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)
   3. In vitro: (Of a biological process) made to occur outside the living organism, i.e. in an artificial environment such as within a glassware, a test tube, etc. (Biology Online, 2021)
   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)
   5. Reading frame: One of the three possible ways of reading a nucleotide sequence. As the genetic code is read in nonoverlapping triplets (codons) there are three possible ways of translating a sequence of nucleotides into a protein, each with a different starting point. For example: given the nucleotide sequence: AGCAGCAGC, the three reading frames are: AGC AGC AGC, GCA GCA, CAG CAG (Biology Online, 2022).

1. 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? A haploid Saccharomyces cerevisiae W303 strain.
   5. What media did they grow them in? What temperature? What type of incubator? For how long? PCR was used to grow the microarrays. The cells were also grown on YPD media. The temperature is not specified in the paper except for the elevated temperature environmental condition which was 30 degrees and then 37 degrees celsius. The time was different depending on the growth conditions and media. The times ranged from 20 minutes to 14 hours.
   6. What controls did they use? Their control was unenriched DNA samples.
   7. How many replicates did they perform per treatment or timepoint? The supplementary methods states that the program was ran 50 times on random sequences on sets of different probes.
   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 raw data can't be downloaded.
   11. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
   • Figure 1:
   • Figure 2:

     Figure 3:

   1. • 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?
   2. How does this work compare with previous studies?
   3. What are the important implications of this work?
   4. What future directions should the authors take?
   5. 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?