The deadline for applications is Friday 10th July, at 4pm.
The application process for the CITI-GENS Programme is different to other PhD application processes within the University - it is important that you read the application pack for details on the application process, which can be found using the link below.CITI-GENS Application Pack
FUNDING AND ELIGIBILITY
These projects are co-funded by the Horizon 2020 programme of the European Union and the Department of the Economy.
The programme will provide funds for both tuition fees and salary - to find out more, click the link below.CITI-GENS eligibility
Dr Stephen Cochrane
CITI-GENS DTP: New tools for new antibiotic targets – The development of novel probes for mechanistic studies on bacterial glycoli
Antibacterial resistance is a major threat to human health. The recent COVID-19 pandemic has highlighted the problem posed by bacterial infections, with a major study showing that half of COVID-19 fatalities were due to a secondary bacterial infection (Lancet 2020, 395, 1054). Therefore, there is a pertinent need for new antimicrobial targets.
Bacteria produce several glycopolymers and glycoproteins that are vital to their survival, including peptidoglycan, which is a key component of the bacterial cell wall. Peptidoglycan biosynthesis involves several glycolipid intermediates, all of which are linked to the cell membrane by the universal lipid carrier, undecaprenyl phosphate. The enzymes that process undecaprenyl-linked biomolecules are hot antibiotic targets, as they are vital and unique to bacteria. However, detailed studies on these enzymes have been limited due to the lack of suitable probes to interrogate their mechanism. An understanding of enzyme mechanism is a vital pre-requisite to the rationale design of inhibitors. This project aims to develop new labelled analogues of undecaprenyl phosphate as probes to perform mechanistic studies on several important enzymes, including enzymes involved in protein O-glycosylation in Burkholderia, a Gram-negative bacterium that can cause life-threatening illnesses, and undecaprenyl pyrophosphate phosphatase (UppP), an essential enzyme in all bacteria. This is a highly interdisciplinary project. Natural product isolation, chemical synthesis of glycolipid probes and enzymatic assays will be performed in the Cochrane Lab. Protein expression, growth of protein crystals and protein/glycolipid co-crystals will be performed in the Valvano Lab (for Burkholderia enzymes) and Caffrey Lab (collaborators at TCD that work with UppP). Macromolecular X-ray crystallography will be performed under the supervision of Dr. Vincent Olieric (non-HEI partner) at the Paul Scherrer Institute. This project will increase our mechanistic understanding of bacterial glycolipid-processing enzymes and could enable the rational design of inhibitors of these enzymes, leading to new classes of antibiotics.
For further information relating to this project, please contact Dr Stephen Cochrane via email (email@example.com).
Dr Meilan Huang
CITI-GENS DTP: Machine-learning based design of light-driven biocatalysts for production of high-value industrial products
Visible light is a cheap and environmentally friendly resource that can be used to accelerate chemical reactions. Despite of the widespread applications in chemistry, photocatalysis in biology is rare. Harnessing photochemistry in biological systems offers a promising route for harnessing clean energy and developing a light-dependent process, so it shows huge potential for biologically based manufacture.
However, it is challenging to harness photochemistry in biomanufacture due to the elusive catalysis mechanism of the photoenzymes and the high cost involved in traditional directed evolution of enzymes. Machine learning, one of the artificial intelligence, has emerged as an promising method in predicting protein structures and function relationship using computers. In this project, a rational protein engineering approach combining computational simulations of enzymatic mechanism, machine-learning based rational design and genetic technique of directed evolution will be developed and tested on engineering an algal enzyme that uses visual light for hydrocarbon production, with the aim to expand the substrate scope and increase the selectivity of the enzyme and to make the laboratory evolution process more efficient. The proposed research would be valuable for developing novel methods for environmentally benign, highly efficient and precise synthesis of chiral hydrocarbon compounds, so as to provide excellent photoenzyme biocatalyst toolbox for selective biosynthesis of high-value hydrocarbon compounds, which are important for pharmaceutical and fine chemical industries. The ECR fellow will work on this interdisciplinary and inter-sectoral project, in close collaboration with the molecular biologists from the school of Biological Sciences, Zhejiang University, China and the Department of Biocatalysis and Isotope Chemistry, Almac, Northern Ireland. Further, the developed novel biotechnology will be handily exploited by Almac because of the long-standing and successful collaboration between Dr Huang and Almac, and therefore would be beneficial for Almac to develop its ultimate goal of becoming a world leading new technology-driven company.
For further information relating to this project, please contact Dr Melian Huang via email (firstname.lastname@example.org)
Dr Andrew Marr
CITI-GENS DTP: Overcoming Enzyme Poisoning in Bioprocesses
Pharmaceutical companies rely heavily on bioprocesses for the manufacture of many of their active ingredients due to environmental, safety and cost factors. Almac Sciences is a world leader in biocatalysis, and is engaged in the development, application and global supply of enzymes for chemicals manufacture.
When removed from its natural environment the performance of an enzyme can become compromised due to stability issues in the presence of chemicals. Many chemicals can affect enzyme activity irreversibly and “poison” the enzyme. Drug companies need to engineer stability into the enzyme at the protein level or protect the enzyme from these poisons during the bioprocess. This project will focus on the latter. Collaborations have been established with Prof. Paul Kamer at Leibniz Institute for Catalysis (LIKAT), Rostock, Germany in order to prepare artificial enzymes1 and with Almac Sciences to access engineered enzymes. The student will work with these enzymes and devise new methods of avoiding poisoning. Material and solvent technologies will be investigated to protect and stabilise the enzyme. The project will combine chemistry, biology, materials and industrial expertise. Marr has developed solvents that sit above a biocatalytic reaction and remove the so-called poisons, thereby increasing productivity of the processes. In collaboration with Dr Patricia Marr, materials will be made to encapsulate enzymes in protective semi-permeable materials, and gels will be used that absorb poisons or selectively release substrates. The project will result in new methodology to support and stabilise enzymes for chemical processing.
For further information relating to this project, please contact Dr Andrew Marr via email (email@example.com)
1Catalytic and biophysical investigation of rhodium hydroformylase. H. T. Imam, A. G. Jarvis, V. Celorrio, I. Baig, C. C. R. Allen, A. C. Marr, P. C. J. Kamer. Catal. Sci. Technol., 2019, 9, 6428-6437. 2019 Catalysis Science & Technology HOT Article
Dr Pamela Walsh
CITI-GENS DTP: Seaweed bioactives for livestock nutrition and methane mitigation
Intense farming practice has resulted in environmental and animal health issues. It is estimated that of the 15% of total GHG emissions that come from livestock, 44% is in the form of methane.
Enteric fermentation from ruminants is considered the primary source of these methane emissions. It has also led to reliance on the use of antibiotics in healthy animals as a routine to prevent infections or speed up their growth. However, this practice has been banned (Regulation (EC) No. 1831/2003) and the antibiotics replaced by zinc oxide, which the EU plan to ban in 2022. Seaweed-supplemented animal feeds have been shown to produce significant improvements in gastrointestinal (GI) health of livestock. They have also shown improved stress resistance, promotion of stronger immune systems, improved productivity, reduced GI tract pathogens, nitrogenous gases and odour emissions. Some recent animal feed studies that supplemented Asparagopsis taxiformis, a red seaweed, into animal diets have showed a significant reduction in methane by up to 80%. Other seaweeds, including brown seaweeds have shown promising methane reduction results in vitro. One of the major challenges of supplementing seaweeds in animal diets is the availability of biomass, given that globally there are almost 1.5 billion head of cattle. Therefore, to use whole seaweeds as a feed ingredient could lead to potential ecological problems. Currently, there is an estimated 25 million tons of seaweed is harvested globally each year for the hydrocolloids, biofertilisers and biostimulants industries. However, in the alginate industry some of these bioactives are undesirable, and are removed and discarded using toxic organic solvents. This studentship will investigate green separation methods, primarily SCO2, to isolate compounds of interest prior to alginate extraction. It is anticipated the extracts produced from this Studentship will be tested in the SEASOLUTIONS projects.
For further information relating to this project, please contact Dr Pamela Walsh via email (firstname.lastname@example.org)