BIOINFORMATICS Seminar 621 62504

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BIOINFORMATICSSeminar 6/21 6/25/04

• Attended by
• Teri Alvarez-Ziegler

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Bioinformatics

• Mining for useful information
• Applications of some rules strategies for
  finding genes

ORF

• Open Reading Frame

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Teaching / Lesson Activities

• Power point presentation
• Video
• Liked Daves example of spacing reading DNA
• Put together DNA models (DNA KNEX)
• Live sliced potato varieties demonstration

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NCBI Steven Pechous

• Synteny comparison between

• Entrez
• Human Genome Resources
• BLAST
• Comparative Genomics
• PubMed

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Teaching / Lesson Activities

• PPT with accompanying handouts
• Hands on computer tutorial within the data bank
• Use of monitor/screen to follow along
• Time for on own exploration

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TIGR Willem Albert Rensink

• Structural Genomics primary sequence (ATGC)
  identification of the genes within an organism
• The omics world genomics, transcriptomics,
  proteomics, metabolomics
• EST Expressed Sequence Tag
• cDNA copy DNA, after RNA
• EST Expressed Sequence Tag

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Outline

• Genomics technologies
• Genome sequencing and annotation
• Microarrays
• Plant Genomics
• Potato functional genomics
• Plant databases
• Microarray data of biotic stress in potato
• Microbial Genomics
• Microbial Genomics resources
• Human Genetics
• DNA fingerprinting
• Ancestry analysis

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Two Different Approaches for Sequencing

• Directed
• Make a clone library.
• Map clones.
• Select a set of overlapping clones to sequence.
• Assemble complete sequences.

• Random Shotgun
• Make library of random inserts.
• Sequence to high redundancy.
• Assemble.
• Close gaps between assemblies.

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Understanding Biological Processes ie. biology
experiment steps

• Biological question of interest
• Plant pathogen interaction
• Describe the process
• Plants get infected and die
• HR response
• Identify components
• Virulence factors
• R-genes
• Explain the process
• The plant can recognize the virulence factors
  biology question of interest

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Use of Microarrays to Detect Pathogens Tim
Straub

• Microarrays - a miniaturization of the former
  high density dot blots on nylon membranes
• FASTA format
• Clustal W
• Box Shade

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Use of Real Time PCR to Detect Pathogens George
Vandemark

• Comparisons between resistant and susceptible
  plants
• Phytophtora Root Rot
• Saranac (S)
• Waph-1 (R)
• SCAR specific examples

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Use of Bioinformatics to Study Biodiversity Ted
Kisha

• NPGS National Plant Germplasm System
• Germplasm diversity available in plant
  
  
• life
• GRIN Germplasm Resources Information
• Network
• Genetic Marker an image or representation of a
  specific, heritable DNA sequence that can be
  mapped to a specific locus

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• AFLP Amplified Fragment Length Polymorphism
• PIC Polymorphism Information Content
• Diversity Analysis Pair-wise comparisons,
  create a matrix of similarity, construct a tree
  using computer algorithm such as UPGMA

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Conclusion of What I Learned

• Review of DNA / genetic processes
• Ability to access use Bioinformatics databases
  within my classroom
• Ideas for different learning activities
• Realized that what I learned is just the tip of
  the iceberg to what is actually out there
• Met a variety of people from different areas,
  ages, levels of educational backgrounds, and
  personal objectives for attending the workshop

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Thank you!