Difference between revisions of "Kzebrows Week 10"
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In order to create an annotated bibliography of genomics papers for my team's species, ''Shigella flexneri'', I visited the following databases/tools and answered the following questions using keyword searches. | In order to create an annotated bibliography of genomics papers for my team's species, ''Shigella flexneri'', I visited the following databases/tools and answered the following questions using keyword searches. | ||
| − | *'''PubMed''' | + | *[http://www.ncbi.nlm.nih.gov/pubmed '''PubMed'''] |
** What original keyword(s) did you use? How many results did you get? | ** What original keyword(s) did you use? How many results did you get? | ||
***When I searched "''Shigella flexneri''" I got 4,832 results. | ***When I searched "''Shigella flexneri''" I got 4,832 results. | ||
** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? | ** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? | ||
***I searched "''Shigella flexneri'' genome" and got 664 results. "''Shigella flexneri'' entire genome" gave me 15 results and adding the word "sequence" gave me only 11 results. | ***I searched "''Shigella flexneri'' genome" and got 664 results. "''Shigella flexneri'' entire genome" gave me 15 results and adding the word "sequence" gave me only 11 results. | ||
| − | *'''Google Scholar''' | + | *[https://scholar.google.com/ '''Google Scholar'''] |
** What original keyword(s) did you use? How many results did you get? | ** What original keyword(s) did you use? How many results did you get? | ||
***I searched "''Shigella flexneri'' genome and received 27,800 results. | ***I searched "''Shigella flexneri'' genome and received 27,800 results. | ||
** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? | ** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? | ||
***I then searched "''Shigella flexneri'' whole genome" and got 23,000 results, which is less but definitely not narrowed down enough. I tried "''Shigella flexneri'' entire genome sequence" and got 21,600. I then tried "''Shigella flexneri'' entire genome sequence RNA" and got 15,600 results. I then searched "''Shigella flexneri'' entire genome sequence cy3 and cy5" and got 676 results. | ***I then searched "''Shigella flexneri'' whole genome" and got 23,000 results, which is less but definitely not narrowed down enough. I tried "''Shigella flexneri'' entire genome sequence" and got 21,600. I then tried "''Shigella flexneri'' entire genome sequence RNA" and got 15,600 results. I then searched "''Shigella flexneri'' entire genome sequence cy3 and cy5" and got 676 results. | ||
| − | *'''Web of Science''' | + | *[https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= '''Web of Science'''] |
** What original keyword(s) did you use? How many results did you get? | ** What original keyword(s) did you use? How many results did you get? | ||
***I originally just searched "''Shigella flexneri''" and got 24,737 results. | ***I originally just searched "''Shigella flexneri''" and got 24,737 results. | ||
Revision as of 22:47, 9 November 2015
Contents
Electronic Lab Notebook
Information for this assignment can be found in the Week 10 assignment page.
Information was further compiled into the group page for the Oregon Trail Survivors.
Creating the Annotated Bibliography
In order to create an annotated bibliography of genomics papers for my team's species, Shigella flexneri, I visited the following databases/tools and answered the following questions using keyword searches.
- PubMed
- What original keyword(s) did you use? How many results did you get?
- When I searched "Shigella flexneri" I got 4,832 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 searched "Shigella flexneri genome" and got 664 results. "Shigella flexneri entire genome" gave me 15 results and adding the word "sequence" gave me only 11 results.
- What original keyword(s) did you use? How many results did you get?
- Google Scholar
- What original keyword(s) did you use? How many results did you get?
- I searched "Shigella flexneri genome and received 27,800 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 then searched "Shigella flexneri whole genome" and got 23,000 results, which is less but definitely not narrowed down enough. I tried "Shigella flexneri entire genome sequence" and got 21,600. I then tried "Shigella flexneri entire genome sequence RNA" and got 15,600 results. I then searched "Shigella flexneri entire genome sequence cy3 and cy5" and got 676 results.
- What original keyword(s) did you use? How many results did you get?
- Web of Science
- What original keyword(s) did you use? How many results did you get?
- I originally just searched "Shigella flexneri" and got 24,737 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 used "Shigella flexneri entire genome" and got 10 results. I then searched "Shigella flexneri entire genome RNA" and received 1 result.
- What original keyword(s) did you use? How many results did you get?
I then used the Advanced search functions for each of the databases/tools and answered the following questions.
- PubMed
- Which advanced search functions were most useful to narrow down the search? How many results did you get?
- To narrow it down, I went to the Advanced search as Dr. Dahlquist instructed us in class and searched "Shigella flexneri genome" by Title/Abstract and received only 5 results.
- Which advanced search functions were most useful to narrow down the search? How many results did you get?
- Google Scholar
- Which advanced search functions were most useful to narrow down the search? How many results did you get?
- Without checking the "patents" box I only got 550 results for "Shigella flexneri entire genome sequence cy3 cy5". I then narrowed it down to the last 4 years (since 2011) and got 142 results. If I clicked on "Since 2015" without patents I received only 17 results.
- Which advanced search functions were most useful to narrow down the search? How many results did you get?
- Web of Science
- Which advanced search functions were most useful to narrow down the search? How many results did you get?
- I searched "Shigella flexneri" as a topic and added "genome" and "RNA" as topics. This gave me 91 results. I added the topic "cy3 cy5" for the dyes and got 2 results.
- Which advanced search functions were most useful to narrow down the search? How many results did you get?
Overview of Genome Paper
I then used the genome sequencing article found by the group to perform a prospective search in the ISI Web of Science/Knowledge database. First, in PubMed, I went to the Advanced Search. Then I entered "Shigella flexneri genome" and filtered by results with those keywords in the Title/Abstract. This gave me 5 results. I clicked on the first one ("Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence") and saw that it had 13 cited references. Upon visiting this reference list I found a paper called "Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T" with 73 cited references, dated May 2003. To see if there was an older paper that this paper possibly got its original genome sequence from I visited its reference list. There was a paper dated from 2002 called "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157" that looked promising and it was dated October 2002. Our group selected this paper as our genome paper.
- Overview of the search:
- How many articles does this article cite? 37
- How many articles cite this article? 303
- 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?
- Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how S. flexneri has been able to develop resistance to multiple drugs. Furthermore, Shigella is suspected to have evolved from Escherichia coli so a lot of research has been done in how and when pathogenic Shigella split from E. coli on the evolutionary tree.
Microarray Paper
Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509
- PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21483688
- PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071730/
- Publisher Full Text (HTML format): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018509 HTML version]
- Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0018509&representation=PDF
- Copyright: 2011 Peng et al. Article is Open Access and the authors own the copyright, not the journal, under a Creative Commons license.
- Publisher: PLOS One
- Is the article available under "Open Access"? Yes
- Availability: online only
- Did LMU pay a fee for this article: no
- Database used to find the data and article: ArrayExpress
- Terms searched: Shigella flexneri
- Filtered by organism: Shigella flexneri
- Filtered by experiment type: RNA assay, array assay
- Search overview
- Results: 7
- Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant Shigella, and virulence plasmid-cured strains amongst others.
- Search in Web of Knowledge
- Number of articles this article cites: 71
- Number of times this article has been cited: 1
- What research directions have been taken since this article has been published? The only article that cited this paper involved detecting infectious diarrheal diseases by chemiluminescence imaging.
- Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22800/samples/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
- What experiment was performed? What was the "treatment" and the "control"?
- The experiment performed was to identify overlooked small RNAs (sRNAs) and small open reading frames (sORFs) in Shigella that were overlooked in the initial genome sequences. Microarrays were performed to search for sRNAs as well as RT-PCR and northern blots were used to identify sRNAs and regions for possible sRNAs. 64 sRNAs that were previously confirmed were used as controls. As a treatment, cells were harvested in the lag, log, and stationary phases at 37C in LB medium and then in the log and stationary phases at 37C in LB medium with 0.01% Congo red, a salt.
- Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Competitive hybridization was conducted three times for each condition. These were technical replicates because the conditions were different samples (treated differently) measured in different conditions.
Assignments
Individual Journal Assignment Pages
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 14
- Week 15
Individual Journal Assignments
- Kzebrows Week 1
- Kzebrows Week 2
- Kzebrows Week 3
- Kzebrows Week 4
- Kzebrows Week 5
- Kzebrows Week 6
- Kzebrows Week 7
- Kzebrows Week 8
- Kzebrows Week 9
- Kzebrows Week 10
- Kzebrows Week 11
- Kzebrows Week 12
- Kzebrows Week 14
- Kzebrows Week 15
- Final Individual Reflection
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 7
- Class Journal Week 8
- Class Journal Week 9
- Oregon Trail Survivors Week 10
- Oregon Trail Survivors Week 11
- Oregon Trail Survivors Week 12
- Oregon Trail Survivors Week 14
Additional Links
- User Page: Kristin Zebrowski
- Class Page: BIOL/CMSI 367-01
- Team Page: Oregon Trail Survivors
