School of Biological Sciences
Faculty of Sciences
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
- My Research
- Grants and Funding
- Professional Activities
Our research integrates biochemistry, genetics and mathematical modelling to characterise fundamental mechanisms of gene control and how these elements are combined to create gene regulatory circuits with complex functions. Having a detailed understanding of the properties of natural regulatory circuits makes it possible to rearrange these components to build circuits with new and interesting behaviours - the emerging discipline of Synthetic Biology. We have a strong focus on using and developing mathematical modelling as a tool to advance understanding of gene regulatory mechanisms and systems, a tool that will be essential for the new ‘systems biology’ as molecular biology tries to move from characterizing the parts of cells and their simple interactions to understanding how these interactions combine to generate complex functions. We find that the process of attempting to construct a mathematical model of a biological system is valuable in itself - helping to clarify ideas, define assumptions and identify missing information. Once a model is made, comparison of the model with available experimental data can reveal shortcomings in either, leading to changes to the model or to improved data collection or interpretation. A consistent mathematical description is a powerful tool, providing precise predictions to aid further experimental tests, and allowing rapid exploration of the range of properties of the system to generate insights into design features.
Our primary experimental systems are two E. coli bacteriophages, lambda and 186. These temperate phages can replicate their genomes using alternative developmental pathways, lysis and lysogeny, and are some of the simplest organisms to make developmental decisions. Despite their relative simplicity, the phage systems combine a wide range of gene control mechanisms in complex ways and have many lessons to teach us. Bacteriophage lambda continues to be a key model system for many molecular biological processes; phage 186 is less well characterised but provides a powerful comparison with lambda, as it achieves similar outcomes using different regulatory circuits. The fundamental biochemistry shared by all living things means that the study of any organism, from phages to humans, continues to illuminate universal principles that apply to all organisms.
Date Position Institution name 2017 Associate Professor University of Adelaide 2010 - 2016 Senior Lecturer University of Adelaide 2005 - 2009 Lecturer B University of Adelaide 2001 - 2005 Research Fellow University of Adelaide 1995 - 2000 ARC Australian Research Fellow University of Adelaide
Date Institution name Country Title 1987 - 1990 University of Queensland Australia PhD 1986 - 1986 Griffith University Australia BSc (Hons) 1983 - 1985 Griffith University Australia BSc
Date Title Institution Country 1993 - 1995 Post-doctoral research University of Adelaide Australia 1990 - 1993 Post-doctoral research Brandeis University United States
Year Citation 2017 Cui, L., & Shearwin, K. (2017). Clonetegration using OSIP plasmids: One-step DNA assembly and site-specific genomic integration in bacteria. In R. Hughes (Ed.), Methods in Molecular Biology (Vol. 1472, pp. 139-155). New York: Humana Press.
2009 Palmer, A., & Shearwin, K. (2009). Guidance for data collection and computational modelling of regulatory networks.. In J. McDermott, R. Samudrala, R. Bumgarner, K. Montgomery, & R. Ireton (Eds.), Computational Systems Biology (Vol. 541, pp. 337-354). United States: Humana Press.
DOI Scopus2 Europe PMC1
Year Citation 2011 Wang, H., Dodd, I., Shearwin, K., Dunlap, D., & Finzi, L. (2011). The 186 Bacteriophage Repressor as a Model System to Study Nucleosome Repositioning by Single Molecule Microscopy. In BIOPHYSICAL JOURNAL Vol. 100 (pp. 230). Baltimore, MD: CELL PRESS.
Year Citation 2017 Hao, N., Shearwin, K., & Dodd, I. (2017). Understanding and Manipulating Chromosomal-Scale DNA Looping in Escherichia coli. Poster session presented at the meeting of 2017 Synthetic Biology: Engineering, Evolution & Design (SEED) : Proceedings. Vancouver, Canada. 2017 Hao, N., Priest, D., Dodd, I., & Shearwin, K. (2017). Programmable DNA looping in vivo. Poster session presented at the meeting of Australia-China Symposium on Synthetic Biology. Brisbane. 2016 Hao, N., Shearwin, K., & Dodd, I. (2016). Road Rules for Traffic on DNA: Gene Regulation by Encounters between Transcribing RNA Polymerases and DNA-bound Proteins. Poster session presented at the meeting of Synthetic Biology: Engineering, Evolution & Design (SEED). Chicago, USA. 2016 Hao, N., Shearwin, K., & Dodd, I. (2016). Understand DNA looping in vivo - a synthetic biology approach. Poster session presented at the meeting of OCE Cutting Edge Conference in Synthetic Biology. Canberra. 2015 Hao, N., Krishna, S., Shearwin, K., & Dodd, I. (2015). Road Rules for Traffic on DNA: Gene Regulation by Encounters between Transcribing RNA Polymerases and DNA-bound Proteins. Poster session presented at the meeting of 2nd International Synthetic & Systems Biology Summer School. Taormina - Sicily, Italy. 2015 Kumar, S., Priest, D. G., Yan, Y., Dodd, I. B., Shearwin, K. E., & Dunlap, D. D. (2015). Estimation of DNA Loop Interactions Supports the Loop Domain Model of Insulator Action. Poster session presented at the meeting of BIOPHYSICAL JOURNAL. CELL PRESS.
2014 Shearwin, K., Cui, L., Murchland, I., & Dodd, I. (2014). Long-range DNA looping in the lambda genetic switch. Poster session presented at the meeting of Abstracts of the 58th Annual Meeting of the Biophysical Society, as published in Biophysical Journal. San Francisco, CA: Cell Press.
2013 Kumar, S., Priest, D., Biton, Y., Swigon, D., Shearwin, K., Dodd, I., & Dunlap, D. (2013). In Silico, In Vitro, and In Vivo Estimation of J-Factors for LAC Repressor-Mediated DNA Loop Formation. Poster session presented at the meeting of BIOPHYSICAL JOURNAL. Philadelphia, PA: CELL PRESS.
2012 Hao, N., Shearwin, K., Dodd, I., Whitelaw, M., & Chapman-Smith, A. (2012). Reverse Bacterial Two Hybrid: A New Tool for Studying Dimeric Protein Interactions. Poster session presented at the meeting of ASBMB ComBio conference. Adelaide. 2010 Wang, H., Dodd, I., Shearwin, K., Dunlap, D., & Finzi, L. (2010). Coliphage 186 genetic switch: a single molecule study. Poster session presented at the meeting of Meeting Abstracts. Biophysical Journal. San Francisco: Cell Press.
2009 Hao, N., Shearwin., Dodd, I., Whitelaw, M., & Chapman-Smith, A. (2009). Reverse Bacterial two Hybrid (RevB2H) method for studying protein-protein interactions. Poster session presented at the meeting of Network in Genes and Environment in Development (NGED) Forum. Palm Cove, Queensland. 2009 Hao, N., Shearwin, K., Dodd, I., Whitelaw, M., & Chapman-smith, A. (2009). A novel Reverse Bacterial two Hybrid (RevB2H) method for studying protein-protein interactions and screening for potential therapeutics. Poster session presented at the meeting of Australian Society for Medical Research (ASMR) SA Scientific Meeting. Adelaide.
Year Citation 1990 Shearwin, K. E. (1990). Effects of thermodynamic non-ideality of protein interactions. 1986 Shearwin, K. (1986). Interaction Between Glycolytic Enzymes and Contractile Proteins. (PhD Thesis).
Synthetic biology tools for integration into bacterial chromosomes. ARC Discovery Grant DP160101450 (2016-2018) Shearwin, K.E. and Bikard, D. $410 000
Understanding and manipulating DNA looping in long range gene regulation. NHMRC Project Grant APP1100651 (2016-2018) Dodd, I.B., Shearwin, K.E., Sneppen, K. and Hao, N. $351 000
Flipping the switch: rational design of genetic circuits that respond to transient signals. ARC Discovery Grant DP150103009 (2015-2017) Shearwin, K.E., Dodd, I.B. and Sneppen, K. $241 000
Quantitative analysis of the DNA loop-domain model for long range regulation of transcription. Human Frontiers Science Program RGP0051 (2009-2012) Shearwin, K.E., Dunlap, D. and Swigon, D. $1 251 000 (total)
Road rules for traffic on DNA - gene regulation by encounters between transcribing RNA polymerases and DNA-bound proteins. ARC Discovery Grant DP110101470 (2011-2013) Dodd, I.B., Shearwin, K.E., and Sneppen, K. $300 000
Synthetic Biology - The Rational Design and Construction of New Genetic Circuits. ARC Discovery Grant DP110100824 (2011-2013) Shearwin, K.E., Dodd, I.B., Finzi, L. and Sneppen, K. $300 000
Understanding and controlling PAS domain interactions in basic helix-loop-helix transcription factors. NHMRC APP627140 (2010-2012) Chapman-Smith, A., Whitelaw, M.L., Shearwin, K.E. and Dodd, I.B. $608 000
Rational design of small genetic circuits for synthetic biology. ARC Discovery Grant DP0665185 (2006-2008) Shearwin, K.E. and Egan, J.B. $368 000
Transcriptional Interference in Gene Regulatory Decisions. NIH R01 (2006-2009) Egan, J.B., Dodd, I.B. and Shearwin, K.E. $526 000
The South Australian Facility for Small and Large Molecule X-Ray Diffraction Structure Determination. ARC LIEF(2009) Sumby, C.J, Shearwin, K.E. and 26 others $560 000
Biophysical Characterisation Facility. ARC LIEF Grant LE0882382 (2008) Brooks, D.A., Shearwin, K.E. (lead CI for University of Adelaide) and 14 others $245 000
Biophysical Characterisation Facility. AIB Labs (2008) Brooks, D.A., Shearwin, K.E. (lead CI for University of Adelaide) and 14 others $50 000
ARC Australian Research Fellowship (1996-2000) Shearwin, K.E. $400 000
In 2018 I am teaching in the following courses
Fundamentals of Biomedical Science (lectures)
Biochemistry II (lectures)
Biomedical Science IIA (lectures)
Biotechnology II (lectures)
Principles and Practice of Research II (mentor, PBLs)
Principles and Practice of Research III (mentor, research placements)
Molecular and Structural Biology III (lectures, tutorials, practicals)
Cancer, Stem Cells and Development (Biomed) (PBL)
Cancer, Stem Cells and Development III (essays)
Masters in Biotechnology: Advanced Research Platforms (lectures)
Honours in Biochemistry (journal club; research grant proposal and thesis assessment)
We host 3rd year laboratory placement students each year.
2018: Smriti Singh, Grace Tulysewski
2017: Khalia Primer
2016: Emi Schutz, Daniel Reed
2015: Jasmine Kelly, Mara Zeissig, Alejandra Isabel, Joe Rossi, Matilda Handsley-Davis
2014: Dominique Jackson, Queenie Tangseefa, Jade Feong, Andrew Hayes, Trang Pham
2013: Byron Shue, Jia Truong, Andelain Erickson
2012: Duncan McKenzie, Dylan Agnew, Grace De La Lande
2011: Emma Rollo, Ashleigh Paparella, Katrina Lee
2010: Emily Higginson, Sofia Xuan, George Dimitroff
Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2018 Co-Supervisor Biochemistry Doctor of Philosophy Doctorate Full Time Ms Stephanie Nguyen 2018 Co-Supervisor Biochemistry Doctor of Philosophy Doctorate Full Time Mr Jordan Luke Pederick 2018 Principal Supervisor Phage based antibacterial proteins Doctor of Philosophy Doctorate Full Time Miss Hannah Rose Bonham 2017 Principal Supervisor Catalytically Inactive Cas Proteins as Transcriptional Roadblocks to Modulate Gene Expression Doctor of Philosophy Doctorate Full Time Miss Alana Jane Donnelly 2017 Principal Supervisor Investigate the Role of 186 Bacteriophage Regulatory Proteins CI and Apl in Prophage Induction Doctor of Philosophy Doctorate Full Time Miss Alejandra Isabel 2016 Co-Supervisor Mas Spectrometric Analysis of Higher Order DNA and Protein Structures Doctor of Philosophy Doctorate Full Time Mr Jiawei Li 2015 Principal Supervisor Structural studies of bacteriophage 186 proteins Doctor of Philosophy Doctorate Full Time Mr Jia Quyen Truong
Past Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2011 - 2014 Principal Supervisor Testing the DNA loop domain model in Escherichia coli Doctor of Philosophy Doctorate Full Time Mr David Priest 2010 - 2014 Principal Supervisor DNA looping mediated transcriptional regulation Doctor of Philosophy Doctorate Full Time Mr Lun Cui 2008 - 2015 Principal Supervisor The Design, Synthesis and Quantitative Analysis of a Bistable Mixed Feedback Loop Gene Network Doctor of Philosophy Doctorate Full Time Mr Julian Pietsch 2006 - 2008 Co-Supervisor Calcium and Phosphoinositides Regulations in Alpha-Actinin-4 F-Actin Binding Doctor of Philosophy Doctorate Full Time Mr Huang-Hui Chen
Date Role Committee Institution Country 2017 - ongoing Member Postgraduate Coordinator The University of Adelaide Australia 2015 - ongoing Chair School of Biological Sciences Research Education Committee — —
Date Role Membership Country 2015 - ongoing Representative Synthetic Biology Australasia Australia 1993 - ongoing Member Australian Society for Biochemistry and Molecular Biology Australia
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