Iskanje mesta začetka podvajanja ter vezavnih mest proteina DnaA pri izbranih probiotičnih bakterijah z uporabo algoritmov

(magistrsko delo)

Larisa Anžel (Author), Domen Mongus (Mentor), Sabina Fijan (Co-mentor)

Abstract

Uvod: Človeško telo je naseljeno s številnimi bakterijami, arhejami, virusi in enoceličnimi evkariotskimi organizmi, ki na različne načine vplivajo na naše zdravje. Probiotične bakterije so tiste, ki v zadostnih količinah pozitivno vplivajo na zdravje gostitelja. Slednje se morajo razmnoževati, da so pozitivni učinki vidni. Bakterije se razmnožujejo s procesom podvajanja, pri čemer je v začetnih fazah vključeno podvajanje DNK. Metode: S pomočjo grafa odklona števila gvaninov in citozinov (GC), ki ga pridobimo iz DNK zaporedja, smo ocenili položaj mesta začetka podvajanja za vsak izbran bakterijski sev. V okolici mesta začetka podvajanja se nahajajo posebna zaporedja, na katera se vežejo DnaA proteini. Z iskanjem najpogostejših motivov v okolici nukleotida z najnižjo vrednostjo na grafu GC smo pridobili možno sekvenco vezavnih mest DnaA, kar omogoča vpogled v sekvenco, ki igra pomembno vlogo pri podvajanju bakterijske DNK. Rezultati: Konsenzna sekvenca vseh izbranih bakterijskih sevov je 5'-TTATCCACA-3', kar sovpada s podatki iz literature, kjer je sekvenca DnaA škatle opredeljena kot 5’-TT(A/T)TNCACA-3'. Razprava in sklep: Izbrane metode se lahko uporablja za določevanje približnega mesta začetka replikacije, vendar so za dokazovanje le-tega potrebni še dodatni laboratorijski poizkusi.

Keywords

probiotične bakterije;mesto začetka replikacije;GC odklon;najpogostejši motivi;

Data

Language:	Slovenian
Year of publishing:	2021
Typology:	2.09 - Master's Thesis
Organization:	UM FZV - Faculty of Health Sciences
Publisher:	[L. Anžel]
UDC:	613.292:579.24:575.112(043.2)
COBISS:	77390595
Views:	260
Downloads:	35
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	English
Secondary title:	Finding the origin of replication and binding sites of dnaa protein in selected probiotic bacteria using algorithms
Secondary abstract:	Introduction: Human body is inhabited with different bacteria, archaea, viruses and unicellular eukaryotic organisms, all of which have ways of affecting human health. Probiotic bacteria are among those, who, in sufficient quantity, benefit the health of the host organism. For positive effects to be seen, probiotic bacteria must replicate. Bacteria replicate with the process of division, which includes DNA replication in its initial steps. Methods: With the help of GC skew diagram, which can be obtained from DNA sequence, we determined position of origin replication site in every selected bacterial variant. In proximity of replication origin, special sequences for binding of DnaA proteins, are paced. While searching for most frequent motifs in proximity of nucleotide with lowest GC skew value, we obtained possible binding sequences of DnaA proteins, which plays an important role in bacterial DNA replication. Results: Consensus sequence of all chosen bacterial variants is 5'-TTATCCACA-3', which coincides with data from literature, where sequence of DnaA box is defined as 5’-TT(A/T)TNCACA-3'. Discussion and conclusion: Selected methods can be used to determine approximate origin replication site, but to prove site of origin replication, additional laboratory experiments are required.
Secondary keywords:	probiotic bacteria;replication origin;GC skew;frequent motifs;Proteins;DNA;Probiotics;Proteini;Probiotiki;
Type (COBISS):	Master's thesis/paper
Thesis comment:	Univ. v Mariboru, Fak. za zdravstvene vede
Pages:	VI, 43 str., 3 f. pril.
ID:	13270910