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Epigenetic and Environmental Influences on the Shellfish Immune Response
- 1. Epigenetic and Environmental Influences on the Shellfish Immune Response Steven B. Roberts Assistant Professor School of Aquatic and Fishery Sciences University of Washington Seattle - Washington - US
- 2. Open Science •You are free to Share! •Our lab practices open notebook science •Slides, links, and related material are available @ oystergen.es/vigo
- 4. Photo credit: Flickr, Creative Commons, dougbrown47
- 17. e Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas). Timmins-Schiffman and Roberts 2012 Immune Function
- 18. e Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure. Roberts et al 2008 Analysis of genes isolated from plated hemocytes of the Pacific Oyster, Crassostrea gigas. Roberts et al 2009 Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas). Timmins-Schiffman and Roberts 2012
- 19. e O c e a n A c i d i f i c a t i o n
- 20. e Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Gavery and Roberts 2012 Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas. Timmins-Schiffman et al 2012 O c e a n A c i d i f i c a t i o n
- 21. e Proteom e Immune Function O c e a n A c i d i f i c a t i o n
- 22. e O c e a n A c i d i f i c a t i o n unpublished Proteomic Response
- 23. e O c e a n A c i d i f i c a t i o n unpublished Proteomic Response oxidation reduction signal transduction oxidative stress response cellular stress & transport Elevated (7.2) Control (8)
- 28. e unpublished Puta%ve cytochrome P450 Isocitrate dehydrogenase [NAD] subunit beta Alpha-‐soluble NSF aCachment protein C16orf62 homolog Radial spoke head protein 4 homolog A Flo%llin-‐2 Small nuclear ribonucleoprotein-‐associated protein ES1 protein homolog Sterile alpha and TIR mo%f-‐containing protein 1 Twinfilin-‐2 Lachesin Syntaxin-‐5 Serine dehydratase-‐like Caspase-‐3 tRNA methyltransferase 112 homolog Circularly permutated Ras protein 1 Contac%n Caspase-‐7 Apopto%c chroma%n condensa%on inducer Calcium-‐binding protein Vacuolar protein sor%ng-‐associated protein 13C Cullin-‐1 Control
- 29. e unpublished O c e a n A c i d i f i c a t i o n Control Elevated
- 32. Photo credit: Flickr, Creative Commons, he-boden Epigenetics
- 33. Epigenetics
- 34. Histone Modification Epigenetics short RNAs DNA Methylation
- 35. Histone Modification Epigenetics short RNAs DNA Methylation m m
- 37. Function?
- 43. traditional - vertebrate model Nature Reviews Genetics 9, 465-476 (June 2008) methylation
- 47. mosaic associated with gene bodies Photo credit: Flickr, Creative Commons, dkeats
- 48. oyster mosaic associated with gene bodies
- 49. oyster mosaic associated with gene bodies methylationmosaic
- 50. Roberts and Gavery 2012 in silico analysis
- 51. Roberts and Gavery 2012 in silico analysis
- 52. Roberts and Gavery 2012 in silico analysis
- 54. Role?
- 56. Biology
- 57. Biology
- 58. Biology In species that experience a diverse range of environmental conditions, processes have evolved to increase the number of potential phenotypes in a population in order to improve the chances for an individual’s survival.
- 59. M M M M M M M M M M germline methylation conventional transcription 5’ UTR promotor ubiquitously expressed, critical genes Transcriptional opportunities
- 60. x x M M M M sparse methylation alternative start sites sequence mutation change AA, premature stop codon conventional transcription transient methylation alternate transcript exon skipping tissue / temporal specific and inducible genes Transcriptional opportunities Roberts and Gavery 2012
- 61. DNA methylation in Crassostrea gigas Gill Sperm
- 62. DNA methylation in Crassostrea gigas Gill Sperm
- 63. If true? Limb Photo credit: Flickr, Creative Commons, csessums
- 64. Could change how we consider tolerance
- 65. Could change how we consider natural variation
- 66. Could change how we consider adaptation
- 69. Profiling the DNA methylomes of plants exposed to bacterial pathogen, avirulent bacteria, or salicylic acid hormone revealed numerous stress-induced differentially methylated regions, many of which were intimately associated with differentially expressed genes.
- 70. ChIP-seq analysis of four histone modifications revealed that the priming treatment altered the epigenomic landscape; .... preferentially targeted transcription factors.
- 73. Open Science
- 75. Photo credit: Flickr, Creative Commons, speechless Sharing
- 76. How? Why?
- 77. Example
- 78. Example
- 79. Example
- 80. Example
- 84. Open Notebook Science ... there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. —Jean-Claude Bradley
- 89. Open Notebook Science Hello, I was doing a search for what concentrations of MgSO4 to use as a bivalve relaxant and came across Katie’s Notebook. What a cool idea! Please say thanks to Katie :). My boss said MgSO4 but most of the literature was MgCl2.... So g’day from the University of Queensland in Brisbane, Australia. Cheers KA email June 22, 2013
- 90. R e p r o d u c i b i l i t y usable data formats Sharing
- 91. R e p r o d u c i b i l i t y usable data formats Sharing Platforms FigShare Dryad GitHub runmycode
- 92. R e p r o d u c i b i l i t y usable data formats Sharing looking for patterns
- 98. Genome Primary Data Table Groupings Expressed Sequence Tags Gene Expression GeneticVariation Epigenetic Features transcripts dynamic RNA-Sequencing Single Nucleotide Polymorphisms Simple Sequence Repeats DNA Methylation Histone Modification miRNA ExpressionExpression Microarrays Amplified Fragment Length Polymorphisms Genomic DataTypes Data Tables static Gene Annotations Sequence Motifs Gene OntologiesPathways Orthologs Transposable Elements Interactions Other species genomes CpG statistics Structural Elements Size Growth Location Environment Stage Treatment Tissue Trait Strain Transcription Factors Binding Sites Publications
- 100. Immune Function e
- 101. Immune Function e I n s i g h t i n t o t h e C o m p l e x i t y
- 103. Acknowledgements Emma Timmins-Schiffman Mackenzie Gavery Claire Ellis Sam White Brent Vadopalas Bill Howe Dan Halperin EPA STAR Aquaculture Program Saltonstall-Kennedy acidification DNA methylation
- 104. Acknowledgements Emma Timmins-Schiffman Mackenzie Gavery Claire Ellis Sam White Brent Vadopalas Bill Howe Dan Halperin EPA STAR Aquaculture Program Saltonstall-Kennedy acidification DNA methylation oystergen.es/vigo