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Mutated zebrafish can answer questions about rare disease A MAGAZINE FROM SCILIFELAB

#1 –– 2018

More Inside Close contact with research engages young people Sex and food odorants for sustainable insect control Loss of chromosome Y: Seeking links between a disrupted immune system and diseases Everything is determined in the expression of genes: The secret life of trees

A handle on

campylobacter A magazine from SciLifeLab

Synergy #1 –– 2018

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Foreword Top research demands cooperation

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ciLifeLab has taken new steps to promote the entire life science ecosystem in Sweden. Last year, more than 1500 users and their research teams gained access to the technologies and expertise offered and being developed within our national infrastructure. The percentage of users from the healthcare services, business community and other actors outside the university world amounted to 17 percent, a significant increase compared with earlier years. As many as four of ten academic researchers who used SciLifeLab’s services came from universities other than our four host universities. At the beginning of 2018, we also launched three calls for proposals to stimulate national research collaboration and update our infrastructure with the latest technologies and instruments. This means that researchers active in Sweden will not only benefit from our improved service offering, but also collaborate as a partner in building SciLifeLab’s research community. One of our new initiatives – establishing Research Community Programs – entails an entirely new way of creating synergy within SciLifeLab. By bringing together top researchers with facilities in our national infrastructure, we aim to create the collaborative conditions that drive Swedish molecular biosciences to the very frontline of global research. In this issue of Synergy, you can be inspired by how others have worked together. Join us as Swedish authorities jointly find the cause of recent years’ campylobacter outbreaks. And meet Nathaniel Street, who created a database with genome sequence information from a variety of trees and plants – for the benefit of research teams around the world.

Editorial staff

Synergy is a magazine about research, published by SciLifeLab twice a year in Swedish and in English. The magazine may be ordered free of cost, or read online at scilifelab.se/infrastructure/synergy Editor : Sara Engström Editorial committee: Susanna Appel, Camilla Breiler, Ellenor Devine and Annica Hulth

Design and production: zellout.se Printing: Danagård Litho Contact: synergy@scilifelab.se

Photo: Daniel Rosik

Enjoy your reading!

Olli Kallioniemi, Director of SciLifeLab director@scilifelab.se

SciLifeLab (Science for Life Laboratory) began its operations in 2010 and is a partnership between KTH Royal Institute of Technology, Karolinska Institutet, Stockholm University and Uppsala University. In 2013, the government tasked SciLifeLab with creating a national center for molecular biosciences. The purpose was to be able to offer researchers throughout Sweden access to technology and expertise for advanced research at a reasonable cost. SciLifeLab is non profit and fully integrated into the higher education institutions’ operations. SciLifeLab’s vision is to be a national hub for mole­c ular biosciences. Today, over a thousand research groups per year benefit from the center’s services.

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A magazine from SciLifeLab


Contents 05 11 15

06 14 12

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#1 –– 2018 02 / Foreword

06 / Reportage

14 / Insight – Chromosome Y

Top research demands cooperation

A handle on campylobacter

04 / In brief

Seeking links between a disrupted immune system and diseases

11 / Insight – Harmful insects

Microorganisms flourish, Extended course offer and prize for young scientists

05 / Insight – Research in school Close contact with research engages young people

A magazine from SciLifeLab

Sex and food odorants for sustainable insect control

12 / Portrait Everything is determined in the expression of genes: The secret life of trees

15 / Insight – CRISPR/Cas9 Mutated zebrafish can answer questions about rare disease

16 / Hello there! Barbara Wohlfarth has mapped DNA in organisms by analyzing sediments from an ancient lake

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Photo: Mikael Wallerstedt

In brief All scientific publications associated with each article in Synergy can be found at scilifelab.se/infrastructure/ synergy

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facilities located at 10 Swedish universities constitute SciLifeLab's research infrastructure.

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Extended course offer

unique users benefited from SciLifeLab’s research infrastructure in 2017, of whom

1428

were academic users with the rest from healthcare, industry or other Swedish authorities.

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further education sessions were organized by SciLifeLab’s research infrastructure in 2017.

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courses were held in locations other than Stockholm/ Uppsala.

SciLifeLab offers courses and workshops for PhD students, postdocs, Principal Investigators and other employees at all Swedish universities. In the autumn of 2018, we will launch four new courses spanning a wide range of topics including proteome analyses, drug discovery, cellular profiling and image processing. The aim of our educational effort is to increase knowledge and understanding about the advanced techniques and data analysis methods available at SciLifeLab’s technical platforms. Read more at scilifelab.se/education

New courses autumn 2018 • Advanced Molecular Technology and Instrumentation for Proteome Analyses • Biophysical methods in drug discovery • Cellular profiling within the Human Protein Atlas/Spatial Proteomics • Single particle Cryo-EM image processing

Latest news! Stay up-to-date on what’s happening at SciLifeLab by subscribing to our newsletter: scilifelab.se/about-us/newsletter

Microorganisms flourish in frozen soil Researchers long assumed assumed that microorganisms in the ground can only break down organic material at temperatures above the freezing point. Now Mats Öquist, researcher at the Swedish University of Agricultural Sciences, together with his team, has discovered that microorganisms can be active and break down soil organic material even when the ground is frozen. How microorganisms work in frozen soil affects the breakdown of carbon deposits in the ground. This process slows down considerably below freezing, but continues nonetheless, and the carbon dioxide formed rises up in the atmosphere. Since the carbon deposits stored in the ground are three times larger than the carbon dioxide in the atmosphere, even small changes

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in the breakdown of soil carbon can affect the amount of atmospheric carbon dioxide. In the latest study published in autumn 2017 in Nature Communications, the researchers were able to show for the first time that large complex macromolecules such as cellulose are broken down by microorganisms even though the ground is frozen. The fact that macromolecules are broken down at such low temperatures means that the effect of winter on the soil carbon balance is greater than previously believed. This study was performed with the help of NMR (nuclear magnetic resonance) technology from SciLifeLab’s Bioimaging and Molecular Structure Services.

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Insight Text: Lisa Thorsén / Photo: Mikael Wallerstedt

Close contact with research engages young people Junior high school-students who have the opportunity to participate in real research projects show an extensive commitment and interest in science. A study from Umeå University reveals that students looking for soil bacteria that can contribute to new antibiotics were clearly engaged by their task.

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any studies show that interest in science decreases in the early teenage years, but this was not the case for students monitored by Jenny Hellgren, a research assistant in educational sciences. In her study, students helped one of SciLifeLab’s facilities at Umeå University to find new soil bacteria belonging to the group actinomycetes as part of Help a Scientist, a collaborative effort between schools, researchers and the Nobel Museum. “The students’ huge commitment surprised me. On a group level, we could see that interest in science didn’t decline during the time that the project was under way,” says Jenny Hellgren. One of the most important results she highlights is that the research project got everyone involved, both those who were already interested in science as well as those who were not. “A society needs scientists and engineers, as well as citizens, who can take conscious and responsible decisions based on knowledge,” reasons Jenny Hellgren. “That’s why it’s important to try to find out what can generate and keep an interest in science.” In total, Jenny Hellgren studied 20 classes with 388 students spread throughout Sweden. They began collecting soil samples in May 2011. Each group took two samples. One they kept in the classroom and one they sent to the researchers. During the autumn semester, they took part in four classes where they found out which bacteria were found in their sample. At the same time, they got to learn more about what research is, what antibiotics are, and why new kinds are needed. The students communicated with the researchers by e-mail and social media. “It’s common that research on students who actively participate in research projects is done on selected young people who are extra diligent or who already attend special high school programs. In Help a Scientist, we meet everyone before they have made their choices.” All students completed two questionnaires. Jenny Hellgren and her team also filmed the lab sessions in three classes and interviewed 24 of the students. The interview focused on how they perceived the Help a Scientist collaboration. “The students appreciated the practical work, getting to do things themselves like digging and looking in a microscope. They also liked the investigative approach, finding out things that lacked ready-made answers. Being able to do things the way real researchers do, things that make a difference and feel important, was also a positive experience.” Technology and service The students helped SciLifeLab’s service area for Chemical Biology and Genome Engineering to gather 200 soil samples, from which around 1000 bacterial species were isolated. Actinomycetes are commonly occurring soil bacteria that frequently produce secondary metabolites— organic molecules that often have anti-bacterial properties. SciLifeLab investigated the bacteria’s ability to produce anti-bacterial substances and maintained continuous contact with the teachers and students throughout the project. SciLifeLab also built up an extra library from the collected samples that can be used for screening, e.g. studying their effect in various infection models.

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Reportage

campylo A handle on

Campylobacter infections in humans often originate from chicken. After the outbreaks of recent years, the Public Health Agency of Sweden, the National Food Agency and the National Veterinary Institute (SVA) began to coordinate sampling and analyses to trace and prevent infection. Hanna Skarin is the coordinating project manager at SVA and group leader of the European reference laboratory for campylobacter. Text: Henrik Möller / Photo: Mikael Wallerstedt

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Synergy # #11–– ––2018 2018

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obacter

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Reportage

T “But something happened in the winter of 2014. An unusually high number of people were infected by campylobacter ”

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he tall chimney over SVA’s large, yellow building complex can be seen from afar. Here, remains of infected animals are incinerated, but today, no smoke is rising towards the blue sky. At the reception desk, visitors are met by a colorful fiberglass cow. Hanna Skarin opens the door to a labyrinth of hallways. Posters with animals and research results hang on the walls. One of them announces that SVA and the Swedish Poultry Meat Association have monitored campylobacter since 2001. The problems are thus well documented: some species of campylobacter can cause serious gastrointestinal problems in humans and infection can also lead to complications such as joint pain and blood poisoning. Infection with campylobacter is a zoonotic disease, meaning a disease that is transmitted between animals and humans. Last year, around 6900 cases of campylobacter infections were reported in Sweden. “Normally, the number of campylobacter-positive chicken broods and human disease cases are fewer in the winter than the summer, when sources of infection are more numerous and people are less cautious about handling meat when barbecuing, for example. But something happened in the winter of 2014. An unusually high number of people were infected by campylobacter,” Hanna Skarin explains. When SVA and the Public Health Agency began sequencing and analyzing genomes from campylobacter during the peak of that winter’s outbreak, they saw that a large number of the bacterial strains in chickens were identical with the strains in infected individuals. In 2016, the number of cases was, as usual, higher all summer but never dropped in the autumn and winter as expected. Now both the poultry industry and the authorities were in agreement that something needed to be done. Could, for example, bacterial isolates in the entire supply chain from farm to table be compared via coordinated sampling? It seemed possible and the project got started at the beginning of 2017 on the initiative of the Public Health Agency. “SVA analyzed campylobacter found in chickens on farms. The National Food Agency collected samples from grocery

stores. The Public Health Agency did the same thing with campylobacter from people who had fallen ill.” Samples were gathered during March and August. Now bacterial strains from farms, through slaughterhouses and on to stores and consumers could be sequenced and compared. What did you conclude? “The results from March showed that most of the bacterial isolates in both chickens and humans were identical and that the campylobacter could be traced to Swedish slaughtered poultry.” A problem that the industry itself identified was an incorrectly installed device for washing cages. What was done about that and what do the statistics look like today? “The industry took several steps. It reviewed hygiene procedures at slaughterhouses and took samples of all broiler broods for the existence of campylobacter. One important measure was that the chicken’s accommodation areas must be kept free from animals for at least 48 hours after they dry out following cleaning and disinfection. Only then can new animals be placed in them. At the affected slaughterhouse, zero percent campylobacter was measured in December 2017. So now we hope that there will not be another peak in infections during the winter.” Will the monitoring continue? “It is under way during 2018 and we hope for continuous monitoring via sequencing. This cooperation gives us a unique overall picture and a handle on the situation in terms of campylobacter.” In a joint strategy document from 2017, which has been signed by the Swedish Board of Agriculture, the National Board of Health and Welfare, the Public Health Agency, the National Food Agency and SVA, the objective is for campylobacter infection and campylobacter prevalence in chicken broods “to show a clear downward trend”.

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or Hanna Skarin, a career in research was not always obvious. She was first accepted to a journalism program with a science specialization, but instead decided to become a

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Reportage

limnologist, an expert on fresh water. “But during an exchange term in Edinburgh, I was completely sold on infectious biology and took all of the courses available in microbiology when I came home.” In 2007, she became a doctoral student at SVA and specialized in botulism in animals. Botulism is poisoning by the botulinum toxin that is produced by the bacteria Clostridium botulinum. It affects the peripheral nervous system and leads to paralysis or death. Eleven years later, she easily finds her way in the endless hallways of SVA. We pass several laboratories with closed doors and a biosafety level that varies between 1 and 3. Warnings for infection keep unauthorized personnel away. “We have strict biosecurity procedures since we also handle bacteria like anthrax, which in the form of spores is entirely encapsulated and can survive an extremely long time.” ➔

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The swab tests (top picture) that arrive to the laboratory are spread on plates with growth medium for culturing of bacteria (bottom picture).

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Reportage

Helena Höök, Sevinc Ferrari and their colleagues prepare samples for proficiency testing, which will be sent to the national reference laboratories for Campylobacter.

”... but ultimately it’s about infections being less of a risk for animals and humans. ” It feels safer to be in the meeting room where the sun is shining through the drapes and no samples of anthrax are in sight. Hanna Skarin emphasizes that Sweden has a good record regarding infection by campylobacter. In many countries, up to 100 percent of chickens can carry the infection, which is harmful to people. In Sweden, the figure is around 12-13 percent. In 2006, the European Commission therefore chose to appoint SVA as the coordinating lab to ensure high quality in labs that examine samples for campylobacter in the EU. “For different hazards, the European Commission may appoint a reference lab. There is one for campylobacter, for which I have been responsible for for two years. Every country also has its own national reference lab. In Sweden, we have two for campylobacter and one of them is here at SVA.” The daily work for the European Union Reference Laboratory (EURL) for Campylobacter means coordinating, training and supporting the national reference labs and reporting to the European Commission. “Right now, we are planning for the annual meeting where some 50 people from all national campylobacter reference labs will meet and exchange experiences.”

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Hanna Skarin’s working group comprises two bioinformaticians, two molecular biologists, one epidemiologist, two laboratory technicians, one administrator, one economist and one veterinarian. “Several of us are new, but we have really united the team and together cover many areas. I manage the project and am involved in the molecular biology side as well.” What drives you in your work? “A desire to know more about the bacteria on which I conduct research, and to share my knowledge with others. This can have different purposes depending on what and which bacteria I am working with, but ultimately it’s about infections being less of a risk for animals and humans.” Every day, new questions come up from the national labs. “I am expected to send quick answers and sometimes it gets hectic because I need to be thorough and check how things have been done in the past, and maybe also discuss with my team. But I am gaining experience and the job therefore gets both easier and more fun.” A colleague stops and greets us in the doorway. It’s laboratory technician Therese Jernberg who is working with a sample that

will test the national labs’ ability to find campylobacter. Hanna Skarin explains: “We are responsible for ensuring that all national labs possess the right expertise. We therefore send them proficiency tests every year to assess their competence and identify if any labs need development assistance. This year, the test includes counting the right number of campylobacter on chicken skin and finding and determining the species of campylobacter in chicken caecal swabs.” We walk back towards the reception desk and the colorful cow. Hanna’s colleagues temporarily leave the unruly campylobacter to their fate in favor of their lunchboxes. Many questions still await them. “Why have different strains been found in every outbreak? Is it purely random or have some strains become better adapted to surviving in oxygen? Are they more resistant to disinfection agents used on chicken farms? Or do they survive longer in products once they have reached the food store?” Continued collaboration between authorities will give us the answers.

Technology and service Both SVA and The Public Health Agency of Sweden have their own instruments for whole genome sequencing, but in the monitoring project, where many isolates were to be sequenced, SciLifeLab assisted in library preparation and sequencing. The sequences were then downloaded as raw data and analyzed using bioinformatics programs developed at the respective authority.

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Insight

Text: Lisa Thorsén / Photo: Cyrus Mahmoudi

Sex and food odorants for sustainable insect control The discovery of how female fruit flies attract other distant fruit flies with a sexual pheromone has incited researchers interest in its feared cousin, the harmful spotted wing Drosophila. The question is: Does the spotted wing Drosophila also emit an attracting scent and, if so, can it be used for traps in fruit and berry farms?

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eter Witzgall, Professor of Chemical Ecology at the

Swedish University of Agricultural Sciences, and his research group, have shown that female fruit flies emit a species-specific sexual pheromone, Z4-11Al. Their study was recently published in the journal BMC Biology. This pheromone attracts males in particular, but also females. Results show that the olfactory receptor of the fruit fly Drosophila melanogaster that binds to the pheromone occurs in two ‘twin variants’, OR69aA and OR69aB. Both send signals to the brain over the same nerve pathways, but one mainly reacts to the sexual pheromone while the other reacts to the scent of fermenting fruit. “The genetic trait for the olfactory receptor is thus affected by both sexual and natural selection and this provides insight into species mechanisms,” says Peter Witzgall. “The sense of smell is fundamental for the survival of sexually reproducing animals. It’s a matter of finding food and a partner with which to procreate.” By observing the behavior of the fruit fly, gathering and analyzing the females’ scents, and identifying and testing the olfactory receptor, the researchers identified the female fruit fly’s sexual pheromone. “Already early in the study, we were surprised to find that we ourselves could smell the difference in the scent of single males and females. The fragrance is difficult to describe, but is very characteristic and reminiscent of mandarin orange,” explains Peter Witzgall. The fact that the human nose could detect the difference in the pheromone led to sensory experiments in cooperation with a German wine research institute in Freiburg. The results showed that it is sufficient for one single female fruit fly to end up in a glass of wine to ruin its taste. Now the researchers are pointing their spotlight on the spotted wing Drosophila, Drosophila suzukii, a species that has spread to Europe and North America through imports of fresh berries from China. “Today, the spotted wing Drosophila is the most important economically harmful insect in Europe and North America. In these new environments, it has no natural enemies,” says Peter Witzgall. The hope is that the spotted wing Drosophila has a pheromone that is similar to the fruit fly’s. In the future, this research may, for example, lead to the development of traps based on pheromones to detect the spotted wing Drosophila in fruit and berry plantations. “This was an unexpected journey for us. We had no plans for applied research, and all that it entails, but this is too promising to pass up,” says Peter Witzgall. Photo: Mikael Wallerstedt Technology and service SciLifeLab’s service in Chemical Biology and Genome Engineering calculated how much energy it costs for various molecules to bind to the olfactory receptor, information that was crucial for comparative studies of structure-activity correlation. The calculations showed that structurally different substances can take on a common bioactive conformation and fit into the same olfactory receptor.

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Portrait

Text: Henrik Möller / Photo: Mikael Wallerstedt

Everything is determined in the expression of genes:

The secret life of trees When Nathaniel Street earned his PhD in the UK and came to Umeå for the first time, he did what he usually does: went for a run. In the forest, he was struck by how the appearance of aspen leaves differed on individual trees. Long, round, angular. Just like people’s faces. Why was this? And what purpose does it serve in evolution?

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en years later, he is seeking the answers among thousands of genes from trees. Nathaniel Street has established himself as Senior lecturer at Umeå University and despite the temperature of minus 22 degrees Celsius, he went running this morning as well. At Umeå Plant Science Centre, he conducts research on gene expression. To help him, he has a self-made website, PlantGenIE.org, which is used by hundreds of research teams around the world. The website contains a database with around 40,000 genes and new information is constantly being added. Nathaniel Street conducts research, teaches and spends a great deal of time in nature, either camping, hiking or collecting samples that are then sent to SciLifeLab for sequencing. “The most important thing for me is to try to understand why the leaves on individual trees look different and also differ from each other functionally. This has always fascinated me. Why this development and what is the meaning behind it?” Can you determine a tree’s characteristics simply by looking at its leaves? Healthy, sick, resilient? “These are exactly the kinds of questions I would like to answer! We compare the shape of the leaves with other characteristics of the aspen. For example, how quickly the tree grows and if this bares a relationship to the leaves’ appearance.” What benefit to society does your research have? “My motivation is to better understand how an organism functions. But there are also useful applications, such as getting trees to grow faster and to handle climate change so that forests can continue to be a useful resource for everyone.”

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Don’t they do that themselves? “Trees adapt very slowly. And people are changing the world quickly. Global warming is the greatest threat. In the long term, trees would be able to adapt, but if we want to continue to have really productive and economically viable forests, they need a little help.” Do trees have a consciousness? “It would be nice to think so, but it’s not true. They clearly communicate with each other through root systems and by emitting various substances into the air. But this is rather a result of a really long-term development of how various organisms interact with each other.” Nathaniel Street’s thesis was about how two poplar species handle a shortage of water. One shuts down its systems and all activities as fast as lightning, and the adjustment therefore goes well: the leaves survive. The other displays no reaction whatsoever and all the leaves die. “I took whole leaves and measured their gene expression. The idea was to find genes whose expression differs between tree species. In this way, we can understand why species are different and in the future cross them to produce a more durable tree. In the end, we did find specific regions in trees that showed differences in gene expression between species. These differences made the trees act in different ways.” Today, Nathaniel Street continues to examine gene expression. A large part of his time is spent analyzing data from genome sequencing of aspen and Norway spruce. Among other things, he wants to understand how fungi and bacteria attack trees and what happens when humans add nitrogen in the form of the fertilization that forestry companies use. “The question is what effect this has on the microorganisms that work together with the trees. In this case, the fungi are not harmful to the trees, quite the contrary. They normally provide nitrogen and receive carbon and sugars in exchange. Fungi also protect the trees from toxic parasites. But if you add nitrogen, this cooperation changes and the harmony is disrupted.” For a while, it looked as if Nathaniel Street’s research career was drowning in time-consuming routine measures: one single tree’s genome contains around 30,000 genes. It was then that he decided to build a website with searchable genomic data open for anyone. In the beginning, it contained just data from poplar and aspen. Now the database includes information from Norway spruce, eucalyptus and other trees and plants often used in research. Nathaniel Street, who had never built websites before, learned web design along the way. Today, members of his research team

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help out and the Plant Genome Integrative Explorer Resource contains sophisticated visualization tools that have made the site popular worldwide. “We have hundreds of users in Europe, China, the USA and other parts of the world that visit the site every day. It feels great to have created something that really helps researchers.” On the website, researchers put the genes they are interested in into a shopping basket and can then see how the gene is expressed in various parts of the tree. A red-to-blue color scale shows how active the gene is. Another tool shows if a group of genes is dedicated to joint activities. “If the genes express themselves in a similar way within a group, we can visualize them as a network with lines that tie them together. That a gene is part of a network indicates that it does something substantial that we are interested in,” explains Nathaniel Street, pointing to blurred red and orange dots linked together by lines. “What we see is an experiment with trees that were infected by harmful fungi and how the various genes respond to the attacks.” As an image, the experiment is rather reminiscent of a piece of abstract art? “Yes, it is, especially how the genes interact with one another. It is only this interaction that provides the end result, the actual cooperation. They dance together in a complex way. The individual is not so interesting in itself; it’s the group’s work that yields results,” says a pleased-looking Nathaniel Street. Outside the window, the temperature is slowly falling and the fog is thick over the campus. But Nathaniel Street has his sights set. In the next few years, he hopes to know which gene group needs to be manipulated to get a tree to develop well in a special environment or handle a certain disease. “There is so much more we need to find out, we still only know a fraction of what is happening.”

Technology and service Nathaniel Street used SciLifeLab’s Genomics service to build up PlantGenIE.org. He also regularly uses SciLifeLab to sequence samples from trees and leaves, including Norway spruce. In another of his projects, SciLifeLab developed a method to study how genes express themselves in different sections of biological samples. For example, thin slices can be cut straight through a bud and the gene expression in the layer and be visualized through spatial transcriptomics. Nathaniel Street received funding from SciLifeLab’s National Sequencing Projects in 2017.

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Insight Text: Lisa Thorsén / Photo: Mikael Wallerstedt

Loss of chromosome Y:

Seeking links between a disrupted immune system and diseases It has previously been shown that men who lose the Y-chromosome in a large number of blood cells have a many-fold elevated risk of early death, several forms of cancer and Alzheimer’s disease. Researchers are now investigating the connection between these diseases and the disruption of the immune system caused by loss of the Y-chromosome.

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hat men can lose their Y-chromosome with age has been known since the 1960s. This loss was previously believed to be a harmless side-effect of aging. When researcher Lars Forsberg and Professor Jan Dumanski at Uppsala University, together with several others, published their first and widely noted study in Nature Genetics in 2014, the map was redrawn. They were able to show that there is a connection between loss of the Y-chromosome (LOY) and cancer. It was the combination of good data,

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coincidence and curiosity that first got Lars Forsberg to think in new ways about LOY. In a discussion with another researcher on the bus to work, he learnt that the fruit fly’s Y-chromosome was significant for gene expression on other chromosomes. The very next day, he was able to test the hypothesis on humans since all the necessary data for conducting the analysis had been compiled for a different research project. The results immediately showed that men who had lost the Y-chromosome die earlier than those who still retain it.

“My first thought was: Why has nobody discovered this earlier? Can it be true?”, explains Lars Forsberg. The conversation on the bus led to the study that showed the connection between LOY and the risk of dying prematurely, as well as the link to several different forms of cancer. In further work, Lars Forsberg and Jan Dumanski showed that LOY is also associated with an elevated risk of being struck by Alzheimer’s disease. Right now, several studies are under way to describe the causal connection. The researchers have strong indications that those who have lost the Y-chromosome in a certain percentage of blood cells have an elevated risk of cancer and Alzheimer’s disease. “The first thing I considered was that the cells we have studied are immune cells. The hypothesis is that these cells lose some of their ability to fight disease when their Y-chromosome disappears,” says Lars Forsberg.

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“Men live shorter lives than women and LOY may help explain why.” The researchers are now following two main tracks. In one, they use cell sorting to see what types of immune cells display LOY among men with cancer and Alzheimer’s disease. This is achieved by separating the immune cells from the patient’s blood, sorting them and comparing them with a control group. The other track is about understanding what happens in a cell that has lost its Y-chromosome. Here the researchers employ single-cell transcriptomics, a technology that makes it possible to map the absolute number of RNA molecules in a cell. “This is a fantastic technology that we have accessed through SciLifeLab for the past year. With this method, we can get answers about exactly what genes

are expressed in thousands of different single cells in just one experiment. The transcriptome reveals a great deal about the cells studied, such as what type of immune cell they are, what functions they have, and how well those functions are executed,” explains Lars Forsberg. So far, no studies have been published, but Lars Forsberg says that the preliminary results look promising. Lars Forsberg and Jan Dumanski are also thinking about how their results could be applied clinically. One suggestion is to develop a simple blood test for clinics to identify LOY. The idea is to identify men with an elevated risk of the most common diseases and to prevent the initial spread of cancer tumors through early diagnosis and treatment. In terms

of Alzheimer’s disease, Lars Forsberg points out that even if a cure or treatment to slow progression is currently lacking, research is advancing quickly and being able to identify an elevated risk will probably be of considerable significance. “If we can also link the risk of developing different diseases with LOY in different cell types, we will really have made progress. Men live shorter lives than women and LOY may help explain why. With future applications of our findings, we might be able to increase men’s survival so that we can age side-by-side with women,” says Lars Forsberg.

Technology and service The project largely builds on data generated through SciLifeLab’s Genomics and Single Cell Biology service areas. The research team is now studying aspects of LOY at the DNA, RNA and protein levels through cooperation with SciLifeLab.

Insight Text: Lisa Thorsén / Photo: Mikael Wallerstedt

Mutated zebrafish can answer questions about rare disease Using CRISPR/Cas9 technology in zebrafish, a research team at Lund University studied a gene of special interest for the very rare disease Dyskeratosis congenita. Dyskeratosis congenita is a hereditary disease that, among other things, can entail premature aging, abnormal skin pigmentation, stains on the mucous membrane of the mouth and failure of bone marrow function. Failure of bone marrow function in turn affects blood formation. “SciLifeLab’s technology has been invaluable to the study’s implementation. Without SciLifeLab, I don’t really see how it could have been possible,” says team leader, pediatrician and assistant researcher Josef Davidsson. To begin with, the researchers screened a patient with a mutation in the gene in question using whole exome

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sequencing to map the entire proteincoding DNA sequence. When they found the mutation, they proceeded by creating a knock-out model in zebrafish. Zebrafish embryos were injected with Guide-RNA and Cas9 to make targeted changes to the genetic material. When the fish were crossbred, the researchers were able to identify mutants that carried defective copies of the gene in which they were interested. This allowed them to study the gene’s significance for morphology, in other words what the fish looks like and how it is formed, as well as its significance for blood and pigment formation. Josef Davidsson feels that CRISPR/ Cas9 is a very effective new tool in the team’s research. “For us, it was very well suited to this case. We only needed to make a simple injection in the fish embryo. The initial results of the study show

that fish that are homozygous for the mutation, i.e. they carry two defective copies of the studied gene, have very clear and similar observable characteristics. Their craniums are compressed, their swim bladder is not fully inflated, and their fins are stunted. Now the research team is continuing its analyses to see exactly what is happening in the cells and how blood formation is affected. Josef Davidsson sees the study as a model project. He hopes that zebrafish could be used to study more widespread diseases.

Technology and service Josef Davidsson used SciLifeLab’s Chemical Biology and Genome Engineering service to create the knock-out model. Sequencing was performed by SciLifeLab’s Genomics service.

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Hello there! Text: Lisa Thorsén / Photo: Mikael Wallerstedt

Barbara Wohlfarth ... ... Professor of Quaternary Geology at Stockholm University. Your research team has mapped DNA in organisms between 10,800 and 13,900 years old by analyzing sediments from an ancient lake. What answers are you looking for?

“Our research team, which is led by Laura Parducci at Uppsala University, Tanja Slotte at SciLifeLab and Stockholm University, and by myself, chose to study this particular time period because it is known for its dramatic climate changes. Our basic question was whether we can decipher ecosystem changes by using metagenome or shotgun sequencing. This method is an effective way of mapping the DNA of all of the organisms found in a sediment.” How have you gone about this? “We took sediment cores from an ancient lake in Blekinge. Under extremely careful and sterile conditions, we then picked out samples from the center of the cores in the laboratory at Stockholm University. We then analyzed the samples at the Centre for GeoGenetics at the University of Copenhagen via shotgun

sequencing according to their very precise protocols.” What have you discovered so far? “In the first part of the project, we studied Archaea. We can see that the biodiversity of the Archaea community shifts during the period studied and that this was related to climatic factors, such as changes in air and water temperature and how long the lake was frozen, but also to how the environment in and around the lake changed.” How will you continue? “We will now investigate which plants we can identify in our sediment samples using DNA analysis. Then we will compare our results with more traditional methods, such as pollen and plant macrofossil analyses. Together, this will give us a picture of how the vegetation around the ancient lake changed

over time. We will make our large database available to other researchers. My vision is that we will be able to analyze ancient sediments using metagenomics much more frequently than we do today. Then, we can better understand how different ecosystems reacted to climate changes in the past. Which organisms adapted? How long did it take for an ecosystem to collapse? Did it recover afterwards?”

Technology and service SciLifeLab’s service area for Bioinformatics contributed with knowledge support in this project. In practice, this included settingup the bioinformatic workflows needed to analyze large-scale sequence data as well as statistical modeling and interpretation of results.

Synergi 1 2018 eng webb  
Synergi 1 2018 eng webb  
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