Model organisms: There's more to life than rats and flies

Article (PDF Available)inNature 491(7422):31-3 · November 2012with106 Reads
DOI: 10.1038/491031a · Source: PubMed
Abstract
The tiny number of model organisms constrains research in ways that must be acknowledged and addressed, warns Jessica Bolker.
COMMENT
HISTORY A masterful take
on the age-old allure of
alchemy p.38
NEUROSCIENCE How does the
mind extract meaning from
language? p.36
DEVELOPMENT Science must
inform UN sustainability
goals p.35
POLITICS US abortion lobby
set to clash with prenatal
diagnostics p.33
F
or most experimental biologists, life
revolves around a handful of species:
the mouse (Mus musculus), the nema-
tode worm (Caenorhabditis elegans), the
fruitfly (Drosophila melanogaster) and
the thale cress (Arabidopsis thaliana). We
assume that model organisms offer universal
insights, and funding agencies largely sup-
port work on a shortlist of favoured species
(www.nih.gov/science/models).
Scientists who submit grant proposals
for a project using a standard model organ-
ism need not use up space to explain their
choice. By contrast, choosing a less common
model that is uniquely suited to the research
demands a lengthy justification to convince
sceptical colleagues. Proposals for projects in
unusual species are often returned with the
suggestion that the applicant use a standard
organism instead, because any worthwhile
question should be accessible in a well-
established model.
Investments in research with a handful of
models have returned rich dividends in basic
knowledge and medical progress. And many
careers, labs and journals are built on the pri-
macy of the fly, mouse and worm
1
.
But studying only a few organisms limits
science to the answers that those organisms
can provide. The extraordinary resolving
power of core models comes with the same
trade-off as a high-magnification lens: a
much reduced field of view. For instance, tra-
ditional models for developmental biology —
such as the fly — were chosen because their
phenotypic traits directly reflect their geno-
type, with minimal environmental input.
These models are poorly suited to questions
asked by scientists in emerging fields such
as ecological developmental biology —
eco-devo’ — which focuses on external influ-
ences on developing phenotypes.
Theres more to life
than rats and flies
The tiny number of model organisms constrains research in ways that
must be acknowledged and addressed, warns Jessica Bolker.
ILLUSTRATION BY PHIL DISLEY
1 NOVEMBER 2012 | VOL 491 | NATURE | 31
© 2012 Macmillan Publishers Limited. All rights reserved
Such limitations have serious
consequences. Disparities between mice and
humans may help to explain why the mil-
lions of dollars spent on basic research have
yielded frustratingly few clinical advances
1–4
.
Narrowing the research focus too far limits
basic understanding, in ways that can lead
directly to clinical failures. For example, an
experimental treatment for multiple sclero-
sis that, in inbred mice, improved symptoms
of induced disease produced unpredicted
— and sometimes adverse — responses in
human patients. The
inbred mouse model
failed to represent the
genetic and immu-
nological diversity of
human cells, a short-
coming that was obvi-
ous in retrospect
2
.
It is time to think
more critically about
how we use models. This means articulat-
ing tacit assumptions, such as the adequacy
of rodent models to fully represent specific
human diseases. It means looking hard at
how we select and use our favoured model
species, and acknowledging both their
strengths and their limitations. And it means
mainstream funders and journals welcom-
ing work in non-standard organisms.
MODELS OF CONVENIENCE
How did a handful of species become
central models? Sometimes it was more about
convenience than strategic planning. Dros-
ophila rose to prominence in the early 1900s
in part because its short generation time was
handy for student projects and its four pairs
of large chromosomes were ideal for the study
of eukaryotic genetics
5
. Yeast, mice, chickens
and other domesticated species became lab
favourites because they were already familiar
and accessible. The existence of lab popula-
tions of frogs (Xenopus laevis) for use in preg-
nancy tests led to their recruitment as a model
for developmental research.
As model-based science grew, these few
species became increasingly dominant,
despite the sometimes haphazard way that
they had initially been chosen. We have now
reached a point where, if researchers cannot
tackle a problem using a familiar species,
they may not study it at all
1
.
Take modern developmental biology. The
field has centred on small, rapidly develop-
ing organisms with short generation times
— most typically, Drosophila and C.elegans.
Much of our current understanding of devel-
opmental principles is based on experiments
in these species. However, evolutionary
selection for rapid development has broad
implications. It seems to favour stronger
genetic control during development and
less plasticity (or flexibility). Compared with
related species, development in the models is
less responsive to external signals, whether
adaptive or disruptive. Because plasticity and
the role of the developmental environment
are particularly hard to study in key mod-
els, these areas receive comparatively little
attention
6
.
A similar narrowing has occurred in
biomedical research. In the case of Parkin-
sons disease, potential treatments are often
assessed by measuring motor function in
a lesioned rat. But the rat model does not
clearly represent other significant symptoms
of Parkinsons that occur in human patients,
such as cognitive decline. This may steer
some researchers away from these aspects
of the disease.
Similar biases rooted in the use of par-
ticular models may also contribute to the
translational disconnect’ with regard to
neuro degenerative diseases such as Alzhei-
mer’s and amyotrophic lateral sclerosis
3,4
.
The inability of highly inbred and often
genetically modified rodent strains to fully
represent the diversity of human patients
and symptoms has called the power of
such models into question, even within the
research communities they serve
1–4,7
.
At the same time, the effects of appar-
ently trivial environmental variations, such
as the details of mouse handling, are often
overlooked
8
. Aggression is the key behav-
ioural phenotype in male mice lacking the
enzyme neuronal nitric oxide synthase.
This was not observed — and could not be
seen — until animals were housed in groups
rather than in standard individual cages
9
.
Few lab models explicitly account for the
environment of organisms, despite increas-
ing recognition that this may affect the
outcome and replicability of experiments
7
.
In short, if we frame a research model or
system too narrowly, leaving out key causal
elements such as environmental influences,
we cannot hope to construct a complete pic-
ture of the mechanisms that underlie crucial
variations, for example in development and
disease. To study environmental influences,
we need to study species in which such fac-
tors matter. So the traits that define a suc-
cessful model must shift as the questions for
which we use them evolve.
BEST FIT
Choosing a research model should be more
than a matter of convenience or conven-
tion. Scientists need to ask more questions
— about the goals of a specific experiment,
how suitable a given model is to reach-
ing those goals, and what environmental
or other external factors might be relevant
to how well the model works. For a given
question, it is crucial to determine which
aspects of human biology are essential (for
example, our genetic diversity, unique char-
acteristics of our immune system or particu-
lar disease symptoms) and assess how well
they are represented in a candidate model
(see ‘Choosing the right candidate’). Where
mismatches appear, we must limit our infer-
ences from animal studies accordingly, and
consider when and how to move to research
in humans. For some kinds of biomedical
“To study
environmental
influences,
we need to
study species
in which
such factors
matter.”
2 Need for additional models
Example: Where there are known
obstacles to translating results from mice
to humans, how do we develop alternative
routes to find new treatments for human
diseases
3
?
Key questions
What aspects of human disease are
poorly represented in current models?
How might the utility of current models
be expanded?
What potential new models are available,
or could be developed?
Research objectives
Develop strategies to assess other
aspects of human disease in current
models.
Identify new candidate models for
specific questions.
Develop criteria for selecting new
models.
1 Matching between the model
and what it represents
Example: Does studying immunology in
highly inbred mouse models shed useful
light on the diversity of human immune
function and disease
1
?
Key questions
What do we need to know about a
disease to develop treatments?
What mechanisms link disease origin to
symptoms?
Research objectives
Discover aetiology of symptoms.
Compare disease initiation and
progression between models and humans.
Assess whether therapeutic targets are
well represented in specific models.
Identify gaps between models and
patients that may be significant with
respect to basic knowledge and to
treatment approaches.
MODEL PROBLEMS
Choosing the right candidate
32 | NATURE | VOL 491 | 1 NOVEMBER 2012
COMMENT
© 2012 Macmillan Publishers Limited. All rights reserved
research, it may not matter that the
damage or symptoms in the model devel-
oped by a different pathway to that which
occurs in patients — orthopaedic injuries
are one example. But in other areas, such
as epidemiology, it matters a great deal.
Recognizing that standard models have
limitations does not mean we should give
them up. Rather, we should deliberately
account for their limitations as part of
study design — for example, by analysing
the role of a gene in mouse strains with
different genetic backgrounds. No single
species, no matter how highly engineered,
can ever serve as a universal model: every
species has unique features that may be
assets or faults, depending on the ques-
tion being asked. For instance, the lack
of developmental plasticity in Drosophila
and of genetic variability in inbred rats
limit what these models can tell us about
ecological effects on development, but
make them powerful tools for studying
gene function during development.
We also need to broaden our range of
models to include species such as Antarc-
tic icefish, comb jellies, cichlids, dune mice
and finches that are naturally endowed by
evolution with features relevant to human
diseases
10
. Studying the basis of unique
adaptive traits in these animals may yield
insight into human disorders such as
osteo porosis, cataracts and cancer.
Immediately and practically, the US
National Center for Advancing Transla-
tional Sciences in Bethesda, Maryland,
should support the development of new
systems for investigating problems that
are not tractable in currently favoured
models. It should also fund investiga-
tions into fundamental questions about
model-based research (see ‘Choosing the
right candidate’). The resulting insights
would help scientists to select the best
models for advancing basic and applied
research, and strengthen the bridges
between them.
Jessica Bolker is an associate professor of
zoology in the Department of Biological
Sciences, University of New Hampshire,
Durham 03824, New Hampshire, USA.
e-mail: jessica.bolker@unh.edu
1. Davis, M. M. Immunity 29, 835–838 (2008).
2. von Herrath, M. G. & Nepom, G. T. J. Exp. Med.
202, 1159–1162 (2005).
3. Geerts, H. CNS Drugs 23, 915–926 (2009).
4. Schnabel, J. Nature 454, 682–685 (2008).
5. Kohler, R. E. Lords of the Fly: Drosophila
Genetics and the Experimental Life (Univ.
Chicago Press, 1994).
6. Bolker, J. A. BioEssays 17, 451–455 (1995).
7. Beckers, J., Wurst, W. & Hrabé de Angelis,
M. H. Nature Rev. Genet. 10, 371–380 (2009).
8. Hurst, J. L. & West, R. S. Nature Methods 7,
825–826 (2010).
9. Nelson, R. J. et al. Nature 378, 383–386
(1995).
10. Maher, B. Nature 458, 695–698 (2009).
I
n the United States, pro-life advocacy
groups, notably Americans United for
Life, based in Washington DC, have been
making headway in their mission
1
to limit
womens access to abortions “state by state,
law by law and person by person. In 2011, 24
US states enacted 92 new provisions restrict-
ing abortion — nearly triple the previous
record of 34 in 2005 (see ‘Clamping down’).
One of the strategies of pro-life advocates is
to target the reasons for which a woman can
have an abortion. Meanwhile, a major devel-
opment in prenatal care, called non-invasive
prenatal genetic testing (NIPT), promises to
increase the genetic information available to
women early during their pregnancy.
The US Food and Drug Administra-
tion (FDA) cannot control how people
use information from genetic tests. But
by developing a clear regulatory framework
for NIPT and improving public under-
standing of NIPT’s benefits and limitations,
the agency could help to allay fears that
the tests will lead to a drastic increase
in selective abortions.
NIPT has the potential to improve
womens reproductive autonomy. But if it
is not integrated cautiously into pre natal
care, the technology could be targeted to
support burgeoning strategies to restrict
abortion.
In recent years, two blood tests combined
with an ultrasound have been the most
common method for determining a fetuss
risk of having a congenital disease such as
Downs syndrome. Results from this type
Politics and fetal
diagnostics collide
Without better regulation, non-invasive prenatal
genetic tests will be targeted by US anti-abortion
lobbyists, argues Jaime S. King.
Pro-choice and pro-life activists clash outside the US Supreme Court in Washington DC.
J. REED/REUTERS/CORBIS
1 NOVEMBER 2012 | VOL 491 | NATURE | 33
COMMENT
© 2012 Macmillan Publishers Limited. All rights reserved
    • "The " traditional " model organisms are very well understood through accumulated knowledge and intense study and have proven broad utility for research in many different fields, but they are unable to cover the full range of biological enquiry. This is because , as Claude Bernard implied 150 years ago, many biological processes are absent, masked, or not accessible in these organisms , and only a tiny fraction of existing molecular and taxonomic biodiversity is represented (Abzhanov et al., 2008; Bolker, 2012, Heidelberg, in March 2012 . The workshop was organized by C.E.C. and P.L. "
    [Show abstract] [Hide abstract] ABSTRACT: Until recently the set of model species used commonly for cell biology was limited to a small number of well-understood organisms, and developing a new model was prohibitively expensive or time-consuming. With the current rapid advances in technology, in particular low-cost high-throughput sequencing, it is now possible to develop molecular resources fairly rapidly. Wider sampling of biological diversity can only accelerate progress in addressing cellular mechanisms and shed light on how they are adapted to varied physiological contexts. Here we illustrate how historical knowledge and new technologies can reveal the potential of nonconventional organisms, and we suggest guidelines for selecting new experimental models. We also present examples of nonstandard marine metazoan model species that have made important contributions to our understanding of biological processes.
    Full-text · Article · Mar 2016
    • "While specialized (e.g., " enhancer " ) screens (Kile and Hilton, 2005; Patton and Zon, 2001) can uncover some of these factors, these are labor intensive and require base knowledge or assumptions about gene action. In all, it is becoming increasingly appreciated (e.g., (Bolker, 2012)) that new approaches and new models are needed to identify the genes that may have been missed by classic forward genetic screens. In addition to disproportionally targeting genes with early essential functions, screens also unequally identify certain types of alleles and mutations. "
    [Show abstract] [Hide abstract] ABSTRACT: We have made great strides towards understanding the etiology of craniofacial disorders, especially for ‘simple’ Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model – African cichlid fishes – can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.
    Full-text · Article · Dec 2015
    • "Model organisms with short generation times and able to tolerate cultivation under laboratory conditions have long captured the attention of biologists, who have used them to test mechanistic hypotheses at the lowest experimental cost and temporal scale possible [1,2]. For instance, the nematode Caenorhabditis elegans Maupas 1900 has for decades served as an animal model for researchers throughout the world [3,4,5]. "
    [Show abstract] [Hide abstract] ABSTRACT: The nematode Pristionchus pacificus is of growing interest as a model organism in evolutionary biology. However, despite multiple studies of its genetics, developmental cues, and ecology, the basic life-history traits (LHTs) of P. pacificus remain unknown. In this study, we used the hanging drop method to follow P. pacificus at the individual level and thereby quantify its LHTs. This approach allowed direct comparisons with the LHTs of Caenorhabditis elegans recently determined using this method. When provided with 5×109 Escherichia coli cells ml–1 at 20°C, the intrinsic rate of natural increase of P. pacificus was 1.125 (individually, per day); mean net production was 115 juveniles produced during the life-time of each individual, and each nematode laid an average of 270 eggs (both fertile and unfertile). The mean age of P. pacificus individuals at first reproduction was 65 h, and the average life span was 22 days. The life cycle of P. pacificus is therefore slightly longer than that of C. elegans, with a longer average life span and hatching time and the production of fewer progeny.
    Full-text · Article · Aug 2015
Show more

  • undefined · undefined
  • undefined · undefined
  • undefined · undefined