Events under 'Dissertations'

The 4th UPSC-INRA (UPRA) bilateral meeting
26 - 28 March 2012, Umeå Plant Science Centre
Chemical Biological Centre (KBC) Umeå University, Sweden

Webpage of the meeting:
http://www.kbc.umu.se/events/upra-meeting

Presentation of Master Thesis
Barbara Terebieniec
Title:
 "Gene Expression Analysis in Populus RNAi lines Targeting Xylan Biosynthesis Gene Family GT43"


Place: KBF30 Welcome!

Supervisors: Ewa Mellerowicz, László Bakó

Docentföreläsning/
Trial lecture for appointment as a docent

Torgeir Hvidsten
Umeå Plant Science Centre/Plant Physiology

Title:
"Is biology more than stamp collecting?"

Place: Lilla hörsalen, KB3A9

Welcome!

Göran Samuelsson

Göran Samuelsson and Stefan Jansson
UPSC

Success factors in grant applications

Slim and Stefan will talk about the writing a grant application and
the evaluation process, respectively

Time: Tuesday 3 April at 13.00
Place: KB3A9 "Lilla hörsalen", KBC

Welcome!

Contact: Jakob Prestele

UPSC Seminars 2012
Speaker: Thierry Delatte
Laboratory of Plant Physiology
Wageningen UR, The Netherlands

Title: "Trehalose 6-phosphate, a local signal with a global impact"
Place: KB3A9 "Lilla hörsalen", KBC

Seminar:

Santiago Gonzalez-Martinez
Center of Forest Research,Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Spain

Strong population genetic structure, recent demographic decline and selection shape diversity of taxol-related genes in European yew (Taxus baccata L.) 

Room: KBF 30

Department of Ecology and Environmental Science

Thesis Defence

Carolina Bernhardsson

Title:
Molecular population genetics of inducible defense genes in Populus tremula. 

Opponent: Santiago Gonzalez-Martinez
Center of Forest Research,Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Spain

Supervisor: Stefan Jansson, UPSC 

Room: KB3B1

Umeå Plant Science Centre UPSC
Half-Time PhD seminar

Speaker
Dmitry Kremnev

Title:
PLASTID REDOX INSENSITIVE 2, is a putative regulatory component that controls PEP transcription

Bastiaan Brouwer is defending his thesis.
Title: Shedding Light on Shade- and Dark-Induced Leaf Senescence
Place: KB3A9

Opponent:
Karin Krupinska, Professor
Department of Plant Cell Biology,
Christian-Albrechts-Universität Kiel/Kiel University

Supervisor: Per Gardeström
 

Department of Chemistry

Seminar

Sacha Baginsky

Martin-Luther-Universität Halle-Wittenberg, Institut für Biochemie und Biotechnologie, Abteilung Pflanzenbiochemie

 

Title:

 Functional characterization of plant proteome dynamics

 

Place : Lilla hörsalen, KB3A9, KBC

Host Christiane Funk

Abstract: 

Different functional proteomics tools are now available that enable the quantitative characterization of proteome dynamics and the mapping of posttranslational modifications. We report here examples how we used these tools to characterize the functional proteome of Arabidopsis and rice cell organelles, with a focus on the plant-specific plastids. We analyzed the Arabidopsis proteome at genome-scale and provide quantitative information about organellar proteomes in different plant organs by "normalized spectral counting" (Science, 320: 938-41). For a functional characterization of plastid protein import, we analyzed the proteomes of plastid protein import mutants and searched for N-terminal acetylated peptides in genome-scale WT, ppi1 and ppi2 proteomics data. These analyses revealed the accumulation of precursor proteins in the cytosol of the import mutants. In order to assess the short-term regulation of the chloroplast proteome in response to environmental signals, we analyzed the chloroplast phosphoproteome and characterized its dynamics during a circadian cycle (Plant Physiol, 150: 889-903). Differential protein phosphorylation was assessed by relative protein quantification with "extracted ion chromatograms". We present here our data, comment on reliability and reproducibility and propose strategies to increase both at a reasonable cost.

Sacha Baginsky

Martin-Luther-Universität Halle-Wittenberg, Institut für Biochemie und Biotechnologie, Abteilung Pflanzenbiochemie, Weinbergweg 22 (Biozentrum),

06120 Halle (Saale)

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Thesis Defence - Department of Chemistry

Harald Aigner

Title:
Characterization of FtsH proteases in the annual plant Arabidopsis thaliana 

Opponent: Sacha Baginski, Professor, Institut fur Biochemie und BioTechnologie, Martin Luther Unitersität, Halle Wittenberg.

Supervisor: Christiane Funk

Lilla hörsalen , KB3A9

UPSC Seminar

Speaker:
Grégory Mouille
Institute JP Bourgin, INRA Versailles, France

Title:
The control of cell wall quality during plant development

Place: Lilla hörsalen KB3A9

UPSC Seminar

Speaker:
Georgia Drakakaki
UC Davis California, USA

Title:
 “Understanding the relation of endomembrane trafficking and polysaccharide deposition using proteomics and chemical genomics”
 
Place: KB3A9 “Lilla hörsalen”, KBC

Host: Stephanie Robert

Presentation of her Master Thesis (30 hp):

Patricia Lang

Title:
KREUZ UND QUER gene function during root epidermal patterning in
Arabidopsis thaliana

Supervisor: Markus Grebe

Room: KBF 30, 14.00
 

Department of Chemistry

 

Seminar

Beverley Green

University of British Columbia, Vancouver, Canada

 

Title: Algal genomics and the evolution of light-harvesting antennae

 

Host: Christiane Funk

Place: Lilla Hörsalen, KB3A9, KBC

 

Abstract:

The ocean is the new frontier in genomics research! The marine algae are particularly important because of their influence on global climate as well as their major contribution to the oceanic food web. The recently sequenced genomes of a number of these algae have illuminated the wide range of photosynthetic biodiversity in the ocean. Particularly interesting are the algae with chlorophyll a/c light-harvesting antennas, such as the diatoms and brown algae, which acquired their plastids by secondary endosymbiosis, and have derived new varieties of light-harvesting antennas.

Seminar

professor Kazuya Kikuchi

Osaka University

Graduate School of Engineering

WPI-Immunology Frontier Research Center

Osaka, Japan

 

Title: Design, synthesis and biological application of in vivo imaging probes with tunable chemical switches

 

Host: Gunnar Öquist

Place: KBC, Large Lecture hall "Stora hörsalen"

 

Abstract: 

One of the great challenges in the post-genome era is to clarify the biological significance of intracellular molecules directly in living cells. If we can image a molecule in action, it is possible to acquire biological information, which is unavailable if we deal with cell homogenates. One possible approach is to design and synthesize chemical probes that can convert biological information to chemical output. Protein fluorescent labeling provides an attractive approach to study the localization and function of proteins in living cells. Recently, a specific pair of a protein tag and its ligand has been utilized to visualize a protein of interest (POI). In this method, a POI is fused with a protein tag and the tag is labeled with the ligand connected to a fluorescent molecule. The advantage of this protein labeling system is that a variety of fluorescent molecules are potentially available as labeling reagents, and that the protein tag is conditionally labeled with its fluorescent ligand. I have designed a protein labeling system that allows fluorophores to be linked to POI. The protein tag (BL-tag) is a mutant class A ?-lactamase (TEM-1) modified to be covalently bound to the designed specific labeling probes and the labeling probes is consisted with a ?-lactam ring (ampicillin, cephalosporin) attached to various fluorophores. A fluorogenetic labeling system can be designed using the unique property of cephalosporin, which release leaving group by subsequent reaction after opening the lactam ring. For further sophisticated application, multicolor imaging was done by adopting the colorful fluorophores.

Umeå Plant Science Centre
Seminar

Speaker:
Janne Lehtiö
Clinical Proteomics Mass Spectrometry, Karolinska Institutet, SciLifeLab Stockholm
Science for Life Laboratory

Title:
Defining human proteome using high resolution peptide isoelectric focusing coupled to mass spectrometry (HiRIEF-LC-MS) and the application of this method to improve cancer treatment

Place: Lilla hörsalen, KB3A9

Host Anders Nordström

Title: The effect of arginine on root system development in Norway spruce (Picea abies L. Karst) somatic embryos.
Date: Wednesday 20/6
Place: KBF30
Time: 13-14

MSc Lorenz Gerber, Department of Forest Genetics and Plant Physiology is defending his dessertation thesis.

Title: Cell Wall Chemotyping for Functional Genomics. Applications of Pyrolysis-Gas Chromatography / Mass Spectrometry.
Opponent: Professor Shawn Mansfield, Department of Wood Science, The University of British Columbia, UBC, Canada
When and Where: 2012-09-14 10:00, Umeå, KB3A9, KBC huset, Umeå universitet

Workshop on Plant Proteomics with Focus on Redox Proteomics

 

The workshop is organized by the KBC Proteomics Facility in collaboration with the International Plant Proteomics Organization (INPPO).

Speakers:

Ian Max Møller (Aarhus University, Denmark)
Per Hägglund (Technical University of Denmark)
Bob Buchanan (University of California, Berkeley)
Thomas Kieselbach (Umeå University)

The workshop will give an introduction into the chemistry of post-translational protein modifications by carbonylation and thiol oxidation and present methods to study them by proteomics. As for carbonylation, a brief introduction to the analysis of stress-induced ROS production and metal-catalyzed protein oxidation and will be given and the consequences of irreversible protein oxidation will be discussed. As for thiol oxidation different, the workshop will provide an introduction to different techniques to study target proteins of thioredoxin (Trx) using mass spectrometry and gel based approaches. This includes the use of ICAT reagents for Trx-target identification and the analysis of Trx-targets using 2-D fluorescence electrophoresis and affinity chromatography by means of monocysteinic Trx-ligands. The opportunities and limitations of these techniques will be discussed using examples from different research projects.

Please register by sending an email to: This email address is being protected from spambots. You need JavaScript enabled to view it.

Location: KBF 31

Special Seminar by Bob Buchanan

Bob Buchanan has kindly offered to present the video of an interview that he recorded some weeks ago with Andrew Benson. The video highlights Andrew Benson's contribution to the discovery of the Benson Calvin cycle, gives credit to less-known persons who made important contributions to the research of Melvin Calvin and gives some interesting insights into how laboratory work looked like in those days. In addition to the video presentation Bob Buchanan offered to give a seminar to introduce the topic. This activity is going to be both a research seminar and a presentation of an interesting chapter of research history.

Place: Lilla hörsalen, KB3A9

Scandinavian Plant Proteomics Day
Organised by Plant Link, International Plant Proteomics Organization, and the KBC Proteomics Platform

Speakers:
Michael Palmgren, Copenhagen University, Denmark
Svante Resjö, Swedish University of Agricultural Sciences, SLU, Alnarp
Ian Max Møller, Aarhus University, Danmark
Per Hägglund, Technical University of Denmark
Bob Buchanan, University of California, Berkeley, U.S.A.
Yogesh Mishra, Umeå Plant Science Centre, Umeå
Gunnar Wingsle, Umeå Plant Science Centre, Umeå
Sven Kjellström, Lund University
Johannes Hansson, Umeå Plant Science Centre, Umeå
Thomas Kieselbach, Department of Chemistry, Umeå University, and Umeå Plant Science Centre

Please register to the workshop by sending an Email to Thomas Kieselbach, This email address is being protected from spambots. You need JavaScript enabled to view it. or by filling in the registration form

Abstract book and programme for download

More information and link to registration form will appear here soon.

Thesis Defence - Tania Tibiletti - Department of Chemistry

Title: Functional studies on the Light-harvesting-Like (LiL) proteins in Cyanobacteria and Cryptophytes

Opponent: Prof. Dr. Martin Hagemann, University of Rostock, Plant Physiology, Germany.

Supervisor: Christiane Funk

Lilla hörsalen , KB3A9

Title: Regulation of Phenology and the Juvenility-to-Maturity Transition in Trees
Opponent: Professor Isabel Allona, Centre for Plant Biotechnology and Genomics U.P.M. -I.N.IA Parque Cientifico y Tecnoloqico de la U.P.M. Campus de Montegancedo, Madrid, Spanien
When and Where: 10 :00, i Aulan, SLU Umeå

UPSC Seminar
Speaker:
Cristian Ibáñez
La Serena University, Chile

Title:
Dissecting the genetic potential of Prosopis chilensis trees in response to salinity stress

Host:
Maria Eriksson

Room:
KB3A9, Lilla hörsalen

In conjunction withe the 1st annual meeting of the EU/FP7 funded project "ProCoGen" (Promoting a functional and comparative understanding of the conifer genome? implementing applied aspects for more productive and adapted forests), there will be a Training workshop organised here in Umeå. The training workshop is open to all interested parties, the schedule for the workshop can be found below.

On Jan 30 the lecture will be given in "Stora Hörsalen (KB3B1)" while the lectures on Jan 31 and Feb 1 the lectures are given in "Lilla Hörsalen (KB3A9)

Programme

Umeå Renewable Energy Meeting 2013 will take place in Umeå from 25 - 27 February at Kemiskt Biologiskt Centrum KBC.

Please go to the conference webpage for more information on the programme and registration:
http://www.kbc.umu.se/events/renewable-energy-meeting-2013.html


Organizing Committee:
Johannes Messinger, Per Gardeström, Hannele Tuominen, Johannes Hanson, Leif Jönsson

UPSC seminar by

Henrik Vibe-Scheller
University of California, Berkeley

Title:

'Optimizing plant cell walls for biofuel production'

Place KB3A9, Lilla hörsalen KBC

Henrik Vibe Scheller is an adjunct professor and vice-President of feedstocks division at JBEI (Joint BioEnergy Institute). He investigates the genes and proteins involved in biosynthesis of complex polysaccharides and glycoproteins in the plant cell wall, using arabidopsis and rice as model plants. Besides the fundamental scientific importance of these studies, understanding wall biosynthesis and regulation may allow us to develop crop plants that are more suitable feedstocks for biofuel production. Techniques used in the lab include biochemistry, spectroscopy, molecular genetics, cell biology and bioinformatics.

Publications from 2012-2013:

Bartley LE, Peck ML, Kim SR, Ebert B, Maniseri C, Chiniquy D, Sykes R, Gao L, Rautengarten C, Vega-Sanchez ME, Benke PI, Canlas PE, Cao P, Brewer S, Lin F, Smith WL, Zhang X, Keasling JD, Jentoft RE, Foster SB, Zhou J, Ziebell A, An G, Scheller HV, Ronald PC. Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification. Plant Physiol. 2013 Feb 7. [Epub ahead of print]

Arabinosylation of a Yariv Precipitable Cell Wall Polymer Impacts Plant Growth as Exemplified by the Arabidopsis Glycosyltransferase Mutant ray1. Gille S, Sharma V, Baidoo EE, Keasling JD, Scheller HV, Pauly M. Mol Plant. 2013 Feb 9. [Epub ahead of print]

Vega-Sanchez M, Verhertbruggen Y, Scheller HV, Ronald P. Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses. Plant Signal Behav. 2013 Jan 8;8(2). doi:pii: e23143. [Epub ahead of print]

Chen X, Vega-Sánchez ME, Bartley L, Verhertbruggen Y, Chiniquy D, Canlas P, Fagerström A, Prak L, Christensen U, Oikawa A, Chen M, Zuo S, Auer M, Willats W G.T., Harholt J, Scheller HV, and Ronald PC. Inactivation of OsIRX10 leads to decreased xylan content in rice stem cell walls and improved biomass saccharification. Mol Plant, in press.

Liwanag AJM, Ebert B, Verhertbruggen Y, Rennie EA, Rautengarten C, Oikawa A, Andersen MCF, Clausen MH, Scheller HV. (2012) Pectin Biosynthesis: GALS1 in Arabidopsis thaliana is a ?-1,4-galactan ?-1,4-galactosyltransferase. Plant Cell, 2012 Dec;24(12):5024-36. doi: 10.1105/tpc.112.106625. Epub 2012 Dec 14.
Petersen PD, Lau J, Ebert B, Yang F, Verhertbruggen Y, Kim JS, Varanasi P, Suttangkakul A, Auer M, Loqué D, Scheller HV. (2012) Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants. Biotechnol Biofuels, 2012 Nov 26;5(1):84. doi: 10.1186/1754-6834-5-84.

Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JK, Sun L, Zheng K, Tang K, Auer M, Scheller HV and Loqué D. Engineering secondary cell wall deposition in plants. Plant Biotechnol J, Published Online: 12 NOV 2012, DOI: 10.1111/pbi.12016

Rennie EA, Hansen SF, Baidoo EEK, Hadi M, Keasling JD, Scheller HV (2012) Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases. Plant Physiol 159, 1408-1417.

Harholt J, Sørensen I, Roberts A, Willats W, Scheller HV, Petersen BL, Banks JA, Ulvskov P. (2012). The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of the cell wall structure. Plos One 7(5): e35846.

Hansen SF, Harholt J, Oikawa A, Scheller HV. (2012) Plant glycosyltransferases beyond CAZy: A perspective on DUF families. Frontiers Plant Physiol, 3:59

Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, xSmith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Christiansen K, Scheller HV, Loque D, Heazlewood JL (2012). Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol 159: 12-26

Vega-Sánchez ME, Verhertbruggen Y, Christensen U, Chen X, Sharma V, Varanasi P, Jobling SA, Talbot M, White, RG, Joo M, Singh S, Auer M, Scheller HV, Ronald PC (2012). Loss of Cellulose Synthase-Like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties and defense responses in vegetative tissues of rice. Plant Physiol 159: 56-69

Harholt J, Jensen JK, Verhertbruggen Y, Søgaard C, Bernard S, Nafisi M, Poulsen CP, Geshi N, Sakuragi Y, Driouich A, Knox JP, Scheller HV (2012). ARAD proteins associated with pectic Arabinan biosynthesis form complexes when transiently overexpressed in planta. Planta. 2012 Jul;236(1):115-28. Epub 2012 Jan 21.

Orfila C, Degan FD, Jørgensen B, Scheller HV, Ray PM, Ulvskov P (2012). Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties. Planta. 2012 Jul;236(1):185-96.

Søgaard C, Stenbæk A, Bernard S, Hadi M, Driouich A, Scheller HV, Sakuragi Y (2012) GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues. PLoS ONE 7: e31324.

Rautengarten C, Ebert B, Ouellet M, Nafisi M, Baidoo EEK, Benke P, Stranne M, Mukhopadhyay A, Keasling JD, Sakuragi Y, Scheller HV (2012). Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for ferulyolation of w-hydroxyfatty acids in cutin polyester. Plant Physiol 158: 654-665.

Chiniquy D, Sharma V, Schultink A, Baidoo EE, Rautengarten C, Cheng K, Carroll A, Ulvskov P, Harholt J, Keasling JD, Pauly M, Scheller HV, and Ronald PC. (2012) XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan. Proc Natl Acad Sci USA 109: 17117-17122.

Oikawa A, Lund CH, Sakuragi Y, Scheller HV. Golgi-localized enzyme complexes for plant cell wall biosynthesis. Published by Elsevier Ltd. http://dx.doi.org/10.1016/j.tplants.2012.07.002 Trends in Plant Science xx (2012) 1–10

Christensen U, Scheller HV (2012) Regulation of (1,3;1,4)-b-d-glucan synthesis in developing endosperm of barley lys mutants. J Cereal Sci 55: 69–76.

Atmodjo MA, Sakuragi Y, Zhu X, Burrell A, Mohanty SS, Atwood JA, Orlando R, Scheller HV, Mohnen D (2011) Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan:galacturonosyl-transferase complex. Proc Natl Acad Sci USA 108:20225-20230.

The Swedish Metabolomics Centre Umeå celebrates it's inauguration with a symposium on
Monday, 11 March and Tuesday 12 March 2013.

More information and programme
Registration

Conference venue: Stora hörsalen, KBC, KB3B1
contact: Jonas Gullberg, This email address is being protected from spambots. You need JavaScript enabled to view it., Manager of the Swedish Metabolomics Centre Umeå