Transcript Biology and computers

Genetics, the Human Genome Project, and
SARS
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June 2, 2003
Learning objectives
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Understand what causes SARS and the life cycle of the
coronavirus.
Understand classical genetics, Mendel’s contributions
Understand the Human Genome Project
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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
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Symptoms
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Fever
Dry cough
Shortness of breath
Headache
Hypoxaemia-low blood oxygen
concentration
Reference: wwwmicro.msb.le.ac.uk/3035/Coronaviruses
.html
SARS-Typical Clinical Course
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Clinical course
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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
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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
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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
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Virus particles are
irregularly shaped
viruses.
Contain clubs on
surface composed
on sugar-modified
proteins
S-Spike protein, receptor binding, cell fusion, major antigen
HE-Envelope protein
M-Membrane protein, for budding and envelope formation
N-phosphoprotein, associates with RNA genome
Coronavirus genome
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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 transcripts
5’ non-translated
leader sequence
3’ polyadenylated
Each mRNA is monocistronic, only one gene can be
translated. Each gene is separated by UCUAAAC. This
intergenic sequence interacts with polymerase plus cellular
proteins to place a leader sequence onto the start of each
ORF.
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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
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1) Serological. Detection by enzymelinked 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
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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)
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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
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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
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Principle of independent assortmentwhen genes are located on separate
chromosomes alleles will distribute
according to predicted 0.25 probability.
Requires genes to be located on
separate chromosomes
Workshop
View Punnett squares of monohybrid and dihybrid
Crosses.
Then take test.
http://www.an.psu.edu/jxm57/irp/mendel.html
Three alleles for a single gene. Two are co-dominant, one
is recessive
Linked genes
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Genes carried on the same
chromosome.
X-linked genes
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Queen Victoria (1819-1901)
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, and
Spain. By the early 20th century, ten of
Victoria's descendents had
hemophilia. All of them were men.
A Pedigree of Hemophilia in the
Royal Families of Europe
Crossing over
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Homologous
chromosomes during
early stages of
meiosis.
Results in
recombination
Nondisjunction
Chromosomes fail
to separate during meiosis.
Sequencing DNA
What is the approach used to
sequence genomes?
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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,
Crick
DNA
structure
1972
Berg,
1st
recombinant
DNA
1977
Maxam,
Gilbert,
Sanger
sequence
DNA
1980
1982
1984
1985
1986
Botstein,
Sinsheimer DOE begins
Wada
MRC
Davis,
genome
proposes to publishes hosts
Skolnick
build
first large meeting to studies with
White
discuss HGP $5.3 million
automated genome
propose to sequencing Epstein-Barrat UCSanta
map human robots
virus (170 Cruz;
genome with
Kary Mullis
kb)
RFLPs
develops
PCR
1987
Gilbert announces
plans to start company
to sequence and
copyright DNA;
Burke, Olson, Carle
develop YACs; DonisKeller publish first
map (403 markers)
History of the Human Genome
Project (continued)
1987 (cont) 1988
1989
Hood
produces
first
automated
sequencer;
Dupont
devolops
fluorescent
dideoxynucleotides
Proposal
Venter
Simon
Hood,
to
sequence
announces develops
Olson,
20
Mb
in
strategy to BACs; US
Botstein
model
sequence
and French
Cantor
propose organism by ESTs. He teams
2005;
plans to
publish first
using
Lipman,
patent
physical
STS’s to map
Myers
partial
maps of
the human
chromosome
genome publish the cDNAs;
BLAST
Uberbacher s; first
algorithm develops
genetic maps
GRAIL, a of mouse and
gene finding human
program
genome
published
NIH
supports the
HGP;
Watson
heads the
project and
allocates
part of the
budget to
study social
and ethical
issues
1990
1991
1992
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
2000
NIH
proposes to
sequence
mouse
genome in 3
years; first
sequence of
chromosome
22 is
announced
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 Microbial
18 Eukaryotes
1275 Viruses
How much of the genome is defined?
Unknown Function
Homework Due June 9
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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