PhD Postdoc Retreat2018 1920x1080"Fighting Swedish mosquitos" - UPSC Phd students and postdocs in Skeppsvik; photo: Niklas Mähler
[2018-08-30] Around 40 of the PhD students and Postdocs working at Umeå Plant Science Centre went on their second retreat to Skeppsvik Herrgård last week. The program of the two days was filled with scientific discussions, team building activities and career coaching. This was the second time that the UPSC PhD students and Postdocs organised a retreat. All participants were very satisfied with the event.

This year’s program was split into two parts: a scientific part with project presentations and creative community building exercises and a training session that introduced strategies for personal career development. All sessions were highly appreciated by the participants even though some parts lead to intense controversial discussions.

Thursday started with a social media competition, in which the researchers were asked to share their impressions, thoughts and upcoming discussion points during the retreat using the hash tag #UPSCretreat2018. The post that achieved most attention got about 100 re-tweets and likes. It was posted by Amit Bajhaiya, who was awarded with 2 cinema tickets.

During a “speed geeking” session, the participants had two and a half minutes to talk one-to-one about their project before changing the partner. “We had to select four to six emojis that describe our project best and discuss this during the speed-geeking”, explained one participant. “That turned out to be much more difficult than I expected but everyone came up with very creative interpretations”. Another participant added: “Especially for new-comers this session was really nice because you easily get in contact with the other people and also obtain a general overview of the ongoing research projects at UPSC.”

In the afternoon session of the first day, mixed teams of postdocs and PhD students were competing in games that simulated daily research and lab-situations. Each team was composed of young and experienced researches that could help each other by discussing ideas and opinions from different perspectives.

“We prepared a game named “waste sorting” where the teams were asked to separate liquid waste appropriately”, said one of the organisers. “Many of us were facing the problem that we do not know how to dispose certain liquid waste. With this game, we wanted to address this problem and improve the situation.”

Other games, such as “Plan your project”, “Guess which researcher chose these emojis for her/his project”, “Critical thinking”, encouraged the participants to exchange their opinions on how to structure a project and how to critically review scientific results. “We all know how it is when you arrive new at an institute. You have so many questions but do not know whom to ask”, describes another one of the organisers. “All those community building games help to get to know each other and this makes it easier to ask someone for support.”

The late afternoon of the first day was reserved for various outdoor activities, such as kayaking, swimming and sauna, and the evening for informal discussions about the role of scientific communication and transparency for society.

On the second day Tina Persson, a former senior researcher at Lund University and now career service coordinator, held a workshop about career development for young researchers. She introduced career development strategies, gave advice on how to figure out what kind of academic or non-academic job is suitable for one´s skills and preferences, and showed how to use social media platforms to find suitable positions. The day was concluded by a final discussion reflecting the retreat in preparation of the next retreat in 2020.

The UPSC PhD and Postdoc retreats are organised by the PhD students and Postdocs themselves with the idea to bring colleagues closer together, while improving work related skills at the same time. The first retreat happened in 2016 and got very positive feedback, encouraging it to become a biannual tradition.

Text: Domenique André, Carolin Seyfferth, Anne Honsel
composite cropped 1920Left photo: porcupine mutant (pcp-2) growing at low ambient temperature (16°C); right photo: close-up showing the malformed “spiky” leaves of a pcp mutant (photos: Giovanna Capovilla; arrangement: Markus Schmid)

A research team led by Markus Schmid has identified a new player regulating plant development under low temperatures. The researchers searched for mutants that have strong growth defects when grown at low temperatures but look otherwise normal. They found the porcupine mutant and showed that the PORCUPINE gene is crucial for normal plant development at low temperatures. Their results are published as Brief Communication article in the journal Nature Plants.

Plants react to changing temperatures by adjusting their development and growth rate. The mutant, that lost the active PORCUPINE gene, grows very slowly at lower temperatures (16°C), displays sever developmental defects and is not able to produce seeds. However, it looks almost like non-mutated plants when growing at favourable temperatures (23°C). The researchers around Markus Schmid concluded that the PORCUPINE gene is required specifically at low temperatures and is crucial for adjusting the plant development and growth to low temperatures.

A recently suggested important mechanism that allows plants to adjust their growth and development to changes in temperature is the so-called alternative splicing (see also below). This process enables a single gene to produce different protein versions depending on which parts of the gene are spliced together and translated. The resulting proteins are altered in their structure and can have different functions. There are factors that regulate which protein variant is synthesised by alternative splicing. PORCUPINE appears to be one of those factors that regulates alternative splicing events under cold temperatures.

Many of the alternative splicing events that take place in the non-mutated plant at lower temperatures are missing in the mutant that lost the active PORCUPINE gene. “We think that PORCUPINE plays a crucial role for connecting plant responses to low temperature with plant development via alternative splicing”, explains Markus Schmid. “This is a new but very complex regulation pathway that we just now start to explore.”

The PORCUPINE gene got its name from the special look of the mutant that lost the functional PORCUPINE gene. The leaves of the mutant are radialised and the hairs (trichomes) on the surface of the mutant are often branched more frequently, giving the mutant a very “spiky” appearance – reminiscent of a porcupine.

What is alternative splicing?
When a gene gets activated its DNA sequence is first transcribed into pre-mRNA (precursor messenger ribonucleic acid). Many pre-mRNAs in plants and animals are than spliced to remove parts (introns) that do not contain information for the encoded protein. The remaining “exons” are stitched together to form a mature mRNA, which is subsequently translated into a protein. Depending on which intros are spliced out and which exons are joined together, different mRNAs can be produced from a single gene, resulting in different protein versions.


The article:
Giovanna Capovilla, Nicolas Delhomme, Silvio Collani, Iryna Shutava, Ilja Bezrukov, Efthymia Symeonidi, Marcella de Francisco Amorim, Sascha Laubinger & Markus Schmid (2018) Nature Plants,
PORCUPINE regulates development in response to temperature through alternative splicing

Link to the publication:

For more information, please contact:

Markus Schmid, professor
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
This email address is being protected from spambots. You need JavaScript enabled to view it.

DariaChrobok IMG 4677 1920x1080Daria Chrobok (middle) and her two supervisor Olivier Keech (right) and Per Gardeström (left); photo: Anne Honsel

Leaves turn yellow naturally, in autumn, when they get old or when the plant is exposed to stresses like darkness or drought. Daria Chrobok compared in her PhD thesis different scenarios of leaf yellowing and analysed what happens on the metabolic level. She showed that mitochondria, the respiratory power stations of the cell, are crucial for a coordinated adjustment of metabolism during leaf yellowing. Mitochondria stay active until the last stages of leaf yellowing to provide the energy that is needed for recycling nutrients from the dying leaf. Daria Chrobok successfully defended her thesis on the 8th of June.

The yellowing of a leaf, also called senescence, occurs naturally in for example deciduous trees in autumn or when annual plants get old and produce seeds. However, also stresses like a lack of nutrients, drought or pathogens can induce senescence. Daria Chrobok compared naturally aging plants with plants where senescence was induced by darkening a single leaf. She showed that in both cases the mitochondria remain intact until the last stages of leaf senescence to provide the energy needed for the mobilisation and transport of nutrients.

In addition, she showed that especially the amino acid glutamate, that can be easily transported within the plant, accumulates during leaf senescence. She hypothesized that this accumulation of glutamate in the mitochondria and its conversion to glutamine in the cytosol are essential steps for the reallocation of nitrogen rich compounds to other parts of the plant.

The export of amino acids with high nitrogen content into developing parts of the plant, e.g. seeds, is of high importance to ensure that those seeds contain enough nitrogen and the survival of the next generation is guaranteed. Nitrogen is often a limiting factor for plant growth and development and therefore the reallocation of nitrogen during senescence is important for plants.

Without light, plants cannot perform photosynthesis and produce energy-rich carbon compounds like sugars. If only one leaf is darkened, the covered leaf will rapidly turn yellow. In contrast, when the whole plant is darkened, the leaves are repressing this induction of senescence, i.e. they stay green. The plant keeps all components needed for photosynthesis alive and intact so that upon sudden light exposure, the plants are ready to start photosynthesis and continue growing.

Daria Chrobok and her colleagues analysed how plants adjust their metabolism to those two darkening conditions and they compared these results with the light-dependent “stay-green” mutant. When one leaf of a stay-green plant is darkened, it stays green, whereas the same treatment in a wild type plant leads to the yellowing of the darkened leaf. This darkened stay-green leaf, as well as the whole darkened plant accumulate amino acids, especially those with high nitrogen and low carbon content.

The understanding of how “stay-green” plants manage to stay green is interesting for the food industry to keep vegetables green for longer time and for agriculture, to ensure proper grain and nutrient filling as well as other improved traits for crop plants.

The public defence took place in Lilla hörsalen at KBC, Umeå University, on Friday, 8th of June 2018. Faculty opponent was David Macherel, IRHS-MitoStress, University of Angers, France. Supervisors were Olivier Keech and Per Gardeström.

Title of Daria Chrobok’s thesis: “To “leaf” or not to “leaf” - Understanding the metabolic adjustments associated with leaf senescence”

Link to the doctoral thesis: urn:nbn:se:umu:diva-147700

Are you interested to read more? Have a look on the comic strip made by Neil E. Robbins II. He illustrated the results from the article Law et al., 2018 (Plant Physiology) that is included in Daria Chrobok’s thesis. The comic explains very nicely the metabolic adjustments during the different dark treatments:

The article:
Simon R Law, Daria Chrobok, Marta Juvany, Nicolas Delhomme, Pernilla Lindén, Bastiaan Brouwer, Abdul Ahad, Thomas Moritz, Stefan Jansson, Per Gardestrom, Olivier Keech (Plant Physiology) 2018; DOI:
Title: Darkened leaves use different metabolic strategies for senescence and survival

UPSC Days2018 Kjell1 070928 0019 1920x1080

The registration to the UPSC Days 2018 is now open! They will take place on September 6-7 at Sliperiet on the Konstnärlig Campus in Umeå.

The first day will start with a session about future visions for UPSC and continue after lunch with an update about the most recent changes of the UPSC infrastructures. We will also have a scientific session with 3 minutes flash talks and end the first day with a barbecue that will take place in front of UPSC.

On the second day, Anna-Karin Byström from DC Consulting AB will give a workshop on intercultural communications. This workshop will include seminars giving theoretical background about cultural understanding and the communication process as well as practical exercises and tools to handle and interpret actions and reactions that arise in meetings with people of different backgrounds. We will finish the second day with the lunch.

The registration is closed. For questions please contact: This email address is being protected from spambots. You need JavaScript enabled to view it.


Preliminary programme

Location:  White boxes, Sliperiet, Konstnärlig campus, Umeå (see on map)

Day 1 - Thursday, 6th September 2018
9:30 - 10:00 Registration and coffee
10.00 - 10.10 Welcome
The future UPSC
10.10 - 10.40 Visions for UCMR (Umeå Centre for Microbial Research)
Bernt Eric Uhlin, UCMR & MIMS, Department of Molecular Biology, Umeå University
10.40 - 11.35 Visions for UPSC
Ove Nilsson (director of UPSC), Karin Ljung (prefect of the Department of Forest Genetics and Plant Physiology, SLU) and Stefan Jansson (prefect of the Department of Plant Physiology, Umeå University) will talk about their visions for UPSC.
11.35 - 12.15 Podiums discussion
Chair: Catherine Bellini, Chairmen of the UPSC board
12.15 - 13.30 Lunch
Infrastructure update
13.30 - 13.50 The new phenotyping platform at UPSC
Ove Nilsson (director of UPSC)
13.50 - 14.10 News from the Bioinformatics platform
Nicolas Delhomme (Manager of the UPSC Bioinformatics platform)
14.10 - 14.40 Coffee break
14.40 - 15.10 Flash-talk competition
Scientific session with 3 min flash talks (max. 1 slide)
15.10 - 15.20 Voting and award presentation
16.30 Barbecue at the Umeå Plant Science Centre (Please bring your own food and drinks)
 Day 2 - Friday, 7th September 2018
Intercultural communications workshop
Anna-Karin Byström, Ph.Lic. Organisational Communication and CEO, DC Consulting AB
9.00 - 9.10 Brief introduction and presentations
9.10 - 10.10 Intercultural communication - introduction to cultural understanding and the communication process
10.10 - 10.55 Coffee and workshop
10.55 - 11.45 Practical tips concerning communication between people of different backgrounds including practical exercises
 11.45 - 12.00 Concluding the workshop and shorter reflection
12.00 - 12.10 Final conclusion by the organisers
12.10 - 13.10 Lunch
HalehHayatgheibi 1920x1080Haleh Hayatgheibi and her PhD supervisor Harry Wu (Photo: Anne Honsel)

On Friday, 18th of May, HalehHayatgheibi successfully defended her PhD thesis. She has worked on lodgepole pine (Pinus contorta), a fast-growing tree that was largely introduced into Sweden in the mid-1960s. One major problem of lodgepole pine trees is that their stems are often bending or even break and this lowers the economic value of the wood. Haleh Hayatgheibi designed breeding strategies to optimize both wood quantity and quality of lodgepole pine to reduce stem bending and breakage. 

Haleh Hayatgheibi estimated genetic parameters which determine wood quality and quantity of lodgepole pine. She measured for example the diameter of the stem as parameter for wood quantity and the stiffness of the stem. A higher stiffness might prevent the breakage of the stem when it bends and decrease the economic loss. This feature is especially interesting for Northern Sweden. 

Lodgepole pine trees from different origin in Canada were planted in different climatic regions in Northern Sweden, e.g. close to the coast or more inland. Haleh Hayatgheibi compared those trees with each other to see which are best suited for which region in Northern Sweden. Based on her results, she can now recommend tree breeders which lodgepole pine trees have the best prerequisites for which climatic region. 

Title of the thesis: “Quantitative genetics of lodgepole pine (Pinus contorta) wood quality traits in Sweden

Link to the doctoral thesis:

The public defence took place in Björken at SLU Umeå on Friday, 18thof May 2018. Faculty opponent was Yousry A. El-Kassaby from the Forest Sciences Centre, University of British Columbia, Canada. The supervisor was Harry Xiaming Wu. 

Six collaborative projects were selected by external reviewers and are now open for application. The postdoctoral fellows will be recruited at the Umeå Plant Science Centre in Sweden but will spend some time at the collaborating partner institute either in France or in Spain. The goal is to intensify the exchange between the three partners of the INUPRAG cooperation

The INUPRAG cooperation exists since 2015 and is a collaboration between the Umeå Plant Science Centre(UPSC, Sweden), the National Institute for Agricultural Research(INRA, France) and the Centre for Research in Agricultural Genomics(CRAG, Spain). The goals are to foster joint research projects in plant science between the different partners and to train young scientists through regular exchanges between the partner laboratories. 

The six granted postdoctoral projects cover different topics within plant science. All group leaders from UPSC could apply with collaborative projects for the postdoctoral fellowships. Three (?) external referees evaluated all submitted projects and selected the six best, three from Umeå University (Department of Plant Physiology) and three from SLU (Department of Forest Genetics and Plant Physiology). 

Are you interested in applying for one of the fellowships? Have a look on the job announcement here

More information about the INUPRAG cooperation 

The granted projects are: 

Project 1: Interactions between Plastid and Light Signalling Pathways

Project leaders: Åsa Strand (UPSC) & Elena Monte (CRAG)

Read more about project 1

Project 2: Regulation of the Master Floral Regulator LEAFY by Ubiquitination through the E3 Ligases UFO and BOP2 

Project leaders: Markus Schmid (UPSC), Ove Nilsson (UPSC) & François Parcy (INRA, Grenoble)

Read more about project 2

Project 3: An evo-devo approach to elucidate the role of PIRIN proteins during non-cell autonomous lignification

Project leaders: Hannele Tuominen (UPSC) and Richard Sibout (INRA, Nantes)

Read more about project 3

Postdoctoral project 4: Unravelling cluster root emergence in white lupin

Project leaders: Stéphanie Robert (UPSC) & Benjamin Péret (INRA, Montpellier)

Read more about project 4

Project 5: Cell wall mediated control of differential cell elongation in Arabidopsis hook Development

Project leaders: Rishikesh Bhalerao (UPSC) and Olivier Hamant (ENS, INRA, Lyon)

Read more about project 5

Project 6: Enabling scale-up of somatic embryogenesis (SE) plant production by physiological analysis of embryos processed in bioreactors and the R&D SE System for harvest

Project leaders: Ulrika Egertsdotter (UPSC) and Marie-Anne Lelu-Walter (INRA, Orleans)

Read more about project 6

IMG 4506 1920x1080Christoffer Johnsson and his supervisor Urs Fischer; photo: Anne Honsel

On Friday, 20th of April, Christoffer Johnsson successfully defended his thesis titled “Elucidating the phytohormonal control of xylem development”. He could show in his thesis that the plant hormones auxin and gibberellin are important signals for normal wood development in poplar trees. The public defence took place in P-O Backströms sal at SLU Umeå. Faculty opponent was Andrea Polle from the Buesgen Institut, Georg-August University Göttingen, Germany. His academic supervisor was Urs Fischer.

Link to the doctoral thesis: 

You can find more background information about Christoffer Johnsson’s work here (in Swedish):

J4A1095 1920x1080 TNasholm photoJohan MarklundTorgny Näsholm is awarded the 2018 Marcus Wallenberg Prize. Photo: Johan Marklund

Torgny Näsholm discovered that amino acids play an important role as nitrogen source for plants. He receives now the Marcus Wallenberg Prize 2018 for his ground-breaking research. 

Please have a look on the Marcus Wallenberg Foundation homepage for more information:

NatStreet teaching 1920x1080Photo: Kathryn Robinson

The plant geneticist and lecturer at the Department of Plant Physiology, Nathaniel Street, is awarded the pedagogical prize from the Faculty of Science and Technology. The prize jury motivated its decision due to his outstanding ambition, good organization and strong interest in developing new ways of teaching. Nathaniel Street will receive the prize during the Spring graduation ceremony of Umeå University on the 19th of May.

“I was on the Ski lift and checked my emails when I found out that I was awarded for the prize”, tells Nathaniel Street. “I was so surprised that I had to read the message twice to be sure that it was true. It is fantastic to know that the efforts made for teaching are acknowledged and appreciated. I really did not expect this, especially because there are so many other excellent teachers in our institute.”

Nathaniel Street came as a postdoc to Umeå University in 2007. In 2011, he became Assistant Professor and is since January 2016 Associate Professor at the Department of Plant Physiology.

During his time at Umeå University, he has fast developed his teaching skills further. He became the course leader of the department’s genomics courses in 2011 and has refined the course since then. Nathaniel Street is also teaching on the courses Bioinformatics and Genome Analysis and Microbiology and Basic Molecular Biology at Umeå University as well as the course Plant Biology for Future Forestry at the Swedish University of Agricultural Sciences (SLU).

The prize motivation emphasizes Nathaniel Street’s extremely careful preparation of his teaching. He gives well prepared and clear lectures that are greatly appreciated by the students and he is continuously improving his teaching methods. Among others, he has introduced interactive and student-led discussions, new practical classes in the lab and discussions on ethics. Several of these initiatives have subsequently been taken over by other teachers at the institution.

“He involves both his own research group and the bioinformatics platform at the Umeå Plant Science Centre in his work and successfully creates extremely smooth ways of teaching, that not only allow the students to get in contact with actual research, but are also very interesting for the research itself”, is stated in the prize motivation. “His high competence in both plant biology and genetics as well as in advanced computing has made this possible.”

Nathanial Street focuses his research on finding the genes that control natural variation and he is analysing microbial communities that are living close together with forest trees. His ambition is to combine his research interest with his educational ambition and strong willingness to develop his teaching methods further.

“My hope is to convey my own fascination and interest in my research area. It can be a challenging area to teach because it is changing very fast, but I try to keep the courses up to date. I do not want the students to just sit and listen to me. It is fun to think of new ways to motivate the students to learn together and from each other and to help them develop skills to learn independently in the future. The courses I have attended at the University Education and Teacher Support (UPL) have been a great inspiration for this.”

Link to the Swedish press release

For more information, please contact:

Nathaniel Street
Associate Professor
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Phone: 090-786 54 73
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Bud from the model organism hybrid aspen (Populus tremula x Populus tremuloides); Photo taken by Pal MiskolcziBud from the model organism hybrid aspen (Populus tremula x Populus tremuloides); Photo: Pal Miskolczi

For trees in boreal and temperate climates, it is important that buds do not burst precociously, but only when it's spring for real. Therefore, the buds are put in dormancy in the autumn, which means they have to go through a long cold period before they slowly become susceptible to the signals of spring. The mechanism behind this is revealed in a new study led by Rishi Bhalerao from UPSC, recently published in the journal Science.

Trees are amongst the longest-living organisms on Earth, and some species can live for thousands of years. One of the key mechanisms that enable such a long life is their synchronization of growth with change in seasons. For example, in temperate and boreal ecosystems, trees stop their growth and establish dormancy prior to the advent of winter. Growth cessation and dormancy establishment is a key adaptive mechanism for winter survival, since failure to cease growth and establish dormancy can result in fatality from extreme low temperatures in the winter.

How trees know when to stop their growth and establish dormancy is a question that has been of interest to researchers since a long time. That growth stops in response to the decrease in daylight during autumn has been well understood. The establishment of dormancy, which means that buds cannot burst before they have experienced a long cold period, and are not awakened by short warm periods during winter, has been more of a mystery. The recent article in Science, however, provides an important insight into how winter dormancy is regulated in perennial trees.

What the researchers could show is that the so-called plasmodesmata, channels that connect different cells with each other, are closed by the deposition of callose, a polysaccharide, in response to the shortening of day length in the autumn. The blockage of the plasmodesmata prevents cells from receiving growth promotive signals, thereby maintaining growth arrest and establishing dormancy in the buds.

The researchers also show that short-day induced dormancy is regulated by the plant hormone abscisic acid which activates (among others) the production of the callose that is used to block the plasmodesmata. Once blocked, a long exposure to low temperatures is needed to slowly re-open the plasmodesmata again, so that the growth-inducing signals can reach the buds and stimulate the growth in the buds in the spring.

"Interestingly, some of the facets of the dormancy regulation mechanism described in our paper have been observed in winter wheat as well as characean algae, suggesting that this mechanism is probably ancient and evolutionarily conserved", says Rishikesh Bhalerao.

The study was conducted using hybrid aspen, which is a model plant in tree research.

The study has been conducted by a research team led by Rishi Bhalerao from SLU's Department of Forest Genetics and Plant Physiology and the Umeå Plant Science Center. The colleagues come from SLU in Alnarp, Uppsala University, University of Helsinki, Cambridge University, Monash University and the University of Environmental and Life Sciences in Norway.

Link to the Swedish press release on the SLU homepage

More information

Contact person
Rishikesh P. Bhalerao, Professor
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences, Umeå
+46 (0)90-786 84 88, +46 (0)70-678 37 32, This email address is being protected from spambots. You need JavaScript enabled to view it.

The article
S. Tylewicz, A. Petterle, S. Marttila, P. Miskolczi, A. Azeez, R. K. Singh, J. Immanen, N. Mähler, T. R. Hvidsten, D. M. Eklund, J. L. Bowman, Y. Helariutta, R. P. Bhalerao. 2018. Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication. Science 10.1126/science.aan8576 (2018). 
DOI: 10.1126/science.aan8576

Direct link to the article in Science

Text: David Stephansson (SLU)