Our first annual workshop at Marholmen 2008
Flyer
Participants
Workshop folder
Activity suggestions from brainstorming session
Photos
Evaluation
Marholmen
Monthly seminars by invited researchers will give an introduction to new technologies covering different aspects of life science. The seminars are scheduled to take place the second Tuesday each month. However, depending on the availability of the lecturers the time may sometimes change. The format will be a 45 minute lecture followed by questions – this part is open for all interested students/researchers. This is followed by a closed discussion where PhD students attending the Emerging Technology course will have a round table discussion with the lecturer. Lunch sandwiches will be served. Time: 11.00-13.00. Place: GC2112.
For registration, contact Fredrik Söderbom.
6/10 Ulf Gyllensten (Dept. of Genetics and Pathology, Uppsala University) – Next generation sequencing.
11/11 Mats Nilsson (Dept. of Genetics and Pathology, Uppsala University) – Molecular diagnosis of single cells and molecules.
9/12 Anke Hermann (Dept. of Chemistry, SLU) - Insights into the underworld with nano-scale secondary ion mass spectrometry.
Syllabus
The graduate school presented a poster and launched the new logotype on the faculty day November 17.
Logotype winner Daniel Vestman
This course in forest pathology covers presentations of important forest pathosystems, identification of causal organisms, general aspects of forest diseases, current development using genomics and experimental approaches on tree –pathogen interactions. The first part of the course, 18-19 Nov 2008, will cover introduction of tree pathogens and presentation of student projects, followed by two field excursions. The second part consists of individual studies while the third part, 16-20 March 2009, includes student project presentations and lectures by invited international teachers. The seminars given during part three of the course will be open for all interested students/researchers.
Registration deadline 11 November 2008, contact Jan Stenlid.
Syllabus
Flyer
Introduction to basic optical theory as well as the practical application of the theory for both conventional light microscopy and fluorescence microscopy; general histological specimen preparation techniques; specific localisation techniques such as immunohistochemistry and in situ hybridisation. Photomicrography with analogue and digital cameras; Digital image processing. The course will be predominantly practical allowing the students to analyze their own samples. Lectures introducing the necessary theory on each aspect will precede the practicals.
The course will be given part time October – December 2008 at the Genetic Centre, in collaboration with Uppsala University. Maximum 20 students.
Registration deadline 3 October 2008, contact Jenny Carlsson.
Syllabus
Schedule
Kost lecture
Summary evaluation
This year we will go to Högbo Brukshotell outside Sandviken for two days of networking. The theme for this year is Interactions. The program includes a number of invited speakers covering different aspects of the theme Interactions, talks putting gender questions in a biological context, networking activities, group discussions about future directions of the graduate school and an evening key note presentation and discussion about biotechnology and GMO. In addition, all students are encouraged to present their research projects in the poster session before lunch the second day. For more details about the program, please have a look at the flyer.
Invited speakers:
Pierre de Wit (Wageningen University) - Fungal effectors
Roger Finlay (Dept. Forest Mycology & Pathology, SLU) - Mycorrhizosphere interactions
Torbjörn Fagerström (Senior advisor, SLU) - Biotechnology for the benefit of the environment
Lars-Erik Nyström (GE Healthcare) - Research in industry - an oxymoron or just weird?
Vadim Kessler (Dept. of Chemistry, SLU) - Bionanotechnology - new tools for study and control of biological processes
Malin Ah-King (Centre for gender research, Uppsala University) - Variation in sex and sexuality in animals - towards a non-normative perspective on biological diversity
Photos
Workshop folder
Reference group feedback
Group discussions
Evaluation
Illustrations are important in all scientific publications. In this course you will get a mainly practical introduction to the handling of computer graphics and digital images. Focus is on photographs and self-made illustrations, but enhancement of graphical output from statistical software will also be covered.
After the course you should be able to edit digital images and create figures and illustrations for publications. Software will first be demonstrated in a mixed lecture-workshop format (March 18-19). You will need to bring your own computer with the appropriate software installed (Adobe PhotoshopTM and Adobe IllustratorTM recommended). You will then work on personal projects for an extended period at your home department. Finally, projects are presented and discussed in a final get-together (May 12).
Syllabus
Schedule
Summary evaluation
For registration on first-serve basis, contact Mattias Thelander.
This course is given by the microscopy core facility at the Evolutionary Biology Centre (EBC) at Uppsala University. After the course the students should have the theoretical and practical knowledge needed to perform analysis of biological specimens with scanning and transmission electron microscopy. The course will be predominantly practical with most time spent on work with own samples.
The number of participants is limited but this year a few slots have been reserved for Organism Biology students. Lectures are scheduled for January 27-29, 2009. For Organism Biology students, the fee for running costs will be covered by the graduate school. For questions and registration on a first-serve basis, contact Stefan Gunnarsson (018-4712638, 018-4712638).
Scanning electron microscopy - oxalate crystals
Have you always though that SEM sounds interesting, but always hesitated to use it because of the difficulties and costs involved? We are now arranging a workshop at Chemistry using the new table top electron microscope. Focus will be on how the instrument works and what type of applications it may be used for.
The course is given part time 11-12 February, and a second time 18-19 February. Maximum 10 participants each time. This activity is primarily open for students within our graduate school, but space provided others may participate. - Workshop summary and evaluation Registration deadline 4th of February. For information and registration on a first-serve basis contact Vadim Kessler.
Evaluation
Monthly seminars by invited researchers will give an introduction to new technologies covering different aspects of life science. The seminars will be followed by a round table discussion where the individual students can ask questions about how the presented techniques can be applied. You may join the course at any time. Registration to Fredrik Söderbom. Place: GC2112. Time: 11.00-13.00
Tuesday 27/1 Gunnar Almkvist (Dept of Chemistry, SLU) - The chemical voyage of the warship Vasa.
Tuesday 10/2 Rolf Danielsson (Dept of Physical and Analytical Chemistry, Uppsala University) - Kemometri.
Tuesday 10/3 Stefan Bertilsson (Dept of Ecology and Evolution, Uppsala University)
Tuesday 14/4 Johan Elf (Dept. of Cell and Molecular Biology, Uppsala University) - Single molecule analysis.
Tuesday 12/5 Fredrik Pontén (Dept. of Genetics and Pathology, Uppsala Universit) - Human Protein Atlas.
This year PhD students will present posters during the day. Please remember to print out the Organsim Biology logo and put that up on your poster if it is not already included. Contact Petra or Mattias if you have any questions.
Half-day workshop on how you -as a PhD student - successfully apply for funding for research projects and travelling. We discuss what a good application looks like and how applications are evaluated. We also discuss what funding possibilities there are at SLU and from various funding agencies. Representatives from our university and an external funding agency (KSLA) will tell us about their experiences. Place: Sal D, basement GC.
Grant list
Programme
Presentations:
Formas - Eva Sundberg
SLU grants - Karin Bennmarker
EU - Grants office
KSLA - Lars-Erik Edqvist
Workshop on how you successfully make your own research homepage. We discuss how you make yourself visible, what information can be put on a homepage and how you use tools (SLU’s verktyg and Mac server tools) for creating a homepage. These are two tools for Windows and Windows/Mac interface where you edit your homepage content in a relatively simple way.
Schedule:
October 26
Place: Ekorummet, Mykopat
9.00-10.00 Introduction, what to put on a homepage and how to make yourself visible
10.00-10.30 Coffee break
10.30-12.00 How to get started, presentation of web tools
Week 44-45 Individual work with text and photos, feedback from supervisor/s
November 9
Place: Lecture hall, Mykopat
9.00-12.00 Presentation of homepages in group
For information and registration contact Petra Fransson.
Invited researchers give presentations about their specific model organism, usually the third Tuesday every month. The seminars are followed by lunch (sandwiches) and further questions/discussions with the lecturer. Review articles describing the specific organisms will be sent out before the lectures. In addition, an article describing the lecturer’s own research will be provided (reading of the research article is optional). Eight or nine seminars will be given during fall-spring. If you attend a minimum of six you will get 2 HEC.
To enroll, please send an email before September 8, including the name of you and your department to Fredrik Söderbom. You may also enroll the first time you attend a seminar.
Place: Room D Genetics Center (unless stated otherwise)
Time: 11.00-13.00
Tuesday 15/9 Andrea Hinas (Uppsala University) - Caenorhabditis elegans (Note: Old library at Genetics Centre)
Review article: Jorgensen and Mangon (2002) Nat. Rev. Gen.
Research article: Jose and Hunter (2007) Annu. Rev. Genet
Tuesday 13/10 Mattias Mannervik (Stockholm University) – Drosophila melanogaster - A model organism in biomedical research
Review article: St Johnston (2002) Nat. Rev. Gen.
Research article: Haecker et al. (2007) PLOS Biol.
Tuesday 10/11 Hans Ronne (Uppsala University) - Yeast
Review article: Menacho-Marquez and Murguia (2007) Clin. Transl. Oncol.
Research article: Gustavsson and Ronne (2008) RNA
Tuesday 8/12 Wolfgang Nellen (Kassel University) - Dictyostelium discoideum
Review article: Loomis (2006) Curr. Issues Mol. Biol.
Research article: Kuhlmann et al. (2005) Nucl. Acids. Res.
Syllabus
Monthly networking seminars by PhD students participating in the Organism biology graduate school. Each time two PhD students will present their research ideas and work in a general context. Take an opportunity to meet the other students under relaxed forms and learn some more about our different subject areas. Presentations will take place from 16.30-17.30 in the VBSG lunch room, then we finish the discussions over dinner pizza and drinks. Food is on Organism Biology while beverages and soft drinks are bought from the fridge bar.
21 January: Gustav Nestor (Chemistry) – Hydrogen bonding in hyaluronic acid oligosaccharides investigated by NMR spectroscopy.
Johanna Boberg (Forest Mycology and Pathology) - Functioning of litter decomposing fungi in N and C circulation in the boreal forest.
19 February: Lotta Avesson (Molecular Biology) - Non-coding RNAs in Dictyostelium discoideum.
Naeem Sattar (Plant Biology and Forest Genetics) - Molecular virus-host interactions of begomoviruses and DNA-satellites infecting cotton.
17 March: Nurun Nahar (Plant Biology and Forest Genetics) - Regulation of sterol and glycoalkaloid biosynthesis in potatoe (Solanum tuberosum) plant.
Kai Wilkinson (Chemistry) - Airborne Impurities: Express Analysis and Health Effects.
20 April: Inga Bödeker (Forest Mycology) - Fungal oxidative enzymes in litter and humus degradation (preliminary title).
Petra Fransson (Forest Mycology) - Elevated CO2, soil carbon fluxes and mycorrhizal fungi.
20 May: Josefin Liew (Crop Production Ecology) - Sleeping buds in perennial weeds. Malin Abrahamsson (Plant Biology and Forest Genetics) - Somatic embryo development in Norway spruce and Scots pine.
21 September at VBSG: Lina Grönberg (Mykopat) - Variation and survival of Phytophthora infestans
Anna Berlin (Mykopat) - Epidemiology and population biology of Puciria graminis for control of stem rust in Sweden.
20 October at Mykopat: Sanjeewani Sooriyaarachchi (MolBiol) - X-ray structures of periplasmic sugar-binding proteins
Maria Karlsson (Mikro) - Syntrophic acetate oxidation in ammonia enriched biogas processes
19 November MolBiol, BMC: Ylva Persson (Mykopat) - Fungi vectored by the bark beetle Ips typographus
Rebecka Strandberg (EBC, Uppsala University) - Evolution of reproductive systems in Neurospora
14 December at Chemistry: Ramesh Vetukuri (VBSG) - Small non-coding RNA in Phytophtora infestans
Jessica Schenck (Mykopat) - Fungi in haylage
For further information, contact Izabela Cierlik or Kai Wilkinson. Register for the session by sending an e-mail to Mattias Thelander.
This course will give a comprehensive overview of plant disease epidemiology and disease control, and includes an introduction to basic concepts and models, disease models, epidemiological basis for plant disease control, disease in space and decision support systems and risk analysis.
The first part of the course, 27-30 April, will cover introduction of plant disease epidemiology, computer based data analysis and presentation of student projects. The second part consists of individual studies and literature reading while the third part of the course, 18 May, includes student project presentations and summarizing. Registration deadline 20th of April, for information contact Jonathan Yuen.
Syllabus
Flyer
Today we often study if a gene is expressed and to what extent by using qRT-PCR and microarrays, which gives us a good overview of the expression profiles in the tissues we have isolated. However, sometimes we need to dissect exactly in which tissues or cell-layers a certain gene is expressed. Using RNA in situ hybridisation it is possible to detect such detailed expression patterns (see example image below). After this course you should be able to design and run a RNA in situ hybridisation experiment and to understand the theories behind the technique.
Syllabus
Schedule
Evaluation summary
The overall objective is to learn enough about protein structure and function to be able to use protein structure information to formulate and to answer biochemical/biological questions. The course includes lectures, exercises, computer graphics/bioinfo-aided literature project on a chosen protein/group of proteins, and will run over ten week with one meeting per week.
Starting October 15, 2009. For registration and information contact Petra Fransson.
Flyer
Schedule
Syllabus
Summary course evaluation
Annual workshop at Älvkarleö
This year we will go to Älvkarleö herrgård north of Uppsala. Emphasis is on active student participation, and all students are expected to give some sort of presentation. You can choose between two possible formats – a short oral presentation or a presentation by a poster that you bring. You can either present your own research or give an overview of your subject area. As further outlined in the attached information, we will have three sessions with different themes, each opened by an invited speaker:
(1) Interactions - from molecules to ecosystems
Dan Funck Jenssen, Forest Mycology and Pathology: Interactions in biological disease control – from ecosystem to molecules and back again
(2) Signalling and regulation
Fredrik Söderbom, Molecular Biology: Small RNAs - ubiquitous regulators of gene expression
(3) Applied sides of research
Johan Schnürer, Microbiology: Quality research - the foundation for biotech applications.
There will also be outdoor networking activities as well as group discussions organized by Per Sandin around the topic: “Who wrote that paper and who did the research? Does it matter? The ethics of authorship credit”. A detailed program will be provided after the application deadline is due. Supervisors – you are also welcome to participate in this workshop. This is a great opportunity to learn what the PhD students within the graduate school are working with and to network with colleagues from other departments in a relaxed atmosphere. To register on first-serve basis, send an e-mail before May 10 to Petra or Mattias.
Handouts incl. programme
Abstracts keynote speakers
Summary evaluation
Illustrations are important in all scientific publications. In this course you will get a mainly practical introduction to the handling of computer graphics and digital images. Focus is on photographs and self-made illustrations, but enhancement of graphical output from statistical software will also be covered. After the course you should be able to edit digital images and create figures and illustrations for publications. Software will first be demonstrated in a mixed lecture-workshop format (March 18-19). You will need to bring your own computer with the appropriate software installed (Adobe PhotoshopTM and Adobe IllustratorTM recommended). You will then work on personal projects for an extended period at your home department. Finally, projects are presented and discussed in a final get-together (May 12). Registration contact Mattias Thelander.
Syllabus
Schedule
Summary evaluation
Forest ecosystems contain the main terrestrial carbon supplies, provide bioenergy, raw materials for a number of industrial applications and serve as a major arena for recreation. In times of globalization and climate change the host pathogen balance has been shifted and we experience new outbreaks of forest diseases. With the use of state-of-the-art technologies, new developments have taken place in the understanding of host-parasite interactions and evolution of forest pathogens.
The course consists of three parts. The first part consists of individual studies, where each PhD student prepares a presentation about one of the Top 10 forest diseases. The second part of the course, 9-14 December 2010, includes student project presentations and lectures by invited international teachers. Lectures cover detection, genomics, host responses, virulence factors, fungal-insect interactions and modeling. The third part (first week of May 2011) consist of two days of field excursions. The seminars given during part two of the course will be open for all interested students/researchers.
Registration deadline 15 November. Fore information and registration contact Petra Fransson.
Syllabus
Schedule
Summary course evaluation
Introduction to basic optical theory as well as practical application of the theory for both conventional light and fluorescence microscopy; general histological specimen preparation techniques; specific localisation techniques such as immunohistochemistry and in situ hibridization; photomicrography with analog and digital camers; digital image processing. The course is predominantly practical allowing students to analyse their own samples, preceeded by lectures.
The course will be given part time October - November at the Dept. of Mycology and Pathology, in collaboration with Uppsala University. Maximum 20 students. Registration deadline October 13, contact Cajsa Lithell.
Schedule
Syllabus
Summary course evaluation
Mass spectrometry is the method of choice for the analysis of biolmolecules within many fields, and this versatile method include for example molecule identification and quantification, proteomics, metabolomics, structure elucidation, doping cotrol and clinical analysis. This course will help you learn and understand the principles and techniques applied in state-of-the-art mass spectrometry and gain insights into what scientific problems can be solved. Methods applied in the analysis of proteins and peptides will be emphasized.
The course is divided in two parts; the first part (4 HEC) representing three weeks full time studies starting on August 16 of lectures, literature seminars, exercises and excursions concluded by a written exam; and a second optional part (2 HEC) is supervised project work finished with presentation and discussions.
Teaching is provided by Jan Eriksson, Lennart Kenne and Suresh Gohil, Dept. of Chemistry, and invited lecturers. Application deadline July 1, maximum participants 15.
Syllabus
Schedule
Summary course evaluation
The aim is to learn and understand the principles and theories applied in molecular evolution. The course covers fundamental concepts, evolutionary changes in nucleotide sequences, molecular phylogeneteics, exon shuffling, genome evolution etc, and is based on reading and discussing the book 'Fundamentals of molecular evolution' by Graur and Li. Exercises are included, covering applications and calculations of models. We meet ten times at the Dept. of Forest Mycology and Pathology, approximately every second week starting September 13, 10.00-12.00 in the lecture hall.
For registration contact Kajsa Himmelstrand, participation is limited to maximum 10. Teaching is provided by MIkael Brandström Durling.
Syllabus
Schedule
Summary course evaluation
Secondary metabolites are compounds that are not necessary for an organism to live, but play a major role in the interaction of the organism with its environment ensuring the survival of the organism in its ecosystem. The function of many secondary metabolites is yet to be determined, but the play important roles in e.g. plant defence and protection, and fungal and bacterial metabolites have antimicrobial properties. Many secondary metabolites have been developed into important pharmaceuticals during the last few decades, whereas others are used as flavors or fragrances.
This course will provide you with a basic understanding of secondary metabolites based on the structural elucidation, biosynthesis of key secondary metabolites and biological activity of representative compounds. At the completion of the course you would have acquired basic knowledge on the structures, occurrence, biosynthesis, properties and functional role of the major secondary metabolites. In addition to theoretical knowledge you would also gain hands-on experience on the use of analytical techniques such as HPLC and GC/MS to identify some secondary metabolites including interpretation of data.
The course is divided into two parts. The first part (3 HEC) starting on November 15 will deal with the different groups of secondary metabolites, including polyketides, terpenes, alkaloids, peptides, phenylpropanoids and carbonhydrates with respect to structure, occurrence, properties, biosynthesis and analytical methods. This part of the course essentially represents two weeks of full time studies and will be given in the form of lectures by specialists at the Uppsala BioCenter and by invited experts (Dr. Alison Hill, University of Exeter; Dr. Ute Wittstock, University of Braunschweig; Prof. Ulf Göransson, Uppsala University), as well as laboratory exercises, group discussions and study visits.
The second optional part of the course (4 HEC) will treat the biosynthesis of secondary metabolites from an organic chemical viewpoint, and will represent part time studies consisting of literature studies and group discussions. The number of participants is limited to 15 and the deadline to register is before November 1, 2010. For further information and registration, please contact organiser Sarosh Bejai or co-organiser Anders Broberg.
Syllabus
Schedule
Study visit
Invited researchers give presentations about their specific model organism, usually the third Tuesday every month. The seminars are followed by lunch (sandwiches) and further questions/discussions with the lecturer. Review articles describing the specific organisms will be sent out before the lectures. In addition, an article describing the lecturer’s own research will be provided (reading of the research article is optional).
Those of you who followed the ET-seminar series but did not attend enough seminars to get your points – if you attend six out of eight constitutive seminars including last spring’s ET seminars you can get your 2 HEC. For more information contact Fredrik Söderbom. Place: Room 2112 Genetics Center (unless stated otherwise). Time: 11.00-13.00.
January 12: Hanna Johannesson (Uppsala University) - Causes and consequenses of reproductive behaviour in Neurospora
Review article: Charlesworth et al. (2005) Nature Heredity
Research article: Menkis et al. (2008) PLOS Genetics
February 9: Jamie Morrison (Stockholm University) - Mending broken hearts - a salamander approach
Review article: Brockes and Kuumar (2002) Nat Rev Mol Cell Biol.
Research article: Morrison et al. (2006) J Cell Biol. and
Morrison et al. (2009) (On-line version)
Please note: Old library GC!
March 9: Johan Ledin (Uppsala University) - Zebra fish - cancelled
April 13: Maud Forsberg (Uppsala University) - Transgenic mice
Review article: Gene modification in mice (2007) The Nobel Assembly
May 5: Mattias Thelander (VBSG) - The moss Physcomitrella patens - a plant model organism for long distance comparative studies
Review article: Rensing et al. (2008) Science
Research article: Eklund et al. (2010) Development
Syllabus
In the autumn the seminar series will continue under a new theme - hot topics in science. For more information contact Magnus Karlsson. Place: Old library, Genetics Center. Time: 11.00-13.00.
September 14: Stefan Knight (Molecular Biology, SLU) - Structure and function of adhesive pili of gram-negative bacteria.
October 12: Örjan Carlborg (Animal Breeding and Genetics, SLU) - Genome wide effects of long-term selection.
November 9: Lena Mäler (Dept. Biochemistry and Biophysics, Stockholm University) - Structure of membrane proteins by nuclear magnetic resonans.
December 14: Elisabeth Fredlund (National Food Administration) - Real-time PCR detection of Fusarium in grain and correlation to toxin production.
January 11: Roger Finlay (Forest Mycology and Pathology, SLU) - Title TBA
February 8: Jarl Vikberg (Dept. of Pharmaceutical Biosciences, Uppsala University) - Proteochemometry
March 8: Sofia Berlin Kolm (Plant Biology and Forest Genetics, SLU) - Linkage mapping and QTL analysis in Salix
April 4: To be announced
May 10: To be announced
Syllabus
Phylogenetic analysis is an important tool in modern biology. It is widely applied in several different areas of research including comparative genomics and epidemiology. A basic understanding of phylogenetics is also necessary to be able to interpret phylogenetic trees and asses their quality when analysing already published data. The aim of the course is to provide students with a basic understanding of phylogenetic analysis as well as an ability to perform phylogenetic analyses on molecular sequences. After completed course the student will be familiar with different software for performing alignments of molecular sequences, know the basics of several different methods (distance methods, parsimony, maximum likelihood and Bayesian inference) and be familiar with different software for performing phylogenetic analyses.
The course is divided into two parts. The first 3 HEC part starting at January 18 consists of lectures and computer exercises describing methodology and invited speakers highlighting applications. The first part is concluded by literature studies and a written examination on February 13. During the second optional 3 HEC part, students will work on individual projects with their own data sets with supervision and weekly follow-ups. Projects are presented and discussed in a concluding get-together on March 3.
There is no tuition fee but participants must bring a copy of the course book and their own (or borrowed) computer (Mac or PC). Appropriate software will be arranged for by the organizers. For more detailed information, see links to the course syllabus and a preliminary schedule below. The number of participants is limited to 20 and registration is on first-serve basis. Deadline for applications is December 18, 2009. For further information and registration, contact Joel Sohlberg.
Syllabus
Schedule
Summary evaluation
Time for the race - team building 2010. Photo: Seth Schwartz.
For the autum the pizza networking seminars continues in its old costume but with new content, with invited former PhD students now worksing outside academia. We meet late in the afternoon to listen to a presentation and then discuss over dinner pizza. Build on your professional network by meetig possible future employers from industry and governmental agencies.
October 21: Kristof Capieau, Swedish board of agriculture (Jordbruksverket)
November 16: Henrik Johannesson, Atlas Antibodies AB, Stockholm
December 6: Mattias Öyen, Nordic BioSite, Stockholm, product specialist
January 18
February 16
March 17
April 21
May 17
Presentations take place in the VBSG lunch room from 16.30-17.30 and then we finish with discussions over food and drinks. For further information contact Petra or Mattias.
Are you planning on doing a post doc? Do you need more information?
On May 10 you are welcome to participate in a half-day workshop where you meet representatives from FORMAS, SULF and four post docs. Come and learn about what is required to apply for funds or positions, why they should do a post doc and what to think about.
The workshop is a joint arrangement by the SLU graduate schools Bioenergy, Ecology and Organism Biology. Share the experience with former or ongoing post docs. Coffee and lunch included. Priority is given to third and fourth year PhD students. Maximum 30 participants. Register by e-mail before May 3.
Summary evaluation
Post doc grants
Introduction
Flyer
Annual Organism Biology workshop 14-15 June 2011
This year we will go to Sätra brunn located about 80 km west of Uppsala. As usual, the program represents a mix of science and network promoting activities. Two broad and hot research areas will be highlighted, PhD students will get a chance to present findings and ideas and the future of the research school will be discussed.
The program is composed of four different sessions:
(1) Epigenetics
Professor Claudia Köhler (VBSG, SLU) and Professor Karl Ekwall (Medical Genetics and Epigenetics, KI) will introduce the topic and give examples from their research before the session is ended with short PhD student presentations.
(2) PhD student presentations
Seven PhD students get a chance to present their research as short oral communications (10+5 minutes). Grab the opportunity - the topic is open and the stage is yours!
(3) Genomics and transcriptomics
Professors Hans Ronne (Microbiology, SLU), Stefan Jansson (Umeå Plant Science Center) and Jan Stenlid (Mykopat, SLU) will together with a few PhD students provide a broad picture of what modern sequencing technologies can be used for.
(4) Future of the research school, group discussions
The four year funding period for faculty-funded research schools is coming to an end. What have we learned and what should be changed for the coming four years?
There will also be a visit to Sala silver mine where we take a guided tour 155 meters below ground. Supervisors – you are also very welcome to participate in this workshop. This is a great opportunity to learn what the PhD students within the graduate school are working with and to network with colleagues from other departments in a relaxed atmosphere. The number of participants is limited to 35 PhD students and 20 supervisors. To register on first-serve basis, send an e-mail before May 10 to Petra or Mattias.
Programme
Handouts
Evaluation
Summary group discussions about our future
Digital images and scientific illustrations (2 HEC)
Illustrations are important in all scientific publications. In this course you will get a mainly practical introduction to the handling of computer graphics and digital images. Focus is on photographs and self-made illustrations, but enhancement of graphical output from statistical software will also be covered.
After the course you should be able to edit digital images and create figures and illustrations for publications. Software will first be demonstrated in a mixed lecture-workshop format (March 30-31). You will need to bring your own computer with the appropriate software installed (Adobe Photoshop and Adobe Illustrator recommended). You will then work on personal projects for an extended period at your home department, preferably figures for a publication or poster. Finally, projects are presented and discussed in a final get-together (May 3).
For registration on a first to serve basis (student number is limited to 12), send an e-mail before March 11 to Mattias.
Schedule
Syllabus
Summary course evaluation 2011
Summary course evaluation 2010
Summary course evaluation 2009
Are you planning on doing a post doc? Do you need more information? On March 3 you are welcome to participate in a half-day workshop where you meet representatives from FORMAS, SULF and four post docs. Come and learn about what is required to apply for funds or positions, why you should do a post doc and what to think about.
The workshop is a joint arrangement by the SLU graduate schools Bioenergy, Ecology and Organism Biology. Share the experience with former or ongoing post docs. Coffee and lunch included. Priority is given to third and fourth year PhD students. Maximum 30 participants. For registration send an e-mail before February 24 to Helena Bylund.
Summary evaluation
Scientific writing is an acquired skill that can be learned. This course provides instructions on how to structure and format each section of a scientific manuscript according to the IMRAD format, based on the book 'How to write and publish a scientific paper' by Robert A. Day and Barbara Gastel (2006). Focus is placed on basic writing skills, particularly on how to write clear and concise sentences, paragraphs and sections.
The students work on their own manuscripts throughout the course, integrating theory and practice. Constructive feedback and analysis of these texts will be given during group meetings before moving on to the next section. In addition to the direct practical training in writing, this setup will also provide the students with a set of tools for the essential text analysis and editing needed to produce a submission ready manuscript.
The course has been filled and run at the Dept. of Forest Mycology and Pathology during winter/spring 2010/2011.
Summary evaluation
Lecture and walk at Skagen
The course is organized as a workshop where lectures and discussion sessions illustrate problems and possibilities in studying secreted proteins in a theoretical fungal-host interaction system. Expertise from each organizing partner will provide lectures in fungal interaction biology, genomics, transcriptomics and the related bioinformatics. Benefits and limitations of available methods such as bioassays, next generation sequencing, bioinformatics and gene knock outs and qPCR will be discussed. The interaction system in focus are1) fungal - fungal, 2) fungal - plant or 3) fungal – insect or fungal - nematode interactions.
The course is organized in collaboration between participating partners from SLU, Lund University, Copenhagen University (KU-Life), Aalborg University and Novozymes A/S, within the framework of the research program “Secreted proteins in fungal parasitic interactions for feed, food and non-food industry”. The number of participants is limited to 10 PhD-students.
Enroll before 25 August 2011, by sending a short application by e-mail to Magnus Karlsson. The application should include the following: Name and address, title of your PhD-project and a short 5-10 line abstract describing your PhD-project.
Syllabus
Preliminary schedule
Summary evaluation
Our seminar series continues during spring, for more information contact Magnus Karlsson. Place: Dept. of Forest Mycology and Pathology. Time: 11.00-13.00.
December 14: Elisabeth Fredlund (National Food Administration) - Real-time PCR detection of Fusarium in grain and correlation to toxin production.
January 11: Roger Finlay (Forest Mycology and Pathology, SLU) - Title TBA
February 8: Jarl Vikberg (Dept. of Pharmaceutical Biosciences, Uppsala University) - Proteochemometry
March 8: Sofia Berlin Kolm (Plant Biology and Forest Genetics, SLU) - Linkage mapping and QTL analysis in Salix
April 4: Anna Palmé, Dept. of Ecology and Genetics, Uppsala University. Title: To be announced
May 10: Petter Melin (Dept. of Microbiology, SLU) - Synthesis and importance of trehalose in filamentous fungi.
Syllabus
Summary evaluation
For spring the pizza networking seminars continues with invited speakers from outside academia. We meet late in the afternoon to listen to a presentation and then discuss over dinner pizza. Build on your professional network by meetig possible future employers from industry and governmental agencies.
February 24: Niklas Nordquist, NL-faculty office, SLU Uppsala
May 12: Johan Allmér, Ekologigruppen, Stockholm
October 26: Natalie von der Lehr, freelancing science journalist
Presentations take place at Uppsala BioCenter from 16.30-17.30 and finish with discussions over food and drinks. For further information contact Petra or Mattias
Interactions involving plant roots and microbes may be beneficial (e.g. symbiotic associations) or pathogenic in their nature. This course focuses on beneficial root-soil-microbe interactions in the rhizoshpere and covers both agricultural and forest ecosystems. The overall aim is to give the students a comprehensive overview of beneficial interactions taking place in the root-soil-microbe interface, as well as provide information on state-of-the-art applications within the subject area.
The course consists of one intense week of full time studies preceded by individual literature studies of selected scientific papers. The scheduled course week includes lectures by invited national and international teachers, literature discussions and PhD student poster presentations.
Scheduled activity periods: 24-28 January 2011, preceded by individual literature studies.
Invited teachers: Phillippe Lemanceau (UMR INRA-Burgundy University), Barbara Drigo (University of Western Sydney,) Katharina Pawlowski (Stockholm University), Håkan Wallander (Lund University), Margareta Hökberg (MASElab) and a number of SLU researchers will participate.
Application deadline: 11 January 2011. Information and application: Petra Fransson.
Schedule
Syllabus
Flyer
Poster abstracts
Summary course evaluation
Plants and microbes interact in many different ways. In the postgraduate course “Plant-microbe interactions”, interactions between plants and microbes are discussed on general and detailed level for both pathogenic and symbiotic interactions. Infection mechanisms, establishment of symbiotic relations, plant defence and stress responses as well as many important problems within agriculture, horticulture and forestry are brought up.
The course is given within the SLU Graduate School in Organism Biology in collaboration with Helsinki University and Norwegian University of Life Sciences. The lectures are given by the three universities and shown through videoconference equipment to the distant sites. The postgraduate course is arranged as a part of the MSc course “Plant-microbe interactions” and contains 20 lectures, literature studies using recent review articles, discussion of study questions and a final written exam.
The course runs from 18 Jan to 25 Mar, 2011. To apply, or for further information, send an e-mail to Anders Kvarnheden latest January 11.
Syllabus
Preliminary schedule