Biology Reference
In-Depth Information
the fly was established at a time when the world of
molecular biology was in darkness, and to ask how a fly
'works' from the molecular perspective was abstract in the
extreme.
In the early 1960s the world was completely different. If
one compares the theorizing and abstraction of Schro-
dinger's What is Life?
[4]
with the concrete molecular
biological knowledge crystallized in Crick's central dogma
[5,6]
, it is clear that biology could be questioned from
a new standpoint. The basic molecular processes under-
pinning life and heredity were known and there were at
least the beginnings of an information theory approach to
genetics, either through the pioneering concepts of Shan-
non
[7,8]
or (amongst other examples) through the exper-
imental dissection of the logic underpinning the lac operon
of Jacob and Monod
[9
genotype
phenotype problem is bounded: both the geno-
type and phenotype are completely known, every base pair,
every cell. While the work of understanding how the
genetic material dictates the phenotype of a worm from
a single-cell fertilized egg through to the 959 cells of the
adult hermaphrodite is immense and ongoing, at least the
start and endpoint of this question are fixed
e
e
in Brenner's
words, complete, accurate, and permanent. In this chapter,
we first set out a brief historical perspective of the advances
in the understanding of worm biology prior to the publi-
cation of the genome sequence, then illustrate how the
genome sequence has driven the systematic studies to
understand how the 20 000-odd coding genes encoded in
six chromosomes coordinate development and function.
We first discuss systematic analyses of gene function
through genetic screens, then set out the key systems
advances in understanding the coordinate regulation of
gene expression at the level of RNA then protein, then end
with computational approaches that attempt to integrate the
vast datasets produced by genomics technologies to
understand how genes are organized into the modules that
ultimately read the genetic code and translate it to the
phenotype.
Before moving into the post-genome world, it is worth
looking again at the map of the neuromuscular system of
the worm as a vignette illustrating the way that systems
principles
e
11]
. It became possible to think
from bottom-up, from the molecule to the system
e
to
attempt to understand how the central molecules and
fundamental processes of molecular biology are organized
to direct the development and function of complex tissues.
The idea to use the worm as a simple model system to
elucidate the molecular mechanisms and genetic logic
underpinning both development and nervous system func-
tion resulted from discussions between Brenner and Crick
in the early 1960s. In effect, Brenner and Crick rejected the
fly as ultimately 'untameable'
e
the cellular complexity of
the fly is immense compared to that of the worm, and this,
coupled to its more complex lifecycle, meant that the goal
of anchoring phenotypic analysis in a complete cellular
lineage was impossible.
The initial phase of worm-taming has been described
extensively elsewhere, most obviously in the Nobel lectures
of 2002, but ultimately rests on four major achievements:
the construction of both the genetic map
[12]
and the
physical genomic map
[13
e
first identify the individual components, then
examine the connections between them, and finally
understand how the systems-level organization explains the
biological properties
e
underpin worm research. There is
a large body of primary literature leading to the insights
outlined here, but ultimately the best overviews can be
found in White et al.
[21]
and in Richard Durbin's Ph.D.
Thesis (
[22]
and online at
http: //www.wormatlas.org/ver1/
durbinv1.2/durbinindex.html
). First,
e
15]
; the complete description
the components,
in
e
of
18]
; the
comprehensive mapping of the physical and chemical
network of the nervous system; and, finally, the complete
genome sequence. This broad summary clearly hides huge
amounts of painstaking work and groundbreaking technical
innovation. Whether one considers the meticulous and
intricate work of tracing the lineage and of reconstructing
the network of cellular contacts of the neuromuscular
system, or the myriad technical achievements necessary to
allow the sequencing of a complex animal genome
(including, among others, the development of PHRED
[19]
and PHRAP, improvements in clone handling and
sequencing technology, and the development of computa-
tional tools such as ACeDB
[20]
to store, query, and
analyze a previously unapproachable level of data), these
steps were heroic.
By the end of 1998, with the publication of the complete
genome sequence, these major early achievements meant
that for the first (and still only) time for any animal, the
the lineage of worm development
[16
this case the neurons, were identified
every adult
hermaphrodite has 302 neurons and the series of divisions
and specific cell deaths that gives rise to these 302 cells is
essentially invariant. Second, the functions of many of
these individual cells was studied through laser ablation
e
e
e
individual neurons were 'deleted' from the developing
animal and the outcome both on the nervous system
structure and on behavior could be studied, thus estab-
lishing the requirements for the correct development and
function of the worm neuromuscular system (reviewed in
[23]
). Third, the connections either between neurons or
between neurons and muscle cells were deduced from
examining electron micrographs of serial sections through
a number of individual worms. The architecture of the
nervous system is highly reproducible between animals,
and in total there are approximately 5000 chemical
synapses, 2000 neuromuscular junctions, and 600 gap
junctions. Finally, having identified the complete set of
cells involved and the complete set of connections between
