Postdoctoral Researcher - Epigenomics as the Next Step in Molecular Diagnostics

Postdoctoral Researcher - Epigenomics as the Next Step in Molecular Diagnostics

DCU - Dublin City University

Dublin, Ireland

Background & Role

Applications are invited from suitably qualified candidates to join the RAPID Institute (Research Advances in Personalised Integrated Diagnostics) Research Group in DCU. The goal of our Institute is to understand and exploit the role of epigenetics in diseases that are particularly governed by temporal changes in the epigenome (e.g. Neurodegenerative & Metabolomic diseases/disorders). The RAPID Institute works across 3 distinct technology pillars/platforms (e.g. benchtop, portable and wearable diagnostic devices) to delve into the emerging power of epigenomics, explore biochemical wearable sensors, and enable POC settings with rapid, affordable testing. These platforms will be interconnected in a way that impacts epilepsy, substance abuse and infectious disease in unprecedented ways.

This advertised Postdoctoral Researcher role falls within research as part of Pillar 1 - Epigenomics as the next step in molecular diagnostics. PILLAR-1 will advance benchtop technologies using Lab- on-a-disc diagnostic devices, to enable users to probe the epigenome for diagnostic information without specialty labs, focusing on epilepsy and addictive behaviour. Epigenomics is the next step in DNA-based molecular diagnostics with recent research increasingly indicating that DNA methylation markers are likely to be important as biomarkers of clinical significance. The appointed candidate will be hosted in the School of Biotechnology, Dublin City University, working under the direction of the Principal Investigator within the Institute’s interdisciplinary research team.

Epigenomics has added a new dimension to DNA analysis highlighting the importance of reversible post-transcriptional modification. One modification is – DNA Methylation – a eukaryotic epigenetic mechanism where gene expression is altered through methylation of the C-5 location on cytosine immediately preceded by a guanidine residue – a ‘CpG site’. Recent research increasingly indicates the DNA methylation markers are likely to be important as biomarkers of clinical significance. The state of methylation at any locus is the genome represents a snapshot in time of the dynamic changes that occur in the genome (not in base sequence) in response to an individual’s environment. These provide information on a vast array of phenotypes including aging, diet, lifestyle, physiology, and even vitamin deficiency, to name a few. It is clear that the ‘methylome’ contains an abundance of diagnostic information pertinent to a number of disorders, and an increasing number of DNA methylation-based biomarkers are being characterised with a particular focus on cancer. While only a small number have been FDA- approved to-date, these markers promise an additional biological dimension to non-invasive disease detection and monitoring. While some clinical labs have the capability for methylated DNA analysis, it is not routinely incorporated into standard clinical testing. In the absence lab setting, there is a clear need for cost-effective, flexible diagnostic device platform, capable of being used for diverse biomarker panels, and designed to integrate into current clinical lab workflows. We will address this directly to open up new vistas in genome-based biomarker detection that can easily be incorporated into current clinical lab workflows.

The proposed Postdoctoral research role will lead the development of core centrifugal Lab-on-a- Disc (LoaD) technologies developed by both Prof. Landers and other members of our interdisciplinary research team to achieve (i) miniaturisation of the cumbersome sample preparation associated with DNA methylation quantitation and (ii) integration the entire workflow through the Sanger sequencing.

Principal Duties and Responsibilities

The duties and responsibilities of the position include, but are not restricted to, the following:

• Conduct a specified programme of research within Pillar 1 involving design and bioassay integration within lab-on-a-chip/disc-based platforms, under the direction of the project PI;
• Leading all activities relating to the mechanical design, system design, implementation and integration of during the development of a flexible diagnostic device platform, capable of being used for target-relevant biomarker panels and designed to integrate into current clinical lab workflows;
• Testing the developed instrument prototype under various conditions and working to validate the performance of the system, informing the system usability and design;
• Responsibility for leading the design and manufacturing of prototype devices, in collaboration with an associated team of postgraduate students;
• Support engagement with industry and other external parties in areas relevant to the project;
• Support reporting of project outcomes to SFI, including development and maintenance relevant design control documentation;
• Authoring of scientific publications, technical reports and marketing activities as may be required to support the commercialisation activities as required by the project;
• Engage in appropriate training and professional development opportunities are recommended/required by Dublin City University.

Minimum Criteria

• Applicants should have a Ph.D. in a relevant discipline In addition, the ideal candidate will have:
  • It is desirable that the successful candidate has a M.Sc. or B.A. degree in Biomechanical/Biomedical/Engineering; Chemistry/Biochemistry, Molecular Biology or a related Engineering/Science degree;
  • Practical laboratory experience designing and building experimental microfluidic/lab-on- chip research platforms/test-rigs/instrumentation. Proven aptitude for laboratory work and a hands-on ability to build, test and validate functional prototypes/breadboard instruments;
  • Experience in microfluidics/Lab-on-a-Chip and micro-fabrication. Experience with heat- transfer in Lab-on-a-Chip;
  • Experience and expertise in SolidWorks CAD, LabVIEW control software and data analysis techniques are highly desirable;
  • Experience in common biochemical and molecular biology (nucleic acid) separation sequencing and amplification techniques/methods (e.g. NAAT, PCR, Sanger Sequencing) are highly desirable;
  • Experience with fluorescence detection of bio-samples particularly developing instrument systems;
  • Experience building, testing, and validating functional prototypes/breadboard of laboratory instruments or test-rigs for biomedical experiments;
  • Good communication and reporting skills.

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