Macroevolution of Complex Cytoskeletal Systems in Euglenids Brian S
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Morphology, Phylogeny, and Diversity of Trichonympha (Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus Punctulatus
J. Eukaryot. Microbiol., 56(4), 2009 pp. 305–313 r 2009 The Author(s) Journal compilation r 2009 by the International Society of Protistologists DOI: 10.1111/j.1550-7408.2009.00406.x Morphology, Phylogeny, and Diversity of Trichonympha (Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus punctulatus KEVIN J. CARPENTER, LAWRENCE CHOW and PATRICK J. KEELING Canadian Institute for Advanced Research, Botany Department, University of British Columbia, University Boulevard, Vancouver, BC, Canada V6T 1Z4 ABSTRACT. Trichonympha is one of the most complex and visually striking of the hypermastigote parabasalids—a group of anaerobic flagellates found exclusively in hindguts of lower termites and the wood-feeding cockroach Cryptocercus—but it is one of only two genera common to both groups of insects. We investigated Trichonympha of Cryptocercus using light and electron microscopy (scanning and transmission), as well as molecular phylogeny, to gain a better understanding of its morphology, diversity, and evolution. Microscopy reveals numerous new features, such as previously undetected bacterial surface symbionts, adhesion of post-rostral flagella, and a dis- tinctive frilled operculum. We also sequenced small subunit rRNA gene from manually isolated species, and carried out an environmental polymerase chain reaction (PCR) survey of Trichonympha diversity, all of which strongly supports monophyly of Trichonympha from Cryptocercus to the exclusion of those sampled from termites. Bayesian and distance methods support a relationship between Tricho- nympha species from termites and Cryptocercus, although likelihood analysis allies the latter with Eucomonymphidae. A monophyletic Trichonympha is of great interest because recent evidence supports a sister relationship between Cryptocercus and termites, suggesting Trichonympha predates the Cryptocercus-termite divergence. -
Biology of Protists Video and DVD Guide. the BIOLOGY of PROTISTS Produced by Biomedia ASSOCIATES ©2003 -- Running Time 20 Minutes
Biology of Protists video and DVD guide. THE BIOLOGY OF PROTISTS Produced by BioMEDIA ASSOCIATES ©2003 -- Running time 20 minutes. Order Toll Free (877) 661-5355 or FAX (843) 470-0237 Or mail orders to eBioMEDIA, P.O. Box 1234, Beaufort, SC 29901–1234 (IMAGES IN THIS GUIDE ARE FROM THE VIDEO PROGRAM) Cosmerium, a green alga Arcella, a shelled ameoba The goal of this program is to show a representative sample of the great diversity of protists, and to show why they need a new classification reflecting our growing understanding of their long evolutionary history. The protists shown can be found in habitats such as: roadside puddles, park duck ponds, aquariums, birdbaths and in the gut of termites. We hope that these observations will encourage students to collect pond water samples and see for themselves this amazing hidden world. The live photography was accomplished using a variety microscope techniques, including dark field (good for showing the natural color of subjects) and the most advanced forms of differential interference contrast (DIC gives contrast to transparent structures that would be invisible in normal bright field microscopy). While these forms of imaging living protists are particularly revealing for some aspects of micro-organism biology, all of the organisms seen here can be studied successfully with student microscopes. IMPORTANT NOTE: This program packs a lot of information and a wealth of observational data into nine different modules. We recommend that the material be viewed module by module, stopping for discussion and replay as needed. “Discussion starters” for the various modules are provided in this guide. -
[3 TD$DIFF]Interdisciplinary Team Science in Cell Biology
TICB 1268 No. of Pages 3 Scientific Life Cell biology, beginning largely as micro- detailed physical–chemical mechanisms Interdisciplinary[3_TD$IF] scopic observations, followed[1_TD$IF]the molec- [7]. The data required for these models ular biology revolution, which viewed are now in sight. New gene editing meth- Team Science in genes, cells, and the machinery that ods are providing endogenous expression underlies their activities as molecular sys- of tagged and mutant cells [8], and new Cell Biology tems that could be fully characterized and live-cell imaging methods are promising Rick Horwitz1,* understood using methods of genetics biochemistry in living cells, measuring con- and biochemistry. Viewing the cell as a centrations, dynamics, equilibria, and complex, dynamic molecular composite organization [9]. Similarly, super-resolution The cell is complex. With its multi- brought insights from chemistry and phys- microscopy and cryoEM tomography, tude of components, spatial– ics to bear on biological problems. Just as which allow structure determination and [6_TD$IF] temporal character, and gene the molecular genetic era was codified by organization in situ [3,4], imaging mass expression diversity, it is challeng- the publication of Watson's book, Molec- spectrometry [10], and single-cell and ing to comprehend the cell as an ular Biology of the Gene [1], two decades spatially-resolved genomic approaches integrated system and to develop later[8_TD$IF]the Molecular Biology of the Cell by [11–13], among other image-based tech- models that predict its behaviors. I Alberts, et al. [2] served a similar purpose nologies, all point to a new golden era of suggest an approach to address for cell biology. -
A Resurgence in Field Research Is Essential to Better Understand
Received Date : 15-Mar-2013 Revised Date : 21-Oct-2013 Accepted Date : 29-Oct-2013 Article type : Symposium Article Heger et al. --- Importance of Field Protistology A Resurgence in Field Research is Essential to Better Understand the Diversity, Ecology, and Evolution of Microbial Eukaryotes Thierry J. Hegera, Virginia P. Edgcombb, Eunsoo Kimc, Julius Lukešd, Brian S. Leandera & Naoji Yubukia a The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada b Woods Hole Oceanographic Institution, Geology and Geophysics Department, Woods Hole, Article MA 02543, USA c Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA d Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic Correspondence T. J. Heger and N. Yubuki, The Departments of Botany and Zoology, Beaty Biodiversity Research Centre and Museum, University of British Columbia, 6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada Telephone number: +1 604 822 4892; FAX number: +1 604 822 6089; emails: [email protected] and [email protected] ABSTRACT The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, -
Evolution and Comparative Morphology of the Euglenophyte
EVOLUTION AND COMPARATIVE MORPHOLOGY OF THE EUGLENOPHYTE PLASTID by PATRICK JERRY PAUL BROWN (Under the Direction of Mark A. Farmer) ABSTRACT My doctoral research centered on understanding the evolution of the euglenophyte protists, with special attention paid to their plastids. The euglenophytes are a widely distributed group of euglenid protists that have acquired a chloroplast via secondary symbiogenesis. The goals of my research were to 1) test the efficacy of plastid morphological and ultrastructural characters in phylogenetic analysis; 2) understand the process of plastid development and partitioning in the euglenophytes; 3) to use a plastid- encoded protein gene to determine a euglenophyte phylogeny; and 4) to perform a multi- gene analysis to uncover clues about the origins of the euglenophyte plastid. My work began with an alpha-taxonomic study that redefined the rare euglenophyte Euglena rustica. This work not only validly circumscribed the species, but also noted novel features of its habitat, cyclic migration habits, and cellular biology. This was followed by a study of plastid morphology and development in a number of diverse euglenophytes. The results of this study showed that the plastids of euglenophytes undergo drastic changes in morphology and ultrastructure over the course of a single cell division cycle. I concluded that there are four main classes of plastid development and partitioning in the euglenophytes, and that the class a given species will use is dependant on its interphase plastid morphology and the rigidity of the cell. The discovery of the class IV partitioning strategy in which cells with only one or very few plastids fragment their plastids prior to cell division was very significant. -
Protist Phylogeny and the High-Level Classification of Protozoa
Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). -
Genomic Divergence and Brain Evolution: How Regulatory DNA Influences Development of the Cerebral Cortex
Prospects & Overviews Review essays Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex Debra L. Silver1)2)3)4) The cerebral cortex controls our most distinguishing higher Introduction cognitive functions. Human-specific gene expression dif- ferences are abundant in the cerebral cortex, yet we have A large six-layered neocortex is a unique feature of only begun to understand how these variations impact brain mammalian brains. This specialized outer covering of the brain controls our higher cognitive functions including function. This review discusses the current evidence linking abstract thought and language, which together help uniquely non-coding regulatory DNA changes, including enhancers, define us as humans. Our distinguishing cognitive capacities with neocortical evolution. Functional interrogation using are specified within discrete cortical areas and are driven by animal models reveals converging roles for our genome in dynamic communication between neurons of the neocortex key aspects of cortical development including progenitor and other brain regions, as well as glial cell populations (including oligodendrocytes, microglia, and astrocytes). cell cycle and neuronal signaling. New technologies, Neurons are initially generated during human embryonic includingiPS cells and organoids, offerpotential alternatives and early fetal development, where they migrate to appropri- to modeling evolutionary modifications in a relevant species ate regions and begin establishing functional connections context. Several diseases rooted in the cerebral cortex during fetal and postnatal stages (Fig. 1). Disruptions to uniquely manifest in humans compared to other primates, cerebral cortex function arising during either development or thus highlighting the importance of understanding human adulthood, can result in neurodevelopmental and neurode- generative disorders. -
The Revised Classification of Eukaryotes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/231610049 The Revised Classification of Eukaryotes Article in Journal of Eukaryotic Microbiology · September 2012 DOI: 10.1111/j.1550-7408.2012.00644.x · Source: PubMed CITATIONS READS 961 2,825 25 authors, including: Sina M Adl Alastair Simpson University of Saskatchewan Dalhousie University 118 PUBLICATIONS 8,522 CITATIONS 264 PUBLICATIONS 10,739 CITATIONS SEE PROFILE SEE PROFILE Christopher E Lane David Bass University of Rhode Island Natural History Museum, London 82 PUBLICATIONS 6,233 CITATIONS 464 PUBLICATIONS 7,765 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Biodiversity and ecology of soil taste amoeba View project Predator control of diversity View project All content following this page was uploaded by Smirnov Alexey on 25 October 2017. The user has requested enhancement of the downloaded file. The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 59(5), 2012 pp. 429–493 © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists DOI: 10.1111/j.1550-7408.2012.00644.x The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. -
MOLECULAR CLOCKS Definition Introduction
MOLECULAR CLOCKS 583 Kishino, H., Thorne, J. L., and Bruno, W. J., 2001. Performance of Thorne, J. L., Kishino, H., and Painter, I. S., 1998. Estimating the a divergence time estimation method under a probabilistic model rate of evolution of the rate of molecular evolution. Molecular of rate evolution. Molecular Biology and Evolution, 18,352–361. Biology and Evolution, 15, 1647–1657. Kodandaramaiah, U., 2011. Tectonic calibrations in molecular dat- Warnock, R. C. M., Yang, Z., Donoghue, P. C. J., 2012. Exploring ing. Current Zoology, 57,116–124. uncertainty in the calibration of the molecular clock. Biology Marshall, C. R., 1997. Confidence intervals on stratigraphic ranges Letters, 8, 156–159. with nonrandom distributions of fossil horizons. Paleobiology, Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., 23, 165–173. and Tavaré, S., 2011. Dating primate divergences through an Müller, J., and Reisz, R. R., 2005. Four well-constrained calibration integrated analysis of palaeontological and molecular data. Sys- points from the vertebrate fossil record for molecular clock esti- tematic Biology, 60,16–31. mates. Bioessays, 27, 1069–1075. Yang, Z., and Rannala, B., 2006. Bayesian estimation of species Parham, J. F., Donoghue, P. C. J., Bell, C. J., et al., 2012. Best practices divergence times under a molecular clock using multiple fossil for justifying fossil calibrations. Systematic Biology, 61,346–359. calibrations with soft bounds. Molecular Biology and Evolution, Peters, S. E., 2005. Geologic constraints on the macroevolutionary 23, 212–226. history of marine animals. Proceedings of the National Academy Zuckerkandl, E., and Pauling, L., 1962. Molecular disease, evolution of Sciences, 102, 12326–12331. -
Parasitology Mgr. Anna Novák Vanclová Evolution of Euglenid Plastid Proteome
Charles University, Faculty of Science Univerzita Karlova, Přírodovědecká fakulta Study program: Parasitology Studijní program: Parazitologie Mgr. Anna Novák Vanclová Evolution of euglenid plastid proteome Evoluce proteomu plastidu euglenidů Summary of the doctoral thesis Thesis supervisor: doc. Vladimír Hampl, Ph.D. Prague, 2019 ABSTRACT Endosymbiotic gain and transfer of plastids is a widespread evolutionary phenomenon and a major driving force of eukaryotic evolution. The integration of a new organelle is accompanied by changes in its structure, gene content, molecular mechanisms for biogenesis and transport, and re-wiring of the host and organelle metabolic pathways. To understand the course and underlying mechanisms of plastid evolution, it is important to study these processes in variety of secondary algae and notice their differences and similarities. Euglenophytes gained their plastids from green eukaryotic algae after a long history of heterotrophic lifestyle. In my thesis, I participated in analyses of newly generated sequence datasets: transcriptomes of Euglena gracilis and Euglena longa and mass spectrometry-determined proteome of E. gracilis plastid with especial regard to the potential novelties associated with plastid gain and incorporation. In the resulting publications we particularly focus on plastid protein import machinery and targeting signals and report extremely reduced TIC and completely absent TOC in euglenophyte plastid. Using the proteomic dataset, we predict potential novel plastid protein translocases recruited from ER/Golgi and re-analyze plastid signal domains, characterizing previously overlooked features. Protein inventory of E. gracilis plastid suggests complex, in some cases redundant metabolic capacity. Chlorophyll recycling is one of the sources of phytol for reactions not connected to MEP/DOXP pathway. -
Biology & Biochemistry
Top Peer Reviewed Journals – Biology & Biochemistry Presented to Iowa State University Presented by Thomson Reuters Biology & Biochemistry The subject discipline for Biology & Biochemistry is made of 14 narrow subject categories from the Web of Science. The 14 categories that make up Biology & Biochemistry are: 1. Anatomy & Morphology 8. Cytology & Histology 2. Biochemical Research Methods 9. Endocrinology & Metabolism 3. Biochemistry & Molecular Biology 10. Evolutionary Biology 4. Biology 11. Medicine, Miscellaneous 5. Biology, Miscellaneous 12. Microscopy 6. Biophysics 13. Parasitology 7. Biotechnology & Applied Microbiology 14. Physiology The chart below provides an ordered view of the top peer reviewed journals within the 1st quartile for Biology & Biochemistry based on Impact Factors (IF), three year averages and their quartile ranking. Journal 2009 IF 2010 IF 2011 IF Average IF ANNUAL REVIEW OF BIOCHEMISTRY 29.87 29.74 34.31 31.31 PHYSIOLOGICAL REVIEWS 37.72 28.41 26.86 31.00 NATURE BIOTECHNOLOGY 29.49 31.09 23.26 27.95 CANCER CELL 25.28 26.92 26.56 26.25 ENDOCRINE REVIEWS 19.76 22.46 19.92 20.71 NATURE METHODS 16.87 20.72 19.27 18.95 ANNUAL REVIEW OF BIOPHYSICS AND 18.95 18.95 BIOMOLECULAR STRUCTURE ANNUAL REVIEW OF PHYSIOLOGY 18.17 16.1 20.82 18.36 Annual Review of Biophysics 19.3 17.52 13.57 16.80 Nature Chemical Biology 16.05 15.8 14.69 15.51 NATURE STRUCTURAL & MOLECULAR 12.27 13.68 12.71 12.89 BIOLOGY PLOS BIOLOGY 12.91 12.47 11.45 12.28 TRENDS IN BIOCHEMICAL SCIENCES 11.57 10.36 10.84 10.92 QUARTERLY REVIEWS OF BIOPHYSICS -
BMC Evolutionary Biology Biomed Central
BMC Evolutionary Biology BioMed Central Research article Open Access Complex distribution of EFL and EF-1α proteins in the green algal lineage Geoffrey P Noble, Matthew B Rogers and Patrick J Keeling* Address: Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada Email: Geoffrey P Noble - [email protected]; Matthew B Rogers - [email protected]; Patrick J Keeling* - [email protected] * Corresponding author Published: 23 May 2007 Received: 5 February 2007 Accepted: 23 May 2007 BMC Evolutionary Biology 2007, 7:82 doi:10.1186/1471-2148-7-82 This article is available from: http://www.biomedcentral.com/1471-2148/7/82 © 2007 Noble et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: EFL (or elongation factor-like) is a member of the translation superfamily of GTPase proteins. It is restricted to eukaryotes, where it is found in a punctate distribution that is almost mutually exclusive with elongation factor-1 alpha (EF-1α). EF-1α is a core translation factor previously thought to be essential in eukaryotes, so its relationship to EFL has prompted the suggestion that EFL has spread by horizontal or lateral gene transfer (HGT or LGT) and replaced EF-1α multiple times. Among green algae, trebouxiophyceans and chlorophyceans have EFL, but the ulvophycean Acetabularia and the sister group to green algae, land plants, have EF-1α.