Kmill104 Week 12

10 Definitions of Terms

1. proteasome: Proteasomes are large multi‐subunit protease complexes that selectively degrade intracellular proteins that are tagged for destruction by ubiquitination. They control cellular processes, such as metabolism and the cell cycle, through signal‐mediated proteolysis of key enzymes and regulatory proteins. They also operate in the stress response, by removing abnormal proteins, and in the immune response, by generating antigenic peptides. The proteolytic activity is due to a 26S protease (a 2 MDa complex), whose ability to degrade proteins generally depends on both the ubiquitination of the substrate and the presence of ATP. At the core is a 20S particle that carries the catalytic activity. When first isolated, it was called ‘multicatalytic proteinase’ because of its ability to cleave peptide bonds carboxy‐terminal to basic, hydrophobic, and acidic residues. The 20S particle does not require ATP for activity. The crystal structure of this core from the archaean Thermoplasma acidophilum has been determined. The core alone is inactive because it requires two specific subunits of a 19S particle to mediate recognition of ubiquitin‐protein conjugates. The core subunits are arranged in four heptameric rings, stacked to form a hollow cylinder with the protease activity on the inside. The active site nucleophile is threonine. The protein substrate first must be unfolded and the disulfide bonds reduced before entry into the cylinder. In Thermoplasma, the two outer rings are composed of seven α subunits, and each inner ring contains seven β subunits. The enzyme catalyses the cleavage at Xaa‐|‐bonds in which Xaa carries a hydrophobic, basic, or acidic side chain. Components of the human proteasome include: c2, c3, c5, c7, c8, c9, β chain, c13, δ chain, ε chain, mecl‐1, τ chain, and ζ chain. (Oxford, 2008).
2. leucine zipper: a domain in a protein structure in which two alpha helices containing leucines (normally four or five) repeating every seventh amino‐acid residue, interdigitate in zipper fashion to stabilize the structure. Such an arrangement was originally found in DNA‐binding proteins, but it is now known to occur also in other proteins, especially adjacent to proposed transmembrane regions, mediating dimerization. The abbreviation ZIP is used, e.g., in designating the bZIP family of proteins. (Oxford, 2008).
3. chromatin immunoprecipitation: abbr.: ChIP; a method used to demonstrate the association between transcription factors or other DNA‐binding proteins and specific regions of genomic DNA. Chromatin is isolated from preparations of nuclei, chemically cross‐linked, and sheared to provide short fragments. Antibodies are used to immunoprecipitate the specific DNA‐binding protein and with it the fragment of DNA to which it is bound. Polymerase chain reaction (PCR) is then used to identify the presence of specific DNA fragments. (Oxford, 2008).
4. lignin: any random phenylpropanoid polymer formed in higher plants by the dehydrogenative radical polymerization of various 4‐hydroxycinnamyl alcohols, in which the residues are joined in differing proportions and by several different linkages, some of which are nonhydrolysable. Lignin is insoluble in water, and occurs in the cell walls of vascular plants (especially of the supporting and conducting tissues), on which it confers strength, rigidity, and resistance to degradation. It is one of the most abundant biopolymers. (Oxford, 2008).
5. capillary electrophoresis: abbr.: CE; a very‐high‐resolution method of electrophoresis, also known as capillary zone electrophoresis (abbr.: CZE) or high‐performance electrophoresis. It is based on the use of long (up to 100 cm), narrow (<100μm) silica columns for separation of peptides, etc. by electro‐osmotic flow. By using sensitive detectors (e.g. laser‐induced fluoresence), sensitivity in the attomole range can be achieved. (Oxford, 2008).
6. k-means clustering: an algorithm for clustering data that allows generation of user‐specified numbers of clusters from a given data set based on distance metrics for similarity. The method is dependent both on the specified value of k, which determines the number of clusters that are created, and on the distance measure employed. It is widely used in the analysis of microarray data. (Oxford, 2008).
7. ChIP: abbr. for chromatin immunoprecipitation. (Oxford, 2008).
8. pentose phosphate pathway: a complex series of cytosolic metabolic reactions by which glucose 6‐phosphate is oxidized with formation of carbon dioxide, ribulose 5‐phosphate, and reduced NADP, the ribulose 5‐phosphate then entering a series of reactions in which a number of sugar phosphates containing between three and seven (or eight) carbon atoms are successively interconverted. One consequence of these interconversions is the nonoxidative regeneration of glucose 6‐phosphate, which then can enter the pathway for another cycle of oxidative decarboxylation and skeletal rearrangement, the eventual result being the complete oxidation of one molecule of glucose with the formation of six molecules of carbon dioxide and 12 molecules of NADPH. The pathway thus provides (in some organisms or tissues) an alternative route to (or shunt of) part of the glycolytic pathway; it also provides ribose 5‐phosphate for nucleotide synthesis and (in some organisms) other intermediates for biosynthesis. Of special importance is d‐erythrose 4‐phosphate, required for the biosynthesis of aromatic amino acids and many other materials by the shikimate pathway. In higher plants many of the pathway enzymes function in the reverse direction as part of the reductive pentose phosphate cycle. (Oxford, 2008).
9. 6-phosphogluconolactonases: an enzyme of the pentose phosphate pathway that catalyses the hydrolysis of 6‐phosphogluconolactone to 6‐phosphogluconic acid. (Oxford, 2008).
10. transketolase: An enzyme that catalyses the transfer of a glycolaldehyde (HOH2C–CHO−) moiety from xylulose 5‐phosphate to ribose 5‐phosphate to form glyceraldehyde 3‐phosphate and sedoheptulose 7‐phosphate, in the pentose phosphate pathway. It requires thiamine diphosphate (TPP) as coenzyme; a glycolaldehyde–TPP intermediate is formed transiently during the reaction. It has broad substrate specificity. Measurement of transketolase activity in a red cell hemolysate, in the presence and absence of thiamin, gives an indication of the thiamin status of the individual (by revealing the degree of activation of the enzyme in the absence of thiamin). (Oxford, 2008).

Question Answers

• Questions About the Article
  1. What is the main result presented in this paper?
  2. What is the importance or significance of this work?
  3. What were the limitations in previous studies that led them to perform this work?
  4. How did they treat the yeast cells (what experiment were they doing?)
  5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
  6. What media did they grow them in? What temperature? What type of incubator? For how long?
  7. What controls did they use?
  8. How many replicates did they perform per treatment or timepoint?
  9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
  10. What mathematical/statistical method did they use to analyze the data?
  11. Are the data publicly available for download? From which web site?
  12. 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 (if applicable)?
      • How were the measurements made?
      • What trends are shown by the plots and what conclusions can you draw from the data?
  13. How does this work compare with previous studies?
  14. What are the important implications of this work?
  15. What future directions should the authors take?
  16. 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?

• Evaluating the Meta Data
  1. The complete bibliographic reference in the APA style
     • Sha, W., Martins, A. M., Laubenbacher, R., Mendes, P., & Shulaev, V. (2013). The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide. PloS one, 8(9), e74939. doi:10.1371/journal.pone.0074939
  2. The link to the abstract from PubMed (LMU-specific link).
     • https://pubmed.ncbi.nlm.nih.gov/24073228/
  3. The link to the full text of the article in PubMedCentral
     • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3779239/
  4. The link to the full text of the article (HTML format) from the publisher web site.
     • https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074939
  5. The link to the full PDF version of the article from the publisher web site.
     • chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0074939&type=printable
  6. Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
     • 2013 Sha et al. hold the copyright
     • Additionally, is the article available under a Creative Commons license?
       • Yes
  7. How is the article available to you?
     • It is an open access article, so it was freely available upon its publication
     • Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
       • Yes
     • If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.
     • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.
     • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
  8. Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
     • It is available online-only
  9. What organization is the publisher of the journal?
     • PLOS One, Public Library of Science
     • What type of organization is it?
       • Nonprofit 501(c)(3) corporation
       • Is the publisher for-profit or non-profit?
         • Non-profit
       • Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
         • No, it is not a scientific society
       • Does the publisher belong to the Open Access Publishers Association?
         • Yes
     • What country is the journal published in?
  10. How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
  11. Are the articles in this journal peer-reviewed?
  12. Provide a link to the scientific advisory board/editorial board of the journal.
  13. What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
  14. On what date was the article submitted?
  15. On what date was the article accepted?
  16. Did the article undergo any revisions before acceptance?
  17. When was the article published?
  18. What is the approximate elapsed time between submission and publication?
  19. What are the institutions with which the authors are affiliated?
  20. Have the authors published other articles on this subject? (How will you find this out?) Hint:
      • Google Scholar
      • PubMed (LMU-specific link)
      • Web of Science (LMU pays subscription fee for access)
  21. Is there a conflict of interest for any of the authors?
  22. Are the data associated with this article available? If so, provide a link to the dataset.
  23. Perform a prospective search on your article in the Web of Science and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):
      • How many articles does this article cite?
      • How many articles cite this article?

Data/Files

Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf