Use Of Model Organisms Research Articles

The hematopoietic stem cell in its place

A signature characteristic of stem cells is their ability to self-renew, affording a theoretically limitless ability to produce daughter cells and their descendents. This near-timeless dimension of stem cell function is not free of the constraints of place. The idea that highly specialized 'microenvironmental' cues participate in the regulation of stem cells has evidence in classic embryology and more recently in adult stem cells through the use of model organisms. There is now ample evidence that an anatomically defined, specifically constituted place represents the niche for hematopoietic and other tissue-specific stem cells. This review provides a conceptual framework and detailed account of the hematopoietic stem cell niche as defined at present. The components are assembling into a more complex view of the niche and may now be amenable to examination as a system and possibly to alteration to affect outcomes in immune regeneration.

Rules for the use of model organisms in antiaging pharmacology

The use of animal models for initially screening anti-aging drugs is a promising approach for drug discovery. However, there a number of potential artifacts, confounds and errors that can arise in such research programs. The following rules are intended to minimize such problems: (1) since aging occupies an increasing proportion of human adulthood, data that conflate aging and late life should not be extrapolated to human aging; (2) the response to candidate medications should show a normal dose-response pattern, although not necessarily a linear response; (3) medicated animal models should not be hypometabolic; (4) medicated animal models should not show pronounced reductions in fertility; (5) medicated animal models should not exhibit general nervous system depression; (6) the effect of the medication should not be highly sensitive to the culture environment; (7) the effect of the medication should not be highly dependent on the genetic ancestry of the stock employed, leaving aside inbreeding, which should be avoided because humans are not generally inbred. While these rules do not guarantee successful extrapolation of successful drug results from the animal model to humans in a clinical setting, the failure to adhere to these rules should raise doubts about such extrapolation.

SPRY1 Is a Negative Regulator of Long-Term In Vivo Engraftment and Ex Vivo Expansion of Primitive Human Umbilical Cord Blood Cells.

Hematopoietic stem cells (HSCs) are functionally defined by their capacity to home to the bone marrow microenvironment, proliferate and differentiate to restore normal hematopoiesis in a myeloablated recipient; however, the molecular determinants of these processes are not well understood. By comparing the gene expression profiles of highly purified human HSC-enriched and HSC-depleted cell populations, and subsequently validating the hematopoietic function of a subset of these differentially expressed genes using zebrafish (Danio rerio), we previously identified human Sprouty 1 (SPRY1), an evolutionarily conserved antagonist of RTK signaling, as a potential regulator of mammalian HSC development and/or cell-fate decisions. To directly assess the role of SPRY1 in mammalian HSC and hematopoietic progenitor cell (HPC) function, we constructed a dual-promoter lentiviral vector to co-express SPRY1 and green fluorescent protein (GFP) (SPRY1-LV) and a control lentiviral vector to express GFP alone (GFP-LV) in the CD34+ fraction of human umbilical cord blood (UCB). While the enforced expression of SPRY1 in CD34+ UCB cells had no effect on the frequency or morphology of colonies generated in short-term in vitro colony-forming cell (CFC) assays (SPRY1-LV = 27.6 ± 12.3% and GFP-LV = 28.4 ± 20.0%; n = 3), it profoundly inhibited the capacity of UCB CD34+ cells to engraft in the bone marrow NOD-SCID mice in vivo. The estimated frequency of week 11 SCID-repopulating cells (SRC) (± 1 standard error) for SPRY1-LV (n = 13 mice) and GFP-LV (n = 15 mice) cells was 1 in 12,678 cells (6,167 – 26,064) and 1 in 3,412 cells (2,272 – 5,124), respectively, as determined using limiting dilution conditions and Poisson statistics. Furthermore, in 14 day cultures designed for the ex vivo expansion and/or maintenance of primitive hematopoietic cells, ectopic expression of SPRY1 in CD34+ UCB cells dramatically inhibited the expansion of total nucleated cells (SPRY1-LV = 37.9 ± 10.1 fold; GFP-LV = 71.1 ± 5.8 fold; n = 3; p<0.05) and CFCs (SPRY1-LV = 5.7 ± 1.2 fold; GFP-LV = 20.8 ± 14.9 fold; n = 3), although it had no effect on expansion of CD34+CD38− cells. We are currently investigating potential mechanisms for the observed affects of SPRY1 on primitive hematopoietic cells, paying particular attention to the possible effects of SPRY1 expression on “early-acting” hematopoietic cytokines and growth factors that activate RTKs - including FGF1, FGF2, VEGF, SCF, FLT3L, and ANGPT1. In conclusion, enforced expression of SPRY1 negatively regulates primitive hematopoietic cell engraftment in vivo and expansion in vitro, thereby presenting the first example of a role for a Sprouty family member, SPRY1, in primitive human hematopoietic cell function. Moreover, this data further validates the use of model organisms, such as zebrafish, for evaluating the functional roles of transcripts identified in large-scale gene expression profiling experiments in mice and humans.

Metabolism, ubiquinone synthesis, and longevity

Until recently, the mechanisms that control the aging process were thought to be immensely complex and nearly impossible to dissect at the molecular level. However, genetic analysis, primarily in model organisms such as yeast, worms, and flies, is dramatically changing this view. It seems that at least three distinct genetic networks control the aging process. These networks include the insulin/IGF-1 signaling pathway, signaling that arises from the mitochondrial electron transport chain, and finally, mechanisms that govern the response to dietary restriction. The use of invertebrates as model organisms to study aging has been extensive, since the ease of genetic manipulation and short life span give them desirable characteristics. However, the question often remains as to whether we can draw the same conclusions in higher organisms. Some of the life-lengthening pathways discovered in invertebrates (i.e., knocking down insulin/IGF-1 signaling) are conserved in mammals; however, distinguishing between species-specific models of aging and universal processes remains a major challenge in the field. Indeed, the conservation of such processes is key to the validation of the use of model organisms to study the aging process. Hekimi and colleagues (Liu et al. 2005) in this issue of Genes and Development substantiates the use of the round worm, Caenorhabditis elegans, as an excellent model for the study of the role of mitochondria in the aging process of mammals.

Genetic analysis of myosin II assembly and organization in model organisms.

Myosins are a large family of actin-based motor proteins that are involved in a variety of cellular processes. Class II, or conventional, myosins are organized into a number of multi-component structures such as muscle thick filaments, non-muscle filaments and the actomyosin ring during cell division. A number of conditions must be met for the proper assembly and organization of myosin II-containing structures, including the correct stoichiometry of myosin and its associated proteins, and the conformation and regulation of the myosin molecule itself by molecular chaperones and protein kinases. In this review we discuss the use of model organisms in the genetic analysis of the assembly and organization of myosin-containing structures.

Selecting representative model micro-organisms

BackgroundMicro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.ResultsWe develop the Best Total Coverage (BTC) method for selecting one or more representative model organisms from a group of interest, given that rough genetic distances between the members of the group are known. Software implementing a "greedy" version of the method can be used with large data sets, its effectiveness is tested using both constructed and biological data sets.ConclusionIn both the simulated and biological examples the greedy-BTC method outperformed random selection of model organisms, and for two biological examples it outperformed selection of model strains based on phylogenetic structure. Although the method was designed with microbial species in mind, and is tested here on three microbial data sets, it will also be applicable to other types of organism.

Molecular genetics of behaviour: research strategies and perspectives for animal production

Genetic factors are undoubtedly involved in inter-individual variability of the behaviours that may be important for livestock production, as shown by pedigree studies, comparison of genetic stocks raised in the same environment, and selection experiments. The knowledge of gene polymorphisms responsible for genetic variability would increase the efficiency of selection, as shown for instance by the identification of the ryanodine receptor gene that harbours the mutations responsible for the porcine stress syndrome, that allows the eradication of the susceptibility allele. One strategy is to screen systematically the genes that are known to be involved in regulation of behaviour (functional candidate genes). This strategy is however very difficult for most behavioural traits, since behaviour is an emerging function from the whole brain/body and the molecular pathways involved in genetic variability are very poorly understood. Another strategy is to investigate linkage between trait variation and genetic markers in a segregating population (usually an intercross or backcross between two strains or breeds contrasting for the trait under study). It allows the detection of genomic regions influencing that trait (quantitative trait loci or QTL), and further investigation aims at the identification of the gene(s) located in each of these regions and the molecular polymorphisms involved in phenotypic variation. Although many QTL have been published for behavioural traits in experimental animals, very few examples are available where strong candidate genes have been identified. Further progress will be very much dependent upon the careful definition of behavioural traits to be studied (including their importance for animal production), on the reliability of their measurement in a large number of animals and on the efficient mastering of environmental factors of variability. The fast increase in the knowledge of genome sequence in several species will undoubtedly facilitate the application to farm animal species of the knowledge obtained in model organisms, as well as the use of model organisms to explore candidate genes detected by QTL studies in farm animals.

Selected contribution: long-lived Drosophila melanogaster lines exhibit normal metabolic rates.

The use of model organisms, such as Drosophila melanogaster, provides a powerful method for studying mechanisms of aging. Here we report on a large set of recombinant inbred (RI) D. melanogaster lines that exhibit approximately a fivefold range of average adult longevities. Understanding the factors responsible for the differences in longevity, particularly the characteristics of the longest-lived lines, can provide fundamental insights into the mechanistic correlates of aging. In ectothermic organisms, longevity is often inversely correlated with metabolic rate, suggesting the a priori hypothesis that long-lived lines will have low resting metabolic rates. We conducted approximately 6000 measurements of CO2 production in individual male flies aged 5, 16, 29, and 47 days postemergence and simultaneously measured the weight of individual flies and life spans in populations of each line. Even though there was a wide range of longevities, there was no evidence of an inverse relationship between the variables. The increased longevity of long-lived lines is not mediated through reduction of metabolic activity. In Drosophila, it is possible to both maintain a normal metabolic rate and achieve long life. These results are evaluated in the context of 100 years of research on the relationship between metabolic rate and life span.

DiGeorge syndrome: the use of model organisms to dissect complex genetics.

The research interest in DiGeorge syndrome (DGS) is partly due to its clinical importance. However, fundamental questions of genetics and developmental biology related to DGS are inspiring investigators to experiment with model systems. Most DGS cases are caused by a heterozygous chromosomal deletion del22q11, and the search for haploinsufficient genes has been successful in mice and led to the discovery of Tbx1 as a major player in the development of the pharyngeal arches and pouches. Whether TBX1 is haploinsufficient in humans, as several other T-box genes are, is yet to be proven. The puzzling clinical variability in patients with del22q11 is also being addressed in model organisms. Consistent with clinical data, experiments in mice indicate that genetics can only explain part of the phenotypic variability. The recent identification of phenotypic modifiers further underscores the complex genetics of this syndrome.

Metabolism and aging in the nematode Caenorhabditis elegans1,2

Research into the causes of aging has greatly increased in recent years. Much of this interest is due to the discovery of genes in a variety of model organisms that appear to modulate aging. Studies of long-lived mutants can potentially provide valuable insights into the fundamental mechanisms of aging. While there are many advantages to the use of model organisms to study aging it is also important to consider the limitations of these systems, particularly because ectothermic (poikilothermic) organisms can survive a far greater metabolic depression than humans. As such, the consideration of only chronological longevity when assaying for long-lived mutants provides a limited perspective on the mechanisms by which longevity is increased. Additional physiological processes, such as metabolic rate, must also be assayed to provide true insight into the aging process. This is especially true in the nematode Caenorhabditis elegans, which has the natural ability to enter into a metabolically reduced state in which it can survive many times longer than its normal lifetime. The extended longevity of at least some long-lived C. elegans mutants may be due to a reduction in metabolic rate, rather than an alteration of a metabolically independent genetic mechanism specific for aging.

Simpson Golabi Behmel Syndrome: Progress toward Understanding the Molecular Basis for Overgrowth, Malformation, and Cancer Predisposition

Simpson Golabi Behmel syndrome (SGBS) is a complex congenital overgrowth syndrome with features that include macroglossia, macrosomia, and renal and skeletal abnormalities as well as an increased risk of embryonal cancers. Most cases of SGBS appear to arise as a result of either deletions or point mutations within the glypican-3 (GPC3) gene at Xq26, one member of a multigene family encoding for at least six distinct glycosylphophatidylinositol-linked cell surface heparan sulfate proteoglycans. As a class of molecules, heparan sulfate proteoglycans have been found to play essential roles in development by modulating cellular responses to growth factors and morphogens. Specifically, mutations in both the murine GPC3 gene and the Drosophila glypican, dally, have been found to modify cellular responses to bone morphogenetic proteins, providing important clues to the molecular basis of SGBS in humans. Despite these advances, there remains a paucity of information about the natural history of SGBS and optimal medical management strategies, and whether select mutations influence the SGBS phenotype and risk of cancer. To this end, an International SGBS Registry has been created and is being maintained to improve the clinical care and understanding of the pathogenesis of SGBS. Using an integrated approach employing epidemiology, molecular genetic characterization of specific GPC3 mutations, and the use of model organisms should rapidly expand the understanding of this complex disorder.

Effects of Cu2+, Ni2+, Pb2+, Zn2+ and pentachlorophenol on photosynthesis and motility in Chlamydomonas reinhardtii in short-term exposure experiments

BackgroundHeavy metals, especially copper, nickel, lead and zinc, have adverse effects on terrestrial and in aquatic environments. However, their impact can vary depending on the nature of organisms. Taking into account the ability of heavy metals to accumulate in sediments, extended knowledge of their effects on aquatic biota is needed. In this context the use of model organisms (often unicellular), which allows for rapid assessment of pollutants in freshwater, can be of advantage. Pentachlorophenol has been extensively used for decades as a bleaching agent by pulp- and paper industry. Pentachlorophenol tends to accumulate in the nature. We aim to determine if photosynthesis and motility can be used as sensitive physiological parameters in toxicological studies of Chlamydomonas reinhardtii, a motile green unicellular alga. It is discussed if photosynthesis and motility can be used as sensitive physiological parameters in toxicological studies.ResultsThe concentrations studied ranged from 0.1 to 2.0 mg l-1 for copper, nickel, lead and zinc, and from 0.1 to 10.0 mg l-1 for pentachlorophenol. Exposure time was set to 24 h. Copper and pentachlorophenol turned out to be especially toxic for photosynthetic efficiency (PE) in C. reinhardtii.ConclusionCopper and pentachlorophenol turned out to be especially toxic for PE in C. reinhardtii. Zinc has been concluded to be moderately toxic while nickel and lead had stimulatory effects on the PE. Because of high variance, motility was not considered a reliable physiological parameter when assessing toxicity of the substances using C. reinhardtii.

Perspectives on Oxygen Sensing

Perspectives on Oxygen Sensing