Дисертації з теми "Proteomic pattern"
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Komori, Mika. "Proteomic pattern analysis discriminates among multiple sclerosis-related disorders." Kyoto University, 2012. http://hdl.handle.net/2433/152501.
Повний текст джерелаLiu, Yiding. "Technologies for Proteomic and Genomic Biomarker Analysis." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1229461302.
Повний текст джерелаAgatea, Lisa. "An integrated proteomic and genomic approach to study FAP patients without APC and MutHY mutations." Doctoral thesis, Università degli studi di Padova, 2016. http://hdl.handle.net/11577/3424509.
Повний текст джерелаLa poliposi adenomatosa familiare (FAP) è una delle più importanti forme cliniche di cancro colo-rettale ereditario ed è caratterizzata dallo sviluppo di centinaia/migliaia di polipi adenomatosi nel colon e nel retto durante la seconda decade di vita. La FAP è causata da una mutazione germinale del gene APC o da varianti bialleliche del gene MutYH. Quasi tutti i pazienti FAP sviluppano il cancro se la patologia non viene precocemente identificata e trattata chirurgicamente. Lo scopo di questo lavoro è stato caratterizzare 4 pazienti in cui, nonostante l’esame colonscopico presentasse una poliposi conclamata, non risultavano mutazioni nei gene APC e MutYH (in questa tesi definiti pazienti FAP irrisolti) utilizzando un approccio integrato di peptidomica e genomica. Riguardo la peptidomica, il MALDI-TOF è stato utilizzato per studiare il profilo peptidico plasmatico di pazienti FAP mutati ed irrisolti comparando i dati ottenuti con quelli derivanti dallo studio di pazienti con adenoma, cancro colo-rettale e soggetti sani di controllo. Dopo analisi statistica è stato ottenuto il fingerprint peptidico dei pazienti FAP mutati. Sono state ottenute 45 specie ioniche differentemente espresse nei quattro gruppi considerati, 12 delle quali peculiari per i pazienti FAP. L’intensità di segnale di quattro di queste specie ioniche è stata trovata statisticamente alterata nello switch tra adenoma e carcinoma maligno. I peptidi potenzialmente prognostici identificati in questo studio derivano principalmente da proteine circolanti, alcune delle quali implicate nella risposta infiammatoria. In particolare è noto dalla letteratura che proteine del sistema del complemento come C3 e C4 vengono tagliate da esoproteasi che sembrano essere patologia correlate. Riguardo ai pazienti FAP irrisolti, per definirne un pattern specifico, i dati derivanti dall’analisi con il MALDI-TOF sono stati combinati con quelli ottenuti dal sequenzia-mento dell’esoma. I dati di peptidomica hanno chiaramente evidenziato le differenze tra pazienti FAP mutati e FAP irrisolti. Infatti i pazienti FAP irrisolti presentano caratteristiche simili a quelle dei soggetti di controllo, dei pazienti con adenoma e cancro colo rettale ma non a quelle dei pazienti FAP mutati. Allo scopo di capire la via di trasduzione del segnale implicata, è stato quindi eseguito il sequenziamento dell'esoma dei pazienti FAP irrisolti. Da questa analisi sono stati selezionati 285 geni variati in tutti i pazienti e tra questi la via di trasduzione del segnale della O-glicosilazione delle mucine è risultata la più rappresentata. In conclusione, in questo studio è stato definito per la prima volta un set peptidico specifico per i pazienti FAP mutati che potrebbe essere utilizzato per monitorare e predire l’evoluzione patologica della malattia. Inoltre è stato possibile caratterizzare un pattern preliminare per i pazienti FAP irrisolti in cui i geni delle mucine potrebbero rappresentare la chiave della via di trasduzione del segnale implicata. Ulteriori studi saranno necessari per correlare i geni delle mucine con la poliposi e costruire l'interatoma (network biologico definito come l’insieme di tutte le interazioni molecolari dirette e indirette che ci sono all'interno di una cellula e di un organismo) di questi pazienti FAP irrisolti.
Wibom, Carl. "Multivariate analyses of proteomic and metabolomic patterns in brain tumors." Doctoral thesis, Umeå universitet, Onkologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-25670.
Повний текст джерелаCerjan, Dijana. "INTRACELLULAR DISTRIBUTION PATTERNS OF ORGANELL SPECIFIC PROTEINS USING IMMUNOHISTOCHEMICAL STAINING OF TISSUE MICRO ARRAYS." Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6154.
Повний текст джерелаThe knowledge of the human genome sequence, as revealed in the HUGO project, has created exciting new possibilities for biomedical research. The Swedish Human Proteome Resource (HPR) program aims to make use of this information to gain further insight into the human proteome. Recombinant proteins are generated from coding sequences identified from the human genome sequence and used to produce specific antibodies to target proteins. Antibodies are subsequently utilized for functional analysis of the corresponding proteins using tissue micro arrays. The aim of my project was to investigate the possibility of distinguishing characteristic distribution patterns of intracellular proteins in the resolution capacity offered by light microscopy. A map of representative distribution patterns was created using immunohistological staining with commercially available antibodies toward well-characterised proteins in the cell. Such a map could then aid in interpreting the results of immunohistological staining of intracellular proteins using antibodies produced within the Human Proteome Resource program. Proteins manifested in nucleus, nuclear membrane and plasma membrane were clearly visible at the expected location. Proteins manifested in different organelles in the cytoplasm however, showed all a similar staining pattern, making determination of exact protein location uncertain. A possible explanation is the resolution of the light microscope not being sufficient to visualize certain proteins specific to organelles in the cytoplasm. Results may also have been influenced by the choice of secondary antibody, where the strenghtened signal generated by an enzyme labelled polymer may have a negative effect on depiction of details in the image generated.
Sabounchi, Schütt Fariba. "Bronchoalveolar lavage and serum protein patterns in healthy individuals and sarcoidosis patients : a proteomics approach /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-790-8/.
Повний текст джерелаÖztürk, Özgür. "Feature extraction and similarity-based analysis for proteome and genome databases." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1190138805.
Повний текст джерелаLindskog, Bergström Cecilia. "Tissue Microarrays for Analysis of Expression Patterns." Doctoral thesis, Uppsala universitet, Molekylär och morfologisk patologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-186272.
Повний текст джерелаGöbel, Thomas. "Identifizierung von Proteom Pattern und Proteinmarkern durch SELDI-TOF MS bei Patienten mit chronischer Hepatitis C." Düsseldorf, 2008. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=016540450&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
Повний текст джерелаPajak, Maciej. "Evolutionary conservation and diversification of complex synaptic function in human proteome." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31108.
Повний текст джерелаStrömberg, Sara. "Antibody-based Profiling of Expression Patterns using Cell and Tissue Microarrays." Doctoral thesis, Uppsala University, Department of Genetics and Pathology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8680.
Повний текст джерелаIn this thesis, methods to study gene and protein expression in cells and tissues were developed and utilized in combination with protein-specific antibodies, with the overall objective to attain greater understanding of protein function.
To analyze protein expression in in vitro cultured cell lines, a cell microarray (CMA) was developed, facilitating antibody-based protein profiling of cell lines using immunohistochemistry (IHC). Staining patterns in cell lines were analyzed using image analysis, developed to automatically identify cells and immunohistochemical staining, providing qualitative and quantitative measurements of protein expression. Quantitative IHC data from CMAs stained with nearly 3000 antibodies was used to evaluate the adequacy of using cell lines as models for cancer tissue. We found that cell lines are homogenous with respect to protein expression profiles, and generally more alike each other, than corresponding cancer cells in vivo. However, we found variability between cell lines in regards to the level of retained tumor phenotypic traits, and identified cell lines with a preserved link to corresponding cancer, suggesting that some cell lines are appropriate model systems for specific tumor types.
Specific gene expression patterns were analyzed in vitiligo vulgaris and malignant melanoma. Transcriptional profiling of vitiligo melanocytes revealed dysregulation of genes involved in melanin biosynthesis and melanosome function, thus highlighting some mechanisms possibly involved in the pathogenesis of vitiligo. Two new potential markers for infiltrating malignant melanoma, Syntaxin-7 and Discs large homolog 5, were identified using antibody-based protein profiling of melanoma in a tissue microarray format. Both proteins were expressed with high specificity in melanocytic lesions, and loss of Syntaxin-7 expression was associated with more high-grade malignant melanomas.
In conclusion, the combination of antibody-based proteomics and microarray technology provided valuable information of expression patterns in cells and tissues, which can be used to better understand associations between protein signatures and disease.
Huang, Yingying. "DATA MINING OF PEPTIDE MS/MS SPECTRA TO ELUCIDATE GAS-PHASE PEPTIDE DISSOCIATION MECHANISMS AND IMPROVE PROTEIN IDENTIFICATION." Diss., Tucson, Arizona : University of Arizona, 2005. http://etd.library.arizona.edu/etd/GetFileServlet?file=file:///data1/pdf/etd/azu%5Fetd%5F1133%5F1%5Fm.pdf&type=application/pdf.
Повний текст джерелаGöbel, Thomas [Verfasser]. "Identifizierung von Proteom Pattern und Proteinmarkern durch SELDI-TOF MS bei Patienten mit chronischer Hepatitis C / Thomas Göbel." Aachen : Shaker, 2009. http://d-nb.info/1159834636/34.
Повний текст джерелаHattingh, Susanna Maria (Suzel). "Ischaemic preconditioning : an investigation of the patterns of kinase activation and protein expression profiles during reperfusion in the rat heart." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/85789.
Повний текст джерелаENGLISH ABSTRACT: Introduction: Coronary heart disease (CHD) is the leading cause of death worldwide with 3.8 million men and 3.4 million women dying globally each year. Although existing myocardial reperfusion strategies such as thrombolysis and percutaneous coronary intervention (PCI), if applied in a timely manner, limit myocardial infarct size, the mortality and morbidity remains significantly high. Ischaemic preconditioning (IPC) may offer the potential to attenuate myocardial ischaemia/reperfusion injury through cardioprotective signaling pathways which is recruited at the time of myocardial reperfusion, thereby improving clinical outcomes in patients with coronary artery disease. Ischaemic preconditioning is a phenomenon whereby short intermittent episodes of coronary occlusion followed by reperfusion protect the myocardium against a subsequent period of sustained ischaemia. This protection is reflected in the limitation of infarct size and improved functional recovery of the ischaemic heart during reperfusion. Despite intensive research efforts, the promise of an effective cardioprotective strategy using the endogenous protective mechanisms of the heart which underlies IPC, has not yet been materialized. Although progress has been made in terms of signaling mechanisms in the preconditioned heart, the identification of the myocardial reperfusion phase as the critical “window” for cardioprotection, requires the elucidation of the signal transduction pathways during the reperfusion phase after IPC. In view of the above, the aims of the present study were to investigate: i. the involvement of the RISK pathway and p38 MAP kinase pathway in IPC during early and late reperfusion ii. the involvement of heat shock protein-27 (HSP-27), heat shock protein-70 (HSP-70), GSK-3β, CAMKII, AMPK and the transcription factor CREB in the context of IPC during early reperfusion iii. the involvement of autophagy and apoptosis during early and late reperfusion after IPC iv. the correlation of the protein kinases with the hemodynamic parameters of the heart v. the mechanism of IPC by means of two-dimensional (2D) proteomics Methods: The isolated perfused working rat heart model was used with functional recovery as end-point. Hearts were preconditioned (IPC) for 3x5 min global ischaemia, alternated with 5 min reperfusion. Hearts were subjected to 25 min sustained global ischaemia, followed by 5, 10, 15 or 30 min reperfusion when hearts were snap-frozen for western blotting analysis. Alternatively, hearts were reperfused for 30 min to record hemodynamic parameters and measure functional recovery. Non-preconditioned (Non-IPC) hearts were stabilized for 30 min and subjected to 25 min sustained global ischaemia followed by 5, 10, 15 or 30 min reperfusion when hearts were snap-frozen. Alternatively Non-IPC hearts were reperfused for 30 min to serve as control for the 30 min reperfused IPC group. Activation of the protein kinases was determined by western blotting analysis. For the proteomic study mitochondrial and cytosolic proteins were isolated from heart tissue and separated in the first dimension by isoelectric focusing, followed by separation in the second dimension by two dimensional gel electrophoresis. The PD Quest software programme was used to identify significantly expressed protein spots. Protein spots of interest were excised and subjected to in-gel digestion and the resulting peptides were analysed by mass spectrometry. Proteins were identified by Mascot and the Swiss Prot database. Results: Western blotting analysis demonstrated that the RISK pathway and p38 MAPK are activated very early in reperfusion, but the activation is not sustained during the reperfusion period. Autophagy is also upregulated during this early reperfusion phase; it is attenuated in the middle reperfusion phase and increase for a second peak of upregulation in the late reperfusion phase. In addition, we identified CAMKII as a novel marker of functional recovery in IPC after reperfusion. The proteomic analysis identified twenty differentially expressed mitochondrial and thirty six differentially expressed cytosolic proteins between Non-IPC and IPC hearts. Functions ascribed to the majority of these individual proteins were directly related to cardiac metabolism. Conclusion: Activation of the majority of the protein kinases investigated in the present study is associated with the hemodynamic parameters of the heart instead of functional recovery. Results indicated that the variable signaling patterns could be attributed to differences in heart rate and the effect thereof (ejection fraction, minimum and maximum rate of contraction), as a result of sympathetic stimulation due to psychological stress in the animals before slaughtering. Proteomics results demonstrated that IPC hearts which failed after ischaemia /reperfusion are metabolically compromised and “worse off” compared to non-IPC hearts.
AFRIKAANSE OPSOMMING: Inleiding: Koronêre hartsiekte is die vernaamste oorsaak van sterftes wêreldwyd met 3.8 miljoen mans en 3.4 miljoen vrouens wat jaarliks sterf. Alhoewel bestaande miokardiale herperfusie strategieë soos trombolise en perkutane koronêre intervensie (PKI), wanneer betyds toegepas, miokardiale infarktgrootte beperk, bly mortaliteit en morbiditeit steeds hoog. Isgemiese prekondisionering (IPK) beskik oor die potensiaal om miokariale isgemie/herperfusie skade te verminder deur beskermende seinoordragpaaie tydens miokardiale herperfusie te aktiveer en sodoende die pasiënte wat aan koronêre arterie siekte ly, se prognose te verbeter. Isgemiese prekondisionering verwys na die verskynsel waartydens kort episodes van isgemie opgevolg deur herperfusie, die miokardium teen ‘n daaropvolgende langdurige isgemiese insident beskerm. Hierdie beskerming word gereflekteer in die beperking van infarktgrootte en verbeterde funksionele herstel van die isgemiese hart tydens herperfusie. Ten spyte van intensiewe navorsingspogings is die presiese meganisme van endogene beskerming tydens IPK nog nie ten volle ontrafel nie. Die identifisering van die miokardiale herperfusie fase se kritiese “vensterperiode” van beskerming, noodsaak ‘n volledige analise van die seinoordragpaaie wat geaktiveer word tydens die herperfusie fase na IPK. In die lig van bogenoemde, was die doel van die huidige studie om die volgende te ondersoek: i. die betrokkenheid van die RISK seinoordragpad en p38 MAP kinase tydens vroeë en laat herperfusie na IPK ii. die betrokkenheid van “heat shock protein-27” (HSP-27), “heat shock protein- 70” (HSP-70), GSK -3β, CAMKII, AMPK en die transkripsie faktor, CREB, in die konteks van IPK tydens vroeë herperfusie iii. die betrokkenheid van outofagie en apoptose tydens vroeë en laat herperfusie na IPK iv. die korrelasie van die proteïenkinases met die hemodinamiese parameters van die hart v. die meganisme van IPK deur middel van twee dimensionele proteomika Metodes: Die geïsoleerde werkende rothart model, met funksionele herstel as eindpunt, is gebruik. Harte is geprekondisioneer (IPK) met 3x5 min globale isgemie, afgewissel met 5 min herperfusie. Daarna is harte blootgestel aan 25 min volgehoue globale isgemie, gevolg deur 5, 10, 15 of 30 min herperfusie, waartydens harte gevriesklamp is. Alternatiewelik, is harte blootgestel aan 30 min herperfusie ten einde funksionele herstel te meet en hemodinamiese parameters te registreer. Nie-geprekondisioneerde (Non-IPK) harte is gestabiliseer vir 30 min, waarna dit onderwerp is aan 25 min volgehoue globale isgemie, gevolg deur 5, 10, 15 of 30 min herperfusie, waartydens harte gevriesklamp is vir westelike klad analise. Alternatiewelik, is Non-IPK harte onderwerp aan 30 min herperfusie om te dien as kontrole vir die 30 min IPK groep. Aktivering van die proteïenkinases is bepaal deur westelike klad analise. Vir die proteomiese studie, is onderskeidelik mitokondriale en sitosoliese proteïene geïsoleer en geskei in die eerste dimensie met behulp van isoelektriese fokusering, gevolg deur skeiding in die tweede dimensie met behulp van twee dimensionele gel elektroforese. Die PDQuest sagteware program is gebruik om proteïenkolle te identifiseer wat statisties beduidende verskille toon. Proteïenkolle van belang is uitgesny en onderwerp aan in-gel tripsinering en die peptiede wat sodoende verkry is, is deur middel van massa spektrometrie geanaliseer. Proteïene is geïdentifiseer deur Mascot en die Swiss Prot databasis. Resultate: Westelike klad analise het aangetoon dat die RISK pad en p38 MAPK geaktiveer is tydens vroeë herperfusie, maar die aktivering word nie volgehou tydens die hele herperfusie periode nie. Outofagie word gestimuleer tydens die vroeë herperfusie fase; dit word onderdruk in die middel herperfusie fase en bereik ‘n tweede piek van stimulering in die laat herperfusie fase. Die proteomiese analise het onderskeidelik twintig differensieel gereguleerde mitokondriale proteïene en ses en dertig differensieel gereguleerde sitosoliese proteïene geïdentifiseer tussen Non-IPK en IPK. Die grootste persentasie van hierdie proteïene is direk betrokke by miokardiale energie metabolisme. CAMKII is geidentifiseer as ‘n unieke merker van funksionele herstel in IPK tydens reperfusie. Gevolgtrekking: Aktivering van die meeste van die proteïenkinases wat ondersoek is in die huidige studie, is geassosieer met die hemodinamiese parameters van die hart, in plaas van funksionele herstel. Die resultate het aangetoon dat die varierende patrone van kinase aktivering toegeskryf kan word word aan verskille in harttempo en die effek daarvan (ejeksie fraksie, minimum en maksimum tempo van kontraksie), as gevolg van simpatiese stimulasie toegeskryf aan sielkundige stres in die diere voor slagting. Proteomiese analise het getoon dat IPK harte wat faal na isgemie/reperfusie metabolies gekompromiseer is en “slegter daaraan toe” is, in vergelyking met Non-IPK harte.
Abbaraju, Naga Vijayalaxmi. "Patterns of protein expression in tissues of the killifish, Fundulus heteroclitus and Fundulus grandis." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/113.
Повний текст джерелаNeves, Simone Cristina Ferreira. "Classificação de câncer de ovário através de padrão proteômico e análise de componentes independentes." Universidade Federal do Maranhão, 2012. http://tedebc.ufma.br:8080/jspui/handle/tede/490.
Повний текст джерелаThe ovarian cancer is difficult to diagnose in the early stages of development. In this work we bring a study of a new method that gave us great accuracy rates based on a bioinformatics tool called surface enhanced for laser desorption and ionization (SELDI-TOF) used to generate proteomic patterns which is one of the technologies advanced in the diagnosis. Our goal is to contribute to effectiveness of this tool, which already helps diagnosis earlier, our methodology uses independent component analysis (ICA) for feature extraction and neural networks to classify between malignancy and no malignancy in a database of the research center cancer in the U.S.A. Our work rates obtained acurracy 97%, 98% specificity and 96% sensitivity.
O câncer de ovário possui difícil diagnóstico nas primeiras fases de desenvolvimento. Neste trabalho trazemos um estudo de um novo método que nos deu ótimas taxas de precisão baseado em uma ferramenta da bio-informática chamada superfície mehorada a laser para ionização e dessorção (SELDI-TOF) usada para geração de padrões proteômicos que é uma das tecnologias mais avançada no auxílio ao diagnóstico. Nosso objetivo é contribuir para eficácia desta esta ferramenta, que já auxilia o dignóstico precoce, nossa metodologia usa análise de componentes independentes (ICA) para extração de caractéristicas e redes neurais para classificar entre malignidade e não malignidade em uma base de dados do centro de pesquisa do câncer nos EUA. Nosso trabalho obteve taxas de 97% de acurária, 98% de especifidade e 96 % de sensibilidade.
Ting, Yang-Chung, and 丁洋中. "A Study of Effects of Growth Substrates for Monascus on Red Pigment Production and Proteomic Pattern Expressions." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/24300750923952941992.
Повний текст джерела實踐大學
食品營養研究所
93
Monascus pigments are important colorings in food application, but Monascus biochemical pathways and regulation of nutrient metabolism concerning pigment production remain unknown. Rice starch and sodium nitrate substrates were firstly reported as better pigment-producing substrates compared to lactose and yeast extract substrates. A comparison of protein expression by proteomic analysis with two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS), tandem mass spectrometry (MS/MS) and database interrogation was conducted on Monascus pilosus grown between the rice nitrate and lactose yeast extract growth substrates. Out of eleven Monascus strains in the screening experiment, M. pilosus BCRC 31527 was selected; it had a maximum pigment production and revealed two types of culture development patterns between this two different growth substrates. In cultivation of M. pilosus BCRC 31527, carbon source in the lactose yeast extract growth substrate remained almost unused during the fermentation and, in the rice nitrate growth substrate, rice starch was consumed gradually. Of the total of measured proteins, 17% of the proteins were identified. The average expression levels of the enzymes in the lactose yeast extract growth substrate showed approximately 3-fold increases when compared to the rice nitrate growth substrate. The occurrence of up-regulation of four glycolytic enzymes, including glyceraldehyde-3-phosphate dehydrogenase, enolase, pyruvate kinase,and adenylate kinase, and three providing reducing equivalent energy enzymes at the initiation of the stationary phase in the lactose yeast extract growth substrate was presumed to result from the release of carbon catabolite repression due to carbon limitaion. Cencerning the NM growth substrate due to lack of the KH2PO4, the NM growth substrate could be considered as a low-potassium and -phosphate complex medium relative to the control. We found that the NM growth substrate induced an up-regulation in aldehyde dehydrogenase and several glycolytic enzymes, including glyceraldehyde-3-phosphate dehydrohygenase, enolase, pyruvate kinase.
Ahmed, Hazem Radwan A. "Pattern Discovery in Protein Structures and Interaction Networks." Thesis, 2014. http://hdl.handle.net/1974/12051.
Повний текст джерелаThesis (Ph.D, Computing) -- Queen's University, 2014-04-21 12:54:03.37
Μπουγιούκος, Παναγιώτης. "Functional classification of proteins using mass spectrometry data and exploration of their frequency of identification in proteomic analysis." Thesis, 2009. http://nemertes.lis.upatras.gr/jspui/handle/10889/2486.
Повний текст джерелаΤα δεδομένα πρωτεομικής τα οποία εξάγονται από φασματογράφο μάζας έχουν ως αποτέλεσμα την δημιουργία ενός μονοδιάστατου σήματος το οποίο στον οριζόντιο άξονα έχει τιμές μάζας/φορτίο και στον κατακόρυφο άξονα έχει τις αντίστοιχες τιμές έντασης. Οι τιμές στον οριζόντιο άξονα (μάζα/φορτίο) οι οποίες αντιπροσωπεύουν πεπτίδια ή πρωτεΐνες έχουν ένα εύρος από 0 έως δεκάδες χιλιάδες. Επομένως τα πρωτεομικά φάσματα θεωρούνται ιδιαίτερα πολύπλοκα. Η διαχείριση της πληροφορίας των πρωτεομικών φασμάτων καθώς και η εξαγωγή διαγνωστικών συμπερασμάτων είναι ένα πεδίο ανοιχτό προς έρευνα. Ο καρκίνος του προστάτη αποτελεί την δεύτερη πιο σημαντική αιτία θανάτου στην Ηνωμένες Πολιτείες Αμερικής και τον Καναδά. Η θνησιμότητα που οφείλεται στον καρκίνο του προστάτη μπορεί να μειωθεί από την έγκαιρη πρόγνωσή του. Όσο ποιο έγκαιρη είναι η πρόγνωσή του τόσο ποιο αποτελεσματική είναι η θεραπεία του. Ο προστάτης είναι ένας αδένας που βρίσκεται στο εσωτερικό του σώματος, κάτω από την ουροδόχο κύστη του άνδρα και περιβάλλει την ουρήθρα. Τον αδένα αυτό τον έχει ένας άνδρας ήδη από την στιγμή που γεννιέται. Με την λειτουργία του συμβάλει, στον έλεγχο της ούρησης, το οποίο το πετυχαίνει λόγω της ανατομικής του θέσης, στον εμπλουτισμό του σπέρματος με χρήσιμα και απαραίτητα συστατικά και στη λειτουργία της εκσπερμάτισης. Ο καρκίνος του προστάτη είναι η ανάπτυξη καρκινικών κυττάρων στον αδένα αυτόν. Τα καρκινικά κύτταρα πολλαπλασιάζονται πολύ πιο γρήγορα από τα φυσιολογικά κύτταρα, και έτσι, η ολοένα αυξανόμενη συγκέντρωσή τους δημιουργεί όγκους. Επιπλέον, τα καρκινικά κύτταρα έχουν την δυνατότητα να μεταφέρονται σε άλλα σημεία του σώματος (κάνουν μετάσταση) και να καταστρέφουν τα υγιή κύτταρα. Η πρωτεομική με την εφαρμογή της φασματογραφίας μάζας έχει βοηθήσει σημαντικά στην πρόγνωση του καρκίνου του προστάτη και στην ανακάλυψη γνωστών βιοδεικτών του καρκίνου του προστάτη όπως είναι το ειδικό αντιγόνο του προστάτη (PSA), η προστατική όξινη φωσφατάση (PAP), το ειδικό πεπτίδιο του προστάτη (PSP) και το ειδικό αντιγόνο μεμβράνης του προστάτη (PSMA). Ο καρκίνος των ωοθηκών είναι μια συνήθεις γυναικολογική κακοήθεια με ποικίλα ιστολογικά χαρακτηριστικά. Είναι η κύρια αιτία θανάτου από καρκίνου ανάμεσα σε όλες τις γυναικολογικές κακοήθειες, καθώς και ο πέμπτος πιο συχνός τύπος καρκίνου μεταξύ γυναικών του δυτικού κόσμου. Η πλειοψηφία των κακοηθών όγκων των ωοθηκών εμφανίζεται σε γυναίκες ηλικίας άνω των 65 χρόνων, ενώ οι καλοήθεις όγκοι είναι συνηθέστεροι σε νεότερης ηλικίας γυναίκες μεταξύ 25 και 45 χρόνων. Λόγω της πολυπαραγοντικής φύσης του καρκίνου, είναι πολύ πιθανό, μια ομάδα βιοδεικτών να είναι πιο ενδεικτικοί για την πρόβλεψη της βιολογικής συμπεριφοράς διαφόρων όγκων, από την χρήση ενός μόνο βιοδείκτη. Το CA-125 είναι ένας δείκτης ο οποίος χρησιμοποιείται για την διάγνωσης και συγκεκριμένα στην πρόγνωση του καρκίνου των ωοθηκών. Η επιβεβαίωση του και αξιοπιστία του βιοδείκτη CA-125 οδήγησε στην ευρέως χρήση του, ως βιοδείκτης για τον καρκίνο των ωοθηκών, καθώς και στην κλινική διάγνωση της ανταπόκρισης του ασθενούς κατά την θεραπεία του καρκίνου. Πρόσφατες προσπάθειες επικεντρώθηκαν στην βελτίωση της διαγνωστικής ακρίβειας του CA-125, είτε χρησιμοποιώντας μόνο τον συγκεκριμένο βιοδείκτη (CA-125), είτε χρησιμοποιώντας τον με νέους βιοδείκτες που έχουν συσχετιστεί με τον καρκίνο των ωοθηκών. Ο βιοδείκτης CA-125 βρίσκεται στο μητρικό γάλα και στο αμνιακό υγρό στις υγιείς γυναίκες. Παρόλα αυτά υπάρχει επίσης σε γυναίκες με γυναικολογικά προβλήματα όπως μητρικό λειομύωμα και ενδομητρίωση μειώνοντας έτσι την ειδικότητα του βιοδείκτη. Επιπροσθέτως άλλοι βιοδείκτες οι οποίοι έχουν βρεθεί είναι οι prostasin, OVX1, CA-15.3, CA-72.4, και inhibin. Έτσι οι στόχοι της παρούσας διατριβής είναι: (i) ο κατάλληλος συνδυασμός των βημάτων, προεπεξεργασίας, εξαγωγής χαρακτηριστικών, επιλογής χαρακτηριστικών και επιλογής ταξινομητή ώστε η διάγνωση να είναι ακριβέστερη από τις υπάρχουσες μεθόδους. (ii) να προταθούν βιοδείκτες (biomarkers) και συγκεκριμένα τιμές φάσματος (μάζας/φορτίου) οι οποίες ενδεχομένως να σχετίζονται με τις ασθένειες προς μελέτη (Καρκίνου του προστάτη και των ωοθηκών). Για την εκπλήρωση των ανωτέρω στόχων σχεδιάστηκαν και αναπτύχθηκαν μεθοδολογίες με στόχο την ακριβή διάκριση των υγειών από ασθενείς με καρκίνο του προστάτη και ωοθηκών. Προτείνονται τιμές μάζας/φορτίο οι οποίες ενδεχομένως να αποτελέσουν χρήσιμους βιοδείκτες για τον καρκίνο του προστάτη και για τον καρκίνο των ωοθηκών. Επίσης υλοποιήθηκε μεθοδολογία για να μπορέσουμε να ερευνήσουμε την διαγνωστική αξία των κορυφών, των πρωτεομικών φασμάτων, με διάφορες τιμές έντασης και κυρίως των χαμηλών, οι οποίες θεωρούνται ως πλούσιες σε πληροφορία από τους βιολόγους.
Luber, Christian A. [Verfasser]. "Pattern recognition receptors are subset specific in dendritic cells : In-vivo quantitative proteomic investigations using label-free analysis and the SILAC mouse / Christian A. Luber." 2009. http://d-nb.info/1006352929/34.
Повний текст джерелаOlipoh, George. "Synthetic cannabinoid method development with Saccharomyces cerevisiae and Escherichia coli proteome patterns." Master's thesis, 2013. http://hdl.handle.net/10400.26/19074.
Повний текст джерелаThe emergence and abuse of new synthetic cannabinoids has been on the rise because legal regulations against particular derivatives of cannabinoids tend to cause the introduction of new variants as the law is made for specific molecules and not for a group of molecules. They come with no clinical indications of use on their labels, and vaguely described intoxicating effects hence they were not banned. Consequently, they are also referred to as ‘Smart Drugs’ or more formally ‘New Psychoactive Substances’ (NPSS). Many classified synthetic cannabinoid agonists remain available to users in many countries mainly through ‘smart’ and online shops. The challenges posed to the regulation of these products are due to their ever-changing composition, adulterants and variable vehicles of distribution. Synthetic cannabinoids are famous for their recreational effects similar to that of marijuana, which has neuropsychiatric effects due to the action of its primary active ingredient, Δ9-tetrahydrocannabinol (Δ9-THC), binding to endogenous cannabinoid receptors. This study was conducted first to find the best microorganism model for the development of a new screening method for the analysis of synthetic cannabinoids by using the proteome expression patterns obtained from proteins of Saccharomyces cerevisiae and E. coli. The research also sought to find an efficient protein extraction and concentration method for expressed microorganism proteins for two-dimension gel electrophoresis. Saccharomyces cerevisiae and Escherichia coli were studied in this work. S. cerevisiae rather than E. coli proved to be a better microorganism model for to be exploited for findings in this research. Diclofenac and JWH-018 standard were used as test drugs. The Amicon® membrane filter concentration method was found to be the most efficient with protein yield greater than 20mg/mL for 500mL cell culture volume. Even though twodimension gels did not show a large number of protein spots, the application of more concentrated protein solution from S. Cerevisiae is paramount to get a better proteomic pattern for use as a sensor.
Ραψομανίκη, Μαρία Άννα. "Ανάπτυξη ολοκληρωμένου συστήματος για προεπεξεργασία και αναγνώριση προτύπων από δεδομένα πρωτεωμικής". Thesis, 2010. http://nemertes.lis.upatras.gr/jspui/handle/10889/4151.
Повний текст джерелаThe rapid developments in mass spectrometry (MS) and the introduction of new experimental ionization methods, like matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI), has made it possible to study protein expression levels in complex mixtures of proteins from various biological samples, like serum plasma and urine. The data generated from these technologies can be used to identify proteomic patterns that can successfully separate states (e.g. normal versus disease) and possibly discover novel disease biomarkers. Those patterns have high diagnostic significance, as they can be used for early diagnosis, prognosis, monitoring disease progression or therapeutic response. This strategy has already been used in various types of cancer, like ovarian, breast and prostate cancer, giving interesting results. However, the complex nature of proteomics data makes their analysis a challenging task, as the initial raw data are very difficult to handle. More specifically, the data retrieved after an MS experiment contain hundreds of samples (i.e. mass spectra), and in each sample correspond tens of thousands of features. In addition to this high dimensionality – small sample size problem, each spectrum contains a great amount of noise and artifacts, mostly due to the high sensitivity of the instrument, sample contamination and electrical noise. Another common problem is the miscalibration of the spectra that makes the data impossible to compare. For all those reasons, it is more than obvious that in order to extract knowledge about the true underlying biological differences in the proteome, various preprocessing steps need to be applied. The main goal of preprocessing is to come up with a matrix of important features (i.e. peaks) and their corresponding intensity values, which can be further analyzed using a variety of computational methods. To achieve this, one must first remove noise, artifacts and systematic bias without loss of information and then detect and quantify a set of peaks. Preprocessing involves various steps that are highly interrelated and it has been shown that if those steps are not applied carefully, it will be difficult to extract meaningful conclusions about the underlying disease. For each step, a number of methods have been proposed making the decision about the best combination of methods a very challenging task. Furthermore, it is difficult to evaluate the performance of each method and come up with a standard strategy, as for each dataset a different set of methods appear to be more effective. This thesis presents a new pipeline method for the analysis of proteomics data, which incorporates a new preprocessing method. This proposed method deals with the problematic characteristics of this type of data and exploits the advantages of various existing methods. More specifically, our proposed strategy focuses on three main problems: correcting the miscalibration of the mass spectra, detecting the peaks in a sensitive yet robust manner and extracting the true intensity values that correspond in each peak. For the peak finding step, we used a method based on the mean spectrum approach, where we first find the peaks per category, then apply certain criteria to ensure their reproducibility and then combine them in a single peak list. Instead of working with peak locations, we propose the use of peak intervals, to ensure that the small shifts present in the data do not interfere with the final results. In order to evaluate the results of our method, a final feature extraction and classification step was applied in the preprocessed data, using the Support Vector Machines classification algorithm. Our proposed pipeline method was applied in a MALDI MS dataset, obtained by the Proteomics Research Unit of the Biomedical Research Foundation. This particular dataset contained approximately 200 samples, concerning patients with bladder cancer (high or low grade) and benign bladder disease. After the application of the proposed preprocessing method we ended up with a matrix of 456 peak bins and corresponding intensities. The application of the classification algorithm achieved extremely high performance in terms of accuracy, sensitivity and specificity. Furthermore, 31 statistically important peaks were identified, some of which are not detected by existing methods.
Chang, Jui-Yun, and 張瑞雲. "Proteomic Approach for Monascus pilosus Treated with Nitrogen Limitation and Translational Inhibitor Cycloheximide Reveals a Difference in Pigment Production and Metabolic Protein Patterns." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/85619979302275776448.
Повний текст джерела實踐大學
食品營養與保健生技研究所
95
Monascus species have the unique ability to economically produce many secondary metabolites. However, most metabolic regulation processes in the production of secondary metabolites in Monascus remain unclear. Nitrogen is a major component of nearly all of the complex macromolecules central to the structure and function of all living organisms. Here, the first objective of this study was to use proteomic analysis to investigate the influence of nitrogen-limited substrate to the medium on the biochemical metabolisms concerning culture growth and pigment production in cultivated Monascus pilosus BCRC 31527. Furthermore, we also found that translational inhibitor cycloheximide (CHX) induced different expression patterns between the pigment production and growth mass in M. pilosus BCRC 31527. We used proteomic approach of two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization time-of-flight/time-of-flight liquid chromatography mass spectrometry (MALDI-TOF/TOF LC-MS), tandem mass spectrometry (MS/MS) to identify the intracellular and mitochondrial proteins of M. pilosus BCRC 31527 among the treatments and the controls. The results revealed that nitrogen limitation to the glucose nitrate medium induced an up-regulation of some transcriptional proteins, such as DNA-directed RNA polymerase and histone deacetylase, and several protein synthesis enzymes in M. pilosus BCRC 31527 relative to the control. The cycloheximide-induced down-regulation proteins were also involved in transcription regulation, peptide translation synthesis, such as valyl-tRNA synthetase and valyl-tRNA synthetase, and other metabolisms, such as 1-aminocyclopropane-1-carboxylate deaminase for the methylation of secondary metabolites. In contrast, several energy-related proteins were up-regulated in the control of cycloheximide treatment. KEYWORDS: Monascus; food pigments; nitrogen-limited; cycloheximide; proteome
Hwang, Kyung Hoon [Verfasser]. "Proteome analysis of Schizosaccharomyces pombe using two-dimensional gel electrophoresis and mass spectrometry : examination of 11-deoxycorticosterone (DOC) induced differential protein patterns / von Kyung Hoon Hwang." 2008. http://d-nb.info/987062107/34.
Повний текст джерела