An analysis of chromosomes in three Primates from India

The chromosomes of three Primates Macaca mulatta, Presbytis entellus and Loris tardigradus have been investigated and the results presented in this paper.     

Impact of <Emphasis Type="Italic">ERCC2</Emphasis> gene polymorphism on HIV-1 disease progression to AIDS among North Indian HIV patients

HIV/AIDS remains to be one of the killing diseases of mankind. Host genetic response is one of the factor which determine susceptibility to HIV and disease progression to AIDS. The aim of the present study was to evaluate the impact of ERCC2 Lyc ⁷⁵¹ Gln (excision repair cross complementing rodent repair deficiency, complementation group 2) polymorphism on HIV-1 susceptibility and disease progression to AIDS, as this gene has been reported to intervene in degrading retroviral cDNA before it integrates with the host DNA. This case control study included 300 HIV seropositive cases and an equal number of HIV seronegative controls. DNA was isolated from the blood samples of study subjects and genotyping of ERCC2 was conducted by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) method. The Gln/Gln genotype showed a significant variation between cases and controls (P = 0.047, OR 1.71, 95% CI 1.00–2.93), indicating a possible role of susceptibility in reference to controls and disease progression when compared within cases.     

Combined effect of GSTM1, GSTT1 and GSTP1 polymorphisms on histological subtypes of lung cancer

Genetic polymorphisms are natural genetic variations in the gene sequence that occur at a frequency of >1% in the population. This genetic variability (polymorphisms) can be a factor in cancer risk. The functional polymorphisms in GST genes play an important role in susceptibility to lung cancer. In our previous study, we reported that the combination of certain genotypes of GSTM1, GSTT1 and CYP1A1 is associated with lung cancer. The study has been extended to investigate the potential role of polymorphism in GSTP1 alone or in combination with the status of GSTM1 and GSTT1 genes in the likelihood of development of lung cancer. A total of 302 subjects (151 cases and 151 controls) were evaluated. Using a case–control design, individuals were genotyped for GSTs using multiplex polymerase chain reaction and restriction fragment length polymorphism techniques. The data obtained were analyzed using multiple logistic regression. The combined ‘at risk’ genotypes of GSTM1 null and GSTT1 null in comparison with ‘wild-type’ genotypes seems to be associated with a greater risk of lung cancer, but the results are not significant (odds ratio (OR) 2.0, 95% confidence interval (CI) 0.68–5.96) and for squamous cell carcinoma (SqCC) it was 1.6-fold (OR 1.6, 95% CI 0.49–5.68). In summary, our case–control study of lung cancer revealed that the effect of these polymorphisms is not very marked for different genotypic combinations of GSTP1, GSTM1 and GSTT1 in the context of developing lung cancer in a north Indian population. However, the increased risk was limited to SqCC, and was not found for other histological subtypes. Further analyses on this topic are needed.     

Phylogenetic position of Indian termites (Isoptera: Termitidae) with their respective genera inferred from DNA sequence analysis of the mitochondrial cytochrome oxidase gene subunit I compared to subunit II

It has been shown that over-expression of Special AT-rich binding protein 1 (SATB1) in breast cancer predicts a poor prognosis. This study was aimed at investigating the effects of silencing SATB1 on mesenchymal derived human osteosarcoma U2OS cells and the underlying mechanisms. The expressions of SATB1 and the related genes in the cells were detected by qRT-PCR and/or Western Blotting. SATB1 silencing was achieved by stable transfection with the vectors expressing small hairpin RNA versus SATB1. Cell proliferation was detected in a microplate reader with Cell Counting Kit-8 and the cell cycle was analyzed by flow cytometry using a cell cycle detection kit. The study found that SATB1 was particularly over-expressed in human osteosarcoma U2OS. Silencing SATB1 inhibited the proliferation of U2OS. It was found that inhibition of cell proliferation resulted from cell cycle arrest due to down-regulated expression of CFGF and JunB. The over-expression of SATB1 is responsible for abnormal proliferation of mesenchymal derived human Osteosatcoma U2OS cells, indicating that silencing SATB1 expression in the cells might be developed as an efficient osteosarcoma therapy. CTGF and JunB were involved in SATB1-mediated proliferation of U2OS cells.     

MspI Allelic Pattern of Bovine Growth Hormone Gene in Indian Zebu Cattle (Bos indicus) Breeds

The MspI allelic variation in intron III of the bovine growth hormone (bGH) gene was explored using PCR-RFLP in 750 animals belonging to 17 well-recognized breeds of Indian zebu cattle (Bos indicus) reared in different geographic locations of the country. Restriction digestion analysis of a 329-bp PCR fragment of the bGH intron III region with MspI restriction enzyme revealed two alleles (MspI− and MspI+) and two genotypes (−/− and +/−) across the 17 cattle breeds studied. The allelic frequency varied from 0.67 to 0.94 for MspI (−) and from 0.06 to 0.33 for MspI (+) across the 17 breeds, with a combined average frequency of 0.87 and 0.13, respectively. No animal with +/+ genotype was detected across the samples analyzed. The chi-square test showed that the difference in MspI allelic frequency was not significant (p > 0.05), regardless of the geographic origin, coat color, or utility of the cattle breed. The high MspI (−) allele frequencies obtained for Indian zebu cattle in this study are in sharp contrast to those reported for taurine breeds from northern Europe, Mediterranean countries, and America. Findings of this study further substantiate the hypothesis that the MspI (−) allele has an Indian origin.     

Identification and expression analysis of <Emphasis Type="Italic">CjLTI</Emphasis>, a novel low temperature responsive gene from <Emphasis Type="Italic">Caragana jubata</Emphasis>

Using rapid amplification of cDNA ends, a full length cDNA (CjLTI) was cloned from apical buds of Caragana jubata, a plant species that grows under extreme cold. The cDNA obtained was 573 bp long consisting of an open reading frame of 351 bp encoding 116 amino acids. Homology analysis did not exhibit significant similarity with any sequence at NCBI database, therefore it was deduced as a novel gene. Secondary structure analysis suggested that the deduced CjLTI contained 25.86% α-helices, 4.31% β-turns, 6.90% extended strands, and 62.93% random coils. The hydropathy profile suggested CjLTI to be a hydrophobic protein having characteristic features of signal peptides at N-terminus. The gene exhibited down-regulation at 5 min of exposure to low temperature (LT, 4 ± 3°C) followed by a strong up-regulation after 15 min and onwards. Methyl jasmonate (MJ) lead to up-regulation of CjLTI starting at 5 min onwards. The gene exhibited up- and down-regulation of expression pattern in response to abscisic acid (ABA) and salicylic acid (SA). Mild drought stress slightly up-regulated gene expression and at severe drought (up to 115% reduction in leaf water potential) slight down-regulation of gene expression was observed. These results suggested CjLTI to be a LT responsive gene wherein MJ, ABA and SA pathways might be involved in regulating the gene expression.     

Crystal structure of Lsm3 octamer from Saccharomyces cerevisiae: implications for Lsm ring organisation and recruitment

Sm and Sm-like (Lsm) proteins are core components of the ribonucleoprotein complexes essential to key nucleic acid processing events within the eukaryotic cell. They assemble as polyprotein ring scaffolds that have the capacity to bind RNA substrates and other necessary protein factors. The crystal structure of yeast Lsm3 reveals a new organisation of the L/Sm β-propeller ring, containing eight protein subunits. Little distortion of the characteristic L/Sm fold is required to form the octamer, indicating that the eukaryotic Lsm ring may be more pliable than previously thought. The homomeric Lsm3 octamer is found to successfully recruit Lsm6, Lsm2 and Lsm5 directly from yeast lysate. Our crystal structure shows the C-terminal tail of each Lsm3 subunit to be engaged in connections across rings through specific β-sheet interactions with elongated loops protruding from neighbouring octamers. While these loops are of distinct length for each Lsm protein and generally comprise low-complexity polar sequences, several Lsm C-termini comprise hydrophobic sequences suitable for β-sheet interactions. The Lsm3 structure thus provides evidence for protein-protein interactions likely utilised by the highly variable Lsm loops and termini in the recruitment of RNA processing factors to mixed Lsm ring scaffolds. Our coordinates also provide updated homology models for the active Lsm[1-7] and Lsm[2-8] heptameric rings.     

Cyclin D1 (G870A) polymorphism and risk of cervix cancer: a case control study in north Indian population

Cyclin D1 (CCND1) is a key regulatory protein, playing a critical role in the transition from G1 to S phase of the cell cycle. We have evaluated the association between CCND1 A870G polymorphism and risk of cervix cancer in north Indian women by using PCR-RFLP method. This association was estimated by computing odds ratio (ORs) and a 95% Confidence Intervals (95% CI) using a Multivariate Logistic Regression Analysis. No significant association was observed between CCND1 genotypes and overall risk of cervix cancer. But when stratified histologically, statistically significant (OR: 3.7, 95% CI: 1.56-8.87, P: 0.001) increased risk of squamous cell carcinoma (SCC) was observed for individuals with AA genotype. Thus our findings suggest that CCND1 (G870A) polymorphism may be associated with increased risk of SCC of the uterine cervix in north Indian women.