Skip navigation

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

 

I HAVE A PHD POSITION AVAILABLE, STARTING IN AUTUMN 2020:

Project title: Predicting the effects of increasing soil temperatures on beneficial plant symbionts and plant pathogens through Synthetic Biology. (Ref: OP20307)

Project Description: The rapid increase in global temperature is already affecting the productivity and composition of natural and agricultural ecosystems. It can also change existing relations between key species, e.g. ongoing coral bleaching is triggered by algal endosymbionts of corals leaving the host because of the increased water temperature. Would increasing soil temperatures change relationships between plants and their microbiota in a similar fashion? Both plants and bacteria could adapt to increasing soil temperatures, bacteria however can evolve much faster than plants. Plant pathogens therefore are likely to adapt much quicker to climate change, which could give them a competitive advantage. At the same time, fastevolving bacterial symbionts of plants could either mitigate or amplify the effects of increased temperature on plant hosts. This project aims to artificially accelerate the evolution of key plant pathogens and symbionts (e.g. Rhizobia for N2 fixation and auxin-producing bacteria) driven by climate change (increasing soil temperature). This will be achieved using a number of Synthetic Biology approaches to precisely induce mutagenesis and selecting for mutants with improved growth at higher temperatures. We will study the effects on plant hosts when cocultured with these artificially-evolved pathogens and symbionts at increasing temperatures. Environmental and ecological data combined with our findings will allow us to predict what changes will occur in bacteria and engineer plants and their symbionts to better resist the climates of the future.

https://research.ncl.ac.uk/media/sites/researchwebsites/oneplanet/OP20307%20-%20KellyKapralov_OnePlanetProjectproposal_Form_2020.pdf

 

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

Project title: Predicting the effects of increasing soil temperatures on beneficial plant symbionts and plant pathogens through Synthetic Biology. (Ref: OP20307) One Planet Research Theme: Climate & Climate Change ☒ | Earth System Processes ☐ | Anthropocene ☒ | Environmental Informatics ☒ Lead Supervisor: Dr Ciarán Kelly, Northumbria University Key Research Gaps and Questions: How will rising global temperatures affect the relationship between plants and their bacterial symbionts? Will the rapid adaptation of key bacterial plant pathogens to increasing soil temperatures increase pathogenesis in slower-to-adapt plant species, or will dormant resistence mechanisms emerge in plants to tackle them? Can we use information obtained to “future proof” important crops? Project Description: The rapid increase in global temperature is already affecting the productivity and composition of natural and agricultural ecosystems. It can also change existing relations between key species, e.g. ongoing coral bleaching is triggered by algal endosymbionts of corals leaving the host because of the increased water temperature. Would increasing soil temperatures change relationships between plants and their microbiota in a similar fashion? Both plants and bacteria could adapt to increasing soil temperatures, bacteria however can evolve much faster than plants. Plant pathogens therefore are likely to adapt much quicker to climate change, which could give them a competitive advantage. At the same time, fastevolving bacterial symbionts of plants could either mitigate or amplify the effects of increased temperature on plant hosts. This project aims to artificially accelerate the evolution of key plant pathogens and symbionts (e.g. Rhizobia for N2 fixation and auxin-producing bacteria) driven by climate change (increasing soil temperature). This will be achieved using a number of Synthetic Biology approaches to precisely induce mutagenesis and selecting for mutants with improved growth at higher temperatures. We will study the effects on plant hosts when cocultured with these artificially-evolved pathogens and symbionts at increasing temperatures. Environmental and ecological data combined with our findings will allow us to predict what changes will occur in bacteria and engineer plants and their symbionts to better resist the climates of the future. Prerequisites: enthusiasm, initiative and an ability to undertake independent research; at least a 2:1 honours degree in biology or related subject is expected. For more information, please contact Dr Ciarán Kelly (ciaran.l.kelly@northumbria.ac.uk) and Dr Maxim Kapralov (maxim.kapralov@ncl.ac.uk).

Ciaran Kelly

Qualifications

Molecular Biology PhD December 07 2013

Key Publications

  • Please visit the Pure Research Information Portal for further information
  • Hanessian-Hullar reaction in the synthesis of highly substituted trans-3,4-dihydroxypyrrolidines: Rhamnulose iminosugar mimics inhibit α-glucosidase., Liu, Z., Yoshihara, A., Jenkinson, S., Wormald, M., Kelly, C., Heap, J., Marqvorsen, M., Estévez, R., Fleet, G., Nakagawa, S., Izumori, K., Nash, R., Kato, A. 6 Nov 2019, In: Tetrahedron
  • 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


+

Northumbria Open Days

Open Days are a great way for you to get a feel of the University, the city of Newcastle upon Tyne and the course(s) you are interested in.

Research at Northumbria
+

Research at Northumbria

Research is the life blood of a University and at Northumbria University we pride ourselves on research that makes a difference; research that has application and affects people's lives.

+

Order your prospectus

If you would like to know more about our courses, or life in general as a student at Northumbria, then we can help you.

Latest News and Features

More news

Back to top