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Functional Analysis of the Homeobox Gene Tur-2 During Mouse Embryogenesis
Functional Analysis of The Homeobox Gene Tur-2 During Mouse Embryogenesis Shao Jun Tang A thesis submitted in conformity with the requirements for the Degree of Doctor of Philosophy Graduate Department of Molecular and Medical Genetics University of Toronto March, 1998 Copyright by Shao Jun Tang (1998) National Library Bibriothèque nationale du Canada Acquisitions and Acquisitions et Bibiiographic Services seMces bibliographiques 395 Wellington Street 395, rue Weifington OtbawaON K1AW OttawaON KYAON4 Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive licence alIowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distri%uteor sell reproduire, prêter' distribuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/nlm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fkom it Ni la thèse ni des extraits substantiels may be printed or otherwise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. Functional Analysis of The Homeobox Gene TLr-2 During Mouse Embryogenesis Doctor of Philosophy (1998) Shao Jun Tang Graduate Department of Moiecular and Medicd Genetics University of Toronto Abstract This thesis describes the clonhg of the TLx-2 homeobox gene, the determination of its developmental expression, the characterization of its fiuiction in mouse mesodem and penpheral nervous system (PNS) developrnent, the regulation of nx-2 expression in the early mouse embryo by BMP signalling, and the modulation of the function of nX-2 protein by the 14-3-3 signalling protein during neural development. -
The Evolution of Cooperation a White Paper Prepared for the John Templeton Foundation
The evolution of cooperation A white paper prepared for the John Templeton foundation Contents Introduction - Darwin’s theory of design - The puzzle of cooperation - This review Cooperation across the tree of life - What is cooperation? - Explanations for Cooperation - The success of inclusive fitness - The debate over inclusive fitness - Alternative ways to measure cooperation - Cooperation between species - The social amoeba: the perfect test case for cooperation Cooperation in Humans - What’s special about humans? - Explanations for cooperation in humans - Cooperative games - Inter-personal and cross-cultural differences in cooperation - Psychological systems designed for cooperation - The origins of cooperation in humans - The How: The mechanism of cooperation Conclusion - The puzzle of cooperation revisited - Open questions in cooperation research 1 Introduction You probably take cooperation for granted. You’d be excused for doing so – cooperation is all around us. Children team up to complete a project on time. Neighbours help each other mend fences. Colleagues share ideas and resources. The very fabric of our society is cooperative. We divide up tasks, with farmers producing food, policemen upholding laws, teachers teaching, so that we may all share the benefits of a functioning society without any one person having to master all domains. What’s more, cooperation is logical, at least to you and me. Two hands are better than one, as the saying goes. If you want something another person has, it makes sense that you might share something of your own. Division of labour efficient. If you have a reputation as a cooperative person, others will likely help you down the line. Cooperation is a straightforward way to achieve more than you ever could on your own. -
How the Evolution of Multicellularity Set the Stage for Cancer’
www.nature.com/bjc CORRESPONDENCE Comment on ‘How the evolution of multicellularity set the stage for cancer’ British Journal of Cancer (2018) 119:133–134; https://doi.org/ multicellular and multicellular evolutionary origins rather than 10.1038/s41416-018-0091-0 pure unicellular evolutionary origin. Ceaseless proliferation is the most characteristic feature of cancer. But, this behaviour is rarely adopted by unicellular organisms in nature. In addition to cell communication, cell-to- We read the paper “How the evolution of multicellularity set the substrate and cell-to-cell adhesions, earlier unicellular organisms stage for cancer” with interest, which was published in a recent (prokaryotes and protists) acquired a variety of anti-proliferative issue of the British Journal of Cancer.1 In this paper, the authors capabilities (cell cycle negative regulation, programmed cell underlined that disruption of gene regulatory networks, which death, contact-dependent inhibition, toxin-antitoxin, etc.) through maintain the multicellular state, induces cancer. The atavistic the pseudo-multicellular mode of life and responses to selective model of cancer is undoubtedly effective in integrating many pressure.6,7 Indeed, exponential growth may lead to species parameters in a performing heuristic framework. It hypothesises extinction due to starvation or destruction of the protective that cancer results from a transition from multicellularity to biofilm. Earlier prokaryotes inevitably faced this problem and unicellularity, through an active constrained process. In this natural evolution proposed different solutions to circumvent schema, dysregulation of a set of fundamental points of them, which were thereafter fixed by heredity. vulnerability, which govern multicellularity maintenance, is Trigos et al.1 underlined that many hallmarks of the malignant sufficient to model carcinogenesis. -
Unit 3 Cells Lesson 6 - Cell Theory What Do Living Things Have in Common?
Unit 3 Cells Lesson 6 - Cell Theory What do living things have in common? Explore and question spontaneous generation, an early belief on the properties of life. Observing Phenomena In the 1600s, this was a recipe for creating mice: Place a dirty shirt in an open container of wheat for 21 days and the wheat will transform into mice. 1) Discuss what you think of this recipe. People may have believed that it worked because they did not notice the mice that were living in and reproducing in the wheat containers and maybe hiding beneath the dirty shirts. Observing Phenomena Another belief of spontaneous generation was that fish formed from the mud of dry river beds. 2) What do you think about the recipe for making fish from the mud of a dried up river bed? Observing Phenomena People believed that these recipes would work because they believed in “spontaneous generation.” 3) Why do you think it is called spontaneous generation? Because a living thing spontaneously came into existence from a mixture of nonliving things. What beliefs about natural phenomena did you have as a young child? For example, some young children might think that clouds are fluffy like cotton balls or the moon is made of cheese. As you have gotten older, how have these beliefs changed as you acquired more knowledge? 4) Discuss why they might have believed these and what has changed people's understanding of living things today. Investigation 1: Categorizing Substances In your notebook, write a list of what you think all living things have in common. -
Sak/Plk4 and Mitotic Fidelity
Oncogene (2005) 24, 306–312 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc Sak/Plk4 and mitotic fidelity Carol J Swallow1,2, Michael A Ko1,2, Najeeb U Siddiqui1,3,4, John W Hudson5 and James W Dennis*,1,3,4 1Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave. R988, Toronto, Ontario, Canada M5G 1X5; 2Department of Surgery, University of Toronto, Ontario, Canada; 3Department of Microbiology and Medical Genetics, University of Toronto, Ontario, Canada; 4Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; 5Department of Biological Sciences, University of Windsor, Ontario, Canada Sak/Plk4 differs from other polo-like kinases in having (Fernebro et al., 2002). Mutation of classical tumor only a single polo box, which assumes a novel dimer fold suppressor genes follows the Knudsen 2-hit model, that localizes to the nucleolus, centrosomes and the whereby loss of the wild-type allele as a ‘second hit’ cleavage furrow.Sak expression increases gradually in S frequently results in relaxed cellular growth controls through M phase, and Sak is destroyed by APC/C (Knudson, 1971). Inherited cancer syndromes such as dependent proteolysis.Sak-deficient mouse embryos Li-Fraumeni (p53, Chk2) and ataxia telangiectasia arrest at E7.5 and display an increased incidence of (ATM) are examples of autosomal recessive mutations apoptosis and anaphase arrest.Sak þ /À mice are haploin- in checkpoint proteins that normally delay the cell cycle sufficient for tumor suppression, with spontaneous tumors in response to DNA damage and environmental stresses developing primarily in the liver with advanced age. -
Cooperation and Conflict During the Unicellular–Multicellular and Prokaryotic–Eukaryotic Transitions
Font-Ch17 8/1/03 6:43 PM Page 195 CHAPTER 17 Cooperation and conflict during the unicellular–multicellular and prokaryotic–eukaryotic transitions Richard E. Michod and Aurora M. Nedelcu Individuals often associate in groups that, under group. Initially, group fitness is taken to be the aver- certain conditions, may evolve into higher-level age of the lower-level fitnesses of its members, but, individuals. It is these conditions and this process as the evolutionary transition proceeds, group fit- of individuation of groups that we wish to under- ness becomes decoupled from the fitness of lower- stand. These groups may involve members of the level components. Witness, for example, colonies of same species or different species. For example, eusocial insects or the cell groups that form organ- under certain conditions bacteria associate to form isms; in these cases, some group members have no a fruiting body, amoebae associate to form a slug- individual fitness (sterile castes, somatic cells) yet like slime mold, solitary cells form a colonial group, this does not detract from the fitness of the group, normally solitary wasps breed cooperatively, birds indeed it is presumed to enhance it. associate to form a colony, and mammals form soci- The essence of an evolutionary transition in indi- eties. Likewise, individuals of different species viduality is that the lower-level individuals must as associate and form symbiotic associations; about it were “relinquish” their “claim” to fitness, that is 2000 million years ago, such an association evolved to flourish and multiply, in favor of the new higher- into the first mitochondriate eukaryotic cell. -
Alternative Splicing Modulates Ubx Protein Function in Drosophila Melanogaster
Copyright Ó 2010 by the Genetics Society of America DOI: 10.1534/genetics.109.112086 Alternative Splicing Modulates Ubx Protein Function in Drosophila melanogaster Hilary C. Reed,* Tim Hoare,† Stefan Thomsen,‡ Thomas A. Weaver,† Robert A. H. White,† Michael Akam* and Claudio R. Alonso‡,1 *Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom, †Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, United Kingdom and ‡School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom Manuscript received November 13, 2009 Accepted for publication December 17, 2009 ABSTRACT The Drosophila Hox gene Ultrabithorax (Ubx) produces a family of protein isoforms through alternative splicing. Isoforms differ from one another by the presence of optional segments—encoded by individual exons—that modify the distance between the homeodomain and a cofactor-interaction module termed the ‘‘YPWM’’ motif. To investigate the functional implications of Ubx alternative splicing, here we analyze the in vivo effects of the individual Ubx isoforms on the activation of a natural Ubx molecular target, the decapentaplegic (dpp) gene, within the embryonic mesoderm. These experiments show that the Ubx isoforms differ in their abilities to activate dpp in mesodermal tissues during embryogenesis. Furthermore, using a Ubx mutant that reduces the full Ubx protein repertoire to just one single isoform, we obtain specific anomalies affecting the patterning of anterior abdominal muscles, demonstrating that Ubx isoforms are not functionally interchangeable during embryonic mesoderm development. Finally, a series of experiments in vitro reveals that Ubx isoforms also vary in their capacity to bind DNA in presence of the cofactor Extradenticle (Exd). -
Biological Atomism and Cell Theory
Studies in History and Philosophy of Biological and Biomedical Sciences 41 (2010) 202–211 Contents lists available at ScienceDirect Studies in History and Philosophy of Biological and Biomedical Sciences journal homepage: www.elsevier.com/locate/shpsc Biological atomism and cell theory Daniel J. Nicholson ESRC Research Centre for Genomics in Society (Egenis), University of Exeter, Byrne House, St. Germans Road, Exeter EX4 4PJ, UK article info abstract Keywords: Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activ- Biological atomism ity of a living organism is thus conceived as the result of the activities and interactions of its elementary Cell theory constituents, each of which individually already exhibits all the attributes proper to life. This paper sur- Organismal theory veys some of the key episodes in the history of biological atomism, and situates cell theory within this Reductionism tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, together with the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the phys- icochemical reductionism of mechanistic biology. -
Symbiogenesis: the New Principle of Evolution
Symbiogenesis: The New Principle of Evolution Boris Mikhailovich KOZO-POLYANSKY 1924 Translated from Russian and edited by Victor Fet, Marshall University, West Virginia Originally published as Novyi printsip biologii: ocherk teorii simbiogeneza [The New Principle of Biology: An Essay of the Theory of Symbiogenesis], Puchina, Leningrad- Moscow, 147 pp. We have changed the title and taken other liberties with the text with one goal in mind: to communicate Kozo-Polyansky’s brilliant work and to show its relevance to modern biology. Table of Contents Introduction Foreword A few words about Kozo-Polyansky Victor Fet Preface I. Non-cellular organisms (cytodes) and the bioblast 1. Bioblast of bacteria 2. Bioblast of Cyanophyceae, or blue-green “algae” 3. Symbiosis among cytodes 4. Symbiosis of cytodes with unicellular organisms 5. Symbiosis of cytodes with multicellular organisms 6. Cytodes as the ancestral organisms II. Cell and its organelles 1. Chlorophyll granules and other plastids, or trophoplasts (a) Chlorophyll granules in animals [and protists] (b) Chlorophyll granules in plants [and protists] 2. Centrosome 3. Cell nuclei 4. Mitochondria 5. Ergastoplasm 6. Reticular apparatus of Golgi 7. Nerve fibrils of N_mecs 8. Physodes 9. Myofibrils (contractile fibers) 10. Blepharoplast 11. Elaioplasts 12. Aleurone 13. Cytoplasm III. Multicellular organism A. First series of examples Lichens Unions of higher plants Unions of animals Sponge-algae B. Second series of examples Mucous glands in aquatic ferns (Azolla) and hornworts Stem glands of Gunnera Protein leaf glands in plants Coralloid organs of cycads Mycorrhiza (fungus root) in various plants Roots, tubers and flowers of orchids Heather in general, and its root in particular Toxic glands of Lolium temulentum C. -
Arxiv:2011.01294V2 [Q-Bio.PE] 23 Nov 2020 of Body Plans
Studying evolution of the primary body axis in vivo and in vitro Kerim Anlas1, Vikas Trivedi1;2;∗ The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process com- monly referred to as gastrulation. While substantial progress has been achieved in terms of characterizing the embryonic development of several model organisms, underlying principles of many early patterning processes nevertheless remain enigmatic. Despite the diversity of (pre-)gastrulating embryo and adult body shapes across the animal kingdom, the body axes, which are arguably the most fundamental features, generally remain identical between phyla. Recently there has been a renewed appreciation of ex vivo and in vitro embryo-like systems to model early embryonic patterning events. Here, we briefly review key examples and propose that similarities in morphogenesis as well as associated gene expression dynamics may reveal an evolutionarily conserved developmental mode as well as provide further insights into the role of external or extraembryonic cues in shaping the early embryo. In summary, we argue that embryo-like systems can be employed to inform previously uncharted aspects of animal body plan evolution as well as associated patterning rules. 1. Introduction In this perspective, we outline metazoan body axes and con- Metazoans display vast morphological diversity, yet body served initial patterning genes Wnt and Bra/T, followed by a plans can universally be distilled to the presence of one to brief review and comparison of mostly recent embryo-like sys- three body axes. Contrasted with protists, a characteristic tems in an evolutionary context. -
HOX CLUSTER INTERGENIC SEQUENCE EVOLUTION by JEREMY DON RAINCROW a Dissertation Submitted to the Graduate School-New Brunswick R
HOX CLUSTER INTERGENIC SEQUENCE EVOLUTION By JEREMY DON RAINCROW A Dissertation submitted to the Graduate School-New Brunswick Rutgers, The State University of New Jersey and The Graduate School of Biomedical Sciences University of Medicine and Dentistry of New Jersey in partial fulfillment of the requirements for the degree of Doctor of Philosophy Graduate Program in Cell and Developmental Biology written under the direction of Chi-hua Chiu and approved by ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ New Brunswick, New Jersey October 2010 ABSTRACT OF THE DISSERTATION HOX GENE CLUSTER INTERGENIC SEQUENCE EVOLUTION by JEREMY DON RAINCROW Dissertation Director: Chi-hua Chiu The Hox gene cluster system is highly conserved among jawed-vertebrates. Specifically, the coding region of Hox genes along with their spacing and occurrence is highly conserved throughout gnathostomes. The intergenic regions of these clusters however are more variable. During the construction of a comprehensive non-coding sequence database we discovered that the intergenic sequences appear to also be highly conserved among cartilaginous and lobe-finned fishes, but much more diverged and dynamic in the ray-finned fishes. Starting at the base of the Actinopterygii a turnover of otherwise highly conserved non-coding sequences begins. This turnover is extended well into the derived ray-finned fish clade, Teleostei. Evidence from our population genetic study suggests this turnover, which appears to be due mainly to loosened constraints at the macro-evolutionary level, is highlighted by evidence of strong positive selection acting at the micro-evolutionary level. During the construction of the non-coding sequence database we also discovered that along with evidence of both relaxed constraints and positive selection emerges a pattern of transposable elements found within the Hox gene cluster system. -
Mechanisms of Epithelial Morphogenesis and Integrity During Nematostella Vectensis Development and Shigella Pathogenesis by ASHL
Mechanisms of epithelial morphogenesis and integrity during Nematostella vectensis development and Shigella pathogenesis BY ASHLEIGH E FRITZ Submitted to the graduate degree program in Cell Biology and Anatomy and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________ Matthew C. Gibson, Ph.D., Co-Chair _______________________________ William H. Kinsey, Ph.D., Co-Chair ________________________________ Lane K. Christenson, Ph.D. _______________________________ Jennifer L. Gerton, Ph.D. ________________________________ Brenda J. Rongish, Ph.D. Date Defended: March 28, 2014 The Dissertation Committee for Ashleigh E Fritz certifies that this is the approved version of the following dissertation: Mechanisms of epithelial morphogenesis and integrity during Nematostella vectensis development and Shigella pathogenesis ________________________________ Matthew C. Gibson, Ph.D., Co-Chair ________________________________ William H. Kinsey, Ph.D., Co-Chair Date approved: April 4, 2014 ii Abstract The transition to animal multicellularity involved the evolution of single cells organizing into sheets of tissue. The advent of tissues allowed for specialization and diversification, which led to the formation of complex structures and a variety of body plans. These epithelial tissues undergo morphogenesis during animal development, and the establishment and maintenance of their polarity and integrity is crucial for homeostasis and prevention of pathogenesis.