Asandle1 Week 12

This journal entry is due on Thursday, April 11, at 12:01am PST.

Grading for this assignment

To User Page: User: Asandle1 To Template: Template:Asandle1

Assignment Pages

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 13

week 14

week 15

Journals

Individual

User:Asandle1

Asandle1 Week 2

SIR2 Week 3

Monarch Initiative Week 4

Asandle1 Week 5

Asandle1 Week 6

Asandle1 Week 8

Asandle1 Week 9

Asandle1 Week 10

Asandle1 Week 12

Asandle1 Week 13

Asandle1 Week 14

Asandle1 Week 15

Class Journals

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 8

Class Journal Week 9

Class Journal Week 10

Class Journal Week 12

• Include both the Acknowledgments and References section as specified by the Week 1 assignment.
• The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, answers to the questions about your article, Data/files, Conclusion, Acknowledgments, and References (as specified by the Week 1 assignment).

Presentation Prep: Individual Journal Pages

1. Make a list of at least 10 biological terms, List full citations in the References section of your journal page.

Biological Term's

In Vivo: In the body (NCI Dictionary of Cancer, 2024)

Amino Acid Transporter: Amino acid transporters are membrane-bound transport proteins that mediate transfer of amino acids into and out of cells or cellular organelles. (Amino acid transporters revisited: New views in health and disease - PubMed, 2024)

Phylogenetic’s: the study of evolutionary relationships among biological entities (Biology Online, 2024)

Phylogenetic Conservation: the keeping of the same genetic processes across organisms. Specifically cis-regulatory sequences in this case. I built this definition myself after finding out the definition of phylogenetic's. Therefor there is no source and it could be incorrect. My source for phylogenetic's is above in the previous definition.

Cis-regulatory Sequences: sequences that control when, where, and with what intensity genes are expressed. Key to this control is the recruitment of transcription factors (TFs) that bind to regulatory sequences, such as promoters, enhancers, repressors, and insulators. (Worsley-Hunt, 2024)

Sensu Stricto: (Science: zoology) In the strict sense, in the narrow sense. most often used to indicate the nominate subordinate taxon etc.). Or it may just indicate exclusion of similar taxa sometimes united with it. (Biology Online, 2024)

Respiratory Electron Transport Chain: The electron transport chain is a series of four protein complexes that couple redox reactions, creating an electrochemical gradient that leads to the creation of ATP in a complete system named oxidative phosphorylation. It occurs in mitochondria in both cellular respiration and photosynthesis. In the former, the electrons come from breaking down organic molecules, and energy is released. In the latter, the electrons enter the chain after being excited by light, and the energy released is used to build carbohydrates. (Ahmad, 2024)

Transcription Initiation Apparatus: the transcription apparatus is a huge molecular machine. It detects the time-varying concentrations of transcriptional activators and initiates mRNA transcripts at appropriate rates. (Wang, 2024)

G1 Phase of the Cell Cycle: G1 is the stage where the cell is preparing to divide. (NIH Glossary of Genomic and Genetic Terms, 2024)

Cell Cycle: The name we give the process through which cells replicate and make two new cells. (NIH Glossary of Genomic and Genetic Terms, 2024)

Chromatin Immunoprecipitation: Combining Genome-Wide Location Analysis + DNA Microarray Analysis to identify protein-DNA interactions within cells. (Lee, 2024)

Answer's to Questions

1) What is the main result presented in this paper?

They created a basic model of yeasts transcriptional regulatory code that shows how the cis-regulatory sequences have transcriptional regulators attach to them and how the interactions are affected by different environmental conditions.

2) What is the importance or significance of this work?

The paper is important because of how comprehensive they were in tackling their studying of gene regulation in yeast. They analyzed over 6000 pieces of. DNA and analyzed TR's under a ton of different conditions. It offered a more expansive map of the TR network in yeast than we had before including the figure that showed how they created a detailed map of the TR network in yeast.

3) What were the limitations in previous studies that led them to perform this work?

They say that people have used comparison across different strains of yeast to try and find regulatory sequences that might be the same.

4) How did they treat the yeast cells (what experiment were they doing?)

They did a genome-wide location analysis to figure out where in the genome the DNA-binding transcription regulators would attach in different environmental conditions.

5) What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?

They used a strain called W303 and then they modified it with a Myc-epitope tag to turn it into a stain of yeast called Z1256. I think this is because any molecules that interact with them get tagged although Im not sure. I don’t think it directly mentioned haploid vs diploid, but it makes more sense to use haploid if they are doing gene editing because of the ability to see the results of the edits. I am very iffy about my answer to this question and I feel like this is not a complete answer but I can't figure out for sure.

6) What media did they grow them in? What temperature? What type of incubator? For how long?

They grew the cells within:

• YPD (1% Yeast Extract, 2% Peptone, 2% Glucose)
• YEP + Galactose or Raffinose:
• Synthetic Complete Medium:

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?

1. 1. Are the data publicly available for download? From which web site?
   2. 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?
   3. How does this work compare with previous studies?
   4. What are the important implications of this work?
   5. What future directions should the authors take?
   6. 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?

Journal Club Presentation

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, April 12.

• Please follow the Presentation Guidelines PowerPoint on Brightspace for how to format your slides.
• You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
• You need to present the information that you answered for the questions above, but organized as a presentation. You will need the following:
  • Title slide with the complete reference to the article, presenter names, date and "BIOL 367".
  • Outline slide (list of key messages for the talk)
  • One or more introduction slides
  • A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
  • A summary/conclusion slide that is a reflection of the outline.
  • Acknowledgments slide
  • References slide
• Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am on Thursday, April 12
  • You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
• Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the Presentation Rubric.
• Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
  1. What is the speaker's take-home message (one short sentence)?
  2. What is the best thing about this presentation?
  3. What needs improvement?
  4. Please comment on the speaking style (language and delivery) of each presenter.
• Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

Evaluating the Meta Data of a Journal Article

Besides evaluating the content of the journal article itself, it is useful to evaluate the meta data about the article to assist in the determination of the article reliability, validity, accuracy, authority, and bias.

Assignment

• For your assigned journal article, answer/provide the following on your individual journal entry.
  1. The complete bibliographic reference in the APA style (see this link), with DOI.
  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.
  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.
     • 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.
  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)
  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?

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

1. Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
2. PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
3. PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
4. Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
5. Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
6. Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article)
   • No Creative Commons license
7. Article is not Open Access, but is freely available 2 months after publication, LMU did not pay for the article
8. Availability: in print and online
9. Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA, published in the United States
10. The journal begain in 1989
11. Peer-reviewed articles: yes
12. Editorial board.
13. Impact factor: 3.512 (2017)
14. Submitted March 1, 2004
15. Accepted September 28, 2004
16. Did the article undergo any revisions before acceptance? no/unknown
17. Published October 13, 2004
18. What is the approximate elapsed time between submission and publication? 6.5 months
19. What are the institutions with which the authors are affiliated?
    • Biotechnology Research Institute, National Research Council of Canada; Department of Biochemistry, McGill University;Institute of Microbiology, Johann Wolfgang Goethe-University; Molecular Oncology Group, Royal Victoria Hospital
20. Have the authors published other articles on this subject? (How will you find this out?) not too much
21. Is there a conflict of interest for any of the authors?
22. Data are not available (dead hyperlink)
23. Web of Science
    • How many articles does this article cite? 73
    • How many articles cite this article? 131

Whole Team Journal Assignment: Creating a Team Wiki Page

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.

1. Select your team's Project Manager.
   • Add the name of your project manager to the Project Manager guild page and Overview pages.
2. Name your team and create your team home page on the wiki.
   • The name of your team home page should simply be the team name.
   • This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
3. Create a link to your team's page on the course Main page.
4. Create a template for your team with useful information and links that you will invoke on all pages that you will create for the project.
   • Include the category "Team Project" in your template.
     • However, please do not add this category to your own individual templates because we want them to precisely mark pages having to do with the Team Project.
5. Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
6. Each team member should reflect on the team's progress:
   1. What worked?
   2. What didn't work?
   3. What will I do next to fix what didn't work?
7. Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.