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What can I learn about the pathogenic mechanisms of Listeria using the tools and resources of the National Microbial Pathogen Data Resource?

The question of pathogenesis in these organisms is overly broad and must be narrowed to one that may be fully interrogated with comparative genomics tools at NMPDR. Your class text and lecture notes are a good place to begin looking for specific proteins or phenotypes to investigate. A good resource for a comprehensive introduction to Principles of Bacterial Pathogenesis is that section of Todar's Online Textbook of Bacteriology.

A concise introduction to mechanisms of pathogenesis provides names and functions of virulence factors such as adhesins, invasins, exotoxins, and endotoxins used by many pathogenic bacteria. Todar's text also has chapters devoted to listeria, which provides the gene names of virulence factors. Virulence factors have been cataloged for many strains of pathogens, including listeria, at the Virulence Factor Database.

Descriptions of the phenotypes of the sequenced strains in NMPDR may be more challenging to locate. A complete understanding of differences and similarities between the genomes will be dependent on the characteristic phenotypes of the strains. For example, which of the strains are virulent, clinical isolates, and which are nonvirulent, laboratory strains? Which are drug resistant, and which are drug sensitive? Some of these strain descriptions have begun to be recorded in the PathInfo section of the NMPDR organism pages, but this project is a work in progress. Descriptions of the strains are frequently associated with their genome project record at NCBI. For example, see the genome project description for strain EGD-e, and follow the genome project link in the lineage for descriptions of other sequenced listerial genomes.

The most recent research on the pathogens is linked under the journals button on the NMPDR organism page. These citations may provide a starting point for inquiry using NMPDR. What kinds of inquries make sense? The comparative genomics tools in NMPDR may be used to discover phenotype-genotype associations, to locate homologs of virulence factor genes in other organisms, to find evidence for co-regulation of clustered genes, or to locate all genes in a functional pathway. From the essential genes page, search for genes identified to be essential in certain model organisms, then find homologs in other genomes. If the gene and its context are conserved, is its essentiality for growth conserved as well? Candidate drug targets for novel therapeutics may be located in multidrug resistant strains.

To formulate an interesting and focused inquiry, you may need to locate a web resource not listed here. If you find a particularly helpful resource, add it to the link list. You may use the comment (dialog balloon) button to describe the site or to give yourself a byline for providing the link.

Before you begin to use the comparative analysis tools at NMPDR, write a well-developed paragraph that states your question and provides a reason why you expect the investigation to be interesting.

Find the protein page for one gene that is the subject of your investigation using either a keyword search for that gene or a neighboring gene, or a homolog in another genome. Report the genome and peg id number, which is located at the top of the protein page in the form of fig|genome.number.peg.number.

Is the protein located in a conserved functional cluster? If so, what is the evidence for functional coupling? If not, use the CL button to determine whether the gene is clustered in other organisms.

Use the bidirectional best hits button to find orthologs. Select several and align them. Provide the reason for your selection. Look at the resulting alignment and phylogenetic tree. Is the tree coherent with what you know about the microbial phylogeny? (The ribosomal phylogeny all genomes in the database is located on the tree of life page.) Copy the alignment. Paste it into your report, making sure to apply a fixed-width font such as courier.

Use the Pins button to investigate homologous regions across the database. How many other genomes have conserved homologous regions? Either count the genomes in the graphic or use the last table on the page launched by the commentary button to determine this. The last table on the commentary page may also be used to select genomes to display. Select a subset and redraw the display to show just those checked. Provide the reason for your selection. Point to the display image and save or copy it as an image. Paste this into your report.

Explore the biological context of your protein either by investigating its subsystem or protein family. Your protein may or may not be included in either a subsystem or protein family. If it is not, speculate on why not. Might it fit into a new subsystem that could be defined by your inquiry?

Your report on this activity should include a well-developed paragraph that states your inquiry and the reason why you expect the investigation to be interesting. Please do this prior to beginning the actual work in NMPDR.

Keep notes while you pursue your inquiry in NMPDR--which tools did you use? Did you reach a dead end with your original subject? Did you find a more interesting tangent? Did your exploration turn up entirely expected results, or did you find something unexpected?

Provide the database id (fig|...) of a protein you explored along with an alignment and subset of pins that includes this protein. Provide answers to the questions asked in the section above. If you used other tools or pursued more than one protein, write about what you did.

Write a concluding paragraph that summarizes your investigation.

Your report should be printed out and handed in to Dr. Wilson. If you find it convenient, you may use this iLab site and the inquiry unit tool to keep track of the process you followed as you formulated your question, to record the initial plan for your inquiry, to keep notes of your progress through the NMPDR tools, and to summarize your experience. The best way to do this is to create a new inquiry unit to record your work, or you may add comments to this one. Regardless of whether you use the iLab to record your progress, you must hand in a hardcopy of your report.

As a research scientist in training, has this inquiry convinced you that bioinformatic tools may be used to formulate hypotheses that are testable at the bench?

Can bioinformatic tools and comparative genomics be used to discover anything new, or just to browse old information?

Are you convinced that the time and resources that have been and continue to be invested in genome sequencing is justified by the utility of the information?