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CONCEPTS OF GENOMIC BIOLOGYPage

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CONCEPTS OF GENOMIC BIOLOGYPage

Table of Contents:

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CONCEPTS OF GENOMIC BIOLOGYPage

Preface

Websites of Interest

Glossary

  1. Introduction
  2. What is a Gene?
  3. What is a Genome?
  4. What is Genomic Biology?
  5. Structural Genomics
  6. Comparative Genomics
  7. Functional Genomics
  8. Genomic Databases
  9. The beginnings of Genomic Biology– classical genetics
  10. Mendel & Darwin – traits are conditioned by genes
  11. Genes are carried on chromosomes
  12. The chromosomal theory of inheritance
  13. Additional Complexity of Mendelian Inheritance
  14. Multiple alleles
  15. Incomplete dominance and co-dominance
  16. Sex linked inheritance
  17. Epistasis
  18. Epigenetics
  19. The Law of Independent Assortment
  20. Meiosis: chromosomes assort independently
  21. Mapping genes on chromosomes
  22. Quantitative Genetics: Traits that are Continuously Variable
  23. Population Genetics: Traits in groups of individuals
  24. The beginnings of Genomic Biology – molecular genetics
  25. DNA is the Genetic Material
  26. Watson & Crick – The structure of DNA
  27. Chromosome structure
  28. Prokaryotic chromosome structure
  29. Eukaryotic chromosome structure
  30. Heterochromatin & Euchromatin
  31. DNA Replication
  32. DNA replication is semiconservative
  33. DNA polymerases
  34. Initiation of replication
  35. DNA replication is semidiscontinuous
  36. DNA replication in Eukaryotes.
  37. Replicating ends of chromosomes
  38. Transcription
  39. Cellular RNAs are transcribed from DNA
  40. RNA polymerases catalyze transcription
  41. Transcription in Prokaryotes
  42. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons
  43. Beyond Operons – Modification of expression in Prokaryotes
  44. Transcriptions in Eukaryotes
  45. Processing primary transcripts into mature mRNA
  46. Translation
  47. The Nature of Proteins
  48. The Genetic Code
  49. tRNA – The decoding molecule
  50. Peptides are synthesized on Ribosomes
  51. Translation initiation, elongation, and termnation
  52. Protein Sorting in Eukaryotes
  53. Genomic Biologists tool kit
  54. Restriction Endonucleases – making “sticky ends”
  55. Cloning Vectors
  56. Simple Cloning Vectors
  57. Expression Vectors
  58. Shuttle Vectors
  59. Phage Vectors
  60. Artificial Chromosome Vectors
  61. Methods for Sequence Amplification
  62. Polymerase Chain Reaction
  63. Cloning Recombinant DNA
  64. Cloning DNA in Expression Vectors
  65. Making complementary DNA (cDNA)
  66. Methods for Sequence Amplification - Cont.
  67. Cloning a cDNA Library
  68. GenomicLibraries
  69. DNA separation – electrophoresis
  70. DNA sequence identification – DNA hybridization
  1. Structural Genomics
  2. Sequencing DNA molecules
  • Sanger sequencing –dideoxy sequencing
  • Automated capillary DNA sequencing robots
  • Next generation sequencing –pyrosequencing
  • Genomic sequence libraries
  • Map-based strategies – molecular polymorphisms
  • Whole genome shotgun sequencing
  • Bioinformatics and gene identification
  • About sequenced genomes
  1. Comparative Genomics
  2. Genomic variation –mutations
  3. Genomic variation – polymorphisms
  4. Phylogenetic trees
  5. The tree of life
  6. Functional Genomics–Overview
  7. Identification of protein structure and function
  8. Non-protein-coding genes
  9. Gene expression – Prokaryotes
  10. Gene expression – Eukaryotes
  11. Gene expression – Signal Transduction
  12. The transcriptome – Measuring gene expression
  • Northern blot
  • RT-PCR
  • Quantitative PCR
  • Microarray
  • The Proteome
  • The Metabolome
  1. Genomic Applications
  2. Human biology
  3. The Environment
  4. Food & fiber production
  5. Evolutionary biology

Epilogue

Preface (RETURN)

Prior to about 1990 few people conceived of the idea of a genome, much less undertakenthe investigation of such. However in 1990 the Human Genome Project (HGP) was initiated as an international scientific research collaboration with the goals of: 1) determining the sequence of nucleotide basesthat make up a haploid copy of human chromosomes; 2) identifying all of the genes of the human genome both physically and functionally; and 3) mapping all of the genes identified to specific human chromosomes. The HGP remains the world's largest collaborative biological project.

The project was proposed and funded by the US government through the National Instutues of Health (NIH). Planning started in 1984, and the project got underway in 1990. In 2003 President Bill Clinton declared the HGP a rousing success and essentially complete with the production of a first draft of the human genome. In fact, work on gene identification, mapping, and function is ongoing even today, and has yielded a treasure trove of knowledge about the human genome as well as the genes and genomes of many other microbes, fungi, plants and animals along the way that is revolutionizing not only health science-related research but virtually every aspect of contemporary biology.

The publicly funded project was led, by Dr. Francis Collins and involved more than in twenty universities and research centers in the United States, the United Kingdom, Japan, France, Germany, and China. A parallel project was conducted in the private sectorled by Dr. Craig Venter of the Celera Genomics (Celera Corporation, which was formally launched in 1998. The dynamics and interaction of these 2 efforts is an interesting study on how we identify and fund science today, and how public sector research is both in competition with and collaboration with privately funded corporate research. This is such an interesting plethora of information that several books have been written describing the HCP and Celera Genomics efforts. A couple of these are given in the book list below:

This eBook is intended to provide knowledge of the technology, achievements, and ongoing activities of what started as the HGP, but now involves much broader considerations that are shaping the future of the study of biology. In order to appreciate this information and to make it maximally useful, a brief synopsis of important concepts from classical and molecular genetics is presented. This followed by an analysis of the technology used by genomic biologists, and a summary of the significant findings in DNA sequencing (structural genomics), sequence comparisons of a wide range of organism (comparative genomics), and information on how genes in genomes produce their phenotype (functional genomics).

Bob Locy, December, 2014

Websites of interest(Return)

General

EMBL (European Bioinformatics Institute)

Gennome News Network

Human Genome Project (HGP)

National Center for Bioltechnology Information (NCBI)

Tree of Life Web Project

Genome Databases

CAMERAResource for microbial genomics and metagenomics

Corn the Maize Genetics and Genomics Database

EcoCycE. coli K-12 database

PATRIC, the PathoSystems Resource Integration Center

FlybaseDrosophila melanogastergenome

JGI Genomesof the DOE-Joint Genome Institute

Mouse Genome Database (MGI)

National Microbial Pathogen Data Resource.

Repbase database for repetitive elements (transposons).

Saccharomyces Genome Database (yeast)

Xenbasegenome of Xenopustropicalis and Xenopuslaevis

WormbaseCaenorhabditiselegans database

Zebrafish Information Network

TAIRThe Arabidopsis Information Resource

Rat Genome Database (RGD)

Banana Genome Hub

Bacterrial Small Regulatory RNA Database

Glossary(Return)