BISC209/S12: Lab12

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=='''LAB 12: Conferences'''==
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==Presentations this week==
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You will not have lab this week but will, instead, have an individual 30 minute conference with your lab instructor. Make sure the that you have a draft of all figures/tables visualizations of evidence ready for critique. There will be time for discussion with your instructor about problematic areas in your paper. If you have completed a draft of your paper BEFORE this conference, it will maximize the effectiveness of this meeting. <BR><BR>
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Room S264. Please make sure that you have emailed your groups' Powerpoint™ to yourself so we can access it in the classroom where we will have our presentations. Make sure to upload a copy to your drop box in Sakai, too.<BR><BR>
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Final Paper and your lab notebook are due in your lab instructor's office by 4pm on your lab day April 24 or April 25. Please make sure there is an electronic copy of your paper uploaded to your folder in your Lab's Drop Box in Sakai.(Electronic copy requirement is in addition to the hard copy submission to your instructor.) <BR>
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'''Turn in your lab notebook''' to your instructor at the beginning of the lab period. She will notify you in an announcement in Sakai when your notebook is graded and ready for pick up. There is a grading rubric posted to Resources in Sakai.<BR>
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More information about the final paper can be found at:
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Lab 12 Assignment: [[BISC209/S12: Assignment_209_Lab12 | Assignment: Final Paper]]. A grading rubric is posted to the Assignments and Rubrics Folder in the Resources section of Sakai. <br>
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Congratulations on completing microbiology lab! <BR>
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'''Group Presentation'''<BR>
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In LAB 12, teams of 3-4 students will prepare and present a 15-20 minute group oral presentation that is worth 15 points. Points awarded the group are based on an assessment of quality of the presentation, judged by the class and by your instructor. You will also evaluate the quality and level of participation of each of your teammates for an individual component of the grade. The penalty for under-participation can be up to 6 points deducted from the 15 point total.  The individual grade is determined by the consensus of your teammates on each member's contribution. Grading rubrics will be provided. You will also be provided with links and handouts of helpful information about making an oral presentation. The Resources section of the wiki contains a tip sheet prepared by PLTC peer-tutors about how to give an effective oral presentation. We will not do these presentations in the lab.
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'''The Theme of our Presentations this year is Methods of Identification of Microorganisms'''<BR>
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'''Choices:'''<BR>
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'''Genome Based Methods:'''<BR>
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Current and next generation: 
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#16s rRNA
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#rpoB gene
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#Multilocus sequence typing (MLST) by next generation DNA sequencing.
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#HIgh throughput:  Examples are Illumina ([http://www.illumina.com/technology/sequencing_technology.ilmn | http://www.illumina.com/technology/sequencing_technology.ilmn]) and 454 Pyrosequencing ([http://www.pyrosequencing.com/DynPage.aspx?id=7454 | http://www.pyrosequencing.com/DynPage.aspx?id=7454])<BR>
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Other genomic methods:<BR>
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#Repetitive sequence-based PCR (rep-PCR)([http://microbeinotech.com/Default.aspx?tabid=178 | http://microbeinotech.com/Default.aspx?tabid=178])<BR>
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#Ribotyping ([http://foodscience.cornell.edu/cals/foodsci/research/labs/wiedmann/lmt/about-ribotyping.cfm | http://foodscience.cornell.edu/cals/foodsci/research/labs/wiedmann/lmt/about-ribotyping.cfm]) <BR>
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#DNA Microarray PhyloChips([http://www.microbial-ecology.net/phylochips.asp | http://www.microbial-ecology.net/phylochips.asp])<BR>
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#Pulsed-field gel electrophoresis(PFGE) [http://www.nphl.org/documents/PFGE.pdf | http://www.nphl.org/documents/PFGE.pdf]<BR>
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#Other?
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'''Non-DNA Based Methods'''<BR>
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#Traditional Culture Based Batteries of Physical and Metabolic Characteristics (Traditional Microbiology)<BR>
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#Analysis of cellular fatty acid methyl esters (FAMEs) by gas chromatography ([http://scholar.google.com/scholar_url?hl=en&q=http://natasha.eng.usf.edu/gilbert/courses/Biotransport%2520Phenomena/pdf/bacteria_gc_1.pdf&sa=X&scisig=AAGBfm0x1rtmNNBwKqkjBDfjNkX7rldQXw&oi=scholarr])<BR>
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#Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight (MaldiTof MS)(http://www.biomerieux-diagnostics.com/servlet/srt/bio/clinical-diagnostics/dynPage?open=CNL_CLN_PRD&doc=CNL_CLN_PRD_G_PRD_CLN_72&pubparams.sform=1&lang=en)<BR>
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#Other?
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<BR><BR>
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'''Congratulations on completing microbiology lab!''' <BR>
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Current revision

Wellesley College-BISC 209 Microbiology -Spring 2012

Presentations this week

Room S264. Please make sure that you have emailed your groups' Powerpoint™ to yourself so we can access it in the classroom where we will have our presentations. Make sure to upload a copy to your drop box in Sakai, too.

Turn in your lab notebook to your instructor at the beginning of the lab period. She will notify you in an announcement in Sakai when your notebook is graded and ready for pick up. There is a grading rubric posted to Resources in Sakai.

Group Presentation
In LAB 12, teams of 3-4 students will prepare and present a 15-20 minute group oral presentation that is worth 15 points. Points awarded the group are based on an assessment of quality of the presentation, judged by the class and by your instructor. You will also evaluate the quality and level of participation of each of your teammates for an individual component of the grade. The penalty for under-participation can be up to 6 points deducted from the 15 point total. The individual grade is determined by the consensus of your teammates on each member's contribution. Grading rubrics will be provided. You will also be provided with links and handouts of helpful information about making an oral presentation. The Resources section of the wiki contains a tip sheet prepared by PLTC peer-tutors about how to give an effective oral presentation. We will not do these presentations in the lab.

The Theme of our Presentations this year is Methods of Identification of Microorganisms

Choices:
Genome Based Methods:

Current and next generation:

  1. 16s rRNA
  2. rpoB gene
  3. Multilocus sequence typing (MLST) by next generation DNA sequencing.
  4. HIgh throughput: Examples are Illumina (| http://www.illumina.com/technology/sequencing_technology.ilmn) and 454 Pyrosequencing (| http://www.pyrosequencing.com/DynPage.aspx?id=7454)

Other genomic methods:

  1. Repetitive sequence-based PCR (rep-PCR)(| http://microbeinotech.com/Default.aspx?tabid=178)
  2. Ribotyping (| http://foodscience.cornell.edu/cals/foodsci/research/labs/wiedmann/lmt/about-ribotyping.cfm)
  3. DNA Microarray PhyloChips(| http://www.microbial-ecology.net/phylochips.asp)
  4. Pulsed-field gel electrophoresis(PFGE) | http://www.nphl.org/documents/PFGE.pdf
  5. Other?

Non-DNA Based Methods

  1. Traditional Culture Based Batteries of Physical and Metabolic Characteristics (Traditional Microbiology)
  2. Analysis of cellular fatty acid methyl esters (FAMEs) by gas chromatography ([1])
  3. Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight (MaldiTof MS)(http://www.biomerieux-diagnostics.com/servlet/srt/bio/clinical-diagnostics/dynPage?open=CNL_CLN_PRD&doc=CNL_CLN_PRD_G_PRD_CLN_72&pubparams.sform=1&lang=en)
  4. Other?



Congratulations on completing microbiology lab!

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