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DTU course #27101 Framework Course in Biotechnology and Food Sciences
- or - Communicating Science: Using Comparative Genomics as an example

Course Programme - Autumn 2008
Link to description of course in DTU course catalogue

The course meets on Thursday and Friday afternoons, from kl. 13.00 until kl. 17.00, and will start on Thursday, 4 September, 2008 at 13:00. Lectures, journal clubs and exercises will take place in buildings 208 and 210, at the Technical University of Denmark, Lyngby. We will meet in the "group room" 008 in building 210 on Thursdays, and in room 062, downstairs in building 208 on Friday afternoons.

Performance will be evaluated by an oral podcast of at least 5 minutes (10%), a poster (15%), a journal club report (25%), and a final written manuscript (50%). The aims and learning objectives for this course are as described at the bottom of this page and also in the DTU course catalog.

Link to DNA Atlas pages List of Prokaryotic Genomes at NCBI version 3.0 of the DNA Atlas pages (still under construction).

Posters due on 7 November, 2008
overview

Thursday, 4 September, 2008

Introductory talks - Please note that on Thursdays the class meets in building 210, room 008.

13.00-13.45: Introduction to the course - some 'housekeeping details'
An overview of the course, working groups, computer exercises, what is expected from this course.
14.00-14.45: Comparative Microbial Genomics: A Brief Overview
Link to pdf file of lecture notes
15.00-16.00: Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics
Link to pdf file of lecture notes

Quiz du jour

Literature: Chapter 1 in the textbook, and 10 Years of Bacterial Genomics

Friday, 5 September, 2008

http://www.cbs.dtu.dk/cbs/dcsc/dcsc_cbs.gif
Introduction to Bioinformatics methods for Comparison of Bacterial Genomes - Please note that on Fridays the class meets in building 208, room 62 (downstairs).

13.00-13.45: Bioinformatics for Microbiologists: An Introduction
Link to pdf file of lecture notes
14.00-14.45: Introduction to podcasts
15.00-17.00: Open discussion on which genomes to compare, how to do this, and how to make a podcast

Link to NCBI BLAST page for Microbial Genomes

Literature: Chapter 2 in the textbook (see internal web pages for chapter)

Thursday, 11 September, 2008

Basics of Computational Genomics
Dave Ussery

13.00-13.45: Microbial Genome Sequences: A New Era in Microbiology
Link to pdf file of lecture notes
13.45-14.00: Break - We will pick up the portable computers for use in the exercises in the office in building 208.
14.00-17.00: Exercise 1: Fetching genomes and predicting protein coding genes.

Literature: Chapter 3 of textbook. 10 Years of Bacterial Genomics

Friday, 12 September, 2008

Basics of Computational Genomics, part 2.


13.00-13.45: An Overview of Genome Databases
Link to pdf file of lecture notes
Three good web sites to visit: Genomes On-Line Database (GOLD) NCBI Genomes page CBS Atlas Pages (v3.0)
13.45-14.00: Break
14.00-14.45: Journal Club - an example for the class
14.45-15.00: Break
15.00-17.00: Sign up sheet for Journal Club presentations, discussion about what is expected, and grading.

Literature: Chapter 4 in the textbook A web-table of "Genome-Database" links.

Thursday, 18 September, 2008

Methods to Compare Genomes

13.00-13.45: Lecture 1 - "Methods to Compare Genomes - with emphasis on AT content"
Link to pdf file of lecture notes
14.00-14.45: Discussion about projects and Journal Club dates
14.45-15.00: Break
15.00-17.00: IMPORTANT: PLEASE SIGN UP YOUR NAMES BEFORE YOUR START; Exercise 2: rRNA and tRNA predictions

Literature: Chapters 5-8 of textbook. DNA Structure: A-, B-, and Z-DNA Families Origins of Replication in Circular Bacterial Chromosomes CBS Genome Atlas database

Friday, 19 September, 2008

Methods to Compare Genomes, part 2

13.00-13.45: Lecture 1 - "Introduction to DNA Atlases"
Link to pdf file of lecture notes
14.00-14.45: Lecture 2 - "non-coding RNA genes"
Link to pdf file of lecture notes
14.45-15.00: Break
15.00-17.00: Work on Projects

Literature: Chapters 7, 8, and 9 in the textbook Link to Hfq paper discussed in class (PLoS Genetics, August, 2008)

Thursday, 25 September, 2008

Food / Nutritional Microbiology - Please note that for the next three Thursdays the class will meet in building 208, room 062.

13.00-13.45: Guest lectures by Associate Professor Alexandr Parlesak
Lecture 1 - "Control of intestinal microbiota by the host, part 1"
Link to pdf file of lecture notes Part 1b
13.45-14.00: Break
14.00-14.45: Lecture 2 - "Control of intestinal microbiota by the host, part 2"
Link to pdf file of lecture notes
14.45-15.00: Break
15.00-17.00: Computer Exercises; Exercise 3: Codon usage, promoters, BLAST atlases

Friday, 26 September, 2008

Food / Nutritional Microbiology.

13.00-13.45: Guest lectures by Associate Professor Alexandr Parlesak Lecture 1 - "Probiotics in human health, part 1"
Link to pdf file of lecture notes
13.45-14.00: Break
14.00-14.45: Lecture 2 - "Probiotics in human health, part 2"
Link to pdf file of lecture notes Part 5
14.45-15.00: Break
15.00-17.00: work on projects

Thursday, 2 October, 2008

First Day of Journal Clubs - Please note that on today the class will meet in building 208, room 062.

13.00-13.30: Mycoplasma group
13.30-14.00: Korarchaeum group
14.00-14.30: Wolbachia group
14.30-14.45: Break
14.45-17.00: Computer Exercises; Exercise 4: Two dimensional clustering, 16S phylogenetic trees, BLAST matrix - Journal Club / poster work

Literature: Chapter 9 of textbook. "CAMERA: A Community Resource for Metagenomics"

Friday, 3 October, 2008

Second Day of Journal Clubs.


13.00-13.30: Cellvibrio group
13.30-14.00: Exiquobacterium group
14.00-14.15: Break
14.15-16.00: Lecture: Expression of Genes and Proteins
Link to pdf file of lecture notes

Literature: Chapter 10 in the textbook

Thursday, 9 October, 2008

Transcription and Translation of Genomes, part 3 - - Please note that on today the class will meet in building 208, room 062.

13.00-13.30: S. auerus group "A" - Phillip and Stine
13.30-14.00: Salmonella group
14.00-14.15: Break
14.15-15.00: Lecture - "On Proteins, Genomes, and Proteomes"
Link to pdf file of lecture notes
15.00-17.00: Computer Exercises

Literature: Chapter 11 of textbook. (see internal web pages for chapter) Sigma Factors Two-component signal transduction systems

Friday, 10 October, 2008

Computational Models of Microbial Communities, part 1.


13.00-13.30: Bifidobacterium group
13.30-14.00: Methylacidiphilum group
14.00-14.30: S. arueus group "B" - Mette og Maria
14.30-14.45: Break
14.45-16.00: Microbial Communities: Core and Pan-genomics

Literature: Chapter 12 in the textbook

Thursday and Friday, 16-17 October, 2008

Autumn Break

Thursday, 23 October, 2008

Computational Models of Microbial Communities, part 2

13.00-13.45: Lecture 1 - "Metagenomics of Microbial Communities"
13.45-14.00: Break
15.00-16.30: Computer Exercises

Literature: Chapter 13 of textbook. rRNA comparisons

Friday, 24 October, 2008

Computational Models of Microbial Communities, part 3.

: Evolution of Microbial Communities - or - On the Origins of Bacterial Species

Literature: Chapter 14 in the textbook

Thursday, 30 October, 2008

Proteome Comparison

13.00-13.30: Stenotrophomonas
13.30-14.00: Staphylococcus, 2nd group
14.00-15.00: Discussion about grades in the course - posters, journal clubs, papers, and podcasts...

Literature: Chapter 12 of textbook. (see internal web pages for chapter)

Friday, 31 October, 2008

Group Projects.


13.00-13.30: Mycobacterium group
13.30-14.00: Pseudomonas group "A"
14.00-14.30: Pseudomonas group "B"
14.30-15.00: Kocuria rhizophila group
15.00-17.00: Group work on projects

Literature: Dave's podcast Text Preprint of Original article in J.Bact.

Thursday, 6 November, 2008

Metagenomics

13.00-13.45: Guest lecture by Professor Francisco Rodriguez-Valera,Division de Microbiologia and Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain
Metagenomics: a short cut to the biology of microbes
13.45-14.00: Break
14.00-14.30: Discussion groups - work on projects
14.30-14.45: Break
14.45-16.30: Computer Exercises

Literature: Chapter 9 of textbook. (see internal web pages for chapter) "Fuzzy species among recombinogenic bacteria" Link to Francisco Rodriguez-Valera's web page

Friday, 7 November, 2008

Group Projects.

: Talk about posters - how to do a poster.

Literature: textbook "Ten Simple Rules for Good Poster Presentation"

Thursday, 13 November, 2008

E. coli Pathogenesis

13.00-13.45: Guest lecture by Viktoria Hancock,Center for Biological Sequence Analysis, Dept. Systems Biology, DTU
13.45-14.00: Break
14.00-14.30: Discussion group - work on projects
14.30-14.45: Break
14.45-16.30: Computer Exercises

Literature: Chapter 10 of textbook. 2-D clustering

Friday, 14 November, 2008

More about E. coli.

13.00-13.45: Guest lecture by Professor Barry Wanner, Dept. Biological Sciences, Purdue University, West Lafayette, Indiana, USA
Part 1 - Development of the www.EcoliHub.org Information Resource and New Ways to Study the E. coli Model Cell
13.45-14.00: Break
14.00-14.45: Part 2 - E. coli Wet lab experiments

Literature: textbook

Thursday, 20 November, 2008

no class

Friday, 21 November, 2008

no class.

Friday, 28 November, 2008

POSTERS due!!!!

kl. 13.00 - kl. 17.00 - Poster party.

Thursday, 4 December, 2008

Papers due kl. 12.00 - the final papers will then be copied and distributed in class, and we will together referee them and hand them back to the groups for final grade, and revision if necessary.

The, final, revised papers and podcasts must be finished and handed in no later than 12:00 noon on 11 December

But of course, groups are encouraged to hand them in anytime before then - in principle, a well-written paper can even be submitted for final grading on the evening of 4 December, provided that it is so good that neither the other student referees nor the course teacher finds any mistakes!

AIMS

The aim of this course is twofold; first it is to give the students a solid knowledge of methods for communication of scientific discoveries, and the second aim is to teach about methods for the comparison of genomes from microorganisms of interest such as those used for bioenergy or biofuels, food biotechnology such as lactic acid bacteria, industrially important filamentus fungi and yeast, as well as organisms with relevance for medical microbiology, biofilms and infection such as Pseudomonas, and other microbial organisms. The idea is to apply this newly gained knowledge of comparative genomics to a specific set of genomes of interest, using various type of communication skills learned in the course. Students that have followed this course should be able to understand and clearly communicate the results of the investigation of their microorganisms of interest to others using four different formats: a short podcast (at least 5 minutes), a journal club report critiquing a recently published paper, a poster, and finally by writing a scientific paper which is formatted and suitable for publication.

The project includes management, organization structure, and strategies for communication of scientific findings. This will be supported by lectures on scientific publications, poster design and presentation, and manuscript writing.

Different disciplines dealing with comparison of microbial genomes will be brought together to produce a manuscript. Specifically the lectures will deal with: introduction to genomics; computational analyses of sequenced microbial genomes; what defines a microbial species; how to choose a set of genomes to compare; and microbial communities and their interactions.

Students that fully have followed the course are able to:

Read, understand and critique a paper published in the scientific literature.
Give a brief description of a new discovery in the field.
Design and produce a poster suitable for showing at a scientific meeting.
Contribute a section to a written scientific paper.
Plan the management and organization of a paper that could be published in a scientific journal.
Obtain up-to-date lists of the most recently sequenced microbial genomes.
Compare two or three genomes to each other.
Compare hundreds of genomes and easily find trends and genomes which are significantly different.
Quickly obtain the core- and pan-genome sets of genes for a given bacterial species or taxonomic group.
Compare metagenomic results to hundreds of projects already available.

Learning objectives

A student who has met the objectives of the course will be able to:

Describe the general methods for comparison of microbial genomes.
Compare a new genome sequence to other genomes already published.
Make a short podcast and use it to communicate to scientific peers the results of a comparison of microbial genomes.
Critique a scientific paper.
Explain basic interactions between microbial organisms within an ecosystem.
Use genomic databases and resources quickly and effeciently to compare genomes.
Make a scientific poster and use it to communicate new findings to scientific peers.
Explain the basic format and important items to include in writing a scientific paper.
Plan a scientific paper.
Write part of a scientific paper.

Student evaluation reports

Over the course of the semester, this course will develop communication skills in several different areas. The students will be divided into small groups to work on various projects. At any time during the semester, students should feel free to ask the course leader (Dave Ussery) if they would like to be assigned to a different group. It is possible that if all in the group are happy with the same members, the same group can work together for most of the projects.

Podcast (10% of grade)		Podcasts will be done by groups throughout the semester. The purpose of the oral "podcast" is to discuss a recent scientific finding / discovery [in our context, this would likely be a newly sequenced genome, for example], explaining the signficance to a general audience. There are several scientific podcasts available, for example, see Nature magazine , Science Times (from The New York Times) , Science magazine , and Scientific American magazine . Early in the semester, example podcasts will be given, and methods will be discussed on how to give good presentations. Students will be divided into small groups (two or three people), which will work together on the podcast. The final podcasts will be available on the course page for evaluation by other students.
Journal Club (15% of grade)		Journal clubs will be done during class, as assigned to groups throughout the semester. During the first few weeks of the course, a set of possible papers to be used for journal club will be distributed over the CampusNet web pages for this course. Students are encouraged to form their own groups of 4 students, and hopefully the first set of journal clubs will begin by the middle of September. Since there are more than 40 students in the course, we will have at least one journal club every week throughout the semester. Students are also encouraged to sign up for dates of their preference.
Poster (25% of grade)		Posters will be done by groups, and are due on 7 November, when they will all be displayed and evaluated. The posters will be (of course) about comparison of bacterial genomes; each group is encouraged to find some genomes of their interest to compare, and use some of the standard tools discussed in the course, such as "BLAST Atlases" for comparison against a reference chromosome, and box and whisker plots for comparison of frequency distribution of genomic properties across large numbers of genomes. A good starting point is the article "Ten Simple Rules for Good Poster Presentation"
Paper (50% of grade)	Link to eJournal.	One of the main goals of this course is to learn to write a scientific manuscript, and in fact we will publish these manuscripts, as part of an "eJournal", in collaboration with a course at the University of Michigan. The papers from our course at DTU will be refereed by students in Michigan, and similarly, the students here at DTU will referee papers submitted by students in Michigan. This is intended to part of the learning process for how to referee (and accept referee's reports) for scientific publications.