Frequently Asked Questions

Research-related questions

How should I cite the use of the Pseudomonas Genome Database?

Please cite our Nucleic Acids Research paper by Winsor et al.,(2011).

I am a researcher studying Pseudomonas. Where can I obtain the PAO1 strain that was sequenced, to use in my research? Where can I obtain the cosmids or other DNA constructs used in the genome sequencing project for Pseudomonas aeruginosa PAO1?

Requests for the P. aeruginosa PAO1 strain that was sequenced for the first Pseudomonas Genome Project should be sent to Dr. Stephen Lory at Harvard Medical School, Boston.

Requests for any other materials associated with the Pseudomonas Genome Project should be sent to Dr. Maynard Olson at the University of Washington, Seattle.

Where can I download a file containing the ORF DNA sequences for Pseudomonas aeruginosa?

A FASTA file containing all of the ORF DNA sequences can be downloaded from the NCBI FTP site. Please note that this file does not contain the updated nucleotide sequence. In addition, our downloadable annotation file (in tab-delimited, excel or CVS format) contains these sequences.

How do I obtain the nucleotide sequence for an intergenic region?

There are a few ways you can go about doing this.

1) If you know the exact coordinates you are interested in, go to the sequence retrieval page and scroll down to a form that is titled "Retrieve a Specific Genomic Range from the Updated Database". Enter the start and stop coordinates of the region of interest and this will return all of the genomic DNA sequence within those coordinates.

2) Visit the intergenic sequences track under GBrowse and click on symbols representing the intergenic regions before or after the gene of interest, which will return the nucleotide sequence for that region.

3) A flat file of all intergenic regions can be downloaded

4) Each gene card contains the nucleotide sequences for the upstream 500 bp and downstream 500 bp regions. In addition, you can link from the same page to a GBrowse track showing all intergenic regions 5000 bp upstream and 5000 bp downstream of the current gene.

What is the difference between protein name confidence rating and localization confidence rating? What are their classifications based on?

The protein name confidence rating summarizes the degree of confidence in the function of a particular protein while the localization rating summarizes the degree of confidence in a protein’s subcellular localization. The protein name rating can be summarized as follows:

Class 1: Function experimentally demonstrated in Pseudomonas aeruginosa.

Class 2: Function of highly similar gene experimentally demonstrated in another organism (and gene context consistent in terms of pathways it is involved in, if known).

Class 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited sequence similarity to an experimentally studied gene.

Class 4: Homologs of previously reported genes of unknown function, or no similarity to any previously reported sequences.

The localization confidence rating can be summarized as follows:

Class 1: Subcellular localization experimentally demonstrated in Pseudomonas aeruginosa.

Class 2: Subcellular localization of highly similar gene experimentally demonstrated in another organism OR to a paralog experimentally demonstrated in the same organism. BLAST expect value of 10e-10 for query within 80-120% of subject length.

Class 3: Subcellular localization computationally predicted by PSORT.

What levels of homology are indicated by "strong homology" in level 2 for your annotation classification system?

There is no short answer to the question of what makes a gene Class 2. Homology counts, context counts, uniqueness of that gene in the genome counts, etc. On a genome annotation scale, consistency in how you decide counts, too. For the sake of space and focus, this issue was not fully addressed in the genome paper, however you may wish to contact those at Chiron (formerly of PathoGenesis) involved in the initial genome annotation (see the genome paper) to speak with them about this further, as they took the lead role in the decision making for Class 2 verses Class 3 annotation designations.

Pseudomonas infection: Patient questions

Please note that we are researchers involved in furthering the understanding of the biology of Pseudomonas aeruginosa. We are not qualified to answer questions regarding treatments for Cystic Fibrosis, and/or Pseudomonas infections. Any medically related questions should be referred to your personal primary care physician or other medical practitioner. For your benefit, we have provided answers to some frequently asked questions.

I am taking a particular drug(s) to treat Pseudomonas infection and its not working. Do you have any suggestions for a better treatment?

Since we are research scientists and not physicians, we cannot provide you with any advice regarding treatment. Unfortunately, Pseudomonas infection can be difficult to treat in some instances; however we hope that our research will provide a better understanding of Pseudomonas aeruginosa so that new drugs or other therapies may be developed to prevent or cure infection. We recommend you bring up any concerns you have with your family doctor. Seek a second medical opinion if you feel strongly that you are being treated incorrectly.

Do you have any drugs you've recently developed that can help cure Pseudomonas infection, but aren't available to the public yet? I'd be willing to be involved in a clinical trial or try out the drug ahead of time, as I am desperate for a cure.

It is unethical for us to allow persons access to any developing medicines before they have first undergone safety tests. There may be clinical trials going on that you may be eligible to participate in; however you will have to contact the relevant agency in your respective country to find out more information. We are not a good starting point for such inquiries - your local or national health department/office is li more suitable. Note that some clinical trials are publicized through Cystic Fibrosis Agencies (due to the susceptibility Cystic Fibrosis patients have for Pseudomonas infection), so you may wish to contact the agency nearest you for more information as well (for example, see the U.S. Cystic Fibrosis Foundation's site at http://www.cff.org/research/ClinicalResearch/ClinicalTrialSites/).

I (or my relative) have a Pseudomonas infection I can't get rid of! Where do I go to for help?

We assume you have already seen your doctor about this, who will likely be prescribing you a treatment. Please follow this treatment carefully, remembering, for example, to always complete all antibiotic pills during a particular treatment (or as prescribed). As we are research scientists, not physicians, we cannot help you with regard to any treatment or giving you medical advice. For such information you are best off seeing a qualified doctor face to face.

Is a person with a Pseudomonas infection at high risk of transmitting their infection to another healthy individual?

No. Pseudomonas infections occur in individuals who have a particular susceptibility to this bacterium - a susceptibility that is not common to most people. The vast majority of people who come in contact with Pseudomonas will not become infected. If you are a healthy individual with no burns, cystic fibrosis disease, or other condition that may compromise your immune system, you should not fear coming into contact with a person who has a Pseudomonas infection. If you have a child (for example) who has a Pseudomonas infection you should not be worried that your child may pass the infection on to other healthy people who have none of the risk factors mentioned above. Also you do not have to worry that you, if a healthy individual, may be the source/cause of a Pseudomonas infection in someone who is infected.

How easily are Pseudomonas infections transmitted? Is it possible for me, as a caregiver, to be the source of this infection that my loved one keeps getting over and over again?

Healthy people do not carry a Pseudomonas infection. The person who became infected with Pseudomonas did not get this from a healthy individual so you do not have to worry that you, as a healthy caregiver, are the cause or source of their Pseudomonas infection.

Where can I find more information about Pseudomonas aeruginosa and the disease it causes?

A good microbiology textbook from your local library or University library will contain some basic information about this bacterium. See your librarian for help. For more detailed information, or information on the latest research, you may wish to do a search of "PubMed" a database of recent medical research papers. You can search PubMed at its website at http://www.ncbi.nlm.nih.gov/entrez using words such as "Pseudomonas aeruginosa", and perhaps clicking on the "Limits" button to only view recent reviews. Note that such detailed information does require a certain level of background knowledge about microbiology and genetics, and so you must be careful, if you do not have such training, to ensure that you do not misinterpret findings. We recommend that you review any such research information with someone who has background training, or is a physician, to ensure that you are interpreting the research results correctly. You may also wish to contact your local Cystic Fibrosis Foundation office for more information. Cystic Fibrosis patients are particularly susceptible to P. aeruginosa and so such agencies may have additional information that is helpful to you.

Where can I find more information about Cystic Fibrosis and its causes?

Visit the Cystic Fibrosis Foundation website for information and links to further resources on this disease. For more detailed information, including discoverer Riordan et al., please read the following articles at NCBI.

1) Cystic Fibrosis Transmembrane Conductance Regulator; CFTR

2) Cystic Fibrosis; CF

*PathoGenesis Corporation, who played a major role in sequencing the first P. aeruginosa genome, is now a part of Chiron and continues its interest in the development of new anti-Pseudomonad drugs.