Week 11 - Revision history

Kdahlquist: /* Grading for this assignment */ update grading info

2019-12-05T21:50:18Z

‎Grading for this assignment: update grading info

Jnimmers: Undo revision 6547 by Jnimmers (talk)

2019-11-14T03:50:21Z

Undo revision 6547 by Jnimmers (talk)

Jnimmers: Answered questions for the outline

2019-11-14T02:41:07Z

Answered questions for the outline

Jnimmers: /* How to Read a Primary Research Article */ Delete section

2019-11-12T23:56:50Z

‎How to Read a Primary Research Article: Delete section

Kdahlquist: link to annotated bib

2019-11-12T23:52:59Z

link to annotated bib

Kdahlquist: add deadline for annotated bib

2019-11-12T23:52:02Z

add deadline for annotated bib

Kdahlquist: /* Assignment */ clarified what goes on team vs individual page

2019-11-12T23:50:28Z

‎Assignment: clarified what goes on team vs individual page

Kdahlquist: /* Annotated Bibliography */ put deadline

2019-11-12T23:48:55Z

‎Annotated Bibliography: put deadline

Kdahlquist: /* Assignment */ add reflection questions

2019-11-12T22:28:47Z

‎Assignment: add reflection questions

Kdahlquist: /* Overview */ add learning objectives

2019-11-12T22:26:14Z

‎Overview: add learning objectives

@@ Line 16: / Line 16: @@
 === Grading for this assignment ===
-* Your individual journal entry for this week is worth a total of 10 points.
+* Your individual journal entry with the outline of the journal club paper is worth a total of 10 points.
 * Your team journal entry for this week is also worth a total of 10 points (instead of 3).  Each member of the team will receive the same grade for the team journal entry.
 * The journal club presentation (delivered on November 14) will be worth a total of 40 points.

@@ Line 22: / Line 22: @@
 === Team Membership ===
-The project groups and roles are:
+The project groups and roles are are:
 # [[FunGals]]: 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
@@ Line 33: / Line 33: @@
 #* Data Analysis: Marcus, Ivy
 #* Designer: DeLisa
-# [[Skinny Genes]]: 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
+# [[Skinny Genes]]: 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: Aby
 #* Quality Assurance: Christina, Jonar
@@ Line 58: / Line 58: @@
 In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
-# 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 its 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.
+# 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.
 #* Online Biological Dictionaries
 #** Web sites
@@ Line 69: / Line 69: @@
 #*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
 #*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
-# 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.
+# 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.
-#What is the main result presented in this paper?
+## What is the main result presented in this paper?
-#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
+## What is the importance or significance of this work?
-#What is the importance or significance of this work?
+## What were the limitations in previous studies that led them to perform this work?
-#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
+## How did they treat the yeast cells (what experiment were they doing?)
-#What were the limitations of previous studies that led them to perform this work?
+## What strain(s) of yeast did they use?  Were the strain(s) haploid or diploid?
-#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
+## What media did they grow them in?  What temperature?  What type of incubator?  For how long?
-#How did they treat the yeast cells (what experiment were they doing?)
+## What controls did they use?
-#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
+## How many replicates did they perform per treatment or timepoint?
-#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
+## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
-#* The researchers used Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, the authors did not specify whether this particular strain was haploid or diploid.
+## What mathematical/statistical method did they use to analyze the data?
-#What media did they grow them in? What temperature? What type of incubator? For how long?
+## Are the data publicly available for download?  From which web site?
 ##Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
-#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
+##* What do the X and Y axes represent?
-#What controls did they use?
+##* How were the measurements made?
-#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
+##* What trends are shown by the plots and what conclusions can you draw from the data?
-#How many replicates did they perform per treatment or timepoint?
+## How does this work compare with previous studies?
-#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
+## What are the important implications of this work?
-#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
+## What future directions should the authors take?
-#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
+## 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?
 === Journal Club Presentation ===

@@ Line 22: / Line 22: @@
 === Team Membership ===
-The project groups and roles are are:
+The project groups and roles are:
 # [[FunGals]]: 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
@@ Line 33: / Line 33: @@
 #* Data Analysis: Marcus, Ivy
 #* Designer: DeLisa
-# [[Skinny Genes]]: 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
+# [[Skinny Genes]]: 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: Aby
 #* Quality Assurance: Christina, Jonar
@@ Line 58: / Line 58: @@
 In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
-# 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.
+# 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 its 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.
 #* Online Biological Dictionaries
 #** Web sites
@@ Line 69: / Line 69: @@
 #*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
 #*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
-# 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.
+# 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.
-## What is the main result presented in this paper?
+#What is the main result presented in this paper?
-## What is the importance or significance of this work?
+#*This paper found that when exposed to arsenite, a chemical compound including arsenic (in varying concentrations), yeast cells see a spike in glutathione synthesis as well as the assimilation of sulfur, which acts to help with the synthesis of glutathione. Using this information, the researchers investigated in order to find what transcriptional factors were responsible for this occurrence and they found that two factors carried out these processes in response to arsenite exposure, Yap1p, and Met4p.
-## What were the limitations in previous studies that led them to perform this work?
+#What is the importance or significance of this work?
-## How did they treat the yeast cells (what experiment were they doing?)
+#* Since arsenite is found naturally in the world, this study works to highlight how cells have evolved to battle the dangerous toxicity of arsenic.
-## What strain(s) of yeast did they use?  Were the strain(s) haploid or diploid?
+#What were the limitations of previous studies that led them to perform this work?
-## What media did they grow them in?  What temperature?  What type of incubator?  For how long?
+#* This study was performed after previous studies found that arsenic trioxide was a key component in helping to treat acute promyelocytic leukemia.
-## What controls did they use?
+#How did they treat the yeast cells (what experiment were they doing?)
-## How many replicates did they perform per treatment or timepoint?
+#* Yeast cells were treated with a sodium arsenite compound that varied in concentration to test the yeast cell’s reaction to the compound (What was released? What was the kinetic response? What genes were activated? What was synthesized? How did it affect cellular processes in general?)
-## What method did they use to prepare the RNA, label it and hybridize it to the microarray?
+#What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
-## What mathematical/statistical method did they use to analyze the data?
+#* The researchers used Saccharomyces cerevisiae in this experiment, and while it can exist as both haploid and diploid, the authors did not specify whether this particular strain was haploid or diploid.
-## Are the data publicly available for download?  From which web site?
+#What media did they grow them in? What temperature? What type of incubator? For how long?
 ##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?
+#* The yeast strains were grown at 30° C on YNB media (0.67% yeast nitrogen base and 2% glucose) for an undisclosed amount of time in an unknown incubator before being hybridized for 12-18 hours at 42° C.
-##* How were the measurements made?
+#What controls did they use?
-##* What trends are shown by the plots and what conclusions can you draw from the data?
+#* In the northern blot analysis, the researchers used an 18s rRNA was used as a loading control to make sure that the blotting bands were not altering due to chance or a mistake in their methods. With no significant change happening in the control row, it was assumed that the bands changed explicitly due to exposure to 0.2 mM As(III), Arsenite.
-## How does this work compare with previous studies?
+#How many replicates did they perform per treatment or timepoint?
-## What are the important implications of this work?
+#*Information on replicates was not explicitly given, however, the authors do state that comparisons consisted of at least three independent experiments.
-## What future directions should the authors take?
+#What method did they use to prepare the RNA, label it and hybridize it to the microarray?
-## 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?
+#* The RNA was isolated from exponentially growing yeast cells that were either untreated or exposed to sodium arsenite. The RNA was primed with a random hexamer (Invitrogen) and anchored oligo(dT)20 primer (ABgene) as well as labeled in a reverse transcription reaction with Cy3-dUTP (Sulfo-Cyanine5 dUTP) or Cy5-dUTP (Sulfo-Cyanine3 dUTP). The labeled cDNA was then cleaned and mixed before being added to a hybridization buffer (DIGeasy). Before the hybridization, the microarray chip was hybridized with 1% BSA (Bovine Serum Albumin) in DIGeasy hybridization buffer at 42°C for 1 h. The hybridization mix was placed at 100°C for 2 min and then at 37°C for 30 min, and then they were hybridized completely for 12-18 hours at 42°C.
 === Journal Club Presentation ===

@@ Line 89: / Line 89: @@
 ## What future directions should the authors take?
 ## 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?
 === Journal Club Presentation ===

@@ Line 3: / Line 3: @@
 '''''There is an interim deadline for Tuesday, November 12 at 12:01am PST, to decide your team name and select your Project Manager.'''''
-'''The Annotated Bibliography is due Tuesday, November 19 at 12:01am PST.'''
+'''The [[Week_11#Annotated_Bibliography_.28Due_Tuesday.2C_November_19.2C_12:01am_PST.29 | Annotated Bibliography]] is due Tuesday, November 19 at 12:01am PST.'''
 == Overview ==

@@ Line 1: / Line 1: @@
-'''This journal entry is due on Thursday, November 14, at 12:01 PST.''' ''(Wednesday night/Thursday morning)''
+'''This journal entry is due on Thursday, November 14, at 12:01am PST.''' ''(Wednesday night/Thursday morning)''
-'''''There is an interim deadline for Tuesday, November 12 at 12:01 PST, to decide your team name and select your Project Manager.'''''
+'''''There is an interim deadline for Tuesday, November 12 at 12:01am PST, to decide your team name and select your Project Manager.'''''
 == Overview ==

@@ Line 173: / Line 173: @@
 ==== Assignment ====
 * 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 [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.

@@ Line 157: / Line 157: @@
 * Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.
-=== Annotated Bibliography ===
+=== Annotated Bibliography (Due Tuesday, November 19, 12:01am PST)===
-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.
+This exercise will be primarily performed in class on Tuesday, November 12.  What is not finished in class is due on Tuesday, November 19, 12:01am PST).
 ==== Resources ====

@@ Line 217: / Line 217: @@
 *#** How many articles does this article cite?
 *#** How many articles cite this article?
 ==== Sample Bibliographic Entry ====

@@ Line 7: / Line 7: @@
 * Everyone will contribute to [[Week_11#Whole_Team_Journal_Assignment:_Creating_a_Team_Wiki_Page | Creating your team's home page,]] and in the process, getting yourselves organized for the final project.
 * To find and use scholarly and discipline-specific professional information, understanding the role of journals and publishers in controlling and providing access to scholarly content.
 * To evaluate resources for reliability, validity, accuracy, authority, and bias.
 * To prepare and give a journal club presentation, critically evaluating an article from the primary literature.