Thursday, February 27, 2014

Report NIH award search link

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

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



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

cluster 175, 214, health diparity

 
Todo: sequence comparison of HSPB1 and CRY proteins



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:

111.089
2
1.407
331.557
441.661
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.







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)


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.




Hassusser hemocytometer, Brightline





http://www.hausserscientific.com/products/hausser_bright_line.html

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

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.


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.








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

Wednesday, February 12, 2014

alignments of MSH2 proteins from various species, cognant sites identification


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

msh2 blastp



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/pubmed/24082110

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)]




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

Youtube screen ratio is 16:9

The 16:9 ratio for youtube means 1280x720 screen.

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). 
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

hotel:
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.

  1. background, gene network, essential and non-essential,
  2. background, what is aging, our quantitative definition
  3. specific aim: how reliable is the yeast gene interaction network.
  4. method: how to generate random networks.
  5. method: evaluate the failure rates of original and random networks
  6. method: how network failure is simulated and evaluated
  7. result: histogram of failure rate, average lifespan of random networks, with original network
  8. result: Gompertz versus Weibull (biological versus machine aging)
  9. summary and conclusions
  10. 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


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')

Thursday, February 6, 2014

online alignment tools

t-coffee
clustalw
muschle

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.




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.

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.

Gram-positive Bacillus megaterium


CYC2E1


cluster 214,CRX ,

macula
黄斑

http://www.nei.nih.gov/eyedata/pbd4.asp

http://omim.org/entry/164500


Tuesday, February 4, 2014

metabolic problem sets


Good biochem problem sets
http://www.uvm.edu/~mcase/courses/chem205/answers_set3.pdf
http://www.uvm.edu/~mcase/courses/chem205/problem_set3.pdf

Some calculation and analysis questions
http://www.ncbi.nlm.nih.gov/books/NBK22432/

mutant enzyme is half effective to covert energy during the succinate to fumarate.
http://en.wikipedia.org/wiki/Succinate_dehydrogenase

Simple recall questions
http://www.faculty.une.edu/com/courses/bionut/distbio/obj-512/Chap22-practice%20questions.htm

ATPase, 10 protons -> 3 ATPs



http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&term=tuininga%20JE%20[au]%20AND%201999%20[dp]%20AND%20Pyrococcus%20furiosus&qd_page_no=0&sourceid=Mozilla-search

bio125, Feb 4, 2014, miniprep


I spent one hour going over the miniprep protocol.  Questions asked by the students include: What does 'resuspend' mean? What is an eppendorf tube? Should samples be done sequentially or in parallel?

Students spent 1.5 hours on doing minipreps. Many students spent too much time at the 'lysis' step which led to poor yields, commented by S. Kioko. I should address this problem next time.

One group turned in their ApE assignment. The two students, both fairly intelligent, are not clear how to calculate protein length from nucleotide coding sequences.





bio233, Feb 4, 2014, morphology and structure

I went over MCAT requirement on microbiology, cell biology, biochemistry, and genetics.

I let students to create spiral shaped bacteria, spherical and rod shapes.

I went through chapter 3 slides, with clicker questions on how to interpret 'rates' from the concentration ~ time plots.



Maverick, bizhub 754, print usage





Moodle grade book, adjust item weight to calculate finale grade

1. Log into your Moodle course page. On the left,  click  a "Grades" icon. 


2. In the "Grader report" window, click the "Categories and items" tab. 

3. Click the 'full view'. 

4. You can adjust the 'Multiplicator' to give weights to each item. 

5. You can go back to the 'view' window to check the student grades, and make sure this what you want. 


6. Before do this, I suggest you to blind the "course total" from students. Make sure the changes are saved. 


Note: The weights are mostly going to change during the course. So, I would do this final grade calculation at least in late part of the semester.