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Evolution: Biology's next top model?
... Some organisms have evolved features which correspond to disease states in humans, such as reduced eyes (microphthalmia) in cave-dwelling fish. Comparing their genomes with those of closely related species without those features can give insights into the processes involved, which can in turn aid in the investigation of human diseases [105,106]. ...
... Another potential application of evolutionary analysis to disease elucidation is the use of evolutionary mutant models. These are species that have evolved traits that mimic human genetic disorders [105,106]. For instance, there are species of Antarctic ice fish which lack hemoglobin and red blood cells. ...
... Comparing their genomes with those of related species that do have red blood cells could give further insights into red blood cell biology and anemic diseases [105]. There are many other examples of evolutionary mutant models involving different species [105,106], and the approach is also applicable to breeds of domestic animals such as dogs [123,124]. Unfortunately, the lack of genome sequences for most such species and breeds is a current limitation to this approach [106]. ...
... The representational scope of an experimental organism can be very narrow and extend only to its own species or those that are closely related: for instance, red-eared terrapins are used to study turtle shell development (Maher 2009) and tamar wallabies are used as a model for reproduction and development in kangaroos, and marsupials more generally (Hickford, Frankenberg, & Renfree 2009). Researchers may hope that the study of these organisms reveals something about behaviour or physiology that is generalisable. ...
... For various sorts of experimental organisms, obtaining the organisms on which to do work involves considerable efforts in the field, let alone to grow, maintain, and manipulate them. Researchers continue to use their organisms of choice in part because they think that they are particularly well-suited for the questions of interest: for instance, turtles have characteristics that make them extremely useful for studying transitions from one cell type to another due to the fact that they convert soft tissue into bone (Maher 2009). In summary, the most important criterion for the selection and development of experimental organisms is the way in which they enable the study of specific questions; experimental tractability is also relevant but will be diversely defined depending on the question of interest and is often subsidiary to it. ...
This Element presents a philosophical exploration of the concept of the ‘model organism’ in contemporary biology. Thinking about model organisms enables us to examine how living organisms have been brought into the laboratory and used to gain a better understanding of biology and to explore the research practices, commitments, and norms underlying this understanding. We contend that model organisms are key components of a distinctive way of doing research. We focus on what makes model organisms an important type of model and how the use of these models has shaped biological knowledge, including how model organisms represent, how they are used as tools for intervention, and how the representational commitments linked to their use as models affect the research practices associated with them.
... Model organisms are those that are widely studied and that are convenient to keep in the laboratory [8]. Prominent amongst these has been a nematode, Caenorhabditis elegans, the first animal to have its genome sequenced [9]. ...
... Bees quickly learn to extend their proboscis to odors following association of that odor with a sucrose reward [6,7]. In a similar manner, flies learn to avoid an odor that was previously associated with an electric shock [8]. Using variants of these established training protocols, both groups investigated parameters of 'trace' conditioning. ...
New work now shows that the dauer larvae of Caenorhabditis elegans can survive anhydrobiotically. The genetic tractability of this model organism may be useful in studying how organisms survive when losing most or all of their water.
... One of the promises of evolutionary medicine is to use non-traditional model organisms, 69 which could be more suitable for a particular health or disease question (Maher, 2009). 70 ...
Evolutionary medicine has been a fast-growing field of biological research in the past decade. One of the strengths of evolutionary medicine is to use non-traditional model organisms which often exhibit unusual characteristics shaped by natural selection. Studying these unusual traits could provide valuable insight to understand biomedical questions, since natural selection likely discovers solutions to those complex biological problems. Because of many unusual traits, the naked mole-rat (NMR) has attracted attention from different research areas such as aging, cancer, and hypoxia- and hypercapnia-related disorders. However, such uniqueness of NMR physiology may sometimes make the translational study to human research difficult. Damaraland mole-rat (DMR) shares multiple characteristics in common with NMR, but shows higher degree of similarity with human in some aspects of their physiology. Research on DMR could therefore offer alternative insights and might bridge the gap between experimental findings from NMR to human biomedical research. In this review, we discuss studies of DMR as an extension of the current set of model organisms to help better understand different aspects of human biology and disease. We hope to encourage researchers to consider studying DMR together with NMR. By studying these two similar but evolutionarily distinct species, we can harvest the power of convergent evolution and avoid the potential biased conclusions based on life-history of a single species.
... To comprehend it, we have compiled a list of those subterranean animals that can be considered as model organisms (Table S1). We selected models based on two these is the cavefish Astyanax mexicanus (Jeffery, 2020;Keene et al., 2016;Torres-Paz et al., 2018), which has been kept in captivity for many generations (Wilkens, 1971) and is increasingly used and recognized as suitable for tackling problems beyond the typical subterranean biology realm (Maher, 2009;McGaugh et al., 2020). ...
• Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.
• Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so-called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.
• We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.
• Our over-arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
... Although mammals have a better similarity to humans, they also show some experimental disadvantages, such as low throughput (Brito-Casillas et al., 2016). Considering these limitations, fish as model organisms are widely used for modeling human disease and drug screening (Maher, 2009;Liang et al., 2013). Zebrafish (Danio rerio) is a low-cost model animal with a rapid lifecycle, small size and optical transparency (Stewart et al., 2014). ...
Ala-Pro (AP), Ile-Pro-Ala (IPA) and Ile-Pro-Ala-Val-Phe (IPAVF) as DPP-IV inhibitory peptides were purified from Antarctic krill protein hydrolysate (AKH). Diabetic zebrafish model was rapidly induced with combination of high glucose immersing and cholesterol diet for evaluation the three DPP-IV inhibitory peptides activity. Physiochemical indexes including DPP-IV activity, glucose, triglyceride and cholesterol; the relative gene (insa, glucagon and pck1) expressions levels were detected. The results showed that after 15 days of peptides treatment, the physiochemical index levels of peptide groups were significantly higher than that of negative control and showed dose-dependent effect. The insa gene expression level would be increased with the enhancement of peptide concentration, whereas gene expression levels of glucagon and pck1 would be decreased. These results indicated that three peptides all had hypoglycemic effects in different degree. It suggested the potential of AKH containing DPP-IV inhibitory peptides could be as functional food supplement to treat diabetes.
... Selecting a natural organism or system might be seen as a trade-off between subjective features making it appealing to study (aesthetic characteristics, peculiar adaptations, etc.) and objective features making it a good model (ease to raise in the lab, generation time, genome size, etc.). And since many of these features are not obvious when selecting a new model organism (Hedges 2002;Maher 2009;Alfred and Baldwin 2015), we cannot deny a certain role of luck in this choice when, for example, a favourite organism turns out to be ideal to tackle an important question or to develop a new method. For example, the status of Arabidopsis thaliana as an anonymous flowering plant or of Caenorhabditis elegans as just-another-round-worm radically changed when pioneering researchers turned them into cutting-edge model systems in evolutionary biology (Mitchell-Olds 2001;Kaletta and Hengartner 2006). ...
Whereas scientists interested in subterranean life typically insist that their research is exciting, adventurous,
and important to answer general questions, this enthusiasm and potential often fade when the results
are translated into scientific publications. This is because cave research is often written by cave scientists
for cave scientists; thus, it rarely “leaves the cave”. However, the status quo is changing rapidly. We analysed
21,486 articles focused on subterranean ecosystems published over the last three decades and observed a
recent, near-exponential increase in their annual citations and impact factor. Cave research is now more
often published in non-specialized journals, thanks to a number of authors who are exploiting subterranean
habitats as model systems for addressing important scientific questions. Encouraged by this positive
trend, we here propose a few personal ideas for improving the generality of subterranean literature,
including tips for framing broadly scoped research and making it accessible to a general audience, even
when published in cave-specialized journals. Hopefully, this small contribution will succeed in condensing
and broadcasting even further the collective effort taken by the subterranean biology community to bring
their research “outside the cave”.
... The intensive study and detailed understanding of specific organisms enables research programs that can address important and timely questions and topics, such as climate change, disease transmission, pest management, and biomaterial engineering (Maher, 2009;Alfred & Baldwin, 2015). The natural world around us harbors surprises that even the most educated and creative minds could not fashion de novo (Bonabeau, Dorigo & Theraulaz, 2000;Sarkar, Phaneendra & Chakrabarti, 2008;Place, Evans & Stevens, 2009;Grzybowski & Huck, 2016). ...
Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students-as well as scientists themselves-into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the "Spider World Records"). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements.
... Nature as a potent "mutagenizing" force While Charles Darwin and other 19 th century biologist embraced the astounding natural diversity of living things, the 20th century became the era of model organisms such as the fly and mouse (Davis, 2004). Technological advances in genome sequencing and molecular techniques have enabled modern biologists to once again turn to natural variation in non-model organisms (discussed in Albertson et al. (2009);Bolker (2012); Mahar (2009);Schartl (2014)), spurring on the current "golden age" of comparative and evolutionary genetics (Nadeau and Jiggins, 2010). We argue that these advances also open up opportunities to use evolutionary systems to better understand the human condition. ...
... Biologen und andere Naturwissenschaftler entdecken auch heute noch Ideal-Modelle um biologische Prozesse sichtbarer zu machen (Maher 2009 Belastung möglich werden (Traunspurger. 1995). ...
Caenorhabditis elegans Modelsysteme für Freiland und Labor
Caenorhabditis elegans ist eines der am intensivsten untersuchten Tiermodelle, dabei weisen die nur unzureichenden Informationen über sein ursprüngliches Habitat eine Vielzahl offener Fragen auf. Deshalb beschäftigt sich der erste Teil vorliegender Arbeit mit einer Überprüfung der Freilandökologie und Biogeographie des Taxons.
Nach den Untersuchungen spricht vieles dafür, dass die Ursprungsart der C. elegans Gruppe ein Begleiter von Gastropoden war, welche auch für ihre Ausbreitung häufig verantwortlich sind. Als Folge der Verschleppung durch Wirtstiere (u.a. die Weinbergschnecke Helix aspersa) erreichte sie ihr heutiges Areal, in allen Kontinenten.
Ein nicht weniger wichtiges Ziel der vorliegenden Arbeit war die Etablierung von C. elegans als Biotest-System für die Indikation von Chemikalien-Wirkungen.
In dieser Arbeit wurden ein ökotoxikologisches Testsystem entwickelt mit den C. elegans als Modellorganismus, das durch Messung von umweltbedingten intrazellulär gebildeten ROS im Gesamtorganismus eine Einschätzung der biologischen Aktivität von Chemikalien und Umweltmedien ermöglichen sollte. Als grundlegender biochemischer Parameter ist eine, die Kapazität der antioxidativen Schutzmechanismen übersteigende, ROS-Bildung ursächlich für oxidative Schädigungen der Zelle verantwortlich und damit Basis für zahlreiche pathologische Effekte. Aus den Resultaten als Bewertungsgrundlage lässt sich folgern, dass sich das erarbeitete Biotestsystem als adäquates Verfahren zur Messung von oxidativem Stress, als Folge exogener Belastung, einsetzen lässt. Damit leistet es einen Beitrag zur Beurteilung des Toxizitätspotentials von Chemikalien und Umweltproben.
Zur Eignung des Einsatzes von C. elegans für Toxizitätstest wurden weitere Untersuchungen mit verschiedenen Chemikalien durchgeführt. Dabei ergibt sich bezogen auf molare Einheiten eine immer gleich bleibende Reihenfolge der Sensitivitäten gegenüber BaP > Cu2+ > AcL, ein Ergebnis welches mit Testergebnissen von anderen Versuchsorganismen zu vergleichen war.
Die Wirkung von Atrazin auf die Entwicklung von C. elegans wurde auch untersucht.
Es wurde festgestellt, dass Atrazin auf Wachstum und Reproduktion von C. elegans konzentrationsabhängig toxisch wirkt.
Die bisherigen Ergebnisse zeigen jedoch, dass das Testsystem C. elegans hervorragend geeignet ist, um Chemikalienwirkungen frühzeitig sichtbar zu machen.
... The organism-centred approach seeks to improve our understanding of critical ecological interactions by focusing on the level of the individual organism. At the time of the Gnettic application, this approach was organised around classical laboratorybased model organisms, i.e. organisms with well-characterised gene expression patterns and large research networks around them, for instance the plant Arabidopsis thaliana and the nematode Caenorhabditis elegans, (Maher 2009, 695; Ankeny and Leonelli 2011, 316). By exposing the model to different environmental conditions (humidity, drought, etc.), the genes and gene functions that matter most in a given ecological interaction were identified (Ungerer et al. 2008). ...
Every field of science, but especially biology, contains particular conceptions of nature. These conceptions are not merely epistemological or ontological, but also have normative dimensions; they provide an ethos, a framework for moral orientation. These normative dimensions, whilst often remaining ‘hidden’ and inarticulate, influence the way in which biologists practice their profession. In this paper, I explore what happens when different versions of these implicit normative frameworks collide. To do so, I will focus on a case study from the field of ecological genomics as it has evolved in one particular country, namely the Netherlands. During an important inaugural meeting, the director of one of the most sizeable Dutch ecogenomics centres gave a presentation in which he introduced the term ‘nature mining’. Part of the audience immediately embraced the term, but others were very reluctant. This mixed response is generally explained as a culmination of growing tension about the future direction of the field: due to new funding demands, a shift had occurred from fundamental research to research more interested in ‘valorisation’.
In addition to this current interpretation, I will argue that the turmoil caused by the use of the term ‘nature mining’ also reveals a more fundamental difference between the various parties involved in the Dutch ecogenomics community. This term is part of a vocabulary that emphasises the beneficial ‘goods’ produced by nature. Whereas part of the audience saw no harm in this commodification of nature, others had difficulties with the reduction of nature to a reservoir to be exploited using the latest technologies. I will conclude by arguing that, although at present, the core of Dutch ecogenomics research reflects a more or less instrumental attitude towards nature, the field also harbours other interpretations of nature as a significant and meaningful order. For instance, ecogenomics might further develop the image of land as a ‘collective organism’, as proposed by Aldo Leopold.
... The notothenioids have undergone resistant and compensatory adaptations to the extreme Antarctic marine environment, as well as regressive evolutionary changes. Thus, they are considered an attractive model species for evolutionary and physiological studies (Eastman 2000;Maher 2009). ...
Notothenia coriiceps, a typical Antarctic notothenioid teleost, has evolved to adapt to the extreme Antarctic marine environment. We previously reported an extensive analysis of the Antarctic notothenioid transcriptome. In this study, we focused on a key component of the innate immune system, the Toll-like receptors (TLRs). We cloned the full-length sequence of 12 TLRs of N. coriiceps. The N. coriiceps transcriptome for TLR homologue (ncTLR) genes encode a typical TLR structure, with multiple extracellular leucine-rich regions and an intracellular Toll/IL-1 receptor (TIR) domain. Using phylogenetic analysis, we established that all of the cloned ncTLR genes could be classified into the same orthologous clade with other teleost TLRs. ncTLRs were widely expressed in various organs, with the highest expression levels observed in immune-related tissues, such as the skin, spleen, and kidney. A subset of the ncTLR genes was expressed at higher levels in fish exposed to pathogen-mimicking agonists, heat-killed Escherichia coli, and polyinosinic-polycytidylic acid (poly(I:C)). However, the mechanism involved in the upregulation of TLR expression following pathogen exposure in fish is currently unknown. Further research is required to elucidate these mechanisms and to thereby increase our understanding of vertebrate immune system evolution.
... Key words: tunicate; Appendicularian (larvacean) husbandry; microalga cryopreservation; fecundity and fertilization success; chordate developmental biology In the last decades, the study of well-established animal models has been crucial for the extraordinary progress of knowledge in the fields of developmental biology and biomedicine, but the scientific challenges of the XXI century, especially those to decipher the evolutionary basis of life diversity, demand the development of new animal models carefully chosen according to their phylogenetic position in the tree of life (Maher, 2009). The larvacean (or appendicularian) Oikopleura dioica, for instance, is a planktonic marine organism that possesses many characteristics that make it attractive as animal model: (i) O. dioica occupies a key phylogenetic position within the chordate phylum as a basally divergent member of the urochordate subphylum (Stach and Turbeville, 2002;Swalla et al., 2000;Wada, 1998), which is the sister group of vertebrates (Delsuc et al., 2006;Delsuc et al., 2008). ...
The genome sequencing and the development of RNAi knockdown technologies in the urochordate Oikopleura dioica are making this organism an attractive emergent model in the field of EvoDevo. To succeed as a new animal model, however, an organism needs to be easily and affordably cultured in the laboratory. Nowadays, there are only two facilities in the world capable to indefinitely maintain Oikopleura dioica, one in the SARS institute (Bergen, Norway) and the other in the Osaka University (Japan). Here, we describe the setup of a new facility in the University of Barcelona (Spain), in which we have modified previously published husbandry protocols to optimize the weekly production of thousands of embryos and hundreds of mature animals using the minimum amount of space, human resources and technical equipment. This optimization includes novel protocols of cryopreservation and solid cultures for long-term maintenance of microalgal stocks - Chaetoceros calcitrans, Isochrysis sp., Rhinomonas reticulata and Synechococcus sp.- needed for Oikopleura dioica feeding. Our culture system maintains laboratory partially inbred lines healthy with similar characteristics to wild animals, and it is easily expandable to satisfy on demand the needs of any laboratory that may wish to use Oikopleura dioica as a model organism. © 2014 Wiley Periodicals, Inc.
... Recent work using the collagen family of genes as markers for cartilage and bone formation also indicates that the delayed branchial and cranial bone development in low-density pelagic and semipelagic notothenioids is associated with heterochronic shifts in skeletal gene expression, specifically persistence of the chondrogenic program and delay in the osteogenic program during larval development (Albertson et al., 2010;Detrich and Amemiya, 2010). This "adaptive osteopenia" has allowed channichthyids to be advanced as evolutionary-mutant model organisms for investigating osteopenia in humans (Albertson et al., 2009;Maher, 2009). ...
Although notothenioid fishes lack swim bladders, some species live temporarily or permanently in the water column. Given its relatively high density, skeletal mass is a key determinant of buoyancy. Notothenioids have reduced skeletal ossification, but there is little quantitative data on the phylogenetic distribution of this trait. We obtained dry skeletal masses for 54 specimens representing 20 species from six notothenioid families. Although comparative data are sparse, notothenioid skeletons comprise a smaller percentage of body mass, <3.5%, than those of three non-notothenioid perciforms. With relatively high skeletal mass, the non-Antarctic Bovichtus diacanthus is similar in skeletal mass to some non-notothenioids. Eleginops maclovinus, the non-Antarctic sister group of the Antarctic clade, has a relatively light skeleton (<2% of body mass) similar to many species in the Antarctic clade. Low skeletal mass is therefore a synapomorphy shared by Eleginops plus the Antarctic clade. We provide gross, histological, and micro-CT documentation of the structure and location of bone and cartilage in skulls, pectoral girdles, and vertebrae, with emphasis on the bovichtid B. diacanthus, the eleginopsid E. maclovinus, and the channichthyid Chaenodraco wilsoni. In Eleginops and the Antarctic clade, most bone is spongy and most species have persisting cartilage in the skull and appendicular skeleton. We also measured the relative size of the notochordal canal in adult vertebral centra of 38 species representing all eight families. There is considerable interspecific variation in this pedomorphic trait and all species show an ontogenetic reduction in the relative size of the canal. However, large persisting canals are present in adults of the Antarctic clade, especially in the nototheniids Pleuragramma and Aethotaxis and in a number of bathydraconid and channichthyid genera. J. Morphol., 2014. © 2014 Wiley Periodicals, Inc.
... Methods for manipulating gene expression in species of biomedical or agricultural interest can enable functional studies in species where we lack detailed genetic information, and/or cannot easily perform breeding experiments (Davis 2004;Vera et al. 2008;Di Stilio 2011;Tulin et al. 2013). Tools developed in chickens can be applied in finches (Abzhanov et al. 2004(Abzhanov et al. , 2006Mallarino et al. 2011), and methods perfected in zebrafish can be used in species from icefish to sticklebacks (Cresko et al. 2006;Maher 2009;Tautz 2011). ...
A model is a representation of or an analogy for something else; in a biological context, the term often refers to organisms or species that serve as a widely used platform for experimental research. In developmental biology, an extraordinarily detailed understanding of fundamental genes and mechanisms has been built around a few core models including Drosophila, mouse, Caenorhabditis elegans, Arabidopsis, and zebrafish. The use of model species entails a series of epistemological issues and commitments regarding similarity, generalization, and the balance between representation and accessibility. In addition, the power of a given model is highly context-dependent, and the core models of developmental biology may not suffice for evo-devo questions. An epistemological perspective can clarify the complementary roles of standard and emerging models in evo-devo, as well as inform decisions about when new models are needed, and criteria for choosing them.
... Examples of this tendency include recent laboratory manuals on " emerging " model organisms ranging from honeybee to wallaby [6]. Many research groups are experiencing pressures as a result of the popularity of the term, for instance due to competitive granting systems that force researchers to focus on these organisms or to rationalise proposed research work on a particular organism by claiming that it is, in some sense, a " model organism " [7, 8]. The model organism concept has thus been accused of " swamping out " research agendas, making it difficult to get funding to do research on nonmodel organisms [9]. ...
This article explains the key role of model organisms within contemporary research, while at the same time acknowledging their limitations as biological models. We analyse the epistemic and social characteristics of model organism biology as a form of "big science", which includes the development of large, centralised infrastructures, a shared ethos and a specific long-term vision about the "right way" to do research. In order to make wise use of existing resources, researchers now find themselves committed to carrying out this vision with its accompanying assumptions. By clarifying the specific characteristics of model organism work, we aim to provide a framework to assess how much funding should be allocated to such research. On the one hand, it is imperative to exploit the resources and knowledge accumulated using these models to study more diverse groups of organisms. On the other hand, this type of research may be inappropriate for research programmes where the processes of interest are much more delimited, can be usefully studied in isolation and/or are simply not captured by model organism biology.
... Analyzing development among diverse organisms under different environments is a departure from how development has previously been studied. Traditionally, research has focused on a few species ("model organisms") in the laboratory ( 3). Because development was typically studied in uniform environments, past research fostered the erroneous view that environmentally contingent development is rare or unimportant. ...
Ecological Developmental Biology Integrating Epigenetics, Medicine, and Evolution by Scott F. Gilbert and David Epel Sinauer Associates, Sunderland, MA, 2009. 496 pp. $49.95. ISBN 9780878932993.
Gilbert and Epel focus on embryonic and larval development of metazoans to explore where "embryology meets the real world."
... Currently the term ''model organism'' not only serves as a descriptor for organisms that have certain attributes, but it also has gained prescriptive power. Many research groups increasingly are experiencing pressures as a result of the popularity of the term, for instance due to competitive granting systems that force researchers to focus on these organisms or to rationalize any proposed research work on a particular organism by claiming that it is, in some sense, a ''model organism'' (e.g., Maher, 2009;Slack, 2009;Sommer, 2009). Some critics have argued that the model organism concept is ''swamping out'' contemporary biological research 0039 2 For an early conceptual examination of model organisms as model systems, see Gest (1995). ...
This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term ''model organism'' does not apply to all organisms used for the purposes of experimental research. We explore the differ-ences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and representational tar-get. We also examine the characteristics of the communities who use these two types of models, includ-ing their research goals, disciplinary affiliations, and preferred practices to show how these have contributed to the conceptualization of a model organism. We conclude that model organisms are a spe-cific subgroup of organisms that have been standardized to fit an integrative and comparative mode of research, and that it must be clearly distinguished from the broader class of experimental organisms. In addition, we argue that model organisms are the key components of a unique and distinctively biolog-ical way of doing research using models. Crown Copyright Ó
... We also need to broaden our range of models to include species such as Antarctic 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. ...
The tiny number of model organisms constrains research in ways that must
be acknowledged and addressed, warns Jessica Bolker.
... On the one hand, model organism databases certainly reinforced the power of popular model organisms over other organisms with less well-organized communities. Indeed, the popularity and usefulness of particular model organisms has tended to grow incrementally with the scale and organisation of their community databases, a principle readily recognised by biologists wishing to promote new organisms as 'biology's next top models', according to whom obtaining funding to build a community database is a crucial step in the process (Maher, 2009; Behringer et al., 2008), and by researchers wishing to highlight the usefulness of model organism research for the future study of human disease (Spradling et al., 2006) and evolutionary developmental biology (Sommer, 2009). At the same time, however, it is important to note how the expansion of community databases has shifted attention away from research on single species to comparative, cross-species research. ...
Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species.
Research with model organisms is often lauded for its putative ability to integrate knowledge at the molecular, physiological, and organismic levels, and across the tree of life. I’ll explore this prima facie surprising assertion (why would working on a single organism better enable us to integrate across multiple levels and multiple organisms?), and then introduce a case study describing the use of ferrets in research in virology. Ferrets, which can be understood as a kind of “model organism in development,” clearly exhibit the different ways that scientists both work to enhance and improve the integrative promise of their work over time and deploy arguments that this integrative promise merits the support of the broader scientific community. I’ll both describe the current state of play in such research and discuss the calls for further enhancement and refinement of the ferret model in order to make the case.
Model organisms are responsible for many important discoveries and advancements in science. This group of species shares a suite of traits making them uniquely suited to be models including being easy to maintain and genetically manipulated within a laboratory setting. Aquatic model organisms are specially positioned for ecotoxicity assessment because of their ability to serve as predictors of toxicity for other organisms, as well as sentinel species for environmental health. The standards of regulatory toxicity assessment and the organisms used in these assays are dictated by environmental agencies. A diversity of freshwater, estuarine, and marine algae, invertebrates, and fish are currently used as model species for ecotoxicity assessment. The popularity of model organism research has created a bias for those studies and limited the diversity of the data produced. However, the expansion of genomic technologies has opened the door to a host of emerging and alternative model organisms. Therefore, though, historically, the number of ecotoxicity model organisms has been limited, the definition is expanding to include a broader range of well-studied organisms.
(1) Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research
(2) Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represent the elective habitat for the so-called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating lab experiments.
(3) We explore the advantages and disadvantages of four general experimental setups (in-situ, quasi in-situ, ex-situ, and in-silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.
(4) Our over-arching goal is to promote caves as model systems where one can perform standardised scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
The use of semi‐isolated habitats such as oceanic islands, lakes and mountain summits as model systems has played a crucial role in the development of evolutionary and ecological theory. Soon after the discovery of life in caves, different pioneering authors similarly recognized the great potential of these peculiar habitats as biological model systems. In their 1969 paper in Science, ‘The cave environment’, Poulson and White discussed how caves can be used as natural laboratories in which to study the underlying principles governing the dynamics of more complex environments. Together with other seminal syntheses published at the time, this work contributed to establishing the conceptual foundation for expanding the scope and relevance of cave‐based studies. Fifty years after, the aim of this review is to show why and how caves and other subterranean habitats can be used as eco‐evolutionary laboratories. Recent advances and directions in different areas are provided, encompassing community ecology, trophic‐webs and ecological networks, conservation biology, macroecology, and climate change biology. Special emphasis is given to discuss how caves are only part of the extended network of fissures and cracks that permeate most substrates, and thus their ecological role as habitat islands is critically discussed. Numerous studies have quantified the relative contribution of abiotic, biotic and historical factors in driving species distributions and community turnovers in space and time, from local to regional scales. Conversely, knowledge of macroecological patterns of subterranean organisms at a global scale remains largely elusive, due to major geographical and taxonomical biases. Also, knowledge regarding subterranean trophic webs and the effect of anthropogenic climate change on deep subterranean ecosystems is still limited. In these research fields, the extensive use of novel molecular and statistical tools may hold promise for quickly producing relevant information not accessible hitherto.
It is well known that extremely cold environments have significant impacts on the ecology, metabolism, and evolution of psychrophilic organisms. However, the relationship between metabolic and biomineralogical processes is not understood. In this chapter, we examine the biomineralization and diversity of selected prokaryotic and eukaryotic psychrophiles. We focus attention on biosilicification (in diatoms, silicoflagellates, radiolarians, sponges) and biocalcification (in bacteria, foraminiferans, sponges, bryozoans, corals, molluscs, echinoderms, crustaceans) as well as pay special attention to the biology and adaptation mechanisms of icefish species. Additionally, we present a wealth of information on references related to the topic that may be a time-saving resource for experts in materials science who are looking for model or key organisms as sources for special scientific and technological inspiration.
A model organism’s value depends on its biological and epistemological contexts. The biological context of a model species comprises all aspects of its environment in the research setting that may influence its biological characteristics. In contrast, the epistemological context is not a matter of the organism’s surroundings, but rather of what question it is supposed to help answer, and the assumptions about its “representativeness” that warrant broader application of results from a unique model. The biological context for model organisms in research is highly controlled and standardized. This strategy has often been productive; however, it risks eliminating essential environmental information and biological mechanisms, including organism-environment interactions that help shape phenotypes. Considering biological context helps us avoid experimental designs that simplify potentially important dimensions out of existence. Clarifying the epistemological context, from background assumptions to the ultimate goal of the research, lets us assess how the research approach we choose—such as employing a particular model—may constrain the range or utility of possible answers. Looking at models in context can enrich understanding of both the history and the practice of biology: how models are selected and evolve to fit questions, and how they in turn influence the direction of future work.
The emerging field of ecological genomics promises to bring about a marriage between ecological and laboratory-based, genomic investigations. In this paper, I will reflect on this promise by exploring how ecology and genomics are integrated in the two approaches that currently dominate this field: the organism-centred approach, focusing on individual (model) organisms, and the metagenomic approach, concentrating on (the metagenome of) entire microbial communities composed of a variety of species. I will show that both approaches have already taken some important steps in bridging the gap between genomics and ecology. Since the introduction of next-generation sequencing methodology in 2007, the organism-centred approach does not need to stick to classical model organisms like Arabidopsis anymore. Instead, it is now able to apply genomic tools to ecologically interesting species (e.g. amphibians, reptiles, birds) as well. The metagenomic approach has been able to give ecology a more prominent place in its investigations, in another way. Contrary to classical microbiology (the field from which it originates), it does not study microbial communities under controlled laboratory settings, but under nature's own conditions. However, in the marriage between genomics and ecology, genomics still appears to be the dominant partner, especially in the case of the organism-centred approach that continues to study the new ecological models in artificial lab environments. Moreover, the organism-centred and metagenomic approaches employ a gene-centred perspective in understanding critical ecological interactions, thus strengthening a reductionist rather than a holistic (systems-oriented) approach.
Although model systems are useful in entomology, allowing generalizations based on a few well-known species, they also have drawbacks. It can be difficult to know how far to generalize from information in a few species: Are all flies like Drosophila? The use of model systems is particularly problematic in studying sexual selection, where variability among taxa is key to the evolution of different behaviors. A bias toward the use of a few insect species, particularly from the genus Drosophila, is evident in the sexual selection and sexual conflict literature over the past several decades, although the diversity of study organisms has increased more recently. As the number of model systems used to study sexual conflict increased, support for the idea that sexual interactions resulted in harm to females decreased. Future work should choose model systems thoughtfully, combining well-known species with those that can add to the variation that allows us to make more meaningful generalizations. Expected final online publication date for the Annual Review of Entomology Volume 59 is January 07, 2014. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.
The nematode Caenorhabditis elegans has been used to study genetics and development since the mid-1970s. Over the years, the arsenal of techniques employed in this field has grown steadily in parallel with the number of researchers using this model. Since the introduction of C. elegans transgenesis, nearly 20 years ago, this system has been extensively used in areas such as rescue experiments, gene expression studies, and protein localization. The completion of the C. elegans genome sequence paved the way for genome-wide studies requiring higher throughput and improved scalability than provided by traditional genetic markers. The development of antibiotic selection systems for nematode transgenesis addresses these requirements and opens the possibility to apply transgenesis to investigate biological functions in other nematode species for which no genetic markers had been developed to date.
The genetic basis of vertebrate morphological evolution has traditionally been very difficult to examine in naturally occurring populations. Here we describe the generation of a genome-wide linkage map to allow quantitative trait analysis of evolutionarily derived morphologies in the Mexican cave tetra, a species that has, in a series of independent caves, repeatedly evolved specialized characteristics adapted to a unique and well-studied ecological environment. We focused on the trait of albinism and discovered that it is linked to Oca2, a known pigmentation gene, in two cave populations. We found different deletions in Oca2 in each population and, using a cell-based assay, showed that both cause loss of function of the corresponding protein, OCA2. Thus, the two cave populations evolved albinism independently, through similar mutational events.
A classic textbook example of adaptive radiation under natural selection is the evolution of 14 closely related species of Darwin's finches (Fringillidae, Passeriformes), whose primary diversity lies in the size and shape of their beaks. Thus, ground finches have deep and wide beaks, cactus finches have long and pointed beaks (low depth and narrower width), and warbler finches have slender and pointed beaks, reflecting differences in their respective diets. Previous work has shown that even small differences in any of the three major dimensions (depth, width and length) of the beak have major consequences for the overall fitness of the birds. Recently we used a candidate gene approach to explain one pathway involved in Darwin's finch beak morphogenesis. However, this type of analysis is limited to molecules with a known association with craniofacial and/or skeletogenic development. Here we use a less constrained, complementary DNA microarray analysis of the transcripts expressed in the beak primordia to find previously unknown genes and pathways whose expression correlates with specific beak morphologies. We show that calmodulin (CaM), a molecule involved in mediating Ca2+ signalling, is expressed at higher levels in the long and pointed beaks of cactus finches than in more robust beak types of other species. We validated this observation with in situ hybridizations. When this upregulation of the CaM-dependent pathway is artificially replicated in the chick frontonasal prominence, it causes an elongation of the upper beak, recapitulating the beak morphology of the cactus finches. Our results indicate that local upregulation of the CaM-dependent pathway is likely to have been a component of the evolution of Darwin's finch species with elongated beak morphology and provide a mechanistic explanation for the independence of beak evolution along different axes. More generally, our results implicate the CaM-dependent pathway in the developmental regulation of craniofacial skeletal structures.
Although induced mutations in traditional laboratory animals have been valuable as models for human diseases, they have some important limitations. Here, we propose a complementary approach to discover genes and mechanisms that might contribute to human disorders: the analysis of evolutionary mutant models in which adaptive phenotypes mimic maladaptive human diseases. If the type and mode of action of mutations favored by natural selection in wild populations are similar to those that contribute to human diseases, then studies in evolutionary mutant models have the potential to identify novel genetic factors and gene-by-environment interactions that affect human health and underlie human disease.
Cataracts, the loss of lens transparency, are the leading cause of human blindness. The zebrafish embryo, with its transparency and relatively large eyes, is an excellent model for studying ocular disease in vivo. We found that the zebrafish cloche mutant, both the cloche(m39) and cloche(S5) alleles, which have defects in hematopoiesis and blood vessel development, also have lens cataracts. Quantitative examination of the living zebrafish lens by confocal microscopy showed significant increases in lens reflectance. Histological analysis revealed retention of lens fiber cell nuclei owing to impeded terminal differentiation. Proteomics identified gamma-crystallin as a protein that was substantially diminished in cloche mutants. Crystallins are the major structural proteins in mouse, human and zebrafish lens. Defects in crystallins have previously been shown in mice and humans to contribute to cataracts. The loss of gamma-crystallin protein in cloche was not due to lowered mRNA levels but rather to gamma-crystallin protein insolubility. AlphaA-crystallin is a chaperone that protects proteins from misfolding and becoming insoluble. The cloche lens is deficient in both alphaA-crystallin mRNA and protein during development from 2-5 dpf. Overexpression of exogenous alphaA-crystallin rescued the cloche lens phenotype, including solubilization of gamma-crystallin, increased lens transparency and induction of lens fiber cell differentiation. Taken together, these results indicate that alphaA-crystallin expression is required for normal lens development and demonstrate that cataract formation can be prevented in vivo. In addition, these results show that proteomics is a valuable tool for detecting protein alterations in zebrafish.
Twenty-nine populations of the blind cavefish, Astyanax mexicanus, are known from different caves in North-Eastern Mexico (Figure 1). They evolved from eyed, surface-dwelling forms which only reached the area in the mid-Pleistocene [1]. Quantitative genetic analyses have shown that the evolutionary impairment of eye development - as well as the loss of pigmentation and other cave-related changes - results from mutations at multiple gene sites ('eye loci') [2,3]. Eye loss has evolved independently at least three times [4,5] and at least some of the eye loci involved differ between the different cave populations [3]. Hybrids between blind cavefish from different caves have larger and better developed eye rudiments than their parents (Figure 2) [6], reflecting these independent origins and complementation [3,7,8]. Given the large number of mutations at different loci that have accumulated in these populations, we reasoned that hybridization among independently evolved populations might restore visual function. Here we demonstrate restoration of vision in cavefish whose immediate ancestors were blind and whose separate lineages may not have been exposed to light for the last one million years.
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