| MBIO
4670 Teaching Assistants:
Damien Rivers
All lab reports must have a completed
Honesty Declaration attached: Group
Lab Assignment or Individual
Lab Assignment. Available as pdf.
Lab starts Monday, January
19, 2012 in rooms 201 and 204 Buller. Lab manuals are handed out in class
the first week of lectures. All essential lab related information is given
in the lab manual.
Lab Manual correction - please correct the lab exam date found on page 3 schedule - Lab exam date is Monday March 26 (not March 27).
Report and Assignment Formats
Read lab report presentation section in general instructions at the beginning of your lab manual before doing your lab report. Lab reports must be typed. This includes calculations. 10% of the mark subtracted for portion of report not typed.
Lab 2 mutant primer design assignment Word format.
Lab 1 report Word format and Excel
spreadsheet. Save and open in Word or Excel to add requested
information. Require information in Lab 2 introduction, Table 1, to do report.
Lab 2 report Word format.
Save and open in Word to add requested information.
Report Data
Lab 1
Southern Blot of Rhizobium leguminosarum
SmaI genomic DNA preps
Agarose Gel Loading plan (pdf): gel 1, gel 2, gel 3, gel 4, gel 5, gel 6
Agarose gel photographs (jpg): gel 1, gel 2, gel 3, gel 4, gel 5, gel 6
Hybridized blots for corresponding agarose gels (jpg): blot 1, blot 2, blot 3, blot 4, blot 5, blot 6. Copy paste
to word Lab 1 report where requested, may need to resize to fit ~1/2 page. If your data is poor,
borrow data from another group (both blot and matching gel)and reference. An example of good data is gel 4 blot lanes 3 to 6 with lanes 3 & 4 transconjugants migrating less than lane 5 negative sample band (should be similar to lane 6 postive sample but migrating slightly less).
Possible reasons for group blots not matching expected pattern, no DNA isolated, samples not labelled as requested (eg on gel blot 4 lanes 10 and 11 and gel blot 6 lanes 5 & 6 are reversed) negative control migrates the furthest, or gel not inverted during prep of Southern blot (possibly gel blot 3).
Lab 2
Agarose gels of plasmid DNA (pMR106
site-directed megaprimer mutant) restriction digested with BamHI and/or
HindIII
Agarose gel loading plan (pdf): gel 1, gel 2, gel 3, gel 4, gel 5, gel 6
Agarose gel digital image (jpg):gel 1, gel 2, gel 3, gel 4, gel 5, gel 6 digests there should only be one band, if this band is present and the most intense, other lighter bands are due to incomplete digestion. For Hind 111/BamHI digest: when the two expected bands are present, other lighter bands due to incomplete digestion. If the expected bands are not present, then plasmid is not acceptable for sequencing.
Student DNA sequences:group 1, group 2, group 3, group 4, group 5, group 6, group 7, group 8, group 9, group 10. group 11, group 12.
Copy/paste file in appropriate location in BLAST (website link below).
ab1 files: Save file before opening in Chromas (link to download below).
Lab References
Oresnik,
IJ, Pacarynuk, LA, O’Brien, SA Yost, CR and Hynes, MF. 1998.
Plasmid-Encoded Catabolic Genes in Rhizobium leguminosarum bv.
trifolii: Evidence for a Plant-Inducible Rhamnose Locus Involved
in Competition for Nodulation. Mol. Plant Microbe Interact. 11:1175-1185.
Richardson,
JS, Hynes, MF, Oresnek, IJ. 2004. A Genetic Locus Necessary for Rhamnose
Uptake and Catabolism in Rhizobium leguminosarum bv. trifolii.
J. Bact. 186:8433-8442
LAB 2 MEGAPRIMER MUTAGENSIS of Rhizobium
leguminosarum rhamnose kinase
Relevant rhamnose catabolism locus genes (pdf format): rhaT,
rhaP,
rhaK, rhaR. Includes both the bp sequence and corresponding amino acid
coding sequence.
pBluescript sequence (primer selection) SK+ SK-
Blast
website (layout may differ from lab manual instructions as the site is continually updated/changed)
Amino
acid codon and abbreviation table
Applied Biosystems Sequence Scanner v1.0 (information and download)
3130 Genetic Analyzer (DNA
sequencer information) Applied Biosystems application note - sequence
nucleotide fluorescent dye output figure
on Applied Biosystems website
Faculty
of Science Cheating, Plagerism,etc
Lab Skill Sheet-
available for students to use for job applications, just check off the
highlighted boxes for the lab course(s) you have taken.
pdf or excel (prior to Fall 2007)
pdf or
excel (starting Fall 2007)
email le_cameron@umanitoba.ca
Emails: subject must contain course number and subject,
eg. 4570 lab 1 report. If no subject given, email is deleted. Emails replies
occur only during working hours. Email must include student name.
phone 474-6542
Department of Microbiology
Buller Bldg
Winnipeg, MB
R3T 2N2
plasmid
pM13 (diagram for 60.457 lab manaul)
Frequently information is available as a
pdf file requiring Adobe Acrobat Reader. Adobe abcrobat reader is available
at UM Software ExpressUM
Software Express.
Lab Skill Sheet-
available for students to use for job applications, just check off the
highlighted boxes for the lab course(s) you have taken.
pdf or excel (prior to Fall 2007)
pdf or
excel (starting Fall 2007)
email le_cameron@umanitoba.ca
phone 474-6542
Department of Microbiology
Buller Bldg
Winnipeg, MB
R3T 2N2
University
of Manitoba calender 2007-2008
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