Newsletter 1/2017 [January - June 2017] issued at the end of June

WP3 Enhancement of research excellence

New people in the NCN projects - welcome newcomers

dr William Truman NCN OPUS "Understanding the role of chitin related defence responses during Plasmodiophora brassicae infection"

Soham Mukhopadhyay

Name: Soham Mukhopadhyay (Ph.D. student; India)

Education: 2010-2015 5 years integrated B.Sc.-M.Sc. from St. Xavier's College, Kolkata, India
                 2015-2016 Research fellow at Bose Institute, Kolkata

Area of interest: molecular plant-microbe interactions

I'm fascinated by the evolutionary arms race that exists between plants and microbes. My 5 year graduate course at St. Xavier's College and 1 year research experience at the Bose Institute exposed me to various theoretical and practical aspects of molecular biology. I developed an abiding interest in plant innate immunity, the different lifestyles of plant pathogens and the tools used to decipher the intricate interactions of pathogen and host. During my Ph.D. tenure in Poznan I wish to apply this knowledge to uncovering the virulence mechanisms of Plasmodiophora brassicae.

Juan Camilo Ochoa

Name: Juan Camilo Ochoa (Ph.D. student; Columbia)

Education: 2009-2011 Master in sciences (Biological Sciences), Universidad Nacional de Colombia - Bogotá
Employment: 2011 - Research Assistant, Archive of Bogotá. Colombia
                   2011-2013 Research Assistant, Universidad Nacional de Colombia, Bogotá
                   2013-2014 Research Assistant, Archive of Bogotá. Colombia
                   2014-2016 CENIPALMA, Barrancabermeja, Colombia.

Area of interest: plant-pathogen interactions

After graduating as a biologist with an emphasis in plant genetics and molecular biology, I have acquired 5 years of experience working in the area of molecular plant-pathogen interactions, specifically in the Xanthomonas – cassava and Phytophthora palmivora – oil palm pathosystems. During these years my main interest has been to develop plant breeding tools by using molecular biology and genetic approaches based on knowledge of plant immunity. During my Ph.D. studies, I hope to take advantage of my previous experiences and learn novel methodologies to elucidate the molecular interactions between the pathogen Plasmodiophora brassicae and the model plant Arabidopsis thaliana.

dr Jorge Paiva NCN SONATA BIS "Purple Walls - Unraveling genome regulation to modulate wood formation in Salix purpurea: an integrative approach"

Mortaza Khodaeiaminjan

Name: Mortaza Khodaeiaminjan (post doc, Iran)

Education: 2013-2017 Ph.D. in Biotechnology Cukurova University, Adana, Turkey
Employment: 2017 - Research Associate in Biotechnology Cukurova University, Adana, Turkey

Area of interest: biotechnology, molecular genetics


The complexity of plant sciences and the technological advances that have been made to decipher the intricate underlying genetics have always fascinated me. I am intrigued by genomics, expression dynamics and the bioinformatics approaches of large-scale data analysis tools. Because of my background in agriculture as an undergraduate in Iran and from spending 6 years studying for my Master’s and Ph.D. in Cukurova University in Tukey, and also working at Queens University Belfast U.K. as a visiting research associate, I have been exposed to a variety of experiences in this field. My master’s thesis was about GMO and I also participated in some breeding programs. During my Ph.D. program my research was focused on pistachio (Pistacia vera L.) which is an important commercial nut, using techniques like: whole genome sequencing and development of SNP markers, in silico SSR marker development and construction of the first genetic reference map in pistachio, development of sex determination markers and mapping the sex locus and RNA-seq analyses for finding the molecular mechanism of periodicity - a very important problem in pistachio cultivation. During my research at Queens University, I worked on a GWAS project with the purpose of finding genes involved in abiotic stress responses in Arabidopsis. My Post-Doc project, PurpleWalls will address new and relevant genetic and molecular mechanisms controlling phenotype determination, and phenotypic adaptation to growing conditions in Salix purpurea as model for other Salicaceae and perennial species used for bioenergy. During my post-doc tenure, I will make use of omics tools to characterize the different expression levels of the genome for identification of regulatory gene network for wood formation. I wish to apply all my knowledge and experience to achieve excellent results in my project.

dr Franklin Gregory NCN OPUS "HyperNano: Understanding plant secondary metabolic changes in response to nanoparticles via an integrated omics approach in Hypericum perforatum"

Dariusz Kruszka

Name: Dariusz Kruszka (PhD student, Poland)

Education: 2010 - 2011 Poznan University of Life Sciences, Biotechnology
                 2011 - 2016  Poznan University of Medical Sciences, Pharmacy MSc
Area of interest: secondary metabolites


My master’s research work has been focused on secondary metabolite  accumulation in cell cultures (callus and cell suspension) under exposure to growth hormones, precursors and elicitors. I concentrated on pharmacologically important metabolites, triterpenoids, steroids and phenolic compounds. In the HyperNano project I will be studying the impact of nanoparticles on the profile of secondary metabolites. I will use chromatographic and spectroscopic techniques (LC, LC-MS, TLC, UV-Vis) for metabolomics works and molecular modeling and docking tools (in cooperation) for bioactivity prediction.                 

R. K. Selvakesavan

Name:  R. K. Selvakesavan (post doc, Indie)

Employment: 2006-2007 QC officer Sterling Biotech Limited, Ooty, India.
    2007-2009 Honorary Research Fellow, Sugarcane Breeding Institute, Coimbatore, India.
    2009-2012 Senior Research Fellow, Institute of Forest Genetics and Tree Breeding, Coimbatore, India
    2012-2013 Research Fellow, University of Minho, Braga, Portugal
    2014-2016 Research Consultant, Monsanto Research Center, Bangalore, India
    2010-2015 PhD in Biotechnology, Manonmaniam Sundaranar University, India
    2016-2017 Senior Research Associate and Lab Manager , Interpretomics India Pvt. Ltd
Area of interest: plant molecular biology

Exposure to abiotic and biotic stresses reduces plant productivity and plant responses to these stresses are very complex. I am interested in understanding the plant responses to different stresses. I am currently working on understanding the impact of nanoparticles on plant metabolism. I have 6 years of research experience in the field of plant molecular biology and four years of industrial experience in three different companies.

New NCN OPUS projects granted to dr Robert Malinowski and dr Franklin Gregory

2016/21/B/NZ9/01980 HyperNano: Understanding plant secondary metabolic changes in response to nanoparticles via an integrated omics approach

PI dr Franklin Gregory

Duration: January 2017- January 2020

Nanomaterial-containing waste released from a wide range of household, industrial and medical products are emerging as a new threat to the environment. Although recent studies have shown that plant growth, development and physiology are significantly affected by these nanoparticles, their impact on plant secondary metabolism is still unclear. Due to the importance of plant secondary metabolites in plant’s performance, communication and adaptation, we propose to investigate the impact of nanoparticles on plant secondary metabolism in this project.

Project team:

Dariusz Kruszka (Ph.D. student) has been working as a Ph.D. student with Dr. Franklin Gregory since April 2017. He obtained his master’s degree in pharmacy form Poznań University of Medical Sciences, Poland. He is currently studying the impact of nanoparticles on plant secondary metabolism.

Dr. R.K Selvakesavan (postdoc) joined Dr. Franklin Gregory’s group in May 2017. He received his doctoral degree in biotechnology from Manonmaniam Sundaranar University, India. His Ph.D. research focused on the isolation and in silico analysis of sodium transporter gene homologues from different tree species. In the HyperNano project, he is studying the changes in plant gene expression upon nanoparticle treatment.

Shakya P, Marslin G, Siram K, Beerhues L, Franklin G (2017) Elicitation as a tool to improve the profiles of high-value secondary metabolites and pharmacological properties of Hypericum perforatum. J Pharm Pharmacol. doi: 10.1111/jphp.12743.

Marslin G, Sheeba CJ, Franklin G (2017) Nanoparticles alter secondary metabolism in plants via ROS burst, Frontiers in Plant Science. 8: 832. doi: 10.3389/fpls.2017.00832


2016/21/B/ZN9/02020 The role of phloem transport in pea plants adaptation to water deficit

PI  dr Robert Malinowski

Duration: January 2017- January 2020

In this project we are aiming to verify the exact role of the structural and functional changes occurring within the phloem tissue in response to drought stress. We hypothesize that the ability of plant to modify osmotic properties in response to drought correlates with cellular/developmental phloem adjustment and increase in phloem transport. Our work will focus on anatomical and functional changes within the phloem as well as studies on sucrose and mannitol transport. We believe that the involvement of particular sugar loading and unloading proteins is essential in this response.

WP4 Cooperation and transfer of knowledge

Lectures, schools, workshops


11.05.2017 Apoplastic and symplastic phloem loading in tree leaves prof. Gertrud Lohaus, University of Wuppertal, Germany


30.03.2017 Quality in an Age of Change: Reference Resources and Big Data dr Paul Kersey, EMBL-EBI, Hinxton, UK

28.04.2017 Massive Analyses of cDNA Ends for simultaneous gene expression profiling and genotyping dr Bjorn Rotter, GenXPro, Frankfurt, Germany

29.05.2017 Plant E-Infrastructures: WheatIS & French Elixir node dr Hadi Quesneville, INRA-Versailles, France

prof. Gertrud Lohaus
dr Paul Kersey
dr Bjorn Rotter


dr Hadi Quesneville


Together with Marcus Sack (RWTH Aachen University) we have organized School of Biotechnology. This hands-on training aimed at practical understanding of modern tools of biotechnology. In particular attendees could learn the strategy of planti-bodies production as well as the new technique of transient gene expression in plant cell suspensions used for mass protein synthesis and purification (Plant-cell pack). Other parts of training covered subjects like chemically inducible gene expression and on field genotyping using “Genie” - the rapid amplification tool (together with Adam Burzynski – Novazyme). By courtesy of Poznan University of Life Sciences (Prof. Tomasz Jankowski) we also had an opportunity to visit the semi-industrial biotech station.

School of biotech. 1
School of biotech. 2


Intercultural communication

8.06.2017 “Intercultural communication – effective communication in an international team” was the topic of the latest workshop from the series of soft skills workshops. Dr. Beata Kozyra from BOMIS company invited the attendees to a world of cultural differences and national stereotypes, which so often create barriers in everyday communication. The workshop supported exchange of knowledge and experiences between international team working at IPG PAS. It also helped to identify possible problems, which might lead to miscommunication and explained what the principles of a good communication process are.


In April 2017 Ph.D. student Sara Blicharz spent 2 weeks at the Department of Molecular Plant Research/ Biochemistry at the University of Wuppertal and the group of Dr. Gertrud Lohaus. The purpose of this training stay was to learn the technique of laser aphid stylectomy and operation of the machine which is used for this technique. The major output of the stay was the opportunity to gain knowledge and practical experience in laser aphid stylectomy to use this technique to verify the exact role of phloem transport in pea plants adaptation to water deficit (NCN OPUS project "The role of phloem transport in pea plants adaptation to water deficit").

Training in Portugal

In June 2017 dr Karolina  Stefanowicz  and dr Jorge Paiva were at ITQB-NOVA (Oeiras, Portugal), in  the frame of the bilateral project “Poland –Portugal Cooperation on Cell Wall remodelling and under stress conditions in Medicago truncatula”. They participated in the training on legume transformation: old and new genetic engineering techniques to scope with environmental challenges”. This Bi-lateral cooperation project is coordinated by Sofia Duque (ITQB-NOVA) and Jorge Paiva (IPG PAS) and lasts two years. The main objective is to create and develop collaborations between the two institutions on cell wall research on legumes and other species.

WP5 Dissemination and outreach

Fatema Bakro


Strategies for the use of legumes, Zakopane, Poland 30 January - 3 February 2017
Based on her early results of M1 generation of the Tilling population, Fatema Bakro (PhD student) attended a conference organised in Zakopane by the Institute of Plant Breeding and Acclimatization National Research Institute in Radzików /IHAR/. She had a poster session under title "Implementation of reverse genetics methods to explore new morphological characteristics potentially useful in the cultivation of peas".

1st Conference of the COST Action 15223
Jorge Paiva participate at the 1st Conference of the Cost Action 15223, in Rome from 15 to 17th February, as Polish delegate  to the Management Committee and as Coordinator  of the Short Term Scientific Missionn of this COST Action Action.

Jorge Paiva

Jorge Paiva participated at The IUFRO Tree biotechnology 2017 from 4th – 9th June of 2017 in  Concepción, Chile with an oral presentation on the “Effect of 5-Azacytdine and Hydroxyaurea on seed germinaton and response of Eucalyptus globulus juvenile plants to water stress”. The IUFRO Tree Biotechnology conferences are held every two years and is the most prestigious international conference on the state of the art in tree biotechnology.

Robert Malinowski and Karolina Stefanowicz attented the conference in Ghent, Belgium presenting their results in the form of posters:
1) Developmental reprogramming of the host accompanying establishment of the successful biotrophy during Plasmodiophora brassicae infection.
2) The importance of cell wall remodelling in host plant for the pathogenesis of Plasmodiophora brassicae

The aims of the VIB conference series are:

  • to showcase cutting edge research and exciting technological solutions presented by leading scientist in the life sciences fields
  • to offer junior researchers the opportunity to present their work during poster sessions and learn from the world’s experts during the Meet the Expert sessions
  • to establish opportunities for collaborations between scientists during an accompanying social program including lunches, conference dinners and reception


Focused Group Training: Spreading Excellence and Widening Participation, 27-28.02.2017, Ankara Turkey
dr Robert Malinowski, ERA Chair holder and dr Anna Stachowiak-Szrejbrowska, Project Manager received an invitation from Turkey in H2020 project to participate in Focused Group Training in Ankara and share their knowledge and experience from the ERA Chair project. During the ERA Chair session they shared their experience from the point of view of the ERA Chair holder and the manager of such type of project. Then dr Stachowiak-Szrejbrowska led the workshop entitled "How to develop a successful ERA Chair Proposal".

dr Anna Stachowiak-Szrejbrowska
dr Robert Malinowski

Visit of Incubator Nunes (Portugal) and Poznan Science and Technology Part at the Institute to meet the ERA Chair
On April 7th, 2017 a group of representatives from Incubator Nunes in Portugal and Poznan Science and technology Park visited the Institute to meet the ERA Chair team, learn about the ERA Chair BIO‑TALENT project, research topics of the Institute and possibilities of commercialisation. The visit was divided into three parts - first dr Anna Stachowiak-Szrejbrowska presented the Institute and the BIO‑TALENT project, then prof. Jędryczka and dr Paiva presented their research. After disscussion moderated by innovation broker - Aleksandra Kempińska, the group visited the laboratories of the BIO‑TALENT group.

dr Jorge Paiva
dr Anna Stachowiak-Szrejbrowska


Entrepreneurship Days

Poznań Entrepreneurship Days
Poznań Entrepreneurship Days is an annual event under the patronage of Poznań City Hall. This year the Institute of Plant Genetics PAS was hosting Ms Marta Koźma, a student from The Karol Marcinkowski Junior High school in Poznań, who wanted to see how scientific research with plants is done. On 26th April she spent a few hours under supervision of Biotalent Innovation Broker – Aleksandra Kempińska. During the time spent at the Institute Ms Koźma had the opportunity to visit laboratory facilities, greenhouses and controlled environment chambers and meet researchers from different countries working at the Institute. She was also allowed to conduct some experiments and joined Institute’s PhD students during the seminar given by invited guests from Scotland’s Rural College.

Regional Intelligent Specialization Forum

Regional Intelligent Specialization Forum
On 9th June 2017 the Institute of Plant Genetics, Polish Academy of Science was visiting the Marshal Office of the Wielkopolska Region in Poznań at the Regional Intelligent Specialization Forum (RIS Forum). The aim of the RIS Forum was to bring regional entrepreneurs representing different RIS and science institutions closer together. IPG PAS, among other institutes like Institute of Bioorganic Chemistry PAS, Institute of Molecular Physics PAS, Institute of Natural Fibres and Medicinal Plants and others, was invited to present its achievements and business offer to visitors of the forum. The forum begun with a presentation of financing opportunities for supporting R&D activities in SMEs and showing a case study of successful business-science cooperation. Afterwards the visitors had the opportunity to meet with science representatives and talk about possible joint projects. The Institute of Plant Genetics PAS was represented by Scientific Secretary – Anna Stachowiak-Szrejbrowska, and Innovation Broker – Aleksandra Kempińska.


Visit to the Centre of Innovations in Łódź:

Centre of Innovations in Łódź
Centre of Innovations in Łódź

On 21st June a group of BIO-TALENT members visited the representatives of the different departments of Medical University of Lodz at the Centre of Innovation and Technology Transfer at the invitation of prof. Lucyna Woźniak. The purpose of the meeting was to present the work and scientific interests of both sides and to find future opportunities to develop a joint project. The BIO-TALENT team was also invited to see the CITT and get to know what its main duties and activities are. The meeting was very fruitful and ended with an agreement to collaborate in the future on healthy ageing topics.

“Breakfast with…” is a series of meetings with different companies organised by Poznan Science and Technology Park. This time the invited guest was Jarosław Rogoża – R&D director and board member at Synthos s.a. one of the biggest chemical firms in Poland. He described how his company is growing through knowledge and showed specific examples of beating the market competition with innovations. After the presentation all participants and the guest were able to discuss interesting points and topics further and also exchange contacts.


Biocafé 16 05 2017
Imagine a small coffin laying on the table and a plume of evaporating liquid nitrogen rising from it. Imagine a strange character in pure white lab coat opening it before your eyes. The ominous music in the background swelling. Imagine as he slowly reaches to its insides and carefully takes out… a cabbage? Yes, a cabbage. That’s how Robert Malinowski the head of BIO-TALENT team started the first Biocafé meeting in Alibi Club on 16th May. He made such a funny show to introduce the audience to a very serious topic of how pathogens are invading the plants, causing many different diseases. The presentation focused on how P. brassicae infection leads to complex reprogramming of core cell cycle gene expression, which was an excellent example of how pathogens are changing the cell cycle to more effectively exploit the host plant, and stimulated further discussion in a bit less formal atmosphere.


On January 13, 2017 we hosted 30 students from various high schools to show them what microscopic methods can be used in plant biology. On-site practical training was held in the laboratories of the BIO-TALENT group by Robert Malinowski, Sara Blicharz, Fatema Bakro and Carolina Gomes. The students had the opportunity to work with our new laser dissecting microscope and learn how to visualize plant cells and gene activity.


On 27th April  Biotalent welcomed 20 students from the International School of Poznan.  After a short presentation of the Biotalent project by dr Anna Stachowiak-Szrejbrowska, dr Jorge Paiva gave a talk about how to be a scientist in a  research market. A guided visit to the laboratories and greenhouses allowed the students to discuss with the Biotalent team researchers activities of the Department of Integrative Plant Biology.

dr Anna Stachowiak-Szrejbrowska
dr Jorge Paiva

BIOTALENT Skills Presentations

Skills Presentations

On 18th May 2017 a class with extended biology programme from International School of Poznan visited the Institute to participate in the BIO-TALENT Skills Presentations and get hands-on experience in the lab. The event was coordinated by dr Jorge Paiva and dr Anna Stachowiak-Szrejbrowska and teaching was done by Ph.D. students: Carolina Gomes, Dariusz Kruszka, Preeti Shakya, Fatema Bakro, Sara Blicharz, Soham Mukhopadhyay, Juan Camilo Ochoa and Marcin Olszak. The class of 20 students was divided into 4 groups to perform following activities in the laboratories: DNA extraction and gel visualisation, preparation of in vitro culture of willows, microscopic methods used in plant biology, experiments with dyes in plants. The ultimate goal of this outreach activities was to give the students the opportunity to work in the lab and conduct their own experiments.


Seminars for PhD students
Dr. William Truman presented a series of four seminars for the IPG PAS Ph.D. students, topics included:

  • Analysis of microarray experiments and mining publicly available gene expression datasets.
  • Presentation skills, handling audience questions.
  • Critical reading of research papers with conflicting results.

Winter student traineeship at DIPB
Since 23th January, Jakub Michalski and Pawel Zaleswski from Poznan University of Life Sciences in Poznań  were  collaboration within the PurpleWalls, project in the frame of the Summer Training program of the UAM, for a training period of 1 month, under supervision of Jorge Paiva and Carolina Gomes.  During this period they participated different activities of the project in  the establishment of a protocol for fast and efficient protocol for multiplication by cuttings,  establishment and maintenance  of in vitro culture of Salix, extractions of nucleic acids and gene expression analysis by RT-qPCR.

PhD thesis jury participation

PhD thesis jury participation
On  6th February 2017, Jorge Paiva participated as member of the jury of the PhD thesis in Biology Molecular  of Pau Boher Genís, at University of Girona (Spain) ( Pau Boher successful concluded PhD studies on "Functional genomics of the periderm: the biosynthetic gene FHT, the transcriptional regulator StRIK and the transcriptome deciphering". The thesis was under co-supervision of Prof.. Mercè Figueras Vall·llosera, Prof. Marisa Molinas de Ferrer and  Dra. Olga Serra Figueras. Congratulations to Dr. Pau Boher Genís.


PhD thesis jury participation

On 17th March 2017, Jorge Paiva participated as member of the jury of the PhD thesis in Biology – Molecular Genetics   of  Carmen Santos, at ITQB-NOVA  ( (Portugal). Carmen Santos  successful concluded PhD studies on “Genomic approaches to understand the genetic response to Phytophthora cinnamomi Rands in Castanea spp.". The thesis was under co-supervision of Dr. Rita Costa (INIAV, Portugal) and Prof. Pedro Feveriro  (ITQB-NOVA) Congratulations to Dr. Carmen Santos!

WP6 Management and sustainability

MIDWAY Review of the BIO-TALENT project by the Advisory Board

Dr. Marie Helene Balesdent

May 2017 is the mid-way of our BIO-TALENT project. According to our plan of milestones, we have asked the Advisory Board (AB) of the Project to review our activities. The AB of the BIO-TALENT project is composed of: 1) Dr. Marie Helene Balesdent, Institute National de la Recherche Agronomique, Thiverval-Grignon, France; 2) Prof. Jaroslav Doležel, Institute of Experimental Botany, Olomouc, Czech Republic, 3) Dr. Robert Matysiak, DuPont Europe, Warsaw, Poland.

Dr. Jaroslav Dolezel

Members of the AB of the BIO-TALENT project decided to evaluate separately each of the work packages, highlighting the achievements and problems with the aim of assisting the Project leadership by providing an independent and critical opinion. They have also evaluated the project as a whole, at the mid-point of its realisation. This review was based on four visits of the AB members to the host institute, as well as the documentation provided by the Coordinator and Administrative Manager of the Project. In Workpackage 1 the AB members highlighted the selection of a suitable candidate (ERA Chair holder – Dr. Robert Malinowski), who built an excellent, international and multidisciplinary research department, which was the overall objective of the project, and his task in Workpackage 2. The members of the AB highlighted that: 1) the recruited team is composed of a well-balanced group of researchers (good gender balance and range of countries of origin); 2) each of the seniors has created his own research group, based on their successful applications to the national Polish funding body (NCN). The Work package 3 “Enhancement of research excellence” led to the submission of several research projects, out of which six have been granted and another two are currently under review. Despite starting from scratch the team of the Department of Integrative Plant Biology has already published two book chapters and eight papers with an impact factor, based on experiments and studies done at IPG PAS. The AB members have highlighted good cooperation with the other departments of the Institute as well as research groups in other scientific institutions located in Poznan and other cities in Poland and abroad. The project goals planned for Workpackage 4 “Cooperation and transfer of knowledge” have also been fulfilled. To date, the BIO-TALENT team, with the help of the Administrative Manager of the Project, have organised two workshops, eleven lectures by foreign experts in integrative plant biology and bioinformatics, two seminars on intellectual property rights and five seminars on the development of soft skills.

Dr. Robert Matysiak

The organisation of these events occupied a lot of time, but it made it possible to broadly transfer the idea of integrative plant biology. Members of AB did highlight one area for potential improvement, suggesting the focus on cooperation with industry should be intensified and become more pro-active. Workpackage 5 “Dissemination and outreach” has also been carried out according to the schedule. A website has been created devoted to the activities within the Project, linked with the Institute website. The information on the website is regularly updated and a Project newsletter is available online. The Newsletter contains project achievements and highlights and it is supported by all members of the team. The BIO-TALENT Project has been receiving good publicity, being selected as an example of a successful project and advertised in the EU leaflet “Spreading excellence and widening participation”. Members of the AB highlighted a good coordination of the Project and the importance of its sustainability (Workpackage 6).

Summary of the successes / drawbacks of the project at its mid-term point
The aim of the Project was to create the Department of Integrative Plant Biology and this goal has been completely fulfilled. The Department has been created, the staff is international, the researchers are at different stages of their scientific careers. The team is multicultural and multi-skilled with a good gender balance. The team is composed of researchers representing different branches of biology with complementary skills and great synergy. The team is relatively large and visible at the local as well as international scale. There are a few business companies interested in cooperation with the members of the Department. In spite of a delayed start of the project it was possible to catch up with most of the activities. To conclude, members of the Advisory Board were impressed by the development of the Project and satisfied with its scientific achievements.


Newsletter 2/2016 [July-December 2016] issued at the end of December

New students:

Carla Gualtieri

Carla Gualtieri (Universitá degli Studi di Pavia, Italy), started at 1st March 2016 her six months ERASMUS + internship at the Department of Integrative Plant Biology, at the team of Jorge A. P. Paiva. Her internship at DIPB is part of her MSc studies, under the supervision of Prof. Alma Ballestrazzi (the Universitá degli Studi di Pavia - Italy), and co-supervision of Jorge A. P. Paiva. Carla will be involved in the identification, characterization and expression analysis of genes involved in salicylate glucosides in Salix spp.

Rasha S. Tawfik and Franklin Gregory

Rasha S. Tawfik PhD (Genetic Engineering and Biotechnology Division, National Research Center, Egypt) has visited Dr. Franklin’s lab during May 1 to June 15, 2016. During her visit, Dr Rasha performed experiments to understand the impact of metallic nanoparticles on plant regeneration and secondary metabolism. Results of her study have revealed that nanoparticles affected plant morphogenesis in a concentration-dependent manner. HPLC analysis of total secondary metabolites extracted from treated tissues showed an increase in chlorogenic acid and caffeoyl quinic acid.


  • International Conference on Arabidopsis Research - GyeongJu South Korea

On 29th of June to 3th of July Robert Malinowski attended the International Conference on Arabidopsis Research held in GyeongJu South Korea. This year vascular development and sugar allocation subjects were very well represented in the program of the conference. What is remarkable also plant biotechnology panel has been organized and we could learn about planti-bodies and plant vaccines. Another good part was the panel devoted to research in which chemistry and biology work together. We could hear talks on strigolactone reporter or chemical compounds influencing plant regeneration potentials. We were presenting poster describing how P. brassicae influences cell cycle progression in hypocotyls of Arabidopsis plants.

IOBC/WPRS Working Group“ Integrated Control in Oilseed Crops “

This year entire team working on clubroot disease decided to join the IOBC/WPRS Working Group“ Integrated Control in Oilseed Crops “ meeting entitled “Prospects and progress for sustainable oilseed crop protection“held at the Institute of Agricultural and Environmental Sciences of the Estonian University of Life Sciences, Tartu, Estonia during September 7–9 2016.

We were very active during the meeting. Dr Robert Malinowski had one of the opening speeches and presented the power of Arabidopsis thaliana as a tool for studying diseases and past responses in brassicas. Arabidopsis thaliana belong to the same family as important crops like oilseed rape, therefore we need to learn how to use it as an efficient tool for plant pathology and crop protection studies.

Also MSc Marcin Olszak from our group gave the talk entitled "Plasmodiophora brassicae infection – usurping the host molecular regulatory networks for feeding site formation". Marcin talked about results of his recent molecular and anatomical studies and tried to describe the developmental changes occurring during infection to give an answer to crucial question: how the pathogen manipulates the host plants to the most effective use and what pathogen needs to alter in host molecular regulatory networks for feeding site formation?

Piotr Walerowski

And Dr Karolina Stefanowicz presented Her recent project “Proteomic approach to study cell wall changes occurring within host plant during clubroot infection”. Karolina had a poster where she described experimental strategy of comparative proteomic studies using 1-D and 2-D protein electrophoresis, followed by the mass spectrometry-based identification of proteins, in order to characterize cell wall remodelling process during P. brassicae infection and to understand the mechanism used by the pathogen for invading the host.

  • PTG Łódź - R. Malinowski

We have presented our work on phloem remodeling by P. brassicae. MSc Piotr Walerowski is a main person involved in this research, so far He managed to describe how the pathogen is hijacking molecular and cellular programs of the infected host to acquire its assimilate. Piotr Walerowski received second award for the best oral presentation during this Congress. The research is funded by the NCN Sonata Bis-2 project entitled “Integrated approach for deciphering the mechanism leading to shift in cell proliferation/differentiation balance accompanying clubroot infection” [PI- Robert Malinowski].

2. Soft skills seminars

  • Individual career plan. Planning, realization, evaluation by dr Justyna Małkuch Świtalska 7 10 2016

To have a good start of the academic year 2016/2017, we invited dr Justyna Małkuch Świtalska from the PolDoc association to teach our PhD students how to plan their career. In the nutshell, PhD students learnt how to deal with different aspects of personal career development, its implementation and evaluation.

  • Scientific career and sucessful applications for grants. ERC grants from my subjective perspective of the laureate and evaluator by prof. Janusz Bujnicki 6 10 2016

On October 6, professor Janusz Bujnicki, the first Polish ERC grant holder, current member of the Science Europe, Life, Environmental and Geo Sciences (LEGS) Scientific Committee and member of the Scientific Policy Committee of the Polish Ministry of Science and Higher Education provided us with the lecture on the successful scientific career development and international research grant application. Special attention was paid to the ERC grants and pros and cons of trying to get this kind of project. The lecture has stimulated lively discussion and reached the attention of our PhD students and perspective young group leaders.

3. IPR seminar by dr Karolina Czarnecka 2 12 2016

On the beginning of December dr Karolina Czarnecka innovation broker from Medical University of Lodz presented a seminar about innovation and technology transfer. During the lecture she explained the process of creating innovative solutions and brought the attention of PhD students to aspects most crucial for successful technology transfer, showing good practices, which could be applied in day to day work.

4. Aleksandra Kempińska - innovation broker

Aleksandra Kempińska

Hi, My name is Aleksandra Kempińska and since July I’m a member of BIO-TALENT team. I graduated biotechnology at the University of Life Sciences in Poznan. During studies in Poznan I participated in BIO-START program at Poznan Science and Technology Park of Adam Mickiewicz University Foundation. There I got basic knowledge about business models and technology transfer. After obtaining Msc diploma I started working at ATERIS SA, where I learned about process management. Simultaneously I continued to develop my knowledge about business-science relations, studying Business in biotechnology jointly at Jagiellonian Center of Innovation and Faculty of Biochemistry, Biophysics and Biotechnology at Jagiellonian University.

Team-play is the most important thing for me, not only in board and computer games, at which I spend most of my free time. Therefore I’m always willing to absorb all new knowledge and I’m interested in entrepreneurship and Polish start-up stage. I spread this knowledge among my friends, bringing help in their smaller and bigger business ventures. My mission at Institute of Plant Genetics, Polish Academy of Science is to inspire people to share their experience with the business world, show their research outside their lab and also to bring innovation inside the Institute.

If you would like to know me better or you have a professional question, please don’t hesitate to contact me at This email address is being protected from spambots. You need JavaScript enabled to view it.. I’ll be very glad to help!

Aleksandra Kempinska

5. Joint photo of the whole team

The whole BIO-TALEN team: Front row: Karolina Stefanowicz, Fatema Bakro, Aleksandra Kempińska; middle row: Piotr Walerowski, Carolina Gomes, Preeti Shakya, Robert Malinowski; back row: Franklin Gregory, Marcin Olszak, Jorge Paiva, Sara Blicharz, Bill Truman

6. Going around the Poznan

The BIO-TALENT integration with scientific community in Wielkopolska. We have visited Poznan BIOCENTER and the Institute of Dendrology of the Polish Academy of Sciences in Kórnik.

BIO-TALENT integration
BIO-TALENT integration


This year part of BIO-TALENT visited Estonia to attend the IOBC meeting. We have also use this opportunity to visit another ERA-CHAIR funded project. It was quite constructive visit and we had an opportunity to talk to Prof. Nicholas Gatherhood – the ERA CHAIR and of course His team of researchers working on green synthesis projects. We have some plans for future cooperation to link chemistry with more biological aspects of science. Thank you very much Nicholas for hosting us in Tallin.


Visiting Estonia

Newsletter 1/2016 [January - June 2016] issued at the end of June

1. New PhD students - Sara Blicharz, Fatema Bakro, Carolina Gomes

Sara Blicharz

New PhD students were appointed. MSc Sara Blicharz will work on drought responses in Pea plants and her appointment is funded by the BIO-TALENT FP7 project. She has an experience in transcriptomics during drought stress in Barley. Her work will focus on the role of the phloem tissue in drought response.

Fatema Azahraa Bakro

Another BIO-TALENT funded student is MSc Fatema Azahraa Bakro. Hold one MSc in plant genetics and biotechnology in university of Aleppo and ICARDA-Syria/Egypt 2011-2014. Another MSc in plant breeding in institute of CIHEAM/IAMZ and lledia university in Spain/2014-2016. Fatema will work on understanding biological mechanisms influencing important agricultural traits related to plant development. In particular, she will develop TILLING population for P. sativum plants and will try to engineer new growth types in Pea with help of molecular biology tools.

Carolina Gomez

MSc Carolina Gomes is the most recent member to integrate the Department of Integrative Plant Biology. Carolina holds a PhD Student fellowship in the frame of the Polish National Science Center funded project- PurpleWalls. Carolina holds the MSc in Biotechnology from the University of Aveiro (Portugal) on the production and analysis of pharmaceutical relevant peptides in Lactuca sativa and Medicago truncatula. She also worked at the ITQB (Portugal) on the optimization of poplar regeneration and transformation protocol. In our Department she will study regulatory mechanisms related to xylogenesis and secondary cell wall biosynthesis in bioenergy producing crops. Her work will be supervised by Dr Jorge A. P. Paiva. Gathered knowledge will be used to improve the productivity of economically relevant crops.

2. New projects

  • Jorge Almiro Pinto Paiva "PurpleWalls - Unraveling genome regulation to modulate wood formation in Salix purpurea: an integrative approach" SONATA BIS 2016 – 2019

The use of bioenergetic plantations of sources of renewable energy is one of the main directives of the energetic policy in Europe. Being part of the natural composition of Polish vegetation, willow has been recommended as bioenergy crop for Poland.

Poland has favourable conditions for production of willow biomass, being estimated that 1.5-to 2.1 Mha the surface that could be dedicated for short rotation coppice plants. Willows plantations are being used primarily for energy and phytoremediation. In 2009, willows plantations for bioenergy surface (6,160 ha) represented 60.5% of total energy crop surface and 95% of all perennial energetic plantations. Willow plantations are expected to play a significant role amongst the energy-dedicated lignocellulosic biomass crops to reach the goal of 14% of energy derived from biomass in Europe in 2020). Understand the molecular mechanisms underlying wood formation and the modulation of the cell wall composition can lead to new breeding strategies of willows for bioenergy purposes. PurpleWalls will address new and relevant insight genetic and molecular mechanisms controlling phenotype determination, and phenotypic adaptation to growing conditions in Salix purpurea as model for other Salicaceae and perennial species used for bioenergy. Until now, most of the research developed on identification of candidate genes and key regulatory gene networks in developing xylem, did not consider the interplay between different levels of regulation in woody plants. At long-term, it is expected that the tools and knowledge gathered in the frame of PurpleWalls project will contribute to reduce production inputs, and to increase productivity of planted forest and quality of the forest raw products, thus contributing to a sustainable mitigation of human pressures on native forests, associated biodiversity, and of the use of marginal land, and to the empowerment of local populations. Moreover, the PurpleWalls potentially able to patentable applications, to be transformed into practical breeding applications with high commercial impact. PurpleWalls will use an Integrative Biology approach to reveal new key genes and regulatory gene networks that modulate xylogenesis and the secondary cell walls biosynthesis. This highly innovative and appealing were able to attract new national and international collaborations, and together with advanced formation (master and PhD thesis) will contribute to reinforce the transfer of knowledge and technology and the capacity building of the new team – Cell Wall by Design.

  • William Truman "Understanding the role of chitin related defence responses during Plasmodiophora brassicae infection" OPUS 2016-2019

The aim of this project is to characterise the role of key host receptors in recognising and responding to this important plant pathogen. Furthermore, we will investigate the potential of putative pathogen effectors in masking spore walls to prevent detection and evade the plant’s surveillance system. Two PhD students will be funded by this project and they will be joining the lab soon: Soham Mukhopadhyay from India and Juan Camilo Ochoa from Colombia.

  • Karolina Stefanowicz "The importance of cell wall changes occuring within host plant for the Plasmodiophora brassicae infection progression" SONATA (2016-2019)

Plasmodiophora brassicae is the obligatory pathogenic protist causing a clubroot disease in agriculturally important Brassica species. The idea behind the project is that expansive gall growth and the formation of giant cells, which constitute final reservoirs of resting spores of the pathogen, must be accompanied by massive cell wall modifications. The project aims to identify the specific protein factors involved in cell wall turnover process observed during infection. Changes in cell wall protein profiles in galls will be monitored by comparative proteomic studies using 1-D and 2-D protein electrophoresis, followed by the mass spectrometry-based identification of proteins differentially present in the studied samples. Ultimately, transgenic lines will be generated with modified activities of the identified and selected cell wall proteins to test potential impact of such modifications on P. brassicae pathogenesis. Detailed characterization of cell wall remodelling process during P. brassicae infection will help to understand the mechanism used by the pathogen for invading plant cells and securing resting spore formation

3. Innovation broker selected - Aleksandra Kempińska, MSc

In April 2016 we started looking for the innovation broker to work at the Institute. There were 5 candidates from Poland and South Africa, and the person that best met our criteria was Aleksandra Kempińska, MSc. She will start her job on July 1, 2016.

4. Kick off meeting of the project March 16, 2016

The inauguration of the BIO-TALENT EU FP7 project took place on 16 March 2016 at the Wielkopolska Centre of Advanced Technologies (WCAT). We have invited representatives of research sector, industry, government granting bodies and local public administration. During the welcome session of the meeting the audience could listen to talks given by prof. Stefan Malepszy - the vice President of the Polish Academy of Sciences, dr Maciej Dohnal -the representative of the City of Poznan, Department of Economic Activity and Agriculture, Prof. Małgorzata Mańka – the Vice-President of the Scientific Board of the Institute and Dr. Krzysztof Pudełko, the representative of WCAT. This has been followed by the presentation of the research scope and perspectives for future BIO-TALENT activity by the newly appointed team members - dr Robert Malinowski, dr Jorge Paiva and dr Franklin Gregory. The BIO-TALENT International Advisory Board members - Dr. Marie-Helene Balesdent (INRA, Paris, France), Dr. Jaroslav Dolezel (IEB, Olomouc, Czech Republic), Dr. Robert Matysiak (DuPont Europe) also commented the current status of the project and expressed their support for the newly created Department. The meeting was concluded by the Discussion mediated by Prof. Małgorzata Jędryczka, the Coordinator of the Project and by Dr Anna Stachowiak-Szrejbrowska, the Administrative Manager of the Project. After lunch we have experienced the Music surprise: the presentation “Music on pictures” illustrated by the music compositions of Maciej Rychły played by Yorgi Quartet. Taken together we have managed to attract country-wide audience and representatives of institutions involved in research management and funding, therefore we believe that the meeting increased the visibility of the project and its future success.

The inauguration of the BIO-TALENT EU FP7

5. Introduction to systems biology workshop March 17, 2016

March 17’th was a big day to all people interested in widening their research perspectives. We have organized the Systems Biology workshop in which Dr Ute Voss [School of Biosciences Division of Plant Sciences, University of Notingham UK] gave a talk on the „Uncovering novel mechanisms controlling root angle using a systems biology approach”. She has presentet how growing roots can be imaged and with help of transgenic lines auxin transport and sensing can be visualized and studied at the systems level.

Dr Wojciech Palubicki [Department of Mathematics and Computer Science, University of Adam Mickiewicz, Poznan, Poland] showed how to represent plant growth and signaling mechanisms with a particle-based modeling paradigm”. Work of Dr Palubicki shows the power of mathematical modelling. He shows how modelling helps to formulate new directions to study complex biological subjects related to auxin signaling. He had presented models for basic developmental events like asymmetric cell divisions or branching in plants. Dr Palubicki has published numerous internationally recognized papers and He is cooperating with leading scientist in the field of plant modelling like Prof. Przemyslaw Prusinkiewicz (Calgary, Canada) and Prof. Ottoline Layser (Cambridge Sainsbury Lab, UK).

Another speaker – Prof. Gerrit Beemster [Department of Biology, University of Antwerp, Antwerp, Belgium] was presenting the power of kinematic analyses as an integrated approach to study plant organ growth regulation. Prof. Gerrit Beemster Has pioneered work of plant development imaging. His good eye, patience and enthusiasm resulted in developing numerous techinques for imaging of plant growth at the cellular and whole organ level. The talk was very exciting and despite all time frames were exceeded the audience was continuing discussion on imaging plant development.

The workshop has been additionally supported by two word leading microscope companies Zeiss and Leica and their R&D specialist were providing new details on the recent cutting edge solutions for microscopy imaging. Our guest was Ms Franziska Klein from the Global Sales Support Life Sciences, Carl Zeiss Microscopy GmbH. She has introduced workshop attendees to the new LSM 880 with Airyscan Superresolution system. Then Polish Leica representative KAWA.SKA specialist Dr Jarosław Korczyński presented the power of White Light Laser confocal microscopy.

In order to make this day even bigger celebration time for all researchers who wants to go behind typical molecular biology work we have invited two other speakers from the Department of Comparaive Genomics and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany. We believe that there are the real frontiers of plant bio-engineering, plant imaging and biophysics. Like Maria Sklodowska-Curie and Her husband Pierre Curie Dr Anne-Lise Routier Kierzkowska and Dr Daniel Kierzkowski French-Polish couple of scientists work very hard to leave their mark in science. So far they have managed to work in leading research groups and publish their work in journals like Science, the Cell and Nature. At present they work in the groups of Professor Miltos Tsiantis (Daniel) and Dr. Richard S. Smith (Anne-Lise). Their work is a mixture of biophysiscs, plant imaging and molecular biology.

Dr Anne-Lise Routier-Kierzkowska presented Her recent work on mechanisms related on the Explosive Seed Dispersal in Cardamine hirsute. This work has just been accepted to the Cell [Hofhuis, H., Moulton, D., Lessinnes, T., Routier-Kierzkowska, A.L., Bomphrey, R.J., Mosca, G., Reinhardt, H., Sarchet, P., Gan, X., Tsiantis, M. and Ventikos, Y. Morphomechanical Innovation Drives Explosive Seed Dispersal. Cell, 166: 222-233]. She also talked on the Morphographics – plant imaging tool which can be used for various applications related to plant development.

Dr Daniel Kierzkowski presented how the Morphographics can be used together with plant genetics tools to unravel mechanisms governing leaf shape determination and its further acquisition. This work has been published by group of Prof. tsiantis and is the milestone for developmental biology of higher plants [Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C, Gan X, Hajheidari M, Hay A, Smith RS, Huijser P, Bailey CD, Tsiantis M. Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene. Science, 343 (6172), 780-783.].

Introduction to systems biology workshop

From the left: Ute Voss [School of Biosciences Division of Plant Sciences, University of Notingham UK]; Daniel Kierzkowski [Department of Comparaive Genomics and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany]; Anne-Lise Routier-Kierzkowska [Department of Comparaive Genomics and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany]; Gerrit Beemster [Department of Biology, University of Antwerp, Antwerp, Belgium];

This was a long and a great day. We believe that BIO-TALENT has managed to organise word leading plant systems biology workshop and panel of lectures in Poznan. For this one day we were the centre of integrative plant science!!!

We would like to say thank you to all attendees, people who gave talks and also people who helped to organise this event. Thank you for attending the workshop, we are hoping that next workshops will also be successful.

6. Lectures:

  • Christian Hardtke - Quantitative and genetic control of vasular tissue formation [28th April 2016]

On the 28th of April we hosted Prof. Christian Hardtke from the Department of Plant Molecular Biology University of Lausanne, Switzerland. Christian is a leading scientist in the area of systems biology of phloem development in plants. His findings led to major progress in understanding how phloem development is orchestrating by the molecular networks. Prof. Hadtke presented His work including unpublished results on the newly discovered phloem related receptor protein. This was a very exciting talk, we were very glad to be a part of it.

Prof. Christian Hardtke lecture
  • Jerzy Paszkowski - Epigenetic regulation and transgenerational inheritance [12th May 2016]

On the 12th of May we hosted Prof. Jerzy Paszkowski – internationally recognized and unquestioned leader of plant methylation mechanisms studies. At present Prof. Jerzy Paszkowski works at the Cambridge Sainsbury Lab and is conducting His experiments funded by ERC Advanced Grant. The main subject of the talk were mechanisms behind transgenerational inheritance of epigenetic regulation. Prof. Paszkowski explained major mechanisms governing plant methylation in plants and what is more important which regulatory patterns can be inherited. He has explained how the epiallelic properties of Arabidopsis plants can be used in rice. He also presented prediction models for epigenetic switches. At the end we were discussing to which degree DNA sequence can influence epigenetic properties of plants. Great and very insightful talk!!!

Prof. Jerzy Paszkowski and BIO-TALENT
  • Vicky Vance - Edible plants as bioreactors to produce and deliver therapeutic microRNAs [23th May]

On the 23th of May we hosted Prof. Vicki Vance from the Department of Biological Sciences of the University of South Carolina. Prof. Vicky Vance is a leading scientist in the field of gene silencing in plants. She has discovered the HC-Pro viral suppressor of gene silencing. Recently she spent substantial amount of time to develop the cancer treatment strategy based on gene silencing concept. Her work led to the discovery that mice provided with plant material expressing hairpin silencing factors targeting colon cancer genes can be in fact cured of colon cancer. This is one of the first evidence for such phenomenon and opens new perspectives for plant biotechnology and medicine. Professor Vance gave a splendid talk and numerous scientist came to listen Her work. She also visited research groups of Professor Szweykowska-Kulinska and Prof. Artur Jarmolowski – leading Polish scientists in the area of molecular regulation of gene silencing and alternative RNA splicing. I believe that was a great time to all of us. Thank you very much Vicky.

Prof. Vicki Vance

7. Soft skills seminars

  • How to write a good article? 14 04 2016 by Fred Stoddard
  • Current GMO status on Poland - legal and ethical aspects 23 02 2016 by Tomasz Twardowski, Sławomir Sowa, Tomasz Zimny

In the BIO-TALENT WP we not only provide current knowledge in the field of plant systems biology, plant genetics, genomics and biotechnology, resistance to stresses or bioinformatics, but also try to develop transferable skills related with our job. Thus, on February 23 we had a seminar on Currect GMO status - legal and ethical aspects by prof. Tomasz Twardowski, Institute of Biooorganic Chemisty of the Polish Academy of Sciences, Poznan; Tomasz Zimny, Institute of Law Sciences of the Polish Academy of Sciences, Warsaw; dr Sławomir Sowa, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow

As it is very important to publish the results of our research, in April we invited prof. Fred Stoddard from the University of Helsinki to learn as much as possible about writing good scientific articles.

Newsletter 2/2015

Newsletter 1/2015