CoMPLEX news 2010








21 November 2010-
We are very pleased to announce another CoMPLEX publication by Remigio Picone (UCL CoMPLEX) . Because many physical processes change with scale, size control is a fundamental problem for living systems. While in some instances the size of a structure is directly determined by the dimensions of its individual constituents, many biological structures are dynamic, self-organising assemblies of relatively small component parts. How such assemblies are maintained within defined size limits remains poorly understood.

In his research, Remigio shows that by confining cells to spread on lines, animal cells reach a defined length that is independent of their volume and width. As Remigio tells us, "In searching for a “ruler” that might determine this axial limit to cell spreading, we identified a population of dynamic microtubule polymers that become oriented along the long axis of cells. This growing population of oriented microtubules drives extension of the spreading cell margin while, conversely, interactions with the cell margin promote microtubule depolymerisation, leading to cell shortening. Using a mathematical model we show that this coupling of dynamic microtubule polymerisation and depolymerisation with directed cell elongation is sufficient to explain the limit to cell spreading and cell length homeostasis. Because microtubules appear to regulate cell length in a similar way in the developing zebrafish neural tube, we suggest that this microtubule-dependent mechanism is likely to be of widespread importance for the regulation of cell and tissue geometry."

Visit Remigio's Homepage at: http://www.homepages.ucl.ac.uk/~ucbprpi/

Head to PLOS Biology to gain access to the full article:
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000542



26 October 2010-
We are very happy to announce a new CoMPLEX publication by Yuval Itan. In his research published in Annals of Human Genetics, Yuval has developed a new bioinformatic method with which he has detected all human-lineage gene duplications. Gene duplications represent an important class of evolutionary events that is likely to have contributed to the unique human phenotype in the short evolutionary time since the human-chimpanzee divergence. The availability of both human and chimpanzee genome drafts in high coverage re-sequencing assemblies and the high annotation quality of most human genes, has made it possible to identify all human lineage-specific gene duplication events (human inparalogues). In his publication, Youval presents a novel set of bioinformatic tools to overcome a number of the conceptual problems that are prevalent in previous studies and a reliable and representative set of human inparalogues.

Head to Annals of Human Genetics to read the article:
http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.2010.00609.x/full



19 October 2010- EPSRC Cross-Disciplinary Landscape Award for UCL & Oxford

We are pleased to announce that Professor Andrew Pomiankowski (Genetics, Evolution and Environment), Professor Peter Coveney (Centre for Computational Science/Chemistry) and Professor Alan Johnston (Cognitive, Perceptual and Brain Sciences) have been awarded a cross-disciplinary EPSRC research grant for a collaborative project between CoMPLEX (UCL) and ComLab (University of Oxford). The project aims to establish a new approach to science at the computational-life science interface. The grant will support a number of interdisciplinary research fellows attached to CoMPLEX’s successful Doctoral Training Centre. The grant begins on 1st April 2011 and will run for 5 years. The EPSRC is contributing £4M and Microsoft Research Cambridge £2M as a third partner, to a total award value of £6M; large scale access to UK national supercomputing resources is also included.


13 October 2010- New Director of CoMPLEX announced

In a recent statement, Professor Andrew Pomiankowski has announced the appointment of Professor Alan Johnston as the new Director of CoMPLEX:

"After 5 years as Director of CoMPLEX, I recently moved sideways to become the Head of the Department of Genetics, Evolution and Environment. It has been a delight to have been involved at a time of great success for CoMPLEX: renewal of the Doctoral Training Centre, expansion of student numbers and range of activities, and the move into new premises in the Physics Building. Thank you to everyone who has made this happen, especially the CoMPLEX students who have made it so worthwhile. I will remain involved in CoMPLEX as Research Strategy Director.

Professor Alan Johnston has taken over as Director of CoMPLEX. Alan has been involved in CoMPLEX since its founding in 1999 and for the last 5 years has been Deputy Director. I wish him well in leading CoMPLEX through what promises to be a difficult funding period. The great news is that Alan starts with the announcement of funding from EPSRC to establish a post-Doctoral Training Centre at CoMPLEX in collaboration with The University of Oxford and Microsoft Research. "

Best wishes,

Andrew Pomiankowski




24 September 2010- NMDA receptors regulate GABAA receptor lateral mobility and clustering at inhibitory synapses through serine 327 on the γ2 subunit

Nerve cells send signals to each other by releasing chemicals at specialized junctions between cells, called synapses. One key neurotransmitter, GABA, acts on special proteins (GABA receptors) to generate inhibition, which stops the brain from becoming too excitable, which would lead to seizures and epilepsy. In a paper published this week in the Proceedings of the National Academy of Sciences, James Muir (UCL NPP and CoMPLEX) and Dr Josef Kittler reveal that GABA receptors, which they visualise by quantum dot tagging, can move rapidly in and out of synapses to control the strength of inhibition, and that this can happen in response to nerve cell signals.

James, the first author on the study, adds: “We show that the stability of GABA receptors at synapses can be controlled by signalling through the excitatory neurotransmitter, glutamate, providing a mechanism for controlling the balance of excitation and inhibition”. In neurological disorders such as epilepsy, too much glutamate can be released from nerve cells which – through the pathway identified in this research – could cause a depletion of GABA receptors from synapses. This phenomenon could therefore make epilepsy worse by decreasing inhibition.

Dr Josef Kittler said: “In collaboration with Lewis Griffin in UCL Computer Science we have been able to develop the tools necessary to detect and analyse the behaviour of single receptors in the surface membrane. Being able to see single receptors moving in nerve cells is incredibly exciting and is a great example of how programmes like UCL’s CoMPLEX bring biologists and mathematicians together to solve difficult problems in the life sciences”.

The article has been published in PNAS:

http://www.pnas.org/content/early/2010/09/01/1000589107.abstract




26 August 2010
- Dynamic filopodia drive pattern refinement via intermittent N-Dl signalling

We are delighted to announce a new publication from a CoMPLEX student. Michel Cohen, who has been recently awarded his PhD, has published his groundbreaking work on the highly prestigious scientific journal Cell. In his paper entitled “Dynamic filopodia drive pattern refinement via intermittent N-Dl signalling”, Michael sheds some light on the organization of bristles on the Drosophila notum. During this process, membrane-tethered Delta activates intracellular Notch signaling in neighboring epithelial cells, which inhibits Delta expression. This induces lateral inhibition, yielding a pattern in which each Delta-expressing mechanosensory organ precursor cell in the epithelium is surrounded on all sides by cells with active Notch signaling. This research shows that conventional models of Delta-Notch signaling cannot account for bristle spacing or the gradual refinement of this pattern. Instead, the pattern refinement that was observed is dependent upon dynamic, basal actin-based filopodia and can be quantitatively reproduced by simulations of lateral inhibition incorporating Delta-Notch signaling by transient filopodial contacts between nonneighboring cells.

To read the entire article, head to Cell journal:

http://www.cell.com/developmental-cell/abstract/S1534-5807%2810%2900296-0




8 July 2010- 2010 Franklin medal and prize

We are very happy to announce that Professor Thomas Duke has been awarded the Franklin Medal of the Institute of Physics for "the application of physical principles to the development of elegant molecular sorting devices, for providing new insights into the organising principles of cells and for his primary contributions to a new generation of theories of how the ear works". News of the award came as Duke was co-hosting a major international meeting entitled "The Physical Cell" at UCL. The award is given biennially for distinguished research in physics applied to the life sciences.

Professor Duke's research on the physical basis of cellular processes has focussed on sensory and motor systems. He first worked on DNA separation technology, providing a theoretical elucidation of the microscopic dynamics underlying the capillary electrophoresis methods. His work has enabled high-throughput DNA sequencing and the pulsed field gel electrophoresis techniques used in DNA fingerprinting. Read more about his exciting news:

Institute of Physics: http://www.iop.org/about/awards/subject/franklin/medallists/page_43963.html

London Centre for Nanotechnology: http://www.london-nano.com/content/newsmedia/recentnews/2010/tomdukefranklinmedal/



23 June 2010- Outcome of PhD+ Application

Good news for some of our students in the PhD+ competition. Remigio Picone and Sam Tazzyman (UCL CoMPLEX) have been awarded with the prestigious PhD+ Fellowships. Commiseration to those who were not successful but clearly the competition was tough with only 3 awarded in this round. One of last year’s fellowships was awarded to CoMPLEX student Alex Stewart.



23 June 2010- A compact acousto-optic lens for 2D and 3D femtosecond based 2-photon microscopy

Paul Kirkby (UCL CoMPLEX) along with top UCL scientists from the fields of Neuroscience, Physiology & Pharmacology, have recently published details of their groundbreaking 3D 2-photon microscope technology, which has many potential applications in biology. In conventional optical microscopes, focusing is slow because it involves physically moving the objective lens.

To overcome this limitation, Paul has helped develop a novel acousto-optic lens to both focus and scan the laser beam. As this is achieved by ultrasonic sound waves crossing  acousto-optic deflectors crystals and does not involve moving a mass, focusing is 300-fold faster than current piezoelectric-based methods. Read more about Paul's significant advance in:





19 May 2010- The Effect of Insertions, Deletions and Alignment Errors on the Branch-Site Test of Positive Selection

On a new publication, William Fletcher (UCL CoMPLEX) sheds light on the detection of positive Darwinian selection affecting protein-coding genes. In his research, William uses a recently developed indel-simulation program to examine the false-positive rate and power of “branch-site test”- a test designed to detect localized episodic bouts of positive selection that affect only a few amino-acid residues on particular lineages. Because the test is sometimes used to analyze divergent sequences, the impact of indels and alignment errors is a major concern. His findings suggest that insertions and deletions do not cause excessive false positives if the alignment is correct, but alignment errors can lead to unacceptably high false positives.

The full publication is accessible through Oxford Journals at: http://mbe.oxfordjournals.org/cgi/content/abstract/msq115


29 February 2010- UCL’s ‘Sophia’ magazine publishes fourth issue

We are thrilled to announce the publication of Issue 4 of Sophia – UCL's magazine for academic journalism – featuring insightful articles on the topics of ‘difficult’ languages, sustainable cities, the future of ethics and a very special piece on the death of editing. Edited by Ed Long (UCL CoMPLEX), the magazine is readily available for download at www.sophiamagazine.co.uk, and (limited) print copies are available in common rooms in various locations around UCL.




12 February 2010- A worldwide correlation of lactase persistence phenotype and genotypes

In a new publication, Yuval Itan, from UCL CoMPLEX, explains how current genetic knowledge may shed some light on the ability of adult humans to digest the milk sugar lactose. Yuval used surface interpolation of Old World lactase persistence genotype and phenotype frequency estimates obtained from all available literature. He then performed a comparison between the predicted and the observed trait frequencies in continuous space.

To find out about the exciting results, read the full article at biomed central: http://www.biomedcentral.com/1471-2148/10/36/abstract



20 January 2010- CoMPLEX Fellowship Report - Andrew Rider

Andrew Rider, from UCL CoMPLEX has just returned from his visit to the Nishida lab in Japan. During his stay, he developed crucial new insights in the field of visual motion processing. To find out more about Andrew's exciting trip to Japan, head to the Case Studies section of the CoMPLEX website.



5 January 2010
- Motion-induced position shifts in global dynamic Gabor arrays

It is known that objects in motion appear shifted in space. For global motion stimuli however, it is of interest to know whether the shift depends on the local or global motion. To help answer this question, Andrew Rider, form UCL CoMPLEX, has recently published his work regarding the construction of arrays of randomly oriented Gaussian enveloped drifting sine gratings (dynamic Gabors). In his experiment, the drifting grating’s speed was set such that the normal component of motion was consistent with a single global velocity. The array thus appears shifted in space in the direction of the global motion. The size of the shift is the same as for arrays of uniformly oriented dynamic Gabors that are moving in the same direction at the same global speed. Subsequently, Andrew noted that arrays made up of vertically oriented gratings, whose speeds were set to the horizontal component of the random array elements, were shifted less far. This showed that motion-induced position shifts of coherently moving surface patches are generated after the completion of the global motion computation.

Read Andrew’s full article in the Journal of Vision: http://journalofvision.org/9/13/8/

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