European Human Genetics Conference 2007 June 16 – 19, 2007 ...

Genomics, technology, bioinformatics
Po08. Genomics, technology, bioinformatics
P1225. Human APP overexpression causes neurodegeneration
and synaptic loss in neural cells in transgenic Drosophila.
S. Sarantseva 1 , O. Bolshakova 1 , S. Timoshenko 1 , M. Vitek 2 , A. Schwarzman 1,3 ;
1 Petersburg Institute of Nuclear Physics Russian Academy of Sciences, Gatchina,
Russian Federation, 2 Division of Neurology, Duke University Medical Center,
Durham, NC, United States, 3 Institute for Experimental Medicine, Russian
Academy of Medical Sciences, St. Petersburg, Russian Federation.
Alzheimer’s disease (AD) is a neurodegenerative disorder characterized
by the loss of neocortical and hippocampal synapses that precedes
amyloidosis and neurodegeneration and closely correlates with
memory impairment. Mutations in the amyloid precursor protein (APP)
cause familial AD and result in the increased production of amyloid-βprotein
(Aβ). However, it is not still clear how Aβ contributes to synaptic
abnormalities in AD.
In our study, transgenic Drosophila melanogaster was established as
a model to analyze AD pathology caused by APP and Aβ. Drosophila
has α- and γ-secretases and does not have activity of β-secretase
(BACE). Therefore, flies do not generate Aβ. We expected that overexpression
of human APP in neural tissues could induces specific effects
of APP independently from Aβ secretion. In contrary, double transgenic
flies expressing human APP and BACE should generate Aβ and Aβspecific
phenotypes. To induce expression of APP in neural cells, we
used elav-GAL4c155 driver and UAS-APP695 expressing system. As
expected, only BACE-containing lines displayed Aβ. Orexpression of
APP resulted in morphological changes and formation of abnormal behavioral
fly phenotypes independently from Aβ generation . Most these
phenotypes has been characterized by progressive neurodegeneration
with numerous vacuoles in the cortex and neuropil and loss of
synaptic density detected by decreased accumulation of presynaptic
protein synaptotagmin in mushroom bodies. Thus, we observed a
classical AD pathology in the absence of Aβ. We suggest that impairment
of cellular functions of APP and secretion of neurotoxic forms of
Aβ may independently contribute to the pathogenesis of AD.
P1226. Performance Comparison of BigDye ® XTerminator Kit &
Conventional DNA Sequencing Purification Methods
S. Pistacchi, G. Amparo, A. Wilson, K. Vashi, M. Harrold;
Applied Biosystems, Foster City, CA, United States.
BigDye® XTerminator is a new post-DNA sequencing reaction purification
kit that removes unincorporated dye-labeled terminators
and salts from completed DNA sequencing reactions prior to electrophoretic
analysis. Adequate removal of these components is crucial
in maximizing high-quality basecalls and useable data. Compared to
conventional purification methods such as ethanol precipitation or spin
columns, DNA sequencing reactions purified with BigDye XTerminator
exhibit very few artifacts from residual dye-labeled terminators (dye
blobs). Read lengths using the BigDye XTerminator kit are also comparable.
Here, the performance of BigDye XTerminator will be compared
to that of other purification techniques across a wide variety of
DNA sequencing reactions.
P1227. Easy-to-use bioinformatic tools for individualized
analyses and data mining in disease gene identification
D. Seelow 1 , T. H. Lindner 2 , S. Mundlos 1,3 , K. Hoffmann 1,3 ;
1 Institute of Medical Genetics, Charite University Medicine, Berlin, Germany,
2 Department of Nephrology and Hypertension, University of Erlangen-Nuremberg,
Nuremberg, Germany, 3 Department Development and Disease, Max
Planck Institute for Molecular Genetics, Berlin, Germany.
Our aim is to create comfortable tools for performing and interpreting
linkage and association analyses, for data mining and expression studies.
Steps that are repeated in several projects are (semi)automated
so that they can be performed by the biologist, student or technician
in charge.
Automated single-/multipoint linkage analysis for microsatellites and
large-scale SNP data: easyLINKAGE Plus is an interface for automated
setup and performance of linkage analyses. We implemented
Allegro, Merlin, SimWalk, GeneHunter, SuperLink, FastSLink, and versions
for several species. Results are given as text files and graphical
outputs.
Web-based exploration of genomic association: Genome-wide association
studies are a challenge to graphically display and interpret the
results. AssociationDB allows interactive graphical exploration of the
results integrating related gene information, tissue-specific expression
and microRNAs. Association results can be imported from other programs
or get calculated within the database.
Automated collection and integration of gene information from multiple
databases: The user can enter a region of interest or a list of genes.
OMIM reports, expression, SNPs etc. are displayed for all candidate
genes at once on a single HTML page or PDF. Results are ready to be
read and discussed with a cup of coffee.
Automated generation of primer sequences for in situ probes: This program
creates primers for either transcript-specific or universal probes
and checks specificity by BLAST.
P1228. “VALAPODYN: Validated Predictive Dynamic Model
of Complex Intracellular Pathways Related to Cell Death and
Survival.”
A. Depaulis 1 , E. Vafiadaki 2 , P. Jackers 3 , D. A. Arvanitis 2 , O. Kel-Margoulis 4 , E.
Wingender 4 , T. Vujasinovic 5 , D. Greenberg 6 , H. Soreq 6 , E. De Pauw 3 , J. B. Dumas
Milne Edwards 5 , D. Sanoudou 2 ;
1 Institut National de la Sante et de la Recherche Medicale, Grenoble, France,
2 Foundation for Biomedical Research, Academy of Athens, Athens, Greece,
3 University of Liege, Liege, Belgium, 4 Biobase, GmbH, Wolfenbuettel, Germany,
5 HELIOS, Paris, France, 6 Hebrew University of Jerusalem, Jerusalem, Israel.
VALAPODYN is a research network funded by the European Commission
(6 th Framework Program) which is developing an original systems
biology approach focused on the development of multidisciplinary
functional genomics related to complex biological processes and cellular
networks. The aim is to generate an innovative approach to model
the dynamics of molecular interaction networks (MIN) in relation to cell
death and survival to detect new therapeutic targets to treat human
brain diseases. The project consists of fundamental genomics research
which is integrating statistical data analysis with real biological
data in order to functionally annotate genes and proteins. Specialized
genomics and proteomics databases for MIN modeling are being used
along with leading microarray and proteomics platform systems to investigate
protein-protein interactions and regulation networks. This will
help to identify and validate biological targets in complex intracellular
pathways to cure multifactorial diseases. Dynamic modeling specifically
addresses the systems biology of complex cellular pathways and
transcriptional networks. The novel dynamic models will be validated
by testing the selected drug targets on innovative in vivo and in vitro
models of CNS pathologies.
As opposed to most current biological data analysis methods, VAL-
APODYN develops a dynamic and quantitative analysis method for
new therapeutic targets through MIN dynamic models. It will provide
a cutting-edge highly accurate in silico tool for identifying novel and
effective therapeutic targets in a much faster, more efficient and more
economical way than it is possible today. (www.valapodyn.eu).
P1229. Evaluation and introduction of new techniques in the
genetic testing service by EuroGentest Unit 5.
N. van der Stoep 1 , C. D. M. Paridon 2 , M. Macek 3 , G. Matthijs 4 , B. Bakker 1 ;
1 Center for Human and Clinical Genetics (EuroGentest), Leiden, The Netherlands,
2 Center for Human and Clinical Genetics, Leiden, The Netherlands,
3 Department of Molecular Genetics and National Cystic Fibrosis Centre (Euro-
Gentest), Prague, Czech Republic, 4 Center for Human Genetics (EuroGentest),
Leuven, Belgium.
At present, the field of genetics is witnessing a fast expansion of new
technologies that could have a strong potential for application in genetic
testing. Unfortunately, implementation of these novel technologies
is often hampered by the lack of complete evaluation of their
technical performance in a diagnostic setting. EuroGenTest (EUGT) is
a European Network of Excellence aiming at harmonizing genetic testing
services throughout Europe. One key objective is to bridge the gap
observed in the chain of new technology-transfer from research into
implementation and ultimate accreditation in genetic diagnostics.
EGT-Unit 5 is specifically involved with the coordination and guidance
of activities required for complete technical evaluation, validation and
subsequent implementation of emerging technologies into diagnostic
application.
In this respect we recruit new techniques in genetic testing at our
EUGT-Unit 5 Website with our “call for technology” and present them
at our Satellite-meeting during the ESHG-conference. As a follow up
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