Group Behavior of Unicellular Organisms for Better Survival Leading to Multi-Cellular Organisms
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Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
Origin and Evolution of Eukaryotic Compartmentalization
TESI DOCTORAL UPF 2016 Origin and evolution of eukaryotic compartmentalization Alexandros Pittis Director Dr. Toni Gabaldon´ Comparative Genomics Group Bioinformatics and Genomics Department Centre for Genomic Regulation (CRG) To my father Stavros for the PhD he never did Acknowledgments Looking back at the years of my PhD in the Comparative Genomics group at CRG, I feel it was equally a process of scientific, as well as personal development. All this time I was very privileged to be surrounded by people that offered me their generous support in both fronts. And they were available in the very moments that I was fighting more myself than the unsolvable (anyway) comparative genomics puzzles. I hope that in the future I will have many times the chance to express them my appreciation, way beyond these few words. First, to Toni, my supervisor, for all his support, and patience, and confidence, and respect, especially at the moments that things did not seem that promising. He offered me freedom, to try, to think, to fail, to learn, to achieve that few enjoy during their PhD, and I am very thankful to him. Then, to my good friends and colleagues, those that I found in the group already, and others that joined after me. A very special thanks to Marinita and Jaime, for all their valuable time, and guidance and paradigm, which nevertheless I never managed to follow. They have both marked my phylogenomics path so far and I cannot escape. To Les and Salvi, my fellow students and pals at the time for all that we shared; to Gab and Fran and Dam, for -
A Unicellular Relative of Animals Generates a Layer of Polarized Cells
RESEARCH ARTICLE A unicellular relative of animals generates a layer of polarized cells by actomyosin- dependent cellularization Omaya Dudin1†*, Andrej Ondracka1†, Xavier Grau-Bove´ 1,2, Arthur AB Haraldsen3, Atsushi Toyoda4, Hiroshi Suga5, Jon Bra˚ te3, In˜ aki Ruiz-Trillo1,6,7* 1Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; 2Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; 3Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway; 4Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; 5Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan; 6Departament de Gene`tica, Microbiologia i Estadı´stica, Universitat de Barcelona, Barcelona, Spain; 7ICREA, Barcelona, Spain Abstract In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an *For correspondence: actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a [email protected] (OD); polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly [email protected] (IR-T) regulated transcriptional activation of genes involved in cell adhesion. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected]. -
Coenocyte Caulerpa Taxifolia
An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia Aashish Ranjan1, Brad T. Townsley1, Yasunori Ichihashi1¤, Neelima R. Sinha1*, Daniel H. Chitwood2* 1 Department of Plant Biology, University of California at Davis, Davis, California, United States of America, 2 Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America Abstract Convergent morphologies have arisen in plants multiple times. In non-vascular and vascular land plants, convergent morphology in the form of roots, stems, and leaves arose. The morphology of some green algae includes an anchoring holdfast, stipe, and leaf-like fronds. Such morphology occurs in the absence of multicellularity in the siphonous algae, which are single cells. Morphogenesis is separate from cellular division in the land plants, which although are multicellular, have been argued to exhibit properties similar to single celled organisms. Within the single, macroscopic cell of a siphonous alga, how are transcripts partitioned, and what can this tell us about the development of similar convergent structures in land plants? Here, we present a de novo assembled, intracellular transcriptomic atlas for the giant coenocyte Caulerpa taxifolia. Transcripts show a global, basal-apical pattern of distribution from the holdfast to the frond apex in which transcript identities roughly follow the flow of genetic information in the cell, transcription-to-translation. The analysis of the intersection of transcriptomic atlases of a land plant and Caulerpa suggests the recurrent recruitment of transcript accumulation patterns to organs over large evolutionary distances. Our results not only provide an intracellular atlas of transcript localization, but also demonstrate the contribution of transcript partitioning to morphology, independent from multicellularity, in plants. -
DU Msc Botany
DU MSc Botany Question Question Sr.No Question Body Options Id Descripti on 1 2345 DU_J19_ Channel proteins that are located in the outer 9377: barrels , MSC_BOT membrane of Gram-negative bacteria are known 9378:murins , _Q01 as 9379:porins, 9380:granules , 2 2346 DU_J19_ Gram-negative bacteria are more resistant to 9381: peptidoglycan wall., MSC_BOT antibiotics than Gram-positive bacteria due to the 9382:outer lipopolysaccharide layer., _Q02 presence of 9383:porin protein., 9384:teichoic acid. , 3 2347 DU_J19_ Dormant, tough, non-reproductive structure, 9385: endospore , MSC_BOT produced by bacteria to tide over unfavourable 9386: sclerotium , _Q03 conditions is known as: 9387:sporocarp , 9388:heterocyst , 4 2348 DU_J19_ Three-dimensional structures of a cell can be 9389: Bright field , MSC_BOT studied by using which of the following 9390: Phase contrast , _Q04 microscopes? 9391:Fluorescent , 9392: Differential interference contrast , 5 2349 DU_J19_ Algae that grow at the interface of water and 9393: epipelic , MSC_BOT atmosphere are called as 9394:neustonic , _Q05 9395: planktonic , 9396: benthic, 6 2350 DU_J19_ Orthorhombic crystals of calcium carbonate are 9397: aragonite., MSC_BOT known as 9398: calcite. , _Q06 9399: detritus. , 9400: stromatolites. , 7 2351 DU_J19_ Which one of the following amino acids has a 9401: Lysine , MSC_BOT nonpolar, aliphatic R group? _Q07 7 2351 DU_J19_ Which one of the following amino acids has a MSC_BOT nonpolar, aliphatic R group? 9402: Histidine , _Q07 9403: Arginine , 9404: Glycine, 8 2352 DU_J19_ -
Can We Understand Evolution Without Symbiogenesis?
Can We Understand Evolution Without Symbiogenesis? Francisco Carrapiço …symbiosis is more than a mere casual and isolated biological phenomenon: it is in reality the most fundamental and universal order or law of life. Hermann Reinheimer (1915) Abstract This work is a contribution to the literature and knowledge on evolu- tion that takes into account the biological data obtained on symbiosis and sym- biogenesis. Evolution is traditionally considered a gradual process essentially consisting of natural selection, conducted on minimal phenotypical variations that are the result of mutations and genetic recombinations to form new spe- cies. However, the biological world presents and involves symbiotic associations between different organisms to form consortia, a new structural life dimension and a symbiont-induced speciation. The acknowledgment of this reality implies a new understanding of the natural world, in which symbiogenesis plays an important role as an evolutive mechanism. Within this understanding, symbiosis is the key to the acquisition of new genomes and new metabolic capacities, driving living forms’ evolution and the establishment of biodiversity and complexity on Earth. This chapter provides information on some of the key figures and their major works on symbiosis and symbiogenesis and reinforces the importance of these concepts in our understanding of the natural world and the role they play in the establishing of the evolutionary complexity of living systems. In this context, the concept of the symbiogenic superorganism is also discussed. Keywords Evolution · Symbiogenesis · Symbiosis · Symbiogenic superorgan- ism · New paradigm F. Carrapiço (*) Centre for Ecology Evolution and Environmental Change (CE3C); Centre for Philosophy of Science, Department of Plant Biology, Faculty of science, University of Lisbon, Lisbon, Portugal e-mail: [email protected] © Springer International Publishing Switzerland 2015 81 N. -
The Origin of Animal Body Plans: a View from Fossil Evidence and the Regulatory Genome Douglas H
© 2020. Published by The Company of Biologists Ltd | Development (2020) 147, dev182899. doi:10.1242/dev.182899 REVIEW The origin of animal body plans: a view from fossil evidence and the regulatory genome Douglas H. Erwin1,2,* ABSTRACT constraints on the interpretation of genomic and developmental The origins and the early evolution of multicellular animals required data. In this Review, I argue that genomic and developmental the exploitation of holozoan genomic regulatory elements and the studies suggest that the most plausible scenario for regulatory acquisition of new regulatory tools. Comparative studies of evolution is that highly conserved genes were initially associated metazoans and their relatives now allow reconstruction of the with cell-type specification and only later became co-opted (see evolution of the metazoan regulatory genome, but the deep Glossary, Box 1) for spatial patterning functions. conservation of many genes has led to varied hypotheses about Networks of regulatory interactions control gene expression and the morphology of early animals and the extent of developmental co- are essential for the formation and organization of cell types and option. In this Review, I assess the emerging view that the early patterning during animal development (Levine and Tjian, 2003) diversification of animals involved small organisms with diverse cell (Fig. 2). Gene regulatory networks (GRNs) (see Glossary, Box 1) types, but largely lacking complex developmental patterning, which determine cell fates by controlling spatial expression -
The Origin of Plastids By: Cheong Xin Chan, Ph.D
A Collaborative Learning Space for Science ABOUT FACULTY STUDENTS INTERMEDIATE CELL ORIGINS AND METABOLISM | Lead Editor: Gary Cote, Mario De Tullio The Origin of Plastids By: Cheong Xin Chan, Ph.D. & Debashish Bhattacharya, Ph.D. (Rutgers, The State University of New Jersey) © 2010 Nature Education Citation: Chan, C. X. & Bhattacharya, D. (2010) The Origin of Plastids. Nature Education 3(9):84 Plastids are core components of photosynthesis in plants and algae. Scientists are currently debating the events leading to the appearance of plastids in eukaryotic cells. Organelles, called plastids, are the main sites of photosynthesis in eukaryotic cells. Chloroplasts, as well as any other pigment containing cytoplasmic organelles that enables the harvesting and conversion of light and carbon dioxide into food and energy, are plastids. Found mainly in eukaryotic cells, plastids can be grouped into two distinctive types depending on their membrane structure: primary plastids and secondary plastids. Primary plastids are found in most algae and plants, and secondary, more-complex plastids are typically found in plankton, such as diatoms and dinoflagellates. Exploring the origin of plastids is an exciting field of research because it enhances our understanding of the basis of photosynthesis in green plants, our primary food source on planet Earth. Primary Plastids and Endosymbiosis Where did plastids originate? Their origin is explained by endosymbiosis, the act of a unicellular heterotrophic protist engulfing a free-living photosynthetic cyanobacterium and retaining it, instead of digesting it in the food vacuole (Margulis 1970; McFadden 2001; Kutschera & Niklas 2005). The captured cell (the endosymbiont) was then reduced to a functional organelle bound by two membranes, and was transmitted vertically to subsequent generations. -
Lynn Margulis
BIOGRAPHY THE INDOMITABLE EVOLUTIONIST: LYNN MARGULIS MEENAKSHI PANT The evolutionary “To me, the human move to take responsibility interest in science. In 1957, she graduated biologist Lynn for the living Earth is laughable — the rhetoric with a degree in Liberal Arts, and moved to Margulis is best of the powerless. The planet takes care of us, the University of Wisconsin to study Biology known for her not we of it. Our self-inflated moral imperative under Walter Plaut (who was to become her work on the Serial to guide a wayward Earth, or heal our sick supervisor) and Hans Ris. In 1960, she graduated Endosymbiotic planet, is evidence of our immense capacity with an MS degree in Zoology and Genetics. Theory (SET) to for self-delusion. Rather, we need to protect She then began her research career in the explain the origins ourselves from ourselves.” University of California, under the guidance of of eukaryotic Max Alfert, earning her doctoral degree in 1965. cells. This article Lynn was offered her first job — a research presents key facets his very courageous statement that assistantship and the position of a lecturer in in the life of Tchallenges the self-acclaimed supremacy Brandeis University — even before she could this avant-garde of humans over nature was made by Lynn finish her dissertation. However, it was only biologist and her Margulis (refer Fig.1). She is believed to be work that has one of the most creative scientific theorists after she had been awarded a PhD that she changed the way of the modern era, who transformed the idea moved to Boston University, where she taught we perceive life on of how life evolved on Earth. -
White-Rot Fungi As Potential Bioremediators of Endocrine Disrupting Compounds – a Mini Review
WHITE-ROT FUNGI AS POTENTIAL BIOREMEDIATORS OF ENDOCRINE DISRUPTING COMPOUNDS – A MINI REVIEW Damian Boer MSc Minor Thesis Department of Plant Breeding Wageningen University & Research 1 WHITE-ROT FUNGI AS POTENTIAL BIOREMEDIATORS OF ENDOCRINE DISRUPTING COMPOUNDS – A MINI REVIEW Student: Damian C.B. Boer Registration number: 941112-081-130 Course: MSc Minor Thesis Plant Breeding (PBR-80424) Study: MSc Plant Biotechnology: Molecular Breeding and Pathology Date of submission: 19-12-2018 Thesis period: 11-06-2018 – 19-12-2018 Mushroom Research Group Department of Plant Breeding Wageningen University & Research Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands Supervisor dr. AF Arend van Peer Examiner: dr. AF Arend van Peer Co-examiner: dr.ir. JC (Jan-Kees) Goud Copyright notice: No information of this report can be used without the consent of the above supervisor and / or examiners 2 ACKNOWLEDGEMENTS First and foremost, a thank you to my supervisor Arend van Peer for entrusting me with this novel and personally challenging topic of my minor thesis. The topic was outside my standard study-related curriculum, which presented a unique experience for me as a student in his final phase of his MSc. Altogether, I am grateful that I was allowed to delve deep into a new subject, having the freedom to explore and being able to fill in the contents of the thesis report. As with the proposal of genetic instability of mushrooms, I sincerely hope that my report will yield some new insights or perhaps inspire the start of a novel research proposal in the future. Second, I would like to thank Jan-Kees Goud for being my second examiner. -
Events with Lynn Margulies Collegium Helveticum STW/D13
Events with Lynn Margulies Prof. Dr. Lynn Margulis Collegium Helveticum STW/D13 Schmelzbergstrasse 25 8092 Zurich T 01 632 3385 F 01 632 1204 Lynn Margulis ist Distinguished University Professor des Departements Geowissenschaften der Universität von Massachusetts in Amherst und wissenschaftlicher Gast des Collegium Helveticum im Sommersemester 2001. My conversion to science occurred in the College of the University of Chicago. No class accepted more than 24 students, labs were frequent, and tests - suggestive only - didn't «count». Rather, a 9-hour final examination in June was the sole requirement for the final grade, and June seemed infinitely distant from that first day of class in autumn. Since textbooks were an anathema to learning, we read unabridged and uncompromised original works. We ignorant chickens accessed the great scientists: Isaac Newton, Francis Bacon, Galileo Galilei, Charles Darwin, Gregor Mendel, Hans Spemann, August Weismann, and the neo-Darwinists. The preoccupation of the great Natural Sciences II class was «What is heredity? What links the generations? How do the materials in fused egg and sperm generate the development of an animal? How does variation in evolution arise? How do organisms originate? Why do they evolve?» These haunting questions drive me still. Ever since I learned about the idea that variation in evolution arises by symbiogenesis, I have worked on it. Symbiosis, coined by the German botanist Anton deBary (1873), refers simply to physical contact between different kinds of organisms - in his words, «living together of differently named organisms.» Cohabitation, long-term living together, it was asserted by many, results in symbiogenesis. Symbiogenesis, the concept developed by the Russian, K.