Evaluation of different generic in silico methods for predicting HLA class I binding peptide vaccine candidates using a reverse approach

Since CD8⁺ T cell response is crucial to combat intracellular infections and cancer, identification of class I HLA binding peptides is of immense clinical value. The experimental identification of such peptides is protracted and laborious. Exploiting in silico tools to discover such peptides is an attractive alternative. However, this approach needs a thorough assessment before its elaborate application. We have adopted a reverse approach to evaluate the reliability of eight different servers (inclusive of 55 predictors) by exploiting experimentally proven data. A comprehensive data set of more than 960 peptides was employed to test the efficacy of the programs. We have validated commonly used strategies to predict peptides that bind to seven most prevalent HLA class I alleles. We conclude that four of the eight servers are more adept in predictions. Although the overall predictions for class I MHC binders were superior to class II MHC binders, individual predictors for different alleles belonging to the same program were highly variable in their efficiencies. We have also addressed whether a consensus approach can yield better prediction efficiency. We observed that combining the results from different in silico programs could not increase the efficiency significantly.     

Abundance and composition of forest-dwelling anurans in cashew plantations in a tropical semi-evergreen forest landscape

Plantation crops in tropical human-modified landscapes provide alternative habitats to biodiversity outside protected areas. The Western Ghats of India are home to a mosaic of closely spaced habitats, including forests and agroecosystems. Cashew is a widely grown plantation crop in the northern Western Ghats and is known to provide economic and societal benefits. However, its role as a supplementary habitat for anurans is not well understood. We assessed the factors that influence understorey anuran composition and abundance in cashew plantations, forest edges, and forest interiors in Tillari Conservation Reserve, Maharashtra. Species composition of cashew plantations differed significantly from forests and was positively influenced by understorey and canopy cover. Cashew plantations had a near equal abundance of anurans as that of forest edges and interiors, which could be due to the preponderance of habitat generalists. Understorey positively influenced anuran abundance while ambient temperature had a negative influence. Reduced understorey and low canopy cover represent habitat modifications that occur in cashew plantations. Such structural changes could lead to reduced environmental refuges for anurans, thereby exposing them to large variations in temperature and moisture. Cashew plantations in Tillari Conservation Reserve serve as supplementary habitats for anurans. That said, cashew cultivation practices and markets must be understood before biodiversity-friendly plantation practices are proposed.     

Assessment of immunological parameters during tumour development in a murine model

Natural Killer activity assessed by 51Cr release assay from K-562 cells showed detectable activity from 5th day after tumour transplantation, reaching a peak on 12th day and thereafter showing a gradual decline in the activity. Antibody dependent cell mediated cytotoxicity estimated by 51Cr labelled sheep red blood cells anti SRBC system demonstrated a peak activity on 5th day. Cytotoxic T lymphocyte activity detected by 51Cr release of Dalton's lymphoma ascites target cells showed a peak on 10th day. Antibody complement mediated cytotoxicity revealed a similar pattern as natural killer cell activity.     

Serum immunoglobulins in patients with carcinoma of the oral cavity,uterine cervix and breast

Summary Serum immunoglobulin levels (IgG, IgA, IgM, IgD and IgE) were estimated in 196 patients with carcinoma of the oral cavity, 172 patients with cervical cancer and 166 patients with breast cancer. The values were compared with those of 50 patients with benign lesions of the breast and cervix and 100 healthy adult controls. Only the serum IgE levels were found to be elevated in the benign group. Serum IgA, IgD and IgE levels were found to be elevated in all the three types of cancers and the levels were found to increase with clinical stage. In carcinoma of uterine cervix IgG levels were also found to be elevated. Immunoglobulins A and D returned to normal after clinical cure whereas IgE remained slightly elevated. IgD and IgE remained high in patients who had residual cancer.