[ { "key": "E6N343WV", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/E6N343WV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/E6N343WV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Qureshi et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "E6N343WV", "version": 1, "itemType": "bookSection", "title": "Nodule Physiology and Proteomics of Stressed Legumes", "creators": [ { "creatorType": "author", "firstName": "M. I.", "lastName": "Qureshi" }, { "creatorType": "author", "firstName": "S.", "lastName": "Muneer" }, { "creatorType": "author", "firstName": "H.", "lastName": "Bashir" }, { "creatorType": "author", "firstName": "J.", "lastName": "Ahmad" }, { "creatorType": "author", "firstName": "M.", "lastName": "Iqbal" }, { "creatorType": "editor", "firstName": "Jean-Claude", "lastName": "Kader" }, { "creatorType": "editor", "firstName": "Michel", "lastName": "Delseny" } ], "abstractNote": "Symbiotic bacteria are harboured in the nodules of the nitrogen-fixing plants. The bacteria, collectively termed rhizobia, include genera such as Rhizobium, Sinorhizobium, Bradyrhizobium, Mesorhizobium and Azorhizobium, and form specialised organs within the plant. Nitrogen fixation occurs via the conversion of N2 into NH3 by bacterial nitrogenases. Knowledge of protein profile (structural and soluble) of bacteria and host may provide information useful in understanding the bacteria-host relationship and improving N2-fixation efficiency in leguminous plants. Although the majority of nitrogen-fixing plants belong to the family Fabaceae, a few non-leguminous plants (like actinorhizal plants) can also fix nitrogen. Proteomics is an ideal tool to study the protein profile and its correlation with nodule-associated metabolic and symbiotic processes. N2-fixing symbioses are well studied but not in terms of proteomic response to abiotic stress. Data obtained in some proteomic studies on Medicago trancatula and few other leguminous plants provide useful information on root nodules, their symbiotic bacteria and the proteins produced by both partners during their constant signal exchange and growth. Mass spectrometric analysis has helped in identifying several proteins, including those associated with molecular regulation, respiration and leghaemoglobin, proteases in the nodule. Differential expression of proteins under different abiotic stresses such as temperature, drought, salinity and toxic metals that affect the profile of nodule proteome is believed to be due to the production of oxidative stress, osmotic imbalance and other direct or secondary consequences of stress. However, nutrient stress also affects proteome profile as in iron deficiency. Iron-containing proteins play a key role in symbiotic nitrogen fixation (SNF) that occurs in the nodule. Several proteins like those related to SNF, predominant components of nitrogenase complexes such as nifD, nifH, nifK, nitrogen regulatory protein II (GlnB) and PIIA (PtsN) and urease accessory protein (UreE) are known to be affected by abiotic stress. Nodules are well equipped with antioxidant enzymes (superoxide dismutase, ascorbate peroxidase and glutathione reductase, etc.) which respond to stress conditions. This review introduces nodule physiology and examines critically the recent developments in the field of nodule proteomics, emphasising, in particular, upon changes brought about by abiotic stresses to the nodule proteome, provides up-to-date information on key metabolic proteins that help to combat stress and discusses the prospects of nodule proteomics.", "bookTitle": "Advances in Botanical Research", "series": "", "seriesNumber": "", "volume": "56", "numberOfVolumes": "", "edition": "", "date": "2010", "publisher": "Academic Press", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "1-48", "ISBN": "0065-2296", "DOI": "", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B7CT0-51GHB12-5/2/fa3be5a5895e93f51bd59ca481d6c8f2", "accessDate": "2011-02-21T15:40:48Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "DOI: 10.1016/B978-0-12-381518-7.00001-7", "tags": [], "collections": [ "TFBB4SRP" ], "relations": {}, "dateAdded": "2011-12-05T09:45:01Z", "dateModified": "2011-12-05T09:45:01Z" } }, { "key": "S2XNTB8J", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/S2XNTB8J", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/S2XNTB8J", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Klawitter et al.", "parsedDate": "2010-02-05", "numChildren": 0 }, "data": { "key": "S2XNTB8J", "version": 1, "itemType": "journalArticle", "title": "Association of Immunosuppressant-Induced Protein Changes in the Rat Kidney with Changes in Urine Metabolite Patterns: A Proteo-Metabonomic Study", "creators": [ { "creatorType": "author", "firstName": "Jost", "lastName": "Klawitter" }, { "creatorType": "author", "firstName": "Jelena", "lastName": "Klawitter" }, { "creatorType": "author", "firstName": "Erich", "lastName": "Kushner" }, { "creatorType": "author", "firstName": "Karen", "lastName": "Jonscher" }, { "creatorType": "author", "firstName": "Jamie", "lastName": "Bendrick-Peart" }, { "creatorType": "author", "firstName": "Dieter", "lastName": "Leibfritz" }, { "creatorType": "author", "firstName": "Uwe", "lastName": "Christians" }, { "creatorType": "author", "firstName": "Volker", "lastName": "Schmitz" } ], "abstractNote": "The basic mechanisms underlying calcineurin inhibitor (CI) nephrotoxicity and its enhancement by sirolimus are still largely unknown. We investigated the effects of CIs alone and in combination with sirolimus on the renal proteome and correlated these effects with urine metabolite pattern changes. Thirty-six male Wistar rats were assigned to six treatment groups (n = 4/group for proteome analysis and n = 6/group for urine 1H NMR metabolite pattern analysis): vehicle controls, sirolimus 1 mg/kg/day, cyclosporine 10 mg/kg/day, cyclosporine 10 mg/kg/day + sirolimus 1 mg/kg/day, tacrolimus 1 mg/kg/day, tacrolimus 1 mg/kg/day + sirolimus 1 mg/kg/day. After 28 days, 24 h-urine was collected for 1H NMR-based metabolic analysis and kidneys were harvested for 2D-gel electrophoresis and histology. Cyclosporine affected the following groups of proteins: calcium homeostasis (regucalcin, calbindin), cytoskeleton (vimentin, caldesmon), response to hypoxia and mitochondrial function (prolyl 4-hydroxylase, proteasome, NADH dehydrogenase), and cell metabolism (kidney aminoacylase, pyruvate dehydrogenase, fructose-1,6-bis phosphate). Several of the changes in protein expression, confirmed by Western blot, were associated with and explained changes in metabolite concentrations in urine. Representative examples are an increase in kidney aminoacylase expression (decrease of hippurate concentrations in urine), up regulation of pyruvate dehydrogenase and fructose-1,6-bisphosphatase, (increased glucose metabolism), and down regulation of arginine/glycine-amidino transferase (most likely due to an increase in creatinine concentrations). Protein changes explained and qualified immunosuppressant-induced metabolite pattern changes in urine.", "publicationTitle": "Journal of Proteome Research", "publisher": "", "place": "", "date": "February 05, 2010", "volume": "9", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "865-875", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/pr900761m", "citationKey": "", "url": "http://dx.doi.org/10.1021/pr900761m", "accessDate": "2010-02-26T08:49:18Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Association of Immunosuppressant-Induced Protein Changes in the Rat Kidney with Changes in Urine Metabolite Patterns", "language": "", "libraryCatalog": "ACS Publications", "callNumber": "", "rights": "", "extra": "PMID: 19994912", "tags": [], "collections": [ "TFBB4SRP" ], "relations": {}, "dateAdded": "2011-12-05T09:45:01Z", "dateModified": "2011-12-05T09:45:01Z" } }, { "key": "83SBCNWU", "version": 1, "library": { "type": "group", "id": 62016, "name": "xavier.robin", "links": { "alternate": { "href": "https://www.zotero.org/groups/xavier.robin", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/62016/items/83SBCNWU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/xavier.robin/items/83SBCNWU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 12953, "username": "Calimo", "name": "Xavier Robin", "links": { "alternate": { "href": "https://www.zotero.org/calimo", "type": "text/html" } } }, "creatorSummary": "Vizcaíno et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "83SBCNWU", "version": 1, "itemType": "journalArticle", "title": "A guide to the Proteomics Identifications Database proteomics data repository", "creators": [ { "creatorType": "author", "firstName": "Juan Antonio", "lastName": "Vizcaíno" }, { "creatorType": "author", "firstName": "Richard", "lastName": "Côté" }, { "creatorType": "author", "firstName": "Florian", "lastName": "Reisinger" }, { "creatorType": "author", "firstName": "Joseph M.", "lastName": "Foster" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Mueller" }, { "creatorType": "author", "firstName": "Jonathan", "lastName": "Rameseder" }, { "creatorType": "author", "firstName": "Henning", "lastName": "Hermjakob" }, { "creatorType": "author", "firstName": "Lennart", "lastName": "Martens" } ], "abstractNote": "The Proteomics Identifications Database (PRIDE, ) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.", "publicationTitle": "PROTEOMICS", "publisher": "", "place": "", "date": "2009", "volume": "9", "issue": "18", "section": "", "partNumber": "", "partTitle": "", "pages": "4276-4283", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1002/pmic.200900402", "citationKey": "", "url": "http://dx.doi.org/10.1002/pmic.200900402", "accessDate": "2009-10-16T09:12:23Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Wiley InterScience", "callNumber": "", "rights": "", "extra": "PMID: 19662629", "tags": [], "collections": [ "TFBB4SRP" ], "relations": {}, "dateAdded": "2011-12-05T09:45:01Z", "dateModified": "2011-12-05T09:45:01Z" } } ]