genetics, the human genome project, and sars june 2, 2003 learning objectives- understand what...
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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