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Dr Ciaran Kelly

Department: Applied Sciences

I was recently recruited to the Department as a Vice-Chancellor's Fellow in Molecular Biosciences. My research focuses on the exciting area of Synthetic Biology. I was recently interviewed by the European Synthetic Biology Society (EUSynBioS) as part of their "Young PIs in Action" series of interviews, which you can read here: https://www.eusynbios.org/blog/2019/7/29/young-pis-in-action-interview-with-ciarn-kelly

Background:

As an undergraduate, I studied genetics at the University of Glasgow, and my Honours Project investigated the central genetic circuits controlling the plant circadian clock; research I continued after graduation in the evenings after work, eventually published in Science [14]. I was lucky to lead research expeditions to the Amazon basin in Ecuador in 2004 and 2005, and it was these trips that instilled my drive to combine genetics/DNA with environmental applications.

I obtained my PhD in Molecular Microbiology at the University of Dundee in 2013. My PhD thesis explored the use of synthetic biology for biohydrogen production in Escherichia coli. This involved the first successful integration of a complex bifurcating hydrogen--producing enzyme into the anaerobic metabolism of E. coli [10], the first evidence that a native E. coli hydrogen enzyme operated bidirectionally in vivo [12], and the first successful reengineering of the native hydrogen--producing enzyme of E. coli to accept electrons from other sources [7].

Following my PhD I focussed on learning and developing approaches and tools enabling predictable engineering of biological pathways and circuits. My postdoctoral experience included positions at the University of Oxford, Imperial College London and Newcastle University. This research focussed on the development of novel tools enabling precise, orthogonal control of gene expression in model and non-model organisms [9,3,1], synthetic metabolic engineering of photosynthetic bacteria for novel light-driven carbon fixation and the first use of engineered Hfq-associated small RNAs in synthetic negative-feedback circuits [2].

Publications:

  1. Kelly, C.L., Taylor, G.M., Šatkutė, A., Dekker, L., Heap, J.T. (2019) Transcriptional terminators allow leak-free chromosomal integration of genetic constructs in cyanobacteria. Microorganisms: 7(8): 263
  2. Kelly, C.L.*, Harris, A.W.K., Steel, H., Hancock, E.J., Papachristodoulou, A. (2018) Synthetic negative feedback circuits using engineered small RNAs. Nucleic Acids Research 46(18): 9875–9889 (*co-corresponding author)
  3. Kelly, C.L., Taylor, G.M., Hitchcock, A., Torres-Méndez, A., Heap, J.T. (2018) A rhamnose-inducible system for precise and temporal control of gene expression in cyanobacteria. ACS Synthetic Biology: 7(4): 1056-1066
  4. Vidal, L.S., Kelly, C.L., Mordaka, P.M., Heap, J.T. (2018) Review of NAD(P)H-dependent oxidoreductases: properties, engineering and application. BBA - Proteins and Proteomics 1866: 327-247
  5. Harris, A.W.K., Kelly, C.L., Steel, H., Papachristodoulou, A. (2017) The Autorepressor: a Case Study of the Importance of Model Selection. 2017 IEEE 56th Annual Conference on Decision and Control (CDC): 1622-1627
  6. Steel, H., Harris, A.W.K., Hancock, E.J., Kelly, C.L., Papachristodoulou, A. (2017) Frequency domain analysis of small non-coding RNAs show summing junction-like behaviour" 2017 IEEE 56th Annual Conference on Decision and Control (CDC): 5328-5333
  7. Lamont, C.M., Kelly, C.L., Pinske, C., Buchanan, G., Palmer, T., Sargent, F. (2017) Expanding the substrates for a bacterial hydrogenlyase reaction. Microbiology. Microbiology 163: 649-653
  8. Liu, Z., Yoshihara, A., Kelly, C.L., Heap, J.T., Marqvorsen, M.H.S., Jenkinson, S.F., Wormald, M.R., Otero, J., Estévez, A., Kato, A., Fleet, G.W.J., Estévez, R.J., Izumori, K., (2016) 6-Deoxyhexoses from l-Rhamnose in the Search for Inducers of the Rhamnose Operon: Synergy of Chemistry and Biotechnology. Chemistry, A European Journal 22: 12557-12565
  9. Kelly, C.L., Liu, Z., Yoshihara, A., Jenkinson, S.F., Wormald, M.R., Otero, J., Estévez, A., Kato, A., Marqvorsen, M.H.S., Fleet, G.W.J., Estévez, R.J., Izumori, K., Heap, J.T. (2016) Synthetic Chemical Inducers and Genetic Decoupling Enable Orthogonal Control of the rhaBAD Promoter. ACS Synthetic Biology 5(10): 1136-1145
  10. Kelly, C.L., Pinkse, C., Murphy, B., Parkin, A., Armstrong, F.A., Palmer, T., Sargent, F. (2015) Integration of an [FeFe]-hydrogenase into the anaerobic metabolism of Escherichia coli. Biotechnology Reports 8: 94-104
  11. Harris, A.W.K., Dolan, J.A., Kelly, C.L., Anderson, J., Papachristodoulou, A. (2015) Designing Genetic Feedback Controllers. IEEE Transactions on Biomedical Circuits and Systems 9(4): 475-484
  12. Pinske, C., Jaroschinsky, M., Linek, S., Kelly, C.L., Sargent, F., Sawers, R.G. (2015) Physiology and Bioenergetics of [NiFe]-Hydrogenase 2-Catalyzed H2-Consuming and H2-Producing Reactions in Escherichia coli. Journal of Bacteriology 197(2): 296-306
  13. Sargent, F., Davidson, F.A., Kelly, C.L., Binny, R., Christodoulides, N., Gibson, D., Johansson, E., Kozyrska, K., Licandro Lado, L., MacCallum, J., Montague, R., Ortmann, B., Owen, R., Dupuy, L., Prescott, A.R., Palmer, T. (2013) A synthetic system for expression of components of a bacterial microcompartment. Microbiology 159(11): 2427-2436
  14. James, A.B., Monreal, J.A., Nimmo, G.A., Kelly, C.L., Herzyk, P., Jenkins, G.I., Nimmo, H.G. (2008) The Circadian Clock in Arabidopsis Roots Is a Simplified Slave Version of the Clock in Shoots. Science 322: 1832-1835

Ciaran Kelly

Qualifications

Molecular Biology PhD December 07 2013

Key Publications

  • Please visit the Pure Research Information Portal for further information
  • Transcriptional Terminators Allow Leak-Free Chromosomal Integration of Genetic Constructs in Cyanobacteria, Kelly, C., Taylor, G., Heap, J., Dekker, L., Satsuke, A. 16 Aug 2019, In: Microorganisms
  • A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria, Kelly, C., Taylor, G., Hitchcock, A., Torres-Méndez, A., Heap, J. 20 Apr 2018, In: ACS Synthetic Biology
  • Review of NAD(P)H-dependent oxidoreductases, Sellés Vidal, L., Kelly, C., Mordaka, P., Heap, J. Feb 2018, In: Biochimica et Biophysica Acta - Proteins and Proteomics
  • Synthetic negative feedback circuits using engineered small RNAs, Kelly, C., Harris, A., Steel, H., Hancock, E., Heap, J., Papachristodoulou, A. 12 Oct 2018, In: Nucleic Acids Research
  • The Autorepressor: a Case Study of the Importance of Model Selection, Harris, A., Kelly, C., Steel, H., Papachristodoulou, A. 23 Jan 2018
  • Expanding the substrates for a bacterial hydrogenlyase reaction, Lamont, C., Kelly, C., Pinske, C., Buchanan, G., Palmer, T., Sargent, F. 10 May 2017, In: Microbiology
  • Synthetic Chemical Inducers and Genetic Decoupling Enable Orthogonal Control of the rhaBAD Promoter, Kelly, C., Liu, Z., Yoshihara, A., Jenkinson, S., Wormald, M., Otero, J., Estévez, A., Kato, A., Marqvorsen, M., Fleet, G., Estévez, R., Izumori, K., Heap, J. 21 Oct 2016, In: ACS Synthetic Biology
  • Integration of an [FeFe]-hydrogenase into the anaerobic metabolism of Escherichia coli, Kelly, C., Pinske, C., Murphy, B., Parkin, A., Armstrong, F., Palmer, T., Sargent, F. 1 Dec 2015, In: Biotechnology Reports

Research Themes and Scholarly Interests

Overall Research Interests:

My aim is to be a leader in harnessing the enormous power of Synthetic Biology approaches and technologies to tackle the many enormous crises facing the planet. I believe that we are now on the cusp of developing biotechnologies that can solve issues such as food and energy provision for a growing global population, and the related problems of unsustainable production and use of fertilisers, and catastrophic greenhouse gas emissions. It is my vision and goal to contribute to a sustainable industrial revolution, where waste is viewed as a valuable commodity, and thus converted through synthetic biology, into value products at high yields and in commercially-attractive processes.

Specific Projects:

  1. I'm interested in constructing synthetic regulation so that we can reliably engineer complex metabolic pathways in industrially-relevant organsms to enable sustainable production of high-value chemicals.
  2. I'm also interested in using small bacterial RNAs (sRNAs) as both synthetic biology tools and as novel antimicrobial therapeutics.

Collaborations:

I am very keen to collaborate with companies on ways to engineer organisms for the reliable scaling-up of bioproduction, as well as companies interested in developing novel antimicrobial approaches using Synthetic Biology. Please get in touch at ciaran.l.kelly@northumbria.ac.uk

Students and Visiting Researchers:

I am always open to hosting undergraduate students for summer placements and visiting researchers for short-term collaborative projects. Studentships are available that we can apply for to host you, but please get in touch as early as possible. Please get in touch at ciaran.l.kelly@northumbria.ac.uk


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