Transcript USDA – National Institute of Food and Agriculture

USDA
National Institute of Food & Agriculture
Grant created to fund late blight control
Caused by Phytophthora infestans
Species of Oomycete (water molds)
P. infestans: Late Blight
Irish potato famine of the mid 1800's
Killed 1.5 million Irish
Almost as many left Ireland
Extensively studied by Anton DeBary
Considered one of the fathering diseases of
plant pathology
Modern Relevance
Still causes over $6 billion dollars in USA
losses alone
Very few effective methods of treatment
Only takes 15 days to decimate a field after
noticeable symptoms appear
Requires extensive fungicide use to control
What Is My Project?
Create a smallRNA database for the public
Expanded to include P. sojae, a soy bean pathogen
This database can be
used as a tool
–
Pathogen control
through smallRNAs
smallRNA?
Broad classification of RNAs that cause RNA
interference, most frequently through
silencing
- Small pieces of RNA bind to target mRNA and block its
translation
- Different types have differing levels of complementarity
Recent focus on microRNA
Uses of microRNA
Extremely powerful research tool
- Can completely silence an undesired gene
- As this technology develops, fewer off-targets are being
affected, leading to a more customizable tool
Disease treatment
- Allows drug-induced gene silencing
miRNA placed in drug which silences a gene
necessary for pathogen survival
Eliminates pathogen!
USDA Goals and My Project
Late blight control is the ultimate goal
Easily accessible smallRNA data will facilitate
this control
Other institutions funded by the same grant
are focusing more on treatment methods
- They will use the data we have organized
Front End
Data Tables
GBrowse
Generic Genome Browse
Creating miRNA
My Co-worker
Deepthika Ennamuri works on the data-end
of the project
- “Back-end”
- Uses Perl scripts to analyze data and get it into
a format usable by Gbrowse
Compared to my work:
- “Front-end”
- Make database easily available
Acknowledgments
USDA – National Institute of Food and Agriculture
NSF – Research Experience for Undergraduates
Howard Hughes Medical Institute (HHMI) and Kevin Ahern
Coworker: Deepthika Ennamuri
Horticulture Research Crops Laboratory
–
Niklaus Grunwald (sponsoring professor)
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Stephanie Bollmann
Center for Genome Research and Biocomputing
–
Josh Cuperus
–
Christopher Sullivan