The Genomic Valley

A brief story of DNA

1865

G. J. Mendel

The basics of heredity

1910

T.H. Morgan

Organization of the genes along chromosomes . The first demonstration of sex-linked characteristics

1928

F. Griffith

His experiments clearly laid the groundwork for the discovery of the genetic material ("transformation")

1944

O.T. Every, C.McLeod & M. McCarty

The DNA was recognized as the factor responsible for transformation. By 1944 it was becoming clear that DNA was the genetic material.

1950

A. Hershey & M. Chase

Studies on bacteriophage

The experiments firmly established that DNA was the genetic material.

1952

Rosalind Franklin

She had all the parameters of the DNA helical backbone (Anatomy of photo 51 by Lexi Krock at http://www.pbs.org/wgbh/nova/photo51/

1953

J. Watson & F.Crick

Helical structure of DNA (the four basic chemicals in DNA paired up as follows: adenine with thymine and guanine with cytosine)

1958

Francis Crick

F. Crick formalized information "as a fundamental property of biological systems and the governing concept in the discipline of molecular biology" - 

"The essence of the problem of protein synthesis was flux: flow of energy, flowof matter, and flow of information" (Crick, 1957)

Late 1950s

Arthur Pardee, Jacques Monod and Francois Jacob

Genetic regulation of enzyme synthesis

1961

J. Heinrich Matthaei ana Marshall W. Nirenberg

Cracking the genetic code

1968

Marshall Nirenberg, Har Gobind Khorana, and Robert Holley

The "Code Words"

1970

S.Cohen

Discovery how to cut and recombine strands of DNA from different organisms, creating the technology for recombuinant DNA

1973

 

First conference to discuss the idea of gene mapping to determine their position on the chromosomes

1980

 

The U.S. Supreme Court approves the first patenting of a genetically engineered organism, an oil eating bacterium, developed by General Electric.

1987

K.A. Hart

First human disease gene (muscolar distrophy) [Hum. Genet 77,88]

1988

 

U.S. Patent Office approves a patent on a genetically engineered mouse developed at Harvard University to be used for cancer studies.

1990

 

Approval in U.S.A. for the first use of gene therapy in which engineered genes are inserted into the blood to cure disease.

1990

 

Scientists launched the human genome project as part of an effort to determine genetic factors behind diseases [(i) to identify all of the more than 100,000 genes in human DNA, (ii) determine the exact order of the 3 billion chemical base pairs]

1995

 

The first complete genome of any free-living organism (Haemophilus influenzae) was published by scientists at the Institute for Genomic Research ( TIGR Microbial database )

1996

 

First eukaryotic genome, S. cerevisiae, sequenced

1997

I. Wilmut

The first cloning of a mammal, the sheep Dolly

1998

R. Yanagimachi

A technique through which 50 mice have been cloned. Some of them are clones of the clones.

1999

X. Su et al.

High-resolution genetic map of Plasmodium falciparum [at National Institute of Allergy and Infectious Diseases (NIAIID)] - Science, 286, 1351 - 1353

<www.ncbi.nlm.nih.gov>

<www.niaid.nih.gov>

1999

 

November 23 - Billion Base Celebration: The completion and deposition into GenBank of one billion base pairs of the human genome DNA sequence (the human genome contains three billion base pairs of DNA)

1999

 

December 2 - The genetic code of the human chromosome 22 has been deciphered by a team of scientists from Britain, Japan Sweden, Canada and USA, as published on Nature 402, 489-495. There are still 11 irritating unsequenced gaps, accounting for about 3% of the sequence.(see comment of N. Loder, page 448).

<www.pebio.com/ab/BioBeat/chr22>

2000

 

Celera Genomics (April 06) finishes sequence of a person's genes, making a human genetic map that could eventually transform medicine and biology..

2000

M. Hattori et al.

The DNA sequence of human chromosome 21 - Nature 405, 311 - 319

Synteny between human chromosome 21 and mouse chromosome 16; Dyrk1A protein kinase is in a down's syndrome critical region and is a candidate gene for causation (see: http://www.ncbi.nlm.nih.gov/Homology/ )

June 26 , 2000

 

The publicly funded HUMAN GENOME PROJECT and the private CELERA GENOMICS Corp. have decoded the 3.1 billion subunits of DNA, the chemical"letters" that make up the recipe of human life (by Sue Leeman,  associated press writer)

February 12, 2001

 

The full text of human genome, as revealed by scientists (Nature 409, 860 - 921 ; Science 291, 1304 - 1351), is surprisingly short, made up of about 31.000 genes (no more than 40.000 genes).  Nature Genome Issue http://www.nature.com/genomics/human/
Science Genome Issue
http://www.sciencemag.org/genome2001

Human Genome Project Working Draft at http://genome.ucsc,edu

April 14, 2003

 

The human genome finally completed (by The Wellcome Trust Sanger Institute)

Post Genome Research

Information  about the human genome

Arrow

Therapeutics & "personal medicine" (?)

2005

 

Details on how the genetic elements interact in various complex ways to produce the effect of life. Process of "gene reshuffling"

October 6, 2007

 

Craig Venter has built a synthetic chromosome out of laboratory chemicals (381 genes long, 580000 base pairs of genetic code) and is poised to announce the creation of the first new artificial life form on Earth. The DNA sequence is based on the bacterium Mycoplasma genitalium. The wholly synthetically reconstructed chromosome was christened mycoplasma laboratorium. It is then transplanted into a living bacterial cell and in the final stage of the process it is expected to take control of the cell and in effect become a new life form (from: The Guardian)

Gene discovery >> Gene Diversity >> Gene products

to dissect the relationship between gene sequence, expression and function and disease predisposition, progression and therapy.

The trend is moving toward personalization of medicine at the genetic level.

In the discovery genetics, the biochemistry of human disease populations permits to identify disease-related susceptibility genes. This represents the basis for pharmacogenetics:

Biochemistry  Arrow    Pharmacogenetics

Genomics is the activity that identifies the relationships between genes, health and disease. Discovery genomics uses the DNA sequence information to identify genes for tractable or screenable targets that are not known to be genetically related to disease. The translation of functional genomics into rational therapy corresponds to pharmacogenomics. The end-point of pharmacogenomics is then the ability to target a drug specifically to those genotypically defined patients who will repond well to the drug with no adverse side effects. Pharmacogenomics may also enable the rescue and retargeting of drugs that failed in clinical trials due to toxicity or low efficacy [W. E. Evans and M. V. Relling - Science 286 (1999), 487 - 491; Allen D. Roses - Nature 405 (2000), 857-865 ].

Genomics  Arrow   Pharmacogenomics

A clinical alternative to the premise of pharmacogenomics and a less costly method (compared to genetics-based pharmacogenomic approach) is that represented by "metaprobes ", chemicals with the function of measuring specific enzyme activity relevant to a disease process or biochemical patway .

 

Proteomics identifies and relates the expression and location of proteins to disease predisposition, progression and drug toxicology and pharmacology.

Expanding the 1950s Biology Dogma

Today:

   One gene  Arrow     More proteins

as a consequence of (i) post-translational processes, (ii) alternative splicing, (iii) rearrangement of the number and the order of proteins domains encoded within genes, (iv) regulation of gene expression (role of the transcription factors), (v) the Wright & Dyson's "intrinsic disorder" under physiological / pathological conditions.

"Like the Greek sea god Proteus, who could change form at will (Homer, in: "The Odyssey", book IV, 349 - 570), proteins can assume myriad shapes and structures, and even shift from begnin to cancer-causing molecules and then back again, so studying them is not so easy task." [in "Protein Shaker" by Stephan Herrera, in: Red Herring 79, 359 - 366 (2000)]

Unlike genomics (which involves the analysis of simple repeating polymers), proteomics involves the study of very complex heteropolymers having a wide range of sizes, physical properties, secondary and tertiary structures, solubilities, and functions (the Karush's configurational adaptability)c.

Eritable changes in gene expression ,that occur without a change in DNA sequence, can complicate the genetic manipulation of living organisms. Epigenetics is the study of these phenomena. "essential for normal development, epigenetic controls become misdirected in cancer cells and other human disease syndromes" ["The organizing principle: microenvironmental influences in the normal and malignant breast" by Mina J. Bissell et al. on: Differentiation 70 ,  537 - 546 (2002); "Epigenetics: Genome, Meet Your Environment" by Leslie A. Pray on: The Scientist 18 (13), 14 - 20 (2004); "Cancer epigenetics enters the mainstream" by Mark Greener on: The Scientist 19 (12), 18 - 19 (2005); " Epigenetics provides a new generation of oncogenes and tumour-suppressor genes" by Esteller M on:  Br J Cancer.96 Suppl:R26-30 (2007)]

Different aspects of epigenetic inheritance

Lamarckism Revisited

RNA interference

Transcriptional silencing

Chromatin-based events

X inactivation

DNA methylation and transposon activity

Cloning of mammals by nuclear transfer (NT)

The centromere

Genetic Disorders in the Year 2007

Alcoholism

Alzheimer's disease

Angioplasty

Brain degeneration [calcium channel regulatory factor(s)]

Cancer (breast, colon)

Cystic Fibrosis

Diabetes

Gender

Hiomosexuality

Huntingtons Chorea

Manic Depression

Multiple sclerosis

Obesity

Orthopedics

 

Selected Human Genetic Disorders: Chromosome Location

http://www.ornl.gov/hgmis/posters/chromosome

http://www.ncbi.nim.nih.gov/Omim

 

Chromosome

Syndrome / Disease

Chromosome

Syndrome / Disease

1

Gaucher disease; Alzheimer's disease

13

Breast cancer; Retinoblastoma

2

Colon cancer; Waardenburg syndrome

14

Alzheimer's disease

3

Von Hippel-Lindau disease; Lung cancer

15

Colorectal cancer; Diabetes mellitus (insulin-dependent)

4

Huntington's disease; Ellis-van Creveld syndrome

16

Polycystic kidney disease

5

Steroid 5-alpha reductase; Diastrophic dysplasia

17

Tumor suppressor TP 53; Breast cancer

6

Spino-cerebellar atrophy; Juvenile onset diabetes

18

Pancreatic cancer

7

Cystic fibrosis; Obesity

19

Apolipoprotein E; Myotonic dystrophy

8

Werner's syndrome; Burkitt's lymphoma

20

Severe combined immunodeficiency

9

Malignant melanoma; Tuberous sclerosis

21

Amyotrophic lateral sclerosis

10

Multiple endocrine neoplasia; Gyrate atrophy of the choroid and retina

22

Di-George syndrome; Neurofibromatosis type2

11

Long-QT syndrome; Harvey RAS oncogene

X

Duchenne muscolar distrophy; Menkes' disease; Fragile X syndrome; Adrenoleukodistrophy

12

Zellweger syndrome; Phenyl ketonuria

Y

Testis determining factor

Steps leading to gene terapy

Target identification

What genes are available to work with?

 
  1. The identification of the defective gene
 
  1. The isolation of the normal gene and its reproduction (reverse genetic technique for functional genomics)
 
  1. The gene and its biological network

Target qualification

How the genes are involved in the disease?

  1. Final phenotype ("the disease") as the result of (i) gene products [proteins / metabolites(accumulation / deficiency)] and (ii) the homeostatic systems (under the influence of the forces of the environment)
  1. Epigenetic inheritance
  1. microRNAs' effects on gene expression, development, and behavior (riboregulators' effects)

Target validation

Is it possible to modify the protein level / activity? Which will be the phenotypic impact?

 
  1. Incorporation of the synthetic gene into a delivery system (retroviruses, liposomes, plasmids)
 
  1. Insertion of the gene preferably where the gene itself is normally espressed, by the use of the delivery systems
 
  1. Production of the required protein by the introduced synthetic gene, in the same way as the normal gene would have done.
 
  1. Shut off the expression of genes, uing RNAi molecules
Note Note Note
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The route to therapeutics and "personal medicine" in the new millennium

Genomics

Transcriptomics

Proteomics

Ribonomics

the RNA analog of proteomics

Conditional systems on the basis of:

  • regulatory proteins
  • aptamers
  • allosteric ribozimes
  • antisense RNA
  • RNA silencing

DNA sequence information

Bioinformatics

Gene identification

Transcriptional gene silencing, Post-transcriptional gene silencing, stRNA, RNA interference

Gene variation

SNPs

The genes states

Personal Genome Network

 

All the DNA transcripts

mRNA

evaluating mRNA and its relationships to functional changes

Spliceosomes

Gene networks pathways

Identification of biological function

 

(Gene)

Study of gene expression through:

(i) identification of the proteins

(ii) quantification of single proteins

(iii) identification of protein networks

(iv) identification of "environmental conditions" that can control the protein expression process

(v) Reverse genetics

Bioinformatics

(i) Protein sequence analysis for homology

(ii) Gene identification / polymorphism

RNA-directed DNA methylation (nucleus)

Transcriptional Gene Silence (cytoplasm)

Post Transcriptional Gene Silence (cytoplasm)

Identify the full complement of natural noncoding RNAs that act as riboregulators

Contribution to epigenetic regulation of gene expression

 

Identification of the biological function

Tissue gene expression

(i) specific protein data banks

(ii) diagnosis of normal & pathol. situations

(iii) specific metabolic functions of protein isoforms

 

Protein expression

Effect of the post-translational process on the full active form

Environmental conditions and protein expression

Gene expression

Environmental conditions and gene expression

Functional genomic screen

Target identification

Target validation

Lead compund screening

High-Throughput Screening

(including x-rays crystallographic techniques)

Promising "hits"

Toxicology

Protein therapeutics

Gene therapy

Protein therapeutics

Protein therapeutics / Gene therapy

Drugs to final approval

"Personal medicine"

Genome

Transcription

Arrow

Transcriptome

pre-messenger RNA

Alternative splicing

Arrow

Spliceome

messenger RNA

Translation

Arrow

Proteome

It is possible to establish the exact correlation between a specific disease and a gene/ protein for a rational therapy (pharmacogenomics / pharmacoproteomics) but it is unrealistic to postulate the possibility to use the same genomics- / proteomics - based product for all the "apparently"  identical pathologies

"The genome is an inventory of function, but not function" Sydney Brenner

How to translate the data into knowledge?

"The future will be the study of  the genes and proteins of organisms in the context of their informational pathways or networks." Leroy Hood

Protein - protein interactions maps

[for Drosophila melanogaster: Science 302:1727 - 1736 (2003)

for Caenorhabditis elegans Science 303: 540 - 543 (2004) ]

 

genes appear to operate in a complex network

Ref.:  Change to gene theory raises new challenges for biotech by Denise Caruso, Int. Herald Tribune (Business) , July 3, 2007

Network

SELECTED GENOME-RELATED WEBSITES

URL ADDRESS

The Human Genome Project at Oak Ridge National Laboratory

http://www.ornl.org

Human Genome Project Information Web Site

http://www.ornl.gov/hgmis

Cat genome resources page

Cat genome project

http://www.ncbi.nlm.nih.gov/projects/genome/guide/cat/

http://home.ncifcrf.gov/ccr/lgd/comparative_genome/catgenome/index_n.as p

DOE JGI

http://www.jgi.doe.gov

GenBank

http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html

Tthe Golden Path at the University of California at Santa Cruz

http://genome.ucsc.edu

http://www.genome.ucsc.edu

The National Center for Biotechnological Information (NCBI)

 http://www.ncbi.nih.gov

http://www.ncbi.nlm.nih.gov

The European Bioinformatics Institute (EBI, Hinxton, UK) (Ensembl by the Wellcome Trust Sanger Institute and the EBI

http://www.ensembl.org)

http://www.ebi.ac.uk

Computational Biology at ORNL

http://genome.ornl.gov/GCat/species.shtml

http://compbio.ornl.gov/channel/

Genome database

http://www.gdb.org

TIGR

http://www.tigr.org

Online Mendelian Inheritance in Man (OMIM TM)

http://www3.ncbi.nlm.nih.gov/omim

http://www.ncbi.nlm.nih.gov/Omim/

Gene Cards

bioinfo.weizmann.ac.il/cards

Gene Tests (formerly HELIX)

http://genetests.org

Protein Dat Bank

http://www.rcsb.org

Human Genome Project - Nature

http://www.nature.com/genomics/

Functional genomics

http://www.sciencegenomics.org

A user's guide to the human genome  by Baxevanis, Collins, Tyra Wolfsberg, Kris Wettenstrand, Mark Guyer on Nature Genetics, 32, supplement , pp 1-79 (2002) ,

http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v32/n1s/inde x.html

Gene Gateway - Exploring genes and genetic disorders

http://www.ornl.gov/hgmis/posters/chromosome/

International Human Genome Organization

http://www.gene.ucl.ac.uk/hugo/

The National Human Genome Research Institute

http://www.nhgri.nih.gov

The American Cancer Society

http://cancer.org

Cancer Genome Anatomy Project

http://www.ncbi.nlm.nih.gov/ncicgap

Genomics : a global resource

http://genomics.phrma.org/legislation/

Genetics Privacy and Legislation (Human Genome Project Information)

http://www.ornl.gov/hgmis/elsi/legislat.html

On-line publication "Signals"

 http://www.signalsmag.com

The Trade Resource Center " (section: "Biotechnology") at the MONTEGEN web site

The Trade Resource Center

Genomes to life (Genomics:GTL)

http://doegenomestolife.org

Genomes to life

http://www.genomes2life.org

Microbial Genome Program

http://www.sc.doe.gov/ober/microbial.html

http://www.ornl.gov/microbialgenomes

Microbial Cell Project

microbialcellproject.org

Environmental Genome Project

http://www.niehs.nih.gov/envgenom/home.htm

SNP Consortium

http://snp.cshl.org