Difference between revisions of "Jwoodlee Week 11"
From LMU BioDB 2015
(→Preparation for Journal Club on Your Species: added definitions) |
(→Preparation for Journal Club on Your Species: added definitions) |
||
| Line 3: | Line 3: | ||
Some steps are taken from [[Week 11 | here.]] | Some steps are taken from [[Week 11 | here.]] | ||
| − | # I made a list of <Insert Number Here> biological terms for which I did not know the definitions when I first read the article. I then defined each of the terms. | + | # I made a list of <Insert Number Here> biological terms for which I did not know the definitions when I first read the article. I then defined each of the terms. |
##enterohemorrhagic - Based on what my teammates have told me and what I've found on [http://www.cdc.gov/ncidod/dbmd/diseaseinfo/enterohemecoli_t.htm the CDC website.] Enterohemorrhagic is used to describe a strain of ''E. coli'' that induces hemorrhagic diarrhea which is a result of bleeding into the intestines. | ##enterohemorrhagic - Based on what my teammates have told me and what I've found on [http://www.cdc.gov/ncidod/dbmd/diseaseinfo/enterohemecoli_t.htm the CDC website.] Enterohemorrhagic is used to describe a strain of ''E. coli'' that induces hemorrhagic diarrhea which is a result of bleeding into the intestines. | ||
| − | ## | + | ##plasmid - Plasmids are circular independent DNA molecules that hold a few genes and can be inserted into genomes. [https://askabiologist.asu.edu/plasmids] |
##inversions - An inversion is a defect in a chromosome. Physically it occurs when a segment of the chromosome breaks off and is reinserted into the chromosome in the same spot. [http://www.biology-online.org/dictionary/Inversion Source] | ##inversions - An inversion is a defect in a chromosome. Physically it occurs when a segment of the chromosome breaks off and is reinserted into the chromosome in the same spot. [http://www.biology-online.org/dictionary/Inversion Source] | ||
##translocations - Translocation is another type of defect in a chromosome when a segment breaks off and is moved to another location within the same chromosome or to another chromosome.[http://www.biology-online.org/dictionary/Translocation Source] | ##translocations - Translocation is another type of defect in a chromosome when a segment breaks off and is moved to another location within the same chromosome or to another chromosome.[http://www.biology-online.org/dictionary/Translocation Source] | ||
| Line 12: | Line 12: | ||
##enteric - I just used the google dictionary for this: [https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=enteric] It means relating to the intestines, so it isn't really strictly a biological term. | ##enteric - I just used the google dictionary for this: [https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=enteric] It means relating to the intestines, so it isn't really strictly a biological term. | ||
##pseudogenes - A pseudogene is the part of the DNA that is not transcribed into mRNA and therefore not translated into protein. [http://www.truthinscience.org.uk/tis2/index.php/evidence-for-evolution-mainmenu-65/277-the-changing-face-of-pseudogenes.html Source] | ##pseudogenes - A pseudogene is the part of the DNA that is not transcribed into mRNA and therefore not translated into protein. [http://www.truthinscience.org.uk/tis2/index.php/evidence-for-evolution-mainmenu-65/277-the-changing-face-of-pseudogenes.html Source] | ||
| − | ## | + | ##accession number - From what I can tell, an accession number in Biology is a unique identifier given to a protein or DNA sequence so it can be tracked. [https://en.wikipedia.org/wiki/Accession_number_(bioinformatics)] |
## | ## | ||
# Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. | # Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article. | ||
Revision as of 04:31, 13 November 2015
Individual Journal Assignment
Preparation for Journal Club on Your Species
Some steps are taken from here.
- I made a list of <Insert Number Here> biological terms for which I did not know the definitions when I first read the article. I then defined each of the terms.
- enterohemorrhagic - Based on what my teammates have told me and what I've found on the CDC website. Enterohemorrhagic is used to describe a strain of E. coli that induces hemorrhagic diarrhea which is a result of bleeding into the intestines.
- plasmid - Plasmids are circular independent DNA molecules that hold a few genes and can be inserted into genomes. [1]
- inversions - An inversion is a defect in a chromosome. Physically it occurs when a segment of the chromosome breaks off and is reinserted into the chromosome in the same spot. Source
- translocations - Translocation is another type of defect in a chromosome when a segment breaks off and is moved to another location within the same chromosome or to another chromosome.Source
- bacteriophage - | Biology Online Dictionary A bacteriophage is a virus that can infect a bacteria.
- pathogenicity islands - The segment of genetic material within an organism(in this case within the bacteria) that gives the organism the ability to cause disease. This helped.
- enteric - I just used the google dictionary for this: [2] It means relating to the intestines, so it isn't really strictly a biological term.
- pseudogenes - A pseudogene is the part of the DNA that is not transcribed into mRNA and therefore not translated into protein. Source
- accession number - From what I can tell, an accession number in Biology is a unique identifier given to a protein or DNA sequence so it can be tracked. [3]
- Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
- What is the importance or significance of this work (i.e., your species)?
- What were the methods used in the study?
- Briefly state the result shown in each of the figures and tables.
- How do the results of this study compare to the results of previous studies (See Discussion).
- For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the NAR assignment. In particular, make sure to answer the following:
- What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
- What individual or organization maintains the database?
- What is their funding source(s)?
- Is there a license agreement or any restrictions on access to the database?
- How often is the database updated?
- Are there links to other databases?
- Can the information be downloaded?
- In what file formats?
- Evaluate the “user-friendliness” of the database.
- Is the Web site well-organized?
- Does it have a help section or tutorial?
- Run a sample query. Do the results make sense?
- What is the format (regular expression) of the main type of gene ID for this species (the "ordered locus name" ID)? (for example, for Vibrio cholerae it was VC#### or VC_####).
- For the microarray paper (GenMAPP Users only), include the following:
- Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
- Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
- Construct a flow chart that illustrates the above.
Journal Club Presentation
Each pair of students will prepare and give a 15 minute PowerPoint presentation for their paper in class on Tuesday, November 17 or Tuesday, November 24.
- Please follow the Presentation Guidelines for how to format your slides.
- You will need to prepare ~15 slides (assume 1 slide per minute of presentation).
- You need to present the information in the outline of your journal article listed above, but organized as a presentation.
- Specifically, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
- Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, November 17, even if you are presenting the following week.
- You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
- Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the Presentation Rubric.
- Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
- What is the speaker's take-home message (one short sentence)?
- What are the best points about the presentation's organization, visuals, and delivery? Please give at least 2 specific examples.
- What points need improvement? Please give at least 2 specific examples.
- Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this presentation.
BIOL 367, Fall 2015, User Page, Team Page
| Weekly Assignments | Individual Journal Pages | Shared Journal Pages |
|---|---|---|
|
|
|
|
