cells (hPBMCs). The hPBMCs were isolated from healthy human volunteers and cultured in collagen coated plates at 37 degrees C. The cells were grouped as Group I (Control), Group II (ox-LDL treated) and Group III (ox-LDLthornCSP treated). Further analysis of inflammatory markers, reactive oxygen species, mRNA and protein expression levels indicated increased expressions of TLR-4, TNF-alpha, IL-6 and VCAM-1 in ox-LDL treated group along with the nuclear translocation of NF-kappa B. Other inflammatory markers such as LOX, PGE2, NO, total COX and lipid peroxidation level were also found to be significantly (p<. 05) increased upon Ox-LDL treatment. The treatment with CSP on the other hand was found to down regulate and reverse the ox-LDL-induced alterations indicating its potential anti-inflammatory effect on hPBMCs via TLR-NF-kappa B signaling pathway