Aporras1 Week 12 - Revision history

Aporras1: /* Acknowledgements */ signed

2017-11-21T07:39:17Z

‎Acknowledgements: signed

Aporras1: pres prep deletion header

2017-11-21T07:37:19Z

pres prep deletion header

Aporras1: /* Conclusions */ last notes

2017-11-21T07:35:24Z

‎Conclusions: last notes

Aporras1: /* Conclusions */ up to cer

2017-11-21T07:29:53Z

‎Conclusions: up to cer

Aporras1: /* Conclusions */ up until 8

2017-11-21T07:21:27Z

‎Conclusions: up until 8

Aporras1: /* Results */ final result

2017-11-21T07:11:01Z

‎Results: final result

Aporras1: /* Terms, Definitions, & Citations */ spacing

2017-11-21T07:06:31Z

‎Terms, Definitions, & Citations: spacing

Aporras1: /* Results */ fig 3

2017-11-21T07:05:31Z

‎Results: fig 3

Aporras1: /* Results */ fig 2

2017-11-21T07:02:27Z

‎Results: fig 2

Aporras1: /* Results */ table 1

2017-11-21T06:57:21Z

‎Results: table 1

← Older revision		Revision as of 07:39, 21 November 2017
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	'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''		'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
		+
		+	[[User:Aporras1\|Aporras1]] ([[User talk:Aporras1\|talk]]) 23:39, 20 November 2017 (PST)

	==References==		==References==

← Older revision		Revision as of 07:37, 21 November 2017
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	Assignment page: [[Week 12\|Week 12 Assignment]]		Assignment page: [[Week 12\|Week 12 Assignment]]
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−	~~==Presentation Prep==~~

	===Terms, Definitions, & Citations===		===Terms, Definitions, & Citations===

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 ***Supports the hypothesis that "lipid modifications are a major contributor to the induced heat and salt tolerance of yeast cells (Mahuaet al.,2000)".
 *There is a dependence on the level of heat shock the cells underwent associated with the number of unregulated genes.
+*Additionally its possible to find genes which are associated with general stress and not just temperature changes.
-# Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser at 100% scale to see 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.
+**These genes are known as "CER" or common environmental response genes.
-#* What is the importance or significance of this work?
+**These genes could be associated with tolerance to changes as the cells treated with pre-adaptation had a double in the gene expression of these CER genes which could point to their association with tolerance or changes in temperature.
-#* Briefly state the result shown in each of the figures and tables.
+*Genes which were upregulated during cold shock were also upregulated during heat shock which could ultimately suggest that these genes are for general stress response and not just cold shock or heat shock alone.
 ===Deliverables===

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 **Cell growth
 **Cell division
+*They were not able to find a common regulatory signal to the promoters of the genes which are down regulated after heat shock.
 # Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser at 100% scale to see 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.

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 ====Conclusions====
+*The profiles in each of the four conditions are different and specific to each shock they were put under.
 # Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser at 100% scale to see 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.

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 *Figure 2: Microarray data of clustering of genes which are regulated by heat shock where the green represents down regulation and the red represents up regulation. The figure further breaks down the genes into their respective major clusters.
 *Figure 3: Venn diagram which puts the ORFs up regulated during heat shock. The pre-adaptation was up to 37◦C. 31 of the 34 have between 1 and 12 copies of the two consensus sequences which haven't yet been identified.
-*Figure 4:
+*Figure 4: Clustering of the genes which were up regulated by heat and cold shock. The higher intensity of the color corresponds with the regulatory ratio and the box provides the number of genes in the respective cluster.
 ====Conclusions====

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 . '''Method of Chomczynski and Sacchi''': "RNA isolation by a single extraction with an acid guanidinium thiocyanate-phenol-chloroform mixture is described. The method provides a pure preparation of undegraded RNA in high yield and can be completed within 4 h" (Chomczynski, P., & Sacchi, N., 1987) Used for large amounts of samples and to isolate RNA from a small amount of cells.
-. '''Correspondence analysis''': "Correspondence analysis is a statistical technique that provides a graphical representation of cross tabulations (which are also known as cross tabs, or contingency tables)"(Yelland, P. M., 2010). Useful when there are two or more categories.
+. '''Correspondence analysis''': "Correspondence analysis is a statistical technique that provides a graphical representation of cross tabulations (which are also known as cross tabs, or contingency tables)" (Yelland, P. M., 2010). Useful when there are two or more categories.
 . '''Glutathione''': "A peptide C10H17N3O6S that contains one amino acid residue each of glutamic acid, cysteine, and glycine..." (Merriam-Webster.com, n.d.) Often found in tissues of animals and plants as it has an essential role as a coenzyme of oxidation-reduction reactions within those tissues.
@@ Line 21: / Line 21: @@
 . '''In silico''': "...an expression used to mean “performed on computer or via computer simulation”" (mpkb.org, n.d.).
-. '''Cluster analysis''': "Statistical classification technique in which cases, data, or objects (events, people, things, etc.) are sub-divided into groups (clusters) such that the items in a cluster are very similar (but not identical) to one another and very different from the items in other clusters"(BusinessDictionary.com, n.d.). Useful to observe or analyze patterns or relationships in data.
+. '''Cluster analysis''': "Statistical classification technique in which cases, data, or objects (events, people, things, etc.) are sub-divided into groups (clusters) such that the items in a cluster are very similar (but not identical) to one another and very different from the items in other clusters" (BusinessDictionary.com, n.d.). Useful to observe or analyze patterns or relationships in data.
 . '''Haploid''': "A cell (especially gametes or germ cells) containing half of the number of homologous chromosomes in somatic cells" (Biology-Online.org, n.d.).

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 ====Results====
-#Figure 1: Biplot created with the use of correspondence analysis of the data by the different conditions of heat shock and cold shocks. The overwhelming black dots represent the individual genes. The colored lines represent the different conditions and their respective temperatures. The more positive values represent up regulation and the more negative values represent down regulation. The medians of the hybridizations are represented by the colored circles in the biplot.
+*Figure 1: Biplot created with the use of correspondence analysis of the data by the different conditions of heat shock and cold shocks. The overwhelming black dots represent the individual genes. The colored lines represent the different conditions and their respective temperatures. The more positive values represent up regulation and the more negative values represent down regulation. The medians of the hybridizations are represented by the colored circles in the biplot.
-#Table 1: The number of genes which respond to the different conditions/changes. Important to note: only genes whose expression changes were high to medium significance were included.
+*Table 1: The number of genes which respond to the different conditions/changes. Important to note: only genes whose expression changes were high to medium significance were included.
-#Figure 2: Microarray data of clustering of genes which are regulated by heat shock where the green represents down regulation and the red represents up regulation. The figure further breaks down the genes into their respective major clusters.
+*Figure 2: Microarray data of clustering of genes which are regulated by heat shock where the green represents down regulation and the red represents up regulation. The figure further breaks down the genes into their respective major clusters.
 ====Conclusions====