Hhinsch Week 12 - Revision history

Hhinsch: invoked the page desiigner template

2017-11-21T04:56:57Z

invoked the page desiigner template

Hhinsch: fixed typo in powerpoint slides

2017-11-21T02:11:14Z

fixed typo in powerpoint slides

Hhinsch: added link to our slides and added my acknowledgments

2017-11-21T02:09:24Z

added link to our slides and added my acknowledgments

Hhinsch: fixed typos so nanometer would be displayed

2017-11-21T00:48:40Z

fixed typos so nanometer would be displayed

Hhinsch: added to my outline

2017-11-19T13:00:53Z

added to my outline

Hhinsch: added to the outline of the article

2017-11-19T12:47:52Z

added to the outline of the article

Hhinsch: saved my outline just in case

2017-11-19T12:10:08Z

saved my outline just in case

Hhinsch: added reference for the article I outlined and wek 12 page

2017-11-19T10:35:36Z

added reference for the article I outlined and wek 12 page

Hhinsch: added part of the introsection to the outline

2017-11-19T10:32:34Z

added part of the introsection to the outline

Hhinsch: added info for outline

2017-11-19T10:21:02Z

added info for outline

← Older revision		Revision as of 04:56, 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.[[User:Hhinsch\|Hhinsch]] ([[User talk:Hhinsch\|talk]]) 18:09, 20 November 2017 (PST)		#While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.[[User:Hhinsch\|Hhinsch]] ([[User talk:Hhinsch\|talk]]) 18:09, 20 November 2017 (PST)

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← Older revision		Revision as of 02:11, 21 November 2017
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−	==Journal Club ~~Presenation~~ Powerpoint ~~Slide~~==	+	==Journal Club Presentation Powerpoint Slides==
	[[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]		[[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]

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+==Journal Club Presenation Powerpoint Slide==
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 ==Acknowledgments==
+#Mary and I worked over text and in person in order to complete the deliverables of this assignment.
 {{hhinsch}}

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 *The commercial wine strain S. cerevisiae var. bayanus EC1118 was used as the wine yeast.
 **Both of these strains were grown in 2 liter chemostats at both 15 and 30 degrees Celsius.
-**The biomass of the two strains was determined by filtering the culture through a  pre-weighed 0.45-�m nitrocellulose filter.
+**The biomass of the two strains was determined by filtering the culture through a  pre-weighed 0.45-nm nitrocellulose filter.
 **The remaining biomass was then dried in a microwave.
-**Culture samples (10 ml) used for determination of glucose, ethanol, glycerol, acetate, pyruvate, and succinate concentrations were immediately filtered through a 0.22-�m-pore-size cellulose acetate filter and then stored at -80 degrees Celsius in order to analyze later in the experiment.
+**Culture samples (10 ml) used for determination of glucose, ethanol, glycerol, acetate, pyruvate, and succinate concentrations were immediately filtered through a 0.22-nm-pore-size cellulose acetate filter and then stored at -80 degrees Celsius in order to analyze later in the experiment.
 *Most of the cultures were stored at very cool temperatures in order to maintain consistency throughout the course of the experiment.
 *Washing and staining of arrays was done using lab equipment: GeneChip fluidics station 400 and scanning with an Affymetrix GeneChip Scanner 3000.
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 **SGD was also used to find the significantly effected gene ontology within the upregulated and downregulated temperature-dependent and strain-dependent genes.
 ** The 5,814 unique S. cerevisiae open reading frames were extracted from the 10,765 transcript features on the Yeast Genome 2.0 arrays.
 ====Results====
 *To compare the difference between the lab yeast and the wine yeast the experimenters used a systems approach.

← Older revision		Revision as of 13:00, 19 November 2017
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	****This wasn't significant at the lower temperature.		****This wasn't significant at the lower temperature.
	*There wasn't a change in levels of ethanol yields on glucose between strains which suggests that this energetic process is strain independent.		*There wasn't a change in levels of ethanol yields on glucose between strains which suggests that this energetic process is strain independent.
		+	*Statistical Analysis of Microarray Data was used in order to find out which genes significantly changed expression.
		+	**A four way analysis was performed. This analysis showed differences in the expressions of the genes at both temperatures.
		+	***This showed differences between temperatures and between strains.
		+	====Conclusions====
		+	*This was the first study to utilize a two-factor design to control for and study the underlying mechanisms for temperature adaptation in wine yeasts compared to laboratory yeasts by using chemostat cultures.
		+	*Growth at the low temperatures altered the biomass compositions of the strains which yielded more nitrogen rich macromolecules.
		+	**This in turn yielded less biomass.
		+	**At the lower temperature, lower sugar uptakes were observed.
		+	**These two factors reduced the efficiency of fermentation.
		+	*The lab yeast and the wine yeast responded differently to growth at the lower temperature.
		+	**The study suggests that the lab yeast uses carbon sources better.
		+	***This could be determined by the increase in fermentation rates of the lab yeast.
		+	**The study suggests that the wine yeast was better adapted for growth in nitrogen limited environments.
		+	***This happened at both temperatures because of the alterations in nitrogen metabolism.

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 **Used DNA microarrays and a sensitive gas chromatography-mass spectrometry (GC-MS) method for quantification of intra- and extracellular metabolites which helped expose a causal relationship between physiological changes and transcription.
 ====Materials and Methods====
+*S. cerevisiae wild-type laboratory strain CEN.PK113-7D (Mata) was used as the lab yeast strain.

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 **Temperatures that are not great for fermentation are consistently used in white wine fermentation for desired sensory effects.
 **Physiological studies of yeast have shown that protein translation rates, cell membrane fluidity, RNA secondary structure stability, enzymatic activity, protein folding rates, and heat shock protein regulation are significantly affected.
+*Used the two-factor design for to show difference in responses between the lab strain and the wine strain of yeast.
+**Used continual chemostat cultures which is different from earlier studies with wine yeast.

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 #(2016). polyploid. In Hine, R., &amp; Martin, E.(Eds.), A Dictionary of Biology. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378-e-3532.
 #(2016). anaerobic respiration. In Hine, R., &amp; Martin, E.(Eds.), A Dictionary of Biology. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378-e-217.
+#Pizarro, F. J., Jewett, M. C., Nielsen, J., & Agosin, E. (2008). Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces cerevisiae . Applied and Environmental Microbiology, 74(20), 6358–6368. http://doi.org/10.1128/AEM.00602-08
+#LMU BioDB 2017. (2017). Week 12. Retrieved November 19, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

← Older revision		Revision as of 10:32, 19 November 2017
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	**Study helps give information that scientists can use to determine how growth temperature affects differential physiological and transcriptional responses.		**Study helps give information that scientists can use to determine how growth temperature affects differential physiological and transcriptional responses.

		+	====Introduction====
		+	*Saccharomyces cerevisiae is an important organism.
		+	**Is used in bakeries, distilleries, breweries, or wineries.
		+	**It is also the first sequenced eukaryote.
		+	**Saccharomyces cerevisiae has also been used as a producer of pharmaceuticals.
		+	*S. cerevisiae S288c is the labratory strain the experimenters used.
		+	**This has been popular for almost a century.
		+	**Used for genetics studies.
		+	**Laboratory yeasts can't produce ethanol so they get stuck in the fermentation process.
		+	*Microarrays have helped determine what effects possible transcriptional regulation among cells.
		+	**Over the past ten years, microarrays have given scientists the ability to study what causal impact different physiological conditions have on the transcription of genes.
		+	*Temperature effects the wine-fermentation.
		+	**Temperatures that are not great for fermentation are consistently used in white wine fermentation for desired sensory effects.
		+	**Physiological studies of yeast have shown that protein translation rates, cell membrane fluidity, RNA secondary structure stability, enzymatic activity, protein folding rates, and heat shock protein regulation are significantly affected.

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 #'''Polyploid''': Describing a nucleus that contains more than two sets of chromosomes (see diploid) or a cell or organism containing such nuclei. For example, triploid plants have three sets of chromosomes and tetraploid plants have four. Polyploidy is far more common in plants than in animals; many crops, in particular, are polyploid (bread wheat, for example, is hexaploid, i.e. 6n). It can be induced chemically with colchicine. [http://electra.lmu.edu:2218/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378-e-3532?rskey=rBb1cc&result=1 ]
 #'''Anaerobic Respiration''': A type of respiration in which foodstuffs (usually carbohydrates) are partially oxidized, with the release of chemical energy, in a process not involving atmospheric oxygen. Since the substrate is never completely oxidized the energy yield of this type of respiration is lower than that of aerobic respiration. It occurs in some yeasts and bacteria and in muscle tissue when oxygen is absent (see oxygen debt). Obligate anaerobes are organisms that cannot use free oxygen for respiration; facultative anaerobes are normally aerobic but can respire anaerobically during periods of oxygen shortage. Alcoholic fermentation is a type of anaerobic respiration in which one of the end products is ethanol. [http://electra.lmu.edu:2218/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378-e-217?rskey=UYLaet&result=1 ]
 ==References==