Thesis defence of Shashank Sane (left); his supervisor was Ove Nilsson (right); photo: Sonali RanadeShashank Sane (left) and his supervisor Ove Nilsson (right) after the dissertation; photo: Sonali Ranade

[2020-04-07] The genetic machinery controlling aging and seasonal growth in hybrid aspen is using at least partly the same molecular components. Shashank Sane, PhD student in Ove Nilsson’s group at UPSC, modified some of these components and characterised their function during those developmental processes. By comparing his results from hybrid aspen with findings in the annual plant thale cress, he demonstrated that the genetic components are similar but the way how the components work together differs. He successfully defended his PhD thesis today in P-O Bäckströms sal at SLU in Umeå.

Shashank Sane has focussed in his PhD thesis on two aspects of vegetative growth in hybrid aspen: the transition from a young to an adult stage and the adaptation to seasonal growth. The underlying regulation networks are very complex but uses similar components that are also involved in the regulation of flowering in thale cress. By genetically modifying three of these components in hybrid aspen, Shashank Sane demonstrated that they can interact in different ways with the other regulatory components of this network than was previously described for thale cress.

In his experiments, Shashank Sane used modified hybrid aspen that were overexpressing microRNA miR156 and others in which microRNA miR172 was inactivated. MicroRNAs are small molecular regulators of gene expression that are found in all plants and animals. MiR156 is in thale cress active in seeds and young plants and inhibits genes that induce flowering. In contrast, miR172 becomes activated with increasing age and blocks genes that repress flowering. The two microRNAs counteract each other in its action and their regulation is closely adjusted to each other.

The two differently modified hybrid aspen trees showed similar characteristics. In the second growing season when the leaves are normally getting a shorter and rounded form and become darker green, the leaves of the modified trees were still longer and lighter green, typical characteristics of young leaves. Shashank and his colleagues concluded that the modified trees need longer to pass from the young state into the adult state than the non-modified trees. They also simulated autumn conditions through shortening of the day length. The modified trees needed one week more than non-modified trees until they stopped their growth.

“We expected that these two gene modifications have similar effects on the growth of the trees as miR156 is once overactive and in the other trees, its antagonist miR172 is blocked,” says Shashank Sane. “But it was really astonishing for us to see that some of the genes that are regulated by those two microRNAs were regulated in the opposite way in hybrid aspen than in thale cress. Our suggestion is that the function of these genes has evolved differently in hybrid aspen than in thale cress, probably to adjust to the perennial growth.”

The researchers made a similar observation when studying the hybrid aspen genes that correspond to the thale cress gene GIGANTEA. In thale cress, this gene is part of a regulation network that senses the day length and regulates flowering. Shashank Sane and his colleagues focussed on the role of the poplar GIGANTEA genes for growth cessation and bud formation. Also here, they demonstrated that the network components interact in different ways to regulate the growth stop and bud set in hybrid aspen than they do during induction of flowering in thale cress.


About the public defence:

The public defence took place on Tuesday, 7th of April at SLU Umeå. The faculty opponent was Professor Miguel Blazquez from the Institute for Plant Molecular and Cellular Biology, Valencia, Spain who participated in the defence remotely. Shashank Sane's supervisor was Prof. Ove Nilsson. The defence was live broadcasted.

Title of the thesis: Molecular Regulation of Bud Phenology and Vegetative Phase Change in Populus Trees

Link to the thesis: https://pub.epsilon.slu.se/16768/


For more information, please contact:

Shashank Sane
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Female scientists working at UPSCSeveral of the female scientists currently working at UPSC (photo: Anne Honsel)

[2020-02-11] Today is the International Day for Women and Girls in Science. Time to reflect on UPSC’s achievements in terms of gender equality. Since 2007, UPSC is working on improving its gender balance among its scientists and has reached now its goal of having 40-60 percent of women throughout the different career stages – from PhD students to full professors.

It all started on initiative of Vinnova and VR who funded a large project, the Berzelii Centre for Forest Biotechnology that continues now as a Vinnova Competence Centre. The funding agencies asked to analyse the gender equality within the centre and which actions were planned to improve the situation. This was when the UPSC management started to think about ways to address a gender imbalance among group leaders. Since then, the percentage of female group leaders at UPSC has increased continuously and is now at 45 percent.

“When we started to analyse the gender balance in 2007, we were pretty much balanced for PhD students, slightly imbalanced for postdocs but at the group leader positions there was a clear bias towards men that got progressively worse as you moved from assistant to associate professors and with just one full professor that was female”, says Ove Nilsson, director of UPSC. “We realized that if we could maintain the balance that we have at the PhD and postdoc level when these people move further on in their career, the imbalance would start to even out.”

That is why the UPSC management started to implement a programme to support specifically newly started group leaders. This was possible due to the funding from Vinnova and VR and the matching funding from the universities. All new group leaders received extra resources to hire e.g. PhD students and postdocs and it ensured that they had six instead of four years of funding for their own positions. The aim was to give them the good conditions to merit themselves and to allow them to establish their group.

“We did not do anything that was specifically targeted towards women”, explains Ove Nilsson. “Just by giving young researchers good starting conditions we managed to level out the gender imbalance among group leaders. The challenge now is to maintain this balance. We continue to support new group leaders with good starting packages but we also hope that now when our environment is more balanced, it becomes more attractive for all genders and like this maintains its balance.”

Special caution is set on the recruitment process. The goal is to prevent any bias but focus on recruiting the best qualified person for the respective position. The UPSC management tries to enforce this all the way from PhD students, to postdocs and group leaders. Of special help for recruiting excellent scientists and especially female scientists is of course Sweden’s family friendliness. “Many foreign scientists are not aware of the support that is offered to families with kids when they come to Sweden but after a while, they appreciate it a lot”, emphasizes Ove Nilsson.

The purpose of the International Day for Women and Girls in Science is to empower women and girls in science to achieve equality. It was established in 2005 by the United Nations General Assembly and implemented by UNESCO and UN-Women. According to UN-Women, 30 percent of researchers world-wide are women and they are still disadvantaged in their career.

Hannele Tuominen and Sacha Escamez in the UPSC greenhouse, watching Arabidopsis seedlings on plateHannele Tuominen (left) and Sacha Escamez (right) in the UPSC greenhouse (photo: Anne Honsel)

[2020-01-16] For long, it was assumed that cell death occurs mainly during animal organ growth but not in plant organs. A research group led by Hannele Tuominen from UPSC demonstrated now that the death of certain cells in the root facilitated the growth of lateral roots. These new findings hint at organ growth of plants and animals might not be so different as thought. The study was published today in the journal Current Biology.

In contrast to animals, plants are forming new organs like lateral roots continuously. These roots grow out from the main root and help to explore the soil for nutrients and give additional stability to anchor the plant in the soil. Elimination of cells plays an important role in animal development, e.g. for the formation of fingers or toes. The cells between the digits die during development to allow the establishment of the individual digits. Also in plants, developmental cell death occurs but so far it was not clear that it is needed to facilitate the emergence of lateral roots like it is shown now in the recent publication.

The researchers around Hannele Tuominen, until 2019 associate professor at Umeå University and now professor at SLU, and her postdoc Sacha Escamez used different methods to demonstrate that cell death is occurring and enables lateral roots to emerge from the main root in the plant thale cress. “We first found that genes, indicating developmental cell death, were activated in cells that are laying over those cells that form the future lateral roots”, says Hannele Tuominen. “That made us curious and we wanted to analyse this in more detail.”

The researchers used different microscopic techniques to show that those cells were actually dying. Among others, they applied dyes that stain either living cells or dead cells and fluorescent markers that are only visible at certain pH values. Important parts of the plant cells become acidic when the cell dies causing the signal from the marker to disappear.

To make the story even more thorough, the researchers used an additional approach. They analysed a thale cress mutant which is lacking a cell death regulating protein. The growth of lateral roots in this mutant was delayed. The researchers could restore the normal development genetically and also physically by using optical tweezers.

In the genetic approach, they introduced a mammalian gene, known to induce cell death, into the mutant and targeted it to only affect those cell types that they observed to die in the non-mutated plants. The lateral roots of the resulting double mutant grew normal without any delay.

In parallel, the researchers applied optical tweezers to wound cells and like this induce the death of the cell. Optical tweezers use a highly focused laser beam to manipulate microscopically small objects. “This is a very precise optical tool. We can target individual cells and wound them. Three hours after we wounded the cells, they died”, explained Sacha Escamez. “When we applied this method to the mutant whose lateral roots normally grow slower, their lateral roots grew significantly faster.”

Researchers from UPSC, from Umeå University, Israel, Germany and the United Kingdom contributed to the publication. “We started this project several years ago and are very pleased that we could now round it up with help of the expertise of all contributing authors”, pointed Hannele Tuominen out. “However, as it is often in science, this will not be the end of the story but it opens up many new questions for further studies.”

About the article:

Sacha Escamez, Domenique André, Bernadette Sztojka, Benjamin Bollhöner, Hardy Hall, Béatrice Berthet, Ute Voß, Amnon Lers, Alexis Maizel, Magnus Andersson, Malcolm Bennett and Hannele Tuominen (2020). Cell death in cells overlying lateral root primordia facilitates organ growth in Arabidopsis. Current Biology.

https://www.cell.com/current-biology/fulltext/S0960-9822(19)31580-5


For more information, please contact:

Hannele Tuominen
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46 90 786 9693
Twitter: @hanneletuominen
https://www.upsc.se/hannele_tuominen

Sacha Escamez
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Twitter: @SachaEscamez

Research on trees is one of our main focus at UPSC. We often use genetically modified trees as tool to understand tree growth and development. Take a look on how we make and work with genetically modified trees!

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Ove Nilsson (Photo: Anne Honsel)

On their meeting on the 12th of December 2019, the Royal Swedish Academy of Agriculture and Forestry (KSLA) elected 30 new fellows. Ove Nilsson, director of UPSC and professor at the Swedish University of Agricultural Science, will be one of eight new fellows that will join the Forestry section of the academy. The fellows are chosen because of their outstanding knowledge and experience in their respective field of work. They are expected to actively participate in the activities of the Academy.

The Forestry section of the Academy works with questions regarding forest management and usage of the forest as natural resource including industrial and market aspects. It takes up specific education and counselling questions and questions related to hunting as well as environmental issues that are associated with the liability of the industry sector. Among the eight new Forestry sector fellows are six Swedish citizens and two foreign fellows. 

The Royal Swedish Academy of Agriculture and Forestry (KSLA) was founded in 1811. Apart from the Forestry section, it comprises two other sections, a General section and an Agricultural section. The Academy is a free and independent network organization working with issues related to agriculture, food, forestry, fishing and hunting. Its independent position shall create a unique opportunity for meetings and constructive discussions, which can be used as starting point for taking initiatives on measures or activities that stimulate development in the respective focus areas. 


Link to the announcement of the Royal Swedish Academy of Agriculture and Forestry (in Swedish)

https://www.ksla.se/senaste-nytt/nyheter/nya-ledamoter-skogsavd-2019/ 


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The newly printed version of the special issue.  (Photo: Carolin Rebernig)

The Scandinavian Journal of Forest Research recently published a special issue on the usage of vegetatively propagated Norway spruce clones in Swedish forestry. The UPSC Centre for Forest Biotechnology, a Vinnova Competence Centre, initiated this publication to disseminate research findings widely within the forest sector. Lately, the large-scale usage of genomically selected, vegetatively propagated plants became technically possible and the researchers want to launch a discussion about the pros and cons of the usage of clones. During 2020, the results of the issue will also be presented and discussed in an open seminar. 

The need of an educated discussion about gains and possible risks advanced the idea of publishing a special issue about the usage of clones in Swedish forestry. “We initiated an extensive literature search on the current knowledge related to the use of clones in forestry and its implications for Swedish forestry. This involves knowledge about the effects from a breeding, silviculture, population genetics and ecology standpoint” explains Ove Nilsson, the Director of the Vinnova Competence Centre and guest editor of the special issue. 

All together the reviews show that not only from an economical viewpoint considerable gains can be made by the use of clonal mixtures, but also that the effect on the genetic diversity in Swedish forests will be very minor during the foreseeable future. Ove Nilsson emphasizes that due to the rapidly changing climate quick selection methods to deploy better adapted plants are needed. “We show that these techniques can be key to be able to meet future rapid changes reacting on for example pathogens and droughts caused by the climate change. This adaptation process is currently very slow.” He also pointed out that it is important for UPSC to discuss this topic. “We have knowledge in this area and we have a goal to make sure that our basic research findings can be used to breed for future generations of tree seedlings with better properties and better adaptation to new climate.”

Norway spruce is one of the economically most important forest trees in Sweden. Efforts to optimize productivity, resistance to diseases and to get more resilient plants adapted to a changing climate are constantly made. One way to get rapid access to the very best material from the operational tree breeding programs is vegetative propagation – especially when this method is used in combination with applications of genomic information through a process called genomic selection. The discussion about gains and possible risks of such applications, especially about the effects of a reduced genetic diversity when using clones, is ongoing. 


Full reference of the publication and link to the online edition:
Special Issue: Using Norway Spruce Clones in Swedish Forestry. Scandinavian Journal of Forest Research, vol. 34, 2019, Issue 5.
https://www.tandfonline.com/toc/sfor20/34/5?nav=tocList

For more information please contact:
Ove Nilsson
Umeå Plant Science Centre 
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

AgriseraPrize2019 1920x1080From left to right: Joanna Porankiewicz-Asplund (Agrisera), Catherine Bellini (Chair of the UPSC board), Jan Karlsson; photo: Anne Honsel

[2019-12-04] This year’s UPSC Agrisera Prize is awarded to Jan Karlsson to acknowledge his ceaseless technical support for everyone working at UPSC. Jan Karlsson works as IT-coordinator at the Department of Plant Physiology, Umeå University, but carries out many additional tasks that are important to keep the research infrastructure at UPSC running. The prize was awarded during today’s traditional UPSC Christmas lunch.

The UPSC board received two independent nomination letters for Jan Karlsson for the UPSC Agrisera Prize 2019. Both letters highlighted his ambition to solve all upcoming technical problems as soon as they appear even if it is challenging and demands to work outside the normal working hours. “He is the one, who we hope to find in his office when we need a solution for a challenging technical issue”, is stated in one of the letters. “His everyday work contributes to the successful research of many of us at UPSC.”

Jan Karlsson is IT-coordinator at one of the two UPSC departments. He is responsible for the growth chambers and cabinets, is technically supporting the new phenotyping platform, helps to fix things that are broken and much else. During the recent renovations at the Department of Plant Physiology, he was one of those who helped to make the moving and the setting up of the new lab as smooth as possible without neglecting his normal responsibilities. “We would like to thank Janne for being so available and make our work doable in this institute. This Agrisera prize is the opportunity for us to do so”, is written in the second nomination that was supported by more than 30 people.

The UPSC Agrisera Prize is awarded every year to a PhD student, a postdoc or a technician for excellent scientific achievement and positive contributions to improve the UPSC work environment. It is sponsored by Agrisera but the members of the UPSC board select the winner of the prize. The name of the winner is traditionally announced during the UPSC Christmas lunch. This year, the board received in total eight nominations for six candidates. The prize was presented by Joanna Porankiewicz-Asplund from Agrisera and by the chair of the UPSC board, Catherine Bellini.

IMG 6458 1920x1080From left to right: Leszek Kleczkowski (chair of the public defence), Tom Beeckman (committee member), Maria Eriksson (commitee member), Abdellah Lakehal, Catherine Bellini (PhD supervisor), Malcolm Bennett (opponent), Alain Goossens (committee member); photo: Anne Honsel

[2019-12-02] When young, dark-grown seedlings of thale cress are given light, they start to form roots from the stem-like part of the plant, called hypocotyl. Abdellah Lakehal used this system to study how the initiation of these adventitious roots is regulated at the molecular level. He identified new components of the complex regulatory network and elucidated further how the main components of the network interact with each other. Abdellah Lakehal successfully defended his PhD thesis on Thursday, 28th of November 2019 at Umeå University.

Plant hormones are growth regulators that play an important role in the regulation of adventitious root initiation. The plant hormones auxin, jasmonate and cytokinin interact with each other to control adventitious root initiation. While auxin promotes adventitious root formation, jasmonate and cytokinins inhibit this process. Abdellah Lakehal now added several new molecular pieces to this complex regulation.

He identified two so-called auxin co-receptors, proteins that fine tune the auxin response during adventitious root initiation. He also showed how jasmonate controls the degradation of auxin in a feedback manner by regulating the expression of another protein. Abdellah Lakehal concluded that this protein mediates a molecular circuit that allows to stabilize the interaction between auxin and jasmonate. In addition, he identified additional components from the jasmonate pathway that prevents the formation of adventitious roots by regulating cytokinin signalling.

Abdellah Lakehal worked with thale cress seedlings. To induce the formation of adventitious roots, he first let the seedlings grow in darkness for three days. Then, the dark-grown seedlings were exposed to light to trigger the development of adventitious roots on the hypocotyl, which is an embryonic stem.

Adventitious roots are important for the vegetative propagation of plants. Many plant species naturally form adventitious roots like for example grasses, cereals or bulb plants but also blackberries or strawberries to propagate without setting seeds. But adventitious roots can also be induced by wounding, flooding or changes in temperature. The vegetative propagation of plants is widely used in forestry and agriculture to clonally multiply elite genotypes.

About the public defence:

The public defence took place on Thursday, 28th of September Umeå. It was chaired by Prof. Leszeck Kleczkowski. The faculty opponent was Malcolm Bennett, Professor, Plant and Crop Sciences, School of Biosciences, University of Nottingham, UK. The defence committee was composed of Docent Maria Ericksson (Umeå University), Prof. Tom Beeckman (VIB, Ghent University, Belgium) and Prof. Alain Goossens (VIB, Ghent University, Belgium). Abdellah Lakehal's supervisor was Prof. Catherine Bellini.

Title of the thesis: A molecular network mediating adventitious root initiation in Arabidopsis thaliana

Link to the thesis: http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A1368017&dswid=6231


For more information, please contact:

Abdellah Lakehal
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

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The UPSC Greenhouse (Photo: Anne Honsel)

In their meeting on the 21st of November 2019, the Kempe Foundations decided to grant a package of six post-doctoral stipends and to approve four additional applications from UPSC. The stipend package is granted to UPSC and it will be used in the frame of a recently started genome sequencing project of Norway spruce and Scots pine that is coordinated by Ove Nilsson. Peter Kindgren and Ewa Mellerowicz receive funding for their research projects, Annika Nordin for doing field work and Stéphane Verger support to buy a new advanced microscope. 

UPSC is currently developing a significantly improved reference version of the spruce genome and a full sequence of the Scots pine genome, together with extensive resequencing of spruce and pine genomes. This project was funded in January 2019 by the Knut and Alice Wallenberg Foundation together with a linked project at the Science for Life Laboratory in Uppsala/Stockholm coordinated by Ulf Gyllensten. The six post-doctoral fellows granted by the Kempe Foundations will allow UPSC groups to take full advantage of the new conifer genomic tools and to help to further improve the resource.

Peter Kindgren (SLU) is investigating the functional role of non-coding transcripts in plants. These transcripts originate from genome regions that do not contain protein information and were first thought to be insignificant noise but have been shown to play diverse biological roles. Peter Kindgren plans to apply a recently developed method to study these non-coding transcripts in tree species like aspen and spruce. He wants to find out how the non-coding DNA of these tree species is used to adapt them to their environment.

Ewa Mellerowicz’s project is focussing on certain lipophilic compounds of the aspen wood which often impact pulping negatively but are interesting for pharmaceutics, cosmetics and the paint industry. Ewa Mellerowicz and her group want to elucidate the nature of these compounds, their link to hemicellulose, one of the main components of wood, and see if they occur also in other tree species. They hope that their results can improve the pulping process. In a parallel approach, they plan to test if these lipids have antibacterial or anticancer properties and might serve as basis to develop new products from the wood. 

Annika Nordin and her co-applicant, Jonas Öhlund from Skogforsk, are planning to study how the choice of planting spot on a forest clear-cut in combination with timing of planting and fertilization of the seedlings can improve the establishment and growth of newly planted trees. The researchers hope that their results will improve the efficiency of forest regeneration practices and contribute to more sustainable forestry. The funding from Kempe Foundations will cover the costs for the field work. 

Stéphane Verger is doing research on plant cell-to-cell adhesion and plant biomechanics.  The Kempe Foundations grant will, together with additional funding from SLU, allow to acquire an Atomic Force Microscope (AFM) to complement the existing high-end microscopy equipment available at UPSC. This technology provides a large array of possibilities to quantify the mechanical properties of plants. The spectrum reaches from measuring the pressure inside living cells, to measuring the stiffness of the plant cell walls in seedlings or in wood, to the nanoscale structure of components making up the plant, like cellulose. The AFM will be used by several research groups at UPSC and KBC. 



Contact information of the project leaders:

Ove Nilsson
Umeå Plant Science Centre 
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/ove_nilsson

Peter Robert Kindgren
Section for Molecular Plant Biology
Department of Plant and Environmental Sciences
University of Copenhagen
e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://plen.ku.dk/english/employees/?pure=en%2Fpersons%2Fpeter-robert-kindgren(525289c6-db78-4032-8942-ade2c82c3792).html

Ewa Mellerovicz
Umeå Plant Science Centre 
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/ewa_mellerowicz

Annika Nordin
Umeå Plant Science Centre 
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/annika_nordin

Stéphane Verger
Umeå Plant Science Centre 
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/stephane_verger

1920 ljung novak
Ondřej Novák and Karin Ljung (Photo: Carolin Rebernig)

On 19th of November 2019, Clarivate Statistics published its annual list of Highly Cited Researchers. This list is based on a citation analysis of the Web of Science databases and identifies highly cited scientific publications. This year two UPSC researcher are on the list – Karin Ljung and Ondřej Novák. Both are listed as authors of highly cited papers that rank among the top one percent in the field of “Plant & Animal Science” during their year of publication.

Since 2002, the list of the world´s most highly cited scientific authors have been presented. Karin Ljung has been on the list for the sixth year in a row, for Ondřej Novák it’s the second time. In total the 2019 list comprises about 6000 Highly Cited Researchers from almost 60 Nations in 21 different categories.


The Clarivate Analytics list of Highly Cited Researchers 2019:

https://recognition.webofsciencegroup.com/awards/highly-cited/2019/

Detailed information about the analysis method Clarivate Analytics is applying can be found here:
https://recognition.webofsciencegroup.com/awards/highly-cited/2019/