CH 564 Resources

CH 564 Resources

Proposal Guidelines

List of species used in this course and their growth media

General resources on microbes

ATCC: The American Type Culture Collection, a global nonprofit bioresource center that provides biological products, technical services and educational programs to private industry, government and academic organizations around the world. You can find general info on the microorganisms that they maintain.
MicrobeWiki: a free wiki resource on microbes and microbiology, edited by students and monitored by microbiologists at Kenyon College
Bergeyπs Manual Trust: homepage of Bergeyπs which publishes the Bergey manuals on prokaryotes

Microbial genome databases

NCBI Microbial Genomes: Microbial Genomes Resources presents public data from prokaryotic genome sequencing projects, organized by the National Center for Biotechnology Information. The sequence collection contains data from finished genomes as well as draft assemblies.
GOLD: Genomes Online Database v2.0, a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world.
Genamics: a software and web development firm dedicated to empowering researchers with modern and innovative solutions related to genomics (especially useful is their GenomeSeek page.)
Integrated Microbial Genomes (IMG): provides a framework for comparative analysis of the genomes sequenced by the Joint Genome Institute. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.
Phototrophic Prokaryotes Sequencing Project: In July 2004, a team led by Arizona State University started sequencing four photosynthetic prokaryotes: Heliobacterium modesticaldum, Roseobacter denitrificans, Rhodocista centenaria and Acaryochloris marina. Finished genome sequences of these organisms will fill large gaps in the available genomic data for photosynthetic prokaryotes and will help to understand the origin and early evolution of photosynthesis. Each organism has unique individual characteristics such as agricultural applications and environmental aspects such as understanding global photosynthetic productivity. BLAST site.

Bacterial phylogeny

Bacterial phylogeny: Presents an alternate view of bacterial phylogeny from the standard rRNA sequencing picture. Run by Dr. Radhey S. Gupta (McMaster Univ.).

Manuals and protocols

Document files for taking notes and writing up reports:

Laboratory Notes

Experiment Reports

Data from Experiments conducted in class (need Logger Pro to open these files)

January 18 (CO₂ fixation by Chlamydomonas reinhardtii)
January 20 (H₂ photoevolution by Chlamydomonas reinhardtii)
January 23 (aerobic respiration by Paracoccus denitrificans)

1. Experiment 1: Initial experiment to see CO₂ production (200 mL/min air)

2. Experiment 2: Low flow rate (10 mL/min) to more easily see O₂ consumption

3. Experiment 3: Low O₂ (10% air at 200 mL/min) to more easily see O₂ consumption

January 25 (anaerobic respiration by Paracoccus denitrificans using nitrate as electron acceptor)

1. Experiment 1: Initial experiment to see NO₃^– concentration of culture (after checking medium + 10 mM NaNO₃)

2. Experiment 2: Measuring CO₂ production of culture (flow = 50 mL/min N₂)

3. Experiment 3: NO₃^– consumption measured using flow cell

January 26 follow-up experiments (after NO₃^– was exhausted) at 6PM

1. Experiment 1: Measuring NO₃^– concentration of culture

2. Experiment 2: Monitoring O₂ and CO₂ from culture (flow = 50 mL/min N₂)

January 30 (anaerobic respiration by Paracoccus denitrificans using nitrate as electron acceptor)

1. Experiment 1

February 1 (anaerobic respiration by Paracoccus denitrificans using nitrate as electron acceptor; H₂ uptake)

1. Experiment 1

February 6 (anoxygenic photosynthesis by Chloroflexus aurantiacus)

1. Experiment 1

2. Experiment 2

February 8 (anoxygenic photosynthesis by Chloroflexus aurantiacus and Chlorobium tepidum using H₂ (or S^2-) as electron donor)

1. Experiment 1

February 15 (anoxygenic photosynthesis by Rhodobacter sphaeroides)

1. Experiment 1

February 20 (Acidithiobacillus ferrooxidans: aerobic oxidation of Fe²⁺)

1. Experiment 1

February 22 (Acidithiobacillus ferrooxidans: mixing electrons donors – probably failed due to drifting CO₂ sensor)

1. Experiment 1 (Fe-grown cells)

2. Experiment 2 (Thiosulfate-grown cells)

February 27 & March 1 (Iron oxidation by Acidithiobacillus ferrooxidans)

1. Experiment 1 (Monitoring Fe²⁺)

a. Protocol (PDF file)

b. Data (PDF file)

2. Experiment 2 (Monitoring Fe³⁺)

a. Protocol (PDF file)

b. Data (Excel file)

March 6-8 (Nitrobacter winogradskyi: aerobic growth with nitrite as electron donor)

1. Description of experiment (PDF doc)

2. Day 1 - Experiment 1 (nitrate measurement on beginning of culture)

3. Day 1 - Experiment 2 (nitrite measurement on beginning culture)

a. calibration file (Excel Doc)

4. Day 2 - Experiment 1 (nitrate & nitrite measurements in morning)

5. Day 2 - Experiment 2 (nitrate & nitrite measurements in evening)

6. Day 3 - Experiment 1 (nitrate & nitrite measurements in morning & start of new experiment)

7. Day 3 - Experiment 2 (nitrite measurements of 2nd time point of new experiment)

8. Day 3 - Experiment 3 (nitrite of 3rd time point and CO2/O2 measurements from chamber)

a. calibration file (Excel Doc)

March 20-22 (Sulfate reduction by Desulfobacterium autotrophicum)

1. Experiment 1 (Monitoring S^2–)

a. Data (Excel file)

March 22 (Methanothermobacter marburgensis) – FAILED due to signal from H₂ in Methane sensor

1. Experiment 1 (initial culture)

2. Experiment 2 (after overnight growth)

March 29 (Methanosarcina barkeri) – FAILED due to low signal from Methane sensor

1. Experiment 1 (initial culture)

April 3-10 (Sulfate reduction by Archeoglobus fulgidus) –

1. Experiment 1 (measuring sulfide concentration over a week)

a. Data (Excel file)

April 3-10 (Sulfate reduction by Archeoglobus fulgidus) –

1. Experiment 1 (measuring sulfide concentration over a week)

a. Data (Excel file)

∑ Heliobacterium modesticaldum CO₂ fixation

1. April 24

2. April 25

3. April 26

a. PYE medium (pyruvate)

b. YE medium (no pyruvate)

4. April 27

5. April 30

6. May 1

Assignments of enzymes for BLAST searches

(Remember to search the Heliobacterium modesticaldum database using "tblastn" (search translated nucleotide database for a protein) on the Phototrophic Prokaryotes Sequencing Project website (see above). Your query sequence should be in FASTA format (first line is "> xxx", where "xxx" can be anything, and the second line is the protein sequence in 1-letter code – no spaces or numbers). You can get the query sequence in a variety of ways, but I would recommend starting with the NCBI website (http://www.ncbi.nlm.nih.gov/) and searching their Protein database.)

The table now has all of our results inserted in it! Good job, everyone!

Reading the literature

Advice from others on how to read a scientific paper:

∑ University of Arizona: a very comprehensive and detailed guide, with emphasis on papers in biochemistry

∑ Hampshire College: a shorter reference

∑ FIU: another short (and somewhat opinionated) guide

∑ UC San Diego: quick reference

Photosystem I is unessential/required papers

∑ 1995 Nature paper (Greenbaum et al.)

∑ 1996 Science paper (Lee et al.)

∑ 1999 JBC paper (Redding et al.)

Paracoccus papers