Sequencing and analysis of a South Asian-Indian personal genome

ABSTRACT: BACKGROUND: With over 1.3 billion people, India is estimated to contain three times more genetic diversity than does Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala. RESULTS: We identified over 3.4 million SNPs in this genome including over 89,873 private variations. Comparison of the SAIF genome with several published personal genomes revealed that this individual shared ~50% of the SNPs with each of these genomes. Analysis of the SAIF mitochondrial genome showed that it is closely related to the U1 haplogroup which has been previously observed in Kerala. We assessed the SAIF genome for SNPs with health and disease consequences and found that the individual was at a higher risk for multiple sclerosis and a few other diseases. In analyzing SNPs that modulate drug response we found a variation that predicts a favorable response to metformin, a drug used to treat diabetes. SNPs predictive of adverse reaction to warfarin indicated that the SAIF individual is not at risk for bleeding if treated with typical doses of warfarin. In addition, we report the presence of several additional SNPs of medical relevance. CONCLUSIONS: This is the first study to report the complete whole genome sequence of a female from the state of Kerala in India. The availability of this complete genome and variant will further aid studies aimed at understanding genetic diversity, identifying clinically relevant changes and accessing disease burden in the Indian population.     

Glucose inhibits development of hamster 8-cell embryos in vitro

Relative preferences of energy substrates (glucose, pyruvate, and lactate) for in vitro development of hamster 8-cell embryos were investigated. Using protein-free modified Tyrode's medium (TLP-PVA) containing 10 mM lactate (L), 0.1 mM pyruvate (P), and amino acids (Phe, Ile, Met and Gln), we found that development of hamster 8-cell embryos to blastocysts was supported better in the absence of glucose than in medium containing (standard) 5 mM glucose (88.1% and 50%, respectively). Addition of even 0.25 mM glucose to the medium significantly inhibited blastocyst formation (54.1%). Medium T-PVA, containing 5 mM glucose as sole energy substrate (without pyruvate, lactate, and amino acids), very poorly supported embryo development (less than or equal to 7.9% blastocysts), but addition of 0.1 mM pyruvate enhanced blastocyst formation (52%). Elimination of pyruvate in TL-PVA medium containing 5 mM glucose and amino acids markedly reduced blastocyst formation by 4-fold (13.5%); the optimal pyruvate concentration was 0.2 mM. However, if the same medium was devoid of glucose, blastocyst formation was high both in the absence (71.1%) and presence (83.3%) of 0.1 mM pyruvate. Similarly, in glucose-free T-PVA medium, addition of either 10 mM lactate or amino acids supported 8-cell embryo development to blastocysts (61.7% and 60.5%, respectively) as opposed to 18.8% and 30.6%, respectively, in the presence of 5 mM glucose. This augmented development in the absence of glucose is suggested to the due to the efficient conversion of lactate to pyruvate and of amino acids to amphibolic intermediates and hence their utilization via the Krebs cycle.(ABSTRACT TRUNCATED AT 250 WORDS)     

Oxidative Stress is Associated with Genetic Polymorphisms in One-Carbon Metabolism in Coronary Artery Disease

In view of growing body of evidence favouring the association of aberrations in one-carbon metabolism and oxidative stress in the aetiology of coronary artery disease (CAD), we investigated the risk associated with polymorphisms regulating the folate uptake and transport such as the glutamate carboxypeptidase II (GCPII) C1561T, reduced folate carrier 1 (RFC1) G80A and cytosolic serine hydroxymethyltransferase (cSHMT) C1420T. We further evaluated the impact of seven putatively functional polymorphisms of this pathway on oxidative stress markers. Genotyping was performed on 288 CAD cases and 266 healthy controls along with the dietary folate assessment. GCPII C1561T polymorphism was found to be an independent risk factor (OR 2.71, 95% CI 1.47–4.98) for CAD, whereas cSHMT C1420T conferred protection (OR 0.51, 95% CI 0.37–0.70). Oxidative stress markers like the plasma levels of malondialdehyde, protein carbonyls and 8-oxo-deoxyguanosine were significantly increased and total glutathione was significantly decreased in CAD cases. Elevated oxidative stress was observed in subjects carrying GCPII 1561T and MTRR 66A-variant alleles and low oxidative stress was observed in the subjects carrying cSHMT 1420T and TYMS 5′-UTR 2R allele. GCPII C1561T, MTHFR C677T and MTRR A66G polymorphisms were observed to influence the homocysteine levels (P < 0.05). SHMT and TYMS variants were found to decrease oxidative stress by increasing the folate pool (r = 0.38, P = 0.003) and also by increasing the antioxidant status (r = 0.28, P = 0.03). Influence of dietary folate status was not observed. Overall, this study revealed elevated oxidative stress that was associated with the aberrations in one-carbon metabolism which could possibly influence the CAD risk.     

Evaluation of glycolamide esters of indomethacin as potential cyclooxygenase-2 (COX-2) inhibitors

A number of novel indomethacin glycolamide esters were synthesized and tested for their cyclooxygenase (COX-1 and COX-2) inhibition properties in vitro. Many of these compounds proved to be selective COX-2 inhibitors, and subtle structural changes in the substituents on the glycolamide ester moiety altered the inhibitory properties as well as potencies significantly. Their in vitro data were rationalized through molecular modeling studies. Few of them displayed anti-inflammatory activity in vivo. Compound 32, [1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3-yl]acetic acid 2-morpholin-4-yl-2-oxo ethyl ester, was identified as a promising compound in this class and its good anti-inflammatory activity was demonstrated in the in vivo model.     

Lysine substitutions convert a bacterial-agglutinating peptide into a bactericidal peptide that retains anti-lipopolysaccharide activity and low hemolytic activity

GL13NH2 is a bacteria-agglutinating peptide derived from the sequence of the salivary protein parotid secretory protein (PSP, BPIFA2, SPLUNC2, C20orf70). The peptide agglutinates both Gram negative and Gram positive bacteria, and shows anti-lipopolysaccharide activity in vitro and in vivo. However, GL13NH2 does not exhibit bactericidal activity. To generate a more cationic peptide with potential bactericidal activity, three amino acid residues were replaced with lysine residues to generate the peptide GL13K. In this report, the antibacterial and anti-inflammatory activities of GL13K were characterized. GL13K had lost the ability to agglutinate bacteria but gained bactericidal activity. Substitution of individual amino acids in GL13K with alanine did not restore bacterial agglutination. GL13K was bactericidal against Pseudomonas aeruginosa, Streptococcus gordonii and Escherichia coli but not Porphyromonas gingivalis. Unlike the agglutinating activity of GL13NH2, the bactericidal activity of GL13K against P. aeruginosa was retained in the presence of saliva. Both GL13NH2 and GL13K exhibited anti-lipopolysaccharide activity. In GL13K, this activity appeared to depend on a serine hydroxyl group. GL13K protected mice from lipopolysaccharide-induced sepsis and the peptide exhibited a low level of hemolysis, suggesting that it may be suitable for in vivo application.     

Active immunization against riboflavin carrier protein results in peri-implantation embryonic loss leading to pregnancy termination in rats: use of alternate adjuvants

To investigate the mechanism of pregnancy termination following immuno-neutralization of riboflavin carrier protein (RCP) and to use acceptable adjuvants, we actively immunized female rats with reduced and carboxymethylated RCP (RCM-RCP) using various adjuvants (during primary immunization) such as sodium phthalylated lipopolysaccharide (SPLPS), purified S. typhi outer membrane proteins (porins) and a combination of them. Rats (5-14 per group) were immunized with alugel adsorbed RCM-RCP (100 microg/dose) either alone or with SPLPS or porins or SPLPS+porins. Control animals received RCM-RCP emulsified with Fruend's completelincomplete adjuvants (FCA/FIA). All animals received five boosters at intervals of 21 days. The lowest (4 X 10(-3)) and the highest (> 70 X 10(-3)) anti-RCM-RCP antibody titers were observed in alugel adsorbed-RCM-RCP group and control groups, respectively. Immunized animals showed reduced fertility following 3rd, 4th and 5th boosters. Reduction in fertility was 30-60% in alugel adsorbed RCM-RCP group, 90-100% in FCA-RCM-RCP group and 80-90% in SPLPS+porins group. Fertility reduction was not strictly correlatable with the serum antibody titers. RCP-specific IgG could be localized in the uterine endometrial glands and luminal epithelial cells in the immunized animals. Animals in the FCA/FIA group showed abnormal implantation/resorption sites and their histological sections showed degenerated embryos. But, day 5 preimplantation embryos were normal. These results show that (a) SPLPS+porins can be used as adjuvants in place of FCA/FIA for active immunization against RCM-RCP and (b) early termination of pregnancy in the immunized animals is due largely to the failure of normal embryo implantation.     

Methanesulfonamide group at position-4 of the C-5-phenyl ring of 1,5-diarylpyrazole affords a potent class of cyclooxygenase-2 (COX-2) inhibitors

The effect of methanesulfonamide (MeSO(2)NH) group on COX-2 inhibitory activity of 1,5-diarylpyrazole is described. While this group being at position-4 of the N(1)-phenyl ring was found to be ineffective, its installation at position-4 of the C-5 phenyl ring offered several potent and selective inhibitors of COX-2 with IC(50) as low as 30 nM.     

Embryo-endometrial proteases during early mammalian development

In mammals, extensive remodeling of uterine endometrial matrix occurs during reproductive cycle and blastocyst implantation. This is regulated by a variety of molecules such as hormones, growth factors, cytokines and proteases. In this article, we review the current state of knowledge available on various proteases and their inhibitors functionally involved in the embryo-endometrial tissues and present some data on endometrial proteases in hamsters and rats during estrous cycle and early pregnancy. We demonstrate the presence of at least four gelatinolytic activities in endometrial samples, belonging to gelatinase-A and -B categories and their dependence on calcium/zinc ions for enzyme activity and, their interrelationships between zymogen and active forms. We believe that the embryo-endometrial proteases are essential for hatching of blastocysts and for the dynamic remodeling of endometrial tissues, occurring during the critical peri-implantation period.     

Phosphate is required for inhibition by glucose of development of hamster 8-cell embryos in vitro

The influence of sodium dihydrogen phosphate (Pi) and glucose on the development of hamster 8-cell embryos mediated by pyruvate (P) or amino acids (A) or lactate (L) was investigated using modified Tyrode's medium, TLP-PVA. When pyruvate was tested as the only energy substrate in medium TP-PVA for embryo development, blastocyst formation ranged from 81.3 to 90.9% whether or not the medium contained 0.35 mM Pi or 5 mM glucose; but, when these two compounds were present together, blastocyst formation fell to 51.8%. Similarly, in TA-PVA medium containing four amino acids: Phe, Ile, Met, and Gln), embryo development to blastocyst ranged from 74.1% to 90.4% whether or not the medium contained 0.35 mM Pi or 5 mM glucose; but, when these compounds were present together, blastocyst formation fell to 16.0%. In TL-PVA medium, 10 mM sodium lactate supported embryo development (84.4% blastocysts); the addition of 0.35 mM Pi decreased blastocyst development to 65.6%. However, addition of glucose to Pi-free TL-PVA medium did not decrease blastocyst formation (81.3%); when the medium contained 0.35 mM Pi, glucose curtailed blastocyst development to 7.5%. When glucose and Pi interactions were studied at different concentrations, glucose up to 1 mM was not inhibitory in Pi-free TL-PVA medium (74.3% blastocysts), but 0.25 mM glucose in the presence of 0.35 mM Pi markedly inhibited embryo development (7.7% blastocysts). Phosphate at a relatively high concentration (1 mM) was inhibitory (37.9% blastocysts), even in the absence of glucose.(ABSTRACT TRUNCATED AT 250 WORDS)     

Pentoxifylline improves sperm capacitation and in vitro fertilization of oocytes in the golden hamster

Pentoxifylline (PF) is used to improve motility of spermatozoa from subfertile or nonfertile males to accomplish in vitro fertilization in humans. The possible adverse effect of PF on pre- and peri-implantation stage embryo development in a suitable rodent model, such as the golden hamster, is yet to be determined. In this study, hamster cauda epididymal spermatozoa were exposed to different concentrations (0.23 to 3.6 mM) of PF, and their quantitative [percentage of motility] and qualitative [Score 0 to 5] motility were assessed and values expressed as the sperm motility index. Upon addition of spermatozoa to dishes containing PF, an immediate increase in sperm motility and sperm motility index was evident, which increased up to 4 to 6 h and then declined. The sperm motility index increase by PF was dose-dependant, and >or= 1.8 mM PF was detrimental after 4 h. The optimum dose of PF was found to be 0.45 mM. To assess the fertilizing ability of PF-treated spermatozoa, in vitro fertilization was carried out. Fertilization rates for spermatozoa treated with 3.6 mM PF were lower (53.8 +/- 7.8) than for the controls (69.5 +/- 10.2), whereas treatment with 0.45 mM PF increased the rates (91.6 +/- 4.3) compared with that of the controls (80.2 +/- 5.9). In conclusion, low concentrations (0.23 to 0.45 mM) of PF improve sperm capacitation and fertilization of oocytes in vitro in the golden hamster.