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  • 1. Agrawal, Ganesh Kumar
    et al.
    Job, Dominique
    Kieselbach, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Barkla, Bronwyn J.
    Chen, Sixue
    Deswal, Renu
    Luethje, Sabine
    Amalraj, Ramesh Sundar
    Tanou, Georgia
    Ndimba, Bongani Kaiser
    Cramer, Rainer
    Weckwerth, Wolfram
    Wienkoop, Stefanie
    Dunn, Michael J.
    Kim, Sun Tae
    Fukao, Yochiro
    Yonekura, Masami
    Zolla, Lello
    Rohila, Jai Singh
    Waditee-Sirisattha, Rungaroon
    Masi, Antonio
    Wang, Tai
    Sarkar, Abhijit
    Agrawal, Raj
    Renaut, Jenny
    Rakwal, Randeep
    INPPO Actions and Recognition as a Driving Force for Progress in Plant Proteomics: Change of Guard, INPPO Update, and Upcoming Activities2013Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 13, nr 21, s. 3093-3100Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    The International Plant Proteomics Organization (INPPO) is a non-profit organization whose members are scientists involved or interested in plant proteomics. Since the publication of the first INPPO highlights in 2012, continued progress on many of the organization's mandates/goals has been achieved. Two major events are emphasized in this second INPPO highlights. First, the change of guard at the top, passing of the baton from Dominique Job, INPPO founding President to Ganesh Kumar Agrawal as the incoming President. Ganesh K. Agrawal, along with Dominique Job and Randeep Rakwal initiated the INPPO. Second, the most recent INPPO achievements and future targets, mainly the organization of first the INPPO World Congress in 2014, tentatively planned for Hamburg (Germany), are mentioned.

  • 2. Agrawal, Ganesh Kumar
    et al.
    Sarkar, Abhijit
    Agrawal, Raj
    Ndimba, Bongani Kaiser
    Tanou, Georgia
    Dunn, Michael J
    Kieselbach, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Cramer, Rainer
    Wienkoop, Stefanie
    Chen, Sixue
    Rafudeen, Mohammed Suhail
    Deswal, Renu
    Barkla, Bronwyn J
    Weckwerth, Wolfram
    Heazlewood, Joshua L
    Renaut, Jenny
    Job, Dominique
    Chakraborty, Niranjan
    Rakwal, Randeep
    Boosting the Globalization of Plant Proteomics through INPPO: Current Developments and Future Prospects2012Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 12, nr 3, s. 359-368Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific).

  • 3. Hansen, Terkel
    et al.
    Albers, Michael
    Abt. Chemische Biologie, Max-Planck-Institut für molekulare Physiologie.
    Hedberg, Christian
    Sickmann, Albert
    Adenylylation, MS, and proteomics-Introducing a "new" modification to bottom-up proteomics2013Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 13, nr 6, s. 955-963Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although the addition of a 5'-adenosine phosphodiester group to proteins, called adenylylation, has been known for decades, the possibility that adenylylation could be a molecular switch in cellular signaling pathways has emerged recently. The distinct mass shift upon adenylation of threonine or tyrosine residues renders it a good target for MS detection and identification; however, the fragmentation of adenylylated peptides derived from proteolytic digestion of adenylylated proteins has not yet been systematically investigated. Here, we demonstrate that adenylylated peptides show loss of parts of the adenosine monophosphate (AMP) upon different fragmentation techniques. As expected, causing the least fragmentation of the AMP group, electron transfer dissociation yields less complicated spectra. In contrast, CID and higher energy collision (HCD) fragmentation caused AMP to fragment, generating characteristic ions that could be utilized in the specific identification of adenylylated peptides. The characteristic ions and losses upon CID and higher energy collision fragmentation from the AMP group turned out to be highly dependent on which amino acid was adenylylated, with different reporter ions for adenylylated threonine and tyrosine. We also investigated how adenylylation is best incorporated into search engines, exemplified by Mascot and showed that it is possible to identify adenylylation by search engines.

  • 4. Havlasová, Jana
    et al.
    Hernychová, Lenka
    Brychta, Martin
    Hubálek, Martin
    Lenco, Jurai
    Larsson, Pär
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi. Swedish Defence Research Agency, Umeå, Sweden.
    Lundqvist, Margaretha
    Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, Mats
    Swedish Defence Research Agency, Umeå, Sweden.
    Kročová, Zulana
    Stulík, Jiri
    Macela, Aks
    Proteomic analysis of anti-Franciselia tularensis LVS antibody response in murine model of tularemia2005Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 5, nr 8, s. 2090-2103Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Francisella tularensis live vaccine strain infection of mice has been established as an experimental model of tularemia that is suitable for studies of immune mechanisms against the intracellular pathogen. In this study, the model was used to explore immunogenic repertoire of F. tularensis with the aim of identifying new molecules able to activate the host immune system, potential bacterial markers with vaccine, and diagnostic applications. Immunoproteomic approach based on the combination of two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry was applied. Globally, 36 different proteins were identified, which strongly reacted with sera from experimentally infected mice, including several putative virulence markers of intracellular pathogens as nucleoside diphosphate kinase, isocitrate dehydrogenase, RNA-binding protein Hfq, and molecular chaperone ClpB. Of them, 27 proteins are described for the first time as immunorelevant Francisella proteins. When comparing murine immunoproteome of F. tularensis with our previous data from human patients, 25 of the total of 50 identified murine sera immunoreactive spots were recognized by human sera collected from patients suffering from tularemia, as well. Immune sera from two Lps gene congenic strains of mice, C3H/HeN (Lpsn) and C3H/HeJ (Lpsd), represented murine immunoproteome in this study. The spectrum of immunoreactive spots detected by two-dimensional immunoblotting varied throughout the course of infection depending on murine strain. Nevertheless, the antibody patterns of the two strains showed significant homogeneity in being directed against almost identical subset of antigens.

  • 5. Hummel, Maureen
    et al.
    Cordewener, Jan H. G.
    de Groot, Joost C. M.
    Smeekens, Sjef
    America, Antoine H. P.
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics2012Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 12, nr 7, s. 1024-1038Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cytosolic ribosomes are among the largest multisubunit cellular complexes. Arabidopsis thaliana ribosomes consist of 79 different ribosomal proteins (r-proteins) that each are encoded by two to six (paralogous) genes. It is unknown whether the paralogs are incorporated into the ribosome and whether the relative incorporation of r-protein paralogs varies in response to environmental cues. Immunopurified ribosomes were isolated from A. thaliana rosette leaves fed with sucrose. Trypsin digested samples were analyzed by qTOF-LC-MS using both MSE and classical MS/MS. Peptide features obtained by using these two methods were identified using MASCOT and Proteinlynx Global Server searching the theoretical sequences of A. thaliana proteins. The A. thaliana genome encodes 237 r-proteins and 69% of these were identified with proteotypic peptides for most of the identified proteins. These r-proteins were identified with average protein sequence coverage of 32% observed by MSE. Interestingly, the analysis shows that the abundance of r-protein paralogs in the ribosome changes in response to sucrose feeding. This is particularly evident for paralogous RPS3aA, RPS5A, RPL8B, and RACK1 proteins. These results show that protein synthesis in the A. thaliana cytosol involves a heterogeneous ribosomal population. The implications of these findings in the regulation of translation are discussed.

  • 6. Lexander, Helena
    et al.
    Franzén, Bo
    Hirschberg, Daniel
    Becker, Susanne
    Hellström, Magnus
    Bergman, Tomas
    Jörnvall, Hans
    Auer, Gert
    Egevad, Lars
    Differential protein expression in anatomical zones of the prostate.2005Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 5, nr 10Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The prostate has three anatomical zones: the peripheral (PZ), the transition (TZ), and the central (CZ) zone. It is proposed that the CZ may be of mesodermal origin, whereas the other two are of endodermal origin. Proteome patterns in the zones were characterized to test for differences. Cells were scraped from macroscopically normal areas of PZ, TZ, and CZ in radical prostatectomy specimens. After exclusion of samples with cancer or prostatic intraepithelial neoplasia, 18 cases remained for analysis. Cells were collected in a medium with protease inhibitors, and the protein material was prepared for two-dimensional gel electrophoresis. The proteins in spots that differed quantitatively between regions were identified via mass spectrometric fingerprinting of tryptic fragments and selected tandem mass spectrometry sequence analysis. Ten proteins with significant zonal differential expression were identified, eight with underexpression in the CZ versus the PZ and the TZ (arginase II, ATP synthase, cytokeratin 8, lamin A/C, peroxiredoxin 4, protein disulfide isomerase A3, tropomyosin, and vimentin), and two with overexpression in the CZ (peroxiredoxin 2 and creatine kinase B). The PZ and TZ, although differing in terms of incidence of cancer and hyperplasia, have epithelium with highly similar major protein expression profiles. However, the protein profile of the CZ differs from that of the other regions, suggesting functional differences.

  • 7.
    Ma, Wei-Juan
    et al.
    Medical College of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases, Xi'an, Shaanxi, China.
    Guo, Xiong
    Medical College of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases, Xi'an, Shaanxi, China.
    Liu, Jiang-Tao
    Medical College of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases, Xi'an, Shaanxi, China.
    Liu, Rui-Yu
    Medical College of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases, Xi'an, Shaanxi, China.
    Hu, Jian-Wen
    Research Center for Proteome Analysis, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.
    Sun, An-Guo
    Research Center for Proteome Analysis, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.
    Yu, Yue-Xiang
    Shaanxi Provincial Institute For Endemic Disease Control, Xi'an, Shaanxi, China.
    Lammi, Mikko
    Department of Biosciences, University of Eastern Finland, Kuopio, Finland.
    Proteomic changes in articular cartilage of human endemic osteoarthritis in China.2011Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 11, nr 14, s. 2881-90, artikkel-id 21681992Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Kashin-Beck disease (KBD) is a chronic endemic osteochondropathy with unclear pathogenesis. It is a degenerative disease similar to osteoarthritis, but with different manifestations of cartilage damage. The aim of this investigation was to show the protein changes in KBD cartilage and to identify the candidate proteins in order to understand the pathogenesis of the disease. Proteins were extracted from the media of primary cell cultures of KBD and normal chondrocytes, and separated by two-dimensional fluorescence difference gel electrophoresis (2-D DIGE). MALDI-TOF/TOF analysis revealed statistically significant differences in 27 proteins from KBD chondrocyte cultures, which consisted of 17 up-regulated and ten down-regulated proteins. The results were further validated by Western blot analysis. The proteins identified are mainly involved in cellular redox homeostasis and stress response (MnSOD, Hsp27, Peroxiredoxin-1, and Cofilin-1), glycolysis (PGK-1, PGM-1, α-enolase), and cell motility and cytoskeletal organization (Actin, Calponin-2, and Keratin). These KBD-associated proteins indicate that cytoskeletal remodeling, glycometabolism, and oxidative stress are abnormal in KBD articular cartilage.

  • 8.
    Piltti, Juha
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB). Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
    Varjosalo, Markku
    Institute of Biotechnology, University of Helsinki, Helsinki.
    Qu, Chengjuan
    Department of Applied Physics, University of Eastern Finland, Kuopio, Finland.
    Häyrinen, Jukka
    Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
    Lammi, Mikko
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Rho-kinase inhibitor Y-27632 increases cellular proliferation and migration in human foreskin fibroblast cells2015Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 15, nr 17, s. 2953-2965Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The idea of direct differentiation of somatic cells into other differentiated cell types has attracted a great interest recently. Rho-kinase inhibitor Y-27632 (ROCKi) is a potential drug molecule, which has been reported to support the gene expressions typical for the chondrocytes, thus restricting their phenotypic conversion to fibroblastic cells upon the cellular expansion. In this study, we have investigated the short-term biological responses of ROCKi to human primary foreskin fibroblasts. The fibroblast cells were exposed to 1 and 10 μM ROCKi treatments. A proteomics analysis revealed expression changes of 56 proteins, and a further protein pathway analysis suggested their association with the cell morphology, the organization, and the increased cellular movement and the proliferation. These functional responses were confirmed by a Cell-IQ time-lapse imaging analysis. Rho-kinase inhibitor treatment increased the cellular proliferation up to twofold during the first 12 h, and a wound model based migration assay showed 50% faster filling of the mechanically generated wound area. Additionally, significantly less vinculin-associated focal adhesions were present in the ROCKi-treated cells. Despite the marked changes in the cell behavior, ROCKi was not able to induce the expression of the chondrocyte-specific genes, such as procollagen α1 (II) and aggrecan.

  • 9. Potrykus, Joanna
    et al.
    Jonna, Venkateswara Rao
    Dopson, Mark
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Iron homeostasis and responses to iron limitation in extreme acidophiles from the Ferroplasma genus2011Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 11, nr 1, s. 52-63Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Extremely acidophilic archaea from the genus Ferroplasma inhabit iron-rich biomining environments and are important constituents of naturally occurring microbial consortia that catalyze the production of acid mine drainage. A combined bioinformatic, transcript profiling, and proteomic approach was used to elucidate iron homeostasis mechanisms in "F. acidarmanus" Fer1 and F. acidiphilum Y(T) . Bioinformatic analysis of the "F. acidarmanus" Fer1 genome sequence revealed genes encoding proteins hypothesized to be involved in iron-dependent gene regulation and siderophore biosynthesis; the Fhu and NRAMP cation acquisition systems; iron storage proteins; and the SUF machinery for the biogenesis of Fe-S clusters. A subset of homologous genes was identified on the F. acidiphilum Y(T) chromosome by direct PCR probing. In both strains, some of the genes appeared to be regulated in a ferrous/ferric iron-dependent manner, as indicated by RT-PCR. A detailed gel-based proteomics analysis of responses to iron depletion showed that a putative isochorismatase, presumably involved in siderophore biosynthesis, and the SufBCD system were upregulated under iron-limiting conditions. No evidence was obtained for iron sparing response during iron limitation. This study constitutes the first detailed investigation of iron homeostasis in extremely acidophilic archaea.

  • 10. Turkina, Maria V
    et al.
    Blanco-Rivero, Amaya
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Vainonen, Julia P
    Vener, Alexander V
    Villarejo, Arsenio
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Biology, Universidad Autónoma de Madrid, Spain.
    CO2 limitation induces specific redox-dependent protein phosphorylation in Chlamydomonas reinhardtii2006Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 6, nr 9, s. 2693-2704Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Acclimation of the green alga Chlamydomonas reinhardtii to limiting environmental CO2 induced specific protein phosphorylation at the surface of photosynthetic thylakoid membranes. Four phosphopeptides were identified and sequenced by nanospray quadrupole TOF MS from the cells acclimating to limiting CO2. One phosphopeptide originated from a protein that has not been annotated. We found that this unknown expressed protein (UEP) was encoded in the genome of C. reinhardtii. Three other phosphorylated peptides belonged to Lci5 protein encoded by the low-CO2-inducible gene 5 (lci5). The phosphorylation sites were mapped in the tandem repeats of Lci5 ensuring phosphorylation of four serine and three threonine residues in the protein. Immunoblotting with Lci5-specific antibodies revealed that Lci5 was localized in chloroplast and confined to the stromal side of the thylakoid membranes. Phosphorylation of Lci5 and UEP occurred strictly at limiting CO2; it required reduction of electron carriers in the thylakoid membrane, but was not induced by light. Both proteins were phosphorylated in the low-CO2-exposed algal mutant deficient in the light-activated protein kinase Stt7. Phosphorylation of previously unknown basic proteins UEP and Lci5 by specific redox-dependent protein kinase(s) in the photosynthetic membranes reveals the early response of green algae to limitation in the environmental inorganic carbon.

  • 11. Walz, Anke
    et al.
    Odenbreit, Stefan
    Stühler, Kai
    Wattenberg, Andreas
    Meyer, Helmut E
    Mahdavi, Jafar
    Borén, Thomas
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Ruhl, Stefan
    Identification of glycoprotein receptors within the human salivary proteome for the lectin-like BabA and SabA adhesins of Helicobacter pylori by fluorescence-based 2-D bacterial overlay2009Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 9, nr 6, s. 1582-1592Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Because gastric infection by Helicobacter pylori takes place via the oral route, possible interactions of this bacterium with human salivary proteins could occur. By using modified 1- and 2-D bacterial overlay, binding of H. pylori adhesins BabA and SabA to the whole range of salivary proteins was explored. Bound salivary receptor molecules were identified by MALDI-MS and by comparison to previously established proteome maps of whole and glandular salivas. By use of adhesin-deficient mutants, binding of H. pylori to MUC7 and gp-340 could be linked to the SabA and BabA adhesins, respectively, whereas binding to MUC5B was associated with both adhesins. Binding of H. pylori to the proline-rich glycoprotein was newly detected and assigned to BabA adhesin whereas the SabA adhesin was found to mediate binding to newly detected receptor molecules, including carbonic anhydrase VI, secretory component, heavy chain of secretory IgA1, parotid secretory protein and zinc-alpha(2)-glycoprotein. Some of these salivary glycoproteins are known to act as scavenger molecules or are involved in innate immunity whereas others might come to modify the pathogenetic properties of this organism. In general, this 2-D bacterial overlay technique represents a useful supplement in adhesion studies of bacteria with complex protein mixtures.

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