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Graduate School of Life Sciences

Master for Life Magazine

This magazine is intended for students and teachers and all other persons interested in the Life Sciences Community Utrecht.

The articles are written by Master’s students following the course Communicating Life Sciences taught by Connie Engelberts and facilitated by de Graduates School of Life Sciences.

Previous issues of the magazine can be found here.
Content

Graduate School news
Research project market
On Tuesday January 15 the annual Research project market takes place. At this market research groups from het UMC Utrecht, the faculty of Veterinary Medicine and Life Sciences groups from the Science faculty are present. Visit this market from 17:00-19:30 to get an overview of all the research project options, to meet with future supervisors and to find your ideal project. Sign up for the market during the evening itself from 17:00 in the ‘Kroonluchter’. Upon this registration you will receive a free meal.

Career services

Do you need some advice about how to start your career? Check out www.uu.nl/careerservices for more information.
Upcoming events: Careers day UU  7th  February, 4th  – 15th  February  Co-challengeLife Sciences Career Event  March 19th, and Life Cycling  May 9th.

Student representation
Problems, complaints, questions about your Master's programme? Contact the Life Sciences Representatives or go to www.facebook.com/GSLSstudents.

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Beers and burn-outs: student life in 2018

Life as a student should be “the best time of your life”, right? But being a student in 2018 can be pretty tough. It is not just about studying anymore; you also need to have an active social life, think about CV building and get a few hours of sleep in between. Student life is becoming increasingly demanding, and more and more students experience feelings of anxiety and depression or even get burn-outs. The University of Utrecht recognizes this and sent out a survey on student well-being called ‘How are UU?’. Master student Lisa Bauer joined the focus group of this survey and shares her opinions.

It was all over the news the past few months: many students suffer from burn-out symptoms. Researchers from Utrecht University are also concerned, which is why they sent out the survey ‘How are UU?’ last May. One of the responders of the questionnaire is Neuroscience and Cognition student Lisa Bauer. She joined the focus group that was organized to pre-test the questions in the survey. When asked why, she explains: “I thought it would help me understand myself better and give me some insight into where my feelings of stress come from.”

Why so stressed?
So what makes students so stressed these days? For students of the Graduate School of Life Sciences, Lisa thinks a big contributor is the working atmosphere research groups tend to have. Passionate as researchers can be, they often make long hours and sometimes take their work home. However, it is important for students to realize that this is not necessarily expected of them.

What can Utrecht University do?
Although initiatives like surveys on well-being are steps in the right direction, Lisa feels like Utrecht University could do more to alleviate the burden on her students. “For 25 euros, you can get a session with a student therapist, but no one knows this. The university could promote it more”, she says. Furthermore, Lisa feels like there is room for improvement in education on career development. “A large part of our worries have to do with uncertainty in the future; we feel insecure about where we are headed and how we can obtain a job that suits us.” In her opinion, career days should bring students in closer contact with alumni that can inform them about the day-to-day activities of their job.

The description of the typical carefree, beer-drinking student does not fit all the graduates of 2018. Universities are acknowledging mental issues amidst students and taking some initiative to monitor student well-being. However, more can be done to alleviate the burden.

By Welmoed van Zuiden

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3 million plastic straws each day

This is the number of straws that the people in the Netherlands alone use each day. Fortunately, the European Parliament has voted on 24 October 2018 to ban all single-use plastics by 2021, to decrease this number of straws and to save the environment. While this ban was already proposed in May this year, an outcry from the public and increased awareness of the plastic problem pushed the European Parliament to finally agreed upon a ban on plastics. It will take some time before this ban is implemented, but we can already start decreasing our daily use of plastic.

Our use of plastics is a big problem: many plastics are not recyclable and eventually end up in the ocean. Scientists say that in de future there will be more plastic than fish in our oceans. More than 8 million tonnes of plastics leak into the ocean every year. In the ocean the plastics are broken down into microplastics by sunlight, waves and animals that try to eat them. These microplastics cannot be digested by animals and will therefore accumulate up the food chain. Some of these microplastics are not toxic in small quantities but will become toxic for humans when they accumulate in the larger fish we eat for dinner.

Thus, the plastic pollution can impact our health. New solutions have to be found to protect our oceans and our livelihoods. All over the world people are trying to find ways to reduce the use of single-use plastics. The ocean clean-up (Website) invented by the Dutch environment activist Boyan Slat is one of these initiatives to save the ocean from plastic pollution. Now all European Union countries agreed to combat plastic pollution together. This sounds very promising and could improve the ocean’s health in the upcoming years.

Personally, I hope that this new ban on the use of plastics could reduce or stop the plastic pollution of our oceans. Despite, 2021 is still a few years ahead, you can try and reduce your plastic waste yourselves. Say no to a straw in your drink and use a re-usable cup for your regular coffee to-go. If we start to reduce our waste ourselves before 2021, this ban can be applied much easier and the ban will have more positive effects on both nature and our health.

By Luc Haverhals

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Genomic studies reveal a rapid spread of ancient humans across the American continent 

Recent investigation of the DNA from ancient inhabitants of North and South America reveals that the first settlers of the American continent moved fast and far. Two articles on this subject appeared on November 8 in Cell and Science and they include genetic data from 64 ancient Americans. This is the first time that such a big genetic study concerning historical findings in the American continent has been reported.

Habitation of the American continent

The spreading of humankind across the globe has interested researchers for many years. It is known that the American continent was the last large land mass to be inhabited by us humans. Previous genomic studies have shown that ancient humans travelled from Asia to Alaska and from then on started populating North and South America. The Native Americans diverged from East Asian and Siberian populations about 25,000 years ago. After this migration, the population diverged into Northern and Southern Native Americans about 17,500 to 14,600 years before present.

Contribution of genomic studies
The comparison of genomes can give insights regarding the genetic similarity between two or more people. It also tells you how these people relate to each other in evolutionary terms. The more differences in their genomic sequences, the less related two people are. This divergence is something that can be observed over time and during evolution.

Genomic studies reveal rapid spread of humans over the American continent
The two recently published studies have investigated the genomes from 64 ancient Americans. More than a dozen of these genomes are over 9000 years old. The researchers compared the genetic data from ancient humans found at various sites on the American continent. They found that the genomes were strikingly similar, although there was a great distance between the places where the remains had been found. This indicates that the first humans who set foot on the American continent spread rapidly and inhabited not only North but also South America in no time.

Nothing could stop us
This knowledge sheds new light on the migration patterns of the ancient inhabitants of North and South America. The fact that these people spread that fast across the continent probably meant that there was nothing else in the way. This is in line with the theory that humans spread over the world without resistance and conquered the globe very early on. In the future, archeologists and researchers will be working together to generate a more detailed model concerning the spread of humans across the American continent by obtaining more data.

By Imke Lankheet

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Sharing Conservation optimism

Future For Nature Academy, that is what we call ourselves, and yes, a future for nature is what we hope to accomplish. Young and idealistic, some might say, but that is what ecologist Ignas Heitkönig from Wageningen University and PhD student Rascha Nuijten from the Netherlands Institute of Ecology hoped to create two years ago. Today, this organization is present across several academic institutions in The Netherlands, including Utrecht University, and unites like-minded students in promoting Nature Conservation optimism.

Most of us have been exposed to the pessimistic scenarios surrounding Nature Conservation news. Just recently, WWF’s Living Planet Report 2018 revealed a 60% decline in animal populations since 1970. In the face of such outcomes, keeping an optimistic view regarding the future is sometimes challenging. That is why I chose to join Future For Nature Academy (FFN Academy), a group of passionate people that strive to inspire others with stories of successful Conservation endeavours.

The work of Future For Nature Academy
By sharing the work of young, talented conservationists through lectures and other activities, the FFN Academy aims to infuse the new generation of conservationists with hope and enthusiasm for a better future. As a student myself, it is easy to feel discouraged and often wonder “What options do I have?” or think that “whatever I’ll end up doing won’t make a difference”. But seeing the work of others bear fruitful results and having the opportunity to engage and share ideas with those people may be just what you need to brighten up your perspectives for the future.

Besides sharing current work, FFN Academy also hopes to make Nature Conservation available and easy for anyone to practice. For instance, you can learn how to build insect hotels in your backyard at a workshop, how to look for bats at night in a nature excursion or participate remotely in ongoing research at a citizen scientist event. And the good news is that everyone can participate! Engaging with the community and participating in fun events with peers is a great way to bring people together while motivating sustainable actions.

Being part of the organization
As a member of the organisation, I get to help organise the events and come up with new ideas for didactic, nature related activities. Seeing everyone enjoying their time while working together makes it all worthwhile. More than that, being part of this movement is very rewarding in itself, because the beauty of it is in every little accomplishment. Recognition is not everything, but it feels good when our efforts are applauded by those who have done so much for the field already, like Jane Goodall did (watch here) after FFN Academy livestreamed her lecture in Amsterdam.

And if nature Conservation is something that speaks to you as well, you can always join the team in your city or stay tuned for upcoming events via our Facebook page.

By Monica Vidal

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From Utrecht straight to the Amazon 

How to save the jungle? Jarno, a student of Environmental Biology has an unusual way of taking action to protect the environment. Together with a newly formed group, he wants to create a reserve in the Amazon of Ecuador. Although the aim is a large reserve, they want to make the initial reserve at least fifteen hectares which equals about 30 soccer fields.

The idea sprouted while he was in Ecuador. The many problems and their reasons became reality. But like the problems, solutions became visible. The people there are positive minded, they also see that this is not the right way. However, they do not always have a choice. Some opportunities already came along to contribute one’s mite. One possibility is the creation of a reserve: “At the moment we think that we can have the largest positive impact by creating a protected area in the Amazon”.

You say the many problems became reality, how bad is it? “Climate change, deforestation etc. are of course topics heard of by everyone. A quick look at google gives us a deforestation rate of 22% and this probably does not halt soon enough. In Ecuador this became visible while watching three trucks a day driving out of a small road leading into the forest. They were loaded with freshly cut wooden planks. With our project we want to add some weight to the opposite side and try to slow down the deforestation and degradation process.”

But the project is not entirely based on the establishment of the reserve. “In order to respect nature, we need to enjoy and understand it“. Therefore, at this project they think it is important to have a good connection with the outside world. “Internet, Instagram and Facebook are of course perfect for this.” They hope to inspire people by sharing their story on a regular base. Curious? Have a look at www.orbitopalo.com.

By Jarno Verdonk

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 Gene drives: promising future or horror scenario?

A gene drive is a genetic technology that can be used to spread specific genes through a population. As an example, this technique can be used to eradicate insects that carry pathogens, such as mosquitos that transmit malaria and dengue. However, this potentially powerful technique could induce devastating consequences. This includes spreading of the genetic variant to other species, such as humans.

The mechanism of gene drive lies in inserting a genomic element, called drive sequence, at a specific site in the DNA. This sequence has the capacity to cut the DNA at the same genomic site on the other allele. This cut is then fixed by using the drive sequence as a template for the repair. This will cause the spreading of the drive component. If they end up in egg cells, the offspring will contain the drive element as well. The gene drive technology therefore provides a way to propagate a specific set of genes throughout a population.

Gene drives have been proposed to provide an effective way of genetically modifying specific populations and entire species. For example, the technique can be used to eradicate insects that carry pathogens, such as mosquitoes that carry malaria. It can also be used to dominate invasive species or exterminate pesticide resistance.

However, gene drives are not used for the above applications since there are some concerns. One complication that might arise when applying the technique is that mutations might emerge. This could allow unwanted traits to spread through a population. The gene drives could also escape to other species, which could have devastating consequences. Even when no unwanted effects on the specific species occur, eliminating species or diseases will have ecological impacts.

As described, a gene drive is a powerful and promising technique to eradicate diseases or species. However, the technique has not been applied yet since there are several hurdles that need to be overcome. Nevertheless, there might come a day that we will apply this technique. At that time, we should have perfect insights in the problems that could arise and we should be able to tackle these problems.

By Imke Lankheet

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Fuelling the homeopathy debate

Since the science advisory council of the European Union (EASAC) advised a ban on homeopathic treatments unless their safety and efficacy has been scientifically proven, the debate around homeopathy was sparked. This September, a criticised article that concludes that homeopathy can ease pain in rats was published. While potentially wrong, in alternative medicine communities, this article has been used as proof that homeopathy works. For me, this article and its impact highlight the importance of scientific integrity and the need for the scientific society to always remain critical towards each other.

Research article
The controversial research article concluded that homeopathic extracts from Toxicodendron pubescens plant ease pain caused by nerve damage in rats. The research was performed by Indian researchers, mostly affiliated with institutes, and published in Scientific Reports, an open access journal from the Nature Publishing Group. The researchers compared high dilutions of the homeopathic treatment to gabapentin, a drug approved for the treatment of pain, in vivo and concluded that the homeopathic drug had a similar effect. They then used in vitro experiments to show that Toxicodendron pubescens extracts had anti-inflammatory and antioxidant properties, and proposed this as a mechanism by which it relieves pain.

Critique on the article
A number of scientists have criticised the article for containing flaws. For example, a short report listing some of these flaws was posted online by Enrico Bucci, adjunct professor at Temple University in Pennsylvania. He stated that the same image was used in two panels of the same figure. Furthermore, the data seemed very similar for two experiments in which pain was measured, so these appear to be duplicated as well. Besides this, other researchers online have expressed doubts about the small number of animals used for the in vivo part of the study.

Impact
Questioning the conclusion of this research article is important as it can have a big impact. One of my main concerns is that the article was reviewed and despite its quite obvious flaws, still got published. Secondly, trials investigating the safety and efficacy of Toxicodendron pubescens extract might be started based on the conclusion of this article. If this conclusion was wrong to begin with, a lot of money might be wasted with these trials. Lastly, this article might influence whether the homeopathic treatment is banned by the European Union or not, if the advice of the science advisory council is followed. However, it is good to keep in mind that the flaws in the research article makes the conclusion questionable but not necessarily incorrect.

By Nadia van der Meijs

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Organ development can now be visualized at single cell level

Scientists from the Howard Hughes Medical Institute have developed a computer-directed light-sheet microscope that can culture and image a whole mouse embryo during its development. It can track single cells in a living organism, opening the door for a variety of new studies.

Current light microscopes are limited by transparency of the embryo and can therefore not be used to investigate organ development inside an embryo. This new microscope can culture a mouse embryo with minimal damage on its development. The microscope continuously measures and adapts to the new optical properties and size of the growing embryo. In addition, the American scientists composed a computer program that tracks single and dividing cells during the development. Thus, allowing an insight in the primitive organ development at single cell resolution for the first time ever.

The computer program maps cell movement and cell division and can track cell fate during growth of the embryo, which is nicely demonstrated in their abstract video. Interestingly, the program is able to measure the differences between individuals and generate an average developmental map.

The microscope and computer program are publicly available, along with all their analyses, so everyone can use them. This new tool is not limited to mouse development, but can also be used to explore what is happening on the inside of organoids and 3D culture systems. Other organisms and time scales can also be imaged. On its own, the software can be used to track live cells in many other species, such as the fruit fly, zebrafish and organ explants.

Thus, the development of this new microscope and the corresponding software allow us to explore a whole new world of single cell tracking inside living organisms.

By Lousanne de Wit

Source: McDole et al. (2018). In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single Cell Level. Cell, 175, 859-876

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Machine learning and Citizen Science join efforts for Ecology.

“What is that species?”, you may ask. A machine may know the answer, and your neighbour could have trained it! No, it is not an overstatement. A multidisciplinary group of scientists has recently used Citizen Science to train computerized AI to quickly identify animal photographs collected from the field.

A group of researchers lead by Physicist dr. Marco Willi from University of Minnesota, has recently tested the accuracy of a computer AI in automatically identifying animal photos and used Citizen Science classified data to inform the machine learning process.

The computer AI employed by dr. Marco Willi and his team was able to match the classification made by Citizen Scientists, on nearly 90% of the images. When the efforts of both machine learning and citizen annotations were combined, the group managed to use only a small number of images to further train, or “teach”, the AI to recognize the animals in the pictures.

Ecologists often collect thousands of photos from strategically placed motion sensitive cameras (camera traps), containing images of all kinds of endangered species from the field. What is hard, if not impossible to do, is going through every inch of image collected to identify the animals in the pictures. Using computer AI to help classify camera trap images is not unheard of, but this is the first time Citizen Science was used to both inform the process on its accuracy and train the AI.

In the field of Artificial Intelligence (AI), machine learning is the process through which a computer system “learns” progressively from data, without being explicitly programmed to do so. That means, a machine can be “trained” to analyse the photos and give back the probabilities of what they are depicting. On the other hand, Citizen Science online platforms, like Zooniverse, have been providing researchers with voluntary manpower from interested citizens to help classify their data. Using citizen classified data to “train” he AI can ensure the process is faster.

For the future, the researchers hope that combining machine learning in the Citizen Science process (online-learning) could further improve the time spent analysing these data, and ultimately allow for massive datasets to be analysed.

By Monica Vidal

Source: Willi, M., Pitman, R. T., Cardoso, A. W., Locke, C., Swanson, A., Boyer, A., ... & Fortson, L. (2018). Identifying animal species in camera trap images using deep learning and citizen science. Methods in Ecology and Evolution.

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Hungry Stomachs, Better Future? – Lunch choices at Utrecht University

It’s lunch time at Utrecht University. Where should you go? Fancy a 4€-sandwich in one of the canteens or maybe a salad for 6€ at the Spar? Installing a canteen that is subsidised by either the city or the university to provide cheap and healthy food for students and employees has not crossed Utrecht University’s mind yet. A plaidoyer for more affordable food for everybody on campus!

Habits be habits
Since Utrecht University attracts a lot of international students, there are as many lunch habits as there are nationalities on campus. With lunch, everybody has their special habits: Some like it hot (e.g. the Germans or the Italians) and some like it cold (e.g. the Dutchies or the Norwegians). Some like early, some like it late. Despite the specific lunch habits, generally everybody needs to eat and likes an attractive price. However, not only the lunch consumers have habits, also the ones that arrange the food stick to their routine, in case of Utrecht University, they stick to the market.

Two Paths – Different Outcomes
In Utrecht, the canteen and multiple kiosk are managed by Sodexo, a market-listed food caterer that supplies universities, hospital and even prisons worldwide. Hence, the price for food is mainly regulated by the market as Sodexo’s revenue was recorded around 18 million euros in the year 2014. Therefore, the piece of the “lunch-cake” is always given away to the market. In the Dutch model, the university’s canteen is basically a student’s restaurant. But there is a cheaper and more social way to serve food for students!

In Germany, for instance, universities’ canteens are subsidised within an institution called Studierendenwerk. The money comes from several parties: the state, the city, the university and also students themselves (embedded into the tuition fees). Further, price categories have been established in a way that students pay the least, followed by employees and external visitors. Consequently, the food can be made available in an affordable way for all social classes and the revenue is recycled back into projects for students such as housing or cultural events.

Affordable lunch? Involvement is needed
So apparently other parties need to get into the picture here. If not the state, then the city should at least care, right? Since students play a substantial part in the economic development of the city of Utrecht, the city council should consider taking better care of their money machines. Unfortunately, the issues of student housing in which the majority of students had troubles finding a suitable and affordable place to live showed many of us the little caring face of Utrecht in the past. So, if change should happen, the students themselves would need to get involved. Involved in protests against profit-oriented food stores such as the Spar. Or in full boycotts of Sodexo’s 4€ sandwiches.

But wait a minute! Protests? Boycotts? Active involvement? The students would need to get up from their comfortable library chairs and actually care about this issue…
Well, maybe a 4€ sandwich does not sound so bad after all.

By Janna Einöder

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Researchers are Step Closer to Bioprinting Organs from Patient Skin Cells

Researchers recently showed that they are able to successfully bioprint a stem cell type that has great potential for engineering bodily tissues, but that could not be printed before. This finding advances the field of regenerative medicine and personalized medicine.

The researchers were able to print induced pluripotent stem cells. These are stem cells that used to be adult cells; they have been manipulated to become stem cells that can develop in each cell type. Stem cells can also proliferate unlimitedly, making them an attractive source for tissue engineering. In theory, a patient’s skin cell can be altered to become a stem cell and this then can be used to replace diseased tissue.

Although promising, these promising cells are very sensitive to changes in their environment. Both their biochemical and mechanical surroundings can affect the efficiency of these cells. During most types of bioprinting cells are exposed to forces, as they are extruded through a nozzle. Hence, it is often not possible to bioprint induced pluripotent stem cells and maintain them after printing.

Currently researchers have explored another, nozzle free, bioprinting technique to print the sensitive cells. They use the help of a laser pulse to selectively deposit drops of cells mixed within a biomaterial (the mixture is called a bio-ink). In this way 3D structures of cell containing biomaterials can be generated by a layer-by-layer manner, without the cells being subjected to extensive forces.

Interestingly, the researchers showed that induced pluripotent stem cells survive well after being laser bioprinted, which was published in the journal ‘Biofabrication’. After printing, the cells were still able to become other cell types, which is an important characteristic for these cells. Nevertheless, the biomaterial the cells are mixed within is crucial for this outcome. The researchers found a biomaterial that works for the cells, but the printed structure is still suboptimal in terms of strength.

The researchers note that their findings have promises for regenerating tissues and innovative disease modeling. However, they also point out that steps have to be taken in optimizing the biomaterial to make the process applicable to the clinic. Regardless, this research did show the potential of bioprinting highly clinically relevant stem cells.

By Marleen Kristen

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