BISC209/S12: Lab12

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==Presentations this week==
==Presentations this week==
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Room TBA. 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. Email a final copy to your instructor, too.
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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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'''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>
'''Group Presentation'''<BR>  
'''Group Presentation'''<BR>  
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In LAB 12, teams of 3-4 students will prepare and present a 20-30 minute group oral presentation that is worth 25 points, based on the assessment of the class and your instructor of the presentation's quality. However, you will also be assessing the quality and level of participation of your peers for a potential loss of no more than 10 individual points from the 25 point total.  This individual grade is determined by the consensus of your group members 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 but in a room TBA.  
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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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'''Your group presentation topic will be '''
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'''Choices:'''<BR>
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'''Genome Based Methods:'''<BR>
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'''Possible Presentation Topics:'''<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>
'''Congratulations on completing microbiology lab!''' <BR>
'''Congratulations on completing microbiology lab!''' <BR>

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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