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AUTOMATION OF DNA SEQUENCING

Objective

THE TECHNIQUES OF DNA SEQUENCING ARE OF CENTRAL IMPORTANCE IN MOLECULAR BIOLOGY AND BIOTECHNOLOGY. DETERMINATION OF THE COMPLETE NUCLEOTIDE SEQUENCES OF LARGE MOLECULES BY THE PRESENT MANUAL METHODS, IS, HOWEVER, A TEDIOUS AND TIME CONSUMING PROCESS AS ARE THE ITERATIVE MANUAL DETERMINATIONS OF RELATIVELY SHORT SEQUENCES. THE REPETITIVE NATURE OF THE TASK MAKES IT AN IDEAL SUBJECT FOR AUTOMATION.

THE AUTOMATION OF THE PROCESS AIMED AT IN THE PRESENT PROPOSAL SHOULD SPEED UP THE DETERMINATION OF NUCLEOTIDE SEQUENCES FOR THE BENEFIT OF BOTH ACADEMIC AND INDUSTRIAL RESEARCH.
Deoxyribonucleic acid (DNA) sequencing is an obvious candidate for automation allowing more rapid access to the genetic data encoded in very large DNA molecules, such as the human genome.
Research was carried out into the production of fast and accurate instrument modules to automate aspects of sequence analysis. A novel machine was designed and built which incorporated a vision controlled robot to identify and select plaques and colonies on Petri dishes for automatic sampling and transfer of candidate material for further growth in individual containers. Electrophoresis and direct blotting were automated and a gas counter was built for directly imaging radiolabelled DNA sequences and mapping gels for genetic data abstraction.

The first robot system (APSCIR) to image mixed randomly disposed arrays of biological specimens and to pick a particular set of these for distribution into an ordered arrangement was produced. Imaging hardware and software were developed jointly with a patented robot picking head to automate this process, which is recognized as a serious bottleneck in many DNA analysis procedures. The direct blotting electrophoresis system was developed into a key technology for the second generation of automatic mappers and sequencers and the gas counter capabilities were extended into the area of sequence and genetic analysis.
AUTOMATION OF PLATING-OUT AND CULTURE INOCULATION IN DNA SEQUENCING WILL BE ACHIEVED BY FIRST CHANGING THE GEOMETRY OF THE MANUAL METHODS PRESENTLY EMPLOYED TO CONFORMATIONS WHICH ARE MORE EASILY INSTRUMENTED AND THEN IMPLEMENTING THESE AS A MACHINE VISION CONTROLLED ROBOT.

PLAQUES WILL BE DEFINED BY THEIR POSITIONAL AND VISUAL CHARACTERISTICS USING A VISION SYSTEM SENSITIVE TO SMALL COLOUR AND LOCATION CHANGES IN A POOR CONTRAST ENVIRONMENT. A HIGH RESOLUTION CCD MATRIX OR LINE CAMERA WILL BE EMPLOYED WITH BACKGROUND ILLUMINATION UNDER USER CONTROL. INTELLIGENT PATTERN RECOGNITION SOFTWARE WILL BE DEVELOPED FOR SEPARATION, CLASSIFICATION, COORDINATE COMPUTATION AND GENERATION OF OVERALL PLAQUE AND CULTURE STATISTICS. THE SYSTEM WILL BE A LOW COST, MENU DRIVEN, DEDICATED MULTI-TASKING DEVICE WITH INTERFACES TO THE MECHANICAL HANDLING ROBOT.

Funding Scheme

CSC - Cost-sharing contracts

Coordinator

University of Manchester Institute of Science and Technology (UMIST)
Address
Sackville Street
M60 1QD Manchester
United Kingdom

Participants (3)

Christian-Albrechts-Universität
Germany
Address
Olshausen Str. 40
24098 Kiel
Rutherford Appleton Laboratory (RAL)
United Kingdom
Address
Chilton
OX11 0QX Didcot
Steinbeis-Transferzentrum System- und Softwareengineering
Germany
Address
Reichenaustraße 81C
78467 Konstanz