Difference between revisions of "GENialOMICS"

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(added goals for this week)
(added microarray paper)
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=Weel 11=
 
=Weel 11=
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==Individual Goals and Progress==
 
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==Other Progress:==
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==Other Progress==
 
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.
 
* A journal using the ''B. cenocepacia'' genome in a microarray experiment titled [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/ Biofilm-Grown ''Burkholderia cepacia'' Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species] was approved for analysis.
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=''Burkholderia cenocepacia'' Genome Paper=
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'''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'''
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* The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103]
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* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/]
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* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long]
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* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html]
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* Who owns the rights to the article? '''American Society for Microbiology'''
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** Does the journal own the copyright? '''Yes'''
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** Do the authors own the copyright? '''No'''
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** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No'''
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** Is the article available “Open Access”? '''Yes'''
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* 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 [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society'''
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* 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.'''
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* How many articles does this article cite? '''It has 150 cited references.'''
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* How many articles cite this article? '''It is cited 128 times.'''
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* 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.'''
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 +
=Microarray Paper=
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'''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
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* This article is suitable for your project.  ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
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* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
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* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
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* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
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**Cannot find HTML format on publisher web site.
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* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
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* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
 +
* Does the journal own the copyright? Yes.
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* Do the authors own the copyright? No.
 +
* Do the authors own the rights under a Creative Commons license? Yes.
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* Is the article available “Open Access”? Yes.
 +
* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
 +
* Is this article available in print or online only? Available in print and online.
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* Has LMU paid a subscription or other fee for your access to this article? No.
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* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
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* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
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* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
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* How many articles does this article cite? This article has 34 cited references.
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* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
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* 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? Most of the articles are related to  antimicrobial therapy, tolerance, and resistance.
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<!-- #'''Sass, A., Marchbank, A., Tullis, E., LiPuma, J. J., & Mahenthiralingam, E. (2011) Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. ''BMC genomics'', 12(1), 373. doi:10.1186/1471-2164-12-373'''
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#* Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:
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#** Control: the wild-type J2315 strain
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#** Treatment: mutant strains which showed antibiotic resistance
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#** Treatment: ET12 outbreak isolates, described as "pan-resistant"
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#* Three biological replicates were used for each experiment.
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#* The raw data does not appear to be directly linked from the article itself. The supplement includes a summary spreadsheet, which only displays values for fold-changes that were statistically significant. However both the raw and processed data files are available on the [https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2747/files/ ArrayExpress entry].
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#* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/21781329
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#* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155924/
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#* Publisher Full Text (HTML): http://www.biomedcentral.com/1471-2164/12/373
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#* Publisher Full Text (PDF):  http://www.biomedcentral.com/content/pdf/1471-2164-12-373.pdf
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#* Copyright:  2011 Sass et al; licensee BioMed Central Ltd. "This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."
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#* Publisher:  BioMedCentral, respected Open Access organization.
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#* Availability:  Article does not initially appear to be available in print, however, BioMedCentral's website mentions that "high quality, bound reprints" can be purchased for any published article.
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#* Did LMU pay a fee for this article: No - open access.
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#* This article cites 64 other articles.
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#* This article has been cited by 29 other articles (across all databases).
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#* The scientific community seems to be particularly interested in this organism's antimicrobial resistance, probably because this is a known pathogen, particularly relevant in the context of cystic fibrosis.
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# '''Mira, N. P., Madeira, A., Moreira, A. S., Coutinho, C. P., & Sá-Correia, I. (2011). Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients’ airways and antimicrobial therapy. PLoS One, 6(12), e28831.'''
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#* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genomic+Expression+Analysis+Reveals+Strategies+of+Burkholderia+cenocepacia+to+Adapt+to+Cystic+Fibrosis+Patients%27+Airways+and+Antimicrobial+Therapy
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#* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244429/
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#* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028831
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#**Cannot find HTML format on publisher web site.
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#* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0028831&representation=PDF
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#* Who owns the rights to the article? Authors of the article: Nuno P. Mira, Andreia Madeira, Ana Sílvia Moreira, Carla P. Coutinho, Isabel Sá-Correia
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#* Does the journal own the copyright? Yes.
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#* Do the authors own the copyright? No.
 +
#* 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? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
 +
#* 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? https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-809/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
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#* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The "treatments" strains were collected from a cystic fibrosis patient. The strain "IST439" was collected first, and the strain "IST4113" was collected 3 years later. The control for this experiment is reference data of Burkholderia cenocepacia.
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#* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? There were 3 replicates of each of the 2 strains and 6 replicates of the reference strain. It is unclear whether these are biological or technical replicates.
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#* How many articles does this article cite? This article has 75 cited references.
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#* How many articles cite this article? This article has been cited 22 times in All Databases, and 22 times in Web of Science Core Collection.
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#* 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? Most articles are related to Burkholderia's pathogenesis and antibiotic resistance.
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#'''Yoder-Himes, D. R., Konstantinidis, K. T., & Tiedje, J. M. (2010). Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One, 5(1), e8724.'''
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#* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20090946
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#* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806911/
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#* Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008724
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#* Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0008724&representation=PDF
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#* Copyright: '''© 2010 Yoder-Himes et al''' (information found on PDF version of article); the article is open-access and is distributed under a '''Creative Commons license'''
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#* Publisher: '''PLOS''' (Public Library of Science); nonprofit open-access publisher/advocate           
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#* Availability: '''online only'''
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#* Did LMU pay a fee for this article: '''No'''
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#* Data Found At: [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15817/ ArrayExpress]
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#* Experiment Information: The transcriptome of a clinical and a environmental strain of ''B. cenocepacia'' was analyzed under conditions mimicking soil versus conditions mimicking the sputum resulting from cystic fibrosis. Identification and observation related to putative virulence factors was conducted. "Treatment" conditions were those mimicking CF sputum and "Control" conditions were those mimicking soil.
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#* Replicate Information: Replicate experiments of the "treatment" and "control" were conducted (quadruplicates were employed using different cultures). These were biological replicates (total of 8 arrays, '''four biological replicates''').
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#* How many articles does this article cite: '''61'''
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#* How many articles cite this article: '''14'''
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#* The papers that cite this article appear to focus upon the aspects of the J2315 strain and other BCC bacteria that are related to virulence and host-pathogen interactions. A few articles also explored the role of certain genes which are related to the pathogenic character of the strain (which were possibly examined in the paper by Yoder-Himes et al).
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#'''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'''
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#* 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.'''
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#* How many results did you get? '''There were 18 experiments that resulted in the search.'''
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#* 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.'''
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#* The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/21357299?dopt=Abstract]
 +
#* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088199/]
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#* The link to the full text of the article (HTML format) from the publisher web site. [http://aac.asm.org/content/55/5/1912.full]
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#* The link to the full PDF version of the article from the publisher web site. [http://aac.asm.org/content/55/5/1912.full.pdf+html]
 +
#*Who owns the rights to the article? '''American Society for Microbiology'''
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#* Does the journal own the copyright? '''Yes'''
 +
#* Do the authors own the copyright? '''No'''
 +
#* Do the authors own the rights under a [http://creativecommons.org/ 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 [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society For Microbiology which is a scientific society.'''
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#* 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'''
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#* How many articles does this article cite? '''It sites 36 other articles.'''
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#* How many articles cite this article? '''32 on Google Scholar and 22 on Web of Science'''
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#* 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?
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#* 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=]
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#* For each of the microarray articles/datasets, answer the following:
 +
#* 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.'''
 +
#*  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.'''
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# '''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: [http://www.ncbi.nlm.nih.gov/pubmed/18801206?dopt=Abstract&holding=f1000,f1000m,isrctn]
 +
#* The link to the full text of the article in PubMedCentral: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559838/]
 +
#* The link to the full text of the article (HTML format) from the publisher web site: [http://www.biomedcentral.com/1471-2334/8/121]
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#* The link to the full PDF version of the article from the publisher web site: [http://www.biomedcentral.com/content/pdf/1471-2334-8-121.pdf]
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#* 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.'''
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#* What organization is the publisher of the article? What type of organization is it? '''BMC Infectious Diseases is an open access, peer-reviewed journal'''
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#* 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? [https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-1261/?keywords=+Burkholderia+cenocepacia+J2315&organism=&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=]
 +
#* 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.'''
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#* How many articles cite this article? '''52 in Google Scholar and 44 in Web of Science.'''
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#* 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.''' -->
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Revision as of 03:01, 15 November 2015

Genialomics-banner.jpg


Weekly Group Assignments Shared Group Journals Project Links Team Members


Week 10


Weel 11

Individual Goals and Progress

Weekly Goals and Progress
Anu Varshneya Goals
  • Complete journal club individual assignment
  • Create and practice journal club presentation with Brandon
  • Find a MOD
  • Create project timeline with soft deadlines for each person/milestone
  • Complete milestone 0: Working Environment Setup
  • Complete milestone 1: Version Control Setup
  • Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build
  • Reformat Home Page with Dr. Dahlquists recommendations
Progress
Brandon Litvak Goals
  • Perform an initial import/export cycle (with Anu)
  • Figure out a file management system (with Anu)
  • Characterize regular expression patterns for ID detection
  • Further explore the found MOD and review it
  • Complete Journal Club presentation on the genome paper
Progress
Veronica Pacheco Goals

Work with Kevin Wyllie

  • Understand experimental design
  • Understand sample-data relationship
    • raw.zip and .sdrf
    • Construct sample-data diagram
  • Develop compiled raw data file
Progress
Kevin Wyllie Goals

Work with Veronica Pacheco

  • Understand experimental design
  • Understand sample-data relationship
    • raw.zip and .sdrf
    • Construct sample-data diagram
  • Develop compiled raw data file
Progress

Other Progress

Burkholderia cenocepacia Genome Paper

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

  • 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

Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. PLoS One, 8(3), e58943.

  • This article is suitable for your project. — Kdahlquist (talk) 10:17, 10 November 2015 (PST)
  • The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
  • The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
  • The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
    • Cannot find HTML format on publisher web site.
  • The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
  • Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
  • 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? Yes.
  • Is the article available “Open Access”? Yes.
  • What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
  • 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? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
  • What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
  • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
  • How many articles does this article cite? This article has 34 cited references.
  • How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
  • 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? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.



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