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Metazoan Ribosome Inactivating Protein Encoding Genes Acquired by Horizontal Gene Transfer Received: 30 September 2016 Walter J
www.nature.com/scientificreports OPEN Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer Received: 30 September 2016 Walter J. Lapadula1, Paula L. Marcet2, María L. Mascotti1, M. Virginia Sanchez-Puerta3 & Accepted: 5 April 2017 Maximiliano Juri Ayub1 Published: xx xx xxxx Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first timein silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms. Ribosome inactivating proteins (RIPs, EC 3.2.2.22) irreversibly modify ribosomes through the depurination of an adenine residue in the conserved alpha-sarcin/ricin loop of 28S rRNA1–4. This modification prevents the binding of elongation factor 2 to the ribosome, arresting protein synthesis5, 6. The occurrence of RIP genes has been exper- imentally confirmed in a wide range of plant taxa, as well as in several species of Gram positive and Gram negative bacteria7–9. -
Is the Germline Immortal and Continuous? a Discussion in Light of Ipscs and Germline Regeneration
Is the Germline Immortal and Continuous? A Discussion in Light of iPSCs and Germline Regeneration 1 1 Kate MacCord and B. Duygu Özpolat 1 - Marine Biological Laboratory, Woods Hole, MA, USA 1 ABSTRACT The germline gives rise to gametes, is the hereditary cell lineage, and is often called immortal and continuous. However, what exactly is immortal and continuous about the germline has recently come under scrutiny. The notion of an immortal and continuous germline has been around for over 130 years, and has led to the concept of a barrier between the germline and soma (the “Weismann barrier”). One repercussion of such a barrier is the understanding that when the germline is lost, soma cannot replace it, rendering the organism infertile. Recent research on induced pluripotent stem cells (iPSCs) and germline regeneration raise questions about the impermeability of the Weismann barrier and the designation of the germline as immortal and continuous. How we conceive of the germline and its immortality shapes what we perceive to be possible in animal biology, such as whether somatic cells contribute to the germline in some metazoans during normal development or regeneration. We argue that reassessing the universality of germline immortality and continuity across all metazoans leads to big and exciting open questions about the germ-soma cell distinction, cell reprogramming, germline editing, and even evolution. 2 1.0 Introduction The germline is the lineage of reproductive cells that includes gametes and their precursors, including primordial germ cells and germline stem cells. Because the germline gives rise to the gametes, it is the hereditary cell lineage, and is ultimately responsible for all cells in an organism’s body, including the next generation of the germline, stem cells, and other somatic cells. -
Reticulate Evolution Everywhere
Reticulate Evolution Everywhere Nathalie Gontier Abstract Reticulation is a recurring evolutionary pattern found in phylogenetic reconstructions of life. The pattern results from how species interact and evolve by mechanisms and processes including symbiosis; symbiogenesis; lateral gene transfer (that occurs via bacterial conjugation, transformation, transduction, Gene Transfer Agents, or the movements of transposons, retrotransposons, and other mobile genetic elements); hybridization or divergence with gene flow; and infec- tious heredity (induced either directly by bacteria, bacteriophages, viruses, pri- ons, protozoa and fungi, or via vectors that transmit these pathogens). Research on reticulate evolution today takes on inter- and transdisciplinary proportions and is able to unite distinct research fields ranging from microbiology and molecular genetics to evolutionary biology and the biomedical sciences. This chapter sum- marizes the main principles of the diverse reticulate evolutionary mechanisms and situates them into the chapters that make up this volume. Keywords Reticulate evolution · Symbiosis · Symbiogenesis · Lateral Gene Transfer · Infectious agents · Microbiome · Viriome · Virolution · Hybridization · Divergence with gene flow · Evolutionary patterns · Extended Synthesis 1 Reticulate Evolution: Patterns, Processes, Mechanisms According to the Online Etymology Dictionary (http://www.etymonline.com), the word reticulate is an adjective that stems from the Latin words “re¯ticulātus” (having a net-like pattern) and re¯ticulum (little net). When scholars identify the evolution of life as being “reticulated,” they first and foremost refer to a recurring evolutionary pattern. N. Gontier (*) AppEEL—Applied Evolutionary Epistemology Lab, University of Lisbon, Lisbon, Portugal e-mail: [email protected] © Springer International Publishing Switzerland 2015 1 N. Gontier (ed.), Reticulate Evolution, Interdisciplinary Evolution Research 3, DOI 10.1007/978-3-319-16345-1_1 2 N. -
The Lamarckian Chicken and the Darwinian Egg Yitzhak Pilpel1* and Oded Rechavi2*
Pilpel and Rechavi Biology Direct (2015) 10:34 DOI 10.1186/s13062-015-0062-9 COMMENT Open Access The Lamarckian chicken and the Darwinian egg Yitzhak Pilpel1* and Oded Rechavi2* Abstract: “Which came first, the Chicken or the Egg?” We suggest this question is not a paradox. The Modern Synthesis envisions speciation through genetic changes in germ cells via random mutations, an “Egg first” scenario, but perhaps epigenetic inheritance mechanisms can transmit adaptive changes initiated in the soma (“Chicken first”). Reviewers: The article was reviewed by Dr. Eugene Koonin, Dr. Itai Yanai, Dr. Laura Landweber. Keywords: Evolution, Darwinian Evolution, Lamarckian Evolution, Modern Synthesis, Weismann Barrier, Epigenetic Inheritance, Transgenerational RNA Interference Background solution. Nevertheless, it is important to discuss why this In this commentary paper we wish to use the well- question is perceived as being paradoxical, and to exam- known “Chicken and Egg” paradox as a gateway for ine the true mystery that it holds; at the base of this discussing different processes of evolution. While in the dilemma stands an extremely important and unsolved biological sense this is not a paradox at all, the metaphor biological question: “Can the phenotype affect the is still useful because it allows examining of the distinc- genotype”? or put differently, “Can epigenetics translate tion between Lamarckian and Darwinian evolution, and into genetics”? specifically, since it enables us to raise an important and Asking the question in this manner allows mapping of unsolved question: “Can the phenotype affect the geno- the “Egg first” vs. the “Chicken first” options onto the type?” or in other words, “can epigenetics translate into distinction between Darwinian and Lamarckian evolu- genetics”? tion. -
Molecular Lamarckism: on the Evolution of Human Intelligence
World Futures The Journal of New Paradigm Research ISSN: 0260-4027 (Print) 1556-1844 (Online) Journal homepage: https://www.tandfonline.com/loi/gwof20 Molecular Lamarckism: On the Evolution of Human Intelligence Fredric M. Menger To cite this article: Fredric M. Menger (2017) Molecular Lamarckism: On the Evolution of Human Intelligence, World Futures, 73:2, 89-103, DOI: 10.1080/02604027.2017.1319669 To link to this article: https://doi.org/10.1080/02604027.2017.1319669 © 2017 The Author(s). Published with license by Taylor & Francis Group, LLC© Fredric M. Menger Published online: 26 May 2017. Submit your article to this journal Article views: 3145 View related articles View Crossmark data Citing articles: 1 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=gwof20 World Futures, 73: 89–103, 2017 Copyright © Fredric M. Menger ISSN: 0260-4027 print / 1556-1844 online DOI: 10.1080/02604027.2017.1319669 MOLECULAR LAMARCKISM: ON THE EVOLUTION OF HUMAN INTELLIGENCE Fredric M. Menger Emory University, Atlanta, Georgia, USA In modern times, Lamarck’s view of evolution, based on inheritance of acquired traits has been superseded by neo-Darwinism, based on random DNA mutations. This article begins with a series of observations suggesting that Lamarckian inheritance is in fact operative throughout Nature. I then launch into a discussion of human intelligence that is the most important feature of human evolution that cannot be easily explained by mutational -
Metazoan Ribotoxin Genes Acquired by Horizontal Gene Transfer
bioRxiv preprint doi: https://doi.org/10.1101/071340; this version posted August 26, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Metazoan ribotoxin genes acquired by Horizontal Gene Transfer Walter J. Lapadula1*, Paula L. Marcet2, María L. Mascotti1, María V. Sánchez Puerta3, Maximiliano Juri Ayub1* 1. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis, IMIBIO-SL-CONICET and Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis Argentina. 2. Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Atlanta, USA. 3. Instituto de Ciencias Básicas, IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina. *Corresponding authors: [email protected], [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/071340; this version posted August 26, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. -
Darwinism and Lamarckism Before and After Weismann: a Historical, Philosophical, and Methodological Analysis
DARWINISM AND LAMARCKISM BEFORE AND AFTER WEISMANN: A HISTORICAL, PHILOSOPHICAL, AND METHODOLOGICAL ANALYSIS by Francis J. Cartieri University of Pittsburgh, BPhil, 2009 Submitted to the Faculty of The College of Arts and Sciences in conjunction with the University Honors College in partial fulfillment of the requirements for the degree of Bachelor of Philosophy University of Pittsburgh 2009 Cartieri 2 UNIVERSITY OF PITTSBURGH COLLEGE OF ARTS AND SCIENCES & THE UNIVERSITY HONORS COLLEGE This thesis was presented by Francis J. Cartieri It was defended on April 21, 2009 and approved by David Denks, Professor, Philosophy Jeffrey Schwartz, Professor, Anthropology Peter Machamer, Professor, History and Philosophy of Science Thesis Director: Sandra Mitchell, Professor and Chair, History and Philosophy of Science Cartieri 3 ABSTRACT Darwinism and Lamarckism before and after Weismann: A Historical, Philosophical, and Methodological analysis. Francis J. Cartieri Chair: Sandra D. Mitchell When exploring the relationship between two reputedly competitive scientific concepts that have persisted, with modification, through time, there are three main features to consider. First, there are historical features of an evolving relationship. Just as a causal story can be reconstructed concerning adaptations in a complex system, an analogous story can be supplied for the historical contingencies that have shaped the organization and development of Lamarckian and Darwinian biological thought, and their interactions, over time. Second, there are philosophical -
Double-Stranded RNA Made in C. Elegans Neurons Can Enter the Germline and Cause Transgenerational Gene Silencing
Double-stranded RNA made in C. elegans neurons can enter the germline and cause transgenerational gene silencing Sindhuja Devanapally, Snusha Ravikumar, and Antony M. Jose1 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 Edited by Gary Ruvkun, Massachusetts General Hospital, Boston, MA, and approved January 9, 2015 (received for review December 10, 2014) An animal that can transfer gene-regulatory information from whether somatic cells in C. elegans can export signals for delivery somatic cells to germ cells may be able to communicate changes in into the germline to cause transgenerational gene silencing. the soma from one generation to the next. In the worm Caeno- The transfer of gene-specific information from one somatic rhabditis elegans, expression of double-stranded RNA (dsRNA) in tissue to another somatic tissue during RNAi has been observed neurons can result in the export of dsRNA-derived mobile RNAs to in C. elegans (22). Such intertissue transfer of gene-regulatory other distant cells. Here, we show that neuronal mobile RNAs can information appears to occur through the transport of forms of cause transgenerational silencing of a gene of matching sequence in dsRNA called mobile RNAs (23). Entry of these mobile RNAs germ cells. Consistent with neuronal mobile RNAs being forms of into the cytosol requires the dsRNA-selective importer SID-1 dsRNA, silencing of target genes that are expressed either in so- (22, 24, 25). Consequently, when dsRNA is expressed in a variety matic cells or in the germline requires the dsRNA-selective importer of somatic tissues such as the gut, muscles, or neurons, SID-1– SID-1. -
Ageing Through Reproductive Death in Caenorhabditis Elegans
Ageing through reproductive death in Caenorhabditis elegans Institute of Healthy Ageing and department of Genetics, Evolution and Environment, University College London Carina Carla Kern Genetics and Evolutionary Biology PhD Thesis Supervisor: David Gems November 2020 1 I, Carina Kern, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. …………………………………………………………………… 2 Abstract The nematode worm Caenorhabditis elegans has emerged as one of the premier model systems for ageing research. Its use has led to the discovery of many biological mechanisms of ageing conserved across species, including acceleration of ageing by insulin/IGF-1 signalling (IIS) and germline signalling. Ageing in C. elegans, however, is unusual in terms of the severity and early onset of senescent pathology, particularly affecting organs involved in reproduction. For example, in post-reproductive hermaphrodites, intestinal biomass is converted into yolk leading to intestinal atrophy and yolk steatosis. While late yolk production has long been viewed as futile, is it possible that it somehow promote fitness? Results in this thesis show that post-reproductive C. elegans hermaphrodites vent yolk that can be consumed by larvae, promoting their growth. Thus, post-reproductive mothers can contribute to reproductive fitness by converting their biomass into milk, suggesting that intestinal atrophy is a cost of lactation. This type of massive reproductive effort involving biomass repurposing leading to organ degeneration is characteristic of semelparous organisms (i.e. that exhibit only a single reproductive episode) ranging from monocarpic plants to Pacific salmon where it leads to rapid death (reproductive death). -
150 Years of Darwin's Theory of Intercellular Flow of Hereditary
COMMENT 150 years of Darwin’s theory of intercellular flow of hereditary information Yongsheng Liu1,2 and Qi Chen 3* In 1868, Charles Darwin published his Pangenesis theory , which proposed a mechanism for the flow of hereditary information between cells and generations. Pangenesis has since been disputed, but emerging evidence of cell-to-cell communication urges the reconsideration of this 150-year-old theory. The theory of Pangenesis each bud, ovule, spermatozoon, and pollengrain”. These In 1868, 9 years after the advent of On the Origin of Species, speculations could not be validated at the time and were Charles Darwin published his two-volume book, The considered as “the fictions of the fancy” by the physician Variation of Animals and Plants under Domestication1, and microscopist Lionel Beale, and as “a pure invention” in which he introduced the theory of Pangenesis. This by the evolutionary biologist August Weismann. In a was an attempt to strengthen the theory of evolution by series of blood transfusion experiments, Francis Galton providing a cellular or molecular mechanism of inheri- failed to detect fur colour changes in the offspring of tance, and to understand the cause of variation upon silver-grey rabbits that were transfused with the blood which natural selection acts. of lop-eared rabbits; he concluded that the blood did not In the Pangenesis theory, Darwin proposed that in carry Darwin’s hypothetical gemmules. addition to cell division as a mean of transferring infor- Second, Pangenesis attempted to explain a range mation, every cell also emits numerous particles or mol- of doubtful phenomena including the inheritance of ecules called ‘gemmules’, which diffuse to and are ‘united’ acquired characteristics; but as the evolutionary bio- with both somatic cells and germ cells. -
Progress in Biophysics and Molecular Biology What Prevents Mainstream
Progress in Biophysics and Molecular Biology xxx (xxxx) xxx Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/jpbm What prevents mainstream evolutionists teaching the whole truth about how genomes evolve? ∗ James Shapiro a, , Denis Noble b a Department of Biochemistry and Molecular Biology, University of Chicago, United States of America b Department of Physiology, Anatomy & Genetics, University of Oxford, United Kingdom article info a b s t r a c t Article history: The common belief that the neo-Darwinian Modern Synthesis (MS) was buttressed by the discoveries Received 31 December 2020 of molecular biology is incorrect. On the contrary those discoveries have undermined the MS. This Received in revised form 31 March 2021 article discusses the many processes revealed by molecular studies and genome sequencing that Accepted 26 April 2021 contribute to evolution but nonetheless lie beyond the strict confines of the MS formulated in the Available online xxxx 1940s. The core assumptions of the MS that molecular studies have discredited include the idea Keywords: that DNA is intrinsically a faithful self-replicator, the one-way transfer of heritable information Evolutionary biology from nucleic acids to other cell molecules, the myth of ``selfish DNA'', and the existence of an Modern Synthesis impenetrable Weismann Barrier separating somatic and germ line cells. Processes fundamental to Molecular biology and evolution modern evolutionary theory include symbiogenesis, biosphere interactions between distant taxa Central Dogma (including viruses), horizontal DNA transfers, natural genetic engineering, organismal stress responses Weismann Barrier that activate intrinsic genome change operators, and macroevolution by genome restructuring (distinct Macroevolution Genomics from the gradual accumulation of local microevolutionary changes in the MS). -
COURS I 2014 Heard.Pptx
CHAIRE ÉPIGÉNÉTIQUE ET MÉMOIRE CELLULAIRE The Weissmann barrier – the germ plasm –germline Année 2013-2014 : Spemann and Mangold - first nuclear transfer, in amphibians Briggs and King – Gurdon – nuclear transfer in Dario then Xenopus “Reprogrammations développementales, Mouse clones – discovery of imprinting Plants – first clones! (here or earlier?) induites et pathologiques ” Animal clones and their problems Cat clones and non randomXCI Plant clone problems Cours I Heterokaryons and Synkaryons Reprogrammation de l’identité cellulaire – introduction historique 10 mars 2014 Seminaire: Sir John Gurdon, le vendredi 14 mars à 17h30 E. Heard, March 10th 2014 the Nobel Prize awarded to John Gurdon and Shinya Yamanaka in 2012 symbolizes the extraordinary contribution that reprogramming experiments have made (and will make) to our understanding of cellular identity and the apparently unlimited practical applications of iPSCs and other reprogrammed cells. 1. l’unité de base de tous les êtres vivants est Omnis cellula e cellula la cellule (Virchow, 1855) 2. Toute cellule provient d’une autre cellule 3. Le noyau de la cellule conen le matériel de l’heredité – l’ADN – le Genome 4. Dans le cycle de vie – on peut considerer la premiere cellule comme l’oeuf fecondé 5. A parr de cee unique cellule, tous les ssues, organes sont elaboré – avec parfois une sophscaon qui nous fascine toujours… “And thus the wonderful truth became manifest that a single cell may contain within its microscopic compass the sum total of the heritage of the species”. EB Wilson, 1900 hp://www.collecve-evoluon.com Et le noyau conent le matériel de l’heredité – les chromosomes… Eye Heart and nerves Macrophage E.