Cdomin12 Week 11 - Revision history

Cdomin12: purpose and conclusion added

2019-11-14T01:25:38Z

purpose and conclusion added

Cdomin12: /* 5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? */ hap

2019-11-13T07:54:40Z

‎5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?: hap

Cdomin12: /* 2. Outline of Article */ answers

2019-11-13T07:49:53Z

‎2. Outline of Article: answers

Cdomin12: added outline

2019-11-12T23:23:25Z

added outline

Cdomin12: /* Bibliographic Entries */

2019-11-12T23:22:58Z

‎Bibliographic Entries

Cdomin12: /* Reflect */ added entries

2019-11-12T23:22:49Z

‎Reflect: added entries

Cdomin12: /* Annotated Bibliography */ added search questions

2019-11-12T23:20:19Z

‎Annotated Bibliography: added search questions

Cdomin12: /* 2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? */ adv

2019-11-12T23:16:35Z

‎2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?: adv

Cdomin12: /* 2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? */ added adv and disadv

2019-11-12T23:15:35Z

‎2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?: added adv and disadv

Cdomin12: /* 19. 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? */ added adv and disadv

2019-11-12T23:05:24Z

‎19. 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?: added adv and disadv

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 {{template:cdomin12}}
 ==Outline==
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 *Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
 *Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.
 ==Acknowledgments==

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 ====5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?====
-Saccharomyces cerevisiae
+Saccharomyces cerevisiae. Haploid or diploid  was not mentioned.
 ====6. What media did they grow them in? What temperature? What type of incubator? For how long?====

@@ Line 17: / Line 17: @@
 ====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.====
-Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.
+Figure 1: This represents induced or expressed gene expression grown on the potassium free medium at the relative time points. These measurements were made through RT-PCR assays. There is a pretty even amount of induced and repressed genes
-====13. What do the X and Y axes represent?====
+Table 1: This table shows the transcriptional changes at minutes 10, 20, 40, 60, and 120. It measured induction/repression also measured through RT-PCR assays. No trend to show here.
-====14. How were the measurements made?====
+Table 2: Where the strains were taken from in regard to work from other papers.
-====15. What trends are shown by the plots and what conclusions can you draw from the data?====
+Figure 2: This pertains to the cellular function of sulfur amino acid metabolism. It has three parts to it. A shows the mechanism of how potassium starvation effects metabolism. B with the X axis representing mRNA change and Y axis being different genes shows the mRNA change in the different time intervals. C (x axis as time min and Y as intracellular levels of methionine and cysteine) shows.
-====16. How does this work compare with previous studies?====
+Figure 3: One graph (x axis- time in minutes and y axis changes in expression) shows different genes and their change in expression over time. The other graph (x axis- time in minutes and y axis glutathione levels) shows glutathione levels over time. Both of these show that there is no general stress response to potassium starvation.
-====17. What are the important implications of this work?====
+Figure 4: (A) This demonstrates the effect of methylglyoxal production as well as trehalose metabolism from potassium starvation. (B) Two graphs (x axis- time in min and y axis- changes in expression fold) shows the change in expression specifically for genes related to trehalose metabolism and methylglyoxal. Measurements were made through the microarray data. (C) A graph (x axis- time in min and y axis- methylglyoxal concentration) showing MG levels remaining higher after 20 minutes potentially linked to genes induced in trehalose metabolism.
-====18. What future directions should the authors take?====
+Figure 5: (A) Graph (x axis- time in min and y axis- change in expression) shows genes seen in mitochondrial retrograde response. Measurements made through microarray data. DIT2 and DLD2 response done through measurements of microarray data. This shows electrophoresis data for it. (B) mitochondria morphology picture with mutant showing different morphology. Measured through GFP microscopy. (C) Graph (x axis- time min and y axis- ammonium concentration) shows concentration increase after being put in potassium free medium. (D) Graph (x axis- time in min and y axis- ammonium concentration) showing mutated Trk1 or Trk2 did not have more concentration. Measured through samples taken with transformed plasmids.
-====19. 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?====
+Figure 6: (A) Graph (x axis- time in min and y axis- changes in expression) shows different genes during potassium starvation. Measured through microarray experiments. (B) mRNA abundance shows of different cyclins measured through RT-PCR. (C) Demonstrates the cyclin data showing that they are almost undetectable. Measured through immunoblot analysis.
 ==Annotated Bibliography==

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 {{template:cdomin12}}
 ===1. Ten Biological Terms===
 *septin: a protein involved in cytokinesis and also functions in maintaining cell morphology (https://www.biology-online.org/dictionary/Septin, Biology Online, 2019)

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 # Primary research article
 # Data are not available (dead hyperlink)
 # 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

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 *#** How many articles does this article cite?
 *#** How many articles cite this article?
 ===Reflect===

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 ====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
-*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations
+*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
-*Pubmed:
+*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
-*Web of Science*
+*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource.
 ==Acknowledgments==

← Older revision		Revision as of 23:05, 12 November 2019
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	====19. 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?====		====19. 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?====
		+
		+	==Annotated Bibliography==
		+	===Reflect===
		+	====1.What impact does the choice of keywords have on your results?====
		+
		+	====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====
		+	*Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations
		+	*Pubmed:
		+	Web of Science

	==Acknowledgments==		==Acknowledgments==