Transcript Evolutionary Biology

Evolutionary Biology
Examples
Polio Virus
• The vaccine now used to immunize
against the disease poliomyelitis is a live
poliovirus that we eat.
• This live virus does not give us the
disease (except to about 1-2 in a million
people vaccinated) because it is
genetically weakened (attenuated) so that
our body can defeat it.
Attenuation
• The attenuated vaccine strains came from
wild, virulent strains of poliovirus, but they
were evolved by Albert Sabin to become
attenuated. Essentially, he grew the
viruses outside of humans, and as the
viruses became adapted to those nonhuman conditions, they lost their ability to
cause disease in people.
This method of attenuation has been
used to create many live vaccines.
• When a person eats the attenuated virus,
it infects his/her gut cells and starts doing
what viruses do -- making copies of itself.
• These viral progeny infect other cells in
your gut, those in turn make other viral
progeny, and so on, until you have a
population of poliovirus growing inside
your gut.
Evolution
• Some of these viruses carry mutations, and
some of those mutations (one or two in
particular) restore most of the virulence to the
virus.
• In your gut, these restored viruses may have a
selective advantage over the weakened viruses,
and in the course of a week or so after eating
the vaccine, you begin shedding virus with
restored virulence.
• In short, an evolutionary process inside your gut
undoes Albert Sabin's attenuation of the virus.
Vaccine
• These restored viruses do not hurt the
person taking the vaccine because by the
time restored viruses get to be abundant in
the gut, the immune system has enough of
a head start to keep the virus from getting
into the central nervous system.
Vaccine
• However, if we were to vaccinate just one
person in a population of non-immunized
people the restored viruses shed from this
one person would infect other people and
could start an epidemic of nasty poliovirus.
• The WHO did all of China in 3 days, and
vaccinated 90,000,000 people in India in
one day.
Evolution leads to resistance
• Isolates of the AIDS virus with up to 15 different
drug-resistance mutations are known, and the
latest drugs are becoming ineffective.
• Some strains of bacteria are resistant to all
available antibiotics.
• For multi-drug resistant tuberculosis, surgery is
the only cure because antibiotics don't work and
only 50% of those infected survive.
• Chemotherapy for cancer often fails because
drug-resistant cells evolve during treatment.
HIV-the great evolver
• The human
immunodeficiency virus
(HIV, shown here budding
from a white blood cell) is
one of the fastest
evolving entities known.
What are the evolutionary origins of
HIV?
• HIV found that it is closely related to other
viruses. Those viruses include SIVs
(simian immunodeficiency viruses), which
infect primates, and the more distantly
related FIVs (the feline strains), which
infect cats.
• primates with SIV and wild cats with FIV
don't seem to be harmed by the viruses
they carry.
History of HIV
Blood Cells
Macrophages
• Macrophages (Greek: "big eaters",
makros = large, phagein = eat) are cells
within the tissues that originate from
specific white blood cells called
monocytes. Monocytes and
macrophages (differentiated
monocytes) are phagocytes, acting in
both nonspecific defence (or innate
immunity) as well as specific defense
(or cell-mediated immunity) of
vertebrate animals. Their role is to
phagocytize (engulf and then digest)
cellular debris and pathogens either as
stationary or mobile cells, and to
stimulate lymphocytes and other
immune cells to respond to the
pathogen.
macrophage of a
mouse stretching its
arms to engulf two
particles, possibly
pathogens
Making of antibodies
• After digesting a pathogen, a macrophage will present
the antigen (a molecule, most often a protein found on
the surface of the pathogen, used by the immune system
for identification) of the pathogen to a corresponding
helper T cell. The presentation is done by integrating it
into the cell membrane and displaying it attached to a
MHC class II molecule, indicating to other white blood
cells that the macrophage is not a pathogen, despite
having antigens on its surface.
• Eventually the antigen presentation results in the
production of antibodies
T-cells
• T cells belong to group of
white blood cells known as
lymphocytes and play a
central role in cell-mediated
immunity. They can be
distinguished from other
lymphocyte types, such as B
cells and NK cells by the
presence of a special receptor
on their cell surface that is
called the T cell receptor
(TCR). The abbreviation "T",
in T cell, stands for thymus
since it is the principal organ
for their development.
Helper T-cells
• They are not cytotoxic or phagocytic; they
activate or direct immune system.
• The importance of helper T cells can be seen
from HIV, a virus that infects cells that are CD4+
(including helper T cells). Towards the end of an
HIV infection the number of functional CD4+ T
cells falls, which leads to the symptomatic stage
of infection known as the acquired immune
deficiency syndrome (AIDS).
Why are some people resistant to
HIV?
• the human genome is littered with the
remnants of our past battles with
pathogens — and one of these
remnants, a mutation to a gene called
CCR5.
• The mutant CCR5 allele probably
began to spread in northern Europe
during the past 700 years when the
population was ravaged by a plague.
The mutant CCR5 is resistant to the
disease, its frequency increased
• In some parts of Europe
today, up to 20% of the
population carry at least
one copy of the protective
allele.
• However, the populations
of Asia and Africa were
not exposed to the same
epidemics; very few
Asians and Africans now
carry the allele
http://evolution.berkeley.edu/evolibrary/article/0_0_0/medicine_04
CCR5
• Two new proteins found on immune cells, CCR5
and fusin (also known as CXCR4), play a key
role in understanding how HIV infects cells.
• One way HIV disables the immune system is by
infecting and destroying CD4+ T-cells that
manage immune responses. HIV actually
attaches to the CD4+ protein on the surface of
these and other cells to gain entry.
CCR5
• CD4+ protein alone is not enough to allow
viral entry into cells. Scientists believe they
have now identified a second doorway that
the virus needs to open to infect a cell,
and they have learned that this receptor
may be different for different types of cells.
One is called CC-CCR5 (CCR5 for short),
and another is called CXCR4 or fusin.
CCR5
• CCR5 is present on a broad range of cells that
can be infected by HIV, including T-cells and
macrophages. Fusin on the other hand, is
primarily found on CD4+ cells and only appears
to serve as a doorway for certain types of HIV.
CCR5 appears to be important for NSI strains of
HIV (the strains most common in early disease),
while CXCR4 appears to be more important for
SI strains (a more aggressive strain seen in
some people with more aggressive disease).
CCR5
• NSI (non-syncitium inducing) strains of
HIV are the most common sexually
transmitted form of the virus. This type of
HIV preferentially infects macrophages
(often found in the skin and mucous
membrane) rather than T-cells. Therefore,
it is macrophage-tropic, or M-tropic.
CCR5
• When HIV is transmitted sexually, it first
establishes itself as an M-tropic virus, later
developing into T-cell-tropic viruses in some
people. These T-tropic strains that prefer to
infect T-cells, are SI (syncitium inducing) viruses
and may become more prevalent during later
stages of the disease. It is unclear why the virus
converts from an NSI to an SI strain in some
people. About 50% of people who die of AIDS
still have a predominant NSI strain of virus.
CCR5
• The SI strain of HIV is more aggressive and its
prevalence correlates with more rapid disease
progression. Additionally, anti-HIV drugs generally have
less activity against SI strains of HIV. The most obvious
difference between someone with an NSI versus an SI
strain, however, is that people with an SI strain
experience more rapid decline in CD4+ counts, as the SI
virus preferentially infects and destroys these cells. Also,
people with the SI strain tend to have a 3- to 5-fold
increase in the rate of disease progression.
Syncitium Inducing
• Syncitium inducing virus (SI) is virus that causes
infected cells to form syncitia (connections) with
other infected cells in tissue culture.
• It is more virulent than non-syncitium inducing
virus (NSI), which means that people with SI
virus tend to progress more rapidly than those
with NSI. Most people are infected with NSI but
at some point experience a conversion to SI,
which usually leads to a rise in viral laod and a
more rapid decline in CD4 count.
Chemokines
beta-chemokines, bind up CCR5 and CXCR4 and help block HIV from infecting cells
MIP-1-alpha, MIP-1-beta and Rantes
Clinical Implications
• When people inherited a defective version
of CCR5 from both parents, they appeared
to be resistant to infection with HIV. (The
gene is considered defective because a
portion of it is missing, and it thus cannot
produce a functional CCR5 receptor.)
Contour Map
Allele originated in Baltic Regions. Another alternative is that the allele may have
arisen in central Europe and increased to a higher frequency in the north because of
a geographical gradient in selection intensity [19].
Perspectives
• A group from Texas has shown that resting
CD4+ cells, despite bearing the CCR5 gene, are
resistant to infection by HIV. Another group
identified a type of cell, called a stem cell, which
had CD4+ and both co-receptors on its surface,
yet remained resistant to infection by HIV. What
this implies is that there are other factors,
beyond the expression of CD4+ and the newly
identified co-receptors, which come into play
with regard to HIV entry into cells.
A case study
• In a highly publicized case in Lafayette,
Louisiana in 1998, a woman claimed that
her ex-boyfriend (a physician) deliberately
injected her with HIV-tainted blood (HIV is
the virus that causes AIDS). There were
no records of her injection and no
witnesses. So how could her story be
tested? Evolutionary trees provide the best
scientific evidence in a case like this.
HIV
• HIV picks up mutations very fast -- even
within a single individual.
• If one person gives the virus to another,
there are few differences between the
virus in the donor and the virus in the
recipient.
HIV
• As the virus goes from person to person, it
keeps changing and gets more and more
different over time.
• Thus, the HIV sequences in two individuals who
got the virus from two different people will be
very different.
• Thus, if the woman's story were true, her virus
should be very similar to the virus in the person
whose blood was drawn but should be very
different from viruses taken from other people in
Lafayette.
A criminal Case
Abstract
• A gastroenterologist was convicted of attempted
second-degree murder by injecting his former
girlfriend with blood or bloodproducts obtained
from an HIV type 1 (HIV-1)-infected patient
under his care.
• Phylogenetic analyses of HIV-1 sequences were
admitted and used as evidence in this case,
representing the first use of phylogenetic
analyses in a criminal court case in the United
States.
Abstract
• Phylogenetic analyses of HIV-1 reverse
transcriptase and env DNA sequences
isolated from the victim, the patient, and a
local population sample of HIV-1-positive
individuals showed the victim’s HIV-1
sequences to be most closely related to
and nested within a lineage comprised of
the patient’s HIV-1 sequences.
Abstract
• Analysis of the victim’s viral reverse
transcriptase sequences revealed
genotypes consistent with known
mutations that confer resistance to AZT,
similar to those genotypes found in the
patient.
Method
• Genomic DNA from each individual was
used to PCR-amplify a 858-bp env gene
fragment and a 1,147-bp reverse
transcriptase (RT) gene fragment
PCR
• 200 ng of genomic DNA from the patient,
victim, or any LA controls were handled
and amplified separately by coamplifying
the pol and env genes regions with
PCR1/PCR2 and PCR5/PCR6 primer
pairs to yield 1,231- and 1,288-bp
fragments.
PCR
• amplified separately a 1,147-bp pol
fragment by using PCR3B/PCR4B primer
pairs and a 858-bp env fragment by using
PCR7B/PCR8B primer pairs. PCR
products from the patient, victim, and the
LA controls were directly sequenced.
Genetic Diversity
• the extent of env genetic diversity of the
suspected transmission pair, 50 molecular
clones were isolated and sequenced at BCM
from their respective PCR products. The
molecular clones for the patient and victim were
designated P01 through P50 and V01 through
V50.
• the most appropriate controls for the current
study were HIV-1-infected individuals from the
Lafayette area.
Tree
Suspect’s Patient
Other HIV patients from
LaFayette
Tree
Tree