Katie Wilkins is a Computational Biology PhD Candidate in the Bogdanove lab in the Plant Pathology and Plant-Microbe Biology section of the School of Integrative Plant Science at Cornell University.
Xanthomonas oryzae pv oryzicola is the causal agent of bacterial leaf streak of rice, a disease that can lead to up to 30% yield loss in this staple crop. Disease progression is mediated in part by the secretion of transcription activator-like (TAL) effectors that upregulate host genes by binding to corresponding promoter regions. Genes upregulated by TAL effectors can confer host resistance or enhance host susceptibility. Knowledge of these important TAL effector-target pairs informs breeding of resistant rice varieties. To determine the distribution of TAL effectors and their candidate targets at the population level, we sequenced 10 strains of Xanthomonas oryzae pv oryzicola and performed RNA-Seq of rice inoculated with each strain. We also used population level conservation to evaluate potential importance of the identified TAL effectors and their candidate targets.
Date: Oct 19, 2015
Time: 11:00 AM
Location: Weill hall, Room 221
Showing posts with label Microbe. Show all posts
Showing posts with label Microbe. Show all posts
Saturday, September 26, 2015
Thursday, October 2, 2014
Date: Oct 13, 2014. Julia Goodrich: Conducting a microbiome study
Julia Goodrich is a PhD student in the lab of Dr. Ruth Ley in the Department of Molecular Biology and Genetics and the Department of Microbiology at Cornell University.
Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Bacterial and archaeal 16S rRNA gene sequence data from complex microbial communities present statistical and computational challenges. She will present some of the standard techniques currently used to characterize microbial communities.
Date: Oct 13, 2014
Time: 11:00 AM
Location: Weill hall, Room 121
Slides
Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Bacterial and archaeal 16S rRNA gene sequence data from complex microbial communities present statistical and computational challenges. She will present some of the standard techniques currently used to characterize microbial communities.
Date: Oct 13, 2014
Time: 11:00 AM
Location: Weill hall, Room 121
Slides
Thursday, July 31, 2014
Date: Aug 11, 2014. Haruo Suzuki: Microbial genome analysis using the G-language system
Haruo Suzuki is an Associate Professor at Yamaguchi University, Japan. You can find his publications here.
He will talk about research on GC skew (predicting the origin and terminus of DNA replication), codon usage (predicting highly expressed or horizontally transferred genes), and dinucleotide composition (classifying DNA sequences and predicting plasmid hosts), followed by an introduction of the data sources (NCBI Genbank and FASTA files) and a hands-on demo of G-language Web services.
The Web services provide URL-based access to all functions of G-language Genome Analysis Environment. For example, information for Staphylococcus aureus N315 genome (NC_002745) is given by http://rest.g-language.org/NC_002745, information for tst gene is shown by http://rest.g-language.org/NC_002745/tst, and GC skew is computed by http://rest.g-language.org/NC_002745/gcskew. Please bring your smart phone, tablet or laptop to follow the demonstration.
Date: Aug 11, 2014
Time: 11:00 AM
Location: Weill hall, Room 321
Slides
He will talk about research on GC skew (predicting the origin and terminus of DNA replication), codon usage (predicting highly expressed or horizontally transferred genes), and dinucleotide composition (classifying DNA sequences and predicting plasmid hosts), followed by an introduction of the data sources (NCBI Genbank and FASTA files) and a hands-on demo of G-language Web services.
The Web services provide URL-based access to all functions of G-language Genome Analysis Environment. For example, information for Staphylococcus aureus N315 genome (NC_002745) is given by http://rest.g-language.org/NC_002745, information for tst gene is shown by http://rest.g-language.org/NC_002745/tst, and GC skew is computed by http://rest.g-language.org/NC_002745/gcskew. Please bring your smart phone, tablet or laptop to follow the demonstration.
Date: Aug 11, 2014
Time: 11:00 AM
Location: Weill hall, Room 321
Slides
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