STEM Summer Research Dublin Courses

You will earn 6 research credits over 8 weeks, conducting faculty supervised, hands-on, directed study research projects with results that will culminate in the preparation of a research paper.  You will complete a minimum of 240 hours on research in and out of the laboratory.

Faculty mentors will work closely with you to direct your continued growth and knowledge development in the chosen research topic discipline.

  • Please review your project with your academic or study abroad advisor to ensure it will transfer back to your home school and that you are following your home school’s policies.

Choosing Your Research Project

  • Review Project titles and descriptions below.
  • List 3 (in order of preference) in your personal essay.
  • Program is highly individualized, with limited enrollment.
  • You will need to complete a brief Literature Review in consultation with your research supervisor prior to departure before the start of the program. More details here.
  • We encourage you to contact Arcadia’s Assistant Dean of STEM programs, Dr. Jessie Guinn, to discuss your particular research interests further.

Biology, Microbiology, Neuroscience, Bioengineering, Genetics and Pharmacology, Computer Science, Environmental Science, Botany, Marine Biology, Ecology

Course ID Title Credits Syllabus
DUBI RSLW 392S International Independent Research in STEM Fields 6 PDF

Summer 2019 Research Projects

Biomedical Science
The role of outer membrane vesicles (OMVs) and their potential as vaccine candidates (read more)
Circulating extracellular vesicles in the very premature infant (read more)
Genotypic and Phenotypic Characterisation of freshly isolated strains of Campylobacter jejuni (read more)
Physiological regulation of human urea transporters (read more)
Association of Gut Barrier Dysfunction with the Microbiome in Colorectal Cancer (read more)
Chemistry
Development of novel continuous flow methods to generate drug-like building blocks (read more)
Design and Development of Transition Metal Catalysts for Promoting Hydrogen Storage (read more)
Synthesis of a pyridine-based, glyoxal urokinase-type plasminogen activator (uPA) inhibitor (read more)
Study of molecular probes of non-canonical DNA (read more)
Development of carbon nanohorn based therapies (read more)
Use of non-natural amino acids to investigate proteins structure-function relationships (read more)
Molecular magnetic behaviour in metal oxalate chains (read more)
Computer SCIENCE
Mobile Immersive VR exploration of the HCI possibilities (read more)
Exploring Educational Programming Data in the Blackbox Dataset (read more)
miRTarPred – microRNA Target Prediction (read more)
What you see is not what you get: spatial audio and the McGuirk effect (read more)
Ecology
Living at the front (read more)
Depicting personality traits in fallow deer (Dama dama) fawns at capture (read more)
Human-deer interactions in the Phoenix Park, Dublin: a study aimed at creating a wildlife management model (read more)
Neuroscience
The effects of trauma-induced neuroinflammation on Alzheimer’s disease-related pathology (read more)
Investigating the role of disease-causing proteins in motor neuron function (read more)
Investigation of Cannabidiol on synaptic excitability in hippocampal slices (read more)
Plant BIOLOGY
Aquaporin expression in roots of barley grown with limited supply of nitrogen and phosphorus (read more)
Nighttime transpirational water loss in barley: its response to photoperiod length, and its molecular basis (read more)
Root water uptake and aquaporin expression in barley plants which have a reduced number of root hairs (read more)
Changes in aquaporin expression in roots of barley in response to a partial reduction (excision) of root system (read more)
Image-based phenotyping of barley under waterlogging conditions (read more)
Optimization of Astaxanthin Production Using Transgenic Tobacco Cell Culture (read more)
Establishing Cannabis as a crop for the future (read more)


2019 Research Project Descriptions

UCD School of Computer Science

Discipline: Computer Science

Mobile Immersive VR exploration of the HCI possibilities

Supervisor: Dr. Abraham Campbell

Consumer level Immersive VR has now become a reality with the Oculus Rift and HTC VIVE head-mounted displays. New mobile versions of these head-mounted displays are being released to the public, one, in particular, the VIVE Focus allows for full 6 Degrees of Freedom tracking. This allows a user to walk around a large area within a VR world without the restrictions of a cable or desktop computer. This project seeks to explore what new areas of human-computer interaction are possible with this new computing paradigm. The student, after a period of study and researching the device, will create a basic VR experience using the device through the VIVE Focus SDK using the UNITY platform. Equipment wise for the project, the student will have access to a HTC FOCUS HMD for the whole duration of the project.

 
Discipline: Computer Science

Exploring Educational Programming Data in the Blackbox Dataset

Supervisor: Dr. Brett Becker

The Blackbox dataset contains the programming activity and source code of hundreds of thousands of users learning to program in Java using the BlueJ IDE. This dataset is relatively new and largely unexplored and underutilised. This project will explore specific facets of a much larger project that is utilising this data. The student will work with a PhD student working on this project and their supervisor, and seek to answer questions like the following: How many users show evidence of following the “Objects First with BlueJ” textbook?; How frequent are source codes that appear to be answering common first-year programming examples such as Fibonacci or Factorial programs?; and How many programs appear to be utilising recursion? The answers to these questions or questions like them will be of practical use to the overall project and also to the computer science education community. The exact nature of the questions to be answered will depend on the progress of the overall project but the student can have a part in shaping these questions. This project is suitable for students who have a strong interest in databases and programming. Some experience with Java programming and SQL databases is required. This project offers an opportunity to contribute to a much larger-scale project and to see how PhD projects work on a daily basis.

 
DISCIPLINE: COMPUTER SCIENCE

What you see is not what you get: spatial audio and the McGuirk effect

Project Supervisor: Dr. Andrew Hines

This project will use the Google Virtual Reality APIs [1] to create a 3D VR spatial audio [1] demo of the McGuirk effect. The McGurk effect [5] is an audio-visual perceptual phenomenon. You can see a video demo on youtube [2]. It demonstrates the fusion of hearing and sight by the human brain. If we combine visual stimuli of a person saying /fa/ with the sound of saying /ba/ the person will hear /ga/ but if they close their eyes they will hear /ba/. In other words, what you see overrides the cues you are hearing. This project will use the javascript APIs to build upon this experiment, allow a virtual speaker's visual and sound sources to diverge. Effectively, the voice moves away from being aligned to the same point as the virtual mouth until the fusion between sound and vision is broken. Undertaking this research will allow a baseline understanding of the fusion thresholds in typical subjects under silent and distraction conditions. The McGuirk effect is useful for research in a range of medical and psychological areas. People who are better at sensory integration have been shown to be more susceptible to the effect and brain damage and neural disorders have been shown to influence it. Using the McGurk Effect it was demonstrated that audio-visual fusion of speech queues is arrested in children with ASD [4].

[1] https://developers.google.com/resonance-audio/

[2] https://www.youtube.com/watch?v=G-lN8vWm3m0

[3] https://en.wikipedia.org/wiki/McGurk_effect

[4] Stevenson et al., 2014. Arrested development of audiovisual speech perception in autism spectrum disorders. Journal of Autism and Developmental Disorders, 44(6), pp.1470-1477

 
 
Discipline: Computer Science

miRTarPred – microRNA Target Prediction

Project Supervisor: Dr. Catherine Mooney

Suits students who like: Machine Learning and Biology microRNAs are a unique class of small (~22 nucleotides) non-coding RNA that regulate gene expression [1]. microRNA function by binding in a sequence-specific manner to protein-coding mRNA. This typically results in a reduction in protein levels. Each microRNA is capable of targeting ~200 mRNAs, potentially bringing about changes to numerous proteins, even within the same pathway. microRNAs have emerged as important contributors to the pathogenesis of numerous diseases.

There are a number of databases with experimentally determined microRNA/mRNA target pairs [2,3]. You will use these databases to collect a set of microRNA and their targets. You will then use this dataset to train a machine learning algorithm to predict the mRNA target of a specific miRNA. You will also test and benchmark your predictor against other similar predictors that are currently available [4, 5].

You will then develop a user-friendly web-server for the new predictor which will be available for the community of biologist who would like to be able to predict which mRNA specific microRNA targets.

You will gain experience in web development and machine learning, both valuable skills that are in high demand in industry and academia.

MicroRNAs stick to mRNA molecules and prevent the mRNAs from being made into proteins. https://www.slideshare.net/yhtaguchi/micrornamrna-interaction-identification-in-wilms-tumor-using-principal-component-analysis-based-unsupervised-feature-extraction

Resources and further reading:

  1. microRNA
  2. miRTarBase
  3. TarBase
  4. The TargetScan web server
  5. Other microRNA Target Prediction methods

UCD School of Biomolecular and Biomedical Science

 
Discipline: Biomedical Science

The role of outer membrane vesicles (OMVs) and their potential as vaccine candidates

Supervisor: Dr. Siobhán McClean

People with cystic fibrosis (CF) experience chronic lung infections right throughout their lives (1). Ultimately these infections lead to lung function decline and premature death. Two of these pathogens are Pseudomonas aeruginosa and Burkholderia cepacia complex (Bcc). The latter, Bcc, is particularly difficult to treat as it is highly multidrug resistant. This means that once a patient is colonised with Bcc it is rarely eradicated. Therefore there is a real need for a vaccine to protect CF patients from this life-threatening infection.

The McClean lab studies the mechanisms by which Bcc attach to lung cells and adapt to successfully colonise in people with CF (2-4). We have discovered a number of proteins that are involved in the infection process that are entrapped in outer membrane vesicles. In other species, OMVs are associated with the transport of virulence factors within the host (5), but little is known about them in Bcc. The OVERALL AIM of this project is to understand the role of outer membrane vesicles (OMVs) in CF lung infection. OMVs have recently been licenced for use in the Neisseria meningitis Men B vaccine, consequently there may be a potential role for Bcc OMVs in a future vaccine to protect people with CF from Bcc and other infections. The project will involve isolating and analysing OMVs from strains of Bcc and examining their role in virulence and the host response in human lung epithelial cells and in an infection model.

References

  1. L. Cullenand S. McClean. Bacterial Adaptation during Chronic Respiratory Infections. Pathogens. 4:66-89 (2015).
  2. S. McClean, M.E. Healy, C. Collins, S. Carberry, L. O'Shaughnessy, R. Dennehy, A. Adams, H. Kennelly, J.M. Corbett, F. Carty, L.A. Cahill, M. Callaghan, K. English, B.P. Mahon, S. Doyle, and M. Shinoy. Linocin and OmpW Are Involved in Attachment of the Cystic Fibrosis-Associated Pathogen Burkholderia cepacia Complex to Lung Epithelial Cells and Protect Mice against Infection. Infect Immun. 84:1424-1437 (2016).
  3. L. Cullen, A. O'Connor, S. McCormack, R.A. Owens, G.S. Holt, C. Collins, M. Callaghan, S. Doyle, D. Smith, K. Schaffer, D.A. Fitzpatrick, and S. McClean. The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection. Scientific reports. 8:13386 (2018).
  4. L. Cullen, A. O'Connor, P. Drevinek, K. Schaffer, and S. McClean. Sequential Burkholderia cenocepacia Isolates from Siblings with Cystic Fibrosis Show Increased Lung Cell Attachment. Am J Respir Crit Care Med. 195:832-835 (2017).
  5. A.J. McBroomand M.J. Kuehn. Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. Mol Microbiol. 63:545-558 (2007).
Discipline: Biomedical Science

Circulating extracellular vesicles in the very premature infant.

Supervisor: Dr. Patricia Maguire

Annually in Ireland, over 600 babies are born prematurely. These babies are at increased risk of developing serious life-threatening complications. Parameters that could predict the onset of these complications in preterm neonates would greatly improve patient care and survival rates in this high-risk patient cohort. Extracellular vesicles (EVs) are small subcellular particles released by cells. The levels of EVs are frequently increased in proinflammatory conditions. They are also rich in proteins, RNAs, and lipids, and are increasingly been seen as potential diagnostic and prognostic biomarkers. In our UCD Conway SPHERE research group, we have demonstrated that preterm babies are characterised by major changes in their plasma EV profile immediately following birth, in the period called the extrauterine transition. From day 1 to Day 3 of life, there are significant changes in the plasma levels of EVs, in the size of plasma EVs, and the expression of protein on EV surface. This project will continue to characterise the changes in EV profiles in preterm neonates during the extrauterine transition period using a variety of state-of-the-art techniques available in the UCD Conway SPHERE research group

 
Discipline: Biomedical Science/Cancer Biology

Association of Gut Barrier Dysfunction with the Microbiome in Colorectal Cancer

Supervisor: Dr. David Hughes

Colorectal cancer (CRC) is a leading cause of cancer illness and death in many world regions, including Ireland. Although the causes of CRC are complex, environmental factors, particularly obesity and lifestyle, are known to play a strong role. Recent compelling evidence, some of which my work has helped generate, suggest that commensal microbial dysregulation and exposures to microbial toxins are involved in CRC development. One recent hypothesis is that this occurs through a weakening of the protective gut barrier by diet, obesity and lifestyle factors.

To help explore this hypothesis, the student will measure a direct biomarker of gut-barrier function by a custom ELISA of the protein zonulin (which modulates the permeability of tight junctions between intestinal tract cells). This will be done in a series (n=304) of matching blood, normal colonic tissue and colon cancer tissues from the same subjects, to assess gut-barrier breakdown from normal to neoplastic. If marker levels in cases/neoplastic tissue are statistically different than those in controls/normal matched tissue, it would mean that the hypothesis is correct. A complementary concurrent study by a Ph.D. student in my lab will assess tissue-DNA markers of a series of microbiota in these same samples. Together, these findings will inform us of the microbiome and gut-barrier function in healthy colorectal epithelium and within colorectal tumors, and how this may contribute to exposure of bacterial toxins from the gut. Blood-based detection of bacteria and gut-barrier health may allow novel screening strategies for CRC prevention, diagnosis and management.

 
Discipline: Neuroscience

The effects of trauma-induced neuroinflammation on Alzheimer’s disease-related pathology

Supervisor: Dr. Derek Costello

Background: Alzheimer’s disease (AD) is characterised by the age-associated accumulation of amyloid-β peptide (Aβ) within the brain, leading to neuronal dysfunction and cognitive impairment. Aβ is a potent activator of microglial cells, inducing inflammatory mechanisms similar to those activated by certain bacterial infections. Interventions which target inflammatory mediators have proven successful in attenuating Aβ-induced changes in microglia and the associated disruption of hippocampal synaptic function. In addition, microglial activation promotes the hyperexcitability of hippocampal neurons, which facilitates the cognitive decline and neurodegeneration characteristic of the disease.

Many patients with sporadic AD, as well as AD animal models, experience recurrent spontaneous seizures which are thought to precede cognitive impairment. Overexpression of Aβ promotes the development of epileptic activity, in turn accelerating cognitive decline. The role of inflammation in epileptogenesis, following disease, trauma and infection, has been highlighted in recent years, which can convey resistance to current anti-epileptic therapies. Enhanced production of inflammatory mediators following seizure further potentiates the activity. This is attributed to the over-activation of microglia and the altered ability of astrocytes to maintain homeostatic function, thus lowering the threshold for neuronal activation.

Aims and Objectives: Our preliminary evidence indicates that certain bacterial agents, in combination with Aβ, differently impact the generation of epileptiform activity in hippocampal neurons. This study will build on this information, to analyse the inflammatory impact of HMGB1, a molecule produced in response to brain trauma, which acts in a similar manner to Aβ. We will investigate inflammatory changes in cultured microglial cells following exposure to these agents, and the potential impact that this may have on neuronal viability. In addition, we will examine the integrity of neurons that have been modified to produce and express different forms of Aβ, as an in vitro model in which to study Alzheimer’s disease pathology.

Experimental design: Microglial and neuronal cells will be cultured and maintained in vitro. Cells will be incubated in the presence or absence of HMGB1, a known mediator of cell damage. The resulting synergistic inflammatory response will be evaluated. Microglial cells will be assessed using PCR and Western immunoblot analysis to determine markers of inflammatory activation and signalling. Supernatants will be analysed by ELISA for evidence of soluble inflammatory mediators. Neurons will be assessed for viability and alterations in homeostasis.

Techniques: In vitro electrophysiology, Western immunoblot analysis, ELISA, PCR

Lab Profile: http://www.ucd.ie/research/people/biomolecularbiomedscience/drderekcostello/

 
Discipline: Neuroscience

Investigating the role of disease-causing proteins in motor neuron function

Supervisor: Dr. Niamh O’Sullivan

My lab studies inherited forms of motor neuron disease, particularly hereditary spastic paraplegia (HSP). Individuals with HSP develop weakness in their legs leading to difficulties walking which is caused by degeneration of the very longest motor neurons. Extensive work in recent years has successfully identified many of the genetic causes underpinning HSP, but there are currently no treatments to prevent, cure or even to slow the course of these diseases. To address this, my lab are using cutting-edge genetic engineering to generate novel animal and cellular models of HSP in which to study the molecular events underpinning this disorder. Recently, researchers in my lab have found that HSP-causing genes play a role in the organisation of the endoplasmic reticulum (ER) network within motor neurons. The aim of your project will be to study how this impaired ER network contributes to neurodegeneration in motor neurons. You will learn various techniques associated with molecular genetics, confocal microscopic image analysis and the assay of behavioural readouts.

Lab website: fniamhy.wixsite.com/osullivanlab

 
Discipline: Biomedical Science

Genotypic and Phenotypic Characterisation of freshly isolated strains of Campylobacter jejuni

Supervisor: Dr. Tadhg Ó Cróinín

Campylobacter jejuni is the major cause of bacterial gastroenteritis worldwide. Although the bacteria is pathogenic in humans it is found in large numbers in chickens without causing any apparent disease. Most raw chicken meat in supermarkets is thus contaminated with this important human pathogen posing a threat to human health. The organism is highly variable on a genetic and phenotypic level with large variation observed in strains isolated from different sources. This project will involve isolating Campylobacter strains from chicken meat from the supermarket and comparing with strains previously isolated from patients in Crumlin Children’s hospital as well as established lab strains. Techniques employed will include growth assays, PCR, Motility assays and Western Immunoblotting. This project would be suitable for a student with an interest in Microbiology and particularly the field of Infection Biology.

 
Discipline: Neuroscience

Investigation of Cannabidiol on synaptic excitability in hippocampal slices

Supervisor: Assoc Prof. Caroline Herron

We have previously shown that cannabidiol (CBD), the non-psycho active component of cannabis sativa is neuroprotective against the effects of beta-amyloid peptide known to be involved in Alzheimer’s disease (Hughes and Herron Neurochem Res. 2018 Mar 24. doi: 10.1007/s11064-018-2513-z). Recently CBD has also been licenced as “Epidiolex” for the treatment of Dravet Syndrome and Lennox Gastaut Syndrome; forms of drug-resistant childhood epilepsy. The mechanism of action of CBD has yet to be determined with a recent publication suggesting it may act as a negative allosteric modulator (NAM)at the Cannabinoid type one receptor (CB1) (Straiker et al Mol Pharmacol. 2018 Jul;94(1):743-748)

We will use in vitro hippocampal slice electrophysiology to investigate the effect of CBD on synaptic depression produced either by electrical stimulation or via application of the metabotropic glutamate receptor agonist Dihydroxy phenyl glycine (DHPG). This will test further the hypothesis that CBD acts as a NAM at CB1. A very low concentration of DHPG is also known to increases epileptiform activity in hippocampal slices and we will test further the effect of CBD on increased levels of synaptic excitability produced by DHPG and other pro-convulsant agents.

The student will be working with an experienced 3rd year Ph.D. student in the laboratory and will learn the basic techniques of extracellular field recordings, use of GraphPad prism and statistical analysis. Hippocampal slices will be prepared by the principal investigator or by the Ph.D. student.

UCD School of Biology and Environmental Science

 
Discipline: Plant Biology

Aquaporin expression in roots of barley grown with limited supply of nitrogen and phosphorus

Supervisor: Dr. Wieland Fricke

Nitrogen and phosphorus are key mineral nutrients which plants need to grow. In particular, they are required for the synthesis of amino acids, proteins, nucleic acids, plant secondary compounds, energy metabolism and have also an important osmotic function to support cell expansion and growth. Less is known about the function of nitrogen and phosphorus in controlling root water uptake. Previous work in our group on barley has shown that low nitrogen and low-phosphate increase the ratio of water-absorbing root surface to water-loosing shoot surface considerably and to a different extent. This is associated with a significant decrease in the water uptake (hydraulic) properties of roots and changes in root anatomy, where the response differs between low-N and low-P conditions. The decrease in root hydraulics is most likely facilitated through aquaporins, water channels in the membrane of cells.

Aim: In this project, we want to test how the combined (!) low supply of N and P affects some of the sizes which we analysed previously. You will grow barley plants under nitrogen/phosphate-sufficient (control) and limiting (low-N/P) conditions and compare the expression of a set of candidate aquaporins between treatments. Expression will be quantified using qPCR. Hydraulic properties of roots will be analysed using exudation measurements. Root anatomy will be analysed through cross-sections. We will address the question, whether any decrease in root hydraulic properties in response to low nitrogen/phosphorus supply is associated with a decrease in the gene expression level of aquaporins.

 
Discipline: Plant Biology

Nighttime transpirational water loss in barley: its response to photoperiod length, and its molecular basis

Supervisor: Dr. Wieland Fricke

It was thought for a long time that plants lose water through transpiration from the shoot only during the day. We know now that this view is wrong, as plants lose typically water during the night through transpiration at 5-20% the rate at which water is lost during the day. Since plants cannot gain carbon and energy at night through photosynthesis, night-time transpiration does not seem to have any obvious advantage to plants, nor to growers. Recent work in our group suggests that night-time transpiration is not so much about water but about losing respiratory carbon dioxide at sufficiently high rates through stomata – otherwise, the carbon dioxide would build up in leaves and cause toxicity. Night-time respiration fuels leaf growth in size during the night and is itself fueled by sugars which are produced during the day. So, one could hypothesise that the shorter the day relative to night-length is, the fewer sugars are available during the night to be respired, the slower growth rates of leaves are in the night and the less water is lost through night-time transpiration. This idea will be tested in the present project.

Aim: In this project, we will grow barley plants under varying day and night length and measure growth, transpiration and sugar content of plants.

 
Discipline: Plant Biology

Root water uptake and aquaporin expression in barley plants which have a reduced number of root hairs

Supervisor: Dr. Wieland Fricke

Root hairs are an outgrowth of individual epidermal cells at the surface of roots. Root hairs increase the surface area of roots for very little investment of resources, and being thin, allow easy access of nutrients and water between soil colloids. Thus, root hairs are thought to have an important role in nutrient and water uptake by plants. There exist mutants of barley which have a very reduced number of root hairs. In this project, we want to test, whether the reduction in root hair number also reduces the water uptake of roots, or whether the remaining part of root increases their water uptake properties (hydraulic conductivity), for example through increased gene expression of aquaporins. These are water channels in the membrane of cells. Also, by comparing expression of aquaporin isoforms in root hair mutants (few root hairs) and wild-type barley plants, we should be able to identify any particular aquaporins which are expressed in root hairs (present in wild-type, almost absent in mutant).

Aim: In this project, we will grow barley plants (wildtype, mutant) until they are two weeks old and compare the gene expression of a set of candidate aquaporin isoforms between plants. Expression will be quantified using qPCR. Hydraulic properties of roots will be analysed using exudation measurements. Leaf and root surface area will be determined by analysing scanned images of roots and leaves with freely-available software (ImageJ). Transpiration will be determined gravimetrically.

 
Discipline: Plant Biology

Changes in aquaporin expression in roots of barley in response to a partial reduction (excision) of root system

Supervisor: Dr. Wieland Fricke

Plants need to adjust the rate of water uptake through the root system to the rate of transpirational water loss through the shoot. It is not clear how this regulation is achieved. The traditional view would be that such a regulation is achieved through the shoot, by means of adjusting the stomatal pore size, yet the discovery of aquaporins (AQPs), membrane water channels, has opened the possibility that this regulation can also be achieved through AQPs in roots. Barley plants which are about two weeks old have five to seven roots. When most of these roots are removed, plants still take up almost as much water as before removal of these roots. We don’t know how barley plants do this, but the most likely possibility is that the activity and possible gene expression of AQPs in the remaining roots is increased. This will enable more water uptake per unit remaining root surface.

Aim: The aim of the project is to test this idea by removing all but one of the roots of 14d-old barley plants and then measure changes in plant water flow and AQP gene expression (qPCR) during the following two days. This is a combined molecular/plant physiological/environmental sciences project.

Discipline: Ecology

Living at the front

Supervisor: Assoc. Prof Mary-Kelly Quinn

The term intermittent to used to describe streams that dry up for a period of time, these include all temporary or intermittent and ephemeral streams. Intermittent streams do not flow for certain parts of a year, whereas ephemeral streams typically only flow during storm events. They are considered to account for more than 30% of the total length and discharge of the global river network. The headwaters of many streams expand and contract in response to fluctuations in surface and groundwater levels. The duration and extent of drying channel is projected to increase in many areas due to climate change and this will have significant consequences for aquatic fauna in the headwaters but also further downstream. Little is known about the ecology of temporary streams in Ireland and the consequences of climate changes for these reaches. Furthermore, there has been no mapping of the expansion and contraction of the wetted channel in headwaters in Ireland. This project will map the expansion-contraction cycle of wetted channel networks in a catchment on the east coast of Ireland and will examine the aquatic macroinvertebrate communities living near the moving front. Useful reading available here.

 
Discipline: Biomedical Science

Physiological regulation of human urea transporters

Supervisor: Dr. Gavin Stewart

Urea transporters, such as UT-B, are used to transport urea across cell membranes and are located in a wide variety of tissues - such as the kidney, bladder, colon and brain. They are known to play important functions in the mammalian urine concentrating mechanism, symbiotic relationships with colonic bacteria, and the removal of the toxic waste product urea from the brain. Recent studies have shown alterations in UT-B transporters to be linked to a wide range of clinical conditions, such as bladder cancer or potentially even Alzheimer's Disease. Utilizing cell culture, RT-PCR, western blotting and immunolocalization techniques, this project will investigate the cellular pathways involved in the normal physiological regulation of UT-B urea transporters. In particular, we will use human cell lines (e.g. RT4 urothelial cells) to investigate the effects of osmolality, urea concentration and/or protein kinase inhibitors on these important transport proteins.

 
Discipline: Ecology

Depicting personality traits in fallow deer (Dama dama) fawns at capture

Supervisor: Dr. Simone Ciuti School of Biology and Environmental Science, Laboratory of Wildlife Ecology and Behaviour LAB LINK

Inter-individual variability in animal behaviour within wild populations is an important component influencing their resilience to external perturbations such as human disturbance, climate and habitat change. When such differences are consistent through time, we typically refer to them as personality traits. Personality differences are indeed a widespread phenomenon throughout the animal kingdom, with important consequences for species ecology and evolution. This project aims to test the hypothesis that behavioural traits recorded at captures (e.g. reaction to capture, vocalization, and behaviour at release) in fallow deer fawns of Phoenix Park (Dublin) are highly repeatable over replicated captures of fawns and are a good proxy for their personality. The student will join the Phoenix Park capture team during the fawning season of June 2019 and will collect behavioural data on more than 100 fawns during their captures. Fieldwork in the Phoenix Park would imply to learn how to capture and handle deer fawns and is expected to be completed by the end of June, leaving the month of July for the data analysis. This is a unique opportunity for students to gain experience in the field of wildlife research and join an experienced team of students and academic staff with long-term experience in animal behaviour. The ultimate goal of the study is to define a protocol for collecting personality traits in wildlife during capture to be linked to life history traits.

 
Discipline: Ecology

Human-deer interactions in the Phoenix Park, Dublin: a study aimed at creating a wildlife management model

Supervisor: Dr. Simone Ciuti School of Biology and Environmental Science, Laboratory of Wildlife Ecology and Behaviour LAB LINK

The feeding of wildlife as a recreational activity is on the rise globally. These interactions result in cases of animal habituation, resultant injuries to visitors caused by close contact, and an unknown impact on target animals health and welfare. There is little consensus on how this should be controlled, which has resulted in a call for an effective management plan that can be replicated across multiple species and countries. Phoenix Park (Dublin) has experienced a recent spike in fallow deer-human feeding interactions and a coinciding rise in reports of human injuries. This is a major human health and safety concern, as well as a deer welfare concern. This study aims to monitor the incidences of human-deer feeding interactions in Phoenix Park effectively, identify the effects of these interactions on the deer, and develop a model management plan that is applicable to other areas experiencing this issue. Data collection from Summer 2018 has shown the extent of the issue, and the first set of management protocols are now being applied (Winter 2018-2019). A follow-up data collection will now occur in Summer 2019, to assess the success of these management techniques. The student will assist in fieldwork and deer behavioural data collection in June 2018, at the height of these interactions, leaving July 2018 free for data analysis. This is a unique opportunity for students to gain experience in the field of wildlife research; including behavioural observation methodology, scan sampling, movement data collection and an expanded comprehension of human-wildlife conflict management.

 
Discipline: Plant Biology

Image-based phenotyping of barley under waterlogging conditions

Supervisor: Dr. Sónia Negrão

Phenotyping, in a nutshell, can be described as a quantitative description of a wide range of traits. Classic plant phenotyping has evolved to high-throughput phenotyping, which uses image-based and non-destructive methods to investigate, for example, plant growth progression. New image-based systems for phenotyping have recently emerged using Raspberry Pi computers, enabling to acquire plant image data at a low cost. However, the use of these systems and its data acquisition for examining plant stress responses is still very new and underexplored.

Barley is a resilient crop plant with higher abiotic stress tolerance than other cereal plants. However, barley is particularly sensitive to waterlogging, leading to severe yield losses. Due to climate change, rainfall is predicted to increase with extreme precipitation and flooding events becoming more frequent. Thus, waterlogging is expected to become a significant problem in the coming decades, and further research on the mechanisms of waterlogging tolerance is required.

The aim of this project is to optimize the image-based phenotyping of barley plants exposed to waterlogging stress. We will use Raspberry Pi computers (and small cameras) to collect images of one barely commercial cultivar, which will be processed using an open-source phenotyping software. By the end of this project, we should be able to collect data from the plant, and its surrounding environment, that will enable the selection of phenotypical traits contributing to waterlogging tolerance mechanisms.

 
Discipline: Plant Biology

Optimization of Astaxanthin Production Using Transgenic Tobacco Cell Culture

Supervisor: Dr. Joanna Kacprzyk, Collaborators: Dr. Paul McCabe, Prof. Jez Simpson

Background: Astaxanthin is considered the most powerful natural carotenoid antioxidant. Named ‘king of antioxidants’, it is more potent than vitamin E and beta-carotene. Astaxanthin is used on a large-scale by the fish farming industry to provide red color to salmon and trout, as well as a food colorant and supplement. It is also a promising biopharmaceutical; research evidence on its anti-inflammatory and antioxidant properties is emerging. The selling price of synthetically produced pure astaxanthin is around $2000 per kilogram, while natural astaxanthin is sold for $7000 -12000 per kg. The new, more cost-effective sources of naturally produced astaxanthin are therefore of significant interest. The astaxanthin biosynethic pathway has been recently cloned into the plastids of Nicotiana tabacum (Liu et al 2017).

Aim: This project will involve optimization of growth protocol of cultured transgenic tobacco cells to maximize the production of this high-value carotenoid. Plant cell culture provides a useful alternative for the production of active ingredients as it offers a contaminant-free, standardized and biosustainable system, which can be scaled up to the industrial level.

Techniques which may be used:

  • Cell culture, aseptic technique, viability assays
  • In vitro characterization of biological activity
  • Solvent extraction, freeze drying, spectrophotometric quantification
  • If sufficient optimization of the protocol is achieved: Use of lab scale bio-reactors

Capacity: Two Students

 
Discipline: Plant Biology

Establishing Cannabis as a crop for the future

Supervisors: Dr. Rainer Melzer and Assoc. Prof Paul McCabe

Lab homepage:  https://ucdflowerpower.org/

Twitter:  @UCDflowerpower

Cannabis, or hemp, is an extraordinarily versatile plant – it has been used for millennia as a source of fibre, oil and for medicinal purpose. However, because Cannabis has psychoactive effects, it has been widely banned throughout the last century. It is now receiving new attention as a sustainable crop for a carbon-neutral society and as an important source for modern medicinal products. However, genetics research on Cannabis is still in its infancy compared to many other crops.

In this project, we aim to establish important molecular genetic analyses for Cannabis. You will be involved in testing different DNA isolation protocols, PCR and gene cloning. We also aim to analyse growth conditions for Cannabis.

UCD School of Chemistry

 
Discipline: Chemistry

Development of novel continuous flow methods to generate drug-like building blocks

Supervisor: Dr. Marcus Baumann, School of Chemistry

This summer project will offer a talented student to acquire novel laboratory skills in a project at the interface of organic chemistry, medicinal chemistry and chemical engineering. The synthesis and spectroscopic characterisation of a focused collection of drug-like heterocycles will be targeted. This will involve exploiting bespoke continuous flow reactors available in the newly established UCD Flow Chemistry lab. Specifically, we will be using a continuous flow photoreactor to generate target compounds in a telescoped manner. This will avoid the isolation of unstable intermediates and provides a readily executed route into important bioactive structures. Using light as a traceless reagent in combination with in-line purification techniques will result in a green and sustainable technology that highlights the power of modern chemical synthesis in delivering important drug-like structures in an automatable fashion without requiring labour-intensive downstream processing to yield clean products.

 
Discipline: Chemistry

Design and Development of Transition Metal Catalysts for Promoting Hydrogen Storage

Supervisor: Dr. Andrew Phillips – School of Chemistry

Integration of energy storage systems that do not involve the release of volatile carbon- or nitrogen-based emissions (CO2, NOx) is key to ensuring environmental sustainability. Hydrogen gas is readily available through water splitting and has a greater energy density of 33.3 kWh/kg as compared to batteries (<0.5 kWh/kg).1 Moreover, electrical energy is harvested by PEM-type fuel cells through the conversion of H2 to water. However, the high-pressure storage of H2 poses significant explosion hazards. Many research organisations recognise that chemically integrated hydrogen provides a safer and more stable method of storage. Ammonia borane (AB) is a lead candidate as it stores up to 12% of accessible H2 (see figure below). An efficient method of dehydrogenation and releasing H2 from AB is through a catalysis rather than thermolysis. The Phillips group developed, synthesised and patented several optimised Ru-diketiminate complexes to dehydrogenate AB with the advantage of producing highly pure H2. This project examines the possibility of incorporating unprecedented molecular-level control into a new generation of catalysts through electrochemical switching. The ability to switch between an active Ru(III) state and inactive Ru(II) state allows for a simplified reactor design involving a single chamber that does not require feeding of AB via a mechanical pump which is susceptible to obstruction.

Design and synthesis of a wide variety of b-diketiminate ligands and associated Ru-complexes are necessary to screen and select a lead complex with the correct balance of redox switching potential and a high rate of catalytic AB dehydrogenation. Through tethering of the Ru-b-diketiminate complex to a graphite electrode, both solid-state support and redox control are incorporated with an added advantage of facile catalyst recovery from spent AB.

 
Discipline: Chemistry

Synthesis of a pyridine-based, glyoxal urokinase-type plasminogen activator (uPA) inhibitor

Supervisors: Nahlah Al-Hadharami, Prof. Paul Malthouse and Dr. Paul Evans

Urokinase-type plasminogen activator (uPA) is an enzyme responsible for the formation of plasmin from plasminogen, an event associated with the development of tumour cells. It is a serine-based protease enzyme resembling trypsin and due to its important role in tumour growth/metastasis is an attractive target for small molecule intervention.1 Studies have demonstrated that peptidomimetic 2-guanidinyl pyridine derivatives (eg. Figure 1, compound 1) are reasonable inhibitors of uPA with good selectivity for uPA over tissue plasminogen activator (tPA).1a This is relevant since tPA plays a pivotal “house-keeping” role in the more general fibrinoyltic cascade. These inhibitors have Ki values of 3-100 μM, depending on their type and the position of the second substituent in the pyridine ring - substitution in the 5-position proving optimal. In addition, substitution in the 3- position, which protrudes into the uPA binding groove, has been shown to further increase the potency of type 1 inhibitors.1

Since the mechanism of plasminogen hydrolysis involves Ser-195, which X-ray crystallographic studies have demonstrated is proximal to the 5-pyridine substituent, the idea behind this proposal is to incorporate a glyoxal functional group in the place of the C-5 halogen atom present in 1. Previous work in the Malthouse group3 has demonstrated that this type of functionality covalently interacts with serine hydroxy groups forming hemiacetals, or ketals, in which the inhibitor is covalently linked in the active site. We believe that this mechanism combined with the pyridine/guanidine-active site recognition elements (eg. The Asp-189 salt bridge) will result in high levels of uPA inhibition. Notably, low nM Ki values are typically encountered for this type of inhibition for different glyoxal containing inhibitors with different serine proteases.

References:

  1. (a) Barber, C. G.; Dickinson, R. P.; Horne, V. A. Bioorg. Med. Chem. Lett., 2002, 12, 181; (b) Barber, C. G.; Dickinson, R. P. Bioorg. Med. Chem. Lett., 2002, 12, 185.
  2. Kelly, B.; O’Donovan, D. H.; O’Brien, J.; McCabe, T.; Blanco, F.; Rozas, I. J. Org. Chem., 2011, 76, 9216; 2012, 417.
  3. Cleary, J. A.; Doherty, W.; Evans, P.; Malthouse, J. P. G. Biochim Biophys. Acta (BBA), Proteins and Proteomics, 2014, 1844, 1119.
 
Discipline: Chemistry

Study of molecular probes of non-canonical DNA

Supervisor: Prof. Susan Quinn https://sites.google.com/site/sjquinngroup/

As the body’s information repository, DNA provides the essential role of programming all biological function. This information is translated through numerous molecular interactions. Proteins and small molecules bind to DNA through a variety of modes that include groove binding, electrostatic interactions and intercalation. The nature of these interactions is influenced by the structure of the molecules and the secondary structure of DNA, which in addition to the common B-DNA form can also adopt other non-canonical forms. Two important structures are guanine-rich quadruplex and cytosine-rich imotif DNA. Quadruplex DNA comprises stacked tetrads of four guanine bases while imotif DNA is an arrangement of alternating interdigitated C:C+ base pairs formed between hemi-protonated cytosines.

In the past 5 years, the presence of both DNA structures in the cell has been confirmed by fluorescence microscopy. The binding interactions of small molecules to these structures is of interest due to our increasing knowledge of the structures potential role in replication, transcription, and recombination. The quadruplex structure is also of interest as it is formed from human telomere DNA. In this project, we aim to investigate the binding of metal complexes to distinguish the different structures, which is essential to resolving their biological roles. The project allows for spectroscopic measurements and DNA binding studies which will provide experience across a range of diverse techniques including circular dichroism, UV-visible and emission spectroscopy. This will build on our extensive experience in this field [Nature Chemistry 2015, 7, 961, Chem. Sci., 2017,8, 4705-4723]

 
Discipline: Chemistry

Development of carbon nanohorn based therapies

Supervisor: Prof. Susan Quinn https://sites.google.com/site/sjquinngroup/

We are interested in preparing gold nanoparticle systems that can be used to complement radiotherapy treatment for resistant cancers. This relies on the fact that X-ray irradiation of gold nanoparticles releases electrons that form reactive oxygen species that can kill cells [Sicard-Roselli, C. et al. Small 2014, 10, 3338–46] see (1) below. Nanoparticles have a high surface area which allows them to carry molecules that can bind to their surface. To get a high concentration of AuNPs to the cell we have developed methods to prepare composite particles using polystyrene nanoparticles with high loadings of Au NPs and demonstrated uptake in cells [Chem. Commun., 2016,52, 14388-14391] (see 2 below). In this project, the aim is to replace polystyrene spheres with carbon nanohorns to prepare gold nanoparticle composites. Carbon nanohorns (CNHs) are spherical carbon nanoparticles (~100 nm) comprising bundles of horn-like rolled carbon sheets (see 3 & 4 below) that can readily enter the cell and our group recently was able to monitor this process through live-cell imaging [Devereux, S. J. et al. Eur. J, 2018, 24, 14162]. Importantly, CNHs are non-toxic and, in time, are degraded by enzymes in the body. The low toxicity, high surface area and ease of functionalisation of carbon nanohorns makes them attractive systems for cellular imaging, diagnostics and therapeutics. The project will involve metal nanoparticle synthesis, spectroscopic characterisation, composite preparation and characterisation as well as assaying the stability of the composites formed to biological media.

 
Discipline: Chemistry

Use of non-natural amino acids to investigate proteins structure-function relationships

Supervisor: Dr. Marina Rubini

Non-natural amino acids represent useful tools to investigate and clarify different biological questions among others protein structure/function relationship, stability and folding. In our laboratory, we synthesize these non-natural building blocks following synthetic routes described in the literature. For elucidating questions regarding protein folding we focus in particular on proline analogues. Proline has no natural counterpart within the pool of the natural amino acids, therefore the direct investigation of the local microenvironment around the proline residue in the peptide chain and its stability contribution is a difficult and challenging task. The non-natural amino acids are then incorporated into the target protein using molecular biology techniques. After purification, using different chromatography techniques, the engineered protein is further characterized by UV-VIS spectroscopy, Circular Dichroism, and Fluorescence spectroscopy.

In the same way, we can also incorporate non-natural amino acids with unique reactive groups to perform bio-orthogonal chemical reactions for the selective modification of therapeutic proteins. After protein purification, bio-conjugation of defined synthetic glycans or of other polymers (i.e. polyethylene glycol) are performed in vitro using different bio-orthogonal reactions (i.e. Copper-catalyzed cycloaddition). The modified protein is then subjected to different assays in order to test its resistance against proteolytic degradation and aggregation.

 
Discipline: Chemistry

Molecular magnetic behaviour in metal oxalate chains

Supervisor: Asst. Prof. Tony D. Keene

This project will involve the synthesis and characterisation of a series of transition metal oxalate coordination polymers. Synthetic techniques will include solvothermal and ambient reactions to produce the coordination polymers and separation techniques to isolate pure products from insoluble mixtures. The coordination polymers synthesised will be structurally characterised using single-crystal and powder X-ray diffraction and magnetically characterised using superconducting quantum interference device (SQUID) magnetometry. The second part of this project will look at the decomposition products of M(ox)(H2O)2 chains and their magnetic properties in conjunction with researchers at the University of Kent.


Grade Scale for University College Dublin - AACRAO EDGE

The following information is vetted and provided by the American Association of Collegiate Registrars and Admissions Officers (AACRAO) on the Electronic Database for Global Education (EDGE).

Letter Grade Percentage Ranking U.S. Equivalent
A+/A/A- 70 - 100% First Class Honours A
B+/B/B- 60 - 69% Second Class Honours Upper B+
C+/C/C- 50 - 59% Second Class Honours Lower B
D+ 45 - 49% Third Class Honours C+
D/D- 40 - 44% Pass C
F 0 - 39% Fail F
Intellectual property copyright AACRAO EDGE