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  Journal of Integrated OMICS
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  This is an Open Access Journal Open Access journal
   ISSN (Print) 2182-0287 - ISSN (Online) 2182-0287
   Published by Proteomass Homepage  [1 journal]
  • Proteomic profiling of the HSPB chaperonome: Mass spectrometric
           identification of small heat shock proteins in stressed skeletal muscles

    • Authors: Sandra Murphy, Kay Ohlendieck
      Abstract: The continuing maintenance of protein homeostasis and the safeguarding of proteomic integrity is essential for the survival of complex cellular systems under stressful conditions. Proteostasis is maintained by a complex system of protective pathways that involve several classes of molecular chaperones, now referred to as the chaperonome. The elaborate interplay of these components averts detrimental protein aggregation and supports proteins in resuming their functional fold. In skeletal muscle tissues, molecular chaperones protect contractile functions throughout fibre adaptations to changed physiological demands and prevent tissue damage during acute phases of protein misfolding or prolonged periods of proteotoxic stress. This results in considerable changes in the expression profile of individual members of the large family of heat shock proteins. Systematic proteomic surveys of skeletal muscle tissues have revealed that the concentration of small heat shock proteins is especially affected following strenuous exercise, in various neuromuscular disorders and during the natural aging process. Of the 10 identified members of the small heat shock protein HSPB family, HSPB1 (Hsp25), HSPB2 (MKBP), HSPB3 (Hsp27), HSPB4 (αA-crystallin), HSPB5 (αB-crystallin), HSPB6 (Hsp20), HSPB7 (cardiovascular cvHsp) and HSPB8 (Hsp22) are clearly present in skeletal muscle tissues. This review outlines the proteomic identification of small heat shock proteins and their muscle-specific expression and induction patterns in health and disease. Since HSPB molecules are of relatively low molecular mass, belong to the markedly soluble type of proteins and represent critical pro-survival proteins that are intrinsically involved in the prevention of stress-induced fibre damage, they present ideal muscle-associated biomarker candidates for the establishment of superior diagnostic and therapy-monitoring approaches to assess stress-related skeletal muscle degeneration.
      PubDate: 2015-07-01
      Issue No: Vol. 5 (2015)
  • Editorial board Vol5, No1 (2015)

    • Authors: Journal of Integrated Omics
      PubDate: 2015-07-01
      Issue No: Vol. 5 (2015)
  • VOL 5, NO 1 (2015)

    • Authors: Journal of Integrated Omics
      PubDate: 2015-07-01
      Issue No: Vol. 5 (2015)
  • Improved reconstitution of Trizol derived protein extracts provides high
           quality samples for comprehensive proteomic characterization of cell

    • Abstract: Background: The study of RNA, DNA, and protein from the same sample is a great advantage but can be challenging. Using Trizol, one can simultaneously extract RNA, DNA, and protein, leading to efficient sample use and more comprehensive analysis. Although it is used routinely for RNA extraction, the frequency of use of Trizol extracts for proteomics applications is low. The aim of our study was to evaluate the results of a simple modification to the Trizol protocol in terms of extraction and protein recovery efficacy and compatibility of the extracts with proteomics technologies in comparison to our standard extraction protocol including freeze/thaw cycles in urea/ thiourea.Method: We used the human airway epithelial cell line S9 and extracted proteins either with a modified Trizol protocol or by freeze/thaw cycles in 8M urea/ 2M thiourea. Extracted proteins were quantified and subjected to 1D- and 2D-gel electrophoresis, Western Blotting and LC-coupled tandem mass spectrometry analysis. Results: Compared to urea/ thiourea extraction, the Trizol-extracted proteins exhibited a similar protein composition and identification rate in LC-coupled tandem mass spectrometry experiments. 1D- and 2D-PAGE of Trizol-extracted proteins revealed excellent protein resolution with better coverage of proteins in the low MW range than urea/ thiourea extraction. Conclusion: The modified Trizol-protocol enabled excellent protein extraction from cell culture samples and high compatibility with proteomics technologies, especially with LC-tandem mass spectrometry. 
      PubDate: 2015-06-09
      Issue No: Vol. 5 (2015)
  • Proteomic and lipidomic analysis of primary mouse hepatocytes exposed to
           metal and metal oxide nanoparticles

    • Authors: Sara Tedesco, Narges Bayat, Gabriela Danielsson, Xabier Buque, Patricia Aspichueta, Olatz Fresnedo, Susana Cristobal
      Abstract: The global analysis of the cellular lipid and protein content upon exposure to metal and metal oxide nanoparticles (NPs) can provide an overview of the possible impact of exposure. Proteomic analysis has been applied to understand the nanoimpact however the relevance of the alteration on the lipidic profile has been underestimated. In our study, primary mouse hepatocytes were treated with ultra-small (US) TiO2-USNPs as well as ZnO-NPs, CuO-NPs and Ag-NPs. The protein extracts were analysed by 2D-DIGE and quantified by imaging software and the selected differentially expressed proteins were identified by nLC-ESI-MS/MS. In parallel, lipidomic analysis of the samples was performed using thin layer chromatography (TLC) and analyzed by imaging software. Our findings show an overall ranking of the nanoimpact at the cellular and molecular level: TiO2-USNPs
      PubDate: 2015-04-26
      Issue No: Vol. 5 (2015)
  • Proteomic analysis of low quantities of cellular material in the range
           obtainable from scarce patient samples

    • Authors: Katja Parapatics, Marie L. Huber, Dorit Lehmann, Christian Knoll, Giulio Superti-Furga, Keiryn L. Bennett, Elena L. Rudashevskaya
      Abstract: The application of proteomics to patient material is increasingly widespread, however, a major shortcoming still are the number of cells or protein material that can be obtained. This study explores the lower limit of cell numbers that can be successfully analysed by liquid chromatography mass spectrometry to determine the protein expression profile that is specific to, and indicative of, the investigated cell type. The aim was to analyse an equivalent quantity of cellular material that can be obtained from, e.g., a fine-needle aspiration biopsy (FNAB). Fifteen thousand and 30,000 cells from adherent (HEK293) and suspension (U937) cell lines were lysed under two different conditions: a ‘native’ and a denaturing buffer. To extend the study to clinical material, human whole PBMCs were also lysed under identical conditions. Proteins from 5,000 and 10,000 cells were analysed by both 1D and 2D-LC-MSMS on an LTQ Orbitrap XL mass spectrometer. In total, 3,219; 1,693 and 659 unique proteins were identified from HEK293, U937 and total PBMCs, respectively. Additionally, an iTRAQ 4-plex experiment was performed to determine the relative quantity of the proteins in the three cell types. In this study, we show that it is feasible to obtain a deep, yet cell-specific protein profile from a very low number of cultured and primary cells. This advancement will enable proteomic-profiling of cellular material from fine needle aspiration biopsies that ultimately can assist cytopathologists in the diagnosis of disease.
      PubDate: 2015-01-28
      Issue No: Vol. 5 (2015)
  • Arabidopsis thaliana and omics approaches: a review

    • Abstract: Arabidopsis thaliana is a small, flowering plant that is widely used as a model organism in plant biology, mainly because it is the first plant to have its entire genome sequenced. It has since proven to be an ideal organism for studying plant development. Arabidopsis is commonly used as a model plant for genomics, metabolomics and proteomics studies, and more recently it has been utilized in metallomic studies. Because of its widespread applications, many methods for Arabidopsis sample preparation, analytes separation and data quantification have been explored. This review briefly describes the Arabidopsis thaliana characteristics, the developed researches and the primary methods using this plant in different fields of OMICS. In the future, the availability of Arabidopsis genomic information may result in its continuous development for nanoparticles and metallomics studies.
      PubDate: 2015-01-28
      Issue No: Vol. 5 (2015)
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