This is the homepage for 27820 - Ph.D course in Medical Biofilm Techniques.
Note: This page will be continuously updated and you should not expect all manuals to be here before a few days before the course starts.
Here you can find the general description of the course: DTU Course base
The course will start August 10th 2014 at 9.00 am in room 056 (ground floor) at DTU, Building 301. For directions, please follow this link.
DIY Sandwich lunch will be provided Sunday Aug 10th, Saturday Aug 16th and Pizza Lunch on Sunday 17th.
- There will be wireless network available. The network is connected to the European EDUROAM collaboartion in which most Western European universities participate. Check with your home university IT department if you can use EDUROAM and get instructions there. Otherwise we will issue a guest login (but EDUROAM is much easier).
- Please note
- Some files require a password to download. This should have been provided to you along with the link to this page. If for some reason you have not received the password, please e-mail Claus Sternberg.
- Manuals and other materials marked with "(PRINTED)" will be given in hard copy at course start
FACEBOOK: We have a Facebook group for present and past participants and instructors/speakers which you can join if you like. Go here: http://www.facebook.com/groups/120786086637/ and apply for membership. Note: The group is not terribly active, but who knows, perhaps someone will make it more interesting some time... :-)
Here we will keep you updated on changes of schedule, and other things you need to know (e.g. where to find result data files)
- 04.08.2014. Eduroam and iPass
- You may want to check out iPass as well as Eduroam. Link to relevant information
- 04.08.2014. Regarding the student presentations
- We will try to do them in the periods of waiting. There will be several occasions where more teams are waiting, e.g. to get to the microscopes. In these periods we suggest the teams not active at the instruments can do their presentations for the other waiting teams. This of course means that you will not hear all presentations, but still most of them.
- 04.08.2012. Bring your own samples
- For the free exercise you can bring your own samples from home. It can be some bacterial strains you work with in your projects, or e.g. a soil sample from home, or a swap from your bath room sink. The oly requirement is that if you bring bacterial samples that they are non-pathogenic.
- 11.08.2014. A new version of the time schedule has been uploaded
- The Timing of the FISH ex (BF system 2) has been changed.
- 12.08.2014. Talks
- The final schedule for speakers has been uploaded.
- 14.08.2014. Comstat
- New version of COMSTAT uploaded.
- 19.08.2014. Presentations
- All group presentations from Sunday now uploaded.
Here we will put changes and errors we detect in the documentation. This document will be updated as the course is progressing (latest update date is shown.
Download the 2014 participant List.
Manuals for the excersises
All manuals will be uploaded shortly. All manuals marked "PRINTED" will be provided to you in print when you arrive. It is generally not nessesary to print the supplementary manuals and documents, but if you want it you can print them before you arrive.
- Biofilm System 1
- Development and architecture of E. coli biofilms: Download (PRINTED)
- Biofilm System 2
- P. aeruginosa: FISH and Cell counting: Download (PRINTED)
- Biofilm System 3
- Differentiation and colistin tolerance in Pseudomonas aeruginosa biofilms: Download (PRINTED)
- Biofilm System 4
- Diversification of Pseudomonas sp. VLB120 when exposed to isobutanol during biofilm growth: Download (PRINTED)
- Biofilm System 5
- Free exercise: Download (PRINTED)
- Exercise 6
- Characterization of clinical isolates from cystic fibrosis: Download (PRINTED)
- Presentation of results (Exercise 7)
- How to present on the last day: Download (Updated 7.Aug 2014) (PRINTED)
Supplementary manuals and recipes
- Biofilm Media Download (Updated)
- Biofilm general manual Download
- FISH Manual Download
- Embedding and FISH on flow chamber biofilms Download
- Adhesion Microtiter Tray Assay (Crystal Violet) Download
- Quorum Sensing assays (from course 27254) Download
- LIVE/DEAD kit manual Download
- Motility assay Download
- Cheat sheet for making Motility assay plates (Excel sheet) Download
- Reading E-Test (Guide) Download
- ROSCO Tablet manuals
- Manuals for the BIOLOG machine
- OmniLog ID User Guide Download (See pages 42-44)
- OmniLog PM User Guide Download
- GEN III Database List and Characteristics Download
- MicroStation System Version 4.2 User Guide Download
Papers of relevance
Note: These papers are also included in the zipped package which you can download below.
- Heydorn, A., Nielsen, A.T., Hentzer, M., Sternberg, C., Givskov, M., Ersbøll, B.K., Molin, S. (2000): Quantification of biofilm structures by the novel computer program COMSTAT. Microbiol. 146(10): 2395-407 (The original Comstat1 paper)
- Heydorn, A., Ersbøll, B.K., Hentzer, M., Parsek, M.R., Givskov, M., and Molin, S. (2000): Experimental Reproducibility in Flow-Chamber Biofilms. Microbiol. 146(10): 2409-15 (The first paper using Comstat)
- Tolker-Nielsen, T., and Sternberg, C.(2011): Growing and Analyzing Biofilms in Flow Chambers. Curr. Prot. Microbiol. Unit 1B.2 (PRINTED)
(The papers are in a zip file on our secure server. Password protected)
- Supplementary papers (general) Download here
- Motility paper by George O'Toole et al 1998 Download here
- Autolysis paper by D'Argenio et al 2007 Download (Updated)
Result Data Files
Your own presentations!
Biofilm System 1
Biofilm System 2
- Raw files from FACS - can be viewed in e.g. flowing software (freeware). The .jpg file gives an overview of the results from all teams
Biofilm System 3
Biofilm System 4
Biofilm System 5
Exercise 6 - Diagnostics
The strains are:
UN1: E. coli
UN2: P. aeruginosa PAO1
UN3: S. epidermidis RP62A
UN4: S. typhimurium
UN5: S. epidermidis 1457
- BIOLOG results
- Sequences for all 5 UN strains
- Link to NCBI BLAST engine
- Protocol for making PCR products of 16S rDNA for sequencing Download
(Note: this is partly from an old course manual, which may show)
List of Speakers and Notes
Powerpoint notes will be placed here as they become available
Speakers and teachers
- Claus Sternberg
- Janus Haagensen
- Anne-Mette Christensen
- Eva Kammer Andresen
- Søren Molin
- Anders Folkesson
- Claus Moser
- Tim Tolker-Nielsen
- Klaus Kirketerp-Møller
- Thomas Bjarnsholt
- Susanne Koefoed
When all that has been done, get the comstat2 program file (Comstat2_.jar): here .
New version of comstat - install_these_in_plugins_folder.zip Download here (to be installed on top of old files)
Note: When you download the comstat2 program file we imply that you accept the license conditions which are set out on www.comstat.dk, namely:
- That you will not distribute the program to others, but refer them to www.comstat.dk where they can obtain a copy for free
- That you will acknowledge the use of Comstat2 in any publication that will be written using Comstat2 generated data in any form.
- Download the program file appropriate for your system
- Imaris 7.7.2 Microsoft Windows XP/Vista/7 32 bit
- Imaris 7.7.2 Microsoft Windows XP/Vista/7 64 bit
- Imaris 7.7.2 Apple MaxOSX
- Demo license for the full Imaris Package - note: Right-click on the link and select "Save as..."
- License file in Zip file, in case you have problems downloading the lic file
- Install the program file. Save the license file somewhere on your computer and when you start Imaris, use the browse button in the license dialog box shown to point to the demo license file.
(Note: the first steps are mac-specific but the rest is common to PC and Mac).
In order to enable Imaris to communicate with MATLAB, ImageJ and Java, you need to download and install these two helper programs:
Note: In this course it is unlikely that you will need the MATLAB/Java functionality of Imaris. But in case you want to check it out we include the links.
and the MATLAB Compiler Runtime (MCR). Please download the MCR version appropriate for your system:
You may also want to download SceneViewer which allows you to show Imaris stacks without a full license. You will, however, need to obtain a permanent license directly from Bitplane, Inc. The program will show how to get that when the demo license has expired.
- SceneViewer 7.7.2 Microsoft Windows 32 bit
- SceneViewer 7.7.2 Microsoft Windows 64 bit
- SceneViewer 7.7.2 Apple MacOSX
Brochures for Imaris:
Zeiss ZEN File Viewer
You can download the viewer program for native Zeiss confocal image stacks here
Leica LAF Viewer
You can download the viewer program for native Leica confocal image stacks here
The flow cell assembly and flow system setup has been documented in JoVE (Journal of Visualized Experiments).
We have made this paper freely accessible without subscription:
- Weiss Nielsen, M., Sternberg, C., Molin, S., Regenberg, B. (2011), Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells. http://www.jove.com/details.php?id=2383 doi: 10.3791/2383. J Vis Exp. 47 (2011).