Difference between revisions of "Kzebrows Week 10"

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(→‎Electronic Lab Notebook: link to assignment page and team page.)
(→‎Annotated Bibliography of Genomics Papers for your Species: Advanced search questions and formatting)
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Information was further compiled into the group page for the [[Team_4 | Oregon Trail Survivors]].
 
Information was further compiled into the group page for the [[Team_4 | Oregon Trail Survivors]].
  
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=== Annotated Bibliography of Genomics Papers for your Species ===
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===Creating the Annotated Bibliography===
  
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For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.
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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.
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*'''PubMed'''
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** What original keyword(s) did you use?  How many results did you get?
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***When I searched "''Shigella flexneri''" I got 4,832 results.
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** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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***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.
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*'''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.
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*'''Web of Science'''
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** 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?
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***I used "''Shigella flexneri'' entire genome" and got 10 results. I then searched "''Shigella flexneri'' entire genome RNA" and received 1 result.  
  
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* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
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* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography.  Specifically, you need to search the literature/biological databases for the following:
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I then used the Advanced search functions for each of the databases/tools and answered the following questions.
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*# The journal article which describes the results of the whole genome sequencing for your species.  ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)''
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*'''PubMed'''
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*#* Use a keyword search for each of these databases/tools and answer the following: 
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** Which advanced search functions were most useful to narrow down the search?  How many results did you get?  
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*#** '''PubMed'''
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***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.
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*#*** What original keyword(s) did you use?  How many results did you get?
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* '''Google Scholar'''
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*#****When I searched "''Shigella flexneri'' genome" I got 664 results.
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** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#*** 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 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.
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***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.  
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*#** '''Google Scholar'''
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* '''Web of Science'''
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*#*** What original keyword(s) did you use?  How many results did you get? I searched "''Shigella flexneri'' genome and received 27,800 results.
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** Which advanced search functions were most useful to narrow down the search?  How many results did you get?  
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*#*** 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.
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***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.
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*#** '''Web of Science'''
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*#*** What original keyword(s) did you use?  How many results did you get?
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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*#* Use the advanced search functions for each of these three databases/tools and answer the following: 
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*#** '''PubMed'''
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#** '''Google Scholar'''
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#** '''Web of Science'''
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
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*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 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).)
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*#** The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
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*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
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*#** The link to the full text of the article (HTML format) from the publisher web site.
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*#** The link to the full PDF version of the article from the publisher web site.
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*#** Who owns the rights to the article?
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*#*** Does the journal own the copyright?
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*#*** Do the authors own the copyright?
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*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
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*#*** Is the article available “Open Access”?
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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.]
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*#** Is this article available in print or online only?
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*#** Has LMU paid a subscription or other fee for your access to this article?
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*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
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==Overview of Genome Paper==
 
==Overview of Genome Paper==

Revision as of 07:57, 6 November 2015

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.
  • 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.
  • 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.


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.
  • 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.
  • 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.

Overview of Genome Paper

  • Used the genome sequencing article to perform a prospective search in the ISI Web of Science/Knowledge database.
  • 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

Shared Journal Assignments

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
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