Analiza metagenoma ekstremnih okoliša

master's thesis

• Title (english): Analysis of metagenomes in extreme environments
• Author: Maša Roller Milošević
• Mentor: Kristian Vlahoviček (mentor)
• Committee member: Mirjana Kalafatić (predsjednik povjerenstva)
• Committee member: Dijana Škorić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2009, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Samo je malen broj bakterija prisutnih u biosferi moguće uzgojiti u laboratorijskim uvjetima, i stoga sve veća količina znanja o raznolikosti genoma prokariota dolaze iz direktne analize DNA iz okoliša pomoću visokoprotočnih metoda skupnog naziva Metagenomika. Metagenomom se naziva skup svih gena nekog mikrobnog okoliša. Poznato je da prokariotski genomi pokazuju značajnu nejednakost u korištenju sinonimnih kodona (CUB) (prema eng. codon usage bias). CUB je izravno povezan s razinom ekspresije gena stoga što su kodoni koje koriste visokoeksprimirani geni komplementarni s najrasprostranjenijim tRNA u organizmu. Dakle, CUB gena se može povezati s razinom ekspresije gena kroz translacijsku optimizaciju. Analizom različitih metagenomskih uzoraka pokazali smo da je moguće primijetiti nejednako iskorištenje kodona unutar pojedinog mikrobnog okoliša, kao i da je takvo svojstvo moguće iskoristiti za predviđanje razine ekspresije gena na razini cjelokupnog mikrobnog ekosustava. Primjena ovog pristupa omogućuje istraživanje genske adaptacije mikrobnih organizama na okoliš.

Abstract (english)

Not all prokaryotes are amenable to cultivation in laboratory conditions, and increasing amounts of knowledge about microbial diversity is gained from direct sampling of DNA from environments. A rapidly developing field that studies whole microbial communities is metagenomics, the culture‐independent genomic study of organisms extracted directly from an ecological niche. Prokaryotic genomes show strong codon usage bias (CUB). CUB is directly correlated with expression levels of genes because codons used by genes expressed at high levels are encoded for by the most abundant tRNAs. Therefore, the CUB of a gene can be linked to its expression level through translational optimization. We show that metagenomes, much like genomes, also show CUB and that this phenomenon can be used to predict the expression level of genes at the level of the entire microbial community. We analyzed adaptation of organisms in metagenomes to their extreme environments through this approach.

• Keywords: metagenomika; nejednakost u korištenju kodona; ekstremni okoliši
• Keywords (english): metagenomics; codon usage bias; extreme environments
• Language: croatian
• URN:NBN: urn:nbn:hr:217:366208
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2018-03-16 11:50:38