SUPFAM: A database of sequence superfamilies of protein domains

BACKGROUND: SUPFAM database is a compilation of superfamily relationships between protein domain families of either known or unknown 3-D structure. In SUPFAM, sequence families from Pfam and structural families from SCOP are associated, using profile matching, to result in sequence superfamilies of known structure. Subsequently all-against-all family profile matches are made to deduce a list of new potential superfamilies of yet unknown structure. DESCRIPTION: The current version of SUPFAM (release 1.4) corresponds to significant enhancements and major developments compared to the earlier and basic version. In the present version we have used RPS-BLAST, which is robust and sensitive, for profile matching. The reliability of connections between protein families is ensured better than before by use of benchmarked criteria involving strict e-value cut-off and a minimal alignment length condition. An e-value based indication of reliability of connections is now presented in the database. Web access to a RPS-BLAST-based tool to associate a query sequence to one of the family profiles in SUPFAM is available with the current release. In terms of the scientific content the present release of SUPFAM is entirely reorganized with the use of 6190 Pfam families and 2317 structural families derived from SCOP. Due to a steep increase in the number of sequence and structural families used in SUPFAM the details of scientific content in the present release are almost entirely complementary to previous basic version. Of the 2286 families, we could relate 245 Pfam families with apparently no structural information to families of known 3-D structures, thus resulting in the identification of new families in the existing superfamilies. Using the profiles of 3904 Pfam families of yet unknown structure, an all-against-all comparison involving sequence-profile match resulted in clustering of 96 Pfam families into 39 new potential superfamilies. CONCLUSION: SUPFAM presents many non-trivial superfamily relationships of sequence families involved in a variety of functions and hence the information content is of interest to a wide scientific community. The grouping of related proteins without a known structure in SUPFAM is useful in identifying priority targets for structural genomics initiatives and in the assignment of putative functions. Database URL:

Evaluation of the performance of SAR and SAR-optical fused dataset for crop discrimination

Crop discrimination and acreage play a vital role in interpreting the cropping pattern, statistics of the produce and market value of each product. Sultan Battery is an area where a large amount of irrigated and rainfed paddy crops are grown along with Rubber, Arecanut and Coconut. In addition, the northern region of Sultan Battery is covered with evergreen and deciduous forest. In this study, the main objective is to evaluate the performance of optical and Synthetic Aperture Radar (SAR)-optical hybrid fusion imageries for crop discrimination in Sultan Bathery Taluk of Wayanad district in Kerala. Seven land use classes such as paddy, rubber, coconut, deciduous forest, evergreen forest, water bodies and others land use (e.g., built-up, barren etc.) were selected based on literature review and local land use classification policy. Both Sentinel-2A (optical) and sentinel-1A (SAR) satellite imageries of 2017 for Kharif season were used for classification using three machine learning classifiers such as Support Vector Machine (SVM), Random Forest (RF) and Classification and Regression Trees (CART). Further, the performance of these techniques was also compared in order to select the best classifier. In addition, spectral indices and textural matrices (NDVI, GLCM) were extracted from the image and best features were selected using the sequential feature selection approach. Thus, 10-fold cross-validation was employed for parameter tuning of such classifiers to select best hyperparameters to improve the classification accuracy. Finally, best features, best hyperparameters were used for final classification and accuracy assessment. The results show that SVM outperforms the RF and CART and similarly, Optical+SAR datasets outperforms the optical and SAR satellite imageries. This study is very supportive for the earth observation scientists to support promising guideline to the agricultural scientist, policy-makers and local government for sustainable agriculture practice

Influence of Cypermethrin on DNA and RNA Content in Different Organs of Fresh Water Fish Cyprinus carpio: Effect of Cypermethrin on DNA and RNA in Fishes

In this study, freshwater fish Cyprinus carpio was exposed to sub lethal concentration of synthetic pyrethroids insecticide cypermethrin to evaluate the impact on nucleic acids in different organs. Fishes were exposed to sub lethal concentration (1/10th of LC50 value) of cypermethrin for three different durations, 7, 14 and 21 days. In seven day exposed fishes, DNA and RNA contents were not altered by cypermethrin. Whereas in 14 day and 21 day exposed fishes the DNA and RNA content decreased significantly in brain, gills and liver. However, the decrease was more in 21 day exposed fishes. The reduction in the DNA and RNA content in cypermethrin exposed fishes is comparatively less in liver when compared to the brain and gills. Cypermethrin treatment diminished RNA/DNA ratio in all the fish organs tested. In all the three organs studied, the influence of cypermethrin was found to be exposure time dependent

Enhanced Metastatic Potential in a 3D Tissue Scaffold toward a Comprehensive in Vitro Model for Breast Cancer Metastasis

Metastasis is clinically the most challenging and lethal aspect of breast cancer. While animal-based xenograft models are expensive and time-consuming, conventional two-dimensional (2D) cell culture systems fail to mimic in vivo signaling. In this study we have developed a three-dimensional (3D) scaffold system that better mimics the topography and mechanical properties of the breast tumor, thus recreating the tumor microenvironment in vitro to study breast cancer metastasis. Porous poly(e-caprolactone) (PCL) scaffolds of modulus 7.0 +/- 0.5 kPa, comparable to that of breast tumor tissue were fabricated, on which MDA-MB-231 cells proliferated forming tumoroids. A comparative gene expression analysis revealed that cells growing in the scaffolds expressed increased levels of genes implicated in the three major events of metastasis, viz., initiation, progression, and the site-specific colonization compared to cells grown in conventional 2D tissue culture polystyrene (TCPS) dishes. The cells cultured in scaffolds showed increased invasiveness and sphere efficiency in vitro and increased lung metastasis in vivo. A global gene expression analysis revealed a significant increase in the expression of genes involved in cell cell and cell matrix interactions and tissue remodeling, cancer inflammation, and the PI3K/Akt, Wnt, NF-kappaB, and HIFI signaling pathways all of which are implicated in metastasis. Thus, culturing breast cancer cells in 3D scaffolds that mimic the in vivo tumor-like microenvironment enhances their metastatic potential. This system could serve as a comprehensive in vitro model to investigate the manifold mechanisms of breast cancer metastasis

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of protein domains in various families. The latest updated version (Release 2.1) comprises of 844 families of homologous proteins involving 3863 protein domain structures with each of these families having at least two members. Each member in a family has been structurally aligned with every other member in the same family using two proteins at a time. In addition, an alignment of multiple structures has also been performed using all the members in a family. Every family with at least three members is associated with two dendrograms, one based on a structural dissimilarity metric and the other based on similarity of topologically equivalenced residues for every pairwise alignment. Apart from these multi-member families, there are 817 single member families in the updated version of PALI. A new feature in the current release of PALI is the integration, with 3-D structural families, of sequences of homologues from the sequence databases. Alignments between homologous proteins of known 3-D structure and those without an experimentally derived structure are also provided for every family in the enhanced version of PALI. The database with several web interfaced utilities can be accessed at: http://pauling.mbu.iisc.ernet.in/~pali

Influence of Aluminium Chloride on Antioxidant System in the Testis and Epididymis of Rats

Background: In recent years, the use of chemicals in agriculture, industry, and public health has become so common that the environment is continuously contaminated by the toxic substance-like metals. Aluminum released due to anthropogenic activities such as mining and industrial uses. Aluminium has several industrial uses. The present study was designed to investigate the effect of aluminium chloride (AlCl3) on enzymatic and non-enzymatic antioxidants in the testis and epididymis of rats. Methods: Adult male rats were administered with aluminium chloride at two different doses, 50 mg and 100 mg/kg body weight, orally, daily for 45 days. At the end of the experimental period, the animals were sacrificed and their testis and the epididymis were removed. Antioxidant enzymes like catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), glutathione reductase (GR), and glutathione-s-transferase (GST) were assayed. Lipid peroxidation (LPO), vitamin C, and vitamin E levels were also determined. Results: Aluminium chloride administration had no effect on the bodyweight of the animals but the weight of the testis and epididymis was decreased. Almost all the antioxidant enzymes studied markedly diminished in the testis and epididymis of aluminium chloride treated animals. The non-enzymatic antioxidants, vitamin C and vitamin E, also declined. Lipid peroxidation, on the other hand, significantly increased. The influence was found to be more in 100 mg treated rats when compared to 50 mg treated rats. Conclusions: The present study suggests the reproductive toxicity of aluminium by inducing the oxidative stress in the testis and epididymis and possible interference in sperm production and further maturational processes