Analize DNA iz okoliša

undergraduate thesis

• Title (english): Environmental DNA analyses
• Author: Nikola Pischiutta
• Mentor: Damjan Franjević (mentor)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2022-09-09, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Okolišna DNA je svaki genetički materijal koji organizam ispusti u okoliš, a da više nije dio tog
organizma. Takva DNA može određeno vrijeme opstati u okolišu iz kojeg se može uzorkovati i
analizirati. Analize DNA iz okoliša uključuju tri glavna koraka: uzorkovanje, laboratorijski rad i
bioinformatička obrada. Metoda uzorkovanja odabire se ovisno o tipu okoliša i supstrata. Nakon
uzorkovanja i izolacije DNA prema standardnim protokolima, DNA se umnaža pomoću metode
lančane reakcije polimerazom (PCR). Kod umnažanja DNA odabiru se odgovarajuće regija DNA
u genomu koje će se umnožiti jer o tome ovisi mogućnost međusobnog razlikovanja vrsta.
Sekvenciranjem dobivenih PCR produkata dobivaju se sljedovi nukleotida koji se obrađuju
bioinformatičkim alatima i uspoređuju s podatcima u referentnim bazama podataka čime se
utvrđuje koje su vrste bile prisutne u uzorku. Metoda identifikacije vrsta prema slijedu nukleotida
naziva se metabarkodiranje. Pomoću ovih metoda moguće je utvrditi sastav vrsta flore i faune na
određenom tipu staništa, istražiti međusobne interakcije između organizama i analizirati
ekosustave iz prošlosti. Danas analize DNA iz okoliša, zbog jednostavnosti i učinkovitosti pristupa,
nalaze sve veću primjenu u područjima ekologije, konzervacijske i evolucijske biologije,
paleontologije i biomonitoringa.

Abstract (english)

Environmental DNA is any genetic material that a living being releases into the environment, but
is no longer a part of that organism. Such DNA can persist for a certain amount of time in the
environment from which it can be sampled and analyzed. Environmental DNA analyses involve
three main steps: sampling, laboratory work, and bioinformatic processing. After following
standard protocols for environmental DNA sampling and isolation, the DNA is amplified using the
polymerase chain reaction (PCR). Before DNA amplification, the appropriate genomic region is
selected to be amplificated, as the possibility of differentiating species depends on it. By
sequencing the PCR products, nucleotide sequences are obtained, which are processed using
bioinformatic tools and compared with existing data in reference databases. This method
determines which species were initially present in the sample and is called metabarcoding. Using
these methods, it is possible to determine the composition of species of flora and fauna in a certain
type of habitat, to investigate mutual interactions between organisms and to analyze ancient
ecosystems. Due to the simplicity and efficiency of the approach, environmental DNA analyses are
increasingly used in the fields of ecology, conservation and evolutionary biology, paleontology and
biomonitoring.

• Keywords: PCR; sekvenciranje; metabarkodiranje; biomonitoring; ekosustavi
• Keywords (english): PCR; sequencing; metabarcoding; biomonitoring; ecosystems
• Language: croatian
• URN:NBN: urn:nbn:hr:217:214268
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/prvostupnica (baccalaureus/baccalaurea) molekularne biologije (sveučilišni/a prvostupnik/prvostupnica (baccalaureus/baccalaurea) molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2022-09-26 14:29:06