Difference between revisions of "Chapter !4 - Comparative Genomics Code : KSI0013"

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imported>김상인
imported>김상인
 
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<p><span style="color:#0000CD"><strong>Introduction&nbsp;</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Introduction&nbsp;</strong></span></p>
 +
 +
<p>It&#39;s likely that life originated on Earth about 3.5 billion years ago. the first cellular life forms were undoubtedly prokaryotes. Eukaryotes appeared about 2 billion year later. There are enough residual similarities among living things to suggest a common ancestory of us all. The great diversity of living forms is therefore, the result of divergence.</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Unity and diversity of life</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Unity and diversity of life</strong></span></p>
 +
 +
<p>Binomial /DNA barcoding</p>
  
 
<p>Taxonomy based on sequences</p>
 
<p>Taxonomy based on sequences</p>
 +
 +
<p>- Traditional linnaean biological nomenclature assigns names to species, and classifies apecies according to evolutionary relationships. It&#39;s often difficult todraw boundaries between species, especially for microorganisms.</p>
 +
 +
<p>- Bacteria/ archaea / Eukarya / phylogenetic tree. / horizontal gene transfer ( Please pass the genes)</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Sizes and organization of genomes</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Sizes and organization of genomes</strong></span></p>
  
 
<p>Genome sizes</p>
 
<p>Genome sizes</p>
 +
 +
<p>Genome sequences/ RNA and protein expression patterns/ The spatial organization of individual macromolecules, their complexes, organelles, entire cells, tissues, and bodies</p>
 +
 +
<p>/ regulatory networs, the internal structure and logic of adaptive control systems.</p>
 +
 +
<p>The term C-value has been used to refer to the amount of DNA in a haploied cell. the letter C refers to the constancy of the amount of DNA per cell in a pspecies.&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Viral genomes</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Viral genomes</strong></span></p>
  
 
<p>Recombinant viruses</p>
 
<p>Recombinant viruses</p>
 +
 +
<p>BOth HIV- 1 and influenza viruses have become major threats to human health after jumping from animal hosts. Their high mutation rates with severe clinical consequences- reflect the fact that their genomes are RNA</p>
  
 
<p>Influenza : a past and current threat</p>
 
<p>Influenza : a past and current threat</p>
 +
 +
<p>Types of viral genome&nbsp;</p>
 +
 +
<p>- SSDNA&nbsp;</p>
 +
 +
<p>- DSDNA</p>
 +
 +
<p>- SSRNA</p>
 +
 +
<p>- DSRNA</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Genome Organization in prokaryotes</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Genome Organization in prokaryotes</strong></span></p>
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<p>Gene transfer</p>
 
<p>Gene transfer</p>
 +
 +
<p>- transformation / conjugation / trnasduction&nbsp;</p>
 +
 +
<p>Some but not all prokaryote genomes contain Insertion sequences mobile genetic elements similar to eukaryotic transposons.</p>
 +
 +
<p>Prokaryotes have several mechanisms for sharing genetic material : Transformation by naked DNA conjugation and transfer via viruses.</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Genome Organization in eukaryotes</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Genome Organization in eukaryotes</strong></span></p>
  
 
<p>Photosynthetic sea slugs : endosymbiosys of chloroplasts</p>
 
<p>Photosynthetic sea slugs : endosymbiosys of chloroplasts</p>
 +
 +
<p>Mitochondria and chloroplasts carry out their own protein synthesis. Chchloroplasts and plant mitochondria translate their genes according to the standard genetic code, but animal mitochondria use variants.&nbsp;</p>
 +
 +
<p>Traffic between the mitochondrial and nuclear genomes.&nbsp;</p>
 +
 +
<p>&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>How genomes differ</strong></span></p>
 
<p><span style="color:#0000CD"><strong>How genomes differ</strong></span></p>
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<p>Comparisions at the chromosome level : synteny</p>
 
<p>Comparisions at the chromosome level : synteny</p>
 +
 +
<p>What can happen to a gene?</p>
 +
 +
<p>- During evolution&nbsp;</p>
 +
 +
<p>-1 A gene may pass to descendants, accumulating favourable or unavourable mutations or dirifting neutrally.</p>
 +
 +
<p>2. A gene may be lost</p>
 +
 +
<p>3. A gene may be dulicated followed by divergence or by loss of one of the pair</p>
 +
 +
<p>4. A gene may undergo horizontal transfer to an organism of another species.</p>
 +
 +
<p>5. A gene may undergo complex patterns of fusion fission or rearrangemnet perhaps involving regions encoding individual protein domains</p>
 +
 +
<p>Homologues / Paralogues/ orthologues&nbsp;</p>
 +
 +
<p>Neutral evolution&nbsp;</p>
 +
 +
<p>Positive selection&nbsp;</p>
 +
 +
<p>Purifying selection&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>What makes us human?</strong></span></p>
 
<p><span style="color:#0000CD"><strong>What makes us human?</strong></span></p>
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<p>Combining the approaches : the <em>FOXP2</em> gene</p>
 
<p>Combining the approaches : the <em>FOXP2</em> gene</p>
 +
 +
<p>Comparative genomics &nbsp;and study of huan diseases</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Genomes of chimpanzees and humans</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Genomes of chimpanzees and humans</strong></span></p>
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<p>The modENCODE project</p>
 
<p>The modENCODE project</p>
  
−
<p>&nbsp;</p>
+
<p>is a systematic development and application of comparative genomics .&nbsp;</p>
 +
 
 +
<p>It has the ultimate goal of developing methods for comprehensive identification of functional regions of the human genome.&nbsp;</p>
 +
 
 +
<p>____________________________________________________________________________________________________________________________KSI&nbsp;</p>

Latest revision as of 03:22, 28 November 2016

<Index of Chapter 4>

Introduction 

It's likely that life originated on Earth about 3.5 billion years ago. the first cellular life forms were undoubtedly prokaryotes. Eukaryotes appeared about 2 billion year later. There are enough residual similarities among living things to suggest a common ancestory of us all. The great diversity of living forms is therefore, the result of divergence.

 

Unity and diversity of life

Binomial /DNA barcoding

Taxonomy based on sequences

- Traditional linnaean biological nomenclature assigns names to species, and classifies apecies according to evolutionary relationships. It's often difficult todraw boundaries between species, especially for microorganisms.

- Bacteria/ archaea / Eukarya / phylogenetic tree. / horizontal gene transfer ( Please pass the genes)

 

Sizes and organization of genomes

Genome sizes

Genome sequences/ RNA and protein expression patterns/ The spatial organization of individual macromolecules, their complexes, organelles, entire cells, tissues, and bodies

/ regulatory networs, the internal structure and logic of adaptive control systems.

The term C-value has been used to refer to the amount of DNA in a haploied cell. the letter C refers to the constancy of the amount of DNA per cell in a pspecies. 

 

Viral genomes

Recombinant viruses

BOth HIV- 1 and influenza viruses have become major threats to human health after jumping from animal hosts. Their high mutation rates with severe clinical consequences- reflect the fact that their genomes are RNA

Influenza : a past and current threat

Types of viral genome 

- SSDNA 

- DSDNA

- SSRNA

- DSRNA

 

Genome Organization in prokaryotes

Replication and transcription

Gene transfer

- transformation / conjugation / trnasduction 

Some but not all prokaryote genomes contain Insertion sequences mobile genetic elements similar to eukaryotic transposons.

Prokaryotes have several mechanisms for sharing genetic material : Transformation by naked DNA conjugation and transfer via viruses.

 

Genome Organization in eukaryotes

Photosynthetic sea slugs : endosymbiosys of chloroplasts

Mitochondria and chloroplasts carry out their own protein synthesis. Chchloroplasts and plant mitochondria translate their genes according to the standard genetic code, but animal mitochondria use variants. 

Traffic between the mitochondrial and nuclear genomes. 

 

 

How genomes differ

Variation at the level of individual nucleotides

Duplications

Comparisions at the chromosome level : synteny

What can happen to a gene?

- During evolution 

-1 A gene may pass to descendants, accumulating favourable or unavourable mutations or dirifting neutrally.

2. A gene may be lost

3. A gene may be dulicated followed by divergence or by loss of one of the pair

4. A gene may undergo horizontal transfer to an organism of another species.

5. A gene may undergo complex patterns of fusion fission or rearrangemnet perhaps involving regions encoding individual protein domains

Homologues / Paralogues/ orthologues 

Neutral evolution 

Positive selection 

Purifying selection 

 

What makes us human?

Comparative genomics

Combining the approaches : the FOXP2 gene

Comparative genomics  and study of huan diseases

 

Genomes of chimpanzees and humans

Genomes of mice and rats

Model organisms for study of human diseases

The genome of Caenorhabditis elegans

The genome of Drosophilia melanogaster

Homologous genes in humans, worms, and flies

The ENCODE project

The modENCODE project

is a systematic development and application of comparative genomics . 

It has the ultimate goal of developing methods for comprehensive identification of functional regions of the human genome. 

____________________________________________________________________________________________________________________________KSI 

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