[Arabidopsis] 8 workshops at the 18th ICAR in Beijing in June

Joanna Friesner via arab-gen%40net.bio.net (by jdfriesner from stanford.edu)
Fri Jun 1 11:59:46 EST 2007

Please note that 8 community-organized scientific workshops on general and
specific topics will be held during the 18th International Conference on
Arabidopsis Research next month (June 20-23, 2007) in Beijing, China.




Wednesday, June 20, 2007 (7:30-9:30 pm)


(1) Linking Stress Signals to Growth: Organizers: Deshpal Verma and  Hong Ma

Overview:All abiotic and biotic stress signals eventually affect plant
growth. How these signals converge to alter translation and transcription
machineries is not known. A body of evidence is accumulating about various
stress pathways and a common thread is evolving which may allow us to
understand how plant growth may be regulated under stress. This workshop
will shed some light on a number of different signaling systems controlling
gene expression and growth of plants.


(2) Ubiquitination in Plant Development and Signaling: Organizers: Qi Xie
and  Minami Matsui

Overview: Ubiquitination has been demonstrated to play important roles in
regulation of broad range of cellular processes, including cell division,
differentiation, signal transduction, protein trafficking, and quality
control in eukaryotic system. In plants, ubiquitination is involved in
hormone signaling, environmental responses and pathogenesis of some
diseases. This workshop will inform the community about the recent progress
in Arabidopsis ubiquitination research. Presentations will focus on
functional genomics and genetics to dissect the roles of SCF complex and
RING finger proteins in plant development and signaling.


(3) Web Services for Arabidopsis Data Integration and Bioinformatics tools
for Arabidopsis microarray databases: Organizers: Chris Town and Anika

Overview: The first part of the workshop will showcase a set of tools
developed at the University of Leeds for mining microarray data, and will be
followed by a series of presentations on the concepts of web services and
their implementation. The ever increasing amount and complexity of
Arabidopsis genomic data presents a growing problem that should be of
concern to both the user and the bioinformatic community. Exploiting the
full potential of these large and diverse datasets is currently hindered by
the limited mechanisms of availability and the lack of integration. Web
services provide a means whereby data residing at many different locations
can be seamlessly integrated to provide the user with richer data sets.
Unlike web pages that are idiosyncratic in their layout and content, and
must be visited by a researcher one at a time, web services (in this case
BioMOBY) provide data in well structured and agreed formats, document their
availability through a central registry and can be combined to provide
richer views of the data. At the workshop, we will present an overview of
what web services are and how they work. This will be followed by a series
of short presentations describing specific examples of web services in
action and mechanisms to encourage a much more widespread use of web
services discussed.



Thursday, June 21, 2007 (7:30-9:30 pm)


(1) Chemical Genetics Organizers: Zhenbiao Yang and Sean Cutler

Overview: Chemical genetics uses small molecules to dissect biological
pathways, analogous to the use of mutations in classical genetics. This
workshop is designed to inform the community of the progress in the
applications of chemical genetic approaches to Arabidopsis research.
Presentations from the leading groups in this area will focus on both the
discovery and use of new small molecules that perturb a variety of
developmental and cell biological processes.


(2) Metabolomics: Organizers: Mike Beale and Jane Ward

Overview: Metabolomics has been defined as the quantitative measurement of
all low molecular weight metabolites in a given sample, cell or tissue and
the integration of the data in the context of gene function analysis. This
type of analysis allows a full and global comparison of the differences
between cell types, tissues, organs and whole organisms (plants, animals and
microbes) to probe unknown aspects of gene function, physiology and
metabolism for a plethora of future research goals. Metabolomics involves
large scale analytical data collection and a range of spectroscopic methods
are available to collect such data. The workshop is designed to inform the
community of the progress in the application of metabolomics in Arabidopsis
research. Presentations from the leading international groups in this area
will focus on using this technology in functional genomic and QTL studies.


(3) Proteomics: Organizers: Wolfram Weckwerth and Harvey Millar
Overview: Plant researchers are gaining more and more interest in
proteomics. This is reflected in the increase in annual numbers of
publications from 11 in 2000 to 92 in 2006. Arabidopsis thaliana is playing
a major role as the plant model system of choice for proteomic studies.
Exploiting classical methods like two-dimensional gel electrophoresis or
emerging techniques like shotgun proteomics in combination with pattern
matching to genome sequences is allowing the connection of whole proteome
dynamics with both genome-wide RNA expression and metabolite dynamics. The
value of accurate genome-wide protein identification and quantification can
not be overestimated given the poor protein:RNA expression correlation
typically observed. Measuring the active players - the proteins - is
therefore a prerequisite to understand molecular dynamics and biochemical
causality in plant systems. In the workshop a general introduction to the
recent and most popular techniques will be followed by four short talks
selected from abstracts covering a range of topics such as combining
transcript and protein analysis, and understanding translational processes,
hormonal signalling and drought and cold stresses through protein analysis.
The workshop will conclude with the participants having a short formal
discussion on trends and needs for the future and an informal discussion
accompanied by a small poster session of proteomics related research from
the conference. 


(4) TAIR (The Arabidopsis Information Resource): Organizers: Eva Huala  and
Donghui Li

Overview: The Arabidopsis Information Resource (TAIR; www.arabidopsis.org)
is a community database for Arabidopsis thaliana. The workshop is designed
for users who wish to more effectively utilize the curated data and software
resources provided by TAIR. Specifically we will address curation of three
major data types: gene structure, gene function and metabolic pathway
annotation. We will describe our progress and give details of the TAIR7
genome release and will outline plans for the TAIR8 release. TAIR curators
annotate gene function using terms developed by the Gene Ontology (GO)
Consortium that describe the molecular function, biological process, and
subcellular location of a gene product. We will use TAIR's GO annotations to
demonstrate how controlled vocabularies allow for standardization of
annotation and assist in comparative genomics. We will describe the process
of GO annotation at TAIR and how the annotations can be used to classify
large data sets or to facilitate annotation of other sequenced plant
genomes. We will demonstrate how to access TAIR's GO annotations in bulk and
to derive a global view of the status of functional annotation of the
Arabidopsis genome. Plant metabolic databases have been developed to
visualize the universe of primary and specialized (secondary) metabolism, to
present the flexibility and interconnectivity of biochemical networks and to
serve as matrix to predict Pathway/Genome Database's (PGDB's) based on
sequenced genomes. We will introduce the contents and curation of the
multi-organism database MetaCyc and the Arabidopsis thaliana specific
database AraCyc. The major functions and applications of MetaCyc and AraCyc
will be presented including the visualization of large-scale data on the
Omics viewer.



Saturday, June 23, 2007 (7:30-9:30 pm)


Peptide Signaling: Organizers: Chun-ming Liu  and Rüdiger Simon

Overview: Peptides represent a very important class of signal molecules in
animals, especially in neural and endocrinal systems. Substantial evidence
accumulated in the last decades or so suggested that plants also use
peptides for intercellular communication, to create position signal and for
defense response. The Workshop for Peptide Signaling will outline some
recent developments in this area. 



Joanna Friesner, PhD

MASC Coordinator


jdfriesner from stanford.edu

jdfriesner from ucdavis.edu


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