Bioinformatics Seminar
Time:
Venue: Na
13 September 2016
NaModelling
Nick HamiltonThe University of Queensland
predicting and understanding kidney development;Kidneys of equal size can vary 10-fold in the number of nephrons at birth. Discovering what regulates such variation has been hampered by a lack of quantitative analysis to define kidney development ; and factors leading to the formation of the ureteric tree and nephrons are still poorly understood. In recent work ; my computational group in collaboration with the developmental biology groups of Melissa Little (MCRI) and Ian Smyth (Monash) created a high-throughput large-scale pipeline for the multi-dimensional analysis and modelling of kidney imaging. Taking advantage of advances in microscopy such as Optical Projection Tomography and high resolution 3D confocal imaging enabled our collaborators to image large numbers of mouse kidneys at high resolution across multiple time points. This has created a massively dense dataset that visualises the multiple stages of kidney development. For example ; in one data set we have some 32 ureteric trees imaged in 3D of normal mouse kidneys at 6 distinct stages of development from which some 90 ;000 measurements have been extracted. In another ; 3D confocal imaging of the cap mesenchyme (which later forms a renal vesicle and goes on to develop into a nephron) with individual cell resolution across multiple time points has also provided a rich data source. In this talk I will outline the mathematical models we created towards making sense these key structures of the kidney and how they develop. The aim is to be able to answer questions such as: how does the cap mesenchyme proliferate and differentiate?; is the ureteric branch formation stereotypic or is there a ''random'' element?; if there is a pattern ; what is the nature of the pattern and what drives its formation?; and does patterning vary in mutants? In this presentation our analysis pipeline and algorithms will be described as well as recent results we have obtained in towards answering these questions in kidney patterning.;Davis Auditorium