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:

20 maart 2024

Jack Pronk receives the 2024 Novozymes Prize

The Novo Nordisk Foundation proudly announces Professor Jack Pronk as the recipient of the 2024 Novozymes Prize for his groundbreaking contributions to industrial biotechnology. His transformative research in yeast physiology and metabolic engineering has not only revolutionised biofuel and chemical production but has also provided critical solutions to longstanding challenges in sustainable bioprocesses. At the turn of the century, as the world faced the looming climate crisis spurred by fossil-fuel consumption, the importance of alternative fuels became increasingly apparent. Bioethanol emerged as a promising solution, yet its production from non-food sources posed significant challenges. “It had been a dream for decades to establish a biobased economy utilising microorganisms. An example is producing fuel ethanol from sugar using yeast, which efficiently converts glucose into ethanol. However, this approach was controversial because unlimited expansion could lead to competition with food production,” explains Jack Pronk, Professor and Head of the Department of Biotechnology at Delft University of Technology (TU Delft) in the Netherlands. Although yeast could efficiently turn sugars from fruits and other edible sources into bioethanol, the metabolism of sugars from agricultural waste streams posed a critical hurdle for economical bioethanol conversion, since traditional yeast strains struggled to utilise pentose sugars, which are abundant in agricultural residues. In a groundbreaking collaboration with fellow microbiologist Huub Op den Camp from Radboud University Nijmegen, Jack Pronk discovered a potential solution in an unlikely source – the anaerobic fungus Piromyces sp. strain E2, isolated from the faeces of an Indian elephant. This fungus harboured a xylose isomerase gene that held the key to unlocking the pentose challenge. “The result initiated years of research, increasingly involving collaboration with the company DSM,” states Jack Pronk. “Through this process, baker’s yeast was adapted for processing pentose sugars from agricultural waste streams.” “Jack Pronk is one of Europe’s foremost leaders in innovative, sustainable biotechnology using microbes for environmentally friendly conversion of waste streams into biofuels and fine chemicals. The fundamental research and the knowledge generated about the functioning of yeast and fungi from Jack Pronk’s laboratory has been the basis for a wide range of commercial applications with clear societal impact, as demonstrated by their full-scale industrial implementation. The Novo Nordisk Foundation is proud to recognise Jack Pronk’s excellence in research with the 2024 Novozymes Prize,” says Professor Mads Krogsgaard Thomsen, CEO of the Novo Nordisk Foundation. By 2010, the modified yeast could efficiently convert the most important sugars from plant residues into ethanol, paving the way for sustainable biofuel production technologies. Despite setbacks in large-scale implementation, Jack Pronk believes that the production of ethanol from agricultural residues will make a comeback. Ethanol is not only useful as a transport fuel but also as a precursor for compounds ranging from ethylene to aviation fuel. “I do see a future for ethanol, produced by low-emission technologies, as a generic feedstock for production of food protein, pharmaceuticals and fine chemicals. There is huge potential for its production from agricultural residues. I am convinced that genetically modified microorganisms, be they yeasts, bacteria or fungi, will enable cost-effective and sustainable ethanol production from these feedstocks.” The 2024 Novozymes Prize therefore celebrates Professor Jack Pronk’s exceptional contributions to industrial biotechnology, highlighting his innovative solutions to longstanding challenges and his enduring commitment to sustainable bioprocesses. His work exemplifies the transformative potential of biotechnology in addressing global challenges and building a more sustainable future. “The advances Jack Pronk has made, especially with using yeast, are based on exceptionally deep knowledge of physiology and metabolism, rooted in rigorous fundamental research. His superb understanding of how a yeast cell operates has directly translated into Jack being able to exploit yeast cells as industrial-level factories for producing fuels and chemicals. He clearly is a world leader in industrial biotechnology and fermentation science, with a specific focus on developing sustainable bioprocesses that help to reduce waste streams and carbon footprint,” concludes Professor Detlef Weigel, Chair of the Committee on the Novozymes Prize. About Professor Jack Pronk 1986 MSc in biology (cum laude), Leiden University 1991 PhD in microbial physiology, TU Delft 1991-1999 Assistant Professor, TU Delft 1999- Professor of Industrial Microbiology, TU Delft 2002-2013 Co-founder and Scientific Director, Kluyver Centre for Genomics of Industrial Fermentation 2015 Fellow of the American Society of Microbiology 2015 Professor of Excellence Award, TU Delft 2018 International Metabolic Engineering Award 2019- Head of the Department of Biotechnology, TU Delft 2020 Member of the Royal Netherlands Academy of Sciences 2021 Knight in the Order of the Netherlands Lion About the Novozymes Prize The Novozymes Prize recognises outstanding research or technology contributions that benefit the development of biotechnological science for innovative solutions. The Prize is awarded annually and is intended to further raise awareness of basic and applied biotechnology research. The Prize is accompanied by DKK 5 million (€672,000) and comprises a DKK 4.5 million (€605,000) research grant and a personal award of DKK 0.5 million (€67,000). The Foundation will award an additional DKK 0.5 million for hosting an international symposium within the recipient’s field(s) of research. Further information TU Delft: Charlotte de Kort, Communications Manager TNW, +31 (0)6 140 15 135, c.g.w.dekort@tudelft.nl Novo Nordisk Foundation: Christian Mostrup, Senior Lead, Corporate Affairs, +45 3067 4805, cims@novo.dk Prof. Jack Pronk Head of department / Full professor +31 15 2783214 j.t.pronk@tudelft.nl Room number: B58.C1.080

News

15 december 2020

Five 20k grants for cross-campus bioengineering research projects

In response to the first call for bioengineering research proposals, Delft Bioengineering Institute received a stunning amount of thirteen interfacultary proposals. After a thorough peer review process, eight very good to excellent proposals surfaced. From these, MT BEI has selected the five winning projects listed below. We want to thank all BEI PIs for submitting proposals and all reviewers for their efforts, knowing they were all quite busy already. We hope that 2021 will see the start of a second five-year term for the institute, so we can continue to support these promising cross-campus collaborations! >> Biochars for reducing methane emissions Methane has a high global warming potential, and landfill is one of the largest contributors of global human-caused methane emissions. Methane treatment using engineered microbial oxidation systems is one of the ways to reduce these emissions. 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, led by Julia Gebert of Geoscience & Engineering (CiTG), BEI PIs of four TU Delft faculties team up to investigate the potential of biochars for enhancing microbial methane oxidation in biofilters. Project title: Effects of biochar on the performance of microbial CH4 oxidation in biofilters to reduce landfill gas emissions. BEI PIs: Julia Gebert (CiTG/GSE), Wiebren de Jong (3mE/P&E), Aljoscha Wahl (TNW/BT), Martin Pabst (TNW/BT), Thomas Abeel (EWI/Bioinformatics) >> Regenerating neuronal circuits using ultrasound People suffering from neurodegenerative disorders such as Alzheimer’s, Parkinson’s Disease and Multiple Sclerosis, have impaired neuronal circuits. Generation of new neuronal circuits by using a patient’s own stem cells may prove helpful in treating the disease. One of the difficulties in inducing neurons from stem cells, is the low efficiency rate we are able to achieve so far. In this project, BEI PIs Tiago Costa of Microelectronics (EWI) and Dimphna Meijer of Bionanoscience (TNW) join forces to explore the use of ultrasound for effectively building active neuronal networks from stem cells. Project title: SoundCircuit: Regeneration of neuronal circuits using ultrasound BEI PIs: Tiago Costa (EWI/ME), Dimphna Meijer (TNW/BN) >> Medical implants to investigate cell mechanobiology In order to study the cell’s behaviour and differentiation, we need to be able to measure the mechanical, electrical and biochemical signals that are dynamically transmitted throughout the cells. This requires the creation of biomaterial models equipped with different sensor types. In this project, BEI PIs Mohammad J. Mirzaali of Biomechanical Engineering (3mE) and Massimo Mastrangeli of Microelectronics (EWI) will team up to design, fabricate and test the proof-of-concept for medical implants equipped with force sensors that can reach a sensitivity level of one micronewton, so the mechanobiology of cells can be effectively investigated. Project title: Sixth Sense Biomaterials BEI PIs: Mohammad J. Mirzaali (3mE/BM), Massimo Mastrangeli (EWI/ME) >> Advanced cellular nanoimaging Structural biology has been essential in understanding the cell. Studying the dynamics of biological systems requires advanced imaging tools, particularly those that can bring both high spatial and temporal resolutions. In this project, BEI PIs Chirlmin Joo of Bionanoscience (TNW) and Carlas Smith of Delft Centre for Systems and Control (3mE) will join forces to develop a novel methodology for fast absolute FRET distance measurement, taking advantage of smFRET (fast but biased molecular dynamics) and localization microscopy (unbiased but static localization). Project title: New structural biology by integrating nanoscopy and single-molecule Forster resonance energy transfer BEI PIs: Chirlmin Joo (TNW/BN), Carlas Smith (3mE/DCSC) >> 3D-printing bacterial electrodes for CO2 conversion In order to achieve a sustainable future, we need to use abundant molecules such as CO2, water and renewable electricity to create our organic chemicals and fuels. Microorganisms have the ability to enable upgrading of CO2 by microbial electrosynthesis. In this project, Ludovic Jourdin of Biotechnology (TNW) and Kunal Masania of the Shaping Matter Lab (LR) will team up to explore strategies to shape carbon electrodes into hierarchical porous electrodes for microbial electrosynthesis and study the role of hierarchical porosity on microbial and electrochemical activity. Project title: BACTRODE: Hierarchical 3D-printing of bacterial electrodes for breakthrough in CO2 conversion BEI PIs: Ludovic Jourdin (TNW/BT), Kunal Masania (LR/SML)

04 december 2020

In Memoriam: Prof.dr.ir. Herman van Bekkum (1932 – 2020)

Met droefheid moet ik je mededelen dat op 30 november 2020 onze zeer gewaardeerde emeritus hoogleraar Herman van Bekkum is overleden. Herman van Bekkum was van 1975-1976 Rector Magnificus van de Technische Universiteit Delft. In de periode van 1955-1998 was hij werkzaam voor de TU Delft. Daarbinnen heeft hij een korte periode bij Shell gewerkt, tussen 1959 en 1961, maar koos uiteindelijk toch definitief en met veel succes voor de TU Delft. Na zijn emeritaat in 1998 is hij nog vele jaren actief gebleven voor onze faculteit, zowel binnen Chemical Engineering als de katalysegemeenschap. Hij betekende veel voor de universiteit, in het bijzonder voor de faculteit Technische Natuurwetenschappen. Herman van Bekkum was een veelzijdig chemicus met een grenzeloze werklust. Hij heeft belangrijke wetenschappelijke bijdragen geleverd vooral met betrekking tot katalytische toepassingen van zeolieten en geordende mesopore materialen en non-food toepassingen van suikers. Daarnaast heeft hij door zijn aanstekelijke enthousiasme bij zijn medewerkers en studenten zijn liefde voor de organische chemie overgebracht en heeft hij hen tot grote prestaties weten te brengen. Terecht is hij daarvoor in 1996 beloond met de TU Delft Leermeesterprijs. Herman van Bekkum heeft altijd samenwerking met de industrie nagestreefd en hij slaagde erin om veel fondsen te verwerven en kon daarmee zijn grote creativiteit en nieuwsgierigheid bevredigen. Hij heeft diverse bestuurlijke functies verricht binnen en buiten de TU Delft. Binnen de TU Delft was hij Rector Magnificus van 1975-1976, en buiten de TU Delft vervulde hij rollen als voorzitter van de Koninklijke Nederlandse Chemische Vereniging (KNCV), en sinds 1995 was hij lid van de KNAW, een belangrijke wetenschappelijke onderscheiding. In 1980 werd hij benoemd tot erelid van de studievereniging het Technologisch Gezelschap (TG). Zijn unieke persoonlijkheid werd gekenmerkt door enthousiasme, grote betrokkenheid, efficiĂŤntie in een soms chaotische omgeving, en een enorme snelheid van bewegen en denken. Medewerkers van TNW hadden soms letterlijk moeite om hem bij te houden in de wandelgangen. Ook wist hij altijd feilloos in zijn volle werkkamer de juiste documenten terug te vinden. Herman van Bekkum zal altijd in onze herinnering blijven en iedereen op de faculteit die het genoegen had hem te ontmoeten en met hem samen te werken koesteren die ervaring. Wij wensen zijn familie veel sterkte toe bij dit grote verlies. Paulien Herder, Afdelingsvoorzitter ChemE

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.