Genetics, the Human Genome Project, and SARS June 2, 2003 Learning objectives- Understand what causes SARS and the life cycle of the coronavirus. Understand.

Genetics, the Human Genome Project, and SARS

June 2, 2003 Learning objectives-

Understand what causes SARS and the life cycle of the coronavirus. Understand classical genetics, Mendel’s contributions Understand the Human Genome Project

The History The technology How is it useful? The ethical questions

Workshop-Work in groups to give a presentation on assigned viruses Homework-see last slide, due June 9.

SARS-Severe Acute Respiratory Syndrome Symptoms-

Fever Dry cough Shortness of breath Headache Hypoxaemia-low blood oxygen concentration

Reference: www-micro.msb.le.ac.uk/3035/Coronaviruses.html

SARS-Typical Clinical Course

Clinical course- Viral pneumonia After a few days one feels the symptoms. Then there is gradual improvement the first week. This is followed by worsening in the second week. This worsening is directly related to the patient’s immune response—not viral replication.

Death results from progressive respiratory failure due to alveolar damage

SARS Mean incubation

period-6.4 days Fatality rate is 13.2%

for patients<60 Fatality rate is 43.3%

for patients>60 Caused by

coronavirus

Pathogenesis Coronaviruses infect mammals and

birds First isolated in chickens in 1937. In 1965, Tyrrell and Bynoe found that

coronaviruses can cause the common cold. The other major virus that does this is the rhinovirus.

Transmitted by respiratory secretions and fecal-oral route

Morphology of Coronavirus

Virus particles are irregularly shaped viruses.

Contain clubs on surface composed on sugar-modified proteins

S-Spike protein, receptor binding, cell fusion, major antigenHE-Envelope proteinM-Membrane protein, for budding and envelope formationN-phosphoprotein, associates with RNA genome

Coronavirus genome Type IV (+) sense RNA viruses Non-segmented, single strand, 27-

31 kilobases long. Genome has a 5’ methylated cap

and 3’ poly-A and functions directly as a mRNA

Keywords:Polymerase Full length(+) sense, (-) sense Nested transcripts5’ non-translated leader sequence3’ polyadenylated

Each mRNA is monocistronic, only one gene can betranslated. Each gene is separated by UCUAAAC. Thisintergenic sequence interacts with polymerase plus cellularproteins to place a leader sequence onto the start of eachORF.

The HCoV that causes SARS is a new type of coronavirus previously unknown

It seems to have originated in the Guangdong province of China.

Civet

Tests for coronavirus in humans 1) Serological. Detection by

enzyme-linked immunosorbent assay (ELISA). Within 14 days of illness onset for positive. Negative result-must wait for 21 days post-onset

2) RT-PCR-can detect within first 10 days after illness onset.

In-class exercise 1) Working in pairs choose one virus and obtain this

information: A) Picture of virus B) Whether it is an RNA or DNA virus C) The virus life cycle D) The symptoms of humans that contract the virus E) What are the tests for viral detection? F) What is the route of viral transmission? G) What is the best treatment for patients with

infection? H) When and where was the last outbreak of the virus?

List of viruses: Ebola, Human papilloma Virus, Human Immunodeficiency Virus-1, Epstein-Barr Virus

Gregor Mendel (1822-1884)

Monk Gardener High School

Teacher Mathematician Scientist Father of Classical

Genetics

Parental generation (P)

First filial (F1)

Second filial (F2)

Key findings of monohybrid cross Genotype dictates phenotype. Dominant trait Recessive trait A gene can have more than one allele Principle of segregation. The F1 generation

contained two alleles that segregated in F2. Homozygous vs. heterozygous Punnett square is used to determine

probabilities

Key findings of dihybrid cross Principle of independent

assortment-when genes are located on separate chromosomes alleles will distribute according to predicted 0.25 probability.

Requires genes to be located on separate chromosomes

Workshop

http://www.an.psu.edu/jxm57/irp/mendel.html

View Punnett squares of monohybrid and dihybridCrosses.Then take test.

Three alleles for a single gene. Two are co-dominant, oneis recessive

Linked genes Genes carried on the same

chromosome.

X-linked genes Queen Victoria of England was a carrier

of the gene for hemophilia.  She passed the harmful allele for this X-linked trait on to one of her four sons and at least two of her five daughters.  Her son Leopold had the disease and died at age 30, while her daughters were only carriers.  As a result of marrying into other European royal families, the princesses Alice and Beatrice spread hemophilia to Russia, Germany, andSpain.  By the early 20th century, ten of Victoria's descendents had hemophilia.  All of them were men.

Queen Victoria (1819-1901)

A Pedigree of Hemophilia in the Royal Families of Europe

Crossing over Homologous

chromosomes during early stages of meiosis.

Results in recombination

Nondisjunction

Chromosomes failto separate during meiosis.

Sequencing DNA

What is the approach used to sequence genomes? Divide and conquer

Split the genome into fragments Clone into vectors that can accept large

fragments: yeast artificial chromosomes (YAC Library)

Landmarks within the genome can be obtained using Sequence Tagged Sites (STS)

Sequences of YAC clones are matched with each other.

Sequences that overlap form contigs.

History of the Human Genome Project

1953

Watson,CrickDNAstructure

1972

Berg,1st recombinantDNA

1977

Maxam,Gilbert,SangersequenceDNA

1980

Botstein,Davis,SkolnickWhitepropose to map humangenome withRFLPs

1982

Wadaproposes tobuild automated sequencingrobots

1984

MRCpublishesfirst largegenomeEpstein-Barrvirus (170 kb)

1985

Sinsheimer hosts meeting to discuss HGP at UCSantaCruz;Kary Mullis develops PCR

1986

DOE begins genome studies with $5.3 million

1987

Gilbert announces plans to start company to sequence and copyright DNA; Burke, Olson, Carle develop YACs; Donis-Keller publish first map (403 markers)

History of the Human Genome Project (continued)

1987 (cont)

Hood producesfirst automated sequencer;Dupont devolops fluorescent dideoxy-nucleotides

1988

NIH supports the HGP;Watson heads the project and allocates part of the budget to study social and ethical issues

1989

Hood, Olson, Botstein Cantor propose using STS’s to map the human genome

1990

Proposal to sequence20 Mb in model organism by 2005;Lipman, Myers publish the BLAST algorithm

1991

Venter announces strategy to sequence ESTs. He plans to patentpartial cDNAs;Uberbacher develops GRAIL, a gene finding program

1992

Simon develops BACs; US and French teams publish first physical maps of chromosomes; first genetic maps of mouse and human genome published

1993

Collins is named director of NCHGR; revise plan to complete seq of human genome by 2005

1995

Venter publishes first sequence of free-living organism:H. influenzae (1.8 Mb);Brown publishes on DNA arrays

1996

Yeast genome is sequenced (S. cerevisiae)

History of the Human Genome Project (continued)

1997

Blattner, Plunket complete E. coli sequence; a capillary sequencing machine is introduced.

1998

SNP project is initiated; rice genome project is started; Venter creates new company called Celera and proposes to sequence HG within 3 years; C. elegans genome completed

1999

NIH proposes to sequence mouse genome in 3 years; first sequence of chromosome 22 is announced

2000

Celera and others publish Drosphila sequence (180 Mb); human chromosome 21 is completely sequenced; proposal to sequence puffer fish; Arabadopsis sequence is completed

2001

Celera publishes human sequence in Science; the HGP consortium publishes the human sequence in Nature

2003

Completed genomes:112 Microbial18 Eukaryotes1275 Viruses

Unknown Function

How much of the genome is defined?

Homework Due June 9 p. 351, problems 1,4 p. 358 1-5 p. 366 Reviewing Ideas: 1, 5-7; Using

Concepts: 1-3 p. 367 Synthesis: 1; Extensions: 1 p. 415 Reviewing Ideas: 7-10, 14; Using

Concepts: 1-3; Synthesis: 1-2; Extensions: 1

Reading for next week: pp.557-569