Volker Brendel vbrendel at iastate.edu
Tue Feb 9 12:43:01 EST 1999

Maize Gene Discovery, DNA Sequencing and Phenotypic Analysis

Open Positions

STANFORD and IOWA STATE UNIVERSITY:  Two postdoctoral positions are
available immediately. The positions are within the context of a study of
maize intron recognition as part of a collaboration between Virginia Walbot
(Stanford University) and Volker Brendel (Iowa State University).  There
are two components to the project

- Design and test new statistical methods for intron prediction in maize
genomic sequence as a pre-requisite to accurate gene annotation in our
"Maize Gene Discovery, DNA Sequencing and Phenotypic Analysis" project (NSF

- Experimental tests of intron splicing patterns. We plan to develop novel
genomics methods to rapidly score splicing patterns in many transcripts
simultaneously based on microarrays containing intron and contiguous exon
sequences. These methods will be used to examine splicing during stress, in
various tissues, and in different inbred lines.

Insights from the bioinformatics and experimental components of the project
will be applied to develop a deeper understanding of intron definition in
maize.  New studies of differential processing under specific physiological
and developmental states will be examined.  Intron inclusion in which
specific introns are retained in processed transcripts is prevalent in
maize (and other plant) transcripts studied to date.  We wish to determine
if this is a general rule.  In addition, the frequency of splicing of
introns with non-canonical splice sites and unusual base compositional
features will be examined.

Literature References:

- Brendel, V., J. C. Carle-Urioste, and V. Walbot.  1998.  Intron
recognition in plants.  In:  J. Bailey-Serres & D. R. Gallie, Eds.  A Look
Beyond Transcription:  Mechanisms Determining mRNA Stability and
Translation in Plants, pp.20-28.  Amer. Soc. Plant Physiol., Rockville, MD.
A review of statistical approaches to intron recognition emphasizing the
comparison of individual introns to their flanking exons.

- Brendel, V., J. Kleffe, J. C. Carle-Urioste, and V. Walbot.  1998.
Prediction of splice sites in plant pre-mRNA from sequence properties.  J.
Mol. Biol.  276:  85-104.   A comprehensive analysis of experiments aimed
at defining intron recognition features.

- Brendel, V. & Kleffe, J. (1998) Prediction of locally optimal splice
sites in plant pre-mRNA with applications to gene identification in
Arabidopsis thaliana genomic DNA.  Nucl. Acids Res. 26, 4748-4757.   The
paper describes our current algorithm for predicting splice sites from
sequence inspection.

- Ko, C. H., V. Brendel, R. D. Taylor and V. Walbot.  1998.  U-richness is
a defining feature of plant introns and may function as an intron
recognition signal in maize.  Plant Mol. Biol. 36:  573-583.   Altering the
8/11 U motif within the Bronze2 intron alters splicing efficiency; tests
were performed in an artificial gene construct examined in electroporated
Black Mexican Sweet Cells.

- Carle-Urioste, J., V. Brendel and V. Walbot.  1997.  A combinatorial role
for exon, intron and splice site sequences in splicing in maize.   Plant J.
6:  1253-1263.   A conceptually rich paper in which the interdependence of
splice site quality, exon base composition and intron base composition were
examined in transient assays using artificial constructs, with Bz2 as the
model intron.

Training Opportunity:  These openings provide an excellent opportunity to
combine experimental molecular biology - using and inventing new tools
along the way - with the opportunity to learn bioinformatics.  You will be
joining an exciting new project, funded for 5 years, by the National
Science Foundation (http://www.zmdb.iastate.edu). Salary:  $32,000 -
40,000, depending on experience; Stanford/ISU benefits.

Qualifications:  Experience in molecular biology is essential.  Work with
splicing and with plants will be an advantage, as will experience in
statistics, software development, and simulation of biological processes.
Candidates will be in residence at either Stanford or ISU but will spend
some time each year in the non-resident to participate in both the
bioinformatics and the experimental aspects of the project.  Travel to
national meetings and to project co-ordination meetings will also be

Application:  Send a cover letter and your resume (cut & paste, no
formatting) by e-mail. Include the names, e-mail addresses, telephone and
FAX numbers of at least 3 professionals who know your work and can be
contacted as references.  Send your complete application materials to both
walbot at stanford.edu and vbrendel at iastate.edu.

Volker Brendel
Iowa State University
Department of Zoology & Genetics
2112 Molecular Biology Building
Ames, Iowa 50011-3260

Tel.: (515) 294-9884
Fax.: (515) 294-6755

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