Backbone Conformation in Nucleic Acids: An Analysis of Local Helicity through Heminucleotide Scheme and a Proposal for a Unified Conformational Plot

Abstract

A relationship has been established to express the local helicity of a polynucleotide backbone directly in terms of the virtual bonds spanning the conformationally equivalent heminucleotide repeats, with a view to provide a better understanding of the cumulative effects of all the chemical bond rotational variations on local helicity. Using this, an analysis made with a few oligodeoxynucleotide crystal structures clearly brings forth that it is the concerted movements manifested in the near neighbour correlations between the pair of chemical bonds C4′—C5′ and P—05′ and C4′-C3′ and P-03′ of the 5′ and 3′ heminucleotides respectively that are primarily responsible for the observed non-uniform helical twists both in A and B type helical backbones. That these need not be restricted to oligodeoxynucleotides but may be a feature of oligoribonucleotides backbone also is shown from an analysis of helical segments of yeast tRNA^Phe. A proposal of a unified or a grand two dimensional conformational plot which would help visualise succinctly the overall effect of the variations in all the repeating six chemical bonds of a polynucleotide backbone is made. Apart from considerable simplification, the plot affords identification on it regions characteristic of helical, and loop and bend conformations of nucleic acid backbone chain.     

CD4 and Viral Load Dynamics in Antiretroviral-Na?ve HIV-Infected Adults from Soweto,South Africa: A Prospective Cohort

BackgroundCD4 count is a proxy for the extent of immune deficiency and declines in CD4 count are a measure of disease progression. Decline in CD4 count is an important component: for estimating benefits of ARV treatment; for individual level counselling on the rapidity of untreated disease progression and prognosis; and can be used in planning demand for health services. Our objective is to report CD4 decline and changes in viral load (VL) in a group of HIV-infected adults enrolled in a randomized trial of preventive treatment for TB in South Africa where clade C infection predominates.MethodsHIV-infected, tuberculin skin test positive adults who were not eligible for antiretroviral (ARV) treatment were randomized to a trial of preventive treatment from 2003–2005. VL and CD4 count were assessed at enrollment and CD4 counts repeated at least annually. During follow-up, individuals whose CD4 counts decreased to <200 cells/mm³ were referred for antiretroviral therapy (ART) and were analytically censored.Results1106 ARV naïve adults were enrolled. Their median age was 30 years and male to female ratio was 1∶5. Median baseline CD4 count was 490 cells/mm³ (IQR 351–675). The overall mean decline in CD4 count was 61 cells/mm³ per annum. Adjusting for age, gender, baseline hemoglobin, smoking and alcohol use had little impact on the estimate of CD4 decline. However, VL at baseline had a major impact on CD4 decline. The percent decline in CD4 count was 13.3% (95% CI 12.0%, 14.7%), 10.6% (95% CI 8.8%, 12.4%), and 13.8% (95% CI 12.1%, 15.5%) per annum for baseline VLs of <10,000 (N = 314), 10,001–100,000 (N = 338), >100,000 (N = 122) copies/ml.ConclusionsOur data suggests that six and a half years will elapse for an individual''s CD4 count to decline from 750 to 350 cells/mm³ in the absence of ART.     

Identification of phosphorylation sites on extracellular corneal epithelial cell maspin

Maspin, a 42-kDa non-classical serine protease inhibitor (serpin), is expressed by epithelial cells of various tissues including the cornea. The protein localizes to the nucleus and cytosol, and is present in the extracellular space. While extracellular maspin regulates corneal stromal fibroblast adhesion and inhibits angiogenesis during wound healing in the cornea, the molecular mechanism of its extracellular functions is unclear. We hypothesized that identifying post-translational modifications of maspin, such as phosphorylation, may help decipher its mode of action. The focus of this study was on the identification of phosphorylation sites on extracellular maspin, since the extracellular form of the molecule is implicated in several functions. Multi-stage fragmentation MS was used to identify sites of phosphorylation on extracellular corneal epithelial cell maspin. A total of eight serine and threonine phosphorylation sites (Thr50, Ser97, Thr118, Thr157, Ser240, Ser298, Thr310 and Ser316) were identified on the extracellular forms of the molecule. Phosphorylation of tyrosine residues was not detected on extracellular maspin from corneal epithelial cell, in contrast to breast epithelial cells. This study provides the basis for further investigation into the functional role of phosphorylation of corneal epithelial maspin.     

Outcomes of multi-drug resistant tuberculosis (MDR-TB) among a cohort of South African patients with high HIV prevalence

Background

Multidrug-resistant tuberculosis (MDR-TB) is a major clinical challenge, particularly in patients with human immunodeficiency virus (HIV) co-infection. MDR-TB treatment is increasingly available, but outcomes have not been well characterized. South Africa has provided MDR-TB treatment for a decade, and we evaluated outcomes by HIV status for patients enrolled between 2000 and 2004 prior to anti-retroviral access.

Methods

We assessed treatment outcomes in a prospective cohort of patients with MDR-TB from eight provincial programs providing second line drugs. World Health Organization definitions were used. Results were stratified by HIV status.

Results

Seven hundred fifty seven patients with known HIV status were included in the final analysis, and HIV infection was documented in 287 (38%). Overall, 348 patients (46.0%) were successfully treated, 74 (9.8%) failed therapy, 177 (23.4%) died and 158 (20.9%) defaulted. Patients with HIV were slightly younger and less likely to be male compared to HIV negative patients. Patients with HIV were less likely to have a successful treatment outcome (40.0 vs. 49.6; P<0.05) and more likely to die (35.2 vs. 16.2; P<0.0001). In a competing risk survival analysis, patients with HIV had a higher hazard of death (HR: 2.33, P<0.0001). Low baseline weight (less than 45 kg and less than 60 kg) was also associated with a higher hazard of death (HR: 2.52, P<0.0001; and HR: 1.50, P<0.0001, respectively, compared to weight greater than 60 kg). Weight less than 45 kg had higher risk of failure (HR: 3.58, P<0.01). Any change in treatment regimen was associated with a higher hazard of default (HR: 2.86; 95% CI 1.55–5.29, P<0.001) and a lower hazard of death (HR: 0.63, P<0.05).

Conclusions

In this MDR-TB treatment program patients with HIV infection and low weight had higher hazards of death. Overall treatment outcomes were poor. Efforts to improve treatment for MDR-TB are urgently needed.     

Studies on New Delhi Metallo-Beta-Lactamse-1 producing Acinetobacter baumannii isolated from donor swab in a tertiary eye care centre, India and structural analysis of its antibiotic binding interactions

Gram-negative bacilli, Enterobacteriaceae and Non-fermentors with resistance to carbapenems and metallo beta-lactams are the major cause of concern in clinical problems in current human healthcare. The most highly emerging dreadful Metallo Beta-lactamses is New Delhi metallo-beta-lactamase (blaNDM-1) which confers resistance to carbapenems; susceptible only to colistin and, less consistently to tigecycline, leading to no therapeutic options. In the present study, we demonstrate the effects of cephalosporins and carbepenems on biofilm producing A. baumanii clinical isolate and also to infer the probable inhibitory binding mode through molecular docking studies. The result of MIC on Biofilm producing A. baumanii and the docking analysis results were found to be concordant. Moreover, we also found cephalosporins and carbepenem groups to interact with 162-166 region of blaNDM-1, which is unique for NDM-1 and also documented to be a potential drug targeting region.     

Reconstitution of specific Na+-dependent D-glucose transport in liposomes by Triton X-100 extracted proteins from purified brush border membranes of hamster small intestine

Liposomes were prepared from soybean phospholipids and were sonicated together with Triton X-100 extracted proteins from purified brush border membranes isolated from hamster small intestine. The treated liposomes showed a specific Na⁺-dependent uptake of D-glucose as compared to L-glucose, which was inhibited by phlorizin and D-galactose.