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Health Technology @ TNW

At the Faculty of Applied Sciences (AS) a lot of research is being done at the interface of technology and healthcare. Scientists at AS use yeast as a model organism for the study of degenerative brain disorders such as Alzheimer's disease, make laser set-ups and models that can visualise the blood flow in a heart chamber, study cellular processes underlying common diseases, develop new imaging techniques that can be used for hospital diagnosis, and more. This page provides an overview of the Health Technology related research carried out at AS. We distinguish four domains, in which the research of certain scientists can simultaneously take place in multiple domains.

How does the Faculty of Applied Sciences work on Health Technology?

Convergence Health and Technology

Diagnostic

Clinical

Process-oriented

Scientific modelling

News

Please click on the buttons to filter the articles below by subtheme.

Pushing the boundaries of ultrasound

Physicist David Maresca has received a Chan Zuckerberg Initiative Dynamic Imaging grant to develop a next-generation medical ultrasound tool. While state-of-the-art ultrasound imaging, known to most as a baby’s first picture, can show our anatomy and organs, the new tool will be able to zoom in much further, all the way down to the level of the cells in our body.

3-in-1 microscope shows researchers the way to proteins

Physicists from TU Delft have developed a 3-in-1 microscope where a light beam, electron beam and ion beam work together to precisely cut out specific slices from biological samples. These slices are indispensable for biomolecular research into new generations of medicines. The invention was published in the journal eLife on 1 December.

ERC Starting Grant for spying on microscopic blood vessels in the heart and brain

The European Research Council (ERC) has awarded a Starting Grant to Delft physicist Sebastian Weingärtner for his research on novel imaging methods to tackle heart and brain diseases.

ERC Synergy Grant to unravel the formation of protein complexes

A prestigious ERC Synergy Grant worth 9.4 million euros has been awarded to a team of researchers that aims to elucidate a new mechanism to explain how protein complexes are formed.

New radiolabelling method for personalised cancer treatment

Researchers from TU Delft have found a new method to efficiently make nano carriers loaded with radioactive salts for both medical imaging and treatment. Because the assembly of these nano carriers is incredibly simple, the innovation is very suitable for clinical research and treatments of cancer patients.

New CRISPR-Cas system with on-off switch cuts proteins

Researchers from TU Delft in the group of Stan Broun have discovered a CRISPR-Cas system that cuts proteins instead of DNA.

NextSkins: EIC Pathfinder grant for collaborative living materials research

A team of researchers from TU Delft, Imperial College London, and Aalto University have received a EIC Pathfinder Challenge grant of 4 million euros for their NextSkins research project on Engineered Living Materials.

Baker’s yeast with human muscle genes

Biotechnologist Pascale Daran-Lapujade and her group at Delft University of Technology managed to build human muscle genes in the DNA of baker’s yeast. This is the first time researchers have successfully placed such a vital human feature into a yeast cell.

Cells: strong at the right place and time

Researchers from TU Delft and NWO institute AMOLF discovered how certain molecular bonds make living cells both flexible, in order to move, as well as strong, in order to withstand forces.

From light spots to supersharp images

Making detailed 3D images of proteins in living cells with a special light microscope, without damaging those cells. That is what Sjoerd Stallinga, winner of an ERC Advanced grant worth 2.3 million euros, wants to achieve. In order to do so he is going to scan samples nanometer by nanometer using a sophisticated 3D light pattern in an approach that requires extensive collaboration between different disciplines.

Dutch Research Council Veni grant for Robin de Kruijff

The Dutch Research Council (NWO) has awarded a Veni grant to researcher Robin de Kruijff of the Reactor Institute Delft (RID) for her research on a new type of radionuclide generator which, among other things, can obviate the global bottleneck in cancer research. The new generator will, moreover, be the first recyclable one of its kind. “I hope that my new type of generator will ultimately make diagnostic treatments much more accessible and less dependent on a handful of reactors”, says De Kruijff.

Bacterial soundtracks revealed by graphene membrane

A of researchers from TU Delft , led by dr. Farbod Alijani, have managed to capture low-level noise of a single bacterium using graphene. Now, their research is published in Nature Nanotechnology.

Spotlight on aggressive cancer cells

Metastases in cancer are often caused by a few abnormal cells. These behave more aggressively than the other cancer cells in a tumour. Miao-Ping Chien and Daan Brinks are working together, from two different universities, on a method to detect these cells. Their research has now been published in Nature.

New Cas9 model maps DNA cutting behaviour for the first time

Researchers from the TU Delft have come up with a physical-based model that establishes a quantitative framework on how gene-editing with CRISPR-Cas9 works, and allows them to predict where, with what probability, and why targeting errors (off-targets) occur. This research, which has been published in Nature Communications, gives us a first detailed physical understanding of the mechanism behind the most important gene editing platform of today.

Cell unstuck: how a glue-like protein can make our cells move

An essential aspect of the cells in our body is their ability to move, to repair certain tissues or chase intruders, for example: but how do they do it? Scientists from TU Delft, AMOLF and Utrecht University reveal how glue-like proteins called crosslinkers could not only help to hold the whole cell together passively, but surprisingly cause the cell to move as well. The research is now published in PNAS.

ERC Proof of Concept Grant for Arjen Jakobi

Arjen Jakobi (Department of Bionanoscience) receives the ERC Proof of Concept Grant for his groundbreaking research on cryogenic electron microscopy (cryo-EM). "This grant will allow us to take our new CryoChip technique for high resolution images of protein molecules to the next level for the development of new drugs," says Jakobi.

Super-fast technique measures heme enzyme reaction as it happens

Researchers from TU Delft found an unexpected new enzyme intermediate at work in enzymes that contain heme, a cofactor that’s vital for many processes in our body such as the breaking down of toxins in the liver. The researchers used new, rapid techniques, which are less invasive than existing methods. The results, published in ACS Catalysis, increase our understanding of heme proteins and enzymes and how they can be engineered.

Scanning a single protein, one amino acid at a time

Using nanopore DNA sequencing technology, researchers from TU Delft and the University of Illinois have managed to scan a single protein: by slowly moving a linearized protein through a tiny nanopore, one amino acid at the time, the researchers were able to read off electric currents that relate to the information content of the protein. The researchers published their proof-of-concept in Science today. The new single-molecule peptide reader marks a breakthrough in protein identification, and opens the way towards single-molecule protein sequencing and cataloguing the proteins inside a single cell.

Mechanism underlying the emergence of virus variants unravelled

An international consortium, led by Delft University of Technology and the University of North Carolina, has for the first time succeeded in probing the molecular origins of recombination in RNA viruses. Hiccups during the copying process of viruses cause recombination to take place: the exchange of segments of viral RNA.

Stronger is not always better

Rather than one key and one strong lock, biology often uses tens or hundreds of weaker links to bind parts together, such as cells membranes. This allows for selectivity and also reversibility: the binding can also be undone. Researcher Christine Linne and colleagues from Leiden University, TU Delft and Imperial College London first caught this phenomenon using spheres or colloids, and published September 1st in the journal PNAS.

Catch me if you can: a revolutionary method to study single proteins

Researchers from the technical universities of Delft and Munich have invented a new type of molecular trap that can hold a single protein in place for hours to study its natural behavior – a million times longer than before.

New CRISPR-Cas system cuts virus RNA

Researchers from the group of Stan Brouns (Delft University of Technology) have discovered a new CRISPR-Cas system that cuts RNA. The study will be published on August 26 in Science and is expected to offer many opportunities for the development of new applications in genetic research and biotechnology.

A new spin on making minimal cells

The ability of a cell to separate its own matter from its surroundings is a basic requirement for life. A team of researchers at AMOLF and Delft University of Technology have managed to create a synthetic container, or lipid vesicle, that is able to hold a range of different biological systems: from a cytoskeleton to entire E.coli bacteria. Their findings on this optimized cDICE method, which has the potential to reveal the inner workings of life, are published in ACS Synthetic Biology on DATE.

Researchers make 3D image with light microscope

For the first time, Delft researchers have succeeded in making a three-dimensional image of a cellular component using light. The component in question is the nuclear pore complex: tunnels that facilitate traffic to and from the cell nucleus. Studying cell components in 3D can help to determine the cause of various diseases, among other things. The researchers have published their findings in Nature Communications.

A new tool to understand the brain

How does our brain work? An international team of researchers, including lead author Daan Brinks of TU Delft, has taken another step towards answering that question. They have created a new tool that allows them to image electrical signals in brains with an unprecedented combination of precision, resolution, sensitivity, and depth.

Researchers discover how a cell’s armour can be both flexible and strong

Medieval knights either had thick, cumbersome armour, or they could wear less protective armour and be flexible in combat – they couldn’t have both. Cells, on the other hand, do have it all. Researchers from Delft University of Technology (TU Delft), Leeds University, Institut Fresnel in Marseille, and Institut Curie in Paris discovered that proteins called ‘septins’ reinforce the fragile membrane of a cell, while still being flexible enough to allow the cell to change shape.

Clever Delft trick enables 20 times faster imaging with electron microscopy

Researchers at TU Delft have expanded upon a clever trick that increases the speed of electron microscope imaging by a factor of twenty. A simple adjustment is all that is needed: applying a voltage to the specimen holder. Through this simple intervention, a specimen that the electron microscope would normally take a week to image can now be inspected in a single night or one working day.

Researchers shed new light on DNA replication

In preparation for cell division, cells need to copy (‘replicate’) the DNA that they contain. A team of researchers from TU Delft, collaborating with investigators from the Francis Crick Institute in London, has now shown that the protein building blocks involved in the initial steps of DNA replication are mobile but reduce their speed at specific DNA sequences on the genome. Their findings, which will be published on 26 March in the open-access journal Nature Communications, were facilitated using an integrated approach involving biophysics and biochemistry that will propel new discoveries in the field.

Decoding movement intentions in the brain using ultrasound waves

An international team of scientists that includes ImPhys researcher David Maresca published an article in Neuron today demonstrating decoding of movement intentions in the brain using ultrasound. The work shows great promises for the development of less invasive brain-machine interfaces.

New test makes detection of genetic material visible to the naked eye

Onderzoekers van de TU Delft hebben een test ontwikkeld waarmee ze specifieke stukjes genetisch materiaal kunnen opsporen, waarna de uitslag met het blote oog af te lezen is. Met de test kunnen onder meer virussen, zoals het coronavirus, en antibioticaresistente bacteriën snel en goedkoop worden gedetecteerd. De resultaten zijn gepubliceerd in Biophysical Journal.

Windsurfing virus particles can bridge 1.5 metres

Can a light breeze nullify the 1.5-metre measure indoors? It looks like it could, says Saša Kenjereš (Chemical Engineering) in a new article in Annals of Biomedical Engineering. He modeled the way virus particles leave a talking person's mouth, as well as how far particles can travel in both quiescent and moving air. In doing so, he found that a virus can surf along on a slight tailwind and thus travel much farther than in an environment in which the air is completely still. In a room with stationary air, 1.5 metres seems to be a safe distance. But a barely perceptible breeze allows virus particles to bridge such a gap with relative ease.

Delft researchers build artificial chromosome

Biotechnologists at Delft University of Technology have built an artificial chromosome in yeast. The chromosome can exist alongside the natural yeast chromosomes, and serves as a platform to safely and easily add new functions to the micro-organism. Researchers can use the artificial chromosome to convert yeast cells into living factories capable of producing useful chemicals and even medicines.

Delft researchers chart the potential risks of 'free-floating DNA'

We don’t realize it, but loose strands of DNA end up in nature via our wastewater. As of yet, it is unclear how much this 'free-floating DNA' impacts environmental and public health. Researchers at Delft University of Technology (TU Delft) have now found a way to determine just how much potentially harmful DNA ends up in our wastewater. They have developed a method that can isolate such ‘free floating DNA’ from wastewater, which gives them the means to determine the extent of the problem. The results of their work will officially be printed in Water Research in February 2021, but have already been pre-published online.

Delft researchers develop blood oxygenation sensor for premature babies

Doctors have to keep a close eye on babies that are born prematurely, and brain oxygenation is perhaps the most important thing to monitor. Up to 50 percent of premature babies suffer brain damage, leading to neurological problems. Researchers at Delft University of Technology have now developed a wireless sensor that monitors the health of the baby's brain in a simple, inexpensive and comfortable way for the child.

From imaging to analysing: how Delmic’s new FAST-EM system is changing electron microscopy

Delmic is launching an automated ultra-fast system, FAST-EM, which uses 64 electron beams. Reliable and extremely fast, FAST-EM is aimed at imaging biological samples without the need to constantly babysit the machine.

Researchers peer deep inside tissue

One of the challenges in optical imaging is imaging the inside of tissue in high resolution. Traditional methods allow us to look to a depth of approximately one millimetre. Researchers at Delft University of Technology have now developed a new method that can penetrate up to four times as deep: up to around four millimetres. The healthcare sector in particular may benefit from the new technique in the future.

Charting the way to minimal cells

Ironically, the closer we get to building a living cell, the less we are able to understand it. During the three-day virtual workshop “Reconstituting biology - charting the way to minimal cells”, cell-building researchers agreed this complexity is what makes cells so interesting.

Monitoring the development of a tumour using the memory of bacteria

New software to better understand conversations between cells

One of the most fascinating and important properties of living cells is their capacity for self-organization. By talking to each other cells can, among other things, determine where they are in relation to each other and whether they need to turn certain genes on or off. Thus, large groups of cells are able to work together and organise into all kinds of tissues. Researchers at Delft University of Technology have now developed software that can predict and visualise conversations between cells on the basis of the molecules involved.

Researchers see rapidly hunting CRISPR system in action

ERC Starting Grant for three AS researchers

Five TU Delft researchers have been selected to receive an ERC Starting Grant. Three of these researchers work at the Faculty of Applied Sciences, the other two are affiliated with QuTech. The grants (1,5 million euros for a five-year programme) are intended to support scientists who are in the early stages of their career and have already produced excellent supervised work.

Yeast against dementia

As our life expectancy increases, more and more people are confronted with different types of dementia, such as Alzheimer's disease. How these brain diseases arise and develop is still unclear, complicating the search for effective treatment.

First phage bank in the Netherlands officially opened

Thanks to alumni of the Faculty of Applied Sciences (AS) and supporters of Delft University Fund, Dr.ir. Stan Brouns today, Tuesday 16 April, has opened the first phage bank in the Netherlands.

Researchers discover mechanism disrupting CRISPR-Cas9 gene editing

The discovery of CRISPR-Cas9 has made gene editing very easy. Unfortunately, the molecular tool has recently been found to be less precise than previously assumed. It can lead to unwanted mutations in a cell’s DNA. Researchers at Delft University of Technology have now identified a mechanism that causes such mutations when CRISPR-Cas9 is used incorrectly. This can cause dormant genes to become expressed, which is potentially very dangerous. The researchers have created a checklist based on their findings. Using this checklist will prevent the harmful mechanism from being activated and makes gene editing using CRISPR-Cas9 safer.

ERC Consolidator grant for Chirlmin Joo and Pouyan Boukany

This year, two ERC Consolidator grants have been awarded to TU Delft researchers. Both these researchers work at the Faculty of Applied Sciences. Dr. Pouyan Boukany from the Department of Chemical Engineering wants to learn when, how and why metastatic tumour cells detach form a tumour. Dr. Chirlmin Joo from the Department of Bionanoscience wants to develop a new gene editing tool based on a system found in a single-celled organism.

AS to coordinate two large new public private research programmes

NWO (The Netherlands Organisation for Scientific Research) has announced the new research programmes that will be part of its ‘Perspective for Top Sectors' funding programme. Six public-private programmes will receive a total of 28 million euros. This amount consists of NWO funding (19 million), plus investments by the companies and organisations involved (9 million). Applied Sciences is involved in three programmes and will act as the coordinator of two of these programmes.

Veni for Jeremy Brown and Zoltán Perkó

NWO has announced the Veni recipients for 2018. Among them are seven Delft scientists, two of whom are from RST: Jeremy Brown and Zoltán Perkó. The Veni grants allow researchers who have recently obtained their PhD to conduct independent research and develop their ideas for a period of three years.

KWF proton research project for Holland PTC

Zoltán Perkó (Radiation, Science & Technology), together with Mischa Hoogeman (project leader, Erasmus MC) and Martijn Eenink (Holland Protonen Therapie Centrum) have been granted a KWF research project named PEARL (PrEcision of proton therapy increased by Advanced Robustness analysis).

Marcel Ottens’ group to participate in new International Training Network

As part of a large European biopharmaceutical consortium, the research group of Marcel Ottens will participate in a 4M€ Marie Curie International Training Network (ITN).

Stories

Medical experts and engineers speak each other’s language in Delft

An outpatients’ centre for cancer patients is certainly not the first thing you would expect to encounter on TU Delft campus. ‘But the decision to choose Delft as the location for the Holland Proton Therapy Centre has actually proved to be a very smart move’, says Medical Director Prof. Marco van Vulpen.

A scale model of the brain

We have ten times more brain cells in our head than the number of people on the earth. Technical neurobiologist Dimphna Meijer is conducting research into these neurons by making scale models of the networks they form. Ultimately she hopes to be able to translate this knowledge into clinical practice. “The neurobiologist of the future is also an engineer.”

A flexible irradiation facility for producing radioisotopes

A breakthrough in the production of microspheres containing the radioactive isotope Holmium-166, used for patients with liver cancer, went hand in hand with the development of a TU Delft innovation: the ‘flexible irradiation facility’. In this new sample holder Holmium-165 is cleverly converted into Holmium-166; the microspheres are irradiated to a high level of activity, without damaging the biodegradable envelope by gamma radiation. The principle of an adjustable irradiation chamber was developed for TU Delft’s research reactor but could be applied in any nuclear reactor. "This has brought the production of isotopes for medical applications closer to the patients," explains TU Delft researcher Dr Antonia Denkova, head of the research project.

Pushing the boundaries of microscopy to understand cells better

Kristin Grußmayer pushes the boundaries of microscopy with new techniques to study the exact location of molecules, and to make extremely fast 3D images of the cell. Her research group will take a look at the early stage of Huntington’s disease on a very small scale, now possible thanks to these advanced microscopy methods: “One of the biggest challenges in the super resolution field is how to work with living cells while making sure they stay happy.”

Bacteriophages as a possible alternative to antibiotics

What is invisible and will kill more people than cancer in thirty years' time? Answer: bacteria. Years of excessive use of antibiotics has enabled certain bacteria to evolve in a way that has become impossible to treat. Stan Brouns from TU Delft is conducting fundamental research into a possible alternative to antibiotics: bacteriophages. These days, researcher Stan Brouns’ mailbox is full of heart-wrenching stories about people who have contracted a superbug. Since he told about the possible use of bacteriophages to tackle antibiotic-resistant bacteria on Dokters van Morgen, patients with these bacteria in their system have been turning to the molecular microbiologist for help. ‘I just spoke to someone who was ringing about his daughter’, says Brouns. ‘She had a skin infection that wouldn't go away.’ Some of the patients have bad infections and are seriously ill. Antibiotics don’t help. As always, the million-dollar question is: can ‘these bacteriophages’ turn the tide? Balanced warfare What are bacteriophages? Quite simply, they are minuscule viruses that infect bacteria, which then use the bacteria cell as an organic factory to multiply themselves. They aren't particularly impressive: an angular head with a bit of DNA, a tubular neck and a couple of wispy legs. That is all they are. But despite their seemingly simple anatomy, bacteriophages are highly efficient killing machines. They kill a staggering third of all bacteria in our oceans. Not per year, not per month, but every single day. Bacteriophages and bacteria have been keeping each other in equilibrium for billions of years. Bacteria have developed an arsenal of defensive measures to fend off their arch enemies during the course of this ongoing war with bacteriophages. But evolution has equipped the phages with even better combat techniques to allow them to cross the bacteria’s defence lines. This biological warfare has enabled bacteriophages to become highly specialised. Most phages (as we call them) cannot infect more than one strain of bacteria. But – they are exceedingly good at it. Bacteria devourer The French-Canadian microbiologist Felix d’Herelle discovered bacteriophages 100 years ago. World War I had turned Europe into a battlefield, and in the midst of this chaos, d’Herelle was investigating an outbreak of dysentery among the soldiers in France. He made filtrates of faeces samples from a number of soldiers who had somehow managed not to succumb to the disease. He then mixed these bacteria- free filtrates with strains of Shigella bacteria, the pathogen that caused the dysentery outbreak. He cultivated the mixture to observe how the bacteria would grow under the influence of the bacteria-free faeces samples. When clear patches appeared in the mixture, d’Herelle instinctively understood what was happening: there was an invisible microbe in the bacteria-free mixtures, he wrote in his notes, which was attacking the bacteria. He thought that it was probably a virus that infiltrated bacteria. Not much later, the scientist gave the ‘bacteria viruses’ the name we still use today: bacteriophage, a compilation of ‘bacteria’ and the Greek word ‘phagein’, which means to ‘eat’ or ‘devour’. So bacteriophage literally means ‘bacteria devourer’. Medical legacy In the same way as he immediately realised what was happening in his Petri dishes, d’Herelle also understood the implications of his discovery. He experimented with the phages as a method for treating dysentery in the Hôpital des Enfants-Malades in Paris, and later developed several drugs based on bacteriophages. As it happened, antibiotics were discovered around the same time. These drugs also killed bacteria, and even more efficiently than phages. As an antibiotic works on a whole spectrum of bacteria rather than one specific strain, doctors did not need to know exactly which bacterium they were dealing with. Efforts were therefore focused on developing antibiotics. What happened to the phages? They slipped into oblivion. At least, they did in the West. But after World War II, doctors behind the iron curtain were finding it difficult to get hold of antibiotics. The Eastern Bloc was only too happy to inherit the Frenchman d’Herelle’s medical legacy. Phages became their most important weapon for fighting infections. Unlike in the West, in countries such as Georgia and Russia they continued developing phages as a medicine, and even set up so-called ‘phage banks’. Bacteriophages attack a bacterium. This image has been made by means of a transmission-elektron-microscope. Unfortunate immutability With the benefit of hindsight, we would clearly have done better to continue the work on phages. As demonstrated by the stories Stan Brouns receives in his mailbox every day, antibiotics are gradually losing their power. Increasingly more bacteria are adapting and making themselves immune to certain types of antibiotics. In fact, superbugs have evolved, with the ability to survive treatment with every type of antibiotic currently known to man. The number of patients dying from a simple infection is rising every year. One of the original advantages of antibiotics, their immutability, has become a serious disadvantage. So what will happen? It is estimated that by 2050, some 10 million people a year will die after being infected with antibiotic-resistant bacteria. The risk of infection from these superbugs will make routine operations life-threatening events in the ‘post-antibiotic era’. Science is doing all it can to develop new antibiotics, but the question is whether – and more importantly when – they will arrive. There is an increasing call for the West to pick up where d’Herelle left off, and start investigating the possibilities of bacteriophage-based drugs. Incorporating information The huge gaps in our knowledge mean that there is still a lot we don't know about phages. Stan Brouns’ research group at TU Delft is conducting fundamental research into the biology of bacteriophages and the way they interact with bacteria. One of the researchers in his group is examining the information exchange between various types of bacteriophages, for example. ‘Phages can incorporate information from other phages into their own genome, which allows them to infect a completely different type of bacterium’, says Brouns. ‘One of the aspects we are studying is the efficiency of this exchange principle.’ Another researcher in his group is trying to find out how bacteria can become resistant to phages. Something that is becoming increasingly obvious is that the minuscule bacteria-killers are much more complex than one would assume. ‘For example, they appear to work alongside our immune system when fighting infections’, explains Brouns. In recent tests, healthy mice and mice with a weakened immune system were infected with a bacterium. Phages were used to see whether they could beat the infection. Brouns: ‘The mice with a healthy immune system recovered, but the mice with a defective immune system did not. This suggests that the immune system and phages sometimes work together.’ Medical tourism So are phages really a wonder drug, the ultimate solution to our problems with antibiotic resistance? If only. ‘Not all problems relating to antibiotic resistance can be solved with phages’, says Brouns. In addition, we do not yet know how phages will affect the human body. Brouns: ‘We may very well develop antibodies against the viral particles, making them increasingly less effective.’ It is even possible that our immune system will attack certain phages, causing an allergic reaction or worse. Aspects like these need to be studied in more detail before bacteriophages can be introduced here as a legal drug. In addition, research must meet our high Western standards, demonstrating evidence of effectiveness and safety from clinical trials on groups of patients and control groups. The phage research conducted in Eastern Europe does not meet these standards. And then, of course, there is the pharmaceutical industry. Unfortunately, phages are tricky customers for a business case. After all, how can you apply for a patent for something that keeps mutating and changes every day? Also: if a drug is so effective that patients are better in no time, is it commercially viable? So Brouns has decided to roll up his own sleeves. ‘I am trying to get the go-ahead for a kind of phage bank here, to put phage therapy on the map.’ Contribution At present, the sad reality is that people in this country who contract an antibiotic-resistant bacterium are sometimes beyond help. If these people want to undergo phage treatment, they have to go abroad. The costs for medical tourists who see phages as a last resort run into thousands of euros. Brouns is convinced that phages may be a lifeline for patients who have already tried everything that regular medicine has to offer. So he uses his www.fagenbank.nl website to answer frequently asked questions about treatment with bacteriophages and advise people about medical trips to the Eliava Institute in Georgia. He hopes that his appearances in the media and initiatives like his website will set the ball rolling. According to Brouns, it would make a huge difference if Dutch healthcare insurance companies were to reimburse the cost of phage treatment abroad. ‘Insurers may be willing to pay for the treatment if they see that it works. Quite a lot of people have already been successfully treated in Georgia, so I am hopeful.’ Stan Brouns +31 15 27 83920 S.J.J.Brouns@tudelft.nl This is a story from Applied Sciences These days, researcher Stan Brouns’ mailbox is full of heart-wrenching stories about people who have contracted a superbug. Since he told about the possible use of bacteriophages to tackle antibiotic-resistant bacteria on Dokters van Morgen, patients with these bacteria in their system have been turning to the molecular microbiologist for help. ‘I just spoke to someone who was ringing about his daughter’, says Brouns. ‘She had a skin infection that wouldn't go away.’ Some of the patients have bad infections and are seriously ill. Antibiotics don’t help. As always, the million-dollar question is: can ‘these bacteriophages’ turn the tide? Balanced warfare What are bacteriophages? Quite simply, they are minuscule viruses that infect bacteria, which then use the bacteria cell as an organic factory to multiply themselves. They aren't particularly impressive: an angular head with a bit of DNA, a tubular neck and a couple of wispy legs. That is all they are. But despite their seemingly simple anatomy, bacteriophages are highly efficient killing machines. They kill a staggering third of all bacteria in our oceans. Not per year, not per month, but every single day. Bacteriophages and bacteria have been keeping each other in equilibrium for billions of years. Bacteria have developed an arsenal of defensive measures to fend off their arch enemies during the course of this ongoing war with bacteriophages. But evolution has equipped the phages with even better combat techniques to allow them to cross the bacteria’s defence lines. This biological warfare has enabled bacteriophages to become highly specialised. Most phages (as we call them) cannot infect more than one strain of bacteria. But – they are exceedingly good at it. Bacteria devourer The French-Canadian microbiologist Felix d’Herelle discovered bacteriophages 100 years ago. World War I had turned Europe into a battlefield, and in the midst of this chaos, d’Herelle was investigating an outbreak of dysentery among the soldiers in France. He made filtrates of faeces samples from a number of soldiers who had somehow managed not to succumb to the disease. He then mixed these bacteria- free filtrates with strains of Shigella bacteria, the pathogen that caused the dysentery outbreak. He cultivated the mixture to observe how the bacteria would grow under the influence of the bacteria-free faeces samples. When clear patches appeared in the mixture, d’Herelle instinctively understood what was happening: there was an invisible microbe in the bacteria-free mixtures, he wrote in his notes, which was attacking the bacteria. He thought that it was probably a virus that infiltrated bacteria. Not much later, the scientist gave the ‘bacteria viruses’ the name we still use today: bacteriophage, a compilation of ‘bacteria’ and the Greek word ‘phagein’, which means to ‘eat’ or ‘devour’. So bacteriophage literally means ‘bacteria devourer’. Medical legacy In the same way as he immediately realised what was happening in his Petri dishes, d’Herelle also understood the implications of his discovery. He experimented with the phages as a method for treating dysentery in the Hôpital des Enfants-Malades in Paris, and later developed several drugs based on bacteriophages. As it happened, antibiotics were discovered around the same time. These drugs also killed bacteria, and even more efficiently than phages. As an antibiotic works on a whole spectrum of bacteria rather than one specific strain, doctors did not need to know exactly which bacterium they were dealing with. Efforts were therefore focused on developing antibiotics. What happened to the phages? They slipped into oblivion. At least, they did in the West. But after World War II, doctors behind the iron curtain were finding it difficult to get hold of antibiotics. The Eastern Bloc was only too happy to inherit the Frenchman d’Herelle’s medical legacy. Phages became their most important weapon for fighting infections. Unlike in the West, in countries such as Georgia and Russia they continued developing phages as a medicine, and even set up so-called ‘phage banks’. Bacteriophages attack a bacterium. This image has been made by means of a transmission-elektron-microscope. Unfortunate immutability With the benefit of hindsight, we would clearly have done better to continue the work on phages. As demonstrated by the stories Stan Brouns receives in his mailbox every day, antibiotics are gradually losing their power. Increasingly more bacteria are adapting and making themselves immune to certain types of antibiotics. In fact, superbugs have evolved, with the ability to survive treatment with every type of antibiotic currently known to man. The number of patients dying from a simple infection is rising every year. One of the original advantages of antibiotics, their immutability, has become a serious disadvantage. So what will happen? It is estimated that by 2050, some 10 million people a year will die after being infected with antibiotic-resistant bacteria. The risk of infection from these superbugs will make routine operations life-threatening events in the ‘post-antibiotic era’. Science is doing all it can to develop new antibiotics, but the question is whether – and more importantly when – they will arrive. There is an increasing call for the West to pick up where d’Herelle left off, and start investigating the possibilities of bacteriophage-based drugs. Incorporating information The huge gaps in our knowledge mean that there is still a lot we don't know about phages. Stan Brouns’ research group at TU Delft is conducting fundamental research into the biology of bacteriophages and the way they interact with bacteria. One of the researchers in his group is examining the information exchange between various types of bacteriophages, for example. ‘Phages can incorporate information from other phages into their own genome, which allows them to infect a completely different type of bacterium’, says Brouns. ‘One of the aspects we are studying is the efficiency of this exchange principle.’ Another researcher in his group is trying to find out how bacteria can become resistant to phages. Something that is becoming increasingly obvious is that the minuscule bacteria-killers are much more complex than one would assume. ‘For example, they appear to work alongside our immune system when fighting infections’, explains Brouns. In recent tests, healthy mice and mice with a weakened immune system were infected with a bacterium. Phages were used to see whether they could beat the infection. Brouns: ‘The mice with a healthy immune system recovered, but the mice with a defective immune system did not. This suggests that the immune system and phages sometimes work together.’ Medical tourism So are phages really a wonder drug, the ultimate solution to our problems with antibiotic resistance? If only. ‘Not all problems relating to antibiotic resistance can be solved with phages’, says Brouns. In addition, we do not yet know how phages will affect the human body. Brouns: ‘We may very well develop antibodies against the viral particles, making them increasingly less effective.’ It is even possible that our immune system will attack certain phages, causing an allergic reaction or worse. Aspects like these need to be studied in more detail before bacteriophages can be introduced here as a legal drug. In addition, research must meet our high Western standards, demonstrating evidence of effectiveness and safety from clinical trials on groups of patients and control groups. The phage research conducted in Eastern Europe does not meet these standards. And then, of course, there is the pharmaceutical industry. Unfortunately, phages are tricky customers for a business case. After all, how can you apply for a patent for something that keeps mutating and changes every day? Also: if a drug is so effective that patients are better in no time, is it commercially viable? So Brouns has decided to roll up his own sleeves. ‘I am trying to get the go-ahead for a kind of phage bank here, to put phage therapy on the map.’ Contribution At present, the sad reality is that people in this country who contract an antibiotic-resistant bacterium are sometimes beyond help. If these people want to undergo phage treatment, they have to go abroad. The costs for medical tourists who see phages as a last resort run into thousands of euros. Brouns is convinced that phages may be a lifeline for patients who have already tried everything that regular medicine has to offer. So he uses his www.fagenbank.nl website to answer frequently asked questions about treatment with bacteriophages and advise people about medical trips to the Eliava Institute in Georgia. He hopes that his appearances in the media and initiatives like his website will set the ball rolling. According to Brouns, it would make a huge difference if Dutch healthcare insurance companies were to reimburse the cost of phage treatment abroad. ‘Insurers may be willing to pay for the treatment if they see that it works. Quite a lot of people have already been successfully treated in Georgia, so I am hopeful.’ Stan Brouns +31 15 27 83920 S.J.J.Brouns@tudelft.nl This is a story from Applied Sciences Related stories Affordable MRI Constructing living cells Tinkering under the bonnet of life

Comparing apples with pears under the microscope

Seeing tiny particles even better through a microscope – Teun Huijben, Best Graduate student of the Faculty of Applied Sciences, managed it for his Master’s thesis.

Solving the worldwide bottleneck in nuclear medicine

Radionuclides are essential in the diagnosis and treatment of cancer and other diseases, because they can detect and destroy specific tumour cells. Yet only a handful of nuclear reactors in the world produce the bulk of these radionuclides. Robin de Kruijff works to solve this medical bottleneck, by developing new ways to produce radionuclides to make sure they become more widely available for medical hospitals and clinics.

Constructing living cells

Scientists across the world are conducting research into cells. But, despite all of their efforts, cells still harbour many secrets. However mind-blowingly complex cells may be, though, increasing numbers of scientists are starting to believe that it should be possible to construct a cell from separate building blocks, one step at a time. TU Delft has the knowledge to play a pioneering role in this process. On one of the walls of Marileen Dogterom's office, head of the department of Bionanoscience in the Faculty of Applied Sciences, there is an enormous drawing of the interior of a cell, with swirling proteins in all shapes, colours and sizes. A long string of DNA winds its way through the clumps. It is quite clear what the primary area of focus is here: the cell. But the research conducted in the department is about more than learning to understand how a cell works. The TU Delft scientists want to go a step further: they want to construct a synthetic cell, together with their counterparts in the Netherlands and abroad. The relatively young field of research that designs new biological systems using existing building blocks is referred to as ‘synthetic biology’. It is a specialist field that is clearly on the rise. Borrowing principles Marileen Dogterom herself primarily conducts research into the physical processes within cells. She addresses such questions as: ‘What forces play a role in processes within a cell?’ and ‘What is it that gives a cell its shape?’. A key area of Dogterom's expertise is microtubules. These are hollow protein tubes that form part of the framework of the cell, the so-called cytoskeleton. ‘We do not plan to precisely mimic any existing cell type,’ says the head of the department about the ambitious plan to create a synthetic cell. ‘Instead, we intend to borrow principles from simple systems such as yeasts or bacteria and then link them together.’ Borrowing principles and linking them together may sound simple, but there is still a lot to research and to learn, even about rudimentary biological systems. Research conducted by Craig Venter, the molecular biologist who became famous for being the first to sequence the human genome, confirms this. In 2010, Venter created what he described as a ‘synthetic life form’ by removing the contents of a bacterial cell, replacing it with DNA developed in the lab and bringing it back to life. It proved to be considerably more difficult than he thought it would be. Minimal cell In 2016, the same Craig Venter also presented a minimal cell. ‘Venter's group had taken a simple bacterium with a genome of around 1,000 genes and started taking bits out of it’, explains Dogterom. ‘After removing a piece of DNA, they would check to see if the cell was still functioning.’ By gradually shaving off the genetic material gene by gene, the group eventually discovered a minimum number of genes that the bacterium needed to keep itself alive. That magic number? 473 genes. Fewer than that and the cell no longer functioned. Craig Venter's ‘minimal bacterium’ is interesting, but also slightly surprising. Because if you look at the separate components that experts believe are needed in order to construct a complete cell from the bottom up, and the genes that code for them, 473 seems like a very large amount. Coordination and timing Christophe Danelon , who also conducts research into synthetic cells with his group in Delft, says he is aiming for a ‘global approach’. Danelon: ‘We do not focus on a single component, but we attempt to construct the different modules we need simultaneously.’ Not so long ago, for example, Danelon's group succeeded in artificially synthesising phospholipids. These fatty chemicals form the ‘vesicles’ in which the other parts of the synthetic cell will soon have to do their work. Danelon estimates that the components needed for a minimal cell can be made using approximately 150 genes, which is not even a third of Craig Venter's 473 genes. This therefore raises a question: will these 150 genes work together when they are combined into one singe strand of DNA? Danelon suspects that the genes in Venter's cell whose purpose is still unknown may be involved in such things as the coordination and timing of cellular processes. Ultimately, everything has to happen in the right sequence. For example, it makes no sense for a cell to start dividing if no copy has yet been made of the genetic material. Cutting through the middle Cees Dekker is the third leading TU Delft researcher involved in the project. Just like Marileen Dogterom, he has a strong physics background. The two scientists also share a refusal to be deterred by the complexity of the cell. ‘It is absolutely true that life is enormously complex’, says Dekker. ‘But does that mean we should say: it is so complicated, let's not even start? Or should we say instead: We see an opportunity to construct test systems and look at what we understand about them? The latter, in my view. I am a scientist because I want to understand how nature works.’ Dekker's group is focused on synthetic cell division, among other things. Some time ago, his group contributed to a study that demonstrated how the protein ring that cuts through the middle of a cell during cell division is constructed. Dekker: ‘I also conduct research into other biophysical processes, such as the spatial structure of DNA and proteins in cells. For example, we manipulated the shape of E. coli cells to see how DNA and proteins organise themselves.’ As well as providing some important scientific insights, this research resulted in the following extraordinary image: living bacteria in the form of the letters TUDELFT. Black box The Delft researchers emphasise that building a synthetic cell is above all a fundamental challenge. It is all about curiosity, about discovering how the cell works. But they are also convinced that the synthetic cell will result in all kinds of practical applications. ‘Just look at microbiology’, says Dekker. ‘In the beginning, research in that field was also driven by curiosity. But since then, a huge industry has emerged that uses bacteria as little factories to make all kinds of different substances.’ Marileen Dogterom expects that research into synthetic cells will result in medical breakthroughs: ‘When you administer a drug to someone, you are doing something with the molecules in their cells. Hopefully, that will have a favourable effect on the disease you are trying to combat. But in fact, you are putting those drugs into a kind of black box, because you do not know exactly what it is they do. This is why side effects are difficult to predict.’ The idea is that a better understanding of how cells work will enable us to intervene more effectively in the processes that make us ill. Ethical discussions Alongside practical applications, the construction of a synthetic cell is also likely to provide us with a greater understanding of what ‘life’ is, exactly, and how it began. ‘We have been doing cellular research for 70 years, and we have made tremendous progress’, says Dekker. ‘But no one knows how, four billion years ago, life first formed from separate biological components such as amino acids and lipids. That is a fascinating scientific question, and building a synthetic cell can help us find the answer.’ It may also raise ethical discussions on the issue of whether, as a scientist, you are permitted to ‘play God’: in other words, whether you should want to create life at all. ‘But’, says Dekker, himself a man of faith, ‘there is a perfectly good answer to that question. Moreover, it is doubtful whether the wider public will have such strong concerns about a primitive form of life. Currently, it is mainly journalists who raise the issue.’ Nevertheless, philosopher Hub Zwart from the Radboud University has now joined the Dutch consortium that has been awarded a prestigious NWO Gravitation grant for research into the synthetic cell. Linking pieces together How long will it be before the synthetic cell is a reality? It is difficult to say. ‘I am optimistic that, on a ten-year time scale, we will be able to make use of minimal components to make a system that can divide autonomously’, says Cees Dekker. Marileen Dogterom is slightly more tentative: ‘I am certain that it is possible to build a synthetic cell, but I am unsure whether that will be achieved within ten years. We are already capable of getting the pieces up and running. The great challenge is how we link these pieces together.’ Christophe Danelon loves his work and is quite happy for the research to take a long time. ‘I think I may have to sabotage the experiments when I sense that we are on the verge of a synthetic cell’, he says jokingly. But even if it proves possible to build a functioning, self-dividing cell, the question is whether that will conclude the project, says Dogterom. ‘Ultimately, it is about how you define success. For example, should a cell also be able to adapt, to evolve? What would you need to add to a synthetic cell to make that possible? And do we not also want to understand the interactions between cells?’ To ask the question is to answer it. And so, Christophe Danelon does not have to worry. There is more than enough work to do. Marileen Dogterom +31 (0)15 27 85937 M.Dogterom@tudelft.nl Cees Dekker +31 15 2786094 c.dekker@tudelft.nl group website Christophe Danelon +31 (0)15 27 88085 c.j.a.danelon@tudelft.nl This is a story from Applied Sciences On one of the walls of Marileen Dogterom's office, head of the department of Bionanoscience in the Faculty of Applied Sciences, there is an enormous drawing of the interior of a cell, with swirling proteins in all shapes, colours and sizes. A long string of DNA winds its way through the clumps. It is quite clear what the primary area of focus is here: the cell. But the research conducted in the department is about more than learning to understand how a cell works. The TU Delft scientists want to go a step further: they want to construct a synthetic cell, together with their counterparts in the Netherlands and abroad. The relatively young field of research that designs new biological systems using existing building blocks is referred to as ‘synthetic biology’. It is a specialist field that is clearly on the rise. Borrowing principles Marileen Dogterom herself primarily conducts research into the physical processes within cells. She addresses such questions as: ‘What forces play a role in processes within a cell?’ and ‘What is it that gives a cell its shape?’. A key area of Dogterom's expertise is microtubules. These are hollow protein tubes that form part of the framework of the cell, the so-called cytoskeleton. ‘We do not plan to precisely mimic any existing cell type,’ says the head of the department about the ambitious plan to create a synthetic cell. ‘Instead, we intend to borrow principles from simple systems such as yeasts or bacteria and then link them together.’ Borrowing principles and linking them together may sound simple, but there is still a lot to research and to learn, even about rudimentary biological systems. Research conducted by Craig Venter, the molecular biologist who became famous for being the first to sequence the human genome, confirms this. In 2010, Venter created what he described as a ‘synthetic life form’ by removing the contents of a bacterial cell, replacing it with DNA developed in the lab and bringing it back to life. It proved to be considerably more difficult than he thought it would be. Minimal cell In 2016, the same Craig Venter also presented a minimal cell. ‘Venter's group had taken a simple bacterium with a genome of around 1,000 genes and started taking bits out of it’, explains Dogterom. ‘After removing a piece of DNA, they would check to see if the cell was still functioning.’ By gradually shaving off the genetic material gene by gene, the group eventually discovered a minimum number of genes that the bacterium needed to keep itself alive. That magic number? 473 genes. Fewer than that and the cell no longer functioned. Craig Venter's ‘minimal bacterium’ is interesting, but also slightly surprising. Because if you look at the separate components that experts believe are needed in order to construct a complete cell from the bottom up, and the genes that code for them, 473 seems like a very large amount. Coordination and timing Christophe Danelon , who also conducts research into synthetic cells with his group in Delft, says he is aiming for a ‘global approach’. Danelon: ‘We do not focus on a single component, but we attempt to construct the different modules we need simultaneously.’ Not so long ago, for example, Danelon's group succeeded in artificially synthesising phospholipids. These fatty chemicals form the ‘vesicles’ in which the other parts of the synthetic cell will soon have to do their work. Danelon estimates that the components needed for a minimal cell can be made using approximately 150 genes, which is not even a third of Craig Venter's 473 genes. This therefore raises a question: will these 150 genes work together when they are combined into one singe strand of DNA? Danelon suspects that the genes in Venter's cell whose purpose is still unknown may be involved in such things as the coordination and timing of cellular processes. Ultimately, everything has to happen in the right sequence. For example, it makes no sense for a cell to start dividing if no copy has yet been made of the genetic material. Cutting through the middle Cees Dekker is the third leading TU Delft researcher involved in the project. Just like Marileen Dogterom, he has a strong physics background. The two scientists also share a refusal to be deterred by the complexity of the cell. ‘It is absolutely true that life is enormously complex’, says Dekker. ‘But does that mean we should say: it is so complicated, let's not even start? Or should we say instead: We see an opportunity to construct test systems and look at what we understand about them? The latter, in my view. I am a scientist because I want to understand how nature works.’ Dekker's group is focused on synthetic cell division, among other things. Some time ago, his group contributed to a study that demonstrated how the protein ring that cuts through the middle of a cell during cell division is constructed. Dekker: ‘I also conduct research into other biophysical processes, such as the spatial structure of DNA and proteins in cells. For example, we manipulated the shape of E. coli cells to see how DNA and proteins organise themselves.’ As well as providing some important scientific insights, this research resulted in the following extraordinary image: living bacteria in the form of the letters TUDELFT. Black box The Delft researchers emphasise that building a synthetic cell is above all a fundamental challenge. It is all about curiosity, about discovering how the cell works. But they are also convinced that the synthetic cell will result in all kinds of practical applications. ‘Just look at microbiology’, says Dekker. ‘In the beginning, research in that field was also driven by curiosity. But since then, a huge industry has emerged that uses bacteria as little factories to make all kinds of different substances.’ Marileen Dogterom expects that research into synthetic cells will result in medical breakthroughs: ‘When you administer a drug to someone, you are doing something with the molecules in their cells. Hopefully, that will have a favourable effect on the disease you are trying to combat. But in fact, you are putting those drugs into a kind of black box, because you do not know exactly what it is they do. This is why side effects are difficult to predict.’ The idea is that a better understanding of how cells work will enable us to intervene more effectively in the processes that make us ill. Ethical discussions Alongside practical applications, the construction of a synthetic cell is also likely to provide us with a greater understanding of what ‘life’ is, exactly, and how it began. ‘We have been doing cellular research for 70 years, and we have made tremendous progress’, says Dekker. ‘But no one knows how, four billion years ago, life first formed from separate biological components such as amino acids and lipids. That is a fascinating scientific question, and building a synthetic cell can help us find the answer.’ It may also raise ethical discussions on the issue of whether, as a scientist, you are permitted to ‘play God’: in other words, whether you should want to create life at all. ‘But’, says Dekker, himself a man of faith, ‘there is a perfectly good answer to that question. Moreover, it is doubtful whether the wider public will have such strong concerns about a primitive form of life. Currently, it is mainly journalists who raise the issue.’ Nevertheless, philosopher Hub Zwart from the Radboud University has now joined the Dutch consortium that has been awarded a prestigious NWO Gravitation grant for research into the synthetic cell. Linking pieces together How long will it be before the synthetic cell is a reality? It is difficult to say. ‘I am optimistic that, on a ten-year time scale, we will be able to make use of minimal components to make a system that can divide autonomously’, says Cees Dekker. Marileen Dogterom is slightly more tentative: ‘I am certain that it is possible to build a synthetic cell, but I am unsure whether that will be achieved within ten years. We are already capable of getting the pieces up and running. The great challenge is how we link these pieces together.’ Christophe Danelon loves his work and is quite happy for the research to take a long time. ‘I think I may have to sabotage the experiments when I sense that we are on the verge of a synthetic cell’, he says jokingly. But even if it proves possible to build a functioning, self-dividing cell, the question is whether that will conclude the project, says Dogterom. ‘Ultimately, it is about how you define success. For example, should a cell also be able to adapt, to evolve? What would you need to add to a synthetic cell to make that possible? And do we not also want to understand the interactions between cells?’ To ask the question is to answer it. And so, Christophe Danelon does not have to worry. There is more than enough work to do. Marileen Dogterom +31 (0)15 27 85937 M.Dogterom@tudelft.nl Cees Dekker +31 15 2786094 c.dekker@tudelft.nl group website Christophe Danelon +31 (0)15 27 88085 c.j.a.danelon@tudelft.nl This is a story from Applied Sciences Related stories Savings lives with mathematics Bacteriophages a possible alternative to antibiotics Tinkering under the bonnet of life

Tinkering under the bonnet of life

A longer life in good health? The end of genetic disorders? Crops that are able to survive in the harshest conditions? CRISPR-Cas9 brings all of this and more within our grasp. The research group of Dr Stan Brouns at the department of Bionanoscience is conducting fundamental research into how CRISPR systems function. What is his take on the forthcoming revolution? “Look, this is a Cascade complex,” says Dr Brouns, turning a strange-looking lump of plastic over in his hands. The object most resembles a chunk of coral, with a contorted and uneven surface. It is, in fact, a model of a cluster of proteins that are to be found in the cytoplasm of certain bacteria. “This protein here,” he points, “is the spine of the complex. And see these blobs here? Those are also proteins. All of them are essential, otherwise the system doesn’t work.” Molecular scissors What is the function of this particular cluster of proteins? Put simply, it is an essential weapon that bacteria use to exterminate viruses, which are professional killing machines that have been bacteria’s nemesis since the dawn of evolution. For example, every day, simple viruses known as ‘bacteriophages’ kill one third of all the bacteria in the oceans. “The virus injects its DNA or RNA into a cell in order to try to take it over,” explains Dr Brouns. “And if this hijacking is successful, the virus is able to use that cell as a little factory to produce copies of itself.” A strategy as simple as it is deadly. Dr Brouns’ protein cluster, the Cascade complex, leaps into action the moment a virus injects its genetic material. It seeks out the virus’s DNA and clamps onto it tightly. It then sends a signal to another protein, which comes along and cuts the virus to ribbons using a pair of molecular scissors. Dr Brouns is investigating how this type of bacterial defence system functions. Mysterious code How does the Cascade complex distinguish between viral DNA and the bacterium's own DNA? That is where something known as CRISPR comes in: ‘Clustered Regularly Interspaced Short Palindromic Repeats’. Researchers discovered these constantly repeating sequences of code (‘repeats’) in the DNA of the well-known E. coli bacteria in the 1980s. “Back then, nobody knew what the sequences meant,” says Dr Brouns. “It was only in 2005 that it was recognised that the DNA segments located between the repeats corresponded with the DNA of viruses.” The DNA of viruses? Yes, indeed. Sometimes a bacterium survives an attack by a virus, for example because the virus was weakened. In those rare cases, the bacterium seizes a trace of the virus’s DNA. By ‘unzipping’ its own DNA at the location of the repeats, the bacterium then builds the virus’s DNA into its own genetic code. The effect is comparable to how a vaccine works. From that moment on, the bacterium has that virus etched into its memory forever. If that same type of virus is foolish enough to try attacking that bacterium again, it recognises its assailant and can dispatch a cutting protein, such as the Cascade complex. Using two strands of RNA as a ‘cheat sheet’, the protein cluster goes on the hunt for enemy DNA. And if the complex finds a match, it is simply a matter of grip, snip and away. Cutting and pasting But CRISPR systems such as the Cascade complex are much more than just a biological curiosity. Scientists have been able to use them to edit DNA since the autumn of 2012, when Professors Jennifer Doudna (UC Berkeley, USA) and Emmanuelle Charpentier (then at Umeå University, Sweden) succeeded in reconstructing the CRISPR system of a streptococcus bacteria that uses the Cas9 protein. The two scientists unravelled the bacteria’s defence mechanism. Then, one of Prof. Doudna’s post-doc researchers managed to combine the two RNA stands into a single ‘guide RNA’ (the cheat sheet alluded to earlier), which he could programme however he wished. This made it possible to use any arbitrary segment of DNA as a guide RNA and therefore to cut DNA wherever required. Of course, rewriting DNA is quite a different challenge than merely cutting it apart. But further research also proved the latter to be possible using CRISPR-Cas9. Researchers are now able to send a segment of DNA along with the Cas9 protein. As soon as the protein snips through a cell’s DNA, the cell tries to repair the strand as quickly as possible. If the ends of the accompanying DNA segment fit with the ends of the cut strand, the cell will use that genetic material to repair the strand. Researchers are able to place other nucleotides (and even complete genes) between the ends of the accompanying DNA segment. Aggressive white blood cells CRISPR-Cas9 is now being used by thousands of research teams around the world to very precisely deactivate or overwrite particular genes. This technology has enormous potential. “One specific example is a clinical trial that is currently in progress in which white blood cells extracted from cancer patients are being modified using Cas9 to be more aggressive,” says Dr Brouns. “The hope is that this will enable the modified white blood cells to get rid of tumours on their own.” It is just one example of the numerous possible applications of CRISPR-Cas9. Naturally, the technology has certain limitations. “Gene editing in living creatures, for example, is a challenge,” he notes. Particularly when trying to introduce changes in tissue that is rarely regenerated. Consider, for example, Duchenne Muscular Dystrophy (DMD), which damages and weakens the muscles. “Setting aside the ethical objections for a moment,” says Dr Brouns, “in theory you could deactivate this disease at the embryonic stage. Or you could select embryos that are unaffected by this disorder, which already happens in clinics. But once a person is born with this disease, it is actually too late.” Still, scientists have already made significant strides towards a cure. “It is possible to embed a repair sequence into a specific virus and inject that virus into a mouse with DMD. The virus will then disseminate the new genetic material.” And the outcome of this procedure? Mice with stronger muscles. But unfortunately not as strong as those of healthy mice, as yet. A kit full of tools What is not widely known is that there are considerably more CRISPR systems in existence than merely the variant that uses the now familiar Cas9 protein. And the functioning of one can be quite unlike the next. For example, instead of a straight cut, one type of protein makes an angular incision in the DNA into which the repair material fits like a puzzle piece, which increases the cell’s chances of successfully repairing its DNA. Furthermore, the size of the Cas proteins varies in each system. Cas9 is relatively large and is therefore not able to operate in every type of cell. Another type of cutting enzyme, known as Cpf1, is also looking promising. “Cpf1 is going to be quite successful as well,” predicts Dr Brouns. “It has a tiny RNA that is capable of cutting through both DNA strands. And since it comprises only 40 nucleotides, compared to Cas9's 100, it is cheaper to produce. Moreover, it makes it easier to cut in multiple locations simultaneously.” In short, CRISPR-Cas is not a single tool, but rather a whole kit full of different kinds of implements. Where one job requires a screwdriver, another requires a hammer. And the good news is, new tools are being added to the kit all the time. Hopefully these new discoveries will eventually lead to a point where scientists can mould all extant cells to their will. Breaking new ground And where will all this end? The first children with a modified DNA have already been born. And while we are at it, will we choose to make these genetically modified children more intelligent? With violet eyes? And maybe add some sweet little dimples to their cheeks? “Yes, well,” says Dr Brouns, “at a certain point you stray beyond the bounds of diseases into areas that people find desirable. That is something we have to consider with great care.” Brouns knows, of course, that it is becoming more and more pressing to answer questions of this nature. However, his goal is to unravel the biology behind CRISPR-Cas systems in order to figure out down to the minutest detail how these extraordinary defence mechanisms function. One question that the Brouns group is now trying to answer, for instance, is why bacteria seem to prefer taking certain strands of a virus’s DNA to build into their own DNA, as opposed to others. These endeavours will keep Brouns and his research group occupied for some time yet. “We have already learned so much, yet I expect that there are many microbial defence mechanisms still to discover.” But the most striking thing remains just how ingenious the CRISPR systems are, which is precisely why they are a source of fascination. “Every time we look at them, their functioning always seems more complex than we first thought,” says Dr Brouns. “They never cease to amaze us.” Stan Brouns +31 15 27 83920 S.J.J.Brouns@tudelft.nl This is a story from Applied Sciences Read more about this project “Look, this is a Cascade complex,” says Dr Brouns, turning a strange-looking lump of plastic over in his hands. The object most resembles a chunk of coral, with a contorted and uneven surface. It is, in fact, a model of a cluster of proteins that are to be found in the cytoplasm of certain bacteria. “This protein here,” he points, “is the spine of the complex. And see these blobs here? Those are also proteins. All of them are essential, otherwise the system doesn’t work.” Molecular scissors What is the function of this particular cluster of proteins? Put simply, it is an essential weapon that bacteria use to exterminate viruses, which are professional killing machines that have been bacteria’s nemesis since the dawn of evolution. For example, every day, simple viruses known as ‘bacteriophages’ kill one third of all the bacteria in the oceans. “The virus injects its DNA or RNA into a cell in order to try to take it over,” explains Dr Brouns. “And if this hijacking is successful, the virus is able to use that cell as a little factory to produce copies of itself.” A strategy as simple as it is deadly. Dr Brouns’ protein cluster, the Cascade complex, leaps into action the moment a virus injects its genetic material. It seeks out the virus’s DNA and clamps onto it tightly. It then sends a signal to another protein, which comes along and cuts the virus to ribbons using a pair of molecular scissors. Dr Brouns is investigating how this type of bacterial defence system functions. Mysterious code How does the Cascade complex distinguish between viral DNA and the bacterium's own DNA? That is where something known as CRISPR comes in: ‘Clustered Regularly Interspaced Short Palindromic Repeats’. Researchers discovered these constantly repeating sequences of code (‘repeats’) in the DNA of the well-known E. coli bacteria in the 1980s. “Back then, nobody knew what the sequences meant,” says Dr Brouns. “It was only in 2005 that it was recognised that the DNA segments located between the repeats corresponded with the DNA of viruses.” The DNA of viruses? Yes, indeed. Sometimes a bacterium survives an attack by a virus, for example because the virus was weakened. In those rare cases, the bacterium seizes a trace of the virus’s DNA. By ‘unzipping’ its own DNA at the location of the repeats, the bacterium then builds the virus’s DNA into its own genetic code. The effect is comparable to how a vaccine works. From that moment on, the bacterium has that virus etched into its memory forever. If that same type of virus is foolish enough to try attacking that bacterium again, it recognises its assailant and can dispatch a cutting protein, such as the Cascade complex. Using two strands of RNA as a ‘cheat sheet’, the protein cluster goes on the hunt for enemy DNA. And if the complex finds a match, it is simply a matter of grip, snip and away. Cutting and pasting But CRISPR systems such as the Cascade complex are much more than just a biological curiosity. Scientists have been able to use them to edit DNA since the autumn of 2012, when Professors Jennifer Doudna (UC Berkeley, USA) and Emmanuelle Charpentier (then at Umeå University, Sweden) succeeded in reconstructing the CRISPR system of a streptococcus bacteria that uses the Cas9 protein. The two scientists unravelled the bacteria’s defence mechanism. Then, one of Prof. Doudna’s post-doc researchers managed to combine the two RNA stands into a single ‘guide RNA’ (the cheat sheet alluded to earlier), which he could programme however he wished. This made it possible to use any arbitrary segment of DNA as a guide RNA and therefore to cut DNA wherever required. Of course, rewriting DNA is quite a different challenge than merely cutting it apart. But further research also proved the latter to be possible using CRISPR-Cas9. Researchers are now able to send a segment of DNA along with the Cas9 protein. As soon as the protein snips through a cell’s DNA, the cell tries to repair the strand as quickly as possible. If the ends of the accompanying DNA segment fit with the ends of the cut strand, the cell will use that genetic material to repair the strand. Researchers are able to place other nucleotides (and even complete genes) between the ends of the accompanying DNA segment. Aggressive white blood cells CRISPR-Cas9 is now being used by thousands of research teams around the world to very precisely deactivate or overwrite particular genes. This technology has enormous potential. “One specific example is a clinical trial that is currently in progress in which white blood cells extracted from cancer patients are being modified using Cas9 to be more aggressive,” says Dr Brouns. “The hope is that this will enable the modified white blood cells to get rid of tumours on their own.” It is just one example of the numerous possible applications of CRISPR-Cas9. Naturally, the technology has certain limitations. “Gene editing in living creatures, for example, is a challenge,” he notes. Particularly when trying to introduce changes in tissue that is rarely regenerated. Consider, for example, Duchenne Muscular Dystrophy (DMD), which damages and weakens the muscles. “Setting aside the ethical objections for a moment,” says Dr Brouns, “in theory you could deactivate this disease at the embryonic stage. Or you could select embryos that are unaffected by this disorder, which already happens in clinics. But once a person is born with this disease, it is actually too late.” Still, scientists have already made significant strides towards a cure. “It is possible to embed a repair sequence into a specific virus and inject that virus into a mouse with DMD. The virus will then disseminate the new genetic material.” And the outcome of this procedure? Mice with stronger muscles. But unfortunately not as strong as those of healthy mice, as yet. A kit full of tools What is not widely known is that there are considerably more CRISPR systems in existence than merely the variant that uses the now familiar Cas9 protein. And the functioning of one can be quite unlike the next. For example, instead of a straight cut, one type of protein makes an angular incision in the DNA into which the repair material fits like a puzzle piece, which increases the cell’s chances of successfully repairing its DNA. Furthermore, the size of the Cas proteins varies in each system. Cas9 is relatively large and is therefore not able to operate in every type of cell. Another type of cutting enzyme, known as Cpf1, is also looking promising. “Cpf1 is going to be quite successful as well,” predicts Dr Brouns. “It has a tiny RNA that is capable of cutting through both DNA strands. And since it comprises only 40 nucleotides, compared to Cas9's 100, it is cheaper to produce. Moreover, it makes it easier to cut in multiple locations simultaneously.” In short, CRISPR-Cas is not a single tool, but rather a whole kit full of different kinds of implements. Where one job requires a screwdriver, another requires a hammer. And the good news is, new tools are being added to the kit all the time. Hopefully these new discoveries will eventually lead to a point where scientists can mould all extant cells to their will. Breaking new ground And where will all this end? The first children with a modified DNA have already been born. And while we are at it, will we choose to make these genetically modified children more intelligent? With violet eyes? And maybe add some sweet little dimples to their cheeks? “Yes, well,” says Dr Brouns, “at a certain point you stray beyond the bounds of diseases into areas that people find desirable. That is something we have to consider with great care.” Brouns knows, of course, that it is becoming more and more pressing to answer questions of this nature. However, his goal is to unravel the biology behind CRISPR-Cas systems in order to figure out down to the minutest detail how these extraordinary defence mechanisms function. One question that the Brouns group is now trying to answer, for instance, is why bacteria seem to prefer taking certain strands of a virus’s DNA to build into their own DNA, as opposed to others. These endeavours will keep Brouns and his research group occupied for some time yet. “We have already learned so much, yet I expect that there are many microbial defence mechanisms still to discover.” But the most striking thing remains just how ingenious the CRISPR systems are, which is precisely why they are a source of fascination. “Every time we look at them, their functioning always seems more complex than we first thought,” says Dr Brouns. “They never cease to amaze us.” Stan Brouns +31 15 27 83920 S.J.J.Brouns@tudelft.nl This is a story from Applied Sciences Related stories Saving lifes with mathematics Bacteriophages as a possible alternative to antibiotics Constructing living cells

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