UNDERGRADUATE SEFS SUMMER RESEARCH BURSARIES 2017

GROUP 1 - ENGINEERING AND COMPUTER SCIENCE

Contact Name Department/School Title

Dr. Guangbo Hao Mechanical Engineering Revisiting and reassessing the kinematic rationality of fitness/exercise equipment

Ms. Orla McKeever Architecture Clarify and illuminate the collective memory of humanity

Prof. Liam Marnane Electrical and Electronic Engineering Algorithim Selection for QRS Complex Detection in Foetal and Neonatal ECG Signals

GROUP 2 – FOOD SCIENCE & NUTRITIONAL SCIENCES; LIFE SCIENCES AND BIOLOGICAL, EARTH &

ENVIRONMENTAL SCIENCE

Contact Name Department/School Title

Dr. Olivia O'Leary Anatomy and Neuroscience Vitamin D as a nutritional strategy for the adolescent brain to counteract stress-induced risk of depression

Dr. Yvonne Nolan Anatomy and Neuroscience The combined impact of brain inflammation and a high fat/high sugar "cafeteria" diet on neuronal plasticity

Dr. Barbara Doyle Prestwich BEES The role of microbial inoculants on the health status of golf greens

Dr. Eoin Lettice BEES Alternative feedstocks for biochar production and effect on crop performance and biodiversity

Dr. Javier Del Barco-Trillo BEES Study of behaviour in urban tardigrades: a novel approach

Dr. Pat Meere BEES Characterising the nature of the Aradian Orogeny in South West Ireland

Prof. Astrid Wingler BEES Establishing Brachypodium sylvaticum as a genetic model for grassland research

Prof. Gavin Burnell BEES Collating Environmental effects on Longline Production of Seaweed (CELPS)

Prof. John Quinn BEES Feeding ecology of an endangered iconic deabird, the Atlantic Puffin

Dr. Kellie Dean Biochemistry and Cell Biology Biochemical characterization of long, non-coding RNAs in colorectal cancer

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. Paul Young Biochemistry and Cell Biology UCC iGEM 2017

Dr. Seamus O'Mahony Food and Nutritional Sciences The effect of calcium phosphate crystal growth on the rheological properties of acid whey concentrate

Dr. Shane Crowley Food and Nutritional Sciences In situ tracking of CO2 bubble dynamics in fermenting Kefir – ‘the Champagne of dairy’

Dr. Martina Scallan Microbiology What role does the cellular protein HABP1 play in alphavirus replication?

Dr. David Clarke Microbiology Bile resistance in Bacteroides

GROUP 3 – MATHEMATICAL SCIENCES; CHEMISTRY AND PHYSICS

Name Department/School Title

Dr. Dean Venables Chemistry Development of spectroscopic instrumentation for a new atmospheric simulation chamber facility

Dr. Florence McCarthy Chemistry Ellipticines: Targetting cancer by a structured approach

Dr. Gerard McGlacken Chemistry Interrupting bacteria talk and switching on antibacterial agents using light

Dr. Tim O'Sullivan Chemistry Molecular modelling, design and synthesis of novel drugs for Chagas disease

Prof John Wenger Chemistry Measurements of Atmospheric Particulate Matter

Dr. Andreas Ruschhaupt Physics Quantum Technologies (Theoretical Physics)

Prof. Denise Gabuzda Physics Helical Magnetic Fields in "Jets" ejected by Active Galactic Nuclei

Prof. Frank Peters Physics Semiconductor Diode Lasers

Prof. Paul Callanan Physics I-LOFAR Exploring the Radio Universe from Ireland

GROUP 1 – ENGINEERING & COMPUTER SCIENCE

PROJECT 1 - REVISITING AND REASSESSING THE KINEMATIC RATIONALITY OF FITNESS/EXERCISE

EQUIPMENT

There are exercise & fitness equipment in outdoor parks and playgrounds where people of almost any ability can challenge their physical fitness and work

toward improving their health from head to toe. However, the rationality of such fitness equipment for different people’s health improvement deserves

revisiting and assessing based on rigorous theoretical calculation and analysis.

(Picture from website)

This project aims to investigate a class of public fitness equipment with mobile parts that are robotic mechanisms such as four-bar linkages (as shown in the

above image). Students are expected to first analyse these mechanisms using mathematics and mechanics plus computational programming, and then to

optimize path generation of the design with consideration of real human body movements (such as gait).

This project is suitable for students with background in Engineering, Mathematics, and Computer Sciences.

Contact Details:

Dr. Guangbo Hao Lecturer In Mechanical Engineering of UCC; Academic Associate of Tyndall National Institute Electrical & Electronic Engineering Electrical Building 1.06 School of Engineering T: +353(0)21 490 3793 F: +353(0)21 427 1698 E: G.Hao@ucc.ie W: https://sites.google.com/site/doctorghao/

PROJECT 2 - CLARIFY AND ILLUMINATE THE COLLECTIVE MEMORY OF HUMANITY

The project aims to reveal the diversity of the setting of the quays of Cork City that they may continue to speak clearly of the progressive human intervention in the development of the City. This proposal will record the antique items of the quays of Cork City and provide design solutions relating to the restoration and repair of the quayside landscape in consideration of proposals to reveal the antique character of the quaysides under pressure of alterations relating to flood relief. Consideration would be given to adaptation of the existing historic elements relating to health and safety, precedent and ingenious, multi-disciplinary design solutions brought about by consideration of increasing water levels and design adaptation. The study is informed by the adaptation of an historic setting for increased public amenity and environmental enhancement. Conclusions will be drawn based on the application of ICOMOS charters on the form and material quality of interventions within an historic environment. It is intended to maintain the specific and authentic nature of the city quaysides and to draw proposals that may then be presented in a publication of design solutions to be publicised through an open event. The development of proposals would be justified through specific analysis of historic items and the drawing and presentation of artefacts and design solutions relating to the different waterside conditions in the City. Solutions would favour the maintenance of artefacts in their original location, restoration only where it may be achieved academically in relation to ICOMOS charters, and consolidation of existing fabric and addition of new works that do not detract from setting, use or future adaptation. The presentation of findings will be the subject of highly considered intervention within the historic setting.

Contact Details:

Ms. Orla McKeever Lecturer in Architecture, Year Four Coordinator, Cork Centre for Architectural Education, 9-10 Copley Street, Cork E: o.mckeever@ucc.ie M: 083 343 6451

PROJECT 3 - ALGORITHM SELECTION FOR QRS COMPLEX DETECTION IN FOETAL AND NEONATAL ECG SIGNALS

The Electrocardiogram (ECG) signal is a measure of the electrical activity of the heart. Monitoring the ECG during labour and delivery gives vital insight into

the state of the baby’s health. Recent research has shown that the variability in the heart rate is a clinically useful indicator of overall health. Such information

is obtained from the raw ECG signal by the use of digital signal processing algorithms, which can be used to detect the QRS complex (the characteristic peak

in the ECG signal that occurs once per heart beat), from which the heart rate and heart rate variability can be derived.

While many QRS detection algorithms exist, particularly for adult ECG, the nature of labour and delivery is such that data collected during this time tends to

be noisy and prone to artefact, including the much stronger ECG signal from the mother. Under the BABYSAFE project conducted at the INFANT centre in UCC,

algorithms are being developed to preprocess this noisy data, removing as much of this noise and artefact as possible. The detection of QRS complexes in this

preprocessed signal is a core component of BABYSAFE.

The proposed project will involve investigating a number of different QRS detection algorithms, implementing them in Matlab or Python and tuning their

parameters for foetal/neonatal ECG. Publicly available online datasets of annotated foetal and neonatal ECG will be used for the parameter tuning. The

successful applicant will be part of the BABYSAFE team within the INFANT centre.

Contact Details:

Prof. Liam Marnane, Electrical & Electronic Engineering T: +353 21 490 2041 E: marnane@ucc.ie

GROUP 2 – FOOD SCIENCE & NUTRITIONAL SCIENCES; LIFE SCIENCES AND BIOLOGICAL, EARTH &

ENVIRONMENTAL SCIENCE

PROJECT 4 - VITAMIN D AS A NUTRITIONAL STRATEGY FOR THE ADOLESCENT BRAIN TO COUNTERACT

STRESS-INDUCED RISK OF DEPRESSION

Depression is the current leading cause of disability worldwide. It is often co-morbid with anxiety disorders which together with depression, cost the global

economy US$1 trillion annually. The burden of these disorders is attributed to high prevalence rates (15-20%) and the lack of effective treatments. Indeed,

60-70% of depressed individuals do not achieve remission with current antidepressants. The cause of depression remains unknown, but stress during early

adolescence (when the brain is still developing) is a major risk factor. There are also abnormalities in the hypothalamic–pituitary–adrenal (HPA) axis which

result in excessive release of the stress hormone cortisol. Animal studies show that excessive exposure to this stress hormone damages cells in areas of the

brain that are affected in depression. Since effective treatments for depression are lacking, it is imperative that we implement preventative approaches during

adolescence to avert this stress-related disorder later in adult life. Modifiable lifestyle factors like dietary interventions represent safe, cost-effective and

easily implementable preventative approaches to ensure optimal brain development during adolescence and thus mental health throughout life. Cross-

sectional epidemiological studies suggest that there is an increased risk of depression in adults who are Vitamin D-deficient and that Vitamin D

supplementation may be of benefit to those individuals. However, there is paucity of studies directly investigating the effect of Vitamin D on depression and

the brains response to stress. This aim of this project is to determine whether Vitamin D can protect adolescent brain cells from the detrimental effects of

cortisol, and thus may represent a dietary intervention that could be applied during adolescence in an effort to reduce the risk for developing depression

later in adulthood

Contact details:

Dr. Olivia O’Leary Senior Lecturer, Department of Anatomy and Neuroscience, 4.114 Western Gateway Building, E-mail: o.oleary@ucc.ie Tel: +353 21 420 5480

PROJECT 5: THE COMBINED IMPACT OF BRAIN INFLAMMATION AND A HIGH FAT/HIGH SUGAR “CAFETERIA”

DIET ON NEURONAL PLASTICITY.

Lon-term over-consumption of palatable high fat/high sugar “cafeteria” diets have been shown to induce obesity, cardiovascular and metabolic disorders as

well as cognitive deficits. Cognitive decline is associated with aging and with neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease

which are also strongly associated with brain inflammation. Inflammation in the hippocampus is well-documented as contributing to the neuronal demise

and cognitive impairments observed in these conditions. The hippocampus is a brain region responsible for learning and memory, as well as mood regulation

and is particularly susceptible to the detrimental impacts of inflammation. It is also a particularly “plastic” region of the brain and is capable to producing new

neurons (neurogenesis). Neuronal plasticity is thus negatively affected with age and by inflammation.

Adolescence is a critical period for the maturation and plasticity of neurons in the hippocampus. It is also a period of the lifespan during which programming

of adult behaviours such as dietary habits occurs. Indeed, lifestyle factors such as dietary habits may have a long-lasting impact on cognitive function through

the lifespan. This, combined with the increased brain inflammation that occurs with aging may be a recipe for an increased risk of developing debilitating

cognitive impairment.

The aim of the proposed study is to assess the impact of a cafeteria diet during adolescence combined with a chronic lentivirus-mediated increase in pro-

inflammatory cytokine interleukin-1β in the hippocampus in adulthood, on hippocampal neuronal plasticity.

The project will be carried out on tissue generated from a currently ongoing in vivo study. Methods employed will be cryostat sectioning of brain tissue,

immunohistochemical staining of hippocampal sections for markers of plasticity, fluorescent/confocal microscopy and cell quantification using appropriate

software.

Contact Details:

Dr. Yvonne Nolan Anatomy & Neuroscience

Room 4.117

Western Gate Building

T: 00 353 21 420 5476

E: y.nolan@ucc.ie

PROJECT 6: THE ROLE OF MICROBIAL INOCULANTS ON THE HEALTH STATUS OF GOLF GREENS.

This project involves an investigation into the role of microbial inoculants on the health status of golf greens. Working together with Muskerry Golf Club and

the company Crop Care (www.cropcare.ie ) we have submitted an application to Enterprise Ireland for an Innovation Voucher to cover the cost of the

consumable work. We cannot use this money for employing a student but we can fund the cost of the research. Only if the innovation voucher application

is successful and if the SEFS bursary application is successful, will this project run. (Enterprise Ireland state that decisions should be made by end of Feb 2017

for the current call).

With the current emphasis on reducing chemical inputs in agriculture and into the environment generally, a sustainable approach is being investigated (and

used) in various industries (both agricultural and leisure) (Velivelli at al. 2014; Velivelli et al. 2015)

In our lab at the moment we are working to isolate soil microbes that can be used in a number of agricultural settings. To date we have successfully isolated

and characterised isolates that aid in plant growth promotion and in disease resistance. We have characterised the isolates under a number of headings

including the types of volatile organic compounds that they emit. The use of these ‘helper’ bacteria are also being employed in a biotech setting for the

generation of genetically altered plants (using ‘traditional’ transgenesis and also the newest CRISPR CAS system). Their use in biofortification is also currently

being investigated in our lab by an MRes student. The successful student for this bursary will be involved in microbial isolations from soil, in vitro

characterisation under a number of headings, liasing with the head green keeper in Muskerry with respect to their deployment under a control setting,

understanding the current situation in relation to the health status of golf greens and will have an opportunity to liaise with Industry i.e. Crop Care in Wicklow.

The student will work alongside a PhD student whose work overlaps with this proposed project and also with two MRes students (one working towards

CRISPR CAS the other on biofortification). The project will be a mixture of lab work and outdoor ‘field work’ with respect to Muskerry Golf Club. I will work

with the student in terms of project planning and supervision and the student will work alongside the postgraduate students in the lab. The student will

undergo a safety induction prior to any work commencing. It is hoped that if the results of the project are interesting, then CROP CARE will work with me

towards applying for a larger ‘proof of concept/commericalisation application’ to Enterprise Ireland.

Contact Details:

Dr. Barbara Doyle Prestwich Lecturer and Principal Investigator School of Biological, Earth and Environmental Sciences Butler Building, Distillery Field, North Mall T: +353 21 490 4559 F: + 353 21 4904664 E: b.doyle@ucc.ie W: http://valoram.ucc.ie;

PROJECT 7: ALTERNATIVE FEEDSTOCKS FOR BIOCHAR PRODUCTION AND EFFECT ON CROP PERFORMANCE

AND SOIL BIODIVERSITY

Biochar is a form of charcoal produced from waste organic material via pyrolysis. It has been demonstrated that biochar has the potential to improve crop

production, sequester carbon and increase soil microbial biodiversity (e.g. Kolton et al., 2016). There is historic evidence for the use of biochar in traditional

agriculture e.g. the terra preta (black soil) of the Amazon basin is due to the incorporation of charcoal by humans between 500 and 2,500 YBP.

Recent research in this laboratory has focussed on the use of biochar as a soil amendment for use in sustainable and organic horticulture. Significant

improvements in crop yields have been recorded in pot-trials and field-scale experiments.

This project is designed to investigate whether the feedstock used for the production of biochar influences its effect on crop yield and soil bacterial biodiversity.

This project will involve:

Sourcing and harvesting (where necessary) appropriate biochar feedstock.

Preparation of feedstock for biochar production.

Production of biochar using pyrolysis.

Design and development of experiments to (a) determine effect of biochar type on the growth of a model crop and (b) measure the effect of biochar

type on soil fertility.

Collection, analysis and reporting of experimental data.

This project is only suitable for a student with very strong and demonstrable practical experience in horticulture and an interest in sustainable crop production.

Reference:

Kolton et al., 2016. Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere. New Phytologist

213: 1393-1404.

Contact Details:

Dr. Eoin Lettice Lecturer - Plant Science School of Biological, Earth and Environmental Sciences Butler Building, Distillery Field, North Mall

T: +353-21-490-4562 E: e.lettice@ucc.ie W: http://www.lettice.eu/

PROJECT 8: STUDY OF BEHAVIOUR IN URBAN TARDIGRADES: A NOVEL APPROACH

Tardigrades, or water bears, are microscopic invertebrates, which live worldwide and across all ecosystems, including urban environments. Terrestrial

tardigrades can be found in almost any sample of moss or lichen, and are thus abundant and easy to collect. Tardigrades are known for surviving under

extreme conditions, including extremely low and high temperatures, lack of oxygen, lack of water, exposure to radiation that would kill most other animals,

extreme high pressure, and exposure to high concentration of pollutants. Despite their extreme capabilities and their bizarre biology, tardigrades are a very

understudied group. We know especially little about their behaviour, even though tardigrades are very mobile. Due to their resistance to pollutants,

tardigrades are likely to thrive in urban environments (although almost nothing is known about urban tardigrades). In urban vertebrates and large-sized

invertebrates (e.g. insects) there are many examples of behavioural adaptations to the urban environment. In contrast, we know absolutely nothing about

the behavioural responses of urban microorganisms like tardigrades. We can predict that changes driven by urbanisation, such as an increase in light pollution

and high population densities, will lead to changes in behaviour. This project will investigate, for the first time, behavioural responses to light pollution and

social environment in tardigrades. Very small, purposely-built Y-mazes, T-mazes and open field arenas will be used to measure different behaviours. The

student will be able investigate, for instance, the preference for dark or lighted areas in tardigrades collected in light-polluted or light-unpolluted urban sites;

and the preference or avoidance of areas containing other tardigrades. This project will allow the student to collect a large dataset, address several research

questions, learn several laboratory techniques, investigate a novel area of research, and have the opportunity to co-author a scientific publication.

Contact details:

Dr. Javier delBarco-Trillo School of Biological, Earth and Environmental Sciences T: +353 (0)21 490 4663 E: javier.delbarcotrillo@ucc.ie

PROJECT 9: CHARACTERISING THE NATURE OF THE ACADIAN OROGENY IN SOUTH WEST IRELAND

The Acadian Orogeny was a relatively short lived mountain building event that deformed the Upper Palaeozoic sedimentary rock sequence of southern Ireland. The timing, nature and extent of this event in Ireland is poorly constrained. This is in some degree due to the up to recently held assumption that the Acadian was a late stage of the Caledonian Orogeny and not a particularly distinct event in itself. The only region in Ireland to study Acadian deformation is on the Dingle Peninsula where the unconformity associated with the associated crustal compression uplift and erosion is very well exposed in the Mount Brandon area at the north western side of the peninsula. This proposed research/mapping project will require the student to adopt a multidisciplinary field and laboratory based approach to elucidate the exact nature of Acadian deformation in southern Ireland. This will involve;

1 Detailed geological mapping of the units above and below the Acadian unconformity on in the Mount Brandon area of the Dingle Peninsula.

2 Detailed structural analysis of the mesoscopic strain regime above and below the unconformity.

3. Detailed petrological and microstructural studies of tectonic fabric development above and below the unconformity.

4. Detailed strain analysis of sandstones above and below the unconformity. This involves the use of newly developed strain analysis analysis techniques and associated software by Dr. Kieran Mulchrone in the School of Mathematics, UCC.

The outputs from this research have the potential to significantly improve our understanding of the Upper Palaeozoic tectono-stratigraphic evolution of southern Ireland and enhance the research skills portfolio of the participating student. Contact details: Dr. Patrick Meere Lecturer School of Biological, Earth & Environmental Sciences T: +353-21-490-3000 F: +353 21 490 3000 E: p.meere@ucc.ie

PROJECT 10: ESTABLISHING BRACHYPODIUM SYLVATICUM AS A GENETIC MODEL FOR GRASSLAND RESEARCH The perennial grass Brachypodium sylvaticum is an excellent model species for temperate perennial grasses, such as forage and bioenergy grasses. It has a small diploid genome, is self-fertile and amenable to genetic engineering. By creating transgenic plants, the role of specific genes in growth, development and response to environmental conditions can be tested. In addition, B. sylvaticum grows naturally over a wide geographic range which makes it an ideal model to study adaptations to climate. In temperate zones, grassland productivity is limited by a combination of low temperature in spring and developmental factors later in the season (Wingler and Hennessy, 2016, Frontiers in Plant Science 7:1130). While extensive physiological analyses have been conducted to determine the growth response of forage grasses, their complex genetics makes it difficult to test hypotheses at the molecular/genetic level, and a good perennial grass model is therefore required. The aims of the project are to:

1. Establish B. sylvaticum as a model for genetic transformation. Embryonic callus will be generated with the aim of setting up a transformation platform using Agrobacterium tumefaciens for creating transgenic plants.

2. Exploit natural genetic variation to determine the response of B. sylvaticum to low temperature. Genotypes from different geographic locations will be grown and their response to low temperature will be analysed to identify traits associated with good performance at low temperature.

Training will be provided in the following techniques: plant cultivation, tissue culture, Agrobacterium-dependent transformation and plant physiological analysis (including chlorophyll fluorescence analysis). Contact details: Professor Astrid Wingler, School of Biological, Earth and Environmental Sciences T: 021 4904660 E: astrid.wingler@ucc.ie

PROJECT 11: COLLATING ENVIRONMENTAL EFFECTS ON LONGLINE PRODUCTION OF SEAWEED (CELPS)

Marine macroalgal (kelp/seaweed) production is a new industry for Ireland and is particularly suitable for coastal regions like West Cork. Marine algae are

primary producers and rely on dissolved organic nutrients (e.g. phosphate and nitrate), light and heat for their growth. In order to optimise production the

best site must be selected with respect to these hydrobiological growth parameters.

At the Daithi O’Murchu Marine Research Station on the Sheep’s Head Peninsula, near Bantry, they are cultivating the kelp species Alaria esculenta in

suspended culture on longlines. We will be collaborating with them to investigate the way in which the position of the longlines and the depth of cultivation

contribute to variability in seaweed growth rates.

The aim of the project is to measure differences in growth rate of the algae with depth, site and current flow as the main variables. Salinity, pH, nutrient levels

and temperature will also be recorded. Once the crop has been harvested its shelf life will be tested under various storage regimes such as freeze drying,

bleaching and air drying.

Training will be provided in laboratory and field analysis of water samples, but the successful candidate must be able to drive and have own transport in

order to collect the samples once every 2 weeks.

Contact details:

Prof. Gavin Burnell School of Biological, Earth and Environmental Sciences T: + 353 21 490 4590 E :g.burnell@ucc.ie

PROJECT 12: FEEDING ECOLOGY OF AN ENDANGERED ICONIC SEABIRD, THE ATLANTIC PUFFIN

Under Ireland’s commitment to Articles 10 and 12 of the Birds Directive, Ireland has an international obligation to protect its seabird populations and yet

does not have reliable population monitoring efforts for most species. The last national census effort ran from 1998-2002 under the JNCC led Seabird 2000

initiative (Mitchell et al., 2004). Seabird monitoring is dependent on the life history traits of the species; thus, multiple techniques are utilized to understand

their population dynamics ranging from census methods to their foraging behaviours.

The seabird research group in the School of BEES is leading both the formation of national census plans for burrow-nesting seabirds, as well as in depth

analysis of telemetry data to understand what drives their distribution at sea. The study will focus on the Atlantic Puffin (Fratercula arctica) that has been

recently described “Endangered” and added to the IUCN’s red list. This project will allow one of the 3rd year undergraduates to link the ongoing work of the

research group, looking at chick provisioning rates to shed light on colony attendance of these birds, informing both monitoring and telemetry studies.

Working on several offshore islands, the student will carry out work to improve our understanding of the type and quality of the bird’s prey species, as this is

known to relate directly to the population’s health.

The proposal expects students to carry out the following:

Demonstrate an understanding of experimental design by aiding in the development of a suitable baseline monitoring scheme at several study sites.

Carry out extended periods of fieldwork in remote conditions, requires excellent team working skills.

Image analysis to determine prey characteristics.

Contact details:

Prof. John Quinn School of BEES, Room 1.25 Distillery Fields, Enterprise Centre T: +353 85 2266122 E: j.quinn@ucc.ie

PROJECT 13: BIOCHEMICAL CHARACTERIZATION OF LONG, NON-CODING RNAS 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 (Yang et al. 2016). While lncRNAs are still being discovered, there is a lack of information regarding molecular interaction partners of existing

lncRNAs, namely what RNA-binding proteins bind to and influence an lncRNA’s structure and function?

To begin to address this question, we are developing the use of a tethered RNA system that will be used as a tool to identify proteins that bind to selected

lncRNAs (Dean, unpublished). Use of this system has been successful with defined RNA-protein interactions (Iioka & Macara 2015; Iioka et al. 2011) , but we

are expanding its utility to identify protein interactors of poorly-characterised lncRNAs expressed in colorectal cancer. In the summer project, the student

will be constructing a tethered lncRNA target of SNHG5 – a cytoplasmic lncRNA that is expressed at high levels in colorectal cancer (Damas et al. 2016).

Tethered SNHG5 lncRNA will be synthesised in vitro and used to create an affinity matrix. Using the SNHG5 affinity matrix, lncRNA-binding proteins will be

isolated from colorectal cancer cell line lysates. Interacting proteins will then be identified by immunoblotting and/or mass spectrometry. By determining

the constituents of lncRNA-protein complexes, we aim to understand how the complexes influence cellular processes that contribute to colorectal cancer.

This research has the possibility of uncovering novel lncRNA-protein networks, contributing to an exciting area of RNA and cancer biology.

References:

Damas, N.D. et al., 2016. SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization. Nature Communications, 7, p.13875. Iioka, H. et al., 2011. Efficient detection of RNA-protein interactions using tethered RNAs. Nucleic Acids Research, 39(8), p.e53. Iioka, H. & Macara, I.G., 2015. Detection of RNA-Protein Interactions Using Tethered RNA Affinity Capture. Methods in Molecular Biology (Clifton, N.J.), 1316, pp.67–73. Yang, Y. et al., 2016. LncRNAs: the bridge linking RNA and colorectal cancer. Oncotarget. Nov 24. doi: 10.18632/oncotarget.

Contact details:

Dr. Kellie Dean College Lecturer and Postgraduate Coordinator School of Biochemistry and Cell Biology, 3.91 Western Gateway Building T: +353 21 420 5421 E: k.dean@ucc.ie

PROJECT 14: INVESTIGATION INTO THE ABILITY OF TH1 INFLAMMATORY AND ANTI-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-g and TNF-a are effectors

of anti-tumour immunity yet their effect on RTK signalling is unclear. We have shown that IFN-g/TNF-a synergise to induce a co-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-g/TNF-a

mediate RTK shutdown by integrating multiple upstream signalling 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 anti-tumour 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-g/TNF-a-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.

Contact Details:

Dr. Ken Nally Lecturer in Biochemistry & Principal Investigator School of Biochemistry & Cell Biology Host Response and Inflammation Group

Alimentary Pharmabiotic Centre Rms. 2.10/4.41, Bioscience Institute T: 353-21-4901302 E: k.nally@ucc.ie Web: http://apc.ucc.ie and http://microbemagic.ucc.ie (for children)

PROJECT 15: UCC iGEM 2017 Project Description: 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 UCC teams have achieved remarkable success in this competition for the past three years. See links below. Are you up for the challenge of being part of the Cork iGEM 2017 team ? The project is student-driven. 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 2017 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 Contact details: Dr. Paul Young Biochemistry & Cell Biology Western Gateway Building Rm. 3.39 / 3.42 T: +353 (0)21 420 5994 E: p.young@ucc.ie

PROJECT 16: THE EFFECT OF CALCIUM PHOSPHATE CRYSTAL GROWTH ON THE RHEOLOGICAL PROPERTIES

OF ACID WHEY CONCENTRATE

In excess of 1.6 billion L of acid whey is produced every year by dairy processors. Acid whey is a waste stream generated during the manufacture of products

such as acid casein and strained yoghurts. The issue of acid whey utilisation has become increasingly pressing with the surge in popularity of Greek-style

yoghurt in recent years. However, it is difficult to add value to acid whey as its high level of minerals, lactic acid and, in some cases, galactose make it extremely

difficult to spray-dry into shelf-stable powders (Chandrapala et al., 2015). There is a need to control the physicochemistry of this dynamic multi-component

system to facilitate the conversion of acid whey from problematic waste stream into value-added whey, lactose and mineral ingredients. Our group is involved

in an active project (led by Kamil Drapala) on acid whey valorisation in collaboration with several industry partners through the Dairy Processing Technology

Centre (DPTC). At commercial scale, acid whey is typically alkalised, concentrated by vacuum evaporation and cooled under agitation in specialised lactose

crystallisation tanks before spray drying. This process creates a multi-phase system of mineral precipitates, lactose crystals and nanoscale proteins with a high

degree of inter-reactivity. Preliminary work from our group has identified that this complex milieu can result in gel network formation, leading to processing

challenges (Fig. 1). In addition, the combined effect of alkalisation and concentration induces super-saturation of Ca3(PO4)2 that drives its precipitation, with

insoluble Ca3(PO4)2 microcrystals subsequently identified at the surface of spray-dried powder particles (Fig. 2). The proposed work aims to develop a

mechanistic understanding of destabilisation phenomena in acid whey concentrates, with a specific focus on the following tasks:

Measurement of the effect of ultrafiltration-assisted deproteinisation on acid whey gelation using rheometry and phase-separation by analytical

centrifugation

Monitoring of lactose crystallisation and Ca3(PO4)2 precipitation at <15°C through light-scattering and pH-drift analysis, respectively

Microstructural analysis of powders using Scanning Electron Microscopy (SEM) and surface composition profiling by Time of Flight-Secondary Ion

Mass Spectrometry (TOF-SIM)

Trialling of in line high-shear rotor-stator device as a stabilising technology

Contact details:

Dr. Seamus O’Mahony

Lecturer In Food Science

School of Food & Nutritional Sciences

T: +353 21 4903625

F: +353 21 4276398

E: sa.omahony@ucc.ie

W: http://www.ucc.ie/en/fns/

Fig. 2. SEM micrograph of acid whey powder with calcium phosphate

crystals, at different stages of crystallisation, present at the powder

surface (i.e., white spots).

Fig. 1. Gelled acid whey with further separation of phases

into lactose crystals-rich fraction (bottom of the

container) and protein-rich fraction (top of the container).

PROJECT 17: IN SITU TRACKING OF CO2 BUBBLE DYNAMICS IN FERMENTING KEFIR – ‘THE CHAMPAGNE OF

DAIRY’

Kefir is a traditional fermented dairy product that is gaining popularity as a refreshing protein-rich drink with probiotic activity and a low level of lactose. Kefir

is manufactured by inoculating milk with ‘Kefir grains’ consisting of yeast and lactic acid bacteria in a protein-carbohydrate matrix. Fermentation of Kefir is

performed at room temperature and leads to the breakdown of 30% of the lactose with the generation of CO2 through the action of bacteria and yeasts on

simple sugars. The formation of CO2 bubbles in Kefir is critical, as these bubbles are responsible for the unique effervescent quality of Kefir, which has led to

it becoming known as the ‘champagne of dairy’. There is a need to develop underpinning knowledge of Kefir fermentation to facilitate the transition from

variable artisan production methods to the consistent manufacturing operations required at commercial level. New insights into CO2 bubble evolution during

fermentation are possible with Broadband Acoustic Resonance Dissolution Spectroscopy (BARDS). BARDS was central to a recent transdisciplinary

collaboration between Food Scientists and Analytical Chemists at UCC that involved measuring air release phenomena in rehydrating milk protein particles

[1]. BARDS will here be used to investigate CO2 bubble dynamics in fermenting Kefir. Grains will be recycled for use as starter in sequential batches of Kefir to

monitor inter-batch viability. Conditions favouring the formation of stable gas bubbles will be determined and linked with acidification rate (pH), ion release

(conductivity) and viscosity development (rheometry). Sub-samples of Kefir will be gel-fixated for later SEM analysis of bubble dimensions and structure. This

project is a great opportunity for students interested in aspects of biochemistry, physics and food science.

[1] Vos, B., Crowley, S. V., O’Sullivan, J., Evans-Hurson, J., McSweeney, S., Krüse, J., Ahmed, M. R., Fitzpatrick, D., and O’Mahony, J. A. (2016). New insights

into the mechanism of rehydration of milk protein concentrate powders determined by Broadband Acoustic Resonance Dissolution Spectroscopy (BARDS).

Food Hydrocolloids, 61, 933-945.

Contact details:

Dr. Shane Crowley Lecturer in Food Processing School of Food and Nutritional Sciences T: +353 21 490 2453 E: shane.crowley@ucc.ie

PROJECT 18: WHAT ROLE DOES THE CELLULAR PROTEIN HABP1 PLAY IN ALPHAVIRUS REPLICATION?

The spread of mosquito vectors beyond their origins in sub-tropical regions of Africa and Asia has made the viruses they carry (arboviruses like Zika virus and

the alphavirus Chikungunya virus) emerging threats to human populations across the globe. Vaccines and antiviral drugs are required.

Antiviral drugs are best targeted towards regions of virus proteins which are conserved, to reduce the rate at which drug resistant viruses evolve. As obligate

intracellular parasites, viruses are dependent on host cells for their replication. Underlying this dependence are direct interactions between virus and cellular

proteins that are essential for replication. Regions of virus proteins with a specific point of interaction with cellular proteins, are particularly well conserved

and make ideal targets for antiviral strategies.

Alphaviruses possess a capsid structure which protects the virus genome. This structure is composed of multiple copies of a single virus-encoded capsid

protein. This protein is likely to also have other roles in virus replication, as viruses are very shrewd with their coding capacity. Previous work in the host

laboratory demonstrated a direct interaction between the alphavirus capsid protein and the multifunctional cellular protein HABP1.

In the proposed summer research project experiments will be performed to elucidate the relevance of this interaction. We will use CRISPR/cas9 technology

to knock out expression of HABP1 in a mammalian cell line. Virus replication will ultimately be compared in knock out and wild-type cell cultures.

Within the overall context of understanding molecular level virus-host cell interactions that may better inform the development of antiviral strategies to

combat arboviral infections:

Fundamental skills of classical cell-culture (maintenance, sub-culture and cell viability assays) and virology (initiation and sampling of experimental infections and plaque assays to quantify virus yields) will be acquired and applied.

Molecular biology techniques (such as transfection, DNA extraction, PCR and agarose gel electrophoresis) required to use CRISPR/cas9 technology to knock out the HABP1/p32 gene in BHK cells will be acquired and applied.

Throughout the project, good laboratory practice in the safe handling of reagents, cells and viruses will be learned and skills of scientific observation and analysis will be developed.

Contact details: Dr. Martina Scallan School of Microbiology, T: +353 21 490 2392 E: m.scallan@ucc.ie

PROJECT 19: BILE RESISTANCE IN BACTEROIDES.

Bacteroides are an important group of Gram negative, anaerobic bacteria found in the mammalian gut. Indeed, recent studies have shown that Bacteroides

make up approximately 50% of the bacterial biomass in the human gut and changes in the level of Bacteroides have been associated with disease. In order to

colonize the gut Bacteroides have to overcome several important host defense mechanisms including the production of bile. 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. However, the

mechanism of bile resistance in Bacteroides is not understood. Therefore, in this study you will undertake comparative studies to measure the level of

resistance of Bacteroides to bile (compared to other Gram negative bacteria) using in vitro screens. You will also screen a mutant library to identify genes in

Bacteroides that encode proteins that are important for bile resistance in this important bacterium.

Contact details:

Dr. David Clarke School of Microbiology T: +353 21 4903624 E: david.clarke@ucc.ie URL: http://publish.ucc.ie/researchprofiles/D010/davidclarke

GROUP 3 – MATHEMATICAL SCIENCES; CHEMISTRY AND PHYSICS

PROJECT 20: DEVELOPMENT OF SPECTROSCOPIC INSTRUMENTATION FOR A NEW ATMOSPHERIC

SIMULATION CHAMBER FACILITY

A world-class atmospheric simulation chamber with a volume of ca. 25 m3 is currently being installed and commissioned in the Centre for Research into

Atmospheric Chemistry. This summer research project will assist in setting up this new facility, the Irish Atmospheric Simulation Chamber facility) and will

focus on developing a sensitive spectrometer for the chamber. The approach followed will build on the group’s experience with incoherent broadband cavity-

enhanced absorption spectroscopy (IBBCEAS) to quantify trace gases such as NO2, NO3, and HONO that have a strong influence on atmospheric chemistry,

even at parts-per-trillion levels. The spectrometer will also be used to measure the light scattering and absorption arising from particles in the chamber;

these measurements are needed to understand the climate-effects of particles arising from both natural and anthropogenic sources. The work will also

include installing, interfacing, and integrating other chamber instrumentation into the overall control system.

This is very much a hands-on project that is geared towards the construction of new research systems. It should suit students in chemistry, physics, and

engineering with good practical skills who like the challenges of developing, testing, and controlling instrumentation.

Contact details:

Dr. Dean Venables Department of Chemistry & Environmental Research Institute Centre for Research into Atmospheric Chemistry T: +353 21 490 2439 E: d.venables@ucc.ie

PROJECT 21: 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.

Figure 1 Synthesis of ellipticine derivatives from indole and a 7-substituted isoellipticine yielding G2-M cell cycle block

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.

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.

Contact details:

Dr. Florence McCarthy Lecturer Chemistry T: +353 21 490 1695 F: +353 21 427 1656 E: f.mccarthy@ucc.ie

PROJECT 22: INTERRUPTING BACTERIA TALK, AND SWITCHING ON ANTIBACTERIAL AGENTS USING LIGHT

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 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. Key to the target molecule is its ability to be switched on and off using light. This could avoid the acquisition of resistance by the bacteria! Additionally, you will acquire skills useful for further PhD studies, or for employment within the Pharmaceutical Industry. Contact details: Dr. Gerard McGlacken Room G21A, Ground Floor, Kane Building Tel: 021-4902866 Email: g.mcglacken@ucc.ie

Check out Prof Bonnie Bassler’s lecture on Youtube at: http://www.youtube.com/watch?v=TVfmUfr8VPA

PROJECT 23: MOLECULAR MODELLING, DESIGN AND SYNTHESIS OF NOVEL DRUGS FOR CHAGAS DISEASE

Between 8 to 11 million people in Mexico, Central America, and South America are estimated to have Chagas disease, most of whom do not know they are

infected. If untreated, infection is lifelong and can be life threatening. The acute phase of the disease is characterised by fever, fatigue, body aches, diarrhoea,

and vomiting. In the chronic phase, the disease may result in cardiac complications such as heart failure. The average life-time risk of developing one of these

complications is about 30% with a fatality rate of around 50,000 people per annum.

The infectious agent of Chagas disease is Trypanosoma cruzi. The parasite usually enters the bloodstream of mammals through blood-sucking insects e.g.

assassin bugs. The disease can be treated in the acute phase by a limited number of drugs such as benznidazole or nifurtimox, although resistance is a growing

problem. These compounds do not completely reduce the parasite load in the bloodstream and may display serious side effects. These side effects, including

anorexia, vomiting, peripheral polyneuropathy and allergic dermopathy, can in some cases lead to treatment discontinuation. For these reasons, there is an

urgent need to develop new therapeutic agents for the treatment of Chagas disease.

In this project, we will use molecular modelling to design novel drugs for Chagas disease based on the naturally occurring compound, quinine. By designing

molecules which fit better in the active receptor site, our compounds should be more potent and display fewer side effects. We will synthesise these

compounds in the lab and work with our colleagues in the Carlos Chagas Institute in Brazil to measure their biological activity.

Contact details:

Dr. Tim O’Sullivan Lecturer in Pharmaceutical Chemistry Department of Chemistry and School of Pharmacy T: 353 (0)21 4901655 E: Tim.OSullivan@ucc.ie

PROJECT 24: MEASUREMENTS OF ATMOSPHERIC PARTICULATE MATTER Atmospheric particulate matter is composed of liquid and solid particles suspended in air. These particles can cause serious effects on air quality, human health and climate. Given the serious nature of the problem, air quality monitoring is required in large urban areas. A new air quality monitoring station has been recently set-up on the UCC campus. The station is equipped with automated analysers for measuring the important pollutant gases (nitrogen oxides and ozone), as well as a range of instruments for determining the size, number, mass and chemical composition of particles. This project will involve operating the instruments in the air quality station, performing data analysis and developing means of transferring/communicating the air quality data to the Irish Air Quality Monitoring Network operated by the Environmental Protection Agency (EPA). The results will also be compared to those obtained at other monitoring stations around Ireland during the same period. This research will therefore provide an excellent grounding in air quality monitoring, data analysis and networking of instruments/data transfer. This project is suitable for students of Chemistry, Chemical Physics, Environmental Science and Physics. Links: 1. http://www.epa.ie/air/quality/#.Vpj_AJqLS70 Contact details:

Prof. John Wenger Professor of Chemistry Department of Chemistry & Environmental Research Institute T: +353 21 4902454 E: j.wenger@ucc.ie http://crac.ucc.ie/ http://publish.ucc.ie/researchprofiles/D004/jwenger http://www.researcherid.com/rid/F-6662-2010

PROJECT 25: 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. Contact details: Dr. Andreas Ruschhaupt Department of Physics Office 216A (Kane building) E: aruschhaupt@ucc.ie

PROJECT 26: 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 analyzing VLBI images of the compact radio jets of a number of AGN, 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.

Contact details:

Prof. Denise C. Gabuzda Physics Department T: +353 21 490 2003 E: d.gabuzda@ucc.ie

PROJECT 27: SEMICONDUCTOR DIODE LASERS

The project is can be tuned to the interests of the student, and could be appropriate for a student in Applied Mathematics, Physics, Chemistry, Chemical

Physics, or Engineering. The actual work would be a selection varying from code based numerical analysis (C++ based) to hands on fabrication of a laser in the

clean room at the Tyndall National Institute, to lab based laser measurements.

Semiconductor lasers are part of our daily lives, as they are a key element in areas as diverse as internet communications, computer mice, and optical storage

(e.g. DVD readers). But, the actual operation of a laser is much more interesting, as semiconductor lasers are nonlinear optical noise amplifiers based on

optical waveguides.

The optical properties of a laser can be calculated by solving the optical wave equation in more than one dimension. This must be done using numerical

techniques such as the Finite Difference, or Finite Element methods. To simulate the actual operation the laser requires the solving non-linear equation using

entirely different techniques. Actual lasers can be designed based on optical resonance techniques coupled with interesting geometry problems.

Once designed, lasers are fabricated in a clean room, where the semiconductor is processed using various techniques, such as wet and dry etching, metal and

dielectric deposition, and the use of optical masks with photoresist. Once complete, lasers are characterised in test labs, where the optical and electrical

properties are evaluated.

Testing a laser bar, using electrical needle probes and a optical lensed fibre

Contact Details:

Prof. Frank Peters Room: Kane 1.16G Physics Department T: +352 21 490 2381 E: f.peters@ucc.ie

PROJECT 28: LOFAR EXPLORING THE RADIO UNIVERSE FROM IRELAND

LOFAR, the LOw Frequency ARray is a new radio observatory (http://www.astron.nl/general/lofar/lofar), with arrays of radio receivers distributed throughout

Europe, but centered in the Netherlands. LOFAR is a significant piece of European research infrastructure, opening up a new window on the universe and

allowing astronomers address fundamental issues in cosmology, the nature of distant galaxies, solar physics, etc. In addition, the very large data volumes (>

50 Gbits per second, requiring a processing power of 10's of terraflops) makes LOFAR an ideal facility for testing new approaches to handling "big" data.

A consortium of astronomers in Ireland (lead by TCD) have started to build a LOFAR station in Ireland (I-LOFAR – www.lofar.ie), in Birr Castle (Co Offaly) –

coincidently the site of the “Birr Leviathan", the largest optical telescope in the world for ~70 years (until the early 1900s).

This telescope will have an area of several 1000 m2, and will be completed this winter.

At this point it will be used as part of the wider LOFAR network, and also in “stand alone” mode, exclusively for astronomers in Ireland.

The project proposed here involves the use of LOFAR survey data of the entire sky (in collaboration with colleagues in Manchester University), and combining

it with surveys of the sky at other wavelengths (eg the optical), to investigate the nature of the new radio sources discovered by LOFAR. The expertise gained

by the student will be of use in the longer term, once we begin to receive our data from I-LOFAR.

The LOFAR network

A LOFAR facility, similar to I-LOFAR when completed this winter.

Image of M51, the “Whirlpool” galaxy, from the current LOFAR network. The quality of this image will be improved with the completion of I-LOFAR

Contact details:

Prof. Paul Callanan Department of Physics T: +353 21 490 3211 E: paulc@ucc.ie