Biotechnology

Innovation is crucial to fulfil the potential of industrial biotechnology for sustainable production of fuels, chemicals, materials, food and feed. Similarly, scientific and technological advances in environmental biotechnology are needed to enable novel approaches to water purification, and ‘waste-to-product’ processes thus contributing to a circular economy. Increased fundamental knowledge encompassing enzymes, microorganisms and processes are essential for progress in this field. The Department of Biotechnology covers this research area and, based on new insights, selects, designs and tests new biobased catalysts, micro-organisms, and processes.

The department encompasses five research sections:

News

25 November 2021

BEI Best MSc Graduate 2021: Alicia Rodríguez Molina!

BEI Best MSc Graduate Awards 2021 Since 2020, Delft Bioengineering Institute (BEI) organizes a cross-campus competition for MSc students who performed remarkably well at their graduation projects in bioengineering. This year, sixteen very impressive theses were submitted. After a strenuous review and discussion, the jury finally agreed that Alicia Rodríguez Molina (MSc Life Science & Technology), Akash Singh (MSc Computer Science) and Jette Bloemberg (MSc Mechanical Engineering) have delivered the most innovative, interdisciplinary bioengineering projects of 2021. On top of eternal fame, they will receive personal cash prizes of €1000, €500 and €250. 1. Alicia Rodríguez Molina (MSc Life Science & Technology) Thesis: "TPR-CHAT is a caspase-like protease that forms a complex with the CRISPR-Cas type III-E endoribonuclease effector gRAMP” Daily supervisor: Sam van Beljouw (Applied Sciences, Bionanoscience) Thesis Committee: Stan Brouns (AS/BN), Peter-Leon Hagedoorn (AS/Biotechnology), Chirlmin Joo (AS/BN) “Alicia has made large contributions to our research discovering a new CRISPR-Cas system with potentially profound implications and new applications. She has been responsible for the major discovery that links a protease (protein cleaving enzyme) to CRISPR-Cas for the first time. The protein complex she identified was named Craspase and can likely trigger cell suicide in bacteria to protect bacteria from virus infection. We anticipate that Craspase can be converted to a tool for applications in molecular diagnostics, targeted knockdown of gene expression and biomolecule activation or deactivation in cells. A patent was also filled to protect some of these ideas. Importantly, her findings were included in a paper published in Science August 26 (attached) on which she was third author.” 2. Akash Singh (MSc Computer Science) Thesis: “Unsupervised Manifold Alignment with TopoGAN” Thesis Committee: Marcel Reinders (EWI/Pattern Recognition and Bioinformatics), Christoph Lofi (EWI/Web Information Systems), Ahmed Mahfouz (EWI/PRB and LUMC/Radiology), Tamim Abdelaal (LUMC/Radiology) “In his thesis, Akash developed TopoGAN, a deep learning method to solve the challenging task of integrating single cell datasets with no matching samples (i.e. cells) or features. Akash’s thesis proposes multiple innovative ideas to address this challenge. First, Akash showed that Topological Autoencoders can capture the heterogeneity of single cell data better than current approaches such as (variational autoencoders, tSNE and UMAP). This on its own is a significant contribution to the field. Second, Akash proposed an approach to tackle the instability of GAN methods in the task of manifold alignment, which can be generally applied in other fields of machine learning. Third, in evaluating the performance of his method, Akash showed that current strategies have severe shortcomings and should as such be revised to faithfully reflect the performance of different methods.” 3. Jette Bloemberg (MSc Mechanical Engineering) Thesis: “MRI-Ready Actuation System for a Self-Propelling Needle” Supervisors: Fabian Trauzettel (3mE/Biomechanical Engineering), Dimitra Dodou (3mE/BmechE), Paul Breedveld (3mE/BmechE) Thesis Committee: Paul Breedveld (3mE/BmechE), Fabian Trauzettel (3mE/BmechE), Dimitra Dodou (3mE/BmechE), Matthijs Langelaar (3mE/Precision and Microsystems Engineering), Jovana Jovanova (3mE/MTT) “Jette did a very interesting research into a new kind of self-propelled steerable needle for prostate interventions under MRI. She developed a perfectly working prototype, bio-inspired on the anatomy of parasitic wasps. (…) Based on a past PhD project in which we developed novel, self-propelling needles based on the ovipositor-anatomy of parasitic wasps, Jette brought this research to an entirely new level. In her project we wanted to evaluate ovipositor-inspired needles on human prostate tissue under MRI. This means that the design should not contain any metallic parts that react on the powerful magnetic MRI-field. To solve this issue, Jette designed an entirely novel manually-driven propulsion mechanism that she printed from plastic on Formlabs and Ulitimaker 3D-printers, thereby gaining a lot of know-how on how to design complex mechanisms with tight tolerances using 3D printers. Driven by her novel propulsion mechanism, Jette designed a very thin (Ø0,81mm) ovipositor needle composed out of six individually moveable NiTi rods. For the experiments in human prostate tissue, Jette set up a very close collaboration with a well-known urology group at the Amsterdam University Medical Center (AUMC), headed by Dr. Daniel Martijn de Bruin. Jette organised many meetings with this group, arranging human prostate tissue, and using an MRI-laboratory scanner at the AUMC for her experiments. As the space within this MRI-scanner was limited, she also developed a special experimental facility in which the tissue could be stored and moved with near zero friction.”

News

01 December 2020

Best Bioengineering MSc Graduate 2020: Nemo Andrea!

“An outstandingly talented biophysicist who seamlessly combines deep biological knowledge with a strong ability for physical abstraction and numerical analysis.” This is how supervisors Marileen Dogterom and Arjen Jakobi (Applied Sciences, Bionanoscience) describe MSc Applied Physics graduate Nemo Andrea. With his thesis “Actin-Microtubule crosstalk studied by cryo electron microscopy” (graded 9.5), Nemo has won Delft Bioengineering Institute’s BEI MSc Graduate Award 2020, comprising of a €1000 personal cash prize. Runners up are MSc Nanobiology graduate Christos Gogou (second prize, €500) and MSc Life Science and Technology graduate Allison Wolder (third prize, €250). Cytoskeleton ‘Actin-microtubule crosstalk’ refers to the functional interactions that exist between these two cytoskeletal systems in living cells. An increasing number of molecular crosslinkers responsible for these interactions are being identified, but detailed mechanistic knowledge on how they connect cytoskeletal filaments is missing. Such knowledge is of great importance for efforts that aim to engineer artificial cells with active cytoskeletal networks from the bottom up. Cryo-EM Taking advantage of recent advances in cryo-electron microscopy, Nemo set out to visualize the architecture of microtubule-actin filament interactions in the presence of an engineered crosslinker. These high-resolution images give valuable insight into how these two filaments affect each other’s dynamic properties, something that was phenotypically observed before with fluorescence microscopy, but not understood at the structural level. In addition, Nemo explored new artificial intelligence methods to reduce the noise level of his cryo-EM images, and independently adapted the algorithm to improve its performance. While the data are too preliminary in terms of statistics to be immediately publishable, the results obtained are completely novel and important for future research in this field. Runners-up Excellent Master thesis work was done as well by runners-up Christos Gogou and Allison Wolder. A short description of their research can be found below. Overall, Delft Bioengineering Institute was impressed by the quality of the ten reports that were submitted, and had a very hard time making a selection. We want to thank all students for their outstanding efforts, and their supervisors for composing their nominations. We hope 2021 will see the start of a second five-year term for the institute, so we can continue to stimulate promising research in the field of bioengineering. BEI Best MSc Graduate Awards 2020 Nemo Andrea – “Actin-Microtubule crosstalk studied by cryo electron microscopy” Supervisors: Marileen Dogterom and Arjen Jakobi (Applied Sciences, Bionanoscience) Taking advantage of recent advances in cryo-electron microscopy, Nemo set out to visualize the architecture of microtubule-actin filament interactions in the presence of an engineered crosslinker. In addition, Nemo explored new artificial intelligence methods to reduce the noise level of his cryo-EM images, and independently adapted the algorithm to improve its performance. Christos Gogou – “Constructing a cryo-EM assay for molecular voltage-sensitivity of liposome-reconstituted membrane proteins” Supervisor: Dimphna Meijer (Applied Sciences, Bionanoscience) Christos bioengineered a novel assay to test if neuronal proteins are sensitive to voltage fluctuations. More specifically, he designed lipid-based vesicles that can be tuned to any membrane potential of choice. Neuronal membrane proteins can then be inserted in these vesicles and visualized at high resolution by cryo-electron microscopy. This assay mimics the action potential of neurons in vitro. Allison Wolder – “Scaling up ene reductase-catalysed selective asymmetric hydrogenation” Supervisor: Caroline Paul (Applied Sciences, Biotechnology) Allison worked on scaling up an incredible enzymatic reaction: hydrogenation. This is notoriously difficult to do, and it requires exploration of the mechanism of the enzyme and its stability. She carried out her thesis in the front seat, thinking outside of the box, suggesting new approaches, making new connections with external companies. The presentation and report were of excellent quality. If you would like to read a thesis, please send a message to N.vanBemmel@tudelft.nl and you will receive a copy.
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