Nutrigenomička analiza metaboličkih putova u kvascu Saccharomyces cerevisiae iščitavanjem reverzne translacije uz pomoć De novo sekvenciranja peptida

doctoral thesis

• Title (english): Nutrigenomics analysis of metabolic pathways in Saccharomyces cerevisiae followed by reading of reverse translation via De novo peptide sequencing
• Author: Janko Diminić
• Mentor: Antonio Starčević (mentor)
• Committee member: Želimir Kurtanjek (predsjednik povjerenstva)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; Zagreb
• Defense date and country: 2014-07-11, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Nutrition
• Universal decimal classification (UDC): 575 - General genetics. General cytogenetics

Abstract

U ovome radu je razvijen novi ekspertni računalni sustav za analizu spektara masa putem kojeg je moguće tehnikom reverznog iščitavanja translacije, odnosno identifikacije proteina u uvjetima de novo, utvrditi promjene na razini proteoma i posredno metaboloma u modelnom organizmu kvascu S. cerevisiae, čiji je genom u potpunosti sekvenciran. Ekspertni sustav razvijen je u Java programskom jeziku te se sastoji od dva djela, jedan koji izvršava analize na strani poslužitelja i drugi koji ima upravljačku funkciju, a nalazi se na strani korisnika. De novo sekvenciranjem peptida možemo identificirati nadeksprimirane peptide (putem spektrometra masa MALDI-TOF/TOF), odnosno proteine. Na temelju identificiranih proteina napravljena je nutrigenomička analiza iščitavanjem reverzne translacije, odnosno određeno je uključivanje i isključivanje pojedinih metaboličkih putova s poveznicom na promjene nastale u proteomu, kod uzgoja kvasca u aerobnim i anaerobnim uvjetima te pri uskraćivanju i obogaćivanju prihrane kvasca. Utvrđeno je da se nadeksprimirani proteini stanice kvasca razlikuju ovisno o načinu uzgoja, čime se može zaključiti da se ekspresija gena te sinteza proteina, a time i aktivnost metaboličkih putova znatno mijenja pod stresnim promjenama prihrane stanica kvasca.

Abstract (english)

As a result of this thesis, expert system for the management and analysis of MALDI-TOF/TOF generated spectra is developed. This bioinformatics tool serves as a support for the derivatisation and analysis of proteoms of any organism by the use of mass spectrometry. The expert system consists of the proprietary database containing gene and protein data from all publicly available resources with their related taxonomic divisions and sub-divisions. Other inovative part of this system is a graphical user interface (client) used for both input and management of data generated from the spectra analyses. All spectra analyses are carried out on the remote server using algortihms and solutions developed during the course of work on this thesis. As a biological model for testing efficiency for the derivatisation and proteome analysis, the proteome of Saccharomyces cerevisiae was used. S. cerevisiae cells were grown in both aerobic and anaerobic conditions with respective food deprivation as well as optimal food content. Finally, proteins were identified which are with their over or under expression responsible for metabolic changes in yeast under the growth in different environmental conditions.

• Keywords: bioinformatika; kvasac; java; programiranje; masena spektrometrija; nutrigenomika; proteomika
• Keywords (english): bioinformatics; yeast; java; programming; mass spectrometry; nutrigenomics and proteomics
• Language: croatian
• URN:NBN: urn:nbn:hr:159:809387
• Promotion: 2014-09-28
• Study programme: Title: Nutrition; Study programme type: university; Study level: postgraduate; Academic / professional title: doktor znanosti/doktorica znanosti (doktor znanosti/doktorica znanosti)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2018-05-18 09:12:58