Genetic Effects on Microsatellite Diversity in Wild Emmer Wheat (Triticum Dicoccoides) at the Yehudiyya Microsite, Israel
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13 Genomics and Bioinformatics
Enderle / Introduction to Biomedical Engineering 2nd ed. Final Proof 5.2.2005 11:58am page 799 13 GENOMICS AND BIOINFORMATICS Spencer Muse, PhD Chapter Contents 13.1 Introduction 13.1.1 The Central Dogma: DNA to RNA to Protein 13.2 Core Laboratory Technologies 13.2.1 Gene Sequencing 13.2.2 Whole Genome Sequencing 13.2.3 Gene Expression 13.2.4 Polymorphisms 13.3 Core Bioinformatics Technologies 13.3.1 Genomics Databases 13.3.2 Sequence Alignment 13.3.3 Database Searching 13.3.4 Hidden Markov Models 13.3.5 Gene Prediction 13.3.6 Functional Annotation 13.3.7 Identifying Differentially Expressed Genes 13.3.8 Clustering Genes with Shared Expression Patterns 13.4 Conclusion Exercises Suggested Reading At the conclusion of this chapter, the reader will be able to: & Discuss the basic principles of molecular biology regarding genome science. & Describe the major types of data involved in genome projects, including technologies for collecting them. 799 Enderle / Introduction to Biomedical Engineering 2nd ed. Final Proof 5.2.2005 11:58am page 800 800 CHAPTER 13 GENOMICS AND BIOINFORMATICS & Describe practical applications and uses of genomic data. & Understand the major topics in the field of bioinformatics and DNA sequence analysis. & Use key bioinformatics databases and web resources. 13.1 INTRODUCTION In April 2003, sequencing of all three billion nucleotides in the human genome was declared complete. This landmark of modern science brought with it high hopes for the understanding and treatment of human genetic disorders. There is plenty of evidence to suggest that the hopes will become reality—1631 human genetic diseases are now associated with known DNA sequences, compared to the less than 100 that were known at the initiation of the Human Genome Project (HGP) in 1990. -
Genomics and Its Impact on Science and Society: the Human Genome Project and Beyond
DOE/SC-0083 Genomics and Its Impact on Science and Society The Human Genome Project and Beyond U.S. Department of Energy Genome Research Programs: genomics.energy.gov A Primer ells are the fundamental working units of every living system. All the instructions Cneeded to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instruc- tions required to create a particular organism with protein complex its own unique traits. The genome is an organism’s complete set of DNA. Genomes vary widely in size: The smallest known genome for a free-living organism (a bac- terium) contains about 600,000 DNA base pairs, while human and mouse genomes have some From Genes to Proteins 3 billion (see p. 3). Except for mature red blood cells, all human cells contain a complete genome. Although genes get a lot of attention, the proteins DNA in each human cell is packaged into 46 chro- perform most life functions and even comprise the mosomes arranged into 23 pairs. Each chromosome is majority of cellular structures. Proteins are large, complex a physically separate molecule of DNA that ranges in molecules made up of chains of small chemical com- length from about 50 million to 250 million base pairs. pounds called amino acids. Chemical properties that A few types of major chromosomal abnormalities, distinguish the 20 different amino acids cause the including missing or extra copies or gross breaks and protein chains to fold up into specific three-dimensional rejoinings (translocations), can be detected by micro- structures that define their particular functions in the cell. -
Gene Prediction and Genome Annotation
A Crash Course in Gene and Genome Annotation Lieven Sterck, Bioinformatics & Systems Biology VIB-UGent [email protected] ProCoGen Dissemination Workshop, Riga, 5 nov 2013 “Conifer sequencing: basic concepts in conifer genomics” “This Project is financially supported by the European Commission under the 7th Framework Programme” Genome annotation: finding the biological relevant features on a raw genomic sequence (in a high throughput manner) ProCoGen Dissemination Workshop, Riga, 5 nov 2013 Thx to: BSB - annotation team • Lieven Sterck (Ectocarpus, higher plants, conifers, … ) • Yao-cheng Lin (Fungi, conifers, …) • Stephane Rombauts (green alga, mites, …) • Bram Verhelst (green algae) • Pierre Rouzé • Yves Van de Peer ProCoGen Dissemination Workshop, Riga, 5 nov 2013 Annotation experience • Plant genomes : A.thaliana & relatives (e.g. A.lyrata), Poplar, Physcomitrella patens, Medicago, Tomato, Vitis, Apple, Eucalyptus, Zostera, Spruce, Oak, Orchids … • Fungal genomes: Laccaria bicolor, Melampsora laricis- populina, Heterobasidion, other basidiomycetes, Glomus intraradices, Pichia pastoris, Geotrichum Candidum, Candida ... • Algal genomes: Ostreococcus spp, Micromonas, Bathycoccus, Phaeodactylum (and other diatoms), E.hux, Ectocarpus, Amoebophrya … • Animal genomes: Tetranychus urticae, Brevipalpus spp (mites), ... ProCoGen Dissemination Workshop, Riga, 5 nov 2013 Why genome annotation? • Raw sequence data is not useful for most biologists • To be meaningful to them it has to be converted into biological significant knowledge -
Biology Dictionary English - Khmer
vcnanuRkm CIvviTüa Gg;eKøs-Exµr Biology Dictionary English - Khmer saklviTüal½yPUminÞPñMeBj ed)a:tWm:g; CIvviTüa e)aHBum<elIkTI 3 ¬EksMrYl¦ 2003 Preface to the Third Edition (Revised) This dictionary is the work of many teachers and some students in the Biology department of The Royal University of Phnom Penh. It has developed over the last three years in response to the need of Biology students to learn Biology from English text books. We have also tried to anticipate the future needs of Biology students and teachers in Cambodia. If they want to join the global scientific community; read scientific journals, listen to international media, attend international conferences or study outside Cambodia, then they will probably need to communicate in English. Therefore, the main aim of this book is to help Cambodian students and teachers at the university level to understand Biology in English. All languages evolve. In the past the main influence on Khmer language was French. Nowadays, it is increasingly English. Some technical terms have already been absorbed from French and have become Khmer. Nowadays new technical terms are usually created in English and are used around the world. Language is also created by those who use it and only exists when it is used. Therefore, common usage has also influenced our translation. We have tried to respond to these various influences when preparing this dictionary, so that it represents many different opinions - old and new, Francophile, Anglophile and Khmer. But there will always be some disagreement about the translation of some terms. This is normal and occurs in all languages. -
Small Variants Frequently Asked Questions (FAQ) Updated September 2011
Small Variants Frequently Asked Questions (FAQ) Updated September 2011 Summary Information for each Genome .......................................................................................................... 3 How does Complete Genomics map reads and call variations? ........................................................................... 3 How do I assess the quality of a genome produced by Complete Genomics?................................................ 4 What is the difference between “Gross mapping yield” and “Both arms mapped yield” in the summary file? ............................................................................................................................................................................. 5 What are the definitions for Fully Called, Partially Called, Half-Called and No-Called?............................ 5 In the summary-[ASM-ID].tsv file, how is the number of homozygous SNPs calculated? ......................... 5 In the summary-[ASM-ID].tsv file, how is the number of heterozygous SNPs calculated? ....................... 5 In the summary-[ASM-ID].tsv file, how is the total number of SNPs calculated? .......................................... 5 In the summary-[ASM-ID].tsv file, what regions of the genome are included in the “exome”? .............. 6 In the summary-[ASM-ID].tsv file, how is the number of SNPs in the exome calculated? ......................... 6 In the summary-[ASM-ID].tsv file, how are variations in potentially redundant regions of the genome counted? ..................................................................................................................................................................... -
Capture of a Recombination Activating Sequence from Mammalian Cells
Gene Therapy (1999) 6, 1819–1825 1999 Stockton Press All rights reserved 0969-7128/99 $15.00 http://www.stockton-press.co.uk/gt Capture of a recombination activating sequence from mammalian cells P Olson and R Dornburg The Dorrance H Hamilton Laboratories, Center for Human Virology, Division of Infectious Diseases, Jefferson Medical College, Thomas Jefferson University, Jefferson Alumni Hall, 1020 Locust Street, Rm 329, Philadelphia, PA 19107, USA We have developed a genetic trap for identifying revealed a putative recombination signal (CCCACCC). sequences that promote homologous DNA recombination. When this heptamer or an abbreviated form (CCCACC) The trap employs a retroviral vector that normally disables were reinserted into the vector, they stimulated vector itself after one round of replication. Insertion of defined repair and other DNA rearrangements. Mutant forms of DNA sequences into the vector induced the repair of a 300 these oligomers (eg CCCAACC or CCWACWS) did not. base pair deletion, which restored its ability to replicate. Our data suggest that the recombination events occurred Tests of random sequence libraries made in the vector within 48 h after transfection. Keywords: recombination; retroviral vector; vector stability; gene conversion; gene therapy Introduction scripts are still made from the intact left LTR, but reverse transcription copies the deletion to both LTRs, disabling Recognition of cis-acting DNA signals occupies a central the daughter provirus.15–17 We found that the SIN vectors role in both site-specific and general recombination path- that could escape this programmed disablement did so 1–6 ways. Signals in site-specific pathways define the by recombinationally repairing the U3-deleted LTR. -
Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine
biomolecules Review Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine Ryuji Hamamoto 1,2,*, Masaaki Komatsu 1,2, Ken Takasawa 1,2 , Ken Asada 1,2 and Syuzo Kaneko 1 1 Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; [email protected] (M.K.); [email protected] (K.T.); [email protected] (K.A.); [email protected] (S.K.) 2 Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan * Correspondence: [email protected]; Tel.: +81-3-3547-5271 Received: 1 December 2019; Accepted: 27 December 2019; Published: 30 December 2019 Abstract: To clarify the mechanisms of diseases, such as cancer, studies analyzing genetic mutations have been actively conducted for a long time, and a large number of achievements have already been reported. Indeed, genomic medicine is considered the core discipline of precision medicine, and currently, the clinical application of cutting-edge genomic medicine aimed at improving the prevention, diagnosis and treatment of a wide range of diseases is promoted. However, although the Human Genome Project was completed in 2003 and large-scale genetic analyses have since been accomplished worldwide with the development of next-generation sequencing (NGS), explaining the mechanism of disease onset only using genetic variation has been recognized as difficult. Meanwhile, the importance of epigenetics, which describes inheritance by mechanisms other than the genomic DNA sequence, has recently attracted attention, and, in particular, many studies have reported the involvement of epigenetic deregulation in human cancer. -
The Economic Impact and Functional Applications of Human Genetics and Genomics
The Economic Impact and Functional Applications of Human Genetics and Genomics Commissioned by the American Society of Human Genetics Produced by TEConomy Partners, LLC. Report Authors: Simon Tripp and Martin Grueber May 2021 TEConomy Partners, LLC (TEConomy) endeavors at all times to produce work of the highest quality, consistent with our contract commitments. However, because of the research and/or experimental nature of this work, the client undertakes the sole responsibility for the consequence of any use or misuse of, or inability to use, any information or result obtained from TEConomy, and TEConomy, its partners, or employees have no legal liability for the accuracy, adequacy, or efficacy thereof. Acknowledgements ASHG and the project authors wish to thank the following organizations for their generous support of this study. Invitae Corporation, San Francisco, CA Regeneron Pharmaceuticals, Inc., Tarrytown, NY The project authors express their sincere appreciation to the following indi- viduals who provided their advice and input to this project. ASHG Government and Public Advocacy Committee Lynn B. Jorde, PhD ASHG Government and Public Advocacy Committee (GPAC) Chair, President (2011) Professor and Chair of Human Genetics George and Dolores Eccles Institute of Human Genetics University of Utah School of Medicine Katrina Goddard, PhD ASHG GPAC Incoming Chair, Board of Directors (2018-2020) Distinguished Investigator, Associate Director, Science Programs Kaiser Permanente Northwest Melinda Aldrich, PhD, MPH Associate Professor, Department of Medicine, Division of Genetic Medicine Vanderbilt University Medical Center Wendy Chung, MD, PhD Professor of Pediatrics in Medicine and Director, Clinical Cancer Genetics Columbia University Mira Irons, MD Chief Health and Science Officer American Medical Association Peng Jin, PhD Professor and Chair, Department of Human Genetics Emory University Allison McCague, PhD Science Policy Analyst, Policy and Program Analysis Branch National Human Genome Research Institute Rebecca Meyer-Schuman, MS Human Genetics Ph.D. -
Conversion Between 100-Million-Year-Old Duplicated Genes Contributes to Rice Subspecies Divergence
Wei et al. BMC Genomics (2021) 22:460 https://doi.org/10.1186/s12864-021-07776-y RESEARCH Open Access Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence Chendan Wei1†, Zhenyi Wang1†, Jianyu Wang1†, Jia Teng1, Shaoqi Shen1, Qimeng Xiao1, Shoutong Bao1, Yishan Feng1, Yan Zhang1, Yuxian Li1, Sangrong Sun1, Yuanshuai Yue1, Chunyang Wu1, Yanli Wang1, Tianning Zhou1, Wenbo Xu1, Jigao Yu2,3, Li Wang1* and Jinpeng Wang1,2,3* Abstract Background: Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution. Results: Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19–5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77–9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
A Long Polymorphic GT Microsatellite Within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a Cpg Island in a Goldfish Inter-Strain Hybrid
International Journal of Molecular Sciences Article A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid 1,2, , 2, 2 Jianbo Zheng * y , Haomang Xu y and Huiwen Cao 1 Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China 2 College of Life Sciences, Zhejiang University, Hangzhou 310058, China * Correspondence: [email protected]; Tel.: +86-572-204-5681 These authors equally contributed to this work. y Received: 26 June 2019; Accepted: 6 August 2019; Published: 12 August 2019 Abstract: It is now widely accepted that allele-specific DNA methylation (ASM) commonly occurs at non-imprinted loci. Most of the non-imprinted ASM regions observed both within and outside of the CpG island show a strong correlation with DNA polymorphisms. However, what polymorphic cis-acting elements mediate non-imprinted ASM of the CpG island remains unclear. In this study, we investigated the impact of polymorphic GT microsatellites within the gene promoter on non-imprinted ASM of the local CpG island in goldfish. We generated various goldfish heterozygotes, in which the length of GT microsatellites or some non-repetitive sequences in the promoter of no tail alleles was different. By examining the methylation status of the downstream CpG island in these heterozygotes, we found that polymorphisms of a long GT microsatellite can lead to the ASM of the downstream CpG island during oogenesis and embryogenesis, polymorphisms of short GT microsatellites and non-repetitive sequences in the promoter exhibited no significant effect on the methylation of the CpG island. -
Mathematical Challenges from Genomics and Molecular Biology Richard M
Mathematical Challenges from Genomics and Molecular Biology Richard M. Karp fundamental goal of biology is to un- algorithms and the role of combinatorics, opti- derstand how living cells function. This mization, probability, statistics, pattern recognition, understanding is the foundation for all and machine learning. higher levels of explanation, including We begin by presenting the minimal information Aphysiology, anatomy, behavior, ecology, about genes, genomes, and proteins required to and the study of populations. The field of molec- understand some of the key problems in genomics. ular biology analyzes the functioning of cells and Next we describe some of the fundamental goals of the processes of inheritance principally in terms of the molecular life sciences and the role of genomics interactions among three crucially important classes in attaining these goals. We then give a series of of macromolecules: DNA, RNA, and proteins. brief vignettes illustrating algorithmic and mathe- Proteins are the molecules that enable and execute matical questions arising in a number of specific most of the processes within a cell. DNA is the car- areas: sequence comparison, sequence assembly, rier of hereditary information in the form of genes gene finding, phylogeny construction, genome re- and directs the production of proteins. RNA is a key arrangement, associations between polymorphisms intermediary between DNA and proteins. and disease, classification and clustering of gene Molecular biology and genetics are undergoing expression data, and the logic of transcriptional revolutionary changes. These changes are guided by control. An annotated bibliography provides point- a view of a cell as a collection of interrelated sub- ers to more detailed information.