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The Populus Genome Program |
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The Populus Genome Program is a part of SCTFG (Swedish Center for Tree Functional Genomics) and is the most comprehensive tree genome program in the world.
The collaborating partners are Umeå Plant Science Center (Department of Plant Physiology, Umeå University and Department of Forest Genetics and Plant Physiology, SLU Umeå) and the Department of Biotechnology, KTH Stockholm.
Databases at UPSC
- PopulusDB - Populus ESTs from 19 cDNA libraries
- UPSC BASE - Microarray gene expression data from Populus
- PopTF DB - Cloning of full length poplar
transcription factor cDNAs and expression in Populus
- PopGenIE - PopGenIE facilitates the exploration of genes and gene function in Populus
- FuncFiber Peptide database - A compendium of peptides
identified in tandem-MS proteomics experiments performed in Populus
Remote Databases
Collaborative Partners
Links
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UPSC Genomics Lab |
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Introduction
The Genomics lab at UPSC has been set up to implement technology and resources generated through a large scale Populus EST sequencing project This project, performed as a collaborative effort between UPSC Genomics lab and the Royal Institute of Technology (KTH), has generated over 100 000 Populus EST sequences. The Genomics lab has a DNA sequence facility, where you can leave template and primer and we run the sequences for you. Except for sequencing, you can also hire us to do other labwork and we have a lot of modern lab equipment.
Included in the Genomics lab is a facility which provides DNA Microarray technology for UPSC personnel and guests.
The work of the Genomics lab is supported mainly by the Knut and Alice Wallenberg Foundation and the Foundation for Strategic Research.
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Poplar Transgenics Facility |
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Introduction
Plant scientists in Umeå were among the first groups in the world to establish a routine protocol for transformation of a forest tree, hybrid aspen. Since then several groups within UPSC have established highly recognised research within developmental tree biology and forest biotechnology. In spite of the time-consuming work to produce and characterise transgenic clones of woody plants, thousands of independently transformed transgenic trees have been processed over the last years. Trees altered in their hormonal balance, light perception and oxidative status have served as excellent experimental material for studying the biology of wood, shoots and roots, as well as annual rhythms and stress responses. Exciting findings include trees with longer fibres, altered cycles of activity and dormancy and increased stress responses. In addition to hybrid aspen, scientists within UPSC use Arabidopsis in their functional genomics research. This species is naturally easier and faster to work with, and the general approach taken is to make most basic studies in this organism. Genes for evaluation in hybrid aspen can then be selected with care for specific targets relevant for woody plants and forest biotechnology. The large scale sequencing of poplar ESTs performed as collaborative effort between UPSC and Royal Institute of Technology (KTH), Stockholm, has generated over 100 000 ESTs that together with our poplar microarrays serve as a base for in depth functional genomics research on Poplar. A core facility was established over 10 years ago in Umeå to facilitate the production of transgenic trees for scientists within Scandinavia. At present the activity is booming and within the academic world, the production of transgenic trees at UPSC is one of the most efficient in the world. Technical support is given to supply the Scandinavian scientists with plant material, perform transformation and to maintain the cultures.
Organisation
3 persons works in the facility, Marie Nygren (60%), Gunilla Malmberg (50%) and Alexander Makoveychuk (50%). The facility is subsidised by the programme for plant development (Foundation for Strategic Research) and Wallenberg Consortium North (WCN), but is also dependent on fees to cover part of the salary costs and consumables. Therefore a predetermined fee structure is used for UPSC and WCN members (see below). A steering committee, Göran Sandberg (chair), Rishi Bhalerao and Catherine Bellini leads the work and also make scientific priorities so that all UPSC- and WCN-groups get a fair chance to get access to this support. The steering committee meets twice a month together with the staff to plan the work.
In order to use the facility you must fill in a request form (will be available on UPSCs homepage) where you state what type of service you request (see below). The group leader must be informed before you submit your application. This you have to do at least two weeks in advance to Gunilla Malmberg.
Contact information:
Steering committee
Staff
Prices
Price list (PDF format)
Request for service (MS Word format)
Request for transformation (pdf Acrobat)
Or use the online request form -->
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Metabolomics Facility |
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The Metabolomics facility at Umeå Plant Science Centre
During the last decade, the sequencing of genomes in different prokaryotic and eucaryotic species has revolutionised biology. The data that these efforts have yielded facilitate analyses that provide insights into the genetic basis of similarities and differences between diverse organisms. They also create new possibilities for investigating the fundamental biology of different organisms, as well as the genetic basis of various diseases.
In the era of post-genomics, elucidation of gene function is a main target. Analysis of gene function by targeted knockouts and mutations and the measurement of gene products such as mRNA and protein species are currently the main methods used in functional genomics. However, these methods do not provide all the information needed to determine how changes in mRNA or proteins are linked to changes in biological function.
Complex regulatory interactions occur at all levels in eukaryotic cells, and a change at one level in the network does not necessarily lead to a significant change in function or phenotype. Instead, single point mutations or alterations in gene expression may often lead to complex responses. Thus, metabolomic analysis is also needed if the final effects of upstream regulatory events on metabolism are to be determined accurately.
Techniques enabling metabolites to be identified and metabolic fluxes to be quantified are essential to complement the information provided by genetic experiments and the large-scale analysis of transcript and protein profiles in living organisms.
Access to the facility
The Metabolomics facility at Umeå Plant Science received substantial support from the Wallenberg Consortium North (WCN; www.wcn.se), and the facility is open for the universities associated to the WCN.
Funding
The facility is now receiving funding from SLU. Wallenberg and The Kempe foundation are highly acknowledged for previous funding.
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Controlled Environment Climate Chambers |
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Within UPSC, we have a number of climate chambers available for controlled environment studies. These include 7 “walk-in” climate chambers on floor 2 and 8 “walk-in” climate chambers on floor 3, within the new high security growth facility. There are 5 smaller controlled environment cabinets located on floor 2, and 5 Percival cabinets on floor 3 (2 for in vitro culture and 3 Arabidopsis chambers for whole plant growth). The cold room on floor 2 is also available for growing and/or winter-hardening large (and small) plants.
These different controlled environment chambers and cabinets are available to all members within UPSC and can be set to a wide range of temperature and irradiance conditions to suit individual experimental requirements.
Organization
One 50% position has been set aside to provide basic services in this facility: such as record keeping, watering, fertilization and insect control. A steering committee oversees the operation of this facility and helps to ensure all UPSC groups get fair access
Steering committee
Staff
Rules and procedures
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Proteomics Facility |
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Scientific coordinator: Gunnar Wingsle,
This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Contact: Thomas Kieselbach,
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The proteomic platform at UPSC is a part of the Umeå Protein Analysis (UPA) Facility. It was initiated in 2003 and provides infrastructure for research in protein science and proteomics. The facility is located at the Chemistry and Biology Center (KBC) of Umeå University and at UPSC. The work of UPA facility has from the beginning had a broad perspective that included the entire range of research in life science at Umeå University, the University hospital, and SLU. As a result of a work that combines education, collaborations, and services relevant advances in the development of research using proteomics and mass spectrometry based protein science were achieved.
The proteomic platform provides infrastructure, service and development for research and education in protein science, proteomics and mass spectrometry. Its instrumental and bioinformatics equipment and infrastructure was enabled through considerable investments from Umeå University, SLU, and The Swedish Research Council. As a result a complete proteomics workflow is now available for the analysis of post-translational modifications (electron dissociation mass spectrometer), which will considerably improve the current opportunities for all research in protein science in Umeå.
For more information about this facility, please, follow the link below.
 
e-link to Proteomics Facility
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Databases & Software |
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Databases at UPSC
- PopulusDB - Populus ESTs from 19 cDNA libraries
- UPSC BASE - Microarray gene expression data from Populus
- PopTF DB - Cloning of full length poplar
transcription factor cDNAs and expression in Populus
- PopGenIE - PopGenIE facilitates the exploration of genes and gene function in Populus
- FuncFiber Peptide database - A compendium of peptides
identified in tandem-MS proteomics experiments performed in Populus
Softwares developed at UPSC
- MASQOT-GUI: spot quality assessment for the two-channel microarray platform
- LAMINA: a tool for rapid quantification of leaf size and shape parameters
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DNA sequencing facility |
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We currently provide capillary sequencing using Beckman CEQ 2000 XL [ http://www.beckman.com ]. The procedure how to prepare samples for sequencing can be found by clicking [Read more] below:
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Read more... [DNA sequencing facility]
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Organisation |
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Scientific director
Thomas Moritz
UPSC, SLU, Umeå.
Tel: 090-786 84 56
Research engineer mass spectrometry and contact person
Krister Lundgren
UPSC, SLU, Umeå
Tel: 090-786 82 42
Chemometrical expertise
Johan Trygg (co-director)
Research group for chemometrics, UmU, Umeå
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Henrik Antti
Research group for chemometrics, UmU, Umeå
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Steering committee
Not decided yet.
The steering committee will, if necessary, be responsible to allocate instrument time to the different projects. |
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General Rules and Access, Security Greenhouses & Arabidopsis Growth Rooms |
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Access
This facility is designed specifically for the controlled growth of transgenic plants. As a result there are special procedures in place to stop the release of transgenic pollen and seed into the environment. Before you get access to this facility you must first go over these procedures with one of the "GMO safety officers" at the two departments, currently Ove Nilsson (SLU) and Stefan Jansson (UmU), and sign a form stating that you have read and understood the rules.
N.B.: Failure to comply with these rules may result in your access to this facility being revoked.
Arabidopsis growth rooms
These rooms are set up with standard growth conditions: approx. 23ºC day and 18ºC night temperature and either short-day (8h) or long-day (16h). These rooms are set up on a rotating basis so that once each room is full it is closed and no new plants are put into the room until ALL plants have completed their growth cycle. The rooms are then steam-cleaned before being re-opened for a new cycle of plants.
Plants can be removed from these rooms for sampling and other experimental reasons throughout their growth cycle – but once plants have begun to flower they MUST NOT be removed from the high security facility for any reason. Furthermore, while it is OK to take plants out of these rooms for experimental reasons - under no circumstances are plants to be shifted between growth rooms. If plants need to be moved for seed collection they can be taken to the greenhouse set aside for Arabidopsis on floor 5.
Watering
Watering of plants growing in these rooms is generally the responsibility of the individual.
Insecticide treatment routines
Treatment for insects is the responsibility of the facility manager (Britt-Marie Åkerman). To control ongoing problems with thrip and fungus gnat (blomflugor) infestations in the controlled growth facility, please observe the following routines:
1. In the growth rooms located on floors 3, 4 and 5, you must flag ALL new pots with a RED tag on the day you put the pots into the growth room. You do not need to write anything on this tag; it is only to alert Britt-Marie that the pot needs to be treated.
2. Once per week Britt-Marie will drench all flagged pots with “Confidor WG70”, which is a systemic insecticide. She will then remove the RED tag.
3. Britt-Marie will give subsequent treatments as required – as either a spray or drench as appropriate.
Obviously, this means that no one should use red tags for any other purpose when growing plants within the controlled growth facility.
Transgenic plants being grown on floor 2 should still be marked with a red tag as usual.
Arabidopsis infertility
A number of groups have experienced problems with low seed production. It is possible that this is caused by inadequate nutrition. A concentrated nutrient solution is available in the lab on floor 5 – along with instructions for diluting it prior to use. For optimum growth, you should fertilize your plants once per week. For seed production, you should certainly fertilize your plants at least once just as they begin to flower.
Soil
At present, we are purchasing different soil for poplar (Torv) and Arabidopsis (Blomjord). The small bags we use for Arabidopsis growth is expensive “ecologically friendly” soil – and hence prone to contain more bugs. Britt-Marie will not be purchasing this anymore – and neither should anyone else. Vermiculite and perlite are available to mix with the soil to lighten it and make it more suitable for Arabidopsis.
Plant maintenance
Users are responsible for maintaining their plants. Flowering plants should be either taped to sticks or bagged to control the spread of seed and to minimize the risk of contaminating other peoples trays.
Activities such as seed collecting, potting and plant transformation should only be done at the designated areas in the laboratory on floor 4 to prevent the possibility of contamination. Once you have finished working at an area it should be cleaned thoroughly either by sweeping up, using the hand held vacuums or with a cloth. Under no circumstances should there be any stray seed or soil left on bench tops.
Waste handling
All garbage containing transgenic materials MUST be put in special double garbage bags. Before being thrown into the container (found in the annex to the growth facility on floor 3), the garbage bag must be marked with "GMO tape".
Identification
All material in the growth facility must be CLEARLY (to others, not just for the sake of the user) identified both with the name of the person running the experiment and the research group. Material not readily identifiable may be thrown out without warning and without consultation.
Costs
Charges for these growth rooms is based on a flat fee per tray per growth cycle. The rooms can take 14 trays per shelf at 6 shelves per room.
Charges have been set at:
Long-day rooms: 100:- per tray
Short-day rooms: 150:- per tray
Arabidopsis greenhouse Floor 5: 100:- per tray per 3 month cycle
Sign up sheets with the names of all registered facility users will be placed on the doors when a room is open for use and you simply need to mark these sheets with the number of trays you have in the room.
Poplar greenhouses Floor 5: charges as per Wallenberg greenhouse.
20:- per table per day with watering
This also equates to 1:- per tray per day (or 100:- per tray per 3 month growth cycle for Arabidopsis)
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Request form