Dwijendra K. Gupta

Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation

Vesiclepedia is a community-annotated compendium of molecular data on extracellular vesicles.

EVpedia: a community web portal for extracellular vesicles research

MOTIVATION Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. RESULTS We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. AVAILABILITY AND IMPLEMENTATION The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info.

Centchroman mediated apoptosis involves cross-talk between extrinsic/intrinsic pathways and oxidative regulation

AIMS Centchroman (CC) has been established as a potent antineoplastic agent in MCF-7 (ER+ve) and MDA MB-231 (ER-ve) Human Breast Cancer Cells (HBCCs) previously by us. To elucidate its antineoplastic action, we investigated the factors involved in cell-cycle progression and apoptosis. MAIN METHODS Tamoxifen (TAM), a widely used antiestrogen was employed as a positive control. Role of Cycloheximide (CHX), Actinomycin-D (Act-D) and caspases were explored using specific inhibitors. Involvement of cell-cycle and apoptosis related factors were explored using western blotting and immunoprecipitation. KEY FINDINGS Metabolic inhibitors viz. CHX, Act-D and pan-Caspase inhibitor, Z-VAD-FMK attenuated CC-induced apoptosis. The upregulation of both p21(Waf1/Cip1) and p27(Kip1) along with p21-CDK6 (Cyclin Dependent Kinase 6) and p21-PCNA (Proliferating Cell Nuclear Antigen) interaction suggests their role in CC-induced cell-cycle arrest. The downregulation of Cyclin-D(1) and -E levels further confirms the antiestrogenic profile of CC. Unlike MDA MB-231, in MCF-7 cells, CC upregulates the level of phospho-p53 (Ser-15) and FasL, suggesting the involvement of extrinsic pathway. CC altered the intracytosolic balance of members of Bcl-2 family along with the cleavage of Poly (ADP-ribose) polymerase (PARP), Bcl-X(L), Bid and AIF (Apoptosis Inducing Factor). The evaluation of Mitogen Activated Protein Kinases (MAPKs) using specific inhibitors and Western blotting confirms CC-induced the upregulation of phospho-c-Jun and phospho-p38. Additionally elevated SOD (Superoxide Dismutase) and unaltered CAT (Catalase) expression further suggest the involvement of oxidative stress. SIGNIFICANCE These results confirm that the antineoplasticity of CC in MCF-7 and MDA MB-231 cells involves the extrinsic and intrinsic pathways of apoptosis along with oxidative stress.

The effect of exposure to low temperature on the metabolism of carbohydrates, lipids and protein in the larvae ofPhilosamia ricini

Exposure of the silkworm(Philosamia ricini) larvae to cold temperature (2‡C) and subsequent exposure to room temperature (29‡ C) resulted in the mortality of the larvae.Cold exposure brought about significant decrease in enzymic activity of proteases, aminotransferases, diacylglycerol lipase and in the amounts of some haemolymph sugars and polyols. However, glycerol increased sharply in response to severe cold exposure. There was also a marked increase in the levels of protein, pyruvate, total free amino acids, total lipid, phospholipid and triacylglycerols.In the colder environment, carbohydrates served as the energy source. Glycerol appears to have conferred cryoprotection to the cold-stressedPhilosamia ricini larvae.

Discriminating lysosomal membrane protein types using dynamic neural network

This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.

Cold shock domain protein from Philosamia ricini prefers single-stranded nucleic acids binding.

The cold shock proteins are evolutionarily conserved nucleic acid-binding proteins. Their eukaryotic homologs are present as cold shock domain (CSD) in Y-box proteins. CSDs too share striking similarity among different organisms and show nucleic acid binding properties. The purpose of the study was to investigate the preferential binding affinity of CSD protein for nucleic acids in Philosamia ricini. We have cloned and sequenced the first cDNA coding for Y-box protein in P. ricini; the sequence has been deposited in GenBank. Comparative genomics and phylogenetic analytics further confirmed that the deduced amino acid sequence belongs to the CSD protein family. A comparative study employing molecular docking was performed with P. ricini CSD, human CSD, and bacterial cold shock protein with a range of nucleic acid entities. The results indicate that CSD per se exhibits preferential binding affinity for single-stranded RNA and DNA. Possibly, the flanking N- and C-terminal domains are additionally involved in interactions with dsDNA or in conferring extra stability to CSD for improved binding.

MEMBRANE FLUIDITY AND LIPID COMPOSITION OF FLUCONAZOLE RESISTANT AND SUSCEPTIBLE STRAINS OF CANDIDA ALBICANS ISOLATED FROM DIABETIC PATIENTS

Ten clinical isolates of Candida albicans, five strains belonging to each of fluconazole resistant and susceptible groups isolated from diabetic patients, were studied for the membrane fluidity and lipid composition. Compared to fluconazole susceptible strains, fluconazole resistant ones exhibited enhanced membrane fluidity as measured by fluorescence polarization technique. The increased membrane fluidity was reflected in the decreased p-values exhibited by the resistant strains. On the other hand, susceptible isolates contained higher amount of ergosterol, almost twice as compared to resistant isolates which might have contributed to their lower membrane fluidity. However, no significant alteration was observed in the phospholipid and fatty acid composition of these isolates. Labeling experiments with fluorescamine dye revealed that the percentage of the exposed aminophospholipid, phosphatidylethanolamine was highest in the resistant strains as compared to the susceptible strains, indicating a possible overexpression of CDR1 and CDR2 genes in resistant strains. The results presented here suggest that the changes in the ergosterol content and overexpression of ABC transporter genes CDR1 and CDR2 could contribute to fluconazole resistance in C. albicans isolated from diabetic patients.

Single-stranded nucleic acid binding in Arabidopsis thaliana cold shock protein is cold shock domain dependent

Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. The CSPs have been shown to play important role in development and stress adaptation in various plant species. The objective of this study was to find out the possible nucleic acid-binding affinities of whole CSP as well as independent domains, so that role of each individual domain may be revealed in Arabidopsis thaliana, the model plant species. The structure of CSP 3 protein from A. thaliana was modeled by homology-based approach and docking was done with different nucleic acid types.

Evolutionary analysis of circumsporozoite surface protein and merozoite surface protein-1 (CSP and MSP-1) sequences of malaria parasites

Malaria, one of the worlds most common diseases, is caused by the intracellular protozoan parasite known as Plasmodium. In this study, we have determined the evolutionary relationship of two single-copy proteins, circumsporozoite protein (CSP) and merozoite surface protein-1 (MSP-1), among Plasmodium species using various bioinformatics tools and softwares. These two proteins are major blood stage antigens of Plasmodium species. This study demonstrates that the circumsporozoite protein of Plasmodium falciparum shows similarity with Plasmodium cynomolgi and Plasmodium knowlesi. The merozoite surface protein-1 of Plasmodium coatneyi forms a monophyletic group with Plasmodium knowlesi, demonstrating their close relationship and these two species also reveal similarity between the human malaria Plasmodium vivax. This Plasmodium phylogenetic arrangement is evidently crucial to identify shared derived characters as well as particular adaptation of plasmodium species from inside and between monophyletic groups.

B(E2) values for transitions from high-spin states in deformed even-even nuclei

SummaryTheB(E2) values of gamma-ray cascades in interrotational-band transitions for high-spin states in deformed even-even nuclei in rare-earth and actinide regions have been calculated in the framework of the rotational vibrational model (RVM) and the Davydov-Rostovsky (DR) model. The transitions involved are 4+→2+, 6+→4+, 8+→6+, 10+→8+, 12+→10+ and 14+→12+. The calculated values have been compared with the experimental ones. In general, the RVM predictions show good agreement with the experimental values. The comparative study indicates that the phase transition of the rotational model from axially symmetric to asymmetric shape appears to take place atI=12 instead ofI=8.RiassuntoNell’ambito del modello vibrazionale rotazionale (RVM) e in quello di Davydov-Rostovsky (DR) sono stati calcolati i valoriB(E2) delle cascate di raggi gamma in transizioni di bande interrotazionali per stati ad alto spin in nuclei deformati pari-pari nelle regioni delle terre rare e degli attinidi. Queste transizioni sono 4+→2+, 6+→4+, 8+→6+, 10+→8+, 12+→10+ and 14+→12+. I valori calcolati sono stati confrontati con quelli sperimentali. In generale, le previsioni dell’RVM mostrano un buon accordo coi valori sperimentali. Uno studio comparativo indica che la transizione di fase del modello rotazionale da una forma assialmente simmetrica ad una asimmetrica sembra avvenire conI=12 invece diI=8.РеэюмеИспольэуя ротационную модель, ротационно-вибраци онную модель и модель Давыдова-Ростовского, вычисляютсяB(E2) величины состояний с больщими спинами для внутриэонных ротационных переходов в деформированных четно-четных ядрах, относяшихся к редкоэемельной области и области актинидов. Вычисленные величины сравниваются с иэвестными зкспериментальными данными. Обнаружено, что реэультаты ротационно-вибрацио нной модели хорощо согласуются с иэвестными зкспериментальными данными. Проведенный аналиэ отражает аксиально-симметри чное описание для зтих ядер со слабо выраженной симметрией приI=12 вместоI=8.