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PubMed | University of Calcutta and Bose Institute
Type: Journal Article | Journal: The Journal of biological chemistry | Year: 2016

, a small protein found in most Gram-positive bacteria was, for a long time, thought to be a subunit of RNA polymerase (RNAP) and was shown to be involved in recycling of RNAP at the end of each round of transcription. However, how participates in both up-regulation and down-regulation of genes in vivo remains unclear. We have recently shown, in addition to the recycling of RNAP, functions as a transcriptional activator by binding to an A-rich sequence located immediately upstream of the -35 element, consequently facilitating the open complex formation. The result had explained the mechanism of up-regulation of the genes by . Here, we show that Bacillus subtilis could also function as a transcriptional repressor. Our results demonstrate that binds to an A-rich sequence located near the -35 element of the spo0B promoter, the gene involved in the regulatory cascade of bacterial sporulation and inhibits the open complex formation due to steric clash with region 4.2. We observed a significant increase in the mRNA level of the spo0B gene in a -knock-out strain of B. subtilis compared with the wild-type. Thus, the results report a novel function of , and suggest the mechanism of down-regulation of genes in vivo by the protein.


News Article | December 27, 2016
Site: www.eurekalert.org

The Biophysical Society has announced the winners of its international travel grants to attend the Biophysical Society's 61st Annual Meeting in New Orleans, February 11-15, 2017. The purpose of these awards is to foster and initiate further interaction between American biophysicists and scientists working in countries experiencing financial difficulties. Recipients of this competitive award are chosen based on scientific merit and their proposed presentation at the meeting. They will be honored at a reception on Sunday, February 12 at the Ernest N. Morial Convention Center. The 2017 recipients of the International Travel Award, along with their institutional affiliation and abstract title, are listed below. Ana F. Guedes, Institute of Molecular Medicine, Portugal, ATOMIC FORCE MICROSCOPY AS A TOOL TO EVALUATE THE RISK OF CARDIOVASCULAR DISEASES IN PATIENTS. Karishma Bhasne Mohali, Indian Institute of Science Education and Research (IISER), A TALE OF TWO AMYLOIDOGENIC INTRINSICALLY DISORDERED PROTEINS: INTERPLAY OF TAU AND α-SYNUCLEIN. Chan Cao, East China University of Science and Technology, DIRECT IDENTIFICATION OF ADENINE, THYMINE, CYTOSINE AND GUANINE USING AEROLYSIN NANOPORE. Venkata Reddy Chirasani, Indian Institute of Technology Madras, LIPID TRANSFER MECHANISM OF CETP BETWEEN HDL AND LDL: A COARSEGRAINED SIMULATION STUDY. Assaf Elazar, Weizmann Institute of Science, Israel, DECIPHERING MEMBRANE PROTEIN ENERGETICS USING DEEP SEQUENCING; TOWARDS ROBUST DESIGN AND STRUCTURE PREDICTION OF MEMBRANE PROTEINS. Manuela Gabriel, University of Buenos Aires, Argentina, 3D ORBITAL TRACKING OF SINGLE GOLD NANOPARTICLES: A NEW APPROACH TO STUDY VESICLE TRAFFICKING IN CHROMAFFIN CELLS. Farah Haque National Centre for Biological Sciences, India, A NEW HUMANIZED MOUSE MODEL FOR STUDYING INHERITED CARDIOMYOPATHIC MUTATIONS IN THE MYH7 GENE. Stephanie Heusser, Stockholm University, Switzerland, STRUCTURAL AND FUNCTIONAL EVIDENCE FOR MULTI-SITE ALLOSTERY MEDIATED BY GENERAL ANESTHETICS IN A MODEL LIGAND-GATED ION CHANNEL. Amir Irani, Massey University, New Zealand, HOMOGALACTURONANS ILLUMINATE THE ROLE OF COUNTERION CONDENSATION IN POLYELECTROLYTE TRANSPORT. Olfat Malak, University of Nantes, France, HIV-TAT INDUCES A DECREASE IN IKR AND IKS VIA REDUCTION IN PHOSPHATIDYLINOSITOL-(4,5)-BISPHOSPHATE AVAILABILITY. CONFORMATIONAL TRANSITION AND ASSEMBLY OF E.COLI CYTOLYSIN A PORE FORMING TOXIN BY SINGLE MOLECULE FLUORESCENCE. Sabrina Sharmin, Shizuoka University, Japan, EFFECTS OF LIPID COMPOSITIONS ON THE ENTRY OF CELL PENETRATING PEPTIDE OLIGOARGININE INTO SINGLE VESICLES. Xin Shi, East China University of Science and Technology, DIRECT OBSERVATION OF SINGLE BIOPOLYMER FOLDING AND UNFOLDING PROCESS BY SOLIDSTATE NANOPORE. Omar Alijevic, University of Lausanne, Switzerland, ANALYSIS OF GATING OF ACID-SENSING ION CHANNELS (ASICS) UNDER RAPID AND SLOW PH CHANGES. Swapna Bera, Bose Institute, India, BIOPHYSICAL INSIGHTS INTO THE MEMBRANE INTERACTION OF THE CORE AMYLOID-FORMING Aβ40 FRAGMENT K16-K28 AND ITS ROLE IN THE PATHOGENESIS OF ALZHEIMER'S DISEASE. Anais Cassaignau, University College London, United Kingdom, STRUCTURAL INVESTIGATION OF AN IMMUNOGLOBULIN DOMAIN ON THE RIBOSOME USING NMR SPECTROSCOPY. Bappaditya Chandra, Tata Institute of Fundamental Research, India, SECONDARY STRUCTURE FLIPPING CONNECTED TO SALT-BRIDGE FORMATION CONVERTS TOXIC AMYLOID-β40 OLIGOMERS TO FIBRILS. Gayathri Narasimhan, Cinvestav, Mexico, ANTIHYPERTROPHIC EFFECTS OF DIAZOXIDE INVOLVES CHANGES IN MIR-132 EXPRESSION IN ADULT RAT CARDIOMYCYTES. Giulia Paci, European Molecular Biology Laboratory, Germany, FOLLOWING A GIANT'S FOOTSTEPS: SINGLE-PARTICLE AND SUPER-RESOLUTION APPROACHES TO DECIPHER THE NUCLEAR TRANSPORT OF HEPATITIS B VIRUS CAPSIDS. Bizhan Sharopov, Bogomoletz Institute of Physiology National Academy of Sciences of Ukraine, DISSECTING LOCAL AND SYSTEMIC EFFECTS OF TRPV1 ON BLADDER CONTRACTILITY IN DIABETES. Chao Sun, East China Normal University, FUNCTION OF BACTERIORUBERIN IN ARCHAERHODOPSIN 4, FROM EXPRESSION TO CHARACTERIZATION. Matthew Batchelor, University of Leeds, United Kingdom STRUCTURAL DYNAMICS IN THE MYOSIN 7A SINGLE α-HELIX DOMAIN. Daniel Havelka, Czech Academy of Sciences, MICROVOLUME DIELECTRIC SPECTROSCOPY AND MOLECULAR DYNAMICS OF AMINO ACIDS. Ivan Kadurin, University College London, United Kingdom, INVESTIGATION OF THE PROTEOLYTIC CLEAVAGE OF α2δ SUBUNITS: A MECHANISTIC SWITCH FROM NHIBITION TO ACTIVATION OF VOLTAGE-GATED CALCIUM CHANNELS? Linlin Ma, University of Queensland, Australia, NOVEL HUMAN EAG CHANNEL ANTAGONISTS FROM SPIDER VENOMS. Ivana Malvacio, University of Cagliari, Italy, MOLECULAR INSIGHTS ON THE RECOGNITION OF SUBSTRATES BY THE PROMISCUOUS EFFLUX PUMP ACRB. Cristina Moreno Vadillo, Cardiovascular Research Institute Maastricht, Netherlands, RESTORING DEFECTIVE CAMP-DEPENDENT UPREGULATION IN LONG-QT SYNDROME TYPE-1 THROUGH INTERVENTIONS THAT PROMOTE IKS CHANNEL OPENING. Melanie Paillard, Claude Bernard University Lyon 1, France, TISSUE-SPECIFIC MITOCHONDRIAL DECODING OF CYTOPLASMIC CA2+ SIGNALS IS CONTROLLED BY THE STOICHIOMETRY OF MICU1/2 AND MCU. Mohammed Mostafizur Rahman, Institute for Stem Cell Biology and Regenerative Medicine, India, STRESS-INDUCED DIFFERENTIAL REGULATION LEADS TO DECOUPLING OF THE ACTIVITY BETWEEN MPFC AND AMYGDALA. Marcin Wolny, University of Leeds, United Kingdom, DESIGN AND CHARACTERIZATION OF LONG AND STABLE DE NOVO SINGLE α-HELIX DOMAINS. Elvis Pandzic, University of New South Wales, Australia, VELOCITY LANDSCAPES RESOLVE MULTIPLE DYNAMICAL POPULATIONS FROM FLUORESCENCE IMAGE TIME SERIES. The Biophysical Society, founded in 1958, is a professional, scientific Society established to encourage development and dissemination of knowledge in biophysics. The Society promotes growth in this expanding field through its annual meeting, monthly journal, and committee and outreach activities. Its 9000 members are located throughout the U.S. and the world, where they teach and conduct research in colleges, universities, laboratories, government agencies, and industry. For more information on these awards, the Society, or the 2017 Annual Meeting, visit http://www.


PubMed | Chromatin, National Center for Cell Science, Ottawa Hospital Research Institute, Bose Institute and Advanced Center for Treatment
Type: Journal Article | Journal: Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

Pre-mRNA splicing is a complex regulatory nexus modulated by various trans-factors and their posttranslational modifications to create a dynamic transcriptome through alternative splicing. Signal-induced phosphorylation and dephosphorylation of trans-factors are known to regulate alternative splicing. However, the role of other posttranslational modifications, such as deacetylation/acetylation, methylation, and ubiquitination, that could modulate alternative splicing in either a signal-dependent or -independent manner remain enigmatic. Here, we demonstrate that Scaffold/matrix-associated region-binding protein 1 (SMAR1) negatively regulates alternative splicing through histone deacetylase 6 (HDAC6)-mediated deacetylation of RNA-binding protein Sam68 (Src-associated substrate during mitosis of 68 kDa). SMAR1 is enriched in nuclear splicing speckles and associates with the snRNAs that are involved in splice site recognition. ERK-MAPK pathway that regulates alternative splicing facilitates ERK-1/2-mediated phosphorylation of SMAR1 at threonines 345 and 360 and localizes SMAR1 to the cytoplasm, preventing its interaction with Sam68. We showed that endogenously, SMAR1 through HDAC6 maintains Sam68 in a deacetylated state. However, knockdown or ERK-mediated phosphorylation of SMAR1 releases the inhibitory SMAR1-HDAC6-Sam68 complex, facilitating Sam68 acetylation and alternative splicing. Furthermore, loss of heterozygosity at the Chr.16q24.3 locus in breast cancer cells, wherein the human homolog of SMAR1 (BANP) has been mapped, enhances Sam68 acetylation and CD44 variant exon inclusion. In addition, tail-vein injections in mice with human breast cancer MCF-7 cells depleted for SMAR1 showed increased CD44 variant exon inclusion and concomitant metastatic propensity, confirming the functional role of SMAR1 in regulation of alternative splicing. Thus, our results reveal the complex molecular mechanism underlying SMAR1-mediated signal-dependent and -independent regulation of alternative splicing via Sam68 deacetylation.


Patent
Bose Institute and West Bengal State University | Date: 2013-09-27

A cancer chemotherapeutic agent that is particularly kinase suppressing and/or any other signaling pathway interfering agents and pharmaceutical formulations/compositions involving the same and its process of manufacture is provided. A potential the cancer chemotherapeutic agent is provided which apart from stated anticancer activity as a proven kinase suppressing and/or any other signaling pathway interfering agent could also involve specific potential binding affinity towards the intramolecular G-Quadruplex DNA structure and/or other potential quadruplex forming sequences over duplex DNA structures favours further diverse end use and application including but not limited to antiaging, antiangiogenic, antiproliferative, antitumor, antibiotic, antiviral, antifungal and multiple anticancer therapeutics, and also possesses favourable cytotoxicity values towards uncontrollably proliferative cells by inducing apoptosis irrespective of cells p53 status, without being cytotoxic to normal cells.


Khan P.,Bose Institute | Manna A.,Bose Institute | Saha S.,Bose Institute | Mohanty S.,Bose Institute | And 4 more authors.
BMC Cancer | Year: 2016

Background: Cancer metastasis is one of the most common causes of treatment failure and death in cancer patients. It has been acknowledged that aberrant activation of epithelial-to-mesenchymal transition (EMT) program, endows cancer cells with metastatic competence for which E-cadherin switch is a well-established hallmark. Suppression of E-cadherin by its transcriptional repressor Slug is thus a determining factor for EMT. Here, we aimed at discerning (i) the molecular mechanisms that regulate Slug/E-cadherin axis in oncogenic K-ras-expressing non-small cell lung carcinoma (NSCLC) cells, and (ii) the effect of aspirin in modulating the same. Methods: The migratory behaviour of NSCLC cell line A549 were deciphered by wound healing assay. Further assessment of the molecular mechanisms was done by western blotting, RT-PCR, confocal microscopy, chromatin immunoprecipitation and small interfering RNA (siRNA)-mediated gene silencing. Results: Here we report that in oncogenic K-ras-expressing A549 cells, Ras/ERK downstream Elk-1 forms p-Elk-1-p300 complex that being directly recruited to SLUG promoter acetylates the same to ensure p65NFκB binding for transcriptional up-regulation of Slug, a transcriptional repressor of E-cadherin. Aspirin inhibits EMT and decelerates the migratory potential of A549 cells by down-regulating Slug and thereby up-regulating E-cadherin. Aspirin impedes activation and nuclear translocation of p65NFκB, essential for this transcription factor being available for SLUG promoter binding. As a consequence, Slug transcription is down-regulated relieving A549 cells from Slug-mediated repression of E-cadherin transcription, thereby diminishing the metastatic potential of these oncogenic Ras-expressing NSCLC cells. Conclusions: Cumulatively, these results signify a crucial role of the anti-inflammatory agent aspirin as a novel negative regulator of epithelial-to-mesenchymal transition thereby suggesting its candidature as a promising tool for deterring metastasis of highly invasive K-ras-expressing NSCLC cells. © 2016 Khan et al.


Sarkar R.,Bose Institute
Journal of complementary & integrative medicine | Year: 2012

The in vitro study of the antioxidant properties of the hydroalcoholic extracts of various Indian medicinal plants can logically help to develop a better and safer way of amelioration from oxidative stress. As aimed, the present study has been done to estimate and thereby conclude regarding the antioxidant activities of a few Indian medicinal plants, viz., Terminalia chebula, Terminalia belerica, Emblica officinalis, Caesalpinia crista, Cajanus cajan, and Tinospora cordifolia. The extracts of the plants have been subjected to the evaluation of antioxidant properties through scavenging assays for reactive oxygen species like superoxide, nitric oxide, peroxynitrite, hypochlorous acid, singlet oxygen, etc. and measurement of TEAC values and other phytochemical parameters. The phenolic and flavonoid contents of each plant have been found to be correlated to their individual antioxidant activity. The results showed the hydroalcoholic extracts of the plants were efficient indicators of their antioxidant capacity thus concreting their basis to be used as natural antioxidant.


Background: Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution. Results: We observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs. Conclusions: Our study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution. © 2016 Acharya and Ghosh.


PubMed | Bose Institute
Type: Journal Article | Journal: Planta | Year: 2014

A growth inhibitor was isolated in crystalline form from the leaf of Vernonia anthelmintica and was found to be identical with abscisic acid by biological activity and physical measurements namely, melting point, mixed melting point, UV-absorption, mass spectra and paper and thin-layer chromatography.


PubMed | Bose Institute
Type: Journal Article | Journal: Indian journal of biochemistry & biophysics | Year: 2013

Alpha-Amylase (EC 3.2.1.1) was purified to homogeneity (specific activity 58,000 micromole min(-1) mg protein(-1)) from the culture filtrate of Bacillus amyloliquefaciens NCIM 2829. Its molecular mass was found to be 67.5 kDa. The activity of the enzyme increased by almost 50% in the presence of Co+2 ion. Hg2+ and Cu2+ acted as strong inhibitors of the enzyme. The tryptophan moities of the enzyme were fairly protected from the aqueous environment. However, the globular interior of the protein was somewhat loosely packed. The protein had nearly an equal amount of alpha-helical and beta-sheet structure in dilute solution. In concentrated solution, its secondary structure had a higher proportion of beta-sheet at the expense of some random coil structure. The protein showed a molten globule state at a low concentration of chaotropic agent. The denaturation profile of the protein showed no cooperativity. Co2+ enhanced the structural stability of the enzyme.


PubMed | Bose Institute
Type: | Journal: Journal of complementary & integrative medicine | Year: 2012

The in vitro study of the antioxidant properties of the hydroalcoholic extracts of various Indian medicinal plants can logically help to develop a better and safer way of amelioration from oxidative stress. As aimed, the present study has been done to estimate and thereby conclude regarding the antioxidant activities of a few Indian medicinal plants, viz., Terminalia chebula, Terminalia belerica, Emblica officinalis, Caesalpinia crista, Cajanus cajan, and Tinospora cordifolia. The extracts of the plants have been subjected to the evaluation of antioxidant properties through scavenging assays for reactive oxygen species like superoxide, nitric oxide, peroxynitrite, hypochlorous acid, singlet oxygen, etc. and measurement of TEAC values and other phytochemical parameters. The phenolic and flavonoid contents of each plant have been found to be correlated to their individual antioxidant activity. The results showed the hydroalcoholic extracts of the plants were efficient indicators of their antioxidant capacity thus concreting their basis to be used as natural antioxidant.

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