Definitions

Organoleptic: A substance which has properties that can be detected by a sensory receptor (Merriam-Webster)
Oenological: Relating to the study of wine (Oxford)
Homocedastic: All variables have equal variances (Merriam-Webster)
Pseudohyphal: Short chain of cells formed by daughter cells not separating entirely (Medical Dictionary)
Metabolome: All of the metabolites in a cell at a certain stage of development (Dictionary of Cell and Microbiology)
Trehalose: Disaccharide sugar found in high numbers in invertebrates (Dictionary of Cell and Microbiology)
Isoform: Protein which functions the same and has a similar sequence to another, but is formed by a different gene (Dictionary of Cell and Microbiology)
Gluconeogenesis:Creation of glucose from substances other than carbohyrates (Dictionary of Cell and Microbiology)
Quadrupole: A situation in which there are four equal poles through which electric charge is distributed (Oxford)
Chemostat: A device which helps to regulate nutrients and the medium in which bacterial cells are grown (Dictionary of Cell and Microbiology)

Outline of Article

Abstract

Saccharomyces cerevisiae has been widely used in research to help understand eukaryotic cells, and their many functions.
Wine yeasts have not been used for many reasons, mainly only to study the properties they have that contribute to making wines.
This experiment grew both the lab strains and the wine strains in 15ºC and 30ºC.
- The environment was purposefully nitrogen-limited and anaerobic, regulated by a chemostat.
Growth temperature had a large affect on the growth or biomass of both of the strains.
The wine strain seemed to be better at forming biomass and the laboratory strain was better at fermenting under these conditions.
Analysis of the results was done by using DNA microarrays as well as metabalome analysis.
- This helped identify genes in each strain which were affected by the different temperatures.
- By doing this, genes could be identified which were different because of the different strains as well as the genes which were different because of the temperatures.
  - 1,007 temperature-dependent genes were found and 473 strain-dependent genes were found.
Nitrogen metabolism and heat shock response were most affected by the temperature dependent genes.
The properties which were most affected by the strain-dependent genes were sugar uptake, nitrogen metabolism, and the organoleptic properties.

Introduction

Saccharomyces cerevisiae is an important bacteria which has many applications such as baking and creation of alcoholic beverages.
- Recently, it has been used in creation of pharmaceuticals.
- S. cerevisiae is a model organism, it is used to represent other organisms which are structured and function in similar ways to it in experiments.
Lab strains of yeast have different functions than wine strains. Lab strains usually have difficulty breaking down sugars from grapes into ethanols compared to wine yeasts, so they cannot be used to make wines.
Wine yeasts are used for wine production because they have high ethanol tolerance, fermentation activity, ability to grow in a wide temperature range, and other properties.
- These properties which these yeasts have more than lab yeasts probably contribute to the differences observed between these two types of yeast.
Previous studies have been done on wine strains of yeast, but the way these tests were done provide results which can be analyzed in multiple ways.
Temperature is a large factor in wine making. Depending on the temperature, the taste, texture, and other characteristics of the wine change.
This study focuses on comparing the differences between the growth of lab yeast and wine yeast in nitrogen limited, anaerobic mediums, as well as differences between the strains and how they grow in different temperatures.
- The environment was purposefully kept static so that it would not be a factor.
DNA microarrays were used to correlate physiological responses with transcriptional changes in each strain.

Materials and Methods

Wild type laboratory and industrial wine strains were used in this experiment.
Grown at 15ºC and 30ºC.
The cultures were grown media that was kept constant in terms of factors such as pH, nitrogen levels, carbon levels, oxygen levels, glucose levels for each temperature, and more.
Biomass was found by taking the mass after filtering, washing, and microwaving to measure the dry mass.
Ammonia content was determined using what's call a Boehringer ammmonia/urea test.
Samples of the cultures were taken to determine the concentrations of other molecules present in the colonies, determined by liquid chromatography.
The Affymetrix Microarray Suite v5.0 along with Microsoft Excel Significance Analysis of Microarrays was used for the microarray.
The SGD GO was used to determine the significant terms related to the genes that were up or down-regulated based on temperature or strain.

Results

Physiological data, transcription profiles, intra- and extracellular metabolome profiles were collected.
Biomass yield at 15ºC:
- 30% decrease for wine strain
- 50% decrease for lab strain
Nitrogen metabolism:
- Same amount of ammonia consumed by all four experiments.
- Both produced lower yields at 15ºC than 30ºC.
- Yield for the wine strain was higher at each temperature than for the lab strain.
  - Wine is made in a nitrogen limited environment, so this may be why the wine strains showed higher biomass.
Biomass yields had different compositions depending on the temperature.
- In both strains, low temperatures had biomass composed of protein and RNA in higher rates than storage carbohydrates.
Glucose uptake was reduced in both strains at 15ºC, but the reduction was larger in the wine strain than the lab strain.
Both strains showed increased ethanol formation in the low temperature.
- There was not a difference in ethanol production between the strains.
Glycerol production:
- Wine strain: production correlates with biomass production.
- Lab strain: glycerol production higher at 15ºC than 30ºC.
The arrays had high levels of reproducibility.
Gene expression determination using Statistical Analysis of Microarray Data (SAM software):
- 1,529 genes changed expression due to at least one of the factors.
- 1,007 changed with both strains depending on temperature.
- 473 genes changed based on the strain.
- 49 genes change based on both temperature and strain.
SGD GO tools were used to determine the genes related to the transcriptional response.
30% of the genes that increased expression in the wine yeast at 15ºC have no known function.
In the wine yeast, genes related to formation of RNA polymerase were higher at 15ºC than for the lab yeast.
The rates of heat shock related genes were higher in both strains at 30ºC.

Discussion

This study had the first design to determine the differences in response to temperature change in wine yeasts compared to lab yeasts.
Both strains produced lower yields at 15ºC.
- But the difference was higher in lab strains than wine strains.
Sugar uptake decreased in both strains at 15ºC.
- The difference was larger in the wine strain.
- Lab strains are used as such because they show fast growth in minima media, possibly why they were less effected by the down-regulation of sugar uptake.

Journal Club Presentation Powerpoint Slides

Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎

Acknowledgements

This week, I worked with the project manager of our group, Hayden Hinsch to create an outline of the article and to make a presentation based on that outline. We also worked with the other members of our team, Arash Lari and Nicole Kalcic on re-designing our team page, Page Desiigner.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Mbalducc (talk) 18:51, 18 November 2017 (PST)

References

LMU BioDB 2017. (2017). Week 12. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

Pizzaro, Jewett, Nielson, Agosin. (2008) Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces Cerevisiae. "Applied and Environmental Microbiology", 74, 6358-6368, doi:10.1128/AEM.00602-08

Merriam Webster. Organoleptic. Retrieved November 16, 2017, from https://www.merriam-webster.com/dictionary/organoleptic

Oxford Dictionary. Oenology. Retrieved November 16, 2017, from https://en.oxforddictionaries.com/definition/oenology

Merriam Webster. Homoscedasticity. Retrieved November 16, 2017 from https://www.merriam-webster.com/dictionary/homoscedasticity

The Free Dictionary. Pseudohypha. Retrieved November 16, 2017 from https://medical-dictionary.thefreedictionary.com/pseudohypha

Dictionary of Cell and Microbiology. Metabolome. Retrieved November 16, 2017, from https://ac.els-cdn.com/B9780123849311000131/3-s2.0-B9780123849311000131-main.pdf?_tid=22708bce-cb18-11e7-969c-00000aacb35e&acdnat=1510869197_22d874b40f288fab293c0b938eff8761

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Dictionary of Cell and Microbiology. Isoform. Retrieved November 16, 2017, from https://ac.els-cdn.com/B978012384931100009X/3-s2.0-B978012384931100009X-main.pdf?_tid=b1fc3576-cb19-11e7-84af-00000aab0f26&acdnat=1510869868_e1c22bf4e9a7bf68f04e8034be410318

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Oxford Dictionaries. Quadrupole. Retrieved November 16, 2017 https://en.oxforddictionaries.com/definition/quadrupole

Dictionary of Cell and Microbiology. Chemostat. Retrieved November 16, 2017, from https://ac.els-cdn.com/B9780123849311000039/3-s2.0-B9780123849311000039-main.pdf?_tid=29137916-cb1b-11e7-bff9-00000aacb35d&acdnat=1510870505_df2671eedcbe815444ad0f824e36e1d6