Spatially resolved in vitro molecular ecology
Authored by JS McCaskill
Date Published: 1997
DOI: 10.1016/s0301-4622(97)00073-2
Sponsors:
German Federal Ministry of Education and Research (BMBF)
Platforms:
No platforms listed
Model Documentation:
Other Narrative
Flow charts
Mathematical description
Model Code URLs:
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Abstract
Sensitive CCD-based fluorescence detection has made spatially resolved
studies of evolving cell-free molecular systems possible. In recent
years our attention has focussed on making the transition to open and
interacting spatially-resolved amplification systems using silicon
microreactor technology and on providing a hardware platform for
individual based simulation of such systems. Significant progress has
been achieved in this direction. Open microflow reactors have been
realized in zero (well-mixed), one and two dimensions with volumes small
enough to allow long-time studies with limited biochemical materials.
The primer directed 3SR reaction (amplifying DNA and RNA) has been used
as a basis for constructing interacting model systems with both
predator-prey and cooperative amplification character. Theoretical work
has demonstrated the need for individual based modeling of such systems:
a significant fraction of the population consists of distinct sequence
polymers in any case. A massively parallel processor-configurable
computer NGEN has been designed and constructed which allows the high
speed simulation in hardware of relatively large populations of locally
interacting individual strings of chosen length (e.g. up to 2000{*}2000
for 64 bases), in addition to its application as an evolvable hardware
machine. Simulations show self-replicating spots to stabilize the
cooperative amplification in evolving systems (a mechanism proposed by
the author in 1994). Both oscillatory kinetics and pattern formation are
expected in the experimental model systems under investigation which
profoundly affect the course of evolution. Such in vitro model systems
serve both to test current theories of cooperative evolution and provide
clues for optimisation strategies in molecular biotechnology. (C) 1997
Published by Elsevier Science B.V.
Tags
Evolution
System
Life
Origin
Waves
Hypercycles
Natural self-organization
Rna replication
Invitro amplification
Dna-polymerase