Were Ancestral Proteins Less Specific?
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Comparative Methods for Reconstructing Ancient Genome Organization Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve
Comparative Methods for Reconstructing Ancient Genome Organization Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve To cite this version: Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Eric Tannier, Cedric Chauve. Comparative Methods for Reconstructing Ancient Genome Organization. Comparative Genomics: Methods and Protocols, pp.343 - 362, 2017, 10.1007/978-1-4939-7463-4_13. hal-03192460 HAL Id: hal-03192460 https://hal.archives-ouvertes.fr/hal-03192460 Submitted on 8 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Chapter 13 Comparative Methods for Reconstructing Ancient Genome Organization Yoann Anselmetti, Nina Luhmann, Se`verine Be´rard, Eric Tannier, and Cedric Chauve Abstract Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses regarding the involved evolutionary processes, inferring ancestral states explaining the similarities and an evolutionary history explaining the differences. In this chapter, we focus on the reconstruction of the organization of ancient genomes into chromosomes. We review different methodological approaches and software, applied to a wide range of datasets from different kingdoms of life and at different evolutionary depths. We discuss relations with genome assembly, and potential approaches to validate computational predictions on ancient genomes that are almost always only accessible through these predictions. -
(12) United States Patent (10) Patent No.: US 7.923,221 B1 Cabilly Et Al
US007.923221B1 (12) United States Patent (10) Patent No.: US 7.923,221 B1 Cabilly et al. (45) Date of Patent: *Apr. 12, 2011 (54) METHODS OF MAKING ANTIBODY HEAVY 4,512.922 A 4, 1985 Jones et al. AND LIGHT CHAINS HAVING SPECIFICITY 4,518,584 A 5, 1985 Mark 4,565,785 A 1/1986 Gilbert et al. FORADESIRED ANTIGEN 4,599,197 A 7, 1986 Wetzel 4,634,665 A 1/1987 Axel et al. (75) Inventors: Shmuel Cabilly, Monrovia, CA (US); 4,642,334 A 2f1987 Moore et al. Herbert L. Heyneker, Burlingame, CA 4,668,629 A 5/1987 Kaplan 4,704,362 A 11/1987 Itakura et al. (US); William E. Holmes, Pacifica, CA 4,713,339 A 12/1987 Levinson et al. (US); Arthur D. Riggs, LaVerne, CA 4,766,075 A 8, 1988 Goeddeletal. (US); Ronald B. Wetzel, San Francisco, 4,792.447 A 12/1988 Uhr et al. CA (US) 4,816,397 A * 3/1989 Boss et al. ...................... 435/68 4,816,567 A 3/1989 Cabilly et al. (73) Assignees: Genentech, Inc, South San Francisco, 4,965,196 A 10, 1990 Levinson et al. 5,081,235 A 1/1992 Shively et al. CA (US); City of Hope, Duarte, CA 5,098,833. A 3/1992 Lasky et al. (US) 5,116,964 A 5/1992 Capon et al. 5,137,721 A 8, 1992 Dallas (*) Notice: Subject to any disclaimer, the term of this 5,149,636 A 9, 1992 Axel et al. patent is extended or adjusted under 35 5,179,017 A 1/1993 Axel et al. -
How the Techniques of Molecular Biology Are Developed from Natural Systems
How the techniques of molecular biology are developed from natural systems Isobel Ronai [email protected] School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia. Abstract A striking characteristic of the highly successful techniques in molecular biology is that they are derived from natural systems. RNA interference (RNAi), for example, utilises a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other examples include restriction enzymes, the polymerase chain reaction, green fluorescent protein and CRISPR-Cas. I propose that biologists exploit natural molecular mechanisms for their effectors’ (protein or nucleic acid) activity and biological specificity (protein or nucleic acid can cause precise reactions). I also show that the developmental trajectory of novel techniques in molecular biology, such as RNAi, is four characteristic phases. The first phase is discovery of a biological phenomenon, typically as curiosity driven research. The second is identification of the mechanism’s trigger(s), the effector and biological specificity. The third is the application of the technique. The final phase is the maturation and refinement of the molecular biology technique. The development of new molecular biology techniques from nature is crucial for biological research. These techniques transform scientific knowledge and generate new knowledge. Keywords: mechanism; experiment; specificity; scientific practice; PCR; GFP. 1 Introduction Molecular biology is principally concerned with explaining the complex molecular phenomena underlying living processes by identifying the mechanisms that produce such processes (Tabery et al. 2015). In order to access the causal structure of molecular mechanisms it is generally necessary to manipulate the components of the mechanism and to observe the resulting effects with sophisticated molecular techniques. -
Reconstruction of Ancestral RNA Sequences Under Multiple Structural Constraints Olivier Tremblay-Savard1,2, Vladimir Reinharz1 and Jérôme Waldispühl1*
The Author(s) BMC Genomics 2016, 17(Suppl 10):862 DOI 10.1186/s12864-016-3105-4 RESEARCH Open Access Reconstruction of ancestral RNA sequences under multiple structural constraints Olivier Tremblay-Savard1,2, Vladimir Reinharz1 and Jérôme Waldispühl1* From 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop Montreal, Canada. 11-14 October 2016 Abstract Background: Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods: In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results: We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions: Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement. Keywords: RNA, Secondary structure, Ancestor reconstruction, Evolution, Phylogeny, Algorithm Background For a long time, most of the attention has been With the development of sequencing technologies given to the reconstruction of ancient protein and DNA emerged the need to elucidate the relationship between sequences, while RNA molecules remained relatively sequences from various organisms. -
Ancestral Reconstruction
TOPIC PAGE Ancestral Reconstruction Jeffrey B. Joy1,2, Richard H. Liang1, Rosemary M. McCloskey1, T. Nguyen1, Art F. Y. Poon1,2* 1 BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, 2 University of British Columbia, Department of Medicine, Vancouver, British Columbia, Canada * [email protected] Introduction Ancestral reconstruction is the extrapolation back in time from measured characteristics of a11111 individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individu- als, populations, or species to their ancestors. In the context of biology, ancestral reconstruction can be used to recover different kinds of ancestral character states, including the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the com- position of a genome (e.g., gene order), a measurable characteristic of an organism (pheno- OPEN ACCESS type), and the geographic range of an ancestral population or species (ancestral range reconstruction). Nonbiological applications include the reconstruction of the vocabulary or Citation: Joy JB, Liang RH, McCloskey RM, Nguyen phonemes of ancient languages [1] and cultural characteristics of ancient societies such as oral T, Poon AFY (2016) Ancestral Reconstruction. PLoS Comput Biol 12(7): e1004763. doi:10.1371/journal. traditions [2] or marriage practices [3]. pcbi.1004763 Ancestral reconstruction relies on a sufficiently realistic model of evolution to accurately recover ancestral states. No matter how well the model approximates the actual evolutionary Published: July 12, 2016 history, however, one's ability to accurately reconstruct an ancestor deteriorates with increasing Copyright: © 2016 Joy et al. -
Species Delimitation in Sea Anemones (Anthozoa: Actiniaria): from Traditional Taxonomy to Integrative Approaches
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 10 November 2019 doi:10.20944/preprints201911.0118.v1 Paper presented at the 2nd Latin American Symposium of Cnidarians (XVIII COLACMAR) Species delimitation in sea anemones (Anthozoa: Actiniaria): From traditional taxonomy to integrative approaches Carlos A. Spano1, Cristian B. Canales-Aguirre2,3, Selim S. Musleh3,4, Vreni Häussermann5,6, Daniel Gomez-Uchida3,4 1 Ecotecnos S. A., Limache 3405, Of 31, Edificio Reitz, Viña del Mar, Chile 2 Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue km. 6, Puerto Montt, Chile 3 Genomics in Ecology, Evolution, and Conservation Laboratory, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, P.O. Box 160-C, Concepción, Chile. 4 Nucleo Milenio de Salmonidos Invasores (INVASAL), Concepción, Chile 5 Huinay Scientific Field Station, P.O. Box 462, Puerto Montt, Chile 6 Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Avda. Brasil 2950, Valparaíso, Chile Abstract The present review provides an in-depth look into the complex topic of delimiting species in sea anemones. For most part of history this has been based on a small number of variable anatomic traits, many of which are used indistinctly across multiple taxonomic ranks. Early attempts to classify this group succeeded to comprise much of the diversity known to date, yet numerous taxa were mostly characterized by the lack of features rather than synapomorphies. Of the total number of species names within Actiniaria, about 77% are currently considered valid and more than half of them have several synonyms. Besides the nominal problem caused by large intraspecific variations and ambiguously described characters, genetic studies show that morphological convergences are also widespread among molecular phylogenies. -
Introduction: the Powers of Association
Copyrighted Material CHAPTER ONE Introduction: The Powers of Association In the summer of 2000, as the rainy season started, I made my way to the poor Dakar suburb of Th iaroye to meet a family with multiple cases of sickle cell anemia. Th ere were no paved sidewalks and my shoes sank in the mud when I jumped off the rusty minibus in a line of other hurried passengers. Stray sewer water bubbled from an opening in the street, creating small puddles of grey that were now being abluted by the downpour. Mr. Seck, the man I had come to see, had his niece keep watch for me, “the American from the hospital.” She surveyed me like sport as I divided my attention between the faulty gutters and locating the house. When we entered the compound, Seck welcomed me with a hard handshake. Th e whole family joined around, every one extending an arm, to introduce themselves with the familiarity and cheer an American usually reserves for a loved one. Doctors in town had recently diagnosed two of Seck’s children, ages eight and twelve, with HbSC sickle cell anemia, a less serious, heterozygous form of the more common homozygous HbSS disease. Both forms of the illness pro duce the hallmark symptom of this hemoglobin disorder: the vascular pain of arterial vessels clogged with sticky, damaged red blood cells, commonly called “the sickle cell crisis.” Th e children were prescribed folic acid for fi ft een days a month and Doliprane, the local name of acetaminophen, for pain when needed. -
Reconstructing Ancestral Gene Content by Coevolution
Downloaded from genome.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Methods Reconstructing ancestral gene content by coevolution Tamir Tuller,1,2,3,4,5 Hadas Birin,1,4 Uri Gophna,2 Martin Kupiec,2 and Eytan Ruppin1,3 1School of Computer Sciences, Tel Aviv University, Ramat Aviv 69978, Israel; 2Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel; 3School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel Inferring the gene content of ancestral genomes is a fundamental challenge in molecular evolution. Due to the statistical nature of this problem, ancestral genomes inferred by the maximum likelihood (ML) or the maximum-parsimony (MP) methods are prone to considerable error rates. In general, these errors are difficult to abolish by using longer genomic sequences or by analyzing more taxa. This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those reconstructed by ML or MP alone (more than 10% in some nodes). -
Molecular Phylogenetics Next Two Lectures
Next two lectures: • What is a phylogenetic tree? • How are trees inferred using molecular data? Molecular phylogenetics • How do you assess confidence in trees and clades on trees? Michael Worobey • Why do trees for different data sets sometimes conflict? • What can you do with trees beyond simply inferring relatedness? Molecular phylogenetics fundamentals Tree terminology All of life is related by common ancestry. Recovering this pattern, the "Tree of Life", is one of the primary goals of evolutionary biology. Even at the A tree is a mathematical structure which is used to model the actual evolutionary population level, the phylogenetic tree is indispensable as a tool for estimating history of a group of sequences or organisms. This actual pattern of historical parameters of interest. Likewise at the among species level, it is relationships is the phylogeny or evolutionary tree which we try and indispensable for examining patterns of diversification over time. First, you estimate. A tree consists of nodes connected by branches (also called need to be familiar with some tree terminology. edges). Terminal nodes (also called leaves, OTUs [Operational Taxonomic Units], external nodes or terminal taxa) represent sequences or organisms for which we have data; they may be either extant or extinct. Phylogenetics interlude Phylogenetics interlude • It’s all about ancestor and All the phylogenetics offspring populations, • Mutations happen when you need to know, in lineages branching genetic material is copied 5 minutes… • The ancestor could -
Climatic Niches in Phylogenetic Comparative Studies: a Review Of
bioRxiv preprint doi: https://doi.org/10.1101/018796; this version posted April 30, 2015. 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. 1 Climatic niches in phylogenetic comparative studies: a review of 2 challenges and approaches 1 1 3 Lara Budic and Carsten F. Dormann 4 Running title: Climatic niche in phylogenetic comparative studies 1 5 Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Str. 4, 6 79106 Freiburg 7 Corresponding author: 8 Lara Budic 9 e-mail: [email protected] 10 Key words: Climatic niche, phylogenetic comparative studies, ancestral niche reconstruction, 11 evolutionary models 1 bioRxiv preprint doi: https://doi.org/10.1101/018796; this version posted April 30, 2015. 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. 12 Abstract Studying the evolution of climatic niches through time in a phylogenetic 13 comparative framework combines species distribution modeling with phylogenies. 14 Phylogenetic comparative studies aid the understanding of the evolution of species' 15 environmental preferences by revealing the underlying evolutionary processes and causes, 16 detecting the differences among groups of species or relative to evolutionary pattern of other 17 phenotypic traits, but also act as a yardstick to gauge the adaptational potential under 18 climate change. -
Electronic Version2
TAIWANESE IDENTITY AND LANGUAGE EDUCATION The Role of Race, Ethnicity, Language, Culture and Nation in the Colonization of Taiwan A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfilment of the Requirements for the Degree of Master of Education In the Department of Education Foundations College of Education University of Saskatchewan Saskatoon By Edmond G. Tetrault Copyright Edmond G. Tetrault July 2003 All Rights Reserved PERMISSION TO USE In presenting this thesis in partial fulfilment of the requirements for a post-graduate degree at the University of Saskatchewan I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for the copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work, or, in their absence, by the Head of the Department or Dean of the College in which my thesis work was done. It is understood that any copying or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use of which may be made of any material in my thesis. Requests for permission to copy or make other use of material in this thesis should be addressed to: Head of the Department of Education Foundations College of Education University of Saskatchewan S7N 0W0 ii ABSTRACT In this thesis I look at the question of Taiwanese identity by focussing on characteristics that have come to be considered natural human identity attributes worldwide. -
History of Genetics Book Collection Catalogue
History of Genetics Book Collection Catalogue Below is a list of the History of Genetics Book Collection held at the John Innes Centre, Norwich, UK. For all enquires please contact Mike Ambrose [email protected] +44(0)1603 450630 Collection List Symposium der Deutschen Gesellschaft fur Hygiene und Mikrobiologie Stuttgart Gustav Fischer 1978 A69516944 BOOK-HG HG œ.00 15/10/1996 5th international congress on tropical agriculture 28-31 July 1930 Brussels Imprimerie Industrielle et Finangiere 1930 A6645004483 œ.00 30/3/1994 7th International Chromosome Conference Oxford Oxford 1980 A32887511 BOOK-HG HG œ.00 20/2/1991 7th International Chromosome Conference Oxford Oxford 1980 A44688257 BOOK-HG HG œ.00 26/6/1992 17th international agricultural congress 1937 1937 A6646004482 œ.00 30/3/1994 19th century science a selection of original texts 155111165910402 œ14.95 13/2/2001 150 years of the State Nikitsky Botanical Garden bollection of scientific papers. vol.37 Moscow "Kolos" 1964 A41781244 BOOK-HG HG œ.00 15/10/1996 Haldane John Burdon Sanderson 1892-1964 A banned broadcast and other essays London Chatto and Windus 1946 A10697655 BOOK-HG HG œ.00 15/10/1996 Matsuura Hajime A bibliographical monograph on plant genetics (genic analysis) 1900-1929 Sapporo Hokkaido Imperial University 1933 A47059786 BOOK-HG HG œ.00 15/10/1996 Hoppe Alfred John A bibliography of the writings of Samuel Butler (author of "erewhon") and of writings about him with some letters from Samuel Butler to the Rev. F. G. Fleay, now first published London The Bookman's Journal