BASIC OUTLINE OF CLASS

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BASIC OUTLINE OF CLASS

• 1) Speculation and research on the origin of
  life.
• 2) The RNA world as an intermediary to the DNA
  world generalities, history and current
• A) What was the RNA world like
• B) Current three domain view
• C) LUCA
• 3) Genome Content and Architecture
• 4) Mutation
• 5) Phylogenetic Reconstruction
• A) Term, definitions and limits
• B) How to determine a phylogenetic tree
• C) Improvements and Extensions to Genome Trees
• Deviation from Tree-like Behavior
• Convergent Evolution
• Evolution of Viruses
• Retroid Agents
• 10) Bioethics

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DEFINITION OF LIFE
BIO 190 Definition of a living system 1)
metabolism 2) organization 3) reproduction 4)
evolution A more sophisticated version of these
requirements Life is a self-sustained chemical
system capable of undergoing Darwinian
evolution. The Darwinian evolutionary process
includes self-reproduction, material
continuity over an historical lineage, genetic
variation and natural selection. Or more
abstractly The attribute of the living state
is defined as the maintenance of a particular
energy relationship of the bounded system (i.e.,
the cell) to its environment.
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McClure, 2002
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The World of Viruses
DNA viruses
RNA viruses
RdDp
ssRNA
dsRNA
ssDNA
dsDNA
RdRp
host Pol II
ssRNA
- ssRNA
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Flavivirae, Caliciviridae, Astroviridae Coronaviri
dae, Arteriviridae, Nodaviridae Tetraviridae
Birna
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Rhabdoviridae
Paramyxoviridae
Filoviridae
Retroviridae
Picornaviridae
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Rhabdoviridae
Paramyxoviridae
The Order Mononegavirales
Filoviridae
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Mononegavirales
OLD FOES rabies (Rhabdoviridae) measles,
RSV, mumps (Paramyxoviridae) EMERGING
THREATS Ebola, Marburg (Filoviridae) equine
morbillivirus, Nipah virus (Paramyxoviridae) MOD
EL AGENT vesicular stomatitis virus
(Rhabdoviridae)
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Rhabdoviridae Genome
Paramyxoviridae Genome
Filoviridae Genome
N VP35 VP40 G
VP30 VP24 RdRp
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• What about DNA viruses?
• Related by
• Multiple chars of large cytoplasmic DNA viruses
  Iver 2001
• Structural similarity Bamford 2002

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Multiple Gene Analysis of Nucleocytoplasmic
Large DNA Viruses Eukaryotic Viruses pox ,
asfar, irido and phyco-viruses Common genes 9
in all, 22 in 3/4 Synapomorphies 5/9 unite
these four virus families to the exclusion of
all other known life forms Monophyly genes
shared by at least 2 viral families
Conclusion multiple cycles of acquisition and
loss with a stable core
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TABLE 2. Predicted Functional Systems of the
Ancestral Nucleocytoplasmic DNA Virus
Function and/or Pathway
Proteins
DNA replication
DNA Polymerase D5R-like helicase, RuvC-like
Holliday junction resolvase, PCNA (DNA clamp),
ATP-dependent DNA ligase, Type II topoisomerase,
dUTPase Ribonucleotide reductase (two subunits),
thymidylate kinase RNA polymerase (two large
subunits and subunit 10), A1L-like and TFIIS-like
transcription factors, D6R-like, A18R-like,
SWI/SNF2-like helicases, capping enzyme, BRO-like
DNA binding protein, Nudix hydrolase A32-like
packaging ATPase, E10R-like thiol-oxidoreductase,
glutaredoxin-thioredoxin F10L-like protein
kinase, H1L-like phosphatase D13L-like capsid
protein, L1R-family and J5L-family virion
membrane proteins BIR-domain-containing protein
DNA precursor synthesis..
Transcription and RNA Processing.
Virion Morphogenesis..
Regulation of Morphogenesis...
Virion Structure....
Inhibition of Apoptosis.
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FIG. 1 Viral lineages and the tree of life. The
upper panel shows the universal phylogenetic tree
of cellular organisms constructed using 16s and
18s ribosomal RNA sequences showing the three
domains of cellular life. The cellular life is
embedded in parasitic viral organisms (blue)
outnumbering the hosts by at least one order of
magnitude. The majority of DNA in higher
eukaryotic organisms may also be of viral origin.
Structurally and functionally related viruses
are discovered infecting hosts from different
domains of life (marked as blue particles at the
branches of the tree) Tree information obtained
from the Ribosomal Database Project. The lower
panels show three distinct emerging lineages of
viruses for which there are representatives of at
least two domains of life (all viruses are
colored according to the domain that they infect
green for prokaryotes, yellow for Archaea, and
red for eukarya). Upper adeno-PRD1. Note
that PBCV-1 (and the iridoviruses) and PRD1
contain lipid bilayers, whereas adenovirus does
not. Note also that there are no proteins
covalently attached to the PBCV-1 (or iridovirus)
genome. Middle reo-?6. Both viruses have
segmented double-stranded RNA genomes, but again
note that the outer layer of ?6 is a membrane,
whereas BTV has proteins. Lower herpes-T4.
This includes the tailed bacteriophages, for
which representatives have been found in bacteria
and Archaea. Herpes virus is the putative member
for the eukarya.
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Retro-transcribing viruses Retroviridae
o Orthoretrovirinae o
Spumaretrovirinae o unclassified
Retroviridae unclassified retroid viruses
o Endogenous sheep retrovirus
Caulimoviridae o Badnavirus o
Caulimovirus o Cavemovirus o
Petuvirus o Soymovirus o
Tungrovirus Hepadnaviridae (hepatitis
B-type viruses) o Avihepadnavirus
(avian hepatitis B-type viruses) o
Orthohepadnavirus (mammalian hepatitis B-type
viruses) o unclassified Hepadnaviridae
Metaviridae o Errantivirus
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Evolution of HIV
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Comparison of HIV evolution in an individual,
cohort and population
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First data indicating that HIV entered the human
population more than once. HIV 1 and 2 phylogeny
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HIV evolves via point mutation AND recombination
in response to the environment of its host. Can
the host evolve away from HIV?
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While the immune system naturally drives the
evolution to the ENV gene, AIDs therapies
artificially drives the evolution of the other
genes
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A 32-nucleotide deletion (delta 32) within the
beta-chemokine receptor 5 (CCR5) gene is found
in subjects who remain uninfected despite
extensive exposure to HIV-1.
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Distribution of CCR5 delta 35
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Was it the plague or smallpox that spread the
CCR5-allele that confers HIV resistance in about
10 of the Caucasian population?
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The Mutualism Continuum
of Retroid Agents
HIV
Endogenous retroviruses
Retroviral LTRs
Endogenous retroviruses
LINEs
TERT
HTLV
Cellular promoters
AIDS
Human T-cell leukemia
Chromosomal repair
Gene regulation
Deadly disease
Disease association
Genetic disease
Reproduction
beneficial symbioant
parasite
commensalism