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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]
  • Preface - Vol3Issue2 - 2013

    • Authors: José Luís Capelo Martínez
      PubDate: 2013-12-28
      Issue No: Vol. 3 (2013)
       
  • VOL 3, NO 2 (2013)

    • Authors: José Luís Capelo Martínez
      PubDate: 2013-12-26
      Issue No: Vol. 3 (2013)
       
  • Editorial board

    • Authors: José Luís Capelo Martínez
      PubDate: 2013-12-26
      Issue No: Vol. 3 (2013)
       
  • Cellular Protein/Peptide Expression Profiles (PEPs): an alternative
           approach for easy identification of cyanobacterial species

    • Authors: Fred Wang-Fat Lee, Kin-Chung Ho, Daniel Yun-Lam Mak, Junrong Liang, Changping Chen, Yahui Gao, Samuel Chun-Lap Lo
      Abstract: Cyanobacterial harmful algal blooms (CyanoHABs) are recognized as an expanding and serious global problem that threatens human health. Timely and accurate identification of cyanobacteria is of vital importance for public health. Morphologic characteristics of cyanobacteria have been used for classical taxonomic studies and identification purposes. However, misidentification may occur either due to subjective judgment by the operators or inability to recognize natural variations of morphotypes. To circumvent problems of  morphology-based identification methods, we reported previously a rapid and simple method for the identification of dinoflagellates using protein/peptide expression profiles (PEPs) of whole cell protein extracts generated by MALDI-TOF-MS (Lee FWF et. al., 2008).  In the present study, we applied this method in the identification of harmful cyanobacteria. Our results showed that various species of the cyanobacteria can be easily distinguished from each other using their PEPs.
      PubDate: 2013-12-23
      Issue No: Vol. 3 (2013)
       
  • Proteomics Analysis of Morphogenic Changes of Human Umbilical Vein
           Endothelial Cells Induced by a Phorbol-Ester Mimicking Angiogenesis

    • Authors: Bruno Baudin, David Ramani, Nelly Bosselut, Paulo Marcelo, Hélène Lecornet, Gary Margoline, Joëlle Vinh, Michel Vaubourdolle
      Abstract: Phorbol 12-myristate 13-acetate (PMA) can induce proliferation and migration of endothelial cells, mimicking vessel formation. We analysed by two-dimensional electrophoresis and MALDI-TOF/TOF the effects of PMA on cultured Human Umbilical Vein Endothelial Cells (HUVECs) to further investigate the complex mechanisms related to protein kinase C activation in this angiogenesis model. At 1 μg/ml for 24 hours, PMA induced transition of HUVECs from quiescent type into the proliferative-migrating phenotype. After 2D gel analysis, 15 differences were detected between PMA-treated samples and controls, including 8 increased proteins and 7 decreased proteins. The three main proteins identified by mass spectrometry and increased after PMA are directly involved in cell stress (α-glucosidase, heat-shock protein 70, and 150 kDa oxygen-regulated protein). Four other proteins varied in function of time, two increasing after PMA (heat shock protein 90β, protein-disulfide isomerase A3), and two other decreasing after this treatment (glucose-related protein 75, cathepsin B). These four proteins are involved in protein folding, apoptosis or tumour dissemination. Our data show that phorbol esters modify a number of proteins involved in multiple and intricate pathways for promoting a phenotype ensuring cell survival and cell migration for new vessels formation.
      PubDate: 2013-10-24
      Issue No: Vol. 3 (2013)
       
  • Proteomic changes in extended-spectrum beta-lactamase-producing
           Escherichia coli strain under cefotaxime selection

    • Authors: Hajer Radhouani, Júlio D. Nunes-Miranda, Ricardo Carreira, Hugo M. Santos, Luís Pinto, Ricardo Monteiro, Carlos Carvalho, Patricia Poeta, Carlos Lodeiro, José-Luis Capelo-Martínez, Gilberto Igrejas
      Abstract: Proteomics can be used to study the metabolic pathways and mechanisms involved in antimicrobial resistance. The aim of this comparative proteomic study was to establish the overall changes in the proteome of a naturally occurring ESBL-producing E. coli strain (C5478) stressed with its minimal inhibitory concentration (2 μg/mL) of cefotaxime, compared to the proteome of the same strain without antimicrobial stress, by using 2-D gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The comparative proteomic analysis revealed that the abundance of numerous protein species changed in the strain stressed by CTX compared to the non-stressed wild-type strain. A total of 188 spots were excised from the 2-DE gel of the wild-type strain, 112 of which were successfully identified by MALDI-TOF MS, representing 110 different proteins. Concerning the 2-DE gel of the CTX-stressed bacteria, 171 spots were excised and 156 were identified, representing 143 different proteins. The proteins identified in both strains were categorized according to their biological functions. These proteins were involved in metabolism, protein synthesis, cell division, stress responses, and antimicrobial resistance, among others. These findings will be helpful to further understand not only the antimicrobial resistance mechanisms, but also the role of wild animals as reservoirs in spreading antimicrobial-resistant bacteria into the environment.
      PubDate: 2013-10-09
      Issue No: Vol. 3 (2013)
       
  • Environmental OMICS: Current Status and Future Directions

    • Authors: Yue Ge, Da-Zhi Wang, Jen-Fu Chiu, Susana Cristobal, David Sheehan, Frédéric Silvestre, Xianxuan Peng, Hui Li, Zhiyaun Gong, Siew Hong Lam, Hu Wentao, Hitoshi Iwahashi, Jianjun Liu, Nan Mei, Leming Shi, Maribel Bruno, Heidi Foth, Kevin Teichman
      Abstract: Objectives: Applications of OMICS to high throughput studies of changes of genes, RNAs, proteins, metabolites, and their associated functions in cells or organisms exposed to environmental chemicals has led to the emergence of a very active research field: environmental OMICS. This developing field holds an important key for improving the scientific basis for understanding the potential impacts of environmental chemicals on both health and the environment. Here we describe the state of environmental OMICS with an emphasis on its recent accomplishments and its problems and potential solutions to facilitate the incorporation of OMICS into mainstream environmental and health research. Data sources: We reviewed relevant and recently published studies on the applicability and usefulness of OMICS technologies to the identification of toxicity pathways, mechanisms, and biomarkers of environmental chemicals for environmental and health risk monitoring and assessment, including recent presentations and discussions on these issues at The First International Conference on Environmental OMICS (ICEO), held in Guangzhou, China during November 8-12, 2011. This paper summarizes our review. Synthesis: Environmental OMICS aims to take advantage of powerful genomics, transcriptomics, proteomics, and metabolomics tools to identify novel toxicity pathways/signatures/biomarkers so as to better understand toxicity mechanisms/modes of action, to identify/categorize/prioritize/screen environmental chemicals, and to monitor and predict the risks associated with exposure to environmental chemicals on human health and the environment. To improve the field, some lessons learned from previous studies need to be summarized, a research agenda and guidelines for future studies need to be established, and a focus for the field needs to be developed. Conclusions: OMICS technologies for identification of RNA, protein, and metabolic profiles and endpoints have already significantly improved our understanding of how environmental chemicals affect our ecosystem and human health. OMICS breakthroughs are empowering the fields of environmental toxicology, chemical toxicity characterization, and health risk assessment. However, environmental OMICS is still in the data generation and collection stage. Important data gaps in linking and/or integrating toxicity data with OMICS endpoints/profiles need to be filled to enable understanding of the potential impacts of chemicals on human health and the environment. It is expected that future environmental OMICS will focus more on real environmental issues and challenges such as the characterization of chemical mixture toxicity, the identification of environmental and health biomarkers, and the development of innovative environmental OMICS approaches and assays. These innovative approaches and assays will inform chemical toxicity testing and prediction, ecological and health risk monitoring and assessment, and natural resource utilization in ways that maintain human health and protects the environment in a sustainable manner.
      PubDate: 2013-09-29
      Issue No: Vol. 3 (2013)
       
  • An integrated proteomic and physiological approach to understand the
           adhesion mechanism of the probiotic Lactobacillus reuteri Lb2 BM DSM 16143
           

    • Authors: Erika Mangiapane, Cristina Lamberti, Alessandro Pessione, Patrizia Ceruti, Francesco Novelli, Eugenio Galano, Ritva Virkola, Timo Korhonen, Enrica Pessione
      Abstract: The adhesion ability of the probiotic Lactobacillus reuteri Lb2 BM DSM 16143 was tested to both enterocyte-like Caco-2 cells and to extracellular matrix proteins (laminin, fibronectin and collagen I and IV). The adhesiveness was lost after an alkaline treatment known to release moonlighting  proteins from lactobacillar cell surface. To characterize the putative adhesive molecules, a 2-DE experiment in the pI range 4-7 was performed on the extracellular proteins. The expression of several moonlighting proteins involved in adhesion (i.e. GAPDH, EF-Tu, phosphoglycerate kinase) was demonstrated. Some of the identified adhesins were able to bind plasminogen (Plg), but did not convert it into plasmin (Plm), in absence of exogenous activators. This indicates that the moonlighting proteome of L. reuteri Lb2 BM DSM 16143 can contribute to adhesion processes.
      PubDate: 2013-09-27
      Issue No: Vol. 3 (2013)
       
  • Iberian Lynx (Lynx pardinus) from the captive breeding program as
           reservoir of antimicrobial resistant enterococci and Escherichia coli
           isolates

    • Authors: Alexandre Gonçalves, Gilberto Igrejas, Hajer Radhouani, Tiago Santos, Ricardo Monteiro, Catarina Marinho, Maria Jose Perez, Rocio Canales, Jose Luis Mendonza, Rodrigo Serra, Carmen Torres
      Abstract: A total of 98 faecal samples from captive specimens of Iberian lynx were collected and analysed for enterococci (96 isolates) and Escherichia coli (90 isolates) recovery. These 186 isolates were tested for antimicrobial resistance, molecular mechanisms of resistance, and detection of virulence genes. Among the enterococci, Enterococcus hirae was the most prevalent species (35 isolates), followed by Enterococcus faecalis (30 isolates), Enterococcus faecium (27 isolates), and Enterococcus durans (4 isolates). High rates of resistance to tetracycline, erythromycin and high-level-kanamycin were detected among enterococcal isolates (41%, 26%, and 19%, respectively). The tet(M) and/or tet(L), erm(B), aac(6′)-Ie-aph(2″)-Ia, ant(6)-Ia, or aph(3′)-IIIa genes were detected among resistant enterococci. Likewise, high rates of resistance were detected in E. coli isolates to tetracycline, streptomycin, sulfamethoxazole-trimethoprim (SXT), nalidixic acid, ampicillin, and ciprofloxacin (34%, 28%, 26%, 21%, 17%, and 16%, respectively). Furthermore, the blaTEM or blaSHV, tet(A) and/or tet(B), aadA or strA-strB, aac(3)-II and/or aac(3)-IV, and different combinations of sul genes were detected among most resistant isolates. Fifteen isolates contained class 1 and/or class 2 integrons and 3 different gene cassette arrays were identified (aadA1, dfrA1+aadA1, and estX+psp+aadA2). The E. coli isolates were ascribed to phylo-groups A (12%); B1 (40%); B2 (37%), and D (11%), being  fimA the most prevalent virulence gene (n=84), followed by aer (n=13), cnf1 (n=13), papC (n=10) and papG-allele III (n=9). This study showed specimens of Iberian lynx acting as reservoirs of resistance genes, and in future (re)introductions they could spread resistant bacteria throughout the environment.  
      PubDate: 2013-07-19
      Issue No: Vol. 3 (2013)
       
  • Inorganic mass spectrometry-based metallomics for environmental monitoring
           of terrestrial ecosystems affected by metal pollution using Mus spretus as
           bioindicator

    • Authors: Miguel Ángel García-Sevillano, Tamara García-Barrera, José Luis Gómez-Ariza
      Abstract: A metallomic approach based on the use of size-exclusion chromatography coupled to inductively coupled plasma-mass spectrometry (SEC-ICP-MS) has been used to characterize the biological response in liver, brain, kidneys, lungs and plasma of the free-living mouse Mus spretus in polluted areas located in Doñana National Park (southwest Spain) and the surroundings, mainly affected by agriculture, mining and industry activities, which are responsible for the presence of metallic contaminants. It is remarkable the high presence of Cu, Zn, Cd, As, Pb and Ni in the cytosolic extracts of different organs and plasma, especially in contaminated areas. In liver extracts, high intensity peaks traced by Cu, Zn, Pb and Cd at 7 kDa (matching with metallothionein I standard) are triggered by the presence of contaminants. In kidney, similar Cu and Cd-peaks at 7 kDa were observed but the equivalent Zn-peak was depleted by the competitive interactions of Cu-Cd-Zn for the active sites of these molecules. In addition, peaks traced by Cu and Zn at about 32 kDa in liver extract match with superoxide dismutase standard (Cu,Zn-SOD), which increase in accordance to contamination. An analogous behavior was observed for a Zn,Cu-peak at about 67 kDa that can be related with the bovine serum albumin standard (Cu,Zn-BSA) or other carrier protein such as transferrin (Cu-Tf) present in liver and plasma. Finally, low molecular mass arsenic metabolites were detected in mice captured in MAT site affected by mine waste.
      PubDate: 2013-07-18
      Issue No: Vol. 3 (2013)
       
  • Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes

    • Authors: Steven Halouska, Bo Zhang, Rosmarie Gaupp, Shulei Lei, Emily Snell, Robert J. Fenton, Raul G. Barletta, Greg A. Somerville, Robert Powers
      Abstract: Over the past decade, metabolomics has emerged as an important technique for systems biology. Measuring all the metabolites in a biological system provides an invaluable source of information to explore various cellular processes, and to investigate the impact of environmental factors and genetic modifications. Nuclear magnetic resonance (NMR) spectroscopy is an important method routinely employed in metabolomics. NMR provides comprehensive structural and quantitative information useful for metabolomics fingerprinting, chemometric analysis, metabolite identification and metabolic pathway construction. A successful metabolomics study relies on proper experimental protocols for the collection, handling, processing and analysis of metabolomics data. Critically, these protocols should eliminate or avoid biologically-irrelevant changes to the metabolome. We provide a comprehensive description of our NMR-based metabolomics procedures optimized for the analysis of bacterial metabolomes. The technical details described within this manuscript should provide a useful guide to reliably apply our NMR-based metabolomics methodology to systems biology studies.
      PubDate: 2013-07-17
      Issue No: Vol. 3 (2013)
       
  • Global proteomic profiling of the membrane compartment of bovine testis
           cell populations

    • Authors: Michelle Lisa Colgrave, Sally Stockwell, Aimee Grace, Mary McMillan, Rhonda Davey, Sigrid Lehnert, Sabine Schmoelzl
      Abstract: Spermatogonial stem cells hold enormous potential in mammalian reproductive medicine through the preservation of gametes, the restoration of fertility, enhancement of germ-lineage genetic manipulation and the improvement in our understanding of stem cell biology. Here we describe the protein profiles of the membrane compartment of bovine testicular cell isolates which were enriched for germ cells using differential plating. The isolated cells were characterised with antibodies to UCHL1 (previously known as PGP9.5) for type A spermatogonia; DDX4 (previously known as VASA) for germ cells and vimentin for Sertoli cells. Ultracentrifugation techniques were used to specifically isolate cell membranes, with membrane protein identifications significantly increased when compared to whole cell lysates. We utilised the filter-aided sample preparation protocol for improved digestion efficiency of membrane proteins. Using ESI-LC-MS/MS, we compared the proteins present in two cell populations. A total of 1,387 proteins were identified in bovine testis cell isolates, of which 39% were membrane-associated. A total of 64 proteins were differentially expressed in the non-adhered fraction (enriched for undifferentiated germ cells), of which 16 were unique to this cell population and the remaining 48 showed a two-fold change as judged by spectral counting. This analysis revealed a number of candidate germ cell markers including the known markers, DDX4 and UCHL1. The proteomic profiles generated in this study support and complement transcriptomics studies and reinforce the potential of proteomics in identifying and characterising the protein effectors of self-renewal and/or differentiation in stem cells.
      PubDate: 2013-07-16
      Issue No: Vol. 3 (2013)
       
  • Determining the C-Terminal Amino Acid of a Peptide from MS/MS Data

    • Authors: Jens Allmer
      Abstract: Proteomics is currently chiefly based on mass spectrometry (MS) which is the tool of choice to investigate proteins. Two computational approaches to derive the tandem mass spectrum precursor’s sequence are widely employed. Database search essentially retrieves the sequence by matching the spectrum to all entries in a database whereas de novo sequencing does not depend on a sequence database. Both approaches benefit from knowledge about the enzyme used to generate the peptides. Most algorithms default to trypsin for its abundant usage. Trypsin cuts after arginine and lysine and thus the c-terminal amino acid is not known precisely and usually either of the two. Furthermore, 90% of protein terminal peptides may not end with either arginine or lysine and may thus contain any of the other amino acids. Here an algorithm is presented which predicts the c-terminal amino acid to be arginine, lysine or any other. Here an algorithm, named RKDecider, to sort the c-terminal amino acid into one of three groups (arginine, lysine, and other) is presented. Although around 90% accuracy was achieved during data mining spectra for rules that determine the c-terminal amino acid, the implementation’s (RKDecider) accuracy is a little less and achieves about 80%. This is due to the fact that the decision trees were implemented as a rule-based system for speed considerations. The implementation is freely available at: http://bioinformatics.iyte.edu.tr/RKDecider.
      PubDate: 2013-07-15
      Issue No: Vol. 3 (2013)
       
 
 
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