Events under 'Seminar'

UPSC Cutting Edge Seminar 2014

Speaker:
Karin Schumacher
Plant Developmental Biology
Faculty of Biosciences, Ruprecht - Karls- University Heidelberg
Germany

Title:
Vacuoles - Pumping up the plant volume

Place: lilla hörsalen KB3A9
Host: Markus Grebe

UPSC Seminars 2014

Seminar (CHANGE of TIME!)

Invited Speaker:
Daniel Van Damme
VIB Ghent

Title:
The TPLATE complex drives clathrin-mediated endocytosis in plants

Host Stephanie Robért

Room KB3A9

Careers Out of Academia Seminar

Speaker:
Johanna Puonti-Kaerlas
European Patent Office

"Working as a scientist at the European Patent Office"

Place: Naturvetarhuset, N230

Host: Delphine Gendre

Careers outsida Academia Seminar

Speaker:
Johanna Puonti-Kaerlas
European Patent Office

Title:
"Introduction to the Intellectual Property Rights"

Place: Lilla hörsalen, KB3A9
Host: Delphine Gendre

UPSC Seminar Series

Half-time Seminars

Syzmon Tylewicz

Title: Photoperiodic control of growth cessation and adaptive response involves tree homologs of bZIP transcription factors

Place: Lilla hörsalen, KB3A9
Host: RB

Cutting Edge Seminar

Speaker
Julia Bailey-Serres
University of California, Riverside

Title:
Waterproofing plants: Sensing, signaling and response mechanisms


Host Johannes Hanson

Room KB3A9

Abstract

The development of crops that can survive extreme weather conditions is imperative due to climate change and population growth. Improving plant yields when there is too little or two much water is especially important. Flooding stress, including soil waterlogging and partial to complete submergence, reduces oxygen availability for ATP production, triggering alterations in gene transcription, mRNA translation and energy metabolism. The plant-specific Group VII Ethylene Response Factor (ERF-VII) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses in plants. In rice (Oryza sativa), ERF-VIIs SUB1A and SNORKEL1/2 enable survival or escape of submergence, respectively. In Arabidopsis thaliana, there are five ERF-VIIs, which are unstable under oxygen-replete conditions due to turnover via the N-end rule of targeted proteolysis. As oxygen levels fall, the ERF-VIIs are stabilized and direct the upregulation of genes associated with anaerobic metabolism. Along with transcriptional regulation in oxygen-deprived cells, there is significant post-transcriptional control. As an energy conserving mechanism, mRNA translation is largely repressed by the sequestration of approximately 90% of the cellular transcripts in large cytosolic granular complexes. We recently reported dynamics in the movement of ribosomes along mRNAs and RNA binding protein that binds many cellular mRNAs that are sequestered during hypoxia. This protein-mRNA association is rapidly reversed upon reoxygenation, allowing stored mRNAs to resume translation. Our efforts to understand low oxygen sensing, signaling and response mechanisms are motivated by the ecological and agronomic relevance of flooding biology in light of the challenges of the 21^st century.

Mustroph, A., Zanetti, M.E., Jang, C.J., Holtan, H.E., Repetti, P.P., Galbraith, D.W., Girke, T. and Bailey-Serres, J. (2009) Profiling the Arabidopsis translatome in discrete cell types resolves altered cell-specific priorities in response to hypoxia. Proceedings of the National Academy of Sciences, USA. 106(44):18843-18848.

Gibbs, D.J., Lee, S.C., Isa, N.M.,Gramuglia, S., Fukao, T., Bassel, G.W., Correia, C.S, Corbineau, F., Theodoulou, F.L., Bailey-Serres, J. and Holdsworth, M.J. (2011) Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature 479(7373):415-418.

Fukao, T., Yeung, E. and Bailey-Serres, J. (2012) The submergence tolerance gene, SUB1A, delays leaf senescence under prolonged darkness through hormonal regulation in rice. Plant Physiology. 160:1795–1807.

Juntawong, P., Girke, T., Bazin, J. and Bailey-Serres, J. (2014) Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis Proceedings of the National Academy of Sciences, USA. 111(1):E203-12.

Sorenson, R. and Bailey-Serres, J. (2014) Selective mRNA sequestration by OLIGOURIDYLATE BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis. Proceedings of the National Academy of Sciences, USA. 111(6):2373-2378.

Cutting Edge Steve McKeand

NOTE Change of Time and Lecture room!!!

KB3B1
Host: Harry Wu

UPSC Seminars 2014 NOTE  Change of TIME!
Half-time seminar

Daniel Decker

Title:
UDP-sugar-utilizing pyrophosphorylases in plants

Host: Leszek Kleczkowski

UPSC Seminars 2014

Half-time Seminar

Speaker:
Chen Zhi-qiang

Title:
Quantitative genetics of wood quality traits in Norway spruce

Speaker
Dr. Andrew J. Tanentzap
Dept. Of Plant Sciences, Cambridge University (http://www.plantsci.cam.ac.uk/research/andrewtanentzap)

Title:
Titel: ECOSYSTEM ECOLOGY NEEDS MORE EVOLUTION

Host: Maria Eriksson
Room: Lilla hörsalen, KB3A9

Abstract: Disturbances associated with global change are degrading natural ecosystems.  But policy-makers and managers need predictions of how ecosystem functioning and patterns of biodiversity might respond to disturbances in order to intervene.  My research group is addressing these needs by tackling problems around water security.  We are focusing on how alterations to vegetation associated with land-use change and water extraction are, respectively, reducing the productivity of food webs in boreal lakes and persistence of biodiversity hotspots in dryland landscapes.  We are finding that the local outcomes of global change may ultimately be driven by the evolutionary history of traits determining species' responses to disturbance and their competitive abilities. 

Older lineages that have had longer to diversify within niche space may lose their ecological advantages as disturbance intensifies.  We are now interested in testing these ideas over much larger macro-ecological scales and linking evolution in the expression of response traits to underlying genetic processes.

UPSC Seminars 2014

Half-time Seminar

Speaker:
Kristoffer Jonsson


Room: KB3B1

UPSC Seminar

Speaker:
Carl Douglas
University of British Columbia
Department of Botany

Title:
Genomic analysis of range-wide collections of Populus trichocarpa and P. balsamifera: connecting phenotype and genotype

Place: Lilla hörsalen KB3A9
Host Björn Sundberg

UPSC Seminars 2014

Post-doc Seminar

Speaker:
Marc Rühl

Title:
The role of EARLY BIRD in the circadian clock of Arabidopsis thaliana

Place: Lilla hörsalen KB3A9

Master Thesis Defence

Guillermo Bañares de Dios

Title:
Eluidating the role of CSK during early light response and chloroplast development

Supervisor: Åsa Strand
place: KB4C10 (lecture room)

UPSC Seminar Series 2014

Cutting Edge Seminar 

Speaker:
Tom Beeckman 
VIB, Department of Plant Systems Biology, University of Ghent, Belgiium

Title:
Root architecture steered by the root cap

Host: Stephanie Robért
Place: Lilla hörsalen, KB3A9

Title : TBA
Were: KB3A9 15.00

Title : Trends of Genomic Researches in Korea
Dr. Park will present an introduction to the activities of KFRI, overview a new Korean Forest Resources Genome Project (in which UPSC is a collaborator) and current work focusing on metabolome-assisted early selection for fast-growing traits in Pinus densiflora.
http://www.researchgate.net/profile/Eung_Jun_Park target

Place: Friday 26th at 14:00 in KB4C10

UPSC Cutting Edge Seminar

Title:
Jasmonates and biosynthesis of defines metabolites, can we break the multiple feedback loops?

Speaker:
Alain Goossens
VIB, Department of Plant Systems Biology, University of Ghent, Belgiium

Host: Catherine Bellini

Time and Place: Monday October 6th - 10:00-11:00.
Place: Lilla hörsalen, KB3A9

UPSC Seminars 2014 presents

Speaker:

Terkel Hansen
University of Tromsø
The Arctic University of Norway

My bioanalytic research in Tromsø
- present and future


Place: KB3A9, Lilla hörsalen, KBC

Hosts: Gunnar Wingsle / Thomas Moritz

Title: TBA
Where: KB3A9 15.00

UPSC Seminar

Speaker:
Kamel Hammani
CNRS-UPR2357
Institute de Biologie Moléculaire des Plantes
Strasbourg, France

Title:
Mode of action of PPR proteins in plant organellar gene expression

Place: KB3A9 Lilla hörsalen

Hosts: Åsa Strand and Olivier Keech

SLU Department of Wildlife, Fish, and Environmental Studies
Seminar

Seminar by Frank & Elin Götmark
University of Gothenburg


Title:
Why produce multiple woody stems? Hypotheses and models for the adaptive significance of the shrub growth form

Place: Lecture room Aspen, SLU

Host: Lars Edenius, SLU

-------------------

Abstract:
Trees are tall woody plants with a single self-supporting woody stem, branching well above ground level, while shrubs are shorter woody plants with multiple self-supporting woody stems, branching at ground level. Shrubs occur in as many plant families as trees, and may have evolved before trees. Shrubs occur in 9 of 11 global biomes according to one classification; in another classification of terrestrial global biomes, shrubs occur 13 of 14 biomes. Shrubs grow in forests, but are also common in many regions and habitats that lack trees. Thus, shrubs are more widespread than trees, and important for many ecosystem functions. Surprisingly, we have not found any detailed analysis of factors that may have selected for the shrub growth form. We will present nine hypothesis, two supported by models, to explain the adaptive significance of shrubs.

 

-----

Frank Götmark is a professor in Animal Ecology and Conservation Biology at Gothenburg University.

His research interests covers:

Ecology and conservation of forest ecosystems, temperate zones
Broadleaved forests and management for biodiversity and biofuel
Oak (Quercus spp.) ecology: regeneration and stand management
Nature reserve systems and conservation policy
Anti-predator adaptations and predation by birds of prey
The less known biodiversity: molluscs, insects, cryptogams (collaboration with other researchers)

For more information about Frank, see: http://bioenv.gu.se/english/staff/Gotmark_Frank/ee

Elin Götmark is a senior lecturer at the department of Mathematical Sciences at Gothenburg University, and her research focuses at complex analysis and partial differential equations.

Welcome!

Lars Edenius

UPSC Seminar:

Speaker:
Rossana Henriques
Career Track Fellow
Centre de Recerca en Agrigenòmica (CRAG)
Edifici CRAG, Campus UAB
Bellaterra (Cerdanyola del Vallés)
Barcelona

Title:
From genome dark matter to biological regulation: uncovering long non-coding RNA function in plants

Host
Laszlo Bako

Place Lilla hörsalen KB3A9

Title: TBA
Where: KB3A9 15.00

UPSC Seminar

Sepaker:
Claudio Stasolla
Dept. Plant Science, University of Manitoba, Winnipeg, Canada

Title:
In vitro plant embryogenesis: improving embryo yield

Place: KB3A9, Lilla hörsalen

Host: Ulrika Egertsdotter

Plant embryogenesis is an essential phase of the plant life cycle and formation of embryos can be stimulated in vitro through the careful selection of media components and environmental conditions. Work in my lab has recently been focussed on the function of plant hemoglobins (Hbs) during somatic embryogenesis in dicots and monocots.   First described in animals, Hbs have now been identified in a variety of organisms including plants where their major function is to scavenge cellular nitric oxide (NO). Suppression of the Arabidopsis class 2 Hb (Hb2) enhances the formation of somatic embryos through the NO-mediated suppression of the transcription factor MYC2. Repression of MYC2 increases IAA accumulation at the sites of embryogenic tissue formation, and favors the formation of Arabidopsis somatic embryos.   In maize the two Hbs: ZmHb1 and ZmHb2 regulate the cell survival/death decision that influences somatic embryogenesis through their cell-specific localization patterns. Suppression of either of the two ZmHbs is sufficient to induce PCD through a pathway initiated by elevated nitric oxide (NO) and zinc (Zn²⁺⁾ levels, and mediated by production of reactive oxygen species (ROS). The effect of the death program on the fate of the developing embryos is dependent upon the localization patterns of the two ZmHbs. During somatic embryogenesis, ZmHb2 transcripts are restricted to a few cells anchoring the embryos to the subtending embryogenic tissue, while ZmHb1 transcripts extend to several embryonic domains. Suppression of ZmHb2 induces PCD in the anchoring cells allowing the embryos to develop further, while suppression of ZmHb1 results in massive PCD leading to abortion. It is concluded that regulation of the expression of these ZmHbs has the capability to determine the developmental fate of the embryogenic tissue during somatic embryogenesis through their effect on PCD. These studies place Hbs as central regulators of in vitro embryogenesis

UPSC Seminar
Speaker:
Carole Dubreuil
Post-doc

Title:
Elucidating the mechanisms involved in chloroplast biogenesis by using an Arabidopsis cell culture system

Host Åsa Strand

UPSC Seminar Series 2014
Cutting Edge Seminar

Speaker:
Sabrina Sabatini
Università degli di Roma "La Sapienza"
Rome, Italy

Title: New insight in root meristem size determination and root zonation

Host: Karin Ljung
Place Lilla hörsalen KB3A9

Abstract:
Understanding the molecular mechanisms through which plant meristems are maintained is a central question in developmental biology. In the root of Arabidopsis thaliana, stem cells in the apical region of the meristem self-renew and produce daughter cells that differentiate in the distal meristem transition zone. To ensure root growth, the rate of cell differentiation must equal the rate of generation of new cells. Cell differentiation takes place in the transition zone that is localized in the distal part of the root meristem, but must be synchronized and balanced with division of the stem cells that are localized in the apical part of the meristem. We have previously shown that maintenance of the Arabidopsis root meristem size - and consequently root growth - is controlled by the interaction between two hormones at the meristem transition zone: cytokinins, which promote cell differentiation, and auxin, which promotes cell division.

New data will be presented on the molecular mechanism by which cytokinin induce cell differentiation influencing auxin distribution and, as a consequence, root zonation

UPSC Seminar

Wendy Heywood
University College London, UK

Title:
Targeted Proteomics: Translating Omics to the clinic

Room: N200, Naturvetarhuset
Host: Jonas Gullberg, Gunnar Wingsle,

She is invited to tell us about her recent progress using targeted proteomic methodology.
Everyone interested in this or general proteomics is welcomed.
Her research profile and publication list can be found here:https://iris.ucl.ac.uk/iris/browse/profile?upi=WEHEY77

UPSC Seminar Series 2014
Cutting Edge Seminar 

Speaker:
Jay J. Thelen
Department of Biochemistry, 
Christopher S. Bond Life Sciences Center
University of Missouri, Columbia, MO, USA

Title:
Phosphoproteomic analysis of seed maturation – from discovering phosphorylation sites to identifying kinase clients

Host: Vaughan Hurry

Place: Lilla hörsalen, KB3A9

Abstract

Although metabolic networks for storage reserve synthesis have been largely characterized in diverse plant seed we are only beginning to understand the complex regulatory processes involved in seed development. Protein phosphorylation is a major form of post-translational regulation in eukaryotes as evidenced by over 1000 protein kinases in the Arabidopsis proteome. To begin studying protein phosphorylation in developing seed we performed large-scale, mass spectrometry-based phosphoproteomic studies on seeds at five stages of development in soybean (Glycine max), rapeseed (Brassica napus), and Arabidopsis (Arabidopsis thaliana). Phosphopeptides were enriched from 0.5 mg total peptides using a combination of immobilized metal affinity and metal oxide affinity chromatography. Enriched phosphopeptides were analyzed by Orbitrap tandem mass spectrometry and spectra mined against cognate genome or cDNA databases in both forward and randomized orientations, the latter to calculate false discovery rate (FDR). We identified a total of 2001 phosphopeptides containing 1026 unambiguous phosphorylation sites from 956 proteins with an average FDR of 0.78% for the entire study (Meyer et al., 2012). The dataset was uploaded into the Plant Protein Phosphorylation Database (P3DB, www.p3db.org), including annotated spectra, for public accession. P3DB is a portal for all plant phosphorylation data and allows for homology-based querying of experimentally-determined phosphosites (Gao et al., 2009). Comparisons to other large-scale studies revealed that 652 of the phosphoproteins are novel to this study. The unique proteins fall into several Gene Ontology categories, some of which are overrepresented in our study as well as other large scale phosphoproteomic studies including metabolic process and RNA binding; while other categories are only overrepresented in our study like embryonic development. Leveraging large-scale phosphoproteomic datasets such as these, we developed a phosphorylation prediction tool called MUSite (http://musite.sourceforge.net/) that incorporates protein disorder as one of three features for prediction (Gao et al., 2010). The sensitivity and accuracy of this prediction algorithm is unmatched, and application to whole plant proteomes such as Arabidopsis TAIR10 indicates greater than 17,000 phosphorylation sites at the 99% confidence interval. Clearly, experimental and bioinformatic prediction of phosphorylation sites is rapidly becoming a facile task. However, confirmation and identification of cognate protein kinases responsible for these events remains challenging. I will also introduce a novel approach to address this problem called the Kinase Client or KiC Assay (Huang et al., 2009). Using this approach we have identified many kinase client relationships, including three different protein kinases responsible for over ten phosphorylation events on a single phosphoprotein.

Ahsan N, Huang Y, Tovar-Mendez A, Swatek KN, Zhang J, Miernyk JA, Xu D, Thelen JJ. (2013) A

Versatile Mass Spectrometry-Based Method to Both Identify Kinase Client-Relationships and Characterize Signaling Network Topology. J Proteome Res. 12:937-48

Meyer LJ, Gao J, Xu D, Thelen JJ (2012) Phosphoproteomic analysis of seed maturation in

Arabidopsis, rapeseed, and soybean. Plant Physiol. 159:517-28

Huang Y, Houston NL, Tovar-Mendez A, Stevenson SE, Miernyk JA, Randall DD, Thelen JJ (2010) A

quantitative mass spectrometry-based approach for identifying protein kinase –clients and quantifying kinase activity. Anal. Biochem. 402:69-76

Gao J, Agrawal GK, Thelen JJ, Xu D (2009) P3DB: A plant protein phosphorylation database. Nucl. Acids

Res. 37:D960-962

Gao J, Thelen JJ, Dunker AK, Xu D (2010) Musite: a tool for global prediction of general and kinase-

specific phosphorylation sites. Mol. Cell. Prot. 9:2586-25600

UPSC Seminar - postdoc seminar

Speaker:
Adeline Rigal

Title:
Unraveling transcriptional regulation of adventitious root formation with a small molecule

Host: Stéphanie Robert

Room: KB3A9, Lilla hörsalen