Difference between revisions of "Malverso Week 11"

From LMU BioDB 2015
Jump to: navigation, search
(defined terms)
(finished defining terms)
Line 21: Line 21:
 
##heme: An iron compound that has oxygen carrying properties and is the non-protein part of hemoglobin. [http://medical-dictionary.thefreedictionary.com/heme Found at this link.]
 
##heme: An iron compound that has oxygen carrying properties and is the non-protein part of hemoglobin. [http://medical-dictionary.thefreedictionary.com/heme Found at this link.]
 
##paralogous genes: Genes that are similar but at two different locations in the chromosome of the organism. This indicates that the sets came from an ancestral gene. [http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-P/paralogous_genes.html Found at this link.]  
 
##paralogous genes: Genes that are similar but at two different locations in the chromosome of the organism. This indicates that the sets came from an ancestral gene. [http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-P/paralogous_genes.html Found at this link.]  
−
##hydrogenases
+
##hydrogenase: A catalyst for the formation/oxidation of H2. [http://www.chemicool.com/definition/hydrogenase.html Found at this link.]
−
##heterodimeric
+
##heterodimeric: An adjective that describes a protein which is comprised of two differing polyeptide chains. [http://www.merriam-webster.com/medical/heterodimer Found at this link.]
−
##aquaporin
+
##aquaporin: A channel that allows water to pass through the membrane (selectively), but not ions. [http://www.medicinenet.com/script/main/art.asp?articlekey=33425 Found at this link.]
−
##efflux
+
##efflux: The process of flowing/flowing out. [http://www.merriam-webster.com/dictionary/efflux Found at this link.]
−
##biofilms
+
##biofilm: A colony of microorganisms that are encased in a protective coating of their own secretions. They can form on solid and liquid surfaces. [http://dictionary.reference.com/browse/biofilm Found at this link.]
−
##virulence determinants
+
##virulence determinants: Factors that allow bacteria to cause disease. [http://www.nature.com/scitable/definition/virulence-factor-53 Found at this link.]
 
#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.
 
#*What is the importance or significance of this work (i.e., your species)?
 
#*What is the importance or significance of this work (i.e., your species)?

Revision as of 05:11, 16 November 2015

Personal Goals

  • Prepare for journal club presentations
  • Set up coding/testing environment
  • Determine the regular expression for the ordered locus ID for your species
  • Identify the appropriate model organism database for your species.
  • Perform an initial Gene Database export and Gene Database Testing Report

Electronic Journal

  • After struggling to find a Model Organism Gene Database for Shewanella oneidensis, I asked Dr.Dahlquist for assistance.
  • The only database link we could find was broken.
  • We decided that our next plan of action would be to use the website bacteria.ensembl.org as our MOD.

Journal Club Presentation

  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. 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 URL citation.
    1. bioremediation: When bacteria, plants, or other biological agents are used to get rid of pollutants in things such as soil or water.Found at this link.
    2. plasmid: DNA that can replicate itself without the chromosomal DNA.Found at this link.
    3. phage: Also known as bacteriophage. Viruses that usually cause the disintegration of a certain bacteria through infection. Found at this link.
    4. cytochromes: A protein whose main function is electron transport. Found at this link.
    5. redox: An abbreviation of reduction which is the loss of oxygen. Found at this link.
    6. heme: An iron compound that has oxygen carrying properties and is the non-protein part of hemoglobin. Found at this link.
    7. paralogous genes: Genes that are similar but at two different locations in the chromosome of the organism. This indicates that the sets came from an ancestral gene. Found at this link.
    8. hydrogenase: A catalyst for the formation/oxidation of H2. Found at this link.
    9. heterodimeric: An adjective that describes a protein which is comprised of two differing polyeptide chains. Found at this link.
    10. aquaporin: A channel that allows water to pass through the membrane (selectively), but not ions. Found at this link.
    11. efflux: The process of flowing/flowing out. Found at this link.
    12. biofilm: A colony of microorganisms that are encased in a protective coating of their own secretions. They can form on solid and liquid surfaces. Found at this link.
    13. virulence determinants: Factors that allow bacteria to cause disease. Found at this link.
  2. 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).
  3. 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_####).


Team Page

Heavy Metal HaterZ

Assignments

Individual Journal Entries

Shared Journal Entries

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Malverso_Week_11&oldid=6242"