Standard free energies of binding of solute to proteins in aqueous medium. Part 1: Thermodynamic analysis for multicomponent system

Using an equilibrium dialysis technique, moles (Gamma(2)(1)) of cationic and anionic surfactants bound per kilogram of proteins of various types in aqueous media have been measured previously in this laboratory under different physicochemical conditions. From a thermodynamic analysis in the present paper, Gamma(2)(1) has been shown to be equal to the Gibbs relative excess of surfactant per kilogram of protein at a measured value of solute activity, a(2). The values of relative solvent excesses, Gamma(2)(1) (which are negative for surfactants) can be estimated from values of Gamma(2)(1) and a(2). Using the Gibbs-Duhem relationship for protein solution inside the dialysis bag and dialysate solutions respectively at equilibrium, an integrated expression for the standard free energy change, DeltaG(o) (in kilojoules per kilogram of protein for binding with ligand as a result of the change of a(2) from zero to unity) can be calculated from experimental data. The isopiestic vapour pressure technique was used extensively for evaluation of negative binding (-Gamma(2)(1)) of inorganic salts to proteins of different types for various values of a(2) of salts present in the bulk media. With some modifications of our derived equations for free energy of binding in such a system, DeltaG(o) has been evaluated for the change of mean activity of electrolyte from zero to unity in the rational scale. DeltaG(o) is positive since Gamma(2)(1) is negative and Gamma(2)(1) is positive for such ionic systems. DeltaG(o) in all cases, however, are expressed in terms of the standard state of reference of unit activity so that their magnitudes and sign can be related to the relative affinities of a solute for binding with proteins in aqueous media.     

Isolation ofThiobacillus ferrooxidans from various habitats and their growth pattern on solid medium

Different strains of iron-oxidizingThiobacillus ferrooxidans were grown and purified on solid medium containing Bapco agar, agarose, and carrageenan (Type 1). These strains produced easily countable isolated colonies that could be transferred after 7 days of incubation at 30°C. Increase in viable cell number in relation to growth and iron oxidation was studied by both microscopic count and direct plating method. Colony morphology of different strains growing on solid medium helped in differentiating the colony types.     

Specificity of Pyrrolysyl-tRNA Synthetase for Pyrrolysine and Pyrrolysine Analogs

Pyrrolysine, the 22nd amino acid, is encoded by amber (TAG = UAG) codons in certain methanogenic archaea and bacteria. PylS, the pyrrolysyl-tRNA synthetase, ligates pyrrolysine to tRNA^Pyl for amber decoding as pyrrolysine. PylS and tRNA^Pyl have potential utility in making tailored recombinant proteins. Here, we probed interactions necessary for recognition of substrates by archaeal PylS via synthesis of close pyrrolysine analogs and testing their reactivity in amino acid activation assays. Replacement of the methylpyrroline ring of pyrrolysine with cyclopentane indicated that solely hydrophobic interactions with the ring-binding pocket of PylS are sufficient for substrate recognition. However, a 100-fold increase in the specificity constant of PylS was observed with an analog, 2-amino-6-((R)-tetrahydrofuran-2-carboxamido)hexanoic acid (2Thf-lys), in which tetrahydrofuran replaced the pyrrolysine methylpyrroline ring. Other analogs in which the electronegative atom was moved to different positions suggested PylS preference for a hydrogen-bond-accepting group at the imine nitrogen position in pyrrolysine. 2Thf-lys was a preferred substrate over a commonly employed pyrrolysine analog, but the specificity constant for 2Thf-lys was 10-fold lower than for pyrrolysine itself, largely due to the change in K_m. The in vivo activity of the analogs in supporting UAG suppression in Escherichia coli bearing genes for PylS and tRNA^Pyl was similar to in vitro results, with l-pyrrolysine and 2Thf-lys supporting the highest amounts of UAG translation. Increasing concentrations of either PylS substrate resulted in a linear increase in UAG suppression, providing a facile method to assay bioactive pyrrolysine analogs. These results illustrate the relative importance of the H-bonding and hydrophobic interactions in the recognition of the methylpyrroline ring of pyrrolysine and provide a promising new series of easily synthesized pyrrolysine analogs that can serve as scaffolds for the introduction of novel functional groups into recombinant proteins.     

Enzymatic transesterification of Jatropha oil

Background  

Transesterification of Jatropha oil was carried out in t-butanol solvent using immobilized lipase from Enterobacter aerogenes. The presence of t-butanol significantly reduced the negative effects caused by both methanol and glycerol. The effects of various reaction parameters on transesterification of Jatropha oil were studied.     

Length-weight relationships of six Nemacheilid fish species (Teleostei: Cypriniformes) from different rivers of Manipur,India

The length-weight relationships (LWRs) of six Nemacheilid species (Schistura chindwinica, S. fasciata, S. khugae, S. minuta, S. reticulata and S. rubrimaculata) have been analyzed. Fish samples were collected on quarterly basis from March 2018 to February 2019. Sampling was performed using cast nets (mesh size 5–10 mm; about 50 sq m area covered each time and water depth was 4 ft approx.), and electrofishing (Ultrasonic Inverter Electro Fisher, 24 volts, 4 m) in the day time. The total length (TL) of individual fish was measured to 0.1 cm with a digital caliper and body weights (BW) were measured to 0.001 g with digital electronic balances. The parameters for the LWR equations were calculated, and the respective statistics such as the 95% confidence interval for parameters “a” and “b” are provided as well as the coefficient of correlation. For five species a new maximum total length has been documented.     

Apoptotic mechanisms of myricitrin isolated from Madhuca longifolia leaves in HL-60 leukemia cells

Molecular Biology Reports - Myricitrin, a naturally occurring flavonoid in Madhuca longifolia, possesses several medicinal properties. Even though our earlier work revealed its role against the...     

Adherence to Antiretroviral Therapy and Its Effect on Survival of HIV-Infected Individuals in Jharkhand,India

Introduction

Research in India has extensively examined the factors associated with non-adherence to antiretroviral therapy (ART) with limited focus on examining the relationship between adherence to ART regimen and survival status of HIV infected patients. This study examines the effect of optimal adherence to ART on survival status of HIV infected patients attending ART centers in Jharkhand, India.

Materials and Methods

Data from a cohort of 239 HIV infected individuals who were initiated ART in 2007 were compiled from medical records retrospectively for 36 months. Socio-demographic characteristics, CD4 T cell count, presence of opportunistic infections at the time of ART initiation and ART regimen intake and survival status was collected periodically. Optimal adherence was assessed using pill count methods; patients who took <95% of the specified regimens were identified as non-adherent. Cox-proportional hazard model was used to determine the relative hazards of mortality.

Results

More than three-fourths of the patients were male, on an average 34 year old and median CD4 T cell count was 118 cells/cmm at the time of ART registration. About 57% of the patients registered for ART were found to be adherent to ART. A total of 104 patients died in 358.5 patient-years of observation resulting in a mortality rate of 29 per 100 patient-years (95% confidence interval (CI): 23.9–35.2) and median survival time of 6.5 months (CI: 2.7–10.9). The mortality rate was higher among patients who were non-adherent to ART (64.5, CI: 50.5–82.4) than who were adherent (15.4, CI: 11.3–21.0). The risk of mortality was fourfold higher among individuals who were non-adherent to ART than who were adherent (Adjusted hazard ratio: 3.9, CI: 2.6–6.0).

Conclusion

Adherence to ART is associated with a higher chance of survival of HIV infected patients, ascertaining the need for interventions to improve the ART adherence and early initiation of ART.