Dbashour Week 12 - Revision history

Dbashour: /* Cold shock and microarray procedures of yeast samples */ syntax

2017-11-21T22:13:17Z

‎Cold shock and microarray procedures of yeast samples: syntax

Dbashour: added template

2017-11-21T19:58:21Z

added template

Dbashour: /* Acknowledgements */ updated with signature

2017-11-21T19:57:34Z

‎Acknowledgements: updated with signature

Dbashour: added flow chart

2017-11-21T19:55:39Z

added flow chart

Dbashour: /* References */ updated

2017-11-21T19:47:20Z

‎References: updated

Dbashour: /* List of 10 Unknown Words and Their Definitions */ finished definitions

2017-11-21T19:43:49Z

‎List of 10 Unknown Words and Their Definitions: finished definitions

Dbashour: finished outline

2017-11-21T17:17:27Z

finished outline

Dbashour: added section 1 of results

2017-11-21T09:48:11Z

added section 1 of results

Dbashour: added methods

2017-11-21T09:16:10Z

added methods

Dbashour: added introduction of outline

2017-11-21T08:43:21Z

added introduction of outline

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 * '''The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells'''
 == Cold shock and microarray procedures of yeast samples ==
-* S. cerevisiae YPH500 was used for all the analyses
+* ''S. cerevisiae'' YPH500 was used for all the analyses
 * Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm
 * 50 ml of the culture were collected for a reference time of 0
@@ Line 45: / Line 45: @@
 * Fluorescence intensities were normalized
 * Data was clustered and referred to the Munich Information Center for Protein Sequences functional database
 * Functional relationships among the genes in each cluster was determined
 == Results and Discussion ==
 === Global Expression Analysis of Low Temperature Response in Yeast Cells Using a cDNA Microarray ===

← Older revision		Revision as of 19:58, 21 November 2017
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	*Shaw, P. E. (2002). Peptidyl‐prolyl isomerases: A new twist to transcription. EMBO reports, 3(6), 521-526. <br>		*Shaw, P. E. (2002). Peptidyl‐prolyl isomerases: A new twist to transcription. EMBO reports, 3(6), 521-526. <br>
	*Witten, D., & Tibshirani, R. (2007). A comparison of fold-change and the t-statistic for microarray data analysis. Analysis, 1776, 58-85. <br>		*Witten, D., & Tibshirani, R. (2007). A comparison of fold-change and the t-statistic for microarray data analysis. Analysis, 1776, 58-85. <br>
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		+	{{template:dbashour}}

← Older revision		Revision as of 19:57, 21 November 2017
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	=Acknowledgements=		=Acknowledgements=
		+	I met with Corrine outside of class to discuss the method of presenting for the journal club. We worked on our presentation together and equally prepared for the assignment.
		+	While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. <br>
		+	[[User:Dbashour\|Dbashour]] ([[User talk:Dbashour\|talk]]) 11:57, 21 November 2017 (PST)

	=References=		=References=

@@ Line 13: / Line 13: @@
 # midlgarithmic - cell numbers increase in a logarithmic fashion but have not reached their full reproduction rate (Rogers & Kadner, 2017)
 # 2-fold - method of reporting statistics using log2 that results in more reproducible gene lists than do the ordinary and modified t-statistics (Witten & Tibshirani, 2007)
 =Outline of Article=
@@ Line 127: / Line 131: @@
 * Other organisms show similar responses in gene expression when exposed to environmental stresses
-==Deliverable==
+=Deliverable=
 [[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation]]
-==Acknowledgements==
+=Acknowledgements=
-==References==
+=References=
 *AccessScience. (2015). Diauxic growth (diauxie). Retrieved November, 2017, from https://www.accessscience.com/content/diauxic-growth-diauxie/BR0105151 <br>
 *Honee, V. (2009). De novo. Retrieved November, 2017, from http://www.biology-online.org/dictionary/De_novo <br>

← Older revision		Revision as of 19:47, 21 November 2017
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	==References==		==References==
		+	*AccessScience. (2015). Diauxic growth (diauxie). Retrieved November, 2017, from https://www.accessscience.com/content/diauxic-growth-diauxie/BR0105151 <br>
		+	*Honee, V. (2009). De novo. Retrieved November, 2017, from http://www.biology-online.org/dictionary/De_novo <br>
		+	*King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). A Dictionary of Genetics. In Oxford Reference. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444<br>
		+	*Lackie, J. M. (2013). The dictionary of cell and molecular biology. Oxford: Academic Press. <br>
		+	*LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
		+	*Lundin, C. (2005). Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks. Nucleic Acids Research, 33(12), 3799-3811. doi:10.1093/nar/gki681 <br>
		+	* National Center for Biotechnology Information (2016). Trehalose. Retrieved November 2017, from https://pubchem.ncbi.nlm.nih.gov/compound/trehalose#section=Top <br>
		+	*Ratini, M. (2016). Hypoxia and Hypoxemia. Retrieved November, 2017, from https://www.webmd.com/asthma/guide/hypoxia-hypoxemia#1 <br>
		+	*Rogers, K., & Kadner, R. J. (2017). Growth of bacterial populations. Retrieved November, 2017, from https://www.britannica.com/science/bacteria/Growth-of-bacterial-populations#ref955458 <br>
		+	*Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
		+	*Shaw, P. E. (2002). Peptidyl‐prolyl isomerases: A new twist to transcription. EMBO reports, 3(6), 521-526. <br>
		+	*Witten, D., & Tibshirani, R. (2007). A comparison of fold-change and the t-statistic for microarray data analysis. Analysis, 1776, 58-85. <br>

@@ Line 3: / Line 3: @@
 =List of 10 Unknown Words and Their Definitions=
+# hypoxia - low oxygen levels in the blood (Ratini, 2016)
+# ubiquitin - plays a role in the heat-shock response, is involved in quality control of nascent proteins, membrane trafficking, cell signalling, cell cycle control, X chromosome inactivation and the maintenance of chromosome structure (Lackie, 2013)
+# Cytosolic - contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
+# diauxic shift - the two-phase growth response seen in a culture of microorganisms making a phenotypic adaptation to the addition of a second substrate (AccessScience, 2015)
+# methyl methanesulfonate - A DNA damaging agent to induce mutagenesis and in recombination experiments (Lundin, 2005).
+# peptidyl-prolyl cis/trans- isomerases - catalyse the cis–trans isomerisation of peptide bonds N-terminal to proline residues in polypeptide chains, play a role in the folding of newly synthesised proteins, and assist in cell cycle control (Shaw, 2002)
+# trehalose - a sugar thought to be implicated in anhydrobiosis - the ability of plants and animals to withstand prolonged periods of desiccation (National Center for Biotechnology Information, 2016)
+# ''de novo'' - New; not present previously; just beginning (Honee, 2009)
+# midlgarithmic - cell numbers increase in a logarithmic fashion but have not reached their full reproduction rate (Rogers & Kadner, 2017)
+# 2-fold - method of reporting statistics using log2 that results in more reproducible gene lists than do the ordinary and modified t-statistics (Witten & Tibshirani, 2007)
 =Outline of Article=

@@ Line 54: / Line 54: @@
 ** Other cells have demonstrated this ^^ when exposed to other environmental stresses
 === Clustering Analysis of Global Expression Data ===
-IV. Conclusion
+* Genes close together were placed into clusters
+* Clusters showed:
+**Similar functions
+**Cooperative regulation
-V. Further Implications
+*Clusters:
 ==Deliverable==

@@ Line 1: / Line 1: @@
-==Article==
+=Article=
 Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
-==List of 10 Unknown Words and Their Definitions==
+=List of 10 Unknown Words and Their Definitions=
+#
+#
@@ Line 14: / Line 14: @@
+#
-==Outline of Article==
+=Outline of Article=
-===Background Information on Purpose of Experiment===
+== Background Information on Purpose of Experiment ==
 * Low temperatures are known to have several effects on biochemical and physiological properties in various cells
 * Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment
@@ Line 21: / Line 21: @@
 *low temperature-dependent gene expression and low temperature response are still unclear
 * '''The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells'''
-===Cold shock and microarray procedures of yeast samples===
+== Cold shock and microarray procedures of yeast samples ==
 * S. cerevisiae YPH500 was used for all the analyses
 * Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm
@@ Line 33: / Line 33: @@
 * Cy3-dUTP and Cy5-dUTP were used as cDNA probes
 * Labeled with fluorophore in order to carry out microarray hybridization
-*Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray
+* Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray
 * Microarrays were scanned by laser microscope
 * Process repeated twice
@@ Line 41: / Line 41: @@
 * Fluorescence intensities were normalized
 * Data was clustered and referred to the Munich Information Center for Protein Sequences functional database
-*functional relationships among the genes in each cluster was determined
+* Functional relationships among the genes in each cluster was determined
-III. Results and Discussion
+== Results and Discussion ==
+=== Global Expression Analysis of Low Temperature Response in Yeast Cells Using a cDNA Microarray ===
+* Changes in expression of genes in yeast after cold shock was analyzed using cDNA of 5,803 genes in a yeast genome
+* Ratio of fluorescent intensities was 2 fold for a mainly all the cDNA spots on the data
 IV. Conclusion
+*

@@ Line 1: / Line 1: @@
 ==List of 10 Unknown Words and Their Definitions==
+#
@@ Line 12: / Line 15: @@
 ==Outline of Article==
-I. Introduction
+I. Background Information on Purpose of Experiment
+* Low temperatures are known to have several effects on biochemical and physiological properties in various cells
+* Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment
+* In yeast, the NSR1, TIP1, and OLE1 genes have been identified as important cold-inducible genes through past research, but their low temperature-dependent gene expression and response are still unclear
+* The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells
-II. Methods
+II. Cold shock and microarray procedures of yeast samples
+*
+*