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SUMMARY:Dynamics of DNA base-pair breathing\, telomere loss and telomere c
 lustering - Jonathan Wattis (University of Nottingham)
DTSTART:20160623T150000Z
DTEND:20160623T154500Z
UID:TALK66557@talks.cam.ac.uk
CONTACT:INI IT
DESCRIPTION:We start by analysing a model of base-pair breathing in DNA us
 ing a system of stochastic ordinary differential equations to describe the
  distances between bases in a sequence of bases that contains a defect.&nb
 sp\; We describe how the parameters in the SODE model are obtained from&nb
 sp\; all-atom MD simulations (AMBER) using a maximum likelihood algorithm.
 &nbsp\; The result is a model which explains how base-pair breathing depen
 ds on the twist of the double helix.&nbsp\; This work is in collaboration 
 with Cipri Duduiala\, Ian Dryden and Charlie Laughton (<i>Phys Rev E</i>\,
  <b>80</b>\, 061906\, 2009 and<i> Physica D</i> <b>240</b>\, 1254-1261\, 2
 011).&nbsp\; <br><br>Telomeres are sequences of bases at the ends of chrom
 osomes. &nbsp\;During replication\, they are shortened due to imperfect re
 plication of the DNA. &nbsp\;We present a variety of models of telomere lo
 ss\, using an evolving distribution of telomere lengths\, and analyse this
 &nbsp\;mechanism of aging in cell populations using a combination of theor
 etical and analytical techniques. This work formed part of the&nbsp\;PhD t
 hesis of Qi Qi\, cosupervised by Helen Byrne&nbsp\;(<a href="http://eprint
 s.nottingham.ac.uk/12258" rel="nofollow" target="_blank">http://eprints.no
 ttingham.ac.uk/12258</a> and <i>Bull Math Biol</i> <b>76</b>\, 1241\, 2014
 ). <br><br>Finally\, we&nbsp\; outline ongoing work modelling (in collabor
 ation with David Holcman) on the formation of protein-telomere clusters in
  yeast cells\, using coagulation-fragmentation equations to describe the c
 luster size and composition.&nbsp\;<br><br><br>
LOCATION:Seminar Room 1\, Newton Institute
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