Science and Health Undergraduate Summer Research Internship 2024

Tuberculosis (TB) is a major cause of morbidity and mortality worldwide. There were 10.6 million new cases of TB in 2022 according to the World Health Organization with low and lower-middle income countries worst affected. Multi-drug resistant (MDR) cases accounted for 3.3% of new TB cases but 12.9% of TB mortalities globally in 2019 due to a higher treatment failure rate. Mathematical modelling analysis has predicted that MDR-TB, as a proportion of incident TB, will increase in high MDR-TB burden countries. As approximately half of TB cases in Ireland today occur in persons born outside the state, we could potentially see an increase in MDR-TB cases in the future without additional health surveillance and preventive measures. Ireland is not unique in this regard and other European countries are also at risk of an increasing prevalence of multi-drug resistance among TB cases. Here, analysis will be completed on a large dataset of Mycobacterium tuberculosis genome sequences that we have assembled from Europe and other countries around the world. The most closely-related international genomes will be identified for each of the isolates using whole genome and core genome variant analysis. This will generate data on the international spread of MDR-TB as well as provide an insight into primary versus acquired sources of MDR-TB isolates. Statistical analyses will then be performed to ascertain the respective contribution of imported versus locally-acquired drug resistance to the burden of MDR-TB. The data generated will assist in identifying preventive measures for minimising the acquisition and transmission of MDR-TB in an European setting including in Ireland. It will also provide a basis for downstream modelling of the effect of future changes in the epidemiology of TB internationally on the incidence of TB in Ireland. 

For further information contact the project lead: 

Assoc Prof Ronan O'Toole | School of Biotechnology 

Email: ronan.otoole@dcu.ie

Background: The structural or sequence conservation among hepatitis C virus (HCV) NS5B and SARS-CoV-2 (SC-2) nsp12 viral proteins could support the hypothesis of having a common ancestor. The HCV non-structural protein (NSP) (NS5b) RdRp and MERS-CoV RdRp share a low sequence similarity but have structural similarity as both have two conserved aspartate residues at the active site (Elfiky and Azzam, 2021). A study by Mönttinen et al. (2021) pointed out possible structural conservation across the viral RdRps thus indicating the potential to target the polymerase for discovering wide spectrum antivirals.

Aim: The aim of the project is to use a molecular modelling approach to identify the structurally conserved binding pockets between HCV (NS5B) and SC-2 (Nsp12). The structurally conserved binding pockets of the proteins will be docked with compounds from the Enamine database to identify possible drug starting points.

Methodology: Week 1 1. Go through CCG MOE 2022 tutorials (computer-aided drug design software). 2. Read relevant literature on structural conservation. Week 2 1. Download the PDB structures of NS5B (HCV) and nsp12 (SC-2) Week 3 1. Use DALI server to look for pairwise structural comparison. 2. Perform pairwise sequence analysis of selected protein sequences. Week 4 1. Prepare the PDB’s and save in relevant folders. 2. Use MOE software to overlay structures. Week 5 1. Map the conserved residues on the 3D protein structures colour code viruses. Week 6 1. Prepare the Enamine dataset including conformer generation. 2. Perform docking with FRED software on the selected protein structures. Week 7 1. Assemble the docked poses for the selected proteins. 2. Correlate the structural conservation with sequence conservation. Highlight the conserved residues. Week 8 1. ESPript for making the secondary structure of protein on a pairwise sequence alignment file. 2. Assemble all the work together and prepare final presentation for the group.

For further information contact the project lead: 

Dr Darren Fayne | School of Chemical Sciences

Email: darren.p.fayne@dcu.ie

Patterns in randomness occur at different scales: watching an ant hill from some distance reveals its shape but not movements of individual ants. Zooming in on the ant hill we may lose the overall shape out of sight but find many individual ants apparently moving erratically, while in fact their collective behaviour can be well described by fluctuation laws like the normal distribution. Zooming in even further, we can only see the movement of individual ants. Probabilistically speaking, these three scales correspond to the law of large numbers, the central limit theorem, and individual marginal distributions, respectively. Other scales and situations are of much interest, too, for example the case of large deviations.

The aim of this project is to understand whether randomness occurring at one scale is independent of randomness occurring at another scale. This will be studied by looking at different weighted sums of n independent random variables as n goes to infinity, the weights encoding the scale. This is original research that should be of considerable interest to the probability and statistics community.

The student intern should have a good knowledge of probability theory, in particular limit theorems. Good knowledge of characteristic functions is preferrable.

The successful candidate will first start with the guidance of the supervisor to explore the easier case of the joint distribution of sums of random variables on the scales of the law of large numbers and the central limit theorem. Then they will investigate the more challenging cases, up to large deviations. The student will be provided with training on how to document their results with the typesetting software LaTeX, as well on how to present them to a scientific audience.

For further information contact the project lead: 

Assist. Prof Martin Venker | School of Mathematical Sciences

Email: martin.venker@dcu.ie

Hamstring strain injuries are extremely common in Gaelic football accounting for 22-24% in ladies’ and men’s Gaelic football respectively with an injury recurrence rate of 36%, which is increasing in recent years. Therefore, primary and secondary hamstring injury prevention is of paramount importance. No studies have examined the mechanism of hamstring injury in Gaelic football, even though this is a critical step in injury prevention. Consequently, hamstring injury prevention programmes in Gaelic football have been based upon the mechanism of injury in soccer, which has different physical demands of Gaelic football and soccer, and so it is possible that the current intervention programmes do not adequately address Gaelic football specific mechanisms of injury.

The aim of this study is to describe the mechanisms of hamstring strain injury in male and female Gaelic footballer players using video analysis. The study involves the analysis of existing videos of LGFA and GAA matches in the 2023 season using a standardised approach. The activity (e.g. running) and the posture (e.g. hip flexed, knee extended) of the player will be determined at the time of injury. If successful, the intern will be educated in this technique and supported in the development of this expertise. An intern will assist with collection, collation and analysis of data and the development of a summary of findings. We aim to use this as a foundation for an academic paper, conference presentation and presentation to the GAA and LGFA, all of which the intern will contribute and have their contribution recognised. He/she will also be integrated into the research team and receive training in data analysis, research methods and statistics. This environment will facilitate the development of the intern as a young researcher with exposure to the interdisciplinary research experience, and the training and mentoring this group can offer.

For further information contact the project lead: 

Assoc. Professor Enda Whyte | School of Health and Human Performance

Email: enda.whyte@dcu.ie

PSR B1259-63 is a millisecond radio pulsar in a highly eccentric 3.4 year orbit with a Be star. The Be stellar disk is highly inclined to the orbital plane, so that the pulsar crosses the disk twice per orbit. The interaction of the pulsar wind with the Be stellar disk/stellar wind is thought to be responsible for the observed broad band emission from radio up to very high-energy (TeV) emission. In both radio and X-ray, the unpulsed emission has a local minimum near the periastron and reaches its maximum when the pulsar passes through the Be stellar disk before and after the periastron. 

This system gives a unique chance to study the structure of the wind from the massive star and the details of the interaction between the relativistic and non-relativistic winds. Intensive observations of the 2021 periastron passage also demonstrated unusual features never observed before like the presence of the 3rd X-ray corresponding to the disappearance of the X-ray/radio correlation. To better understand the physical process taking place we are organising an extensive multi-wavelength monitoring of this system in 2024, with already approved intensive radio ( MeerKAT and ATCA ), optical (SALT), X-ray ( Swift, INTEGRAL) and gamma-ray (FERMI) facilities. The role of the student within this project would be to take part in ATCA radio observations and their further analysis and modelling in order to better understand the origin of the observed emission.

Dr Chernyakova's main research is based on the studies of broadband emission from the various sources of very high energy emission. In particular, Dr Chernyakova is very interested in the gamma-ray binaries. Gamma-ray binaries are a subclass of high-mass binary systems whose energy spectrum peaks at about 100 MeV and extends up to TeV energies.Currently, fewer than ten such systems were discovered in the gamma-ray band by the current generation of Cherenkov telescopes. Therefore gamma-ray binaries represent a relatively new and unexplored class of astrophysical object. Only for PSR B1259-63, LSI +61 303 and PSR J2032+4127 is the compact object firmly established as a pulsar. It is possible that the other systems also harbour radio pulsars, but that the optical depth is too high to detect the radio signal. Since the orbital period of PSR J2032+4127 is ~50 yrs, and the radio emission from LSI +61 303 is heavily obscured, PSR B1259-63, is the only gamma-ray binary with a known compact object, where both the pulsed and unpulsed non-thermal emission can regularly be studied with multi-wavelength observations. 

The next periastron passage in PSR B1259-63 will happen this summer and Dr Chernyakova has already organised an intensive multi wavelength campaign with lots of observations. In particular, there willl be intensive radio observations (will be done online) where the student can help both with the observations and the following analysis. In the campaigns like this usually the first goal is to perform all the analysis as soon as possible in order to inform the community on the observational results to be used in future modelling, and a help with the analysis of the radio data will be extremely useful. In addition, I hope that student will be interested in the project and will continue to work on the project afterwards which will be a clear path to the IRC funding.

For further information contact the project lead: 

Dr Masha Chernyakova | School of Physical Sciences

Email: masha.chernyakova@dcu.ie

The internship project will serve as an important component within the IRC Coalesce PANO Prehabilitation for Peritoneal Malignancy Cancer Patients feasibility trial (2022-2024), targeting the enhancement of support mechanisms for cancer patients undergoing surgery. The primary aim is to develop a Patient and Public Involvement (PPI) co-designed pre-surgery information resource pack, tailored to empower patients, combat misinformation, and foster self-confidence in adopting health behaviors conducive to recovery and survivorship.

Within the framework of the PANO trial, there's a PPI recognized imperative to address the informational and supportive needs of patients preparing for surgery. Through close collaboration with PPI representatives, the internship project will harness their insights from their lived experience as cancer patients, and also from participating in the trial. This collaboration will inform the creation of a comprehensive resource pack comprising PPI co-created podcasts, expert-led videos encompassing support strategies, physical activity guidelines, and nutritional optimization, alongside easy-to-understand informational sheets and consent forms. Furthermore, the resource pack will equip patients with tools to identify and circumvent cancer-related misinformation, thereby fostering informed decision-making and proactive engagement in their health journey.

The internship endeavor not only serves to co-develop this invaluable resource with PPI but also lays the groundwork for future initiatives. It will play a pivotal role in shaping an upcoming PPI Ignite grant application, aimed at expanding PPI involvement within the healthcare landscape. By establishing a strong foundation through collaborative efforts, this project sets the stage for subsequent endeavors, including the pursuit of a Definitive Interventions Award (DIF) to further extend the reach and impact of PPI initiatives in facilitating improved patient outcomes and healthcare delivery. 

For further information contact the project lead: 

Dr Lorraine Boran | School of Psychology

Email: lorraine.boran@dcu.ie

This project will have scope to explore content and modes for the teaching of practical skill and theory in Chemistry in virtual environments. This will include testing a VR App being developed by DCU for lab practical training. This could involve some practical work to develop procedures for replication in this App. The internship will also involve the creation of environments in immersive applications (e.g. Spatial, Engage) for teaching Chemistry where we will use the software Blender to create 3D models, e.g. molecular structures to use as interactive teaching tools. It is envisaged that the intern will be mostly computer-based (PC-simulations or VR) but the link to the practical laboratory will be important and so there may be some use/testing of instrumentation. 
 

The PI is leading a project on assessing Digital and Virtual Laboratory content for its effectiveness in teaching practical skill. This project has been rolled out in 3rd year practical chemistry modules in School of Chemical Sciences for the last 3 years. This roll out has involved developing new pedagogical approaches to teaching practical skill - including new pre-lab preparatory content, eg quizzes, videos; assessment of lab techniques via video-making, virtual twin development of instrumentation in VR; and introduction to simulations. The Summer Intern will get the opportunity to explore and look at developing out some of these approaches to support the teaching of practical skill to ensure our graduating students have the excellent practical and transversal skills needed for the workplace.

For further information contact the project lead: 

Dr Aoife Morrin | NCSR

Email: aoife.morrin@dcu.ie

The ProtoSigns Lab lead by Dr. Seán Jordan is focused on investigating the formation of the first cell membranes from simple organic molecules and their potential preservation in the geological record. We have shown previously that single chain amphiphilic molecules such as fatty acids form stable bilayer membranes in simulated early Earth environments. Others have demonstrated that mineral catalysts relevant to the early Earth can facilitate the reduction of CO2 under hydrothermal conditions leading to the production of long-chain fatty acids. We will now investigate a plausible pathway for in situ production of amphiphilic organics leading directly to the formation of bilayer membranes. This would elucidate a sequential progression from molecules to membranes – one of the first steps on the path to living cells. We will modify the CO2 reduction experiments to generate conditions which favour membrane self-assembly. We will analyse the resulting solutions using UV-Vis spectroscopy, gas chromatography-mass spectrometry, and phase contrast, fluorescence, confocal, and electron microscopy. This will enable us to characterise and quantify both the organic molecules produced in the initial CO2 reduction, and the resulting membrane structures. This project is in collaboration with Dr. Nessan Kerrigan in the SCS, an expert in metal catalysis and organic synthesis, and Dr. Martina Preiner at the Max Planck Institute for Terrestrial Microbiology, an expert in prebiotic mineral catalysis and protometabolic pathways. The student will meet regularly with collaborators and work closely with PhD students and Postdocs in the lab as part of a supportive research environment. They will gain valuable skills in organic chemistry and state-of-the-art analytical techniques. This project will provide the student with the opportunity to work at the cutting edge of prebiotic chemistry and astrobiology research, enhancing our understanding of the origin of life on Earth and supporting our search for life on other planetary bodies.

For further information contact the project lead: 

Dr Seán Jordan | Life Science Institute

Email: sean.jordan@dcu.ie