Search Calendar
Seminar - Wendy Heywood: Targeted Proteomics: Translating Omics to the clinic
25-Nov-2014 10:30 - 11:30
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
Cutting Edge Seminar - Jay J. Thelen: Phosphoproteomic analysis of seed maturation – from discovering phosphorylation sites to identifying kinase clients
01-Dec-2014 10:00 - 11:00
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
Thesis Defence - Dmitry Kremnev: Get in tune: Chloroplast and nucleus harmony
03-Dec-2014 13:00 - 14:00
Thesis Defence
Dmitry Kremnev
Title:
Get in tune: Chloroplast and nucleus harmony
Faculty Examiner: Professor Francis Andre Wollman, Institut de Biologie Physico-Chimique (IBPC), Paris, Frankrike.
Supervisor: Åsa Strand.
Room: KB3B1 Stora hörsalen
Seminar - Adeline Rigal: Unraveling transcriptional regulation of adventitious root formation with a small molecule
08-Dec-2014 10:00 - 11:00
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
PhD half-time - Zsofia Reka Stangl
15-Dec-2014 10:00 - 11:00
Speaker:
Zofia Stangl
Title:
Tree growth is affected by temperature and nutrient interactions
Host: Vaughan Hurry
Room: KB3A9, Lilla hörsalen
PhD-Halftime seminar - Tomas Bergström New insights in botulinum toxin analysis by mass spectrometry
16-Dec-2014 13:00 - 14:00
Forest Genetics and Plant Physiology, SLU/ The Swedish Defence Research Agency (FOI)
Speaker
Tomas Bergström
Title:
New insights in botulinum toxin analysis by mass spectrometry
Supervisor: Gunnar Wingsle
Room: Lilla hörsalen, KB3A9, KBC
Seminar - Alison Smith: The leaf at night
16-Dec-2014 14:00 - 15:00
Speaker:
Alison Smith
John Innes Centre, Norwich, UK
Title:
The leaf at night
Room. Lilla Hörsalen, KB3A9
Host: Eduoard Pesquet
Dissertation Sabine Kunz
17-Dec-2014 10:00 - 11:00
Opponent: Prof. Alison Smith (Dept. of Metabolic Biology, John Innes Centre, Norwich, UK)
Seminar - Manuela Jurca: The role of NFX-like proteins as circadian clock regulators
12-Jan-2015 10:00 - 11:00
Postdoc Seminar
Speaker:
Manuela Jurca
Title: The role of NFX-like proteins as circadian clock regulators
Host: Maria Eriksson
Place: NOTE! Stora hörsalen KB3B1
Seminar - Robert Turgeon: Phloem loading in trees and herbs: Why is there more than one mechanism?
16-Jan-2015 10:00 - 11:00
Speaker:
Robert Turgeon
Cornell University, USA
Title. Phloem loading in trees and herbs: Why is there more than one
mechanism?
Host: Totte Niittylä
Place: Stora hörsalen, KB3B1
Thesis Defence - Mir Amir Hossein Mahboubi: New insights into carbon transport and incorporation to wood
16-Jan-2015 13:00 - 15:00
Thesis Defence
Mir Amir Hossein Mahboubi
Title:
New insights into carbon transport andincorporation to wood
Faculty Examiner/Opponent: Prof Robert Turgeon from Cornell University, USA
Supervisor: Totte Niittylä
Place: P-O. Bäckströms sal, SLU.
Seminar - Daniel Pacurar: Digging for genes controlling adventitious root formation in Arabidopsis thaliana
19-Jan-2015 10:00
Postdoc Seminar
Speaker
Daniel Pacurar
Title: Digging for genes controlling adventitious root formation in Arabidopsis thaliana
Host: Catherine Bellini
Place Lilla hörsalen
Seminar- Anne Honsel: Deciphering energy signaling in plants
26-Jan-2015 10:00 - 11:00
postdoc seminar
Speaker:
Anne Honsel
Title: Deciphering energy signaling in plants
Host: Johannes Hanson
Place: Lilla hörsalen KB3A9
Seminar - Judith Felten:Cell wall remodelling during ectomycorrhiza development
02-Feb-2015 10:00 - 11:00
Speaker:
Judith Felten
Title:
Cell wall remodelling during ectomycorrhiza development
Host: Björn Sundberg
Place: Lilla hörsalen KB3A9
Thesis Defence - Malgorzata Pietrzykowska: Lhcb1 och Lhcb2 in regulation of photosynthetic light harvesting
06-Feb-2015 13:00 - 14:00
Thesis Defence
Malgorzata Pietrzykowska
Title:
Lhcb1 och Lhcb2 in regulation of photosynthetic light harvesting
Faculty Examiner: Jean-David Rochaix, professor, Department of Molecular Biology, University of Geneva.
Supervisor: Stefan Jansson
Place: Biologihuset, BiA201
NOTE TIME CHANGE! Seminar - Beata Kmiec: Shredding the signal: targeting peptide degradation in mitochondria and chloroplasts
09-Feb-2015 11:00 - 12:00
Speaker:
Dr. Beata Kmiec,
Department of Biochemistry and Biophysics
Stockholm University
Title: "Shredding the signal: targeting peptide degradation in mitochondria and chloroplasts.”
Host: Per Gardeström
Room: KB3A9 Lilla hörsalen
NOTE TIME CHAMGE! 11.00 instead of 10.00!
UPSC Seminar - Peter Kindgren: PPR proteins: an emerging tool to control defined RNA targets
13-Feb-2015 10:00 - 11:00
Speaker:
Peter Kindgren
Plant Energy Biology, ARC Centre of Excellence
The University of Western Australia
Title:
PPR proteins: an emerging tool to control defined RNA targets
Room: KBF30
Host : Åsa Strand
Half-time Seminar - Shashank Sane: To Investigate pathways that regulate Bud Set and Bud Flush in Poplar
16-Feb-2015 10:00 - 11:00
Half-time Seminar
Speaker:
Shashank Sane
Title: To Investigate pathways that regulate Bud Set and Bud Flush in Poplar
Host: Ove Nilsson
Room Lilla hörsalen, KB3A9
Dissertation - Szymon Tylewicz
20-Feb-2015 10:00 - 12:00
Place: P.O. Bäckströms sal, SLU Umeå
Time: 10.00 2015-02-20
Respondent: MSc Szymon Tylewicz, SKOGLIG GENETIK O VÄXTFYSIOLOGI
Opponent: Professor Isabel Allona, Centre for Plant Biotechnology and Genomics U.P.M. - I.N.I.A. Parque Cientifico y Tecnológico de la U.P.M. Madrid, Spanien.
Seminar - Siamsa Doyle: Identifying Compounds Regulating Auxin Transport
23-Feb-2015 10:00 - 11:00
Speaker:
Siamsa Doyle, postdoc
Title: Identifying Compounds Regulating Auxin Transport
Host: Stephanie Robert
Room: Lilla hörsalen, KB3A9
Half-time Seminar - Stefano Papazian: Metabolomics of plant defense under multiple stress conditions
02-Mar-2015 10:00 - 11:00
Half-time Seminar
Speaker:
Stefano Papazian
Title: Metabolomics of plant defense under multiple stress conditions
Host: Benedicte Albrectsen
Room: Lilla hörsalen KB3A9
Seminar - Barbara Terebieniec: A Systems Genetics Approach to Understanding the Genetic Control of Leaf Shape Variation in SwAsp
09-Mar-2015 10:00 - 11:00
Half-time Seminar
Speaker:
Barbara Terebieniec
Title: A Systems Genetics Approach to Understanding the Genetic Control of Leaf Shape Variation in SwAsp
Host: Nathanial Street
Room: Lilla hörsalen KB3A9
Cutting Edge Seminar - Miguel Blazguez: Oxygen as a positional signal during seedling development
16-Mar-2015 14:00 - 15:00
Cutting Edge Seminar
Speaker:
Miguel Blazguez
Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
Title: Oxygen as a positional signal during seedling development
Room: NOTE! Stora hörsalen KB3B1
Host: Hannele Tuominen
Seminar-Jörg Nickelsen: Biogenesis and Biomedical Utilization of the Photosynthetic Apparatus
16-Mar-2015 15:00 - 16:00
Seminar
Speaker:
Jörg Nickelsen
Biozentrum der LMU München, AG Molekulare Pflanzenwissenschaften, Botanik, Munich Germany
Title:
Biogenesis and Biomedical Utilization of the Photosynthetic Apparatus
Host: Christiane Funk
Room: KB3A9, Lilla hörsalen KBC
Abstract:
Cyanobacteria, algae and plants can convert light energy to chemical energy using a very similar type of photosynthetic membrane system, named thylakoids. Current molecular analyses suggest that the initial steps of the biogenesis of the cyanobacterial energy conversion system, in particular photosystem (PS) II, progress in a membrane subfraction representing a biosynthetic center which is marked by the PS II assembly factor PratA. This factor binds and delivers manganese (Mn) to PS II and, consequently, is involved in the assembly of its oxygen evolving Mn4CaO5 cluster.
Also in chloroplasts of the eukaryotic alga Chlamydomonas reinhardtii, PSII biogenesis centres – so called translation (T) zones – have been described. We have recently identified the DLA2 factor which appears to target the chloroplast psbA mRNA to these T-zones. Interestingly, DLA2 represents the E2 subunit of the plastid pyruvate dehydrogenase enzyme suggesting a crosstalk between gene expression and carbon metabolism via this protein.
In an applied approach, the oxygen evolving activity of PSII is used to provide a constant source of oxygen supply to engineered mammalian skin tissues which usually suffer from hypoxia due to poor vascularization. In particular, our data suggest that bioartificial scaffolds can be loaded with the microalgae Chlamydomonas reinhardtii, showing high biocompatibility and photosynthetic activity in vitro. The results of this study represent a first step towards the establishment of engineered autotrophic tissues and suggest that the use of photosynthetic cells can overcome a broader spectrum of hypoxic stress conditions.
Half-time Seminar - Unmut Rende: Sucrose Cleavage During Wood Formation
23-Mar-2015 10:00 - 11:00
Half time Seminar
Speaker:
Unmut Rende
Title: Sucrose Cleavage During Wood Formation
Host Totte Niittylä
Room Lilla hörsalen, KB3A9
Cutting Edge Seminar - Chrisanto Gutierrez: A chromatin perspective of cell cycle and genome replication during Arabidopsis organogenesis
30-Mar-2015 10:00 - 11:00
Cutting Edge Seminar
Speaker:
Chrisanto Gutierrez
Title:
A chromatin perspective of cell cycle and genome replication during Arabidopsis organogenesis
Host: László Bakó
Room: Lilla hörsalen KB3A9
Abstract:
A chromatin perspective of cell cycle and genome replication during Arabidopsis organogenesis
Crisanto Gutierrez
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM)
The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes. It is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this talk, I will briefly review the results supporting a chromatin perspective of the cell cycle. Also I will focus on events related to genome replication and cell division control in the meristems linked to chromatin dynamics.
Seminar - Delphine Gendre: Dissection of root hair formation – How ECH and YIP4 intervene
27-Apr-2015 10:00 - 11:00
Speaker:
Delphine Gendre, postdoc
Title: Dissection of root hair formation – How ECH and YIP4 intervene
Host: Rishi Bhalerao
Room Lilla hörsalen, KB3A9