IGEM:Harvard/2010/Team Allergy

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==Description==
==Description==
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[[Image:Strawberries_iGEM_2010.png‎|250px|left]]Allergies to fruits and vegetables are (increasingly) common, affecting millions of people around the world with symptoms ranging from mild itchiness to life-threatening anaphylaxis. Allergy is caused by an inappropriate immune response to harmless proteins present in the environment. Several common food allergens are structurally similar to pollens that cause seasonal allergies and are present in a wide range of fruits and vegetables. Many of these proteins have been knocked down in plants using RNA interference, leading to plants with reduced allergenicity. As part of our iGarden project we are designing modular BioBrick  intron-containing self-complementary hairpin forming RNA (ihpRNA) constructs for the targeted knockdown of proteins with homology to allergens in arabidopsis and strawberry, as well as designing ihpRNA constructs against allergens in a range of other plants common in home gardens, including lettuce, carrots, celery, tomato, and several herbs. Our goal is to use genetic engineering to make food safer, and to specially tailor gardens to the needs of each person with a different set of allergies.
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We are designing shRNA constructs against common allergens in fruits and vegetables.  
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<br>
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==Bibliography==
==Bibliography==
===Plant shRNA===
===Plant shRNA===
<biblio>
<biblio>
#1 pmid=11576441
#1 pmid=11576441
 +
#2 pmid=16531494
</biblio>
</biblio>
===Allergen silencing===
===Allergen silencing===
<biblio>
<biblio>
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#2 pmid=17784907
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#3 pmid=17784907
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#3 pmid=18467156
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#4 pmid=18467156
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#4 pmid=17088146  
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#5 pmid=17088146  
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#5 pmid=19356919
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#6 pmid=19356919
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#6 pmid=16950292
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#7 pmid=16950292
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#7 pmid=12746509
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#8 pmid=12746509
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#8 pmid=15696096
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#9 pmid=15696096
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#9 pmid=14962769
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#10 pmid=14962769
</biblio>
</biblio>
===Allergen proteins===
===Allergen proteins===
<biblio>
<biblio>
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#10 pmid=12811016
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#11 pmid=12811016
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#11 pmid=12757453
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#12 pmid=12757453
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#12 pmid=15347364
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#13 pmid=15347364
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#13 pmid=8946858
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#14 pmid=8946858
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#14 pmid=16650053
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#15 pmid=16650053
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#15 pmid=15507096
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#16 pmid=15507096
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#16 pmid=16945416
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#17 pmid=16945416
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#17 pmid=10887301
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#18 pmid=10887301
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#18 pmid=12169176
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</biblio>
</biblio>
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|''CCTTGAATTCGCGGCCGCATCTAGA''
|''CCTTGAATTCGCGGCCGCATCTAGA''
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==Protocols==
 
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===Isolating Genes From Plants===
 
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*[http://labs.fhcrc.org/fero/Protocols/RNeasy_Mini_Handbook.pdf Qiagen RNeasy Plant Mini Kit]
 
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*[http://cshprotocols.cshlp.org/cgi/reprint/2007/4/pdb.kit23.pdf iScript cDNA Synthesis]
 
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===Strawberry Transformation===
 
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<biblio>
 
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#1 pmid=17147614
 
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#2 pmid=16320068
 
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#3 pmid=19956955
 
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#4 pmid=7581659
 
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</biblio>
 
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==Plasmids==
 
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*[https://spreadsheets.google.com/ccc?key=0AnjFW9ZXw2djdFc0YXl4Tmw0SHFLdzZOVHVtQi10Znc&hl=en Spreadsheet]
 

Revision as of 09:31, 17 June 2010

Contents

Description

We are designing shRNA constructs against common allergens in fruits and vegetables.

Bibliography

Plant shRNA

  1. Wesley SV, Helliwell CA, Smith NA, Wang MB, Rouse DT, Liu Q, Gooding PS, Singh SP, Abbott D, Stoutjesdijk PA, Robinson SP, Gleave AP, Green AG, and Waterhouse PM. . pmid:11576441. PubMed HubMed [1]
  2. Schwab R, Ossowski S, Riester M, Warthmann N, and Weigel D. . pmid:16531494. PubMed HubMed [2]
All Medline abstracts: PubMed HubMed

Allergen silencing

  1. Dodo HW, Konan KN, Chen FC, Egnin M, and Viquez OM. . pmid:17784907. PubMed HubMed [3]
  2. Singh MB and Bhalla PL. . pmid:18467156. PubMed HubMed [4]
  3. Le LQ, Mahler V, Lorenz Y, Scheurer S, Biemelt S, Vieths S, and Sonnewald U. . pmid:17088146. PubMed HubMed [5]
  4. Gallo M and Sayre R. . pmid:19356919. PubMed HubMed [6]
  5. Lorenz Y, Enrique E, Lequynh L, Fötisch K, Retzek M, Biemelt S, Sonnewald U, Vieths S, and Scheurer S. . pmid:16950292. PubMed HubMed [7]
  6. Herman EM, Helm RM, Jung R, and Kinney AJ. . pmid:12746509. PubMed HubMed [8]
  7. Gilissen LJ, Bolhaar ST, Matos CI, Rouwendal GJ, Boone MJ, Krens FA, Zuidmeer L, Van Leeuwen A, Akkerdaas J, Hoffmann-Sommergruber K, Knulst AC, Bosch D, Van de Weg WE, and Van Ree R. . pmid:15696096. PubMed HubMed [9]
  8. Bhalla PL and Singh MB. . pmid:14962769. PubMed HubMed [10]
All Medline abstracts: PubMed HubMed

Allergen proteins

  1. Chardin H, Mayer C, Sénéchal H, Wal JM, Poncet P, Desvaux FX, and Peltre G. . pmid:12811016. PubMed HubMed [11]
  2. San Miguel-Moncín M, Krail M, Scheurer S, Enrique E, Alonso R, Conti A, Cisteró-Bahíma A, and Vieths S. . pmid:12757453. PubMed HubMed [12]
  3. Salcedo G, Sanchez-Monge R, Diaz-Perales A, Garcia-Casado G, and Barber D. . pmid:15347364. PubMed HubMed [13]
  4. Gajhede M, Osmark P, Poulsen FM, Ipsen H, Larsen JN, Joost van Neerven RJ, Schou C, Løwenstein H, and Spangfort MD. . pmid:8946858. PubMed HubMed [14]
  5. Zuidmeer L, Salentijn E, Rivas MF, Mancebo EG, Asero R, Matos CI, Pelgrom KT, Gilissen LJ, and van Ree R. . pmid:16650053. PubMed HubMed [15]
  6. Karlsson AL, Alm R, Ekstrand B, Fjelkner-Modig S, Schiött A, Bengtsson U, Björk L, Hjernø K, Roepstorff P, and Emanuelsson CS. . pmid:15507096. PubMed HubMed [16]
  7. Musidlowska-Persson A, Alm R, and Emanuelsson C. . pmid:16945416. PubMed HubMed [17]
  8. Breiteneder H and Ebner C. . pmid:10887301. PubMed HubMed [18]
All Medline abstracts: PubMed HubMed


Primers and Sequences

name GenBank Accession forward sense primer reverse sense primer forward antisense primer reverse antisense primer
pdk intron AJ311872 CCTTGAATTCGCGGCCGCATCTAGA tcttttttccttttagtata AAGGCTGCAGCGGCCGCTACTAGT CAATCCAAATGTAAGATCAA
GFP AF218816.1 CCTTGAATTCGCGGCCGCATCTAGA atggtgagcaagggcgagga AAGGCTGCAGCGGCCGCTACTAGT gaagatggtgcgctcctgga AAGGCTGCAGCGGCCGCTACTAGT atggtgagcaagggcgagga CCTTGAATTCGCGGCCGCATCTAGA gaagatggtgcgctcctgga
A. thaliana LTP1 ATHSEQB CCTTGAATTCGCGGCCGCATCTAGA ATGGCTGGAGTGATGAAGTT AAGGCTGCAGCGGCCGCTACTAGT CAGCTGCACGGCCAGCGTTG AAGGCTGCAGCGGCCGCTACTAGT ATGGCTGGAGTGATGAAGTT CCTTGAATTCGCGGCCGCATCTAGA CAGCTGCACGGCCAGCGTTG
Fra a 1A (Bet v 1) DQ385511 CCTTGAATTCGCGGCCGCATCTAGA ATGGGTGTTTACACTTATGA AAGGCTGCAGCGGCCGCTACTAGT GTAGTCGATCTTCTCGATGT AAGGCTGCAGCGGCCGCTACTAGT ATGGGTGTTTACACTTATGA CCTTGAATTCGCGGCCGCATCTAGA GTAGTCGATCTTCTCGATGT
L. sativa LTP 1.1 EF101532.1 CCTTGAATTCGCGGCCGCATCTAGA ATGGCAAGGATGGCAACGAT AAGGCTGCAGCGGCCGCTACTAGT TGACACCACACTTGCCGGGG AAGGCTGCAGCGGCCGCTACTAGT ATGGCAAGGATGGCAACGAT CCTTGAATTCGCGGCCGCATCTAGA TGACACCACACTTGCCGGGG
L. sativa LTP 1.2 EF101531.1 CCTTGAATTCGCGGCCGCATCTAGA GTGACATGTGGTCAGGTGGT AAGGCTGCAGCGGCCGCTACTAGT CTGGATCCTATTGCAGTCGG AAGGCTGCAGCGGCCGCTACTAGT GTGACATGTGGTCAGGTGGT CCTTGAATTCGCGGCCGCATCTAGA CTGGATCCTATTGCAGTCGG
S. lycopersicum Lyc E 1.01 (profilin) AJ417553 CCTTGAATTCGCGGCCGCATCTAGA ATGTCGTGGCAAACATATGT AAGGCTGCAGCGGCCGCTACTAGT AGCCTGATTGGTCTTCTTAA AAGGCTGCAGCGGCCGCTACTAGT ATGTCGTGGCAAACATATGT CCTTGAATTCGCGGCCGCATCTAGA AGCCTGATTGGTCTTCTTAA
D. Carota Dau C 1 Z84376.1 CCTTGAATTCGCGGCCGCATCTAGA ATGGGTGCCCAGAGCCATTCAC AAGGCTGCAGCGGCCGCTACTAGT GGTTTCAATGGATTCGATGA AAGGCTGCAGCGGCCGCTACTAGT ATGGGTGCCCAGAGCCATTCAC CCTTGAATTCGCGGCCGCATCTAGA GGTTTCAATGGATTCGATGA
Api g 4 (celery profilin) AF129423.1 CCTTGAATTCGCGGCCGCATCTAGA ATGTCGTGGCAGGCGTACGT AAGGCTGCAGCGGCCGCTACTAGT GGTTCATCATAGACTCCGAA AAGGCTGCAGCGGCCGCTACTAGT ATGTCGTGGCAGGCGTACGT CCTTGAATTCGCGGCCGCATCTAGA GGTTCATCATAGACTCCGAA
Api g 1.0201 (celery) Z75662.2 CCTTGAATTCGCGGCCGCATCTAGA ATGGGTGTCCAAAAGACCGT AAGGCTGCAGCGGCCGCTACTAGT CACCACTGACTCGAGTACGT AAGGCTGCAGCGGCCGCTACTAGT ATGGGTGTCCAAAAGACCGT CCTTGAATTCGCGGCCGCATCTAGA CACCACTGACTCGAGTACGT
Api g 1 (celery) Z48967.1 CCTTGAATTCGCGGCCGCATCTAGA ATGGGAGTGCAGACACATGT AAGGCTGCAGCGGCCGCTACTAGT GTTTTCAATGGATTCGATAA AAGGCTGCAGCGGCCGCTACTAGT ATGGGAGTGCAGACACATGT CCTTGAATTCGCGGCCGCATCTAGA GTTTTCAATGGATTCGATAA
A. Thaliana (BLAST) Bet v 1 (#1) :12937059-12937689 CCTTGAATTCGCGGCCGCATCTAGA ATGATAGAAGAGGAGATTGA AAGGCTGCAGCGGCCGCTACTAGT TACCATATTAAAAAATACGT AAGGCTGCAGCGGCCGCTACTAGT ATGATAGAAGAGGAGATTGA CCTTGAATTCGCGGCCGCATCTAGA TACCATATTAAAAAATACGT
A. Thaliana (BLAST) Bet v 1 (#2) :12937059-12937689 CCTTGAATTCGCGGCCGCATCTAGA AAATTCATTTATAAACGCAT AAGGCTGCAGCGGCCGCTACTAGT TTAATCCTTAGACAAGAGGT AAGGCTGCAGCGGCCGCTACTAGT AAATTCATTTATAAACGCAT CCTTGAATTCGCGGCCGCATCTAGA TTAATCCTTAGACAAGAGGT
A. thaliana GER3 NM_122070 CCTTGAATTCGCGGCCGCATCTAGA ATGAAGATGATAATCCAAAT AAGGCTGCAGCGGCCGCTACTAGT GATGACACCACCACCGGCTA AAGGCTGCAGCGGCCGCTACTAGT ATGAAGATGATAATCCAAAT CCTTGAATTCGCGGCCGCATCTAGA GATGACACCACCACCGGCTA
CCTTGAATTCGCGGCCGCATCTAGA AAGGCTGCAGCGGCCGCTACTAGT AAGGCTGCAGCGGCCGCTACTAGT CCTTGAATTCGCGGCCGCATCTAGA
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