2058 research outputs found
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Co-Activation of TGFβ and Wnt Signalling Pathways Abrogates EMT in Ovarian Cancer Cells
Full text linkThe aggressive property of ovarian cancer (OC) in terms of epithelialmesenchymal transition (EMT), proliferation and metastasis are of major concern. Different growth factors including TGFβ are associated with regulating these molecular events but the underlying mechanisms remain unclear. The aim of this report is to decipher the regulation of EMT by co-activation of TGFβ and Wnt signalling cascades in gaining malignancy. Methods:
The expression of the different components of signalling events were analyzed by QPCR, Western blot, Immunofluorescence microscopy and flow cytometry. β-catenin promoter activity was checked by luciferase assay. Results: We observed reduced EMT in ovarian cancer cells upon co-activation with TGFβ1 and LiCl as shown by the expressions of epithelial/ mesenchymal markers and the EMT promoting factor, Snail1, accompanied by decrease in the invasion and migration of the cells compared to individual pathway activation. A detailed study of the mechanism suggested reduction in the β-catenin and p-GSK3b (Ser 9) levels
to be the driving cause of this phenomenon, which was reversed upon co-activation with higher concentrations of LiCl. Conclusions: Therefore, tumourigenesis might be affected by the concentration of ligand/ growth factors for the respective signalling pathways activated in the tumour microenvironment and interaction between them might alter tumourigenesis
C11/C9 Helical Folding in ab Hybrid Peptides Containing 1-Aminocyclohexane acetic acid (b3,3-Ac6c)
No full textThe present study describes the solid-state conformation
of ab hybrid peptides, Boc-Leu-b3,3-Ac6c-OH,
P1; Boc-Leu-b3,3-Ac6c-Leu-b3,3-Ac6c-OMe, P2; and Boc-Leub
3,3-Ac6c-Leu-b3,3-Ac6c-Leu-OMe, P3. The dipeptide P1
adopts extended conformations, whereas tetrapeptide P2
and pentapeptide P3 favor a helical conformation stabilized by mixed types of C11/C9 intramolecular hydrogen bonds. In peptide P3, the amino group of b3,3-Ac6c(2) and b3,3-Ac6c(4) residues occupies axial orientation, whereas in P2 it occupies axial and equatorial orientations for residues b3,3-Ac6c(2) and b3,3-Ac6c(4), respectively. The self-assembly of P3 forms channels filled with solvent molecules that present interesting patterns
Chromatin Remodeling Protein SMAR1 Is a Critical Regulator of T Helper Cell Differentiation and Inflammatory Diseases
Full text linkT cell differentiation from naïve T cells to specialized effector subsets of mature cells is determined by the iterative action of transcription factors. At each stage of specificT cell lineage differentiation, transcription factor interacts not only with nuclear proteins
such as histone and histone modifiers but also with other factors that are bound to the chromatin and play a critical role in gene expression. In this review, we focus on one
of such nuclear protein known as tumor suppressor and scaffold matrix attachment region-binding protein 1 (SMAR1) in CD4+ T cell differentiation. SMAR1 facilitates Th1
differentiation by negatively regulating T-bet expression via recruiting HDAC1–SMRT complex to its gene promoter. In contrast, regulatory T (Treg) cell functions are dependent
on inhibition of Th17-specific genes mainly IL-17 and STAT3 by SMAR1. Here, we discussed a critical role of chromatin remodeling protein SMAR1 in maintaining a fine-tuned
balance between effector CD4+ T cells and Treg cells by influencing the transcription factors during allergic and autoimmune inflammatory diseases
Interaction of KMP-11 with Phospholipid Membranes and Its Implications in Leishmaniasis: Effects of Single Tryptophan Mutations and Cholesterol
No full textKMP-11 is a small protein that is believed to
control the overall bilayer pressure of the Leishmania parasite.Recent results have suggested that membrane binding and the presence of cholesterol affect the efficacy of Leishmanial infection, in which KMP-11 plays an important role. Nevertheless, there exists no systematic study of membrane interaction with KMP-11 either in the absence or presence of cholesterol. In this article, we investigated the interaction between KMP-11 and phospholipid membranes using an unsaturated (PC 18:1; 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)) and saturated (PC 12:0; 1,2-dilauroyl-snglycero- 3-phosphocholine (DLPC)) lipid as membrane mimics. Additionally, we studied the effect of cholesterol on the protein−membrane interaction. Steady-state as well as timeresolved fluorescence spectroscopy, isothermal titration calorimetry (ITC), and ζ-potential measurements were used for the determination of the binding constants for the wild-type (WT) and single-site tryptophan mutants. Single-site tryptophan mutants were designed to make sure that the tryptophan residues sample different surface exposures in different mutants. In the
absence of cholesterol, the membrane-binding affinities of the partially exposed and buried tryptophan mutants (Y5W and Y48W, respectively) were found to be greater than those of the WT protein. In the presence of cholesterol, the binding constants of the
WT and Y48W mutant were found to decrease with an increase in cholesterol concentration. This was in contrast to that in the Y5W and F77W mutants, in which the binding constants increased on adding cholesterol. The present study highlights the interplay among the conformational architecture of a protein, its interaction with the membrane, and membrane composition in
modulating the survival of a Leishmania parasite inside host macrophages
Fiaud’s Acid: A Brønsted Acid Catalyst for Enantioselective Friedel− Crafts Alkylation of Indoles with 2‑Alkene-1,4-diones
No full textFiaud’s acid (trans-1-hydroxy-2,5-diphenylphospholane
1-oxide), a phospholane-based phosphinic acid, is
introduced as an efficient chiral Brønsted acid catalyst that mediates the asymmetric Friedel−Crafts alkylation of indoles with 2-butene-1,4-diones. With a catalyst loading of 10 mol %,the reaction proceeded smoothly to afford 2-(indol-3-yl)butane-1,4-diones in high yield (up to 82%) and high enantioselectivity(up to 91% ee, one such product showed enhanced ee of 98% after ecrystallization). The reaction conditions are sufficiently mild to tolerate sensitive functionality at room temperature and are therefore suitable for the synthesis of complex targets
Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India
No full textBackground: Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia.
Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the
varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA
methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and
validated in an additional 53 well-differentiated OSCC and adjacent normal samples.
Results: Genome-wide DNA methylation analysis identified several novel differentially methylated regions
associated with OSCC. Hypermethylation is primarily enriched in the CpG-rich regions, while hypomethylation is
mainly in the open sea. Distinct epigenetic drifts for hypo- and hypermethylation across CpG islands suggested
independent mechanisms of hypo- and hypermethylation in OSCC development. Aberrant DNA methylation in the
promoter regions are concomitant with gene expression. Hypomethylation of immune genes reflect the
lymphocyte infiltration into the tumor microenvironment. Comparison of methylome data with 312 TCGA HNSCC
samples identified a unique set of hypomethylated promoters among the OSCC patients in India. Pathway analysis
of unique hypomethylated promoters indicated that the OSCC patients in India induce an anti-tumor T cell
response, with mobilization of T lymphocytes in the neoplastic environment. Survival analysis of these
epigenetically regulated immune genes suggested their prominent role in OSCC progression.
Conclusions: Our study identified a unique set of hypomethylated regions, enriched in the promoters of immune
response genes, and indicated the presence of a strong immune component in the tumor microenvironment.
These methylation changes may serve as potential molecular markers to define risk and to monitor the prognosis
of OSCC patients in India
Cholesterol and Its Derivatives Reversibly Inhibit Proteinase K
No full textMicroorganisms express a variety of proteases that degrade many proteins of the host body and subvert host immune response. While elucidating the mechanism/s of an immune stimulatory drug that contains bile lipid, regulation of proteolytic activity was investigated. The drug and bile lipids both stabilize Proteinase K, an aggressive protease of fungal origin against auto-digestion. Among the components of bile lipids, only cholesterol and its derivatives stabilize the enzyme. Biophysical evidences such as scattering of light, intrinsic and extrinsic
fluorescence emission spectra, circular dichroism spectra, atomic force microscopy, and transmission electron microscopy images indicated that cholesterol and its derivatives interact with Proteinase K. Inhibition kinetics using esterolysis of ATEE revealed noncompetitive
inhibition by cholesterol. Surface Plasmon Resonance and mass spectrometric analysis indicated 1:1 stoichiometry of binding and with dissociation constant in the mM range. Further, the presence of four cholesterol recognition amino acid consensus motifs (CRAC motifs I–IV) was identified in Proteinase K. Bioinformatics analysis revealed that the whole stretch of cholesterol interacts very well with
the hydrophobic groove of motif II only among the four CRAC motifs. Variation of cholesterol content of HepG2 human liver carcinoma cells showed positive correlation with binding of fluorescence tagged Proteinase K. Under these conditions, binding of Proteinase K to the cells did not affect their morphology, viability and growth kinetics. Cell bound Proteinase K could be released by an excess of its substrate, thereby restoring reversibly its proteolytic activit
Understanding Bio-molecular Networks of Cellular Processes Using Computational Biology Approach
No full textWhile experimental research forms the foundation of biological science, computational biology concepts and mathematical models have become crucial to understand the observed phenomena underlying complex systems. Particularly in molecular biology, mathematical models of networks help to extend knowledge of single interactions and connect to a systems-level analysis. Well-structured knowledge database source for interaction and other biomedical data are important for systems level analysis. This knowledge database source plays important role in simplifying the access to information and its further processing. In biomedical domain, results and other important information (like association between bio-entity terms) are present in the form of unstructured text. To advance the scientific research it is crucial to extract the information from unstructured to structured format. I have developed a literature and data mining platform PALM-IST (Pathway Assembly from Literature Mining - an Information Search Tool). This platform provides users to extract biomedical research articles for their searched term and at the same time build relationship/pathways between bio-entity terms like genes, proteins, drugs, diseases and biological processes. Information is extracted using literature mining methods i.e. from unstructured text (literature resources like PubMed) and from existing databases i.e. structured resources (like protein-protein interaction database STRING and pathway resources KEGG and other).
The main theme of this thesis is modeling and analysis of biological networks. In this thesis different types of networks are analyzed using context specific experimental datasets (like expression data) and mathematical models. Further a systems biology based network information flow model unlike previous is developed and discussed. The resulting model was utilized to study the roles of constituently active EGFR (EGFRvIII mutated) in GBM (Glioblastoma) condition. Model developed for information flow analysis incorporates experimental data, biological information and network properties into biological network analysis for identification of molecular signatures of disease phenotypes. These signature proteins and connections identified from the model were further tested and validated using cell culture experiments. The model is flexible to apply on diverse data and conditions in a combination with a suitable molecular network. By the integration of diverse sources of information and molecular events from different points of view, new and exhaustive insights into biological processes can be acquire
A Smart Molecule for Selective Sensing of Nitric Oxide: Conversion of NO to HSNO; Relevance of Biological HSNO Formation
No full textA smart molecule, QT490, containing thiosemicarbazide
moiety acts as a highly selective turn-on in vitro NO sensor through the unprecedented NO-induced transformation of thiosemicarbazide moiety to 1,3,4-oxadiazole heterocycle with the concomitant release of HSNO, thereby eliminating any interference from various endogenous biomolecules including dehydroascorbic acid, ascorbic acid, etc. The
kinetic studies of the reactions between QT490 and NO provide a mechanistic insight into formation of HSNO/RSNO from the reaction between H2S/RSH and NO in the biological system. This novel probe is non-cytotoxic, cell permeable, water-soluble, and appropriate for intracellular cytoplasmic NO sensing with the possibilities of in vivo
applications
SILAC-based quantitative proteomic analysis revealswidespread molecular alterations in human skinkeratinocytes upon chronic arsenic exposure
No full textChronic exposure to arsenic is associated with dermatological and nondermatological disor-ders. Consumption of arsenic-contaminated drinking water results in accumulation of arsenicin liver, spleen, kidneys, lungs, and gastrointestinal tract. Although arsenic is cleared from thesesites, a substantial amount of residual arsenic is left in keratin-rich tissues including skin. Epi-demiological studies suggest the association of skin cancer upon arsenic exposure, however,the mechanism of arsenic-induced carcinogenesis is not completely understood. We developeda cell line based model to understand the molecular mechanisms involved in arsenic-mediatedtoxicity and carcinogenicity. Human skin keratinocyte cell line, HaCaT, was chronically ex-posed to 100 nM sodium arsenite over a period of 6 months. We observed an increase in basalROS levels in arsenic-exposed cells. SILAC-based quantitative proteomics approach resultedin identification of 2111 proteins of which 42 proteins were found to be overexpressed and 54downregulated (twofold) upon chronic arsenic exposure. Our analysis revealed arsenic-inducedoverexpression of aldo-keto reductase family 1 member C2 (AKR1C2), aldo-keto reductase fam-ily 1 member C3 (AKR1C3), glutamate-cysteine ligase catalytic subunit (GCLC), and NAD(P)Hdehydrogenase [quinone] 1 (NQO1) among others. We observed downregulation of severalmembers of the plakin family including periplakin (PPL), envoplakin (EVPL), and involucrin(IVL) that are essential for terminal differentiation of keratinocytes. MRM and Western blotanalysis confirmed differential expression of several candidate proteins. Our study providesinsights into molecular alterations upon chronic arsenic exposure on skin