Clonal crayfish as biological model: a review on marbled crayfish

Since the mid-twentieth century, numerous vertebrates and invertebrates have been used as model organisms and become indispensable tools for exploring a broad range of biological and ecological processes. Crayfish seem to be adequate models which resulted in their involvement in research. In the two decades since its discovery, ongoing research has confirmed that the marbled crayfish (Procambarus virginalis Lyko, 2017) is an ideal taxon in this regard, especially due to its almost continuous asexual reproduction providing a source of genetically identical offspring. This review provides an overview of the occurrence, biology, ecology, ethology, and human exploitation of marbled crayfish with primary focus on its use as a laboratory model organism as well as potential risks to native biota in case of its introduction. Genetic uniformity, ease of culture, and a broad behaviour repertoire fosters the use of marbled crayfish in epigenetics and developmental biology, as well as physiological, ecotoxicological, and ethological research. Marbled crayfish could be further exploited for basic and applied fields of science such as evolutionary biology and clonal tumour evolution. However, due to its high invasive potential in freshwater environments security measures must be taken to prevent its escape into the wild.     

Echinococcus as a model system: biology and epidemiology

The introduction of Echinococcus to Australia over 200 years ago and its establishment in sheep rearing areas of the country inflicted a serious medical and economic burden on the country. This resulted in an investment in both basic and applied research aimed at learning more about the biology and life cycle of Echinococcus. This research served to illustrate the uniqueness of the parasite in terms of developmental biology and ecology, and the value of Echinococcus as a model system in a broad range of research, from fundamental biology to theoretical control systems. These studies formed the foundation for an international, diverse and ongoing research effort on the hydatid organisms encompassing stem cell biology, gene regulation, strain variation, wildlife diseases and models of transmission dynamics. We describe the development, nature and diversity of this research, and how it was initiated in Australia but subsequently has stimulated much international and collaborative research on Echinococcus.     

New data and collaborations at the Saccharomyces Genome Database: updated reference genome,alleles, and the Alliance of Genome Resources

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.     

Expanding our scientific horizons: utilization of unique model organisms in biological research

During the past century, research studies using animal models have contributed to numerous scientific discoveries and have been vital for the understanding of numerous biological processes, including disease. Over the past decades, the scientific community has defined a small number of model organisms that includes a few mammals, fish (mainly zebrafish), birds (mainly chicken), frogs, flies, and nematodes. Rodents are by far the most commonly employed laboratory animals in biomedical research. Mice share many biological similarities to humans and can be genetically manipulated to express mutations linked to human diseases. Mice and rats reproduce relatively quickly and have a short life span, which allows scientists to study progressive disorders, including aging. A large range of inbred mice strains enables accurate and reproducible experiments by decreasing the variability often associated with animal models and biological systems in general. Finally, mice are cost‐effective, small, and relatively easy to handle, transport, and house. All of these advantages combine to make mice the major species for recapitulating and studying human diseases. However, focusing exclusively on one or very few animal models may lead researchers to lose sight of other species with vastly different biology that might inform and affect our understanding of disease pathogenesis.     

The mouse as a model for investigation of human granulocytic ehrlichiosis: current knowledge and future directions

The use of laboratory mice to investigate correlates of infectious disease, including infection kinetics, cellular alterations, cytokine profiles, and immune response in the context of an intact host has expanded exponentially in the last decade. A marked increase in the availability of transgenic mice and research tools developed specifically for the mouse parallels and enhances this research. Human granulocytic ehrlichiosis (HGE) is an emerging, zoonotic disease caused by tick-borne bacteria. The HGE agent (Anaplasma phagocytophila) is one of two recognized pathogens to cause human granulocytic ehrlichiosis (HGE). The mouse model of HGE complements in vitro tissue culture studies, limited in vivo large animal studies, and ex vivo studies of human and ruminant neutrophils, and promises new avenues to approach mechanisms of disease. In the overview reported here, we focus principally on current research into HGE pathogenesis using the mouse model. Included is a discussion of current changes in ehrlichial classification and nomenclature, a review of ehrlichial biology and ecology, and highlights of clinical disease in animals and people.     

New tricks for an old-favorite model

A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009.The international yeast meetings are highly interactive conferences attracting scientists from diverse disciplines of fungal research. The 24th yeast meeting held in the University of Manchester presented recent advances ranging from basic cell biology to the use of yeast for industrial purposes and translational research. Here, I summarize a few highlights related to systems and synthetic biology, yeasts as model organisms in gene expression, aging and human disease studies and the use of yeast cells as factories.     

Model organisms in molecular nutrition research

The complexity of food organism interactions necessitates the use of model organisms to understand physiological and pathological processes. In nutrition research, model organisms were initially used to understand how macro and micronutrients are handled in the organism. Currently, in nutritional systems biology, models of increasing complexity are needed in order to determine the global organisation of a biological system and the interaction with food and food components. Originally driven by genetics, certain model organisms have become most prominent. Model organisms are more accessible systems than human beings and include bacteria, yeast, flies, worms, and mammals such as mice. Here, the origin and the reasons to become the most prominent models are presented. Moreover, their applicability in molecular nutrition research is illustrated with selected examples.     

Mouse models in neurological disorders: Applications of non-invasive imaging

Neuroimaging techniques represent powerful tools to assess disease-specific cellular, biochemical and molecular processes non-invasively in vivo. Besides providing precise anatomical localisation and quantification, the most exciting advantage of non-invasive imaging techniques is the opportunity to investigate the spatial and temporal dynamics of disease-specific functional and molecular events longitudinally in intact living organisms, so called molecular imaging (MI). Combining neuroimaging technologies with in vivo models of neurological disorders provides unique opportunities to understand the aetiology and pathophysiology of human neurological disorders. In this way, neuroimaging in mouse models of neurological disorders not only can be used for phenotyping specific diseases and monitoring disease progression but also plays an essential role in the development and evaluation of disease-specific treatment approaches. In this way MI is a key technology in translational research, helping to design improved disease models as well as experimental treatment protocols that may afterwards be implemented into clinical routine. The most widely used imaging modalities in animal models to assess in vivo anatomical, functional and molecular events are positron emission tomography (PET), magnetic resonance imaging (MRI) and optical imaging (OI). Here, we review the application of neuroimaging in mouse models of neurodegeneration (Parkinson's disease, PD, and Alzheimer's disease, AD) and brain cancer (glioma).     

生命科学与人类疾病研究的重要模型——果蝇

黑腹果蝇(Drosophilamelanogaster)是生物学研究中最重要的模式生物之一,它在遗传的染色体理论建立中起到非常重要的作用。由于果蝇自身独特的优势,20世纪70年代以来,它又在发育生物学、神经科学、人类疾病研究等领域得到广泛应用,作出许多新的重要贡献。果蝇在神经退行性疾病研究中是非常有用的模型。可以预期,随着研究手段的丰富及科学的发展,果蝇将作为一种理想的模式生物在生物医学中发挥更大的作用。     

Bibliometric analysis of personalized humanized mouse and Drosophila models for effective combinational therapy in cancer patients

Research performed using model organisms such as mice and the fruit fly, Drosophila melanogaster has significantly enhanced our knowledge about cancer biology and the fundamental processes of cancer. This is because the major biological properties and genes associated with cancer including signaling pathways, oncogenes, tumor suppressors, and other regulators of cell growth and proliferation are evolutionary conserved. This review provides bibliometric analysis of research productivity, and performance of authors, institutions, countries, and journals associated with personalized animal cancer models, focussing on the role of Drosophila in cancer research, thus highlighting emerging trends in the field. A total of 1469 and 2672 original articles and reviews for Drosophila cancer model and patient-derived xenograft (PDX) respectively, were retrieved from the Scopus database and the most cited papers were thoroughly analyzed. Our analysis indicates a steadily increasing productivity of the animal models and especially of mouse models in cancer research. In addition to the many different systems that address almost all aspects of tumor research in humanized animal models, a trend towards using tailored screening platforms with Drosophila models in particular will become widespread in the future. Having Drosophila models that recapitulate major genetic aspects of a given tumor will enable the development and validation of novel therapeutic strategies for specific cancers, and provide a platform for screening small molecule inhibitors and other anti-tumor compounds. The combination of Drosophila cancer models and mouse PDX models particularly is highly promising and should be one of the major research strategies the future.     

Patient-derived model systems and the development of next-generation anticancer therapeutics

Anticancer drug discovery and development using conventional cell line and animal models has traditionally had a low overall success rate. Despite yielding game-changing new therapeutics, 10–20 new molecules have to be brought to the clinic to obtain one new approval, making this approach costly and inefficient. The use of in vitro experimental models based on primary human tumour tissues has the potential to provide a representation of human cancer biology that is closer to an actual patient and to ‘bridge the translational gap’ between preclinical and clinical research. Here, we review recent advances in the use of human tumour samples for preclinical research through organoid development or as primary patient materials. While challenges still remain regarding analysis, validation and scalability, evidence is mounting for the applicability of both models as preclinical research tools.     

The mouse as a model for human biology: a resource guide for complex trait analysis

The mouse has been a powerful force in elucidating the genetic basis of human physiology and pathophysiology. From its beginnings as the model organism for cancer research and transplantation biology to the present, when dissection of the genetic basis of complex disease is at the forefront of genomics research, an enormous and remarkable mouse resource infrastructure has accumulated. This review summarizes those resources and provides practical guidelines for their use, particularly in the analysis of quantitative traits.     

Zebrafish information network,the knowledgebase for Danio rerio research

The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.     

Mouse models of neurological disorders—A comparison of heritable and acquired traits

Human neurological disorders include a wide range of illnesses which have a disproportionately high prevalence in the increasingly populous geriatric community. Any research effort directed at discovering the aetiology of neurological disease is greatly enhanced with in vivo models of the disease of interest. Scientific research incorporating the use of mice has advanced rapidly in the last three decades. Relatively simple to breed, maintain and train, mice have many advantages over other species for use in research. More than a century of selective breeding has provided investigators with a rich gene pool and sub-strain diversity from which to choose for their research. Thus the dramatic increase in genetic screening and gene engineering that has occurred in research in recent decades has enabled the generation of a multitude of mouse models. This review discusses the relative utility of mouse models in which a heritable or non-heritable (acquired) manipulation has been used to model a specified trait of a human neurological disorder. The techniques used in deriving useful genetic alterations or modifications and in generating acquired mouse models are outlined with examples of each provided.     

A call to fins! Zebrafish as a gerontological model

Among the wide variety of model organisms commonly used for studies on aging, such as worms, flies and rodents, a wide research gap exists between the invertebrate and vertebrate model systems. In developmental biology, a similar gap has been filled by the zebrafish (Danio rerio). We propose that the zebrafish is uniquely suited to serve as a bridge model for gerontology. With high fecundity and economical husbandry requirements, large populations of zebrafish may be generated quickly and cheaply, facilitating large-scale approaches including demographic studies and mutagenesis screens. A variety of mutants identified in such screens have led to modelling of human disease, including cardiac disorders and cancer. While zebrafish longevity is at least 50% longer than in commonly used mouse strains, as an ectothermic fish species, its life span may be readily modulated by caloric intake, ambient temperature and reproductive activity. These features, coupled with a growing abundance of biological resources, including an ongoing genome sequencing project, make the zebrafish a compelling model organism for studies on aging.     

MouseCyc: a curated biochemical pathways database for the laboratory mouse

Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc . MouseCyc has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human.     

Fish as model systems for the study of vertebrate apoptosis

Apoptosis is a process of pivotal importance for multi-cellular organisms and due to its implication in the development of cancer and degenerative disease it is intensively studied in humans and mammalian model systems. Invertebrate models of apoptosis have been well-studied, especially in C. elegans and D. melanogaster, but as these are evolutionarily distant from mammals the relevance of findings for human research is sometimes limited. Presently, a non-mammalian vertebrate model for studying apoptosis is missing. However, in the past few years an increasing number of studies on cell death in fish have been published and thus new model systems may emerge. This review aims at highlighting the most important of these findings, showing similarities and dissimilarities between fish and mammals, and will suggest topics for future research. In addition, the outstanding usefulness of fish as research models will be pointed out, hoping to spark future research on this exciting, often underrated group of vertebrates.     

Re-thinking organisms: The impact of databases on model organism biology

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.