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--- aree:proteomica:ms:bibliografia [2017/02/16 15:32]
Gianluca Frustagli Modifica "bottoni"
+++ aree:proteomica:ms:bibliografia [2017/11/09 10:30] (versione attuale)
Federica Fratini [Sub-Proteomes, Extra-cellular vesicles and membrane microdomains]
@@ Linea 1: / Linea 1: @@
 **Area Proteomica**
 ====== MassSpec ======
-<wrap button>[[:aree:proteomica:ms:richiesta|Richiesta servizio]] [[:aree:proteomica:ms:linee_guida|Linee guida]] [[:aree:proteomica:ms:protocolli|Protocolli]] [[:aree:proteomica:ms:bibliografia|Bibliografia]] [[:aree:proteomica:ms:faq|FAQ]] [[:aree:proteomica:ms:chi_siamo|Chi siamo]]</wrap>
+<WRAP tabs>
+  * [[:aree:proteomica:ms:richiesta|Richiesta servizio]]
+  * [[:aree:proteomica:ms:linee_guida|Linee guida]]
+  * [[:aree:proteomica:ms:protocolli|Protocolli]]
+  * [[:aree:proteomica:ms:bibliografia|Bibliografia]]
+  * [[:aree:proteomica:ms:link_tutorial|Link & Tutorial]]
+  * [[:aree:proteomica:ms:faq|FAQ]]
+</WRAP>
+===== BIBLIOGRAFIA =====
+===== Sub-Proteomes, Exosomes and membrane microdomains =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/28288760|Isolation and characterization of exosomes derived from fertile sheep hydatid cysts.]] \\
+Siles-Lucas M, Sánchez-Ovejero C, González-Sánchez M, González E, Falcón-Pérez JM, Boufana B, Fratini F, Casulli A, Manzano-Román R. \\
+<wrap lo>Vet Parasitol. 2017 Mar 15;236:22-33. doi: 10.1016/j.vetpar.2017.01.022. Epub 2017 Jan 23.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/24045696|Proteomic analysis of detergent-resistant membrane microdomains in trophozoite blood stage of the human malaria parasite Plasmodium falciparum.]] \\
+Yam XY, Birago C, Fratini F, Di Girolamo F, Raggi C, Sargiacomo M, Bachi A, Berry L, Fall G, Currà C, Pizzi E, Breton CB, Ponzi M. \\
+<wrap lo>Mol Cell Proteomics. 2013 Dec;12(12):3948-61. doi: 10.1074/mcp.M113.029272.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/23496850|Global proteomic analysis of the oocyst/sporozoite of Toxoplasma gondii reveals commitment to a host-independent lifestyle.]] \\
+Possenti A*, Fratini F*, Fantozzi L, Pozio E, Dubey JP, Ponzi M, Pizzi E, Spano F. \\
+<wrap lo>BMC Genomics. 2013 Mar 15;14:183. doi: 10.1186/1471-2164-14-183.</wrap>
+===== Biomarkers =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/22855863|Increased levels of acute-phase inflammatory proteins in plasma of patients with sporadic CJD.]] \\
+Fratini F, Principe S, Puopolo M, Ladogana A, Poleggi A, Piscopo P, Bruno G, Castrechini S, Pascone R, Confaloni A, Minghetti L, Cardone F, Pocchiari M, Crescenzi M. \\
+<wrap lo>Neurology. 2012 Sep 4;79(10):1012-8. doi: 10.1212/WNL.0b013e318265a55d.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/22081349|Serum low-molecular-weight protein fractionation for biomarker discovery.]] \\
+VanMeter AJ, Camerini S, Polci ML, Tessitore A, Trivedi N, Heiby M, Kamal Y, Hansen J, Zhou W. \\
+<wrap lo>Methods Mol Biol. 2012;823:237-49. doi: 10.1007/978-1-60327-216-2_15.</wrap>
+===== Quantitative proteomics: Label free =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/28798222|An Integrated Approach to Explore Composition and Dynamics of Cholesterol-rich Membrane Microdomains in Sexual Stages of Malaria Parasite.]] \\
+Fratini F, Raggi C, Sferra G, Birago C, Sansone A, Grasso F, Curr C, Olivieri A, Pace T, Mochi S, Picci L, Ferreri C, Di Biase A, Pizzi E, Ponzi M. \\
+<wrap lo>Mol Cell Proteomics. 2017 Oct;16(10):1801-1814. doi: 10.1074/mcp.M117.067041. Epub 2017 Aug 10.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/26675863|Mass spectrometry detection of fraudulent use of cow whey in water buffalo, sheep, or goat Italian ricotta cheese.]] \\
+Camerini S, Montepeloso E, Casella M, Crescenzi M, Marianella RM, Fuselli F. \\
+<wrap lo>Food Chem. 2016 Apr 15;197 Pt B:1240-8. doi: 10.1016/j.foodchem.2015.11.073.</wrap>
+===== Protein identification from 2D gel spot - Immunoproteomics =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/27213890|Anti-GAPDH Autoantibodies as a Pathogenic Determinant and Potential Biomarker of Neuropsychiatric Diseases.]] \\
+Delunardo F, Soldati D, Bellisario V, Berry A, Camerini S, Crescenzi M, Alessandri C, Conti F, Ceccarelli F, Francia A, Valesini G, Cirulli F, Siracusano A, Siracusano A, Niolu C, Alex Rubino I, Ortona E, Margutti P. \\
+<wrap lo>Arthritis Rheumatol. 2016 Nov;68(11):2708-2716. doi: 10.1002/art.39750.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/25623267|Autoantibodies specific to D4GDI modulate Rho GTPase mediated cytoskeleton remodeling and induce autophagy in T lymphocytes.]] \\
+Barbati C, Alessandri C, Vomero M, Vona R, Colasanti T, Vacirca D, Camerini S, Crescenzi M, Pendolino M, Truglia S, Conti F, Garofalo T, Sorice M, Pierdominici M, Valesini G, Malorni W, Ortona E. \\
+<wrap lo>See comment in PubMed Commons belowJ Autoimmun. 2015 Apr;58:78-89. doi: 10.1016/j.jaut.2015.01.005. Epub 2015 Jan 24.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/23663103|Streptococcal-vimentin cross-reactive antibodies induce microvascular cardiac endothelial proinflammatory phenotype in rheumatic heart disease.]] \\
+Delunardo F, Scalzi V, Capozzi A, Camerini S, Misasi R, Pierdominici M, Pendolino M, Crescenzi M, Sorice M, Valesini G, Ortona E, Alessandri C. \\
+<wrap lo>Clin Exp Immunol. 2013 Sep;173(3):419-29. doi: 10.1111/cei.12135.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/22222975|An insight into the abundant proteome of 46BR.1G1 fibroblasts deficient of DNA ligase I.]] \\
+Giuliano S, Iadarola P, Leva V, Montecucco A, Camerini S, Crescenzi M, Salvini R, Bardoni A. \\
+<wrap lo>Electrophoresis. 2012 Jan;33(2):307-15. doi: 10.1002/elps.201100332.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/21984412|Phosphorylation of SRSF1 is modulated by replicational stress.]] \\
+Leva V, Giuliano S, Bardoni A, Camerini S, Crescenzi M, Lisa A, Biamonti G, Montecucco A. \\
+<wrap lo>Nucleic Acids Res. 2012 Feb;40(3):1106-17. doi: 10.1093/nar/gkr837.</wrap>
+===== Protein – protein interaction =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/27512140|The telomeric protein AKTIP interacts with A- and B-type lamins and is involved in regulation of cellular senescence.]] \\
+Burla R, Carcuro M, Torre ML, Fratini F, Crescenzi M, D'Apice MR, Spitalieri P, Raffa GD, Astrologo L, Lattanzi G, Cundari E, Raimondo D, Biroccio A, Gatti M, Saggio I. \\
+<wrap lo>Open Biol. 2016 Aug;6(8). pii: 160103. doi: 10.1098/rsob.160103.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/27322472|Exogenous Alpha-Synuclein Alters Pre- and Post-Synaptic Activity by Fragmenting Lipid Rafts.]] \\
+Emanuele M, Esposito A, Camerini S, Antonucci F, Ferrara S, Seghezza S, Catelani T, Crescenzi M, Marotta R, Canale C, Matteoli M, Menna E, Chieregatti E. \\
+<wrap lo>EBioMedicine. 2016 May;7:191-204. doi: 10.1016/j.ebiom.2016.03.038.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/26492376|Pur-alpha functionally interacts with FUS carrying ALS-associated mutations.]] \\
+Di Salvio M, Piccinni V, Gerbino V, Mantoni F, Camerini S, Lenzi J, Rosa A, Chellini L, Loreni F, Carrì MT, Bozzoni I, Cozzolino M, Cestra G. \\
+<wrap lo>Cell Death Dis. 2015 Oct 22;6:e1943. doi: 10.1038/cddis.2015.295.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/24561067|Megalencephalic leukoencephalopathy with subcortical cysts protein-1 modulates endosomal pH and protein trafficking in astrocytes: relevance to MLC disease pathogenesis.]] \\
+Brignone MS, Lanciotti A, Visentin S, De Nuccio C, Molinari P, Camerini S, Diociaiuti M, Petrini S, Minnone G, Crescenzi M, Laudiero LB, Bertini E, Petrucci TC, Ambrosini E. \\
+<wrap lo>Neurobiol Dis. 2014 Jun;66:1-18. doi: 10.1016/j.nbd.2014.02.003.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/24046450|The nebulin SH3 domain is dispensable for normal skeletal muscle structure but is required for effective active load bearing in mouse.]] \\
+Yamamoto DL, Vitiello C, Zhang J, Gokhin DS, Castaldi A, Coulis G, Piaser F, Filomena MC, Eggenhuizen PJ, Kunderfranco P, Camerini S, Takano K, Endo T, Crescenzi M, Luther PK, Lieber RL, Chen J, Bang ML. \\
+<wrap lo>J Cell Sci. 2013 Dec 1;126(Pt 23):5477-89. doi: 10.1242/jcs.137026.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/22452640|Interaction network of the 14-3-3 protein in the ancient protozoan parasite Giardia duodenalis.]] \\
+Lalle M, Camerini S, Cecchetti S, Sayadi A, Crescenzi M, Pozio E. \\
+<wrap lo>J Proteome Res. 2012 May 4;11(5):2666-83. doi: 10.1021/pr3000199.</wrap>
+===== Post translational modifications (PTM) =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/25948553|Src inhibitors modulate frataxin protein levels.]] \\
+Cherubini F, Serio D, Guccini I, Fortuni S, Arcuri G, Condò I, Rufini A, Moiz S, Camerini S, Crescenzi M, Testi R, Malisan F. \\
+<wrap lo>Hum Mol Genet. 2015 Aug 1;24(15):4296-305. doi: 10.1093/hmg/ddv162.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/25210797|HIPK2 sustains apoptotic response by phosphorylating Che-1/AATF and promoting its degradation.]] \\
+De Nicola F, Catena V, Rinaldo C, Bruno T, Iezzi S, Sorino C, Desantis A, Camerini S, Crescenzi M, Floridi A, Passananti C, Soddu S, Fanciulli M. \\
+<wrap lo>Cell Death Dis. 2014 Sep 11;5:e1414. doi: 10.1038/cddis.2014.381.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/24658679|The crystal structure of Giardia duodenalis 14-3-3 in the apo form: when protein post-translational modifications make the difference.]] \\
+Fiorillo A, di Marino D, Bertuccini L, Via A, Pozio E, Camerini S, Ilari A, Lalle M. \\
+<wrap lo>PLoS One. 2014 Mar 21;9(3):e92902. doi: 10.1371/journal.pone.0092902.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/24147113|Interkingdom complementation reveals structural conservation and functional divergence of 14-3-3 proteins.]] \\
+Lalle M, Leptourgidou F, Camerini S, Pozio E, Skoulakis EM. \\
+<wrap lo>PLoS One. 2013 Oct 11;8(10):e78090. doi: 10.1371/journal.pone.0078090.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/23485397|HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation.]] \\
+Siepi F, Gatti V, Camerini S, Crescenzi M, Soddu S. \\
+<wrap lo>Biochim Biophys Acta. 2013 Jun;1833(6):1443-53. doi: 10.1016/j.bbamcr.2013.02.018.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/23103755|Phosphorylation and nitration of tyrosine residues affect functional properties of Synaptophysin and Dynamin I, two proteins involved in exo-endocytosis of synaptic vesicles.]] \\
+Mallozzi C, D'Amore C, Camerini S, Macchia G, Crescenzi M, Petrucci TC, Di Stasi AM. \\
+<wrap lo>Biochim Biophys Acta. 2013 Jan;1833(1):110-21. doi: 10.1016/j.bbamcr.2012.10.022.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/22978324|Phosphorylation on threonine 11 of β-dystrobrevin alters its interaction with kinesin heavy chain.]] \\
+Fratini F, Macchia G, Torreri P, Matteucci A, Salzano AM, Crescenzi M, Macioce P, Petrucci TC, Ceccarini M. \\
+<wrap lo>FEBS J. 2012 Nov;279(22):4131-44. doi: 10.1111/febs.12006.</wrap>
+===== Protein adducts and protein-drug interaction =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/28366863|Proteomic and functional analyses reveal pleiotropic action of the anti-tumoral compound NBDHEX in Giardia duodenalis.]] \\
+Camerini S, Bocedi A, Cecchetti S, Casella M, Carbo M, Morea V, Pozio E, Ricci G, Lalle M. \\
+<wrap lo>Int J Parasitol Drugs Drug Resist. 2017 Aug;7(2):147-158. doi: 10.1016/j.ijpddr.2017.03.006. Epub 2017 Mar 29.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/26082764|The FAD-dependent glycerol-3-phosphate dehydrogenase of Giardia duodenalis: an unconventional enzyme that interacts with the g14-3-3 and it is a target of the antitumoral compound NBDHEX.]] \\
+Lalle M, Camerini S, Cecchetti S, Finelli R, Sferra G, Müller J, Ricci G, Pozio E. \\
+<wrap lo>Front Microbiol. 2015 Jun 1;6:544. doi: 10.3389/fmicb.2015.00544.</wrap>
+[[https://www.ncbi.nlm.nih.gov/pubmed/23815439|Carbon monoxide signaling in human red blood cells: evidence for pentose phosphate pathway activation and protein deglutathionylation.]] \\
+Metere A, Iorio E, Scorza G, Camerini S, Casella M, Crescenzi M, Minetti M, Pietraforte D. \\
+<wrap lo>Antioxid Redox Signal. 2014 Jan 20;20(3):403-16. doi: 10.1089/ars.2012.5102.</wrap>
-===== Bibliografia =====
+===== Protein redox state characterization =====
-  * //[[http://www.sciencedirect.com/science/article/pii/S0003269702956770|Intact glucosinolate analysis in plant extracts by programmed cone voltage electrospray LC/MS: performance and comparison with LC/MS/MS methods]]// - FA Mellon, RN Bennett, B Holst, G Williamson - **Analytical Biochemistry, 2002** - Elsevier
+[[https://www.ncbi.nlm.nih.gov/pubmed/24925315|Gaucher disease due to saposin C deficiency is an inherited lysosomal disease caused by rapidly degraded mutant proteins.]] \\
+Motta M, Camerini S, Tatti M, Casella M, Torreri P, Crescenzi M, Tartaglia M, Salvioli R. \\
+<wrap lo>Hum Mol Genet. 2014 Nov 1;23(21):5814-26. doi: 10.1093/hmg/ddu299.</wrap>
-  * //[[http://www.sciencedirect.com/science/article/pii/S0003269798928093|Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography–microspray and …]]// - CL Gatlin, GR Kleemann, LG Hays, AJ Link… - **Analytical biochemistry, 1998** - Elsevier
+[[https://www.ncbi.nlm.nih.gov/pubmed/23726996|Genotype-phenotype analysis of S326C OGG1 polymorphism: a risk factor for oxidative pathologies.]] \\
+Simonelli V, Camerini S, Mazzei F, Van Loon B, Allione A, D'Errico M, Barone F, Minoprio A, Ricceri F, Guarrera S, Russo A, Dalhus B, Crescenzi M, Hübscher U, Bjørås M, Matullo G, Dogliotti E. \\
+<wrap lo>Free Radic Biol Med. 2013 Oct;63:401-9. doi: 10.1016/j.freeradbiomed.2013.05.031.</wrap>
-  * //[[http://www.sciencedirect.com/science/article/pii/S1044030503005749|Matrix effect in bio-analysis of illicit drugs with LC-MS/MS: influence of ionization type, sample preparation, and biofluid]]// - R Dams, MA Huestis, WE Lambert… - **Journal of the American …, 2003** - Elsevier
-  * //[[http://www.sciencedirect.com/science/article/pii/S0003269796903139|Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry]]// - SA Carr, MJ Huddleston, RS Annan - **Analytical biochemistry, 1996** - Elsevier
+===== Proteomics Review =====
+[[https://www.ncbi.nlm.nih.gov/pubmed/25618357|The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics.]] \\
+Camerini S, Mauri P. \\
+<wrap lo>J Chromatogr A. 2015 Feb 13;1381:1-12. doi: 10.1016/j.chroma.2014.12.035. Review.</wrap>