BioDate 2020: 15 interdisciplinary MSc projects supported with 2,5k

The call for interdisciplinary MSc project proposals attached to BioDate 2020 ­yielded the stunning amount of twenty submissions. In peer review, fifteen of these were rated very good to excellent, and were consequently supported with €2500 by Delft Bioengineering Institute. BEI wants to thank all PIs who submitted a proposal, as well as the reviewers who kindly helped us out to select the best ones. Students who are interested in applying for one of the projects, can contact the supervisors via email.

MSc Graduation Project	Supervisor #1	Supervisor #2
Ultrasonic Scalp – high-precision transcranial brain stimulation with a flexible ultrasound transmitter	Tiago Costa (EWI/ME)	Mohammad J. Mirzaali (3mE/BME)
Chambering a method for screening drugs against microbial pathogen membrane proteins	Duncan McMillan (TNW/BT)	Murali Ghatkesar (3mE/PME)
Engineering of a thrombus-on-chip model for stroke prevention	Gijsje Koenderink (TNW/BN)	Frank Gijsen (3mE/BME)	Supervisor #3: Massimo Mastrangeli (EWI/ME)
Diving in the geysers of Enceladus, an icy moon from Saturn	Jovana Jovanova (3mE)	Stéphanie Cazaux (LR)
Haloperoxidase catalyzed hydrogen peroxide activation for targeted drug release	Rienk Eelkema (TNW/ChemE)	Frank Hollmann (TNW/BT)
Nitrate-dependent iron oxidation for groundwater treatment	Doris van Halem (CiTG/WM)	Mark van Loosdrecht (TNW/BT)
3DNacre: Three-dimensional printing of biologically fabricated mineral bridges in nacre-like composites	Marie-Eve Aubin-Tam (TNW/BN)	Kunal Masania (LR)	Student: Kevin Krüger (LR)
Sustainable bio-based polymers from wastesludge for wastewater purification	Hanieh Bazyar (3mE/P&E)	Mark van Loosdrecht (TNW/BT)	Supervisor #3: Andres Hunt (3mE/MNE)
How 'deep' can neurons 'feel' within hybrid soft/stiff engineered 3D microstructures?	Angelo Accardo (3mE/PME)	Eduardo Mendes (TNW/ChemE)
Quantifying biophysical and biochemical characteristics of neuronal social networks (QUANTINETS)	Murali Ghatkesar (3mE/PME)	Dimphna Meijer (TNW/BN)
Engineering (sub)surface nature-based treatment of urban & rural run-off for climate adaptation & water re-use	Boris van Breukelen (CiTG)	David Weissbrodt (TNW/BT)	Student: Vita Marquenie (TNW/LST)
2.5D Hybrid polymer/metal neuron-on-chip architectures fabricated by two-photon polymerization and multi-focal lithography	Angelo Accardo (3mE/PME)	Massimo Mastrangeli (EWI/ME)
Effects of biochar on gas transport properties and CH4 oxidation capacity of landfill cover soils	Julia Gebert (CiTG)	Thomas Abeel (EWI)
Topological transitions during tissue formation	Timon Idema (TNW/BN)	Lisanne Rens (EWI)
Enhanced acoustic biosensors for deep molecular imaging in living organisms	David Maresca (TNW/ImPhys)	Valeria Garbin (TNW/ChemE)

 

>> One step closer to ultrasonic scalps

Neuroscience and medicine would benefit greatly from ‘ultrasonic scalps’: wearable, high-precision transcranial brain stimulators. Promising ultrasound technologies are available to use in such a device, but the transmitter technology needs advancing. In this project, Tiago Costa of EWI and Mohammad J. Mirzaali of 3mE will supervise a master student of Microelectronics, Biomedical Engineering or Mechanical Engineering, who will explore multi-material 3D printing techniques to investigate materials with different ratios of density and speed of sound, in order to acoustically match ultrasound transmitters and the skull.

Project: Ultrasonic Scalp – high-precision transcranial brain stimulation with a flexible ultrasound transmitter
Supervisors: Tiago Costa (EWI/ME) and Mohammad J. Mirzaali (3mE/BME)
Student: to be recruited

>> Towards a new rapid drug-screening platform

As the ongoing pandemic demonstrates, it is of great importance that we develop rapid drug screening platforms against membrane proteins – such as the covid-19 spike protein. It’s both necessary and challenging to study membrane protein function in a native lipid environment. To this end, Duncan McMillan of TNW/BT has been working on an attolitre chamber system, while Murali Ghatkesar of 3mE/PME has developed a device capable of delivering attolitres of fluid containing biological materials. A student with a proclivity for biochemistry, nanosciences and materials chemistry will try and combine the systems to take the next step towards a new drug-screening platform.

Project: Chambering a method for screening drugs against microbial pathogen membrane proteins
Supervisors: Duncan McMillan (TNW/BT) and Murali Ghatkesar (3mE/PME)
Student: to be recruited

>> A thrombus-on-chip model for stroke prevention

In a thrombotic stroke, a blood clot (thrombus) forms inside a brain artery. The clot prevents blood flow to a part of the brain, which causes cells in that area to die. It’s possible to surgically remove the clot, but outcomes are not yet optimal. To be able to improve revascularisation techniques aimed at preventing stroke, it’s important to understand the mechanical properties of the thrombi. A student with a background in (bio)engineering, (bio)physics or (bio)nanoscience will work on that in the labs of Gijsje Koenderink (TNW/BN), Frank Gijsen (3mE/BME) and Massimo Mastrangeli (EWI/ME).  

Project: Engineering of a thrombus-on-chip model for stroke prevention
Supervisors: Gijsje Koenderink (TNW/BN), Frank Gijsen (3mE/BME) and Massimo Mastrangeli (EWI/ME)
Student: to be recruited

>> Looking for life underneath Enceladus’ icy surface

Enceladus is one of Saturn’s 82 moons, and a critical science target, for the icy moon has a subsurface salty ocean that contains complex organic molecules. This fairly recent discovery raises questions: is there life on Enceladus? And if so, how can we find it? Supervised by Jovana Jovanova (3mE) and Stephanie Cazaux (LR), a student with interest in bio-inspired design and application of smart materials will develop a prototype robot based on the latest advancements in bio-inspired soft robotics that would be able to dive into Enceladus’ crevasses and reach its subsurface ocean to collect samples. 

Project: Diving in the geysers of Enceladus, an icy moon from Saturn
Supervisors: Jovana Jovanova (3mE) and Stéphanie Cazaux (LR)
Student: to be recruited

>> Using enzymes for targeted drug release

Many current medication is highly effective, yet also extremely toxic. This is why targeted drug delivery seeks to concentrate the medication only in the diseased tissues, leaving the surrounding healthy tissues intact. Releasing of the drug often relies on a chemical reaction that is initiated by a chemical signal present in the diseased area. Hydrogen peroxide can function as such a signal, but it requires high concentrations to effectively start the reaction. In this project, a master student with a chemistry, chemical engineering or LST background, supervised by Rienk Eelkema of TNW/ChemE and Frank Hollmann of TNW/BT, will use haloperoxidase enzymes to activate hydrogen peroxide at biologically relevant concentrations, and use that to trigger drug release.

Project: Haloperoxidase catalyzed hydrogen peroxide activation for targeted drug release
Supervisors: Rienk Eelkema (TNW/ChemE) and Frank Hollmann (TNW/BT)
Student: to be recruited

>> Nitrate-dependent iron oxidation for groundwater treatment

Groundwater is the source of sixty percent of the drinking water consumed in the Netherlands. Its quality and temperature are constant, and it’s considered hygienically safe. The main contamination sources of anaerobic groundwater are the decomposition of natural organic matter, producing ammonium and methane, and the dissolution of soil minerals, introducing manganese, iron and trace metals. The aim of this interdisciplinary MSc project is to separate the removal process of each contaminant to get control of the system, increase the operating flow rates and recover pure iron and manganese solids. To do so, the use of anaerobic iron removal coupled to nitrate will be explored. Supervised by Doris van Halem (CiTG/WM) and Mark van Loosdrecht (TNW/BT), a Life Science & Technology master student will carry out the project.

Project: Nitrate-dependent iron oxidation for groundwater treatment
Supervisors: Doris van Halem (CiTG/WM) and Mark van Loosdrecht (TNW/BT)
Student: to be recruited

>> 3D printing strong, lightweight biomaterials

Nacre, commonly called mother of pearl, is a biological composite that is both lightweight and strong. Given that brittle calcium carbonate is its main constituent, this is quite unexpected. Inspired by nature, experts in biomaterials (Marie-Eve Aubin-Tam, TNW/BN) and additive manufacturing techniques (Kunal Masania, LR) will join forces to design lightweight biomaterials with enhanced fracture resistance, using naturally abundant chemicals. Supervised by the two PIs, master student Kevin Krüger of LR will develop a printer and utilize bacterial cultures to produce the desired novel materials.

Project: 3DNacre: Three-dimensional printing of biologically fabricated mineral bridges in nacre-like composites
Supervisors: Marie-Eve Aubin-Tam (TNW/BN) and Kunal Masania (LR)
Student: Kevin Krüger (LR)

>> Using bio-based polymers for a smart water treatment membrane

Bio-based polymers, such as Kaumera Nereda Gum, developed from waste sludge at TU Delft, are emerging materials that perfectly meet the need for renewable alternatives that are necessary in order to achieve a carbon-neutral polymer industry. In this project, Kaumera will be used to create a smart membrane for wastewater treatment. The project will join the expertise in bio-based/microbial polymers (Mark van Loosdrecht, TNW/BT), membrane separation technology (Hanieh Bazyar, 3mE/P&E) and smart material transducers (Andres Hunt, 3mE/MNE). A student of TNW or 3mE in a curriculum that links to material science, chemistry, engineering or similar, will be supervised by these three PIs.

Project: Sustainable bio-based polymers from wastesludge for wastewater purification
Supervisors: Hanieh Bazyar (3mE/P&E), Mark van Loosdrecht (TNW/BT) and Andres Hunt (3mE/MNE)
Student: to be recruited

>> How ‘deep’ can neurons ‘feel’ within engineered 3D microstructures?

Mechanical cues and substrate stiffness affect the growth and behaviour of cells, especially neurons, cultured in vitro. In the human brain, neurons reside in a complex 3D environment, the brain tissue being extremely soft compared to other tissues in the body. However, to date, cell biologists mostly study neurons in 2D petri dish environments that lack resemblance to the native environment of neurons. In this project, Angelo Accardo (3mE/PME) and Eduardo Mendes (TNW/ChemE) aim to develop hybrid two-photon polymerization based fabrication protocols resulting in 3D stiff scaffolds, coated with micrometric soft hydrogel layers, in order to study neuronal cell properties. A student of the Precision and Microsystems Engineering department at 3mE will carry out the project.

Project: How 'deep' can neurons 'feel' within hybrid soft/stiff engineered 3D microstructures?
Supervisors: Angelo Accardo (3mE/PME) and Eduardo Mendes (TNW/ChemE)
Student: to be recruited

>> Quantifying characteristics of neuronal social networks

Brain circuits function by virtue of precise connections between nerve cells. The functional neural circuits in our brain control intricate processes such as learning and memory, while failure in neural circuitry formation can lead to developmental disorders. On the cellular level, we don’t understand how single-cells are organised into complex neural circuits. In this project, BEI PIs Murali Ghatkesar (3mE/PME) and Dimphna Meijer (TNW/BN) team up to develop methods to perform single-cell sampling for genomic analysis and measure cell-cell adhesion in a neuronal social network. An MSc student will learn how to use micro-nano engineering tools to perform precise quantification in biology. He or she will try and answer the question: what is the adhesion strength between individual cells and how does it evolve spatially and temporally between single neuronal cells during a social network formation?

Project: Quantifying biophysical and biochemical characteristics of neuronal social networks (QUANTINETS)
Supervisors: Murali Ghatkesar (3mE/PME) and Dimphna Meijer (TNW/BN)
Student: to be recruited

>> Engineering treatment of urban and rural run-off

Managed Aquifer Recharge (MAR) aims to capture the abundant winter rainfall before it is lost, and stores it temporarily in aquifers below ground for later re-use in dry periods when water demand and shortage are highest. The captured water does however not fulfil the water quality requirements in both urban and rural areas, and profits from further treatment and biogeochemical processing. In this project, the role of the microbial community in engineered (sub)surface systems treating run-off before re-use is investigated. Supervised by Boris van Breukelen (CiTG) and David Weissbrodt (TNW/BT), master student Vita Marquenie (TNW/LST) performs the research in her master thesis.

Project: Engineering (sub)surface nature-based treatment of urban & rural run-off for climate adaptation & water re-use
Supervisors: Boris van Breukelen (CiTG) and David Weissbrodt (TNW/BT)
Student: Vita Marquenie (TNW/LST)

>> Towards 2.5D neurons-on-chip to study neuronal networks

The electrical activity of neurons holds a crucial role in the evaluation of cellular network functionality. To study it, so far, most of the current approaches rely on micro-electrode arrays, which are limited to 2D topologies. Recently, the group of Massimo Mastrangeli (EWI/ME) added the option of using metal layers grown on the sidewalls of 2.5D silicon structures, while Angelo Accardo (3mE/PME) showed how polymeric and hydrogel materials can be shaped very precisely to promote the formation of ramified 3D neuronal networks. A MSc student of either Precision and Microsystems Engineering (3mE) or Microelectronics (EWI) will work on a combined micro/nanofabrication approach, paving the way for the creation of unprecedented 2.5D hybrid polymer/metal neuron-on-chip architectures for functional readout of neuronal networks.

Project: 2.5D Hybrid polymer/metal neuron-on-chip architectures fabricated by two-photon polymerization and multi-focal lithography
Supervisors: Angelo Accardo (3mE/PME) and Massimo Mastrangeli (EWI/ME)
Student: to be recruited

>> Biochars to improve methane reduction

Biochars, carbon-rich materials produced from sources such as municipal solid wastes, wastewater sludge and wood, have gained interest in the waste management industry as media to enhance control of landfill gas emissions. In this project, a student supervised by Julia Gebert of CiTG and Thomas Abeel of EWI will investigate the effect of biochar on soil compaction behaviour, gas transport, water retention properties and methane oxidation capacity. The research will include hands-on experimental work at the Geo Lab at CiTG and application of bioinformatics tools at EWI.

Project: Effects of biochar on gas transport properties and CH4 oxidation capacity of landfill cover soils
Supervisors: Julia Gebert (CiTG) and Thomas Abeel (EWI)
Student: to be recruited

>> Topological transitions during tissue formation

During gastrulation, a multi-cellular embryo undergoes major structural change, transitioning from a spherical to a toroidal topology, while simultaneously differentiating into multiple cell types. Gastrulation is crucial to life, but hard to study, especially in mammals. A possible solution is the use of gastruloids, assemblies of stem cells that mimic gastrulation. In this project, Timon Idema of TNW/BN and Lisanne Rens of EWI will join forces to simulate the gastrulation process in a binary gastruloid, and determine the optimal conditions to facilitate gastrulation. A student of applied physics, applied mathematics or nanobiology will work on the project and be supervised by both PIs.  

Project: Topological transitions during tissue formation
Supervisors: Timon Idema (TNW/BN) and Lisanne Rens (EWI)
Student: to be recruited

>> Acoustic biosensors for deep molecular imaging in living organisms

Gas vesicles (GVs) are air-filled protein nanostructures that, as recent research shows, can be deployed to enable deep molecular ultrasound imaging in living organisms. To maximize the potential of this novel nanotechnology, a diversification of GV acoustic properties is needed. The goal of this MSc project will be to develop new biosensor formulations based on gas vesicles with enhanced acoustic performance. The project is supervised by David Maresca (ImPhys) and Valeria Garbin (ChemE), and is suitable for an MSc student Applied Physics or Chemical Engineering.

Project: Enhanced acoustic biosensors for deep molecular imaging in living organisms
Supervisors: David Maresca (TNW/ImPhys) and Valeria Garbin (TNW/ChemE)
Student: to be recruited