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

15 January 2016

Algae prove promising candidates for biodiesel production via 'survival of the fattest'

Smart methods for cultivating algae bring the efficient production of biodiesel using algae in sight. On Tuesday 19 January, Peter Mooij will obtain his doctorate at TU Delft for his work on this subject. CO 2 neutral There is huge scientific interest in the use of microalgae to produce carbohydrates and in particular lipids (fats), as lipids from microalgae can be converted into biodiesel. The amount of CO 2 released by the combustion of this biodiesel is equal to the amount of CO 2 that was previously extracted from the atmosphere by the microalgae. Thus the use of biodiesel does not lead to an increase in CO 2 in the atmosphere. 'Microalgae offer two huge advantages over other biological oil production platforms', says doctoral candidate Peter Mooij from TU Delft. 'Firstly, after cultivation, microalgae can be made up relatively largely of lipids. And secondly, relatively little fresh water and agricultural land is required to cultivate microalgae.' Survival of the fattest Mooij uses a smart method to cultivate suitable algae that is economically viable for large-scale algae production: survival of the fattest. The fattest algae survive. 'In the reactor we give a competitive advantage to the algae with the required characteristics, in this case the production of carbohydrates and fats. We start with a collection of 'ordinary' algae. During the day we provide them with light and CO 2 . This is enough for them to produce oil, however they are unable to divide. They need nutrients for cell division and they are only given these in the dark. To absorb these nutrients, the algae need energy and carbon. This means that only the fattest algae can divide, as they have stored these during the day. By removing some of the algae every day, the culture will eventually exist of only the fattest algae.' Starch 'All of our experiments led to systems in which carbohydrates (starch) formed the primary energy storage compounds', continues Mooij. 'So we have found a suitable environment in which carbohydrate production by algae is rewarded.' Unfortunately this environment is not yet selective for the storage of fats. The culture environment needs to be made even more specific to achieve this. 'But a greater understanding of the ecological role of lipids and carbohydrates in microalgae clears the way for the creation of lipid-specific selective environments. Rewarding a microalga for showing the desired behaviour by using a selective environment, one of the central concepts in my research, will be shown to be a valuable approach once there is a better understanding of the ecological role of lipids.' More information For further information please contact Peter Mooij tel. +31 6 - 483 826 35 or p.r.mooij@tudelft.nl or Wendy Batist, press officer TU Delft via tel. +31 - 15 - 27 884 99 or g.m.batist@tudelft.nl . Please read Peter Mooij's blogs on Faces of Science (only in Dutch).
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