Nstojan1 Week 12

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
   1. Blotting: The transfer of protein, rna, dna molecules from a relatively thick acrylamide or agrose gel or to a paper like membrane (usually nylon or agarose gel) by capillarity or an electric field, preserving the spatial arrangment. Once on the membrane, the molecules are immobilised, typically by baking or by ultra violet irradiation and can then be detected at high sensitivity by hybridisation (in the case of dna & rna) or antibody labelling (in the case of protein). Rna blots are called northern blots, dna blots, southern, protein blots, western (Biology Online, 2022).
   2. Filamentous growth: The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape (AmiGO 2)
   4. Respiratory electron transport chain: A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. (AmiGO 2)
2. Answer the following questions about your article. Your answers need to be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's answers either. Even if you work together to understand the article, your individual entries need to be in your own words.
   1. What is the main result presented in this paper?
   • The main result presented in the paper is that they were able to identify the DNA sequences bound by transcriptional regulators under different growth conditions. They were also able to classify the regulatory binding behaviors into condition-invariant, condition-enabled, condition-expanded, and condition-altered. They discussed the different mechanisms for the different binding behaviors such as nuclear exclusion and increased protein levels and why the regulatory elements were organized the way they were in yeast promoters.
   1. What is the importance or significance of this work? This work is important because it discusses the advancement in understanding the regulatory mechanisms that controls gene expression in yeast. Under the different growth conditions, they were able to identify the specific DNA sequences that were bound by transcriptional regulators which provided a map of the transcriptional regulatory code.
   2. What were the limitations in previous studies that led them to perform this work? Previously, they weren't;t able to map the transcriptional regulatory code because there was limited understanding if the specific DNA sequenced that were bound by transcriptional regulators. They also didn't understand how the different growth conditions affected transcriptional regulators which was important in order to understand the regulatory mechanism. There was also little understanding about regulatory elements and how they were used by regulators in different environments in yeast promoters.
   3. How did they treat the yeast cells (what experiment were they doing?) The yeast cells were treated in a couple of ways: with the Myc-epitope coding which allowed for all of the 203 regulators to be tagged for further analysis. Crosslinkng and Immunoprecipitation, cross linking stabilized interactions between the target DNA sequence and transcriptional regulators, using immunoprecipitation, they were able to isolate specific DNA fragments that were tagged with the myc-tagged regulators. Then the ligation-medicated PCR was used to augment the DNA for further analysis. Using microarray hybridization, they were able to detect the DNA sequence that was bound by transcriptional regulators in the yeast.
   4. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid? They don't specify if the strain was haploid or diploid but it was the W303 strain.
   5. What media did they grow them in? What temperature? What type of incubator? For how long? They did not specify this
   6. What controls did they use? They do not specify this
   7. How many replicates did they perform per treatment or timepoint? They do not specify this
   8. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
   9. What mathematical/statistical method did they use to analyze the data? Probability scores were used to determine the significance of the binding interactions
   10. Are the data publicly available for download? From which web site? The data can be downloaded from the National Library of Medicine.
   11. 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?
   12. How does this work compare with previous studies?
   13. What are the important implications of this work?
   14. What future directions should the authors take?
   15. 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 Meta Data

1. The complete bibliographic reference in the APA style (see this link), with DOI.
   • Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J. B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, P. A., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E., & Young, R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99–104. https://doi.org/10.1038/nature02800
2. The link to the abstract from PubMed (LMU-specific link.
3. The link to the full text of the article in PubMedCentral (if not available, write N/A).
4. The link to the full text of the article (HTML format) from the publisher web site. https://www.nature.com/articles/nature02800
5. The link to the full PDF version of the article from the publisher web site.
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.
   • Additionally, is the article available under a Creative Commons license?
7. How is the article available to you?
   • 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. I don't see "open access" or "unlocked" icon. Once I open the full text, I do see "Public Access".
   • 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. I could not find "open access" or "unlocked" icon, however I could see "free full text" and was able to access the article.
   • 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.
9. What organization is the publisher of the journal?
   • What type of organization is it?
   • Is the publisher for-profit or 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)
   • Does the publisher belong to the Open Access Publishers Association?
   • 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)
    • Since 1989
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.) 60.9 was the 5 year impact factor (2022)
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? no/unknown, all it says is that it was published in final edited form 2004, Sept 2.
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? Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA 2Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

3MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar Street, Cambridge, Massachusetts 02139, USA 4Broad Institute, One Kendall Square, Building 300, Cambridge, Massachusetts 02139, USA

1. 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)
2. Is there a conflict of interest for any of the authors?
3. Are the data associated with this article available? If so, provide a link to the dataset.
4. 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?