Vpachec3 Week 10

Tuesday November 3, 2015

We came together as a team to choose our species, Project Manager and our team name.

Additional Class Notes:

• Genome sequence paper
• Microarray data/paper
• There will be duplicated information on user page and teams page
• Make use of LibGuide through the library; databases section on class's LibGuide page for very useful links
• Use APA style because that is closest to the usual format used in biology
• DOI is a primary id or unique identifier that is specific for each article
• Pubmed Central contains the full text of papers in it, while Pubmed just has abstracts of articles
• Copyright-who owns the work, owns the right to distribute the work
• For microarray, find datasets then find paper- would be easier

Thursday November 5,2015

Demonstration of PubMed

• go straight to advanced search; its the front end of SQL
• use filters to narrow down the search

Demonstration of Google Scholar

• has a wider range
• can see how many times a paper has been cited in other papers
• also has filters to narrow down search

Demonstration of Web of Science

• prospective search: you can see where the paper is being cited; google can do this too
• Web of Science is better for organization and retrieval

Demonstration of ArrayExpression

• filter by experiment type
• high number of arrays are better

So first we needed to decide on a genome sequence paper. Brandon was the first one to find the paper through web of science. He shared it on the group page. He used the key search as Burkholderia cenocepacia genome and filtered by number of citations. The paper with the highest citations will appear first.

Search Methods

Genome Paper Search Method

The way I decided to approach finding a genome paper was by first finding a data set then use the data set to link us to a paper

1. Starting in ArrayExpress, I typed in a a key term the name of the species: Burkholderia cenocepacia
2. With that keyword alone, the results were 35 experiments. To narrow down the results, I used the filters where I chose to filter by experiment type which had two drop down bars. The first bar I selected RNA assay and the second bar I selected Array assay. This led to having 24 experiments.
3. Within this search, my teammates made a note that looking through the titles, there were experiments using different strains. We decided to use the J2315 strain.
4. Adding the J2315 into the keyword search, narrowed down the experiment results to 16.
5. To select through the 16, we are looking at the assays column. We want a number greater than or equal to 9 to ensure better quality data.
6. I took a took a title from the results and used in the other search engines. But then I got confused and didn't really understand what the next step would be. So, I just started to use the other search engines independently.
7. Looking at Web of Science, I typed in the key term Burkholderia cenocepacia genome.

There were 22 results. Before adding any filter, I want to read through the first five papers to get an idea of how to filter. The first paper was recent, Oct 13 2015 and hasn't been cited. However, it was looking at the particular strain we want: J2315.

1. I opened another tab and used google scholar. Again, I typed in the same key term just to get an idea of how to filter based on the first few results.

There were 18,200 results. The first two didn't seem particularly helpful and they were past or almost past the 10 year mark. However, the third article looked golden. The title was looked like the paper would have the genome data needed, it was within the 10 year mark, it was cited 163 times and the full text could be found at the LMU library. This one I was definitely going to come back to.

1. Finally, I did the same key term search into PubMed. There were 150 results.

I noticed that on the right side there was a section that says "Titles with your search terms" and the first paper was the same paper from the Google Scholar search. I would take a that one first.

1. At this point, Brandon had already found a paper and as a group we wanted to take a look at it so he posted on the group page. I clicked on the link and it was the golden paper. So we had agreed to use that one as our genome paper.

Microarray Search Methods

• 1. • Use a keyword search for each of these databases/tools and answer the following:
       • PubMed
         • What original keyword(s) did you use? How many results did you get? I used the keywords Burkholderia cenocepacia J2315 microarray and got 4 results
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? I deleted the key term microarray to see how many results I would get and it got 67 hits. So the term microarray narrowed down the search very much. I also added a filter for the free full text because it would be what I need to read the article. And after that I got 3 hits. However, the one with was taken away actually seems like a pretty good candidate for an article so I am going to save that and see if I can find the full text elsewhere.

• 1. • • Google Scholar
         • What original keyword(s) did you use? How many results did you get? I used the keywords Burkholderia cenocepacia J2315 microarray. Since Google has a wider range, there 210 results.
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? To narrow down the search, I filtered by time range. I had a 5 year limit from 2005 to 2015 and this brought the hits down to 191. I then added the key terms biofilm and genome. This narrowed down the search to 93. I also unchecked the patents but it did not affect the number.

• 1. • • Web of Science
         • What original keyword(s) did you use? How many results did you get? I started off the the full search:Burkholderia cenocepacia J2315 microarray genome biofilm and it only got 2 hits.
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? I reentered the search without the terms genome and biofilm. I also added the time span to ten years from 2005 to 2015. This got me 32 results. After I added the key term biofilm and it went down to 21 hits.

• 1. • Use the advanced search functions for each of these three databases/tools and answer the following:
       • PubMed
         • Which advanced search functions were most useful to narrow down the search? How many results did you get?Since the search that resulted in 4 hits, I wasn't able to narrow down the search even further. However, in the advanced section, it was pretty neat to see that the web site save my search histories so you can see the thought process and the actions to get to the final search.

• 1. • • Google Scholar
         • Which advanced search functions were most useful to narrow down the search? How many results did you get? In the advanced search option, I was able to arrow down the search by saying I just wanted my key terms in my titles. I also deleted the word microarray. It got it down to 26.

• 1. • • Web of Science
         • Which advanced search functions were most useful to narrow down the search? How many results did you get? Using the advanced search option, I was able to type in my keywords a bit differently. I used the formula TS=(Burkholderia cenocepacia J2315 AND microarray) and also refined by using dataset documents only. This got 16 hits. The datasets linked back to the abstracts so I can find the relating articles through there.

Final Paper Choice and the Annotated Bibliography

GENOME PAPER

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

• 1. • • The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)

Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08

• 1. • • The link to the abstract from PubMed. [1]
       • The link to the full text of the article in PubMedCentral. [2]
       • The link to the full text of the article (HTML format) from the publisher web site. [3]
       • The link to the full PDF version of the article from the publisher web site. [4]
       • Who owns the rights to the article? American Society for Microbiology
         • Does the journal own the copyright? Yes
         • Do the authors own the copyright? No
         • Do the authors own the rights under a Creative Commons license? No
         • Is the article available “Open Access”? Yes
       • What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here. American Society for Microbiology which is a scientific society
       • Is this article available in print or online only? It is both available in print and online.
       • Has LMU paid a subscription or other fee for your access to this article? Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.
       • How many articles does this article cite? It has 150 cited references.
       • How many articles cite this article? It is cited 128 times.
       • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? A lot of the papers revolved around antibiotic resistance and therapeutic strategies.

MICROARRAY PAPER

Molecular Mechanisms of Chlorhexidine Tolerance in Burkholderia cenocepacia Biofilms

• 1. • State what you used as search terms and what type of search terms they were. Used the search bar in Array Express and used the terms Burkholderia cenocepacia J2315. I used the filters RNA assay and Array assay.
       • How many results did you get? There were 18 experiments that resulted in the search.
       • Give an assessment of how relevant the results were. A good chunk of the experiments we weren't going to look at because the assay numbers were smaller than 9 which was as low as we were going to test.

• 1. • • The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)

Coenye, T., Van Acker, H., Peeters, E., Sass, A., Buroni, S., Riccardi, G., & Mahenthiralingam, E. (2011). Molecular Mechanisms of Chlorhexidine Tolerance in Burkholderia cenocepacia Biofilms. Antimicrobial Agents and Chemotherapy, 55(5), 1912–1919. http://doi.org/10.1128/AAC.01571-10

• 1. • • The link to the abstract from PubMed. [5]
       • The link to the full text of the article in PubMedCentral. [6]
       • The link to the full text of the article (HTML format) from the publisher web site. [7]
       • The link to the full PDF version of the article from the publisher web site. [8]
       • Who owns the rights to the article? American Society for Microbiology
         • Does the journal own the copyright? Yes
         • Do the authors own the copyright? No
         • Do the authors own the rights under a Creative Commons license? No
         • Is the article available “Open Access”? Yes
       • What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here. American Society For Microbiology which is a scientific society.
       • Is this article available in print or online only? Both online and in print.
       • Has LMU paid a subscription or other fee for your access to this article? No
       • How many articles does this article cite? It sites 36 other articles.
       • How many articles cite this article? 32 on Google Scholar and 22 on Web of Science
       • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
     • In addition, you must also link to the web site where the microarray data resides.[ https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2502/?keywords=Burkholderia+cenocepacia+J2315&organism=&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=]
       • For each of the microarray articles/datasets, answer the following:
         1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment? B. cenocepacia J2315 cells were treated by exposure to high levels of H2O2, NaOCl or chlorhexidine. In addition differences in gene expression were examined between untreated B. cenocepacia sessile cells and B. cenocepacia planktonic cells.
         2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? There were 20 assays.Hybridizations for all experimental conditions were performed in 4 replicates.

1. Drevinek, P., Holden, M. T., Ge, Z., Jones, A. M., Ketchell, I., Gill, R. T., & Mahenthiralingam, E. (2008). Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BMC Infectious Diseases, 8, 121. http://doi.org/10.1186/1471-2334-8-121
   • The link to the abstract from PubMed: [9]
   • The link to the full text of the article in PubMedCentral: [10]
   • The link to the full text of the article (HTML format) from the publisher web site: [11]
   • The link to the full PDF version of the article from the publisher web site: [12]
   • Who owns the rights to the article? Authors of the article: Copyright © 2008 Drevinek et al; licensee BioMed Central Ltd.
   • Does the journal own the copyright? No
   • Do the authors own the copyright? Yes
   • Do the authors own the rights under a Creative Commons license? Yes.
   • Is the article available “Open Access”? Yes.
   • What organization is the publisher of the article? What type of organization is it? BMC Infectious Diseases is an open access, peer-reviewed journal
   • Is this article available in print or online only? Available in print and online.
   • Has LMU paid a subscription or other fee for your access to this article? No.
   • Where does MicroArray Data reside? [13]
   • What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The genome of Burkholderia cenocepacia J2315 and transcriptomics used to identify genes that were differentially regulated when the pathogen was grown in a CF sputum-based infection model. Sputum samples from CF individuals infected with the same B. cenocepacia strain as genome isolate were used, hence, other than a dilution into a minimal growth medium (used as the control condition), no further treatment of the sputum was carried out.
   • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? A replicate self-hybridization control experiment was performed. There were 8 essays and 4 biological replicates.
   • How many articles does this article cite? 50 references cited.
   • How many articles cite this article? 52 in Google Scholar and 44 in Web of Science.
   • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? It has been working on antibiotic resistance in cystic fibrosis patients and how the bacteria had evolves and reacts to different extreme treatments.

Links

Vpachec3 User Page