Difference between revisions of "Hhinsch Week 12"

Revision as of 12:10, 19 November 2017

Outline

Article Info

• The journal club article I reviewed is: 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
• The full text can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570279/pdf/0602-08.pdf

Definitions

1. Metabolome: the sum of all small molecular weight metabolites in a biological sample of interest. The metabolome of a given cell will vary greatly depending on its physiological or developmental state, its age, or its response to disease or drugs. [1]
2. Polyketide: any natural product synthesized via linear poly‐β‐ketones, which are themselves formed by repetitive head‐to‐tail addition of acetyl (or substituted acetyl) units indirectly derived from acetate (or a substituted acetate) by a mechanism similar to that for fatty‐acid biosynthesis but without the intermediate reductive steps. In many cases, acetyl‐CoA functions as the starter unit and malonyl‐CoA as the extending unit. Various molecules other than acetyl‐CoA may be used as starter, often with methylmalonyl‐CoA as the extending unit. The poly‐β‐ketones so formed may undergo modification by alkylation, cyclization, glycosylation, oxidation, or reduction. Polyketides include: coniine (of hemlock) and orsellinate (of lichens) – acetyl‐CoA; flavanoids and stilbenes – cinnamoyl‐CoA; tetracyclines – amide of malonyl‐CoA; urushiols (of poison‐ivy) – palmitoleoyl‐CoA; erythronolides – propionyl‐CoA and methylmalonyl‐CoA as extender. Polyketide synthases are large multidomain proteins that contain phosphopantheteine. [2]
3. Gas Chromatography/Mass Spectrometry: abbr.: GC/MS; an analytical technique that combines the separation process of gas chromatography with the highly selective detection technique of mass spectrometry.[3]
4. Metabolite: a chemical compound that is produced or consumed during metabolism. Polymeric biological molecules are excluded from this definition. Metabolites include low-molecular-weight compounds that are produced or converted by enzymes during metabolism or the precursors or breakdown products of biopolymers. [4]
5. Fermentation: an energy-yielding enzymatic breakdown of sugar molecules that takes place in bacteria and yeasts under anaerobic conditions.[5]
6. Gluconeogenesis: the formulation of glucose or other carbohydrates such as glycogen (glyconeogenesis) from noncarbohydrate precursors such as glycogenic amino acids, lactate, and Krebs TCA cycle intermediates. Gluconeogenesis occurs in the mammalian liver under conditions such as starvation or low carbohydrate intake. [6]
7. Diploid: referring to the situation or state in the life cycle where a cell or organism has two sets of chromosomes, one from the mother and one from the father. Diploidy results from the fusion of the haploid egg nucleus and a haploid sperm nucleus. [7]
8. Aneuploid: Describing a nucleus, cell, or organism in which one or more chromosomes have been added to or deleted from the complete set, so that the total number of chromosomes is not an exact multiple of the haploid number. [8]
9. 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. [9]
10. 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. [10]

Outline

Abstract

• The scientists studied two different strains of Saccharomyces cerevisiae.
  • A wine strain and a lab strain.
    • The lab strains are primarily studied for mapping of eukaryotic cells and possible understanding of diseases.
    • The wine strains are primarily used for making wine that has organoleptic properties.
• A two-factor experiment was done to examine the responses of a laboratory strain and an industrial wine strain at a temperature of 15 and 30 degrees Celsius.
  • The studies were done in nitrogen-limited, anaerobic, steady-state chemostat cultures.
• Results showed that the biomass of each strain was effected greatly.
  • Laboratory strains were found to yield higher fermentation rates.
  • Industrial wine strains were found to yield higher biomass production at the lower temperatures.
• DNA Microarrays and targeted metabolome analysis were used.
  • Experimenteries identified 1,007 temperature-dependent genes and 473 strain-dependent genes.
  • 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.
• 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.
  • 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

References

1. King, R., Mulligan, P., & Stansfield, W.(2013). A Dictionary of Genetics. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444.
2. (2006). polyketide. In Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J.(Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-15977.
3. (2006). gas chromatography/mass spectrometry. In Cammack, R., Atwood, T., Campbell, P., Parish, H., Smith, A., Vella, F., & Stirling, J.(Eds.), Oxford Dictionary of Biochemistry and Molecular Biology. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-7653.
4. King, R., Mulligan, P., & Stansfield, W.(2013). metabolite. In A Dictionary of Genetics. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-4071.
5. King, R., Mulligan, P., & Stansfield, W.(2013). fermentation. In A Dictionary of Genetics. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-2328.
6. King, R., Mulligan, P., & Stansfield, W.(2013). gluconeogenesis. In A Dictionary of Genetics. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-2707.
7. King, R., Mulligan, P., & Stansfield, W.(2013). diploid. In A Dictionary of Genetics. : Oxford University Press. Retrieved 19 Nov. 2017, from http://electra.lmu.edu:2218/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444-e-1796.
8. (2016). aneuploid. In Hine, R., & 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-230.
9. (2016). polyploid. In Hine, R., & 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.
10. (2016). anaerobic respiration. In Hine, R., & 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.
11. 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
12. LMU BioDB 2017. (2017). Week 12. Retrieved November 19, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

Acknowledgments

Assignments

Week 1
Week 2
Week 3
Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Week 11
Week 12
Week 14
Week 15

Hayden's Individual Journal Entries

hhinsch Week 1
hhinsch Week 2
hhinsch Week 3
hhinsch Week 4
hhinsch Week 5
hhinsch Week 6
hhinsch Week 7
hhinsch Week 8
hhinsch Week 9
hhinsch Week 10
hhinsch Week 11
hhinsch Week 12
hhinsch Week 14
hhinsch Week 15
Page Desiigner Deliverables Page

Class Journal Entries

Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
Class Journal Week 10
Page Desiigner

Electronic Notebook

Hhinsch Electronic Notebook

Hayden's User Page

Hayden Hinsch