The Laboratory Robotics Interest Group
February 2000 Meeting
Bioinformatics:
Agricultural and Pharmaceutical Perspectives
Date: Tuesday, February 15, 2000
Place: Rohm and Haas Research Site in Spring House, PA
Itinerary: Social Period - 5:00 to 6:30 PM in the atrium
cafeteria
Presentations & Panel Discussion - 6:30 to 9:00 PM
Registration: Requested, not required.
Pre-registering will allow us to more accurately gauge seating requirements and
refreshment needs. Indicate names of attendees and company affiliation.
Pre-register by email with <>
or by phone at (732)302-1038. In order to speed sign-in at the meeting, please bring
a business card to drop into the registration box. There will be a
business card drawing for a prize.
Agenda:
Social time from 5-6:30pm in the Rohm and Haas atrium cafeteria; cold
sandwiches, hot strombolis, fruit salad, green salad, soda and coffee,
make-your-own ice cream sundae; Posters will focus on ag apps and ag-related
bioinformatics. Oral presentations in our conference area starting about
6:30.
Members interested in presenting a poster are encouraged to do so. Open
career positions at your company may be announced or posted. There is no
registration or fee associated with this LRIG function.
Presentation: Data Management in
Transition: An Ag Chem Perspective.
Ted T. Fujimoto, Research Fellow, Rohm and Haas Company, Spring House, PA 19477
Presentation: Where's
that data?! - Data Management in High Throughput Screening. Michael H.
Chin, Sr. Biological Information Specialist/ActivityBase Administrator, Research Data Management, Aventis Pharmaceuticals Inc., Bridgewater, NJ
08807
Managing data efficiently and accurately in High Throughput Screening (HTS)
and in Therapeutic Areas is crucial to making timely decisions on compounds
throughout the selection process. Recent technical advances in methodology and
equipment have enabled HTS teams to screen more compounds faster and better than
in earlier times. Scientists are oftentimes backlogged in processing the data
resulting from bottlenecks in the area(s) of data capture, analysis, and
reporting. This talk will focus on the importance of getting the right tools and
people involved to "get that data!"
Presentation: Can Pharmacoinformatics Accelerate
Drug Discovery?
Janet Cohen, Sr Group Leader, Software Development, Pharmacopeia,
Inc.
How can we use the information and data that we gather in the drug discovery
process to help develop new drugs faster? How do we categorize and classify that
data so that we can mine the information needed? With the use of DSS systems and
data visualization techniques we can use the data that we collect in our current
data collection (OLTP) systems to facilitate faster and more productive lead
discovery and lead optimization which will lead to faster and more productive
drug discovery.
Presentation: Preparation of Agricultural Soil for
GC/MS analysis with Dionex Accelerated Solvent Extraction and Zymark XP Robot
System
Robert Plaisance, Aventis, North Carolina
Twenty grams of soil is mixed with hydromatrix and sodium sulfate prior to
extraction with acetonitrile:acetone:ethyl acetate. When the ASE sequence is
completed, the ASE sample vials are organized on Zymark XP robot number one for
transfer w/ rinsing into 200 mL Zymark Turbo-Vap tubes which receive a timed
concentration to less than/equal to ten milliliters. The processed samples are
organized on Zymark XP robot number two for automated solid phase extraction (SPE)
or open tubular chromatography. The Zymark Turbo-Vap tube which receives the
sample after SPE is concentrated prior to GC/MS analysis.
Poster: Choosing the
Right Compounds for Ag Chem HTS: Do Lipinki's Rules apply to Agrochemicals?
Colin M. Tice; Rohm and Haas Company; Spring House, PA
Lipinski's "Rule of 5" has played an influential role in
the design of compound libraries and the purchase of compounds for
pharmaceutical screening. Examination of the structures of commercial
postemergence herbicides and insecticides showed that some modifications to
"The Rule of 5" are appropriate when designing libraries or purchasing
compounds for agrochemical screening.
Poster: Phenotype MicroArrays?/font>
for High Throughput Cell-Based Testing.
Barry R. Bochner, Ph.D., Chairman and Vice President of R&D, Biolog,
Inc., Hayward, CA
Phenotype MicroArrays and companion high-throughput instruments
have been developed for testing hundreds of cell traits simultaneously. The
current set of phenotypes that are tested include carbon, nitrogen, phosphorus,
and sulfur sources used by the cell, biosynthesis of small molecules, and
sensitivity or resistance to a wide range of toxic organic and inorganic
chemicals. The breathing rate of the cells is measured quantitatively and
kinetically as the reporter that indicates the cells' response in each well of
the MicroArray. This technology can be used to determine the function of genes
by doing a simultaneous comparison of a normal cell to a daughter cell in which
the gene of interest is either inactivated or over-expressed. The readout of the
cell detects aspects of cell function that are altered due to the genetic change
(i.e. Genotype --->Phenotype). In this poster we show data collected
from E. coli strains. Individual genes have been altered and in all cases
the expected phenotypic changes, along with some unexpected phenotypic changes,
were be detected. Phenotype MicroArray technology can also be used to test drugs
on cells to determine (a) mode of action, (b) specificity of action, and (c)
interactions with other drugs.
Poster: Universal Approach for Automation
of LC-MS Combichem Library Analysis.
Enrique Michelotti, Bernard Choi, Mark Eisenschmied, Tianlan Zhang, Blanca
Martinez, David M. Hercules, Arkady I. Gusev; Rohm and Haas Company; Spring
House, PA
High efficiency and fast turnaround for liquid chromatography-mass
spectrometry (LC-MS) screening of large combinatorial libraries requires
automation of sample submission, signal acquisition, data interpretation and
report generation. However, the sample database may not be directly compatible
with the instrument data acquisition and interpretation software, thereby
hindering automation of direct sample submission and reporting. One universal
approach which can be used to automate the entire analytical screening procedure
is through the application of Excel Visual Basic macros to coordinate data
exchange between databases which are not directly compatible with the LC-MS
instrument software.
This presentation will describe the application of Visual Basic macros to
extract sample information from an Accord database/worksheet (i.e. target
compound, reagent, intermediate exact masses) and send sample information
(sample location, target analyte mass, injection volume, LC and MS acquisition
parameters and report formats) directly to the instrumentation for immediate
characterization and reporting. This approach has been successfully implemented
on different type of LC/MS instruments (e.g. Micromass, Finnigan) and can be
customized for other applications, such as metabolism studies and trace
analysis.
Poster: Automated Results Determination
in Antifungal Bioassays.
M. Elizabeth Miller and Judith A. Rolling; Rohm and Haas Company; Spring
House, PA
Results determination from whole-cell fungal assays frequently rely
on spectrophotometric detection of growth. The growth habits of certain fungi,
however, are not always homogenous in a microplate well, and therefore results
acquired spectrophotometrically can be unreliable in some instances. As our
screening rates increase, the practice of manually inspecting and editing growth
results from each microplate becomes impractical. Recently we have made
improvements to our data collection method. By altering the spectrophotometric
reading pattern geographically within each well of a microplate, it is possible
to more reliably detect fungal growth in the wells, reduce the number of false
positives and eliminate the need to manually inspect each microplate.
Poster: Instrumentation for Agricultural
High Throughput Screening.
Robert Bisbing, Ted T. Fujimoto and M. Elizabeth Miller, Rohm and Haas
Company, Spring House, PA 19477
Poster: The Herbicide High Throughput
Screen, Improvements for Opportunities.
Bridget Donohue, Rohm and Haas Company, Spring House, PA 19477
