Lecturers - Baylor College of Medicine



Lecturers

|Term 1 |

|Genetics A |

|FullName |Phone |Room |Email |

|*Susan Rosenberg |713-798-6924 |S809 |smr@bcm.edu |

|*Zheng Zhou |713-798-6489 |322B |zhengz@bcm.edu |

|Richard Kelley |713-798-4526 |T728 |rkelley@bcm.edu |

|Method & Logic in Molecular Biology |

|FullName |Phone |Room |Email |

|*Graeme Mardon |713-798-8731 |T222 |gmardon@bcm.edu |

|Adam Kuspa |713-798-8278 |S338A |akuspa@bcm.edu |

|David Moore |713-798-3313 |N61006 |moore@bcm.edu |

|E. Zechiedrich |713-798-5126 |220A |elz@bcm.edu |

|Gad Shaulsky |713-798-8082 |S430 |gadi@bcm.edu |

|John Wilson |713-798-5760 |T342 |jwilson@bcm.edu |

|Richard Kelley |713-798-4526 |T728 |rkelley@bcm.edu |

|Rui Chen |713-798-5194 |N1519 |ruichen@bcm.edu |

|Scott Pletcher |713-798-5524 |N803 |pletcher@bcm.edu |

|Timothy Palzkill |713-798-5609 |223A |timothyp@bcm.edu |

|Xiangwei He |713-798-2093 |T926 |xhe@bcm.edu |

|Molecular Methods |

|FullName |Phone |Room |Email |

|*Hiram Gilbert |713-798-5880 |371A1 |hgilbert@bcm.edu |

|*Sarah Highlander |713-798-6311 |219A |sarahh@bcm.edu |

|Jun Qin |713-798-1507 |T303 |jqin@bcm.edu |

|Michael Metzker |713-798-7565 |N1409 |mmetzker@bcm.edu |

|Xin-Hua Feng |713-798-4756 |137D |xfeng@bcm.edu |

|Organization of the Cell |

|FullName |Phone |Room |Email |

|*Richard Sifers |713-798-3169 |T228 |rsifers@bcm.edu |

|*Steen Pedersen |713-798-3888 |T428 |pedersen@bcm.edu |

|Theodore Wensel |713-798-6994 |N430 |twensel@bcm.edu |

|Xiangwei He |713-798-2093 |T926 |xhe@bcm.edu |

|Zheng Zhou |713-798-6489 |322B |zhengz@bcm.edu |

|Science as a Profession Term 1 |

|FullName |Phone |Room |Email |

|*Hiram Gilbert |713-798-5880 |371A1 |hgilbert@bcm.edu |

|Barbara Slaughter |713-798-6644 |N204 |gayles@bcm.edu |

|Bill Brinkley |713-798-5263 |204GA |brinkley@bcm.edu |

|Scott Basinger |713-798-4100 |N204D |scottb@bcm.edu |

|Term 2 |

|Cancer |

|FullName |Phone |Room |Email |

|*Sharon Plon |832-824-4251 |120020 |splon@bcm.edu |

|Francesco Demayo |713-798-6241 |M725A |fdemayo@bcm.edu |

|Cell Division |

|FullName |Phone |Room |Email |

|*Shelley Sazer |713-798-4531 |375A |ssazer@bcm.edu |

|John Wilson |713-798-5760 |T342 |jwilson@bcm.edu |

|Pumin Zhang |713-798-1866 |T411 |pzhang@bcm.edu |

|Xiangwei He |713-798-2093 |T926 |xhe@bcm.edu |

|Development |

|FullName |Phone |Room |Email |

|*Armin Schumacher |713-798-6865 |S803 |armins@bcm.edu |

|Kathleen Mahon |713-798-5550 |M804 |kmahon@bcm.edu |

|Paul Overbeek |713-798-6421 |N620.0 |overbeek@bcm.edu |

|Ramiro Ramirez-Solis |713-798-3454 |T903 |solis@bcm.edu |

|Genetics B |

|FullName |Phone |Room |Email |

|*Graeme Mardon |713-798-8731 |T222 |gmardon@bcm.edu |

|*Tae-Ho Shin |713-798-4683 |N604.0 |tshin@bcm.edu |

|Alison Bertuch |832-824-4579 |124008 |abertuch@bcm.edu |

|Arthur Beaudet |713-798-4795 |T619 |abeaudet@bcm.edu |

|Monica Justice |713-798-5440 |S413A |mjustice@bcm.edu |

|Science as a Profession-Ethics |

|FullName |Phone |Room |Email |

|*Hiram Gilbert |713-798-5880 |371A1 |hgilbert@bcm.edu |

|Barbara Slaughter |713-798-6644 |N204 |gayles@bcm.edu |

|Bill Brinkley |713-798-5263 |204GA |brinkley@bcm.edu |

|Lloyd Michael |713-798-6825 |N104 |lmichael@bcm.edu |

|Morey Haymond |713-798-6776 |7062 |mhaymond@bcm.edu |

|Term 3 |

|Gene Regulation |

|FullName |Phone |Room |Email |

|*Jeffrey Rosen |713-798-6210 |M638A |jrosen@bcm.edu |

|Andrew Rice |713-798-5774 |824DB |arice@bcm.edu |

|Bert O'Malley |713-798-6205 |M613 |berto@bcm.edu |

|Christophe Herman |713-798-2126 |S909 |herman@bcm.edu |

|Jiemin Wong |713-798-6294 |M732 |jwong@bcm.edu |

|Richard Lloyd |713-798-8993 |860E |rlloyd@bcm.edu |

|Thomas Cooper |713-798-3141 |268B |tcooper@bcm.edu |

|Immunology |

|FullName |Phone |Room |Email |

|*Biao Zheng |713-798-8796 |N90305 |bzheng@bcm.edu |

|David Spencer |713-798-6475 |N903.0 |dspencer@bcm.edu |

|Molecular Interactions |

|FullName |Phone |Room |Email |

|*B Prasad |713-798-5686 |N410 |vprasad@bcm.edu |

|*Joseph Bryan |713-798-4007 |112C |jbryan@bcm.edu |

|Steen Pedersen |713-798-3888 |T428 |pedersen@bcm.edu |

|Neuroscience |

|FullName |Phone |Room |Email |

|*Tony Pham |713-798-9174 |M822A |tapham@bcm.edu |

|Term 4 |

|Research Design |

|FullName |Phone |Room |Email |

|*Hiram Gilbert |713-798-5880 |371A1 |hgilbert@bcm.edu |

|*Michael Schmid |713-798-5734 |N420 |mschmid@bcm.edu |

|B Prasad |713-798-5686 |N410 |vprasad@bcm.edu |

|E. Zechiedrich |713-798-5126 |220A |elz@bcm.edu |

|Joseph Bryan |713-798-4007 |112C |jbryan@bcm.edu |

|Olivier Lichtarge |713-798-5646 |T921 |lichtarg@bcm.edu |

|Structure of Macromolecules |

|FullName |Phone |Room |Email |

|*Michael Schmid |713-798-5734 |N420 |mschmid@bcm.edu |

|*Nancy Weigel |713-798-6234 |M515 |nweigel@bcm.edu |

|E. Zechiedrich |713-798-5126 |220A |elz@bcm.edu |

|Francis Tsai |713-798-8668 |315BA |ftsai@bcm.edu |

|Hiram Gilbert |713-798-5880 |371A1 |hgilbert@bcm.edu |

|Jun Qin |713-798-1507 |T303 |jqin@bcm.edu |

|Olivier Lichtarge |713-798-5646 |T921 |lichtarg@bcm.edu |

|Richard Sifers |713-798-3169 |T228 |rsifers@bcm.edu |

|Steven Ludtke |713-798-9020 |N420 |sludtke@bcm.edu |

|Theodore Wensel |713-798-6994 |N430 |twensel@bcm.edu |

Lecture Calendar

|Term 1 |

|Date |10:00-12:00 |1:15-2:15 |2:30-3:30 |1:00-4:00 |5:15-6:30 |

|Mon Jul 30 | |MM1 |OC1 | | |

|Tue Jul 31 | | |1SP1 | | |

|Wed Aug 01 | |MM2 |OC2 | |MMTA1 |

|Thu Aug 02 |ML1 | | | |OCTA1 |

|Fri Aug 03 | |MM3 |OC3 | | |

|Mon Aug 06 | |MM4 |OC4 | | |

|Tue Aug 07 |ML2 |GA1 |1SP2 | | |

|Wed Aug 08 | |MM5 |OC5 | |OCTA2 |

|Thu Aug 09 |ML3 |GA2 | | | |

|Fri Aug 10 | |MM6 |OC6 | | |

|Mon Aug 13 | |MM7 |Traber 2:30-5:30 | | |

|Tue Aug 14 |ML4 |GA3 |1SP3 | |MMTA2 |

|Wed Aug 15 | |OC - Midterm Review 1:15-3:00 | |

|Thu Aug 16 |ML5 |OC - Midterm Exam 1:15-3:45 | |

|Fri Aug 17 | |MM - Midterm Review 1:15-3:00 | |

|Mon Aug 20 | |MM - Midterm Exam 1:15-3:45 | |

|Tue Aug 21 |ML6 |GA4 |1SP4 | |GATA1 |

|Wed Aug 22 | |MM8 |OC7 | | |

|Thu Aug 23 |ML7 |GA5 | | |OCTA3 |

|Fri Aug 24 | |MM9 |OC8 | | |

|Mon Aug 27 | |MM10 |OC9 | | |

|Tue Aug 28 |ML8 |GA6 |1SP5 | |MMTA3 |

|Wed Aug 29 | |MM11 |OC10 | |OCTA4 |

|Thu Aug 30 |ML9 |GA7 | | | |

|Fri Aug 31 | |MM12 |OC11 | | |

|Mon Sep 03 | |Labor Day | | | |

|Tue Sep 04 |ML10 |GA8 |1SP6 | |GATA2 |

|Wed Sep 05 | |MM13 |OC12 | |OCTA5 |

|Thu Sep 06 |ML11 |GA9 | | | |

|Fri Sep 07 | |MM14 |OC13 | | |

|Mon Sep 10 | |MM15 |Traber 2:30-5:30 | | |

|Tue Sep 11 |ML12 |GA10 |1SP7 | | |

|Wed Sep 12 | |MM16 |OC14 | |MMTA4 |

|Thu Sep 13 |ML13 | | | | |

|Fri Sep 14 | |MM17 |OC15 | | |

|Mon Sep 17 | | | | | |

|Tue Sep 18 |ML14 |GA11 |1SP8 | | |

|Wed Sep 19 | |OC ER | | | |

|Thu Sep 20 |ML15 |OC - Final Exam 1:15-3:45 |MMTA5 |

|Fri Sep 21 | |MM - Evaluation/Review 1:15-3:00 | |

|Mon Sep 24 | |MM - Final Exam 1:15-3:45 | |

|Tue Sep 25 | | | | |GATA3 |

|Wed Sep 26 | |GA - Evaluation/Review 1:15-3:00 | |

|Thu Sep 27 | |GA - Final Exam 1:15-3:45 | |

|Fri Sep 28 | | | | | |

|Term 2 |

|Date |10:00-12:00 |1:15-2:15 |2:30-3:30 |1:00-4:00 |5:15-6:30 |

|Mon Oct 08 | |CD1 | | | |

|Tue Oct 09 | |GB1 |2SP1 | | |

|Wed Oct 10 | |CD2 | | | |

|Thu Oct 11 | |GB2 | | | |

|Fri Oct 12 | |CD3 | | | |

|Mon Oct 15 | |CD4 |Traber 2:30-5:30 | | |

|Tue Oct 16 | |GB3 |2SP2 | |CDTA1 |

|Wed Oct 17 | |CD5 | | | |

|Thu Oct 18 | |GB4 | | | |

|Fri Oct 19 | |CD6 | | | |

|Mon Oct 22 | |GB5 |DE1 | |CDTA2 |

|Tue Oct 23 | |GB6 |2SP3 | |GBTA1 |

|Wed Oct 24 | |CD - Midterm Review 1:15-3:00 | |

|Thu Oct 25 | |CD - Midterm Exam 1:15-3:45 | |

|Fri Oct 26 | |CD7 |DE2 | | |

|Mon Oct 29 | |CD8 |DE3 | |GBTA2 |

|Tue Oct 30 | |GB7 |2SP4 | | |

|Wed Oct 31 | |CD9 |DE4 | | |

|Thu Nov 01 | |GB8 | | |DETA1 |

|Fri Nov 02 | |CD10 |DE5 | | |

|Mon Nov 05 | |CD11 |DE6 | | |

|Tue Nov 06 | |GB9 |2SP5 | |GBTA3 |

|Wed Nov 07 | |CD12 |DE7 | |CDTA3 |

|Thu Nov 08 | |GB10 |2SP6 | | |

|Fri Nov 09 | |GB11 |DE8 | |DETA2 |

|Mon Nov 12 | |CD - |Traber 2:30-5:30 | | |

| | |Evaluation/Review | | | |

| | |1:15-3:00 | | | |

|Tue Nov 13 | |CD - Final Exam 1:15-3:45 |GBTA4 |

|Wed Nov 14 | |CA1 |DE9 | | |

|Thu Nov 15 | | |GrdSymp | | |

|Fri Nov 16 | |CA2 |DE10 | | |

|Mon Nov 19 | |CA3 |DE11 | | |

|Tue Nov 20 | |GB12 |2SP7 | |DETA3 |

|Wed Nov 21 | |CA4 |DE12 | | |

|Thu Nov 22 | |Thanksgiving | | | |

|Fri Nov 23 | |Thanksgiving | | | |

|Mon Nov 26 | |CA5 | | |DETA4 |

|Tue Nov 27 | |GB13 |2SP8 | |GBTA5 |

|Wed Nov 28 | |DE - Evaluation/Review 1:15-3:00 | |

|Thu Nov 29 | |DE - Final Exam 1:15-3:45 | |

|Fri Nov 30 | | | | | |

|Mon Dec 03 | | | | | |

|Tue Dec 04 | |CA - Evaluation/Review 1:15-3:00 | |

|Wed Dec 05 | |CA - Final Exam 1:15-3:45 | |

|Thu Dec 06 | |GB - Evaluation/Review 1:15-3:00 | |

|Fri Dec 07 | |GB - Final Exam 1:15-3:45 | |

|Term 3 |

|Date |10:00-12:00 |1:15-2:15 |2:30-3:30 |1:00-4:00 |5:15-6:30 |

|Mon Dec 31 | |NewYears | | | |

|Tue Jan 01 | |NE1 |MI1 | | |

|Wed Jan 02 | |GR1 | | | |

|Thu Jan 03 | |NE2 |MI2 | |NETA1 |

|Fri Jan 04 | |GR2 |MI3 | | |

|Mon Jan 07 | |GR3 |Traber 2:30-5:30 | | |

|Tue Jan 08 | |NE3 | | |GRTA1 |

|Wed Jan 09 | |GR4 |MI4 | | |

|Thu Jan 10 | |NE4 |MI5 | |MITA1 |

|Fri Jan 11 | |GR5 |MI6 | | |

|Mon Jan 14 | |MLKDay | | | |

|Tue Jan 15 | |NE5 | | |NETA2 |

|Wed Jan 16 | |GR6 |MI7 | | |

|Thu Jan 17 | |GR7 |MI8 | |NETA3 |

|Fri Jan 18 | |GR8 |MI9 | | |

|Mon Jan 21 | |NE - Evaluation/Review 1:15-3:00 | |

|Tue Jan 22 | |NE - Final Exam 1:15-3:45 | |

|Wed Jan 23 | |GR9 |MI10 | | |

|Thu Jan 24 | |GR10 | | |GRTA2 |

|Fri Jan 25 | |GR11 |MI11 | | |

|Mon Jan 28 | | | | | |

|Tue Jan 29 | |GR - Midterm Review 1:15-3:00 |MITA2 |

|Wed Jan 30 | |GR - Midterm Exam 1:15-3:45 | |

|Thu Jan 31 | |GR12 |MI12 | | |

|Fri Feb 01 | |GR13 | | | |

|Mon Feb 04 | |GR14 |MI13 | | |

|Tue Feb 05 | | | | |MITA3 |

|Wed Feb 06 | |GR15 |MI14 | | |

|Thu Feb 07 | |GR16 |IM4 | |GRTA3 |

|Fri Feb 08 | |GR17 |MI15 | |IMTA1 |

|Mon Feb 11 | |GR18 |Traber 2:30-5:30 | | |

|Tue Feb 12 | | |IM5 | |MITA4 |

|Wed Feb 13 | |MI - Evaluation/Review 1:15-3:00 | |

|Thu Feb 14 | |MI - Final Exam 1:15-3:45 | |

|Fri Feb 15 | |GR19 | | | |

|Mon Feb 18 | |PresDay | | | |

|Tue Feb 19 | |IM - Evaluation/Review 1:15-3:00 | |

|Wed Feb 20 | |IM - Final Exam 1:15-3:45 | |

|Thu Feb 21 | |GR20 | | |IMTA2 |

|Fri Feb 22 | |DB Retreat | | | |

|Mon Feb 25 | |GR21 | | | |

|Tue Feb 26 | | | | |GRTA4 |

|Wed Feb 27 | |GR - Evaluation/Review 1:15-3:00 | |

|Thu Feb 28 | |GR - Final Exam 1:15-3:45 | |

|Fri Feb 29 | | | | | |

|Term 4 |

|Date |10:00-12:00 |1:15-2:15 |2:30-3:30 |1:00-4:00 |5:15-6:30 |

|Mon Mar 10 | |SM1 |Traber 2:30-5:30 | | |

|Tue Mar 11 | | | |RD1 | |

|Wed Mar 12 | |SM2 | | | |

|Thu Mar 13 | | | | | |

|Fri Mar 14 | |SM3 | | | |

|Mon Mar 17 | |SM4 | | | |

|Tue Mar 18 | | | |RD2 |SMTA1 |

|Wed Mar 19 | |SM5 | | | |

|Thu Mar 20 | |CareerDay | | | |

|Fri Mar 21 | |SM6 | | | |

|Mon Mar 24 | |SM7 | | | |

|Tue Mar 25 | | | |RD3 | |

|Wed Mar 26 | |SM8 | | | |

|Thu Mar 27 | | | | | |

|Fri Mar 28 | |SM9 | | | |

|Mon Mar 31 | |SM10 | | | |

|Tue Apr 01 | | | |RD4 |SMTA2 |

|Wed Apr 02 | |SM11 | | | |

|Thu Apr 03 | | | | | |

|Fri Apr 04 | |GoodFri | | | |

|Mon Apr 07 | |SM12 |Traber 2:30-5:30 | | |

|Tue Apr 08 | | | |RD5 |SMTA3 |

|Wed Apr 09 | |SM13 | | | |

|Thu Apr 10 | | | | | |

|Fri Apr 11 | |SM14 | | | |

|Mon Apr 14 | |SM15 | | | |

|Tue Apr 15 | | | |RD6 | |

|Wed Apr 16 | |SM16 | | | |

|Thu Apr 17 | | | | | |

|Fri Apr 18 | |SM17 | | | |

|Mon Apr 21 | |SM18 | | | |

|Tue Apr 22 | | | |RD7 | |

|Wed Apr 23 | |SM19 | | | |

|Thu Apr 24 | | | | | |

|Fri Apr 25 | |SM20 | | | |

|Mon Apr 28 | | | | | |

|Tue Apr 29 | | | |RD8 | |

|Wed Apr 30 | | | | |SMTA4 |

|Thu May 01 | |SM - Evaluation/Review 1:15-3:00 | |

|Fri May 02 | |SM - Final Exam 1:15-3:45 | |

|Term 5 |

|Date |10:00-12:00 |1:15-2:15 |2:30-3:30 |1:00-4:00 |5:15-6:30 |

|Mon May 12 | | |Traber 2:30-5:30 | | |

|Tue May 13 | | | | | |

|Wed May 14 | | | | | |

|Thu May 15 | | | | | |

|Fri May 16 | | | | | |

|Mon May 19 | | | | | |

|Tue May 20 | | | | | |

|Wed May 21 | | | | | |

|Thu May 22 | | | | | |

|Fri May 23 | | | | | |

|Mon May 26 | |MemDay | | | |

|Tue May 27 | | | | | |

|Wed May 28 | | | | | |

|Thu May 29 | | | | | |

|Fri May 30 | | | | | |

|Mon Jun 02 | | | | | |

|Tue Jun 03 | | | | | |

|Wed Jun 04 | | | | | |

|Thu Jun 05 | | | | | |

|Fri Jun 06 | | | | | |

|Mon Jun 09 | | |Traber 2:30-5:30 | | |

|Tue Jun 10 | | | | | |

|Wed Jun 11 | | | | | |

|Thu Jun 12 | | | | | |

|Fri Jun 13 | | | | | |

|Mon Jun 16 | | | | | |

|Tue Jun 17 | | | | | |

|Wed Jun 18 | | | | | |

|Thu Jun 19 | | | | | |

|Fri Jun 20 | | | | | |

|Mon Jun 23 | | | | | |

|Tue Jun 24 | | | | | |

|Wed Jun 25 | | | | | |

|Thu Jun 26 | | | | | |

|Fri Jun 27 | | | | | |

|Mon Jun 30 | | | | | |

|Tue Jul 01 | | | | | |

|Wed Jul 02 | |IndDay | | | |

|Thu Jul 03 | | | | | |

|Fri Jul 04 | | | | | |

|Mon Jul 07 | | |Traber 2:30-5:30 | | |

|Tue Jul 08 | | | | | |

|Wed Jul 09 | | | | | |

|Thu Jul 10 | | | | | |

|Fri Jul 11 | | | | | |

|Mon Jul 14 | | | | | |

|Tue Jul 15 | | | | | |

|Wed Jul 16 | | | | | |

|Thu Jul 17 | | | | | |

|Fri Jul 18 | | | | | |

Lecture Schedule

|Term 1 | |

|Genetics A |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Aug 07 |1:15 |Principles, Model Systems and Nomenclature - Mendel's laws. The chromosomal |Kelley |

| | | |basis of inheritance, definitions of genes, alleles, mutants. Sex linkage. Life| |

| | | |cycles and nomenclature of key model systems. Haploid vs. diploid genetics, | |

| | | |tetrad analysis in yeast. | |

|2 |Thu Aug 09 |1:15 |Genetic Linkage - Building a genetic map based on recombination frequency. |Kelley |

| | | |Ordering genes by three factor crosses. Ordering genes by deletion mapping. | |

|3 |Tue Aug 14 |1:15 |Complementation - Complementation tests, allelism. Verification by linkage |Kelley |

| | | |mapping. Genetic interactions of unlinked loci. Allelic series, penetrance, and| |

| | | |expressivity. | |

|4 |Tue Aug 21 |1:15 |Bacterial Genetics I - Genetic transmission: haploid and circular genomes, |Rosenberg |

| | | |P1-transduction, F-factors, HFRs, conjugation. | |

|1 |Tue Aug 21 |5:15 |GA-TA1 - General Genetic Principles | |

|5 |Thu Aug 23 |1:15 |Bacterial Genetics II - Phage lambda: lysis versus lysogeny, Campbell model of |Rosenberg |

| | | |integration, site specific recombination, establishing repression, host factors, | |

| | | |specialized transduction, induction. | |

|6 |Tue Aug 28 |1:15 |Bacterial Genetics III - Phage lambda in recombination studies. |Rosenberg |

|7 |Thu Aug 30 |1:15 |Bacterial Genetics IV - SOS response. |Rosenberg |

|8 |Tue Sep 04 |1:15 |Genetic Screens Molecular Basis of the Phenotype - Conception and design of |Zhou |

| | | |genetic screens. Verification and evaluation of results. Modern genetic | |

| | | |philosophy and practice. Classes of mutations. | |

|2 |Tue Sep 04 |5:15 |GA-TA2 - Bacterial Genetics | |

|9 |Thu Sep 06 |1:15 |Classes of mutations - Genetics as a study of how proteins interact, fold, and |Zhou |

| | | |function. Nonsense suppression of null alleles. Partial loss of function | |

| | | |alleles. Conditional alleles | |

|10 |Tue Sep 11 |1:15 |Delineating a Pathway - How to identify genes that are functionally related to |Zhou |

| | | |your favorite gene. Suppression analysis. Synthetic lethal mutants | |

|11 |Tue Sep 18 |1:15 |Enhancer screens and Pathway Analysis - Enhancer screens. Epistasis grouping and |Zhou |

| | | |epistasis analysis. Establishing the order of gene functions. | |

|3 |Tue Sep 25 |5:15 |GA-TA3 - Phenotype, pathway analysis and genetics screens | |

| |Wed Sep 26 |1:15 |Faculty Review - | |

| |Thu Sep 27 |1:15 |Final Exam - 1:15-3:45 - | |

|Method & Logic in Molecular Biology |

|No |Date |Time |Lecture |Lecturer |

|1 |Thu Aug 02 |10:00 |Method and Logic Meeting - |Mardon |

|2 |Tue Aug 07 |10:00 |Method and Logic Meeting - |Chen |

|3 |Thu Aug 09 |10:00 |Method and Logic Meeting - |Shaulsky |

|5 |Thu Aug 16 |10:00 |Method and Logic Meeting - |Kelley |

|6 |Tue Aug 21 |10:00 |Method and Logic Meeting - |Moore |

|7 |Thu Aug 23 |10:00 |Method and Logic Meeting - |Zechiedrich |

|8 |Tue Aug 28 |10:00 |Method and Logic Meeting - |Kuspa |

|9 |Thu Aug 30 |10:00 |Method and Logic Meeting - |He |

|10 |Tue Sep 04 |10:00 |Method and Logic Meeting - |Palzkill |

|11 |Thu Sep 06 |10:00 |Method and Logic Meeting - |Pletcher |

|12 |Tue Sep 11 |10:00 |Method and Logic Meeting - |Wilson |

|13 |Thu Sep 13 |10:00 |Method and Logic Meeting - |Staff |

|14 |Tue Sep 18 |10:00 |Method and Logic Meeting - |Staff |

|15 |Thu Sep 20 |10:00 |Method and Logic Meeting - |Staff |

|Molecular Methods |

|No |Date |Time |Lecture |Lecturer |

|1 |Mon Jul 30 |1:15 |Introduction - Objectives of course, expectations, problem sets |Gilbert |

|2 |Wed Aug 01 |1:15 |Properties of DNA - DNA structure, melting, annealing, hybridization, blots |Highlander |

| | | |(Northern, Southern), probes and labeling | |

|1 |Wed Aug 01 |5:15 |MM-TA1 - Intro - cover 5'-3' ends, intron/exon boundaries, 5' and 3' overhangs | |

| | | |from restriction enzymes, plasmid, screen vs selection, oligonucleotides, | |

| | | |labeling (why it's done rather than how), vector/host, library, clone/cloning | |

| | | |(various definitions), exonucleas | |

|3 |Fri Aug 03 |1:15 |DNA Analysis - Gels for DNA Analysis, restriction mapping, cloning, ligation |Highlander |

|4 |Mon Aug 06 |1:15 |DNA manipulation - PCR, quantitative PCR, rtPCR, DNA sequencing (small scale), |Highlander |

| | | |site directed and random mutagenesis | |

|5 |Wed Aug 08 |1:15 |Vectors&Hosts - Plasmids (properties, purification); preparation of insert DNA |Highlander |

| | | |(restriction fragments, PCR, cDNA); transformation and selection in E. coli and | |

| | | |yeast; M13 (life cycle; derived vectors). Phagemids, vector switching; lambda | |

| | | |(biology, vectors, recombinant construction, in vitro packaging); cosmids and | |

| | | |fosmids; BACs and PACs (bkgrd; vectors); YACs (vectors, construction); EBV-based | |

| | | |human articial chromosome vectors, recombination cloning | |

|6 |Fri Aug 10 |1:15 |Protein Expression - Expression in E. coli; transcription and translation |Gilbert |

| | | |signals, production of native proteins,fusion proteins, baculovirus expression | |

| | | |systems, in vitro translation | |

|7 |Mon Aug 13 |1:15 |Protein Purification - Opening the cell, inhibition of proteolysis, precipitants,|Gilbert |

| | | |chromatography (gel filtration, ion exchange, hydrophobic interaction, affinity, | |

| | | |HPLC, reversed phase), ultracentrifugation, isoelectric focusing and | |

| | | |electrophoresissucrose density gradient,deterg | |

|2 |Tue Aug 14 |5:15 |MM-TA2 - go over general scheme by which you would detect a gene | |

| | | |(hybridization/blots including end labeling), map its restriction sites, PCR it | |

| | | |from cDNA, and insert it into a vector), define BACs, PACs, YAC and describe | |

| | | |preparation of cDNA library including conc | |

| |Fri Aug 17 |1:15 |Midterm Review - | |

| |Mon Aug 20 |1:15 |Midterm Exam - | |

|8 |Wed Aug 22 |1:15 |Isolation/Refolding Strategies - Affinity tags, inclusion bodies, refolding, |Gilbert |

| | | |disulfide formation | |

|9 |Fri Aug 24 |1:15 |Libraries and screening - Construction and handling of libraries with different |Metzker |

| | | |vectors; cDNA libraries (statistics, subtracted libraries, normalized libraries, | |

| | | |reference libraries such as IMAGE); immunological and hybridization screening; | |

| | | |genomic libraries (sizes, PCR- and hybridization methods for analyzing) | |

|10 |Mon Aug 27 |1:15 |Genomics I - mapping strategies (FISH mapping, RH mapping), genome sequencing |Metzker |

| | | |strategies (BAC-by-BAC, library construction, STS or FP, contig assembly, minimum| |

| | | |tiling paths, whole genome shotgun), HTP instrumentation (96 capillary machines),| |

| | | |data analysis (bsecalling, | |

|3 |Tue Aug 28 |5:15 |MM-TA3 - Go over purpose of large-scale physical mapping, contig assembly, FISH | |

| | | |in locating the position/sequence of a gene of interest, approaches to large | |

| | | |scale sequencing, genebank, BLASTA and internet tools for searching sequence. | |

|11 |Wed Aug 29 |1:15 |Genomics II - annotation of sequences, EST's, specific organism databases |Metzker |

|12 |Fri Aug 31 |1:15 |Proteomics II - mass spectometery (MALDI-TOF, electrospray) protein |Qin |

| | | |identification | |

|13 |Wed Sep 05 |1:15 |Proteomics III - identification of protein species in large complexes |Qin |

|14 |Fri Sep 07 |1:15 |Proteomics I - protein arrays, interaction networks |Feng |

|15 |Mon Sep 10 |1:15 |Molecular Biology Database Use - pattern searches, domains, paralogs and |Feng |

| | | |orthologs, sequence-function relationships | |

|16 |Wed Sep 12 |1:15 |Interaction cloning - systems, false positives and negatives happen, limitations,|Feng |

| | | |combinatorial screens, phage display, two-hybrid screen, lambda gt11 screens | |

|4 |Wed Sep 12 |5:15 |MM-TA4 - review BLAST/FASTA searches (purpose/output), mutagenesis (deletion, | |

| | | |insertion, random, directed), protein expression in coli (fusion and non-fusion | |

| | | |proteins), induction of expression, baculovirus | |

|17 |Fri Sep 14 |1:15 |Protein Localization/Identification - Purification of antigen, polyclonal |Feng |

| | | |antibodies, monoclonal antibodies, anti-peptide antibodies, Western blots, GFP | |

| | | |fusions, FRAP | |

|5 |Thu Sep 20 |5:15 |MM-TA5 - review protein purification, chromatography, protein quantitation, | |

| | | |refolding of inclusion bodies, phage display /two-hybrid screens, antibody | |

| | | |production and characterization, proteomics. | |

| |Fri Sep 21 |1:15 |Faculty Review - | |

| |Mon Sep 24 |1:15 |Final Exam - 1:15-3:45 - | |

|Organization of the Cell |

|No |Date |Time |Lecture |Lecturer |

|1 |Mon Jul 30 |2:30 |Overview and the Secretory Pathway - Course organization, outline etc. General |Sifers |

| | | |protein expression and maturation. The secretory pathway and nature of various | |

| | | |organelles. | |

|2 |Wed Aug 01 |2:30 |Nuclear Transport - Overall structure of the nucleus and nuclear pore complexes. |Sifers |

| | | |Transport of proteins and RNAs into and out of the nucleus. Nuclear transport | |

| | | |and the control of gene expression | |

|1 |Thu Aug 02 |5:15 |OC-TA1 - Review general cell structures, their function and generation. Concepts | |

| | | |of vesicular transport and protein import and export for the organelles | |

|3 |Fri Aug 03 |2:30 |Mitochondria, Choloroplasts, Peroxisomes - Structure and biogenesis of |Sifers |

| | | |mitochondria, chlorplasts, and peroxisomes. Protein import into these organelles| |

|4 |Mon Aug 06 |2:30 |The Endoplasmic Reticulum - quality control checkpoint and mother of the |Sifers |

| | | |endomembrane system | |

|5 |Wed Aug 08 |2:30 |The Golgi Complex - regulated vesicular trafficking in the endomembrane system |Sifers |

|2 |Wed Aug 08 |5:15 |OC-TA2 - Review of protein trafficking | |

|6 |Fri Aug 10 |2:30 |Vesicular Transport in Reverse - the plasma membrane-endoxome-lysosome connection|Sifers |

| |Wed Aug 15 |1:15 |Midterm Review - | |

| |Thu Aug 16 |1:15 |Midterm Exam - | |

|7 |Wed Aug 22 |2:30 |Energy Transduction and Bioenergetics - Membrane permeability, mechanisms of |Pedersen |

| | | |transport, bio-energetics, mitochondrial and chloroplast function, chemiosmosis | |

|3 |Thu Aug 23 |5:15 |OC-TA3 - Review of Lipid synthesis and transport. Energy transduction and | |

| | | |bioenergetics, membrane transport and ion channel | |

|8 |Fri Aug 24 |2:30 |Transport Mechanisms - Active and passive transport, synporters, antiporters, |Pedersen |

| | | |ATPases | |

|9 |Mon Aug 27 |2:30 |Ion channels - Nernst potential, electrical properties of excitable membranes, |Pedersen |

| | | |action potential | |

|10 |Wed Aug 29 |2:30 |G Proteins - Signalling mechanisms, ligand recognition and conformation changes |Wensel |

| | | |by receptors, GDP release kinetics, G protein structure and function, effectors, | |

| | | |signal processing, inactivation and desensitization, receptor kinases and | |

| | | |arrestins, putative roles for PKC | |

|4 |Wed Aug 29 |5:15 |OC-TA4 - Review of G-proteins, growth factors, Tyr-kinase signalling and ion | |

| | | |channel | |

|11 |Fri Aug 31 |2:30 |Growth Factors/Tyrosine Kinase Signaling - Ligands and signals, structure of |Wensel |

| | | |families of membrane receptors with intrinsic tyrosine kinase activity and | |

| | | |introduction to cascades activated by binding to phosphotyrosines, SH2 and SH3 | |

| | | |domains, tyrosine kinases associated with membrane bound receptors | |

|12 |Wed Sep 05 |2:30 |Calcium and phospholipase signaling - Calcium and its protein complexes |Wensel |

| | | |Phosphoinositides, phospholipase C, protein kinase C, IP3 receptors, proteins | |

| | | |regulated by Ca, calmodulin, Ca-regulated channels, annexins, overview of methods| |

| | | |for monitoring intracellular Ca and phosphoplipase activity | |

|5 |Wed Sep 05 |5:15 |OC-TA5 - Review of calcium and phospholipase signaling, cytoskeleton | |

|13 |Fri Sep 07 |2:30 |Cytoskeleton I - Actin, microtubules, intermediate filaments, junctional |He |

| | | |complexes and cellular architecture, cell motility. | |

|14 |Wed Sep 12 |2:30 |Cytoskeleton II - Actin, microtubules, intermediate filaments, junctional |He |

| | | |complexes and cellular architecture, cell motility. | |

|15 |Fri Sep 14 |2:30 |Apoptosis - Apoptosis versus necrosis, mechanisms of programmed cell death, |Zhou |

| | | |regulators of apoptosis. | |

| |Thu Sep 20 |1:15 |Final Exam - 1:15-3:45 - | |

|Science as a Profession Term 1 |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Jul 31 |2:30 |Setting goals for your scientific development - Career paths for the professional|Basinger |

| | | |scientist, career decisions (how and when to make them), what to do in your first| |

| | | |year to ensure your success, developing curiosity, coursework(what to expect in | |

| | | |gradschool), lifelong learning, the scientific literature, finding a | |

| | | |lab/rotation, selecting a mentor, where to get help and information, thinking now| |

| | | |about the next step | |

|2 |Tue Aug 07 |2:30 |Organization of the literature - Organization and purpose of a paper, how to read|Slaughter |

| | | |the current literature, what is contained in the various sections of a paper, | |

| | | |computer searching vs browsing, parts of a scientific paper and what you can | |

| | | |learn from each | |

|3 |Tue Aug 14 |2:30 |The Scientific Method - thinking like a scientist - The scientific method |Gilbert |

| | | |(hypothesis vs results-driven science), elements of experimental design | |

| | | |(developing models/hypotheses), designing experimental tests of your hypotheses, | |

| | | |fishing expeditions, controls , replication of experiments and data selection - | |

| | | |ethical considerations, Interpreting your results | |

|4 |Tue Aug 21 |2:30 |The Mentor/Student relationship - What you should expect from your mentor, |Slaughter |

| | | |getting along with your mentor, your advisory committee, accumulating references | |

| | | |for your next step | |

|5 |Tue Aug 28 |2:30 |Coping with challenges - Social/Emotional adjustment to grad school, coping with |Basinger |

| | | |stress, dealing with your peers, dealing with faculty, where to go for help | |

|6 |Tue Sep 04 |2:30 |The funding structure of science - Government organizations, private funding |Brinkley |

| | | |sources, applying for fellowships, structure of a grant, grant review system | |

|7 |Tue Sep 11 |2:30 |Scientific Societies/Public Policy - advantages of membership, participation in |Brinkley |

| | | |committee activity, science advocacy ( what you can do), how Congress manages its| |

| | | |scientific effort | |

|8 |Tue Sep 18 |2:30 |Grievance procedures - When you have problems with: courses/exams, program |Basinger |

| | | |administration, graduate school administration, other students or lab personnel, | |

| | | |mentor, thesis committee, health/safety concerns, when your research isn't | |

| | | |progressing | |

|Term 2 | |

|Cancer |

|No |Date |Time |Lecture |Lecturer |

|1 |Wed Nov 14 |1:15 |Introduction to Cancer Vocabulary - epidemiology and carcinogenesis - lung cancer|Plon |

| |Thu Nov 15 |2:30 |Graduate Student Symposium - No Class - | |

|2 |Fri Nov 16 |1:15 |Cancer as a Multi-step process - tumor suppressor genes - colon cancer |Demayo |

|3 |Mon Nov 19 |1:15 |Activation of Oncogenes - leukemia/lymphoma |Plon |

|4 |Wed Nov 21 |1:15 |Animal Models in Cancer Research - prostate cancer |Demayo |

| |Thu Nov 22 |1:15 |Thanksgiving Holiday - No Class - | |

| |Fri Nov 23 |1:15 |Thanksgiving Holiday - No Class - | |

|5 |Mon Nov 26 |1:15 |Use of familial cancers to define molecular events - breast cancer, course |Plon |

| | | |summary | |

| |Tue Dec 04 |1:15 |Faculty Review - | |

| |Wed Dec 05 |1:15 |Final Exam - 1:15-3:45 - | |

|Cell Division |

|No |Date |Time |Lecture |Lecturer |

|1 |Mon Oct 08 |1:15 |Course Introduction/Cell Cycle Overview - Discovery of cell cycle |Sazer |

| | | |regulation--Cell cycle stages, mitosis and meiosis, discovery of CDK/cyclin/MPF | |

|2 |Wed Oct 10 |1:15 |G1/S - G1 phase and the G1 to S phase transition, CDK regulation by |Zhang |

| | | |phosphorylation and protein degradation, CDK regulation of initiation of DNA | |

| | | |replication | |

|3 |Fri Oct 12 |1:15 |S phase - Initiation and control of DNA replication at origins of replications |Wilson |

|4 |Mon Oct 15 |1:15 |DNA Damage - DNA damage and repair |Wilson |

|1 |Tue Oct 16 |5:15 |CD-TA1 - Review of DNA replication |Wilson |

|5 |Wed Oct 17 |1:15 |DNA Repair - Repair of double strand breaks by homologous and non-homologous |Wilson |

| | | |recombination | |

|6 |Fri Oct 19 |1:15 |G2/M - G2 phase and the G2 to M phase transition |Zhang |

|2 |Mon Oct 22 |5:15 |CD-TA2 - Review of recombination |Wilson |

| |Wed Oct 24 |1:15 |Faculty Review Midterm - Lectures 1-6 | |

| |Thu Oct 25 |1:15 |Exam I - Lectures 1-6 | |

|7 |Fri Oct 26 |1:15 |Cell Cycle Checkpoints - Introduction to cell cycle checkpoints, the DNA damage |Zhang |

| | | |checkpoint | |

|8 |Mon Oct 29 |1:15 |M phase chromosomes - chromosomes (centromeres, telomeres), chromosome pairing |He |

| | | |and cohesion, chromosome condensation | |

|9 |Wed Oct 31 |1:15 |M phase spindle - mechanics of spindle formation and function, |He |

| | | |kinetochore/spindle attachment | |

|10 |Fri Nov 02 |1:15 |Spindle Assembly Checkpoint - the spindle assembly checkpoint |Sazer |

|11 |Mon Nov 05 |1:15 |Exit from mitosis - Exit from mitosis, coordination of exit from mitosis with |Sazer |

| | | |cytokinesis | |

|12 |Wed Nov 07 |1:15 |Growth regulation - The cell cycle in growth regulation, development and cancer |Zhang |

|3 |Wed Nov 07 |5:15 |CD-TA3 - Review of cell cycle regulation, mitosis, mitotic entry and exit, |Zhang, Sazer, He |

| | | |cytokinesis | |

| |Mon Nov 12 |1:15 |Faculty Review - | |

| |Tue Nov 13 |1:15 |Exam II - Lectures 7-12 | |

| |Thu Nov 15 |2:30 |Graduate Student Symposium - No Class - | |

| |Thu Nov 22 |1:15 |Thanksgiving Holiday - No Class - | |

| |Fri Nov 23 |1:15 |Thanksgiving Holiday - No Class - | |

|Development |

|No |Date |Time |Lecture |Lecturer |

|1 |Mon Oct 22 |2:30 |Introduction - Overview and objectives of the course. Introduction to major |Schumacher |

| | | |animal models used in developmental studies and relative advantages of each. | |

| | | |Brief description of Drosophila oogenesis and embryogenesis | |

|2 |Fri Oct 26 |2:30 |Embryonic patterning in Drosophila I - Introduction to the genetic hierarchy that|Schumacher |

| | | |subdivides the embryo into progressively smaller units. The concept of gradients | |

| | | |and asymmetric distribution of morphogenetic determinants in organizing the | |

| | | |Drosophila embryo. Maternal-effect genes and the establishment of the | |

| | | |anteroposterior axes. | |

|3 |Mon Oct 29 |2:30 |Embryonic patterning in Drosophila II - Maternal-effect genes and the |Schumacher |

| | | |establishment of the dorsoventral axes. | |

|4 |Wed Oct 31 |2:30 |Embryonic patterning in Drosophila III - The role of the wingless and hedgehog |Schumacher |

| | | |signaling pathways in the formation of embryonic segments and compartments. The | |

| | | |concept of segments as developmental compartments. | |

|1 |Thu Nov 01 |5:15 |TA-DE1 - | |

|5 |Fri Nov 02 |2:30 |Embryonic patterning in Drosophilia IV - Homeotic selector (HOM) genes and their |Schumacher |

| | | |role in defining positional identity in each of the segments of the fly embryo | |

| | | |along the A-P axis | |

|6 |Mon Nov 05 |2:30 |Early embryonic development in vertebrates - Mammalian germline development. |Ramirez-Solis |

| | | |Fertilization and pre-implantation mammalian development | |

|7 |Wed Nov 07 |2:30 |Formation of the vertebrate body plan I - Gastrulation. Somitogenesis and somite |Ramirez-Solis |

| | | |differentiation | |

|8 |Fri Nov 09 |2:30 |Formation of the vertebrate body plan II - Development of the cardiovascular and |Ramirez-Solis |

| | | |urogenital system | |

|2 |Fri Nov 09 |5:15 |TA-DE2 - | |

|9 |Wed Nov 14 |2:30 |Establishment of left-right asymmetry in vertebrates - Regulatory and signaling |Overbeek |

| | | |pathways involved in establishing left-right asymmetry in the vertebrate embryo. | |

| | | |The relationship between heart looping and asymmetric positioning of other | |

| | | |organs. | |

| |Thu Nov 15 |2:30 |Graduate Student Symposium - No Class - | |

|10 |Fri Nov 16 |2:30 |Introduction to neural development in vertebrates - Developmental anatomy of the |Mahon |

| | | |nervous system. Molecular aspects of neural induction, formation of the neural | |

| | | |plate and neurogenesis | |

|11 |Mon Nov 19 |2:30 |Regionalization of the vertebrate nervous system - Molecular mechanisms of |Mahon |

| | | |dorsal-ventral and anterior-posterior patterning. Combinatorial and antagonistic | |

| | | |signaling involved in dorsoventral patterning of the neural tube. The role of Hox| |

| | | |genes in regional specification along the anterior-posterior axis. | |

|3 |Tue Nov 20 |5:15 |TA-DE3 - | |

|12 |Wed Nov 21 |2:30 |Development of the vertebrate brain - Integration of conserved genetic networks |Mahon |

| | | |and signaling centers in the formation and specification of the forebrain, | |

| | | |midbrain and hindbrain. | |

| |Thu Nov 22 |1:15 |Thanksgiving Holiday - No Class - | |

| |Fri Nov 23 |1:15 |Thanksgiving Holiday - No Class - | |

| |Wed Nov 28 |1:15 |Faculty Review - | |

| |Thu Nov 29 |1:15 |Final Exam - 1:15-3:45 - | |

|Genetics B |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Oct 09 |1:15 |Introduction - Comparisons of classical genetics, reverse genetics, and genomics.|Shin |

| | | |Strengths and weaknesses of model systems. Nomenclature. | |

|2 |Thu Oct 11 |1:15 |Yeast I - Basic molecular manipulations in reverse genetics: cloning by |Bertuch |

| | | |complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffle| |

|3 |Tue Oct 16 |1:15 |Yeast II - Genome analysis and functional genomics. The impact of the yeast |Bertuch |

| | | |genome project. Systematic manipulation of entire gene sets to monitor mRNA | |

| | | |expression and protein localization in vivo. | |

|4 |Thu Oct 18 |1:15 |Mouse Genetics I - Inbred mice. Microsatellite markers. Mapping genes in mice |Justice |

| | | |using crosses. | |

|5 |Mon Oct 22 |1:15 |Mouse Genetics II - Insertion of DNA and retrotransposons. Knock-outs and ins. |Justice |

| | | |Conditional knock-outs. | |

|6 |Tue Oct 23 |1:15 |Drosophila I - Isolation of lethal mutations that affect pattern formation. |Mardon |

| | | |Modifier (enhancer and suppressor) screens. P-elements as mutagens. Positional | |

| | | |cloning, P-element transformation. Aim of the Drosophila genome project: a | |

| | | |P-element insertion in every gene. | |

|1 |Tue Oct 23 |5:15 |GB-TA1 - | |

|2 |Mon Oct 29 |5:15 |GB-TA2 - | |

|7 |Tue Oct 30 |1:15 |Drosophila II - Genetic tricks: Mosaic analysis, autonomy vs. non-autonomy. |Mardon |

| | | |Ectopic expression using heat shock, FLP-out and GAL4-UAS. | |

|8 |Thu Nov 01 |1:15 |Drosophila III - |Mardon |

|9 |Tue Nov 06 |1:15 |C. elegans I- - Advantages and special considerations of hermaphrodite genetics. |Shin |

| | | |Significance of having the detailed fate map of the organism. Developmental | |

| | | |genetics at the single cell level. | |

|3 |Tue Nov 06 |5:15 |GB-TA3 - | |

|10 |Thu Nov 08 |1:15 |C. elegans II - C. elegans transformation. Positional cloning and |Shin |

| | | |complementation. Impact of the C. elegans genome project. Reverse genetics | |

| | | |using RNA interference. | |

|11 |Fri Nov 09 |1:15 |Human Genetics I - Disease loci and pedigrees. |Beaudet |

|4 |Tue Nov 13 |5:15 |GB-TA4 - | |

| |Thu Nov 15 |2:30 |Graduate Student Symposium - No Class - | |

|12 |Tue Nov 20 |1:15 |Human Genetics II - Mapping with DNA markers. Sources of polymorphisms. Simple |Beaudet |

| | | |vs. complex traits. Genome scans for quantitative trait loci. | |

| |Thu Nov 22 |1:15 |Thanksgiving Holiday - No Class - | |

| |Fri Nov 23 |1:15 |Thanksgiving Holiday - No Class - | |

|13 |Tue Nov 27 |1:15 |Human Genetics III - Effect of imprinting on pedigrees. Models for specific |Beaudet |

| | | |mechanisms of imprinting. Model for evolutionary significance. | |

|5 |Tue Nov 27 |5:15 |GB-TA5 - | |

| |Thu Dec 06 |1:15 |Faculty Review - | |

| |Fri Dec 07 |1:15 |Final Exam - 1:15-3:45 - | |

|Science as a Profession-Ethics |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Oct 09 |2:30 |Data Management/Ownership - Keeping a laboratory notebook, maintaining other |Slaughter |

| | | |records/computer files, ownership of scientific materials/data, sharing results | |

| | | |and reagents | |

|2 |Tue Oct 16 |2:30 |Scientific Misconduct- Part 1 - Definitions - Falsification, fabrication, |Gilbert |

| | | |plagiarism (case studies) | |

|3 |Tue Oct 23 |2:30 |Research with Human Subjects - definition of research with human subjects, |Haymond |

| | | |experiments with human material, confidentiality of medical data, experiments | |

| | | |involving humans, informed consent, the role of the IRB | |

|4 |Tue Oct 30 |2:30 |Scientific Misconduct - Part 2 - Policies of the college –allegations, inquiries,|Gilbert |

| | | |investigations, penalties (case studies) | |

|5 |Tue Nov 06 |2:30 |Publishing your Work - Authorship/Peer Review - Organizing your paper, preparing |Brinkley |

| | | |manuscripts, who should be an author?, responsibilities of an author, manuscript | |

| | | |review systems, responsibilities of a reviewer, dealing with criticism | |

|6 |Thu Nov 08 |2:30 |Experimental error and honesty - Experimental measurements and error, replication|Gilbert |

| | | |of experiments, influence of statistics on experimental design, how errors affect| |

| | | |your conclusions, statistical significance, correlations, when is it ethical to | |

| | | |ignore some experiments | |

| |Thu Nov 15 |2:30 |Graduate Student Symposium - No Class - | |

|7 |Tue Nov 20 |2:30 |Ethics of Experiments with Animals - when can animals be used ethically in |Michael |

| | | |research, avoiding unnecessary pain/suffering and euthanasia, appropriate | |

| | | |selection of numbers/types of animals in research, animal use approval | |

| |Thu Nov 22 |1:15 |Thanksgiving Holiday - No Class - | |

| |Fri Nov 23 |1:15 |Thanksgiving Holiday - No Class - | |

|8 |Tue Nov 27 |2:30 |Plagiarism/Conflicts of Interest - Plagiarism (definition and examples), |Slaughter |

| | | |attributing credit to others, financial conflicts of interest, conflicts of | |

| | | |interest in peer review, plagiarasm and computers, copyright, acceptable use | |

| | | |policies of the College | |

|Term 3 | |

|Gene Regulation |

|No |Date |Time |Lecture |Lecturer |

|1 |Wed Jan 02 |1:15 |Introduction to Gene Regulation - Sites of Gene Regulation: transcription |Rosen |

| | | |initiation, termination, alternative RNA splicing, 3' end processing, nuclear | |

| | | |export, cytoplasmic mRNA stability, translational regulation, protein | |

| | | |degradation, Methods of Assessing Levels of Regulation, | |

|2 |Fri Jan 04 |1:15 |RNA Polymerase - the bacterial enzyme summarizing the kinetics and |Herman |

| | | |thermodynamics of the protein and its interactions with DNA., subunit function of| |

| | | |the bacterial enzyme compared with the subunit structure of the eukaryotic | |

| | | |enzyme, Regulatory functions of the polymerase pol. | |

|3 |Mon Jan 07 |1:15 |Control of transcription in bacterias - degradation and sequestration of |Herman |

| | | |initiation factors, riboswitches, noise in transcription and logic of | |

| | | |transcriptional circuits. | |

|1 |Tue Jan 08 |5:15 |GRTA1 - Overview of regulation of transcription and translation including review | |

| | | |of overall process of transcription and translation, introduce reporter genes | |

| | | |(rationale) | |

|4 |Wed Jan 09 |1:15 |Mammalian RNA Polymerase and Co-factors and Promoters - Mammalian RNA Polymerase-|O’Malley |

| | | |Structure- function complexity of mammalian RNA pol II. Chromatin is a tough | |

| | | |substrate for Pol II to transcribe, and many proteins and much energy is | |

| | | |required. The Cis- and Trans- regulation of transcription at the TATA box. The | |

| | | |chemistry and biology of General Transcription Factors (GTFs). | |

|5 |Fri Jan 11 |1:15 |Transcription factors: Upstream Activation Sequences and Enhancers - Enhancer |O’Malley |

| | | |regulatory proteins and their structure-function relationships. Introduction to | |

| | | |integrator coregulators, such as CBP/p300.Structure-function characteristics of | |

| | | |coactivators. Description of the SRC family of coactivators. Coactivators as | |

| | | |enzymes. | |

| |Mon Jan 14 |1:15 |Martin Luther King Day Holiday - No Class - | |

|6 |Wed Jan 16 |1:15 |Mechanisms of action of coactivators and corepressors - Coactivators function in |O’Malley |

| | | |high molecular weight complexes. The kinetics of coactivator complex interactions| |

| | | |with target gene promoter regions; association and dissociation of the complex. | |

| | | |The functional diversity of coactivators. Regulation of substeps of transcription| |

| | | |by coactivators. Coactivators have evolved to regulate genes that function | |

| | | |together. Regulation of coactivator levels by the proteasome and activities by | |

| | | |phosphorylation cascades. | |

|7 |Thu Jan 17 |1:15 |Biology and Pathologies of Coactivators and Corepressors - Structure-function |O’Malley |

| | | |relationships of corepressors. Signaling to coregulators from the environment. | |

| | | |Coordinate steps in transcription factor (e.g., NR) and coactivator (egg SRC-3) | |

| | | |function in signaling pathways. The role of secondary coactivators. Tissue | |

| | | |specificity and transcription factor specificity of coregulators. The role of | |

| | | |coregulators in pharmaceutical drugs. The role of coactivators in pathologies | |

| | | |such as cancer, genetic disease, CVS disease. | |

|8 |Fri Jan 18 |1:15 |Local Chromatin Changes - histones, nucleosomes, covalent modification of |Wong |

| | | |histones, DNAase hypersensitive sites, insulators, locus control regions, | |

| | | |polytene chromosomes | |

|9 |Wed Jan 23 |1:15 |Global Chromatin Changes - chromatin subdomains, silencing, position effect |Wong |

| | | |variegation, epigenetic inheritance, X-inactivation, imprinting | |

|10 |Thu Jan 24 |1:15 |Regulation of RNA Polymerase II Elongation - Transcriptional elongation – an |Rice |

| | | |important regulatory step; Negative factors that limit elongation (NELF, DSIF); | |

| | | |Positive factor that activates elongation (P-TEFb); HIV system (Tat, TAR RNA, | |

| | | |P-TEFb); Drosophila heat shock genes and elongation; Current questions in this | |

| | | |area | |

|2 |Thu Jan 24 |5:15 |GR TA2 - Review of assembly of transcription complex including order and identity| |

| | | |of factor loading Identify major transcriptional activator families and | |

| | | |mechanisms | |

|11 |Fri Jan 25 |1:15 |Nuclear export of RNA - Nuclear pores – structure and dynamics; Retroviral |Rice |

| | | |systems: Retroviral life cycle, HIV system (Rev, RRE RNA, CRM1, RAN/GTP), | |

| | | |Mason-Pfizer Monkey Virus (MMPV; CTE, TAP); Experimental methods to study RNA | |

| | | |export; Export pathways of different classes of cellular RNAs; Current questions | |

| | | |in this area. | |

| |Tue Jan 29 |1:15 |Midterm Faculty Review - | |

| |Wed Jan 30 |1:15 |MIDTERM EXAM - | |

|12 |Thu Jan 31 |1:15 |Splicing of Pre-mRNA (I) - Overview of RNA chemistry (basis for lability and |Cooper |

| | | |reactivity), overview of RNA structure, comparisons of intron/exon architecture, | |

| | | |Autocatalytic RNA: Group I & II autocatalytic introns and hammerheads, The | |

| | | |spliceosome; U12-dependent introns, domain structure of RNA binding proteins | |

|13 |Fri Feb 01 |1:15 |Splicing of Pre-mRNA (II) - How the spliceosome finds vertebrate exons, intron |Cooper |

| | | |definition vs exon definition, splicing enhancers and silencers, SR proteins, | |

| | | |Exon junction complex (EJC), Trans-splicing, | |

|14 |Mon Feb 04 |1:15 |3’ end formation / Polyadenylation - 3' end formation of pol II genes, |Cooper |

| | | |transcription termination; cotranscriptional 3’ end formation; relationship | |

| | | |between 3' end formation and splicing, histone 3' end formation; spatial | |

| | | |relationship between splicing and transcription within nucleus | |

|15 |Wed Feb 06 |1:15 |Alternative splicing - Drosophila paradigms, yeast and vertebrate systems; |Cooper |

| | | |splicing microarrays; effects on coding potential; regulatory factors and | |

| | | |mechanisms of regulation; signaling pathways; splicing and human disease (direct | |

| | | |cause and as genetic modifier) | |

|16 |Thu Feb 07 |1:15 |Editing - RNA editing, Insertional/deletion editing (Mitochondrial mRNA editing, |Rosen |

| | | |contrast with trans-esterifiction, editsome complex, spliceosome), Substitutional| |

| | | |or modification editing in the nucleus (Apoliprotein B and cytidine deaminase, | |

| | | |AMPA receptor and adenosine deaminase. | |

|3 |Thu Feb 07 |5:15 |GR TA3 - Splicing and poyadenylation general overview; define mechanisms for | |

| | | |alternative splice-site selection, intron vs exon selection | |

|17 |Fri Feb 08 |1:15 |Posttranscriptional Regulation - Short RNAs, RNAi and miRNAs. History, Biogenesis|Rosen |

| | | |of RNAi and miRNAs, miRNAs in development and cancer. RNAi and heterochromatin | |

| | | |silencing. RNAi reagents, forward genetic screens and shRNA libraries | |

|18 |Mon Feb 11 |1:15 |Posttranscriptional Regulation - mRNA Turnover I & II- Multilevel regulation: |Rosen |

| | | |e.g. histone gene expression during the cell cycle. Translation Coupled mRNA | |

| | | |Degradation. Poly A shortening and 5' -> 3' degradation, P-bodies and mRNA | |

| | | |decay. Non-polyA shortening mechanisms. Nonsense-mediated mRNA decay. mRNA | |

| | | |stability in prokaryotes -genetics and biochemistry, Role of 3'UTR sequences in | |

| | | |mRNA localization. | |

|19 |Fri Feb 15 |1:15 |Translational Regulation I - Review of protein synthesis and initiation steps, |Lloyd |

| | | |Cap-dependent and cap independent translation. 5'-3' interactions and recycling. | |

| | | |Global regulation mechanisms; eIF2 kinase mechanisms, eIF4E inhibitors, viral | |

| | | |mechanisms, mTOR, TOP mRNAs. | |

| |Mon Feb 18 |1:15 |President's Day Holiday - No Class - | |

|20 |Thu Feb 21 |1:15 |Translational Regulation II Mechanisms - mRNA-specific regulation; scanning |Lloyd |

| | | |blockers, (uORFs, IRE, autoregulatory systems), cellular IRESs, shunt | |

| | | |mechanisms, 3' UTR-based regulation (CPEB in oocytes and neurons) - stress | |

| | | |mechanisms (stress granules and P bodies), Frameshifting. | |

|21 |Mon Feb 25 |1:15 |Regulation of Protein Turnover - Ubiquitin-proteosome mediated degradation., |Rosen |

| | | |Importance of regulation, protein motifs, PEST sequences, etc. | |

|4 |Tue Feb 26 |5:15 |GR-TA4 - RNA self-splicing overview, concept of regulating synthesis and | |

| | | |degradation of mRNA, review of ribosome assembly and initiation and termination | |

| | | |of translation | |

| |Wed Feb 27 |1:15 |Faculty Review - | |

| |Thu Feb 28 |1:15 |Final Exam - 1:15-3:45 - | |

|Immunology |

|No |Date |Time |Lecture |Lecturer |

| |Mon Jan 14 |1:15 |Martin Luther King Day Holiday - No Class - | |

|1 |Thu Jan 24 |3:30 |Principles of Specific Immunity - innate vs. specific immunity, cells of the |Spencer |

| | | |immune system, clonal selection principle, strategies for self-nonself | |

| | | |discrimination | |

|2 |Thu Jan 31 |3:30 |Antigen-Recognition - Antigens for B and T cells, Antigen-binding molecules, |Zheng |

| | | |Antibody/T Cell receptor structure and genetics, Generation of diversity: Gene | |

| | | |rearrangements, MHC Complex Genes, Antigen presentation | |

|3 |Tue Feb 05 |3:30 |Cellular Differentiation and Selection in the Immune system - B/T cell |Zheng |

| | | |development and selection. Self vs. nonself selection, Tolerance | |

|4 |Thu Feb 07 |2:30 |Lymphocyte Activation - B/T cell activation, signal transduction, convergence and|Spencer |

| | | |integration of signal transduction pathways, anergy, apoptosis | |

|1 |Fri Feb 08 |5:15 |IM TA Review 1 - Overview of response to pathogen: Anatomy and function of | |

| | | |organs of lymphatic system: general overview of B and T cell development and | |

| | | |function | |

|5 |Tue Feb 12 |2:30 |Integration of an Immune Response - T cell effector functions, transplantation, |Spencer |

| | | |autoimmunity, tumor immunology | |

| |Mon Feb 18 |1:15 |President's Day Holiday - No Class - | |

| |Tue Feb 19 |1:15 |Faculty Review - | |

| |Wed Feb 20 |1:15 |Final Exam - 1:15-3:45 - | |

|2 |Thu Feb 21 |5:15 |IM TA Review 2 - MHC I and MHC II - functions, derivation; B cells - antibody | |

| | | |structure - subtypes, receptors and surface molecules, VDJ recombination; T cells| |

| | | |- receptor and surface molecules, maturation, subtypes/function; T and B cell | |

| | | |interactions | |

|Molecular Interactions |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Jan 01 |2:30 |Course Introduction -Ligand Binding - Definition of Kd. Mass action, basic |Pedersen |

| | | |thermodynamics. | |

|2 |Thu Jan 03 |2:30 |Forces in solution and thermodynamics - Enthalpy and entropy, forces in solution,|Pedersen |

| | | |competitive inhibition. | |

|3 |Fri Jan 04 |2:30 |Allosterism and protein conformations - Regulation of activity and binding, |Pedersen |

| | | |multiple binding sites and the Hill equation | |

|4 |Wed Jan 09 |2:30 |Allosterism and linkage analysis - Heterotropic allosteric interaction and |Pedersen |

| | | |thermodynamic linkage analysis. | |

|5 |Thu Jan 10 |2:30 |Cooperativity - Koshland-Nemethy-Filmer models. Negative cooperativity |Pedersen |

|1 |Thu Jan 10 |5:15 |MI-TA Review 1 - | |

|6 |Fri Jan 11 |2:30 |Binding kinetics I - reactions and reaction order |Pedersen |

| |Mon Jan 14 |1:15 |Martin Luther King Day Holiday - No Class - | |

|7 |Wed Jan 16 |2:30 |Binding kinetics II - better kinetics through computation |Pedersen |

|8 |Thu Jan 17 |2:30 |Protein-Ligand Interactions - Molecular basis of specificity, protein ligand |Prasad |

| | | |interactions - structural basis of H-bonding, salt bridges and other interactions| |

|9 |Fri Jan 18 |2:30 |Protein-Protein Interactions - Protein-protein interactions. Structural motifs |Prasad |

| | | |that serve as protein-protein interaction domains, structural basis of surface | |

| | | |complementarity, engineering tight binding | |

|10 |Wed Jan 23 |2:30 |Protein DNA Interactions - Protein-DNA interactions. DNA binding motifs, |Prasad |

| | | |structural basis of base recognition, backbone interactions | |

|11 |Fri Jan 25 |2:30 |Enzyme Kinetics and Catalysis - Michaelis-Menten kinetics, Inhibition, kcat and |Bryan |

| | | |kcat/Km, allosteric enzymes, inhibition, practical features of an assay | |

|2 |Tue Jan 29 |5:15 |MI-TA Review 2 - | |

|12 |Thu Jan 31 |2:30 |Mechanisms of Enzyme Catalysis - Acid base catalysis, covalent catalysis, |Bryan |

| | | |stabilization of transition states, transition state analogs, coenzymes, suicide | |

| | | |inhibitors | |

|13 |Mon Feb 04 |2:30 |Protein Machines I - Stable and Dynamic Assemblies. Oligomers and Polymers.  ATP |Bryan |

| | | |synthases | |

|3 |Tue Feb 05 |5:15 |MI-TA Review 3+G133 - | |

|14 |Wed Feb 06 |2:30 |Protein Machines II - Actin-myosin motors |Bryan |

| |Wed Feb 13 |1:15 |Faculty Review - | |

| |Thu Feb 14 |1:15 |Final Exam - 1:15-3:45 - | |

| |Mon Feb 18 |1:15 |President's Day Holiday - No Class - | |

|Neuroscience |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Jan 01 |1:15 |Information processing in neurons. - The electrical properties of neurons. Ion |Pham |

| | | |channel distriution. Coupling electrical signals to neurotransmitter release | |

|2 |Thu Jan 03 |1:15 |Synaptic plasticity - Structure of the synapse. Ligand gated ion channels. |Pham |

| | | |Neuortransmitter release. Activity-dependent plasticity | |

|1 |Thu Jan 03 |5:15 |NE TA Review 1 - Brain anatomy, anatomy of eye and nose, neuron types, action | |

| | | |potentials (including review of neurotransmitters) | |

|3 |Tue Jan 08 |1:15 |Learning and memory - forms of learning and memory. Molecular coincidence |Pham |

| | | |detectors. Perpetuation of biochemical signals. Alterations in gene expression.| |

| | | |Structural changes. | |

|4 |Thu Jan 10 |1:15 |Sensory systems - specialized sensory receptors, encoding of information, |Pham |

| | | |circuits for information processing, face cells, behavioral control | |

| |Mon Jan 14 |1:15 |Martin Luther King Day Holiday - No Class - | |

|5 |Tue Jan 15 |1:15 |Cognition - Split brain studies, amnesia, PET imaging in cognition, cortical |Pham |

| | | |plasticity, diseases of cognition and affect | |

|2 |Tue Jan 15 |5:15 |NE TA Review 2 - Basis of methods used (voltage clamp, imaging of brain); Visual | |

| | | |receptors (rods, cones), receptive fields | |

| |Mon Jan 21 |1:15 |Faculty Review - | |

| |Tue Jan 22 |1:15 |Final Exam - 1:15-3:45 - | |

| |Mon Feb 18 |1:15 |President's Day Holiday - No Class - | |

|Term 4 | |

|Research Design |

|No |Date |Time |Lecture |Lecturer |

|1 |Tue Mar 11 |1:00 |Research Design Introduction - Introduction to the design of research projects |Gilbert |

|2 |Tue Mar 18 |1:00 |Research Design Workgroup 2 - |Schmid |

|3 |Tue Mar 25 |1:00 |Research Design Workgroup 3 - |Zechiedrich |

|4 |Tue Apr 01 |1:00 |Research Design Workgroup 4 - |Bryan |

|5 |Tue Apr 08 |1:00 |Research Design Workgroup 5 - |Lichtarge |

|6 |Tue Apr 15 |1:00 |Research Design Workgroup 6 - |Prasad |

|7 |Tue Apr 22 |1:00 |Research Design Workgroup 7 - |Staff |

|8 |Tue Apr 29 |1:00 |Research Design Workgroup 8 - |Staff |

|Structure of Macromolecules |

|No |Date |Time |Lecture |Lecturer |

|1 |Mon Mar 10 |1:15 |Hydrodynamic methods - methods for estimating size, shape compactness and |Schmid |

| | | |oligomeric state of proteins (and interactions among them)--analytical | |

| | | |ultracentrifugation, native gels, size exclusions chromatorraphy, dynamical light| |

| | | |scattering, small angle x-ray scattering | |

|2 |Wed Mar 12 |1:15 |Spectroscopic methods for estimating compactness and foldedness of proteins - CD,|Schmid |

| | | |FTIR, proton exchange | |

|3 |Fri Mar 14 |1:15 |NMR of proteins and DNA - Basic theory and instrumentation, NOSEY, COSY methods, |Gilbert |

| | | |distance geometry, multi-diminsional NMR, sample requirements | |

|4 |Mon Mar 17 |1:15 |DNA Structure and topology I - Structure of B, Z and A DNA, topology, structural |Zechiedrich |

| | | |effects on electrophoretic properties of DNA, R-loops, D-loops, Literature | |

| | | |project on DNA structure/function | |

|1 |Tue Mar 18 |5:15 |TA-1 - | |

|5 |Wed Mar 19 |1:15 |DNA Structure and topology II - Methods of analyzing DNA structure, future goals |Zechiedrich |

| | | |in field of DNA structure/topology, literature project | |

| |Thu Mar 20 |1:15 |Career Day - No Class - | |

|6 |Fri Mar 21 |1:15 |Protein Taxonomy - Discussion of protein motifs, domains and general structural |Tsai |

| | | |features. Approaches to function from structure. | |

|7 |Mon Mar 24 |1:15 |Protein Folding - Mechanisms for attaining the correct 3D structure of proteins, |Gilbert |

| | | |experimental approaches to observing protein folding, catalysis of protein | |

| | | |folding | |

|8 |Wed Mar 26 |1:15 |Cryoelectron microscopy - a scattering (diffraction)-based structural technique |Ludtke |

|9 |Fri Mar 28 |1:15 |Xray crystallography - a scattering (diffraction)-based structural technique. |Tsai |

| | | |Crystallization and synmetry. Theory of diffraction | |

|10 |Mon Mar 31 |1:15 |Convolution - The diffraction pattern as a Fourier Transform. Some simple |Schmid |

| | | |examples. | |

|2 |Tue Apr 01 |5:15 |TA-2 - | |

|11 |Wed Apr 02 |1:15 |The Phase Problem - solving the phase problem, one way or another. EM |Schmid |

| | | |techniques. | |

| |Fri Apr 04 |1:15 |Good Friday Holiday - No Class - | |

|12 |Mon Apr 07 |1:15 |Mass spec I - mass spectrometers, ionization methods, the use of MS in protein |Qin |

| | | |identification | |

|3 |Tue Apr 08 |5:15 |TA3 - | |

|13 |Wed Apr 09 |1:15 |Mass spec II - use of mass spec in protein interaction, proteomics |Qin |

|14 |Fri Apr 11 |1:15 |Regulatory post-translational modification - Protein phosphorylation and other |Weigel |

| | | |reversibale regulatory post-translational modification | |

|15 |Mon Apr 14 |1:15 |Post-translational modification - irreversible, lipid modifications, |Weigel |

| | | |ubiquitination | |

|16 |Wed Apr 16 |1:15 |Protein glycosylation and quality control - biosynthetic quality control, |Sifers |

| | | |additional roles for glycosylation, analysis of glycoproteins | |

|17 |Fri Apr 18 |1:15 |Fluorescence Methods for Structure analysis - principles of photon absorption and|Wensel |

| | | |emission, fluorescence energy transfer, anisotropy, lifetime, instrumentation, | |

| | | |optics | |

|18 |Mon Apr 21 |1:15 |Structure of Lipids and Glycolipids - Major lipids of biomembranes, diversity of |Ludtke |

| | | |composition, relationships between lipid structures and functional properties | |

|19 |Wed Apr 23 |1:15 |Membrane Protein Structure - integral and peripheral membrane proteins, |Ludtke |

| | | |protein-lipid interactions, structural features of transmembrane proteins | |

|20 |Fri Apr 25 |1:15 |Sequence to Structure - primary structure analysis, domain classifications, |Lichtarge |

| | | |prediction of secondary and tertiary structure | |

| |Thu May 01 |1:15 |Faculty Review - | |

| |Fri May 02 |1:15 |Final Exam - 1:15-3:45 - | |

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