Skilled and internationally recognised leaders will guide the Early Stage Researchers

In addition to the academic merits, our supervisors have ample experience supervising BSc, MSs and PhD students. Our principal investigators have together supervised over 90 graduated PhD students and almost 100 postdoctoral fellows.

David Alabadí

Research Scientist at the Instituto de Biología Molecular y Celular de Plantas (CSIC/UPV)

David Alabadí (PhD, 1998) is Research Scientist of the Spanish Research Council at the IBMCP since 2007. His research interest has focused on understanding the contribution of hormones gibberellins/DELLA proteins to the plant response to the environment. One of the main contributions was the finding that DELLAs act as signalling hubs, connecting the environment with developmental and growth pathways by interacting with many transcription factors involved in many different processes. This finding allowed answering two relevant questions, what are the mechanisms by which gibberellins control so many different processes, and what are the mechanisms by which the gibberellin pathway interacts with other signalling pathways. His work has also uncovered a gibberellin-independent mechanism to degrade DELLA proteins in response to changes in temperature or light quality, which is mediated by COP1 and provides a faster response capacity than the canonical pathway. In recent years, his research interests have gravitated towards investigating other mechanisms through which DELLA regulate transcription, for example through interaction with transcription elongation factors, and the characterization of a small group of co-chaperones, the prefoldin and prefoldin-like proteins, which participate in transducing information from the cellular environmental in animals and yeast and whose role in plants is largely unknown.

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Javier Gallego-Bartolomé

“Ramón y Cajal” Fellow (CSIC) at Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV)

Javier Gallego-Bartolomé (PhD, 2011) graduated as Agronomical Engineer at the Polytechnic University of Valencia (UPV) in 2004. Then he joined the lab of Drs Blázquez and Alabadí (IBMCP, Valencia, Spain), where he studied different molecular mechanisms by which the plant hormones gibberellins interact with other signaling pathways to control gene expression. After a short postdoc in the Chory lab (The Salk Institute, La Jolla, USA), he moved in 2013 to the Jacobsen lab (UCLA, Los Angeles, US) where he worked on targeted manipulation of DNA methylation and on the mechanistic aspects of the de-novo silencing machinery in plants. In 2019 he joined the IBMCP as a junior group leader, where he is working on the epigenetic regulation of gene expression in plants. His group is currently focused on the evolution and function of the SWI/SNF chromatin remodelers, as well as the development of biotechnological tools to manipulate the epigenome and gene expression in a locus-specific manner.

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Joint Project

DELLA-dependent chromatin features during seedling adaptation to drought

DELLAs are transcriptional regulators that can act on histone modifiers and on the transcription machinery and that are degraded in response to gibberellins (GAs). DELLA activity improves plant’s performance under drought. To better understand the mechanism underlying this role, F2 will investigate if DELLAs modify the epigenetic landscape in response to drought and if they mediate seed priming. We will increase DELLA levels with the GA-inhibitor paclobutrazol (PAC) in oilseed rape and Arabidopsis and with mutants in the latter. F2.O1. F2 will evaluate seedling traits (biomass, photosynthetic parameters) in response to seed priming, drought, and both, with and without PAC-treatment and in DELLA mutants. F2.O2. F2 will examine DELLA-dependent changes in the transcriptome (RNA-seq) in seedlings of both species subjected to drought. F2.O3. F2 will profile H3K4me3 and RNAPII (ChIP-seq) and chromatin accessibility (MOA-seq) to determine the effect of DELLAs in the chromatin response to drought in both species. F2.O4. F2 will define the differential genomic occupancy of the DELLA RGA (ChIP-seq) and its differential interactome (quantitative AP-MS) in response to drought in Arabidopsis. F2.O5. F2 will perform meta-analysis with results from F2.O2, F2.O3 and F2.O4 to infer the mechanisms through which DELLAs operate under drought.

F2.R1. Seedling traits improved by DELLA activity under drought and DELLA’s role in seed priming. F2.R2. DELLA-dependent changes in the transcriptome in response to drought. F2.R3. DELLA-dependent chromatin features triggered by drought. F2.R4. Mechanism for DELLA-dependent regulation of chromatin features under drought.

Fredy Barneche

CNRS Research Director, IBENS, France

Fredy Barneche (PhD) has been leading an independent research axis at IBENS, CNRS/Ecole Normale Supérieure (ENS-PSL), France, since 2008, with promotion as Research Director in 2016. He is interested in determining how chromatin-based or epigenetically-controlled mechanisms influence plant adaptive responses to environmental cues, with a specific emphasis on light. He has discovered that the initial light perception event by the germinating plantlet has a rapid and spectacular influence on chromatin organisation and composition, from single genes to higher order nuclear architecture. He further identified that large-scale chromatin rearrangements during Arabidopsis photomorphogenesis co-occur with a general increase of the transcriptional regime, altogether underlying a profound reprogramming of genome and epigenome organisation induced by light. In a collaborative work with the Rubio team, he also identified a functional role for the long-known DET1 light-signalling component at the chromatin level. The latter study revealed a light-regulated mechanism that controls the abundance of specific epigenetic marks over the whole plant genome.

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Sujeeth Neerakkal

Head of Plant Research, BioAtlantis Ltd.

Dr. Sujeeth Neerakkal (PhD): is leading the Plant Biology Department, BioAtlantis Ltd. Sujeeth undertakes and oversees the production of natural products and functional bioactives as plant stress solutions. He has a strong background in plant molecular biology research, extensive experience in the elicitor-abiotic and biotic plant stress responses, oxidative stress biology and programmed cell death in plants. He played a key role in coordinating BioAtlantis role in EU FP7 projects (Biofector, Grant Agreement n°312117 & COFREE, Grant Agreement n°KBBE.2011.1.2-06, CropStrengthen, Grant Agreement n°642901). His current research programmes are based around development of novel molecular-based methods to understand stress mechanisms in biostimulant – plant interactions. His group at BioAtlantis has recently developed an innovative technology “AgriPrime®”. Naturally-derived and unique stress tolerance enhancing compounds are used in this technology to prime and modulate metabolic and physiological responses in plants, resulting in protection against subsequent stresses. A key product from this platform, named Super Fifty Prime®, is being launched for use in climate-smart strategies to alleviate oxidative stress-induced damages in crops, associated with heat, drought and cold.

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Sara Farrona

Lecturer, National University of Ireland Galway (NUI Galway)

Sara Farrona (PhD) has been leading an independent research group at the Plant and Agricultural Bioscience Centre-Ryan Institute, NUI Galway, Ireland, since 2015. Her research focuses on how plants adapt their development in response to the environment through the regulation of gene expression by epigenetic mechanisms. Her group has contributed to discover novel components of the epigenetic machinery that regulate chromatin structure and subsequently transcription. Her lab is highly multidisciplinary and to develop their research aims they apply a combination of biochemistry, biotechnology, epigenetics and molecular biology techniques. The ultimate goal is to identify molecular tools that may help to breed crops with a higher adaptability to different environments including stressful ones due to climate change.

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Klaus Grasser

Professor, Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg

Klaus Grasser (PhD) has been leading an independent research group at the University of Freiburg, Germany (from 1995), then at Aalborg University, Denmark (from 2000) and since 2009 at the University of Regensburg, Germany. His research focuses on the regulation of RNA polymerase II transcriptional elongation as well as co-transcriptional processes. Transcript elongation factors (i.e. regulators of polymerase activity, histone chaperones) are studied in the Arabidopsis model to elucidate their role in plant development and in response to environmental conditions.

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Ueli Grossniklaus

Full professor, Department DirectorDepartment of Plant and Microbial Biology (IPMB)University of Zurich

Our long-term goal is to elucidate the molecular basis of plant reproduction with a special focus on cell specification, cell-cell communication, and epigenetic gene regulation. We cover diverse aspects of reproduction at the physical, molecular, cellular, organismal, and ecological level. A major focus is on understanding signaling during pollen tube growth and reception, and we have identified many players of a novel, plant-specific signaling pathway, which turned out to be involved in a multitude of physiological and developmental processes. We have also made significant contributions towards elucidating the role of epigenetics in seed development and are interested in ecological and evolutionary aspects, in particular in the role and inheritance of epigenetic variation. Finally, a considerable effort is placed on the engineering of apomixis, the clonal reproduction through seeds, which has a tremendous potential for agriculture. Over the last decade, our research has become increasingly interdisciplinary, including collaborations with ecologists, evolutionary biologists, engineers and physicists. This has allowed us to develop novel approaches to address fundamental questions, e.g., how physical contraints affect cellular morphogenesis or how the mode of reproduction affects genome evolution.

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Manuel Piñeiro

Senior Scientist. Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC

Dr. Manuel Piñeiro is a senior scientist in the Instituto Nacional de Investigaciones Agrarias-Consejo Superior de Investigaciones Científicas (INIA-CSIC). After graduating in Biology in the Universidad de Sevilla (1986), he earned his PhD in Sciences in the Universidad Autónoma de Madrid (UAM, 1991) working in the Centro de Biología Molecular-Severo Ochoa – CSIC. His research group is interested in understanding the regulation of plant developmental transitions such as the initiation of flowering or the balance between seed dormancy and germination that have a direct impact on crop yield. His laboratory is contributing to unveil epigenetic mechanisms involved in the regulation of these plant developmental processes, and in the adaptation of plants to fluctuating environmental conditions with emphasis in the increase on ambient temperature associated with the current scenario of climate change. Currently he serves as representative of INIA in the European Plant Science Organization (EPSO).

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José Antonio Jarillo Quiroga

Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC

Dr. Jose A. Jarillo is a Research Professor in INIA-CSIC. After graduating in Biology in the Universidad Autónoma de Madrid (UAM) (1988), he earned his PhD in Biological Sciences in UAM (1994). Later he moved to the Univ. of Pennsylvania as postdoc. In 1999 he came back to Spain and join INIA, where he obtained a staff scientist position in 2001. Since then, the interest of his group has been to deepen in the understanding of the molecular mechanisms that regulate plant phase developmental transitions, and in particular, of those factors that are required to repress flowering initiation until plants are under favourable environmental conditions or reach the appropriate developmental stage to flower. Currently, his research interest is focused in the role of epigenetic regulation in the control of different plant developmental processes, and in the adaptation of plants to high ambient temperatures associated with climate change.

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Aline Probst

CNRS Research director, iGReD

Aline PROBST (PhD, HDR) is leading a research group at the Genetics, Reproduction and Development Institute (iGReD), located in Clermont-Ferrand, France. She aims to understand the role of chromatin organisation in the dynamic changes in gene expression that take place during development and in response to environmental stimuli. To this aim her research focuses on the mechanisms involved in deposition and eviction of histone variants and in the recruitment of histone modifiers in plants. As an example, she characterized the functions of H3 histone chaperones in plants (ATRX, NASP, HIRA…) and demonstrated their involvement in chromatin organisation and gene expression control in early seedling development. Now, she is concentrating on chromatin organization in seeds using Arabidopsis thaliana and Brassica napus (oilseed rape) to better understand histone variant dynamics and their role in transcriptional reprogramming during seed germination using genetics, molecular biology and epigenomic techniques coupled to 3D-bioimaging approaches.

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Vicente Rubio

Research Scientist (CSIC) at Centro Nacional de Biotecnología (CNB-CSIC)

Vicente Rubio (PhD, 2001) is a Research Scientist in the Plant Molecular Genetics Dept. at CNB-CSIC. He studied Biochemistry at Universidad de Murcia (MSc, 1996) and then moved to the CNB-CSIC for a PhD in plant mineral nutrition at the group of Javier Paz-Ares. Afterwards, he carried out a postdoc at Yale University in the group of Xing Wang Deng, working in plant ubiquitination machineries and light signalling. Upon moving back to the CNB-CSIC in 2005 his group has been focused on the characterisation of new functions of the ubiquitination machinery in plants, particularly of E3 ubiquitin ligases that act as hubs to integrate signals from different abiotic stresses and environmental stimuli in plants to trigger coherent adaptive and developmental responses. Currently, the group’s objectives include the characterisation of ubiquitination machineries that control the accumulation of specific epigenetic marks over the plant genome in response to environmental changes, to regulate expression of specific sets of genes that lead to plant adaptation to changing climate conditions.

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Maike Stam

Associate Professor, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam (UvA), The Netherlands

m.e.stam@uva.nl

Website link to the University of Amsterdam: https://www.uva.nl/en
Website link to the Swammerdam Institute for Life Sciences: https://sils.uva.nl/
Website link to group site: https://www.uva.nl/en/profile/s/t/m.e.stam/m.e.stam.html

Maike Stam (PhD) has joined the UvA in 2002 as KNAW fellow, became Assistant Professor in 2006, and was later promoted to Associate Professor. She has been leading her own research team since 2002. From 2012-2014 she coordinated the EU FP7 Marie Curie ITN EpiTRAITS. Research in her team focuses on gene regulation through (distant) regulatory sequences, and epigenetic and chromatin-based mechanisms. She discovered the first known distant cis-regulatory sequence in plants, an enhancer 100 kb upstream of the maize b1 gene. This enhancer is also required for an epigenetic phenomenon called paramutation, in which inactivated alleles can inactivate homologous active alleles when combined by crossing. Her team has been studying this model system for several years, and as part of EpiTRAITS performed the first identification of distant regulatory sequences in maize.

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