Difference between revisions of "Rlegaspi Week 11"

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(→‎Journal Club Preparation: Microarray Paper: Added experimental design section, added biological terms that are unique compared to Emily's)
 
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{{Heavy Metal Haterz}}
 
{{Heavy Metal Haterz}}
  
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'''This journal entry is due on Tuesday, November 17, at midnight PST.''' ''(Monday night/Tuesday morning)''
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= Journal Club Preparation: Microarray Paper =
  
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== Overview ==
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== Bibliographic Information of Microarray Paper ==
  
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For this week, your team has two main tasks:
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Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. ''BMC genomics, 10''(1), 131.
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*The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed/?term=Yang%2C+Y.%2C+Harris%2C+D.+P.%2C+Luo%2C+F.%2C+Xiong%2C+W.%2C+Joachimiak%2C+M.%2C+Wu%2C+L.%2C+...+%26+Zhou%2C+J.+%282009%29.+Snapshot+of+iron+response+in+Shewanella+oneidensis+by+gene+network+reconstruction.+BMC+genomics%2C+10%281%29%2C+131. PubMed].
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*The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667191/ PubMedCentral]
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*The link to the full text of the article (HTML format) from the publisher [http://www.biomedcentral.com/1471-2164/10/131 web site].
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*The link to the full [http://www.biomedcentral.com/content/pdf/1471-2164-10-131.pdf PDF] version of the article from the publisher web site.
  
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# Prepare for journal club presentations in Weeks 12 and 13
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== Experimental Design of the Study ==
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#* You will deeply explore and perform a critical review of the genome paper (coder/QA) and microarray paper (GenMAPP users) for your team's species.
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Purpose: Examining the iron response of ''Shewanella oneidensis'' through the depletion and repletion of iron.
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#* You will communicate your findings in an effective oral presentation.
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Sample: Wild-type ''Shewanella oneidensis'' MR-1 (grown to mid-log phase, diluted in LB medium)
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# Begin initial tasks on your research project
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Treatment: Iron chelator 2,2'-dipyridyl diluted in water to 80, 160, 240, and 320 micro-molar concentrations (Iron chelator depletes iron)
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#* Coder/QA
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Biological treatments - all of the studies were done in triplicates
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#** Set up coding/testing environment
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3 samples per treatment
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#** Determine the regular expression for the ordered locus ID for your species
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Number of chips: 12 (3 samples x 4 treatments = 12)
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#** Identify the appropriate model organism database for your species.
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Dye swaps - Undetermined
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#** Perform an initial Gene Database export and Gene Database Testing Report
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<!-- Thank you Emily for info, confirmed info through more reading of paper -->
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#* GenMAPP Users
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#** Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
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#** Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
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#** Compile the raw data in preparation for normalization and statistical analysis.
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== Individual Journal Assignment ==
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== Defining Unfamiliar Biological Terms ==
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#Proteobacterium: comprise one of the largest divisions within prokaryotes and account for the vast majority of the known Gram-negative bacteria; great biological significance as it includes a large number of known human, animal and plant pathogens
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#*[[http://femsre.oxfordjournals.org/content/24/4/367.long Citation]]
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#Methanogenesis: Bacterial conversion of methanogenic substrates [acetate, formate, hydrogen, carbon dioxide] into methane and carbon dioxide
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#*[[http://toxics.usgs.gov/definitions/methanogenesis.html Citation]]
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#Ferric Uptake Regulator: a transcription factor which utilizes Fe(2+) as a corepressor and represses siderophore synthesis in pathogens
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#*[[http://www.ncbi.nlm.nih.gov/pubmed/24106689 Citation]]
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#RT-PCR (reverse transcriptase-PCR): a reaction applied when the target sequence is RNA, such as viral RNA or messenger RNA. Reverse transcriptase that copies DNA from an RNA template is present in the first round.
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#*[[http://medical-dictionary.thefreedictionary.com/Real-Time+PCR Citation]]
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#Cytochrome: any of a class of hemoproteins, widely distributed in animal and plant tissues, whose main function is electron transport using the heme prosthetic group; distinguished according to their prosthetic groups
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#*[[http://medical-dictionary.thefreedictionary.com/cytochrome Citation]]
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#Palindromic: In molecular biology, a self-complementary nucleic acid sequence; a sequence identical to its complementary strand, if both are "read" in the same 5' to 3' direction, or inverted repeating sequences running in opposite directions (for example, 5'-AGTTGA-3') on either side of an axis of symmetry
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#*[[http://medical-dictionary.thefreedictionary.com/palindrome Citation]]
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#Mutagenesis: act of mutating by deleting or changing the nucleotide sequence
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#*[[http://www.biology-online.org/dictionary/Mutagenesis Citation]]
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#Spectrophotometric quantification: The determination of the structure or quantity of substances by measuring their capacity to absorb light of various wavelengths
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#*[[http://medical-dictionary.thefreedictionary.com/spectrophotometric+analysis Citation]]
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#Chi square test: a statistical method of assessing the significance of a difference, as when the data from two or more samples is represented by a discrete number
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#*[[http://www.biology-online.org/dictionary/Chi-square_test Citation]]
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#Hybridization: The process of forming a double stranded nucleic acid from joining two complementary strands of DNA (or RNA).
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#*[[http://www.biology-online.org/dictionary/Hybridization Citation]]
  
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* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
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== Article Outline ==
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* Link from your user page to this Assignment page.
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* Link to your journal entry from your user page.
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* Link back from your journal entry to your user page.
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* Link from your journal entry to your team's home page.
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* Link from your team's home page to your journal entry.
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* Don't forget to add the categories "Journal Entry", "Group Projects", and your team's category to the end of your wiki page.
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**'''''Note: you can easily fulfill all of these links by adding them to your template (and your team's template) and then using your template on your journal entry.'''''
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* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week.  An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
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=== Preparation for Journal Club on Your Species ===
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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.
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Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 17 and Tuesday, November 24.  The Coder and Quality Assurance person will present the genome paper for your species and the GenMAPP Users will present the microarray paper for your species.  You will decide within your team who will present on which day.  Please edit the schedule on the [[Main Page]] to show who is presenting on which day.
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In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
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# 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.'''''
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# 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.
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#* 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)?
 
#* What were the methods used in the study?
 
#* What were the methods used in the study?
 
#* Briefly state the result shown in each of the figures and tables.
 
#* 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).
 
#* How do the results of this study compare to the results of previous studies (See Discussion).
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#* 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:
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#*# 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])?
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#*# What individual or organization maintains the database? 
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#*# What is their funding source(s)? 
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#*# Is there a license agreement or any restrictions on access to the database?
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#*# How often is the database updated? 
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#*# Are there links to other databases? 
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#*# Can the information be downloaded? 
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#*#* In what file formats?
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#*# Evaluate the “user-friendliness” of the database. 
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#*#* Is the Web site well-organized? 
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#*#* Does it have a help section or tutorial? 
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#*#* Run a sample query.  Do the results make sense?
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#*# 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_####).
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#* For the microarray paper (GenMAPP Users only), include the following:
 
#* 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.
 
#*# Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
Line 63: Line 56:
 
#*# Construct a flow chart that illustrates the above.
 
#*# Construct a flow chart that illustrates the above.
  
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=== Journal Club Presentation ===
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= Links to User Page and Journal Pages =
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{{Template:Rlegaspi}}
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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. 
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[[Category:Heavy Metal HaterZ]]
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* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
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* You will need to prepare ~15 slides (assume 1 slide per minute of presentation).
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* You need to present the information in the outline of your journal article listed above, but organized as a presentation.
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** 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.
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* '''''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.'''''
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** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
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* Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the [[Presentation Rubric]].
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* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
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*# What is the speaker's take-home message (one short sentence)?
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*# What are the best points about the presentation's organization, visuals, and delivery?  Please give at least 2 specific examples.
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*# What points need improvement? Please give at least 2 specific examples.
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* 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.
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== Team Journal Assignment ==
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* Please make the requested changes to your team's wiki pages.
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** Please "comment out" the microarray papers that you won't be using for the project, just leaving the annotated bibliographic information for your genome paper and the microarray paper you will be using.
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* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
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* Set up a system for managing team files, including a filename system that keeps track of versions of files.
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[[Category:Assignment]]
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[[Category:Group Projects]]
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Latest revision as of 08:49, 17 November 2015

HeavyMetal.jpg

Shewanella oneidensis

Our Gene Database Testing Report

Group Paper - File:Final Report 20151218 2 HMH.docx

Group Members

Important Links

Our Files

Our Deliverables

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors
Individual Journal Entries
Mary Alverson Week 11 Week 12 Week 14 Week 15
Emily Simso Week 11 Week 12 Week 14 Week 15
Ron Legaspi Week 11 Week 12 Week 14 Week 15
Josh Kuroda Week 11 Week 12 Week 14 Week 15

Journal Club Preparation: Microarray Paper

Bibliographic Information of Microarray Paper

Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC genomics, 10(1), 131.

  • The link to the abstract from PubMed.
  • The link to the full text of the article in PubMedCentral
  • The link to the full text of the article (HTML format) from the publisher web site.
  • The link to the full PDF version of the article from the publisher web site.

Experimental Design of the Study

Purpose: Examining the iron response of Shewanella oneidensis through the depletion and repletion of iron. Sample: Wild-type Shewanella oneidensis MR-1 (grown to mid-log phase, diluted in LB medium) Treatment: Iron chelator 2,2'-dipyridyl diluted in water to 80, 160, 240, and 320 micro-molar concentrations (Iron chelator depletes iron) Biological treatments - all of the studies were done in triplicates 3 samples per treatment Number of chips: 12 (3 samples x 4 treatments = 12) Dye swaps - Undetermined

Defining Unfamiliar Biological Terms

  1. Proteobacterium: comprise one of the largest divisions within prokaryotes and account for the vast majority of the known Gram-negative bacteria; great biological significance as it includes a large number of known human, animal and plant pathogens
  2. Methanogenesis: Bacterial conversion of methanogenic substrates [acetate, formate, hydrogen, carbon dioxide] into methane and carbon dioxide
  3. Ferric Uptake Regulator: a transcription factor which utilizes Fe(2+) as a corepressor and represses siderophore synthesis in pathogens
  4. RT-PCR (reverse transcriptase-PCR): a reaction applied when the target sequence is RNA, such as viral RNA or messenger RNA. Reverse transcriptase that copies DNA from an RNA template is present in the first round.
  5. Cytochrome: any of a class of hemoproteins, widely distributed in animal and plant tissues, whose main function is electron transport using the heme prosthetic group; distinguished according to their prosthetic groups
  6. Palindromic: In molecular biology, a self-complementary nucleic acid sequence; a sequence identical to its complementary strand, if both are "read" in the same 5' to 3' direction, or inverted repeating sequences running in opposite directions (for example, 5'-AGTTGA-3') on either side of an axis of symmetry
  7. Mutagenesis: act of mutating by deleting or changing the nucleotide sequence
  8. Spectrophotometric quantification: The determination of the structure or quantity of substances by measuring their capacity to absorb light of various wavelengths
  9. Chi square test: a statistical method of assessing the significance of a difference, as when the data from two or more samples is represented by a discrete number
  10. Hybridization: The process of forming a double stranded nucleic acid from joining two complementary strands of DNA (or RNA).

Article Outline

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 microarray paper (GenMAPP Users only), include the following:
      1. Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
      2. Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
      3. Construct a flow chart that illustrates the above.

Links to User Page and Journal Pages

Ron Legaspi
BIOL 367, Fall 2015

Assignment Links
Individual Weekly Journals
Shared Weekly Journals
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