Normative genetic profiles of RAAS pathway gene polymorphisms in North Indian and South Indian populations

Population-based genetic association studies, popularly known as case-control studies, have continued to be the most preferred method for deciphering the genetic basis of various complex diseases, even in the post-human genome sequencing era. However, interpopulation differences in allele, genotype, and haplotype frequencies and linkage disequilibrium patterns lead to inconsistent results in candidate gene association studies. Therefore, for any meaningful disease association study, knowledge of the normative genetic background of the baseline population is a prerequisite. In addition, such genetic variation data also provide a ready-made menu of allele frequencies and linkage disequilibrium patterns of various polymorphisms in specific candidate genes in a particular population, which is a useful reference for further genetic association studies. Such genetic variation data are lacking for the Indian population, which represents about one-sixth of the world's population. In the present study we have reported the allele, genotype, and haplotype frequencies, Hardy-Weinberg equilibrium status, and linkage disequilibrium patterns of 12 polymorphisms in six candidate genes from the renin-angiotensin-aldosterone system among Indians. Because of their different history of origin, the Indian population is broadly divided into two subpopulations: North Indians (Caucasian Europeans) and South Indians (Dravidians). Considering this well-documented difference in gene pools, we have presented a comparative account of the normative genetic data of North Indian and South Indian populations with at least four individuals of urban and suburban origin from each of the representative states of northern and southern India.     

The taxonomic status of <Emphasis Type="Italic">Opegaster</Emphasis> Ozaki, 1928 and the description of four new species of <Emphasis Type="Italic">Opecoelus</Emphasis> Ozaki, 1925 (Digenea: Opecoelidae) from marine teleosts in Australian waters

The similarities between Opecoelus Ozaki, 1925, Coitocaecum Nicoll, 1915, Opegaster Ozaki, 1928 and Paropecoelus Pritchard, 1966 and the difficulty of separating Opecoelus and Opegaster are discussed. It is proposed that Opegaster be reduced to synonymy with Opecoelus and the diagnosis of the latter amended to accommodate both forms. Four new species of Opecoelus are described from marine teleosts in Australian waters. These are Opecoelus woolcockae n. sp. from Acanthopagrus butcheri and A. australis from off South Australia, New South Wales and southern Queensland, O. pomatomi n. sp. from Pomatomus saltatrix off New South Wales, O. crowcrofti n. sp. from Atherinomorus ogilbyi off southern Queensland and O. queenslandicus n. sp. from Apogon fasciatus off southern Queensland. The following new combinations are formed: Opecoelus gonorhynchi (Gavrilyuk, 1979) n. comb., O. elongatus (Yamaguti, 1959) n. comb., O. pentadactylus (Manter, 1940) n. comb., O. apogonichthydis (Yamaguti, 1938) n. comb., O. cameroni (Caballero & Caballero, 1969) n. comb., O. dendrochiri (Yamaguti, 1970) n. comb., O. hawaiiensis (Yamaguti, 1970) n. comb., O. jamunicus (Srivastava, 1968) n. comb., O. longivesiculus (Yamaguti, 1952) n. comb., O. mastacembalii (Harshey, 1937) n. comb., O. mehrii (Harshey, 1937) n. comb., O. synodi (Manter, 1947) n. comb., O. tamori (Yamaguti, 1938) n. comb., O. bothi (Yamaguti, 1970) n. comb., O. caulopsettae (Manter, 1954) n. comb., O. beliyai (Pande, 1937) n. comb., O. brevifistulus (Ozaki, 1928) n. comb., O. cryptocentri (Yamaguti, 1958) n. comb., O. dactylopteri (Yamaguti, 1970) n. comb., O. dermatogenyos (Yamaguti, 1970) n. comb., O. ditrematis (Yamaguti, 1942) n. comb., O. gobii (Yamaguti, 1952) n. comb., O. hippocampi (Shen, 1982) n. comb., O. iniistii (Yamaguti, 1970) n. comb., O. lobulus (Wang, 1977) n. comb., O. macrorchis (Yamaguti, 1938) n. comb., O. parapristipomatis (Yamaguti, 1934) n. comb., O. pritchardae (Overstreet, 1969) n. comb., O. syngnathi (Yamaguti, 1934) n. comb., O. lutiani (Bravo-Hollis & Manter, 1957) n. comb., O. ovatus (Ozaki, 1928) n. comb., O. plotosi (Yamaguti, 1940) n. comb. and O. rectus (Ozaki, 1928) n. comb.; all the new combinations were previously species of Opegaster.     

Differential Effects of Fluoride During Osteoblasts Mineralization in C57BL/6J and C3H/HeJ Inbred Strains of Mice

The behavior of fluoride ions in biological systems has advantages and problems. On one hand, fluoride could be a mitogenic stimulus for osteoblasts. However, high concentrations of this element can cause apoptosis in rat and mouse osteoblasts. Toward an understanding of this effect, we examined the role of sodium fluoride (NaF) in two mouse calvaria osteoblasts during the mineralization process. The animals used were C3H/HeJ (C3) and C57BL/6J (B6) mice. The calvaria cells were cultured for 28 days in the presence of several doses of NaF (0, 5, 10, 25, 50, and 75 μM), and we performed the assays: mineralized nodule measurements, alkaline phosphatase (ALP) activity, determination of type I collagen, and matrix metalloproteinase-2 (MMP-2) activity. The results showed no effects on alkaline phosphatase activity but decreased mineralized nodule formation. In B6 cells, the NaF effect was already seen with 10 μM of NaF and a greater increase of cellular type I collagen, and MMP-2 activity was upregulated after 7 days of NaF exposure. C3 osteoblasts showed a reduction in the mineralization pattern only after 50 μM of NaF with a slight increase of type I collagen and downregulation of MMP-2 activity during the mineralization period. In conclusion, fluoride affects the production and degradation of the extracellular matrix during early onset and probably during the mineralization period. Additionally, the genetic factors may contribute to the variation in cell response to fluoride exposure, and the differences observed between the two strains could be explained by an alteration of the bone matrix metabolism (synthesis and degradation).     

Limited Evidence for Parent-of-Origin Effects in Inflammatory Bowel Disease Associated Loci

Background

Genome-wide association studies of two main forms of inflammatory bowel diseases (IBD), Crohn’s disease (CD) and ulcerative colitis (UC), have identified 99 susceptibility loci, but these explain only ∼23% of the genetic risk. Part of the ‘hidden heritability’ could be in transmissible genetic effects in which mRNA expression in the offspring depends on the parental origin of the allele (genomic imprinting), since children whose mothers have CD are more often affected than children with affected fathers. We analyzed parent-of-origin (POO) effects in Dutch and Indian cohorts of IBD patients.

Methods

We selected 28 genetic loci associated with both CD and UC, and tested them for POO effects in 181 Dutch IBD case-parent trios. Three susceptibility variants in NOD2 were tested in 111 CD trios and a significant finding was re-evaluated in 598 German trios. The UC-associated gene, BTNL2, reportedly imprinted, was tested in 70 Dutch UC trios. Finally, we used 62 independent Indian UC trios to test POO effects of five established Indian UC risk loci.

Results

We identified POO effects for NOD2 (L1007fs; OR = 21.0, P-value = 0.013) for CD; these results could not be replicated in an independent cohort (OR = 0.97, P-value = 0.95). A POO effect in IBD was observed for IL12B (OR = 3.2, P-value = 0.019) and PRDM1 (OR = 5.6, P-value = 0.04). In the Indian trios the IL10 locus showed a POO effect (OR = 0.2, P-value = 0.03).

Conclusions

Little is known about the effect of genomic imprinting in complex diseases such as IBD. We present limited evidence for POO effects for the tested IBD loci. POO effects explain part of the hidden heritability for complex genetic diseases but need to be investigated further.     

Potential of Ayurgenomics Approach in Complex Trait Research: Leads from a Pilot Study on Rheumatoid Arthritis

Background

Inconsistent results across association studies including Genome-wide association, have posed a major challenge in complex disease genetics. Of the several factors which contribute to this, phenotypic heterogeneity is a serious limitation encountered in modern medicine. On the other hand, Ayurveda, a holistic Indian traditional system of medicine, enables subgrouping of individuals into three major categories namely Vata, Pitta and Kapha, based on their physical and mental constitution, referred to as Prakriti. We hypothesised that conditioning association studies on prior risk, predictable in Ayurveda, will uncover much more variance and potentially open up more predictive health.

Objectives and Methods

Identification of genetic susceptibility markers by combining the prakriti based subgrouping of individuals with genetic analysis tools was attempted in a Rheumatoid arthritis (RA) cohort. Association of 21 markers from commonly implicated inflammatory and oxidative stress pathways was tested using a case-control approach in a total cohort comprising 325 cases and 356 controls and in the three subgroups separately. We also tested few postulates of Ayurveda on the disease characteristics in different prakriti groups using clinico-genetic data.

Results

Inflammatory genes like IL1β (C-C-C haplotype, p = 0.0005, OR = 3.09) and CD40 (rs4810485 allelic, p = 0.04, OR = 2.27) seem to be the determinants in Vata subgroup whereas oxidative stress pathway genes are observed in Pitta (SOD3 rs699473, p = 0.004, OR = 1.83; rs2536512 p = 0.005; OR = 1.88 and PON1 rs662, p = 0.04, OR = 1.53) and Kapha (SOD3 rs2536512, genotypic, p = 0.02, OR = 2.39) subgroups. Fixed effect analysis of the associated markers from CD40, SOD3 and TNFα with genotype X prakriti interaction terms suggests heterogeneity of effects within the subgroups. Further, disease characteristics such as severity was most pronounced in Vata group.

Conclusions

This exploratory study suggests discrete causal pathways for RA etiology in prakriti based subgroups, thereby, validating concepts of prakriti and personalized medicine in Ayurveda. Ayurgenomics approach holds promise for biomarker discovery in complex diseases.     

Looking over toxin-K(+) channel interactions. Clues from the structural and functional characterization of α-KTx toxin Tc32, a Kv1.3 channel blocker

α-KTx toxin Tc32, from the Amazonian scorpion Tityus cambridgei, lacks the dyad motif, including Lys27, characteristic of the family and generally associated with channel blockage. The toxin has been cloned and expressed for the first time. Electrophysiological experiments, by showing that the recombinant form blocks Kv1.3 channels of olfactory bulb periglomerular cells like the natural Tc32 toxin, when tested on the Kv1.3 channel of human T lymphocytes, confirmed it is in an active fold. The nuclear magnetic resonance-derived structure revealed it exhibits an α/β scaffold typical of the members of the α-KTx family. TdK2 and TdK3, all belonging to the same α-KTx 18 subfamily, share significant sequence identity with Tc32 but diverse selectivity and affinity for Kv1.3 and Kv1.1 channels. To gain insight into the structural features that may justify those differences, we used the recombinant Tc32 nuclear magnetic resonance-derived structure to model the other two toxins, for which no experimental structure is available. Their interaction with Kv1.3 and Kv1.1 has been investigated by means of docking simulations. The results suggest that differences in the electrostatic features of the toxins and channels, in their contact surfaces, and in their total dipole moment orientations govern the affinity and selectivity of toxins. In addition, we found that, regardless of whether the dyad motif is present, it is always a Lys side chain that physically blocks the channels, irrespective of its position in the toxin sequence.     

Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography

The genus Alcantarea comprises near 30 species endemic to rocky outcrops from eastern Brazil. Most species are ornamental and several are threatened due to habitat loss and over collection. In this paper we examine the phylogenetics of Alcantarea and its relationship with the Brazilian members of Vriesea, a genus of which Alcantarea has been treated as a subgenus. We discuss the morphological evolution of the stamen position and its implication for pollination and the occurrence of Alcantarea in the Espinha?o mountain range rocky savanna-like habitat vegetation. DNA sequence data derived from two plastid markers (trnK-rps16, trnC-petN) and from a low copy nuclear gene (Floricaula/Leafy) together with 20 nuclear microsatellite loci were the data source to perform analyses and construct phylogenetic and Neighbor Joining trees for the genus. Alcantarea is well supported as monophyletic in both Bayesian and parsimony analyses, but sections of Vriesea, represented by the eastern Brazilian species, appear paraphyletic. Microsatellites delimit geographically isolated species groups. Nevertheless individuals belonging to a single species may appear related to distinct clusters of species, suggesting that hybridization and/or homoplasy and/or incomplete lineage sorting are also influencing the analysis based on such markers and may be the reasons for some unexpected results. Alcantarea brasiliana is hypothesized as putative hybrid between A. imperialis and A. geniculata. Spreading stamens, a morphological floral characteristic assumed to be related to Chiropterophily, apparently evolved multiple times within the genus, and invasion of rocky savanna-like habitat vegetation by Atlantic rainforest ancestors seems to have occurred multiple times as well.     

Design and synthesis of dihydroindazolo[5,4-a]pyrrolo[3,4-c]carbazole oximes as potent dual inhibitors of TIE-2 and VEGF-R2 receptor tyrosine kinases

Fused dihydroindazolopyrrolocarbazole oximes have been identified as low nanomolar, potent dual TIE-2 and VEGF-R2 receptor tyrosine kinase inhibitors with excellent cellular potency. Development of the structure-activity relationships (SAR) led to identification of compounds 35 and 40 as potent, selective dual TIE-2/VEGF-R2 inhibitors with favorable pharmacokinetic properties. Compound 35 was orally active in tumor models with no observed toxicity.     

The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interaction

The outer membrane lipoprotein A (OmlA) belongs to a family of bacterial small lipoproteins widely distributed across the beta and gamma proteobacteria. Although the role of numerous bacterial lipoproteins is known, the biological function of OmlA remains elusive. We found that in the citrus canker pathogen, Xanthomonas axonopodis pv. citri (X. citri), OmlA is coregulated with the ferric uptake regulator (Fur) and their expression is enhanced when X. citri is grown on citrus leaves, suggesting that these proteins are involved in plant-pathogen interaction. To gain insights into the function of OmlA, its conformational and dynamic features were determined by nuclear magnetic resonance. The protein has highly flexible N- and C- termini and a structurally well defined core composed of three beta-strands and two small alpha-helices, which pack against each other forming a two-layer alpha/beta scaffold. This protein fold resembles the domains of the beta-lactamase inhibitory protein BLIP, involved in protein-protein binding. In conclusion, the structure of OmlA does suggest that this protein may be implicated in protein-protein interactions required during X. citri infection.     

Molecular genetics of schizophrenia: past, present and future

Schizophrenia is a severe neuropsychiatric disorder with a polygenic mode of inheritance which is also governed by non-genetic factors. Candidate genes identified on the basis of biochemical and pharmacological evidence are being tested for linkage and association studies. Neurotransmitters, especially dopamine and serotonin have been widely implicated in its etiology. Genome scan of all human chromosomes with closely spaced polymorphic markers is being used for linkage studies. The completion and availability of the first draft of Human Genome Sequence has provided a treasure-trove that can be utilized to gain insight into the so far inaccessible regions of the human genome. Significant technological advances for identification of single nucleotide polymorphisms (SNPs) and use of microarrays have further strengthened research methodologies for genetic analysis of complex traits. In this review, we summarize the evolution of schizophrenia genetics from the past to the present, current trends and future direction of research.