Drosophila and C. Elegans the Molecular
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L. Lacey Knowles
Curriculum Vitae L. Lacey Knowles Department of Ecology and Evolutionary Biology E-mail: [email protected] Museum of Zoology, University of Michigan Orcid ID: 0000-0002-6567-4853 Ann Arbor, MI 48109-1079 POSITIONS 2015-present, Robert B. Payne Collegiate Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan 2012-2015, Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan 2008-2012, Associate Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan 2003-2008, Assistant Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan ACADEMIC APPOINTMENTS: Science Communication Fellow, Museum of Natural History, University of Michigan Member, Center for statistical Genetics, University of Michigan NIH Training Program in Genome Sciences, University of Michigan EDUCATION 2001-2002 NIH Postdoctoral Fellowship (PERT: Postdoctoral Excellence in Research and Teaching) awarded through the Center for Insect Science at the University of Arizona 1999-2001 Postdoctoral Fellowship from the National Science Foundation Research Training Group in the Analysis of Biological Diversification at the University of Arizona 1999 Ph.D., Ecology and Evolution, State University of New York at Stony Brook Dissertation title: Genealogical portraits of Pleistocene speciation and diversity patterns in montane grasshoppers 1993 M.S., Zoology, University of South Florida. Thesis title: Effects of habitat structure on community assemblages of epifaunal macroinvertebrates in seagrass systems. 1989 B.S., cum laude with honors in Marine Biology, University of North Carolina, Wilmington RESEARCH INTERESTS Speciation and processes that promote divergence Phylogenomics and statistical phylogeography Evolutionary consequences of climate change HONORS AND AWARDS *Fulbright U.S. -
Network Access to the Genome and Biology of Caenorhabditis Elegans
82–86 Nucleic Acids Research, 2001, Vol. 29, No. 1 © 2001 Oxford University Press WormBase: network access to the genome and biology of Caenorhabditis elegans Lincoln Stein*, Paul Sternberg1, Richard Durbin2, Jean Thierry-Mieg3 and John Spieth4 Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA, 1Howard Hughes Medical Institute and California Institute of Technology, Pasadena, CA, USA, 2The Sanger Centre, Hinxton, UK, 3National Center for Biotechnology Information, Bethesda, MD, USA and 4Genome Sequencing Center, Washington University, St Louis, MO, USA Received September 18, 2000; Accepted October 4, 2000 ABSTRACT and a page that shows the locus in the context of the physical map. WormBase (http://www.wormbase.org) is a web-based WormBase uses HTML linking to represent the relationships resource for the Caenorhabditis elegans genome and between objects. For example, a segment of genomic sequence its biology. It builds upon the existing ACeDB data- object is linked with the several predicted gene objects base of the C.elegans genome by providing data contained within it, and each predicted gene is linked to its curation services, a significantly expanded range of conceptual protein translation. subject areas and a user-friendly front end. The major components of the resource are described below. The C.elegans genome DESCRIPTION WormBase contains the ‘essentially complete’ genome of Caenorhabditis elegans (informally known as ‘the worm’) is a C.elegans, which now stands at 99.3 Mb of finished DNA small, soil-dwelling nematode that is widely used as a model interrupted by approximately 25 small gaps. In addition, the system for studies of metazoan biology (1). -
Lower Organisms As Alternatives for Toxicity Testing in Rodents with a Focus on Ceanorhabditis Elegans and the Zebrafish (Danio Rerio)
Report 340720003/2009 L.T.M. van der Ven Lower organisms as alternatives for toxicity testing in rodents With a focus on Ceanorhabditis elegans and the zebrafish (Danio rerio) RIVM report 340720003/2009 Lower organisms as alternatives for toxicity testing in rodents With a focus on Caenorhabditis elegans and the zebrafish (Danio rerio) L.T.M. van der Ven Contact: L.T.M. van der Ven Laboratory for Health Protection Research [email protected] This investigation has been performed by order and for the account of the Ministry of Health, Welfare and Sport, within the framework of V/340720 Alternatives for animal testing RIVM, P.O. Box 1, 3720 BA Bilthoven, the Netherlands Tel +31 30 274 91 11 www.rivm.nl © RIVM 2009 Parts of this publication may be reproduced, provided acknowledgement is given to the 'National Institute for Public Health and the Environment', along with the title and year of publication. RIVM report 340720003 2 Abstract Lower organisms as alternatives for toxicity testing in rodents With a focus on Caenorhabiditis elegans and the zebrafish (Danio rerio) The nematode C. elegans and the zebrafish embryo are promising alternative test models for assessment of toxic effects in rodents. Tests with these lower organisms may have a good predictive power for effects in humans and are thus complementary to tests with in vitro models (cell cultures). However, all described tests need further validation. This is the outcome of a literature survey, commissioned by the ministry of Health, Welfare and Sport of the Netherlands. The survey is part of the policy to reduce, refine and replace animal testing (3R policy). -
Hypothesis As an Alternative. the Distribution Of
Heredity (1976), 36 (3), 293-304 REASSOCIATIONPATTERNS AMONG SEGMENTAL INTERCHANGES IN MAIZE D.B. WALDEN and R. C. JANCEY Department of Plant Sciences,Universityof WesternOntario,London, Ontario N6A 3K7 Received2.iv.75 SUMMARY Data from Longley (1961) and Burnham (1969) on the cytological position of the break-points in chrornosomal rearrangements in maize were re-expressed in terms of segment lengths and analysed. After correction for the deviation of the distribution of break-points from an equidistribution, it was shown that highly significant excesses and deficits occurred among some but not all segment length classes. It was concluded that the pattern of reassociation shows: (i) that reassociation involves non-homologues whose interstitial segments are of similar length more frequently than expected; (ii) that the two interchange segments involved in a translocation are of similar length more frequently than expected. 1. INTRODUCTION AN extensive literature exists on the genetic effects and consequences of exposure to radiation and radiomimetic and radiochemical compounds. The origin of chromosomal aberrations had long been considered to be the consequence of" breakage and reunion" until Revell (1955) proposed an "exchange" hypothesis as an alternative. The distribution of the "breakage" or "exchange" events has been approximately determined in several species, with a" random "distribution being claimed by some workers and a "non-random" distribution favoured by several recent investigators (e.g. Caspersson et al., 1972). It is important for the present communication to note that most of the studies record observations made one or a few cell generations after exposure to the mutagen and that only limited information is available about the survival of the aberrations so induced. -
Effects of Gut-Associated Yeasts on Drosophila Melanogaster Performance
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 12-6-2016 12:00 AM Effects of gut-associated yeasts on Drosophila melanogaster performance Yanira Jiménez Padilla The University of Western Ontario Supervisor Brent Sinclair The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Yanira Jiménez Padilla 2016 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Biology Commons Recommended Citation Jiménez Padilla, Yanira, "Effects of gut-associated yeasts on Drosophila melanogaster performance" (2016). Electronic Thesis and Dissertation Repository. 4285. https://ir.lib.uwo.ca/etd/4285 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract I used Drosophila melanogaster as a model to study the role of the gut microbiota, specifically yeasts, in animal physiology. I used Saccharomyces cerevisiae, the yeast commonly included in Drosophila diet, and Lachancea kluyveri, isolated from some Drosophila in the wild, and generated axenic (germ-free) and gnotobiotic (yeast-fed) flies. I found that L. kluyveri persists in the crop, as ascospores and vegetative cells, longer than S. cerevisiae. Some L. kluyveri vegetative cells survive passage through the gut. Egg to adult development time is reduced by 14% in vials containing live L. kluyveri or S. cerevisiae, whereas heat-killed yeasts reduced development time by 3.5-4.5%. -
DROSOPHILA MELANOGASTER - the MODEL ORGANISM of CHOICE for the COMPLEX BIOLOGY of MULTI-CELLULAR ORGANISMS Kathleen M
DROSOPHILA MELANOGASTER - THE MODEL ORGANISM OF CHOICE FOR THE COMPLEX BIOLOGY OF MULTI-CELLULAR ORGANISMS Kathleen M. Beckingham 1*, J. Douglas Armstrong2, Michael J. Texada1, Ravi Munjaal1, Dean A. Baker2 1 Department of Biochemistry and Cell Biology, MS-140, Rice University, Houston, Texas 77251. 2 School of Informatics, Institute for Adaptive and Neural Computation Edinburgh, EH1 2QL, UK. ABSTRACT Although the route from mutation to sequenced gene may Drosophila melanogaster has been intensely studied for almost be long and hard, genetics is an extremely powerful 100 years. The sophisticated array of genetic and molecular approach because it can be applied to much more tools that have evolved for analysis of gene function in this complex biological processes than biochemistry. Clearly organism are unique. Further, Drosophila is a complex multi- for fundamental, universal processes that can be studied cellular organism in which many aspects of development and behavior parallel those in human beings. These combined in cell-free extracts, the biochemical approach is highly advantages have permitted research in Drosophila to make effective. But for complex processes, such as seminal contributions to the understanding of fundamental developmental events or behavioral responses, in which biological processes and ensure that Drosophila will continue to many components of the whole organism are in play, provide unique insights in the genomic era. An overview of the genetics offers perhaps the only viable route to dissecting genetic methodologies available in Drosophila is given here, out the protein components. together with examples of outstanding recent contributions of Drosophila to our understanding of cell and organismal biology. The genetic approach has been used to probe gene/protein The growing contribution of Drosophila to our knowledge of function in many organisms. -
Patterns and Potential Mechanisms of Thermal Preference in E. Muscae-Infected Drosophila Melanogaster
Western Washington University Western CEDAR WWU Honors Program Senior Projects WWU Graduate and Undergraduate Scholarship Spring 2020 Patterns and potential mechanisms of thermal preference in E. muscae-infected Drosophila melanogaster Aundrea Koger Western Washington University Carolyn Elya Ph.D. Harvard University Jamilla Akhund-Zade Ph.D. Harvard University Benjamin de Bivort Ph.D. Harvard University Follow this and additional works at: https://cedar.wwu.edu/wwu_honors Recommended Citation Koger, Aundrea; Elya, Carolyn Ph.D.; Akhund-Zade, Jamilla Ph.D.; and de Bivort, Benjamin Ph.D., "Patterns and potential mechanisms of thermal preference in E. muscae-infected Drosophila melanogaster" (2020). WWU Honors Program Senior Projects. 406. https://cedar.wwu.edu/wwu_honors/406 This Project is brought to you for free and open access by the WWU Graduate and Undergraduate Scholarship at Western CEDAR. It has been accepted for inclusion in WWU Honors Program Senior Projects by an authorized administrator of Western CEDAR. For more information, please contact [email protected]. Patterns and potential mechanisms of thermal preference in Entomophthora muscae-infected Drosophila melanogaster 1 2 2 Aundrea Koger , Carolyn Elya, Ph.D. , Jamilla Akhund-Zade, Ph.D. , and Benjamin de Bivort, Ph.D.2 1 2 Honors Program, Western Washington University, Department of Organismic and Evolutionary Biology, Harvard University Abstract Animals use various strategies to defend against pathogens. Behavioral fever, or fighting infection by moving to warm locations, is seen in many ectotherms. The behavior-manipulating fungal pathogen Entomophthora muscae infects numerous dipterans, including fruit flies and house flies, Musca domestica. House flies have been shown to exhibit robust behavioral fever early after exposure to E. -
Helical Insertion of Peptidoglycan Produces Chiral Ordering of the Bacterial Cell Wall
Helical insertion of peptidoglycan produces PNAS PLUS chiral ordering of the bacterial cell wall Siyuan Wanga,b, Leon Furchtgottc,d, Kerwyn Casey Huangd,1, and Joshua W. Shaevitza,e,1 aLewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; bDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544; cBiophysics Program, Harvard University, Cambridge, MA 02138; dDepartment of Bioengineering, Stanford University, Stanford, CA 94305; and eDepartment of Physics, Princeton University, Princeton, NJ 08854 AUTHOR SUMMARY Cells from all kingdoms of wall growth to demonstrate life face the task of that patterning of cell-wall constructing a specific, synthesis by left-handed mechanically robust three- MreB polymers leads to a dimensional (3D) cell shape right-handed chiral from molecular-scale organization of the glycan components. For many strands. This organization bacteria, maintaining a rigid, produces a left-handed rod-like shape facilitates a twisting of the cell body diverse range of behaviors during elongational growth. including swimming motility, We then confirm the detection of chemical existence of right-handed gradients, and nutrient access Fig. P1. Helical insertion of material into the bacterial cell wall (green) glycan organization in E. coli during elongational growth, guided by the protein MreB (yellow), leads and waste evacuation in by osmotically shocking biofilms. The static shape of to an emergent chiral order in the cell-wall network and twisting of the cell that can be visualized using surface-bound beads (red). surface-labeled cells and a bacterial cell is usually directly measuring the defined by the cell wall, a difference in stiffness macromolecular polymer network composed of glycan strands between the longitudinal and transverse directions. -
Interactions Between Drosophila and Its Natural Yeast Symbionts---Is
Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship? Don Hoang1,2 , Artyom Kopp1 and James Angus Chandler1,3 1 Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA, USA 2 Current aYliation: Program in Genomics of DiVerentiation, NIH/NICHD, Bethesda, MD, USA 3 Current aYliation: Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA ABSTRACT Yeasts play an important role in the biology of the fruit fly, Drosophila melanogaster. In addition to being a valuable source of nutrition, yeasts aVect D. melanogaster behavior and interact with the host immune system. Most experiments investigating the role of yeasts in D. melanogaster biology use the baker’s yeast, Saccharomyces cerevisiae. However, S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species. Moreover, the strain of S. cerevisiae used most often in D. melanogaster experiments is a commercially and industrially important strain that, to the best of our knowledge, was not isolated from flies. Since disrupting natural host–microbe interactions can have profound eVects on host biology, the results from D. melanogaster–S. cerevisiae laboratory experiments may not be fully representative of host–microbe interactions in nature. In this study, we explore the D. melanogaster-yeast relationship using five diVerent strains of yeast that were isolated from wild Drosophila populations. Ingested live yeasts have variable persistence in the D. melanogaster gastrointestinal tract. For example, Hanseniaspora occidentalis persists relative to S. cerevisiae, while Submitted 25 April 2015 Brettanomyces naardenensis is removed. -
Model Organisms
RESEARCH HIGHLIGHTS Nature Reviews Genetics | Published online 30 Aug 2017; doi:10.1038/nrg.2017.70 P. Morgan/Macmillan Publishers Limited Morgan/Macmillan P. its caste-specific RNA expression is conserved in other insect species with different social systems. In ants undergoing the worker–gamergate transition, high corazonin peptide levels promoted worker-specific behaviour and inhibited behaviours associated with progression to the MODEL ORGANISMS gamergate caste; as expected, short interfering RNA (siRNA) knockdown of the corazonin receptor (CrzR) gene New tools, new insights — had the opposite phenotypic effect. The researchers went on to identify the vitellogenin gene as a key regula- probing social behaviour in ants tory target of corazonin; its expres- sion is consistently downregulated Eusocial insects display complex strategy of Harpegnathos saltator to in response to increased corazonin social behaviours, but the underlying increase the number of reproducing levels, suggesting that corazonin and Until now, molecular mechanisms are largely ants to enable them to establish orco vitellogenin have opposing effects functional unknown. Now, a trio of papers in mutant lines. In the absence of a on caste identity. Consistent with genetic studies Cell decribe two genes (orco and queen, non-reproductive H. saltator this hypothesis, siRNA knockdown corazonin) that control social behav- workers can become ‘gamergates’, of vitellogenin gene expression pro- have not been iour in ants. Furthermore, two of which lay fertilized eggs. This caste moted worker-specific behaviours. possible in the studies describe the first mutant transition can be replicated in the lab Based on these observations, the ants lines in ants, which were generated by simply by isolating workers. -
The Antennapedia Gene
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Control elements of the P2 promoter of the Antennapedia gene Anne M. Boulet I and Matthew P. Scott Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, 80302 USA Antennapedia (Antp), a homeotic gene of Drosophila required for proper differentiation of the thorax of the fly, is expressed in complex spatial patterns during development. The gene is > 100 kb long and has two independently regulated promoters. To characterize cis-acting regulatory elements responsible for the expression pattern, fusions of the Antp promoter 2 cap site and upstream sequences to an Adh-lacZ gene were introduced into flies. A 10-kb sequence directs ~-galactosidase production in a pattern that closely resembles the endogenous P2 pattern. Transcription from the 10-kb fusions is regulated by three genes that regulate Antp transcription. Control elements, including a target of action of homeo-domain-containing proteins, were mapped by deleting parts of the 10-kb sequence. [Key Words: Homeotic; Antennapedia; Drosophila; promoter] Received July 19, 1988; revised version accepted October 18, 1988. The homeotic genes of Drosophila are required for the 1987; Mahaffey and Kaufman 1987; Martinez-Arias et specification of segmental identity during embryonic de- al. t987; Regulski et al. 1987). The complexity of ho- velopment and metamorphosis. Mutations in homeotic meotic mutant phenotypes and the elaborate spatial pat- genes lead to the transformation of one part of the em- terns in which the genes are expressed suggest that bryo or adult fly into another. -
Genes Controlling Essential Cell-Cycle Functions in Drosophila Melanogaster
Downloaded from genesdev.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Genes controlling essential cell-cycle functions in Drosophila melanogaster Maurizio Gatti I and Bruce S. Baker 2 ~Dipartimento de Genetica e Biologia Molecolare, Universit/l di Roma 'La Sapienza', 00185 Roma, Italy; 2Department of Biological Sciences, Stanford University, Stanford, California 94305 USA On the basis of the hypothesis that mutants in genes controlling essential cell cycle functions in Drosophila should survive up to the larval-pupal transition, 59 such 'late lethals' were screened for those mutants affecting cell division. Examination of mitosis in brain neuroblasts revealed that 30 of these lethals cause disruptions in mitotic chromosome behavior. These mutants identify genes whose wild-type functions are important for: (1) progression through different steps of interphase, (2) the maintenance of mitotic chromosome integrity, (3) chromosome condensation, (4) spindle formation and/or function, and (5) completion of cytokinesis or completion of chromosome segregation. The presence of mitotic defects in late lethal mutants is correlated tightly with the presence of defective imaginal discs. Thus, the phenotypes of late lethality and poorly developed imaginal discs are together almost diagnostic of mutations in essential cell-cycle functions. The terminal phenotypes exhibited by these Drosophila mitotic mutants are remarkably similar to those observed in mammalian cell-cycle mutants, suggesting that these diverse organisms use a common genetic logic to regulate and integrate the events of the cell cycle. [Key Words: Cell-cycle mutants; Drosophila; mitosis] Received November 30, 1988; revised version accepted February 7, 1989. The exquisitely precise cyclic changes that eukaryotic review, see Simchen 1978; Ling 1981; Oakley 1981; chromosomes and cells undergo during mitotic and Wissmger and Wang 1983; Marcus et al.