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Marine Animal Health Genes and Genomics Paul S. Gross, Ph.D. Marine Biomedicine and Environmental Sciences Program Medical University of South Carolina.

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Presentation on theme: "Marine Animal Health Genes and Genomics Paul S. Gross, Ph.D. Marine Biomedicine and Environmental Sciences Program Medical University of South Carolina."— Presentation transcript:

1 Marine Animal Health Genes and Genomics Paul S. Gross, Ph.D. Marine Biomedicine and Environmental Sciences Program Medical University of South Carolina Charleston, South Carolina, USA

2 “Genome Projects”

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4 THE PARADIGM OF GENETICS DNARNAProteins Everything Else

5 Genomics defined: the scientific study of genomes, esp. of their organization and evolution. - OED the comprehensive study of the genetic information of a cell or organism - NIH the study of how an individual's genes interact with each other and with the environment to create the complexity of life. - Mayo Clinic

6 “OMICS” (a.k.a. Genomics in the generic sense) (a.k.a. Biology with fancy machines) Genomics (strictly referring to the “genome” or DNA) Transcriptomics (expressed sequences or RNA a.k.a ESTs) Proteomics (referring to expressed proteins) Lipidomics (referring to lipid manufacture) Metabolomics (referring to metabolism cascades) Ecogenomics Toxicogenomics etc…

7 “OMICS” Genomics (strictly referring to the “genome” or DNA) Transcriptomics (expressed sequences or RNA a.k.a ESTs) Proteomics (referring to expressed proteins) Lipidomics (referring to lipid manufacture) Metabolomics (referring to metabolism cascades) Ecogenomics Toxicogenomics etc…

8 “OMICS” Genomics (strictly referring to the “genome” or DNA) Transcriptomics (expressed sequences or RNA a.k.a ESTs) Proteomics (referring to expressed proteins) Lipidomics (referring to lipid manufacture) Metabolomics (referring to metabolism cascades) Ecogenomics Toxicogenomics etc…

9 “OMICS” Genomics (strictly referring to the “genome” or DNA) Transcriptomics (expressed sequences or RNA a.k.a ESTs)

10 478 Bacterial genomes 49 Eukaryotic genomes WHOLE GENOME SEQUENCING: Genomes available

11 The Human Genome Project using the ‘Celera’ Scheme of 10 X coverage –Regions not covered –Regions very densely covered –Contigs kb –# Gaps? >100,000? –Base Quality High or Low? –Mis-Assemblies? –Duplications? WHOLE GENOME SEQUENCING: problems, pitfalls and failures

12 Other projects: –Zebrafish: used more than one individual to “try to simultaneously capture variability with the draft genome sequence” –Ciona: selected a wild animal off a rock so not lineage to go back to for further analysis WHOLE GENOME SEQUENCING: problems, pitfalls and failures

13 “OMICS” Genomics (strictly referring to the “genome” or DNA) Transcriptomics (expressed sequences or RNA a.k.a ESTs)

14 TRANSCRIPTOMICS Transcript libraries Microarrays

15 FUNCTIONAL GENOMICS CONCEPT STIMULUS PHYSIOLOGICAL Hormonal, Metabolic INFECTION RESPONSE ENVIRONMENT Physical, Chemical, Biological stress SYSTEMIC: Development? Differentiation? IMMUNITY: Survival? Mortality? STRESS: Physiological? Pathological? GENOME GENE EXPRESSION

16 EXPRESSED SEQUENCE TAGS (ESTS) What are they? - Randomly selected clones from a cDNA library - Single-pass uncorrected sequences, usually from the 5’ end What is their value? - Novel Gene Discovery - Transcript profiling- distribution of metabolic energy - Source of “unigenes” for microarrays

17 Whole transcriptome is not really possible only a general representation Incomplete and short sequences Redundancy Gene identification <60% for most organisms (human is still 30-40% unknown) TRANSCRIPTOMICS: problems, pitfalls and failures

18 Number of ESTs at NCBI = 61,132,599 Number of Unigenes at NCBI > 17,960,667 Number of bases at NCBI > 65,369,091,950 Searching resources abound –NCBI –EMBL (Swissprot) –Etc…(over a million hits on the web) TRANSCRIPT LIBRARIES: sequences

19 TRANSCRIPTOMICS cDNA libraries Microarrays

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22 Snap shot of the status of all gene expression for those genes (features) on the array Comprehensive? Massive data collection Repeatable? Microarrays

23 Overview Quantification of gene expression Test Animal Microarray Analysis Predictive Models Classical Health Assessment + Environmental Parameters

24 Atlantic bottlenose dolphin: Tursiops trucatus Class: Mammalia Superorder: Cetartiodactyla Order: Cetacea Suborder: Odontoceti Family: Delphinidae Genus: Tursiops Species: Tursiops truncatus Length is from 8-12 feet ( m). May weigh as much as 1,430 pounds (650 kg) (Great Britain). Males are larger than females. An adult bottlenose dolphin may consume pounds (8-15 kg) of food each day (fish; squid; crustaceans). The average lifespan is estimated to be about 25 years, although some live to their late 40's. Bottlenose dolphins are found worldwide in temperate and tropical waters (harbors, bays, lagoons, estuaries, and river mouths). There appear to be two ecotypes: a coastal and an offshore form. The bottlenose dolphin is protected in U.S. waters by the Marine Mammal Protection Act (1972).

25 Good sentinel organism in aquatic and coastal environments (Bossart, 2005): - Long life span - Feed at a high trophic level - Have extensive fat stores deposit for anthropogenic toxin (Reddy et al, 2001; Wells et al., 2004) Sentinels for: - Infectious diseases such as toxoplasmosis, urogenital cancer (Goldston et al., 1990; Jenson et al., 2006) - Anthropogenic pollutants such as organohalogen and heavy metal contaminants (Stein et al., 2003; Houde et al., 2005) - Harmful Algal Blooms (HABs) and their toxins such as brevetoxins, saxitoxins, okadaic acid and others (Gulland, 2000; Bossart et al., 2002; Flewelling et al., 2002; Landsberg, 2002) Why the dolphin?

26 Pattern and intensity of the spots TRANSCRIPTOMIC SIGNATURE Dolphin Peripheral Blood Leukocyte cDNA Microarray 3600 clones from cDNA libraries IL-2 and LPS stimulated PBL (T and B cell biased) and targeted PCR 52 TARGETED STRESS & IMMUNE FUNCTION GENES

27 Analysis of differential gene expression in wild dolphins: What can a microarray tell us? Association with location, sex, stress, health?

28 Experimental design Samples: summary Blood samples from 20 dolphins 2 samples for each animal: pre and post 40 samples: microarray hybridization and analysis FB833 time pre blood sample 0 post blood sample 30’-40’ Samples collection CAPTURERELEASE

29 RNA samples from Wild Dolphins CHS: Charleston, SC IRL: Indian River Lagoon, FL CHS IRL

30 Cluster analysis: pre samples CHS, SC IRL, FL 122 genes differentially expressed


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