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Twelve PhD students presented their research projects with short pre-recorded video pitches during the KBC DAYS 2020 last week. The video pitches were the outcome of a course in science communication that the students participated in before. An evaluation committee evaluated all pitches and awarded Lill Eilertsen, PhD student in Judith Lundberg-Felten’s group at UPSC, with the prize for the best presentation.
Every year, the best PhD student presentation is awarded during the KBC DAYS but normally they are presenting their research with a scientific poster. Due to the online format of the KBC DAYS 2020, the organisation committee decided against a poster presentation but instead asked for short pre-recorded video pitches and offered in combination with this a course in science communication. Twelve PhD students affiliated with KBC took the chance and participated in the course. Their video-pitches were evaluated during the KBC DAYS by an evaluation committee of six people and the best presentation was awarded with a travel voucher sponsored by Agrisera AB.
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Photos of Rishikesh Bhalerao (top left), Stéphanie Robert (top middle), Åsa Strand (top right), Hannele Tuominen (bottom left) and Stéphane Verger (bottom right) whos project proposals were granted by the Swedish Research Council in 2020.
On Thursday last week, the Swedish Research Council announced which project proposals in the field of natural and engineering sciences receive financial support in 2020. Five projects from UPSC were approved. Stéphane Verger receives a starting grant and Rishikesh Bhalerao, Stéphanie Robert, Åsa Strand and Hannele Tuominen project grants.
The topics of the five projects from UPSC deal with seasonal growth, cell shape, cell internal communication, lignin biosynthesis and cell-to-cell adhesion. The focus is for all on the molecular level but using different plant model organisms and applying a wide range of different methods. In total, the Swedish Research Council approved this year 324 of 1668 applications in the field of natural and engineering sciences including research project grants and starting grants.
More information about the individual approved projects:
Project: Unravelling the genetic network mediating temperature control of dormancy release and bud break in hybrid aspen
Bud break in perennial trees starts in spring after trees have been exposed to extended period of cold temperatures that release dormancy, followed by a period of increasing temperatures that signal spring onset. The exact timing of bud break is very crucial for the trees to prevent damage to young leaves and meristems enclosed in the buds from sudden late frosts. Rishikesh Bhalerao is researching on how temperature regulates the release of the dormant state to allow bud break in spring. In the approved project, he plans to identify the genetic framework that controls these temperature-mediated processes in the model tree hybrid aspen.
Contact:
Rishikesh Bhalerao
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/rishikesh_bhalerao
Project: Molecular mechanisms regulating shape acquisition in plants
How does a cell receive its final shape? Stéphanie Robert wants to answer this question focusing on leaf epidermal pavement cells. These cells form the outer layer of the leaf and have a very specific jigsaw puzzle shape. The mechanical and chemical properties of the cell wall but also cell internal factors like the plant growth regulator auxin determine the final shape of a cell. In her project, Stéphanie Robert aims at finding new molecular players involved in the development of cell shape and at looking deeper into the interactions between the different factors involved in this development.
Contact:
Stéphanie Robert
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
http://www.upsc.se/stephanie_robert
Project: Establishment of Photosynthesis, a Tale of Two Genomes
Åsa Strand focusses in her project on cell internal communication, specifically on the communication between the chloroplast and the nucleus. The chloroplast is the place were photosynthesis is conducted. Some of the genetic information that is needed for chloroplast development is stored in the nucleus. That is why a synchronised exchange of information between the chloroplast and the nucleus is indispensable for proper chloroplast development. Åsa Strand wants to understand in more detail how this communication between the chloroplast and the nucleus is regulated.
Contact:
Åsa Strand
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email:
http://www.upsc.se/asa_strand
Project: Cell-type specific lignification in plant vasculature
Lignin is used by plants to increase stability and provide a water repellent surface in the water transporting system. However, for industrial applications, it often reduces the accessibility of the favoured cellulose. Hannele Tuominen aims on identifying the molecular mechanisms behind lignin biosynthesis and on characterising lignin composition in different cell types. To understand how and why cell-type specific lignification is established might help to improve the properties of lignocellulosic raw material for bioprocessing.
Contact:
Hannele Tuominen
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
http://www.upsc.se/hannele_tuominen
Project: Mechanics and dynamics of cell-to-cell adhesion in plants
Stéphane Verger focusses in his research on how neighbouring cells in a tissue interact and attach to each other, a dynamic process called cell adhesion. To maintain cell adhesion despite changes in the surrounding is very important to keep a tissue functioning and Stéphane Verger wants to reveal the dynamic mechanisms that are involved in this process. He plans to apply genetical, pharmaceutical but also mechanical and microscopic approaches to understand how cell adhesion is maintained in plants.
Contact:
Stéphane Verger
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
http://www.upsc.se/stephane_verger
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Pieter Nibbering and his PhD supervisor Totte Niittylä after the successful defence (photo: Anne Honsel)
[2020-10-30] Plant cell walls need to be flexible and at the same time rigid to give stability but also allow growth. Glycoproteins, proteins with attached carbohydrates, are only a minor component of the cell wall which consists mainly of cellulose, hemicellulose, pectin and lignin. Nevertheless, modifications of such glycoproteins can have a strong impact on the properties of the plant cell wall. This was shown by Pieter Nibbering, PhD student in Totte Niittylä’s group, who studied cell wall formation in the herbal plant Arabidopsis and in poplar. Pieter Nibbering successfully defend his PhD thesis at the Swedish University of Agricultural Sciences on Friday, 30th of October.
Your thesis focuses on plant cell wall formation in Arabidopsis and aspen. What was interesting you about doing research on cell walls?
I find cell walls very interesting because they so complex. It is very challenging to work with them and I wanted to take on this new challenge. Another reason why I decided for this PhD project was that you cannot just use one or two methods when studying cell walls but need to use many different tools like e.g. molecular cloning, chemistry and protein expression to come closer to an answer of your questions. This diversity was also very interesting for me because it allowed me to learn a lot of different techniques.
You worked with certain glycoproteins that are lesser known components of the cell wall. Why are these glycoproteins important?
That is actually the question we tried to answer during my PhD. We do not know yet why they are important. The difficulty is that approximately 1200 proteins in Arabidopsis are predicted to have this kind of carbohydrates called arabinogalactan glycans attached - not only those ones we worked with. The attached glycans fulfil many different functions. They can e.g. stabilize the protein to make sure that the protein can perform the right function, they can interact directly with the cell wall or with cell wall components or they can bind salts for instance calcium and be involved in signal transduction. For our experiments, we used mutants in which the biosynthesis of some glycoproteins is impaired meaning that the glycans are not added properly to the proteins. The mutants clearly showed growth defects and/or defects in stress response and this let us conclude that the impaired glycoproteins are important for normal growth and stress responses.
Which of your results is the most fascinating for you?
Some of our mutants only showed an obvious difference to our control plants when they were grown under stressful conditions. This is rather what you expect if you modify minor components of the cell wall. However, the growth of other mutants was strongly affected also under optimal growth conditions. This was really unexpected for me because I did not think that a modification of a protein that is adding glycans to some of the 1200 predicted glycoproteins has such a severe effect on the cell wall. We still do not fully understand this result, but we have some ideas and are hopefully close to figure out what the cause is.
What was the biggest challenge you faced during your PhD?
The biggest challenge in my whole PhD was to transfer those proteins to bacteria or tobacco which allows to multiply and isolate these proteins and do functional studies. They need a very specific environment to be active which made the full procedure very challenging. We are still struggling with this, but I will continue on optimizing the process in the next couple of weeks.
Do you think your results might lead to practical applications in future?
We still need to do more research before we come closer to practical applications. When we understand better how modifications of the glycoproteins affect cell wall properties, we might be able to alter the interaction between cell wall components and like this change the properties of the cell wall. We could for example make cellulose or hemicellulose easier to extract which could be interesting for the pulp and paper industry or make the cell walls a bit more bendable or allow that it can expand more. Beside of the mutant studies with Arabidopsis, we also performed a bioinformatic analysis where we predicted which proteins in poplar are glycoproteins and where these proteins are expressed in the wood. Also this study does not result in direct applications but it is groundwork for future research in poplar and closely related species there is the potential for possible future applications.
Do you plan to continue doing research on cell wall or do you have already other plans for your future?
My plan is to go back to the Netherlands, and I am currently searching a postdoc there. It is quite difficult now during the Corona crisis because not many positions open up. I would like to continue doing research on cell walls. There is still a lot to uncover. Unfortunately, not many research groups in the Netherlands are working on cell walls. That is why I am also thinking to write my own postdoc proposal focusing on the role of the cell wall in abiotic stress responses in Arabidopsis but also in crops. I have never worked with crops before and I would like to start with that. On the long run, I would like to do research in a breeding company and working with crops hopefully will help me to come closer to that.
About the public defence:
The public defence took place on Friday, 30th of October at SLU in Umeå. Faculty opponent was Grégory Mouille, Institut Jean-Pierre Bourgin, UMR 1318 INRAE-AgroParisTech, France. Pieter Nibbering's supervisor is Totte Niittylä. The dissertation was live broadcasted on SLU Play: https://play.slu.se.
Title of the thesis: The role and synthesis of β1,3-galactans in plant cell wall formation
Link to the thesis: https://pub.epsilon.slu.se/17817/
For more information, please contact:
Pieter Nibbering
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
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Pinus densata is the dominant forest-forming species in the southeastern Qinghai-Tibetan Plateau. Photo: Wei Zhao
The plant journal New Phytologist has selected a study led by Umeå University researcher Xiao-Ru Wang as its cover story in the October issue. The paper is about effects of landscapes and range expansion on population structure and local adaptation.
“Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates”, says Xiao-Ru Wang, professor at the Department of Ecology and Environmental sciences at Umeå University and associated group leader at UPSC.
The study addresses a fundamental question in landscape genetics: the relative roles of population history, geography and natural selection in shaping genetic diversity in wild populations.
In the study, Xiao-Ru and a Chinese research group analyzed diversity and population structure in the pine tree Pinus densata, a keystone species on the Qinghai-Tibetan Plateau. They mapped the genetic variation to geographical and climate variables across the distribution range to establish the contribution of geo- and eco-factors to the observed spatial genetic pattern. Based on this information, the study further simulated how its genetic legacy may limit the persistence of P. densata in future climates.
The results illustrate that significant adaptation to extreme environment, when coupled with reduced diversity as a result of past demographic history, constrains potential evolutionary response to climate change.
As the dominant forest-forming species in the southeastern Qinghai-Tibetan Plateau, the resilience of P. densata underlies regional ecosystem function. Qinghai-Tibetan Plateau is the largest plateau on earth and also the most vulnerable ecosystem. While the deep valleys and high mountain ridges of the Qinghai-Tibetan Plateau have helped to create a global biodiversity hotspot, these same features can constrain adaptive responses to climate change. This is a particular concern for organisms with limited dispersal ability.
“The strong signal of genomic vulnerability in P. densata may be representative for other plateau endemics. As we accumulate further examples, it will become possible to gain a more general understanding of how demography and landscape factors constrain or promote adaptation to novel and changing environments,” Prof. Xiao-Ru Wang explains.
The study was performed in close collaboration with Beijing Forestry University; the joint team has been working together on this study system for more than 20 years.
The original article
Zhao, W., et al: Effects of landscapes and range expansion on population structure and local adaptation. New Phytologist Volume 228, Issue 1, October 2020. Pages 330-3432020. https://doi.org/10.1111/nph.16619
More information about Xiao-Ru Wang's research
More information about evolutionary biology research at Umeå University
Text: Ingrid Söderbergh
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An international research team led by Colin Turnbull from Imperial College London and Karin Ljung from UPSC showed that cytokinin, a substance that regulates plant growth, can be sensed on the outside of the plant cell. For a long time, researchers were convinced that cytokinin is mainly perceived within the cell, initiating reactions to adjust the cell’s development. These new findings, that were published last week in the journal Nature Communications, will fuel a 20-year-old discussion.
Cytokinins have many different functions in the plant. They control root and shoot growth, autumn senescence, they regulate cell division and much more. Within the plant cell, cytokinins bind to cytokinin receptors and these proteins then initiate a reaction that leads to, for example, enhanced shoot growth. This was the common view so far. In the current publication, the research team found a proportion of cytokinin receptors also sitting on the surface of the cell and they showed that they are fully functional there.
“The discussion about cytokinin receptor localization started almost 20 years ago when the first receptor was discovered. The recent view was that the receptors were mainly localised in the endoplasmic reticulum, which is a membrane system located within the cell,” explains Ioanna Antoniadi, who is postdoc in Karin Ljung’s group and first author of the article. “However, it was never excluded that the receptors might also sit in the plasma membrane, the membrane surrounding the cell.”
Initially, the researchers wanted to identify which of the different existing cytokinin forms is the active one that regulates root growth and development. They isolated individual cells from the root of thale cress, measured the cytokinin contents within and were really surprised to find similar amounts of active cytokinins inside and outside of the cell.
“We were wondering what these active cytokinins are doing out there and if they could actually be perceived,” says Ioanna Antoniadi, who started this work as part of her PhD thesis in London in 2013. “We started a collaboration with Karel Doležal and his team from the Palacký University in Olomouc, Czech Republic, who developed an incredible tool to answer our question.”
The Czech group synthesized active cytokinin molecules and attached them to sepharose beads that were bigger in size than a plant cell. These bound cytokinins could not enter the plant cell but were still able to activate a cytokinin response in the cell.
During their latest experiments, the researchers got in touch with yet another research team that was coming to the same conclusions as them but used a completely different approach. They were able to publish their results at the same time in the same journal fuelling the ongoing discussion even more.
Left: Microscopic photo of isolated plant cells from Thale cress roots (protoplasts, small circles) next to sepharose beads with bound cytokinin molecules (big circles). The cell wall of the plant cells was removed with digesting proteins leaving only the cell surrounding plasma membrane. Right: Graphic illustrating the results of the Nature Communications article. The common view was that active cytokinin binds to cytokinin receptors that are located in the endoplasmic reticulum - a membrane system in the plant cell. The researchers showed that active cytokinins are available outside and inside of the plant cell and that cytokinin receptors are also located in the plasma membrane of the cell. They used active cytokinin molecules bound to sepharose beads that are bigger than the plant cell to prove that the receptors in the plasma membrane are fully functional and can also initiate a typical cytokinin response in the cell. (Figure: Ioanna Antoniadi)The article
Antoniadi I, Novák O, Gelová Z, Johnson A, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communication 11, 4284 (2020).
https://doi.org/10.1038/s41467-020-17700-9
The corresponding article that was published at the same time:
Kubiasová K, Montesinos JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communication 11, 4285 (2020).
https://doi.org/10.1038/s41467-020-17949-0
For more information, please contact:
Ioanna Antoniadi
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
Karin Ljung
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
Phone: +46 (0)90 786 8355
https://www.upsc.se/karin_ljung
Colin Turnbull
Department of Life Sciences
Imperial College london
Email:
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Linghua Zhou (right) and her supervisor Rosario García Gil (left) after Linghua Zhou's PhD defence (Photo: Sonali Ranade)
Norway spruce is one of the industrially most important trees, also here in Sweden. Its generation time is with about 20 years relatively long making traditional breeding tedious. Linghua Zhou, PhD student in Rosario García Gil’s group, investigated the potential of different genomic-based breeding methods to assist in Norway spruce breeding. She showed that several of these new breeding methods have the potential to improve and speed up the breeding process of Norway spruce in future. Linghua Zhou successfully defended her PhD thesis at SLU on Friday last week, 28th of August.
Tree breeders look for individuals with the most favourable characteristics and use these then as parents in the next breeding cycle. Tree height, stem diameter, wood quality parameters and also resistance to fungi infection are traits the breeders are interested in. Genomic-based breeding methods try to relate such traits to the genetic information of the tree and use then the genetic information to select the best tree candidates for the breeding. Often this can speed up the breeding cycle because the genetic information can be analysed already in young trees when differences in a certain trait might not be seen yet on the tree.
“Genomic selection as one of genomic-based breeding method is applied almost routinely in animal and crop breeding, like for example for cattle, maize or wheat and also the breeding cycle of fast-growing trees like eucalypts and poplar could be shortened using these methods”, explains Linghua Zhou. “Another advantage is that the most interesting trees can be selected more accurately than with just traditional methods.”
Linghua Zhou and her colleagues firstly tried to identify marker regions in the DNA sequence that are determining how a certain trait is expressed in the tree. They focussed on different wood quality traits, like for example wood density and stiffness, but also looked for marker regions that determine the resistance to fungi. Their results showed that the genomic information of a tree partly determines which fungi species colonise the tree’s buds causing potentially a huge financial lost due to fungal infection.
“By genome-wide association study, another genomic-based breeding method, we successfully identified some genes associating with some traits we were interested in. However, they cannot describe the major variance that we see for the trait which means we cannot use them for breeding directly,” says Linghua Zhou. “That is why we moved from genome-wide association studies to genomic selection which uses the full genomic information instead of just certain DNA regions to predict the trait values of our population of trees.”
The main challenge Linghua Zhou and her colleagues faced during their analyses was the still low quality of the sequenced Norway spruce genome which limits the power of the genomic-based breeding methods. Also, the number of tree individuals that were analysed was partly too small to really use some of the methods to their full extent.
“Our results help to improve the understanding of genetic structure for some complex traits for Norway spruce. And even though genomic-based breeding has limited power at this state, I believe that it will be the trend in future for Norway spruce breeding,” concludes Linghua Zhou.
About the public defence:
The public defence took place on Friday, 28th of September at SLU Umeå. Faculty opponent was Marcio Resende from the Horticultural Sciences Department of the University of Florida, USA. Linghua Zhou's supervisor was María Rosario García Gil. The dissertation was live broadcasted on https://play.slu.se/.
Title of the thesis: Towards genomic-based breeding in Norway spruce
Link to the thesis: https://pub.epsilon.slu.se/17349/
For more information, please contact:
Linghua Zhou
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email:
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Field site with transgenic hybrid aspen trees, taken 2017 (Photo: Marta Derba-Maceluch)
Researchers from the Swedish University of Agricultural Sciences and Umeå University have developed genetically modified hybrid aspen that have a higher energy yield for the production of biofuels. The trees have grown well in greenhouses, and were now tested for the first time under more stressful field conditions. Some of the modified trees were more susceptible to insect infestation but others grew very well also in the field. The results were published in the journal Frontiers in Plant Sciences.
Hybrid aspen, a crossing between European and American aspen, is one of Sweden's most productive tree species which grows better than the usual aspen. Rapidly growing deciduous trees are used as an important resource for energy supply, but some of the properties of woody cell walls limit the possibility to produce biofuels and "green" chemicals from it.
To use the energy stored in the wood, cellulose first needs to be digested by enzymes releasing sugars that are then converted into bioethanol by microorganisms. The problem is that the cell wall component xylan is often extensively acetylated in hardwoods like hybrid aspen making the cellulose of the wood less accessible and thus the bioethanol production less efficient.
Ewa Mellerowicz and her group at the Umeå Plant Science Centre have reduced the acetylation of xylan by modifying hybrid aspen transgenically. The transgenic trees performed well in greenhouse experiments and the cellulose in their wood was easier to digest by enzymes to release more sugars. 18 of these different transgenic hybrid lines have now been evaluated for the first time in field trials, where they are subjected to much greater stress coming from the environment.
“The field trial was performed in agreement with the Swedish and European rules for handling genetically modified plants,” says Ewa Mellerowicz, professor SLU. “The most important outcome of the study was that we could demonstrate that reduction of acetylation, when targeted to wood tissue is a viable strategy to improve hardwood for biorefinery.”
The researchers used different strategies to modify the acetylation of xylan. They either prevented that the acetylation of xylan takes place or they cleaved off the acetyl group with the help of fungal enzymes that were introduced in the tree, and the modification was either directed specifically to the wood or introduced to the whole tree.
Most of the tested hybrid aspen trees grew similar to non-modified control trees planted in the same field. However, the researchers could see that trees in which the genetic modification was limited to the wood performed better than trees in which the modification was active in the whole tree.
“The trial showed the importance of testing modified aspen trees under field conditions to follow up results from lab and greenhouse experiments. It is urgent to continue and develop the field-testing programs”, points out Ulf Johansson, experimental manager at the Unit for Field-based Forest Research at SLU. Marta Derba-Maceluch, first author of the article and researcher at UPSC adds: “Our study shows that early field testing can be worth more than investing in extensive greenhouse experimentations.”
Especially those trees in which the fungal gene was active in the whole plant suffered much more from insect attacks. These trees were growing slower than the controls and their leaves had an altered amount and composition of phenolic compounds, chemical compounds that are important for plants to defend themselves against insect attacks or other types of stress.
“Our study confirmed that cell wall acetylation may alter both, the composition and concentrations of phenolic compounds in hybrid aspen”, explains Benedicte R. Albrectsen, researcher in chemical ecology and plant defence dynamics at Umeå University. “However, the main finding to me is that reduced cell wall acetylation did not cause any outstanding general differences in growth and resistance to herbivores and pathogens when compared to the untransformed wild type.”
The field site, where the experiment was done, was located in Våxtorp in the south of Sweden. 636 trees were planted there in August 2014. In the coming four years, their growth and the damage by insects, fungi, frost or other environmental stresses was monitored regularly until the harvest in 2018. Currently, researchers from Umeå University, lead by Professor Leif Jönsson, evaluate the harvested samples to see if the cellulose is still easier to digest. The best improved trees will be further tested at a larger scale in a biorefinery in Örnsköldsvik.
The article
Derba-Maceluch Marta, Amini Fariba, Donev Evgeniy N., Pawar Prashant Mohan-Anupama, Michaud Lisa, Johansson Ulf, Albrectsen Benedicte R., Mellerowicz Ewa J. (2020). Cell Wall Acetylation in Hybrid Aspen Affects Field Performance, Foliar Phenolic Composition and Resistance to Biological Stress Factors in a Construct-Dependent Fashion. Frontiers in Plant Science 11: 651
https://doi.org/10.3389/fpls.2020.00651
For more information, please contact:
Ewa Mellerowicz
Professor
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences (SLU)
Email:
Phone: +46 (0)90 786 8367
https://www.upsc.se/ewa_mellerowicz
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Jean Claude Nzayisenga and his supervisor Anita Sellstedt after the defence (Photo: Anne Honsel)
Microalgae have a high potential for biodiesel production and in parallel benefit domestic sewage treatment. Jean Claude Nzayisenga, PhD student in Anita Sellstedt’s group at the Department of Plant Physiology, validated a method to rapidly analyse the lipid, carbohydrate and protein content of microalgae. He also tested different growth conditions that improve quality of algal biodiesel and in parallel treat sewage. He successfully defended his PhD thesis at Umeå University on Monday, 15th of June.
Microalgae are photosynthetic, fast growing single cell organisms that live mostly in water and produce high amounts of proteins, fatty acids and carbohydrates. To measure the amount of these compounds produced during the growth of microalgae, Jean Claude Nzayisenga and his colleagues coupled the optical method Fourier-transform infrared spectroscopy (FTIR) with the complex mathematical modelling method Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS). They demonstrated that the combination of the two methods is useful to monitor changes in fatty acid, carbohydrates and protein contents.
“FTIR was already shown to allow measuring fatty acid and carbohydrate contents of microalgae but used alone, it relied on the assumption that the protein content remains constant during cultivation, which may not always be true”, says Jean Claude Nzayisenga. “We compared our results with the ones gained by using other standard techniques and showed that FTIR is a useful method for monitoring changes of the biochemical composition in microalgae. As FTIR is a relatively fast method, it could be even applied on a daily basis to monitor a microalgae cultivation system.”
Jean Claude Nzayisenga worked with microalgae species that were isolated in Northern Sweden and are adjusted to the long winters with low temperatures and only a few hours of light. Some of these microalgae are able to grow even without light as long as an alternative carbon-source is given. Jean Claude Nzayisenga and his colleagues grew microalgae either with light and carbon dioxide to allow doing them photosynthesis, with light and glucose or glycerol as carbon source so that they were still able to make photosynthesis but not completely rely on it, or they grew them without light but with glucose or glycerol, so that they were fully depended on the external carbon source.
“When we grew microalgae without light but with glycerol as carbon source, we could see that the microalgae are able to produce high amounts of fatty acids and that the composition of these fatty acids looks promising for biodiesel production”, explains Jean Claude Nzayisenga. “We chose glycerol because it is a cheaper carbon source than glucose and it is a by-product of biodiesel production offering a more sustainable and cost-effective production circuit. In future, it would be interesting to test also other carbon sources that are produced as industrial by-products or come from food waste.”
In another experiment, Jean Claude Nzayisenga tested the effect of different light intensities on the production of fatty acids. Under high light intensity, the microalgae produced more fatty acids than under low light intensities and also here the composition of fatty acids looked promising for biodiesel production. The team around Jean Claude Nzayisenga took a closer look and analysed which biochemical changes were associated with the accumulation of fatty acids. When growing without light and with glycerol, fatty acids accumulated on the expense of carbohydrates, while under high light conditions the content of proteins decreased instead.
In most of his experiments, Jean Claude Nzayisenga used not just one microalgae strain but compared different strains and evaluated which strain has the best properties for biodiesel production under the respective growth conditions. He also analysed the capability of the microalgae strains to take up nutrients from municipal wastewater to see if they could benefit sewage treatment. All tested microalgae strains were able to take up most of the nitrogen and phosphor from the wastewater which are the main contaminants in municipal wastewater. This offers the possibility to use microalgae for the wastewater treatment and in parallel produce raw material for biodiesel production.
About the public defence:
The public defence took place on Monday, 15th of June at Umeå University. Faculty opponent was Professor Ashton Keith Cowan from the Institute for Environmental Biotechnology, Rhodes University, South Africa. Jean Claude Nzayisenga 's supervisor was Anita Sellstedt from the Department of Plant Physiology (UPSC). The dissertation was broadcasted via Zoom.
Title of the thesis: Autotrophic and heterotrophic culture of Nordic microalgae in wastewater for lipid production
Link to the thesis: https://www.diva-portal.org/smash/record.jsf?pid=diva2%3A1430620&dswid=1987
For more information, please contact:
Jean Claude Nzayisenga
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email:
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PhD Student Bastian Schiffthaler (Photo: Alena Aliashkevich)
Most plant and animal features arise from complex interactions of genes, proteins and metabolites. The identification and analysis of these complex genetic traits is very challenging, especially when the sequenced genomes are fragmented. Bastian Schiffthaler, PhD student in Nathanial Street’s group, improved the genome information from European aspen and developed bioinformatic tools that help to analyse complex genetic traits in plants. He has successfully defended his PhD thesis at Umeå University today, on the 12th of June.
For sequencing a genome, the DNA is normally cut into small pieces, the sequence is read and then bioinformatic software assembles the whole sequence information using overlapping regions of these small pieces in an iterative process that ideally yields full length chromosomes. For trees, which often have very complex genomes and most available genome assemblies are therefore not very contiguous. Bastian Schiffthaler worked on improving the contiguity of such genomes focussing on European aspen.
When Bastian Schiffthaler started, the genome sequence of European aspen was already quite good compared to for example Norway spruce. However, it was still fragmented which made it difficult to carry out analyses that depend on a highly contiguous assembly. Examples of this are the detection of DNA signatures that relate to traits via genome wide association, or studying evolutionary history by looking at large scale genomic rearrangements. “Our strategy included modern long read sequencing, polished with highly accurate short-read data and combined with an optical and a genetic map to further link the initially assembled scaffolds into fully assembled chromosomes. At close to 20,000 genetic markers, the genetic map is one of the most comprehensive ones created for any organism to date. This was an overwhelming mass of information that most of the commonly used free software programmes were not able to handle.”
Ordering markers on a genetic map is a classic application of the travelling salesman problem, which aims to find the shortest between a set of points or locations. To derive the perfect order for only sixty markers would take more calculations than are atoms in the universe, hence all software relies on approximations, but even those were too slow for a dataset of this size. To overcome this problem, Bastian Schiffthaler developed “BatchMap”, a software package that speeds up the computations required to find the order of genetic markers with the highest likelihood given their inheritance patterns.
“BatchMap” divides calculations into small batches, which are easy to compute and can run in parallel. This drastically decreased the calculation time and Bastian Schiffthaler could produce a dense map of genetic signatures on the European aspen chromosomes. Since the creation of BatchMap, it has now been adopted by other genome projects such as those assembling the Norway spruce or a strawberry genome, which comprises eight chromosome sets.
“We wanted to evaluate our improved assembly in the context of genome wide association studies to look for genes that are involved in the salicinoid metabolism. These metabolites are only available in Populus and Salix species and help to protect the plant against herbivores,” explains Bastian Schiffthaler. “When compared to previous attempts using the more fragmented assembly, we could see that our new genome version improved the analysis of this complex trait a lot and we were able to gain new insights into the evolution of the different Populus species.”
To identify genes that are controlling complex traits is very challenging. Bastian Schiffthaler and his colleagues studied leaf shape variation in European aspen, a complex trait that is inherited from the parents but still highly diverse between individuals. Their results show that leaf shape is controlled by a complex network of many different genes, but the individual gene often exerted only a minor influence on the final leaf shape.
Bastian Schiffthaler believes that it in order to better understand the workings of traits like leaf shape, an integrative approach, where traits are analysed at all stages that contribute to their emergence. He therefore developed “Seidr”, a toolkit to study the interactions of genes that are actively being made into protein within an organism. He hopes that integrating “Seidr” with other layers of data will enable scientists to better predict complex traits in the future.
About the public defence:
The public defence took place on Friday, 12th of June at Umeå University. The faculty opponent was Marek Mutwil from The School of Biological Sciences at Nanyang Technological University in Singapore, who participated remotely in the defence. Supervisor was Nathaniel Street. The defence was broadcasted live. Interested people could participate via Zoom.
Title of the thesis: Embracing the Data Flood – Integrating Diverse Data to Improve Phenotype Association Discovery in Forest Trees.
Link to the thesis in DIVA: http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A1429905&dswid=8163
For more information, please contact
Bastian Schiffthaler
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email:
- Details
The Swedish Foundation for Strategic Research (SFF) approved last week four SSF Agenda 2030 Research (ARC) Centers on Future Advanced Technology for Sustainability. The project “Re-designing photosynthesis for future food security” with Åsa Strand from UPSC as main applicant was granted. Åsa Strand and her three co-applicants want to improve photosynthesis and apply CRISPR/Cas9 and other genetic modification techniques to increase crop productivity.
The world-wide crop production is stagnating while the population is growing which threatens food security. “Zero hunger” is defined as one of 17 Sustainable Development Goals that are addressed by the Agenda 2030. Åsa Strand and her co-applicants plan to target this goal by improving crop productivity through optimising the efficiency of photosynthesis. Because plants are only using a fraction of the light energy that they perceive, the researchers want to optimise the harvest of the light energy by plants and identify limiting steps during carbon fixation.
Åsa Strand’s co-applicants are Alexey Amunts from Stockholm University, Paul Hudson from the Royal Institute of Technology (KTH) and Alizée Malnoë who is like Åsa Strand working at the Department of Plant Physiology at Umeå University. All of them are internationally recognized and bring in different competences to the project. They will closely collaborate with the biotechnology company SweTree Technologies which will help them to test their engineering strategies in transformable crop species that are relevant to the Swedish agriculture.
The researchers will use cyanobacteria and Arabidopsis as two model systems in parallel. Cyanobacteria use the light energy much more efficiently compared to plants and also their carbon fixation rates are higher. The plant chloroplasts, the place where photosynthesis takes place, share the same ancestor as todays cyanobacteria. During evolution, photosynthesis in the chloroplast was adjusted to coordinate it with the more complex development and growth of plants – on the expense of the photosynthetic efficiency. The researchers hope that they can transfer knowledge from cyanobacteria to the chloroplasts of plants and maybe even re-introduce genes that were lost or modified in plants during evolution.
Their assumption is that photosynthesis in Cyanobacteria is adapted first and foremost to biomass formation. They think that the comparison between Cyanobacteria and plants will allow them to define the bottlenecks that restrict the light harvesting efficiency and limits the carbon fixation rate. Using multiple research lines and genetic engineering, they hope to break the bottlenecks and improve the efficiency of photosynthesis in plants and like this increase their productivity. Several initiatives are working internationally on improving biological photosynthetic efficiency using different approaches and the researchers hope to complement these efforts with their novel approach.
Four strategic areas have been identified by the Swedish Foundation for Strategic Research in the frame of their call for SSF-ARC Centers. These were “Future Nuclear Power”, “Plant Biotechnology including GMO and CRISPR/Cas9” which is the area that Åsa Strand applied for, “Hydrogen/Fuel Cells and Next Generation of Antibiotics and/or Actions to prevent pandemics”. In every strategic area, one application was granted. The four centers will share 200 million SEK.
The researchers plan to compare cyanobacteria and plant chloroplasts. Both have common ancestors, but their evolution separated about 1 billion years ago (1bya). The researchers want to transfer knowledge from the photosynthetic more efficient cyanobacteria to the plant chloroplast and like this improve crop productivity (Figure: Daria Chrobok, DC SciArt).Link to the Swedish press release from SSF:
https://strategiska.se/pressmeddelande/har-ar-de-ssf-arc-center-som-far-dela-pa-200-miljoner-kronor/
Information about the applicants:
Alexey Amunts
Associate Professor
Department of Biochemistry and Biophysics
Stockholm University
E-mail:
Phone: +46(0)8161003
https://www.su.se/english/profiles/aamun-1.219419
Paul Hudson
Associate Professor
Division of Systems Biology
KTH Royal Institute of Technology
E-mail:
Phone: +46 (0)70 783 95 07
https://www.kth.se/profile/huds
Alizée Malnoë
Assistant Professor
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
E-mail:
Phone: +46(0)907869314
https://www.upsc.se/alizee_malnoe
Åsa Strand
Professor
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
E-mail:
Phone: +46 (0)90 786 9314
https://www.upsc.se/asa_strand