Course27820

From teaching

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

General information

The course will start August 11th 2011 at 9.00 am in room 056 (ground floor) at DTU, Building 301. For directions, please follow this link.

Click here for the General time table in short, version 1.10 Subject to changes. (PRINTED)

Laboratory rules for work in the P2 Lab Download and READ (PRINTED)

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... :-)

Messages

Thank you to all the students of 27820 PhD course 2012. It was a great pleasure having you here!

Class of 2012

ERRATA

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.

Participant List

Download the 2012 participant List.

Course manuals

Manuals for the excersises

Manuals

Biofilm System 1: E.coli development: Download (PRINTED)
Biofilm System 2: P. aeruginosa: FISH and Cell counting: Download (PRINTED)
Biofilm System 3: P. aeruginosa: Differentiation and colistin tolerance: Download (PRINTED)
Biofilm System 4: Monitoring gene expression in microbial biofilms: Download (PRINTED)
Biofilm System 5: Free exercise: Download (PRINTED)
Microbial Diagnostics: Chip technlology and antibiotics screening (Exercise 6): Download (PRINTED)
Presentation of results (Exercise 7): How to present on the last day: Download

Supplementary manuals and recipes

General

Biofilm Media Download
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

Diagnostic Excersise

Short manual for analysis of AT Chip data Download
Excel spreadsheet for AT Chip data Download
Data Analysis Example Download
Reading E-Test (Guide) Download

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

Scientific Papers

Note: These papers are also included in the zipped package which you can download below.

Supplementary Papers

(The papers are in a zip file on our secure server. Password protected)

Supplementary papers (general) Download here
Supplementary papers (Diagnostic exercise) Download here
Motility paper by George O'Toole et al 1998 Download here

Result Data Files

Your own presentations!

Biofilm System 1: Presentation from Team 4
Biofilm System 2: Presentation from Team 5
Biofilm System 3: Presentation from Team 3
Biofilm System 4: Presentation from Team 2
Diagnostic Exercise: Presentation from Team 1

Data files

Mixed files from the confocals

Here are mixed files from Wednesday and Thursday. The label of the files and directoryies do not nessesarily reflect what data is there...
E.g. the file "free ex.lif" contains both some images of the free ex and the FISH images.

Mixed files

Biofilm System 1

Biofilm System 2

Files for FISH

Biofilm System 3

Biofilm System 4

LSM files for BF4

Biofilm System 5

Diagnostic Exercise

Chip Images: Download

List of Speakers and Notes

Powerpoint notes will be placed here as they become available

Speakers and teachers

Janus Haagensen

Tools and Biofilms

Claus Sternberg

Rasmus Marvig

Rasmus Bojsen
Henrik Fallesen
Anders Folkesson

Biofilm Formation and antibiotics. Also includes intro to BF system 4

Søren Molin

No slides

Claus Moser
Klaus Kirketerp-Møller
Michael Kühl
Niels Høiby

Cystic Fibrosis, Biofilms and the clinic

Morten Alhede

Biofilms and Quorum Sensing

Additional teachers

Susanne Koefoed

Download Software

Comstat 2

First - go to http://www.comstat.dk/helperfiles and get all nessesary support files. Please read the instructions in the HOW-TO-INSTALL document.

When all that has been done, get the comstat2 program file (Comstat2_.jar): here.

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.

Imaris 7.5

Download the program file appropriate for your system:

Imaris 7.5.1 Microsoft Windows XP/Vista/7 32 bit
Imaris 7.5.1 Microsoft Windows XP/Vista/7 64 bit
Imaris 7.5.1 Apple MaxOSX
Demo license for the full Imaris Package - note: Right-click on the link and select "Save as..."

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. The demo license is valid until the end of September 2011. If you need testing after that, please contact Bitplane.
See also: Installation Instructions on bitplane.com

QuickStart Tutorial 7.3 Download
Imaris Reference Manual 7.3 Download

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.

Java Runtime Environment JRE 6

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.

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

Analysis of AT chip Images

A plugin for ImageJ have been developed to analyse the images from the AT Reader. The plugin evaluate the pattern and produce the corresponding "bar code". The plugin can be downloaded by clicking here (AT Chip Analyzer Plugin, and a manual is provided by clicking here (plugin manual).

In short: First install ImageJ (http://rsbweb.nih.gov/ij/). Then place the plugin in the plugin folder of ImageJ. And you are then able to run the plugin from ImageJ's plugin menu.

Video files

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).

Web links

27820 Wiki page from 2011