Genome Sequences Answer Interesting Questions

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Genome Sequences Answer Interesting Questions
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Outline

• Evolution of Genomes
• Genomic Identification
• Biomedical Genome Research

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2.1 Evolution of Genomes

• Use genomes to understand the evolution of
  eukaryotes.
• Analyze sequences to deduce human evolution.

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Six Archaea genomes Nine EuBacteria genomes
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What Is An E-value?

• A BLASTn search returns hits, sequences that
  produce significant alignments to the query
  sequence.
• The significance of a hit is measured by its
  E-value, or expect value.
• Biological significance hits will tend to have
  E-values much less than 1.0.
• The larger the E-value, the greater the chance
  that the similarity between the hit and the query
  is due to more coincidence.

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Are the hit numbers significantly different?

• Use t-test to determine whether a separation
  between grey and blue lines is statistically
  significant.
• t-statistic values greater than 1.771 favor an
  Archaeal origin, and t-statistic values less than
  -1.771 favor a Eubacterial origin.

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Severe Acute Respiratory Syndrome (SARS)

• The severe acute respiratory syndrome (SARS) has
  recently been identified as a new clinical
  entity.
• SARS is thought to be caused by an unknown
  infectious agent.
• A novel coronavirus (????) was identified in
  patients with SARS.

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SARS Cases and Deaths
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March 14
March 20
March 17
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SARS Genomes
Science, 300, pp.715
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When a New Virus Emerging?

• Clinics
• Diagnosis
• Treatment Trials
• Genomics
• Genome sequencing
• Genome organization
• Phylogenetic analysis
• Predicted replicase gene products
• Analysis of the predicted structural proteins

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Virus Proteins

• The genomic organization is typical of
  coronavirus, with the characteristic gene order
  (5-replicase rep, spike S, envelope E,
  membrance M, nucleocapsid N-3), and short
  untranslated regions at both termini.
• Coronaviruses encode a chymotrypsin-like
  protease, 3CLpro.
• Polymerase POL
• Helicase HEL

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Coronovirus Genome Organization
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Phylogenetic Analysis
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Exercise
Transmissible gastroenteritis virus (TGEV) Human
coronavirus 229E (HcoV-229E) Feline infectious
peritonitis virus (FIPV) Canine coronavirus 
(CCoV) Porcine respiratory coronavirus
(PRCoV) Bovine coronavirus  (BcoV) Murine
hepatitis virus  (MHV) Human coronavirus OC43
(HCoV-OC43) Porcine hemagglutinating
encephalomyelitis virus (PHEV) Avian infectious
bronchitis virus (IBV)
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2.2 Genomic Identification

• Explore new technologies for faster forensic
  identification.
• Discover challengers of working with ancient
  DNA.
• Use genomes to track emerging diseases.

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How can we identify biological weapons?

• Anthrax (???) is a spore-forming bacterium,
  Bacillus anthracis, that occurs in wild and
  domestic mammals (cattle, sheep, goats, camels,
  antelopes, and other herbivores) but can infect
  humans as well.

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PCR (Overview)

• PCR (Polymerase Chain Reaction)
• To amplify the target DNA sequence in the
  exponential manner

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• Temperature
• 94?-Denature the double strand DNA
• 50-60?-Attach the primers to target DNA sequence
• 72?-Synthesize the DNA

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PCR (The first stage)
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The synthesis of 'short' products
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How Long Can DNA Survive?
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Bacteria Survives in 250-Million-Year-Old Salt
Crystal
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Chromosomal DNA was isolated from 2-9-3, the
complete rDNA region was sequenced and compared
with other sequences.
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How Did Tuberculosis Reach North America?

• Knowing the transmission mechanism enables us to
  better combat the causative agent.
• Knowing how the disease was first introduced into
  humans would provide a more complete
  understanding of its life history.

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A segment of DNA unique to Mycobacterium
tuberculosis called IS6110
Lane 1 DNA extracted from nodule N1 Lane 2
DNA extracted from lung nodule L Lane 3 control
reaction Lane 4 was empty Lane 5 reaction
control Lane 6 molecular weight standards
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Using PCR, a 133 bp fragment is amplified. The
fragment encodes a surface protein expressed in
M. tuberculosis and M. leprae.
(?????)
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How Are Newly Emerging Disease Identified?

• Many viral genomes have been sequenced, enabling
  a better understanding of viral diseases.

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(??????)
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(??????)
Encephalitis (??)
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