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Laxmi Mishra has used weed Arabidopsis thaliana as model organism in her research about proteases. Photo: Anna-Lena Lindskog
Climate change with its extreme temperatures and fluctuating precipitations is affecting agricultural land conditions and crop yields. Therefore it is essential to understand and improve the details of plant growth. Laxmi Mishra has developed new knowledge about a family of chloroplast proteases called FtsH. She is defending her dissertation at Umeå University.
Proteases are proteins that degrade other proteins; they either clean the cell from malfunctioning enzymes, activate them or generate signals. Hence its the inevitable fate of a protein to meet a protease in its lifetime.
“While the importance of proteases for cell survival and for various diseases is well known, my work deals with inactivated proteases (pseudo-proteases), which therefore could be seen as “anti-heros””, Laxmi laughs.
Laxmi Mishra’s work focuses on a family of proteases called FtsH, which are present in human, animals, plants and bacteria. She is using the annual weed Arabidopsis thaliana as model organism. Plants do not only contain active FtsH proteases, but even some with mutations rendering them proteolytically inactive (termed FtsHis; i for inactive).
“Even though these enzymes are not functioning as proteases, we found them to be extremely important for the survival of plants.” says Laxmi.
Laxmi Mishra used molecular biological, biochemical and physiological methods to reveal the role of these inactive FtsH pseudo-proteases. She compared wild-type Arabidopsis thaliana plants with mutants depleted in single FtsHi proteins and exposed these plants to various stresses in controlled laboratory conditions, but even outside in the field.
Interestingly, Laxmi found that absence of one of the Ftshi enzyme improves drought tolerance in Arabidopsis thaliana. In a collaborative study carried out partly at UC Berekely/USDA in Professor Devin Coleman-Derr lab, she showed that the mutant plants sense the drought stress, but do not act according to it.
About the dissertation:
On Thursday, the 2nd of December, Laxmi Mishra, Department of Chemistry at Umeå University, defends her PhD thesis titled FtsH metalloproteases and their pseudo-proteases in the chloroplast envelope of Arabidopsis thaliana. Her supervisor is Christiane Funk who is associated group leader at UPSC.
The dissertation takes place at 14.00 in Glasburen, KBC Building, Umeå University and be live broadcasted via Zoom. Faculty opponent is professor Catherine de Vitry, Institut de Biologie Physico-Chimique, Sorbonne University, France.
For more information, please contact:
Laxmi Mishra
Department of Chemistry
Umeå University
E-mail:
Phone: +46 90 786 60 13
Text: Anna-Lena Lindskog
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Building up a greenhouse in Nepal (Photo: Dhurva Gauchan)
Last week, SLU Global awarded Rosario García Gil from UPSC with seed funding for a collaboration project with Associate Professor Dhurva Gauchan from Kathmandu University. They plan to start a programme to sustainably marketize local medicinal plants from Nepal and such preserve such plants from extinction. Local communities will be the basis of the project. They shall be provided with knowledge and skills about plant nursing and marketing.
Many medicinal plants in Nepal are on the risk of extinction because of overexploitation for medicinal uses. The project of Rosario García Gil and Dhurva Gauchan aims on preventing species extinction and reducing the negative consequences of it on the local communities. Their idea is to involve the local communities in the preservation of endangered plants by training them on how to grow and nurse these plants in a sustainable way. In parallel they will be introduced to marketing and connected to national and international markets to enable them to rise an income by selling the plants.
“The indigenous people in Nepal are directly dependent on plant resources for food, shelter, medicine, and other needs which is one of the big reasons behind forest destruction and environmental degradation,” says Rosario García Gil, researcher at UPSC and Swedish University of Agricultural Sciences. “We hope that we can counteract this development by activating this programme.”
One of the competence-building activities will be a training programme on herbal cultivation and nursery management for school children and local communities. The researchers plan to build a school medicinal plant garden. The students will be responsible for looking after the plants as part of their extra-curricular activities. This shall provide them not only with knowledge and gardening skills but also help to develop a bond with nature.
“My role has been to design the project and raise the funding. Now my colleague Dhurva Gauchan will take care of the operative aspects. Basically, he will conduct the project and I will supervise it”, explains Rosario García Gil. “I especially plan to keep an eye on the involvement of women. We want to ensure a fifty percent female participation as they are more disadvantaged in Nepal. If this project can help to improve their situation a little bit for example by facilitating them to start their own micro business by cultivating and commercializing medicinal plants, I will call the project successful.”
SLU Global awarded in total six of twenty submitted projects initiated by SLU employees. The projects are transdisciplinary and incorporate strong collaborations with researchers and practitioners in low-income or lower middle-income countries. The goal of the annual call from SLU Global is to support SLU’s work for global development and contribute to the UN’s sustainability goals and Agenda 2030.
Title of the project: Rescue, collection, and conservation of rare, endangered and threatened medicinal plants of Nepal
More information about SLU Global
For questions, please contact:
Rosario García Gil
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
E-mail:
Twitter: @GarciaGilllab1
https://www.upsc.se/rosario_garcia
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PhD student Evgeniy Donev
Evgeniy Donev, PhD student in Ewa Mellerowicz group at UPSC, investigated different modification strategies to genetically improve hybrid aspen for biofuel production. The idea is to make sugars in wood cell walls that are the basis for biofuel production, better accessible by modifying the cell wall structure. Based on his results, Evgeniy Donev suggests using gentle modifications restricted to certain tissues and test them both in the greenhouse and under field conditions. He also advices to be cautious when introducing fungal proteins because they can trigger an immune response just by its presence. Evgeniy Donev will defend his PhD thesis at the Swedish University of Agricultural Sciences on Tuesday, 16th of November 2021.
How did you get to know about your PhD project and what aroused your interest in it?
Nicolas Delhomme and Nathaniel Street from UPSC were teachers of mine during my master’s degree in Civil Engineering in Biotechnology at Umeå University. Via a student bioinformatic project, I met my PhD supervisor Ewa Mellerowicz. Already during my studies, I realized that I do not only want to do bioinformatics but also know more about the biology behind. Ewa Mellerowicz planned a whole series of experiments and wanted to analyse them with a broad range of different techniques including also complex methods that produce a vast amount of data and require some bioinformatic knowledge. I was very interested in this and when I finished my master thesis in her group, I did not want to finish the project. Luckily, she thought the same and offered me to continue as a PhD student.
You chose as subtitle of your thesis “From design to the field”. Why do you think is this important?
My thesis addresses several problems important for improving trees - in our case hybrid aspen - for biorefinery and biofuel production. We identified the best engineering strategies based on experiments in the greenhouse and outside in the field. To evaluate the performance of promising genetically improved plants, it is important to test them in an environment which represents their usual cultivation conditions. In many cases, genetically modified plants grow well in the greenhouse but show undesirable reactions in the field conditions where they must cope with a multitude of different stresses like drought or pathogen attacks. Such undesirable reactions or off-target effects can erase all positive effects coming from the gene modification.
What is the best engineering strategy to modify hybrid aspen trees for biofuel production?
We investigated a collection of hybrid aspen in which cell wall properties were modified in different ways to make cellulose and the contained sugars better accessible for biofuel production. Trees in which the modification was introduced to the whole plant developed stronger off-target effects than trees in which the modification was restricted to certain tissues of the plant like for example the wood.
Some of our trees grew better in the greenhouse and in the field. The relative sugar amount that we extracted from those trees was not much higher than in non-modified trees, but they contributed with more biomass. So, the total amount of sugars was higher. On the contrary, we saw that we lose already all wins gained through the modification when the modified trees grew twenty percent less than non-modified trees. Our conclusion is that nothing can replace reduction in growth, and we should therefore choose gentle and more specific engineering strategies.
Which of your results was the most unexpected for you?
We expressed a protein from a wood decaying fungus in hybrid aspen that is supposed to loosen up the cell wall structure and thus make cellulose better accessible. It looked like the improvement worked because we could extract more sugar from these trees, but the off-target effects were really strong. The trees were dwarf, dropped their leaves very early and showed strong immune defence reactions. Only when we restricted the activity of the protein to the wood, all off-target effects were avoided, and the plants looked normal. However, I started to wonder if just the presence of the fungal gene could be recognised by the plant and trigger an immune response. To test this, we introduced an inactive version of the protein into hybrid aspen, and we saw the same strong effects on the plant. It turned out that the protein we introduced is recognized by the plant as pathogenic and causes an immune response. Sugars are remobilized as part of this response to supply the plant immune system with the necessary energy, which could possibly affect the sugar concentration extracted from the wood of these plants.
What were the biggest challenges you faced during your PhD?
My group is focussing on cell wall formation in the wood and not on plant-pathogen interaction. It was very challenging to convince them that the changes we saw in those trees in which the fungal protein was active all over the plant, is coming from the reaction of the immune system and not from the activity of the introduced fungal protein. I had to dig deep into the available literature and develop my analytical skills, think through my story thoroughly and keep on discussing with my group. I am very grateful to Ewa Mellerowicz because her support and trust in my skills combined with her positively demanding attitude was motivating me a lot during this time.
What are you planning to do now?
Research in plant science will be in one way or the other part of my future, not least that I see that there are many open questions that are not answered yet. I plan to stay in the group of Ewa Mellerowicz for the next year. We have several very exciting projects which we are currently working on, and I hope that we generate useful knowledge that helps to better understand the complex plant system.
About the public defence:
Evgeniy Donev, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, will defend his PhD thesis on Tuesday, 16th of November 2021. Faculty opponent will be Sharon Regan, Department of Biology, Queens University, Kingston Ontario, Canada. The thesis was supervised by Ewa Mellerowicz. The dissertation will be live broadcasted via Zoom.
Title of the thesis: Modification of forest trees by genetic engineering - From design to the field
Link to the thesis: https://pub.epsilon.slu.se/25690/
For more information, please contact:
Evgeniy Donev
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
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Stefan Jansson (top left; photo: Fredrik Larsson), Karin Ljung (top middle; photo: Fredrik Larsson), Petra Marhava (bottom left; photo: Peter Marhavy), Ewa Mellerowicz (bottom middle) and Olivier Keech (right; photo: Fredrik Larsson)
The Swedish Research Council granted last week four projects from UPSC. Stefan Jansson, Karin Ljung and Ewa Mellerowicz received a project grant and Petra Marhava receives a starting grant to establish her own group at UPSC. All four will address basic research questions aiming on understanding plant development and their interaction with their environment. In addition, Formas approved one applied project the week before where Olivier Keech is involved and that aims to use artificial intelligence to make urban food production more sustainable.
Stefan Jansson, professor at the Department of Plant Physiology at Umeå University, focuses in his research on the mechanisms that allow trees to survive the winter. The new project is based on previous research. It aims to use a systems biology approach to understand how autumn leaf senescence is regulated on the molecular level. A second part of the project focusses on a novel regulatory mechanism that allows conifers to keep their needles green during winter. Stefan Jansson and his group want to look deeper into this mechanism in conifer trees and also try to see which role it plays in leaf shedding trees.
The group of Karin Ljung, who is professor at the Department of Forest Genetics and Plant Physiology at SLU, is researching on root development and shoot-root communication. In the new project, they will investigate how lateral roots are initiated focusing on the processes that are happening within the root cells, particularly on the role of the different cell compartments. They aim to develop new methods to analyse plant growth regulators, metabolites, proteins and gene activity on the cellular and subcellular level in the model plant Arabidopsis thaliana to better understand the complex interplay between these components during later root initiation.
Petra Marhava, who is currently working as researcher affiliated with Stéphanie Robert’s group at SLU, is also working with Arabidopsis thaliana roots but wants to understand how cold or heat stress affects the transport of auxin, a plant growth regulator involved in root formation. High or low temperatures change the physical properties of the cell membrane and Petra Marhava wants to see with the help of advanced imaging techniques how these physical changes influence auxin transport components that are integrated in the cell membrane. A second part of the project focuses on identifying those genes that are activated during temperature stress and that coordinate auxin transport in different root cells.
The project from Ewa Mellerowicz, who is professor at the Department of Forest Genetics and Plant Physiology at SLU, is based on a recent finding that she and her group made. They found so far unnoticed lipidic compounds in the cell walls of wood and want now to characterize these compounds further. They want to investigate which role these compounds play in the wood cell walls, how they are synthesized and to develop methods to efficiently extract them. Their hope is that this knowledge will help to reduce damages to the machinery in biorefineries that are caused by such lipidic compounds but also develop new products derived from wood like for example natural waxes or environmentally friendly packaging.
The applied project that was granted by Formas, the Swedish Research Council for Sustainable Development, comprises several partners from industry and academia and is designed in partnership with the municipality in Boden, in Northern Sweden. The goal is to improve energy fluxes in a large-scale symbiosis project, called the Boden Symbiosis Cluster, by using artificial intelligence. Energy, in form of heat and low-heat waters, that is released from server halls and other local industries shall be channelled into an aqua-agro farming system to establish a sustainable food production site.
Olivier Keech, associate professor at the Department of Plant Physiology at Umeå University, will focus on the plant components of the project while his colleagues from Luleå University of Technology (LTU) and Swedish University of Agricultural Sciences will concentrate more on microbial and animal production systems. Together with the division of Machine Learning at LTU, they will integrate the different energy flows using artificial intelligence to improve sustainability and cost-efficiency. They hope to create an urban food competence platform of commercial size that can be used for implementing and testing innovative solutions for future food production systems.
The four projects approved by the Swedish Research Council within Natural and Engineering Sciences:
• How do trees survive winter?
Stefan Jansson
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/stefan_jansson
• Cell type and organelle specificity in cytokinin and auxin signalling and metabolism during Arabidopsis lateral root initiation
Karin Ljung
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/karin_ljung
• How plants deal with heat and cold: molecular mechanism of auxin transport in response to temperature stress
Petra Marhava
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
• Wood suberin? Unravelling biosynthesis and chemical structure of wood lipophilic compounds
Ewa Mellerowicz
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Umeå University
Email:
https://www.upsc.se/ewa_mellerowicz
The Formas project in the call on “From research to implementation for a sustainable society”
• AI for improved efficiency and sustainability of closed land-based integrated food production Systems – a case study in Boden project – iCFPS (intelligent Circular Food production Systems)
Olivier Keech
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/olivier_keech
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Anne Bünder (right) together with her supervisor Totte Niittylä (left) after the defence (Photo: Anne Honsel)Nanocellulose forms the basis of many novel materials and is used already now for a wide range of different applications. Anne Bünder, PhD student in Totte Niittylä’s group, investigated how wood properties influence the extraction of nanocellulose from wood material. She showed that modification of cellulose and the amount of lignin influence the efficiency of the nanocellulose extraction. Anne Bünder has defended her PhD thesis at the Swedish University of Agricultural Sciences on Friday, 29th of October 2021.
Different raw material resources have been already tested for nanocellulose production but not much was known about how the chemical composition of the wood source affects the yield and final properties of nanocellulose. In close collaboration with material scientists from Luleå University of Technology, Anne Bünder examined in her PhD how modified chemical structures of wood influence the efficiency of nanocellulose production. She used material from genetically modified hybrid aspen trees in which the cellulose synthesis is impaired and from trees that have naturally different composition of the three main components of wood - cellulose, hemicellulose and lignin.
The modified trees were mechanically weaker
“We used hybrid aspen trees in which a protein that is involved in cellulose biosynthesis is genetically reduced. This protein makes sure that the cellulose fibres are aligned correctly in the primary cell wall, but it is not clear if it also plays a role for secondary cell walls,” explains Anne Bünder. “We saw that the wood of these modified trees is mechanically weaker, but we could not see any changes in wood anatomy. Also the cell wall structure in the secondary cell wall, which contributes most to the mechanical performance of wood, was not changed. So, we were wondering if this protein is really needed for a proper alignment of cellulose in the secondary cell walls.”
In wood, cell walls consist of different layers. The outer layer is the primary cell wall which is much thinner and more flexible than the more rigid secondary cell wall that consist of three layers. In each cell wall layer, cellulose macrofibrils are aligned together with hemicellulose, lignin and proteins in a specific pattern that provides mechanical strength and also flexibility. Long glucose chains are the building blocks of cellulose microfibrils which bundle together to cellulose macrofibrils.
Cell wall features of the trees affect nanocellulose properties
When the researchers searched further for explanations for the mechanical weakness, they noticed that the cellulose chains in the modified trees were shorter, and this also affected the properties of cellulose nanofibrils. This fibrous form of nanocellulose is obtained when cellulose microfibrils from wood material are mechanically disrupted during nanocellulose extraction. Different methods are used to extract nanocellulose from wood material and the properties of the resulting nanocellulose depend on the used method.
“When we used wood material from those trees to isolate nanofibrils, we ended up with a lower amount of fine nanofibrils and we think that this is related to the structural differences of the cell wall,” says Anne Bünder. “We also saw that the isolated cellulose nanofibrils were shorter like the cellulose in the cell wall. This demonstrates that also cell wall properties and cellulose structure of the wood material used to manufacture nanofibrils are influencing the efficiency of the nanocellulose production process and also the final properties.”
Lignin might facilitate nanocellulose extraction from wood
In a next step, the researchers wanted to see if also other wood components affect the nanocellulose production. They used wood from field grown hybrid aspen trees that contained different amounts of lignin and they also used a naturally occurring phenomenon to induce changes in the wood composition. When trees that are bend down grow, they produce wood with more cellulose, longer cellulose chains and less hemicellulose and lignin on the outer side of the bending. The researchers used such wood material to produce nanofibrils and assumed that the higher amount of cellulose and a lower amount of lignin will make the isolation of nanofibrils easier. However, the opposite was the case.
“Cellulose is the component of interest for industry, and the common opinion is that a lot of lignin is making cellulose less accessible. Our results put lignin into a completely new light,” explains Anne Bünder. “Our hypothesis is that the cell wall becomes more porous when lignin is removed which is one of the first steps in nanocellulose production. The more lignin in the cell wall, the more porous the cell wall gets when it is removed making cellulose better accessible in further treatments.”
The researchers think that these results open up new opportunities for tree breeding programs. So far, the focus was set on reducing lignin or changing its structure in the wood to make cellulose better accessible for extraction, but this was often on expense of tree health and viability. The new findings illustrate that lignin might not be such a big problem for nanocellulose extraction as thought so far. They also show that a better understanding of the composition of wood can help to improve the isolation and also the performance of nanocellulose extracted from this material.
From wood to nanocellulose: a scale guide (figure created by Anne Bünder with BioRender.com)About the public defence:
Anne Bünder, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, has defended her PhD thesis on Friday, 29th of October 2021. Faculty opponent will be Ingo Burgert, Institute for Building Materials, ETH Zurich, Switzerland. The thesis was supervised by Totte Niittylä. The dissertation was live broadcasted via Zoom.
Title of the thesis: The biology and properties of wood for nanocellulose production
Link to the thesis: https://pub.epsilon.slu.se/25573/
For more information, please contact:
Anne Bünder
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
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Emmanuelle Charpentier, Nobel laureate and mentor of the new 'Excellence by Choice' Postdoctoral Programme (photo: Hallbauer&Fioretti)
Umeå University is establishing a postdoctoral programme in Life Science research to attract prominent young researchers and stimulate cutting-edge research. Umeå Centre for Microbial Research (UCMR) is managing the programme in collaboration with UPSC and other research centres. The mentor for the new programme will be Nobel laureate Emmanuelle Charpentier, who was affiliated with The Laboratory for Molecular Infection Medicine Sweden (MIMS) and UCMR and discovered the ground-breaking CRISPR-Cas9 gene editing technology during her time in Umeå.
The aim of the new programme ‘Excellence by Choice’ Postdoctoral Programme (EC Postdoctoral Programme) is to strengthen world-class research activities in Umeå and attract excellent young researchers. UCMR and UPSC, the two national Centres of Excellence, are launching the life science programme in collaboration with other research centres. 17 new postdoctoral researchers will be recruited to Umeå over a five-year period. The objective is to train next-generation scientists and encourage new synergies and collaborations to strengthen life science research in Umeå.
“We are very grateful to Emmanuelle Charpentier who serves as the patron and mentor of the programme. She was one of the first MIMS group leaders and was active within UCMR when she was working in Umeå. We were very proud of her when she received the Nobel Prize in 2020,” says Yaowen Wu, director of UCMR. “Her role model is inspiring us a lot in our research and will inspire more next-generation scientists in the future.”
The two national Centres of Excellence in Umeå, UCMR and UPSC, have joined their forces to attract funding for this new programme. The research focus will be on molecular and translational life science research with the goal to enhance international competitiveness. The postdoctoral researchers will receive a two-year fellowship and additional funding for project running costs as well as for their career development. This individual support will be complemented with jointly organised programme activities to extend the networking and collaboration possibilities for the young researchers.
“Postdoctoral researchers are an important part of the research landscape in Sweden, and we aim to strengthen their competence by providing them with good work conditions”, emphasizes Ove Nilsson, director of UPSC. “It might look on the first hand that UCMR and UPSC do not have much overlap research-wise, but we believe that our collaboration creates new and innovative synergies that will be beneficial not only for the involved postdoctoral researchers but for all our researchers.”
The new Excellence by Choice programme is largely financed with donations from the Knut and Alice Wallenberg Foundation and the Kempe Foundations, as well as with direct funding from Umeå University and the Swedish University of Agricultural Sciences (SLU). It is managed by UCMR and based on the format of a previous programme that was established at MIMS. The former programme started in 2015 and provided already several young researchers the opportunity to conduct postdoctoral research at Umeå University.
The programme has opened a call for postdoctoral projects to Principal Investigators:
Read more about the open call and the postdoctoral programme on the UCMR homepage
Link to the Swedish news on the Umeå University homepage
For more information, please contact:
Yaowen Wu
Umeå Centre for Microbial Research
Department of Chemistry
Umeå University
Phone: + 46 (0)90 786 5531
e-mail:
https://www.umu.se/en/staff/yaowen-wu/
Ove Nilsson
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Phone: +46 (0)90 786 8487
e-mail:
https://www.upsc.se/ove_nilsson
Text: Ola Nilsson, Anne Honsel
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Judith Lundberg-Felten presenting her research at the Researcher's Night Stand-up Comedy (photo: Gabriella Beans Picón)
How funny can science be? Judith Lundberg-Felten and four other scientists showed their comedy skills in the first science-themed stand-up comedy show in Umeå and entertained the audience with stories from their life as a researcher. The event was arranged, as part of the Researchers Night at Curiosum, Umeå’s science centre, and took place on the last Saturday in September.
Can the relationship between tree roots and fungi teach you how to date online? What do design anthropologists learn from being followed by a masked man? Can you explain the evolution of complexity with your family’s history? What can you learn from guerrilla gardening about “transdisciplinary” design, and can snails help you to cope with stress? Using daily life stories, the five scientists comically explained their research in eight minutes and made the audience laugh.
“It was a lot of fun and exciting to be part of Researchers’ Friday Stand up," says Judith Lundberg-Felten, group leader at UPSC. "It is a new way to talk about my research and rewarding to experience how positively the event was received by the audience. Such events are an excellent opportunity for me as a researcher to continue building a trustful relationship with society."
"We attracted especially young adults to this event, a group that we have previously not reached with other outreach formats," continues she. "I want to encourage also other people working in science, irrespective of position or age, to participate in such events. It’s an inspiring experience for the presenter and a fantastic way to keep fostering our interaction with people that may eventually become the decision-makers of tomorrow.”
The overall goal of the Researchers’ Night is to bring research closer to the public and show that researchers are just ordinary people even though their jobs might be extraordinary. The concept for the stand-up comedy derived from the comedy club Bright Club from St Andrews University in Scotland. The organizers from Curiosum worked close together with the people from Bright Club and offered an online workshop on comedy stand-up to the researchers followed by repeated rehearsals. The show on the 25th of September was moderated by comedian Monica Lindgren.
The full Stand-up comedy show was recorded, and you can still watch it on YouTube:
Researcher’s Night Stand-up Comedy in Umeå
More about the Stand-up comedy event at Curiosum and interviews with all five participants:
https://www.curiosum.umu.se/en/discover/aktuella-evenemang/past-events/forskarfredag-2021/standup/
https://www.umu.se/nyheter/stauppkomedi-gor-forskning-roligare_10945335/ (in Swedish)
More about the Researchers Night:
https://www.curiosum.umu.se/upptack/aktuella-evenemang/sparade-evenemang/forskarfredag-2021/ (in Swedish)
https://forskarfredag.se/researchers-night/
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From bud burst to bud set: The different stages of the annual growth cycle in a juvenile aspen tree (Illustration: Domenique André).
Why are flowering genes important for non-flowering young aspen trees? PhD student Domenique André started to work in Ove Nilsson’s group because she was interested in flowering, but the research led her to studying the annual growth cycle. She showed that key genes that regulate flowering in other plants are crucial for proper bud set and burst in young aspen trees and they control growth during summer. Domenique André will defend her PhD thesis at SLU on Friday this week, 27th of August.
You came to UPSC as Bachelor student about ten years ago and did your master thesis at UPSC. How does it feel to finish your PhD now after all this time?
It is a weird feeling, like “the end of an era”. I have been here now for nine and a half years. UPSC is the place where I grew up academically and scientifically and it feels like my home in a way. And because of that, I also tried to give back as much as possible. For example, I was PhD representative of my department and attended the UPSC Board meetings. I also helped organising events and participated in various outreach activities like Soapbox Science and Fascination of Plants Day. I will miss UPSC for sure.
In your thesis, you studied the annual growth cycle in aspen trees concentrating on the molecular regulation. What interested you about this project?
I started in Ove Nilsson’s group during my master. At that time, I was mainly interested in flowering, and he was the only person working on it at UPSC. But then, Ove’s group started to shift focus from flowering towards the annual growth cycle because it turned out that the genes we were focussing on played a different role in aspen. So, I kind of slipped into this topic together with the group and the flowering topic moved more to the side. To be honest, it took me some time to understand how the annual growth cycle works because I had no previous experience with trees. Aspen trees look very different after they have gone through the first growth cycle and there were big changes between the start and the end of our experiments. That can be confusing. I tried to illustrate this in my thesis: why the growth cycle exists, what stages the tree goes through and how all this is regulated. I really enjoyed the time during my master thesis in Ove’s group and we both agreed that it would be cool if I could continue the project during my PhD and in the end, there is even a little bit about flowering included in my PhD thesis.
You focussed in your research on FLOWERING LOCUS T genes which are most known for their role in regulating flowering, but you studied their role in non-flowering juvenile aspen trees. What are your key findings?
The key findings are that the FLOWERING LOCUS T or FT genes have mainly functions unrelated to flowering but rather control the annual growth cycle in juvenile aspen trees. There are in total three FT genes in aspen. The first one, FT1, is important during winter and makes sure that the tree can wake up from its dormancy during spring. The other two, we call them FT2a and FT2b, are important during summer making sure that the tree grows. Whether they are involved in flowering at all in nature is currently not clear.
What makes it so difficult to prove that the FT genes are important to regulate flowering in aspen?
When we enhanced the gene activity of either of the three FT genes by mutation, the trees started to flower very early. Those flowers did not look normal and were sterile. This is the one flowering part in my thesis. But just because we could induce flowering with more FT, it does not mean that FT is important for flowering in nature. To prove that FT is indeed required, we would have to block FT activity and show that flowering is delayed or doesn’t occur at all. And we have indeed removed FT activity with the CRISPR-Cas9 technology, but the problem is that flowering takes too much time. A normal tree will flower only after 5 years (if you’re lucky), so how long would we have to wait to see it in our mutants? And given how important FT is for the annual growth cycle, it is unlikely that the mutated trees would survive for so long anyway.
Which of your results was most surprising for you?
We did not know that there were two FT2 genes when I started. When we wanted to block the FT2 gene activity using the CRISPR technology, it worked perfectly. We had no FT2 gene activity, but the trees looked absolutely normal. That was really surprising because we knew from mutant lines with reduced gene activity that even if you have only twenty percent of the expression left, you get a very significant effect and in our CRISPR lines there was nothing. It turned out then that there was a second copy of the FT2 gene and when we blocked the activity of both genes at the same time, we got a really, really strong effect. The trees were just around five centimetres tall and almost do not grow. They are alive and they can be propagated in tissue culture, but they grow very slow. This shows that the genes are very important for the trees.
Studying aspen can be demanding because it can be very time-consuming. Was this the biggest challenge you faced during your PhD?
Yes, indeed. People studying wood for example grow their trees in the greenhouse for about two to three months. For us, it takes ten months to do one growth cycle experiment. We simulate the seasons in a growth chamber by adjusting daylength and temperature so that we can see the different seasonal stages on the trees like bud set and bud burst. The most limiting factor during my PhD was the lack of space in growth chambers because I could only do one of these long-lasting experiments at once. I had no problem keeping myself busy with other things while waiting for the experiment to be done but it took very long to get results and move on with my research questions. It was also challenging to decide which experiment to focus on and to plan them very detailed to get as much out as possible, but I learned a lot and became more independent. Overall, I liked my time as a PhD student. I felt it was a nice and relaxed time and I got the freedom to do what I wanted.
What are your plans now? Would you like to stay longer at UPSC?
I will stay at UPSC until the end of the year to hopefully get our manuscripts out. After that I will see. I would like to stay in Umeå, and I like to work in the university environment. I am very interested in teaching and took basically all teaching courses that I was allowed to take as a PhD student. I would love to be a lecturer or head of a lab. I would like to learn new things and develop, but also do something I’m already good at. I’m sure I will find something fun.
About the public defence:
Domenique André will defend her thesis on Friday, 27th of August 2021 in P-O Bäckströms sal at SLU Umeå. Faculty opponent will be Professor Soraya Pelaz from the Centre for Research in Agricultural Genomics in Barcelona, Spain. Supervisor is Ove Nilsson. The dissertation will be live broadcasted via Zoom.
Title of the thesis: Molecular Regulation of the Annual Growth Cycle in Populus Trees
Link to the thesis: https://pub.epsilon.slu.se/24748/
For more information, please contact:
Photo: Rory Shelton
Domenique André
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
Twitter: @FloweringLocusT
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Using cryoelectron microscopy, Umeå researchers have succeeded in producing a high-resolution image of photosystem II in the plant thale cress. Image: Wolfgang Schröder, © 2020 andre
For the first time, Umeå researchers have, with the help of cryogenic electron microscopy, succeeded in producing a high-resolution image of photosystem II - the central complex of photosynthesis - of the model plant Arabidopsis. The enormous complex is responsible for the vital oxygen production in photosynthesis that once made life possible on our planet. The study is published in Scientific Reports.
"The structure gives us detailed information about the various cofactors such as chlorophyll and the lipid molecules in photosystem II. We have also managed to show exactly where and how detergents bind and affect the stability of the complex," says Wolfgang Schröder, professor at the Department of Chemistry at Umeå University Sweden and associated researcher at UPSC, who led the study.
The plant researchers' "experimental rat" has for the past 25 years been the plant thale cress/mouse-ear cress Arabidopsis thaliana. The reason for this is that this "weed" grows rapidly even at our northern latitudes in Sweden and in 2000, researchers succeeded in sequencing all its genes.
At the heart of the photosynthetic process is the Photosystem II complex. It contains almost 30 different proteins and a number of cofactors such as different pigments and metals and it is without any doubt one of the largest complexes in plant chloroplasts. The now published structure from this study has the same high-resolution as the two previous structures obtained from spinach and pea, which for the first time enables a comparison of plants' photosystem II complex with the same level of detail.
"I have worked with this complex since I became a PhD student in plant protein chemistry at Lund University in 1983,” says Wolfgang Schröder. “I remember that as a doctoral student I joked at the coffee break “think if you could dive into photosystem II and look around”. Today, with new technology and my extremely talented doctoral student André Graça and my two fantastic research colleagues Michael Hall and Karina Persson, we have now been able to do this."
Karina Persson, André Graça, Wolfgang Schröder and Michael Hall (from left to right) constitute the successful research group at Umeå University. Photo: André Graça
The technology that the researchers have used is called cryogenic electron microscopy (Nobel Prize in Chemistry 2017) and it briefly means that biological samples are shot down into liquid ethane (-190 degrees Celsius). Nearly 100,000 two-dimensional EM particle images from random orientations are selected. Using several computational resources, the collection of 2D images can then be used to reconstruct a three-dimensional structure.
"Additionally, it was extremely exciting to see if our previous biochemical analyses of the complex were correct. Usually, the privilege of publishing structures with this size and resolution is only possible to larger research teams from different laboratories, as it requires a lot of data, time, and effort. In our case we are four Umeå researchers within the network Integrated Structural Biology, ISB, who created this structure, so it is "locally" produced research," says Wolfgang Schröder with a smile.
See moving image on the photosynthesis complex
The research is mainly funded by the Carl Tryggers Foundation. Data were collected at Umeå Core Facility for Electron Microscopy, UCEM, which is part of the National Microscopy Infrastructure, NMI.
About the scientific study:
Graça, A.T., Hall, M., Persson, K. and Schröder W.P.: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin extraction. Sci Rep 11, 15534 (2021).
https://doi.org/10.1038/s41598-021-94914-x
More reading:
About Umeå Core Facility for Electron Microscopy
The network Integrated Structural Biology, ISB
About cryo-Electron microscopy and the Nobel prize 2017
For more information, please contact:
Wolfgang Schröder
Department of Chemistry
Umeå University
Email:
Phone: +46 90 786 69 74
https://www.umu.se/en/staff/wolfgang-schroder/
https://www.upsc.se/wolfgang_schroder
André Graça
Department of Chemistry
Umeå University
Email:
Phone: +46 90 786 66 87
https://www.umu.se/en/staff/andre-graca/
Text: Ingrid Söderbergh
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Photo: Kanchan Vishwakarma
Raghuram Badmi, postdoc in Judith Lundberg-Felten’s group at UPSC, was granted a Career-Fit PLUS fellowship from Enterprise Ireland, an Irish governmental organisation that leads the national support network for Horizon Europe. The fellowship will be for three years and is oriented on experienced researchers to work on applied research projects. Raghuram Badmi will study how Botrytis cinerea, a fungus, causes fruit rot in strawberries. He will start his new position in autumn this year in Cork, Ireland.
What was motivating you to apply for this competitive fellowship and how did you choose your project?
Raghuram Badmi: One of the main attractive features of this Career-Fit Plus fellowship is that it is designed for researchers who want to transition into industry as a ‘Marie Skłodowska-Curie Fellow’ as well as a ‘Career-FIT PLUS Fellow’. I realized that my skill set could be valuable in developing solutions to agricultural problems and this fellowship provided me with the right platform to act as a bridge between the academic university and the company partners. My previous work on strawberry-Botrytis interactions left me with quite a few exciting questions to pursue. I chose the most exciting and most pressing problems that the agricultural sector is currently facing and proposed to solve them by employing advanced techniques such as non-transgenic (footprint-free/DNA-free) genome editing.
With whom will you work in your future project and what do you plan to do?
Raghuram Badmi: The project involves three partners, an academic university partner, the University College Cork, a company partner, Plantedit, and a Technology Center, Shannon ABC, all based in Ireland. The main goal of this project is to develop non-transgenic genome edited strawberry plants that have higher resistance against grey mould disease caused by Botrytis cinerea fungus. The project involves interdisciplinary computational approaches to better understand the strawberry-Botrytis interactions and I also plan to employ some beneficial microbial interactions to improve disease resistance, strawberry growth and yield.
Do you think your experiences from your current research project in Judith Lundberg-Felten’s group will benefit your future project?
Raghuram Badmi: Yes of course, I plan to use my experience in working with mycorrhizal fungus to develop bioinoculant based solutions to improve strawberry growth and disease resistance. In this respect, I wish to continue my association with UPSC by collaborating with my supervisor Judith Lundberg-Felten, whose support and recommendation was crucial in obtaining this fellowship.
Which were the biggest challenges writing your proposal?
Raghuram Badmi: This proposal is the result of at least four years of continuous grant applications and the rejections that followed. I got to learn a lot on how to develop a project that perfectly fits my expertise, develop compelling arguments, and present myself as the perfect fit for the project. I would like to thank my previous supervisors at the Norwegian Institute of Bioeconomy Research, whose guidance on proposal writing was invaluable in developing this proposal.
Do you have some tips for other postdocs or PhD students applying for similar fellowships that are funded by the European Union?
Raghuram Badmi: My suggestions to my younger self would be to identify a specific niche area and develop oneself around it. Writing is hard, and the earlier you start the better. Proposal/grant writing training programs such as for Marie Curie Individual Fellowships, Young Research Talent grants, ERC grants have benefitted me a lot and this could be helpful to many others wanting to apply for fellowships.
Career-FIT PLUS programme is launched by Enterprise Ireland and is aimed for experienced researchers from all over the world to work on research projects that are of interest for Irish enterprises. The fellows will work three years in Ireland hosted by a Third Level Institution, like e.g., a university, that is associated with a Technology Centre/Gateway. During this time, they will have the opportunity to spend a six to twelve months long secondment in a partner company.
The Career-FIT PLUS fellowship programme has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847402.
Read more about the Career-FIT PLUS programme
For more information, please contact:
Raghuram Badmi
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Sweden
Email:
Twitter: @raghubadmi
Text: Raghuram Badmi and Anne Honsel