GENE 3210:
Genetics Laboratory
Fall 2006, Dawe portion |
Tues-Thurs 2:00-4:45 pm Rm C104 |
The goal of this lab is to identify a Centromeric Retroelement (CR element) from a new monocot, sequence it, and submit it to GenBank. The syllabus describes the basic outline of the course and how grades will be assigned. It really works -- the successes from prior years are listed below the course outline.
| Week 8: INTRO, MAKE DNA | |
| Oct 10 | Introduction |
| Oct 12 | Make monocot DNA (protocol) |
| Week 9: PCR | |
| Oct 17 | Design primers (protocol) (get sequence of CRs) |
| Oct 19 | PCR parameters (protocol) |
| Week 10: PCR ON YOUR DNA | |
| Oct 24 | PCR on your plant DNA |
| Oct 26 | No class Fall break |
| Week 11: CHECK PCR | |
| Oct. 31 | Check PCRs from your plant DNA on gels |
| Nov. 2 | New PCRs or start cloning as appropriate (protocol for ligation and transformation) |
| Week 12: PLASMIDS | |
| Nov. 7 | Purify plasmids from E. coli (protocol) |
| Nov. 9 | GRADE NOTEBOOKS |
| Week 13: SEND TO SEQUENCE | |
| Nov. 14 | Continue as appropriate |
| Nov. 16 | First Paper: Mobile Elements: Drivers of Genome Evolution |
| Week 14: ANALYZE SEQUENCE | |
| Nov. 21 | GRADE NOTEBOOKS |
| Nov. 24 | No class Thanksgiving |
| Week 15: ANALYZE SEQUENCE | |
| Nov. 28 | Do BLAST searches on your CR sequences (protocol for BLASTING and submitting to GenBank) |
| Nov. 30 | Do BLAST searches on your CR sequences (protocol for BLASTING and submitting to GenBank) |
| Week 16 &17: FINISH UP | |
| Dec. 5 | Second Paper: Jin et al 2004 see also example exam |
| Dec. 12 | Final Exam 3:30-6:30 |
| Dec. 14 | Paper due, follow these guidelines |
These are the sequences from prior years
| Students | Primers | Species | GenBank |
--------------------------------2003--------------------------------------- |
|||
| Weiner,T.P., Bassett,G.H. | 5F, 5R | Avena sativa | AY495547 |
| Luhring,T.M., Green,P.A. | 4F, 2R | Spartina alterniflora | AY487345 |
| Fisher,J.A., Marchand,S.J., Johnson,P.M. | 2F, 3R | Imperata cylindrica | AY495545 |
| Oshansky,C.M. and Wilson,M.N. | 4F, 4R | Avena sativa | AY495544 |
| Odeh,R.N. and Kamran,D.M. | 9F, 9R | Uniola paniculata | AY495546 |
| Williams,J.L., Swart,L.M | 5F, 5R | Uniola paniculata | AY495543 |
| Johnson,H.L., Asher,L. | 5F, 8R | Digitaria ischaemum | AY495542 |
--------------------------------2004 (class photo)-------------------- |
|||
| Mollere,O.B., Rigamer,M.C. | RMF, MAR | Setaria pumila | AY846847 |
| Baxter,V.Z., Amin,R.V | 2F, RZR | Uniola paniculata | AY846845 |
| McCalla,A.D., Courtwright,P.W. | 5F, 5R | Pennisetum alopecuroides | AY845397 |
| Shivas,J.M., Wagnon,J.M. | 7F, MAR | Cymbopogon citratus | AY845418 |
| Robertson,J., Rosario,S.C. | RMF, RZR | Sorghum propinquum | AY845417 |
| Van Duys,I.J., Goforth,A | 5F, 5R | Ophiopogon japonicus | AY849797 |
| Goforth,A., Van Duys,I.J. | 5F, 5R | Pennisetum alopecuroides | AY849781 |
| Hill,M.E., Luce,A.C | JJF, 4R | Pennisetum alopecuroides | AY846846 |
| Reinemeyer,I.C., Petree,K.E. | RMF, RMR | Tripsacum dactyloides | AY845426 |
--------------------------------2005 (class photo)-------------------- |
|||
| Bosdell,M.H. | RMF, MAR | Fargesia robusta | DQ301877 |
| Burgos,B., Godwin,C. | RMF, MAR | Bambusa multiplex | DQ316316 |
| Farhat,N., Wrenn,W.B. III | 4F, 9R | Alocasia longiloba | DQ316317 |
| Wrenn,W.B. III | 7F, 7R | Alocasia longiloba | DQ320316 |
| Blankenhagen,K.J., Bosdell,M.H. | 5F,5R | Fargesia robusta | DQ320315 |
| Chatfield,M.K. | 5F, 5R | Panicum virgatum | DQ316318 |
| Sadosky,L.N., Wrenn,W.B. III | RMF, MAR | Alocasia Longiloba | DQ322243 |
| Furlong,J.M., Chatfield,M.K. | P1, P2 | Panicum virgatum | DQ322242 |
--------------------------------2006(blurry class photo)-------------------- |
|||
| Trivett,L.R., Hong,S. | 2F, LTSHR | Aristolochia gigantea | EF151087 |
| Johnson,E.M., Jones,T.E. | JJF, 4R | Arundinaria gigantea | EF153457 |
| Le,N.L., Kay,W.L. | 5F, 5R | Arundinaria gigantea | EF182739 |
| Randolph,M.E., Hadj-Moussa,M., Free,A.M., Mulyadi,A.R. | 2F, LTSHR | Panicum virgatum | EF182744 |
| Randolph,M.E., Hadj-Moussa,M., Free,A.M., Mulyadi,A.R. | 2F, LTSHR | Panicum virgatum | EF182743 |
| Free,A.M., Mulyadi,A.R., Wolfe,R. and Norman,M. | 2F, LTSHR | Arundinaria gigantea | EF182741 |
| Desai,A.R. and Schmidt,B.W. | 2F, LTSHR | Panicum virgatum | EF153458 |
| Wiley, D., Ford, B. | 7F, 4R | Panicum virgatum | EF182742 |
| Lopez, K.E., Smith, R. | 2F, 8R | Musa X paradisiaca | EF182740 |
