Marmas Week 11
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Contents
Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray
Team Information Project Manager: Michael Armas Quality Assurance: Iliana Crespin Data Analysis: Emma Young, Kaitlyn Nguyen Coder: Michael Armas
Purpose
The purpose of this assignment is to begin in-depth analysis of the paper assigned for the final project and presentation of BIOL 367-01. The article assigned to this group, FunGals, is titled "Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray." This week, ten unknown terms from the paper will be defined for clarification, and an outline of the article will be posted to summarize the reading.
Ten Terms
- Thiuram: "The counting and/or measuring of cells in a fluid suspension" (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Mutagen: "Any physical or chemical agent that is capable of increasing the frequency of mutation above the spontaneous, background level"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Disulfiram: "Trivial name for tetraethylthiuram disulfide; bis(diethylthiocarbamoyl) disulfide; a drug used to deter alcohol abuse in the treatment of alcoholism. Alcohol ingestion after disulfiram causes vasomotor disturbances, nausea, vomiting, and even unconsciousness and death. It acts by inhibiting the enzyme acetaldehyde dehydrogenase and hence slows the removal of acetaldehyde. It occurs naturally in the otherwise edible fruit body of the agaric mushroom Coprinus atramentarius. One proprietary name is Antabuse" (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Erythrocyte: "A mature red blood cell; in mammals it is non‐nucleated and lacks mitochondria. Erythrocytes contain, but are no longer capable of synthesizing, hemoglobin and they function in the transport of oxygen. Mammalian erythrocytes obtain energy from anaerobic glycolysis and also metabolize glucose via the phosphogluconate pathway"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Cytometry: "The counting and/or measuring of cells in a fluid suspension"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Glutathione: "A tripeptide that is widely distributed in most if not all cells. It acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide and oxidized ascorbate, and it participates in the γ ‐glutamyl cycle. Oxidation links two molecules by a disulfide bond (represented as GSSG). For clarity, glutathione is sometimes termed reduced glutathione (or the reduced form of glutathione). It is involved in the synthesis of certain leukotrienes"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Glutathione Dehydrogenase: "An enzyme that catalyses the reduction by two molecules of glutathione of dehydroascorbate to form oxidized glutathione and ascorbate"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Base Excision Repair: "One of the intracellular mechanisms for the repair of DNA lesions (single‐strand breaks, damaged bases, etc.). It occurs in the following stages: (1) recognition of the damaged region; (2) removal of the damaged oligonucleotide by two enzymic nucleolytic reactions (excision); (3) synthesis by DNA polymerase of the excised oligonucleotide using the second (intact) DNA strand as template; and (4) covalent joining by DNA ligase of the newly synthesized segment to the existing ends of the originally damaged DNA strand. The process is light‐independent"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Transformant: "A bacterial cell that has undergone transformation, i.e. one that contains integrated donor genes that can be detected by plating on media selective for some or all of the donor genes"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
- Oxidative Stress: "A state of metabolic imbalance within cells that favours pro‐oxidant substances (e.g. superoxide, hydrogen peroxide, hypochlorous acid, nitric oxide, peroxynitrite) rather than antioxidants (e.g. glutathione, ascorbic acid) and antioxidant enzyme systems (e.g. superoxide dismutases, catalase). This leads to oxidative damage to all classes of the major biomolecules. Depending on the degree of imbalance, a cell may die or it might survive in a changed state. Such stress can be important in causing a wide variety of degenerative states, including atherosclerosis, ischemia/reperfusion injury in heart and brain, mutagenesis, and chronic inflammatory disease"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
Article Outline
- What is the main result presented in this paper?
- What is the importance or significance of this work?
- What were the limitations in previous studies that led them to perform this work?
- How did they treat the yeast cells (what experiment were they doing?)
- What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
- What media did they grow them in? What temperature? What type of incubator? For how long?
- What controls did they use?
- How many replicates did they perform per treatment or timepoint?
- What method did they use to prepare the RNA, label it and hybridize it to the microarray?
- What mathematical/statistical method did they use to analyze the data?
- Are the data publicly available for download? From which web site?
- Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
- What do the X and Y axes represent?
- How were the measurements made?
- What trends are shown by the plots and what conclusions can you draw from the data?
- How does this work compare with previous studies?
- What are the important implications of this work?
- What future directions should the authors take?
- Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
