Postgraduate Seminars

2016 Postgraduate Seminars

An investigation of the role of Rab11A and Rab11B in EGFR endosomal trafficking

Supervisor: Professor Mary McCaffrey, School of Biochemistry and Cell Biology

Investigation of the underlying mechanisms of stop codon UGA read-through

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology & Dr John Mackrill, Department of Physiology

Obtaining ribosomal complexes for structural insights into the mechanism of translational frameshifting

PhD Candidate: Pramod Bhatt

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

Investigation of mechanisms by which PINK1 protects against Parkinson’s disease: to develop better biomarkers and treatment targets for the disease

PhD Candidate: Rachel Furlong

Supervisor: Dr Cora O’Neill, School of Biochemistry and Cell Biology

Translation termination in diverse ciliates depends on stop codon proximity to 3’ polyA tails

PhD Candidate: Stephen Heaphy

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

The Host Response towards Bifidobacteria breve UCC2003

PhD Candidate: Ana Hickey

Supervisor: Dr Ken Nally, School of Biochemistry and Cell Biology & Professor Douwe Van Sinderen, School of Microbiology

G-quadruplex mediated translation regulation and ribosome pause detection

PhD Candidate: Romika Kumari

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

Subcellular localisation of the FLT3-ITD oncogene and NOX4 is critical in the production of pro-survival reactive oxygen species in acute myeloid leukaemia

PhD Candidate: Jennifer Moloney

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Self-assembling protein-based nanoparticle biosensors for microscopy imaging

PhD Candidate: Neil O’Donnell

Supervisor: Dr Ruslan Dmitriev & Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Investigation of the role of the brain-gut axis in the pathophysiology of Parkinson’s disease

MSc Candidate: Sarah O’Donovan

Supervisor: Dr Cora O’Neill, School of Biochemistry and Cell Biology

The investigation of putative recoding events in Streptomyces

PhD Candidate: Sinead O’Loughlin

Supervisor: Professor John Atkins & Dr Pasha Baranov, School of Biochemistry and Cell Biology

Progesterone analog-mediated Redox response enhances cell survival in stressed 661W photoreceptor cells

PhD Candidate: Ana Ruiz Lopez

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Identification of the molecular pathways that mediate cytokine-induced immunopathology of the gut epithelium

PhD Candidate: Nisha Saini

Supervisor: Dr Ken Nally, School of Biochemistry and Cell Biology

Mechanisms of immune tolerance in mice

PhD Candidate: Sreeram Udayan

Supervisor: Dr Ken Nally, School of Biochemistry and Cell Biology & Professor Paul O’Toole, School of Microbiology

2015 Postgraduate Seminars

An investigation of the role of Rab11A and Rab11B in EGFR endosomal trafficking

PhD Candidate: Patrycja Artemiuk

Supervisor: Professor Mary McCaffrey, School of Biochemistry and Cell Biology

Isolation and characterization of Selenoprotein P: A multiple Selenocysteine-containing protein in Crassostrea gigas

PhD Candidate: Janinah Baclaocos

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology & Dr John Mackrill, Department of Physiology

Obtaining ribosomal complexes for structural insights into the mechanism of translational frameshifting

PhD Candidate: Pramod Bhatt

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

IGF1 inducible mitochondrial nucleotide carrier PNC1, regulates invasiveness in breast cancer

PhD Candidate: Michael Coleman

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Widespread abrogation of triplet translation continuity and stop codon mediated termination in Euplotes ciliates

PhD Candidate: Stephen Heaphy

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

Host response towards Bifidobacteria breve UCC2003 and the effect of sortase-dependent pili on this interaction

PhD Candidate: Ana Hickey

Supervisor: Dr Ken Nally, School of Biochemistry and Cell Biology & Professor Douwe Van Sinderen, School of Microbiology

Use of PLIM imaging to investigate the effect of oxygen on the expression of SPCA2

PhD Candidate: James Jenkins

Supervisor: Dr Ruslan Dmitriev & Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Luminescent optical oxygen sensors with food packaging applications

PhD Candidate: Caroline Kelly

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

G-quadruplex mediated translation regulation

PhD Candidate: Romika Kumari

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

Mislocalized activation of FLT3-ITD induces the production of reactive oxygen species in MV4-11 cells

PhD Candidate: Jennifer Moloney

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Computational analysis of ribosome profiling data in order to examine short term translation response

PhD Candidate: Patrick O’Connor

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

Nanoparticle biosensors for imaging

PhD Candidate: Neil O’Donnell

Supervisor: Dr Ruslan Dmitriev & Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Recoding in Streptomyces

PhD Candidate: Sinead O’Loughlin

Supervisor: Professor John Atkins & Dr Pasha Baranov, School of Biochemistry and Cell Biology

Neurotrophic factor profile in mouse retina following stress and treatment with Norgestrel

PhD Candidate: Ana Ruiz Lopez

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Identification of the molecular pathways that mediate cytokine-induced immunopathology of the gut epithelium

PhD Candidate: Nisha Saini

Supervisor: Dr Ken Nally, School of Biochemistry and Cell Biology

Understanding the role of TLR2 in inflammation using TLR2 knockout mice as a model system

PhD Candidate: Sreeram Udayan

Supervisor: Dr Ken Nally, School of Biochemistry and Cell Biology & Professor Paul O’Toole, School of Microbiology

Elucidating the mechanism of action behind the neuroprotective compound ‘Norgestrel’ in the treatment of stressed photoreceptor cells

PhD Candidate: Alice Wyse Jackson

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

2014 Postgraduate Seminars

Investigation of the role of PDLIM2 in breast cancer metastasis and tumor microenvironment regulation

PhD Candidate: Milán Bustamante Garrido (PhD Scholars Programme in Cancer Biology)

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Characterisation of presenilins in innate immune receptor signalling

PhD Candidate: Caroline Coleman

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

IGF1 inducible mitochondrial nucleotide carrier PNC1, regulates invasiveness in breast cancer

PhD Candidate: Michael Coleman

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Altered regulation of adipogenesis in disease process

PhD Candidate: Stephanie Davies (PhD Molecular and Cell Biology)

Supervisor: Professor Tommie McCarthy, School of Biochemistry and Cell Biology

Presenilin ubiquitination and CUE domain function

PhD Candidate: Stephen Duggan

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

Ribosomal frameshifting is a standard feature of translation in Euplotes ciliates

PhD Candidate: Stephen Heaphy

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

New systems for oxygen imaging in tissues

PhD Candidate: James Jenkins

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Novel optical oxygen sensors for smart food packaging systems

PhD Candidate: Caroline Kelly

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Role of RNA G-quadruplexes role in translation

PhD Candidate: Romika Kumari

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

Cellular regulation of the ubiquitin conjugating enzyme Ubc6

PhD Candidate: Selina Lam (PhD Scholars Programme in Cancer Biology)

Supervisor: Dr Eoin Fleming, School of Biochemistry and Cell Biology

LNX1 and LNX2 in the nervous system: a study of molecular interactions and regulation of expression

PhD Candidate: Joan Lenihan

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

Investigation of the role of Trib2 in T-cell development and T-ALL

PhD Candidate: Kai-Ling Liang

Supervisor: Professor Tommie McCarthy, School of Biochemistry and Cell Biology

IGF-1R signalling is essential for mitochondrial maintenance and function

PhD Candidate: Amy Lyons (PhD Molecular and Cell Biology)

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Alpha-Actinin: characterisation and synthetic biology applications

PhD Candidate: Anita Murphy

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

Characterisation of the role of ST2/IL-33 in colon cancer

PhD Candidate: Charlotte O'Donnell

Supervisor: Dr Aileen Houston, Department of Medicine

Oxygen and glucose deprivation induces both global and gene-specific alterations in mRNA translation within 20 minutes

PhD Candidate: Patrick O’Connor

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

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PhD Candidate: Sandra O'Shea

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Investigating the effect of 5'UTR on translational efficiency and mTOR inhibition

PhD Candidate: Anjali Pai (PhD Scholars Programme in Cancer Biology)

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

The effect of Isoellipticines on leukaemia

PhD Candidate: Eileen Russell (PhD Molecular and Cell Biology)

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Development of tumour therapy and imaging strategies utilising bacteria

PhD Candidate: Mike Stanton (PhD Scholars Programme in Cancer Biology)

Supervisor: Dr Mark Tangney, Cork Cancer Research Centre

Investigating the potential role of GRAB as a Guanine Exchange Factor (GEF) for Rab8 and Rab3 and the functional outcome of these interactions

PhD Candidate: Jennifer Timoney (PhD Scholars Programme in Cancer Biology)

Supervisor: Professor Mary McCaffrey, School of Biochemistry and Cell Biology

Using ribosomal profiling to study translation regulation

PhD Candidate: Ioanna Tzani (PhD Scholars Programme in Cancer Biology)

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

Neuroprotection of retinal photoreceptors

PhD Candidate: Alice Wyse Jackson

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

2013 Postgraduate Seminars

Investigation of the role of PDLIM2 in colorectal cancer metastasis and tumor microenvironment regulation

PhD Candidate: Milán Bustamante Garrido (PhD Scholars Programme in Cancer Biology)

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Gene 60 Bypassing: The Nascent Peptide Effect

PhD Candidate: Arthur Coakley

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

A study of the role of presenilins in the innate immune response

PhD Candidate: Caroline Coleman

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

IGF1 inducible mitochondrial nucleotide carrier PNC1, regulates invasiveness in breast cancer

PhD Candidate: Michael Coleman

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Altered regulation of adipogenesis in disease processes

PhD Candidate: Stephanie Davies (PhD Molecular and Cell Biology)

Supervisor: Professor Tommie McCarthy, School of Biochemistry and Cell Biology

Presenilin Ubiquitination and gamma-secretase activity

PhD Candidate: Stephen Duggan

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

Proteomics approaches to environmental stress in Mytilus edulis due to emerging classes of anthropogenic pollutants

PhD Candidate: Tahirah Ja'Afar

Supervisor: Professor David Sheehan, School of Biochemistry and Cell Biology

Measurement of cell respiration and oxygenation with novel phosphorescent probes

PhD Candidate: Alina Kondrashina

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Steady state expression of the human ubiquitin conjugating enzyme Ubc6 (UBE2J2) is regulated by JNK and P38 MAP kinase signalling pathways

PhD Candidate: Selina Lam (PhD Scholars Programme in Cancer Biology)

Supervisor: Dr Eoin Fleming, School of Biochemistry and Cell Biology

LNX1 and LNX2 function in the central nervous system: A Study of Molecular Interactions

PhD Candidate: Joan Lenihan

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

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PhD Candidate: Kai-Ling Liang

Supervisor: Professor Tommie McCarthy, School of Biochemistry and Cell Biology

IGF-1R Signalling Is Essential for Mitochondrial Maintenance and Function

PhD Candidate: Amy Lyons (PhD Molecular and Cell Biology)

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Nano-Meccano: Using Protein-Based Elements as Building Blocks to Generate Synthetic Nanostructures

PhD Candidate: Anita Murphy

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

The Potential Role of ST2 and its Ligand IL-33 In colon carfinogenesis

PhD Candidate: Charlotte O'Donnell

Supervisor: Dr Aileen Houston, Department of Medicine

Phosphorylation of Critical Tyrosine residue Y1250 in the C terminal Domain of IGF-1R is dependent on IGF-1

PhD Candidate: Sandra O'Shea

Supervisor: Professor Rosemary O'Connor, School of Biochemistry and Cell Biology

Investigation of the mechanism of TOP genes regulation at the level of translation

PhD Candidate: Anjali Pai (PhD Scholars Programme in Cancer Biology)

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

Isoellipticines: Novel Molecules for the Treatment of Leukaemia

PhD Candidate: Eileen Russell (PhD Molecular and Cell Biology)

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Nox4-generated H₂O₂ translocates to the nucleus to cause DNA oxidation and DNA double strand breaks in FLT3-ITD AML

PhD Candidate: Joanna Stanicka

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Development of tumour therapy and imaging strategies utilising bacteria

PhD Candidate: Mike Stanton (PhD Scholars Programme in Cancer Biology)

Supervisor: Dr Mark Tangney, Cork Cancer Research Centre

Investigating a novel interaction and the functional relationship between Rab25 and TGF Beta Receptor I in the context of cell motility and invasion

PhD Candidate: Jennifer Timoney (PhD Scholars Programme in Cancer Biology)

Supervisor: Professor Mary McCaffrey, School of Biochemistry and Cell Biology

Ribosome profiling in Merkel Cell Polyomavirus induced Merkel Cell Carcinoma

PhD Candidate: Ioanna Tzani (PhD Scholars Programme in Cancer Biology)

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

Role of mitochondrial activity and hypoxia in mitochondrial calcium turnover in colon cancer cells

PhD Candidate: Alicia Waters

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

2012 Postgraduate Seminars

Investigation of the p75 neurotrophin receptor and the role of its post-translational modifications in tumour cell motility and invasiveness

PhD Candidate: Janina Berghoff (PhD Scholars in Cancer Biology Programme)

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

Presenilin and Regulated Intramembrane Proteolysis of Interleukin-1 receptor, type 1 and Tumor Necrosis Factor (TNF) receptor-1

PhD Candidate: Jyoti Chhibber

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

Identifying the nature of reading frame transitions observed in prokaryotic genomes

PhD Candidate: Arthur Coakley

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

The effect of oxidative stress on the iron regulatory HFE protein and the ubiqutin-conjugating enzyme Ubc6e

PhD Candidate: Louise Foley

Supervisor: Dr Eoin (John) Fleming, School of Biochemistry and Cell Biology

Proteomics approaches to environmental stress in Mytilus edulis due to emerging classes of anthropogenic pollutants

PhD Candidate: Tahirah Ja’Afar

Supervisor: Professor David Sheehan, School of Biochemistry and Cell Biology

Monitoring of cell oxygenation with new phosphorescent based probes and techniques

PhD Candidate: Alina Kondrashina

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

Observation of dually decoded regions of the human genome using ribosome profiling data

PhD Candidate: Audrey Michel

Supervisor: Dr Pasha Baranov and Professor John Atkins, School of Biochemistry and Cell Biology

Functional consequence of FIP3 interactions with the dynein motor complex

MSc Candidate: Sylvia O’Sullivan

Supervisor: Professor Mary McCaffrey, School of Biochemistry and Cell Biology

Elucidation of the role of Evi5 in the Rab11/Rab25 mediated endosomal trafficking and cell migration events

MSc Candidate: Lydia Riordan

Supervisor: Professor Mary McCaffrey, School of Biochemistry and Cell Biology

Assessment of contribution of key metabolites to cell bioenergetics, responses to stimulation and hypoxia

PhD Candidate: Alicia Waters

Supervisor: Professor Dmitri Papkovsky, School of Biochemistry and Cell Biology

A nascent peptide stimulates the regulatory frameshifting on antizyme mRNA

PhD Candidate: Martina Yordanova

Supervisor: Professor John Atkins, School of Biochemistry and Cell Biology

2011 Postgraduate Seminars

A novel role of Presenilin2 in determining IL1β and LPS mediated responsiveness and gene regulation

PhD Candidate: Vishal Agrawal

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

The regulation of NF-κB by Promyelocytic Leukaemia (PML) protein

PhD Candidate: Abrar Ahmed

Supervisor: Dr Ruaidhri Carmody, School of Biochemistry and Cell Biology

The SREBP Pathway in Cancer

PhD Candidate: Kathy Barriscale

Supervisor: Professor Tommie McCarthy, School of Biochemistry and Cell Biology

Investigation of p75 neurotrophin receptor and the role of its post-translational modifications in tumour cell motility and invasiveness

PhD Candidate: Janina Berghoff

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

Development of an integrated microfluidic system for genetic analysis

PhD Candidate: Desmond Brennan

Supervisor: Dr Paul Galvin, ASSERT for Health Research Group, UCC

Targeting regulatory T cells in cancer

PhD Candidate: William Byrne

Supervisor: Professor Gerry O’Sullivan, Cork Cancer Research Centre

Presenilin and regulated intramembrane proteolysis of Interleukin-1 receptor, type 1

PhD Candidate: Jyoti Chhibber

Supervisor: Dr Justin McCarthy, School of Biochemistry and Cell Biology

Investigation of the molecular determinants of NF-κB p50 ubiquitination

PhD Candidate: Patricia Collins

Supervisor: Dr Ruaidhri Carmody, School of Biochemistry and Cell Biology

FLT3-driven redox signalling in acute myeloid leukemia

PhD Candidate: Aoife Corcoran

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Investigating the function of heme-binding protein HRG-1 in pH equilibrium and invasive cancer cells

PhD Candidate: Fionola Fogarty

Supervisor: Professor Rosemary O’Connor, School of Biochemistry and Cell Biology

Investigation of the role of the α-actinin family of actin-binding proteins in cell adhesion and motility

PhD Candidate: Kate Foley

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

The effect of oxidative stress on the iron regulatory HFE protein

PhD Candidate: Lousie Foley

Supervisor: Dr Eoin (John) Fleming, School of Biochemistry and Cell Biology

Regulation of TRIB2 gene expression in normal and AML Cells

PhD Candidate: Maura Hannon

Supervisor: Dr Karen Keeshan, School of Biochemistry and Cell Biology

Investigating IRS/RACK1 complexes in IGF-IR pathway in cancer cells

PhD Candidate: Catherine Harrington

Supervisor: Professor Rosemary O’Connor, School of Biochemistry and Cell Biology

A SLICK technique for the study of neuronal activity-dependent competition

PhD Candidate: Victoria Heimer-McGinn

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

Redox effects on sub-proteomes targeted by oxidative stress

PhD Candidate: Wentao Hu

Supervisor: Professor David Sheehan, School of Biochemistry and Cell Biology

Development of public databases and large-scale analysis of RNA editing in humans

PhD Candidate: Anmol Kiran

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

The interactions of Nox4 and Bcr-Abl in the survival of leukaemia cells

PhD Candidate: William Landry

Supervisor: Professor Tom Cotter, School of Biochemistry and Cell Biology

Mechanism of Trib2 mediated degradation of C/EBP-α in Acute Myelogenous Leukaemia

PhD Candidate: Fiona Lohan

Supervisor: Dr Karen Keeshan, School of Biochemistry and Cell Biology

Development of a computational technique to detect reading frame transitions using ribo-seq data

MSc Candidate: Audrey Michel

Supervisor: Dr Pasha Baranov and Professor John Atkins, School of Biochemistry and Cell Biology

Regulation of LPS tolerance in macrophages

PhD Candidate: Christine O’Carroll

Supervisor: Dr Ruaidhri Carmody, School of Biochemistry and Cell Biology

Investigating the role of PTEN-induced Kinase 1 in cancer development and pathogenesis

PhD Candidate: Ciara O’Flanagan

Supervisor: Dr Cora O’Neill, School of Biochemistry and Cell Biology

Pregnancy-Specific Glycoproteins: search for a receptor mediating pro-angiogenic and immunomodulatory properties

PhD Candidate: Ronan O’Riordan

Supervisor: Dr Tom Moore, School of Biochemistry and Cell Biology

Proteomic approach of oxidative stress in Daphnia magna

PhD Candidate: Louis Charles Rainville

Supervisor: Professor David Sheehan, School of Biochemistry and Cell Biology

Analysis of expression and function of LNX1 and LNX2 in the central nervous system

PhD Candidate: Orthis Saha

Supervisor: Dr Paul Young, School of Biochemistry and Cell Biology

Analysis of evolutionary conserved recoded genes in bacteria

PhD Candidate: Virag Sharma

Supervisor: Dr Pasha Baranov, School of Biochemistry and Cell Biology

NF-κB p105 and IκBγ are nucleocytoplasmic shuttling proteins

PhD Candidate: Jamie Urquhart

Supervisor: Dr Ruaidhri Carmody, School of Biochemistry and Cell Biology

TRAF6-mediated ubiquitination of the γ-secretase protease complexes and its substrates

Postgraduate Seminars