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2 annual report

2012

annual report

2012

Published by:

Gregor Mendel Institute

of Molecular Plant Biology GmbH

Dr. Bohr-Gasse 3

1030 Vienna, Austria

E: [email protected]

Editor: Thomas Friese

Photographers: Herbert Blazejovsky,

Ruben Gutzat, Oliver Zehner

GMI logo: Lo Breier

Graphic design: Atelier Blazejovsky

Printing house: Riedel Druck GmbH, 2214 Auersthal© Gregor Mendel Institute of Molecular Plant Biology 2013

The GMI is a basic research institute of the

Austrian Academy of Sciences

2 ANNUAL REPORT 2012

Contents

4 Directors’ Statement

6 Introducing the GMI

RESEARCH GROUPS

8 Busch Group

12 Greb Group

16 Jonak Group

20 Mittelsten Scheid Group

24 Nodine Group

28 Nordborg Group

32 Riha Group

36 Tamaru Group

GENERAL

40 GMI Key Facts

40 Publications

44 Grants

46 PhD Program

48 Seminars

50 Professional Training &

Personal Development

51 Alumni

52 Events

54 Management

54 Administration & Services

56 Scientific Advisory Board

56 Supervisory Board

58 The Austrian Academy of Sciences

59 The City of Vienna

60 Location & Travel Directions

ANNUAL REPORT 2012 3

Directors’ Statement

Dr Magnus NordborgScience Director

Dr Markus KiessBusiness Director

This report covers our third year as Directors of the Gregor Mendel Institute (GMI), which means we have now been here longer than most of the graduate students. During these three

years, we have seen constant improvement, and although there is much left to do, the GMI is already a fantastic place to do research, comparable to other world-leading institutions. Our scientific reputa-tion continues to grow. During the last year, 37 papers were pub-lished, including several in absolute top journals; we continued to recruit successfully worldwide, including a new Junior Group Leader, Michael Nodine, from the Whitehead/MIT; and we played a leading role in organizing the very successful 23rd International Conference on Arabidopsis Research in Vienna’s Hofburg.

We are proud to be one of a relatively small number of institu-tions world-wide focusing on basic research in plant biology, a field we are convinced will play an increasingly important role in years to come.

In conclusion, we want to thank the Austrian Academy of Sciences for its continued support, without which the GMI would not exist; the Federal Ministry of Science, and the City of Vienna for their general support of the VBC; and everyone, especially those at the GMI, for making this a fantastic place to work.

Magnus Nordborg Markus Kiess

4

Profile

The Gregor Mendel Institute of Molecular Plant Biology (GMI) was founded in 2000 by the Austrian Academy of Sciences (ÖAW) to promote research excellence in plant molecular biology. The GMI is the only international center for basic plant research in Austria. Located in Austria’s leading address for life sciences research, the Vienna Biocenter Campus (VBC), the GMI co-owns and occupies part of the purpose-built ÖAW Life Sciences Center Vienna, along with the Institute for Molecular Biotechnology (IMBA). The Center was completed in 2006.

As a complex incorporating both academic research institutes and biotech-nology companies, the VBC provides an environment brimming with exciting intellectual and infrastructural synergies for GMI researchers. In addition to the IMBA, other campus institutes include the Research Institute of Molecu-lar Pathology (IMP), the Max F. Perutz Laboratories (MFPL) of the University of Vienna and the Medical University of Vienna, and companies such as Affiris, Haplogen, and Intercell.

Block funding is received from the GMI’s shareholder, the Austrian Academy of Sciences (ÖAW), with additional resources provided by a mix of national, European, and other international funding agencies.

Our research

Research at the GMI is curiosity driven and covers many aspects of molecular plant genetics, including basic mechanisms of epigenetics, population genetics, chromosome biology, developmental biology, and stress signal transduction. GMI research focuses primarily, but not exclusively, on Arabi-dopsis thaliana, an unassuming member of the mustard family, which has become the worldwide model organism of choice for molecular plant biology, due to its rapid life cycle, small simple genome, and prolific seed production.

Research is carried out by independent research groups, led by senior group leaders with permanent contracts, or junior group leaders with tempo-rary (5+3 years) appointments. The focus is on scientific excellence and publication in high impact journals. Notably, GMI researchers have one of the highest publications rates in top journals such as Nature and Science in Austria.

The importance of plant research

The vital importance of plant biology can hardly be overstated, and it has two aspects. Firstly, it is obvious that all life on earth, human life not least,

Introducing theGregor Mendel Institute


depends directly on the growth of plants. And yet, because of its so central role, its importance can easily be taken for granted. This is not an option today – in a world faced with mounting nutritional and energy deficiencies, with climate change and soil depletion, understanding how plants grow, and how they might be better grown to address these prob-lems, is more important than ever – it is indeed a question of survival.

At the GMI, we understand our first mission in this context: to conduct basic plant research that will have direct or indirect implications for improving world nutrition, developing biofuels and plant-based medicines, and manag-ing climate change.

Secondly, it must be remembered that basic research on plants can led to fundamental breakthroughs not only for plant biology but also for human biology – Gregor Mendel’s elucidation of the basic principles of genetics, Barbara McClintock’s discovery of transposons, and the recent work on epigenetics and RNA silencing are good examples. GMI research aims to be fruitful in this aspect too.

Infrastructure

Our research activities are supported by an efficient administration team and a truly world-class infrastructure, consisting of rapidly expanding in-house services, including state-of-the-art plant growth chambers and bioinformatics facilities, of shared scientific services with IMP and IMBA, and lastly of a wide range of services offered by the Campus Science Support Facilities GmbH (CSF), a non-profit organization funded by the Austrian Ministry of Science and the City of Vienna.

CSF services of special relevance to GMI researchers include Electron Microscopy, Next Generation Sequencing, and Structural Biology. In 2012, the foundation for a new Plant Growth and Phenotyping facility was also laid, with the decision to build 6 new state-of-the-art plant growth chambers, include CO2-controlled and pathogen chambers. For more information, please visit www.csf.ac.at.

Education

The GMI offers PhD positions within the framework of the prestigious Vienna Biocenter International PhD Program. In addition, GMI members present lectures and organize journal clubs and laboratory courses at the University of Vienna. The GMI is also committed to taking part in outreach activities to promote the importance of plant science for the general public.

Working at the Gregor Mendel Institute

The GMI provides a lively, international working environment with some 95 staff from over 20 countries. Our working language is English. Research is complemented by scientific events, such as seminars, an annual scientific retreat and GMI-organized conferences, and social events, such as ski trips to the nearby Alps, sports events, and festivities.


“The Busch group has been part of the

GMI community for less than two years, but has done a

tremendous job in establishing and developing technologies

for the quantitative assessment of multiple

characteristics of plant roots.”

GMI Scientific Advisory Board Report 2012

Regulation ofroot development in ArabidopsisAlthough the roots of plants are obscured from view, they are of utmost

importance for plants. Roots explore the soil and gather all essential

nutrients for plants. Thus the regulation of the continuous and highly

plastic development of the root is essential to any plant. During the

past decade the root has been successfully used as model for organ

development. Applying quantitative genetics tools coupled with novel

tools for automated image acquisition and analyses, we are using natu-

ral variation of hundreds of Arabidopsis accessions to uncover novel

classes of regulators and regulatory networks of root development. We

are using genetics and systems biology tools to dissect the functions

of these novel regulators and regulatory networks.

Plants have been highly successful in colonizing the vast majority of the earth’s land surfaces. Intriguingly, this was achieved without the presence of fast chemo-electrical information processing systems

such as a central nervous system or significant motility. A key to this success was presumably the evolution of organismal development towards an un-matched plasticity. Most of the development in plants happens post-embryoni-cally after a short and stereotypical embryogenesis. In almost all vascular plants this development includes the periodic formation of new organs above and below ground, as well as the growth of these initiated organs. Organ initiation and growth is highly influenced by environmental conditions. The orchestration of development within and between tissues and organs is realized using a highly complex system of intercellular communication that relies on chemical signaling such as hormones, receptor/ligand based signal-ing and moving proteins.

To understand the molecular basis of this development and how environmental information is integrated into it, the root of Arabidopsis thaliana has proven to be an excellent model. Much of this progress was facilitated by the discrete arrangement of tissues and developmental zones in the Arabidopsis root that made it possible to determine the stage of development and the tissue identify of a cell simply by its position in the root (Fig 1). Using this simple model, remarkable progress has been made in understanding regulatory processes that underlie plant development. However, it is to a large extent still unclear how those networks and pathways interact to coordinately regulate root development. Furthermore, there is a gap in understanding how growth processes are modulated in a quantitative manner.

Group Leader:

Wolfgang [email protected] ac.at

Joined GMI in Jan 2011PhD: Max Planck Institute for Developmental Biology/Eberhard-Karls-Universität,Tübingen, Germany

Previously– Postdoctoral Fellow, IGSP Center for Systems Biology, Duke University, USA, 2008. Laboratory of Philip Benfey

Group members:

Postdoctoral Fellows Takehiko Ogura Mónica Meijon Vidal* Santosh Satbhai

Technicians Aaron Appleyard Christian Göschl Bonnie Wolhrab

PhD Student Radka Slovak

(*left the lab in 2012)

9ANNUAL REPORT 2012

Fig. 1.Medial longitudinal section of an Arabidopsis root illustrating the progression of development along the longitudinal axis, as well as the tissue architecture around the radial axis (additionally illustrated with schematic of a cross-section).

Fig. 2.Example of imaging pipeline to extract quantitative data at the organ level of the root. Depicted are four isogenic roots in a time course over five days (left to right). Upper panel: Original im-ages; lower panel: Images after automated processing. Grey areas: Above ground parts of seedling. Blue dot: Detected root start point. Red dot: Detected root end points.

B U S C H

A promising avenue to fill these gaps is to explore the phenotypic space created by natural variation and to identify the causal genes using quantitative genetics. Due to the large number of lines that need to be screened to conduct any quantitative genetics, it is highly desirable to acquire quantitation of phenotypes as automated as possible. The root of Arabidopsis lends itself very nicely to automation since it can be easily grown in a way amendable to image acquisition, and due to its simple structure the images are suitable for computational analysis.

By acquiring large phenotypic datasets and using these in conjunction with quantitative genetics, we aim to identify novel regulatory genes and net-works. For this we developed a toolbox of resources to enable large-scale phenotyping of Arabidopsis accessions, as well as to acquire, process, and analyze phenotypic data of Arabidopsis roots. Using these data we aim to identify novel developmental regulators and their networks, which we then characterize functionally, using genetics and systems biology approaches.

HIGH-THROUGHPUT IMAGING PLATFORMS FORqUANTITATIVE PHENOTyPING OF ROOTS

To phenotype large numbers of plant roots in a highly standardized manner, we established a lab seed resource and custom phenotyping pipelines. To enable experimental designs to deal with maternal effects that might confound statistical analyses, the high quality seed resource contains several hundred Arabidopsis accessions. We have developed several highly standardized imaging pipelines to quantitatively phenotype a very large number of plants. These pipelines use custom growth racks to grow verti-cally oriented agar plates or growth chambers containing Arabidopsis plants in a standardized manner. For image acquisition we use CCD scanners in conjunction with custom plate alignment frames, or, for high-resolution data at the cellular level, an automated laser confocal microscope in conjunction with a custom growth chamber

day 1

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Fig. 3.Histogram of root growth rates of 274 Arabidopsis accessions under standard growth conditions.

Fig. 4.Natural variation at the cellular level. Laser confocal microscope images of representative roots for two accessions that display differ-ent cellular root architectures. Left: Root of accession with long mer-istem and large cells. Right: Root of accession with short meristem and short cells. Images are of the same scale. Roots were stained with the cell wall tracer propidium iodine. Colors represent signal intensity (cool colors: low intensity, warm colors: high intensity).

B U S C H

To deal with the challenges caused by the large number of images, we developed custom software that automatically segments and quantifies several growth related traits from roots at the organ level. This software uses shape and color information to identify roots with high confidence and then automatically measures total length and measures of root topology (Fig. 2). Using the software we can currently recover quantitative data from around 80-90% of all germinated roots under standard growth conditions. Recently, we have quantified data from images of more than 500,000 single roots using this pipeline. For the extraction of biometric measurements at the cellular scale (Fig. 3), we developed semi-automatic procedures that facilitate a high-throughput image processing. These methods allowed us to build the basis of a comprehensive atlas of the natural variation of root development, which is already one of the largest collections of quantitative phenotypes for the Arabidopsis root.

NATURAL VARIATION AND DEVELOPMENTOF THE ARABIDOPSIS ROOT

Using our high throughput image acquisition pipelines and automated image analyses, we were able to assess the natural variation of root development in Arabidopsis, under both standard growth conditions and a variety of stresses, as well as perturbation of hormone signaling pathways. This extensive phenomic dataset showed significant variation of root development at the whole organ scale (Fig 3) and at the cellular level (Fig 4). Using genome wide association mapping we have already identified several genomic regions and genes that contribute significantly to this variation. We are currently setting up a multilevel data mining pipeline to identify multiple components of regulatory networks in these data. We will functionally analyze these candidate genes and regulatory networks using genetics and systems biology tools. Besides the identification of novel regulators and their networks, this will be an excellent starting point to understand the role of networks in natural variation.


“The Greb lab made excellent progress

over the last year. In 2011, they published several

important papers describing key regulators of

cambial development and establishing a strong

record of productivity. Ongoing work

builds on these discoveries.”


Growth and cellfate regulation

Lateral growth in plants is essential for the formation of extended

shoot and root systems, and, thus, for the creation of biomass on earth.

Our lab uses this process as an example to reveal principles of growth

and cell fate regulation in multicellular organisms.

Multi cellularity is a fundamental concept of life on our planet. The concept of single units (cells) taking over special functions in interaction with other units of a multicellular body is striking and

requires an extreme degree of complexity with respect to cell-to-cell com-munication during growth and activity of such a system. Elucidating holistic concepts of the development and function of multicellular systems is there-fore challenging, but also essential to understand the functionality of higher organisms. Lateral growth of plant shoots and roots is based on the tissue-forming properties of a lateral meristem called the cambium, the activity of which leads to the production of secondary vascular tissue (wood and bast, Fig. 1). Considering its function as a stem cell niche that is essential for the constant production of new tissues, as well as its dependence on environ-mental cues, the cambium represents an ideal model for addressing ques-tions concerning the regulation of cell identity and how growth processes are aligned with endogenous and exogenous requirements. Given these attractive properties, our laboratory investigates lateral plant growth in order to reveal general concepts of growth and development of multicellular organisms.

Despite its herbaceous growth habit, Arabidopsis thaliana has been shown to be an excellent model for the analysis of secondary growth. Simi-larly to more woody species, secondary growth in Arabidopsis is initiated by the establishment of the interfascicular cambium in the elongating shoot (Fig. 2A, B). To explore the molecular control of secondary growth initiation, we concentrate on the formation of the interfascicular cambium (IC) between primary bundles, a prominent and easy to follow mark for the establishment of a closed cambium cylinder and the initiation of secondary growth. A selection of our approaches aiming at the molecular characterisation of this process is given below.

Group Leader:

Thomas [email protected]

Joined GMI in Feb 2006PhD: Max Planck Institute for Plant Breeding Research, Cologne, Germany

Previously– Postdoctoral Fellow, John Innes Centre, Norwich, UK, 2003-2006. Caroline Dean Lab

Group members:

Postdoctoral Fellows Javier Agusti Nial Rau Gursanscky Virginie Jouannet Branislav Kusenda (25%) Stefanie Suer

Technicians Karin Grünwald Julia Riefler* Martina Schwarz*

PhD Students Klaus Brackmann Ivan Lebovka Pablo Sánchez



14

G R E B

HORMONAL CONTROL OF SECONDARy GROWTHPlant hormones play a crucial role in the long- and short-distance

control of developmental processes, and secondary growth is no excep-tion in this respect. Information about the growth stage of the plant, day length, temperature and mechanical stress are mediated by the action of auxin, ethylene, gibberellins, brassinolides and cytokinin and integrated by still unknown cambium regulators. In our research group, we revealed the influence of two additional hormones, namely strigolactones (SLs) and jasmonate (JA), further increasing our picture of the complexity of cambium regulation. SLs are connected to auxin signalling and seem to mediate information about the stage of general shoot growth. In contrast, we hypothesise that JA signalling translates tissue tension within the stem into cell division, a process essential to avoid tissue disruption during expansion of growth axes. The characterisation of the role of these hormone signalling pathways and their interactions represents a challenging but fundamental task in understanding how secondary growth is integrated into the general growth of the plant.

ISOLATION OF NOVEL CAMBIUM REGULATORSThe number of genes known to be involved in cambium regulation

is rather limited to date. The isolation of novel regulators is therefore one essential step towards the understanding of secondary growth regulation. We established an in vitro system by which we are able to induce secondary growth in isolated stem fragments of Arabidopsis in a very controlled man-ner (Fig. 3A). For us, this system represents an invaluable tool to dissect molecular mechanisms regulating secondary growth. We took advantage of this system in particular to monitor tissue-specific changes in transcriptional profiles during the initiation of the IC and to identify regulating genes by following a Laser Capture Microdissection (LCM) approach. During this process, we collected RNA specifically from cells in interfascicular regions at three different time points during the initiation process (Fig. 3B). Micro array hybridisations with amplified RNA were performed, providing us with a repertoire of genes specifically changing expression during cambium initia-tion. By analysing plants defective for the identified genes, we are currently elucidating their role in cambium regulation. Here we focus primarily on factors involved in cell-to-cell signalling.

Fig. 1.Schematic cross sections through the stem of a dicotyledonous plant. The initiation of cambium activity (red, B) between primary vascular bundles (i.e. interfascicu-lar regions) transforms a primary stem (A) into a secondary stem (C). This process is essential for the establishment of a closed cambial cylinder which produces phloem (assimilate and signal-ling molecule transporting tissue, yellow) towards the outside and xylem (water transporting tissue, blue) towards the centre of the shoot axis, resulting in an in-crease of shoot diameter (C).

G R E B

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Fig. 4.Comparison between Arabidopsis (left)and Brachypodium (right).

auxin

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GMI Report 2010_Kern_23.02.11_1 06.03.11 20:09 Seite 15

G R E B

INVESTIGATION OF THE ADAPTIVE VALUE OFSECONDARy GROWTH The innovation of secondary growth during evolution allowed plants to overcome hydraulic constraints, to increase their repertoire of possible growth forms and to thereby colonize an extended range of ecological niches. In order to explore the adaptive value of secondary growth in various environmental contexts and to reveal the underlying molecular changes, we exploit natural variation in Arabidopsis thaliana as a powerful tool for study-ing the selection pressure acting on this process (Fig. 4). Genetic variation between Arabidopsis strains collected at different sites of the northern hemisphere and appropriate association studies allow the identification of molecular basis of phenotypic variations. By aligning identified loci and the natural growth regimes of particular accessions, we investigate the ecologi-cal significance of variation in secondary growth. This approach helps us to understand how plant growth forms are modified during evolution and why a certain growth strategy is beneficial in a given environment.

Fig. 4.Examples of natural variation in secondary growth in Arabidopsis thaliana. A) Cross-section col-lected from the main stem of the Rou-0 strain. B) Cross-section from the main stem of the Pla-1 strain. Note that Pla-1 displays more tissue production than Rou-0 (indicated by red brackets).

Fig. 3.Transcriptional profiling taking advantage of an in vitro system to induce secondary growth.(A) Incubation of stem fragments on split-plates in the presence ofthe phytohormone auxin induces secondary growth in a verycontrollable manner.(B) After harvesting the fragments at different time points and subse-quent sectioning, cells transform-ing into the cambium are collected by LCM (red labelled area). Stars label primary vascular bundles.

Fig. 2.Comparison of a primary (A) and secondary (B) stem from Arabidopsis thaliana. Histological analyses show that secondary growth is initiated similarly to more woody species by initiating cambium activity in interfascicular regions. Colour coding as in Fig. 1. Molecular markers (in this case the expression of the histone H4, visualised by RNA in situ hybridisations) identify cam-bium cells as actively dividing. Arrows: dividing cell in primary bundles; arrowheads: dividing cells in interfascicular regions. Stars label primary vascular bundles.

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“Claudia Jonak’s work aiming to link thoroughly

studied kinase signal transduction pathways with cell

metabolism and chromatin modulation has especially

high potential for revealing novel,

unknown mechanisms.“


Stress signal trans-duction and cellular responsesA key question in biology is how organisms cope with changing envi-

ronmental conditions. Research in our group focuses on the mecha-

nisms of signal transduction and physiological adaptations in

unfavorable environments. We take an integrative approach to better

understand fundamental molecular processes at the interface between

signal transduction and coordinated responses of cellular metabolism

and gene expression in stress situations.

Plant growth and development largely depend on the environment. Drought, extreme temperatures, soil contamination with salts or heavy metals, and pathogen infections are examples of environmen-

tal constraints that determine the yield and reproductive success, and thus, the geographical distribution of plants. Over time, plants have evolved sophisticated inducible adaptation and defense systems. Environmental cues and pathogen infections are communicated by integrated signaling path-ways, which delicately coordinate diverse cellular and physiological re-sponses, ultimately determining stress resistance (Fig. 1). Protein kinases are key players of the signal transduction network.

ADAPTIVE REGULATION OF CELLULAR METABOLISM By STRESS SIGNALING KINASES

In a changing environment, metabolism needs to be adjusted to enable a fast, adaptive physiological response. Protein phosphorylation rep-resents an important means of fine tuning the activity of metabolic enzymes. However, our knowledge about how environmental stress-triggered signal transduction modulates the activity of metabolic enzymes remains limited.

In our recent work we established the Arabidopsis GSK3/shaggy-like kinase, ASKa, as critical regulator for the cellular stress response by regulating the antioxidant system to counteract oxidative stress (Fig. 2). We showed that ASKa is post-translationally activated by salt stress, and used a high-throughput metabolic screen to identify possible targets of ASKa. With a combination of genetic and biochemical approaches we revealed that ASKa regulates stress tolerance by activating glucose-6-phosphate dehydrogenase (G6PD), which is essential for maintaining the cellular redox balance. Loss of stress-activated ASKa leads to reduced G6PD activity, elevated levels of ROS (reactive oxygen species), and enhanced sensitivity to salt stress. Conversely, plants overexpressing ASKa have increased G6PD activity and

Group Leader:

Claudia [email protected]

Joined GMI in Feb 2004PhD: Institute of Microbiology and Genetics, University of Vienna, Austria

Previously– Research Assistant: Institute of Microbiology and Genetics, University of Vienna, Austria, 1994-1995

– EMBO Postdoctoral Fellow: Institute National de la Recherche Agronomique (INRA), Versailles, France, 1995-1997. Jan Traas Lab

– Research Assistant: Institute of Microbiology and Genetics, University of Vienna, Austria, 1997-2000

– Hertha Firnberg Position: University of Vienna, Austria, 2001-2004

Group members:

Postdoctoral Fellows Branislav Kusenda (25%) Aladar Pettko-Szandtner* Olga Popova

Technicians Caroline Broyart Bettina Dekrout

PhD Students Iulia Danciu Agnes Eder Julia Krasensky Juliane Mayerhofer Hansjörg Stampfl Sascha Waidmann


ANNUAL REPORT 2012 17ANNUAL REPORT 2012

J O N A K

Fig. 1.Plants respond to environmental stress. Plants are permanently exposed to a multitude of external stimuli, which plant cells have to transform into physiologically intelligible signals. Extracellular stimuli are perceived and internal-ized by various cellular receptors and are subsequently transduced by signaling cascades to induce appropriate cellular responses that ultimately lead to physiologi-cal and developmental modifica-tions determining the sensitivity or tolerance of a plant.

Fig. 2.ASKa-mediated phosphorylation of G6PD contributes to maintaining the cellular redox balance under stress conditions.(A) The crystal structure of human G6PD suggests that the threonine residue phosphorylated by ASKa influences coenzyme binding. The threonine (stick presentation with carbon atoms colored in yellow) is positioned in close proximity to the βE–βe loop (in green) which is part of the NADP binding region (NADP highlighted in stick representation with carbon atoms colored in white).

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Adaption of Physiologyand Development

(B) Threonine (T) phosphorylation is necessary and sufficient for enhanc-ing G6PD6 activity. G6PD activity was enhanced by ASKa but not by loss-of-function ASKa LOF in cells expressing G6PD6. However, when protoplasts were transformed with the non-phosphorylatable mutant G6PD6 T/A, ASKa was unable to stimulate G6PD activity. Cells expressing the phosphomimicking mutant G6PD6 T/E showed consti-tutively high G6PD activity, which could not be further stimulated by ASKa.

(C) ASKa is an important regula-tor of ROS detoxification and, thus, acclimation to salt stress. High salinity activates ASKa, which in turn, phosphorylates G6PD6, thereby stimulating its activity. Enhanced G6PD activity provides NADPH for the antioxidant system to remove excess ROS. Reduction of H2O2 to H2O can then be mediated by the glutathione peroxidase cycle or by the ascorbate-glutathione cycle.

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J O N A K

Fig. 3.Brassinosteroid (BR) and MAPK signaling pathways concertedly control SPCH activity to regulate stomatal development: a model. BRs bind to the BRI1 membrane receptor, thereby triggering BIN2 inactivation. When active, BIN2 phosphorylates and thus inacti-vates and/or targets for degrada-tion the transcription factor SPCH required for stomatal development. The MAPK signaling cascade, genetically downstream of the ERECTA and TMM receptors, and the BR-regulated BIN2 signaling pathway act in coordination to regulate SPCH activity.

low levels of ROS in response to stress, and are more tolerant to salt stress. ASKa stimulates the activity of a specific cytosolic G6PD isoform (G6PD6) by phosphorylating the evolutionarily conserved threonine 467. Analysis of structural data shows that the threonine residue targeted by the ASKa is in close proximity to the active site cleft of G6PD, suggesting that phosphoryla-tion of G6PD6 might alter co-substrate binding and thus G6PD activity.

G6PD is a major determinant of cellular redox homeostasis, which plays a pivotal role in determining cellular responsiveness to stress. ROS generation and redox imbalance are closely linked to aging and a wide range of diseases including inflammation, cancer, and neurodegenerative disorders. Our data not only provide novel mechanistic insights into the regulation of G6PD6 activity by phosphorylation, but also offer a starting point for future studies beyond metabolic adaptation of plants to adverse environments.

INTEGRATION OF BRASSINOSTEROID AND STOMATA SIGNALING PATHWAyS

Stomata, small pores on the aerial parts of plants, regulate photosynthetic carbon dioxide uptake and transpiration under changing environmental conditions. Stomatal development is regulated by various signals, but mechanisms controlling stomatal development are not fully understood. In a collaboration with E. Russinova (VIB, Gent), we have shown that brassinosteroids (BR) promote stomatal development and that the GSK3/shaggy-like kinase BIN2 (a negative regulator of BR signaling) phosphorylates and thus negatively regulates the basic helix-loop helix transcription factor SPEECHLESS (SPCH) that is crucial for establishing the stomatal lineage. BIN2 phoshorylates SPCH on residues, which partially overlap with those phosphorylated by the MAP kinases MPK3 and MPK6, suggesting integration of GSK3 and MAPK signaling pathways at the level of SPCH to coordinately regulate stomata development (Fig. 3).


“Members of the Mittelsten Scheid group are continuing their

high quality work on the genetic consequences of polyploidy, the

epigenetic control of DNA damage repair, and the epigenetic and

genetic consequences of stress. Ortrun is well-known and respected

in the plant biology community. Former members have obtained

positions at first rate institutions.”


Epigenetic changes in plants

Epigenetic changes contribute significantly to diversity in gene ex-

pression and, thereby, to adaptation potential. Using the model plant

Arabidopsis, we investigate the influence of stress exposure on chro-

matin configuration, gene expression, DNA repair and recombination,

and study inheritance and natural variation of stress responses.

Epigenetic regulation controls a broad range of heritable, yet revers-ible, changes in gene expression. It generates an additional level of transmitted information and gene expression diversity in many

eukaryotes. It is involved in defence against intruding DNA and RNA mol-ecules, in genome stabilisation, and in the regulation of development and morphology. Our group is interested in the interplay between genetic and epigenetic changes, in epigenetic diversity in different ecotypes and after exposure to abiotic stress. We study these aspects in Arabidopsis thaliana with well-established genetic, cytological and molecular methods, using mutants, reporter genes, chromatin analysis, flow sorting, fluorescence in situ hybridisation, defined stress treatments, specific and genome-wide expression assays and bioinformatic approaches.

EPIGENETIC CONTROL OF DNA DAMAGE REPAIRAND RECOMBINATION

DNA damage, especially in the form of double strand breaks, is deleterious if not repaired before replication and cell division and can cause malfunction or cell death. Like other organisms, plants have diverse, efficient and highly interactive repair enzymes. However, DNA lesions must be accessible for these proteins even in a tightly packed heterochromatic environment. There is growing evidence that epigenetic features influence this accessibility and thereby determine genome stability, recombination and mutation rates. The density of chromatin is governed in part by multimeric chromatin remodeling complexes that can shift, remove, or insert nucle-osomes, or exchange histone variants. We analyzed the role of one of these complexes by assaying DNA repair potential in mutants that lacked either one of three subunits. All mutants showed increased sensitivity to several types of DNA damage, compared to the wild type (Fig. 1). Combining the mutations with other defects in genes coding for known repair factors points towards a specific role of the complex in repair via homologous recom-

Group Leader:

Ortrun MITTELSTEN [email protected]

Joined GMI in Jan 2004PhD: University of Hamburg, Germany

Previously– Postdoctoral Fellow: Max Planck Institute for Cell Biology, Ladenburg, Germany, 1985-1987. Hans-Georg Schweiger Lab

- Postdoctoral Fellow: Institute for Plant Sciences at the Federal Institute of Technology (ETH), Zurich, Switzerland, 1988-1992. Ingo Potrykus Lab

- Research Associate: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, 1992-2003. Jerzy Paszkowski Lab

- Interim Scientific Director: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria, 2007-2009

Group members:

Postdoctoral Fellows Riccardo Aiese Cigliano Ruben Gutzat Branislav Kusenda (25%) Marie-Luise Zielinski

Technician Nicole Lettner

PhD Students Jasmin Bassler Vanja Cavrak Huy Quang Dinh* Marisa Rosa* Laura Sedman*



M I T T E L S T E N S C H E I D

bination. This was confirmed by assays revealing reduced homologous recombination in somatic cells. Reduced fertility and impaired gametes in the mutants indicate that the chromatin remodeling complex ist also required for efficient double strand break repair and homologous recombination during meiosis. We are currently investigating the mechanism and kinetics of chromatin remodeling during repair and attempting to disclose more details of this vital process.

GENETIC AND EPIGENETIC ASPECTS OF ABIOTIC STRESS EFFECTS

Many exogenous conditions causing stress responses in plants can provoke genome instability, resulting in local mutations, transposon activation, or larger genome rearrangements. Recently, it became evident that external factors can also result in epigenetic destabilization, changing chromatin features and expression of genes that are under epigenetic control. Arabidopsis thaliana has several genes and repetitive elements that, at ambient temperatures, are usually not expressed. However, they become transiently activated by prolonged heat stress. Among them is one retrotransposon family that is transcribed after several hours of heat expo-sure and forms extrachromosomal DNA. We found substantial differences in copy number of the element and the extent of its epigenetic response among different Arabidopsis ecotypes from varying geographical origin. We used the retrotransposon as a marker to analyze the kinetics of activation and re-silencing and its requirement for different epigenetic regulators.

Fig. 1.Growth response after DNA dam-age: resistant plants can develop the first pair of true leaves (white arrow), in contrast to sensitive plants (orange arrow) (A, B). Mutants lacking subunits of a chromatin remodeling factor (2, 3, 4) are significantly more sensitive to physical and chemical DNA damage (C, D) than wild type plants (1) and resemble mutants lacking repair proteins (5).


M I T T E L S T E N S C H E I D

Fig. 2.Stress conditions (A) with and without hormone signaling (B) can change gene expression and modify chromatin via DNA meth-ylation, histone tail modifications, histone variant replacements, or nucleosome loss and chromatin de-condensation (C, D). These changes are largely reversible but can modify metabolic or morpho-logic plant features. Usually, the new phenotypes are not transmit-ted to progeny. However, chroma-tin-associated changes have the potential to be heritable and to create epigenetic diversity (E).

A striking consequence of heat stress was the dissociation of nucle-osomes from the DNA at several of the activated genes, but also at other sites. However, once a sublethal stress exposure is terminated, silencing is restored and the nucleosomes are reloaded onto the DNA. This suggests that histone chaperones are involved in the reconstitution of chromatin organization, and indeed, the absence of chromatin assembly factor CAF1 subunits delays silencing and reloading. However, histone chaperones and histone variants in Arabidopsis are manifold, partially specialized and partially redundant. We are now extending the analysis of the role of histone chaperones and variants during and after stress treatments. This work is part of a grant-supported Graduate Program on “Chromosome Dynamics” and a binational collaboration.

Although the dissociation of chromatin during prolonged heat stress seems reversible to a large extent, reconstitution might not be perfect. If some stochastic errors during the reassembly occur in nuclei of germ line cells, epigenetic changes could potentially be transmitted to the next generation (Fig. 2). However, the number of well-documented cases of so-called “transgenerational effects” based on epigenetic features is limited, and careful analysis is necessary to distinguish a hypothetical epigenetic memory from parental effects during seed set. To challenge the hypothesis, and in a multinational collaboration, we have exposed different ecotypes to diverse stress or control treatments over several generations and pheno-typed plants for morphological changes. The results indicate high diversity of the responses between ecotypes and stress treatments. The material was not yet subjected to molecular analysis but so far we have not obtained phenotypically recognizable evidence for a transgenerational memory.


“Although still in its infancy, Michael Nodine’s group

has a clear research direction and well-focused plans …

The SAB congratulates the GMI on his appointment and

looks forward to following the development of his program

in the coming years.”


Small RNA functionsin plant embryosMicroRNAs (miRNAs) are a class of small regulatory RNAs that are

essential for plant embryo development. Our major goal is to under-

stand how miRNAs shape the gene regulatory networks that control

plant embryogenesis. We are using a combination of cutting-edge

experimental and computational approaches to achieve this aim.

The basic plant body plan is established during early embryogenesis. After this morphogenesis phase, embryos transition to a maturation phase during which they accumulate proteins, starch, lipids and

sugars. Not only are these macromolecules required for successful germina-tion, but they are also the major nutritional component of several key crops. Despite its fundamental importance to developmental biology and agricul-ture, the molecular mechanisms that regulate embryonic patterning and maturation remain largely uncharacterized.

MicroRNAs are required for both embryonic pattern formation and the timing of the morphogenesis-to-maturation phase transition (Figs 1 and 2). Because plant miRNAs specifically repress transcription factors and other key developmental regulators, they likely have a large influence on the gene regulatory networks that control plant embryogenesis. Character-izing the embryonic functions of miRNAs and their corresponding targets should therefore yield insight into the mechanistic basis of plant embryo development. More broadly, investigating the roles of embryonic miRNAs will contribute to our general understanding of how small regulatory RNAs influence cellular differentiation.

Group Leader:

Michael [email protected]

Joined GMI in July 2012PhD: University of Arizona, Tucson AZ, USA

Previously– Postdoctoral Research Fellow, Whitehead Institute for Biomedical Research, USA, 2007-2012. David Bartel Lab

Group members:

Postdoctoral Fellow Olga Bannikova

Technician Ulf Naumann

PhD Student Aleksandra Plotnikova


dcl1

wild type

8-cell

WOX2 ATML1pSHR::GFP

globular and early heart

pWOX5::YFPWOX8

wild type dcl1

*

*

**

***

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A B

16-cell

earlyglobular

earlyheart

dcl1

wild type

8-cell

WOX2 ATML1pSHR::GFP


pWOX5::YFPWOX8

wild type dcl1

*

*

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A B

16-cell

earlyglobular

earlyheart

N O D I N E

A

B

wild type

8-cell

wild type

WOX2 pSHR::GFP ATML1 WOX8 pWOX5::YFP

dc/1


16-cell

earlyglobular

earlyheart

dc/1Fig. 1.MicroRNAs are required forembryonic pattern formation.

(A) Representative Nomarski imges of wild-type embryos and dicer-like1 (dcl1) mutant embryos, which lack miRNAs. DCL1, and by inference miRNAs, are required for morphogenesis beginning at the 16-cell stage. Asterisks indicate products of abnormal divisions, and carets designate positions where cell divisions did not take place. Nuclei were false-colored blue for clarity.

(B) Representative micrographs of RNA in situ hybridizations and confocal scanning laser microsco-py images of cell-specific markers in wild-type and dcl1 embryos. Loss of miRNAs in dcl1 mutants results in differentiation defects beginning at the 8-cell stage. By mid-embryogenesis almost every embryonic cell-type has inap-propriate expression of cell-spe-cific markers. This indicates that miRNAs are required for multiple embryonic patterning events. Adapted from Nodine and Bartel, Genes & Development, 2010.


Fig. 2.Model of plant miRNA functions during early embryogenesis. In wild-type Arabidopsis embryos, miR156-mediated repression of SPL10/11 transcription factors prevents precocious expression of maturation phase genes. Early dcl1 embryos lack miR156 and over-express SPL10/11, which in turn induce premature gene expression. We hypothesize that additional plant miRNAs also fore-stall expression of differentiation-promoting transcription factors. Adapted from Nodine and Bartel, Genes & Development, 2010.

N O D I N E


“The Nordborg group continues to work as a

power house for quantitative genetics and genomics,

with the overall goal of understanding the genetic

basis for evolutionary change …

Overall the program is exceptional in

its breadth and depth.”


Population GeneticsOur group studies natural variation, the genetic basis for evolutionary

change. Our research is quantitative, and involves computational

analysis of genomic data in addition to field and bench work. While we

focus on the model plant Arabidopsis thaliana, we also work on other

species, including primates.

One of the most important challenges facing biology today is making sense of genetic variation. Understanding how genetic variation translates into phenotypic variation, and how this translation

depends on the environment, is fundamental to our understanding of evolution, and has enormous practical implications for both medicine and agriculture. Our group studies this mapping from genotype to phenotype, primarily to understand evolution better. We also work directly at the se-quence level, seeking to understand the forces that have shaped genomic variation within and between species. Our research is usually quantitative, with several group members doing exclusively computational work. The following is an overview of some of the many projects in which my group is involved.

GWAS IN A. THALIANA AND THE 1001GENOMES PROJECT

Thanks to decreasing genotyping costs, there is currently great interest in so-called genome-wide association studies (GWAS), in which one attempts to identify genes responsible for variation simply by correlating genotype (typically in the form of single nucleotide polymorphisms) with phenotype. The model plant A. thaliana is ideally suited for such studies in that it naturally occurs as inbred lines which can be genotyped once and phenotyped repeatedly. For several years, my group has been spearhead-ing a multi-group effort to make genome-wide association in A. thaliana a reality. We have genotyped a set of roughly 1,300 lines using close to 250,000 SNPs, and play a major role in the 1001 Genomes project that aims to fully sequence over 1,000 lines. In total, we will make over 2,000 densely genotyped or sequenced lines available to the Arabidopsis community, and we are also developing a public website that will allow anyone to carry out GWAS and coordinate as much phenotypic information as possible.

STATISTICAL METHODOLOGy FOR ASSOCIATIONMAPPING

Our work on genome-wide association in A. thaliana has forced us to confront the problem of confounding in structured populations, which is much more severe in this organism than it is in standard human case-control studies. As the costs of genotyping and sequencing continue to decrease, genome-wide association will become an obvious choice for investigating

Group Leader:

Magnus [email protected]

Joined GMI in Feb 2006PhD: Department of Biological Sciences, Stanford University, USA

Previously– Research Associate, Department of Ecology & Evolution, University of Chicago, USA, 1994-1997. Advisors: J. Bergelson, B. Charlesworth & D. Charlesworth

- Research Assistant Professor (“forskarassistent”), Department of Genetics, Lund University, Sweden, 1997-2000

- Assistant Professor, Molecular & Computational Biology, USC, USA, 2000-2004

- Associate Professor (tenured), Molecu- lar & Computational Biology, USC, 2004-present

Group members:

Postdoctoral Fellows Ashley Farlow Daniele Filiault Arthur Korte Quan Long* Eriko Sasaki

Technicians Pamela Korte Viktoria Nizhynska Viktor Voronin

Programmers/Bioinformaticians Alexander Platzer Ümit Seren

PhD Students Matthew Horton Envel Kerdaffrec Dazhe Meng Polina Novikova


Hannes SvardalTakashi TsuchimatsuQingrun Zhang*

Fernando RabanalPei ZhangBjarni Vilhjálmsson*Pei Zhang


Fig. 1.a Common garden experiment

Fig. 1.b A.thaliana in natural beach habitat

N O R D B O R G

the genetics of natural variation in many species, and methodology for dealing with confounding will be crucial. We are exploring a wide range of methods for handling this problem, focusing in particular on the effect of having several major loci under selection present.

THE GENETICS OF ADAPTATIONWe are carrying out large-scale GWAS seeking to understand the

genetic basis of variation for adaptively important traits like flowering time, dormancy, and cold tolerance. The GWAS results are complemented with a variety of methods to confirm results. Our goal is to achieve as complete and understanding of the genetics of these traits as is possible.

Investigating the adaptive significance of any trait also requires field studies. We are using field sites in northern and southern Sweden (Fig. 1) for reciprocal transplant competition experiments of both natural inbred lines and the offspring of crosses. The objective is to map the genes responsible for fitness differences, and to molecularly characterize them.

GENOMIC ANALySIS OF THE GENOTyPE-PHENOTyPE MAPWe are a major part of an NIH-funded ‘Center of Excellence in

Genomic Science’ that aims to investigate the regulatory networks by which genetic variation leads to phenotypic variation in traits like flowering time. Our group has carried out genome-wide expression profiling of 200 lines under different environment conditions, and are complementing this information with genome-wide epigenetic profiling. The goal is to integrate the resulting multi-level data to infer causal relationships. Rather than simply finding associations between genotype and phenotype, we seek to infer how the genotype affects the phenotype.

MOLECULAR EVOLUTION OF ARABIDOPSISWe are heavily involved in the comparative analysis of the genomes of A. thaliana and its close relatives. Questions include the evolution of genome size, the effects of polyploidy or switching to self-fertilization. For example, we are currently exploring the pattern of polymorphism in A. suecica, an allotetraploid hybrid between A. thaliana and A. arenosa (Fig. 2) that seems to have involved a massive bottleneck and complete loss of genetic variation.

THE GENETICS OF SPECIES DIFFERENCESIN AQUILEGIA

As part of an international collaboration, we are studying the genetics of species differences in the columbine genus, Aquilegia (Ranunculaceae). The genus is an excellent example of a recent, rapid adaptive radiation and offers many opportunities to study genetic changes at different stages in the speciation process. We have focused on two North American species, A. formosa and A. pubescens. As illustrated in Figure 3, the species exhibit distinct differences in floral characters that influence pollinator preference, thereby restricting gene flow between them. However, the two species are


Fig. 2. The origin ofA. suecica.

A. thaliana2n = 10

EUROPE ASIA

North America

A. arenosa4n = 32

Sister group

Semiaquilegiaadoxoides

A. chrysantha A. pubescens A. coerulea

A. formosa

A. jonesii A. canadensis A. pinetorum A. bamebyiA. longissima

A. aurea A. vulgaris A. sibiricaA. flabellata A. oxysepala A. ecalcarata

X =

A. suecica2n = 26

Fig. 3. Columbine species currently being sequenced by JGI.We focus in particular on the sympatric A. formosa and A. pubescens. (Courtesy of Scott Hodges, UCSB)

N O R D B O R G

completely inter-fertile and form natural hybrid zones. We have demon-strated that the two species are very closely related at the genetic level, with most polymorphisms shared between the species, and little divergence in allele frequencies, and we are now trying to identify the genes responsible for the phenotypic differences through GWAS.

POPULATION GENETICS OF AFRICAN GREEN MONKEySThe African green monkey (Cercopithecus sp.) is a common Old

World monkey, spread throughout much of Africa, and introduced by humans to the Caribbean. It is also kept in large colonies for behavioral and biomedi-cal research. We are part of an international consortium to develop genomic resources for African green monkeys through extensive sequencing and SNP typing of samples from wild-collected samples. Our primary interest is the genetics of subspecies differences across the African continent.


“The Riha group made impressive progress during

the last year, distinguishing it from other research groups in

its fields. This was clearly achieved through Karel Riha’s

excitement for science, his creative thinking and his ability

to encourage all group members to explore

novel hypotheses.”


Genome stability:Telomeresand meiosisChromosome integrity and their proper partitioning to daughter cells

are essential prerequisites for stable inheritance of genetic informa-

tion over multiple cell divisions. Our two main research interests are

molecular mechanisms that govern stability of chromosome ends and

regulation of chromosome behavior during meiosis.

MECHANISMS OF CHROMOSOME END PROTECTION

Telomeres are indispensable elements of eukaryotic chromosomes that are important for the complete replication of linear genomes and for chromosome end protection. These functions are essential for

genome stability and long-term cell survival. The key feature of telomeres is their capability to differentiate native chromosome ends from deleterious DNA double-strand breaks. This is achieved by assembling chromosome termini in elaborate, high-order nucleoprotein structures, which in most organisms encompass telomeric DNA, specific telomere-associated pro-teins, and general chromatin and DNA repair factors. We developed a number of techniques for detailed structural analysis of telomeric DNA, which we use in combination with genetic tools available in Arabidopsis to decipher mechanisms that govern chromosome end protection. In our work we discovered that the opposite ends of a chromosome adopt different end protective structures, whose formation is dictated by the mode of DNA replication (Fig. 1). The telomeres replicated by the lagging-strand mecha-nism end with single stranded DNA protrusions and their maintenance depends on CST, a recently identified protein complex, mutations of which underlie several human genetic disorders. The telomeres replicated by the leading-strand mechanism terminate as blunt-ended DNA that is protected by the evolutionarily conserved DNA repair complex Ku. In our research we aim to understand how Ku mediates protection of these telomeres without triggering a DNA repair reaction.

GETTING INTO, THROUGH, AND OUT OF MEIOSISThe alteration of haploid and diploid cell generations during the

sexual life cycle requires meiosis, a specialized cell division that enables the formation of haploid gametes from diploid cells. Meiosis occurs only once during the life cycle, and the transition from the mitotic to meiotic mode of chromosome partitioning requires extensive remodeling of the cell cycle machinery. We devote part of our research efforts to deciphering mechanisms that define meiosis in plants. The cell cycle progression is driven by cyclin-dependent kinases and associated cyclins that regulate

Group Leader:

Karel [email protected]

Joined GMI in June 2003PhD: Masaryk University, Brno,Czech Republic

Previously– Postdoctoral Research Associate: Department of Biochemistry & Biophysics, Texas A&M University, USA, 1999-2002. Dorothy Shippen Lab

– Senior Postdoctoral Fellow: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria, 2003-2005

Group members:

Postdoctoral Fellows Petra Bulankova Nick Fulcher Anita Kazda Branislav Kusenda (25%) Matt Watson

Technician Svetlana Akimcheva

PhD Students Elisa Derboven Jiradet Gloggnitzer Sona Valuchová Claudio Capitao


Fig. 1.Cartoon illustrating our view on chromosome end protection in Arabidopsis. The shoelace depicts a chromosome and differently coloured aglets indicate distinct telomere architectures formedat the opposite ends of thechromosome.

Fig. 2. Inactivation of cyclin B3;1 affects cell wall formation in male meiotic cells (pollen mother cells, PMC). Transversal section through the anther lobe of an Arabidopsis cycb3;1 mutant visualised by transmission electron microscopy. PMCs in the centre of the anther lobe are surrounded by the layer of tapetum cells (Tp). PMCs are characterized by a thick layer of callose (c) that forms beneath the cell wall. Arrow points to an aber-rant cell wall invasion into PMC, which is one of the characteristic features of cycb3;1 mutants. Scale bar indicates 5µm.

R I H A

CDK activity and confer substrate specificity. The cyclin gene family has undergone a massive expansion in angiosperm plants, which has raised the question whether some of these cyclins evolved specific meiotic func-tions. We systematically analyzed two cyclin gene families in Arabidopsis and identified eight cyclins that are meiotically expressed and involved in diverse meiotic processes (Fig. 2). Furthermore, we have discovered a genetic module, consisting of SMG7 and TDM1, that inhibits meiotic CDKs and facilitates transition from meiosis to mitosis (Fig. 3). Our current work is directed towards molecular understanding of the SMG7/TDM1 function and characterization of additional genes that are involved in meiotic progression.

NONSENSE MEDIATED RNA DECAy AND ITS ROLE IN PATHOGEN RESPONSE

Errors that occur during transcription and splicing of mRNA may lead to translation of aberrant proteins and thereby severely impair cellular metabolism. RNA quality control mechanisms are therefore important for long-term cell survival. Nonsense mediated RNA decay (NMD) is a key pathway involved in degradation of aberrant transcripts that contain premature stop codons. NMD is essential in higher eukaryotes, but its physiological function is still not fully understood. Besides its role in meiosis, SMG7 is also an important NMD factor. In the course of our functional analysis of this gene, we noticed that smg7 mutations trigger strong patho-gen response in Arabidopsis. Our further work revealed that activation of the pathogen signaling pathway is a general physiological response to impaired NMD. In addition, we discovered that NMD efficiency is decreased upon bacterial infection, suggesting a regulatory role of NMD in the plant immune response. Considering the evolutionarily conserved nature of the NMD mechanism, modulation of this pathway may provide an attractive strategy for enhancing plant disease resistance (Fig. 4).


Fig. 3.Plants with dysfunctional TDM1 protein are infertile due to an aber-rant meiotic exit. Instead of leaving meiosis and entering mitotic cell cycle, tdm1 mutants initiated another meiotic division after formation of haploid nuclei. The attempt to separate unreplicated chromatids results in genome frag-mentation and cell death. Picture shows third meiotic division in tdm1 mutants. Chromatin is shown in red, spindle detected with the alpha-tubulin antibody is stained in green.

Fig. 4.Activation of a defence response in NMD deficient plants leads to increased resistance to bacterial pathogen Pseudomonas syringae. Growth of bacteria in wild type and upf1-5 mutant plants was monitored by using a light emitting strain of P. syringae that contains the lucipherase operon from a bio-luminescent bacterium Photorhab-dus luminescens.

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“To address various questions relating to the

epigenome of sperm and vegetative cells, the Tamaru group

has developed considerable technical expertise and

know-how in the area of epigenetic profiling and cyto-

genetic analyses of these two cell types.”


Control and functionof epigenetic reconfi-gurations in the male gametophyteResearch in the group focuses on investigating epigenetic reprogram-ming in the male gametophyte, pollen, of Arabidopsis thaliana.

A unique and vital feature of gametogenesis is resetting the genetic and epigenetic plan for totipotency toward the next generation. Current evidence suggests that genome-wide epigenetic repro-gramming occurs in the germ cell lineage of both animals and plants, involving active DNA demethylation and replacement of histones and their modifications. Epigenetic modifications of the genome play impor-tant roles in gene imprinting, control of transposons, and normal devel-opment of animals and plants. Unlike the situation in animals, where the male gamete (sperm) represents the direct product of meiosis, flowering plants form the male gametophyte (pollen) by post-meiotic mitotic divisions. A pollen grain contains one vegetative cell and two sperm cells. The primary role for the vegetative cell in plant reproduction is to germinate and form a pollen tube that brings the sperm cells to the female gametophyte for double fertilization. The model plant Arabidopsis thaliana provides powerful genetic and molecular approaches not pos-sible in other plants. Recent studies in A. thaliana have revealed exten-sive reconfiguration of chromatin dynamics, DNA methylation and small RNAs in the vegetative cell that impacts on the integrity of the sperm cell genome and pollen function.

ROLE FOR ACTIVE DNA DEMETHyLATIONIN CONTROLLING TRANSPOSONS IN POLLEN

DNA glycosylase enzymes catalyze active DNA demethylation by excising 5-methylcytosine. The Arabidopsis DEMETER (DME) DNA glyco-sylase is primarily expressed in the central cell in the female gametophyte, the companion cell of the egg, prior to fertilization. A functional maternal DME allele is required for seed viability and maternal allele DNA demethyla-tion in the endosperm that establishes gene imprinting. By contrast, little is known about the function of DME in the male gametophyte, pollen. We showed previously that DME is active also in the vegetative cell in pollen, the companion cell of the sperm, and demethylates imprinted genes MEA and FWA and a transposon Mu1a. DME is required for normal pollen tube formation in certain ecotypes.

Group Leader:

Hisashi [email protected]

Joined GMI in April 2006PhD: Saitama University, Japan

Previously– Postdoctoral Fellow, Max Planck Institute for Molecular Genetics, Berlin, Germany, 1994-1996 Vincenzo Russo Lab

- Postdoctoral Fellow, Max Planck Institute for Molecular Genetics, Germany, 1996. Thomas Trautner Lab

- Postdoctoral Fellow, University of Oregon, Eugene, OR, USA, 1996-2004. Eric Selker Lab

- Postdoctoral Fellow, National Institute of Genetics, Japan, 2004-2006. Tetsuji Kakutani Lab

Group members:

Postdoctoral Fellows Adriana Machlicova Vera Schoft Zsuzsanna Merai

Technician Lucyna Slusarz

PhD Students Nina Chumak* Atil Saydere



T A M A R U

To elucidate the target preferences, mechanism, and biological signifi-cance of the DME-mediated DNA demethylation in the female and male gamete companion cells, we extended our study to genome-wide profiling of DNA methylation using deep bisulfite sequencing in collaboration with Drs Robert

L. Fischer and Daniel Zilberman (UC Berkeley, USA). We found that DME preferentially demethylates small AT-rich euchromatic transposons near genes in the vegetative and central cells (Fig. 1). Our results reveal that active DNA

Fig. 1.DME demethylates small, AT-rich euchromatic TEs. (A) Box plots showing absolute fractional demethylation of 50-bp windows within transposons. Each box encloses the middle 50% of the dis-tribution, with the horizontal line marking the median, and vertical lines marking the minimum and maximum values that fall within 1.5 times the height of the box. Differences between each size category are significant (p

T A M A R U

demethylation mediated by DME in the vegetative cell reinforces de novo DNA methylation in the sperm cells in pollen (Fig. 2) and likely assures stable silencing of transposable elements across generations.

IDENTIFICATION OF GENES REqUIRED FORREPROGRAMMING CHROMATIN DyNAMICS IN POLLEN

Although quite a lot is known about the mechanisms and biological signifi-cance of heterochromatin formation and gene silencing, little is known about the reverse process of developmentally-programmed heterochromatin decondensation. We found that the vegetative cell nucleus in pollen undergoes loss of centromere-specific histone H3 variant (CenH3) and large-scale decondensation of centromeric heterochromatin. Following a forward genetic mutant screen using an automated microscopy and image processing system, we isolated a mutant defective in heterochromatin decondensation and pollen tube formation, which we named izanagi (igi) after a Nippon god of fertility (Fig. 3). We are currently mapping the causative mutation in the igi mutant plant using a combination of high-throughput whole genome sequencing and conventional DNA sequencing.

Fig. 3. Analysis of pollen from IGI / igi heterozygous mutant plants. (A and B) Images of an IGI wild-type (A) and igi mutant (B) pollen grain in the Col-0 ecotype carry-ing pCenH3::CenH3::GFP and pLAT52::H2B::RFP. igi mutant pollen displays five CenH3-GFP centromeric foci in the vegetative cell nucleus. Images were taken by an epifluorescent microscope with 63x magnification. (C) (Left panel) Representative images of a germinated (top) and non-germinated (bottom) IGI wild-type pollen. (Right panel) The in-ability of igi mutant pollen grains to germinate and form a pollen tube on solid media. Germinated and non-germinated pollen from a IGI / igi heterozygous mutant plant were inspected for the igi phenotype showing CenH3-GFP foci in the vegetative cell nucleus. Green bar represents percentage of non-germinated pollen. Orange bar represents percentage of ger-minated pollen. Numbers on the bars indicate the number of pollen inspected.


Busch Group

Busch Wolfgang, Moore Brad, Martsberger Bradley, Mace Daniel, Twigg Richard, Jung Jee, Pruteanu-Malinici Iulian, Kennedy Scott, Fricke Gregory, Clark Robert, Ohler Uwe, Benfey Philip (2012) A microfluidic device and computational platform for high-throughput live imaging of gene expression. Nat. Methods 9(11):1101-6.

Greb Group

Agusti Javier, Greb Thomas (2012) Going with the wind - Adaptive dynamics of plant secondary meristems. Mech. Dev.

Brandt Ronny, Salla-Martret Mercè, Bou-Torrent Jordi, Musielak Thomas, Stahl Mark, Lanz Christa, Ott Felix, Schmid Markus, Greb Thomas, Schwarz Martina, Choi Sang-Bong, Barton M, Reinhart Brenda, Liu Tie, Quint Marcel, Palauqui Jean-Christophe, Martínez-García Jaime, Wenkel Stephan (2012) Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses. Plant J. 72(1):31-42.

Businge Edward, Brackmann Klaus, Moritz Thomas, Egertsdotter Ulrika (2012) Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies). Tree Physiol. 32(2):232-44.

GMI Staff by Functions (Head Count)

GMI Expenditures (%)

GMI Staff by Nationality (%)

Research Grants (%)

Group Leaders

Postdocs

PhD Students

Scientific Support

Administration

Research

Core Facilities

Building

Administration

Investments

Austria

Europe (excl. Austria)

North America

Asia

Others

Austrian Grants

EU Grants

Other Grants (e.g., NSF, NIH)

Key Facts(as of 31 December 2012)

Publications


Jouannet Virginie, Moreno Ana, Elmayan Taline, Vaucheret Hervé, Crespi Martin, Maizel Alexis (Epub: 2012) Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis. EMBO J. 31(7):1704-13.

Marshall Alex, Aalen Reidunn, Audenaert Dominique, Beeckman Tom, Broadley Martin,Butenko Melinka, Caño-Delgado Ana, de Vries Sacco, Dresselhaus Thomas, Felix Georg, Graham Neil, Foulkes John, Granier Christine, Greb Thomas, Grossniklaus Ueli, Hammond John, Heidstra Renze,Hodgman Charlie, Hothorn Michael, Inzé Dirk, Ostergaard Lars, Russinova Eugenia, Simon Rüdiger,Skirycz Aleksandra, Stahl Yvonne, Zipfel Cyril, De Smet Ive (2012) Tackling drought stress:receptor-like kinases present new approaches. Plant Cell 24(6):2262-78.

Rasmussen Amanda, Mason Michael, De Cuyper Carolien, Brewer Philip, Herold Silvia, Agusti Javier, Geelen Danny, Greb Thomas, Goormachtig Sofie, Beeckman Tom, Beveridge Christine (2012)Strigolactones suppress adventitious rooting in Arabidopsis and pea. Plant Physiol. 158(4):1976-87.

Jonak Group

Dal Santo Silvia, Stampfl Hansjörg, Krasensky Julia, Kempa Stefan, Gibon Yves, Petutschnig Elena,Rozhon Wilfried, Heuck Alexander, Clausen Tim, Jonak Claudia (2012) Stress-induced GSK3 regulatesthe redox stress response by phosphorylating glucose-6-phosphate dehydrogenase in Arabidopsis.Plant Cell 24(8):3380-92.

Gudesblat Gustavo, Schneider-Pizoń Joanna, Betti Camilla, Mayerhofer Juliane, Vanhoutte Isabelle,van Dongen Walter, Boeren Sjef, Zhiponova Miroslava, de Vries Sacco, Jonak Claudia, Russinova Eugenia (Epub: 2012) SPEECHLESS integrates brassinosteroid and stomata signalling pathways.Nat. Cell Biol. 14(5):548-54.

Krasensky Julia, Jonak Claudia (2012) Drought, salt, and temperature stress-induced metabolicrearrangements and regulatory networks. J. Exp. Bot. 63(4):1593-608.

Riehs-Kearnan Nina, Gloggnitzer Jiradet, Dekrout Bettina, Jonak Claudia, Riha Karel (2012)Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors iscaused by autoimmune-like response. Nucleic Acids Res. 40(12):5615-24.

Matzke Group

Eun C, Lorkovic Z, Sasaki T, Naumann U, Matzke A, Matzke M (2012) Use of Forward Genetic Screens to Identify Genes Required for RNA-Directed DNA Methylation in Arabidopsis thaliana. Cold Spring Harb. Symp. Quant. Biol.

Lee Tzuu-fen, Gurazada Sai, Zhai Jixian, Li Shengben, Simon Stacey, Matzke Marjori, Chen Xuemei, Mey-ers Blake (2012) RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7(7):781-95.

Lorković Zdravko (2012) MORC proteins and epigenetic regulation. Plant Signal Behav 7(12).


Lorković Zdravko, Naumann Ulf, Matzke Antonius, Matzke Marjori (2012) Involvement of a GHKL ATPase in RNA-directed DNA methylation in Arabidopsis thaliana. Curr. Biol. 22(10):933-8.

Sasaki Taku, Naumann Ulf, Forai Petar, Matzke Antonius, Matzke Marjori (2012) Unusual Case of Apparent Hypermutation in Arabidopsis thaliana. Genetics 192(4):1271-80.

You Wanhui, Tyczewska Agata, Spencer Matthew, Daxinger Lucia, Schmid Marc, Grossniklaus Ueli, Simon Stacey, Meyers Blake, Matzke Antonius, Matzke Marjori (Epub: 2012) Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol. 12:51.

Mittelsten Scheid Group

Dinh Huy, Dubin Manu, Sedlazeck Fritz, Lettner Nicole, Mittelsten Scheid Ortrun, von Haeseler Arndt (2012) Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS ONE 7(7):e41528.

Gutzat Ruben, Mittelsten Scheid Ortrun (2012) Epigenetic responses to stress: triple defense? Curr. Opin. Plant Biol. 15(5):568-73.

Pecinka Ales, Mittelsten Scheid Ortrun (2012) Stress-induced chromatin changes: a critical view ontheir heritability. Plant Cell Physiol. 53(5):801-8.

Zielinski Marie-Luise, Mittelsten Scheid Ortrun (2012) Meiosis in polyploidy plants. In: Polyploidy andGenome Evolution (Soltis PS, Soltis DE, eds.) Springer Publisher.

Yáñez-Cuna J Omar, Dinh Huy Q, Kvon Evgeny, Shlyueva Daria, Stark Alexander (2012)Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.Genome Res. 22(10):2018-30.

Kalyna Maria, Simpson Craig G, Syed Naeem H, Lewandowska Dominika, Marquez Yamile, Kusenda Branislav, Marshall Jacqueline, Fuller John, Cardle Linda, McNicol Jim, Dinh Huy Q, Barta Andrea, Brown John WS (2012). Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidosis. Nucl Acid Res. 40(6):2454-69.

Voigt-Zielinski Marie-Luise, Piwczyński Marcin, Sharbel Timothy (2012) Differential effects of polyploidy and diploidy on fitness of apomictic Boechera. Sex. Plant Reprod. 25(2):97-109.

Nodine Group

Nodine, Michael D., Bartel, David P. (2012) Maternal and paternal genomes contribute equally tothe transcriptome of early plant embryos. Nature, 482: 94-97.

Nordborg Group

Chao Dai-Yin, Silva Adriano, Baxter Ivan, Huang Yu S., Nordborg Magnus, Danku John,Lahner Brett, Yakubova Elena, Salt David (2012) Genome-wide association studies identifyheavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium inArabidopsis thaliana. PLoS Genet. 8(9):e1002923.


Horton Matthew, Hancock Angela, Huang Yu, Toomajian Christopher, Atwell Susanna, Auton Adam, Muliyati N, Platt Alexander, Sperone F, Vilhjálmsson Bjarni, Nordborg Magnus, Borevitz Justin, Bergelson Joy (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat. Genet. 44(2):212-6.

Korte Arthur, Vilhjálmsson Bjarni, Segura Vincent, Platt Alexander, Long Quan, Nordborg Magnus (2012) A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat. Genet. 44(9):1066-71.

Platzer Alexander, Nizhynska Viktoria, Long Quan (2012) TE-Locate: A Tool to Locate and Group Transpos-able Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology 1(2):395-410.

Segura Vincent, Vilhjálmsson Bjarni, Platt Alexander, Korte Arthur, Seren Ümit, Long Quan, Nordborg Magnus (Epub: 2012) An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat. Genet. 44(7):825-30.

Seren Ü, Vilhjálmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M (2012) GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis. Plant Cell Online,December 2012 tpc.112.108068.

Vilhjálmsson Bjarni, Nordborg Magnus (2012) The nature of confounding in genome-wideassociation studies. Nat. Rev. Genet. 14(1):1-2.

Riha Group

Kazda Anita, Zellinger Barbara, Rössler Max, Derboven Elisa, Kusenda Branislav, Riha Karel (2012)Chromosome end protection by blunt-ended telomeres. Genes Dev. 26(15):1703-13.

Riehs-Kearnan Nina, Gloggnitzer Jiradet, Dekrout Bettina, Jonak Claudia, Riha Karel (2012) Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused byautoimmune-like response. Nucleic Acids Res. 40(12):5615-24.

Siomos MF, Riha K (2012) Telomeres and their biology. In: Plant Genome Diversity (eds. Wendel FW,Greilhuber J, Leitch IJ, Dolezel J), Springer, pp. 71 - 82.

Tamaru Group

Adhvaryu KK, Berge E, Tamaru H, Freitag M, Selker EU (Epub: 2011) Substitutions in the amino-terminal tail of Neurospora histone H3 have varied effects on DNA methylation. PLoS Genetics:7:e1002423.

Ibarra Christian, Feng Xiaoqi, Schoft Vera, Hsieh Tzung-Fu, Uzawa Rie, Rodrigues Jessica, Zemach Assaf, Chumak Nina, Machlicova Adriana, Nishimura Toshiro, Rojas Denisse, Fischer Robert, Tamaru Hisashi,Zilberman Daniel (2012) Active DNA demethylation in plant companion cells reinforces transposonmethylation in gametes. Science 337(6100):1360-4.

Mérai Zsuzsanna, Benkovics Anna, Nyikó Tünde, Debreczeny Mónika, Hiripi László, Kerényi Zoltán,Kondorosi Eva, Silhavy Dániel (2012) The late steps of plant nonsense-mediated mRNA decay. Plant J.


Grants

Thomas Greb

• FWF: Austrian Science Fund (2009-2012). Regulation of secondary growth initiation in Arabidopsis thaliana• FWF: Austrian Science Fund (20011-2015). The role of strigolactones in secondary growth regulation• DFG fellowship (2012-2013). Identification and characterization of CBI1, a novel repressor of cambium identity in Arabidopsis thaliana (Stefanie Suer)• EMBO (2012-2014). Identification of the WOX4 downstream network essential for the regulation of lateral plant growth (Virginie Jouannet)

Claudia Jonak

• European Union: COSI (2008-2012). Chloroplast Signals – Marie Curie Initial Training Network Project• FWF: Austrian Science Fund (2010-2013). Arabidopsis GSK3/SHAGGY-LIKE KINASE β in drought stress signalling• FWF: Austrian Science Fund (2008-2012). Linking stress signaling and metabolism in plants• FFG (2012-2013). Stresstoleranz

Antonius & Marjori Matzke

• FWF: Austrian Science Fund (2008-2012). Genetic analysis of RNA-directed DNA methylation• FWF/SFB: Austrian Science Fund (2011-2015). Role of non-coding RNAs and different RNA polymerases in epigenetic regulation in plants

Ortrun Mittelsten Scheid

• FWF: Austrian Science Fund (2010-2013). EPICOL – Ecological and evolutionary plant epigenetics• FWF: Austrian Science Fund – Lise Meitner fellowship (2012-2013). An epigenome-wide association study in plants (Manu Dubin)• FWF: Austrian Science Fund (2012-2016). Graduate program “Chromosome Dynamics”• DAAD (May-Oct 2012). Erasmus fellowship (Suraj Jamge)• DAAD (September 2012-January 2013) Erasmus fellowship (Dominik Ewald)


Magnus Nordborg

• NIH: National Institutes of Health (2008-2013). The molecular basis of local adaptation in Arabidopsis thaliana• NIH: National Institutes of Health (2009-2013). Genomic analysis of the genotype-phenotype map• NIH: National Institutes of Health, Laboratory of Molecular Genetics, NICHD, NIH (2009-2012). Integrated genetic and genomic resources for a model system• ERC: European Research Council (2011-2016). Developing maximum-resolution genotype-phenotype maps using whole-genome polymorphism data – MAXMAP• DFG: German Research Fund - DFG fellowship (2011-2013). Genome-wide association analysis of drought tolerance in seedlings of A. thaliana (Arthur Korte)• DFG: German Research Fund (2001-2014). Starting from scratch: adaptation to variable environments after an extreme bottleneck• ERC: European Research Council (2011-2015). Trans-national infrastructure for plant genomic science – transPLANT• 7th EU Frame Program – Marie Curie Integration Grant (2012-2016). Genetic adaptions to climate in Arabidopsis thaliana (Angela Hancock)• FWF: Austrian Science Fund – Lise Meitner fellowship (2012-2014) The genomics of buffering and canalization in Arabidopsis (Eriko Sasaki)• EMBO (2011-2012). Fellowship (Takashi Tsuchimatsu)

Karel Riha

• FWF: Austrian Science Fund (2009-2014). Mechanisms of chromosome end protection• ÖAD: Österreichischer Austauschdienst (2011-2012). Gene targeting in green algae Chlamydomonas reinhardtii• FWF: Austrian Science Fund (2011-2014). Dissecting the mechanisms governing meiotic progression• FWF: Austrian Science Fund (2012-2016). Graduate program “Chromosome Dynamics”

Hisashi Tamaru

• FWF: Austrian Science Fund (2009-2012). Genetic and epigenetic aspects of the plant male gametophyte• FWF: Austrian Science Fund (2012-2015). Control and function of epigenetic reconfiguration in pollen


Vienna BiocenterInternational PhD Program

The Gregor Mendel Institute offers PhD positions within the framework of the prestigious Vienna Biocenter International (VBC) PhD Program, providing students the opportunity to undertake research at the cutting

edge of modern plant biology. Modest group sizes ensure students receive excellent supervision, plenty of interaction with fellow students, and unhindered access to top-notch infrastructure. Students are selected twice-yearly with an emphasis on academic and technical excellence. The official language of the program is English, and students are enrolled through the University of Vienna. PhD salaries are offered at an internationally competitive level for up to 4 years.

A number of GMI faculty are also involved in giving lectures, seminars, and practical courses in Molecular Plant Biology in the context of this program, all in English language.

The Institute of Molecular Biotechnology (IMBA), the Research Institute of Molecular Pathology (IMP), and the Max F. Perutz Laboratories (MFPL) also participate in the program. For detailed information and application procedure, please consult the program’s website (www.vbcphdprogramme.at).


January19. 01. 2012 Sharon Kessler, University of Zurich, Switzerland Finding love: intercellular communication during plant reproduction30. 02. 2012 Dong-Ha Oh, University of Illinois at Urbana-Champaign, USA Life in extreme environments: learning from crucifer genomes

February02. 02. 2 012 Lisa Smith, Max Planck Institute, Tübingen, Germany Genome evolution and hybrid incompatibility

07. 02. 2012 Outi Savolainen, University of Oulu, Finland Genetics of local adaptation and incipient reproductive isolation between Arabidopsis lyrata ssp. lyrata and ssp. petraea

13. 02. 2012 Nicolas Schauer, Metabolomic Discoveries GmbH, Germany Plant Metabolomics – From Academic to Industry Research

13. 02. 2012 Michael Nodine, Whitehead Institute, Cambridge, USA RNA biology of plant embryos14. 02. 2012 Javier Palatnik, University of Rosario, Argentina Biogenesis and function of plant microRNAs

20. 02. 2012 Miguel Ferreira, Instituto Gulbenkian de Ciência, Oeiras, Portugal Telomere protection in cancer and aging

21. 02. 2012 Anna Amtmann, University of Glasgow, UK Histone modifications: a role for somatic stress memory in plants?

March05. 03. 2012 Pascal Braun, Technische Universität München, Germany Evolution, systems organization, and pathogen perturbation of a plant protein-interactome

05. 03. 2012 Murat Tasan, University of Toronto, Canada Identifying disease-causing subnetworks from genome-wide association studies

12. 03. 2012 Sabrina Sabatini, University of Roma Sapienza, Italy Spatial coordination between stem cell division and cell differentiation in the root meristem

21. 03. 2012 Frederic Berger, National University of Singapo More than a scaffold, histone variants orchestrate chromatin states

26. 03. 2012 Robert Sablowski, John Innes Centre, Norwich, UK Floral organs: growth and regulatory evolution

April12. 04. 2012 Richard Clark, University of Utah, USA Understanding Ecologically Relevant Traits in Arabidopsis and Spider Mites

14. 04. 2012 Teva Vernoux, CNRS/Ecole Normale Supérieure de Lyon, France Integration of cell behavior by hormonal signaling during plant morphogenesis

16. 04. 2012 Stephen Wright, University of Toronto, Canada How much selection is acting on plant genomes

21. 04. 2012 Christian Fleck, University of Freiburg, Germany Quantitative Approaches to Plant Development

24. 04. 2012 Christian Breuer, RIKEN Plant Science Center, Japan Transcriptional regulation of ploidy-dependent cell growth in Arabidopsis

30. 04. 2012 Brad Till, International Atomic Energy Agency, Austria Induction and retent

annual - austrian academy of sciences · 2018. 11. 26. · 2 annual report 2012. contents...

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