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Model Organisms (model + organism)
Kinds of Model Organisms Selected AbstractsPROPOSAL OF ECTOCARPUS SILICULOSUS (ECTOCARPALES, PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS,JOURNAL OF PHYCOLOGY, Issue 6 2004Akira F. Peters The emergence of model organisms that permit the application of a powerful combination of genomic and genetic approaches has been a major factor underlying the advances that have been made in the past decade in dissecting the molecular basis of a wide range of biological processes. However, the phylogenetic distance separating marine macroalgae from these model organisms, which are mostly from the animal, fungi, and higher plant lineages, limits the latters' applicability to problems specific to macroalgal biology. There is therefore a pressing need to develop similar models for the macroalgae. Here we describe a survey of potential model brown algae in which particular attention was paid to characteristics associated with a strong potential for genomic and genetic analysis, such as a small nuclear genome size, sexuality, and a short life cycle. Flow cytometry of nuclei isolated from zoids showed that species from the Ectocarpales possess smaller haploid genomes (127,290 Mbp) than current models among the Laminariales (580,720 Mbp) and Fucales (1095,1271 Mbp). Species of the Ectocarpales may complete their life histories in as little as 6 weeks in laboratory culture and are amenable to genetic analyses. Based on this study, we propose Ectocarpus siliculosus (Dillwyn) Lyngbye as an optimal choice for a general model organism for the molecular genetics of the brown algae. [source] Evolution of Ecological and Behavioural Diversity: Australian Acacia Thrips as Model OrganismsAUSTRALIAN JOURNAL OF ENTOMOLOGY, Issue 2 2005Myron P Zalucki No abstract is available for this article. [source] Fish proteome analysis: Model organisms and non-sequenced speciesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2010Ignasi Forné Abstract In the last decade, proteomic technologies have been increasingly used in fish biology research. Proteomics has been applied primarily to investigate the physiology, development biology and the impact of contaminants in fish model organisms, such as zebrafish (Danio rerio), as well as in some commercial species produced in aquaculture, mainly salmonids and cyprinids. However, the lack of previous genetic information on most fish species has been a major drawback for a more general application of the different proteomic technologies currently available. Also, many teleosts of interest in biological research and with potential application in aquaculture hold unique physiological characteristics that cannot be directly addressed from the study of small laboratory fish models. This review describes proteomic approaches that have been used to investigate diverse biological questions in model and non-model fish species. We will also evaluate the current possibilities to integrate fish proteomics with other "omic" approaches, as well as with additional complementary techniques, in order to address the future challenges in fish biology research. [source] Dynein light chain family in Tetrahymena thermophilaCYTOSKELETON, Issue 2 2007David E. Wilkes Abstract Dyneins are large protein complexes that produce directed movement on microtubules. In situ, dyneins comprise combinations of heavy, intermediate, light-intermediate, and light chains. The light chains regulate the locations and activities of dyneins but their functions are not completely understood. We have searched the recently sequenced Tetrahymena thermophila macronuclear genome to describe the entire family of dynein light chains expressed in this organism. We identified fourteen genes encoding putative dynein light chains and seven genes encoding light chain-like proteins. RNA-directed PCR revealed that all 21 genes were expressed. Quantitative real time reverse transcription PCR showed that many of these genes were upregulated after deciliation, indicating that these proteins are present in cilia. Using the nomenclature developed in Chlamydomonas, Tetrahymena expresses two isoforms each of LC2, LC4, LC7, and Tctex1, three isoforms of p28, and six LC8/LC8-like isoforms. Tetrahymena also expresses two LC3-like genes. No Tetrahymena orthologue was found for Chlamydomonas LC5 or LC6. This study provides a complete description of the different genes and isoforms of the dynein light chains that are expressed in Tetrahymena, a model organism in which the targeted manipulation of genes is straightforward. Cell Motil. Cytoskeleton 2006. © 2006 Wiley-Liss, Inc. [source] Mutation in the abcb7 gene causes abnormal iron and fatty acid metabolism in developing medaka fishDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 9 2008Akimitsu Miyake The medaka fish (Oryzias latipes) is an emerging model organism for which a variety of unique developmental mutants have now been generated. Our recent mutagenesis screening of the medaka isolated a unique mutant that develops a fatty liver at larval stages. Positional cloning identified the responsible gene as medaka abcb7. Abcb7, a mitochondrial ABC (ATP binding cassette) half-transporter, has been implicated in iron metabolism. Recently, human Abcb7 was found to be mutated in X-linked sideroblastic anemia with cerebellar ataxia (XLSA/A). The homozygous medaka mutant exhibits abnormal iron metabolism in erythrocytes and accumulation of lipid in the liver. Microarray and in situ hybridization analyses demonstrated that the expression of genes involved in iron and lipid metabolisms are both affected in the mutant liver, suggesting novel roles of Abcb7 in the development of physiologically functional liver. The medaka abcb7 mutant thus could provide insights into the pathogenesis of XLSA/A as well as the normal function of the gene. [source] Investigations of the Morphogenesis of Filamentous Microorganisms,ENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 5 2006S. Kelly Abstract Several biotechnological production processes are based on the cultivation of filamentous microorganisms like the fungus Aspergillus niger. The morphological development plays an important role for transport phenomena and the related productivity. The description of filamentous morphogenesis of A. niger as a model organism, given here, is structured in three morphological growth processes, a very fast conidial aggregation, followed by a second slower aggregation step promoted by germination and hyphal tip growth, and the growth of pellets as the last process. [source] Drosophila melanogaster: the model organismENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 2 2006David B. Roberts Abstract In the 20th century, there were two decades during which Drosophila melanogaster was the most significant model organism and each decade led to the establishment of new scientific disciplines. The first decade was roughly from 1910 and during this period a small group at Columbia University, headed by Thomas Hunt Morgan, established the rules of transmission genetics with which we are all familiar. In the second decade, roughly from 1970, many of the principles and techniques of the earlier period were used to determine the genetic control of basic aspects of the biology of organisms, notably their development and their behaviour. In this review I will show that it was not only the genius of the research workers (five were awarded Nobel Prizes and it has been argued, with justification, that at least one more should have been awarded) but also the special features of D. melanogaster that led to these advances. While Drosophila is still a significant model organism, the advent of molecular biology permits the investigation of organisms less amenable to genetic analysis, but the principles applied in these investigations were in the main principles laid down during the earlier work on Drosophila. [source] Techniques for continuous rearing and assessing host preference of a multivoltine leaf-mining moth, Acrocercops transecta (Lepidoptera: Gracillariidae)ENTOMOLOGICAL SCIENCE, Issue 3 2005Issei OHSHIMA Abstract Techniques for rearing the leaf-mining moth Acrocercops transecta successively over several generations are described. Based on continuous rearing, some life historical parameters in A. transecta were determined. Because of its short generation time, successive rearing makes the moth suitable for mating experiments and a model organism to elucidate the mechanism of host-associated speciation. [source] Ion transport and osmotic adjustment in Escherichia coli in response to ionic and non-ionic osmoticaENVIRONMENTAL MICROBIOLOGY, Issue 1 2009Lana Shabala Summary Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using Escherichia coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above ,1.0 Os kg,1 causes a dose-dependent K+ leak from the cell, resulting in a substantial decrease in cytosolic K+ content and a concurrent accumulation of Na+ in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K+ uptake. Ion flux data are consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K+ uptake to efflux. Microarray experiments reveal that about 40% of upregulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic and non-ionic osmotica. The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K+ transporters for bacterial adaptation to hyperosmotic stress. [source] Calcium and magnesium competitively influence the growth of a PMR1 deficient Saccharomyces cerevisiae strainFEMS MICROBIOLOGY LETTERS, Issue 2 2005Réka Szigeti Abstract PMR1, the Ca2+/Mn2+ ATPase of the secretory pathway in Saccharomyces cerevisiae was the first member of the secretory pathway Ca2+ ATPases (SPCA) to be characterized. In the past few years, pmr1, yeast have received more attention due to the recognition that the human homologue of this protein, hSPCA1 is defective in chronic benign pemphigus or Hailey,Hailey disease (HHD). Recent publications have described pmr1, S. cerevisiae as a useful model organism for studying the molecular pathology of HHD. Some observations indicated that the high Ca2+ sensitive phenotype of PMR1 defective yeast strains may be the most relevant in this respect. Here we show that the total cellular calcium response of a pmr1, S. cerevisiae upon extracellular Ca2+ challenge is decreased compared to the wild type strain similarly as observed in keratinocytes. Additionally, the novel magnesium sensitivity of PMR1 defective yeast is revealed, which appears to be a result of competition for uptake between Ca2+ and Mg2+ at the plasma membrane level. Our findings indicate that extracellular Ca2+ and Mg2+ competitively influence the intracellular Ca2+ homeostasis of S. cerevisiae. These observations may further our understanding of HHD. [source] ,-Synuclein, oxidative stress and apoptosis from the perspective of a yeast model of Parkinson's diseaseFEMS YEAST RESEARCH, Issue 8 2006Stephan N. Witt Abstract The neuronal protein ,-synuclein (,-syn) has been suggested to be one of the factors linked to Parkinson's disease (PD). Several organisms, including the rat, mouse, worm, and fruit fly, are being used to study ,-syn pathobiology. A new model organism was recently added to this armamentarium: the budding yeast Saccharomyces cerevisiae. The yeast system recapitulates many of the findings made with higher eukaryotes. For example, yeast cells expressing ,-syn accumulate lipid droplets, have vacuolar/lysosomal defects, and exhibit markers of apoptosis, including the externalization of phosphatidylserine, the release of cytochrome c, and the accumulation of reactive oxygen species. This MiniReview focuses on the mechanisms by which ,-syn induces oxidative stress and the mechanisms by which yeast cells respond to this stress. Three classes of therapeutics are discussed. [source] Selenium metabolism in zebrafish: multiplicity of selenoprotein genes and expression of a protein containing 17 selenocysteine residuesGENES TO CELLS, Issue 12 2000Gregory V. Kryukov Fish are an important source of selenium in human nutrition and the zebrafish is a potentially useful model organism for the study of selenium metabolism and its role in biology and medicine. Selenium is present in vertebrate proteins in the form of selenocysteine (Sec), the 21st natural amino acid in protein which is encoded by UGA. We report here the detection of 18 zebrafish genes for Sec-containing proteins. We found two zebrafish orthologs of human SelT, glutathione peroxidase 1 and glutathione peroxidase 4, and single orthologs of several other selenoproteins. In addition, new zebrafish selenoproteins were identified that were distant homologues of SelP, SelT and SelW, but their direct orthologs in other species are not known. This multiplicity of selenoprotein genes appeared to result from gene and genome duplications, followed by the retention of new selenoprotein genes. We found a zebrafish selenoprotein P gene (designated zSelPa) that contained two Sec insertion sequence (SECIS) elements and encoded a protein containing 17 Sec residues, the largest number of Sec residues found in any known protein. In contrast, a second SelP gene (designated zSelPb) was also identified that contained one SECIS element and encoded a protein with a single Sec. We found that zSelPa could be expressed and secreted by mammalian cells. The occurrence of zSelPa and zSelPb suggested that the function of the N-terminal domain of mammalian SelP proteins may be separated from that of the C-terminal Sec-rich sequence: the N-terminal domain containing the UxxC motif is likely involved in oxidoreduction, whereas the C-terminal portion of the protein may function in selenium transport or storage. Our data also suggest that the utilization of Sec is more common in zebrafish than in previously characterized species, including mammals. [source] Ethanol preference in C. elegansGENES, BRAIN AND BEHAVIOR, Issue 6 2009J. Lee Caenorhabditis elegans senses multiple environmental stimuli through sensory systems and rapidly changes its behaviors for survival. With a simple and well-characterized nervous system, C. elegans is a suitable animal model for studying behavioral plasticity. Previous studies have shown acute neurodepressive effects of ethanol on multiple behaviors of C. elegans similar to the effect of ethanol on other organisms. Caenorhabditis elegans also develops ethanol tolerance during continuous exposure to ethanol. In mammals, chronic ethanol exposure leads to ethanol tolerance as well as increased ethanol consumption. Ethanol preference is associated with the development of tolerance and may lead to the development of ethanol dependence. In this study, we show that C. elegans is a useful model organism for studying chronic effects of ethanol, including the development of ethanol preference. We designed a behavioral assay for testing ethanol preference after prolonged ethanol exposure. Despite baseline aversive responses to ethanol, animals show ethanol preference after 4 h of pre-exposure to ethanol and exhibit significantly enhanced preference for ethanol after a lifetime of ethanol exposure. The cat-2 and tph-1 mutant animals have defects in the synthetic enzymes for dopamine and serotonin, respectively. These mutants are deficient in the development of ethanol preference, indicating that dopamine and serotonin are required for this form of behavioral plasticity. [source] Opened brood chamber with embryos of different stages from the demosponge Amphimedon queenslandica.GENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 11 2009Article first published online: 19 NOV 200 Opened brood chamber with embryos of different stages from the demosponge Amphimedon queenslandica. This poriferan species has its genome sequenced, assembled, and annotated and serves as a model organism for sponge developmental biology. Image supplied by Bernie Degnan (University of Queensland). [source] Cloning and sequence analysis of a zebrafish cDNA encoding DNA (cytosine-5)-methyltransferase-1GENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 4 2001Aizeddin A. Mhanni Abstract Summary: The zebrafish has become a well-established animal model for the analysis of development and of several disease phenotypes. Several of the favorable traits that make it a popular model organism would also be beneficial for the study of normal and abnormal vertebrate development in which DNA methylation may play a role. We report the determination of the full-length cDNA sequence corresponding to the zebrafish DNA (cytosine-5-) methyltransferase gene, Dnmt1. It is 4,907 bases long and has an open reading frame predicted to encode a 1,499 amino acid protein that is similar in size and sequence to a number of other methyltransferases identified in other organisms. genesis 30:213,219, 2001. © 2001 Wiley-Liss, Inc. [source] Halloween genes and nuclear receptors in ecdysteroid biosynthesis and signalling in the pea aphidINSECT MOLECULAR BIOLOGY, Issue 2010O. Christiaens Abstract The pea aphid (Acyrthosiphon pisum) is the first whole genome sequenced insect with a hemimetabolic development and an emerging model organism for studies in ecology, evolution and development. The insect steroid moulting hormone 20-hydroxyecdysone (20E) controls and coordinates development in insects, especially the moulting/metamorphosis process. We, therefore present here a comprehensive characterization of the Halloween genes phantom, disembodied, shadow, shade, spook and spookiest, coding for the P450 enzymes that control the biosynthesis of 20E. Regarding the presence of nuclear receptors in the pea aphid genome, we found 19 genes, representing all of the seven known subfamilies. The annotation and phylogenetic analysis revealed a strong conservation in the class of Insecta. But compared with other sequenced insect genomes, three orthologues are missing in the Acyrthosiphon genome, namely HR96, PNR-like and Knirps. We also cloned the EcR, Usp, E75 and HR3. Finally, 3D-modelling of the ligand-binding domain of Ap-EcR exhibited the typical canonical structural scaffold with 12 ,-helices associated with a short hairpin of two antiparallel ,-strands. Upon docking, 20E was located in the hormone-binding groove, supporting the hypothesis that EcR has a role in 20E signalling. [source] Apolipoprotein D is involved in the mechanisms regulating protection from oxidative stressAGING CELL, Issue 4 2008Maria D. Ganfornina Summary Many nervous system pathologies are associated with increased levels of apolipoprotein D (ApoD), a lipocalin also expressed during normal development and aging. An ApoD homologous gene in Drosophila, Glial Lazarillo, regulates resistance to stress, and neurodegeneration in the aging brain. Here we study for the first time the protective potential of ApoD in a vertebrate model organism. Loss of mouse ApoD function increases the sensitivity to oxidative stress and the levels of brain lipid peroxidation, and impairs locomotor and learning abilities. Human ApoD overexpression in the mouse brain produces opposite effects, increasing survival and preventing the raise of brain lipid peroxides after oxidant treatment. These observations, together with its transcriptional up-regulation in the brain upon oxidative insult, identify ApoD as an acute response protein with a protective and therefore beneficial function mediated by the control of peroxidated lipids. [source] Trade-offs between longevity and pathogen resistance in Drosophila melanogaster are mediated by NF,B signalingAGING CELL, Issue 6 2006Sergiy Libert Summary The innate immune response protects numerous organisms, including humans, from the universe of pathogenic molecules, viruses and micro-organisms. Despite its role in promoting pathogen resistance, inappropriate activation and expression of NF,B and other immunity-related effector molecules can lead to cancer, inflammation, and other diseases of aging. Understanding the mechanisms leading to immune system activation as well as the short- and long-term consequences of such activation on health and lifespan is therefore critical for the development of beneficial immuno-modulating and longevity-promoting interventions. Mechanisms of innate immunity are highly conserved across species, and we take advantage of genetic tools in the model organism, Drosophila melanogaster, to study the effects of acute and chronic activation of immunity pathways on pathogen resistance and general fitness of adult flies. Our findings indicate that fat body specific overexpression of a putative pathogen recognition molecule, peptidoglycan recognition protein (PGRP-LE), is sufficient for constitutive up-regulation of the immune response and for enhanced pathogen resistance. Primary components of fitness are unaffected by acute activation, but chronic activation leads to an inflammatory state and reduced lifespan. These phenotypes are dependent on the NF,B-related transcriptional factor, Relish, and they establish a mechanistic basis for a link between immunity, inflammation, and longevity. [source] The function of mate choice in sticklebacks: optimizing Mhc genetics,JOURNAL OF FISH BIOLOGY, Issue 2003M. Milinski Sexual reproduction is an evolutionary ,puzzle'. A sexual female ,throws away' half of her genes (during meiosis), and ,fills up' what she lost with genes from a male. Thus, sexual reproduction can only be successful if the offspring with the new mixture of genes should be more than twice as fit as if she had just made a copy of herself. A challenging hypothesis assumes that infectious diseases select for females that reshuffle the immune genes for their offspring in each generation. The required increase in quality could be achieved by females selectively ,smelling out' suitable immune-genes (i.e. Mhc alleles) in potential partners, which, in combination with the female's genes, offer optimal resistance against quickly changing infectious diseases. It was found that most three spined sticklebacks Gasterosteus aculeatus in natural populations around Plön, Germany, had intermediate instead of maximal numbers of different Mhc class IIB alleles. Furthermore, fish with an intermediate number of different Mhc alleles were infected with the lowest number of both parasite species and parasites per species. This suggests that Mhc heterozygosity was optimized instead of maximized. Can this immunogenetic optimum be achieved through female choice? In a flow channel design that allowed the detection of olfactory signals only, it was found that female three-spined sticklebacks that were ready to spawn preferred males as mates that in combination with their Mhc alleles would allow the production of offspring with the optimal number of Mhc alleles. Thus, mate choice in three-spined sticklebacks could have the two-fold advantage over asexual reproduction that is required to maintain sexual reproduction. The interaction of olfactory with visual signals in three-spined stickleback mate choice is discussed. The three-spined stickleback is a suitable model organism for studying the evolution of sexual reproduction in relation to optimizing offspring immune genetics although other fishes may be as suitable. [source] Patterns of spatial and temporal cranial muscle development in the African clawed frog, Xenopus laevis (Anura: Pipidae)JOURNAL OF MORPHOLOGY, Issue 9 2007Janine M. Ziermann Abstract The African Clawed Toad, Xenopus laevis, has been a major vertebrate model organism for developmental studies for half a century. Because most studies have focused on the early stages of development, this has had the effect that many aspects of organogenesis and later development remain relatively poorly known in this species. In particular, little is known about cranial muscle development even at the level of morphology and histological differentiation of muscle anlagen and muscle fibers. In this study, we document the morphogenesis and histological differentiation of cranial muscles in X. laevis. We provide a detailed account of the timing of development for each of the cranial muscles, and also describe a new muscle, the m. transversus anterior. The cranial musculature of X. laevis larvae generally develops in a rostrocaudal sequence. The first muscles to differentiate are the extrinsic eye muscles. Muscles of the mandibular and hyoid arches develop almost simultaneously, and are followed by the muscles of the branchial arches and the larynx, and by the mm. geniohyoideus and rectus cervicis. Despite the fact that differentiation starts at different stages in the different muscles, most are fully developed at Stage 14. These baseline data on the timing of muscle differentiation in the X. laevis can serve as a foundation for comparative studies of heterochronic changes in cranial muscle development in frogs and other lissamphibians. J. Morphol., 2007. © 2007 Wiley-Liss, Inc. [source] INTERCOLONIAL VARIABILITY IN MACROMOLECULAR COMPOSITION IN P-STARVED AND P-REPLETE SCENEDESMUS POPULATIONS REVEALED BY INFRARED MICROSPECTROSCOPY,JOURNAL OF PHYCOLOGY, Issue 5 2008Philip Heraud Macromolecular variability in microalgal populations subject to different nutrient environments was investigated, using the chlorophyte alga Scenedesmus quadricauda (Turpin) Bréb. as a model organism. The large size of the four-cell coenobia in the strain used in this study (,35 ,m diameter) conveniently allowed high quality spectra to be obtained from individual coenobia using a laboratory-based Fourier transform infrared (FTIR) microscope with a conventional globar source of IR. By drawing sizable subpopulations of coenobia from two Scenedesmus cultures grown under either nutrient-replete or P-starved conditions, the population variability in macromolecular composition, and the effects of nutrient change upon this, could be estimated. On average, P-starved coenobia had higher carbohydrate and lower protein absorbance compared with P-replete coenobia. These parameters varied between coenobia with histograms of the ratio of absorbance of the largest protein and carbohydrate bands being Gaussian distributed. Distributions for the P-replete and P-starved subpopulations were nonoverlapping, with the difference in mean ratios for the two populations being statistically significant. Greater variance was observed in the P-starved subpopulation. In addition, multivariate models were developed using the spectral data, which could accurately predict the nutrient status of an independent individual coenobium, based on its FTIR spectrum. Partial least squares discriminant analysis (PLS-DA) was a better prediction method compared with soft independent modeling by class analogy (SIMCA). [source] PROPOSAL OF ECTOCARPUS SILICULOSUS (ECTOCARPALES, PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS,JOURNAL OF PHYCOLOGY, Issue 6 2004Akira F. Peters The emergence of model organisms that permit the application of a powerful combination of genomic and genetic approaches has been a major factor underlying the advances that have been made in the past decade in dissecting the molecular basis of a wide range of biological processes. However, the phylogenetic distance separating marine macroalgae from these model organisms, which are mostly from the animal, fungi, and higher plant lineages, limits the latters' applicability to problems specific to macroalgal biology. There is therefore a pressing need to develop similar models for the macroalgae. Here we describe a survey of potential model brown algae in which particular attention was paid to characteristics associated with a strong potential for genomic and genetic analysis, such as a small nuclear genome size, sexuality, and a short life cycle. Flow cytometry of nuclei isolated from zoids showed that species from the Ectocarpales possess smaller haploid genomes (127,290 Mbp) than current models among the Laminariales (580,720 Mbp) and Fucales (1095,1271 Mbp). Species of the Ectocarpales may complete their life histories in as little as 6 weeks in laboratory culture and are amenable to genetic analyses. Based on this study, we propose Ectocarpus siliculosus (Dillwyn) Lyngbye as an optimal choice for a general model organism for the molecular genetics of the brown algae. [source] 71 Proteomics of haematococcus pluvialis: new opportunities for study of genomics of a non-sequenced speciesJOURNAL OF PHYCOLOGY, Issue 2003Q. Hu The green alga, Haematococcus pluvialis, has become a model organism for commercial production of the high-value carotenoid astaxanthin. H. Pluvialis has also drawn significant scientific attention because fundamental biological questions relating to the massive cellular accumulation of astaxanthin have to be addressed in order to improve the yield and quality of the algal biomass. However, research has been impeded by the lack of molecular background information on this non-sequenced species. A combination of classical biochemistry with a state-of-the-art proteomic approach was used to address these questions. This was possible by taking advantage of information already available for homologous genes/gene-products in organisms whose genomes have been sequenced. The approach involved isolation of subsets of the proteome from subcellular compartments/organelles of an organism by one- or two-dimensional electrophoresis (1-DE or 2-DE) and their identification by N-terminal sequencing and peptide mass fingerprinting (PMF), involving matrix-assisted laser desorption/ionization and time-of-flight (MALDI-TOF) mass spectrometry coupled with bioinformatics. Based upon the information obtained from the combined methods, expression and physiological functions of specific genes/encoded proteins may be deduced. Examples include profiling of cell wall proteins, biogenesis and protein composition of lipid bodies, and expression patterns of soluble proteins under stress conditions. Advantages and limitations of the method for non-sequenced organisms and for cross-species protein identification will also be discussed. [source] Long-Term Behavioral Changes in Response to Early Developmental Exposure to Ethanol in ZebrafishALCOHOLISM, Issue 4 2009Yohaan Fernandes Background:, Zebrafish is becoming an important research tool for the analysis of brain function and behavior. It has been proposed to model human alcoholism as well as fetal alcohol syndrome. Previous studies investigating the consequences of exposure to ethanol during early development of zebrafish employed robust dosing regimens (high ethanol concentration and long exposure) that may model a rare situation in the human clinic. These studies found major structural abnormalities developing in the exposed fish. Methods: Here we hope to avoid such gross changes and administer only low doses of ethanol (0.00, 0.25, 0.50, 0.75, 1.00 vol/vol %) at 24-hour postfertilization and for only a short period of time (for 2 hours). We analyze the behavior of exposed fish at adult stage using computerized stimulus presentation and automated videotracking response quantification. Results: Despite the short ethanol exposure period and the modest concentrations, significant behavioral alterations were found: fish exposed to higher doses of ethanol swam at an increased distance from a computer-animated zebrafish shoal while their activity levels did not change. Conclusions: Although the interpretation of and the mechanisms underlying this finding will require further investigation, the results suggest that zebrafish will be an appropriate model organism for the analysis of the effects of moderate to mild prenatal ethanol exposure. [source] Genetic Control of Acute Ethanol-Induced Behaviors in DrosophilaALCOHOLISM, Issue 8 2000Carol M. Singh Background: In most organisms in which acute ethanol exposure has been studied, it leads to similar changes in behavior. Generally, low ethanol doses activate the central nervous system, whereas high doses are sedative. Sensitivity to the acute intoxicating effects of ethanol is in part under genetic control in rodents and humans, and reduced sensitivity in humans predicts the development of alcoholism (Crabbe et al., 1994; Schuckit, 1994). We have established Drosophila melanogaster as a model organism to study the mechanisms that regulate acute sensitivity to ethanol. Methods: We measured the effects of ethanol vapor on Drosophila locomotor behaviors by using three different assays. Horizontal locomotion was quantified in a locomotor chamber, turning behavior was assayed in narrow tubes, and ethanol-induced loss of postural control was measured in an inebriometer. Mutants with altered sensitivity to the acute effects of ethanol were generated by treatment with ethyl methane sulfonate and isolated by selection in the inebriometer. We ascertained the effects of these mutations on ethanol pharmacokinetics by measuring ethanol levels in extracts of flies at various times during and after ethanol exposure. Results: Among nearly 30,000 potentially mutant flies tested, we isolated 19 mutant strains with reduced and 4 strains with increased sensitivity to the acute effects of ethanol as measured in the inebriometer. Of these mutants, four showed changes in ethanol absorption. Two mutants, named barfly and tipsy to reflect their reduced and increased ethanol sensitivity in the inebriometer, respectively, were analyzed for locomotor behaviors. Both mutants exhibited ethanol-induced hyperactivity that was indistinguishable from wild type. However, barfly and tipsy displayed reduced and increased sensitivity to the sedative effects of ethanol, respectively. Finally, both mutants showed an increased rate of ethanol-induced turning behavior. Conclusions: The effects of acute ethanol exposure on Drosophila locomotor behaviors are remarkably similar to those described for mammals. The analysis of mutants with altered sensitivity to ethanol revealed that the genetic pathways which regulate these responses are complex and that single genes can affect hyperactivity, turning, and sedation independently. [source] A new model organism among the lower Bilateria and the use of digital microscopy in taxonomy of meiobenthic Platyhelminthes: Macrostomum lignano, n. sp. (Rhabditophora, Macrostomorpha)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2005P. Ladurner Abstract Macrostomum lignano n. sp. is a member of the Macrostomorpha, the basal-most subtaxon of the Platyhelminthes,Rhabditophora. This new species can be easily cultured in the laboratory and has been already the subject of several developmental/evolutionary studies. The small size, with only about 25 000 cells constituting the major bilaterian organ systems, makes this simultaneous hermaphrodite a possible candidate for a new model organism that is phylogenetically more basal than any of the model organisms currently used in such studies within the Bilateria. M. lignano belongs to the largest genus of the Macrostomorpha. Over 100 marine, fresh water and brackish water species are contained in the genus Macrostomum, some of them with worldwide distribution pattern. Within it, M. lignano is a member of the M. tuba -species group, which we have summarized here. In the species description, we have used a novel approach to document such small soft-bodied meiobenthic organisms: we provide extensive digital micrographical documentation, which are deposited as a CD together with the type material. Zusammenfassung Macrostomum lignano n. sp. gehört zu den Macrostomorpha, dem ursprünglichsten Subtaxon der Plathelminthes-Rhabditophora. An der neuen Art, die sich im Labor besonders einfach züchten lässt, wurden bereits zahlreiche entwicklungsbiologische und evolutionsbiologische Studien durchgeführt. Die kleinen simultan-hermaphroditischen Tiere, bei denen nur etwa 25'000 Zellen alle wichtigen Organsysteme der Bilateria ausbilden, sind für derartige Untersuchungen ein möglicher Modellorganismus, der phylogenetisch weit ursprünglicher ist als die üblichen Modellorganismen. Macrostomum ist die größte Gattung der Macrostomorpha. Sie umfasst mehr als 100 Meer-, Süss- und Brackwasser-Arten, einige davon mit weltweiter Verbreitung. Innerhalb der Gattung ist M. lignano der M. tuba -Artengruppe zuzurechnen, die zusammenfassend dargestellt wird. Zur Charakterisierung dieser meiobenthischen neuen Art wird als neuartige Dokumentationsform digitales Bildmaterial verwendet, das als CD zusammen mit dem Typenmaterial hinterlegt wird. [source] Proteome analysis of non-model plants: A challenging but powerful approachMASS SPECTROMETRY REVIEWS, Issue 4 2008Sebastien Christian Carpentier Abstract Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 354,377, 2008 [source] Pigment pattern formation in zebrafish: A model for developmental genetics and the evolution of formMICROSCOPY RESEARCH AND TECHNIQUE, Issue 6 2002Ian K. Quigley The zebrafish Danio rerio is an emerging model organism for understanding vertebrate development and genetics. One trait of both historical and recent interest is the pattern formed by neural crest,derived pigment cells, or chromatophores, which include black melanophores, yellow xanthophores, and iridescent iridophores. In zebrafish, an embryonic and early larval pigment pattern consists of several stripes of melanophores and iridophores, whereas xanthophores are scattered widely over the flank. During metamorphosis, however, this pattern is transformed into that of the adult, which comprises several dark stripes of melanophores and iridophores that alternate with light stripes of xanthophores and iridophores. In this review, we place zebrafish relative to other model and non-model species; we review what is known about the processes of chromatophore specification, differentiation, and morphogenesis during the development of embryonic and adult pigment patterns, and we address how future studies of zebrafish will likely aid our understanding of human disease and the evolution of form. Microsc. Res. Tech. 58:442,455, 2002. © 2002 Wiley-Liss, Inc. [source] Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at ,Evolution Canyon', Mount Carmel, IsraelMOLECULAR ECOLOGY, Issue 9 2009ZUJUN YANG Abstract ,Evolution Canyon' (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unravelling evolution in action highlighting the twin evolutionary processes of adaptation and speciation. A major model organism in ECI is wild barley, Hordeum spontaneum, the progenitor of cultivated barley, which displays dramatic interslope adaptive and speciational divergence on the ,African' dry slope (AS) and the ,European' humid slope (ES), separated on average by 200 m. Here we examined interslope single nucleotide polymorphism (SNP) sequences and the expression diversity of the drought resistant dehydrin 1 gene (Dhn1) between the opposite slopes. We analysed 47 plants (genotypes), 4,10 individuals in each of seven stations (populations) in an area of 7000 m2, for Dhn1 sequence diversity located in the 5, upstream flanking region of the gene. We found significant levels of Dhn1 genic diversity represented by 29 haplotypes, derived from 45 SNPs in a total of 708 bp sites. Most of the haplotypes, 25 out of 29 (= 86.2%), were represented by one genotype; hence, unique to one population. Only a single haplotype was common to both slopes. Genetic divergence of sequence and haplotype diversity was generally and significantly different among the populations and slopes. Nucleotide diversity was higher on the AS, whereas haplotype diversity was higher on the ES. Interslope divergence was significantly higher than intraslope divergence. The applied Tajima D rejected neutrality of the SNP diversity. The Dhn1 expression under dehydration indicated interslope divergent expression between AS and ES genotypes, reinforcing Dhn1 associated with drought resistance of wild barley at ,Evolution Canyon'. These results are inexplicable by mutation, gene flow, or chance effects, and support adaptive natural microclimatic selection as the major evolutionary divergent driving force. [source] Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfish Engaeus sericatus Clark (Decapoda: Parastacidae)MOLECULAR ECOLOGY, Issue 24 2008MARK B. SCHULTZ Abstract Historical sea levels have been influential in shaping the phylogeography of freshwater-limited taxa via palaeodrainage and palaeoshoreline connections. In this study, we demonstrate an approach to phylogeographic analysis incorporating historical sea-level information in a nested clade phylogeographic analysis (NCPA) framework, using burrowing freshwater crayfish as the model organism. Our study area focuses on the Bass Strait region of southeastern Australia, which is marine region encompassing a shallow seabed that has emerged as a land bridge during glacial cycles connecting mainland Australia and Tasmania. Bathymetric data were analysed using Geographical Information Systems (GIS) to delineate a palaeodrainage model when the palaeocoastline was 150 m below present-day sea level. Such sea levels occurred at least twice in the past 500 000 years, perhaps more often or of larger magnitude within the last 10 million years, linking Victoria and Tasmania. Inter-locality distance measures confined to the palaeodrainage network were incorporated into an NCPA of crayfish (Engaeus sericatus Clark 1936) mitochondrial 16S rDNA haplotypes. The results were then compared to NCPAs using present-day river drainages and traditional great-circle distance measures. NCPA inferences were cross-examined using frequentist and Bayesian procedures in the context of geomorphological and historical sea-level data. We found distribution of present-day genetic variation in E. sericatus to be partly explained not only by connectivity through palaeodrainages but also via present-day drainages or overland (great circle) routes. We recommend that future studies consider all three of these distance measures, especially for studies of coastally distributed species. [source] | ||||||||||||||||||||||||||||||||||||||||||||||