Rotation Opportunities presented at the BCB Faculty Seminar

Event
Wednesday, September 14, 2016 - 4:10pm
Event Type: 

 


Justin Walley

Plant Pathology and Microbiology Department


Research in my lab investigates molecular mechanisms that underpin plant-microbe interactions.  Our research focuses on immune signaling in corn and Arabidopsis. We specialize in mass spectrometry based proteomics to globally quantify protein abundance and post-translational modifications (including phosphorylation and acetylation). Using systems biology we integrate these data with other types of omics datasets, such as transcriptome profiling, to generate hypotheses to test using various biochemical and genetic approaches. 


Area of Expertise: 


  • proteomics

Education: 


  • PhD, University of California - Davis, 2009
  • MS, Miami University, 2005

Teaching: 


BCBIO 402: Fundamentals of Bioinformatics and Computational Biology II


Contact:


 


Roger Wise

Plant Pathology and Microbiology Department


Research in the Wise laboratory is focused on the high-throughput functional analysis of important agronomic genes in cereal crops. We use a variety of interdisciplinary approaches, including plant and microbial genetics, molecular biology, plant pathology, and bioinformatics & computational biology. 


Host-pathogen interactions:


Plant diseases are among the greatest deterrents to crop production worldwide. Historically, cereal crops have laid the foundation for numerous classical genetic studies in host-pathogen interactions, resulting in many model biological systems. We have focused on the well-characterized, barley-powdery mildew pathosystem as our entry point to address fundamental questions regarding host resistance. In this system, resistance to the obligate biotroph, Blumeria graminis f. sp. hordei, is governed by gene-for-gene-specified interactions of barley Ml (Mildew resistance locus) genes and cognate powdery mildew avirulence (Avr) genes. (Wei et al. 1999; Halterman et al. 2001; Zhou et al. 2001; Wei et al. 2002; Halterman et al. 2003; Halterman and Wise 2004; Halterman and Wise 2006).


Bioinformatics and Agricultural Genomics:


In the area of molecular plant - microbe interactions, small RNA and mRNA transcript profiling, proteomics, and protein-protein inteactions have provided unparalleled perception into the mechanisms underlying gene-for-gene resistance and basal defense, host vs. non-host resistance, or biotrophy vs. necrotrophy. 


Historically, we used the Affymetrix Barley1 GeneChip genome array for large-scale genetical genomics and parallel expression profiling (Caldo et al. 2004; Eckardt 2004).  The Barley1 GeneChip includes 22,792 probe sets derived from 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the NCBI non-redundant database (Close et al. 2004).  


We have now moved into smallRNA and mRNA-Seq, proteomics, and genome-wide yeast two hybrid interactions to provide the data sets necessary for genome-wide dissection of host-pathogen interaction networks.


Area of Expertise: 


  • Molecular Plant-Microbe Interactions
  • Plant Genetics & Genomics
  • Transcriptomics

 


Other Affiliations: 


Education: 


  • B.S., Physiology, Michigan State University, 1976
  • Ph.D., Genetics, Michigan State University, 1983
  • Postdoctoral, Plant Molecular Biology, University of Florida, 1984-1986
  • Postdoctoral, Plant Molecular Biology, Max Planck Institut, Köln, Germany, 1987-1989

 


Contact:


 


Eric Henderson

Genetics, Development and Cell Biology Department


Eric Henderson’s path in science is:


  • B.A. in Biology UCLA
  • Ph.D. in Molecular Biology UCLA
  • Post-Doc studying telomere biology, UC Berkeley
  • Professor, ISU

Eric teaches, promotes and practices rule breaking (when appropriate), fearlessness, and entrepreneurship in all facets of life. He has been involved in several companies including:


  • Bio Force Nanosciences, Inc., (biotech)
  • Aspera Corp (biotech)
  • Creodyne, llc (tech development)
  • Bumblefunk Music (media)
  • Hello Holdings (Griffle, GriffleGames, Griffle TV; media)
  • eMoJoCo, llc (art and media)

Eric is always looking for challenges and opportunities to work with young entrepreneurs. On the side Eric is a performing musician, fiction writer, tinkerer, and gadget freak.


Research


We are interested in the interface between biology and nanotechnology. This has recently been labeled either bionanotechnology or synthetic biology. The label is of no importance. What is important is that 3.6 billion years of biological evolution has resulted in fantastic developments that are the stuff of which the dreams of nanotechnology is made. The challenge is to understand and, in a practical fashion, transfer these insights to the emerging field of nanotechnology so that the wheel (and eyeball, nose, etc. ) need not be invented twice. This is no small challenge. We have created a few tools that will facilitate this effort and a portion of my time is spent determining how best to provide these tools to researchers. A conclusion I have drawn is that a commercial enterprise accomplishes this and also provides an avenue (in theory) by which future developments may be funded and manifest. This theory is far from proven, however.


More on the Henderson Lab Research


Using the magic of DNA hybridization we design and build self-assembling DNA Nanodevices like the Pathogen Sentinel.


DNA Nanostructures and Devices: We make functional nanodevices out of DNA. Our most current device is a pathogen sentinel that can detect, measure and report the presence of a variety of pathogen-related biomarkers. Billions of these sentinels can be created for pennies in a few microliters of saltwater. Even better, since they are made out of DNA they are extremely robust.


We also developed a new method for creating 2D and 3D DNA nanostructures. This method uses DNA origami as a design tool but does not require a single-stranded scaffold of biological origin. In this way, our method allows the creation of any number of DNA nanostructures with much fewer restrictions on size and, importantly, simultaneous assembly in a single reaction ("single pot" self-assembly). Creating useful machines and expanding the general method of DNA-based nanodevice construction are currently the main objectives.


Recent publications


  • R. Lutz, J. Lutz, J. Lathrop, T. Klinge, E. Henderson, D. Mathur, and D. Abo Sheasha, (2012) Engineering and verifying requirements for programmable self-assembling nanomachines, Proceedings of the Thirty-Fourth International Conference on Software Engineering (ICSE 2012, Zurich, Switzerland, June 2-9, 2012), pp. 1361-1364.
  • Lutz, Robyn R., Lutz, Jack H., Lathrop, James I., Klinge, Titus H., Mathur, Divita, Stull, Don M., Bergquist, Taylor G. and Henderson, Eric R. (2012) Requirements analysis for a product family of DNA nanodevices, Proceedings of the Twentieth IEEE International Requirements Engineering Conference (RE 2012, Chicago, IL, September 24-28, 2012), pp. 211-220.
  • Mathur, D. and Henderson, E. (2013) Complex DNA Nanostructures from Oligonucleotide Ensembles, ACS Synthetic Biology, 2, 180-185.
  • Ellis, Samuel J., Henderson, Eric R., Klinge, Titus H., Lathrop, James I., Lutz, Jack H., Lutz, Robyn R., Mathur, Divita, and Miner, Andrew S. (2014) Automated Requirements Analysis for a Molecular Watchdog Timer In Proceedings of the 29th ACM/IEEE international conference on Automated software engineering (ASE '14). ACM, New York, NY, USA, 767-778. DOI=10.1145/2642937.2643007 (Awarded the "Manfred Paul Award for Excellence in Software: Theory and Practice").

Area of Expertise: 


  • Nanotechnology

Other Affiliations: 


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