Aantekeningen en leerdoelen van hoorcollege 7 t/m 15 van het eerstejaarsvak Genomica aan de Universiteit Utrecht. De leerdoelen met daaronder de besproken theorie in het hoorcollege geven een goed overzicht van de te leren stof. Dit is handig ter voorbereiding op deeltoets 2 over bio-informatica! H...
hc7. resultaten practicum & informatie poster & prijsuitreikingen
in het bioinformatica-gedeelte gaan we de sequenties analyseren
● wet-lab & dry-lab (in silico / bioinformatica) resultaten komen op de poster
hc8. quantifying evolution | intro to bioinformatics & BLAST
wekelijkse bb-toetsen
● telt 5% mee aan het eindcijfer; highest scoring attempt counts
● available Friday noon, have to be done on Wednesday
e.hauptfeld@uu.nl voor vragen over de inhoud van de cursus
explain why a biologist should know bioinformatic data analysis
researches cannot directly look at bacteria and archaea, so to learn how they work
● they need to be grown in the lab (culture) in order to be sequenced and analyzed
using bioinformatics: study of informatic processes in biotic systems
● bioinformatic data analysis uses computational methods to analyze biological data
describe the omics
genomics: sequentie van al het DNA van 1 organisme
● metagenomics: sequentie van het DNA van alle organismen in een monster
○ take a sample (e.g. from corals) and filter it to get rid of non-biotic particles
(sand, leaves) → filtraat: microbes and/or viruses → DNA extraheren en
sequencen (e.g. illumina sequencing)→ illumina reads
transcriptomics: sequentie van al het mRNA in een organisme/weefsel/cel
● metatranscriptomics: sequentie van het mRNA van alle organismen in een monster
proteomics: sequentie van al het eiwit in een organisme/weefsel/cel
● metaproteomics: sequentie van de eiwitten van alle organismen in een monster
metabolomics; ‘meta’ komt van metabolism en hoort dus niet bij de bovenstaande termen
sequence data volume
● HumanGenome Project was all done with Sanger sequencing (first-generation)
● eerste keer duurde het 13 jaar, hedendaags maar een paar dagen
● sinds next-generation sequencing zijn er veel genomen snel/helemaal gesequenced
number of proteins: the longer its genome, the more genes it has (for virus and prokaryotes)
● eukaryoten - meeste hebben een groter genoom dan bacteriën
○ vooral planten hebben een groot genoom vanwege duplicatie
● bacteria and archaea – prokaryoten hebben een ‘gemiddelde’ genoomgrootte
● virussen - klein genoom, laag aantal protein coding genes
, explain the biology behind the ‘omics revolution: reduce bias by measuring all of a thing
Because of the omics revolution, we have more different genomes of different organisms in
the databases, and do not focus on few, well-known organisms.
microbioom: alle micro-organismen die het menselijk lichaam bevolken
● bacteria associated to humans in some way are usually well-studied → bias
● some don't even have a single cultured representative → can’t be grown in the lab
● metagenomics allows unbiased sampling of all microbes
○ metagenomics zorgt ervoor dat organismen kunnen worden gesequenced
zonder ze eerst in het lab te groeien → verminderde bias
compare the 2 ways a bioinformatician exploits existing data to make new discoveries
bioinformaticians use data in 2 ways
1) top-down
● eerst vraag → dataset(s)
● met een biologische vraag denkt een bio-informaticus na over welke datasets
gebruikt kunnen worden om deze te beantwoorden
2) bottom-up
● eerst dataset → biologische hypothese (vraag)
● met een dataset denk een bio-informaticus na over welke biologische
hypothese hij zou kunnen helpen testen
list the mechanisms of DNA mutation
evolution happens when organisms reproduce (vertical reproduction) and the copies are a
little bit different from the parents → selection
● mutations happen all the time
○ nucleotide substitution
■ replication error
■ physical or chemical reaction
○ insertions or deletions (indels)
■ unequal crossing-over during meiosis
■ replication slippage: polymerase slips (starts at a later/earlier repeat)
○ inversions or rearrangements (e.g. transposons that ‘jump around’)
○ duplications of:
■ partial or whole gene
■ partial (polysomy) or whole (aneuploidy, polysomy) chromosome
■ whole genome (polyploidy, e.g. plants)
○ horizontal gene transfer (HGT)
■ transfer between individuals of the same generation
● microsatellites: regions full of STR (number of copies)
○ fast-evolving regions: microsatelites with short tandem repeats (components)
○ most rapidly evolving characters on the genome
■ to distinguish individuals at short evolutionary distances
■ to distinguish 2 organisms/different members of the same species
○ are the most variable genome regions → have the highest resolution
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