IGEM:PennState/Labbook/GalenLynch
Contents
- 1 Galen Lynch Lab Notebook
- 1.1 Calender
- 1.2 April 30th, 2007: Project Proposal Presentations
- 1.3 May 30th, 2007: Project Proposal Presentation
- 1.4 June 4th, 2007: Lab Meeting Presentation
- 1.5 June 13th, 2007: XylR Biobricks and Primers
- 1.6 June 28th, 2007: Lambda Biobricks and Primers
- 1.7 Oligo Order results:
- 1.8 June 30th, 2007: Competency Transformations
Galen Lynch Lab Notebook
- Penn State iGEM 2007
- Penn State Undergraduate
- Email gfl110@psu.edu
Calender
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<calendar> name=iGEM:PennState/Labbook/GalenLynch date=2007/04/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>
<calendar> name=iGEM:PennState/Labbook/GalenLynch date=2007/07/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>
<calendar> name=iGEM:PennState/Labbook/GalenLynch date=2007/10/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>
<calendar> name=iGEM:PennState/Labbook/GalenLynch date=2008/1/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>
April 30th, 2007: Project Proposal Presentations
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Bacterial Magnetosomes
<table|left>Bacterial Magnetosomes Information
Biogenic Nanotubes
Disclaimer: It turns out this presentation was looking under the wrong name, and thus is not an accurate portrayal of literature avaliability <table|left>Search for Biogenic Nanotubes
May 30th, 2007: Project Proposal Presentation
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Bio-Dosimetry
<table|left>Preliminary Dosimetry Feasibility Investigation
June 4th, 2007: Lab Meeting Presentation
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iGEM Meeting
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June 13th, 2007: XylR Biobricks and Primers
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Note: Start codons are in green, stop codons are in read, translational terminators are in blue. All sequences are shown without biobrick restriction sequences
XylR with promoter, rbs and terminator (Forward)
<html><pre>GCAACCAAAC GCCGTTCTTG ATTTTGATAA AAATTTTCTC AAAGCCGGTT ACGTATTACC GGTTTTGAGT TTTTGCATGA TTCAGCAGGA AAAGAACC<font color=green>AT G</font>TTTACTAAA CGTCACCGCA TCACATTACT GTTCAATGCC AATAAAGCCT ATGACCGGCA GGTAGTAGAA GGCGTAGGGG AATATTTACA GGCGTCACAA TCGGAATGGG ATATTTTCAT TGAAGAAGAT TTCCGCGCCC GCATTGATAA AATCAAGGAC TGGTTAGGAG ATGGCGTCAT TGCCGACTTC GACGACAAAC AGATCGAGCA AGCGCTGGCT GATGTCGACG TCCCCATTGT TGGGGTTGGC GGCTCGTATC ACCTTGCAGA AAGTTACCCA CCCGTTCATT ACATTGCCAC CGATAACTAT GCGCTGGTTG AAAGCGCATT TTTGCATTTA AAAGAGAAAG GCGTTAACCG CTTTGCTTTT TATGGTCTTC CGGAATCAAG CGGCAAACGT TGGGCCACTG AGCGCGAATA TGCATTTCGT CAGCTTGTCG CCGAAGAAAA GTATCGCGGA GTGGTTTATC AGGGGTTAGA AACCGCGCCA GAGAACTGGC AACACGCGCA AAATCGGCTG GCAGACTGGC TACAAACGCT ACCACCGCAA ACCGGGATTA TTGCCGTTAC TGACGCCCGA GCGCGGCATA TTCTGCAAGT ATGTGAACAT CTACATATTC CCGTACCGGA AAAATTATGC GTGATTGGCA TCGATAACGA AGAACTGACC CGCTATCTGT CGCGTGTCGC CCTTTCTTCG GTCGCTCAGG GCGCGCGGCA AATGGGCTAT CAGGCGGCAA AACTGTTGCA TCGATTATTA GATAAAGAAG AAATGCCGCT ACAGCGAATT TTGGTCCCAC CAGTTCGCGT CATTGAACGG CGCTCAACAG ATTATCGCTC GCTGACCGAT CCCGCCGTTA TTCAGGCCAT GCATTACATT CGTAATCACG CCTGTAAAGG GATTAAAGTG GATCAGGTAC TGGATGCGGT CGGGATCTCG CGCTCCAATC TTGAGAAGCG TTTTAAAGAA GAGGTGGGTG AAACCATCCA TGCCATGATT CATGCCGAGA AGCTGGAGAA AGCGCGCAGT CTGCTGATTT CAACCACCTT GTCGATCAAT GAGATATCGC AAATGTGCGG TTATCCATCG CTGCAATATT TCTACTCTGT TTTTAAAAAA GCATATGACA CGACGCCAAA AGAGTATCGC GATGTAAATA GCGAGGTCAT GTTG<font color = red>TAG</font>CGA TGATGAGAAT TGTCGGCGTC ACATCAGGTA ACGCTGCGTG GTTGTCGGAT GCGGCGTGAA CGCCTTATCC GACCTACCCG CCAGGCATGA TAAAACGCAC CAACAACGCT TCAGGCTCGT AGCTCAACTG CCTGAGACAA AGTAAAA<font color=blue>AGC CTTATCCGAC TGACAAGTCG GATAAGGCT</font>C AAGGAAATGC AAT</pre></html>
Primers:
ggaattcgcg gccgcttcta gag GCAACCAAAC GCCGTTCT (left side) Sequence for operations: ggaattcgcggccgcttctagagGCAACCAAACGCCGTTCT
- TmC 63,81
ctgcagcggc cgctactagt a ATTGCATTTC CTTGAGCCTT ATCC (right side) Sequence for operations: ctgcagcggccgctactagtaATTGCATTTCCTTGAGCCTTATCC
- TmC 63,78
XylR with promoter, rbs and terminator (Reverse)
<html><pre>ATTGCATTTC CTTG<font color=blue>AGCCTT ATCCGACTTG TCAGTCGGAT AAGGCT</font>TTTT ACTTTGTCTC AGGCAGTTGA GCTACGAGCC TGAAGCGTTG TTGGTGCGTT TTATCATGCC TGGCGGGTAG GTCGGATAAG GCGTTCACGC CGCATCCGAC AACCACGCAG CGTTACCTGA TGTGACGCCG ACAATTCTCA TCATCG<font color=red>CTA</font>C AACATGACCT CGCTATTTAC ATCGCGATAC TCTTTTGGCG TCGTGTCATA TGCTTTTTTA AAAACAGAGT AGAAATATTG CAGCGATGGA TAACCGCACA TTTGCGATAT CTCATTGATC GACAAGGTGG TTGAAATCAG CAGACTGCGC GCTTTCTCCA GCTTCTCGGC ATGAATCATG GCATGGATGG TTTCACCCAC CTCTTCTTTA AAACGCTTCT CAAGATTGGA GCGCGAGATC CCGACCGCAT CCAGTACCTG ATCCACTTTA ATCCCTTTAC AGGCGTGATT ACGAATGTAA TGCATGGCCT GAATAACGGC GGGATCGGTC AGCGAGCGAT AATCTGTTGA GCGCCGTTCA ATGACGCGAA CTGGTGGGAC CAAAATTCGC TGTAGCGGCA TTTCTTCTTT ATCTAATAAT CGATGCAACA GTTTTGCCGC CTGATAGCCC ATTTGCCGCG CGCCCTGAGC GACCGAAGAA AGGGCGACAC GCGACAGATA GCGGGTCAGT TCTTCGTTAT CGATGCCAAT CACGCATAAT TTTTCCGGTA CGGGAATATG TAGATGTTCA CATACTTGCA GAATATGCCG CGCTCGGGCG TCAGTAACGG CAATAATCCC GGTTTGCGGT GGTAGCGTTT GTAGCCAGTC TGCCAGCCGA TTTTGCGCGT GTTGCCAGTT CTCTGGCGCG GTTTCTAACC CCTGATAAAC CACTCCGCGA TACTTTTCTT CGGCGACAAG CTGACGAAAT GCATATTCGC GCTCAGTGGC CCAACGTTTG CCGCTTGATT CCGGAAGACC ATAAAAAGCA AAGCGGTTAA CGCCTTTCTC TTTTAAATGC AAAAATGCGC TTTCAACCAG CGCATAGTTA TCGGTGGCAA TGTAATGAAC GGGTGGGTAA CTTTCTGCAA GGTGATACGA GCCGCCAACC CCAACAATGG GGACGTCGAC ATCAGCCAGC GCTTGCTCGA TCTGTTTGTC GTCGAAGTCG GCAATGACGC CATCTCCTAA CCAGTCCTTG ATTTTATCAA TGCGGGCGCG GAAATCTTCT TCAATGAAAA TATCCCATTC CGATTGTGAC GCCTGTAAAT ATTCCCCTAC GCCTTCTACT ACCTGCCGGT CATAGGCTTT ATTGGCATTG AACAGTAATG TGATGCGGTG ACGTTTAGTA AA<font color<font color=green>CAT</font>GGTTC TTTTCCTGCT GAATCATGCA AAAACTCAAA ACCGGTAATA CGTAACCGGC TTTGAGAAAA TTTTTATCAA AATCAAGAAC GGCGTTTGGT TGC</pre></html>
Primers:
ggaattcgcg gccgcttcta gag ATTGCATTTC CTTGAGCCTT ATCC (right side) Sequence for operations: ggaattcgcggccgcttctagagATTGCATTTCCTTGAGCCTTATCC
- TmC 63,79
ctgcagcggc cgctactagt a GCAACCAAAC GCCGTTCT (left side) Sequence for operations: ctgcagcggccgctactagtaGCAACCAAACGCCGTTCT
- TmC 63,80
XylR open reading frame (Forward)
<html><pre><font color=green>ATG</font>TTTACTA AACGTCACCG CATCACATTA CTGTTCAATG CCAATAAAGC CTATGACCGG CAGGTAGTAG AAGGCGTAGG GGAATATTTA CAGGCGTCAC AATCGGAATG GGATATTTTC ATTGAAGAAG ATTTCCGCGC CCGCATTGAT AAAATCAAGG ACTGGTTAGG AGATGGCGTC ATTGCCGACT TCGACGACAA ACAGATCGAG CAAGCGCTGG CTGATGTCGA CGTCCCCATT GTTGGGGTTG GCGGCTCGTA TCACCTTGCA GAAAGTTACC CACCCGTTCA TTACATTGCC ACCGATAACT ATGCGCTGGT TGAAAGCGCA TTTTTGCATT TAAAAGAGAA AGGCGTTAAC CGCTTTGCTT TTTATGGTCT TCCGGAATCA AGCGGCAAAC GTTGGGCCAC TGAGCGCGAA TATGCATTTC GTCAGCTTGT CGCCGAAGAA AAGTATCGCG GAGTGGTTTA TCAGGGGTTA GAAACCGCGC CAGAGAACTG GCAACACGCG CAAAATCGGC TGGCAGACTG GCTACAAACG CTACCACCGC AAACCGGGAT TATTGCCGTT ACTGACGCCC GAGCGCGGCA TATTCTGCAA GTATGTGAAC ATCTACATAT TCCCGTACCG GAAAAATTAT GCGTGATTGG CATCGATAAC GAAGAACTGA CCCGCTATCT GTCGCGTGTC GCCCTTTCTT CGGTCGCTCA GGGCGCGCGG CAAATGGGCT ATCAGGCGGC AAAACTGTTG CATCGATTAT TAGATAAAGA AGAAATGCCG CTACAGCGAA TTTTGGTCCC ACCAGTTCGC GTCATTGAAC GGCGCTCAAC AGATTATCGC TCGCTGACCG ATCCCGCCGT TATTCAGGCC ATGCATTACA TTCGTAATCA CGCCTGTAAA GGGATTAAAG TGGATCAGGT ACTGGATGCG GTCGGGATCT CGCGCTCCAA TCTTGAGAAG CGTTTTAAAG AAGAGGTGGG TGAAACCATC CATGCCATGA TTCATGCCGA GAAGCTGGAG AAAGCGCGCA GTCTGCTGAT TTCAACCACC TTGTCGATCA ATGAGATATC GCAAATGTGC GGTTATCCAT CGCTGCAATA TTTCTACTCT GTTTTTAAAA AAGCATATGA CACGACGCCA AAAGAGTATC GCGATGTAAA TAGCGAGGTC ATGTTG<font color=red>TAG</font></pre></html>
Primers:
ggaattcgcg gccgcttcta gag ATGTTTACTA AACGTCACCG CATCA left side Sequence without spaces: ggaattcgcggccgcttctagagATGTTTACTAAACGTCACCGCATCA
- TmC 65,79
ctgcagcggc cgctactagt a CTACAACATG ACCTCGCTAT TTACAT right side Sequence wihout spaces: ctgcagcggccgctactagtaCTACAACATGACCTCGCTATTTACAT
- TmC 62,77
XylR open reading frame (Reverse)
<html><pre><font color=red>CTA</font>CAACATG ACCTCGCTAT TTACATCGCG ATACTCTTTT GGCGTCGTGT CATATGCTTT TTTAAAAACA GAGTAGAAAT ATTGCAGCGA TGGATAACCG CACATTTGCG ATATCTCATT GATCGACAAG GTGGTTGAAA TCAGCAGACT GCGCGCTTTC TCCAGCTTCT CGGCATGAAT CATGGCATGG ATGGTTTCAC CCACCTCTTC TTTAAAACGC TTCTCAAGAT TGGAGCGCGA GATCCCGACC GCATCCAGTA CCTGATCCAC TTTAATCCCT TTACAGGCGT GATTACGAAT GTAATGCATG GCCTGAATAA CGGCGGGATC GGTCAGCGAG CGATAATCTG TTGAGCGCCG TTCAATGACG CGAACTGGTG GGACCAAAAT TCGCTGTAGC GGCATTTCTT CTTTATCTAA TAATCGATGC AACAGTTTTG CCGCCTGATA GCCCATTTGC CGCGCGCCCT GAGCGACCGA AGAAAGGGCG ACACGCGACA GATAGCGGGT CAGTTCTTCG TTATCGATGC CAATCACGCA TAATTTTTCC GGTACGGGAA TATGTAGATG TTCACATACT TGCAGAATAT GCCGCGCTCG GGCGTCAGTA ACGGCAATAA TCCCGGTTTG CGGTGGTAGC GTTTGTAGCC AGTCTGCCAG CCGATTTTGC GCGTGTTGCC AGTTCTCTGG CGCGGTTTCT AACCCCTGAT AAACCACTCC GCGATACTTT TCTTCGGCGA CAAGCTGACG AAATGCATAT TCGCGCTCAG TGGCCCAACG TTTGCCGCTT GATTCCGGAA GACCATAAAA AGCAAAGCGG TTAACGCCTT TCTCTTTTAA ATGCAAAAAT GCGCTTTCAA CCAGCGCATA GTTATCGGTG GCAATGTAAT GAACGGGTGG GTAACTTTCT GCAAGGTGAT ACGAGCCGCC AACCCCAACA ATGGGGACGT CGACATCAGC CAGCGCTTGC TCGATCTGTT TGTCGTCGAA GTCGGCAATG ACGCCATCTC CTAACCAGTC CTTGATTTTA TCAATGCGGG CGCGGAAATC TTCTTCAATG AAAATATCCC ATTCCGATTG TGACGCCTGT AAATATTCCC CTACGCCTTC TACTACCTGC CGGTCATAGG CTTTATTGGC ATTGAACAGT AATGTGATGC GGTGACGTTT AGTAAA<font color=green>CAT</font></pre></html>
Primers:
ggaattcgcg gccgcttcta gag CTACAACATG ACCTCGCTAT TTACAT left side Sequence for operations: ggaattcgcggccgcttctagagCTACAACATGACCTCGCTATTTACAT
- TmC 62,78
ctgcagcggc cgctactagt a ATGTTTACTA AACGTCACCG CATCA right side Sequence for operations: ctgcagcggccgctactagtaATGTTTACTAAACGTCACCGCATCA
- TmC 65,78
June 28th, 2007: Lambda Biobricks and Primers
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Lambda control region (OR)
- Contains OR1, OR2, and OR3, shown in reverse order (i.e. the leftmost binding region below is OR3)
- Bi directional promoter
- in the lambda phage, CI is to the left(PRM), cro is to the right(PR)
- recognized by cro, CI
- cro binding affinities: OR3, OR2 ~ OR1 (OR1 is slightly less)
- CI binding affinites: OR1, OR2 ~ OR3 (OR3 is slightly less)
- CI acts as a positive regulator for PRM when bound to OR2, but and a negative regulator for PR when bound to OR3
<html><pre>ACGTTA<font color=cyan>AATC </font><font color= blue>TA</font><font color=green>TCACCGCA AGGGATA</font>AA<font color=cyan>T ATC</font><font color = blue>TA</font><font color = green>ACACC GTGCGTG</font><font color =blue>TTG</font><font color=cyan> ACT</font>ATTT<font color=green>TAC CTCTGGCGGT </font><font color=blue>GATA</font><font color=cyan>AT</font>GGTT GC</pre></html> Cro and CI binding regions are depicted in green, -10 and -35 sequences in cyan, and shared regions are in blue
Primers
Readable primer:ggaattcgcg gccgcttcta gag ACGTTAAATC TATCACCGC (left side) Primer sequence:ggaattcgcggccgcttctagagACGTTAAATCTATCACCGC
- Mp: 57,77
Readable primer:ctgcagcggc cgctactagt a GCAACCATTA TCACCGC (right side) Primer sequence:ctgcagcggccgctactagtaGCAACCATTATCACCGC
- Mp: 58,78
Lambda Repressor (CI)
- Forms dimers
- Dimers associate to form tetramers, octamers etc
- Binds to OL and OR operators in bacteriophage genome
- Cleaved by activated RecA protein (activates with ssDNA exposure)
<html><pre><font color=green>ATG</font>AGCACAA AAAAGAAACC ATTAACACAA GAGCAGCTTG AGGACGCACG TCGCCTTAAA GCAATTTATG AAAAAAAGAA AAATGAACTT GGCTTATCCC AGGAATCTGT CGCAGACAAG ATGGGGATGG GGCAGTCAGG CGTTGGTGCT TTATTTAATG GCATCAATGC ATTAAATGCT TATAACGCCG CATTGCTTGC AAAAATTCTC AAAGTTAGCG TTGAAGAATT TAGCCCTTCA ATCGCCAGAG AAATCTACGA GATGTATGAA GCGGTTAGTA TGCAGCCGTC ACTTAGAAGT GAGTATGAGT ACCCTGTTTT TTCTCATGTT CAGGCAGGGA TGTTCTCACC TGAGCTTAGA ACCTTTACCA AAGGTGATGC GGAGAGATGG GTAAGCACAA CCAAAAAAGC CAGTGATTCT GCATTCTGGC TTGAGGTTGA AGGTAATTCC ATGACCGCAC CAACAGGCTC CAAGCCAAGC TTTCCTGACG GAATGTTAAT TCTCGTTGAC CCTGAGCAGG CTGTTGAGCC AGGTGATTTC TGCATAGCCA GACTTGGGGG TGATGAGTTT ACCTTCAAGA AACTGATCAG GGATAGCGGT CAGGTGTTTT TACAACCACT AAACCCACAG TACCCAATGA TCCCATGCAA TGAGAGTTGT TCCGTTGTGG GGAAAGTTAT CGCTAGTCAG TGGCCTGAAG AGACGTTTGG C<font color=red>TGA</font></pre></html> Start codon is in green and stop codon is in red
Primers
Readable Primer:ggaattcgcg gccgcttcta gag ATGAGCACAA AAAAGAAACC (left side) Primer sequence:ggaattcgcggccgcttctagagATGAGCACAAAAAAGAAACC
- Mp: 56,77
Readable primer:ctgcagcggc cgctactagt a TCAGCCAAAC GTCTCTTC (right side) Primer sequence:ctgcagcggccgctactagtaTCAGCCAAACGTCTCTTC
- Mp: 58,78
Lambda Repressor (CI) with degredation tag (LVA)
Part BBa_C0051 on MIT's parts registry
- same as CI repressor, but with degredation tag on the N terminus to promote degredation
Lambda AntiRepressor (Cro)
- Binds to OR and OL operators
- transcriptional activator, repressor
- favors lytic pathway in lambda bacteriophage
<html><pre><font color=green>ATG</font>GAACAAC GCATAACCCT GAAAGATTAT GCAATGCGCT TTGGGCAAAC CAAGACAGCT AAAGATCTCG GCGTATATCA AAGCGCGATC AACAAGGCCA TTCATGCAGG CCGAAAGATT TTTTTAACTA TAAACGCTGA TGGAAGCGTT TATGCGGAAG AGGTAAAGCC CTTCCCGAGT AACAAAAAAA CAACAGCA<font color=red>TA A</font></pre></html> Start codon is in green and stop codon is in red
Primers
Readable primer:ggaattcgcg gccgcttcta gag ATGGAACAAC GCATAACC (left side) Primer sequence:ggaattcgcggccgcttctagagATGGAACAACGCATAACC
- Mp: 57,78
Readable primer:ctgcagcggc cgctactagt a TTATGCTGTT GTTTTTTTGT TACT (right side) Primer sequence:ctgcagcggccgctactagtaTTATGCTGTTGTTTTTTTGTTACT
- Mp: 58,75
Oligo Order results:
- Primer 260 LBOrL 75.48 nm, 1046.19 ug, 100nM
- Primer 261 LBOrR 79.09 nm, 991.83 ug, 100nM
- Primer 262 LBClL 73.48 nm, 1042.71 ug, 100nM
- Primer 263 LBClR 79.76 nm, 1026.56 ug, 100nM
- Primer 264 LBCroL 79.42nm, 1074.55 ug, 100nM
- Primer 265 LBCroR 81.02 nm, 1206.56 ug, 100nM
June 30th, 2007: Competency Transformations
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<table|left>
Transformations of frozen competent cells
Note that all images above have had their contrast levels adjusted in photoshop to highlight colonies, for originals contact me.
