NCBI10-12-09-Handout

NCBI10-12-09-Handout - Bioinformatics and NCBI Dr Jacob...

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1 Bioinformatics and NCBI Dr. Jacob Mayfield October 12th, 2009 We have been liberated from the tyranny of the life cycles of organisms, from their modes of reproduction. We can do genetics now on everything, anything. Giant redwoods, grapes and, most importantly, human beings. - Nobel Laureate Sydney Brenner on DNA sequence. Acknowledgements Meara Davies Jane O John Gahagan Atoosa Firouzian Sarah Mogri Mark Andre Rachel Doran Sean McCarthy Ankur Narain Nick Pleskaz Elizabeth Boydston Lecture Overview I. How do you define a species? II. How do plants define a species? III. How does mutation cause disease? How Do You Define a Species? Systema Naturae , Carolus Linnaeus, 1758
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2 Is Form a Good Definition? The Genetic and Endocrinic Basis for Differences in Form and Behavior , Charles R. Stockard, 1941 Ribosomal RNA: Conserved and Diverged Woese C. 1987 Bacterial Evolution Microbiological Reviews , 51/2 221-271 Bacteria Archaea Eukaryotes E. Coli M. vannielli S. cerevisiae The Tree of Life Woese C. 1987 Bacterial Evolution Microbiological Reviews , 51/2 221-271 The Tree Keeps Growing Pace 1997 Jackson et al 2006 Science 276 734 BMC Bioinformatics 7 1471
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3 Bioluminescence is a Phenotype Light Dark Protocol to Identify Bioluminescent Bacteria by 16S Single colony purified bioluminescent bacterium PCR of 16S rDNA using bacterial universal primers Sequence of the amplified fragment Assemble, edit and align sequence Determine sequence homology The B asic L ocal A lignment S earch T ool BLAST: www.ncbi.nlm.nih.gov/blast/Blast.cgi BLAST Nucleotide Query Page BLAST: www.ncbi.nlm.nih.gov/blast/Blast.cgi
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4 Patience… BLAST Greatest Hits BLAST: www.ncbi.nlm.nih.gov/blast/Blast.cgi BLAST Hits List BLAST: www.ncbi.nlm.nih.gov/blast/Blast.cgi BLAST Alignment BLAST: www.ncbi.nlm.nih.gov/blast/Blast.cgi
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5 A Species or an Individual? Shore Pole 16 16S Sequence Isn’t Perfect Pascual et al Int. J. Syst. Evol. Microbiol, 2009 [Epub ahead of Print] Percentage Nucleotide Difference Between Vibrio Species More Sequence Means Better Resolution Is It Something in the Air? Mate Recognition by Plants
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6 Flowering Plant Anatomy Pollen Pistil Anther Ovule Ovary Stigma Pollination: Coat Conversion Conversion Adhesion Pollination: Hydration Hydration Pollination: Tube Germination Germination
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7 Pollination: Tube Guidance Guidance Pollination Conversion Hydration Germination Guidance Fertilization Adhesion A Pollination-Defective Mutant in Arabidopsis thaliana cer6-2 Lacks a Pollen Coat
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8 Purification of Pollen Coat Proteins by Organic Extraction 97 66 45 31 21.5 14.5 Size (kD) Pollen Coat Proteins Sequenced IKKSKAKSKGGLKAXQKKM GMSGSGGGKHKIGGGKHK BLAST Query Page, Restricted A Perfect Match
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9 A Not So Perfect Match More Than A List What is GRP17: Entrez Gene Knows Entrez Gene Links
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This note was uploaded on 02/24/2010 for the course BIO General Bi taught by Professor Mehgian during the Fall '09 term at Berkeley.

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NCBI10-12-09-Handout - Bioinformatics and NCBI Dr Jacob...

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