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SCIENCE
And a few suggestions...
Uncle Tungsten
by Oliver Sacks
In this charming biography, Sacks gives a wonderfully
vivid account of his earlier years and his fascination
with chemistry. Evoking memories of his
family and their fascination with science, he paints
a picture of the environment that fostered his curiosity
and inquisitiveness. Sacks proves himself to be a
brilliant storyteller; his accounts of boarding school
and the return to home life where he nurtured his
passion for science are witty and endearing.
Particularly poignant are his dry humour and careful
comedy, a welcome addition to what is a highly
emotive biography (apparently moving some readers
to tears). What is most inspiring is the innocence of
Sack’s early fascination with chemistry; he is now
a highly distinguished neurologist and a respected
figure in popular science. This innocence leaves us
with a sense of resolve; after all, this brilliant mind
was once a child too. Katya-yani Vyas
Schrödinger’s lolcat
Fantastic phenomenon from the
Natural World
A boa constrictor has given birth without mating. ZZ
chromosomes produce males and ZW produce females,
but these baby snakes have WW. She gave
birth through parthenogenesis (half-cloning) when
there were four courting males in her enclosure.
FELIX
Science Editors: James Goldsack
Katya-yani Vyas
science.felix@imperial.ac.uk
The retrovirus conundrum
How do retroviruses insert their genome into host DNA?
Victoria Bignet
Imperial College researchers from the Department
of Infectious Diseases have just succeeded
in determining the mechanism of retroviral
integration, using x-rays to analyse the key molecular
structures involved in this process.
The Diamond synchrotron in Oxfordshire
was the researchers’ main tool to produce intense
X-ray beams enabling them to observe
molecular interactions. “This kind of fundamental
research is vital if we are to advance
our understanding of the viruses and diseases
that affect millions of people around the world.
Knowing the 3D structure of the mechanisms
involved is like being able to see inside the engine
of your car. If you can actually see what
is happening, you get an idea of how you can
fi x it”, says Professor Thomas Sorensen, who
is Principal Beamline Scientist at the Diamond
synchrotron.
A retrovirus relies on its host-cell machinery
to replicate its genome. The latter is in the
form of RNA, and is converted to DNA once in
the host cell. Viral DNA must then be inserted
within host-cell chromosomal DNA. The way
this insertion is carried out has, up till now,
been a biological enigma. The Imperial College
researchers have managed to describe a
key agent in this vital step for the virus: the
intasome, a nucleoprotein complex composed
of an integrase tetramer (IT). Integrase is a formerly
known enzyme which confi nes and fuses
the ends of viral and host DNA together.
Prototype foamy virus (PFV) is very similar
to HIV in its way of integrating its genome.
With the synchrotron, the authors analysed
crystal structures of host DNA in complex with
the intasome of PFV. That is, the 3D structures
of integrase bound to both viral and host DNA
in atomic detail. From this observation, the authors
elucidated the confi nement mechanism
of target DNA before integration, as well as
the intermediary steps of post-catalytic strand
transfer. “Only 18 months ago we had a rather
sketchy understanding of retroviral integration”,
says Dr Peter Cherepanov from the Department
of Medicine.
Two integrase tetramers (ITs) come together
to form a narrow cleft, which accommodates
the host DNA in a highly bent confi guration,
facilitating access for IT active sites to the scissile
phosphodiester bonds. For insertion into
chromatin, the ITs are thought to interact with
host nucleosomal DNA , and/or the histone octamer.
Once this is performed, the phosphodiester
linking viral and host DNA gets ejected
out of the active site. As expected from knowl-
edge on the relatively low degree of sequence
selectivity of retroviruses for chromosomal
DNA, interactions between IT and host DNA
bases are sparse. Indeed, strong selectivity for
chromosomal DNA would limit possible integration
sites and thus reduce viral fi tness. Yet
two sites of close contact were identifi ed.
In the context of gene-therapy, Cherepanov
stresses that: “one of the main problems with
the current method is that retroviral integration
is too random. [...] Ideally, we want to insert
therapeutic genes in predefi ned, safe locations
of the human genome”. With these fi ndings,
one could theoretically create site-specifi c
retroviral vector systems by designing an integrase
with higher selectivity for a wanted target
DNA sequence.
The synthetic retrovirus could insert a functional
copy of a desired gene into a human chromosome
by greater certainty of insertion site.
This greatly improves the technique’s safety by
for instance reducing the risk of activating an
oncogene, thereby avoiding the reoccurrence
of former cases such as leukaemia in treated
patients. The discoveries would also help improving
existing antiviral strategies, facilitate
the design of better drugs to combat AIDS, and
stimulate novel approaches to blocking viral
replication.
Huge leap in quantum computing
Kelly Oakes
Do you think you could make sense of this
sentence if every fourth word was missing?
How about trying to hold a conversation when
you can only hear three quarters of what the
other person is saying? Cutting out a fraction
of the information being transferred in a given
situation may make life slightly diffi cult, but it
certainly doesn’t stop the meaning being conveyed
in most cases. This is because of the redundancy
built into language. However, redundancy
is not only useful for conversations on a
dodgy phone line - it can also come in handy
in the world of quantum computing, as two
researchers explained in a paper published in
Physical Review Letters last week.
The research was carried out by Sean Barrett,
of Imperial College, and Thomas Stace, at the
University of Queensland in Brisbane, Australia.
They found that if a quarter of the qubits
(the quantum equivalent of bits, which store information
in a classical computer) are lost, the
computer can still function as normal. Barrett
and Stace looked at the remaining information
and used a code that could check for errors to
decipher what was missing. “It’s surprising,
because you wouldn’t expect that if you lost
a quarter of the beads from an abacus that it
would still be useful,” said Dr Barrett.
One of the main differences between a classical
bit and its quantum equivalent is that the
latter can exhibit entanglement. This means
that, no matter how far away two entangled
qubits are, if one changes so will the other - instantaneously.
Quantum computers take advantage
of this effect, as well as another property
of quantum systems known as superposition,
to perform complicated calculations much
faster than classical computers. At the moment,
though, the largest quantum computers have
only two or three qubits.
It had previously been thought that large
quantum computers would be very sensitive to
missing information, but this research shows
that they should be much more robust than
we’d imagined. At this stage, the work is theoretical
and scientists must do a lot more in order
Friday 19 November 2010
See? The future isn’t ‘orange’ at all! Idiots... It’s quite obviously blue and whooshy
to make quantum computers bigger than a few
qubits in the lab.
When large quantum computers are a reality,
they may have the potential to revolutionise
fi elds as far apart as drug modelling, electronics
and code breaking. However, we won’t
know exactly what applications quantum computers
will be best suited to until we’re able to
make one.
“At the moment quantum computers are good
at particular tasks, but we have no idea what
these systems could be used for in the future,”
said Dr Barrett. “They may not necessarily be
better for everything, but we just don’t know.
They may be better for very specifi c things that
we fi nd impossible now.”