Inference and Analysis of Population Structure Using Genetic Data and Network Theory
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
Gene Linkage and Genetic Mapping 4TH PAGES © Jones & Bartlett Learning, LLC
© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Gene Linkage and © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 4NOTGenetic FOR SALE OR DISTRIBUTIONMapping NOT FOR SALE OR DISTRIBUTION CHAPTER ORGANIZATION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR4.1 SALELinked OR alleles DISTRIBUTION tend to stay 4.4NOT Polymorphic FOR SALE DNA ORsequences DISTRIBUTION are together in meiosis. 112 used in human genetic mapping. 128 The degree of linkage is measured by the Single-nucleotide polymorphisms (SNPs) frequency of recombination. 113 are abundant in the human genome. 129 The frequency of recombination is the same SNPs in restriction sites yield restriction for coupling and repulsion heterozygotes. 114 fragment length polymorphisms (RFLPs). 130 © Jones & Bartlett Learning,The frequency LLC of recombination differs © Jones & BartlettSimple-sequence Learning, repeats LLC (SSRs) often NOT FOR SALE OR DISTRIBUTIONfrom one gene pair to the next. NOT114 FOR SALEdiffer OR in copyDISTRIBUTION number. 131 Recombination does not occur in Gene dosage can differ owing to copy- Drosophila males. 115 number variation (CNV). 133 4.2 Recombination results from Copy-number variation has helped human populations adapt to a high-starch diet. 134 crossing-over between linked© Jones alleles. & Bartlett Learning,116 LLC 4.5 Tetrads contain© Jonesall & Bartlett Learning, LLC four products of meiosis. -
Unit 2 Cell Biology Page 1 Sub-Topics Include
Sub-Topics Include: 2.1 Cell structure 2.2 Transport across cell membranes 2.3 Producing new cells 2.4 DNA and the production of proteins 2.5 Proteins and enzymes 2.6 Genetic Engineering 2.7 Respiration 2.8 Photosynthesis Unit 2 Cell Biology Page 1 UNIT 2 TOPIC 1 1. Cell Structure 1. Types of organism Animals and plants are made up of many cells and so are described as multicellular organisms. Similar cells doing the same job are grouped together to form tissues. Animals and plants have systems made up of a number of organs, each doing a particular job. For example, the circulatory system is made up of the heart, blood and vessels such as arteries, veins and capillaries. Some fungi such as yeast are single celled while others such as mushrooms and moulds are larger. Cells of animals plants and fungi have contain a number of specialised structures inside their cells. These specialised structures are called organelles. Bacteria are unicellular (exist as single cells) and do not have organelles in the same way as other cells. 2. Looking at Organelles Some organelles can be observed by staining cells and viewing them using a light microscope. Other organelles are so small that they cannot be seen using a light microscope. Instead, they are viewed using an electron microscope, which provides a far higher magnification than a light microscope. Most organelles inside cells are surrounded by a membrane which is similar in composition (make-up) to the cell membrane. Unit 2 Cell Biology Page 2 3. A Typical Cell ribosome 4. -
Chapter 13 Protein Structure Learning Objectives
Chapter 13 Protein structure Learning objectives Upon completing this material you should be able to: ■ understand the principles of protein primary, secondary, tertiary, and quaternary structure; ■use the NCBI tool CN3D to view a protein structure; ■use the NCBI tool VAST to align two structures; ■explain the role of PDB including its purpose, contents, and tools; ■explain the role of structure annotation databases such as SCOP and CATH; and ■describe approaches to modeling the three-dimensional structure of proteins. Outline Overview of protein structure Principles of protein structure Protein Data Bank Protein structure prediction Intrinsically disordered proteins Protein structure and disease Overview: protein structure The three-dimensional structure of a protein determines its capacity to function. Christian Anfinsen and others denatured ribonuclease, observed rapid refolding, and demonstrated that the primary amino acid sequence determines its three-dimensional structure. We can study protein structure to understand problems such as the consequence of disease-causing mutations; the properties of ligand-binding sites; and the functions of homologs. Outline Overview of protein structure Principles of protein structure Protein Data Bank Protein structure prediction Intrinsically disordered proteins Protein structure and disease Protein primary and secondary structure Results from three secondary structure programs are shown, with their consensus. h: alpha helix; c: random coil; e: extended strand Protein tertiary and quaternary structure Quarternary structure: the four subunits of hemoglobin are shown (with an α 2β2 composition and one beta globin chain high- lighted) as well as four noncovalently attached heme groups. The peptide bond; phi and psi angles The peptide bond; phi and psi angles in DeepView Protein secondary structure Protein secondary structure is determined by the amino acid side chains. -
Course Outline for Biology Department Adeyemi College of Education
COURSE CODE: BIO 111 COURSE TITLE: Basic Principles of Biology COURSE OUTLINE Definition, brief history and importance of science Scientific method:- Identifying and defining problem. Raising question, formulating Hypotheses. Designing experiments to test hypothesis, collecting data, analyzing data, drawing interference and conclusion. Science processes/intellectual skills: (a) Basic processes: observation, Classification, measurement etc (b) Integrated processes: Science of Biology and its subdivisions: Botany, Zoology, Biochemistry, Microbiology, Ecology, Entomology, Genetics, etc. The Relevance of Biology to man: Application in conservation, agriculture, Public Health, Medical Sciences etc Relation of Biology to other science subjects Principles of classification Brief history of classification nomenclature and systematic The 5 kingdom system of classification Living and non-living things: General characteristics of living things. Differences between plants and animals. COURSE OUTLINE FOR BIOLOGY DEPARTMENT ADEYEMI COLLEGE OF EDUCATION COURSE CODE: BIO 112 COURSE TITLE: Cell Biology COURSE OUTLINE (a) A brief history of the concept of cell and cell theory. The structure of a generalized plant cell and generalized animal cell, and their comparison Protoplasm and its properties. Cytoplasmic Organelles: Definition and functions of nucleus, endoplasmic reticulum, cell membrane, mitochondria, ribosomes, Golgi, complex, plastids, lysosomes and other cell organelles. (b) Chemical constituents of cell - salts, carbohydrates, proteins, fats -
Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris Rarus) in a Successive Generation Closed Colony
diversity Article Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony Lei Cai 1,2,3, Miaomiao Hou 1,2, Chunsen Xu 1,2, Zhijun Xia 1,2 and Jianwei Wang 1,4,* 1 The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China; [email protected] (L.C.); [email protected] (M.H.); [email protected] (C.X.); [email protected] (Z.X.) 2 University of Chinese Academy of Sciences, Beijing 100049, China 3 Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China 4 National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China * Correspondence: [email protected] Received: 10 November 2020; Accepted: 11 December 2020; Published: 18 December 2020 Abstract: The complex genetic architecture of closed colonies during successive passages poses a significant challenge in the understanding of the genetic background. Research on the dynamic changes in genetic structure for the establishment of a new closed colony is limited. In this study, we developed 51 single nucleotide polymorphism (SNP) markers for the rare minnow (Gobiocypris rarus) and conducted genetic diversity and structure analyses in five successive generations of a closed colony using 20 SNPs. The range of mean Ho and He in five generations was 0.4547–0.4983 and 0.4445–0.4644, respectively. No significant differences were observed in the Ne, Ho, and He (p > 0.05) between the five closed colony generations, indicating well-maintained heterozygosity. -
Multidisciplinary Design Project Engineering Dictionary Version 0.0.2
Multidisciplinary Design Project Engineering Dictionary Version 0.0.2 February 15, 2006 . DRAFT Cambridge-MIT Institute Multidisciplinary Design Project This Dictionary/Glossary of Engineering terms has been compiled to compliment the work developed as part of the Multi-disciplinary Design Project (MDP), which is a programme to develop teaching material and kits to aid the running of mechtronics projects in Universities and Schools. The project is being carried out with support from the Cambridge-MIT Institute undergraduate teaching programe. For more information about the project please visit the MDP website at http://www-mdp.eng.cam.ac.uk or contact Dr. Peter Long Prof. Alex Slocum Cambridge University Engineering Department Massachusetts Institute of Technology Trumpington Street, 77 Massachusetts Ave. Cambridge. Cambridge MA 02139-4307 CB2 1PZ. USA e-mail: [email protected] e-mail: [email protected] tel: +44 (0) 1223 332779 tel: +1 617 253 0012 For information about the CMI initiative please see Cambridge-MIT Institute website :- http://www.cambridge-mit.org CMI CMI, University of Cambridge Massachusetts Institute of Technology 10 Miller’s Yard, 77 Massachusetts Ave. Mill Lane, Cambridge MA 02139-4307 Cambridge. CB2 1RQ. USA tel: +44 (0) 1223 327207 tel. +1 617 253 7732 fax: +44 (0) 1223 765891 fax. +1 617 258 8539 . DRAFT 2 CMI-MDP Programme 1 Introduction This dictionary/glossary has not been developed as a definative work but as a useful reference book for engi- neering students to search when looking for the meaning of a word/phrase. It has been compiled from a number of existing glossaries together with a number of local additions. -
Cmse 520 Biomolecular Structure, Function And
CMSE 520 BIOMOLECULAR STRUCTURE, FUNCTION AND DYNAMICS (Computational Structural Biology) OUTLINE Review: Molecular biology Proteins: structure, conformation and function(5 lectures) Generalized coordinates, Phi, psi angles, DNA/RNA: structure and function (3 lectures) Structural and functional databases (PDB, SCOP, CATH, Functional domain database, gene ontology) Use scripting languages (e.g. python) to cross refernce between these databases: starting from sequence to find the function Relationship between sequence, structure and function Molecular Modeling, homology modeling Conservation, CONSURF Relationship between function and dynamics Confromational changes in proteins (structural changes due to ligation, hinge motions, allosteric changes in proteins and consecutive function change) Molecular Dynamics Monte Carlo Protein-protein interaction: recognition, structural matching, docking PPI databases: DIP, BIND, MINT, etc... References: CURRENT PROTOCOLS IN BIOINFORMATICS (e-book) (http://www.mrw.interscience.wiley.com/cp/cpbi/articles/bi0101/frame.html) Andreas D. Baxevanis, Daniel B. Davison, Roderic D.M. Page, Gregory A. Petsko, Lincoln D. Stein, and Gary D. Stormo (eds.) 2003 John Wiley & Sons, Inc. INTRODUCTION TO PROTEIN STRUCTURE Branden C & Tooze, 2nd ed. 1999, Garland Publishing COMPUTER SIMULATION OF BIOMOLECULAR SYSTEMS Van Gusteren, Weiner, Wilkinson Internet sources Ref: Department of Energy Rapid growth in experimental technologies Human Genome Projects Two major goals 1. DNA mapping 2. DNA sequencing Rapid growth in experimental technologies z Microrarray technologies – serial gene expression patterns and mutations z Time-resolved optical, rapid mixing techniques - folding & function mechanisms (Æ ns) z Techniques for probing single molecule mechanics (AFM, STM) (Æ pN) Æ more accurate models/data for computer-aided studies Weiss, S. (1999). Fluorescence spectroscopy of single molecules. -
The Structure and Function of Large Biological Molecules 5
The Structure and Function of Large Biological Molecules 5 Figure 5.1 Why is the structure of a protein important for its function? KEY CONCEPTS The Molecules of Life Given the rich complexity of life on Earth, it might surprise you that the most 5.1 Macromolecules are polymers, built from monomers important large molecules found in all living things—from bacteria to elephants— can be sorted into just four main classes: carbohydrates, lipids, proteins, and nucleic 5.2 Carbohydrates serve as fuel acids. On the molecular scale, members of three of these classes—carbohydrates, and building material proteins, and nucleic acids—are huge and are therefore called macromolecules. 5.3 Lipids are a diverse group of For example, a protein may consist of thousands of atoms that form a molecular hydrophobic molecules colossus with a mass well over 100,000 daltons. Considering the size and complexity 5.4 Proteins include a diversity of of macromolecules, it is noteworthy that biochemists have determined the detailed structures, resulting in a wide structure of so many of them. The image in Figure 5.1 is a molecular model of a range of functions protein called alcohol dehydrogenase, which breaks down alcohol in the body. 5.5 Nucleic acids store, transmit, The architecture of a large biological molecule plays an essential role in its and help express hereditary function. Like water and simple organic molecules, large biological molecules information exhibit unique emergent properties arising from the orderly arrangement of their 5.6 Genomics and proteomics have atoms. In this chapter, we’ll first consider how macromolecules are built. -
Cancer Genomics Terminology
Cancer Genomics Terminology Acquired Susceptibility Mutation: A mutation in a gene that occurs after birth from a carcinogenic insult. Allele: One of the variant forms of a gene. Different alleles may produce variation in inherited characteristics. Allele Heterogeneity: A phenotype that can be produced by different genetic mechanisms. Amino Acid: The building blocks of protein, for which DNA carries the genetic code. Analytical Sensitivity: The proportion of positive test results correctly reported by the laboratory among samples with a mutation(s) that the laboratory’s test is designed to detect. Analytic Specificity: The proportion of negative test results correctly reported among samples when no detectable mutation is present. Analytic Validity: A test’s ability to accurately and reliably measure the genotype of interest. Apoptosis: Programmed cell death. Ashkenazi: Individuals of Eastern European Jewish ancestry/decent (For example-Germany and Poland). Non-assortative mating occurred in this population. Association: When significant differences in allele frequencies are found between a disease and control population, the disease and allele are said to be in association. Assortative Mating: In population genetics, selective mating in a population between individuals that are genetically related or have similar characteristics. Autosome: Any chromosome other than a sex chromosome. Humans have 22 pairs numbered 1-22. Base Excision Repair Gene: The gene responsible for the removal of a damaged base and replacing it with the correct nucleotide. Base Pair: Two bases, which form a “rung on the DNA ladder”. Bases are the “letters” (Adenine, Thymine, Cytosine, Guanine) that spell out the genetic code. Normally adenine pairs with thymine and cytosine pairs with guanine. -
Linkage & Genetic Mapping in Eukaryotes
LinLinkkaaggee && GGeenneetticic MMaappppiningg inin EEuukkaarryyootteess CChh.. 66 1 LLIINNKKAAGGEE AANNDD CCRROOSSSSIINNGG OOVVEERR ! IInn eeuukkaarryyoottiicc ssppeecciieess,, eeaacchh lliinneeaarr cchhrroommoossoommee ccoonnttaaiinnss aa lloonngg ppiieeccee ooff DDNNAA – A typical chromosome contains many hundred or even a few thousand different genes ! TThhee tteerrmm lliinnkkaaggee hhaass ttwwoo rreellaatteedd mmeeaanniinnggss – 1. Two or more genes can be located on the same chromosome – 2. Genes that are close together tend to be transmitted as a unit Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 2 LinkageLinkage GroupsGroups ! Chromosomes are called linkage groups – They contain a group of genes that are linked together ! The number of linkage groups is the number of types of chromosomes of the species – For example, in humans " 22 autosomal linkage groups " An X chromosome linkage group " A Y chromosome linkage group ! Genes that are far apart on the same chromosome can independently assort from each other – This is due to crossing-over or recombination Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 3 LLiinnkkaaggee aanndd RRecombinationecombination Genes nearby on the same chromosome tend to stay together during the formation of gametes; this is linkage. The breakage of the chromosome, the separation of the genes, and the exchange of genes between chromatids is known as recombination. (we call it crossing over) 4 IndependentIndependent assortment:assortment: -
Genetic Distance
NBER WORKING PAPER SERIES THE DIFFUSION OF DEVELOPMENT Enrico Spolaore Romain Wacziarg Working Paper 12153 http://www.nber.org/papers/w12153 NATIONAL BUREAU OF ECONOMIC RESEARCH 1050 Massachusetts Avenue Cambridge, MA 02138 March 2006 Spolaore: Department of Economics, Tufts University, 315 Braker Hall, 8 Upper Campus Rd., Medford, MA 02155-6722, [email protected]. Wacziarg: Graduate School of Business, Stanford University, Stanford CA 94305-5015, USA, [email protected]. We thank Alberto Alesina, Robert Barro, Francesco Caselli, Steven Durlauf, Jim Fearon, Oded Galor, Yannis Ioannides, Pete Klenow, Andros Kourtellos, Ed Kutsoati, Peter Lorentzen, Paolo Mauro, Sharun Mukand, Gérard Roland, Antonio Spilimbergo, Chih Ming Tan, David Weil, Bruce Weinberg, Ivo Welch, and seminar participants at Boston College, Fundação Getulio Vargas, Harvard University, the IMF, INSEAD, London Business School, Northwestern University, Stanford University, Tufts University, UC Berkeley, UC San Diego, the University of British Columbia, the University of Connecticut and the University of Wisconsin-Madison for comments. We also thank Robert Barro and Jim Fearon for providing some data. The views expressed herein are those of the author(s) and do not necessarily reflect the views of the National Bureau of Economic Research. ©2006 by Enrico Spolaore and Romain Wacziarg. All rights reserved. Short sections of text, not to exceed two paragraphs, may be quoted without explicit permission provided that full credit, including © notice, is given to the source. The Diffusion of Development Enrico Spolaore and Romain Wacziarg NBER Working Paper No. 12153 March 2006 JEL No. O11, O57 ABSTRACT This paper studies the barriers to the diffusion of development across countries over the very long-run.