News: Bioteknik related to Chalmers University of TechnologyTue, 22 Jun 2021 11:56:35 +0200 dipping solution turns the whole fish into food<p><b>​​When herring are filleted, more than half their weight becomes a low-value ‘side stream’ that never reaches our plates – despite being rich in protein and healthy omega-3 fatty acids. Now, scientists from Chalmers University of Technology, Sweden, have developed a special dipping solution, with ingredients including rosemary extract and citric acid, which can significantly extend the side streams’ shelf life, and increase the opportunities to use them as food.  ​</b></p><p class="chalmersElement-P">​<span>Techniques for upgrading these side-streams to food products such as minces, protein isolates, hydrolysates and oils are already available today, and offer the chance to reduce the current practices of using them for animal feed, or, in the worst cases, simply throwing them away. </span></p> <p class="chalmersElement-P"><span style="background-color:initial">However, the big challenge is that the unsaturated fatty acids found in fish are very sensitive to oxidative degradation, meaning that the quality starts to decrease after just a few hours. This results in an unpleasant taste, odour, colour and texture </span><span style="background-color:initial">in the final product. The reason why side stream parts from the fish such as backbones and heads are so sensitive is because they are rich in blood, which in turn contains the protein haemoglobin, which accelerates the fatty acid degradation process.</span></p> <h2 class="chalmersElement-H2"><span>Solution including rosemary and citric acid </span></h2> <p class="chalmersElement-P"><span style="background-color:initial"><img src="/SiteCollectionImages/Institutioner/Bio/Food/Ingrid%20Undeland_I0A0740_350x305.jpg" alt="Photo od Ingrid Undeland" class="chalmersPosition-FloatRight" style="margin:5px;width:250px;height:218px" />“Our new technology offers a valuable window of time for the producer, where the side-streams remain fresh for longer, and can be stored or transported before being upgraded into various food ingredients,” explains<strong> Ingrid Undeland</strong>, Professor of Food Science at the Department of Biology and Biological Engineering at Chalmers.</span></p> <p class="chalmersElement-P"><span style="background-color:initial">The new technology is based on a dipping solution containing ingredients including for example rosemary extract and citric acid. Within the frame of a European project called WaSeaBi, and together with colleagues Haizhou Wu and Mursalin Sajib, Ingrid Undeland recently published a scientific study exploring the possibilities of the method.  </span></p> <h2 class="chalmersElement-H2"><span>Recycling the solution up to ten times</span></h2> <p class="chalmersElement-P"><span style="background-color:initial">The results showed that dipping the side stream parts from the herring filleting process into the solution, prior to storage, significantly extended the time before rancidity developed. At 20 degrees, the storage time could be extended from less than half a day to more than 3 and a half days, and at 0 degrees, from less than 1 day to more than 11 days.</span></p> <p class="chalmersElement-P"><span style="background-color:initial">“And because the dipping solution covers the surface of side stream parts with a thin layer of antioxidants, these are carried over to the next stage of the process, providing more high-quality minces, protein or oil ingredients,” explains Ingrid Undeland.</span></p> <p class="chalmersElement-P"><span style="background-color:initial">To make the technology cost-effective, the possibility of re-using the solution was also investigated. Results showed that even after reusing the solution up to 10 times, rancidity was completely inhibited at 0 °C. In addition, it was found that the solution kept the fish haemoglobin in a form that was more stable and less reactive with the fatty acids, which the researchers believe explains the decrease in oxidation.</span></p> <p class="chalmersElement-P"><span style="background-color:initial"><strong>Photo of Ingrid Undeland:</strong> Anna-Lena Lundqvist/Chalmers</span></p> <p class="chalmersElement-P"><span style="background-color:initial"><br /></span></p> <p class="chalmersElement-P"> <span><strong>More on the study, and the possibilities of side-streams </strong></span></p> <p class="chalmersElement-P"></p> <ul><li>The study, <a href="">Controlling hemoglobin-mediated lipid oxidation in herring (<em>Clupea harengus</em>) co-products via incubation or dipping in a recyclable antioxidant solution</a>, was published with open access in the journal Food Control. </li> <li>It was based on herring side-streams from Sweden Pelagic, however, results obtained with dipping of cod-side streams from Royal Greenland also confirm that rosemary-based antioxidant mixtures are good at protecting against oxidation. This means that the solution can be used to prevent rancidity of different kinds of fish side-streams.</li> <li>Examples of valuable side streams from fish include, for example, the backbones and heads, which are rich in muscle and therefore suitable for fish mince or pr<span style="background-color:initial">otein ingredients. As the belly flap and intestines are rich in omega-3 fatty acids, they can be used for oil production. The tail fin has a lot of skin, bones and connective tissue and is therefore well suited for, for example, the production of marine collagen, which is a much sought-after ingredient on the market right now. In addition to food, marine collagen is also used in cosmetics and ‘nutraceuticals’ with documented good effects on the health of our joints and skin.</span></li></ul> <br /><p></p> <p class="chalmersElement-P"><strong>About the project</strong></p> <p class="chalmersElement-P"></p> <ul><li><span style="background-color:initial"><a href="">WaSeaBi ​</a>is a four-year project that aims to optimise the utilisation of seafood side-streams by developing new methods to produce nutritious and tasty ingredients. The project brings together an interdisciplinary team of 13 partners from five European nations which include Technical University of Denmark, Food &amp; Bio Cluster Denmark, Chalmers University of Technology, AZTI, EIT Food, Sweden Pelagic, Royal Greenland, Alfa Laval, Pescados Marcelino, Jeka Fish, Barna, Nutrition Sciences, Ghent University</span></li> <li>The project receives funding from the Bio Based Industries Joint Undertaking (JU) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 837726. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and the Bio Based Industries Consortium. </li></ul> <div><strong>Read more: </strong><a href="/en/departments/bio/news/Pages/More-of-the-catch-to-end-up-on-the-plate.aspx">More of the catch to end up on the plate​</a><br /> <p></p> <p class="chalmersElement-P"></p> <div><br /></div></div>Thu, 10 Jun 2021 08:00:00 +0200 mRNA to time its great escape perfectly<p><b>​​The ease by which mRNA-based drugs are taken up by cells in tissues is crucial to their therapeutic effectiveness. Now, a new detection method developed by researchers at Chalmers and AstraZeneca could lead to faster and better development of the small droplets known as lipid nanoparticles, which are the main method used to package mRNA for delivery to the cells.​</b></p><p class="chalmersElement-P"><span><img src="/SiteCollectionImages/Institutioner/Bio/ChemBio/" alt="Photo of Michael Munson" class="chalmersPosition-FloatRight" style="margin:5px;width:250px;height:218px" />“We have developed an automated process to monitor and test large numbers of different lipid nanoparticles simultaneously, which we hope will streamline the development of new medicines,” says <strong>Michael Munson</strong>, Postdoctoral Fellow at AstraZeneca R&amp;D, who is affiliated to the research centre FoRmulaEx, and is the first author of the study that was recently published in the journal Nature Communications Biology.</span></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><span>Messenger RNA, or mRNA, is the code used by cells to produce proteins. When it is introduced as a drug or a vaccine, it is interpreted by the cells as a set of instructions, to then use their own systems to produce the desired proteins.</span></p> <p class="chalmersElement-P"><span style="background-color:initial">mRNA-based technologies are</span><span style="background-color:initial"> being explored for their potential to help treat chronic diseases in various ways, such as by encoding therapeutic proteins, and potentially be tailored for specific tissues, for example to replace incorrect proteins or regulate cellular malfunctions that cause disease.</span></p> <h2 class="chalmersElement-H2"><span>mRNA molecules are packed into lipid nanoparticles ​</span></h2> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"><span>But the</span><span>re are several major challenges associated with this new technology. First, the cells must be ‘tricked’ into taking in the mRNA molecules. One of the most advanced ways of doing this is to pack the mRNA into a small droplet, known as a lipid nanoparticle. The nanoparticles enter cells in a large bubble called an endosome, which transports its contents to the cell's ‘lysosomes’, or degradation stations. </span></p> <p class="chalmersElement-P"><span>The lipid nanoparticles containing the mRNA must exit the endosome at just the right moment, to reach the cell's cytoplasm, where the proteins are made, before the endosome reaches the degradation station. Otherwise, the mRNA will break down and no longer be able to work. This vital step is called ‘endosomal escape’ and timing it correctly is the most decisive factor for mRNA-based medicines to work. </span></p> <div> </div> <div> </div> <div> </div> <h2 class="chalmersElement-H2"><span>Tracking the escape</span></h2> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P">The new study describes a method that the researchers developed to screen lipid nanoparticles for optimization of mRNA delivery. The method makes it possible to monitor the cell uptake, endosomal escape and delivery of mRNA in hundreds of samples at a time. To achiev​e this, the researchers combined fluorescence reporters to track the movement of the lipid nanoparticles through the cell, for protein expression and the endosomal escape events. The endosomal escape marker consists of a fluorescent variant of the protein Galectin-9 which accumulates at ruptured endosomes and <a href="">was adapted from work published by a research group in Lund​</a>.</p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial">“Instead of just seeing which lipid nanoparticles work best, we can now also understand what makes them work optimally, and use that knowledge to develop and test new improved nanoparticle formulations,” says Michael Munson.</span></p> <div> </div> <div> </div> <div> </div> <h2 class="chalmersElement-H2"><span>Endosomal escape must be optimally timed​</span><span><br /></span></h2> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial"><strong>Elin Esbjörner</strong>, Associate Professor of Chemical Biology at Chalmers and co-author of<img src="/SiteCollectionImages/Institutioner/Bio/ChemBio/Elin%20Esbjorner_1_350x305.jpg" class="chalmersPosition-FloatRight" alt="Photo of Elin Esbjörner" style="margin:5px;width:250px;height:218px" /> the study, explains the importance of delivering the mRNA to the target cells as precisely as possible: </span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial">“To redu</span><span style="background-color:initial">ce the risk of side effects, such as the immune system being triggered by the lipid particles, we want to use the lowest possible dose. This is particularly true for diseases which require long term treatment. In those cases, it is vital that the moment of endosomal escape is optimally timed, to allow the mRNA to get out into the cytoplasm with maximum effect,” she says. </span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial">In addition to allowing the researchers to evaluate a large number of lipid particles at the same time, the new method can also help examine how efficiently the lipid particles are delivered and how well they function in different types of cells. This could allow for tailoring the drugs to target specific tissues, such as in the lungs or the liver.</span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial">“The lipid nanoparticles work differently in different cell types. A formulation that works well for delivery to liver cells, for example, could be significantly different in lung cells. Our new method could help us understand why such differences exist, and to harness this knowledge to design new lipid nanoparticles tailored for different targets in the body,” says Elin Esbjörner.</span></p> <p class="chalmersElement-P"><span style="font-weight:700">Photo of Michael Munson: </span>AstraZeneca<br /><span style="font-weight:700">Ph</span><span style="font-weight:700">oto of</span><span style="font-weight:700"> Elin Esbjörner: </span>Mikael WInters​<span style="background-color:initial"><br /></span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial"><br /></span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><span style="background-color:initial"><strong>Read the scientific article: </strong><a href="">A high-throughput Galectin-9 imaging assay for quantifying nanoparticle uptake, endosomal escape and functional RNA delivery</a></span></p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"><strong style="background-color:initial">About FoRmulaEx:</strong><span style="background-color:initial"> <br /></span><a href="/en/centres/FoRmulaEx/Pages/default.aspx"><span>FoRmulaEx ​</span>​</a><span style="background-color:initial">is an industrial research center for functional RNA delivery. The three academic partners are Chalmers University of Technology, the University of Gothenburg and the Karolinska Institutet in Stockholm, carrying out research in close collaboration with AstraZeneca, Vironova, Camarus and Nanolyze. The purpose is to contribute the foundational knowledge required to design safe and effective drug deliveries for the next generation of nucleotide drugs.</span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> </p>Wed, 09 Jun 2021 09:00:00 +0200' Robot Scientist ready for drug discovery<p><b>The robot scientist Eve has been assembled and is now operating at Chalmers University of Technology. Eve’s f​irst mission is to identify and test drugs against covid-19.​</b></p><p class="chalmersElement-P">​<span>A robot scientist is a laboratory system that uses artificial intelligence (AI) to automate scientific research. It autonomously forms hypothesis, plans experiments, executes the experiments using laboratory automation equipment, analyses the results, and repeats the cycle. </span></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><img src="/SiteCollectionImages/Institutioner/Bio/SysBio/RossKing_191003_02_350x305px.jpg" alt="Professor Ross King" class="chalmersPosition-FloatRight" style="width:250px;height:218px" />AI systems now have superhuman scientific skills that are complementary to human scientists.</p> <h2 class="chalmersElement-H2">​Human scientists free to make creative leaps</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“My vision when developing robot scientists  is not to replace human scientists, but rather to make them orders of magnitude more productive through collaborating with AI systems,” says <strong>Ross King</strong>, Professor of Machine Intelligence at the Department of Biology and Biological Engineering, continuing: </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“This will free human scientist to make the high-level creative leaps at which they excel, and thus contribute to solving societal challenges.” </p> <div> </div> <h2 class="chalmersElement-H2">The first machine to discover scientific knowledge</h2> <div> </div> <p class="chalmersElement-P">His first robot scientist, Adam, was the first machine to autonomously discover scientific knowledge. Eve was developed for automatic early-stage drug development and has previously discovered novel drugs against several tropical diseases including malaria. </p> <div> </div> <p class="chalmersElement-P"></p> <div> </div> <p class="chalmersElement-P">Moving Eve from the University of Manchester to the Division of Systems and Synthetic Biology at Chalmers has enabled Ross King to collaborate with Per Sunnerhagen, Professor at Gothenburg University, to search for drugs against covid-19. </p> <div> </div> <p class="chalmersElement-P"></p> <div> </div> <p class="chalmersElement-P">“It is deeply shocking how little effort large pharmaceutical companies have put into finding drugs against covid-19. If such drugs were available now, they would save many lives in places such as India,” says Ross King.</p> <div> </div> <h2 class="chalmersElement-H2">New robot scientist under development​</h2> <div> </div> <p class="chalmersElement-P"></p> <div> </div> <p class="chalmersElement-P"></p> <div> </div> <p class="chalmersElement-P">The new robot scientist Genesis, which is under development,  is funded by the Wallenberg AI, Autonomous Systems and Software Program. It is designed to better understand how human cells work.​<br /><br /></p> <div> </div> <p class="chalmersElement-P"><strong>Text:</strong> Susanne Nilsson Lindh<br /><strong>Photo of Ross King: </strong>Johan Bodell<br /><strong>Photo of Eve and researcher </strong><strong>Ievgeniia Tiukova (below): </strong>Martina Butorac</p> <div> </div> <p class="chalmersElement-P"><br /></p> <div> </div> <p class="chalmersElement-P"><img src="/SiteCollectionImages/Institutioner/Bio/SysBio/robotscientist_750.jpg" alt="Chalmers' Robot Scientist ready for drug discovery" style="margin:5px;width:650px;height:379px" /><br /></p> <div> </div> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"><strong><br /></strong></p> <p class="chalmersElement-P"><strong>About Eve</strong></p> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"></p> <div> </div> <ul><li>Eve is a laboratory automation work cell with equipment for liquid handling, drug maintenance, yeast growth profiling brough together by robotic arms. </li> <li>Eve has vacuum sealed mechanics of robotic arms which can operate in six axis orientation and were designed for continuous use under heavy loads for months at a time. </li> <li>Eve has an intelligent drug discovery mode using algorithms of active machine learning to untangle quantitative structure/activity relationship. </li> <li>Eve enables ultra-precise, reproducible, and high-throughput experimentation to facilitate early drug discovery and assists researchers with repetitive tasks.</li> <li>Watch <a href="" style="background-color:rgb(255, 255, 255)">Eve at work</a></li></ul> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"><strong>Read more:</strong></p> <div> </div> <p class="chalmersElement-P"></p> <div> </div> <ul><li><a href="/en/departments/bio/news/Pages/I-want-to-transform-the-way-science-is-done.aspx"><span style="background-color:initial">&quot;I want to transform the way science is done”</span>​</a><span style="background-color:initial"> </span></li> <li><span style="background-color:initial"><a href="/en/news/Pages/43-Chalmers-researchers-receive-funding-for-more-research.aspx">43 Chalmers researchers receive funding for more research​</a><br /></span></li></ul> <div> <strong></strong></div> <p></p> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"><br /></p> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <p class="chalmersElement-P">   </p> <div> </div> <p class="chalmersElement-P"> ​</p>Thu, 03 Jun 2021 11:00:00 +0200 and oats in study with heart patients<p><b>​Bilberries and oats are already proven to be healthy for your heart. But do you get an additional positive effect if you combine them? This will now be investigated in a large study, which includes 900 heart attack patients.</b></p>​<span style="background-color:initial">Researchers from Chalmers, in collaboration with clinics in Örebro, Karlstad, Lund and Umeå, will after the summer launch a study, where patients with acute myocardial infarction will be recruited for a diet trial. The patients will be given bilberries – the kind of blueberries that grow in Sweden – and oats.</span><div>“They are recruited within five days after undergoing balloon dilation in connection with their infarction. The procedure usually takes place immediately when they arrive at the hospital, or within a couple of days”, says Rikard Landberg, Professor at Chalmers’ division of Food and Nutrition Science, and adds:<img src="/SiteCollectionImages/Areas%20of%20Advance/Health/Udda%20format/Rikard_Landberg_300.jpg" class="chalmersPosition-FloatRight" alt="" style="margin:5px" /><br /></div> <div>“It is important to know that this is not an alternative treatment, but of course an addition to the standard medical treatment they will receive by their care givers”.</div> <h2 class="chalmersElement-H2">Healthy but in different ways</h2> <div>No previous study has been performed on the combination of oats and bilberries. But their separate health effects have been shown, and the effects of bilberries have been investigated in a pilot study by the research group involved in the new trial.</div> <div>“We were able to demonstrate great effects, even though the patients were already on drug treatment. This is what stimulated us to design this study”, says Rikard Landberg.<br /><span style="background-color:initial">Oats and </span>bilberries <span style="background-color:initial">seem to have positive effects on risk factors via different body mechanisms. Dietary fibre in oats has well-known cholesterol-lowering effects, and certain polyphenols in bilberries – substances that give the berry its color, taste and smell – have positive effects on blood pressure, as the polyphenols have bo</span><span style="background-color:initial">th a vasodilating and an anti-inflammatory effect. That is why the researchers believe that the two together can give a synergy effect, or at least an added effect.</span><br /></div> <h2 class="chalmersElement-H2">Individualized treatment a goal</h2> <div>The cholesterol levels, but also other metabolic risk factors of the 900 patients, will be monitored. Stool tests will show if the intestinal bacterial flora is affected, and if it modifies the effect of bilberries and oats on the risk factors studied. The research team will also follow metabolites, the body’s markers in the blood, to possibly find specific molecules that can be linked to the individual’s response to the dietary supplement. Bilberries​ are compared to oats, the combination of bilberries and oats in a special made beverage (picture), and to a placebo product.</div> <div>“Our study opens up for a more specific, individualized preventive treatment of people who have had a myocardial infarction”, Rikard Landberg says.<img src="/SiteCollectionImages/Areas%20of%20Advance/Health/Udda%20format/Blåbär-havre-dryck_300.jpg" class="chalmersPosition-FloatRight" alt="" style="margin:5px" /><br /></div> <h2 class="chalmersElement-H2">Food an important factor</h2> <div>He is hoping for preliminary results in 2023. And Rikard Landberg is happy to be able to contribute to future evidence-based additional treatment and prevention for a large group of patients:</div> <div>“Each year, a large number of individuals suffer heart attacks. Eating habits are one of the most important factors, but as of today, we lack evidence to show how we should relate to this. This research is an example where we from Chalmers can contribute with specific competence and experience, while we also must collaborate with medical expertise as the study is performed on patients. Together, I hope we can contribute to future improved healthcare for myocardial infarction patients”, he concludes.</div> <div><br /></div> <div>Text: Mia Malmstedt</div> <div>Photo: Shutterstock, Annika Söderpalm (picture of Rikard Landberg), Rikard Fristedt (picture of the beverage used in the study)</div>Tue, 01 Jun 2021 15:00:00 +0200 enzymes help gut bacteria compete for food<p><b>​The bacterial composition of the human gut can affect health. To investigate this, researchers need increased knowledge of this diverse bacterial ecosystem. In a recently published study in the Journal of Biological Chemistry, researchers at Chalmers investigated the strategy used by one bacterial species in the gut to compete for nutrients in dietary fibre. The study was selected as one of the journal’s top ranked publications, the so-called Editors’ Picks.</b></p><p class="chalmersElement-P"><span style="background-color:initial">The systems and strategies used by gut bacteria to digest dietary fibre in our food varies between different species. Research has shown connections between bacterial composition to both health and different diseases. Thus, basic understanding of how the “good” gut bacteria work is important, for example how well they compete with other bacteria for nutrients in the gut.</span><br /></p> <h2 class="chalmersElement-H2">Protective groups complicates degradation of dietary fibre</h2> <p class="chalmersElement-P"><span style="background-color:initial">​In</span><span style="background-color:initial"> the gut, bacteria use enzyme</span><span style="background-color:initial">s, proteins that catalyse chemical reactions, to break down the complex polysaccharides, i.e. long carbohydrate chain</span><span style="background-color:initial">s, in dietary fibre into simple sugars. However, some of these polysaccharides are prot</span><span style="background-color:initial">ected by chemical groups, that hinder enzymatic degradation. </span></p> <p class="chalmersElement-P"><span style="background-color:initial">“How gut bacteria handle these protective groups has not been studied in detail. In our study, we have explored how the gut bacter</span><span style="background-color:initial">ium </span><span style="background-color:initial"><em>Dysgonomona's mossii</em> </span><span style="background-color:initial">degrades the complex plant polysaccharide xylan. This is an important compone</span><span style="background-color:initial">nt in dietary fibre, but the carbohydrate chains are protected by several chemical groups that make them difficult to degrade,” says Johan Larsbrink, Associate Professor of Industrial Biotechnology at the Department of Biology and Biotechnological Engineering.</span></p> <p class="chalmersElement-P"><span style="background-color:initial"></span></p> <h2 class="chalmersElement-H2" style="font-family:&quot;open sans&quot;, sans-serif">Found three enzymes used to remove protective groups </h2> <p class="chalmersElement-P"><span style="background-color:initial"><em>Dysgonomonas mossii </em></span><span style="background-color:initial">belongs to in the phylum Bacteroidetes, which is a dominant group in the gut microbiota of humans, and they are considered &quot;good&quot; bacteria. Previous research has shown that in these species, the genes encoding enzymes for degrading carbohydrate chains are often found in large gene clusters in the DNA, so-called polysaccharide utilisation loci (PULs).</span></p> <p class="chalmersElement-P"><span style="background-color:initial">“We found three interesting enzymes, carbohydrate esterases, with different properties in a PUL in the bacterium, and we have shown how they are used to remove protective groups from xylan,” says Cathleen Kmezik, doctoral student at the Department of Biology and Biotechnological Engineering.</span></p> <p class="chalmersElement-P"><span style="background-color:initial">The PUL with the esterase genes also contains several other enzymes which degrade complex xylan chains. The clustering of the studied esterases with these other enzymes indicates that the ability to remove protective groups from carbohydrate chains is important for the bacteria to obtain nutrients.</span></p> <p class="chalmersElement-P"><span style="background-color:initial"></span></p> <h2 class="chalmersElement-H2" style="font-family:&quot;open sans&quot;, sans-serif">Solved one enzyme's 3D structure</h2> <p class="chalmersElement-P"><span style="background-color:initial">One of the esterases consists of two fused, catalytic, domains, which is rare. If you compare an enzyme to a pair of scissors that cuts specific chemical bonds, this esterase consists of two pairs of scissors physically connected to each other.</span></p> <p class="chalmersElement-P"><span style="background-color:initial"></span><span style="background-color:initial">“This enables the esterase to cut different chemical bonds that are situated very close to each other. However, one part of this enzyme was not very active on the molecules we tested in our lab experiments, but Scott Mazurkewich, a post-doctoral researcher managed to solve its 3D structure by X-ray crystallography. This means that we can see exactly what the enzyme looks like down to a tenth of a nanometre scale and provides us with a better understanding of what the enzyme is actually doing in the gut,” says Cathleen Kmezik.</span></p> <p class="chalmersElement-P"><span style="background-color:initial"></span></p> <h2 class="chalmersElement-H2" style="font-family:&quot;open sans&quot;, sans-serif">Removal of protective groups may be important for survival</h2> <p class="chalmersElement-P"><span style="background-color:initial">The ability to remove protective groups from polysaccharides may be important for survival in the gut, according to the researchers. More research is needed, though, to determine which niches different bacteria have in terms of what they can eat in the gut − and whether it leads to increased survival and persistence under certain conditions.</span></p> <p class="chalmersElement-P"><span style="background-color:initial">Future studies could allow different species of bacteria to grow simultaneously on different carbohydrates with many or few protective groups and compare wh</span><span style="background-color:initial">o &quot;wins&quot; the battle for nutrition. There is also potential for the enzymes to be used industrially to accelerate the enzymatic degradation of plant biomass in the production of biofuels.</span></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <div> </div> <div> </div> <div><p class="chalmersElement-P"><strong>Read the article in the Journal of Biological Chemistry</strong>: <a href=""><span>A</span><span> polysaccharide utilization locus from the gut bacterium <em>Dysgonomonas mossii </em>encodes functionally distinct carbohydrate esterases</span></a></p> <p class="chalmersElement-P"><img src="/SiteCollectionImages/Institutioner/Bio/IndBio/Scott%20Cathleen%20Johan_750x340.jpg" alt="Scott Mazurkewich, Cathleen Kmezik and Johan Larsbrink at IndBio" style="margin:5px;width:650px;height:295px" /><br /><br /><span style="background-color:initial">F</span><span style="background-color:initial">rom Chalmers the researchers <span></span><strong>Scott Mazurkewich, </strong></span><span style="background-color:initial;font-weight:700">Cathleen Kmezik </span><span style="background-color:initial">and <strong>Johan Larsbrink</strong> (above)from the Division of Industrial Biotechnology, <strong>Alexander Idström</strong> from Applied Chemistry, and <strong>Marina Armeni</strong> and</span><span style="background-color:initial"> <strong>Otto Savolainen</strong> from CMSI, participated in the study.</span></p></div> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><br /></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><strong>More about the esterases:</strong></p> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"><strong> </strong></p> <div> </div> <div> </div> <div> </div> <div><ul><li><p class="chalmersElement-P"><em>Dm</em>CE1A: enzyme from carbohydrate esterase family 1 (CE1), active on acetyl esters and cleaving coumaryl-like molecules of unknown structure from plant biomass.</p></li> <p class="chalmersElement-P"> </p> <li><p class="chalmersElement-P"><em style="background-color:initial">Dm</em>CE1B: enzyme consisting of two fused CE1 domains – <em>Dm</em>CE1B_nt and <em>Dm</em>CE1_ct, connected through a carbohydrate-binding module. Out of the three enzymes, <em>Dm</em>CE1B_nt is the only one with clear activity on feruloyl esters, which can crosslink xylan polysaccharides, and it was also active on acetyl esters. <em>Dm</em>CE1B_ct was only weakly active on acetyl esters. Its 3D structure was solved together with the carbohydrate-binding module. The structure indicates that the enzyme targets larger molecules than those tested in the lab (see figure).</p></li> <p class="chalmersElement-P"> </p> <li><p class="chalmersElement-P"><em style="background-color:initial">Dm</em>CE6A: enzyme from carbohydrate esterase family 6 (CE6), with significant activity on acetyl esters, both in model substrates and in complex biomass. The enzyme was shown to strongly contribute to a faster xylan degradation by enzymes targeting the polysaccharide itself (xylanases).</p></li></ul> <p class="chalmersElement-P"> <strong>Text:</strong> Susanne Nilsson Lindh<br /><strong style="background-color:initial">Illustration:</strong><span style="background-color:initial"> Scott Mazurkewich<br /><strong>Photo: </strong>Martina Butorac</span></p></div> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> </p> <div> </div> <div> </div> <div> </div> <div></div> <div> </div> <div> </div> <div> </div> <p class="chalmersElement-P"> ​</p>Thu, 20 May 2021 09:00:00 +0200's-100-list.aspx's-100-list.aspxInnovations for global health and sustainable textiles at IVA' s 100 list <p><b>​Three Chalmers research project​ in chemistry and chemical biology​, are highlighted by the Royal Swedish Academy of Engineering Sciences on this year's IVA's 100 list. The innovations can contribute to great progress for the development of RNA drugs and vaccines, reduce the textile industry's negative environmental impact and protect us against one of the world's major health threats – antibiotic resistant bacteria.</b></p>​The Royal Swedish Academy of Engineering Sciences (IVA), releases a national list of the 100 research projects that have the greatest potential to translate strong research into actual societal benefits and increased competitiveness for Swedish business, annually. This year's list focuses on research and innovations that contribute to increasing society's resilience to crises, and that’s where the projects from the Department of Chemistry and Chemical Engineering and the Department of Biology and Biotechnology, is now taking place.<div><div> </div> <h2 class="chalmersElement-H2">New method to overcome obstacles for full development of RNA drugs </h2> <div>What if it was possible to observe RNA-based therapeutics and vaccines as they do their job to enter and reprogram human cells, through a microscope in real-time. Thanks to a new method, developed by a group of researchers led by Marcus Wilhelmsson and Elin Esbjörner at Chalmers it is now possible! They have developed a method that makes RNA visible, using new minimalistic probes that do not alter its natural functions. The new method makes RNA visible without effecting its natural functions in the cell. The researchers’ innovation can contribute to solve the largest remaining challenge for taking also other RNA-based therapeutics to the clinic – their low functional cellular uptake. Similarly, the method facilitates research regarding new RNA-vaccines so that the world can be better prepared the next time it is hit by a pandemic.​​​<br /><br /></div> <div>“First of all, it feels great to be part of IVA's 100 list! It also confirms that others, apart from ourselves, consider this very interesting. It is especially exciting that people with other expertise than a researcher's, for example entrepreneurs in the field of technology, have evaluated our project and see the potential. We are currently in the process of starting a company to enable our research and ideas to be utilized, and we have submitted a patent application. Of course, this also verifies the high quality of what we do &quot;, says Marcus Wilhelmsson Professor at the Department of Chemistry and Chemical Engineering, and Elin Esbjörner, Associate Professor at the Department of Biology and Biotechnology, in a joint comment.<br /></div> <div><br /></div> <div><h2 class="chalmersElement-H2">Reversible coloring technology to extend the use of textile  </h2> <div>The textile industry is experiencing big changes, as increasing pressure from consumers and policy makers is forcing companies to act more sustainably. Today’s textile coloring processes don’t allow efficient removal of textile color to facilitate reuse and recycling. To tackle these issues, has a reversible coloring technology, a new combined coloring / decoloring process for textiles, been developed by researchers at Chalmers University of Technology to tackle these issues. Through the startup company Vividye the technology has been further developed. This unique solution will help the industry to extend the use of textile, and to pave the way for a green but colorful future.<br /><br /></div></div> <div><p class="MsoNormal"><span lang="EN-GB">“Six years ago, when we started the research project behind Vividye, we had no idea that we would end up on the IVA100 list.”, says Romain Bordes, </span><span lang="EN-US">Associate Professor </span><span lang="EN-US">at the Department of Chemistry and Chemical Engineering and one of Vividye’s co-founders​ </span></p> <h2 class="chalmersElement-H2"><span lang="EN-US">New materials to protect us against antibiotic-resistant bacteria<br /></span></h2> <p class="chalmersElement-P"><span lang="EN-US">​The increasing number of antibiotic-resistant bacteria is one of the greatest threats to humanity. To deal with this challenge, we need to develop new technical solutions. That’s why Martin Andersson and his research group develop new antibacterial materials that are suitable for medical devices, which can reduce the use of systemic antibiotics. The material is inspired by the way our immune system defeat infections and has shown good effect on all types of bacteria, including antibiotic-resistant ones. Clinical studies on the material have been initiated, and the material is getting closer to the researchers' goal of utilization.  <br /><br /></span></p> <p class="MsoNormal"><span lang="EN-US">“Utilization is an important part of our work, and this is a great example when research create value to the society. In recent years, we have worked in parallel with both research on the antimicrobial material and product development of the innovation in a spin-off company. We are now getting close to introduce the material on the market, so it is perfect timing to be selected on IVA's 100 list. Being part of the list is a great opportunity for us to show how our research can contribute to fight antibiotic resistance” says Martin Andersson, Professor at the Department of Chemistry and Chemical Engineering​​​</span></p> <p class="MsoNormal"><span lang="EN-US"><br /></span></p> <h3 class="chalmersElement-H3"><span lang="EN-US">Read more<br /></span></h3> <p class="MsoNormal"><span lang="EN-US">On the new method for developing RNA drugs  <br /><a href="">Scientific article recently published in ​Journal of Chemical Society (JACS)</a></span></p> <p class="MsoNormal"><br /></p> <p class="MsoNormal">On the innovation coloring / decoloring process for textiles <br /><a href="" title="Link to external webiste ">Startup company Vividye websites</a><br /><a href="" title="Link to external webiste ">Press release ”Vividyes teknologi kan förändra textilindustrin” (in Swedish)</a></p> <p class="MsoNormal"><span style="background-color:initial"><a href="" title="Link to external webiste "></a></span><span style="background-color:initial">​</span><br /></p> <p class="MsoNormal"><a href="" title="Link to external webiste ">​</a>​<span style="background-color:initial">On the material that works against all types of bacteria, including antibiotic-resistant ones<br /></span><span style="background-color:initial"><a href="" title="Link to scientific article">Scientific article recently published in ACS Biomaterials Science &amp; Engineering </a><br /></span><span style="background-color:initial"><font color="#1166aa"><b><a href="" title="link to external website ">Startup company Amferia website</a></b></font></span><span style="background-color:initial"><a href="" title="Link to scientific article"></a>​</span></p> <p class="MsoNormal"><span lang="EN-US"><br /></span></p></div> <div> </div> <div><br /></div></div> ​Mon, 10 May 2021 10:00:00 +0200–-with-computer-analysis.aspx healthy diets – with computer analysis<p><b>​A new mathematical model for the interaction of bacteria in the gut could help design new probiotics and specially tailored diets to prevent diseases. The research, from Chalmers University of Technology, was recently published in the journal PNAS.</b></p><p class="chalmersElement-P"><img src="/SiteCollectionImages/Institutioner/Bio/SysBio/Jens%20Nielsen_NNF_340.jpg" alt="Photo of Jens Nielsen" class="chalmersPosition-FloatRight" style="margin:5px;width:240px;height:240px" /><span style="background-color:initial">“Intesti</span><span style="background-color:initial">nal bacteria have an imp</span><span style="background-color:initial">ortant role to play in health and the development of diseases, and our new mathematical model could be extremely helpful in these areas,” says <strong>Jens Nielsen</strong>, Professor of Systems Biology at Chalmers, who led the research. </span></p> <p class="chalmersElement-P"><span style="background-color:initial">The <a href="">new paper </a>describes how the mathematical model performed when making predictions relating to two earlier clinical studies, one involv</span><span style="background-color:initial">ing Swedish infants, and the other adults in Finland with obesity. </span></p> <p class="chalmersElement-P"><span style="background-color:initial">The studies involved regular measurements of health indicators, which the researchers compared with the predictions made from their mathematical model – the m</span><span style="background-color:initial">odel proved to be highly accurate in predicting multiple variables, including how a switch</span><span style="background-color:initial"> from liquid to solid food in the Swedish infants affected their intestinal bacterial composition. </span></p> <p class="chalmersElement-P"><span style="background-color:initial">T</span><span style="background-color:initial">hey also measured how the obese adults’ intestinal </span><span style="background-color:initial">bacteria changed after a move to a more restricted diet. Again, the model’s predictions proved to be reliably accurate.  </span></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“These are very encouraging results, which could enable computer-based design for a very complex system. Our model could therefore be used to for creating personalised healthy diets, with the possibility to predict how adding specific bacteria as novel probiotics could impact a patient’s health,” says Jens Nielsen.</p> <p class="chalmersElement-P"> </p> <h2 class="chalmersElement-H2">Many factors at play</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">There are many different things that affect how different bacteria grow and function in the intestinal system. For example, which other bacteria are already present and how they interact with each other, as well as how they interact with the host – that is to say, us. The bacteria are also further affected by their environmental factors, such as the diet we eat.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">All of these variables make predicting the effect that adding bacteria or making dietary changes will have. One must first understand how these bacteria are likely to act when they enter the intestine or how a change in diet will affect the intestinal composition. Will they be able to grow there or not? How will they interact with and possibly affect the bacteria that are already present in the gut? How do different diets affect the intestinal microbiome?</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“The model we have developed is unique because it accounts for all these variables. It combines data on the individual bacteria as well as how they interact. It also includes data on how food travels through the gastrointestinal tract and affects the bacteria along the way in its calculations. The latter can be measured by examining blood samples and looking at metabolites, the end products that are formed when bacteria break down different types of food,” says Jens Nielsen.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">The data to build the model has been gathered from many years’ worth of pre-existing clinical studies. As more data is obtained in the future, the model can be updated with new features, such as descriptions of hormonal responses to dietary intake.</p> <p class="chalmersElement-P"> </p> <h2 class="chalmersElement-H2">A potential huge asset for future healthcare</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Research on diet and the human microbiome, or intestinal bacterial composition, is a field of research that generates great interest, among both researchers and the general public. Jens Nielsen explains why:</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“Changes in the bacterial composition can be associated with or signify a great number of ailments, such as obesity, diabetes, or cardiovascular diseases. It can also affect how the body responds to certain types of cancer treatments or specially developed diets.”</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Working with the bacterial composition therefore offers the potential to influence the course of diseases and overall health. This can be done through treatment with probiotics – carefully selected bacteria that are believed to contribute to improved health.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">In future work, Jens Nielsen and his research group will use the model directly in clinical studies. They are already participating in a study together with Sahlgrenska University Hospital in Sweden, where older women are being treated for osteoporosis with the bacteria<em> Lactobacillus reuteri</em>. It has been seen that some patients respond better to treatment than others, and the new model could be used as part of the analysis to understand why this is so.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Cancer treatment with antibodies is another area where the model could be used to analyse the microbiome, helping to understand its role in why some patients respond well to immunotherapy, and some less so.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“This would be an incredible asset if our model can begin to identify bacteria that could improve the treatment of cancer patients. We believe it could really make a big difference here,” says Jens Nielsen.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Text: </strong>Susanne Nilsson Lindh and Joshua Worth<br /><strong>Illustration:</strong> Yen Strandqvist<br /><strong>Photo:</strong> Martina Butorac</p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"><strong>Read the whole study in PNAS: </strong><a href="">CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention</a></p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"><strong>More about the study</strong></p> <p class="chalmersElement-P"></p> <ul><li><span style="background-color:initial">The article's authors ar</span><span style="background-color:initial">e Jun Geng, Boyang Ji, Gang Li, Felipe López-Isunza and Jens Nielsen. </span></li> <li>The researchers are active at Chalmers University of Technology and the Wallenberg Center for Protein Research in Sweden, the Novo Nordisk Foundation Center for Biosustainability and BioInnovation Institute, DTU in Denmark, and Universidad Autónoma Metropolitana-Iztapalapa in Mexico. </li> <li>The research has been financed by the Bill &amp; Melinda Gates Foundation, Novo Nordisk Foundation and the Knut and Alice Wallenberg Foundation.</li></ul> <p></p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"> </p>Tue, 20 Apr 2021 07:00:00 +0200 science and biotech explore new territory<p><b>​Researchers in Materials Science and Industrial Biotechnology at Chalmers University of Technology will combine forces to produce sustainable light-weight materials of the future. The project, led by Chalmers, has been awarded the prestigious EU-grant FET Open. ​</b></p><p class="chalmersElement-P">​<span>The aim of the FET Open-project is to develop lightweight materials from wood-based components, involving metabolically engineered microorganisms in the process. </span></p> <p class="chalmersElement-P"><span>There is an urgent need to reduce causes of climate change, microplastic pollution and raw material shortages, and this may be achieved by replacing fossil-based resources with renewable ones. At the same time environmentally friendly processing technologies to create safe products with minimum impact on the environment must be developed. </span></p> <h2 class="chalmersElement-H2"><span>Light-weight materials for transportation and sports</span></h2> <p class="chalmersElement-P">”Our project is a unique opportunity for materials engineering to meet biotechnology for  production of light-weight materials,” says project co-ordinator Tiina Nypelö, Associate Professor at the Department of Chemistry and Chemical Engineering at Chalmers, continuing:  </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“We see transportation and sports as application fields to contribute to.”</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">In her work Tiina Nypelö combines forest products technology, material science and renewable resources for advancing sustainable materials engineering. Her appointment at Chalmers is affiliated with <a href="" style="font-family:inherit">Wallenberg Wood Science Center </a><span style="background-color:initial;font-family:inherit">(WWSC).</span></p> <h2 class="chalmersElement-H2"><span>Research expertise will be used in complet​ely new ways</span></h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">In the project, she is collaborating with Chalmers researchers Cecilia Geijer, Assistant Professor at the Department of Biology and Biological Engineering and Lisbeth Olsson, Professor in Industrial Biotechnology, and Co-Director of WWSC. Their research focus is on the design and use of microorganisms in processes where plant cell wall materials are converted to biofuels, biochemicals and material.  </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">”Even though Lisbeth, Tiina and I are already working with sustainability issues, the approach we have to this challenge is new territory, which I personally think is very cool. We will all be applying our research expertise in completely new ways to create novel light-weight material, and we are aiming for this project to have a great impact on society in the future. The interdisciplinary aspect of the project is exciting and very important as it will build bridges between our research groups, divisions and departments,” says Cecilia Geijer. </p> <p></p> <h2 class="chalmersElement-H2">Potential of great societal impact​</h2> <p></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">The EU-grant FET Open supports science and technology research and innovation towards radically new future technologies with the potential of great societal impact. The Chalmers’ co-ordinated project has been granted three million Euros, involves three Chalmers research groups from two departments, together with four partners from Austria and Spain, and will run for four years. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Text: </strong>Susanne Nilsson Lindh<br /><span style="background-color:initial"><strong>Photo:</strong> Ma</span><span style="background-color:initial">rtina Butorac</span></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"> </p> <h2 class="chalmersElement-H2">​More about: The Collaboration Partners</h2> <p class="chalmersElement-P"> </p> <h3 class="chalmersElement-H3">TU Graz</h3> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"></p> <ul><li><strong>Wolfgang Bauer</strong> and <strong>Stefan Spirk</strong>, both professors at the Institute of Bioproducts and Paper Technology at Graz University of Technology in Austria, will support project by developing tailored cellulose starting materials. <br /> “We are very excited to work together with the Chalmers team to create the next generation of cellulose light-weight materials. Our decade long experience to work with cellulosic pulps and in fibre and paper physics will be invaluable for this cooperation,” says Wolfgang Bauer.</li> <li><strong>Hermann Steffan</strong> and <strong>Florian Feist,</strong> TU Graz, Institute for Vehicle Safety, Austria, will provide the expertise in the field of crashworthy materials to make the biogenic materials ready-for-action in mechanical engineering. <br />&quot;In automotive engineering sustainability when developing materials, is playing an increasingly important role. For a novel material to be applied in contemporary automotive development, it must be assessable through computer simulation. This requires comprehensive characterization of the material's physical properties and adequate materials models,” says Hermann Steffan. </li></ul> <p></p> <p class="chalmersElement-P"> </p> <h3 class="chalmersElement-H3">TEC​NALIA</h3> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"></p> <ul><li><strong>​Dr. Sonia </strong><strong>García-Arriet</strong><strong>a</strong><strong></strong><strong></strong><strong></strong>, from the Composite Materials Department of the Industry and Transport division of TECNALIA in Spain, will work on the demonstration of cellulose material for a real application. <br />&quot;Tecnalia aims to bring innovative developments in new materials to the industry. Our pilot plant has a wide variety of semi-industrial machines for the automotive, aeronautical or sports sectors where composite materials have their main application. In the project we will scale up the manufacturing process, we will validate the moulding capacity to adapt to complex shapes and we will study the parameters that influence upscaling. The goal objective will be to obtain a large component for sports application and to validate it under similar mechanical conditions to those of its final application,&quot; she says. </li></ul> <p></p> <p class="chalmersElement-P"> </p> <h3 class="chalmersElement-H3">BioNanoNet Forschungsgesellschaft mbH</h3> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"></p> <ul><li>T​​he BioNanoNet Forschungsgesellschaft mbH (BNN), an RTO based in Austria, complements the consortium with its safe-and-sustainable-by-design (SSbD) expertise, will thus look into the manufacturing processes to identify potential hotspots to outdesign these already during early stages of the development. Furthermore, BNN will support the project through its unique global network to gain maximum of visibility and thus boosting the impact of the project.</li></ul> <p></p> <p class="chalmersElement-P"> </p> <h3 class="chalmersElement-H3">University ​of Vienna</h3> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"></p> <ul><li><strong>Alexa</strong><strong>nder Bismarck</strong>, Head of the Institute of Materials Chemistry and Research, Faculty of Chemistry at the University of Vienna, will lead the work on material processing and performance optimisation. His team contributes with an extensive expertise in material and composites engineering and with access to the recently established Institute’s Core Facility Interface Characterisation with high-end methods for the investigation of material properties. <br />“We develop a strong, renewable material for a c<span style="background-color:initial">ool application. The question is: how can we go from the lab side to application? Based on our interdisciplinary approach, combining basic chemistry, materials science, engineering, and processing, we aim at establishing a viable material process that will guide us towards a highly functional and sustainable light-weight material for future applications,” he says.</span></li></ul> <p></p> <p class="chalmersElement-P"> </p>Tue, 06 Apr 2021 07:00:00 +0200 generated proteins will speed up drug development<p><b>​Artificial Intelligence is now capable of generating novel, functionally active proteins, thanks to recently published work by researchers from Chalmers. “What we are now able to demonstrate offers fantastic potential for a number of future applications, such as faster and more cost-efficient development of protein-based drugs,” says Aleksej Zelezniak, Associate Professor at the Department of Biology and Biological Engineering. ​</b></p><p class="chalmersElement-P">​P<span>roteins are large, complex molecules that play a crucial role in all living cells, building, modifying, and breaking down other molecules naturally inside our cells. They are also widely used in industrial processes and products, and in our daily lives. </span></p> <p class="chalmersElement-P">Protein-based drugs are very common – the diabetes drug insulin is one of the most prescribed. Some of the most expensive and effective cancer medicines are also protein-based, as well as the antibody formulas currently being used to treat COVID-19.</p> <p class="chalmersElement-P"> </p> <h2 class="chalmersElement-H2">From computer design to wo​rking proteins in just a few weeks</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Current methods used for protein engineering rely on introducing random mutations to protein sequences. However, with each additional random mutation introduced, the protein activity declines. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“Consequently, one must perform multiple rounds of very expensive and time-consuming experiments, screening millions of variants, to engineer proteins and enzymes that end up being significantly different from those found in nature,” says research leader Aleksej Zelezniak, continuing: </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“This engineering process is very slow, but now we have an AI-based method where we can go from computer design to working protein in just a few weeks.” </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">The new results from the Chalmers researchers were recently published in the journal Nature Machine Intelligence and represent a breakthrough in the field of synthetic proteins. Aleksej Zelezniak’s research group and collaborators have developed an AI-based approach called ProteinGAN, which uses a generative deep learning approach. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">In essence, the AI is provided with a large amount of data from well-studied proteins; it studies this data and attempts to create new proteins based on it. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">At the same time, another part of the AI tries to figure out if the synthetic proteins are fake or not. The proteins are sent back and forth in the system until the AI cannot tell apart natural and synthetic proteins anymore. This method is well known for creating photos and videos of people who do not exist, but in this study, it was used for producing highly diverse protein variants with naturalistic-like physical properties that could be tested for their functions.</p> <p class="chalmersElement-P"><span style="background-color:initial;font-family:inherit">The proteins widely used in everyday products are not always entirely natural but are made through synthetic biology and protein engineering techniques. Using these techniques, the original protein sequences are modified in the hope of creating synthetic novel protein variants that are more efficient, stable, and tailored towards particular applications. </span></p> <p class="chalmersElement-P">The new AI-based approach is of importance for developing efficient industrial enzymes as well as new protein-based therapies, such as antibodies and vaccines.</p> <p class="chalmersElement-P"> </p> <h2 class="chalmersElement-H2">A cost-efficient and sustainable model</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Assistant Professor Martin Engqvist, also of the Department of Biology and Biological Engineering, was involved in designing the experiments to test the AI synthesised proteins. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“Accelerating the rate at which we engineer proteins is very important for driving down development costs for enzyme catalysts. This is the key for realising environmentally sustainable industrial processes and consumer products, and our AI model, as well as future models, will enable that. Our work is a vital contribution in that context” says Martin Engqvist.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“This kind of work is only possible in the type of multidisciplinary environment that exists at our Division – at the interface of computer science and biology. We have perfect conditions to experimentally test the properties of these AI-designed proteins,” says Aleksej Zelezniak. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">The next step for the researchers is to explore how the technology could be used for specific improvements to protein properties, such as increased stability, something which could have great benefit for proteins used in industrial technology. </p> <p class="chalmersElement-P"><span style="font-weight:700">Text</span><span>: Susanne Nilsson Lindh, Mia Halleröd Palmgren &amp; Joshua Worth</span><br /></p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>More about: The research project </strong></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"></p> <ul><li>The study was conducted within a collaboration between Chalmers University of Technology, Vilnius University Life Sciences Centre in Lithuania, and the company Biomatter Designs. </li> <li>Read the article <a href="">“Expanding functional protein sequence spaces using generative adversarial networks&quot;​</a> in Nature Machine Intelligence. </li></ul> <p></p> <div> </div> <div> <span style="background-color:initial"></span></div>Tue, 30 Mar 2021 07:00:00 +0200 advice depends on your gut<p><b>​In the future, a blood sample may show how you should eat to stay healthy. But the road to personalized recommendations is long and winding. It passes through the gut, where bacteria make us react differently to the food we eat.</b></p>​<span style="background-color:initial">Researchers are working hard, attempting to come up with personalized or group-based dietary advice. It’s not easy. Much depends on the gut microbiota that is unique to us all.<br /><br /></span><div>One example is dietary fiber, which is an established component of a healthy diet. In a research study that attracted attention last year, Chalmers’ researchers show that whole grains from rye lowered cholesterol levels more than whole grain wheat, but that this effect was dependent of individual’s gut microbiota composition. The study clearly showed that the dietary advice is not equally effective for everyone – but that there is a great potential to increase the health benefits by matching the foods with gut microbiota of the individual.</div> <h2 class="chalmersElement-H2">Hot research area</h2> <div>According to Rikard Landberg, Professor of Food and Nutrition science at Chalmers and one of the speakers at the two-day event Engineering Health in April, research relating the importance of the gut bacteria to diet, dietary advice and health is hot right now.<img src="/SiteCollectionImages/Areas%20of%20Advance/Health/Udda%20format/Rikard_Landberg_300.jpg" class="chalmersPosition-FloatRight" alt="" style="margin:5px" /><br /></div> <div>“How and when should we take the gut microbiome into account? How do we design a diet that is optimal for the individual? We are yet quite far from individual dietary advice. There is a lot more we need to know first”, he says.<br /><br /></div> <div>At the same time, there are already commercial apps where you can try to identify your ideal diet. But these tests are often not to be trusted, says Rikard Landberg. They are based on nothing more than existing knowledge about general effects of lifestyle and diet, and the connections between these and the gut microbiota. But already in five to ten years, the situation may be completely different:<br /><br /></div> <div>“By then, I believe we will have the opportunity to identify groups of individuals who, for example, benefit from a certain diet”, says Rikard Landberg and explains:</div> <div>“We should be able to identify the profile of a certain group, using gut microbiome and metabolites – molecules formed by bacteria. Then, we can also measure the body’s response to a certain diet through a blood sample. Based on such data, we can determine whether you belong to a particular profile that would benefit from, for example, eating vegetarian food or a certain type of dietary fiber. And knowing which diet is ideal for your group will of course be helpful if you have reason to review your diet, for example if you’re at increased risk of cardiovascular disease.”</div> <h2 class="chalmersElement-H2">Food and gut experts working together</h2> <div>Rikard Landberg collaborates with Fredrik Bäckhed, Professor at the Department of Molecular and Clinical Medicine at the University of Gothenburg. Fredrik Bäckhed is an expert on gut microbiome and its role in health and disease. Among other things, he is trying to optimize probiotic bacterial strains that can improve the health of our gut, and reduce risk of developing diseases. A permanent change in the intestinal microbiome is difficult to achieve, but vary between different parts of the bacterial flora.</div> <div>“This autumn, we will start a study start where we take a closer look at diets that are composed to promote a healthy intestinal bacterial flora. The diet is designed based on a systematic literature review, where we have reviewed 8,000 scientific articles. We want to investigate whether it is possible, with an optimal diet based on “ordinary food”, to influence intestinal bacteria linked to an increased risk of cardiovascular disease. Strangely enough, this has not been done in any previous scientific study”, says Rikard Landberg.</div> <h2 class="chalmersElement-H2">New and climate friendly guidelines</h2> <div>A revision of Nordic Nutrition Recommendations and the Swedish dietary guidelines is currently underway. Around 100 experts review, and evaluate, research results. Among other things, they look at health impact of different nutrients and foods. The dietary advice is also put in a Nordic context, to take into account which nutrients we, in the Nordic countries, may need to boost – such as vitamin D, which we could lack in our sun-depraved countries – based on the type of food we normally eat. In addition, the dietary advice is climate-adapted; the guidelines should not only focus on what’s healthy, but also what is sustainable from a climate perspective.<br /><br /></div> <div>But while waiting for updated dietary advice, and research on gut microbiota: What can we really say about what to eat in order to stay healthy? One problem is that many researchers – as well as the media – try to give advice based on individual studies, says Rikard Landberg, as there is a desire to go directly from research results to recommendations.</div> <div>“Unfortunately, this might give people the perception that advices change all the time. Results from different studies often show different results, for varied reasons.”</div> <h2 class="chalmersElement-H2">Vegetarian diet possibly healthier</h2> <div>Still, if he would dare to give any advice, in addition to the official dietary guidelines, Rikard Landberg gives one that is aligned with a recent study performed together with Örebro University and Fredrik Bäckhed:<br /><br /></div> <div>“I am quite convinced that a diet with more vegetarian food, and less meat, is better for most of us. But this will vary between individuals, and moreover, we must not forget the risks associated with such a diet for certain groups. Many women, for example, have an iron deficiency. For them, a vegetarian diet might lead to they getting too low intake of available iron – and that will not be healthy”, he says.<br /></div> <div>“Then, of course, the usual advice applies; for example, not eating too much, and avoiding sugar-sweetened beverages. People also tend to think that physical activity plays a large part in keeping a healthy weight, but diet is the most important thing for those who need to watch the kilos. But with that said, we need to be active in order to feel good and prevent illness. Furthermore, we should not forget that diet is much more than health! For example, we do not eat chocolate to be healthy, but because it tastes good. That’s also allowed!”<br /><br /></div> <div><strong>FACTS: Want to know more about diet and intestinal flora?</strong></div> <div>Watch Rikard Landberg’s and Fredrik Bäckhed’s lecture “Diet meets the gut microbiome - implications for cardiometabolic disease” at Engineering Health on April 14 at 11.00. The event will be broadcast live via YouTube. <a href="">More information can be found here</a>.<br /><br /></div> <div>Text: Mia Malmstedt</div> <div>Photo: Pixabay and Annika Söderpalm</div> <div>​<br /></div> Fri, 26 Mar 2021 09:00:00 +0100 model predicts metabolic response to metals<p><b>​Metal ions, for example iron, are vital to many cellular functions in all organisms. Researchers at Chalmers University of Technology have now developed a mathematical model to identify the role of metal ions in baker’s yeast. This model can be used to optimise industrial yeast strains producing a variety of bioproducts, or to design new diet supplements. ​</b></p><p class="chalmersElement-P">​<span>Baker’s yeast, <em>Saccharomyces cerevisiae</em>, is used as a model organism for human cells and different cellular systems, such as metabolism. But the microorganisms can also be used as so-called cell factories, for sustainable industrial production where renewable sources are turned into different bioproducts, such as bioethanol, drugs, and chemicals. </span><span style="background-color:initial">K</span><span style="background-color:initial">nowledge abo</span><span style="background-color:initial">ut the metabolism is used to optimise the production rate and viability of the yeast cell factories, through genetic editing and by providing the best growth conditions.</span></p> <h2 class="chalmersElement-H2"><span>Predict metabolic respons to reduced availability of metals</span></h2> <p class="chalmersElement-P"><span style="background-color:initial">Metal ions play an important role in metabolism by serving as cofactors, helper molecules, to numerous metabolic enzymes, such as respiration but also many enzymes playing a role in detoxification. Although many enzymes have been reported to interact with metal ions, the quantitative relationships between metal ions, and metabolism, are lacking. </span></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><img src="/SiteCollectionImages/Institutioner/Bio/SysBio/Yu-Chen_2019-09-02_350.jpg" alt="Photo of Yu Chen" class="chalmersPosition-FloatRight" style="margin:5px;width:250px;height:218px" />&quot;We generated a model by applying the framework to <em>Saccharomyces cerevisiae</em>. The model showed good performance in terms of predicting intracellular metal ion abundances and predicting metabolic responses upon reduced availability of metal ions&quot;, says <strong>Yu Chen</strong>, postdoc at the Department of Biology and Biological Engineering and first author of the <a href="">scientific publication​</a> recently published in PNAS. </p> <h2 class="chalmersElement-H2">Iron deficiency leads to resource allocation </h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">The research group also investigated the role of iron in metabolism and found that the model captured resource re-allocation upon iron deficiency. This suggests that yeast allocates iron based on optimisation principles. This means that yeast aims to always ensure allocation of iron to enzymes engaged in biosynthesis of amino acids that essential for cell growth. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">In addition, the researchers validated one of the model predictions experimentally in the field of metabolic engineering. </p> <p class="chalmersElement-P">These experiments showed that insufficient supply of iron could limit biosynthesis of <em>p</em>-coumaric acid, a chemical of great commercial interest used for production of dyes and polymers that are used in many materials, which relies on an iron-containing enzyme.</p> <h2 class="chalmersElement-H2">&quot;Improve cell factories and diets&quot;</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">&quot;We believe that our model can be used to guide improvement of yeast cell factories and optimisation of growth conditions. More importantly, the framework can be easily applied to study metal ions within human metabolism, which can hopefully aid in explaining mineral deficiency and designing diets,&quot; says Yu Chen.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Text:</strong> Susanne Nilsson Lindh </p> <p class="chalmersElement-P"></p> <p class="chalmersElement-P"><strong>Read the scientific article in PNAS:</strong> <a href="">Yeast optimizes metal utilization based on metabolic network and enzyme kinetics </a></p> <div><br /></div> <p class="chalmersElement-P"> </p>Thu, 25 Mar 2021 00:00:00 +0100 repair studied with molecular precision<p><b>​If DNA breaks and is not correctly repaired it may pose devastating consequences to humans, not only on the cellular level but for the whole body, as the breaks may cause disease, such as cancer. Using a combination of unique methods, researchers at Chalmers have investigated a mechanism for repairing DNA-breaks in bacteria, which can potentially increase the general understanding of DNA repair in human cells.​</b></p><p class="chalmersElement-P">​<span>Fredrik Westerlund, Professor in Chemical Bi​ology at the Department of Biology and Biological Engineering, was in 2019 awarded the European Research Council's prestigious research grant ERC Consolidator Grant for the project &quot;Next Generation Nanofluidic for Single Molecule Analysis of DNA Repair Dynamics&quot;. </span></p> <p class="chalmersElement-P"><span>​​His research group has now published <a href="">a study</a> linked to the project, where they have characterised the bacterial DNA-repair system responsible for so-called Non-Homologous End-Joining (NHEJ).</span></p> <p class="chalmersElement-P"><strong>What is NHEJ and why are you interested in this system?</strong></p> <p class="chalmersElement-P"><strong> </strong></p> <p class="chalmersElement-P"><strong><img src="/SiteCollectionImages/Institutioner/Bio/ChemBio/FredrikWesterlund_340x400.jpg" alt="Photo of Fredrik Westerlund" class="chalmersPosition-FloatRight" style="margin:5px;width:200px;height:235px" />Fredrik Westerlund: </strong>DNA molecules can break − it happens all the time in all cells – and the consequences of these breaks can be severe. So-called double-strand breaks can, among other things, stall life-sustaining processes in the cell. If the DNA molecule is not correctly repaired, the cell can potentially lose or change genetic information, i.e. the information that controls all the cellular functions. In turn, this can lead to lethality or the initiation of various diseases, such as cancer. It is important that DNA-breaks are repaired as quickly and efficiently as possible, therefore all cells have developed efficient repair systems.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">There are two different mechanisms for repairing DNA-breaks; &quot;Homologous Recombination&quot; − where the enzymes involved use an identical copy of the broken DNA molecule as a template − and NHEJ where enzymes join the DNA ends, without using a template.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">NHEJ was first discovered in human cells. However, it has also been found to exist in bacteria, which use a smaller set of components. Thus, we realized that the bacterial mechanism might serve as an interesting model system.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>What is a model system?</strong></p> <p class="chalmersElement-P"><strong> </strong></p> <p class="chalmersElement-P"><strong><img src="/SiteCollectionImages/Institutioner/Bio/ChemBio/Robin-Oz_20200825_340x400.jpg" alt="Photo of Robin Öz" class="chalmersPosition-FloatRight" style="margin:5px;width:200px;height:235px" />Robin Öz, postdoc at the Division of Chemical Biology, and first author of the study:</strong> It means that we study a simpler system, in this case the bacterial repair mechanism, with the aim to eventually gain a better understanding of how the more complex human cells, repair broken DNA. Since inaccurate repair of DNA-breaks plays a major role in, for example, cancer, the model system can potentially help us understand how such disease develop and how they can be prevented from further spreading. We use a simpler model, which consists of only two components, to better understand important features of the more complex human system, consisting of at least ten different proteins.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>What are the results of the study?</strong></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Fredrik Westerlund: </strong>In the study, we focused mainly on one of the two proteins that are part of the bacterial NHEJ system. Together with our collaborators in France we have identified important differences between the bacterial and human systems. Previous studies have shown that a protein, called Ku, binds to broken ends of the DNA, and protects them from systems that may destroy free DNA ends in the cell. Ku can bring the DNA strands together and then recruit, Ligase D, which finally repairs the DNA. In our group we have developed a method where the DNA molecules are stretched out in nanochannels, thin glass tubes, without obstructing the ends. This allow us to study processes and interactions that take place at the free ends when different proteins are added to the solution. In this way, we have been able to show previously unknown mechanisms for the interaction between Ku and DNA.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Robin Öz: </strong>The study has shown that there are very interesting similarities between DNA-repair systems in bacteria and human cells, while the mechanisms are very different. Previously, it has been unclear what happens to the proteins attached to the DNA after the repair. We have now shown, among other things, that Ku is actually entrapped on the DNA up to several hours after the repair has finished, which means that there are potentially other, currently unknown systems that are involved in the final phase of the repair process.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><span style="background-color:initial"><strong>What is the next step?</strong></span><br /></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Fredrik Westerlund: </strong>The next step is to show how the ligase that binds to Ku works. NHEJ in bacteria could be an important target for new antibacterial drugs. Different variants of combined treatments have become very relevant in the fight against antibiotic-resistant bacteria. For example, one can imagine a combination of drugs that damage DNA − and knock out the DNA-break repair system.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><strong>Text:</strong> Susanne Nilsson Lindh<br /><span style="background-color:initial"><strong>Photo: </strong>Pixabay, </span><span style="background-color:initial">Johan Bodell &amp; Martina Butorac</span></p> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <p class="chalmersElement-P"><br /></p> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <p class="chalmersElement-P"><span style="background-color:initial"><b>Read the study in</b></span><span style="font-weight:700"> <em>Nucleic Acid Research</em>: </span></p> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <p class="chalmersElement-P"><a href="/sv/institutioner/bio/nyheter/Sidor/Ny-teori-om-snabb-spridning-av-antibiotikaresistens.aspx" style="font-weight:300"><img class="ms-asset-icon ms-rtePosition-4" src="/_layouts/images/ichtm.gif" alt="" /></a> <a href="">Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis​</a></p> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <p class="chalmersElement-P"><span style="font-weight:700;background-color:initial">Read more: </span><br /></p> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <p class="chalmersElement-P"><a href="/sv/institutioner/bio/nyheter/Sidor/Ny-teori-om-snabb-spridning-av-antibiotikaresistens.aspx" style="font-weight:300"><img class="ms-asset-icon ms-rtePosition-4" src="/_layouts/images/ichtm.gif" alt="" /></a><span style="background-color:initial"><font color="#1166aa"><a href="/en/departments/bio/news/Pages/ERC-grant-for-next-generation-DNA-repair-analysis.aspx">ERC-grant for next generation DNA-repair analysis</a></font></span></p> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <div></div> <p class="chalmersElement-P"><a href="/sv/institutioner/bio/nyheter/Sidor/Ny-teori-om-snabb-spridning-av-antibiotikaresistens.aspx" style="font-weight:300"><img class="ms-asset-icon ms-rtePosition-4" src="/_layouts/images/ichtm.gif" alt="" /></a><span></span><span style="background-color:initial"><font color="#1166aa"><a href="/en/departments/bio/news/Pages/New-Chalmers-method-sheds-light-on-DNA-repair-.aspx">New Chalmers method sheds light on DNA-repair</a></font></span></p> <p class="chalmersElement-P"> ​</p>Wed, 10 Mar 2021 07:00:00 +0100 antibiotic resistance with new diagnostics<p><b>​Bacteria become resistant to antibiotics through changes in their DNA – changes which can now be found, through the use of modern DNA sequencing technology. A new international research network, led by Chalmers and Erasmus University Medical Center in the Netherlands, will help bring recent advances in DNA sequencing to bacterial diagnostics in healthcare settings. </b></p><p>​<img class="chalmersPosition-FloatRight" alt="Erik Kristiansson" src="/SiteCollectionImages/Institutioner/MV/Nyheter/ErikKristiansson2021.jpg" style="margin:5px" />Clinical microbiology laboratories rely today mainly on cultivation to identify bacteria resistant to antibiotics. Bacteria collected from the patient are grown alongside various types of antibiotics to find drugs that work against them – a method that can take days, or in some cases, weeks.</p> <p>“Cultivation will remain important, but with the increasing number of infections caused by resistant bacteria, it may not be enough,” explains Erik Kristiansson, Professor of Mathematical Sciences at Chalmers. “We need to improve diagnostics to provide faster and more accurate results.”</p> <p>DNA sequencing – a technology that can be used to characterise all the genes a bacterium carries in its genome – can provide just that. But even though the technology is rapidly improving, several challenges need to be solved before it can be effectively applied in routine diagnostics.</p> <h2>Big data expertise a key requirement </h2> <p>Erik Kristiansson is one of two leaders for the new research network, <a href="">Integrating Microbial Sequencing and Platforms for Antimicrobial Resistance</a>, which aims to provide solutions for these challenges. In this work, an action plan will be developed to increase the adoption rate of sequencing-based diagnostics.</p> <p>As an expert in bioinformatics and artificial intelligence, he works with key questions in how the vast and complex data generated by DNA sequencing of bacteria should be handled and properly interpreted. Here, a major task is to develop and implement data analysis methods that can correctly identify the changes that make bacteria resistant to antibiotics.</p> <p>Other challenges are to ensure that the execution of the DNA sequencing is done properly and accurately and that the genetic databases – which the methods rely upon – are of sufficient quality.</p> <p>“One strength of our network is that it is interdisciplinary,” says Erik Kristiansson. “There are experts from both academia and industry as well as from scientific areas including infectious diseases, bacteriology, computer science and statistics. This will allow us to take a holistic approach to the many factors that affect the spread of resistant bacteria.”</p> <p>“We aim to facilitate the implementation of DNA sequencing as a technique in routine diagnostics in hospitals globally. Here, training personnel to utilise this new technique is an important task. Knowledge dissemination and education will therefore be a part of the network.”</p> <h2>Methods for both fighting resistance and managing outbreaks</h2> <p>DNA sequencing has the potential to reduce antibiotic use and thereby make it harder for bacteria to become resistant. By analysing the entire genome of an infecting bacterium, physicians can be provided with all the information needed for starting a patient-tailored antibiotic treatment at an early stage.</p> <p>In the best-case scenario the bacterium is not resistant and the patient can receive a narrow-spectrum antibiotic, that is, an antibiotic that is more specific and only kills a limited number of bacterial species at the same time. This reduces the risk that other bacteria, for example those that live naturally in and on the human body, become resistant. In the worst case, the infection is instead caused by a bacterium that has developed resistance against a wide range of antibiotics.</p> <p>“It can then become a matter of finding a type of antibiotic that will work at all. In the event of a serious infection, rapid and accurate diagnosis can be life-saving,” says Erik Kristiansson. DNA sequencing can also be instrumental in preventing outbreaks of bacterial infections in hospitals. By monitoring the bacteria that spread within health care settings, resistant and virulent pathogens can be identified at an early stage. Various management strategies, such as isolation of patients, can then be used to disrupt the chain of transmission.</p> <h2>Virus sequencing is carried out with the same technology and expertise</h2> <p>The work done by the network will enable healthcare and clinical laboratories to adopt DNA sequencing for all kinds of microorganisms. This also applies to viruses – a very relevant area during the current pandemic – where sequencing can be used as a tool to monitor coronavirus mutations. In the long run, veterinary medicine may also be able to benefit from the results of the network.</p> <p>Practices for the use of antibiotics vary greatly between countries, and there is a link between widespread use and serious problems with antibiotic resistance. But even though antibiotic resistance can be partially combated within a country through measures such as restrictive antibiotic use, the problem is in essence global. Indeed, antibiotic-resistant bacteria spread rapidly around the world as a result of international travel. The network therefore has a global perspective and includes 14 experts from 8 different countries.</p> <p>“When we present our results in two years, we aim especially to contribute with solutions to countries that still have a long way to go when it comes to sustainable antibiotic use,” says Erik Kristiansson. “Determining the most efficient way to reach this point is an important part of the holistic approach the network will use.”<br /><br /><strong>Text</strong>: Johanna Wilde and Joshua Worth<br /><strong>Photo</strong>: Nachiket P Marathe<br /><br /><strong>More about the network: Integrating Microbial Sequencing and Platforms for Antimicrobial Resistance</strong></p> <strong></strong><ul><li>Coordinated by Erik Kristiansson at the <a href="/en/departments/math/Pages/default.aspx">Department of Mathematical Sciences</a> at Chalmers ( and John P. Hays at Erasmus University Medical Center Rotterdam ( </li> <li>Financed nationally by Sweden and the Netherlands, through the organisation <a href="">Joint Programming Initiative on Antimicrobial Resistance</a>. The organisation is a global cooperation platform of 28 countries for combatting antibiotic resistance. The secretariat is located at the Swedish Research Council.</li> <li>The network and the organisation operate from a One Health-perspective, where the many disparate factors that affect the development and spread of resistant bacteria are considered jointly.</li></ul> <p><img class="chalmersPosition-FloatLeft" alt="Logo Seq4AMR" src="/SiteCollectionImages/Institutioner/MV/Nyheter/Seq4AMRLogo200x.png" style="margin:5px" /><img width="320" height="120" class="chalmersPosition-FloatLeft" alt="Logo jpiamr" src="/SiteCollectionImages/Institutioner/MV/Nyheter/JPIAMR-logo320x.jpg" style="margin:5px" /><br /><br /><br /><br />​<br /></p>Fri, 05 Mar 2021 07:00:00 +0100 and development in focus for new Head of Department at BIO <p><b>​Maria Faresjö, Professor of Biomedical Laboratory Science, will be the new Head of the Department of Biology and Biological Engineering (BIO) from 1 May. With her passion for research, and her curious and open approach as a leader, she hopes to find ways to develop the research at the department and create new arenas for collaboration.​</b></p><p class="chalmersElement-P">​<span>“It is incredibly exciting with this relatively young department, which has expanded rapidly and conducts excellent and innovative research. I look forward to being a part of, and leading and developing a research environment with a stable foundation and many prominent researchers,” she says.</span></p> <p class="chalmersElement-P">Maria Faresjö will succeed the current Head of Department, Stefan Hohmann, when he retires in September after six years in the position. She has been involved in research and education in biomedicine for 25 years and will bring this experience, together with her solid experience of strategic development of research and visions, to her new workplace. </p> <h2 class="chalmersElement-H2">Eager to meet the employees at the department </h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">She has been working at Jönköping University, JU, since 2009, with issues regarding development high on the agenda <span style="background-color:initial">− </span><span style="background-color:initial">a priority which will remain valid for her future work at BIO. Top priority, though, is to get to know the organisation.</span></p> <p class="chalmersElement-P"></p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“The greatest challenge for me, a positive challenge, is to get to know the research and all the members of BIO. Initially, I want to meet with the management and faculty to understand the direction in which the Department is heading, and how to achieve existing goals. In the long run, I also want to investigate how new strategies for further development could be implemented”, she says.  </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“Of course, I also wish to contribute with the experiences I have gained from my own research. I know that my knowledge in biomedicine can contribute, for example, to development in health engineering. But we need to find ways to do that in tandem with the needs and routines of the organisation.” </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">The position as Head of BIO also includes participation in the University Management Group.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“I am looking forward to being part of the management group, to participate in discussions about development, strategies and Chalmers' vision. I hope that my knowledge and experience can be useful for Chalmers' operations and development in the future,” Maria Faresjö says.</p> <h2 class="chalmersElement-H2"><span>​Professor of Biomedical Laboratory Science</span>​</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Maria Faresjö already knew that she wanted to become a researcher at the age of ten. How would she otherwise get the answers to all her questions? At that time, she was perhaps not fully aware of what a researcher does, but as the years passed it became very clear. </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">After achieving a bachelor’s degree in biomedical laboratory sciences at the School of Health and Welfare in Jönköping, her research career took off. She defended her thesis at Linköping University in 2000 and stayed there as a researcher. In 2009 she changed workplace after a total of 15 years in the Faculty of Medicine and Health Sciences. That year, she returned to Jönköping and JU and was appointed Professor of Biomedical Laboratory Science.</p> <h2 class="chalmersElement-H2">Research focus: the immune system in children with type 1 diabetes</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Maria Faresjö's focus in research has always been the immune system and how it behaves when activated. By studying biomarkers, she has been able to monitor the immune system in children with type 1 diabetes. In her research she has also worked on finding precise biomarkers to identify infections in new-borns as early as possible to, in order to avoid, if possible, antibiotic treatments. An additional project has involved using biomarkers for identification of inflammation due to pressure problems when using prostheses and orthoses.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“Trying to understand the mechanisms of the immune system in diseases such as type 1 diabetes has always been relevant and important to me. In addition, being part of research that can contribute to better treatment and possibly also prevention has given me motivation to continue forward in this field of research”, she says.</p> <p class="chalmersElement-P"> </p> <h2 class="chalmersElement-H2">Listening to people important for development</h2> <p class="chalmersElement-P">At JU, she was appointed Head of Research at the School of Health and Welfare at JU (corresponding to a department at Chalmers), with the responsibility for strategic development of research in health and welfare issues. She was also in charge of the development of a new vision and strategies for JU for the period 2020− 2025.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“During the process of developing a new vision, I got to spend time on what I love the most − meeting, talking to, and above all, listening to people, from researchers to students and administrative staff, to form an overall picture of the university”, she says, continuing: </p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“That experience really suited me, as I always try to stay open and interested in the people I work with. I really want to listen to and understand the organisation and the people in it. It enables me to stake out a positive direction for development. This is also how I would like to work at BIO.”</p> <h2 class="chalmersElement-H2">Believes in collaboration with many actors​</h2> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">Cooperation is the key to all development, says Maria Faresjö. Therefore, she strongly believes in interdisciplinary and interprofessional collaboration in research − but also in education and utilisation. Successfully reaching out to society is a way of creating additional value from new knowledge. In addition to finding ways to collaborate internally at BIO, there is great potential in collaboration with different societal actors, such as regions, other universities, businesses, and industry.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">“In this area Chalmers is at the forefront. It is one of Chalmers' strengths and why the university’s research has such great impact on society. Even though my experience is modest, I think it is essential for the future of research to expand and enhance collaboration with wider society,” she says.</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P">As spring arrives, so does BIO’s new Head of Department, and all members of BIO will have the opportunity to get to know her better. With focus on collaboration with all the department, Maria Faresjö hopes to create great conditions for further development. </p> <p class="chalmersElement-P"><strong>Text: </strong>Susanne Nilsson Lindh<br /><strong>Photo:</strong> Privat</p> <p class="chalmersElement-P"> </p> <p class="chalmersElement-P"><br /></p> <p class="chalmersElement-P"> </p>Wed, 03 Mar 2021 13:00:00 +0100 up to solve healthcare challenges<p><b>​Research on the border between technology and health is becoming increasingly important. Chalmers and Sahlgrenska Academy have now started a new collaboration, where researchers will work in pairs to solve healthcare challenges.</b></p>​<span style="background-color:initial">As our population grows and we live longer, and previously fatal diseases can be cured or become chronic, the healthcare sector faces major challenges. New technology can support and provide solutions, and technology focusing on health is also rapidly developing. At the same time, collaboration between healthcare and engineering is prioritised. Chalmers University of Technology currently has a number of collaborations, in both research and education, with Sahlgrenska University Hospital and Sahlgrenska Academy at the University of Gothenburg.</span><h2 class="chalmersElement-H2">Working in pairs</h2> <div>The recently started Gothenburg Research School of Health Engineering is a new way of tackling healthcare challenges. Doctoral students from Sahlgrenska Academy and Chalmers will work in pairs, one participant from each university. Together, they will solve problems identified by healthcare professionals. The initiative is partly funded by Region Västra Götaland.</div> <div>“We are very happy to now expand our collaboration through student pairs, which enables doctoral students in the fields of medicine and technology to work together with important research topics. At Chalmers, we would like to develop technology that will help the healthcare sector to meet future challenges, and we also see that close collaborations with both Sahlgrenska University Hospital and Sahlgrenska Academy strengthen our competences and make us an even more attractive choice for researchers and students”, says Stefan Bengtsson, Chalmers’ President.</div> <div>The universities are now, together, educating a new type of researcher and expert with knowledge in the areas of health, medicine and technology, says Agneta Holmäng, Dean of Sahlgrenska Academy.</div> <div>”This makes it possible to increase interdisciplinary collaborations in many different research areas, which in turn increases the chances of addressing healthcare challenges and specific topics where technical competence is becoming increasingly important.”</div> <h2 class="chalmersElement-H2">First: improved image analysis<img src="/SiteCollectionImages/Areas%20of%20Advance/Health/Udda%20format/Malin-Barman_300.jpg" class="chalmersPosition-FloatRight" alt="" style="margin:5px;width:220px;height:293px" /><br /></h2> <div>Malin Barman, researcher at the department of Biology and Biological Engineering, is Chalmers’ coordinator<br />for the so-called research school. She is also part of a pair constellation; her counterpart Justin Schneiderman, who is also a researcher and coordinator, works at Sahlgrenska Academy.</div> <div>“Many of the doctoral students at Sahlgrenska work as physicians part-time, and researchers part-time. At Chalmers, our doctoral students do full-time research”, says Malin Barman.</div> <div>“The first projects are in the medtech field, focusing on improved image analysis. With the help of AI, new programmes for image analysis is developed, and this makes it possible to identify signs of, for example, incipient cardiovascular disease. Then, the idea is to expand and develop the research school to include, for example, biotechnology and data analysis, and also to apply AI in more areas. There are clearly many research topics that would benefit from close collaboration.”<br /><br /></div> <div>The overall goal of the research school is to increase collaboration and points of contact. But the initiative is also about shaping a broader research competence; individuals at the intersection of health and technology,<img src="/SiteCollectionImages/Areas%20of%20Advance/Health/Udda%20format/Justin-Schneiderman_300.jpg" class="chalmersPosition-FloatRight" alt="" style="margin:5px;width:220px;height:293px" /><br /> who can understand and “talk to” both disciplines. To achieve this, each doctoral student has supervisors at both universities, and they will give lectures to each other, thereby sharing their skills. They also take a course together; a seminar series covering cross-border topics such as ethics, innovation, utilisation and AI.</div> <div>“The seminar series is also open to other doctoral students in the field of health”, says Malin Barman.</div> <div>A clear purpose of the seminar series is to provide time and opportunity for networking between researchers from different disciplines. The students will work in groups, but also get the chance to share experiences and skills in more unofficial contexts, such as over a lunch or around the coffee table.</div> <div>“We now hope for a big interest, from both Chalmers and Sahlgrenska Academy!”</div> <h2 class="chalmersElement-H2">Research made useful</h2> <div>There are many benefits of participating in the research school, according to Malin Barman. Chalmers’ doctoral students will gain increased knowledge about research and innovation – and challenges – within the hospital. They will also learn more about the organisation and structure of healthcare, and gain new medical knowledge. For Chalmers as a university, the initiative will be a way to get additional input from the healthcare sector, making it easier for researchers to focus on the right issues and use their expertise in a way that will benefit healthcare and society.</div> <div>“We will, without a doubt, strengthen our competence in the area of health. In addition, we get a clear link to utilisation of our research; we will make technical solutions that can be implemented more quickly in healthcare”, Malin Barman concludes.<br /><br /></div> <div><strong>About the seminar series within Gothenburg Research School of Health Engineering</strong></div> <div>The seminar series in the field of health and technology will start in February 2021. The aim is to give doctoral students an in-depth study in areas that connect health and technology, such as innovation, utilisation, ethics and AI. The participants get three higher education points, and the plan is to give the series continuously each year.</div> <div>The seminar series include 10+ seminars, approximately one each month, held by various both external and internal lecturers with expert knowledge in each area.<br /><br /></div> <div>The goal is that the students after completing the course should: </div> <div>• Have gained a broader perspective and understanding of how one’s own research can be utilised and disseminated.  </div> <div>• Gain a greater understanding of how AI and medtech solutions can be helpful in healthcare.  </div> <div>• Be able to identify and discuss ethical aspects of their research.  </div> <div>• Know how to go about translating results from the research project into utilisation.  </div> <div>• Demonstrate and discuss their research project with key players and stakeholders from a utilisation and innovation perspective.<br /></div> <div><div>The seminar series is obligatory for doctoral students at the Gothenburg Research School of Health Engineering, but also open to other doctoral students working in the field of technology and health, at Chalmers and Sahlgrenska Academy. For questions, please get in touch with <a href="">Malin Barman</a>.</div> <h2 class="chalmersElement-H2">Three questions for Roman Naeem, Chalmers' doctoral students at <span>Gothenburg Research School of Health Engineering:</span></h2> <div><span style="background-color:initial"></span><span style="background-color:initial"><strong>What is your work about?<br /><br /></strong></span></div></div> <div>&quot;These days, most Artificial Intelligence systems utilise Deep Learning methods because of their recent advancements showing significant performance gains over traditional methods. Deep learning models are usually trained in a way called Supervised Learning, in which a large amount of data with sufficient variation is required to learn useful data features, and give appropriate outputs that could be used by medical<img src="/SiteCollectionImages/Areas%20of%20Advance/Health/Udda%20format/Roman_Naeem_300.jpg" class="chalmersPosition-FloatRight" alt="" style="margin:5px;width:220px;height:288px" /><br />professionals. However, in medical imaging, such as MRI, CT scans and ultrasounds, labeling a large amount of data can be very time consuming and quite expensive, as we need highly-qualified individuals like doctors to label the data. A potential way of tackling this hurdle is utilising Semi-supervised Learning (SSL), which is the main subject of my work.<br /><br /></div> <div>As the name suggests, in SSL we only partly use supervised learning using the limited data that we have, and focus more on using the much more unlabeled data available to train the models. Specifically, I am working on developing algorithms that utilise SSL for analysing a dataset of CT examinations of around 30,000 individuals, collected in a population study by a few Swedish hospitals. Through this analysis, we hope to find and locate atherosclerosis in coronary arteries, which will help us in improving risk predictions for future myocardial infarction, or heart attack in layman’s terms.&quot;<br /><br /></div> <div><strong>What part/-s of your work is the most challenging?</strong></div> <div><br />&quot;Computer vision, like SSL, has seen a major rise in popularity in the recent years, so a lot of research is being done in the field. I think the most challenging aspect of my work is keeping track of and staying updated with all the new research that is being published, and taking inspiration and incorporating ideas in the new research with my own work to improve it.&quot;<br /><br /></div> <div><strong>What are the benefits (for you) in being a part of the Gothenburg Research School of Health Engineering?</strong><br /><br /></div> <div>&quot;There are quite a few benefits! But the main benefit would be being a part of a multidisciplinary group, which makes it easier to learn more about the characteristics and peculiarities of the downstream tasks – like automatic detection of features in a medical exam, that could lead to benefits like early diagnosis and preventive measures – for which my work will be used. My colleagues, coordinators and supervisors at Gothenburg Research School of Health Engineering are also a great asset in helping me further in my research.&quot;</div> <div>​<br />Text: Mia Malmstedt, Elin Lindström​<br /></div> <div>Photo, Malin Barman: Chalmers</div> <div>Photo, Justin Schneiderman: Malin Arnesson</div> <div>Photo, Roman Naeem: Siri Norelius<br /><span style="background-color:initial">Photo, x-ray: Pixabay</span></div>Mon, 15 Feb 2021 13:00:00 +0100