GÉNialOMICS Week 10 - Revision history

Anuvarsh: /* Microarray Paper */ fixed formatting

2015-11-11T18:57:55Z

‎Microarray Paper: fixed formatting

Anuvarsh: /* Microarray Paper Annotated Bibliography */ changed title

2015-11-11T18:56:21Z

‎Microarray Paper Annotated Bibliography: changed title

Anuvarsh: spacing edits

2015-11-11T18:55:55Z

spacing edits

Blitvak: commented out the other papers

2015-11-10T22:59:20Z

commented out the other papers

Kdahlquist: /* Ranked Microarray Papers' Annotated Bibliographies */ fixed spelling

2015-11-10T18:20:05Z

‎Ranked Microarray Papers' Annotated Bibliographies: fixed spelling

Kdahlquist: /* Ranked Microarray Papers' Annotated Bibliographies */ paper suitable for project

2015-11-10T18:17:48Z

‎Ranked Microarray Papers' Annotated Bibliographies: paper suitable for project

Vpachec3: /* Ranked Microarray Papers' Annotated Bibliographies */ Added second article in ranking

2015-11-10T07:10:41Z

‎Ranked Microarray Papers' Annotated Bibliographies: Added second article in ranking

@@ Line 19: / Line 19: @@
 ==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.'''
+'''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.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
+* This article is suitable for your project.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk: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 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 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
+* 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.
+**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
+* 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
+* 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.
+* Does the journal own the copyright? Yes.
-#* Do the authors own the copyright? No.
+* Do the authors own the copyright? No.
-#* Do the authors own the rights under a Creative Commons license? Yes.
+* Do the authors own the rights under a Creative Commons license? Yes.
-#* Is the article available “Open Access”? 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
+* 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.
+* 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.
+* 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=
+* 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.
+* 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.
+* 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 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.
+* 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.
+* 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.
 <!-- #'''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'''
 #* Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:

@@ Line 18: / Line 18: @@
 * 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 Annotated Bibliography==
+==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.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''

@@ Line 135: / Line 135: @@
 #* 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.''' -->
+<br>
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@@ Line 18: / Line 18: @@
 * 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.'''
-==Ranked Microarray Papers' Annotated Bibliographies==
+==Microarray Paper Annotated Bibliography==
 # '''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.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
@@ Line 40: / Line 40: @@
 #* 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.
-#'''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'''
+<!-- #'''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'''
 #* Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:
 #** Control: the wild-type J2315 strain
@@ Line 134: / Line 134: @@
 #* 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.'''
+#* 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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@@ Line 20: / Line 20: @@
 ==Ranked Microarray Papers' Annotated Bibliographies==
 # '''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 you project.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:17, 10 November 2015 (PST)''
+#* This article is suitable for your project.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk: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/

@@ Line 115: / Line 115: @@
 #* 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.'''
+# '''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'''
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