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Journal of Integrated OMICS
  This is an Open Access Journal Open Access journal
     ISSN (Print) 2182-0287 - ISSN (Online) 2182-0287
     Published by Proteomass Homepage  [1 journal]
  • VOL 4, NO 1 (2014)

    • Authors: José Luís Capelo Martínez
      PubDate: 2014-07-07
      Issue No: Vol. 4 (2014)
  • Editorial board

    • Authors: José Luís Capelo Martínez
      PubDate: 2014-07-07
      Issue No: Vol. 4 (2014)
  • A Novel High Throughput High Content Analysis Assay for Intermediate
           Filament Perturbing Drugs

    • Authors: Joanna Chowdry, Gareth J. Griffiths, Rod P. Benson, Bernard Michael Corfe
      Abstract: Keratins form the intermediate filament (IF) component of the epithelial cytoskeleton. Depolymerisation of these filaments causes the cell to collapse and become more plastic. We have previously shown that short chain fatty acids may trigger depolymerisation of keratins through altered protein acetylation. Currently, there is no single functional assay for screening of the cytoskeleton. The aim of this study is to develop a high-throughput assay to quantify IF depolymerisation and to apply as a screen for IF-perturbing nutrients and drugs. Three treatments were used in a proof-of-principle study: the anti-fungal drugs griseofulvin and cordycepin (the former a c-mitotic drug known to suppress microtubule growth, the latter inducing abnormal mitosis by suppressing microtubule dynamics) and sodium butyrate, a histone deacetylase inhibitor which disrupts IF formation in cancer cells via post-translational modification of keratins. Methods were optimised for cell fixation using methanol or formalin, permeabilising agents for Keratin 8 (krt8) antibody (triton-x100, digitonin and saponin) and blocking of non-specific binding prior to cell staining using BSA. High Content Analysis (HCA) was employed to quantify cell staining intensities by comparing co-occurrence of adjacent pixel intensities. Immunocytochemistry was used to identify Krt 8 intermediate filaments. Indicators of depolymerisation include Krt 8 fluorescence intensity, filamentousness or texture intensity, fibre spot count and fibre spot total area. All treatments resulted in significant decreases for texture intensity. Assessment of this assay using a Z prime calculation recorded gace a statistic of 0.95, indicating suitability for high-throughput applications. In conclusion, a HCA assay for intermediate filament integrity has been demonstrated, establishing proof of principle with griseofulvin, and cross-validating with two further treatments assayable using this method.
      PubDate: 2014-07-01
      Issue No: Vol. 4 (2014)
  • 2D DIGE proteomic analysis of multidrug resistant and susceptible clinical
           Mycobacterium tuberculosis isolates

    • Authors: Phong Quoc Truong, Elke Hammer, Manuela Gesell Salazar, Do Thi Thu Ha, Nguyen Lan Huong, Dang Minh Hieu, Nguyen Thanh Hoa, Phung Thi Thuy, Uwe Volker
      Abstract: Tuberculosis (TB) is the leading cause of infectious disease related mortality worldwide. Infection of Mycobacterium tuberculosis (Mtb) leads to nearly 3 million deaths every year due to tuberculosis. Rifampicin and Isoniazid (RH) are the key drugs to being used for the treatment of tuberculosis. Reports in recent years indicate that the increasing emergence of resistance to these drugs. The resistance to these drugs severely affects options for effective treatment. The current vaccine for tuberculosis has variable protective efficacy and there is no commercially available serodiagnostic test for this disease with acceptable sensitivity and specificity for routine laboratory use, especially in case of multidrug resistance. In order to develop a new diagnostic tool for detection of Mtb, multidrug resistant Mtb as well and improve the tuberculosis vaccine, it is necessary to indentify novel antigenic candidates, especially in identification of multidrug resistant associated protein antigens. Here, we present a 2-D gel-based proteomic survey of the changes in RH resistant Mtb. The proteins extracted from RH resistant and susceptible Mtb clinical isolates were analyzed by two-dimensional differential in gel electrophoresis (2D-DIGE). Protein intensities of 41 spots were found to be regulated in RH resistant isolates. A total of 28 proteins were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Twelve proteins of interest are NADH-dependent enoyl-[acyl-carrier-protein] reductase, 60 kDa chaperonin 2, Chaperone protein DnaK, 3-oxoacyl-(Acyl-carrier-protein0 reductase, Probable acetyl-CoA acyltransferase FadA2, two Acetyl/propionyl-CoA carboxylase, alpha subunit, Universal stress protein Rv1636/MT1672, Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, Glutamine synthetase 1 and two uncharacterized proteins (Rv2557 and Rv1505c).
      PubDate: 2014-07-01
      Issue No: Vol. 4 (2014)
  • Differential proteomics has emerged as a tool to understand carbapenem
           resistance in Acinetobacter baumannii

    • Authors: Vishvanath Tiwari
      PubDate: 2014-07-01
      Issue No: Vol. 4 (2014)
  • Quantification Technologies for Circulating Tumour Cells

    • Authors: Ho Kah Fai, Natasha E. Gouw, Gao Zhiqiang
      Abstract: Circulating tumour cells (CTCs) are tumour cells dislodged from tumours into the bloodstream. In the past two decades, numerous studies have suggested that CTCs play a major role in cancer metastasis. As such, CTCs are currently considered as potentially important cancer biomarkers that may significantly improve cancer diagnosis and prognosis, aid drug development, and offer personalized treatments for cancer patients. Therefore, accurate enumeration or detection of CTCs is a highly sought after technology to improve cancer management. The rarity of CTCs, however, poses significant challenges to their sensitive and reliable detection. A thorough review of the state-of-the art detection technologies for CTCs will be helpful to researchers in the development of more efficient CTC detection technologies. In this review recent advances in the detection of CTCs are summarized. Also, emerging techniques for CTC detection like telomerase-based and aptamer-based assays are also assessed.
      PubDate: 2014-07-01
      Issue No: Vol. 4 (2014)
  • Subtoxic concentrations of benzo[a]pyrene induce metabolic changes and
           oxidative stress in non-activated and affect the mTOR pathway in activated
           Jurkat T cells

    • Authors: Sven Baumann, Maxie Rockstroh, Jörg Bartel, Jan Krumsiek, Wolfgang Otto, Harald Jungnickel, Sarah Potratz, Andreas Luch, Edith Willscher, Fabian Theis, Martin von Bergen, Janina Tomm
      Abstract: Although the activation of immune cells is the first and thereby pivotal step in the immunological cascade, the current knowledge about the details of this process is quite limited. Recent studies have shown that aromatic compounds, such as B[a]P, influence the immune system even at low concentrations. We investigated the effect of a subtoxic B[a]P concentration (50 nM) on the proteome and the metabolome of non-activated and activated Jurkat T cells. The GeLC-MS/MS analysis yielded 2624 unambiguously identified proteins. In addition to typical regulatory pathways associated with T cell activation, pathway analysis by Ingenuity IPA revealed several metabolic processes, for instance purine and pyruvate metabolism. The activation process seems to be influenced by B[a]P suggesting an important role of the mTOR pathway in the cellular adaptation. B[a]P exposure of non-activated Jurkat cells induced signaling pathways such as protein ubiquitination and NRF2 mediated oxidative stress response as well as metabolic adaptation involving pyruvate, purine and fatty acid metabolism. Thus, we validated the proteome results by determining the concentrations of 183 metabolites with FIA-MS/MS and IC-MS/MS. Furthermore, we were able to show that Jurkat cells metabolize B[a]P to B[a]P-1,6-dione. The combined evaluation of proteome and metabolome data with an integrated, genome-scale metabolic model provided novel systems biological insights into the complex relation between metabolic and proteomic processes in Jurkat T cells during activation and subtoxic chemical exposure.
      PubDate: 2014-02-17
      Issue No: Vol. 4 (2014)
  • Molecular cloning and protein characterization of a heme-binding globin
           predicted in a sugar cane EST database

    • Authors: Daniel H.A. Corrêa, Silvia L.F Silva, Carlos H.I. Ramos
      Abstract: A very large and representative sugar cane expression sequence tag (EST) library (SUCEST) was sequenced by a Brazilian consortium, opening the possibility to study important proteins, such as hemoglobins, which are largely present across the plant kingdom. The widespread presence and long evolutionary history of plant hemoglobins suggest a major role for this protein family in plants; however, little is known about their functional roles. In this study, we report the identification and characterization of a putative non-symbiotic hemoglobin cDNA clone that was identified in SUCEST. The cDNA was cloned, and the recombinant protein was purified and folded, as shown by its circular dichroism and emission fluorescence spectra. The expressed globin protein was able to bind hemin, as a characteristic Soret band was observed in the absorbance spectrum and increases were seen in the amount of secondary structure and in the stability of the protein. A model for the structure of the sugarcane hemoglobin was created using the crystal structure of a rice hemoglobin, and this model showed a conserved globular conformation.
      PubDate: 2014-01-31
      Issue No: Vol. 4 (2014)
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