BISC209/S12: Lab12

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=="Virtual" Poster Presentations this week==
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==Presentations this week==
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Room TBA. Please make sure that you have emailed your poster 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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'''Virtual Poster Presentation'''<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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In LAB 12, teams of 3-4 students will prepare and present a Powerpoint™ slide in the style of a poster that would be presented informally and talked about at a scientific research conference. You and your partners will not print the poster and stand by it at a conference but, instead, you will show it to the class "virtually" on a projection screen and use it in a 20-30 minute group oral presentation that is worth 25 points, based on the assessment of the class and your instructor of the poster and 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. The contribution grade includes the data collection, data analysis, and the preparation of the poster and presentation. Grading rubrics will be provided. You will also be provided with links and handouts of helpful information about making a poster. There are examples of effective posters to look at from the following web site: [http://www.ncsu.edu/project/posters/examples | http://www.ncsu.edu/project/posters/examples/]. The Resources section of the wiki contains a tip sheet prepared by the PLTC oral presentation 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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'''Your group poster presentation topic will be to compare soil microbial communitiesYou have explored the composition and behavior of one through 16srRNA sequencing and and other analyses.'''
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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 totalThe 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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'''Possible Presentation Topics:'''<BR>
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'''The Theme of our Presentations this year is Methods of Identification of Microorganisms'''<BR>
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All of your soil samples were taken from a greenhouse in New England in mid-winter but the soil microbial community may or may not be typical of a soil community found outside the greenhouse. One line of investigation might be to compare your soil's microbial community to that of a more a natural environment. What natural environments might be appropriate for this comparison? What might be differences and similarities to look for?
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This greenhouse tropical habitat comprises many, many microenvironments. Do you think there are major differences among them as far as abundance and richness of microbial members of each community? What are the factors that might contribute to differences? How do bacteria travel from one community to another? Might there be greater differences among those farther away than closer together? How would you test this hypothesis? What characteristics would you look for among common members or unique members of different soil communities in the same habitat?
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'''Choices:'''<BR>
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'''Genome Based Methods:'''<BR>
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Note that we attempted to get soil samples in the rhizosphere (including the roots of plants). Might the plants adjacent or in your sampling site influence the bacterial membership of the community? How so? How would you test this hypothesis?
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Current and next generation: 
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What other factors might influence or control the make-up or behavior of bacteria in soil communities? How might you use our data to test other hypotheses?  
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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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If you consider all the soil communities we tested as members of one habitat and members of one eco-system, do we have evidence to support the “great plate count anomaly”? Do we have evidence to support or refute any of the wide ranging, published estimates of the diversity and abundance of bacteria in a gram of soil?
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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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Congratulations on completing microbiology lab! <BR>
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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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<div class=noprint>
==Links to Labs==
==Links to Labs==

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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