Newsletter 1/2018 [January-June 2018] issued at the end of June
WP3 Enhancement of research excellence
New NCN OPUS projects granted to dr Franklin Gregory
HyperAgro: Pathogenesis-related (PR) defence mechanisms in plant recalcitrance (2018-2021)
New people in the NCN projects - welcome newcomers
Dr Gupta is a new Post-doctoral fellow at Dr. Franklin’s team. She obtained her Ph. D. degree in Plant Genetics from the Department of Genetics at University of Delhi-South Campus (India). She was a postdoctoral fellow at National Institute of Plant Genome Research (Delhi, India). With a strong background in plant physiology and plant molecular biology, she has published 13 research articles and has also reviewed articles and scientific projects for journals and funding agencies. Her current research focus is combined biotic and abiotic stress response in plants.
Mr. Maqbool started as a PhD scholar at Dr. Franklin’s team. He will be working in the frame of Nano-biotechnology and integrative plant sciences. He has published many high impact articles in peer reviewed international journals. He is a Gold medalist in MSc-Biology and won 2018 outstanding research paper of the year award by HEC (Higher Education Commission, Pakistan).
Ms. Gharari is a Ph.D student at the Department of Agricultural and Plant Breeding, University of Zanjan, Zanjan, Iran. She will be working at Dr. Franklin’s lab for six months on sabbatical leave. Her visit to Poland is sponsored by the Ministry of Science, Research and Technology, Iran.
WP4 Cooperation and transfer of knowledge
LECTURES & WORKSHOPS
23.04.2018 Stephen Long
"Engineering Photosynthesis for Global Food Security. Why, How and Will You Let Me Do It?" Stephen Long, Department of Plant Biology, University of Illinois, USA
28.04.2018 Edward Farmer
"Rapid long distance signalling in the plant wound response" Edward Farmer, University of Lausanne, Switzerland
24.05.2018 Laura Ragni
"Novel tools to measure secondary growth: the quantitative histology approach" Laura Ragni, University of Tubingen, Germany
Applications of CRISPR system in plants workshop 18.01.2018 by Anindya Bandyyopadhyay and Shamik Mazumdar (IRRI)
IPR – Industrial property goods and how to find them 24.01.2018 by Łukasz Wściubiak, Patent Attorney
Soft skills – Boost your creativity 29.01.2010 by dr Anna Czerwoniec
STUDY VISITS AND TRAININGS ABROAD
Preeti Shakya (Luknow, India) 15.01- 05.03.2018
The academic training was received in the Institute of Engineering & Technology, Dr. A.P.J. Abdul Kalam Technical University under the supervision of Dr. Amrika Singh, Professor & Dean Research, Head of department of Applied Sciences, in the area of Environmental Bio-Technology, which included participation in seminars and different teaching activities. She was offered to be part of Academic Developmental Programme for young researchers, which is a platform for PhD students to enhance their academic and teaching skills with the team of experienced professors and researchers. The objective of the training was to learn about the Bioenergy production from Jatropha curcus (JC), a worldwide growing plant that belongs to Euphorbiaceae family, which has versatile potential for renewable energy, biodiesel production and various medicinal uses.
Sara Blicharz (Antwerp, Belgium) 22.01-23.02.2018
In Januarty 2018 a PhD student Sara Blicharz went for training to the Integrated Molecular Plant physiology Research group in the Department of Biology of University of Antwerp, Belgium. The purpose of this training stay was study of number and size of plant cells as well as learn new microscopy technique which will be used to carry out the OPUS11 project and Sara’s PhD thesis.
Jorge Paiva (Oslo, Norway) 27-30.01.2018
The visit to NMBU (Oslo, Norway) by invitation of Prof. Hilde-Gunn Opsahl Sorteberg. The visit was done in the frame of the preparation of one international application to submit to the H2020 "CLC-SFS-15-2018: Future proofing our plants" call. During the four days meeting it was possible to define the structure of the project and advance with establishment of the Consortium. The project was submitted on 13th February, being Jorge Paiva leader of one of the workpackages of the project.
Jorge Paiva (Toulouse, France) 11-21.03.2018
Jorge Paiva visited Laboratoire de Recherche en Science Vegetales (LRSV, UMR 5546 UPS/CNRS), the laboratory of Dr. Jacqueline Grima-Pettenati. Dr. Grima-Pettenati is an expert on lignin biosynthesis regulation, being one of the pioneers on the identification of these lignin related genes in Eucalyptus. The visit has as objective to learn new methodologies of analysis of transcriptome data. WGCNA and Cytoscape was used to generate and visualized co-expression modules, using transcriptomic data of Eucalyptus differential xylem.
WP5 Dissemination and outreach
III International Symposium on Nanoparticles/Nanomaterials and Applications
Dariusz Kruszka and Franklin Gregory attended the III International Symposium on Nanoparticles/Nanomaterials and Applications 22nd – 25th January 2018, Caparica, Portugal. They presented a communication entitled "Arabidopsis thaliana plant secondary metabolism in response to silver nanoparticles" co-authored by researchers participating in the project namely R. Selvakesavan and P. Kachilicki.
2nd iPLANTA (COST Action CA15223) Conference: RNAi: The Future Of Cross Talk, Focus on RNAi Technology (WG1) and Applications (WG2)
The 2nd Conference COST Action iPlanta was held at the Faculty of Biology of Adam Mickiewicz University, Poznań, Poland from 14th to 16th February 2018, in collaboration with the KNOW program of this Faculty. The conference brought together 101 experts from 25 European countries involved in the iPlanta COST network were invited to present and discuss the state of the art focused on RNAi technology (WG1) and the application of RNAi technology in GM plants (WG2), among the other issues such as biosafety, socio-economics and communication on RNAi. The conference was organized by Dr. Jorge Paiva and Prof. Zofia Szweykowska-Kulińska, head of Gene Expression of the the Faculty of Biology at UAM. At the end of the conference, Jorge Paiva participated at the MC meeting COST of the Cost Action 15223 (iPlanta) as Poland delegate, and also STSM coordinator of this Cost Action.
More information available at http://iplanta2018.home.amu.edu.pl/
COST Action CA15223 meeting
Jorge Paiva participate in the Core Group meeting held in Bruxelles, Belgium on 23 March 2018, at the Cost Head Quarter. The objective of the meeting was to define the planning of the iPLANTA Grant period 3 and also the communication plan of this Cost Action.
Bio-based Industries Joint Undertaking’s (BBI JU) Info Day 2018
Dr. Franklin attended the Bio-based Industries Joint Undertaking’s (BBI JU) Info Day 2018 and brokerage event on 17 April 2018. He had face-to-face meetings with representatives from academy and industry and discussed about the Hypexplor project. Dr. Franklin as coordinator will submit this project in the near future.
7th International Food Legume Research Conference (IFLRC-VII)
Jorge Paiva participated in the "7th International Food Legume Research Conference (IFLRC-VII)" from 6th to 8th May 2018 at Palais des Congrès, Marrakech, Morocco. The event was hosted by ICARDA and INRA Morocco and will continue from past conferences in promoting international collaboration on basic, applied, and strategic research on food legumes. Jorge Paiva presented the poster "Paiva J A P, Ana Barradas, Fevereiro P. 2018. . Transcriptome of Trifolium resupinatum.", resulting from the collaboration with the team of prof. Pedro Fevereiro on on development of genomics resources for Trifolium. Before the conference, (2nd to 4th May) J. Paiva had the possibility to visit the lab of Prof. Pedro Fevereiro at ITQB-NOVA (Oeiras, Portugal) to discuss the results already obtained and to plan new collaborative activities on this domain.
More information at: http://www.iflrc.org/
Gordon Research Seminars & Conference
In the first week of June 2018 Sara Blicharz gave a talk entitled "The role of the phloem in drought stress responses in pea" during the 2018 Gordon Research Seminars (GRS) on Salinity and Waters Stress in Plants as an invited speaker. She also presented her work on poster entitled "Phloem-mediated sugar redistribution is a vital component of drought response in pea" during Gordon Research Conference (GRC). Both events brought together researchers from academia, government and industry with expertise from molecular system to trait development to discuss progress in elucidating mechanisms and managing challenges associated with water availability and salinity on both agriculture and ecosystems. GRS and GRC took place in Waterville Valley, NH, US.
2. Konferencja Naukowa. Biologia I Ekologia Roślin Drzewiastych
Jorge Paiva and Carolina Gomes participate in the 2. Konferencja Naukowa. Biologia I Ekologia Roślin Drzewiastych held at Kórnik and Poznań, Poland from 11th to 15th June 2018. Jorge Paiva gave a oral presentation on his current project on Eucalyptus (EgoSelf, funded by FCT, Portugal): "Susana Araújo, Ana R. Guedes, Andreia Amaral, Ehsan Valiollahi, PedroFevereiro, Jorge A. Pinto Paiva. 2018. egoSELF: An Integrative Biology approach to study the molecular basis of inbreeding depression in Eucalyptus globulus. ".
Carolina Gomes, a PhD student under the supervision of Jorge Paiva presented (oral communication) the results already obtained in the project PurpleWalls "Carolina Gomes, Mortaza Khodaeiaminjan, Jorge A. Pinto Paiva. 2018. Unfolding the role of DNA methylation on xylogenesis modulation in Salix purpurea."
More information at: http://www.idpan.poznan.pl/images/stories/konferencja_pl_2018/2018-materialykonferencyjne-highresolution.pdf
Plant Biology Europe 2018
Carolina Gomes, a PhD Student under the supervision of Jorge Paiva and fellow of the project PurpleWalls participated in the PBE 2018 conference in Copenhagen, Danemark from 18 to 21 June. She presented a communication in the form of panel on "Unraveling the Cytosine-5 methylation machinery in Salix purpurea" (Carolina Gomes, Mortaza Khodaeiaminjan, Jorge A. Pinto Paiva). Carolina Gomes was awarded with the "PBE2018 Support grants for PhD students and Post Docs" This grants were offered on basis of the submitted abstract to the PBE2018 conference. Congratulations Carolina!
More information at: http://www.europlantbiology2018.org/
BioCafe 16.01.2018 – Franklin at Poznan University of Life Sciences
Dr Franklin Gregory gave an invited lecture entitled "Prospects and Problems of Plant Genetic Engineering" at Poznan University of Life Sciences on 16th January 2018. The meeting was organized by BIO-TALENT in cooperation with the scientific association of students and PhD students of PULS who actively participated in the BioCafe.
BioCafe 7.05.2018 - Preeti at Adam Mickiewicz University in Poznan
Biocafe talk entitled "The Art of Designing life by Synthetic Biology& The Indian Wedding Tale" has been organized on 7 may 2018. The main idea of talk was to give few glimpses on the application of synthetic biology in designing new life forms for useful purposes, currently researched worldwide, which has various solutions to global health, energy and environmental problems. The other part of the talk was about the tradition and rituals about marriages in India, which gave a beautiful insight of wedding customs in India to audience.
Marslin G, Siram K, Maqbool Q, Selvakesavan RK, Kruszka D, Kachlicki P, Franklin G (2018) Secondary Metabolites in the Green Synthesis of Metallic Nanoparticles. Materials 2018, 11, 940.
Marslin G, Jose P, Qi S, Franklin G (2018) Oral Delivery of Curcumin Polymeric Nanoparticles Ameliorates CCl4-induced Subacute Hepatotoxicity in Wistar Rats. Polymers, 10, 541; doi:10.3390/polym10050541
IPG-PAS seminar, 27th April 2018
Dr Franklin Gregory gave an invited lecture entitled "The Emerging Avenues of Phyto-nanotechnology" at the IPG PAS on 27th April 2018. It was in the frame of Scientific Seminar of the Institute that are open to public.
Jury member at PhD thesis defence at Universidad Politecnica de Madrid (Spain)
On 22th May 2018, Jorge Paiva participated as member of the jury of the PhD thesis Víctor Manuel Chano Gonzáles, in the frame of the Doctoral Program "Doctorado en investigación Florestal Avanzada" of "E.T.S De Ingenieria de Montes, Forestal y del Medio Natural" do the Polytechnic University of Madrid (UPM, Universidad Politecnica de Madrid). Victor Chano successful concluded PhD studies on "Xyloegeneis in response to severe traumatism in the Canary Island pine (Pinus canariensis C. Sm. Ex DC). The thesis was under supervision of Prof.Dr. Alvaro Soto de Viana and Prof. Dr. Carmen Collada Collada. Congratulations to Dr. Víctor Chano!
Dr. Franklin is editing a special issue entitled "Nanoformulations containing Phytochemicals/ Herbal extracts" for the Journal Frontiers in Pharmacology (IF 3.8) In collaboration with Prof. Fernandez-Ferreira (Portugal) and Dr. Dureja (India)
BIO-TALENT CONFERENCE IS COMING!
The Institute of Plant Genetics, Polish Academy of Sciences (IPG PAS) Poznan, Poland cordially invites you to join the Integrative Plant Biology IPG PAS Conference, held 7-9 November 2018 in Poznan, Poland. To find more information and register please go to the www.conference.biotalent.eu
Newsletter 2/2017 [July-December 2017] issued at the end of December
WP3 Enhancement of research excellence
New NCN OPUS projects granted to dr Franklin Gregory
OPUS13 HyperiSyn: Unravelling the molecular/ genetic network of hypericin biosythesis by employing innovative tools (2017-2020)
Hypericin is an important multifunctional lead drug molecule in new therapies. Being a light sensitive molecule, photoexcitation properties of hypericin are under exploitation for use as fluorescent diagnostic tool and to treat tumors via photodynamic therapy. In spite of several applications in the pharmaceutical industry and medical field, the biosynthesis of hypericin is not understood yet, mainly due to the lack of information about the genes involved in this pathway. This project is proposed to elucidate hypericin biosynthesis pathway using several contemporary tools developed at Dr. Franklin’s laboratory. Results of this project would not only benefit the basic research but also the applied sciences. Since H. perforatum is one of the most consumed medicinal plants in the world and would contribute to the knowledge-based bio economy, it is worth investing in the characterization of its biosynthesis pathways.
OPUS13 HyperAgro: Understanding the relevance of pathogenesis-related defence mechanisms in plant recalcitrance against Agrobacterium mediated transformation (2018-2021)
Agrobacterium tumefaciens mediated plant transformation is an indispensable tool for crop improvement, plant functional genomics, genome editing and synthetic biology. Unfortunately, several economically important plant species (example: members of legumes, cereals, biofuel crops, fruit trees, medicinal plants) remain difficult to transform using this bacterium (plant recalcitrance), a phenomenon yet to be understood. Moreover, the widespread of plant recalcitrance phenomenon in the plant kingdom makes the use of such contemporary tools as CRISPR / Cas9 or RNAi limited to only a few plant species. Although the mechanism of plant recalcitrance is still unknown, activation of plant defense response against A. tumefaciens seems to be the prevailing cause. In this project, we will analyze the relevance of PR defense mechanisms in plant recalcitrance.
Marslin G, Siram K, Liu X, Khandelwal VKM, Xiaolei S, Xiang W, Franklin G (2017) Solid lipid nanoparticles of Albendazole for enhancing cellular uptake and cytotoxicity against U-87 MG glioma cell lines. Molecules 2017, 22(11), 2040; doi:10.3390/molecules22112040
Marslin G, Sarmento B, Franklin G, Martins JAR, Silva CJR, Gomes AFC, Sárria MP, Coutinho O, Dias ACP (2017). Curcumin Encapsulated into Methoxy Poly(Ethylene Glycol) Poly(ε-Caprolactone) Nanoparticles Increases Cellular Uptake and Neuroprotective Effect in Glioma Cells. Planta Medica 83(5): 434-444 DOI: http://dx.doi.org/10.1055/s-0042-112030
Boher, P., Soler, M., Sánchez, A. Hoede, C., Noirot, C., Paiva, JAP, Serra, O, Figueras, M (2017) A comparative transcriptomic approach to understanding the formation of cork. Plant Molecular Biology https://doi.org/10.1007/s11103-017-0682-9
Hypericum is an important genus of the family Hypericaceae and includes almost 500 species of herbs, shrubs and trees. Being the home for many important bioactive compounds, these species have a long traditional value as medicinal plants. Currently, several species of this genus have been used in ailments as knowledge-based medicine in many countries. A special topic entitled “Molecular and Biotechnological Advancements in Hypericum Species” has been co-edited by Dr. Franklin with Professors Ludger Beerheus (Germany) and Eva Cellárová (Slovakia) for the Frontiers in Plant Science journal.
Citation: Franklin, G., Beerhues, L., Cellárová, E., eds. (2017). Molecular and Biotechnological Advancements in Hypericum Species. Lausanne: Frontiers Media. doi: 10.3389/978-2-88945-117-3
Dr. Franklin Gregory received an award from the director of IPG-PAS for his scientific performance during the years 2015-2016.
WP4 Cooperation and transfer of knowledge
LECTURES & WORKSHOPS
Series PLANT SYSTEMS BIOLOGY
16.10.2017 Cyril Zipfel
Light and dissection microscopy workshop
4.12. – Introduction to light microscopy – an introductory lecture by Robert Malinowski
5.12. practical exercises by Karolina Stefanowicz and Marcin Olszak
Workshop on cytogenetics and LCM applied to legumes
Jorge Paiva and Karolina Stefanowicz organised the Workshop on cytogenetics and LCM applied to legumes, held at the IGR PAN between 5th to 8th December 2017. The workshop was organized in the frame of the bi-lateral Poland Portugal project “Cell wall remodelling under stress conditions in Medicago truncatula” in collaboration with the Biotalent project.
The project “Cell wall remodelling under stress conditions in Medicago truncatula” is a project developed in the frame of the Programme for Cooperation in Science between Portugal and Poland (2017/2018, signed between FCT (Portugal) and MNiSW (Poland). This project aims to: 1) develop a strong collaborative network on legume cell walls responses to abiotic stress, towards a better understanding of this response; 2) generate important synergistic opportunities to combine the knowledge, expertise and resources between the Polish and Portuguese teams; 3) establish the bases for common international research projects.
During the 5 days of the workshop the Portuguese and Polish team members (4 PhDs, 3 PhD students, and a MSc) and two invited participants for IGR PAN (Karolina Susek and Mortaza Khoedeaminjan) were been trained in cytogenetics and Laser Capture Microscopy. The theoretical lectures of the workshop were open to the community, while the practices were reserved to the members of the consortium and invited participants.
More details bout the workshop can be found at the Bi-lateral project (https://bilateralplptcellwall.wordpress.com/aims/).
STUDY VISITS AND TRAININGS ABROAD
In October 2017 Robert Malinowski visited IPK, Gatersleben, Germany to perform joint experiments using new imaging methods for plant-pathogen interactions and lay the grounds for further collaboration.
Robert Malinowski gave a talk entitled – “Understanding P. brassicae – driven molecular and cellular reprogramming in plants”
In October 2017 Fatema Bakro spent one week in Prague taking part in the bioinformatics course.
WP5 Dissemination and outreach
18-22 September 2017 Conference IUFRO 2017 “125th Anniversary Congress 2017”
The Cell Walls by Design Team was represented by Jorge Paiva and Carolina Gomes at the IUFRO “125th Anniversary Congress 2017” held in Freiburg, Germany from 18th – 22th September of 2017. Jorge Paiva presented a poster communication the “Effect of 5-Azacytdine and Hydroxyaurea on seed germinaton and response of Eucalyptus globulus juvenile plants to water stress” (project EgoSelf, Portugal). Carolina Gomes present an oral communication on the recent work on the identification and the characterization of DNA methyltransferases and demethylases in Salix purpurea in the frame of her PhD studies (project PurpleWalls, funded by NCN, Poland). The IUFRO World conference is the most prestigious world conference on the state of the art in the difference domains of the forest.
18-22 September 2017 Conference ICLGG
The biannual meetings of ICLGG were launched in 2002 in St. Paul, Minnesota by the initiative of prominent scientists and professionals in the field with the aim to promote the international dissemination and discussion of the most recent research results and achievements of the legume sciences, to support the scientific community and help the breeders and stakeholders with applications and partnership. Fatema Bakro participated in the 8th International Conference on Legume Genetics and Genomics (ICLGG) in Budapest, Hungary. She presented a poster entitled “Implementation of reverse genetics tools for improvement of pea cultivation in Poland” co-authored by Sara Blicharz and Robert Malinowski.
6-10 December 2017 Nano Today conference
Nano Today journal, Institute of Bioengineering and Nanotechnology (IBN) and Elsevier organized the 5th Nano Today Conference (Nano Today 2017) focusing on the latest developments in the area of nanoscience and nanotechnology. Dr Franklin presented the results of HyperNano project as a poster communication entitled “Silver nanoparticles modulate secondary metabolism in Arabidopsis thaliana” co-authored by researchers participating in the project namely D. Kruszka, R. Selvakesavan and P. Kachilicki.
NETWORKING & PROMOTION
Anna Stachowiak-Szrejbrowska, Karolina Stefanowicz and Aleksandra Kempińska participated in Projekt Naukowiec (18-19.10.2017). It was a country-wide event organised by the EU Framework Programmes National Contact Point and Regional Contact Points. The main aim of this event was to promote the career in research among students and support young researchers in their career development by sharing best practice and experience.
BIOM 20.11.2017 – BIO-TALENT Monday for a class from the Junior High School comprising theory by Anna Stachowiak-Szrejbrowska, Aleksandra Kempińska and RK Selvakesavan (Technology Transfer and Work in the Biotech Company) and practice (DNA isolation) complemented by visiting the labs of the Institute.
BIOM 11.12.2017 – BIO-TALENT Monday for a class from the Junior High School comprising theory by Anna Stachowiak-Szrejbrowska and Robert Malinowski (Plants go on war) and practice (DNA isolation) complemented by visiting the labs of the Institute.
BIOCAFE 13.12.2017 - a talk by Fatema Bakro on Short trip to discover the magic behind the variation in our food (Legumes around the world) was given at Adam Mickiewicz University in Poznan together with traditional Christmas Polish food and Syrian sweets prepared by Fatema.
SCIENTIFIC CONTEST – Daria Budzyńska, a the student of fifth year of Biotechnology on Poznan University of Life Sciences on the Scientific Contest and had a 1 month training at the DIPB.
TEACHING – dr Robert Malinowski and dr William Truman provided a theoretical course Introduction to Molecular Plant Signalling for the Biology part of PhD programme at the Institute of Bioorganic Chemistry. The main idea of this course is to provide a comprehensive introduction to the world of plant signalling. Understanding the dynamics, both spatial and temporal, of particular molecules as well as the biochemical and molecular character of their interactions will help establish a more holistic view of plant biology.
The course consists of the following lectures:
- Introduction: Signalling Molecules in Plants [Dr hab. Robert Malinowski]
- Signalling Pathways and Molecules Co-ordinating Plant Development [Dr hab. Robert Malinowski]
- Responses to External Stimuli [Dr hab. Robert Malinowski]
- Nutrient Uptake and Distribution [Dr hab. Robert Malinowski]
- Pathogen Detection Mechanisms and Signalling in Defence Responses [Dr William Truman]
- Mini-Project Review and Discussion
Summer student traineeship at DIPB (July-October 2017)
Cell Walls by design Team held, during July 2017 Marcin Drzewiecki and during August Malwina Wegner both students from the from Poznan University of Life Sciences for one month Summer training period, under the supervision of Jorge Paiva, Carolina Gomes and Mortaza Khodeaiaminjan. During this period they participated different activities of the PurpleWalls project were they developed competences 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.
Ms. Sophia Bałdysz, an undergraduate student from Adam Mickiewicz University, Poznan pursued her internship program at Dr. Franklin’s lab from 3rd July 2017 to 2nd October 2017. Under the supervision of Dr. RK Selvakesavan, she did a project on the Characterization of Agrobacterium transposon mutants. She got trained in screening of Agrobacterium mutants using Rapid Amplification of Transposon Ends (RATE), sequence analysis (BLAST and CLUSTALW), bacterial transformation, Agrobacterium- mediated Plant transformation and screening of plants for transient GUS gene expression.
Erasmus student from the University of Pavia (August-October 2017)
Following the collaboration between the Cell Walls team and the University of Pavia, Monah Abou Alezz (Universitá degli Studi di Pavia, Italy), started at 1st August 2017 his 3 months ERASMUS + internship at the Department of Integrative Plant Biology, at the Cell Walls by Design. Monah was involved in the identification, characterization and expression analysis of some coding and non-coding genes in Salix spp.
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"
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.
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"
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"
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.
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.
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
Series INTEGRATIVE PLANT BIOLOGY
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
29.05.2017 Plant E-Infrastructures: WheatIS & French Elixir node dr Hadi Quesneville, INRA-Versailles, France
SCHOOL OF BIOTECHNOLOGY
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.
SOFT SKILLS WORKSHOPS
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.
STUDY VISITS AND TRAININGS ABROAD
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").
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
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.
IUFRO TREEBOTECH, CONCEPCION, CHILE, 4-9 JUNE 2017
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.
AT THE FOREFRONT OF PLANT RESEARCH, GHENT, BELGIUM 15-16 JUNE 2017
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
SHARING GOOD PRACTICE
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".
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.
NETWORKING & PROMOTION
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
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:
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.
BIOM BIO-TALENT Monday
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.
BIOTALENT 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
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) (www.udg.edu). 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.
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 (www.itqb.unl.pt) (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
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.
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.
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
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 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?
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
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.
5. Joint photo of the whole team
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.
7. BIO-TALENT Meets TUTIC-GREEN
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.
Newsletter 1/2016 [January - June 2016] issued at the end of June
1. New PhD students - Sara Blicharz, Fatema Bakro, Carolina Gomes
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.
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.
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.
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.].
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.
- 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.
- 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!!!
- 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.
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.