DSundell 1920x1080
[2017-05-18] David Sundell has developed novel interactive web tools that can visualize and perform statistical analysis of gene expression data based on two high-spatial resolution datasets of wood development. One tool that can compare expression between species may help identify genes with conserved biological function. David Sundell will defend his thesis at Umeå University today.

David Sundell has analysed two high-spatial resolution datasets profiling wood development from the angiosperm tree aspen (Populus tremula) and from the conifer species Norway spruce (Picea abies). For each of the datasets he developed a web resource (AspWood och NorWood ) including tools for the exploration of gene expression, co-expression and functional enrichment of gene sets.

One developed resource (ComPlEx) allows interactive, comparative co-expression analysis between species to identify conserved and diverged co-expression modules. These tools make it possible to identifying conserved regulatory modules that can focus downstream research and provide biologists with a resource to identify regulatory genes for targeted trait improvement.

 “The goal was to provide a platform (PlantGenIE) where scientists can investigate the processes underlying wood formation including comparative analysis between species”, says David Sundell. “My research has resulted in a set of powerful resources for identifying genes controlling wood development and the functional properties of wood. This probably allows to develop new varieties with increased biomass or optimal properties for downstream uses such as bioenergy uses in a more targeted way.”

Research on wood development conducted in conifer tree species is limited. The majority of research has been conducted in model angiosperm species such as Arabidopsis thaliana. Using model organisms such as aspen and Norway spruce is possible due to the fact that all living organisms derive from a common ancestor. This means that a gene that exists in two species had the same function at the time of divergence from their last common ancestor. Throughout evolution, the function of the two gene copies may diverge, but a signature of the shared ancestry remains in the DNA sequence of the two gene copies.

The identification of such orthologous genes and of the regulatory pathways controlling those genes by comparing sequences similarities from angiosperms and gymnosperms is limited due to the large evolutionary distance between these two plant groups. The have diverged hundreds of millions of years ago. At such large evolutionary distances additional information, such as gene expression data, is required for functional annotation.

Lignocellulose from plants is the most abundant source of terrestrial biomass and is one of the energy sources that can potentially replace fossil fuels. For a country such as Sweden, where the forest industry accounts for 10% of total economic export, increased plant biomass yields would not only be beneficial for the environment, but also for the economy of the country.

About the defence:

Thursday, the 18th of May, David Sundell, Department of Plant Physiology, Umeå University, will defend his thesis with the title: Novel resources enabling comparative regulomics in forst tree species. Swedish titel: Nya verktyg för komparativ regulomik i skogsträd.

The public defence will be in Lilla hörsalen KB3A9, KBC-huset.

Faculty opponent is Professor Klaas Vandepoele, VIB/Ghent University, Belgium.

For more information, please contact:

David Sundell, 
Phone: +46705943742
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Text: David Sundell
 
 
[2017-05-15] Seoljong Kim, student of Master’s programme in Plant and Forest Biotechnology, is Umeå University’s Global Swede for 2017. The annual recognition of Global Swede is a joint initiative by the Ministry of Foreign Affairs, and the Swedish Institute. This is the seventh year this recognition is awarded.

Seoljong Kim from South Korea is in his final term of Master’s programme in Plant and Forest Biotechnology. He was selected for this recognition after distinguishing himself during his studies.

“One quality sets him apart from other top students: his curiosity towards peculiar, hidden subjects in plant biology. This is best illustrated by his selection of master thesis work to study edible orchids in Zambia. He unearthed the topic for himself, approached the group working on the field, designed the thesis project, conducted the work in Africa and done the lab work back in Sweden. To organise the whole project required enthusiasm, lots of time, effort and a strong drive that he has”, says programme director Laszlo Bako.

See the full text on the homepage of Umeå University here: http://www.umu.se/english/news/.cid282572

Link to the Swedish news: http://www.umu.se/nyhet//.cid282547
[2017-05-11] Journalist Vanessa Hill has interviewed experts around the world about gene engineering with CRIPSR techniques. Stefan Jansson, Professor at Umeå University and group leader at the UPSC, is one of the interview partners.  The documentary which is freely available on YouTube aims to be a starting point for discussing the pro and contra of gene editing methods and their use in society.

Link to the documentary: https://m.youtube.com/watch?v=NrDM6Ic2xMM
170320 PNAS MKKL 2 1920x1080The organic electronic ion pump positioned in vivo next to the Arabidopsis root. Macro and micro view, with highlighted delivery channel. Picture: Michal Karady

A drug delivery ion pump constructed from organic electronic components also works in plants. Researchers from the Laboratory of Organic Electronics at Linköping University and from the Umeå Plant Science Centre have used such an ion pump to control the root growth of a small flowering plant, the thale cress (Arabidopsis thaliana).

In the spring of 2015, researchers from the Laboratory of Organic Electronics at Linköping University presented a microfabricated ion pump with the ability to pump in the correct dose of a naturally occurring pain-relief agent exactly where it was needed. This was a first step towards effective treatment of such conditions as chronic pain. In the autumn of the same year, the researchers presented results showing how they had caused roses to absorb a water-soluble conducting polymer, enabling them to create a fully operational transistor in the rose stem. The term “flower power” suddenly took on a whole new meaning.

Delivering hormones to plants

“Around 10 years ago, we started considering applying our ion pump drug delivery devices to plants. It wasn´t until several years later that we teamed up with Professor Markus Grebe and colleagues at the Umeå Plant Science Centre and finally discovered that the ion pump could be of great use to plant biologists", says Daniel Simon, Associate Professor and head of the organic bioelectronics research area in the Laboratory of Organic Electronics, Linköping University.

Assistant Professor David Poxson, Laboratory of Organic Electronics, teamed up with the group´s chief chemist, Assistant Professor Roger Gabrielsson, to develop new ion pump materials capable of transporting and delivering powerful plant signalling compounds such as the hormone auxin.

Dr. Poxson then worked closely with biologists at the Umeå Plant Science Centre to investigate highly-resolved delivery of auxin to the roots of living thale cress, Arabidopsis thaliana. This plant is to plant biologists what the fruit fly Drosophila is to researchers working in animal research: a major model organism.

The result: Electronically-controlled gradients of plant hormone were taken up by the roots. Dr. Poxson and co-author Dr. Michal Karady followed the internal auxin response with the help of fluorescent reporter proteins that change their fluorescence intensity in the presence of auxin. They observed that the internal auxin response and even the roots´ growth rate could be controlled by the ion pump delivery of auxin.

A ground-breaking step for plant research

“We have accomplished a ground-breaking step for plant research by our multidisciplinary effort”, says Markus Grebe. “Several research groups from Umeå Plant Science Centre and Linköping University have been involved. The pump will likely allow us to locally apply not only auxin but also a variety of other hormones to plants in an electronically controlled manner. This will help us to study the impact of these hormones on plant growth and development at tissue and cellular resolution.”

“These new DendrolyteTM materials also pave the way for future ion pump capabilities in a variety of areas, for example delivery of larger aromatic compounds like plant hormones or even certain pharmaceuticals,” says Daniel Simon.

The results have now been published in the prestigious scientific journal Proceedings of the National Academy of Sciences of the United States of America (PNAS).

“This is an important advance: we now know not only that we can use the ion pump in plants, but also that we can regulate their physiology and growth,” says Professor Magnus Berggren, head of the Laboratory of Organic Electronics.

The research has been funded by the Knut and Alice Wallenberg Foundation as part of the ShapeSystems project.

The article:
Regulating plant physiology with organic electronics, David Poxson, Michal Karady, Roger Gabrielsson, Aziz Alkattan, Anna Gustavsson, Siamsa Doyle, Stéphanie Robert, Karin Ljung, Markus Grebe, Daniel T Simon and Magnus Berggren, Linköping University, Umeå University and Swedish University of Agricultural Sciences 2017, PNAS, doi/10.1073/pnas.1617758114

Contact at Linköping Unversity:
Daniel Simon
Department of Science and Technology
Division of Physics and Electronics
This email address is being protected from spambots. You need JavaScript enabled to view it.
+46 11 363476

Contact at Umeå Plant Science Centre:
Markus Grebe (at UPSC)
Department of Plant Physiology
Umeå University
This email address is being protected from spambots. You need JavaScript enabled to view it.

For more information about Markus Grebe, see also here:
http://www.uni-potsdam.de/en/ibb/researchgroups/fullprofessors/plant-physiology.html

Karin Ljung
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
This email address is being protected from spambots. You need JavaScript enabled to view it.
+46 (0)90 786 8355

Text: Monica Westman Svenselius (Linköping University)

The model plant thale cress acquires organic nitrogen from the soil, although its roots do not form symbiosis with mycorrhizal fungi. This is shown in a study, led by SLU researchers. They also show that plants can acquire organic nitrogen in competition with microorganisms in soil, which previously has been questioned. This means that organic nitrogen can contribute to the plant’s nitrogen supply, and raises the question if agricultural crops could be modified to become more efficient in using organic nitrogen as a source of nutrients. The study is published in a recent issue of the scientific journal Plant, Cell & Environment.

The classic science on plant nutrition states that plants acquire nitrogen from the soil as nitrate or ammonium, or as nitrogen gas if the plant forms symbiosis with nitrogen-fixing bacteria. Today we know that there are plants that also can make use of organic nitrogen, but the consensus has been that it only applies to certain mycorrhiza-forming plants growing in nutrient-poor soils. Together with colleagues from Austria and Australia the SLU researchers show that a plant that does not form mycorrhiza acquires organic nitrogen when grown in nutritious agricultural soil.

The new findings show that the plant is dependent on a specific protein for this to work. The protein is an amino acid transporter, and the researchers have performed a number of experiments on genetically modified thale cress (Arabidopsis thaliana) that either lack the transporter or over produces it. Torgny Näsholm, Professor in ecophysiology at the Swedish University of agricultural sciences in Umeå, led the study.

"We grew the plants in greenhouses in agricultural soil, and could follow the way of the amino acid glutamine from the soil into the plant by labelling the glutamine with carbon and nitrogen isotopes. It turned out that the uptake of the amino acid is much more efficient in plants that overproduce the amino acid transporter, and very low in plants lacking the transporter", he explains.

Additionally, the plants that were lacking the transporter had the lowest carbon/nitrogen ratios, and the plants overproducing the transporters had the highest ratios. Theoretically, the amino acids should result in a higher carbon concentration, which indicates that the plants have been taking up organic nitrogen from the soil continuously. "This study is a milestone in our research. With the use of genetically modified model plants we have been able to show that amino acids in soil are used as nitrogen sources by plants. We also aim to increase the plant capacity to take up nitrogen from the soil, and our results show that an optimization of organic nitrogen uptake is a possible way to achieve this", says Torgny Näsholm.

Thale cress is not an agricultural crop, but a model plant which is often used to predict the effects of genetic modifications in agricultural plant species. As part of the research programme Mistra Biotech, the research group now investigates how the uptake of organic nitrogen can be improved in potato. "We are now testing if it is possible to use the same strategy to increase the uptake of organic nitrogen in an agricultural crop. We have propagated modified potato clones to see if we get the same increase in potato as in thale cress."

PCE article Ganeteg 1920x1080 1Photos: Iftikhar Ahmad; Illustration: Ulrika Ganeteg

Scientific article:
Ganeteg, U., Ahmad, I., Jämtgård, S., Aguetoni-Cambui, C., Inselsbacher, E., Svennerstam, H., Schmidt, S., and Näsholm, T. (2017) Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil. Plant, Cell & Environment 40: 413–423. doi: 10.1111/pce.12881.


Link to the Swedish press release on the SLU homepage

More information about Mistra Biotech: http://www.slu.se/mistrabiotech

Contacts:

Torgny Näsholm, Professor
Department of Forest Ecology and Management, SLU
Phone: +46-90-786 8205
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Ulrika Ganeteg, researcher
Department of Forest Genetics and Plant Physiology, SLU
Phone: +46 (0)90 786 8431
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Henrik Svennerstam, researcher
Department of Forest Genetics and Plant Physiology, SLU
Phone: +46 (0)90 786 8641
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Mistra Biotech
This email address is being protected from spambots. You need JavaScript enabled to view it.
+4618 672232

Olivier Keech 151127 141033 JGS IG Webb 1920x1080
The Scandinavian Plant Physiology Society (SPPS), announced last week that Olivier Keech, assistant professor at Umeå University and group leader at UPSC, receives the SPPS Early Career Award 2017. This award honours young scientists in Scandinavia who proceed well in their scientific career and contribute significantly and independently to plant biology.

Olivier Keech established his research group in 2014 when he became assistant professor at the Department of Plant Physiology, Umeå University. His research focuses on the regulation of metabolism in response to abiotic stresses, notably in response to stress-induced senescence. Olivier Keech wants to understand why and how plants “decide” to sacrifice an organ such as a leaf for the benefit of the rest of the plant. He wants to know how this decision is communicated within the plant body and how the associated metabolic changes, e.g. the recycling and reallocation of valuable nutrients, are regulated.

There were all together four SPPS Award Winners announced by SPPS last week. The SPPS Award goes to Michael Broberg Palmgren from the Department of Plant Environmental Sciences, University of Copenhagen. Chuanxin Sun from the Department of Plant Biology, Swedish University of Agricultural Science in Uppsala receives the Physiologia Plantarum Award and Kurt Fagerstedt from the Department of Biosciences from the University of Helsinki the SPPS Popularisation Prize. All awards are monetary rewards as well as invitations to the SPPS Congress this summer in Naantali, Finland, where the certificates will be officially presented to the winners.

For more information about the winners and the awards please have a look on the SPPS homepage.

You can find more information about Oliver Keech's research here.

Here you can find a Swedish press release from Umeå University.
Mycorrhiza-project_1920x1080Group picture with the students from Dragonskolan who participated in the Mycorrhiza project, Sabine Kunz (2nd from left in the front row), Elisabeth Uppsäll (5th from left in the front row) and Judith Felten (1st from right in the first row)

[2017-03-24] Today, twenty students from Dragonskolan presented their results from the “Mycorrhiza project”, a six-month project together with Judith Felten’s group from the Umeå Plant Science Centre (UPSC). The project aimed to teach scientific methodology based on the interaction between mycorrhizal fungi and plant roots.

Do forest trees grow better when their roots are growing in interaction with mycorrhizal fungi? How do those roots look like? How many different fungal species are growing in forest soils and how can we detect them? These were questions the students tried to find answers to. Sabine Kunz, postdoctoral researcher at the UPSC, and Judith Felten, assistant professor at the Swedish University of Agricultural Sciences, developed this project in collaboration with Dragonskolan.

“We designed the project together with the biology teacher Elisabeth Uppsäll from Dragonskolan in Umeå. Our idea was to bridge the gap between biology lessons at school and scientific research,” says Sabine Kunz. “The students got access to specific scientific methods we are using for our research and gain insight into our work as researchers. There are many things you need to consider when planning experiments. This is best experienced when you do the experiment yourself and evaluate your results.”

“It has been great for us to participate in this project”,Students greenhouseStudents working with fir trees in the greenhouse (Photo: Sabine Kunz)adds Elisabeth Uppsäll. “It is important to get students to understand how scientists work and what methods are used to answer scientific questions. Sabine has been an invaluable link between the students and the UPSC because she is not only researcher but has also experience with teaching at school and she knows how to address students. We have had many nice meetings developing this project and exciting discussions during the full course of the project, weather we were digging up roots in nature or during the final seminar today.”

The students worked in smaller groups with different research questions. They went into the forest and dug up roots and soil and brought it to the lab. There, they used among others, DNA analyses to detect different fungal species in the soil. They tested whether young spruce trees grow differently in forest soil that contained mycorrhizal fungi than spruce trees in commercial planting soil. They observed roots from the forest under the microscope and they investigated whether the architecture of the plant root system changes when it is in symbiosis with the fungi.

“The mycorrhizal symbiosis is really fascinating. It is not visible until you dig up a root and look at it under the microscope but it is very important for the forest ecosystem,” says Judith Felten. “We hope that we could inspire the students by our project and that they now see the forest with different eyes.” 
 
After the experimental part, the students got a crash course in scientific data analysis. They learned how to edit a microscopic image, how to present data in diagrams and graphs and how to interpret results. They presented their results today in short talks to researchers and staff members of the UPSC.

The project was financially supported by the Kempe Foundations.

For more information, please contact:

Judith Felten
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
This email address is being protected from spambots. You need JavaScript enabled to view it.
+46 (0)90 786 8435
http://www.upsc.se/judith_felten

Sabine Kunz
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
This email address is being protected from spambots. You need JavaScript enabled to view it.
+46 (0)90 786 8628

Elisabeth Uppsäll
Dragonskolan Umeå
Dragongatan 1
903 22 Umeå
This email address is being protected from spambots. You need JavaScript enabled to view it.
+46 (0)90 16 24 92

More information about Dragonskolan
Vetenskapslunch2017 SJansson 1920x1080 2Vetenskapslunch February 2017 (Umeå University)
Stefan Jansson, plant scientist at the UPSC and Professor at Umeå University, was awarded the 2017 ÅForsk “Kunskapspris”. He is being honoured for his commitment to transfer scientific knowledge to the public.

The ÅForsk foundation awards every year “kunskapspriset”, a price that values
outstanding contributions to the dissemination of knowledge. Stefan Jansson was awarded this year with the following motivation:

“Stefan Jansson is a committed and untiring public educator who fights well and hard for knowledge. He is constantly active in the public debate, taking part not only in humoristic programmes but also in political debates. He informs about both his own and other’s research to school kids as well as to pensioners. He is active in bringing knowledge into the debate on GMO and organic farming to counteract fact resistance.”

“I feel incredibly honoured and glad”, says Stefan Jansson. “Actually, I think there should be more prizes that encourage researchers to use their knowledge in the public debate. It’s probably never been more important than at present.”

The candidates for the ÅForsk price are nominated by the Universities . One very prominent awardee was Hans Rosling, a Swedish role model in the debate on fact resistance who has received the price in 2006 but has recently passed away. “He has left great footsteps to follow in”, says Stefan Jansson. “very many like me will be needed to fill his shoes”.

Link to the press release from Umeå University 
 
About ÅForsk
 
For more information, please contact:
Stefan Jansson, Department of Plant Physiology
Phone: +46 70-677 23 31
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Six researchers from UPSC developed a concept for more sustainable urban farming. They presented their idea last November at PLATSEN in Umeå, a conference that aims to bring together different actors to discuss about sustainable developments. A short video describing their so-called eMTE concept is now available online.

The concept called eMTE (electronic Multi-Trophic Ecosystem) comprises several stages of a food chain like aquaculture, compost recycling, bioreactors as well as aero-/hydroponics. These so-called trophic layers are electronically controlled and interconnected with each other to form a small-scale ecosystem. Like this, nutrients produced in one trophic layer can support another layer reducing the amount of waste and energy that needs to be invested to produce food. Employing electronics offers great possibilities to monitor the different trophic layers and therefore makes the entire ecosystem more modular, which thus eases its use within complex structures such as found in cities.schemeSchematic overview of the eMTE concept

The eMTE project was initiated by Olivier Keech, assistant professor at Umeå University. His team, namely Nicolas Delhomme, Simon Law, Stefano Papazian, Alonso Serrano, Bastian Schiffthaler and Bernard Wessels, consists of fundamental scientists with different specialisations. All of them are driven by the idea to improve urban farming and urban food production while in parallel increasing the awareness about human relationship to ecosystems.

“It was great to get the opportunity to present our eMTE concept at PLATSEN”, says Olivier Keech, leader of the eMTE project. “We got lots of positive feedback as well as new contacts to collaborate with, which is encouraging. Our idea is to develop this project further so it can be soon integrated into existing and novel urban farming projects.”

PLATSEN is thought as a platform where decision makers, politicians, scientists, NGOs and people from public and private sectors can meet and exchange and discuss ideas about sustainability in an urban environment. The event is initiated by the Swedish Scientific Council for Sustainability in collaboration with several other actors from the public and private sectors e.g. Umeå Municipality and Umeå University.

For more information have a look to the video or contact Olivier Keech: This email address is being protected from spambots. You need JavaScript enabled to view it.
OveNilsson 1920x1080
Six new members were elected at the General Meeting of the Royal Swedish Academy of Science on the 11th of January 2017. Ove Nilsson, director of the UPSC and professor at the Swedish University of Agricultural Sciences, is one of them. The membership honours exclusive recognition of successful achievements in research and outstanding services to science.

The other new members are Rikard Holmdahl from Karolinska Institutet, Ruth Palmer from the University of Gothenburg and Jarone Pinhassi from Linnaeus University and the two Nobel laureates May-Britt Moser and Edvard Moser, both from the Norwegian Kavli Institute for Systems Neuroscience. All members are divided according to their scientific focus into different scientific disciplines, called classes. Ove Nilsson and Jarone Pinhassi are assigned to the class for bioscience while the other four belong to the class for medical sciences.

There have been three other UPSC researcher elected to the Academy previously: Gunnar Öquist, Göran Sandberg and Stefan Jansson. Today, the Academy has about 625 members, 450 from Sweden and 175 foreign members. It is a non-governmental scientific organisation that awards every year the Nobel Prizes in Physics and Chemistry, the Sveriges Riksbank Prize in Economic Sciences and many other prizes. The members take part in the Academy’s committees and panels and in the selection process for the prizes. The main goal of the Academy is to promote sciences and strengthen their influence in society.

Link to the announcement at the Royal Swedish Academy of Science:
http://www.kva.se/en/News/2017/sex-nya-ledamoter-invalda/