TNFα regulates the localization of CD40 in lipid rafts of glioma cells

Resistance of glioblastoma multiforme (GBM) to TNFα induced apoptosis is attributed to NFκB activation. As TNF-receptor family member CD40 regulates NFκB activation, we investigated the role of CD40 in NFκB activation in GBM. We observed elevated CD40 levels in human glioma samples as compared to the surrounding normal tissue. Treatment with TNFα elevated CD40 levels in glioma cells and inhibition of CD40 signaling failed to abrogate TNFα induced NFκΒ activity. While TNFα increased the interaction between TRAF2/6, IκBα, IKKα/β in the CD40 signalosome, the level of CD40 in the signalosome remained unaffected upon TNFα treatment. Interestingly, TNFα decreased the spatial localization of CD40 and increased TRAF2/6 co-localization with lipid raft marker Caveolin. As localization of CD40 signalosome in lipid raft is crucial for NFκB activation, TNFα mediated decreased clustering of CD40 in lipid rafts could have possibly contributed to its non-involvement in NFκB activation.     

Tagging SNPs in the kallikrein genes 3 and 2 on 19q13 and their associations with prostate cancer in men of European origin

Two of the classical kallikrein genes KLK3 and KLK2 on 19q13.4 are plausible candidates in prostate cancer susceptibility. They are expressed almost exclusively in prostate tissue. We have performed a comprehensive analysis of association of variants in these two genes with prostate cancer among men of European descent using a tagging SNP approach. Thirteen SNPs selected from the HapMap database were analyzed in a sample of 596 histologically verified prostate cancer cases and 567 ethnically matched controls. Five SNPs showed significant association at single marker level. Linkage disequilibrium (LD) analysis revealed four LD blocks. We performed a haplotype analysis within each LD block. A major haplotype in block 1 that contains the first two significantly associated SNPs was significantly underrepresented in the prostate cancer cases; a second haplotype in block 3 also showed significant frequency differences between cases and controls. Four of the studied SNPs show positive associations with serum PSA levels. A structure analysis revealed no population stratification in our samples that could have confounded the association results. These findings suggest a plausible role of kallikrein gene variants in the etiology of prostate cancer among men of European ancestry.     

Lipolysis and lipophagy play individual and interactive roles in regulating triacylglycerol and cholesterol homeostasis and mitochondrial form in zebrafish

Neutral lipases-mediated lipolysis and acid lipases-moderated lipophagy are two main processes for degradation of lipid droplets (LDs). However, the individual and interactive roles of these metabolic pathways are not well known across vertebrates. This study explored the roles of lipolysis and lipophagy from the aspect of neutral and acid lipases in zebrafish. We established zebrafish strains deficient in either adipose triglyceride lipase (atgl^?/?; AKO fish) or lysosomal acid lipase (lal^?/?; LKO fish) respectively, and then inhibited lipolysis in the LKO fish and lipophagy in the AKO fish by feeding diets supplemented with the corresponding inhibitors Atglistatin and 3-Methyladenine, respectively. Both the AKO and LKO fish showed reduced growth, swimming activity, and oxygen consumption. The AKO fish did not show phenotypes in adipose tissue, but mainly accumulated triacylglycerol (TAG) in liver, also, they had large LDs in the hepatocytes, and did not stimulate lipophagy as a compensation response but maintained basal lipophagy. The LKO fish reduced total lipid accumulation in the body but had high cholesterol content in liver; also, they accumulated small LDs in the hepatocytes, and showed increased lipolysis, especially Atgl expression, as a compensatory mechanism. Simultaneous inhibition of lipolysis and lipophagy in zebrafish resulted in severe liver damage, with the potential to trigger mitophagy. Overall, our study illustrates that lipolysis and lipophagy perform individual and interactive roles in maintaining homeostasis of TAG and cholesterol metabolism. Furthermore, the interactive roles of lipolysis and lipophagy may be essential in regulating the functions and form of mitochondria.     

Crystal structure of the nucleotide‐binding domain of mortalin,the mitochondrial Hsp70 chaperone

Mortalin, a member of the Hsp70‐family of molecular chaperones, functions in a variety of processes including mitochondrial protein import and quality control, Fe‐S cluster protein biogenesis, mitochondrial homeostasis, and regulation of p53. Mortalin is implicated in regulation of apoptosis, cell stress response, neurodegeneration, and cancer and is a target of the antitumor compound MKT‐077. Like other Hsp70‐family members, Mortalin consists of a nucleotide‐binding domain (NBD) and a substrate‐binding domain. We determined the crystal structure of the NBD of human Mortalin at 2.8 Å resolution. Although the Mortalin nucleotide‐binding pocket is highly conserved relative to other Hsp70 family members, we find that its nucleotide affinity is weaker than that of Hsc70. A Parkinson's disease‐associated mutation is located on the Mortalin‐NBD surface and may contribute to Mortalin aggregation. We present structure‐based models for how the Mortalin‐NBD may interact with the nucleotide exchange factor GrpEL1, with p53, and with MKT‐077. Our structure may contribute to the understanding of disease‐associated Mortalin mutations and to improved Mortalin‐targeting antitumor compounds.     

Roundup: a multi-genome repository of orthologs and evolutionary distances

SUMMARY: We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that has been shown to improve upon alternative approaches of ortholog detection, such as reciprocal blast. Presently, the Roundup repository contains all possible pair-wise comparisons for over 250 genomes, including 32 Eukaryotes, more than doubling the coverage of any similar resource. The orthologs are accessible through an intuitive web interface that allows searches by genome or gene identifier, presenting results as phylogenetic profiles together with gene and molecular function annotations. Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data. AVAILABILITY: http://rodeo.med.harvard.edu/tools/roundup.     

CO-WOA: Novel Optimization Approach for Deep Learning Classification of Fish Image

The most significant groupings of cold-blooded creatures are the fish family. It is crucial to recognize and categorize the most significant species of fish since various species of seafood diseases and decay exhibit different symptoms. Systems based on enhanced deep learning can replace the area's currently cumbersome and sluggish traditional approaches. Although it seems straightforward, classifying fish images is a complex procedure. In addition, the scientific study of population distribution and geographic patterns is important for advancing the field's present advancements. The goal of the proposed work is to identify the best performing strategy using cutting-edge computer vision, the Chaotic Oppositional Based Whale Optimization Algorithm (CO-WOA), and data mining techniques. Performance comparisons with leading models, such as Convolutional Neural Networks (CNN) and VGG-19, are made to confirm the applicability of the suggested method. The suggested feature extraction approach with Proposed Deep Learning Model was used in the research, yielding accuracy rates of 100 %. The performance was also compared to cutting-edge image processing models with an accuracy of 98.48 %, 98.58 %, 99.04 %, 98.44 %, 99.18 % and 99.63 % such as Convolutional Neural Networks, ResNet150V2, DenseNet, Visual Geometry Group-19, Inception V3, Xception. Using an empirical method leveraging artificial neural networks, the Proposed Deep Learning model was shown to be the best model.     

Morphological alterations in erythrocytes treated with silver nanoparticles biomineralized by marine sediment-derived Bacillus sp. VITSSN01

Biomineralization-inspired preparation of nanoparticles by marine microorganisms is in the limelight of modern nanotechnology. In recent years, the use of marine microorganisms for the synthesis of nanoparticles has been gaining importance due to the simplicity and eco-friendliness of the approach. Here we describe the synthesis of silver nanoparticles using halotolerant Bacillus sp. isolated from the southern coastal waters of India. Our selective and enriched isolation technique resulted in the isolation of a silver nitrate-resistant novel marine Bacillus sp. isolated from sediments collected at Ennore Port, Chennai, India. The strain was characterized by the polyphasic taxonomic approach, and phenotypic and phylogenetic analysis identified the strain as Bacillus sp. VITSSN01. The resistant strain was further assayed for the synthesis of silver nanoparticles and its biological activity evaluated. Nanoparticles were synthesized under optimized nutritional and cultural conditions with shaking and the production continuously monitored. The nanoparticles thus produced were then characterized by atomic force microscopy, X-ray diffraction, Fourier transform-infrared spectrophotometer and transmission electron microscopy. The mean particle size was 46 nm. Hemotological toxicity of nanoparticles is very severe form and less studied. We therefore checked the synthesized silver nanoparticles for toxicity against erythrocytes and found that the silver nanoparticles exhibited moderate hemolytic activity against human erythrocytes, with a half maximal effective concentration (EC₅₀) value of 60 μg/ml. Microscopic studies of the treated erythrocytes showed slight structural perturbations. The results of our study strongly suggest that marine microorganisms could be a potential source for the rapid and eco-friendly synthesis of nanoparticles.     

Potential Therapeutic Agents on Alzheimer's Disease through Molecular Docking and Molecular Dynamics Simulation Study of Plant-Based Compounds

Globally Alzheimer's disease (AD) is a highly complex, heterogeneous, and multifactorial neurological disease. AD is categorized clinically through a steady loss in memory and progressive decline of cognitive function. So far, there is no effective cure is available for the treatment of AD. Here, we identified Plant-based compounds (PBCs) from seven therapeutic plants through pharmacophore and pharmacokinetics approaches. Subsequently, we retrieved 65 AD associated proteins by Text Mining approach .We observed the interactions between 39 PBCs with 65 AD-associated targets by using molecular docking. Further, we carried out Molecular dynamics simulation analysis to predict the steady binding of top drug-target complexes. The entire MD simulation results analysis was evidence that seven drug-target complexes consistently interacted during the in silico experiment. The top complexes were the target CHLE interacted with 2 PBCs (Pseudojujubogenin and Anahygrine), target VDAC1 interacted with Withanolide R, target THOP1 interacted with Withaolide R, target AOFB interacted with 2 PBCs (Nardostachysin and Viscosalactone B), and target ACHE interacted with the drug (12-Deoxywithastramonolide). These PBCs have stably and flexibly interacted at the protein‘s active site region. Our results suggest that these PBCs and targets are potential therapeutic candidates for molecular development in AD.