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Poster Full Abstracts - Techniques and Functional Genomics
Poster board number is above title. The first author is the presenter
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assays, but it can also be easily adapted for DNA extractions as well. The robotic system comprises a device to grind the flies, a scale (under an anti-vibratic
plate) to weight them and a mechanism to remove major debris (through 2 sequential centrifugations). All of these components are incorporated in a single
platform system that in the end will provide the material in a 96-well plate. We believe that the robotic system here presented represents a major advantage
for laboratories because not only it improves quality and consistency in the samples, avoiding Human- errors and variability, but because it also releases
personnel to be devoted to other tasks or projects in the lab.
861C
Accessing fly data from the modENCODE project: modMine, GBrowse and dataset search.
Sergio Contrino
1
, Daniela Butano
1
, Seth Carbon
2
, Adrian
Carr
1
, Fengyuan Hu
1
, Ellen Kephart
2
, Paul Lloyd
2
, Rachel Lyne
1
, Marc Perry
3
, Peter Ruzanov
3
, Richard Smith
1
, E.O. Stinson
2
, Radek Stepan
1
, Julie
Sullivan
1
, Alex Kalderimis
1
, Zheng Zha
3
, Suzanna Lewis
2
, Gos Micklem
1
, Lincoln Stein
3
. 1) university of cambridge, cambridge1.Department of Genetics,
University of Cambridge, Cambridge, UK; 2) Lawrence Berkeley National Laboratory; Genomics Division, Berkeley, CA, USA; 3) Ontario Institute for
Cancer Research, Toronto, ON, Canada.
The goal of the modENCODE project is to provide the biological research community with a comprehensive encyclopedia of genomic functional elements
in the model organisms
C. elegans
and
D. melanogaster
. Its data span the main domains of genomic functions, including gene structure, mRNA and ncRNA
expression profiling, transcription factor binding sites, histone modifications, chromatin structure and origins of DNA replication.
modMine
is the main
gateway to the project data, and allows researchers to navigate easily through modENCODE experiments, to view and export data and to perform
sophisticated, ad hoc queries. External data are incorporated in modMine to complement modENCODE data, including genome annotations from FlyBase
and WormBase, Gene Ontology annotations, physical and genetic interactions, and details on proteins, protein domains and orthology. modMine is based on
the InterMine data warehousing system and allows users, among other things, to create and analyse lists of data items.
GBrowse
is a genome browser giving
a graphical view of all of the datasets created by modENCODE, plus a number of reference tracks such as annotated genes from FlyBase. It is integrated
within modMine or accessible independently for all the Drosophila species used in the project.
Dataset Search
: a faceted search index to find and download
specific data set from the project. Datasets can be filtered by organism, category of experiment, experimental factors, technique, target elements, etc. An FTP
site is also available to download datasets. All the tools illustrated are available from www.modencode.org.
862A
Organically Modified Silica nanoparticles are biocompatible and can be targeted to Drosophila neurons in vivo.
Shermali Gunawardena
1,2
, Farda
Barandeh
1
, Phuong-Lan Nguyen
1
, Rajiv Kumar
1
, Gary Iacobucci
1
, Michelle L Kuznicki
1
, Andrew Kosterman
1
, Earl J. Bergey
2
, Paras N. Prasad
2
, Shermali
Gunawardena
1,2
. 1) Biological Sciences, SUNY at Buffalo, Buffalo, NY; 2) 2Institute of Laser, Photonics and Biophotonics, The State University of New
York at Buffalo, Buffalo, NY, 14260.
The application of nanotechnology in biological research is beginning to have a major impact leading to the development of new types of tools for human
health. One focus of nanobiotechnology is the development of nanoparticle based formulations for use in drug or gene delivery systems. However most of
the nano probes currently in use have varying levels of toxicity in cells or whole organisms and therefore are not suitable for in vivo application or long-term
use. Here we test the potential of a novel silica based nanoparticle (organically modified silica, ORMOSIL) in living neurons within a whole organism. We
show that feeding ORMOSIL nanoparticle suspension to Drosophila has no effect on viability. ORMOSIL nanoparticles penetrate into living brains,
neuronal cell bodies and axonal projections. In the neuronal cell body, nanoparticles are present in the cytoplasm, but not in the nucleus. Strikingly,
incorporation of ORMOSIL nanoparticles into the brain did not induce aberrant neuronal death or interfere with normal neuronal processes. Our results in
Drosophila indicate that these novel silica based nanoparticles are biocompatible and not toxic to whole organisms, and has potential for the developed of
long-term applications.
863B
pΔTubHA4C: a new versatile vector for constitutive expression in
Drosophila
.
Barbara Perez
1,2,4
, Stephanie Arcia
1,3,4
, Yan Zhang
4
, Pedro Fernandez-
Funez
4
, Diego Rincon-Limas
4
. 1) Undergraduate Dept of Microbiology; 2) McNair Scholar; 3) HHMI/Science for Life Program; 4) Dept of Neurology,
University of Florida, Gainesville, FL.
Control of gene expression relies on a variety of strategies, including gene overexpression, gene rescue, and gene silencing. The binary UAS/GAL4 system
has become a popular choice for genetic manipulation. However, there are cases in which ubiquitous expression is desirable independently of GAL4.
Traditionally, constitutive expression has been achieved by cloning cDNAs under control of ubiquitous promoters such as the Actin5C or Hsp70 genes.
Unfortunately, the Actin5C promoter displays heterogeneous expression and the Hsp70 promoter requires heat induction, which may affect certain
experiments. In a search for more homogeneous expression, the promoters of α1-Tubulin, Armadillo or EF-1αF1 were isolated. Since the first intron of these
genes contain essential regulatory information, they were used together with the first exon containing the ATG and a fragment of the second exon for
ligation of the cDNA. Thus, expression under these promoters requires the creation of a fusion with their first amino acids. Additionally, exon 2 contains few
suitable restriction sites, complicating cDNA cloning. To overcome these limitations we created pΔTubHA4C. This plasmid was designed for expression of
cDNAs in flies under control of a simplified Tubulin promoter. For this, we cloned and fused the critical regulatory regions of the promoter and intron 1 of
α1-Tubulin, producing a shorter, optimized Tub promoter (880 nt). Then, we incorporated an optimized polylinker to offer flexible cloning options. Finally,
we added the option of double labeling the expressed proteins with two C-terminal tags, the viral epitope hemagglutinin (HA) and a synthetic tetracysteine
(4C) tag that binds small fluorescent compounds. We have cloned the LacZ gene under control of both the ΔTub and unmodified α1-Tubulin (2.6 Kb)
promoter to compare their strengths and spatial regulation in cell culture and transgenic flies. The properties and advantages of the new pΔTubHA4C vector
will be presented.
864C
The FlyMine Project: New Developments and Interoperation.
Julie Sullivan, Daniela Butano, Adrian Carr, Sergio Contrino, Hu Fengyuen, Alex
Kalderimis, Rachel Lyne, Mike Lyne, Richard Smith, Radek Stêpán, Gos Micklem. Genetics Dept, University of Cambridge, Cambridge, UK.
FlyMine is a well-established, open-source database of genomic, expression and protein data for Drosophila species. A powerful and flexible query