Difference between revisions of "Laurmagee: Week 10"

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#''""''
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#''"Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid"''
 
#*I used GoogleScholar and entered into the search bar, "Sinorhizobium meliloti".  
 
#*I used GoogleScholar and entered into the search bar, "Sinorhizobium meliloti".  
−
#*Give an overview of the results of the search.
+
#*In this article, the authors conclude that Sinorhizobium meliloti contains nucleotide sequences characteristic of nitrogen fixating bacteria. They confirm this conclusion through sequencing the nucleotides of Sinorhizobium meliloti and determining the subsequent proteins that illicit a particular function.  
 
#*There was a total of 16,800 results.  
 
#*There was a total of 16,800 results.  
−
#*Give an assessment of how relevant the results were.
+
#*This article was published in 2001, so quite a while has passed since, but I think that the results are still fairly relevant. The researchers identified the function of certain genes in Sinorhizobium meliloti, which is information that will never be outdated, but may be improved with further details of the specific function.  
−
#*Record the full bibliographic citation of the relevant paper(s), formatted according to the Guidelines for Literature Citations in a Scientific Paper.
+
#*rnett, M. J., Fisher, R. F., Jones, T., Komp, C., Abola, A. P., Barloy-Hubler, F., & Long, S. R. (2001). Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proceedings of the National Academy of Sciences, 98(17), 9883-9888. Retrieved from http://www.pnas.org/content/98/17/9883.abstract
−
#*Create a link to the HTML version of your journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
+
#*[[http://www.pnas.org/content/98/17/9883.full]]
−
#*Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.
+
#*[[http://www.pnas.org/content/98/17/9883.full.pdf]]
−
#*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
+
#*I searched the web of science database with the key terms nucleotide sequence, Sinorhizobium meliloti, and the the first author of the article Barnett. I got two results from this search and the first was the article I have noted above.
−
#*Give an overview of the results of the search.
+
#*This article has been cited 156 times in Wed of Science and 282 times total included all other databases.  
−
#*How many results did you get?
+
#*It appears that many of these articles have expanded upon the research done in the article above, by continuing to identify functions of Sinorhizobium meliloti from its nucleotide sequence. Many of the articles deal with genomics in an environmental setting, because as the article notes, Sinorhizobium meliloti is greatly involved with nitrogen fixation. Therefore, the term nitrogen comes up a lot in these articles as well.
−
#*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?
+
−
#*The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.  
+
−
#*State which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). It may actually be easier to find the microarray data first and then find the corresponding journal article.  
+
−
#*State what you used as search terms and what type of search terms they were.
+
−
#*Give an overview of the results of the search. How many results did you get?
+
−
#*Give an assessment of how relevant the results were.  
+
−
#*Record the full bibliographic citation of the relevant papers, formatted according to the Guidelines for Literature Citations in a Scientific Paper.  
+
−
#*Create a link to the HTML version of the journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
+
−
#*Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.  
+
−
#*You must also link to the web site where the microarray data resides.  
+
−
#*Download the microarray dataset file, upload it to the wiki, and link to it on your individual and team pages. Remeber, microarray data is not centrally located on the web. Some major sources are:
+
−
#*What experiment was performed?
+
−
#*What was the "treatment" and what was the "control" in the experiment?
+
−
#*Were replicate experiments of the "treatment" and "control" conditions conducted?
+
−
#*Were these biological or technical replicates?
+
−
#*How many of each?
+
 
#''"The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti"''
 
#''"The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti"''
 
#*I used GoogleScholar and entered into the search bar, "Sinorhizobium meliloti".  
 
#*I used GoogleScholar and entered into the search bar, "Sinorhizobium meliloti".  
−
#*Give an overview of the results of the search.
+
#*The article outlines the entire sequence of the specific strain of N2-fixing endosymbiont Sinorhizobium meliloti.
 
#*There was a total of 16,800 results.  
 
#*There was a total of 16,800 results.  
−
#*Give an assessment of how relevant the results were.
+
#*This article was also published in 2001, so again, the results had not been published recently, but the information it offers is still very much applicable to present day research as well.  
−
#*Record the full bibliographic citation of the relevant paper(s), formatted according to the Guidelines for Literature Citations in a Scientific Paper.
+
#*Finan, T. M., Weidner, S., Wong, K., Buhrmester, J., Chain, P., Vorholter, F. J., . . . Puhler, A. (2001). The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proceedings of the National Academy of Sciences, 98(17), 9889-9894. Retrieved from http://www.pnas.org/content/98/17/9889.abstract
−
#*Create a link to the HTML version of your journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
+
#*[[http://www.pnas.org/content/98/17/9889.full]]
−
#*Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.
+
#*[[http://www.pnas.org/content/98/17/9889.full.pdf]]
−
#*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
+
#*I entered in the following terms into the search field on the Web of Science database: complete sequence, Sinorhizobium meliloti, and the author Finan. I come up with three results and the article I was looking for that is noted above, was number three on the list.
−
#*Give an overview of the results of the search.
+
#*This article was cited 167 time in web of science and 282 times total in all databases available.  
−
#*How many results did you get?
+
#*This article has been cited in many of the same articles that were previously listed in my search of the first article on this page. The deal with exploring the functions of Sinorhizobium meliloti more closely and unique to this article, there are some papers that worked on the interactions this bacteria might play in natural environments.  
−
#*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?
+
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 15:04, 1 November 2013 (PDT)
−
#*The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.  
+
[[Category:Journal Entry]]
−
#*State which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). It may actually be easier to find the microarray data first and then find the corresponding journal article.  
+
−
#*State what you used as search terms and what type of search terms they were.
+
−
#*Give an overview of the results of the search. How many results did you get?
+
−
#*Give an assessment of how relevant the results were.
+
−
#*Record the full bibliographic citation of the relevant papers, formatted according to the Guidelines for Literature Citations in a Scientific Paper.  
+
−
#*Create a link to the HTML version of the journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.  
+
−
#*Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.  
+
−
#*You must also link to the web site where the microarray data resides.
+
−
#*Download the microarray dataset file, upload it to the wiki, and link to it on your individual and team pages.  Remeber, microarray data is not centrally located on the web. Some major sources are:  
+
−
#*What experiment was performed?
+
−
#*What was the "treatment" and what was the "control" in the experiment?
+
−
#*Were replicate experiments of the "treatment" and "control" conditions conducted?
+
−
#*Were these biological or technical replicates?
+
−
#*How many of each?
+

Latest revision as of 23:21, 12 November 2013

  1. "Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid"
    • I used GoogleScholar and entered into the search bar, "Sinorhizobium meliloti".
    • In this article, the authors conclude that Sinorhizobium meliloti contains nucleotide sequences characteristic of nitrogen fixating bacteria. They confirm this conclusion through sequencing the nucleotides of Sinorhizobium meliloti and determining the subsequent proteins that illicit a particular function.
    • There was a total of 16,800 results.
    • This article was published in 2001, so quite a while has passed since, but I think that the results are still fairly relevant. The researchers identified the function of certain genes in Sinorhizobium meliloti, which is information that will never be outdated, but may be improved with further details of the specific function.
    • rnett, M. J., Fisher, R. F., Jones, T., Komp, C., Abola, A. P., Barloy-Hubler, F., & Long, S. R. (2001). Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proceedings of the National Academy of Sciences, 98(17), 9883-9888. Retrieved from http://www.pnas.org/content/98/17/9883.abstract
    • [[1]]
    • [[2]]
    • I searched the web of science database with the key terms nucleotide sequence, Sinorhizobium meliloti, and the the first author of the article Barnett. I got two results from this search and the first was the article I have noted above.
    • This article has been cited 156 times in Wed of Science and 282 times total included all other databases.
    • It appears that many of these articles have expanded upon the research done in the article above, by continuing to identify functions of Sinorhizobium meliloti from its nucleotide sequence. Many of the articles deal with genomics in an environmental setting, because as the article notes, Sinorhizobium meliloti is greatly involved with nitrogen fixation. Therefore, the term nitrogen comes up a lot in these articles as well.
  2. "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti"
    • I used GoogleScholar and entered into the search bar, "Sinorhizobium meliloti".
    • The article outlines the entire sequence of the specific strain of N2-fixing endosymbiont Sinorhizobium meliloti.
    • There was a total of 16,800 results.
    • This article was also published in 2001, so again, the results had not been published recently, but the information it offers is still very much applicable to present day research as well.
    • Finan, T. M., Weidner, S., Wong, K., Buhrmester, J., Chain, P., Vorholter, F. J., . . . Puhler, A. (2001). The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proceedings of the National Academy of Sciences, 98(17), 9889-9894. Retrieved from http://www.pnas.org/content/98/17/9889.abstract
    • [[3]]
    • [[4]]
    • I entered in the following terms into the search field on the Web of Science database: complete sequence, Sinorhizobium meliloti, and the author Finan. I come up with three results and the article I was looking for that is noted above, was number three on the list.
    • This article was cited 167 time in web of science and 282 times total in all databases available.
    • This article has been cited in many of the same articles that were previously listed in my search of the first article on this page. The deal with exploring the functions of Sinorhizobium meliloti more closely and unique to this article, there are some papers that worked on the interactions this bacteria might play in natural environments.

Laurmagee (talk) 15:04, 1 November 2013 (PDT)

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