Our research

Description

This project develops and analytically and clinically validates bioelectronic assays on magnetic beads (MB) for accurate monitoring of therapy efficacy in patients with metastatic breast, prostate, gastric and colorectal cancers. The DC will develop electrochemical ELASA on MBs with novel electrocatalytic labels and apply them for liquid biopsy analysis of cancer patients’ samples for PTM of selected proteins. Assays will be integrated within the bioelectronic MB-based strip test device for PoC monitoring of the cancer treatment efficacy and characterizing the type of tumor and resistance to treatment

Research fields: Electrochemistry, Surface Science, Biochemistry, Biotechnology, Molecular Biology

Main Supervisor: Elena Ferapontova (elena.ferapontova@inano.au.dk)

Host Institution:

Description

The aim of this project is to create a multianalyte, multi-replicate, multianalyte device for measuring PTM biomarkers with ECL detection. In particular, to create novel ECL luminophore dyes for labelling aptamers and antibodies enabling multiplexed assays with target discrimination; to develop highly sensitive ECL assays for methylated DNA and proteins with aberrant glycosylation patterns; to test the analytical performance of the assays using serum samples collected from patients to integrate the assays within a 384 microwell electrode array and determine the performance required from an optical reader to identify the feasibility of using a mobile phone camera as the detector.

Research field: Electrochemistry, Surface Science, Biochemistry, Molecular Biology

Main Supervisor(s): Robert Forster (Robert.Forster@dcu.ie)

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Description

This project aims to create ECL luminophore – nanoparticle (NP) pairs where a fraction of the ECL generated activates the plasmon of metal NP, generating an intense electric field that amplifies the ECL generated by the other luminophores immobilised on NP, and to develop new approaches for the deposition of aptamer and antibody receptors onto individual electrodes and within microwell electrode arrays. The objective is to establish high performance antibody based ECL assays for methylated DNA and test the assay performance using real patient samples.

Research field: Electrochemistry, Surface Science, Biochemistry, Molecular Biology

Main Supervisor(s): Robert Forster (Robert.Forster@dcu.ie)

Host Institution:

Description

The aim of this PhD project is the selection and characterization of aptamer receptors for the O-glycosylation site of glycoproteins, such as mucins, overexpressed in colorectal cancer, and their application to develop diagnostic tools for early detection of cancer. The DC will select the aptamers and will design and optimize sensing platforms using them to detect aberrant glycosylated forms of the selected proteins, evaluating their diagnostic potential by testing clinical samples.

Research field: Electrochemistry, Surface Science, Biochemistry, Molecular Biology

Main Supervisor(s): María Jesús Lobo-Castañón (mjlc@uniovi.es)

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Description

This PhD project aims to obtain and characterize a panel of aptamers mimicking lectins to recognize aberrant glycosylation patterns of proteins, using them to develop aptamer microarrays and other platforms for profiling specific N-linked glycoforms of protein biomarkers. The DC will evaluate differential glycoforms of selected glycoproteins, such as carcinoembryonic antigen, in colorectal tumor tissues and normal tissues, assessing their diagnostic/prognostic performance in serum samples.

Research field: Electrochemistry, Surface Science, Biochemistry, Molecular Biology

Main Supervisor(s): María Jesús Lobo-Castañón (mjlc@uniovi.es)

Host Institution:

Description

The aims of this project are (i) the development of femto-second laser ablation technology for surface nano-patterning of gold electrodes in the biosensor microarray for electrochemical cancer detection; (ii) creation of nano-patterned PEDOT electrodes in the biosensor microarray for electrochemical cancer detection by soft nano-imprint of photo-curable PEDOT formulation. The surface nano-pattern will be optimized to achieve antifouling properties and long-life time of Au electrodes for electrochemical sensors. The photo-curable PEDOT formulation and characteristics of the surface nano-pattern will be adjusted for improved antifouling properties and long-life time of the polymeric electrodes. The nano-patterned gold electrodes and nano-patterned polymeric electrodes will be fabricated and tested with assays developed by the STRIM partners.

Research field: Physics, Laser Physics, Nanoscience, Electrochemistry, Surface Science, Biochemistry, Molecular Biology

Main Supervisor(s): Prof. Dr. Boris Chichkov (chichkov@iqo.uni-hannover.de)

Host Institution:

Description

The aim of this project is to develop novel nanocomposite polymer-based screen-printing inks and electrodes to act as platforms for electrocatalytic and ECL assays, for which the successful candidate will establish the data protocols for multiplexed assay data analysis in the Z&P DjuliTM cloud database. Anti-fouling properties of electrodes will be explored by micro- and nano-patterning and tested in industrial environment. Finally, analysis of multiplexed assay data in DjuliTM will be used as a pan-cancer screening tool.

Research field: Electrochemistry, Surface Science, Biochemistry, Molecular Biology

Main Supervisor(s): Sindre Søpstad (sindre@zimmerpeacock.com)

Host Institution:

Description

The DC will apply the integrated stakeholder-centric impact evaluation framework to investigate expectations and requirements with respect to pan-cancer screening among all stakeholders (patients, payers and commissioners) involved in cancer screening. The DC start by mapping all relevant stakeholders, will collect user expectations and requirements with respect to pan-cancer screening and will elicit population preferences by making use of discrete choice experiments, focusing on the potential harms of pan-cancer screening (e.g. false-positive test results, overdiagnosis and complications), related to mortality reduction, test frequency and screening setting/location.

Research field: Health Sciences, Public Health, Epidemiology, Medicine.

Main Supervisor(s): Prof. Harry de Koning (h.dekoning@erasmusmc.nl) and Esther Toes-Zoutendijk (e.toes-zoutendijk@erasmusmc.nl)

Host Institution:

Description

The DC will evaluate the cost-effectiveness of different screening policy scenarios for pan-cancer approaches and will estimate the long-term benefits of screening and early detection (i.e. incidence and mortality reduction, quality-adjusted life-years gained). The DC will compare these outcomes to those of the existing cancer screening programs. In addition, the DC evaluates potential improvements to the pan-cancer test, and how these impact the comparative effectiveness of pan-cancer screening. This way, the DC can help define thresholds int test performance, acceptability and costs for pan-cancer screening to provide good value for money. For this, the DC will be trained in health technology assessment and microsimulation modeling for cancer screening.

Research field: Mathematics, Econometrics, Biostatistics.

Main Supervisor(s): Prof. dr. Iris Lansdorp-Vogelaar (i.vogelaar@erasmusmc.nl) and Esther Toes-Zoutendijk (e.toes-zoutendijk@erasmusmc.nl)

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Description

The aim of this PhD project is the development of bioinformatic pipelines and molecular modeling approaches to analyzed glycoproteomics data produced during the projects by other collaborators or available in literature to identify suitable markers for aptamer design

Research field: Bioinformatics, Biochemistry, Molecular Modeling, Computational Biology.

Main Supervisor(s): Assoc. Prof. Elena Papaleo (elenap@cancer.dk)

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Description

This PhD project aims to expand the Moonlight framework for integrative -omics analyses to support the analyses of glycoproteomics data and integrate them with other available quantitative biological data as gene expression, mutational data, methylation. Additionally, the project aims to include machine-learning solution to streamline the selection of the candidate markers using features from different quantitative data and clinical phenotypes. The DC will analyze data provided by other collaborators in the consortium or already available in public available repositories.

Research field: Bioinformatics, Biochemistry, Molecular Modeling, Computational Biology.

Main Supervisor(s): Assoc. Prof. Elena Papaleo (elenap@cancer.dk)

Host Institution:

Description

Main goal is to develop novel FET-based electronic measurements system for real-time potentometric and amperometric DNA detection. Important milestone is in the establishing of the bioreceptor functionalization, calibration and measurement formats for detection of methylated DNA of interest, using both, traditional molecular and nanoparticles-amplified formats. Finally, a demonstrator of the measurements system, enabling up to 10² pads monitored at the same time is expected.

Research field: Electrochemistry, Electronic biosensors, Electronic engineering, Materials Science.

Main Supervisor(s): Prof. Larysa Baraban (l.baraban@hzdr.de)

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