Assessment of Toluidine Blue in Oral Leukoplakia

Squamous cell carcinoma is the most common cancer of the oral cavity and the prognosis of the tumor depends on the early detection of the carcinoma. Toluidine blue is a metachromatic die of the thiazine group that has been effectively used as a nuclear stain because of its binding capacity with DNA. The objective of the study was to find the specificity and sensitivity of the toluidine blue supra vital staining technique in oral leukoplakia. The study comprised of 17 clinically suspicious cases of oral leukoplakia. The effect of toluidine blue staining and histopathological features were also studied. The toluidine blue staining is a sensitive vital staining method for leukoplakia. It is the useful chair side diagnostic test with the sensitivity of 92% and specificity of 100%.   KEYWORDS:  Oral Leukoplakia, toluidine blu

Enabling ab initio Hessian and frequency calculations of large molecules

A linear scaling method, termed as cardinality guided molecular tailoring approach, is applied for the estimation of the Hessian matrix and frequency calculations of spatially extended molecules. The method is put to test on a number of molecular systems largely employing the Hartree-Fock and density functional theory for a variety of basis sets. To demonstrate its ability for correlated methods, we have also performed a few test calculations at the Moller-Plesset second order perturbation theory. A comparison of central processing unit and memory requirements for medium-sized systems with those for the corresponding full ab initio computation reveals substantial gains with negligible loss of accuracy. The technique is further employed for a set of larger molecules, Hessian and frequency calculations of which are not possible on commonly available personal-computer-type hardware.Financial support from the Center for Development of Advanced Computing C-DAC, Pune, Naval Research Board NRB, New Delhi, and Council of Scientific and Industrial Research CSIR, New Delhi is gratefully acknowledged

Many-body interaction analysis: Algorithm development and application to large molecular clusters

A completely automated algorithm for performing many-body interaction energy analysis of clusters (MBAC) [M. J. Elrodt and R. J. Saykally, Chem. Rev. 94, 1975 (1994); S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996)] at restricted Hartree-Fock (RHF)/MA Plesset 2nd order perturbation theory (MP2)/density functional theory (DFT) level of theory is reported. Use of superior guess density matrices (DM's) for smaller fragments generated from DM of the parent system and elimination of energetically insignificant higher-body combinations, leads to a more efficient performance (speed-up up to 2) compared to the conventional procedure. MBAC approach has been tested out on several large-sized weakly bound molecular clusters such as (H(2)O)(n), n=8, 12, 16, 20 and hydrated clusters of amides and aldehydes. The MBAC results indicate that the amides interact more strongly with water than aldehydes in these clusters. It also reconfirms minimization of the basis set superposition error for large cluster on using superior quality basis set. In case of larger weakly bound clusters, the contributions higher than four body are found to be repulsive in nature and smaller in magnitude. The reason for this may be attributed to the increased random orientations of the interacting molecules separated from each other by large distances.Financial support from the Council of Scientific and Industrial Research (CSIR), New Delhi, India and the Center for Development of Advanced Computing (C-DAC), Pune, India, is gratefully acknowledged

Molecular tailoring approach for geometry optimization of large molecules: Energy evaluation and parallelization strategies

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including alpha-tocopherol, taxol, gamma-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.The authors thank C-DAC, UGC (CAS program to the University of Pune) and the Council of Scientific and Industrial Research (CSIR), New Delhi for financial assistance

Molecular tailoring approach for exploring structures, energetics and properties of clusters

Molecular Tailoring Approach (MTA) is a method developed for enabling ab initio calculations on prohibitively large molecules or atomic/molecular clusters. A brief review of MTA, a linear scaling technique based on set inclusion and exclusion principle, is provided. The Molecular Electrostatic Potential (MESP) of smaller clusters is exploited for building initial geometries for the larger ones, followed by MTA geometry optimization. The applications of MTA are illustrated with a few test cases such as (CO2)n and Lin clusters employing Density Functional theory (DFT) and a nanocluster of orthoboric acid at the Hartree-Fock (HF) level. Further, a discussion on the geometries and energetics of benzene tetramers and pentamers, treated at the Moller-Plesset second order (MP2) perturbation theory, is given. MTA model is employed for evaluating some cluster properties viz. adiabatic ionization potential, MESP, polarizability, Hessian matrix and infrared frequencies. These property evaluations are carried out on a series of test cases and are seen to offer quite good agreement with those computed by an actual calculation. These case studies highlight the advantages of MTA model calculations vis-a-vis the actual ones with reference to the CPU-time, memory requirements and accuracy

The CD8 Antiviral Factor (CAF) can suppress HIV-1 transcription from the Long Terminal Repeat (LTR) promoter in the absence of elements upstream of the CATATAA box

Background: The CD8 Antiviral Factor (CAF) suppresses viral transcription from the HIV-1 Long Terminal Repeat (LTR) promoter in a non-cytolytic manner. However, the region on the LTR upon which CAF acts is unknown. Our objective was to determine the region on the LTR upon which CAF acts to suppress HIV-1 transcription. Methods. Serial deletions of the LTR from the 5' end and inactivating point mutations were made

Comprehensive analysis of preeclampsia-associated DNA methylation in the placenta

Background:A small number of recent reports have suggested that altered placental DNA methylation may be associated with early onset preeclampsia. It is important that further studies be undertaken to confirm and develop these findings. We therefore undertook a systematic analysis of DNA methylation patterns in placental tissue from 24 women with preeclampsia and 24 with uncomplicated pregnancy outcome

Construction of a series of vectors for high throughput cloning and expression screening of membrane proteins from Mycobacterium tuberculosis

<p>Abstract</p> <p>Background</p> <p>One of the major challenges for membrane protein structural genomics is establishing high-throughput cloning and expression screening methods to obtain enough purified protein in a homogeneous preparation for structural and functional studies. Here a series of ligation independent cloning based vectors were constructed to address this challenge.</p> <p>Results</p> <p>The feasibility of these vectors was tested with 41 putative membrane proteins from <it>Mycobacterium tuberculosis</it>. The efficiency for direct cloning of these target genes from PCR products was 95% (39/41). Over 40% of cloned genes were overexpressed in <it>Escherichia coli </it>BL21 (DE3)-RP codon plus strain in the first round of expression screening. For those proteins which showed no expression, three protein fusion partners were prepared and it was found that each of the target proteins could be overexpressed by at least one of these fusions, resulting in the overexpression of two thirds of the cloned genes.</p> <p>Conclusion</p> <p>This expression platform features high throughput cloning, high flexibility for different constructs, and high efficiency for membrane protein overexpression, and is expected to be useful in membrane protein structural and functional studies.</p

Climate change awareness, preparedness, adaptation and mitigation strategies: Fisherfolks perception in Coastal Kerala

Coastal environments cover 8 per cent of the world’s surface, house 70 per cent of the human population, provide 90 per cent of the global f ish catch, and deliver 40 per cent of the estimated economic value derived from ecosystem goods and services. In addition to increasing population pressure and demand for marine protein, climate change is modifying coastal environments and increasing the vulnerability of marine-dependent communities around the world. Climate change is modifying the distribution, productivity of marine and freshwater species thereby impacts the sustainability of f isheries and aquaculture, eventually on the livelihoods of the communities that depend on f isheries. The effect of sea level rise means that coastal f ishing communities are vulnerable and are in the front line of the deleterious effects of climate change. Changing seawater temperature and current flows will likely bring increases, decreases and shifts in the distribution of marine f ish stocks, with some areas benef iting while others lose. These changes may have impacts on the nature and value of commercial f isheries. Many artisanal f ishers are extremely poor with social and political marginalization with limited access to healthcare, education and other public services. With little capacity to adapt, the small-scale and migrant f ishers are highly vulnerable to losses of natural capital consequent to climate impacts. The impacts of climate change going to affect economy as well the social standards of f isher folk with implications for food security and sustainablelivelihoods . Thus the climate change effects impact the environment, f ishery, social, economic and development drivers..Consequently, it is important to understand factors that contribute to vulnerability of coastal biological and human systems in order to develop sustainable adaptation pathways; and develop effective mechanisms and expertise to translate f indings into management guidelines and policy advice addressing natural, social and economic implications. Globally each government are looking for pragmatic time-bound strategies and plans for mitigation and adaptatio

Transgenic Strategies for Improved Drought Tolerance in Legumes of Semi-Arid Tropics

Water deficit is the most prominent abiotic stress that severely limits crop yields, thereby reducing opportunities to improve livelihoods of poor farmers in the semi-arid tropics (SAT) where most of the legumes, including groundnut and chickpea, are grown. Sustained long-term efforts in developing these legume crops with better drought tolerance through conventional breeding have been met with only limited success mainly because of an insufficient understanding of the underlying physiological mechanisms and lack of sufficient polymorphism for drought tolerance-related traits. Exhaustive efforts are being made at the International Crop Research Institute for Semi-Arid Tropics (ICRISAT) to improve crop productivity of the SAT crops by comprehensively addressing the constraints caused by water limitations. The transgenic approach has been used to speed up the process of molecular introgression of putatively beneficial genes for rapidly developing stress-tolerant legumes. Nevertheless, the task of generating transgenic cultivars requires success in the transformation process and proper incorporation of stress tolerance into plants. Hence, evaluation of the transgenic plants under stress conditions and understanding the physiological effect of the inserted genes at the whole plant level is critical. This review focuses on the recent progress achieved in using transgenic technology to improve drought tolerance, which includes evaluation of drought-stress response and protocols developed for testing transgenic plants under near-field conditions. A trait-based approach was considered, in which yield was dissected into components