Difference between revisions of "Eyoung20 journal week 11"

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== Individual Journal Assignment ==
 
== Individual Journal Assignment ==
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===Annotated Bibliography===
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APA + DOI number
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* PubMed Abstract: 
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* PubMed Central:
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* Publisher Full Text (HTML): 
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* Publisher Full Text (PDF): 
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* Copyright: 
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* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
 +
 +
APA + DOI number
 +
* PubMed Abstract: 
 +
* PubMed Central:
 +
* Publisher Full Text (HTML): 
 +
* Publisher Full Text (PDF): 
 +
* Copyright: 
 +
* Publisher: 
 +
* Availability: 
 +
* Did LMU pay a fee for this article:
  
 
* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
 
* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).

Revision as of 15:30, 12 November 2019

Individual Journal Assignment

Annotated Bibliography

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:

APA + DOI number

  • PubMed Abstract:
  • PubMed Central:
  • Publisher Full Text (HTML):
  • Publisher Full Text (PDF):
  • Copyright:
  • Publisher:
  • Availability:
  • Did LMU pay a fee for this article:
  • Store this journal entry as "username Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
  • Invoke your template on your journal entry page so that you:
    • Link from your journal entry page to this Assignment page.
    • Link from your journal entry to your user page.
    • Add the "Journal Entry" category to the end of your wiki page.
  • Because you have invoked your template on your user page, you should also have a:
    • Link from your user page to this Assignment page.
    • Link to your journal entry from your user page.
  • Note that this week, we will add two new categories, "Group Projects" and a category for your team's name. Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.
  • Include both the Acknowledgments and References section as specified by the Week 1 assignment.
  • The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Conclusion, Acknowledgments, and References (as specified by the Week 1 assignment).
    • All files generated in the protocol must be uploaded to the wiki and linked to from your journal entry page in a "Data and Files" section.
    • You will write a summary paragraph that gives the conclusions from this week's analysis.

Team Membership

The project groups and roles are are:

  1. Team 1: Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
    • Project Manager: Mike
    • Quality Assurance: Iliana
    • Data Analysis: Emma, Kaitlyn
    • Coder: Mike
  2. Arseknights: Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
    • Project Manager: Naomi
    • Quality Assurance: Naomi, Joey
    • Data Analysis: Marcus, Ivy
    • Designer: DeLisa
  3. Team 3: Barreto, L., Canadell, D., Valverde‐Saubí, D., Casamayor, A., & Ariño, J. (2012). The short‐term response of yeast to potassium starvation. Environmental microbiology, 14(11), 3026-3042. DOI: 10.1111/j.1462-2920.2012.02887.x
    • Project Manager: TBA
    • Quality Assurance: Christina, Jonar
    • Data Analysis: David, Aby
    • Coder: Mihir

Presentation Prep: Individual Journal Pages

In preparation for your journal club presentation, you will each individually complete the following assignment on your individual journal page.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
  2. Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
    1. What is the main result presented in this paper?
    2. What is the importance or significance of this work?
    3. What were the limitations in previous studies that led them to perform this work?
    4. How did they treat the yeast cells (what experiment were they doing?)
    5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    6. What media did they grow them in? What temperature? What type of incubator? For how long?
    7. What controls did they use?
    8. How many replicates did they perform per treatment or timepoint?
    9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
    10. What mathematical/statistical method did they use to analyze the data?
    11. Are the data publicly available for download? From which web site?
    12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
      • What do the X and Y axes represent?
      • How were the measurements made?
      • What trends are shown by the plots and what conclusions can you draw from the data?
    13. How does this work compare with previous studies?
    14. What are the important implications of this work?
    15. What future directions should the authors take?
    16. Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
How to Read a Primary Research Article

A primary research article is divided into sections that each have a different purpose. Articles in Science and Nature are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there.

Abstract

The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on PubMed and may be the only part of the text publicly available.

Introduction

The introduction gives the background information necessary to understand the paper. The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

Funnel.jpg
  • States importance of the problem
  • States what is known about the problem
  • States what is unknown about the problem
  • States clues that suggest how to approach the unknown
  • States the question the paper is trying to address
  • States the experimental approach
  • Sometimes briefly states the answer they found
Materials and Methods

Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in Science and Nature severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.

Results

Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.

Discussion

States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.

References

List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.

Caveat Emptor

Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

Journal Club Presentation

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.

  • Please follow the Presentation Guidelines PowerPoint on Brightspace for how to format your slides.
  • You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
  • You need to present the information in the outline of your journal article listed above, but organized as a presentation.
  • Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am on Thursday, November 14
    • You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
  • Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the Presentation Rubric.
  • Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
    1. What is the speaker's take-home message (one short sentence)?
    2. What is the best thing about this presentation?
    3. What needs improvement?
    4. Please comment on the speaking style (language and delivery) of each presenter.
  • Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this one.

Annotated Bibliography

This exercise will be primarily performed in class on Tuesday, November 12. The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.

Resource: BIOL/CMSI 367 LibGuide

  1. Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member).
    • Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
      • The complete bibliographic reference in the APA style (see this link). 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).)
      • The link to the abstract from PubMed.
      • The link to the full text of the article in PubMedCentral.
      • The link to the full text of the article (HTML format) from the publisher web site.
      • The link to the full PDF version of the article from the publisher web site.
      • Who owns the rights to the article and what is the availability?
        • Does the journal or the authors own the copyright?
        • Is the article available “Open Access” upon publication under a Creative Commons license?
        • If the article is not Open Access, is it available for free after a certain period of time has elapsed?
      • 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 http://oaspa.org/membership/members/ for a list of members of the Open Access Scholarly Publishers Association)
      • Is this article available in print or online only?
        • Has LMU paid a subscription or other fee for your access to this article?
      • Are the data associated with this article available? If so, provide a link to the dataset.
  2. You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
    • Use a keyword search for the first three databases/tools and answer the following:
      • PubMed
        • What original keyword(s) did you use? How many results did you get?
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • Google Scholar
        • What original keyword(s) did you use? How many results did you get?
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • Web of Science
        • What original keyword(s) did you use? How many results did you get?
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • Use the advanced search functions for each of these three databases/tools and answer the following:
      • PubMed
        • 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?
      • Web of Science
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • Perform a prospective search on the following three review articles in Web of Science and answer the following:
        • Aguilera, J., Randez-Gil, F., & Prieto, J.A. (2007). Cold Response in Saccharomyces cerevisiae: New Functions for Old Mechanisms. FEMS Microbiological Reviews, 31, 327–341. doi: 10.1111/j.1574-6976.2007.00066.x
          • How many articles does this article cite?
          • How many articles cite this article?
        • Al-Fageeh, M.B. & Smales, C.M. (2006). Control and Regulation of the Cellular Responses to Cold Shock: the Responses in Yeast and Mammalian Systems. Biochemical Journal, 397, 247–259. doi: 10.1042/BJ20060166
          • How many articles does this article cite?
          • How many articles cite this article?
        • Thieringer, H.A., Jones, P.G.,& Inouye, M. (1998). Cold shock and adaptation. BioEssays, 20, 49–57. doi: 10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.0.CO;2-N
          • How many articles does this article cite?
          • How many articles cite this article?

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167


Eyoung20 user page

Assignment pages Individual Journal Class Journal
week 1 Eyoung20 journal week 1 Class Journal Week 1
week 2 Eyoung20 journal week 2 Class Journal Week 2
week 3 ASP1/YDR321W Week 3 Class Journal Week 3
week 4 Eyoung20 journal week 4 Class Journal Week 4
week 5 Ancient mtDNA Week 5 Class Journal Week 5
week 6 Eyoung20 journal week 6 Class Journal Week 6
week 7 Eyoung20 journal week 7 Class Journal Week 7
week 8 Eyoung20 journal week 8 Class Journal Week 8
week 9 Eyoung20 journal week 9 Class Journal Week 9
week 10 Eyoung20 journal week 10 Class Journal Week 10
week 11 Eyoung20 journal week 11 FunGals
week 12/13 Knguye66 Eyoung20 Week 12/13 FunGals
week 15 Knguye66 Eyoung20 Week 15 FunGals
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