Lec2-Jan6-2010-MolecToolbox-Ernest

Lec2-Jan6-2010-MolecToolbox-Ernest - Ecologys molecular...

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Announcements Homework-1 due Friday Jan 8 at 1pm Homework-2 available Friday by 5pm and due next Wed Jan 13 at 1pm UCD Bodega Phylogenetics course http://bodegaphylo.wikispot.org/Front_Page WORKSHOP IN APPLIED PHYLOGENETICS Bodega Bay Mar 6-13, 2010 Applications due Jan 8 (today) Today’s Session Ecology’s molecular toolbox Planning for term project Today’s Plan Ecology’s molecular toolbox ECL242 / PHR 242 Ecological Genetics Jan 6 2010
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Molecular Markers in Ecology Detection of Genomic Variation Thanks to Bernie May and students of past PHR242/ECL242, ECL290 courses for ideas and some slides Ecology’s Molecular Toolbox
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Nucleic Acids DNA and RNA Everybody has them! All life forms have some system of genetic molecules * Library and instruction manual for the organism stays same over time and across tissue types * *Well, there might be exceptions – give it some thought
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Organization of DNA Genome : all of the genetic information contained within a cell or organism Chromosome : composed of DNA & associated proteins that carry portions of the genetic information of an organism must contain centromere, origin of replication & telomeres Human chromosome karyotype using fluorescent dye
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Visualizing a Human Genome One genome = a library of 3000 books Each book with 300 pages 3500 characters per page each char. = 1 base pair (bp) One book = one million bp the DNA content of one person = 3 Billion bp One protein locus = 28 pages (100,000 bp) mtDNA = 5 pages (18,000 bp) One microsatellite = short sentence (~100-300 bp)
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Molecular Markers The common ones Nuclear DNA • Microsatellites – Repetitive DNA • SNP – Single Nucleotide Polymorphisms Mitochondrial DNA sequence Chloroplast DNA sequence
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Nuclear DNA Other repetitious DNA – minis atellites Sex chromosome markers Immune system markers Mhc – Major histocompatibility Complex and others Coding genes Introns Alphabet Soup Markers: AFLP, RAPD, RFLP, etc Any many more classes of markers! RNA Biochemical markers – such as allozymes More Molecular Markers AFLP = Amplified Fragment Length Polymorphism RAPD = Random Amplified Polymorphic DNA RFLP = Restriction Length Polymorphism We’ll learn more about them soon
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mtDNA cpDNA nDNA Alphabet Soup Of Molecular Markers Proteins A cell mtDNA = mitchondrial cpDNA = chloroplast nDNA = nuclear
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mtDNA cpDNA nDNA allozymes Total DNA Sequence Alphabet Soup Of Molecular Markers Proteins cpDNA & mtDNA
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mtDNA cpDNA nDNA allozymes Total DNA Sequence Alphabet Soup Of Molecular Markers Proteins PCR Gene sequence Microsat SNP
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mtDNA cpDNA nDNA allozymes PCR Total DNA multi-locus RFLP ( and blots) single-locus Restriction Enzyme Restriction analysis cloning develop probe develop primers Sequence Restriction Enzyme Alphabet Soup Of Molecular Markers Gene sequence Microsat SNP Proteins AFLP
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Locus : a specified region of DNA -alternative forms of a locus are referred to as alleles Ploidy : # of complete sets of chromosomes in a genome Chromosome terms
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This note was uploaded on 01/18/2010 for the course PHR 242 taught by Professor Ernest during the Spring '09 term at UC Davis.

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Lec2-Jan6-2010-MolecToolbox-Ernest - Ecologys molecular...

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