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UNDERGRADUATE SEFS SUMMER RESEARCH BURSARIES 2018
GROUP 1 - ENGINEERING AND COMPUTER SCIENCE
Name Department/School Title
Dr Pádraig Cantillon-Murphy Engineering Tracking sensor design for image-guided surgery
Dr Kevin McCarthy/Prof Paul Callanan EE & Physics*
Tracking the stars with The Crawford Observatory
Dr Jason Quinlan/ Professor Cormac Sreenan, (Principal Investigator Computer Science
A System Architecture for Edge Computing in Cellular Networks
Dr Bill Wright Mechanical Engineering Development of a hardware controller for a Nd:YAG laser
GROUP 2 – FOOD SCIENCE & NUTRITIONAL SCIENCES; LIFE SCIENCES AND BIOLOGICAL, EARTH & ENVIRONMENTAL SCIENCE
Name Department/School Title
Dr Jean O’Dwyer BEES
In situ assessment of GRappLE: Groundwater Risk application for Local Evaluations
Dr Eoin Lettice BEES Examining the effect of soil compaction on root morphology and crop yield
Prof Douwe van Sinderen Microbiology
How to understand and prevent beer spoilage
Dr David Clarke Microbiology Bile resistance in Bacteroides
Dr Susan Joyce Biochemistry and Cell Biology Bile acid metabolising ability: examining enzymes from the microbiome
Dr Paul Young Biochemistry and Cell Biology The International Genetically Engineered Machine (iGEM) competition is a Synthetic Biology competition for interdisciplinary teams of undergraduate students
Dr Kellie Dean Biochemistry and Cell Biology Deciphering a potential coding role of SNHG5 RNA in colorectal cancer
Dr Pat Meere BEES The development and timing to tectonic cleavage from the Variscides of SW Ireland
Dr John Weatherill BEES
Conceptualising shallow groundwater contaminant pathways in high vulnerability fractured bedrock aquifers
Prof Cora O’Neill Biochemistry and Cell Biology Understanding gut inflammatory responses in Parkinson’s
Prof Mairead Kiely Food and Nutritional Sciences Exploring relationships between maternal mental health and early infant feeding
Dr Lucía Hermida González/Dr Paul Leahy Enviornmental
Can Recent Severe Weather Events in Ireland be Attributed to Global Climate Change?
Dr. Shane Crowley/Mr. Dave Waldron Food and Nutritional Sciences
Why are Ouzo hazy, spirit?’ –Spontaneous Emulsification in Aniseed-flavoured Distilled Beverages
Dr Ken Nally Biochemistry and Cell Biology
Investigation into the ability of Th1 Inflammatory and Anti-Tumour Cytokines to Sensitize Resistance Colon Cancer Cell Lines to the EGFR targeted therapy Cetuximab
Dr Barbara Doyle BEES The influence of LEDs on plant growth under in vitro and in vivo conditions
GROUP 3 – MATHEMATICAL SCIENCES; CHEMISTRY AND PHYSICS
Name Department/School Title
Prof. Denise Gabuzda Physics Helical Magnetic Fields in "Jets" ejected by Active Galactic Nuclei
Dr Gerard McGlacken Chemistry Interrupting bacteria communication systems as a strategy to avoid the evolution of bacteria resistance.
Dr Martin Kilian Mathematical Sciences Minimal Surfaces
Dr. Tim O'Sullivan Chemistry
The design and synthesis of DSF mimetics - new weapons in the battle against bacterial resistance
Dr Dean Venables Chemistry Spectroscopy of Semi-Volatile Organic Species
Dr Andreas Ruschhaupt Physics Quantum Technologies (Theoretical Physics)
Dr Kevin McCarthy/Prof Paul Callanan EE & Physics*
Tracking the stars with The Crawford Observatory
Prof Colm O’Dwyer Chemistry
Colour-Coding Battery Performance – Electrochemical and Photonics for Understanding Electrochemical Energy Storage
Prof Bernard Hanzon Mathematical Sciences Computation of Critical Value Polynomials and their Galois Groups
Dr Elizabeth Gilchrist Chemistry
Determination of trace toxic ionic species in drinking water using ion chromatography-mass spectrometry
Dr. Florence McCarthy Chemistry Ellipticines: Targetting cancer by a structured approach
Dr Davide Tiana Chemistry Computational study of the Aldol-Tishchenko reaction catalysed by metal-organic frameworks
Prof. John McInerny/ Dr Pierpaolo Porta Physics
DIODE LASER-BASED LIDAR FOR AUTONOMOUS VEHICLES
GROUP 1 - ENGINEERING AND COMPUTER SCIENCE
PROJECT 1 - TRACKING SENSOR DESIGN FOR IMAGE-GUIDED SURGERY
Electromagnetic tracking (EMT) is the gold standard for non line-of-sight tracking in image-guided surgery. Tracking of surgical instruments is achieved by using a combination of a transmitter board, usually located beneath the patient, and a receiving sensor, usually attached to the tip of the instrument. UCC School of Engineering has been developing advanced electromagnetic tracking tools for image-guided and robotic surgery for six year and launched the Anser EMT platform in 2017 (http://anser.io).
To date, tracking is achieved with off-the-shelf commercial sensors which provide 5 degree-of-freedom accuracy (5DOF) and there has been no customised coil development. The goal of this project is to design, built and test a new sensor type for use with electromagnetic tracking. The sensor will combine simulated design (Matlab and Maxwell) with experimental work (inductive coil winding and characterisation), as well as testing of coils for tracking of position and orientation in a realistic pre-clinical benchtop setting. The end goal is a working sensor coil which can be used for 6 degree-of-freedom tracking and is integrated within the tip of a surgical instrument for proof-of-concept testing. The student will work with the Anser design team to integrate the sensor within the tracking platform and validate pre-clinical performance.
The ideal candidate will have a background in electromagnetics and experimental electronics as well as an interest in biomedical applications. For additional background visit https://www.researchgate.net/profile/Padraig_Cantillon-Murphy2
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Padraig Cantillon-Murphy
PROJECT 2 - TRACKING THE STARS WITH CRAWFORD OBSERVATORY
The Crawford Observatory at University College Cork (e.g. https://en.wikipedia.org/wiki/Crawford_Observatory) was built in 1878 and extensively renovated in 2006. Of its three telescopes, the equatorial, sitting directly under the 15-foot dome, is the largest: exhibited at the Paris Exhibition in 1878, its design won the gold medal. These telescopes represent state of the art 19th C astronomical technology, and were built by the pioneering engineer Sir Howard Grubb (http://astro.ucc.ie/?page_id=763)
Although the equatorial telescope is designed to track stars throughout the night by means of a gearing mechanism, in practice this has not worked very effectively. Last year, as part of a collaboration between UCC Physics and Electrical Engineering, a small stepper motor was attached to the clockwork drive, allowing the telescope track successfully for the first time in decades (e.g. see http://astro.ucc.ie/equatorial_tracking.m4v for Betelgeuse - motor switched off at ~6 sec into movie). With this, the telescope can now remain pointed at targets over extended periods, allowing deeper images to be obtained (see attached).
The next challenge is to improve the pointing of the telescope, and our ability to centre a star in the field of view. This requires an ability to maneuver the telescope precisely on the sky, which is not currently feasible. The best way to do this is to modify the motor so that it can drive the telescope at a user controlled rate, allowing the telescope slew to the star much more easily. This work is feasible as a summer project, and builds on the successful Physics/EE collaboration of last year.
We confirm that all facilities required for the proposed research project are available and that we are available to personally supervise the project during an 8 week period during June -September 2018. Prof Paul Callanan, Department of Physics, UCC, ([email protected], x3211)
Dr Kevin McCarthy, Electrical and Electronic Engineering, UCC ([email protected], x2072)
Moon from Crawford Observatory
PROJECT 3 - A SYSTEM ARCHITECTURE FOR EDGE COMPUTING IN CELLULAR NETWORKS
In current wireless systems, we are seeing a trend towards mobile applications demanding high data rates, low network delay and local contextual information (GPS locations, user interactions). Use cases of these emerging applications are IoT devices (machine-2-machine), Video consumption (Gaming, Streaming, Augmented Reality), and geo-dependent analytics (CCTV, law enforcement, drones). These applications produce large amounts of data, which is subject to low-latency analysis, typically in the Cloud, but usually with delays in redistribution to the device. To counteract these excessive delays in communication and video analysis, we are seeing active research into the offloading of mobile data, via localised cloud computing virtualisation at the edge of the wireless network, which is collectively known as Edge Computing (EC). EC offers the promise of low latency, location awareness and access to radio network information which are crucial for real-time, time-sensitive and safety critical applications.
In the Mobile and Internet Systems Laboratory, under the iVID project, we are investigating how exposing the state of the network provides an insight into the capabilities of systems resources, which can be optimised to ultimately improve the quality of video delivered over wireless cellular networks. We have currently investigating how the judicious placement of supportive systems within, or close to the network edge, can alleviate video delivery issues such as delay and congestion. The goal of this project is to build upon our existing testbed, which incorporates simulation and emulation element utilised to stream video over a 4G cellular network, and by using off-the-shelf tools, investigate issues such as video analysis, latency of local versus Cloud processing, and underlying device interactions, which are needed to support the vision of Edge Computing. This project would suit a student with strong programming and systems skills, and a passion for innovation.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018
Dr Jason Quinlan Professor Cormac Sreenan, (Principal Investigator) Senior Post-Doctoral Researcher, Head of Department, Mobile and Internet Systems Laboratory, Department of Computer Science, Rm 2.09, University College Cork, Western Gateway Building, Cork email: [email protected] University College Cork, Western Road, Cork email: [email protected]
PROJECT 4 – DEVELOPMENT OF A HARDWARE CONTROLLER FOR A Nd:YAG LASER
This project requires the design and construction of a hardware controller for a Q-switched NdYAG laser that was recently refurbished in the Ultrasonics Research Laboratory. Pulsed lasers may be used to remotely generate ultrasonic waves in many materials without physical contact – either by rapid thermal expansion or material ablation from the irradiated surface causing either shear or compression waves to propagate.
The laser is presently underused for research applications as the main in-built control unit requires the following multiple input signals, which are currently provided by separate laboratory benchtop power supplies and function generators;
0-5V variable dc input to control the depth of Q-switch modulation;
TTL gating signal to quickly open and close the Q-switch and release a laser pulse from the optical cavity, with a minimum duty cycle of 1% and a maximum frequency of 5 MHz;
TTL input to set the flash tube lamp current using a variable frequency square wave between 25 kHz and 125 kHz;
12 V dc supply for a HeNe alignment laser.
The hardware controller circuitry should be designed and constructed using discrete analog components in a dedicated housing for reliability, and should also incorporate a manual button or switch to fire a single laser pulse– this may be a separate circuit in the same housing if desired.
Once constructed and fully tested, the controller may then be used with the laser to determine the optimum settings to generate non-contact ultrasonic signals in various test materials as part of a larger research project.
“I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8 week period during June – September 2018”
Dr Bill Wright
Project Supervisor
W: http://ultrasonics.ucc.ie/
GROUP 2 – FOOD SCIENCE & NUTRITIONAL SCIENCES; LIFE SCIENCES AND BIOLOGICAL, EARTH & ENVIRONMENTAL SCIENCE
PROJECT 5 - IN SITU ASSESSMENT OF GRappLE: GROUNDWATER RISK APPLICATION FOR LOCAL EVALUATIONS
GRappLE is a mobile phone application that has recently been developed through a Geological Survey Ireland funded research grant (PI: Dr. Jean O’Dwyer). Recent studies by GRappLE team members examined and modelled the presence of faecal indicator organisms in Irish groundwater sources, with several of these models capable of >85% predictive accuracy [1-4]. By combining these studies and associated data, a scientifically robust and extrapolative database has been created, thus permitting significantly improved groundwater resource protection at a national scale. The rationale underpinning the GRAppLE project is to effectively place scientific quantification and assessment in the hands of those most affected (i.e. private well users) via technological applications. As a result of combining scientific data, online shapefiles (GIS) and databases in combination with ‘pocket technology’, it is now feasible to provide a ‘live’ source-specific risk assessment tool for private well owners (overview in Figure 1).
To assess the accuracy and sensitivity of the application (and contained risk model), this summer placement will coordinate a targeted sampling regime of private wells, in low, medium and high vulnerability regions, recruited through the National Federation of Group Water Schemes
(NFGWs). Water samples will be taken in accordance with Standard Methods and assayed for Total Coliforms and E. coli using a US Environmental Protection Agency (EPA) approved commercial culture kit (Colilert, IDEXX Laboratories Inc., Westbrook, ME, USA). In total, ~100 samples will be processed and the results will be analysed in terms of accuracy relative to the corresponding ‘Risk’ from GRAppLE. Finally, a sensitivity assessment will be undertaken which can be used to provide a degree of confidence in the accuracy of GRAppLE for private well utilisers in Ireland.
Contact Details:
Dr. Jean O’Dwyer
Ext: 4590
Email: [email protected]
References:
1. O’Dwyer, J., Hynds, P., Byrne, K.A., Ryan, M.P., Adley, C. (2018) Development of a Hierarchical Model for Predicting Microbiological Contamination of Private Groundwater Supplies in a geologically heterogeneous region. Environmental Pollution [In press]
2. O'Dwyer, J., Dowling, A., Adley, C. C. (2014) Microbiological assessment of private groundwater- derived potable water supplies in the Mid-West Region of Ireland. Journal of Water and Health, 12(2):310-317.
3. Hynds PD., Misstear BD., Gill LW., Murphy H. (2014) Groundwater source contamination mechanisms: Physicochemical profile clustering, risk factor analysis and multivariate modelling. Journal of Contaminant Hydrology, 159:47-56
4. Hynds PD., Misstear BD., Gill LW. (2012) Development of a microbial contamination susceptibility model for private domestic groundwater sources. Water Resources Research, 48(12)
5. Supervisor Statement:
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Signed: 6th February 2018
PROJECT 6 - EXAMINING THE EFFECT OF SOIL COMPACTION ON ROOT MORPHOLOGY AND CROP YIELD
Ongoing work in this laboratory is examining the effect of differing levels of soil compaction on root growth and development in perennial rye grass. There is considerable evidence that severe soil compaction can have significant effects on the ability of roots to penetrate the soil; leave the crop more susceptible to abiotic stresses (e.g. drought, waterlogging); and lead to an overall reduction in yields. Soil compaction is one of the major problems facing world agriculture.
This project will examine changes to root morphology in perennial rye grass brought about by soil compaction in a mini-rhizotron system. The student will use image analysis software to characterise and quantify such changes. The impact of abiotic stresses on plants growing in soil with different levels of compaction will also be explored.
This project will provide training in experimental design, plant management in a rhizotron system, use of the ImageJ image processing and analysis software as well as data handling and statistical analysis.
SEFS Summer Research Bursary Project 2018
Supervisor: Dr Eoin Lettice (School of BEES)
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018
Eoin Lettice
PROJECT 7 - HOW TO UNDERSTAND AND PREVENT BEER SPOILAGE
The brewing process and the natural composition of beer make this beverage a challenging environment for bacterial organisms to survive. Nonetheless, certain bacteria have evolved and adapted the ability to grow in this environment. Approximately 70 % of microbial beer-spoilage incidents are reported to be caused by Lactic Acid Bacteria (LAB), in particular certain strains of Lactobacillus brevis. Although these bacteria are in principle harmless for human health they are responsible for the production of undesirable flavours, acidity and/or turbidity, thus affecting negatively the aesthetic and organoleptic qualities of the final product. The proposed project aims to understand how Lb. brevis can grow in beer, while it will also apply naturally occurring bacterial viruses to combat this beer-spoiling microbe.
Lb. brevis beer spoiler strains are known to carry plasmids which have been associated with their beer-spoilage phenotype. The proposed research would involve plasmid-curing of fully sequenced Lb. brevis beer spoiler strains (obtained from a major brewery) using various established
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8 week period during June – September 2018.
Prof Douwe van Sinderen
School of Microbiology
Email [email protected] phone ext 1365
PROJECT 8 - BILE RESISTANCE IN BACTEROIDS
Bacteroides are important Gram negative, anaerobic bacteria found in the human gut. Indeed, recent studies have shown that Bacteroides make up approximately 50% of the bacterial biomass in the human gut and decreases in the level of Bacteroides have been associated with conditions such as obesity and diabetes. In order to colonize the gut Bacteroides have to overcome several important host defense mechanisms including the production of bile in the small intestine. Bile is a molecule produced in the liver and stored in the gall bladder of humans. Bile acts as an emulsifier that solubilizes dietary lipids making them accessible for digestion. Bile also has important anti-microbial activity and any bacteria that colonizes the gut must have a certain degree of resistance to the action of bile. Bacteroides have been shown to be resistant to high levels of bile although the mechanism of bile resistance in Bacteroides is not understood. Therefore, in this study you will construct a mutant library in Bacteroides thetaiotaomicron (a strain of Bacteroides isolated from the human gut) using a mariner-based transposon. You will then use this library to screen for mutants in B. thetaiotaomicron that are sensitive to bile and, in this way, you will identify genes that are necessary for bile resistance in this important beneficial gut commensal.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Dr David Clarke
School of Microbiology
Phone: (021) 4903624
Email: [email protected]
URL: http://publish.ucc.ie/researchprofiles/D010/davidclarke
PROJECT 9 - BILE ACID METABOLISING ABILITY: EXAMINING ENZYMES FROM THE MICROBIOME
Bile acids are an indication of gut microbial changes and they have different signatures in disease and health states. The hypothesis is that athletes contain altered bile acid metabolism compared to weight matched counterparts. We have shown that bile acids are altered in these athletes. However, we have not identified and matched strains and genetics with activity. This project will examine a selection of fosmid (large plasmid) harbouring DNA encoding bile acid altering enzymes for specific activity against a range of bile acids. We will delimit activity of 227 bile active fosmids isolated from a single athlete. Fosmids will be grouped according to their specific activity. In collaboration with Dr Paul Cotter and Dr. Orla O’Sullivan representatives from each group of interest will be end sequenced and the corresponding bile altering enzymes identified will be assigned to taxa
“I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.”
Dr Susan Joyce, Lecturer, School of Biochemistry and Cell Biology, UCC
Email: [email protected]
Tel: 021 4901343
PROJECT 10 - CORK iGEM 2018
The International Genetically Engineered Machine (iGEM) competition is a Synthetic Biology competition for interdisciplinary teams of undergraduate students. Q. What is Synthetic Biology? A. The design and construction of biological devices and systems for useful purposes. Some examples of what is/ may be possible with synthetic biology:
High performance protein fibres produced in bacteria
Bacterial detection of DNA sequences for diagnostics
Genetically encoded logic gates
DNA origami templates for nanoelectronic circuitry
Computational Design of Protein Nanomaterials
Data storage in DNA
An artificial leaf for hydrogen fuel production
Designed enzymes for gluten destruction
Diesel production in E. coli
Bacterial biosensor for arsenic
A bacterial red blood cell substitute
Self-Assembling Nanoreactors
Biohybrid materials from viruses
Bacteria as sensitivity tuners You can see why the team needs to bring together students from Mathematics, Computer Science, Engineering, Physics, Chemistry as well as the Biological Sciences. Are you up for the challenge of being part of the Cork iGEM 2018 team?
The School of Biochemistry and Cell Biology hope to facilitate a team to enter the competition, but the project is student-driven. Supervisors will advise the team and provide a crash course in molecular biology for non-biologists. Teams are given a toolkit of biological parts. Using these parts and applying principles from diverse scientific fields, the challenge is to build biological systems and operate them in living cells. The team will devise, design and implement the project. They will also promote and fundraise for the project, so as to be able to travel to the iGEM 2018 Jamboree in Boston in Oct! Links: http://igem.org/About http://2014.igem.org/Team:UCC_Ireland http://2015.igem.org/Team:Cork_Ireland http://2016.igem.org/Team:UCC_Ireland http://2017.igem.org/Team:UCC_Ireland “I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8 week period during June – September 2015” Signed
Paul Young Dr. Paul Young, School of Biochemistry and Cell Biology. Email: [email protected] Phone: 4205994
PROJECT 11 - DECIPHERING A POTENTIAL CODING ROLE OF SNHG5 RNA IN COLORECTAL CANCER
Colorectal (bowel) cancer is one of the most common types of cancer in Ireland and worldwide (WHO http://gco.iarc.fr/today/home). Long, non-coding RNAs (lncRNAs) are a large group of RNAs that are transcribed, but not translated into proteins. Due to advances in sequencing technologies, the cellular contribution of the non-coding transcriptome is expanding, and lncRNAs have emerged as regulators of normal cellular events and disease states, including colorectal cancer 1. One lncRNA specifically associated with CRC is small, nucleolar, RNA host human gene 5 (SNHG5), which was found at high levels in CRC tumours and promotes cancer cell survival 2.
Intriguingly, several studies indicate that ‘non-coding’ RNAs have coding potential, serving as templates for protein synthesis, often from small, open reading frames (sORFs) 3–6. As reported, SNHG5 is a cytoplasmic, with no polyribosome association 2,7,8. However, upon closer examination, we believe that SNHG5 RNA can be occupied by one or two translating ribosomes. Using RiboGalaxy 9, we visualized ribosome profiling data from HCT116 CRC cells 10 and discovered an sORF that could produce a 35-amino acid peptide. Therefore, we hypothesize that SNHG5 lncRNA is bifunctional, with both coding/non-coding functions.
To begin to assess SNHG5 sORF translation, this project will involve cloning the 5’ leader sequence of SNHG5 sORF, along with mutant variants, upstream of firefly luciferase in a dual-luciferase reporter system 11. Following transfection into HCT116 and SW620 CRC cell lines, luciferase activity will be monitored using a luminometer. This system will allow us to determine the influence of the SNHG5 5’ sORF leader on translation, providing supporting evidence that it might be a peptide, not the long, non-coding RNA itself that is contributing to CRC.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Signature: Date: 09 February 2018
Kellie Dean, PhD College Lecturer and Postgraduate Director School of Biochemistry and Cell Biology, 3.91 Western Gateway Building University College Cork, Cork, Ireland ph: +353 21 420 5421; e: [email protected]
References:
1. Yang, Y. et al. LncRNAs: the bridge linking RNA and colorectal cancer. Oncotarget 8, 12517–12532. (2016).
2. Damas, N. D. et al. SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization. Nat. Commun. 7, 1–14 (2016).
3. Makarewich, C. A. & Olson, E. N. Mining for Micropeptides. Trends Cell Biol. 27, 685–696 (2017).
4. Nam, J., Choi, S. & You, B. Incredible RNA: Dual Functions of Coding and Noncoding. Mol. Cells 39, 367–374 (2016).
5. Anderson, D. M. et al. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160, 595–606 (2015).
6. Aspden, J. L. et al. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. Elife 3, e03528 (2014).
7. Zhao, L. et al. Long non-coding RNA SNHG5 suppresses gastric cancer progression by trapping MTA2 in the cytosol. Oncogene 35, 5770–5780 (2016).
8. Carlevaro-Fita, J. et al. Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. Rna 1–16 (2016). doi:10.1261/rna.053561.115
9. Michel, A. M. et al. RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data. RNA Biol. 13, 316–319 (2016).
10. Crappe et al. PROTEOFORMER: Deep proteome coverage through ribosome profiling and MS integration. Nucleic Acids Res. 43, e29 (2015).
11. Loughran, G., Howard, M. T., Firth, A. E. & Atkins, J. F. Avoidance of reporter assay distortions from fused dual reporters. RNA 23, 1285–1289 (2017).
PROJECT 12 – THE DEVELOPMENT AND TIMING TO TECTONIC CLEAVAGE FROM THE VARISCIDES OF SW IRELAND
Understanding the development of tectonic cleavage is fundamental to gaining an insight to how rocks deform in general. Attempting to understand the key physical/chemical processes of tectonic foliation formation has occupied the minds of some of the leading geologists for nearly 200 with answers to some fundamental questions still outstanding. Research since the early seventies has revealed significant insights into the central role pressure dissolution plays in the formation of tectonic cleavage. As a consequence cleavage foliations are typically domainal with alternating phyllosilicate-rich dissolution cleavage domains and lithon domains of relatively un-deformed host lithology. Deformation mechanisms involved in the formation of these fabrics include grain rigid body rotation producing grain shape preferred orientation (GSPO), crystal-plastic deformation and pressure dissolution (Vernon, 1998). The current orthodoxy is that these processes predominantly operate to produce a slaty cleavage after the host lithology has become fully lithified. The key research question to be addressed by this research centers on identifying the controls of the development domainal structure of cleavage fabrics from the Variscides of SW Ireland. There is also a need to address the significant degree of uncertainty with regards to the timing of cleavage development with respect to the other main phases (folding, reverse faulting) of Variscan deformation.
Field Structural Studies: A detailed structural analysis of a selected key localities exhibiting Variscan cleavage will be carried out. The primary objective of this field based phase of research is to fully characterise the structural controls on the development of these tectonic fabrics.
Micro-structural Studies: Cleavage development histories will be elucidated with the aid of conventional petrographic and Raman spectroscopy studies.
PROJECT 13 – CONCEPTUALISING SHALLOW GROUNDWATER CONTAMINANT PATHWAYS IN HIGH VULNERABILITY FRACTURED BEDROCK AQUIFERS
Groundwater supplies one in four people in Ireland with drinking water. Approximately two thirds of the island of Ireland is underlain by thin aquifers which are highly vulnerable to pollution. These aquifers are critical for rural water provision and maintenance of headwater stream flow during dry weather. The proposed project will develop an integrated conceptual understanding of contaminant migration pathways within a stream catchment draining a vulnerable aquifer subject to diffuse nitrate and geogenic arsenic pollution. The study area is currently being by developed by UCC as an experimental research site for groundwater-surface water interactions.
The research will employ state-of-the-art 2D electrical resistivity tomography to map shallow pollutant pathways in high resolution which will be integrated as a 3D conceptual model. These pathways include the bedrock-subsoil transition zone, fault zones and weathered bedrock which act as conduits for pollutant transfer. Contaminant residence times along pathways will be evaluated using point-dilution tracer studies in groundwater monitoring boreholes. A high-resolution streambed temperature and hydrochemical survey will be completed over a 1 km reach of the stream. The survey will integrate the 3D conceptual understanding of the surrounding groundwater system with preferential contaminant pathways at the aquifer-stream interface.
The proposed research will link into a funded MRes studentship which will investigate reactive transport of geogenic arsenic. The research will form a key part of a peer-reviewed publication for submission to the high-impact journal Water Resources Research.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Dr. John Weatherill
Lecturer in Hydrogeology Environmental Research Institute School of Biological, Earth and Environmental Sciences Phone: +353 (0)21 490 4578 Email: [email protected]
PROJECT 14 – UNDERSTANDING GUT INFLAMMATORY RESPONCES IN PARKINGSON’S DISEASE
Parkinson’s disease is the second most common brain degenerative disease, after Alzheimer’s disease, and affects 10 million people worldwide. The disease primarily impairs movement/motor function. However, 80% of people with Parkinson’s disease experience problems with their gut and digestive system. Importantly these impairments in gut function also occur several years before the motor defects. This has led many scientists to hypothesise that communication between the gut enteric and the brain nervous system is a key component of Parkinson’s disease and that the disease may even originate in the gut nervous system. It is thus of major importance to develop a better understanding of communication between enteric gut nervous system and brain central nervous system in Parkinson’s to develop better disease diagnostics and treatments for this disease which is a major interest of our research.
-synuclein builds up and aggregates abnormally in neurons that degenerate and control movement in Parkinson’s disease and this protein spreads between specific neurons slowly over time as these brain neurons die. The mechanism underlying this are being
-synuclein is believed to be a major cause of Parkinson’s and is also found in the gut neurons in the disease. This project will investigate -synuclein and how it affects the gut with a focus on inflammation and immune systems. Several cell and molecular approaches will be employed and the summer bursary will allow the student to develop these practical skills and to better understand research in the area of Parkinson’s disease and neurodegeneration. The research will add to the work of a PhD student working with a multidisciplinary team of supervisors and funded by the APC Microbiome Institute UCC.
I confirm that all facilities required for the proposed research project are available and that I available to personally supervise the project during an 8 week period during June-September 2018.
Prof Cora O’Neill,
School of Biochemistry and Cell Biology,
Biosciences Institute, UCC.
Email [email protected];
021 4901380
PROJECT 15 – EXPLORING RELATIONSHIPS BETWEEN MATRENAL MENTAL HEALTH AND EARLY INFANT FEEDING
Background It is estimated that up to 1 in 7 new mothers will experience postnatal depression (Health Service Executive, 2008), which has been strongly associated with infant feeding problems and early breastfeeding cessation. On the other hand, there is some evidence to support the notion that expert support to minimise early breastfeeding difficulties may help to improve postpartum mental health among mothers, with benefits for both mother and baby.
Aim This study will explore associations between maternal mental health assessed at 2 months postpartum and early feeding practice and behaviour among mother-infant dyads participating in the COMBINE study. An a priori sensitivity analysis of maternal feeding intention will be included.
Methods The project will undertake analysis of data from the subgroup of 300 women who have completed assessment of Postnatal Attachment, Adult Attachment Style and Depression in the COMBINE prospective birth cohort, which is currently undertaking postnatal follow-up of 400 maternal-infant dyads. Using a combination of clinical data and electronic data collected from our infant nutrition MiChild mobile application, the analysis will provide a detailed longitudinal description of early infant feeding throughout the first six months of life and will investigate putative associations between maternal anxiety and depression and the initiation and maintenance of breastfeeding over this period.
Expected outcomes First data of associations between maternal mental health and attachment style and early infant feeding in an Irish birth cohort. These data will inform health care practitioners about the bi-directional links between maternal post-natal anxiety and depression and infant nutrition.
Learning outcomes Participation and training in cutting edge research environment; database construction and analysis; report writing and presentation; interpersonal; organisational and professional skills.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Mairead Kiely | Professor of Human Nutrition,Cork Centre for Vitamin D and Nutrition Research Room 127, School of Food and Nutritional Sciences | College of Science Engineering and Food Science UCC | Ireland
P +353214903394 | [email protected]
PROJECT 16 – CAN RECENT SEVERE WEATHER EVENTS IN IRELAND BE ATTRIBUTED TO GLOBAL CLIMATE CHANGE?
The human-induced warming of the global climate system since the 1950s is already beyond reasonable doubt. This warming is altering not only long-term trends but also is changing the patterns of extreme weather and climate events. An increase in temperature would lead to more atmospheric water vapour, which increases annual average precipitation as well as the frequency of heavy precipitation.
An increase has already been detected in annual precipitation and in the occurrence of extreme precipitation events since the second half of the 20th century, particularly affecting the western half of Ireland. Increases in winter precipitation will lead to increases in stream flow from October to April with a final consequence of an increase in the risk of floods.
The student will gain knowledge in a relatively new subfield of climate science, called attribution studies. This involves comparison of the frequency and/or magnitude of a specific past extreme event between two climate model experiments: (1) simulations of the world’s climate as we know it today (factual world) and (2) a world as it would be without anthropogenic human emissions (counterfactual world).
A suitable event will be selected based on the student’s background and interests, for example, the case of the floods of November 2009 on the river Lee in Cork City, or the so-called Fodder Crisis of 2012/2013 when farmers ran out of animal feed due to sustained poor growing conditions.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018
Supervisor: Dr. Lucía Hermida González, Environmental Research Institute
Co-Supervisor (Principal Investigator, ClimAtt Project): Dr. Paul Leahy, School of Engineering/ERI
PROJECT 17 – ‘WHY ARE OUZO HAZY, SPIRIT?’ – SPONTANEOUS EMULSIFICATION IN AINISEED-FLAVOURED DISTILLED BEVERAGES
Ouzo is a Greek anise-flavoured alcoholic drink manufactured by distillation. At its natural alcohol content (~40% abv) Ouzo is transparent, but when diluted with water it is transformed into an opaque white solution. The same phenomenon is observed for anise-flavoured spirits from Italy (Sambuca), Switzerland (Absinthe) and France (Pastis). This so-called ‘Ouzo Effect’ involves spontaneous emulsification of anethole, a flavour compound with poor water solubility. This remarkable property is not only of interest to cocktail enthusiasts, however; food and pharmaceutical scientists see tremendous potential in the Ouzo Effect as a micro-encapsulation technology for the stabilisation and delivery of sensitive bioactive molecules to the body. What makes these spontaneously-formed emulsions so unusual is their almost indefinite stability, requiring no additional ingredients (e.g., emulsifiers) or processing operations (e.g., homogenisation). These factors make the Ouzo Effect a highly promising emulsion design strategy that potentially offers unprecedented levels of microdroplet control and stabilisation. This project will involve an in-depth study of the physical chemistry of spontaneous emulsification. Anise-flavoured spirits will be procured and diluted to various alcohol contents (confirmed by hydrometry). The evolution of anethole droplets from the nano- to the micron-scale will be tracked in situ using dynamic light-scattering. Equilibrium droplet size will be measured using static light scattering. Kinetics of droplet flotation for anethole microdroplets will be
determined for the first time using a novel analytical centrifugation technique. Tensiometry will be utilised to probe surface tension effects caused by the Ouzo Effect. During the project, model anise-flavoured liquors will be prepared using distillation and solvent extraction of aniseseed and ‘stressed’ under various conditions, including pH, temperature and ionic strength, of relevance to real food and pharmaceutical systems.
This project will be of interest to students interested in topics including physical-chemistry, food science and molecular gastronomy.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Dr. Shane Crowley Mr. Dave Waldron
Dr. Shane Crowley, Lecturer in Food Processing, & Mr. Dave Waldron, Senior Technical Officer, School of Food and Nutritional Sciences
PROJECT 18 – INVESTIGATION INTO THE ABILITY OF Th1 INFLAMMATORY AND NTI-TUMOUR CYTOKINES TO SENSITIZE RESISTANCE COLON CANCER CELL LINES TO THE EGFR TARGETED THERAPY CETUXIMAB
Redundancy between oncogenic receptor tyrosine kinase (RTK) signalling pathways represents a key mechanism of acquired resistance to targeted cancer therapies such as the anti-EGFR biological therapy (cetuximab) in colon cancer. In particular, targeting one RTK may result in compensatory upregulation of bypass RTK genes, which turns otherwise sensitive cells refractory to the initial treatment. The pro-inflammatory Th1 cytokines IFN- - -tumour immunity yet their effect on RTK signalling is unclear. We have shown that IFN- -
-ordinated shutdown of multiple RTK genes in colon cancer cell lines. This transcriptional response is seen across various human cancer cell types and involves up-regulation of EGFR – the target of cetuximab - coupled with repression of a conserved set of RTKs, including HER2/3, FGFR3, INSR and IGF1R. Mechanistically, IFN- -inputs such as (i) acute transactivation of EGFR, HER2, INSR and IGF1R, which drives activation of PI3K/AKT signalling as well as (ii) RTK-independent induction of p38 and MEK/ERK pathways. Our results suggest that therapies promoting T-cell-mediated antitumour immunity (e.g. immune checkpoint blockers) may produce similar effects as a part of their overall efficacy. This could provide a rationale for combining such immunotherapies with RTK-based targeted therapies in order to overcome acquired resistance to the latter.
Aim
The aim of this project is to test whether IFN- - -induced rewiring of RTK signalling pathways sensitizes resistant colon cancer cell lines to the anti-EGFR targeted therapy cetuximab.
References
(1) Resistance to anti-EGFR therapy in colorectal cancer: from heterogeneity to convergent evolution.
Misale S, Di Nicolantonio F, Sartore-Bianchi A, Siena S, Bardelli A. Cancer Discov. 2014 Nov;4(11):1269-80. Review.
(2) Acquired resistance to EGFR-targeted therapies in colorectal cancer.
Van Emburgh BO, Sartore-Bianchi A, Di Nicolantonio F, Siena S, Bardelli A. Mol Oncol. 2014 Sep 12;8(6):1084-94. Review.
Supervisor Contact Details:
Ken Nally, Ph.D. Tel: 353-21-4901302
Lecturer in Biochemistry & Principal Investigator Email: [email protected]
School of Biochemistry & Cell Biology Web: http://apc.ucc.ie and http://microbemagic.ucc.ie (for children)
Host Response and Inflammation Group
Alimentary Pharmabiotic Centre
Rms. 2.10/4.41, Bioscience Institute
Supervisor Declaration:
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8 week period during June – September 2018.
PROJECT 19 – THE INFLUENCE OF LEDS ON PLANT GROWTH UNDER IN VITRO AND IN VINO CONDITIONS
This project will examine the impact of light emitting diodes on plant growth in both growthroom and glasshouse scenarios. We have a small
Enterprise Ireland funded project (Innovation voucher ) which has allowed us to purchase two LED units from Heliospectra in Sweden. This units
can be controlled remotely and allow us to switch between different wavelengths. Working with a former medical physicist Dr Graham Manson
and myself, the student will, under our supervision, carry out a series of experiments from seed germination, growth performance and
photosynthetic capacity of selected plant species.
We have sectioned part of the existing growthroom in BEES to carry out the experiments over the summer period and in addition we are having
the second unit installed in the glasshouses in BEES. This short project will generate a lot of interesting data for a student project over the time
period and we expect lead to a poster presentation for the autumn. There have been a number of excellent reviews in this area and also the
former bomb shelters in London (along with other vertical urban farming settings ) are using LEDs to grow vegetables and supply local markets.
http://www.independent.co.uk/Business/indyventure/growing-underground-london-farm-food-waste-first-food-miles-a7562151.html
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project
(with Graham) during an 8 week period during June – September 2018
Dr Barbara Doyle Prestwich
GROUP 3 – MATHEMATICAL SCIENCES; CHEMISTRY AND PHYSICS
PROJECT 19 - HELICAL MAGNETIC FIELDS IN “JETS” EJECTED BY ACTIVE GALACTIC NUCLEI
The centres of Active Galactic Nuclei (AGN) generate huge amounts of energy, whose source is believed to be accretion onto a central supermassive (~109 solar masses) black hole. These objects sometimes produce oppositely directed “jet” outflows, which emit radio synchrotron radiation, produced by highly energetic electrons accelerated by magnetic fields. Synchrotron radiation is intrinsically linearly polarized, and the observed polarization can provide information about the orientation of the synchrotron magnetic field. Fine details of the jet structures can be studied using Very Long Baseline Interferometry (VLBI), a technique in which radio telescopes around the world are used together in synchrony to obtain images with extremely high angular resolution.
The Summer project will involve making VLBI images of the compact radio jets of a number of AGN with sensitive, new 6cm+13cm+18cm data, with the aim of studying the jet magnetic fields and the distribution of material in the immediate vicinity of the jets. The jets of AGN are predicted theoretically to have helical magnetic fields, produced by the combination of the rotation of the central black hole and the jet outflow; the project will focus on analyzing the jet structure in the framework of a model for these helical magnetic fields, in order to estimate fundamental parameters of the jets and their helical fields. Such studies are of considerable importance in the field, and tie in with the fundamental question of how the relativistic jets are generated and launched. The summer project will begin with a brief tutorial in the basics of AGN and radio astronomy.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8 week period during June – August 2018.
Denise C. Gabuzda – Physics Department
[email protected]; 490-2003
PROJECT 20 - ORGANIC SYNTHESIS SUMMER PLACEMENT 2018
Title: Interrupting bacteria communication systems as a strategy to avoid the evolution of bacteria resistance. Background: It has been recently discovered that bacteria use a communication system known as Quorum Sensing (bacteria talk!).
Using quorum sensing, the bacteria communicate with each other and coordinate behaviour to the benefit of their colony. For example, in the formation of protective biofilms. In this way the antibiotic resistant bacteria Pseudomonas aeruginosa, which particularly affects Cystic Fibrosis patients, communicate and cooperate to help defend against the body’s responses. You will make ‘signal molecules’ that are similar but different to that used by P. aeruginosa. In this way we will try and interrupt bacteria conversation and take a new look at controlling infection. This could avoid the acquisition of resistance by the bacteria! Additionally, you will acquire skills useful for PhD studies, or for employment within the Pharmaceutical Industry. We frequently publish our findings and this month we are on the inside front cover of Organic and Biomolecular Chemistry! Contact: Dr Gerard McGlacken Email: [email protected] Check out Prof Bonnie Bassler’s lecture on Youtube at: http://www.youtube.com/watch?v=TVfmUfr8VPA I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
PROJECT 21 - MINIMAL SURFACES 2018
The study of minimal surfaces goes back to Lagrange in the year 1762, and has since then matured into a beautiful body of knowledge linking mathematical disciplines like differential geometry, calculus of variations, potential theory, complex analysis and mathematical physics. Minimal surfaces are still a very active research area: they are used in molecular engineering and materials science, due to their stability in self-assembly of complex materials. Minimal surfaces also play a role in general relativity: The apparent horizon is a minimal hypersurface, linking the theory of black holes to minimal surfaces and the Plateau problem. In architecture there has been much interest in tensile structures, which are closely related to minimal surfaces.
The aim of this project is to study aspects of the local as well as global theory of minimal surfaces. Minimal surfaces are surfaces whose mean curvature is zero at every point. Topics to be studied include the variational characterisation, the Gauss map, isothermal coordinates and the Enneper-Weierstrass representation. Examples of minimal surfaces include the helicoid, catenoid, Enneper surfaces and Scherk towers amongst many others. One aspect of the project will be to implement the Weierstrass representation in mathematical software to generate images of minimal surfaces. Useful prerequisite for this project are good foundations in the differential geometry of curves and surfaces, and some complex analysis.
Project Supervisor:
Dr Martin Kilian School of Mathematical Sciences University College Cork Email: [email protected]
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018
PROJECT 22 - THE DESIGN AND SYNTHESIS OF DFS MIMETIC- NEW WEAPONS IN THE BATTKE AGAINST BACKTERIAL RESISTANCE
The increasing prevalance of bacterial resistance has been identified by the World Health Ogranisation as a “global threat” to humanity. As more and more strains of bacteria develop resistance to existing antibiotics, novel approaches are required to tackle this challenge. In this project, we will synthesise molecules which disrupt the bacterial communication system and halt the resistance mechanism.
Over the course of their evolution, bacteria have developed many different strategies for countering the effects of synthetic antibiotics. Some bacteria have evolved a special type of defence where they excrete a chemical messenger on treatment with an antibiotic. These chemical messengers are cis-2-unsaturated fatty acids, with the most important being Diffusible Signal Factor (DSF). We have demonstrated that the presence of DSF leads to increased biofilm formation and resistance to antibiotics, factors that prolong the infection. Effectively, DSF acts a warning signal by behaving as an ‘emergency flare’ to other bacteria, which then produce a biofilm in response. The biofilm works as a shield which protects the bacteria from the effects of the antibiotic.
In the same way as a key fits in a lock causing it to open, DSF fits into a biological receptor and “turns on” biofilm formation. This project aims to synthesise molecules which mimic DSF and fit into the same biological receptors but do not “turn on” biofilm formation. These novel molecules will act by jamming the lock closed and shut down the bacterias’ defences.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8 week period during June – September 2018.
Dr Tim O’Sullivan,
School of Chemistry
PROJECT 23 - SPECTROSCOPY OF SEMI-VOLATILE ORGANIC SPECIES
The near-ultraviolet is the highest energy solar radiation delivered to the lower atmosphere and the earth’s surface. Near-UV radiation plays a critical role in the atmosphere because it initiates most major atmospheric chemistry processes. Many semi-volatile organic compounds from biomass burning emissions are known to absorb in the near-UV. The effect of this absorption is to alter radiation levels and thereby influence other atmospheric processes that impact on atmospheric composition, air quality, and climate forcing.
The gas phase absorption spectra of semi-volatile organic compounds (SVOCs) are unusually unknown because such compounds are difficult to keep suspended in the gas phase. This project will use a new approach to record high quality reference absorption spectra of SVOCs. The experimental system will be based on a heated spectrometer cell and a unique measurement protocol that is ideally suited to low volatility compounds. The work will validate the method against the spectra of reference compounds and record the first spectra of atmospherically-important species like nitroaromatics. This work is intended to contribute towards the first publication of these spectra and of the new method.
Supervisor: Dean Venables
[email protected] 490-2439 (W)
Affiliation: Department of Chemistry & Environmental Research Institute
Centre: Centre for Research into Atmospheric Chemistry
“I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.”
PROJECT 24 - QUANTUM TECHNOLOGIES (THEORETICAL PHYSICS)
This project is set in the field of theoretical quantum physics. There is currently a significant interest in developing new technologies based on quantum-mechanical effects. Many real systems or new materials are so complex that it is impossible to simulate them on today’s “classical” computers and it can be shown that it will continue to be impossible in the future. This lack of ability to simulate complex physical systems often prevents the application of these systems or new materials to future technologies. Therefore, the goal of quantum computing is to take advantage of quantum mechanics to overcome the limitations of classical computers. A related idea is quantum simulations where quantum systems are used to simulate these critical quantum systems or new materials and so overcome the limitations of classical computers. In addition, there is the field of quantum cryptography where working devices are already commercially available. An important requirement for all these new quantum technologies is the capability of a fast and stable control of quantum systems. This project is to be carried out in the research group “Shortcuts to adiabaticity in quantum optics”; the group develops new schemes for such a fast and stable control of quantum systems. The task of this project is to get an overview of the theoretical background of the most promising quantum technologies today. The first part of the project will be to understand the required basics of quantum information and to get into the quantum-mechanical formalism required for this. In the second part, the task of the student will be to study the literature and to understand the different existing quantum technologies and especially understand the quantum-theoretical background that underpins these. I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018. Supervisor: Dr. Andreas Ruschhaupt (Department of Physics) Office 216A (Kane building)
PROJECT 25 - COLOUR-CODING BATTERY PERFORMANCE – ELECTROCHEMICAL AND PHOTONICS FOR UNDERSTNDING
ELECTROCHEMICAL ENERGY STORE
For consumer electronic devices, long-life, stable, and reasonably fast charging Li-ion batteries with good stable capacities, are a necessity. For exciting advances in electrochemical energy storage (EES) for small power cells, or wearable technology of the future, real-time analysis and an accurate picture of battery material performance and health is crucial. A need for a better understanding of new material behaviour in batteries is urgently needed. This project will contribute to the development of a ground-breaking approach to high performance, Li-ion materials that provides a colour-coded read-out of the battery behaviour in real time to determine the true nature of charge storage process for accurate performance metrics. This colour-coded ‘chameleon’ battery material will distinguish the type of process, the voltage, chemical phase changes, remaining capacity, cycle health and state-of-charge or discharge by looking at its colour. The new science is possible for any material made an order 3D porous electro-photonic architecture. This approach is designed to permit ultrafast optical read-out by probing the variation in periodicity and order that controls the diffraction of visible light, and the materials chemical and structural modification that are fundamentally linked to their composition, but also performance. OptiCharge addresses the primary challenges in EES materials in a real-time, amenable way. By marrying optical physics and materials electrochemistry, electro-photonic battery circuitry can fundamentally describe the very mechanism of energy storage or conversion for a range of technologies, and how advanced EES nanomaterials really behave. OPTICHARGE is also generally applicable as a new materials diagnostic toolset for in-situ and operando profiling for emerging battery chemistries.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Contact: Prof. Colm O’Dwyer, School of Chemistry, email: [email protected], web: www.appliednano.ie
PROJECT 26 - COMPUTATION OF CRITICAL VALUE POLYNOMIAL AND THEIR GALOIS GROUPS
This project will be based around the topic of algebraic optimisation, which is an area of abstract mathematics that holds many interesting applications in several other fields, such as financial mathematics, systems and control theory, engineering and computer science.
In many instances of optimisation problems, one is dealing with a rational goal function (a quotient of two polynomials) in one or more variables in which case the critical value polynomial (CVP) is a well-defined univariate polynomial which is associated with the goal function, and which has the property that the zeros of the CVP are the critical values of the goal function.
If the rational goal function is limited to quotients of polynomials with rational coefficients, then the CVP will also have rational coefficients and this allows much information to be extracted from the Galois group of the CVP, which would tell us of the algebraic complexity of the optimisation problem.
The main goal of this project will be to apply the machinery described above, to a number of algebraic optimisation problems, and using the Galois group of the CVP, try to determine whether or not an algebraic simplification of the problem is possible. This will involve advanced computer algebraic calculations using appropriate software such as MATHEMATICA.
An application we would like to explore would be model order reduction problems for linear systems, which can allow for significant reduction in computing time for numerical models.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018
Professor Bernard Hanzon
Department of Mathematics, UCC
Room WGB G40
E-mail [email protected]
Tel nr 4205839/5819(secr)
PROJECT 27 – DETERMINATION OF TRACE TOXIC IONIC SPECIES IN DRINKING WATER USING ION CHROMATOGRAPHY-MASS SPECTOMETRY
The proposed project will be in the area of analytical and environmental chemistry under the supervision of Dr. Elizabeth Gilchrist in the School of Chemistry.
The SEFS bursary student will be working on the development and improvement of the detection and identification of new and emerging contaminants within the Irish environment. Currently on the priority list, released by the Irish Environmental Protection Agency (EPA), are contaminants such as pesticides and pharmaceuticals, with ‘safe water’ an important research theme at the moment. These new and emerging contaminants can potentially occur down to trace concentrations within water (drinking, standing, river, waste, etc.) and can be detrimental to the environment and biological systems, including food sources and humans.
The student will have the opportunity to work on new analytical technology, a high pressure ion chromatography (HPIC) system coupled to mass spectrometry (MS) to identify and sensitively determine trace concentrations of potentially harmful contaminants. Analytes present in water samples include common anions, oxyhalides and haloacetic acids (HAAs). HAAs and oxyhalides are possible by products of water disinfection and include bromate (BrO3
-), a potential carcinogen, and perchlorate (ClO4-), which inhibits the uptake of iodide in the thyroid, highlighting the
need for sensitive and selective monitoring techniques.
For more information please contact Dr. Elizabeth Gilchrist [email protected]
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June - September 2018.
PROJECT 28 - ELLIPTICINES: TARGETING CANCER BY A STRUCTURED APPROACH
Ellipticine (Fig. 1) is a natural plant alkaloid, isolated from berries of the Ochrosia Elliptica tree.1 The ellipticine family of compounds (including isoellipticine and olivacine) possess potent anticancer activity and have clinical pedigree in the treatment of breast and colon cancer. Like many clinical anticancer agents, ellipticines are thought to have multi-modal mechanisms of action – DNA intercalation, topoisomerase II inhibition and adduct formation via bio-oxidation amongst other potential mechanisms. The multimodal activity of ellipticines is inherently related to its relatively simple planar structure and consequent ability to bind to multiple targets. It is possible however to modify the behaviour of this family of compounds by substitution.1,2
To date, tailored functionalization of the pharmacophore has led to reports of specific effects on CNS cell selectivity, specific cell cycle effects, biooxidation to form adducts, AKT and c-Kit kinase inhibition.1,3,4 A program of research within this laboratory to generate diverse ellipticines has produced remarkable success in the treatment of acute myeloid leukaemia amongst other cancer types and this is currently in development.4,5,6,7 It can clearly be seen that ellipticines have diverse medicinal functions related to cell viability and cytotoxicity.
This project sets out to design and synthesise novel substituents and heterocycles on the tetracyclic ellipticine template to increase biological potency, solubility and specificity. We aim to produce and evaluate structurally diverse novel and specific ellipticine agents using the innovative chemistry we have developed. We will evaluate the novel compounds generated by this project for anticancer activity by biochemical and cellular means.
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018
Figure 1 Synthesis of ellipticine derivatives from indole and a 7-substituted isoellipticine yielding G2-M cell cycle block
References 1. E.C. O’ Sullivan et al. (2013) Stud. Nat. Prod. Chem. 39 (6), 189-232. 2. C.M. Miller et al. (2012) RSC Adv., 2 (24), 8883-8918. 3. D. Thompson et al. (2008) Biochemistry, 47, 10333-10344. 4. F.M. Deane et al. (2013) Org. Biomol. Chem., 11 (8), 1334-1344. 5. C.M. Miller et al. (2012) Org. Biomol. Chem, 10 (39), 7912-7921 6. E.G. Russell et al. (2014) Invest. New Drugs 32(6), 1113-1122. 7. E.G. Russell et al. (2016) Invest. New Drugs 34(1):15-23.
Signed: School of Chemistry, University College Cork. [email protected]; 021 4901695
PROJECT 29 – COMPUTATIONAL STUDY OF THE ADOL-TISHCHENKO REACTION CATALYSED BY METAL-ORGANIC FRAMEWORKS
In our group we use computational chemistry for understanding chemical interactions,[1] rationalise compounds properties that would have not been explainable otherwise,[2] and design new materials with targeted properties leading their synthesis.[3] Particularly, we are interested in the forefront and challenging chemistry of metal-organic frameworks (MOFs): hybrid crystalline materials made by combining inorganic cluster and organic molecules.
Due to their porosity, as well as to the possibility of engineering the pore shape, MOFs have been widely used for gas-adsorption and separation. [CITE] However, another big advantage of MOFs is that their internal surface can be designed and functionalised as desired; that is why MOFs has been recently proposed as a powerful alternative to traditional catalyst. [4] In fact, MOFs are ideally tunable, and, by selecting the correct combination of inorganic cluster and organic ligand, we can create our catalytic active centre ad-hoc: i.e. we can think to crystal engineering our material to promote a specific chemical reaction.
For instance, we have recently demonstrated how, by using MOFs, the products of the reaction between n-alkyl aldehydes and methylvinylketone can be modified promoting an electrophilic reaction (i.e. Aldol-Tishchenko) instead of the classical nucleophilic attack (i.e. Morita-Baylis-Hillman reaction) that would be observed in the presence of the standard catalyst (i.e. triphenylphosphine). [5]
Nevertheless, the reaction mechanism of this new reaction has still to be clarified. Using state-of-the-art computational chemistry this project will further investigate the Aldol-Tishchenko reaction profile.
[1] D. Tiana and co-workers Chemical Science 2013, 4, 4278-4284.
[2] D. Tiana and co-workers Nature Comm. 2017, 8, 13945.
[3] D. Tiana and co-workers J. Am. Chem. Soc. 2013, 135, 10942-10945.
[4] L. Xamena and co-workers ACS Catalysis, 2014, 4, 361-378.
[5] D. Tiana and co-workers J. Am. Chem. Soc., 2017, 139, 18166–18169.
“I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.”
Davide Tiana, School of Chemistry. Email: [email protected]
PROJECT 30 – DIODE LASER-BASED LIDAR FOR AUTONOMOUS
There is currently great interest in autonomous (driverless) and driver-assistive vehicles. A key element of driving autonomously is the ability to scan and identify path markers and hazards. This is most effectively done by LIDAR, the optical equivalent of radar, which is difficult, delicate and expensive to incorporate into road vehicles. Current LIDARs use separate lasers and detectors with mechanical scanners, and cost more than the vehicles themselves. We will investigate miniature, integrable semiconductor laser diodes as sensitive, compact, rugged, inexpensive LIDAR modules.
The project exploits the extreme sensitivity of laser diodes to minute reflections. This is due to the microscopic physics of the laser material and the amplifying laser cavity. Normally it is an expensive nuisance, requiring delicate, bulky and expensive magneto-optical isolators to maintain stability and minimise noise in most applications, notably fibre optics. We intend to turn this behaviour to our advantage. A variety of laser diodes will be subjected to reflections to establish sensitivity, signal-to-noise ratio, and ability to resolve velocity (Doppler shift) information. The observed behaviour will be modelled using basic physics, and extrapolated to meet requirements of real LIDAR systems. If time permits, system integration and non-mechanical scanning possibilities will be explored.
LOGISTICS
Project requires 6-8 weeks’ laboratory work, including safety training and orientation. Prior knowledge of optics, electromagnetics, lasers and solid state electronics will be an advantage. Students should have good experimental and theoretical skills, including manual dexterity, coordination and visual acuity for laser alignment and pattern analysis.
AVAILABILITY
I confirm that all facilities required for the proposed research project are available and that I am available to personally supervise the project during an 8-week period during June – September 2018.
Dr Pierpaolo Porta, Prof John McInerney
