Dr Gib Bogle
BSc DIC Lond., PhD
After completing a Bachelor of Science in physics and mathematics and a PhD in Engineering Science at the University of Auckland, and a post-doc in the Environmental Quality Lab at Caltech, Gib Bogle left the world of pure research behind. He worked for engineering consulting firms in New Zealand and the United States, applying mathematical modelling to a range of physical problems, particularly in hydrodynamics and water quality.
Joining the Auckland Bioengineering Institute in 2004 meant a radical redeployment of Gib’s mathematical and computational skills into fundamental biological research. Since then his focus has been almost exclusively on modelling the adaptive immune response at the level of cell populations.
Research | Current
Agent based models
In collaboration with Professor Rod Dunbar at the School of Biological Sciences, he has developed an agent-based model for T cell activation in a lymph node. The model incorporates processes at a range of scales: cell receptor-ligand dynamics, cell motility, TCR stimulation leading to T cell activation and proliferation, and cell trafficking. Simulation results are being compared with mouse experiments carried out by Philippe Bousso and Helene Moreau at the Pasteur Institute in Paris.
The T cell model has been modified and extended to simulate processes involved in the formation of the germinal centre in a B cell follicle, work carried out in collaboration with Dr Takaharu Okada at the RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. The motivations for this work are: to aid understanding of the immune response by integrating knowledge, to build an in silico laboratory for biological experiments, and to provide an educational tool for teaching immunology.
Dr Bogle is collaborating with Professor William Wilson’s group at the Auckland Cancer Society Research Centre, to develop an agent-based model for tumour spheroids – human tumours grown from single cancer cells in vitro. The aim of this project is to create tools to support the Wilson group’s development of hypoxia-activated pro-drugs. The model will enable exploration of complex treatment protocols combining multiple drugs and radiation. This video shows cells on a slice through the centre of a growing spheroid.
With the help of Professor Jillian Cornish, Dr Bogle has initiated the development of an agent-based model for bone remodelling. This model aims to simulate the behaviour and interaction of three cell types: monocytic osteoclast-precursor cells, the osteoclasts that are created by the fusing of precursor cells, and osteoblasts. Working as a team, osteoclasts dissolve old or fractured bone, while osteoblasts follow behind laying down new bone.
Dr Bogle has developed a number of tools for processing the large 3D images of tissue vasculature captured by Professor Ian LeGrice’s team with the computer-controlled confocal microscope system known as the “structural rig”. This work was initially focussed on lymph node vasculature, with the aim of characterizing the changes that occur during an adaptive immune response. This video created by Inken Kelch displays the raw image of a mouse lymph node captured by the rig (left) and the extracted and reconstructed vascular network represented as a collection of tubes (right).
Recently the same methods have been extended to processing images of xenograft human tumours grown on mice. This work is a multidisciplinary collaboration between the Wilson group at the ACSRC, the Dunbar group at the SBS, and the LeGrice group at the ABI, with the aim of extracting detailed descriptions of the vascular networks of xenograft tumours. The project links with the Wilson group’s drug development programme. Understanding and predicting oxygen levels in tumours is crucial to predicting the activity of their hypoxia-activated anti-cancer drugs. A key contributor to this programme is Professor Tim Secomb at the University of Arizona, an expert in simulating angiogenesis, blood flow in capillary networks and the corresponding oxygen levels in tissue.
Gib is also providing mathematical modelling assistance to Professor David Williams in his research into conducting polymers.
Areas of expertise
- Immunology, the adaptive immune response,
- Agent-based modelling at the cell level,
- Modelling conducting polymer systems.
Selected publications and creative works (Research Outputs)
- Kelch, I. D., Bogle, G., Sands, G. B., Phillips, A. R. J., LeGrice, I. J., & Dunbar, P. R. (2019). High-resolution 3D imaging and topological mapping of the lymph node conduit system. PLoS biology, 17 (12)10.1371/journal.pbio.3000486
Other University of Auckland co-authors: Anthony Phillips, Inken Kelch, Gregory Sands, Rod Dunbar, Ian LeGrice
- Saghian, R., Bogle, G., James, J. L., & Clark, A. R. (2019). Establishment of maternal blood supply to the placenta: insights into plugging, unplugging and trophoblast behaviour from an agent-based model. Interface focus, 9 (5)10.1098/rsfs.2019.0019
Other University of Auckland co-authors: Jo James, Alys Clark
- Kelch, I., Bogle, G., Sands, G., Phillips, A., LeGrice, I., & Dunbar, R. (2019). High-resolution 3D imaging and topological mapping of the lymph node conduit system. 10.1101/752972
Other University of Auckland co-authors: Rod Dunbar, Gregory Sands
- Saghian, R., Bogle, G., James, J., & Clark, A. (2019). HOW DO THE MECHANICAL INFLUENCES OF BLOOD FLOW IMPACT TROPHOBLAST PLUGGING AND UNPLUGGING OF THE SPIRAL ARTERIES IN EARLY PREGNANCY?. Paper presented at Meeting of the International-Federation-of-Placenta-Associations (IFPA), Tokyo, JAPAN. 21 September - 24 September 2018. PLACENTA. (pp. 1). 10.1016/j.placenta.2019.06.089
- James, J., Bogle, G., Sagian, R., & Clark, A. (2019). Trophoblast plugs: How do they stay together and why do they break up?. Paper presented at 35th Annual Meeting of the European-Society-of-Human-Reproduction-and-Embryology (ESHRE), Vienna, AUSTRIA. 24 June - 26 June 2019. HUMAN REPRODUCTION. (pp. 2).
- Mao, X., McManaway, S., Jaiswal, J. K., Patel, P. B., Wilson, W. R., Hicks, K. O., & Bogle, G. (2018). An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids. PLoS computational biology, 14 (10)10.1371/journal.pcbi.1006469
Other University of Auckland co-authors: Kevin Hicks, Jagdish Jaiswal
- Hong, C. R., Bogle, G., Wang, J., Patel, K., Pruijn, F. B., Wilson, W. R., & Hicks, K. O. (2018). Bystander Effects of Hypoxia-Activated Prodrugs: Agent-Based Modeling Using Three Dimensional Cell Cultures. Frontiers in pharmacology, 910.3389/fphar.2018.01013
Other University of Auckland co-authors: Kevin Hicks, Frederik Pruijn, Cho Rong Hong
- Hong, C. R., Bogle, G., Wilson, W. R., & Hicks, K. O. (2017). Investigation of bystander effects of hypoxia activated prodrugs using three dimensional cell cultures. Paper presented at AACR (American Association For Cancer Research) Annual Meeting 2017, Washington, DC. 1 April - 4 April 2017. Proceedings of the American Association for Cancer Research.
Other University of Auckland co-authors: Kevin Hicks, Cho Rong Hong