Emmatyrnauer Week 12 - Revision history

Emmatyrnauer: /* Introduction */ rewording

2017-11-21T08:02:43Z

‎Introduction: rewording

Emmatyrnauer: /* Introduction */

2017-11-21T08:01:54Z

‎Introduction

Emmatyrnauer: /* Journal Outline */ significance

2017-11-21T08:00:08Z

‎Journal Outline: significance

Emmatyrnauer: adding small electronic notebook and definition references

2017-11-21T07:55:18Z

adding small electronic notebook and definition references

Emmatyrnauer: /* Materials and Methods */ linking to flow chart

2017-11-21T07:42:51Z

‎Materials and Methods: linking to flow chart

Emmatyrnauer: /* Definitions */ adding definitions

2017-11-21T07:34:56Z

‎Definitions: adding definitions

Emmatyrnauer: /* Definitions */ adding definitions

2017-11-21T07:24:14Z

‎Definitions: adding definitions

Emmatyrnauer: /* Discussion */ typo

2017-11-21T07:06:26Z

‎Discussion: typo

Emmatyrnauer: /* Discussion */ finishing discussion

2017-11-21T07:05:07Z

‎Discussion: finishing discussion

Emmatyrnauer: /* Discussion */ adding to discussion

2017-11-21T06:52:19Z

‎Discussion: adding to discussion

@@ Line 23: / Line 23: @@
 **Cluster analysis performed
 ***Results include gene expression between 6 and 48 hours after 4C cold shock differs from culture kept at 35C or 4C. After cold shock, expression of certain genes was induced (e.g. energy preservation genes, phospholipid synthesis genes, and cell rescue genes)
-*Now the question is how does this compare to the cellular responses of yeast which have already adapted to/able to survive at 4C; significant in understanding preservation
+*Now the question is how does this compare to the cellular responses of yeast which have already adapted to/able to survive at 4C; significant in understanding  and carrying out preservation of samples
 ===Materials and Methods===

@@ Line 20: / Line 20: @@
 *Currently there aren't any studies that examine the effects of cold shock below 10 deg C on gene expression in yeast
 *Interested in this because preservation of organisms often occurs at less than 10 deg C (i.e. 4 deg C)
-'''*This study exposed yeast to temperature of 4 deg C and examines changes in gene expression using cDNA microarray
+*This study exposed yeast to temperature of 4 deg C and examines changes in gene expression using cDNA microarray
 **Cluster analysis performed
 ***Results include gene expression between 6 and 48 hours after 4C cold shock differs from culture kept at 35C or 4C. After cold shock, expression of certain genes was induced (e.g. energy preservation genes, phospholipid synthesis genes, and cell rescue genes)
-*Now the question is what are the cellular responses of yeast which have already adapted to/able to survive at 4C
+*Now the question is how does this compare to the cellular responses of yeast which have already adapted to/able to survive at 4C; significant in understanding preservation
 ===Materials and Methods===

@@ Line 20: / Line 20: @@
 *Currently there aren't any studies that examine the effects of cold shock below 10 deg C on gene expression in yeast
 *Interested in this because preservation of organisms often occurs at less than 10 deg C (i.e. 4 deg C)
-*This study exposed yeast to temperature of 4 deg C and examines changes in gene expression using cDNA microarray
+'''*This study exposed yeast to temperature of 4 deg C and examines changes in gene expression using cDNA microarray
 **Cluster analysis performed
 ***Results include gene expression between 6 and 48 hours after 4C cold shock differs from culture kept at 35C or 4C. After cold shock, expression of certain genes was induced (e.g. energy preservation genes, phospholipid synthesis genes, and cell rescue genes)
 *Now the question is what are the cellular responses of yeast which have already adapted to/able to survive at 4C
 ===Materials and Methods===

@@ Line 70: / Line 70: @@
 # Methionine synthesis genes induced after cold shock in this study. Some of these genes were found to allow for sulfur assimilation (Thomas and SurdinKerjan1997).
 #* These capabilities may be required for glutathione synthesis after cold shock.
 ==Acknowledgements==
@@ Line 78: / Line 84: @@
 ==References==
-#LMU BioDB 2017. (2017). Week 12. Retrieved November 19, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
+# LMU BioDB 2017. (2017). Week 12. Retrieved November 19, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
-#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. Retrieved November 19, 2017 from http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
+# Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
 {{Emmatyrnauer}}

@@ Line 26: / Line 26: @@
 ===Materials and Methods===
 # Strain and growth conditions
 #* ''Saccharomyces cerevisia'' S288c grown in YPD medium at 25C in a shaker.

@@ Line 1: / Line 1: @@
 ==Definitions==
-# consortium: a two- (or more) membered bacterial culture (or natural assemblage) in which each organism benefits from the other. (http://www.biology-online.org/dictionary/Consortium)
+# consortium: a two- (or more) membered bacterial culture (or natural assemblage) in which each organism benefits from the other (http://www.biology-online.org/dictionary/Consortium)
-# desaturase: An enzyme that converts an unsaturated fatty acid chain to one that includes at least one carbon-carbon double bond. (https://medical-dictionary.thefreedictionary.com/desaturase)
+# desaturase: an enzyme that converts an unsaturated fatty acid chain to one that includes at least one carbon-carbon double bond (https://medical-dictionary.thefreedictionary.com/desaturase)
-# glycosyl phosphatidyl inositol: Glycosylphosphatidylinositol (GPI) is a lipid anchor for many cell-surface proteins. The GPI anchor represents a posttranslational modification of proteins with a glycolipid and is used ubiquitously in eukaryotes and most likely in some Archaea, but not in Eubacteria. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689333/)
+# glycosyl phosphatidyl inositol: a lipid anchor for many cell-surface proteins; represents a posttranslational modification of proteins with a glycolipid (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689333/)
 # mannoproteins: glycoproteins that contain 15 to 90% mannose by weight (https://link.springer.com/chapter/10.1007%2F978-3-642-68234-6_18)
 # hybridization: act of binding (https://www.genome.gov/10000533/dna-microarray-technology/)
 # Subcellular localization: the act of proteins moving to a particular position in a cell (e.g. how anchor proteins end up in particular locations) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845201/)
 # thioredoxin peroxidases: a member of a newly discovered family of proteins that are conserved from yeast to mammals and to which natural killer enhancing factor belongs; these proteins are antioxidants that function as peroxidases only when coupled to a sulfhydryl reducing system. (https://www.ncbi.nlm.nih.gov/pubmed/9388194)
-# alkylhydroperoxide
+# glutathione: a peptide C10H17N3O6S that contains one amino acid residue each of glutamic acid, cysteine, and glycine, that occurs widely in plant and animal tissues, and that plays an important role in biological oxidation-reduction processes and as a coenzyme (https://www.merriam-webster.com/dictionary/glutathione)
-# ubiquitious
+# ubiquitious: present everywhere (https://www.medicinenet.com/script/main/art.asp?articlekey=26111)
 ==Journal Outline==

@@ Line 67: / Line 67: @@
 #* This is because both heat shock and cold shock are acute stresses and interfere with proper protein folding
 # Homma et al. 2003 found that these heat shock proteins are also expressed when yeast cells are cultured at 4C for months.
-# Methionine synthesis genes induced after cold shock in this study. Some of these genes were found to allow for sulfur assimilation (by Thomas and SurdinKerjan1997).
+# Methionine synthesis genes induced after cold shock in this study. Some of these genes were found to allow for sulfur assimilation (Thomas and SurdinKerjan1997).
 #* These capabilities may be required for glutathione synthesis after cold shock.

@@ Line 58: / Line 58: @@
 #*Therefore, preservation via low temperatures is a viable option
 #Transcription patterns differed between cells continuously grown in 4C versus cells shifted to 4C
-# At low temperatures, membrane fluidity and permeability decrease so induction of genes (e.g OLE1) involved with fatty acid desaturase help to prevent these drastic changes (Aguilar et al. 1999; Inaba et al. 2003;
+# At low temperatures, membrane fluidity and permeability decrease so induction of genes (e.g OLE1) involved with fatty acid desaturase help to prevent these drastic changes (Aguilar et al. 1999; Inaba et al. 2003; Nakagawa et al. 2002). However, this study did not observe this large induction.
 #* Northern blot demonstrated by Nakagawa et al. 2002 showed activation of OLE1 at 10C so it is possible that induction occurred before the 6 hour mark
 # Murata et al. 2003 found that phospholipid synthesis and methionine synthesis are integrated mechanisms. This relates to this study as both molecules were induced
 # Trehalose and glycogen have been found to accumulate during exposure to stressful environments (Lillie and Pringle 1980)
 ==Acknowledgements==

← Older revision		Revision as of 06:52, 21 November 2017
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	===Discussion===		===Discussion===
		+	# Yeast cells were able to maintain colony forming ability for more that one year after being stored at 4C
		+	#*Therefore, preservation via low temperatures is a viable option
		+	#Transcription patterns differed between cells continuously grown in 4C versus cells shifted to 4C
		+	# At low temperatures, membrane fluidity and permeability decrease so induction of genes (e.g OLE1) involved with fatty acid desaturase help to prevent these drastic changes (Aguilar et al. 1999; Inaba et al. 2003;
		+	Nakagawa et al. 2002). However, this study did not observe this large induction.
		+	#* Northern blot demonstrated by Nakagawa et al. 2002 showed activation of OLE1 at 10C so it is possible that induction occurred before the 6 hour mark
		+	# Murata et al. 2003 found that phospholipid synthesis and methionine synthesis are integrated mechanisms. This relates to this study as both molecules were induced
		+	# Trehalose and glycogen have been found to accumulate during exposure to stressful environments (Lillie and Pringle 1980)

	==Acknowledgements==		==Acknowledgements==