A homology/ab initio hybrid algorithm for sampling near‐native protein conformations

One of the major challenges for protein tertiary structure prediction strategies is the quality of conformational sampling algorithms, which can effectively and readily search the protein fold space to generate near‐native conformations. In an effort to advance the field by making the best use of available homology as well as fold recognition approaches along with ab initio folding methods, we have developed Bhageerath‐H Strgen, a homology/ab initio hybrid algorithm for protein conformational sampling. The methodology is tested on the benchmark CASP9 dataset of 116 targets. In 93% of the cases, a structure with TM‐score ≥ 0.5 is generated in the pool of decoys. Further, the performance of Bhageerath‐H Strgen was seen to be efficient in comparison with different decoy generation methods. The algorithm is web enabled as Bhageerath‐H Strgen web tool which is made freely accessible for protein decoy generation ( http://www.scfbio‐iitd.res.in/software/Bhageerath‐HStrgen1.jsp ). © 2013 Wiley Periodicals, Inc.     

Formic acid oxidation at platinized platinum electrodes: Part IV. Effect of preadsorbed sulfur and related studies

A study has been made of the effect of preadsorbed sulfur layer on the anodic oxidation of formic acid at a platinized platinum electrode. It is shown that, in the presence of the preadsorbed s sulfur layer, the oxidation process obeys the following rate expression,i=nFkc^αg(θ_s) exp(α_anF?r/RT)where α≈0.75 and α_an≈0.5. This is explained in terms of the following rate-determining step,

${\left(HCOOH\right)}_{ads}\to \underset{*}{C}OOH+H^{+}+e$

and involves the adsorption of formic acid on the sulfur-covered electrode surface. A strong catalytic effect of the sulfur layer is observed; the function g(θ_S) is greater than unity at all θ_S and exhibits two maxima at г_S values of 0.3 and 0.6. It is suggested that these effects arise from a coverage-dependent variation of bond strength between adsorbed sulfur and platinum. Evidence is adduced that the adsorption of sulfur from H₂S solutions involves 2-site adsorption at low coverages and 1-site adsorption at higher coverages. Possibility of multilayer adsorption under appropriate conditions is also discussed in the light of the results obtained.     

A colorimetric method of estimating hydrolyzable chlorine in lindane (γ-hexachlorocyclohexane)

A rapid colorimetric method of determining hydrolyzable chlorine content of lindane has been developed. The region of maximum absorption, Beer's law is obeyed between 80 and 320 μg/ml of solution. The sensitivity of this method is compared with Volhard's titration method and is found to be superior. With the above method, the insecticide can be estimated in pure form with an accuracy of ±0.8 to 1.9%.     

LIGHT-INDUCED CAROTENE SYNTHESIS IN MUTANTS OF PHYCOMYCES WITH ABNORMAL PHOTOTROPISM

Mutants of Phycomyces. abnormal in their phototropic responses (the mad mutants), have been tested for their responses in light-induced carotene synthesis (LICS). The amount of carotene synthesized at any given fluence is significantly lower in the madA, madB and madD mutants than in the wild type. The amount of carotene is not lower in other mad mutants ( madC, madE, madF and madG ). The double mutant mad A madB and the triple mutant mad A madB madC show stronger effects. The wild type strain, as well as those carrying a single mad mutation ( madA and madB ) or those carrying two or three mad mutations ( madA madB. madA madB madC ) show closely similar sensitivity to LICS. This contrasts with phototropism and photoinitiation of sporangiophores which are sensitive to extremely small signals in the wild type and in which the madA mutation decreases the sensitivity by nearly a factor of 10⁴ and madB mutation by a factor of 10⁵. It appears that LICS does not share the signal amplification mechanisms characteristic of the other two responses.     

On the acceptance ratio in Monte Carlo computer simulations

The functional form of acceptance probabilities in Monte Carlo algorithms bears a resemblance to the distance functions which are specifically defined to be bracketed by the unit interval. This observation led us to seek the average distance between any two points on the unit interval and this by analogy resulted in a suggestion of an upper and a lower bound of 1/2 and 1/3, respectively, for the acceptance ratio or the average acceptance probability in Monte Carlo computer simulations.     

Core level X-ray photoelectron emission spectra and structure-surface related multi-excitonic photoluminescence with reduced recombination rate in mesoporous TiO2/RuO2/CuO nanomaterials

Journal of Sol-Gel Science and Technology - Highly textured mixed metal oxide nano systems consisting of TiO2, RuO2, and CuO (TiO2/RuO2/CuO) were developed through triblock copolymer and Pluronic...     

Kinetics and mechanism of chlorination of p-aminobenzoic acid by chloramine-B

The chlorination of p-aminobenzoic acid (PABA) by chloramine-B (CAB) in HCl medium at 303 K indicates simultaneous catalysis by H⁺ and Cl^–. The reaction is first order in [CAB] and [HCl], but fractional order in [PABA]. The observed solvent isotope effect is 1.52. A suitable mechanism is proposed.

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- (PABA) -B (CAB) HCl 303 H⁺ Cl^–. [PABA]. 1,52. .

     

Choline chloride·2ZnCl2 ionic liquid: an efficient and reusable catalyst for the solvent free Kabachnik–Fields reaction

The choline based Zn containing deep eutectic mixture was applied as an efficient and eco-friendly ionic liquid catalyst for the one pot three-component synthesis of α-aminophosphonates under solvent-free condition at room temperature. The reactions were completed in short times and products were obtained in good to excellent yields.     

Wound infection kinetics probed by MALDI-MS: rapid profiling of Staphylococcus aureus in mice

Using direct matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS), we were able to investigate the role of the clinically important bacteria, Staphylococcus aureus, in wound infections using mice. The infection kinetics of S. aureus at the wound site and the host immune response has been investigated using MALDI-MS. In this study, for the first time, we report the growth pattern of S. aureus infection at a wound site. Using mice wound infection models; the following study fingerprints the bacterial-host (mice) response at the wound site as a function of increasing wound infection in order to establish the infection pattern of Staphylococcus aureus in wounds. The current approach is extremely simple, rapid, highly selective, sensitive and established MALDI-MS as a versatile tool for detecting bacteria in clinical samples, such as those collected from wound sites.