http://report.nih.gov/award/index.cfm?ot=&fy=2014&state=&ic=&fm=&orgid=7693101&distr=&rfa=&om=y&pid=&view=data
NIH Report search
Thursday, February 27, 2014
bio125, review for midterm, ApE exercises, transformation, Feb 27, 2014
I led the students to SOD1 yeast sequences to work on ApE.
1) Find out where is the mutation in DNA sequences.
2) Find an RE that can distinguish WT from mutant.
3) Use the RE of your choice, describe digestion results of WT and mutant genes.
4) Translate the genes into proteins and identify the nature of the mutation.
5) Figure which gene this is using blastp.
I then worked on math assignment3 and 2.
At the end of the class, I explained transformation. The key is to how force cells to keep the plasmid. We need to make cells dependent on the plasmid, like people depndent on cigarettes. By using auxotrophic marker, cells without the HIS3 of plasmid will not live in the absence of histidine.
I then explained pSH44, the reporter plasmid and URA3 fused with micro-satellite. How FOA is converted to a toxic stuff by normal URA3 that kills the cell. Only when URA3 is disfunctional due to failed MSH2, can cells surive on FOA plates. This is negative selection. I then added TRP5 of pSH44 into the mix, explained what kind of media should be use for FOA plates.
See:
http://www.youtube.com/watch?v=NxLhXF_jS8o
1) Find out where is the mutation in DNA sequences.
2) Find an RE that can distinguish WT from mutant.
3) Use the RE of your choice, describe digestion results of WT and mutant genes.
4) Translate the genes into proteins and identify the nature of the mutation.
5) Figure which gene this is using blastp.
I then worked on math assignment3 and 2.
At the end of the class, I explained transformation. The key is to how force cells to keep the plasmid. We need to make cells dependent on the plasmid, like people depndent on cigarettes. By using auxotrophic marker, cells without the HIS3 of plasmid will not live in the absence of histidine.
I then explained pSH44, the reporter plasmid and URA3 fused with micro-satellite. How FOA is converted to a toxic stuff by normal URA3 that kills the cell. Only when URA3 is disfunctional due to failed MSH2, can cells surive on FOA plates. This is negative selection. I then added TRP5 of pSH44 into the mix, explained what kind of media should be use for FOA plates.
See:
http://www.youtube.com/watch?v=NxLhXF_jS8o
bio233, discussion of term project, Feb 27, 2014
Led students discussed their term project and worked on abstracts using googleDoc.
See
http://www.youtube.com/watch?v=ibaCASRiEL4
See
http://www.youtube.com/watch?v=ibaCASRiEL4
dummy sequence analysis
>WT ORF ATGGTTCAAGCAGTCGCAGTGTTAAAGGGTGATGCCGGTGTCTCTGGTGTTGTCAAGTTC GAACAGGCTTCCGAATCCGAGCCAACCACTGTCTCTTACGAGATCGCTGGTAACAGTCCT AACGCAGAACGTGGGTTCCACATTCATGAGTTTGGAGATGCCACCAATGGTTGTGTCTCT GCTGGTCCTCACTTCAATCCTTTCAAGAAGACACATGGTGCTCCAACTGACGAAGTCAGA CATGTCGGTGACATGGGTAACGTAAAGACGGACGAAAATGGTGTGGCCAAGGGCTCCTTC AAGGACTCTTTGATCAAGCTTATCGGTCCTACCTCCGTTGTAGGCAGAAGCGTCGTTATC CACGCCGGCCAAGATGACTTAGGTAAGGGTGACACTGAAGAATCTTTGAAGACTGGTAAT GCCGGTCCAAGACCAGCCTGTGGTGTCATTGGTCTAACCAACTAA
>mutant1 ATGGTTCAAGCAGTCGCAGTGTTAAAGGGTGATGCCGGTGTCTCTGGTGTTGTCAAGTT
CGAACAGGCTTCCGAATCCGAGCCAACCACTGTCTCTTACGAGATCGCTGGTAACAGTC
CTAACGCAGAACGTGGGTTCCACATTCATGAGTTTGGAGATGCCACCAATGGTTGTGTC
TCTGCTGGTCCTCACTTCAATCCTTTCAAGAAGACACATGGTGCTCCAACTGACGAAGT
CAGATATGTCGGTGACATGGGTAACGTAAAGACGGACGAAAATGGTGTGGCCAAGGGCT
CCTTCAAGGACTCTTTGATCAAGCTTATCGGTCCTACCTCCGTTGTAGGCAGAAGCGTC
GTTATCCACGCCGGCCAAGATGACTTAGGTAAGGGTGACACTGAAGAATCTTTGAAGAC
TGGTAATGCCGGTCCAAGACCAGCCTGTGGTGTCATTGGTCTAACCAACTAA
>mutant2
ATGGTTCAAGCAGTCGCAGTGTTAAAGGGTGATGCCGGTGTCTCTGGTGTTGTCAAGTTC
GAACAGGCTTCCGAATCCGAGCCAACCACTGTCTCTTACGAGATCGCTGGTAACAGTCCT
AACGCAGAACGTGGGTTCCACATTCATGAGTTTGGAGATGCCACCAATGGTTGTGTCTCT
GCTGGTCCTCACTTCAATCCTTTCAAGAAGAGACATGGTGCTCCAACTGACGAAGTCAGA
CATGTCGGCTGAATGGGTAACGTAAAGACGGACGAAAATGGTGTGGCCAAGGGCTCCTTC
AAGGACTCTTTGATCAAGCTTATCGGTCCTACCTCCGTTGTAGGCAGAAGCGTCGTTATC
CACGCCGGCCAAGATGACTTAGGTAAGGGTGACACTGAAGAATCTTTGAAGACTGGTAAT
GCCGGTCCAAGACCAGCCTGTGGTGTCATTGGTCTAACCAACTAA
>WT protein MVQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVS AGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVI HAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN*
>mutant1 X###Y
MVQAVAVLKGDAGVSGVVKF EQASESEPTTVSYEIAGNSP NAERGFHIHEFGDATNGCVS AGPHFNPFKKRHGAPTDEVR HVGDMGNVKTDENGVAKGSF KDSLIKLIGPTSVVGRSVVI HAGQDDLGKGDTEESLKTGN AGPRPACGVIGLTN*
sod1p, yeast, truncation
>YJR104C s288c MVQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVS AGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVI HAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN*
>YJR104C_RM11-1a [source=Broad] MVQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVS AGPHFNPFKKTHGAPTDEVRHVGDMGNVKDGRKWCGQGLLQGLFDSSLSVLPPL*
>YJR104C_Kyokai7 [source=NRIB] MVQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIHEFGDATNGCVS AGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVI HAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN*
Download sequences
http://www.yeastgenome.org/cgi-bin/FUNGI/getSeq.pl?seq=YHR008C_AWRI1631
sir2, yeast strains, highly conserved.
>YDL042C S288c MTIPHMKYAVSKTSENKVSNTVSPTQDKDAIRKQPDDIINNDEPSHKKIKVAQPDSLRET NTTDPLGHTKAALGEVASMELKPTNDMDPLAVSAASVVSMSNDVLKPETPKGPIIISKNP SNGIFYGPSFTKRESLNARMFLKYYGAHKFLDTYLPEDLNSLYIYYLIKLLGFEVKDQAL IGTINSIVHINSQERVQDLGSAISVTNVEDPLAKKQTVRLIKDLQRAINKVLCTRLRLSN FFTIDHFIQKLHTARKILVLTGAGVSTSLGIPDFRSSEGFYSKIKHLGLDDPQDVFNYNI FMHDPSVFYNIANMVLPPEKIYSPLHSFIKMLQMKGKLLRNYTQNIDNLESYAGISTDKL VQCHGSFATATCVTCHWNLPGERIFNKIRNLELPLCPYCYKKRREYFPEGYNNKVGVAAS QGSMSERPPYILNSYGVLKPDITFFGEALPNKFHKSIREDILECDLLICIGTSLKVAPVS EIVNMVPSHVPQVLINRDPVKHAEFDLSLLGYCDDIAAMVAQKCGWTIPHKKWNDLKNKN FKCQEKDKGVYVVTSDEHPKTL*
>YDL042C_RM11-1a MTIPHMKYAVSKTSENKVSNTVSPTQDKDAIRKQPDDIINNDEPSHKKIKVAQPDSLRET NTTDPLGHTKAALGEVASMELKPTNDMDPLAVSAASVVSMSNDVLKPETPKGPIIISKNP SNGIFYGPSFTKRESLNARMFLKYYGAHKFLDTYLPEDLNSLYIYYLIKLLGFEVKDQAL IGTINSIVHINSQERVQDLGSAISVTNVEDPLAKKQTVRLIKDLQRAINKVLCTRLRLSN FFTIDHFIQKLHTARKILVLTGAGVSTSLGIPDFRSSEGFYSKIKHLGLDDPQDVFNYNI FMHDPSVFYNIANMVLPPEKIYSPLHSFIKMLQMKGKLLRNYTQNIDNLESYAGISTDKL VQCHGSFATATCVTCHWNLPGERIFNKIRNLELPLCPYCYKKRREYFPEGYNNKVGVAAS QGSMSERPPYILNSYGVLKPDITFFGEALPNKFHKSIREDILECDLLICIGTSLKVAPVS EIVNMVPSHVPQVLINRDPVKHAEFDLSLLGYCDDIAAMVAQKCGWTIPHKKWNDLKNKN FKCQEKDKGVYVVTSDEHPKTL*
>YDL042C_BY4742 MTIPHMKYAVSKTSENKVSNTVSPTQDKDAIRKQPDDIINNDEPSHKKIKVAQPDSLRET NTTDPLGHTKAALGEVASMELKPTNDMDPLAVSAASVVSMSNDVLKPETPKGPIIISKNP SNGIFYGPSFTKRESLNARMFLKYYGAHKFLDTYLPEDLNSLYIYYLIKLLGFEVKDQAL IGTINSIVHINSQERVQDLGSAISVTNVEDPLAKKQTVRLIKDLQRAINKVLCTRLRLSN FFTIDHFIQKLHTARKILVLTGAGVSTSLGIPDFRSSEGFYSKIKHLGLDDPQDVFNYNI FMHDPSVFYNIANMVLPPEKIYSPLHSFIKMLQMKGKLLRNYTQNIDNLESYAGISTDKL VQCHGSFATATCVTCHWNLPGERIFNKIRNLELPLCPYCYKKRREYFPEGYNNKVGVAAS QGSMSERPPYILNSYGVLKPDITFFGEALPNKFHKSIREDILECDLLICIGTSLKVAPVS EIVNMVPSHVPQVLINRDPVKHAEFDLSLLGYCDDIAAMVAQKCGWTIPHKKWNDLKNKN FKCQEKDKGVYVVTSDEHPKTL*
Wednesday, February 26, 2014
Bio233, lab, serial dilution Feb 26, 2014
I had 10 minutes to set up this lab, because of another class in the same room.
Grow yeast SGU57 overnight. I then tried to create 5 OD value for standard curve analysis.
5, 4, 3, 2, 1 ml culture + 1,2,3,4,5 ml of fresh YPD.
OD600nm:
Serial dilutions were finished quickly. One student mistook 90ul as 900ul, and use P1000 to pick 100ul. One group labeled the yeast strain as 'bacteria'.
Student then worked on using hemocytometer in 5 groups. Initially, the challenge is what to look for, and which grid should be used. I tried Proscope on the screen but there were too many grid lines under the 10X and 40X. I had to switch to white board and sketch a picture to illustrate what to look for. SGU57 yeast cells have many interconnected group like cell clumps. I asked students to count each individual cell, in order to show the different between hemocytometer and CFU.
The lab was video recorded to observe student engagement during the lab.
2014 March 19, added note:
Students can use googleDoc master sheet to input data, but have trouble to convert them to Excel for plot. I decided to convert the googleSheet to Excel and posted it on Moodle
Grow yeast SGU57 overnight. I then tried to create 5 OD value for standard curve analysis.
5, 4, 3, 2, 1 ml culture + 1,2,3,4,5 ml of fresh YPD.
OD600nm:
| 1 | 1 | 1.089 |
| 2 | 1.407 | |
| 3 | 3 | 1.557 |
| 4 | 4 | 1.661 |
| 5 | 1.733 |
Serial dilutions were finished quickly. One student mistook 90ul as 900ul, and use P1000 to pick 100ul. One group labeled the yeast strain as 'bacteria'.
Student then worked on using hemocytometer in 5 groups. Initially, the challenge is what to look for, and which grid should be used. I tried Proscope on the screen but there were too many grid lines under the 10X and 40X. I had to switch to white board and sketch a picture to illustrate what to look for. SGU57 yeast cells have many interconnected group like cell clumps. I asked students to count each individual cell, in order to show the different between hemocytometer and CFU.
The lab was video recorded to observe student engagement during the lab.
2014 March 19, added note:
Students can use googleDoc master sheet to input data, but have trouble to convert them to Excel for plot. I decided to convert the googleSheet to Excel and posted it on Moodle
sequences of various yeast strians, SGD
http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=YHR008C&seq_type=dna
http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=SOD1&submit=Submit&rm=display_result
compare oxidative response genes versus house-keeping genes.
http://www.yeastgenome.org/cgi-bin/blast-sgd.pl
It looks genomes are assembled. Many of these genomes are sequenced by Wustl.
Tuesday, February 25, 2014
bio125, RE of pcr fragment to verify mutation in msh2, Feb 25, 2014, research day abstract.
Each group choose an RE to cut the PCR fragment of pmsh2, pMSH2, vector. We started with reading protocol and write the procedure. This took about 45 minutes.
Set up reaction, takes about 30 minutes. One student mistook ladder as load dye. Some are not clear what what sample goes to what tubes.
During the digestion, we worked on abstract. "What's our topic" is a common question. Most groups are behind on their lab report.
During the gel loading, some students loaded sample to the running buffer, and some punctured into the agarose gel. The gel were run under 120 Volts. Dr. Kioko took the pictures around 5pm.
Set up reaction, takes about 30 minutes. One student mistook ladder as load dye. Some are not clear what what sample goes to what tubes.
During the digestion, we worked on abstract. "What's our topic" is a common question. Most groups are behind on their lab report.
During the gel loading, some students loaded sample to the running buffer, and some punctured into the agarose gel. The gel were run under 120 Volts. Dr. Kioko took the pictures around 5pm.
fix a double-inverse bug in network simulation
file: net-aging-sim-2014Feb24.R
line 78: lambda = 1/c(100,50,25) #it was 1/c(1/100, 1/50, 1/25)
line 78: lambda = 1/c(100,50,25) #it was 1/c(1/100, 1/50, 1/25)
Bio233, microbial growth, part 1. Chapter 5.
Emphasized on binary fission and asymmetric mechanism. A brief reading on 'a bacterial kind of aging'. Mentioned 'mother's sacrifice', and 'why new-born babies are not as old as their parents'.
Drew on the board 'Old pole and new pole' during mitosis, and explained that old pole always stay in the end. I should found a movie on 'mother machine' next time.
For Haussier hemocytomer usage, I project a image on the board, asked students to work out the calculations.
Spent some time on research day abstract writing and googleDoc usage.
Drew on the board 'Old pole and new pole' during mitosis, and explained that old pole always stay in the end. I should found a movie on 'mother machine' next time.
For Haussier hemocytomer usage, I project a image on the board, asked students to work out the calculations.
Spent some time on research day abstract writing and googleDoc usage.
Hassusser hemocytometer, Brightline
http://www.hausserscientific.com/products/hausser_bright_line.html
Monday, February 24, 2014
stochasticity X average degee > 1 for cells to be alive.
# Notice that degree*p > 1 if the cells are to be alive. >2 should sufficient redundancy.
Sunday, February 23, 2014
Online primer design tools
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
http://primer3.ut.ee/cgi-bin/primer3/primer3web_results.cgi
Thursday, February 20, 2014
Bio125, figure out RE to distinguish wildtype and mutant MSH2
NEB Cutters
http://www.youtube.com/watch?v=Cju7vxDKL4M&list=TLWmctTNuKSBQkNaB2qK6WXhZVa1P9nrXl
http://www.youtube.com/watch?v=Cju7vxDKL4M&list=TLWmctTNuKSBQkNaB2qK6WXhZVa1P9nrXl
Bio233, reflection of exam1, electron transport chain, rate change,
Wednesday, February 19, 2014
single_network_failure = function(lambda, p, pairs, runningORFs)
##########################################
# single network failure simulation
# lambda: exponential constant failure rate for edges
# pairs: network in pairwide format
# runningORFs: GooddEssentialORFsPPI
single_network_failure = function(lambda, p, pairs, runningORFs) {
inpairs = pairs[,1:2] #bookkeeping
names(inpairs) = c('id1','id2')
#stochasticity into pairs
inpairs$active = runif(length(inpairs[,1])) #uniform
# tmp = pairs$active > 1-p
# table(tmp) / length(tmp) ; #double-check, very good.
inpairs$age = rexp( length(inpairs[,1]), rate=lambda ) #exponential ages for pairs
inpairs$age = ifelse(inpairs$active > (1-p), inpairs$age, NA ) #if not active, intxn is excluded.
#pairs$age = ifelse(pairs$active > (1-p), pairs$age, 0 ) # in what situations, can non-ative intxn be treat as 0-age?
ModuleTb = data.frame(runningORFs) #buffer for module ages
#loop every essential genes to identify the module age
for (i in 1:length(runningORFs)) {
myORF = runningORFs[i]
pos1 = grep(myORF, inpairs$id1)
pos2 = grep(myORF, inpairs$id2) #id1,2 to ORF1,2 is a really bad choice.
if( length( c(pos1,pos2))>=1 ) {
ModuleTb$age.m[i] = max( inpairs$age[c(pos1,pos2)], na.rm=T ) #maximal intxn age -> module age
} else {
ModuleTb$age.m[i] = NA;
}
}
#head(ModuleTb);
summary(ModuleTb)
ModuleTb$age.m[ ModuleTb$age.m== -Inf] = 0; #dead births occur when links are not active
currentNetworkAge = min(ModuleTb$age.m)
}
This function was added to "lifespan2014Feb19.r". Test run passed. I need to run some dummy test-netowkrs to double-check the results.
Seagate + Desktop external drive, vista
Seagate + Desktop usb 3.0 recognized by Vista but now shown on Explore.
I installed Seagate Dashboard (after many trials), and "Drive test" is passed. So, the drive is OK, but configuration is the problem.
I installed Seagate Dashboard (after many trials), and "Drive test" is passed. So, the drive is OK, but configuration is the problem.
Tuesday, February 18, 2014
bio125, PCR reaction
things covered: pcr principle, primer design. dilution of plasmid to 5ng/ul. GC content, annealing temperature and DNA melting temperature.
students asked for MSH2 alignments. I took the opportunity and give an overview of the MSH2 project.
pcr ready to go beads can fly out of the tube if they are electrostatic.
students asked for MSH2 alignments. I took the opportunity and give an overview of the MSH2 project.
pcr ready to go beads can fly out of the tube if they are electrostatic.
p-value, Nature, 2014
http://www.nature.com/polopoly_fs/1.14700!/menu/main/topColumns/topLeftColumn/pdf/506150a.pdf
clustering based prediction of human disease genes
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030143/pdf/ijbsv07p0061.pdf
multiNet
Things to do:
various clustering methods
compare I=1.4 and 2.0.
visualization, say by cytoscape.
What is Disease ID, and where to obtain this information?
Monday, February 17, 2014
2014 Research Day prep
http://www.spelman.edu/academics/research-programs/research-day
http://princess.spelman.edu/researchday.nsf
mathramp, 2014 Feb 17
The student used link-switch to generate random network. I went over '20131221.DIPandGIN.sim.aging_v2.R' with the student. The code is 5 1/2 pages, much longer than I thought.
MSH2 protein sequences in human, yeast, worm
>yeastMSH2 gi|6324482|ref|NP_014551.1| mismatch repair ATPase MSH2 [Saccharomyces cerevisiae S288c]
MSSTRPELKFSDVSEERNFYKKYTGLPKKPLKTIRLVDKGDYYTVIGSDAIFVADSVYHTQSVLKNCQLDPVTAKNFHEP
TKYVTVSLQVLATLLKLCLLDLGYKVEIYDKGWKLIKSASPGNIEQVNELMNMNIDSSIIIASLKVQWNSQDGNCIIGVA
FIDTTAYKVGMLDIVDNEVYSNLESFLIQLGVKECLVQDLTSNSNSNAEMQKVINVIDRCGCVVTLLKNSEFSEKDVELD
LTKLLGDDLALSLPQKYSKLSMGACNALIGYLQLLSEQDQVGKYELVEHKLKEFMKLDASAIKALNLFPQGPQNPFGSNN
LAVSGFTSAGNSGKVTSLFQLLNHCKTNAGVRLLNEWLKQPLTNIDEINKRHDLVDYLIDQIELRQMLTSEYLPMIPDIR
RLTKKLNKRGNLEDVLKIYQFSKRIPEIVQVFTSFLEDDSPTEPVNELVRSVWLAPLSHHVEPLSKFEEMVETTVDLDAY
EENNEFMIKVEFNEELGKIRSKLDTLRDEIHSIHLDSAEDLGFDPDKKLKLENHHLHGWCMRLTRNDAKELRKHKKYIEL
STVKAGIFFSTKQLKSIANETNILQKEYDKQQSALVREIINITLTYTPVFEKLSLVLAHLDVIASFAHTSSYAPIPYIRP
KLHPMDSERRTHLISSRHPVLEMQDDISFISNDVTLESGKGDFLIITGPNMGGKSTYIRQVGVISLMAQIGCFVPCEEAE
IAIVDAILCRVGAGDSQLKGVSTFMVEILETASILKNASKNSLIIVDELGRGTSTYDGFGLAWAIAEHIASKIGCFALFA
THFHELTELSEKLPNVKNMHVVAHIEKNLKEQKHDDEDITLLYKVEPGISDQSFGIHVAEVVQFPEKIVKMAKRKANELD
DLKTNNEDLKKAKLSLQEVNEGNIRLKALLKEWIRKVKEEGLHDPSKITEEASQHKIQELLRAIANEPEKENDNYLKYIK
ALLL
>humanMSH gi|4557761|ref|NP_000242.1| DNA mismatch repair protein Msh2 isoform 1 [Homo sapiens]
MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFGNNDMSASIGVVGVKMSAVDGQRQ
VGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQD
LNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYMKLDIAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREIMNDLEKKMQSTLISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSKLTSLN
EEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHA
CVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQG
EKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVNEIISRIKVTT
>flyMSH2 gi|24584320|ref|NP_523565.2| spellchecker1, isoform A [Drosophila melanogaster] >gi|386769639|ref|NP_001246031.1| spellchecker1, isoform D [Drosophila melanogaster]
MQAKATDSRQEPTLNMDTNARRNFIKFHAKLGEKPATTVRFFDHTDRYTVHGSDDCELVAKIVYKSTAFIGALLPDDKKE
TLQFVSMSKGNFELAVRELLLVRNYRVEVYVKNSSDWEIEYRGSPGNLLQFEDILFSNKEVLVGNSIISLLVKLDGGGQR
RVGVASVEQNDCKFQLLEFLDDDFFTELEATVVLLGPKECLLPSIEGEYSAVKTLLDRNGVMITMPKKSGDNDLLQDLNR
LLRFAKGQQEDATGLKELQLQLASNALKTAIKYLDLVNDAGNLGHYEIKQLDLNRFVHLDSAAVAALNIMPKPGTHPSMP
SYRWQSVLGVLDHCRTPQGHRLMGQWVKQPLRSRNILNDRHNIVQCLLESPDTMETLSLDYLKRIPDILMLTKKLMRRKA
NLQDLFRIYQVILRTPKILKVLHELDNSTIESVICAPFKSFLKDLTGLKQMVEQVVDFEAIERGEYLVKASFDSRLMELQ
QMMTELYSKMEELQFKCSQELNLDGKNQVKLESVAKLGHHFRITVKDDSVLRKNKNYRIVDVIKGGVRFTSDKLEGYADE
FASCRTRYEEQQLSIVEEIIHVAVGYAAPLTLLNNELAQLDCLVSFAIAARSAPTPYVRPKMLEEGARELVLEDVRHPCL
ELQEHVNFIANSVDFKKEECNMFIITGPNMGGKSTYIRSVGTAVLMAHIGAFVPCSLATISMVDSILGRVGASDNIIKGL
STFMVEMIETSGIIRTATDKSLVIIDELGRGTSTYEGCGIAWSIAEHLAKETKCFTLFATHFHEITKLAETLSTVKNCHM
AAVADADDFTLLYQVRSGVMEKSFGIQVARLANFPEHVVQNAQEVYNEFEDEHVDKQKKEDKALLEKIQVAIQQLSTAGN
NVDINVEDLTQLVTQFTKDIEQLDSDYFKSVLATSEA
>wormMSH2 gi|17508445|ref|NP_491202.1| Protein MSH-2 [Caenorhabditis elegans]
MSGGKDEASDKALLKILKSKSPNTIAIFSRGEYFSVYGDDATFVATNIFKSDVCVKTFTLSTDNSQQMKYISVNRGQYEK
VVRETIVLLRCSVELYSSEQGEWKMTKRGSPGNTVDFEQEIGVSDQAPILAIYIHPGDDDNRVTLCAWDAGNVRIVISEY
IDTPSFSQTEQCIFGLCPTEYILVNEGSVAPKAKKIASMFTRMEVHNKQQLKPKSQWSDVIESVHLDYKDEAEKQNENIK
ECLQILHSNAADEYSISEKYSIFNYGTHGNMLIDSCAVEALELFQLNYNYLEKSNNLTLYNVLNKCKTLPGEKLLRDWLS
RPLCQIDHINERLDIVEALFENQTIRQKLRDSILARMPDCSQLARRLMRKCTLQDLNRFYQAATLLETVEMQLIQLSEAE
QFAPSINRLLKSEITEILKKVERFQVLCDEFFDFDYEKENKEIRVRVDFVPEIQEISEKLEQMERVAEKLRKKYSAKFEC
DNLKLDKNSQYGFYFRVTLKEEKSIRKKDVHILETTKGSGVKFSVGELSDINDEFLEFHLKYTRAEEEVISMLCKKAEEF
IPLIPAMAQLIATLDVFVSLSTFAATSSGIYTRPNLLPLGSKRLELKQCRHPVIEGNSEKPFIPNDVVLDKCRLIILTGA
NMGGKSTYLRSAALSILLAQIGSFVPCSSATISVVDGIFTRVGASDKQSQGISTFMAEMLDCSAILQRATKNSFVVIDEL
GRGTSTFDGFGIASAIAQDILNRIQCLSIFATHFHEMGKLAEQPGAVALQMGVQIENNEIHMLYKVFEGVAQCSFGLQVA
KMVGIDENVINKAAQLLEGLEKKLVIDSKKKKELLESADIRQAILSLVK
>mouseMSH2 gi|6678938|ref|NP_032654.1| DNA mismatch repair protein Msh2 [Mus musculus]
MAVQPKETLQLEGAAEAGFVRFFEGMPEKPSTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGSKTLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNKAGNKASKENEWYLAFKASPGNLSQFEDILFGNNDMSASVGVMGIKMAVVDGQRH
VGVGYVDSTQRKLGLCEFPENDQFSNLEALLIQIGPKECVLPGGETTGDMGKLRQVIQRGGILITERKRADFSTKDIYQD
LNRLLKGKKGEQINSAALPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELATFDFSQYMKLDMAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTAQGQRLVNQWIKQPLMDRNRIEERLNLVEAFVEDSELRQSLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPSVIQALEKYEGRHQALLLAVFVTPLIDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREVMDGLEKKMQSTLINAARGLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSELSSLN
EEYTKNKGEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAHLDAIVSFAHVSNAAPVPYVRPVILEKGKGRIILKASRHA
CVEVQDEVAFIPNDVHFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISDYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPRHVIACAKQKALELEEFQNIGTSLGCDEAEPAAKRRCLEREQG
EKIILEFLSKVKQVPFTAMSEESISAKLKQLKAEVVAKNNSFVNEIISRIKAPAP
MSSTRPELKFSDVSEERNFYKKYTGLPKKPLKTIRLVDKGDYYTVIGSDAIFVADSVYHTQSVLKNCQLDPVTAKNFHEP
TKYVTVSLQVLATLLKLCLLDLGYKVEIYDKGWKLIKSASPGNIEQVNELMNMNIDSSIIIASLKVQWNSQDGNCIIGVA
FIDTTAYKVGMLDIVDNEVYSNLESFLIQLGVKECLVQDLTSNSNSNAEMQKVINVIDRCGCVVTLLKNSEFSEKDVELD
LTKLLGDDLALSLPQKYSKLSMGACNALIGYLQLLSEQDQVGKYELVEHKLKEFMKLDASAIKALNLFPQGPQNPFGSNN
LAVSGFTSAGNSGKVTSLFQLLNHCKTNAGVRLLNEWLKQPLTNIDEINKRHDLVDYLIDQIELRQMLTSEYLPMIPDIR
RLTKKLNKRGNLEDVLKIYQFSKRIPEIVQVFTSFLEDDSPTEPVNELVRSVWLAPLSHHVEPLSKFEEMVETTVDLDAY
EENNEFMIKVEFNEELGKIRSKLDTLRDEIHSIHLDSAEDLGFDPDKKLKLENHHLHGWCMRLTRNDAKELRKHKKYIEL
STVKAGIFFSTKQLKSIANETNILQKEYDKQQSALVREIINITLTYTPVFEKLSLVLAHLDVIASFAHTSSYAPIPYIRP
KLHPMDSERRTHLISSRHPVLEMQDDISFISNDVTLESGKGDFLIITGPNMGGKSTYIRQVGVISLMAQIGCFVPCEEAE
IAIVDAILCRVGAGDSQLKGVSTFMVEILETASILKNASKNSLIIVDELGRGTSTYDGFGLAWAIAEHIASKIGCFALFA
THFHELTELSEKLPNVKNMHVVAHIEKNLKEQKHDDEDITLLYKVEPGISDQSFGIHVAEVVQFPEKIVKMAKRKANELD
DLKTNNEDLKKAKLSLQEVNEGNIRLKALLKEWIRKVKEEGLHDPSKITEEASQHKIQELLRAIANEPEKENDNYLKYIK
ALLL
>humanMSH gi|4557761|ref|NP_000242.1| DNA mismatch repair protein Msh2 isoform 1 [Homo sapiens]
MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFGNNDMSASIGVVGVKMSAVDGQRQ
VGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQD
LNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYMKLDIAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREIMNDLEKKMQSTLISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSKLTSLN
EEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHA
CVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQG
EKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVNEIISRIKVTT
>flyMSH2 gi|24584320|ref|NP_523565.2| spellchecker1, isoform A [Drosophila melanogaster] >gi|386769639|ref|NP_001246031.1| spellchecker1, isoform D [Drosophila melanogaster]
MQAKATDSRQEPTLNMDTNARRNFIKFHAKLGEKPATTVRFFDHTDRYTVHGSDDCELVAKIVYKSTAFIGALLPDDKKE
TLQFVSMSKGNFELAVRELLLVRNYRVEVYVKNSSDWEIEYRGSPGNLLQFEDILFSNKEVLVGNSIISLLVKLDGGGQR
RVGVASVEQNDCKFQLLEFLDDDFFTELEATVVLLGPKECLLPSIEGEYSAVKTLLDRNGVMITMPKKSGDNDLLQDLNR
LLRFAKGQQEDATGLKELQLQLASNALKTAIKYLDLVNDAGNLGHYEIKQLDLNRFVHLDSAAVAALNIMPKPGTHPSMP
SYRWQSVLGVLDHCRTPQGHRLMGQWVKQPLRSRNILNDRHNIVQCLLESPDTMETLSLDYLKRIPDILMLTKKLMRRKA
NLQDLFRIYQVILRTPKILKVLHELDNSTIESVICAPFKSFLKDLTGLKQMVEQVVDFEAIERGEYLVKASFDSRLMELQ
QMMTELYSKMEELQFKCSQELNLDGKNQVKLESVAKLGHHFRITVKDDSVLRKNKNYRIVDVIKGGVRFTSDKLEGYADE
FASCRTRYEEQQLSIVEEIIHVAVGYAAPLTLLNNELAQLDCLVSFAIAARSAPTPYVRPKMLEEGARELVLEDVRHPCL
ELQEHVNFIANSVDFKKEECNMFIITGPNMGGKSTYIRSVGTAVLMAHIGAFVPCSLATISMVDSILGRVGASDNIIKGL
STFMVEMIETSGIIRTATDKSLVIIDELGRGTSTYEGCGIAWSIAEHLAKETKCFTLFATHFHEITKLAETLSTVKNCHM
AAVADADDFTLLYQVRSGVMEKSFGIQVARLANFPEHVVQNAQEVYNEFEDEHVDKQKKEDKALLEKIQVAIQQLSTAGN
NVDINVEDLTQLVTQFTKDIEQLDSDYFKSVLATSEA
>wormMSH2 gi|17508445|ref|NP_491202.1| Protein MSH-2 [Caenorhabditis elegans]
MSGGKDEASDKALLKILKSKSPNTIAIFSRGEYFSVYGDDATFVATNIFKSDVCVKTFTLSTDNSQQMKYISVNRGQYEK
VVRETIVLLRCSVELYSSEQGEWKMTKRGSPGNTVDFEQEIGVSDQAPILAIYIHPGDDDNRVTLCAWDAGNVRIVISEY
IDTPSFSQTEQCIFGLCPTEYILVNEGSVAPKAKKIASMFTRMEVHNKQQLKPKSQWSDVIESVHLDYKDEAEKQNENIK
ECLQILHSNAADEYSISEKYSIFNYGTHGNMLIDSCAVEALELFQLNYNYLEKSNNLTLYNVLNKCKTLPGEKLLRDWLS
RPLCQIDHINERLDIVEALFENQTIRQKLRDSILARMPDCSQLARRLMRKCTLQDLNRFYQAATLLETVEMQLIQLSEAE
QFAPSINRLLKSEITEILKKVERFQVLCDEFFDFDYEKENKEIRVRVDFVPEIQEISEKLEQMERVAEKLRKKYSAKFEC
DNLKLDKNSQYGFYFRVTLKEEKSIRKKDVHILETTKGSGVKFSVGELSDINDEFLEFHLKYTRAEEEVISMLCKKAEEF
IPLIPAMAQLIATLDVFVSLSTFAATSSGIYTRPNLLPLGSKRLELKQCRHPVIEGNSEKPFIPNDVVLDKCRLIILTGA
NMGGKSTYLRSAALSILLAQIGSFVPCSSATISVVDGIFTRVGASDKQSQGISTFMAEMLDCSAILQRATKNSFVVIDEL
GRGTSTFDGFGIASAIAQDILNRIQCLSIFATHFHEMGKLAEQPGAVALQMGVQIENNEIHMLYKVFEGVAQCSFGLQVA
KMVGIDENVINKAAQLLEGLEKKLVIDSKKKKELLESADIRQAILSLVK
>mouseMSH2 gi|6678938|ref|NP_032654.1| DNA mismatch repair protein Msh2 [Mus musculus]
MAVQPKETLQLEGAAEAGFVRFFEGMPEKPSTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGSKTLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNKAGNKASKENEWYLAFKASPGNLSQFEDILFGNNDMSASVGVMGIKMAVVDGQRH
VGVGYVDSTQRKLGLCEFPENDQFSNLEALLIQIGPKECVLPGGETTGDMGKLRQVIQRGGILITERKRADFSTKDIYQD
LNRLLKGKKGEQINSAALPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELATFDFSQYMKLDMAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTAQGQRLVNQWIKQPLMDRNRIEERLNLVEAFVEDSELRQSLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPSVIQALEKYEGRHQALLLAVFVTPLIDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREVMDGLEKKMQSTLINAARGLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSELSSLN
EEYTKNKGEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAHLDAIVSFAHVSNAAPVPYVRPVILEKGKGRIILKASRHA
CVEVQDEVAFIPNDVHFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISDYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPRHVIACAKQKALELEEFQNIGTSLGCDEAEPAAKRRCLEREQG
EKIILEFLSKVKQVPFTAMSEESISAKLKQLKAEVVAKNNSFVNEIISRIKAPAP
Wednesday, February 12, 2014
MSH2 in different species
>scMSH2 gi|6324482|ref|NP_014551.1| mismatch repair ATPase MSH2 [Saccharomyces cerevisiae S288c]
MSSTRPELKFSDVSEERNFYKKYTGLPKKPLKTIRLVDKGDYYTVIGSDAIFVADSVYHTQSVLKNCQLDPVTAKNFHEP
TKYVTVSLQVLATLLKLCLLDLGYKVEIYDKGWKLIKSASPGNIEQVNELMNMNIDSSIIIASLKVQWNSQDGNCIIGVA
FIDTTAYKVGMLDIVDNEVYSNLESFLIQLGVKECLVQDLTSNSNSNAEMQKVINVIDRCGCVVTLLKNSEFSEKDVELD
LTKLLGDDLALSLPQKYSKLSMGACNALIGYLQLLSEQDQVGKYELVEHKLKEFMKLDASAIKALNLFPQGPQNPFGSNN
LAVSGFTSAGNSGKVTSLFQLLNHCKTNAGVRLLNEWLKQPLTNIDEINKRHDLVDYLIDQIELRQMLTSEYLPMIPDIR
RLTKKLNKRGNLEDVLKIYQFSKRIPEIVQVFTSFLEDDSPTEPVNELVRSVWLAPLSHHVEPLSKFEEMVETTVDLDAY
EENNEFMIKVEFNEELGKIRSKLDTLRDEIHSIHLDSAEDLGFDPDKKLKLENHHLHGWCMRLTRNDAKELRKHKKYIEL
STVKAGIFFSTKQLKSIANETNILQKEYDKQQSALVREIINITLTYTPVFEKLSLVLAHLDVIASFAHTSSYAPIPYIRP
KLHPMDSERRTHLISSRHPVLEMQDDISFISNDVTLESGKGDFLIITGPNMGGKSTYIRQVGVISLMAQIGCFVPCEEAE
IAIVDAILCRVGAGDSQLKGVSTFMVEILETASILKNASKNSLIIVDELGRGTSTYDGFGLAWAIAEHIASKIGCFALFA
THFHELTELSEKLPNVKNMHVVAHIEKNLKEQKHDDEDITLLYKVEPGISDQSFGIHVAEVVQFPEKIVKMAKRKANELD
DLKTNNEDLKKAKLSLQEVNEGNIRLKALLKEWIRKVKEEGLHDPSKITEEASQHKIQELLRAIANEPEKENDNYLKYIK
ALLL
>hsMSH2_1 gi|4557761|ref|NP_000242.1| DNA mismatch repair protein Msh2 isoform 1 [Homo sapiens]
MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFGNNDMSASIGVVGVKMSAVDGQRQ
VGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQD
LNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYMKLDIAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREIMNDLEKKMQSTLISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSKLTSLN
EEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHA
CVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQG
EKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVNEIISRIKVTT
>hsMSH2_2 gi|384871702|ref|NP_001245210.1| DNA mismatch repair protein Msh2 isoform 2 [Homo sapiens]
MGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFGNNDMSASIG
VVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITE
RKKADFSTKDIYQDLNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYMKLDIAA
VRALNLFQGSVEDTTGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPD
LNRLAKKFQRQAANLQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVENH
EFLVKPSFDPNLSELREIMNDLEKKMQSTLISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQK
NGVKFTNSKLTSLNEEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVRPAILE
KGQGRIILKASRHACVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVD
CILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHE
LTALANQIPTVNNLHVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQGYDIM
EPAAKKCYLEREQGEKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVNEIISRIKVTT
>dmMSH2 gi|24584320|ref|NP_523565.2| spellchecker1, isoform A [Drosophila melanogaster] >gi|386769639|ref|NP_001246031.1| spellchecker1, isoform D [Drosophila melanogaster]
MQAKATDSRQEPTLNMDTNARRNFIKFHAKLGEKPATTVRFFDHTDRYTVHGSDDCELVAKIVYKSTAFIGALLPDDKKE
TLQFVSMSKGNFELAVRELLLVRNYRVEVYVKNSSDWEIEYRGSPGNLLQFEDILFSNKEVLVGNSIISLLVKLDGGGQR
RVGVASVEQNDCKFQLLEFLDDDFFTELEATVVLLGPKECLLPSIEGEYSAVKTLLDRNGVMITMPKKSGDNDLLQDLNR
LLRFAKGQQEDATGLKELQLQLASNALKTAIKYLDLVNDAGNLGHYEIKQLDLNRFVHLDSAAVAALNIMPKPGTHPSMP
SYRWQSVLGVLDHCRTPQGHRLMGQWVKQPLRSRNILNDRHNIVQCLLESPDTMETLSLDYLKRIPDILMLTKKLMRRKA
NLQDLFRIYQVILRTPKILKVLHELDNSTIESVICAPFKSFLKDLTGLKQMVEQVVDFEAIERGEYLVKASFDSRLMELQ
QMMTELYSKMEELQFKCSQELNLDGKNQVKLESVAKLGHHFRITVKDDSVLRKNKNYRIVDVIKGGVRFTSDKLEGYADE
FASCRTRYEEQQLSIVEEIIHVAVGYAAPLTLLNNELAQLDCLVSFAIAARSAPTPYVRPKMLEEGARELVLEDVRHPCL
ELQEHVNFIANSVDFKKEECNMFIITGPNMGGKSTYIRSVGTAVLMAHIGAFVPCSLATISMVDSILGRVGASDNIIKGL
STFMVEMIETSGIIRTATDKSLVIIDELGRGTSTYEGCGIAWSIAEHLAKETKCFTLFATHFHEITKLAETLSTVKNCHM
AAVADADDFTLLYQVRSGVMEKSFGIQVARLANFPEHVVQNAQEVYNEFEDEHVDKQKKEDKALLEKIQVAIQQLSTAGN
NVDINVEDLTQLVTQFTKDIEQLDSDYFKSVLATSEA
>ceMSH2 gi|17508445|ref|NP_491202.1| Protein MSH-2 [Caenorhabditis elegans]
MSGGKDEASDKALLKILKSKSPNTIAIFSRGEYFSVYGDDATFVATNIFKSDVCVKTFTLSTDNSQQMKYISVNRGQYEK
VVRETIVLLRCSVELYSSEQGEWKMTKRGSPGNTVDFEQEIGVSDQAPILAIYIHPGDDDNRVTLCAWDAGNVRIVISEY
IDTPSFSQTEQCIFGLCPTEYILVNEGSVAPKAKKIASMFTRMEVHNKQQLKPKSQWSDVIESVHLDYKDEAEKQNENIK
ECLQILHSNAADEYSISEKYSIFNYGTHGNMLIDSCAVEALELFQLNYNYLEKSNNLTLYNVLNKCKTLPGEKLLRDWLS
RPLCQIDHINERLDIVEALFENQTIRQKLRDSILARMPDCSQLARRLMRKCTLQDLNRFYQAATLLETVEMQLIQLSEAE
QFAPSINRLLKSEITEILKKVERFQVLCDEFFDFDYEKENKEIRVRVDFVPEIQEISEKLEQMERVAEKLRKKYSAKFEC
DNLKLDKNSQYGFYFRVTLKEEKSIRKKDVHILETTKGSGVKFSVGELSDINDEFLEFHLKYTRAEEEVISMLCKKAEEF
IPLIPAMAQLIATLDVFVSLSTFAATSSGIYTRPNLLPLGSKRLELKQCRHPVIEGNSEKPFIPNDVVLDKCRLIILTGA
NMGGKSTYLRSAALSILLAQIGSFVPCSSATISVVDGIFTRVGASDKQSQGISTFMAEMLDCSAILQRATKNSFVVIDEL
GRGTSTFDGFGIASAIAQDILNRIQCLSIFATHFHEMGKLAEQPGAVALQMGVQIENNEIHMLYKVFEGVAQCSFGLQVA
KMVGIDENVINKAAQLLEGLEKKLVIDSKKKKELLESADIRQAILSLVK
>mmMSH2 gi|6678938|ref|NP_032654.1| DNA mismatch repair protein Msh2 [Mus musculus]
MAVQPKETLQLEGAAEAGFVRFFEGMPEKPSTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGSKTLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNKAGNKASKENEWYLAFKASPGNLSQFEDILFGNNDMSASVGVMGIKMAVVDGQRH
VGVGYVDSTQRKLGLCEFPENDQFSNLEALLIQIGPKECVLPGGETTGDMGKLRQVIQRGGILITERKRADFSTKDIYQD
LNRLLKGKKGEQINSAALPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELATFDFSQYMKLDMAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTAQGQRLVNQWIKQPLMDRNRIEERLNLVEAFVEDSELRQSLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPSVIQALEKYEGRHQALLLAVFVTPLIDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREVMDGLEKKMQSTLINAARGLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSELSSLN
EEYTKNKGEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAHLDAIVSFAHVSNAAPVPYVRPVILEKGKGRIILKASRHA
CVEVQDEVAFIPNDVHFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISDYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPRHVIACAKQKALELEEFQNIGTSLGCDEAEPAAKRRCLEREQG
EKIILEFLSKVKQVPFTAMSEESISAKLKQLKAEVVAKNNSFVNEIISRIKAPAP
MSSTRPELKFSDVSEERNFYKKYTGLPKKPLKTIRLVDKGDYYTVIGSDAIFVADSVYHTQSVLKNCQLDPVTAKNFHEP
TKYVTVSLQVLATLLKLCLLDLGYKVEIYDKGWKLIKSASPGNIEQVNELMNMNIDSSIIIASLKVQWNSQDGNCIIGVA
FIDTTAYKVGMLDIVDNEVYSNLESFLIQLGVKECLVQDLTSNSNSNAEMQKVINVIDRCGCVVTLLKNSEFSEKDVELD
LTKLLGDDLALSLPQKYSKLSMGACNALIGYLQLLSEQDQVGKYELVEHKLKEFMKLDASAIKALNLFPQGPQNPFGSNN
LAVSGFTSAGNSGKVTSLFQLLNHCKTNAGVRLLNEWLKQPLTNIDEINKRHDLVDYLIDQIELRQMLTSEYLPMIPDIR
RLTKKLNKRGNLEDVLKIYQFSKRIPEIVQVFTSFLEDDSPTEPVNELVRSVWLAPLSHHVEPLSKFEEMVETTVDLDAY
EENNEFMIKVEFNEELGKIRSKLDTLRDEIHSIHLDSAEDLGFDPDKKLKLENHHLHGWCMRLTRNDAKELRKHKKYIEL
STVKAGIFFSTKQLKSIANETNILQKEYDKQQSALVREIINITLTYTPVFEKLSLVLAHLDVIASFAHTSSYAPIPYIRP
KLHPMDSERRTHLISSRHPVLEMQDDISFISNDVTLESGKGDFLIITGPNMGGKSTYIRQVGVISLMAQIGCFVPCEEAE
IAIVDAILCRVGAGDSQLKGVSTFMVEILETASILKNASKNSLIIVDELGRGTSTYDGFGLAWAIAEHIASKIGCFALFA
THFHELTELSEKLPNVKNMHVVAHIEKNLKEQKHDDEDITLLYKVEPGISDQSFGIHVAEVVQFPEKIVKMAKRKANELD
DLKTNNEDLKKAKLSLQEVNEGNIRLKALLKEWIRKVKEEGLHDPSKITEEASQHKIQELLRAIANEPEKENDNYLKYIK
ALLL
>hsMSH2_1 gi|4557761|ref|NP_000242.1| DNA mismatch repair protein Msh2 isoform 1 [Homo sapiens]
MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFGNNDMSASIGVVGVKMSAVDGQRQ
VGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITERKKADFSTKDIYQD
LNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYMKLDIAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREIMNDLEKKMQSTLISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSKLTSLN
EEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHA
CVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQG
EKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVNEIISRIKVTT
>hsMSH2_2 gi|384871702|ref|NP_001245210.1| DNA mismatch repair protein Msh2 isoform 2 [Homo sapiens]
MGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDILFGNNDMSASIG
VVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKECVLPGGETAGDMGKLRQIIQRGGILITE
RKKADFSTKDIYQDLNRLLKGKKGEQMNSAVLPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELTTFDFSQYMKLDIAA
VRALNLFQGSVEDTTGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPD
LNRLAKKFQRQAANLQDCYRLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVENH
EFLVKPSFDPNLSELREIMNDLEKKMQSTLISAARDLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQK
NGVKFTNSKLTSLNEEYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAVVSFAHVSNGAPVPYVRPAILE
KGQGRIILKASRHACVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVD
CILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHE
LTALANQIPTVNNLHVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQGYDIM
EPAAKKCYLEREQGEKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIAKNNSFVNEIISRIKVTT
>dmMSH2 gi|24584320|ref|NP_523565.2| spellchecker1, isoform A [Drosophila melanogaster] >gi|386769639|ref|NP_001246031.1| spellchecker1, isoform D [Drosophila melanogaster]
MQAKATDSRQEPTLNMDTNARRNFIKFHAKLGEKPATTVRFFDHTDRYTVHGSDDCELVAKIVYKSTAFIGALLPDDKKE
TLQFVSMSKGNFELAVRELLLVRNYRVEVYVKNSSDWEIEYRGSPGNLLQFEDILFSNKEVLVGNSIISLLVKLDGGGQR
RVGVASVEQNDCKFQLLEFLDDDFFTELEATVVLLGPKECLLPSIEGEYSAVKTLLDRNGVMITMPKKSGDNDLLQDLNR
LLRFAKGQQEDATGLKELQLQLASNALKTAIKYLDLVNDAGNLGHYEIKQLDLNRFVHLDSAAVAALNIMPKPGTHPSMP
SYRWQSVLGVLDHCRTPQGHRLMGQWVKQPLRSRNILNDRHNIVQCLLESPDTMETLSLDYLKRIPDILMLTKKLMRRKA
NLQDLFRIYQVILRTPKILKVLHELDNSTIESVICAPFKSFLKDLTGLKQMVEQVVDFEAIERGEYLVKASFDSRLMELQ
QMMTELYSKMEELQFKCSQELNLDGKNQVKLESVAKLGHHFRITVKDDSVLRKNKNYRIVDVIKGGVRFTSDKLEGYADE
FASCRTRYEEQQLSIVEEIIHVAVGYAAPLTLLNNELAQLDCLVSFAIAARSAPTPYVRPKMLEEGARELVLEDVRHPCL
ELQEHVNFIANSVDFKKEECNMFIITGPNMGGKSTYIRSVGTAVLMAHIGAFVPCSLATISMVDSILGRVGASDNIIKGL
STFMVEMIETSGIIRTATDKSLVIIDELGRGTSTYEGCGIAWSIAEHLAKETKCFTLFATHFHEITKLAETLSTVKNCHM
AAVADADDFTLLYQVRSGVMEKSFGIQVARLANFPEHVVQNAQEVYNEFEDEHVDKQKKEDKALLEKIQVAIQQLSTAGN
NVDINVEDLTQLVTQFTKDIEQLDSDYFKSVLATSEA
>ceMSH2 gi|17508445|ref|NP_491202.1| Protein MSH-2 [Caenorhabditis elegans]
MSGGKDEASDKALLKILKSKSPNTIAIFSRGEYFSVYGDDATFVATNIFKSDVCVKTFTLSTDNSQQMKYISVNRGQYEK
VVRETIVLLRCSVELYSSEQGEWKMTKRGSPGNTVDFEQEIGVSDQAPILAIYIHPGDDDNRVTLCAWDAGNVRIVISEY
IDTPSFSQTEQCIFGLCPTEYILVNEGSVAPKAKKIASMFTRMEVHNKQQLKPKSQWSDVIESVHLDYKDEAEKQNENIK
ECLQILHSNAADEYSISEKYSIFNYGTHGNMLIDSCAVEALELFQLNYNYLEKSNNLTLYNVLNKCKTLPGEKLLRDWLS
RPLCQIDHINERLDIVEALFENQTIRQKLRDSILARMPDCSQLARRLMRKCTLQDLNRFYQAATLLETVEMQLIQLSEAE
QFAPSINRLLKSEITEILKKVERFQVLCDEFFDFDYEKENKEIRVRVDFVPEIQEISEKLEQMERVAEKLRKKYSAKFEC
DNLKLDKNSQYGFYFRVTLKEEKSIRKKDVHILETTKGSGVKFSVGELSDINDEFLEFHLKYTRAEEEVISMLCKKAEEF
IPLIPAMAQLIATLDVFVSLSTFAATSSGIYTRPNLLPLGSKRLELKQCRHPVIEGNSEKPFIPNDVVLDKCRLIILTGA
NMGGKSTYLRSAALSILLAQIGSFVPCSSATISVVDGIFTRVGASDKQSQGISTFMAEMLDCSAILQRATKNSFVVIDEL
GRGTSTFDGFGIASAIAQDILNRIQCLSIFATHFHEMGKLAEQPGAVALQMGVQIENNEIHMLYKVFEGVAQCSFGLQVA
KMVGIDENVINKAAQLLEGLEKKLVIDSKKKKELLESADIRQAILSLVK
>mmMSH2 gi|6678938|ref|NP_032654.1| DNA mismatch repair protein Msh2 [Mus musculus]
MAVQPKETLQLEGAAEAGFVRFFEGMPEKPSTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGSKTLQSVVL
SKMNFESFVKDLLLVRQYRVEVYKNKAGNKASKENEWYLAFKASPGNLSQFEDILFGNNDMSASVGVMGIKMAVVDGQRH
VGVGYVDSTQRKLGLCEFPENDQFSNLEALLIQIGPKECVLPGGETTGDMGKLRQVIQRGGILITERKRADFSTKDIYQD
LNRLLKGKKGEQINSAALPEMENQVAVSSLSAVIKFLELLSDDSNFGQFELATFDFSQYMKLDMAAVRALNLFQGSVEDT
TGSQSLAALLNKCKTAQGQRLVNQWIKQPLMDRNRIEERLNLVEAFVEDSELRQSLQEDLLRRFPDLNRLAKKFQRQAAN
LQDCYRLYQGINQLPSVIQALEKYEGRHQALLLAVFVTPLIDLRSDFSKFQEMIETTLDMDQVENHEFLVKPSFDPNLSE
LREVMDGLEKKMQSTLINAARGLGLDPGKQIKLDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQKNGVKFTNSELSSLN
EEYTKNKGEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAHLDAIVSFAHVSNAAPVPYVRPVILEKGKGRIILKASRHA
CVEVQDEVAFIPNDVHFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLK
GVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISDYIATKIGAFCMFATHFHELTALANQIPTVNNL
HVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPRHVIACAKQKALELEEFQNIGTSLGCDEAEPAAKRRCLEREQG
EKIILEFLSKVKQVPFTAMSEESISAKLKQLKAEVVAKNNSFVNEIISRIKAPAP
Translational fidelity / transcriptional fidelity, a collection
http://www.yeastgenome.org/go/GO:1990145/overview
EFB1 essential gene
SUI1 essential gene
EFT1 YOR133W non-essential gene, null has very short lifespan
EFT2 is a paralog of EFT1, non-essential.
Michael Sovaneau's 1979 PNAS paper on tRNA aminocylation proofread.
High fidelity translation in nude mouse, Nature paper 2013.
Yeast, SUP45 (essential gene)
http://www.yeastgenome.org/reference/S000043151/overview
Overexpression SUP45 leads to decreased vegetative growth
"SUP45 TCH tetO"
http://www.yeastgenome.org/reference/S000151121/overview
http://www.ncbi.nlm.nih.gov/
Proc Natl Acad Sci U S A. 2013 Sep 30. [Epub ahead of print]
Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage.
Source
Department of Biology, University of Rochester, Rochester, NY 14627.
Abstract
The naked mole-rat (Heterocephalus glaber) is a subterranean eusocial rodent with a markedly long lifespan and resistance to tumorigenesis. Multiple data implicate modulation of protein translation in longevity. Here we report that 28S ribosomal RNA (rRNA) of the naked mole-rat is processed into two smaller fragments of unequal size. The two breakpoints are located in the 28S rRNA divergent region 6 and excise a fragment of 263 nt. The excised fragment is unique to the naked mole-rat rRNA and does not show homology to other genomic regions. Because this hidden break site could alter ribosome structure, we investigated whether translation rate and amino acid incorporation fidelity were altered. We report that naked mole-rat fibroblasts have significantly increased translational fidelity despite having comparable translation rates with mouse fibroblasts. Although we cannot directly test whether the unique 28S rRNA structure contributes to the increased fidelity of translation, we speculate that it may change the folding or dynamics of the large ribosomal subunit, altering the rate of GTP hydrolysis and/or interaction of the large subunit with tRNA during accommodation, thus affecting the fidelity of protein synthesis. In summary, our results show that naked mole-rat cells produce fewer aberrant proteins, supporting the hypothesis that the more stable proteome of the naked mole-rat contributes to its longevity.
H3K36 methylation promotes longevity by enhancing transcriptional fidelity.
Epigenetic mechanisms, including histone post-translational modifications, control longevity in diverse organisms. Relatedly, loss of proper transcriptional regulation on a global scale is an emerging phenomenon of shortened life span, but the specific mechanisms linking these observations remain to be uncovered. Here, we describe a life span screen in Saccharomyces cerevisiae that is designed to identify amino acid residues of histones that regulate yeast replicative aging. Our results reveal that lack of sustained histone H3K36 methylation is commensurate with increased cryptic transcription in a subset of genes in old cells and with shorter life span. In contrast, deletion of the K36me2/3 demethylase Rph1 increases H3K36me3 within these genes, suppresses cryptic transcript initiation, and extends life span. We show that this aging phenomenon is conserved, as cryptic transcription also increases in old worms. We propose that epigenetic misregulation in aging cells leads to loss of transcriptional precision that is detrimental to life span, and, importantly, this acceleration in aging can be reversed by restoring transcriptional fidelity.
Educational problems
Student cheating problems
http://www.nytimes.com/2012/09/08/education/studies-show-more-students-cheat-even-high-achievers.html?_r=0
http://www.nytimes.com/2013/08/04/education/edlife/educators-study-online-dishonesty.html
http://www.nytimes.com/2013/09/17/education/students-accused-of-cheating-return-awkwardly-to-a-changed-harvard.html
http://education-portal.com/articles/75_to_98_Percent_of_College_Students_Have_Cheated.html
http://abcnews.go.com/Primetime/story?id=132376
Honor code
http://www.nytimes.com/2014/04/13/education/edlife/the-fading-honor-code.html?WT.mc_id=D-NYT-MKTG-MOD-70311-06-10-HD&WT.mc_ev=click&WT.mc_c=${CAMPAIGN_ID}
ms02 R, batch run
# ms02-2014Feb12.R
#permuate merged yeast PPI+GIN
#2014 Feb 12, re-name function to ms02_singlerun
#2014 Jan 31, fixed a bug that inserted "NA" into new network. The bug seems to be caused by spliting the
# arrays. I rewrote the spliting portion.
#require(igraph)
rm(list=ls())
debug = 0
setwd("~/projects/0.ginppi.reliability.simulation/ms02GINPPI")
#set.seed(2014)
#permute.pairs.wo.selfpairs = function( inpairs, ncycles=10, debug=1 ) {
ms02_singlerun = function( inpairs, ncycles=10, indebug=0 ) { # Renamed, 2014 Feb 12
if (ncycles >= 1 ) {
if(indebug>0) {
print(paste('ncycles=', ncycles))
}
longids = c(as.character(inpairs[,1]), as.character(inpairs[,2]) )
longids = sample(longids)
len = length(inpairs[,1])
newpairs = data.frame( cbind( longids[1:len], longids[(len+1): (2*len)]) )
names(newpairs) = c('id1', 'id2')
newpairs$id1 = as.character( newpairs$id1)
newpairs$id2 = as.character( newpairs$id2)
newpairs$selfpairs = ifelse( newpairs$id1 == newpairs$id2, 1, 0 )
self.tb = newpairs[ newpairs$selfpairs==1, ]
nonself.tb = newpairs[newpairs$selfpairs==0, ]
if(indebug>0) {
print(paste("===selfpairs===="),NULL)
print(self.tb)
print(paste("================="),NULL)
}
if( length(self.tb[,1])>=1 ) {
if ( ncycles == 0) {
#return (c(NA,NA, NA) );
print(paste("ncycles reached zero, ncycles"),ncycles)
print(paste("Abort!"),NULL)
stop;
} else {
ncycles = ncycles - 1
splitPos = round( length(self.tb[,1]) * sqrt(ncycles) ) + 5 #2014Jan31 change
splitPos = min( splitPos, (length(nonself.tb[,1])-1 ) )
selectedpairs = rbind(self.tb, nonself.tb[1: splitPos, ] )
restpairs = nonself.tb[ (splitPos + 1): length(nonself.tb[,1]), ]
#return( rbind(restpairs, permute.pairs.wo.selfpairs(selectedpairs, ncycles)))
return( rbind(restpairs, ms02_singlerun(selectedpairs, ncycles))) #2014 Feb 12
}
} else {
return (newpairs)
}
} else {
return( c(NA,NA,NA ))
}
}
#net = read.table("repeat.tab")
#write.table(pairs, "merged_PPIGIN_2014Jan20.tab", quote=F, row.names=F, col.names=F, sep='\t')
net = read.table( "merged_PPIGIN_2014Jan20.tab", header=F, sep="\t", colClass = c("character", "character") )
head(net)
if(debug==9) {
#net = read.table('pair.tab',header=F)
net = net[1:90000,]
}
for( i in 1:100) {
net.ms02 = ms02_singlerun( net, indebug=0 )
cmnd = paste( "mkdir dipgin.ms02.output/", i, sep="")
system( cmnd )
outputname = paste( 'dipgin.ms02.output/', i, '/', "ms02_",i,".tab", sep="")
write.csv(net.ms02, outputname)
}
#do they have the same degree?
#t1 = table(c(net[,1],net[,2]))
#t2 = table(c(net.ms02[,1],net.ms02[,2]))
#comp <- t1 == t2
#table(comp)
#tf = comp[comp==F]; tf
#t1[names(tf)[1]]
#t1[names(tf)]
#t2[names(tf)]
#permuate merged yeast PPI+GIN
#2014 Feb 12, re-name function to ms02_singlerun
#2014 Jan 31, fixed a bug that inserted "NA" into new network. The bug seems to be caused by spliting the
# arrays. I rewrote the spliting portion.
#require(igraph)
rm(list=ls())
debug = 0
setwd("~/projects/0.ginppi.reliability.simulation/ms02GINPPI")
#set.seed(2014)
#permute.pairs.wo.selfpairs = function( inpairs, ncycles=10, debug=1 ) {
ms02_singlerun = function( inpairs, ncycles=10, indebug=0 ) { # Renamed, 2014 Feb 12
if (ncycles >= 1 ) {
if(indebug>0) {
print(paste('ncycles=', ncycles))
}
longids = c(as.character(inpairs[,1]), as.character(inpairs[,2]) )
longids = sample(longids)
len = length(inpairs[,1])
newpairs = data.frame( cbind( longids[1:len], longids[(len+1): (2*len)]) )
names(newpairs) = c('id1', 'id2')
newpairs$id1 = as.character( newpairs$id1)
newpairs$id2 = as.character( newpairs$id2)
newpairs$selfpairs = ifelse( newpairs$id1 == newpairs$id2, 1, 0 )
self.tb = newpairs[ newpairs$selfpairs==1, ]
nonself.tb = newpairs[newpairs$selfpairs==0, ]
if(indebug>0) {
print(paste("===selfpairs===="),NULL)
print(self.tb)
print(paste("================="),NULL)
}
if( length(self.tb[,1])>=1 ) {
if ( ncycles == 0) {
#return (c(NA,NA, NA) );
print(paste("ncycles reached zero, ncycles"),ncycles)
print(paste("Abort!"),NULL)
stop;
} else {
ncycles = ncycles - 1
splitPos = round( length(self.tb[,1]) * sqrt(ncycles) ) + 5 #2014Jan31 change
splitPos = min( splitPos, (length(nonself.tb[,1])-1 ) )
selectedpairs = rbind(self.tb, nonself.tb[1: splitPos, ] )
restpairs = nonself.tb[ (splitPos + 1): length(nonself.tb[,1]), ]
#return( rbind(restpairs, permute.pairs.wo.selfpairs(selectedpairs, ncycles)))
return( rbind(restpairs, ms02_singlerun(selectedpairs, ncycles))) #2014 Feb 12
}
} else {
return (newpairs)
}
} else {
return( c(NA,NA,NA ))
}
}
#net = read.table("repeat.tab")
#write.table(pairs, "merged_PPIGIN_2014Jan20.tab", quote=F, row.names=F, col.names=F, sep='\t')
net = read.table( "merged_PPIGIN_2014Jan20.tab", header=F, sep="\t", colClass = c("character", "character") )
head(net)
if(debug==9) {
#net = read.table('pair.tab',header=F)
net = net[1:90000,]
}
for( i in 1:100) {
net.ms02 = ms02_singlerun( net, indebug=0 )
cmnd = paste( "mkdir dipgin.ms02.output/", i, sep="")
system( cmnd )
outputname = paste( 'dipgin.ms02.output/', i, '/', "ms02_",i,".tab", sep="")
write.csv(net.ms02, outputname)
}
#do they have the same degree?
#t1 = table(c(net[,1],net[,2]))
#t2 = table(c(net.ms02[,1],net.ms02[,2]))
#comp <- t1 == t2
#table(comp)
#tf = comp[comp==F]; tf
#t1[names(tf)[1]]
#t1[names(tf)]
#t2[names(tf)]
DMG problem in Snow Leopard
RStudio-0.98.501.dmg file is not automatically mounted on a snow leopard laptop. Open it with "Disk Utility", then click "Mount". It worked.
VPN Spelman
http://princess.spelman.edu/accountreq.nsf/vpninstructions
sudo sh *.sh
install 'Cisco' folder to Application, which contains Cisco Anyconnect client.
Tuesday, February 11, 2014
Bio125, Feb 11, Tue, 2014, ApE, identify mutations, gel electrophoresis
I manually generated mutations and give students for analysis. I made two mistakes and were found out by studetns.
I posted a youtube tutorial and asked student finish the ApE assignment in class. This seems to push student to focus on the work. At 1:30pm, the college was closed and some student left. Others stay and kept working on the ApE exercieses.
Gel were poured by lab instructor. Student loaded their samples, and gels were run. I found that ApaI and Xab I gave two similar-sized bands for pMSH2 and one sized-band for pRS413. When the plasmid are overloaded, the one 4.5kb smear band is similar to the 4.4 and 4.9 kb bands. We decided to run the gel longer to get better resolution. (Next time we should pick different RE, or we can ask student to pick better RE. 0.8% gel might be used).
Because of the HA tag, locations can be different between MSH2 and HA-MSH2, (info based on D. Wang).
I posted a youtube tutorial and asked student finish the ApE assignment in class. This seems to push student to focus on the work. At 1:30pm, the college was closed and some student left. Others stay and kept working on the ApE exercieses.
Gel were poured by lab instructor. Student loaded their samples, and gels were run. I found that ApaI and Xab I gave two similar-sized bands for pMSH2 and one sized-band for pRS413. When the plasmid are overloaded, the one 4.5kb smear band is similar to the 4.4 and 4.9 kb bands. We decided to run the gel longer to get better resolution. (Next time we should pick different RE, or we can ask student to pick better RE. 0.8% gel might be used).
Because of the HA tag, locations can be different between MSH2 and HA-MSH2, (info based on D. Wang).
1. G704S: AG41_G693S
2. R542P: AG29_R542P
3. H669Y: AG33_H658Y
4. G704D: AG91_G693D
5. M718I: AG371_M707I
6. H669R: AG372_H658R
7. A618V: AG421_A618V
8. D621N: AG422_D621N
Monday, February 10, 2014
GAS 2014 annual meeting prep, math ramp research
Friday and Saturday, 28-29 March, 2014 at Georgia Regents University, Augusta, GA.
meeting registration site
http://www.gru.edu/trends/gas/accommodations.php
http://www.gaacademy.org/annualmeeting10.htm
Hilton Garden Inn Augusta Meeting rate ($89) but not available anymore.
1065 Stevens Creek Road, Augusta, Georgia, 30907
Sheraton Augusta Hotel , prepaid rate $107 per night, refundable rate $119
1069 Stevens Creek Road, Augusta, GA 30907
Sheraton Augusta Hotel
1069 Stevens Creek Road
Augusta, Georgia 30907 United States
Phone: (706) 396-1000 Fax: (706) 396-1001
Parking?
-------------------------
Prepare of a 10 minutes talk.
Research talk:
10 slides.
- background, gene network, essential and non-essential,
- background, what is aging, our quantitative definition
- specific aim: how reliable is the yeast gene interaction network.
- method: how to generate random networks.
- method: evaluate the failure rates of original and random networks
- method: how network failure is simulated and evaluated
- result: histogram of failure rate, average lifespan of random networks, with original network
- result: Gompertz versus Weibull (biological versus machine aging)
- summary and conclusions
- future directions:
acknowledge, funding support
things to do:
->flow chart to generate 100 random networks and simulate their failures.
-> run the two R codes on network aging simulation and network permutation.
BIO125, FOA plate media and western blot media
=> For FOA plates, the media is -HIS-TRP-LEU-THR+URA
-LEU -THR for URA3's LEU2 promoter to be active. The presence of Leucine and Theorine lead to 10 fold drop of LEU2 expression.
-HIS to keep pMSH2
-TRP to keep pSH44 reporter plasmid
+URA for FOA assay, because we are selecting for mutant URA3.
So the FOA media is HIS-TRP-LEU-THR + URA
However, before the FOA plate, yeast cells should be grown in - URA to ensure intact dinucleotide repeat in pSH44.
So the regular media is -URA-HIS-TRP (-LEU-THR)
See Gammie04CBE
=> For MSH2 expression:
Gammie07,
Three type of pMSH2 was mentioned. pMSH2, pGBD-MSH2, and pGAL-MSH2.
The pMSH2 is under endogenous promoter. So, the media should be -His to keep pMSH2.
The pGBD-MSH2 was designed to have a constitutive expression of MSH2 protein with HA tag. This plasmid seems to be used for two-hybrid.
The pGAL-MSH2 contains a GAL10 promoter.
References
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC294742/pdf/jbacter00572-0372.pdf
-LEU -THR for URA3's LEU2 promoter to be active. The presence of Leucine and Theorine lead to 10 fold drop of LEU2 expression.
-HIS to keep pMSH2
-TRP to keep pSH44 reporter plasmid
+URA for FOA assay, because we are selecting for mutant URA3.
So the FOA media is HIS-TRP-LEU-THR + URA
However, before the FOA plate, yeast cells should be grown in - URA to ensure intact dinucleotide repeat in pSH44.
So the regular media is -URA-HIS-TRP (-LEU-THR)
See Gammie04CBE
=> For MSH2 expression:
Gammie07,
Three type of pMSH2 was mentioned. pMSH2, pGBD-MSH2, and pGAL-MSH2.
The pMSH2 is under endogenous promoter. So, the media should be -His to keep pMSH2.
The pGBD-MSH2 was designed to have a constitutive expression of MSH2 protein with HA tag. This plasmid seems to be used for two-hybrid.
The pGAL-MSH2 contains a GAL10 promoter.
References
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC294742/pdf/jbacter00572-0372.pdf
self-pairing test, ms02, R, network permutation
test network:
Expectation: When ncycles run to 1, the last row should be "NA"
Summary: the code 'ms02' passed the test. No extra row or self-pairs are found.
2014April 7. 'ms02' did not check id1-id2 versus id2-id1.
exercises on rate, R code
MM = function(x, Km, Vmax) {
ret = Vmax /(1 + (Km/x)^10);
}
x = seq(-0.1,90, by=0.1);
Km = 40;
Vmax = 45;
y = MM( x,Km,Vmax);
plot( y ~ x, type='l', lwd=4, ylab='concentration', xlab='time'); #sigmoid shape transport
#get the rate
dy = NA;
for ( i in 2:length(y)) {
dy[i]= y[i] - y[i-1]
}
plot( dy ~ x, type='l', lwd=4, ylab='rate', xlab='time')
dy2 = 0.25 - dy
plot( dy2 ~ x, type='l', lwd=4, ylab='rate', xlab='time')
KM2 = 40
Vmax2 = 0.25
y2 = MM( x,KM2,Vmax2);
plot( y2 ~ x, type='l', lwd=4, ylab='rate', xlab='time'); #sigmoid shape transport
y2b = 0.25 - y2
plot( y2b ~ x, type='l', lwd=4, ylab='rate', xlab='time'); #sigmoid shape transport
y3 = c(rep(0,40),rep(0.25,40))
x3 = seq(1,80,by=1)
plot( y3 ~ x3, type='l', lwd=4, ylab='rate',xlab='time')
y3b = 0.25 - y3
plot( y3b ~ x3, type='l', lwd=4, ylab='rate',xlab='time')
ret = Vmax /(1 + (Km/x)^10);
}
x = seq(-0.1,90, by=0.1);
Km = 40;
Vmax = 45;
y = MM( x,Km,Vmax);
plot( y ~ x, type='l', lwd=4, ylab='concentration', xlab='time'); #sigmoid shape transport
#get the rate
dy = NA;
for ( i in 2:length(y)) {
dy[i]= y[i] - y[i-1]
}
plot( dy ~ x, type='l', lwd=4, ylab='rate', xlab='time')
dy2 = 0.25 - dy
plot( dy2 ~ x, type='l', lwd=4, ylab='rate', xlab='time')
KM2 = 40
Vmax2 = 0.25
y2 = MM( x,KM2,Vmax2);
plot( y2 ~ x, type='l', lwd=4, ylab='rate', xlab='time'); #sigmoid shape transport
y2b = 0.25 - y2
plot( y2b ~ x, type='l', lwd=4, ylab='rate', xlab='time'); #sigmoid shape transport
y3 = c(rep(0,40),rep(0.25,40))
x3 = seq(1,80,by=1)
plot( y3 ~ x3, type='l', lwd=4, ylab='rate',xlab='time')
y3b = 0.25 - y3
plot( y3b ~ x3, type='l', lwd=4, ylab='rate',xlab='time')
Saturday, February 8, 2014
Thursday, February 6, 2014
Bio125, Xba1 Apa1, pRS413, pMSH2
1hour, went through protocol for XbaI and Apa1 cutting.
Use ApE to do XbaI and ApaI mapping. Dr. Kioko ordered FastDigest enzyme and buffer. Both enzyme work at 37C. The 37C incubation did not finish because the heat block somehow could not reach 37C.
Explained why 6bp cutters have fewer sites than 4bp cutters. Most students use plus instead of multiplication to do the calculation. I used 3 colored play dough again to enumerate the 9 possibility for 2 positions. I initially tried 2 colored play dough, but ran into the problem of 2+2 and 2x2 yield the same result.
Kioko mixed XbaI and ApaI. Student took 1ul of the mixture.
Use ApE to do XbaI and ApaI mapping. Dr. Kioko ordered FastDigest enzyme and buffer. Both enzyme work at 37C. The 37C incubation did not finish because the heat block somehow could not reach 37C.
Explained why 6bp cutters have fewer sites than 4bp cutters. Most students use plus instead of multiplication to do the calculation. I used 3 colored play dough again to enumerate the 9 possibility for 2 positions. I initially tried 2 colored play dough, but ran into the problem of 2+2 and 2x2 yield the same result.
Kioko mixed XbaI and ApaI. Student took 1ul of the mixture.
Bio233, Feb 6 2014
Played music science video on glycolysis and Kreb cycle.
Emphasized electron transport chain, went through the calculation of 38 ATP.
Emphasized negative feedbacks.
Summarized key learning objectives at the end.
Emphasized electron transport chain, went through the calculation of 38 ATP.
Emphasized negative feedbacks.
Summarized key learning objectives at the end.
Wednesday, February 5, 2014
BIO233, Gram stain lab, Feb 5, 2014
Lab started around 2:05pm.
Two students explained procedures on board. I did demo on preparing smear and gram stain.
Problems and issues that need to be addressed in the future:
Some slides are oily, and cells could not be spread on them.
Some students are not sure how much water they would put on slides, or how to spread the water thinly.
Some students will do Gram stain in their own space instead of the sink.
Some over-decolorized the stain with 95% EtOH.
Some did not sufficiently decolorize the stain or add too much stain. Some crytal violet and safranin contain too much debris. New bottles of reagent should be bought when funds are available.
Several students did know how to use microscope properly.
Most students finished the lab within 40 minutes. Three students worked on their own and spent about 20 more minutes. Overall, the lab finished at 4:30pm.
Students could use their iPhones and took picture from the eye-pieces.
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| Gram-positive Bacillus megaterium |
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