Department of Biochemistry University of Oxford Department of Biochemistry
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Anaphase bridges in fission yeast cells
Whitby lab
Lactose permease represented using bending cylinders in Bendix software
Caroline Dahl, Sansom lab
Epithelial cells in C. elegans showing a seam cell that failed to undergo cytokinesis
Serena Ding, Woollard lab
Collage of Drosophila third instar larva optic lobe
Lu Yang, Davis lab
First year Biochemistry students at a practical class
Image showing the global movement of lipids in a model planar membrane
Matthieu Chavent, Sansom lab
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Glycolipid modeling wins student inaugural prize

Image showing the atomistic structure for the lipid GM3 next to the equivalent structure that David developed using the coarse-graining method

Image showing the atomistic structure for the lipid GM3 next to the equivalent structure that David developed using the coarse-graining method (Click to enlarge)

DPhil student David Shorthouse has won the SCI Young Lipid Scientist Award for his work on glycolipids.

David, a student in the lab of Mark Sansom, was shortlisted for the award along with three other students from across the country. He presented his work in June at a conference in Reading run by the SCI lipid group and was chosen as the inaugural winner of the competition.

David's research is to develop computational models of cell membrane lipids using a 'course-grained' method. This lumps atoms together, enabling researchers to carry out large-scale simulations.

'We're trying to simulate more physiologically relevant membrane systems, which means they need to be bigger and run for longer periods of time than all-atom simulations will allow,' David explains. 'To get around this we use a system called 'coarse-graining' where roughly four atoms are represented by a single particle.'

Image showing the bilayer of the red blood cell membrane from the side, with the lipid GM3 in pink (from Heidi Koldsoe)

Image showing the bilayer of the red blood cell membrane from the side, with the lipid GM3 in pink (from Heidi Koldsoe)
(Click to enlarge)

'This means that the system needs roughly four-fold fewer particles, and the energy landscape, and computations that are involved with this, are very much smoothened.'

David's work has been focused on trying to improve the library of membrane components such as glycoplipids. The aim is to simulate systems such as a mammalian red blood cell membrane and entire viruses.

'I've designed a series of glycolipids which are generally very poorly studied and parameterised them – that's making sure all the components in the structure match correctly with what experiments tell us they should be. This has allowed others to go on and do exciting research.'

His work has contributed to a number of studies in the lab. Heidi Koldsoe is carrying out simulations of a lipid-complete mammalian red blood cell membrane, looking at the membrane's curvature. Another colleague, Tyler Reddy, is doing large-scale simulations of a flu virion.

 

 

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