Recommended Readings: Lora Hooper, Ph.D. April 2

Wednesday, April 2, 2014
4:00 p.m., Carson Family Auditorium

Lora Hooper, Ph.D.
University of Texas Southwestern Medical Center
Investigator, HHMI

Circadian Regulation of Intestinal Immunity

Recommended Readings:

Empirical Articles

Bäckhed, F., Ding, H., Wang, T., Hooper, L. V, Koh, G. Y., Nagy, A., … Gordon, J. I. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences, 101(44), 15718–15723. doi:10.1073/pnas.0407076101

Cash, H. L., Whitham, C. V, Behrendt, C. L., & Hooper, L. V. (2006). Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science, 313(5790), 1126–1130. doi:10.1126/science.1127119

Scheer, F. a J. L., Hilton, M. F., Mantzoros, C. S., & Shea, S. A. (2009). Adverse metabolic and cardiovascular consequences of circadian misalignment. Proceedings of the National Academy of Sciences, 106(11), 4453–4458. doi:10.1073/pnas.0808180106

Yu, X., Rollins, D., Ruhn, K. a, Stubblefield, J. J., Green, C. B., Kashiwada, M., … Hooper, L. V. (2013). TH17 cell differentiation is regulated by the circadian clock. Science, 342(6159), 727–730. doi:10.1126/science.1243884

Review Papers

Arjona, A., Silver, A. C., Walker, W. E., & Fikrig, E. (2012). Immunity’s fourth dimension: approaching the circadian-immune connection. Trends in Immunology, 33(12), 607–612. doi:10.1016/

Hooper, L. V, & Macpherson, A. J. (2010). Immune adaptations that maintain homeostasis with the intestinal microbiota. Nature Reviews Immunology, 10(3), 159–169. doi:10.1038/nri2710

Korn, T., Bettelli, E., Oukka, M., & Kuchroo, V. K. (2009). IL-17 and Th17 cells. Annual Review of Immunology, 27, 485–517. doi:10.1146/annurev.immunol.021908.132710

Recommended Readings: Andrew Kruse Ph.D. March 3

Monday, March 3, 2014
4:00 p.m., Carson Family Auditorium

Andrew Kruse, Ph.D.
Department of Molecular and Cellular Physiology
Stanford University School of Medicine

Structural insights into G protein-coupled receptor activation and allosteric modulation

Recommended Readings:

Empirical Papers

Haga, K., Kruse, A. C., Asada, H., Yurugi-Kobayashi, T., Shiroishi, M., Zhang, C., … Kobayashi, T. (2012). Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist. Nature, 482(7386), 547–551. doi:10.1038/nature10753

Kruse, A. C., Hu, J., Pan, A. C., Arlow, D. H., Rosenbaum, D. M., Rosemond, E., … Kobilka, B. K. (2012). Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature, 482(7386), 552–556. doi:10.1038/nature10867

Kruse, A. C., Ring, A. M., Manglik, A., Hu, J., Hu, K., Eitel, K., … Kobilka, B. K. (2013). Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature, 504(7478), 101–106. doi:10.1038/nature12735

Kruse, A. C., Weiss, D. R., Rossi, M., Hu, J., Hu, K., Eitel, K., … Shoichet, B. K. (2013). Muscarinic receptors as model targets and antitargets for structure-based ligand discovery. Molecular Pharmacology, 84(4), 528–540. doi:10.1124/mol.113.087551

Ring, A. M., Manglik, A., Kruse, A. C., Enos, M. D., Weis, W. I., Garcia, K. C., & Kobilka, B. K. (2013). Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody. Nature, 502(7472), 575–579. doi:10.1038/nature12572

Review Articles

Kruse, A. C., Li, J., Hu, J., Kobilka, B. K., & Wess, J. (2013). Novel insights into M3 muscarinic acetylcholine receptor physiology and structure. Journal of Molecular Neuroscience. doi:10.1007/s12031-013-0127-0

Kruse, A. C., Manglik, A., Kobilka, B. K., & Weis, W. I. (2013). Applications of molecular replacement to G protein-coupled receptors. Acta Crystallographica. Section D, Biological Crystallography, 69(11), 2287–2292. doi:10.1107/S090744491301322X

Recommended Readings: Rob Knight, Ph.D. Wednesday, Oct. 30, 2013

Wednesday, October 30, 2013
4:00 p.m., Carson Family Auditorium

Rob Knight, Ph.D.
HHMI Early Career Scientist and Professor
Department of Chemistry & Biochemistry, Department of Computer Science, and BioFrontiers Institute
University of Colorado at Boulder

Gut Microbes and their Role in Malnutrition and Obesity

Recommended Readings:

Review Papers

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012). The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), 1258–1270. doi:10.1016/j.cell.2012.01.035

Gevers, D., Knight, R., Petrosino, J. F., Huang, K., McGuire, A. L., Birren, B. W., … Huttenhower, C. (2012). The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biology, 10(8), e1001377. doi:10.1371/journal.pbio.1001377

Hamady, M., & Knight, R. (2009). Microbial community profiling for human microbiome projects : Tools , techniques , and challenges, Genome Research, 19(7), 1141–1152. doi:10.1101/gr.085464.108.19

Ley, R. E., Lozupone, C. a, Hamady, M., Knight, R., & Gordon, J. I. (2008). Worlds within worlds: evolution of the vertebrate gut microbiotaNature Reviews Microbiology6(10), 776–788. doi:10.1038/nrmicro1978

Empirical Articles

Costello, E., Lauber, C., & Hamady, M. (2009). Bacterial community variation in human body habitats across space and time. Science, 326, 8–11.

The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–14. doi:10.1038/nature11234

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A, Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102(31), 11070–5. doi:10.1073/pnas.0504978102

Lozupone, C. A., Stombaugh, J., Gonzalez, A., Ackermann, G., Jansson, J. K., Gordon, J. I., … Knight, R. (2013). Meta-analyses of studies of the human microbiota, Genome Research, 23,1704–1714. doi:10.1101/gr.151803.112

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., … Gordon, J. I. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480–484. doi:10.1038/nature07540

Turnbaugh, P. J., Ley, R. E., Mahowald, M. a, Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–31. doi:10.1038/nature05414

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–7. doi:10.1038/nature11053

Recommended Readings: Eran Segal Ph.D. October 9, 2013

Special Seminar Series
Deciphering the Code of Gene Regulation
Eran Segal, Ph.D.
Incumbent of the Soretta and Henry Shapiro Career Development Chair
Department of Computer Science and Applied Mathematics
4:00 p.m. – 5:00 p.m. Carson Family Auditorium (CRC)
Refreshments: 3:45 p.m. – 4:00 p.m., Lower Level Greenberg Building (CRC)

Recommended Readings:

Review Papers

Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013). Eukaryotic transcriptional dynamics: from single molecules to cell populationsNature Reviews Genetics14(8), 572-584. doi: 10.1038/nrg3484.

De Smet, R., & Marchal, K. (2010). Advantages and limitations of current network inference methodsNature Reviews Microbiology8(10), 717-729. doi: 10.1038/nrmicro2419

Segal, E., & Widom, J. (2009). From DNA sequence to transcriptional behaviour: a quantitative approachNature Reviews Genetics10(7), 443-456. doi: 10.1038/nrg2591

Jiang, C., & Pugh, B. F. (2009). Nucleosome positioning and gene regulation: advances through genomicsNature Reviews Genetics10(3), 161-172. doi: 10.1038/nrg2522

Empirical Articles

Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., … & Segal, E. (2008). The DNA-encoded nucleosome organization of a eukaryotic genomeNature458(7236), 362-366. doi: 10.1038/nature07667

Schones, D. E., Cui, K., Cuddapah, S., Roh, T. Y., Barski, A., Wang, Z., … & Zhao, K. (2008). Dynamic regulation of nucleosome positioning in the human genomeCell132(5), 887-898. doi: 10.1016/j.cell.2008.02.022

Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., … & Widom, J. (2006). A genomic code for nucleosome positioningNature,442(7104), 772-778. doi: 10.1038/nature04979

Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003). Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics34(2), 166-176. doi: 10.1038/ng1165

Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., & Sidow, A. (2011). Determinants of nucleosome organization in primary human cellsNature474(7352), 516-520. doi: 10.1038/nature10002

Structural Biology Lecture Series: Venki Ramakrishnan Ph.D. Wed Sept 28 2011

Structural Biology Lecture Series

The Structural Basis of Decoding by the Ribosome

Dr. Venki Ramakrishnan

2009 Nobelist

Medical Research Council Laboratory of Molecular Biology

Wednesday September 28, 11 am, Caspary Hall

Recommended Readings:

Voorhees RM; Schmeing TM; Kelley AC; Ramakrishnan V. 2010. The mechanism for activation of GTP hydrolysis on the ribosome. Science 330:835-838.

Schmeing TM; Voorhees RM; Kelley AC; et al.  2009. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.  Science  326(5953):688-694.

Gao Y-G; Selmer M; Dunham CM; Weixlbaumer A; Kelley AC; Ramakrishnan V. 2009. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326:694-699.

Weixlbaumer A; Hong J; Neubauer C; Voorhees RM; Sabine P; Kelley AC; Ramakrishnan V. 2008. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322:953-956.

Selmer M; Duham CM; Murphy FV; Weixlbaumer A; Sabine P; Kelley AC; Weir JR; Ramakrishnan V. 2006. Science 313:1935-1942.

Petry S; Brodeson DE; Murphy FV; et al.  2005.  Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.  Cell  123(7):1255-1266.

Ogle, JM; Murphy FV; Tarry MJ; et al.  2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form.  Cell  111(5):721-732.

Wimberly BT; Brodeson DE; Clemons WM; et al.  Structure of the ribosomal subunit. 2000. NATURE   407(6802): 327-339.

Carter AP; Clemons WM; Broderson DE; et al.  2000.  Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics.  NATURE  407(6802):340-348.

Recommended Readings: Uri Alon, Ph.D.

Special Seminar Series

Design Principles of Biological Circuits/on Science and Nurturing

Uri Alon, Ph.D.

Principal Investigator, Depts. of Molecular Cell Biology and Physics of Complex Systems

Weizmann Institute of Science

Wednesday, January 28, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Book and Journal Articles:

Alon, Uri.  An Introduction to Systems Biology: Design Principles of Biological Circuits.  Boca Raton, FL: Chapman & Hall/CRC, 2007.  (2 copies of this book are available at the Markus Library Circulation Desk.

Geva-Zatorsky, N., N. Rosenfeld, S. Itzkovitz, R. Milo, A. Sigal, E. Dekel, T. Yarnitzky, et al. 2006. Oscillations and variability in the p53 system. Molecular systems biology [electronic resource]. 2.
Request PDF from Markus Library

Kalir, S., S. Mangan, and U. Alon. 2005. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Molecular systems biology [electronic resource]. 1.
Request PDF from Markus Library

Kalisky, T., E. Dekel, and U. Alon. 2007. Cost-benefit theory and optimal design of gene regulation functions. Physical Biology. 4(4):229-245.

Kaplan, S., A. Bren, E. Dekel, and U. Alon. 2008. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Molecular Systems Biology. 4.

Mangan, S., and U. Alon. 2003. Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences of the United States of America. 100(21):11980-11985.

Mangan, S., S. Itzkovitz, A. Zaslaver, and U. Alon. 2006. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. Journal of Molecular Biology. 356(5):1073-1081.

Rosenfeld, N., J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz. 2007. Accurate prediction of gene feedback circuit behavior from component properties. Molecular Systems Biology. 3. article #3.

Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S., and Elowitz, M.B. 2005. Gene regulation at the single-cell level. Science. 307(5717):1962-1965.

Recommended Readings: Anne Brunet, Ph.D.

Special Seminar Series

Evolution, Ecology & Developmental Biology

Mechanisms of stem cell maintenance during aging

Anne Brunet, Ph.D.

Assistant Professor, Department of Genetics, Stanford School of Medicine 

3:45 pm – Refreshments

4:00 pm – 5:00 pm – Lecture

Wednesday, December 17, 2008

Welch Hall, 2nd Floor

Recommended Readings:

Carter, M. E., and A. Brunet. 2007. FOXO transcription factors. Current Biology. 17(4):R113-R114.

Greer, E. L., and A. Brunet. 2008. Signaling networks in aging. Journal of Cell Science. 121(4):407-412.

Calnan, D. R., and A. Brunet. 2008. The FoxO code. Oncogene. 27(16):2276-2288.

Salih, D. A., and A. Brunet. 2008. FoxO transcription factors in the maintenance of cellular homeostasis during aging. Current Opinion in Cell Biology. 20(2)126-136.

Greer, E. L., P. R. Oskoui, M. R. Banko, J. M. Maniar, M. P. Gygi, S. P. Gygi, and A. Brunet. 2007. The energy sensor AMP-activated protein kinase directly regulates the mammalian FOXO3 transcription factor. Journal of Biological Chemistry. 282(41)30107-30119.

Maiese, K., Z. C. Zhao, and C. S. Yan. 2007. “Sly as a FOXO”: New paths with forkhead signaling in the brain. Current Neurovascular Research. 4(4)295-302.
(Order copy from Markus Library)

Related Readings: Constance Scharff, Ph.D.

Special Seminar Series

Gene Function Studies in Songbirds:

Case Study FoxP2

Constance Scharff, Ph.D.

University Professor of Animal Behavior

Department of Biology, Chemistry, and Pharmacy

Free University of Berlin;

Neurobiology Group Leader

Max Planck Institute for Molecular Genetics

3:45 – Refreshments

4:00 – 5:00 pm – Seminar

Wednesday, October 22, 2008

Second Floor, Welch Hall

Recommended Articles:

Haesler, S., Rochefort, C., Georgi, B., Licznerski, P., Osten, P., Scharff, C. 2007. Incomplete and inaccurate vocal imitation after knockdown of FoxP2 in songbird basal ganglia nucleus area X. PLoS Biology 5(12):2885-2897.

Rochefort, C., He, X., Scotto-Lomassese, S., Scharff, C. 2007. Recruitment of FoxP2-expressing neurons to area X varies during song development. Developmental Neurobiology 67(6)809-817.

White, S.A., Fisher, S.E., Geschwind, D.H., Scharff, C., Holy, T.E. 2006. Singing mice, songbirds, and more: Models for FOXP2 function and dysfunction in human speech and language. Journal of Neuroscience 26(41):10376-10379.

Teramitsu, I., White, S.A. 2006. FoxP2 regulation during undirected singing in adult songbirds. Journal of Neuroscience 26(28):7390-7394.

Scharff, C., Haesler, S. 2005. FoxP2 in song-learning birds and vocal-learning mammals. Current Opinion in Neurobiology 15 (6):694-703.

Scharff, C., White, S.A. 2004. Genetic components of vocal learning. Annals of the New York Academy of Sciences 1016:325-347.

Teramitsu, I., Kudo, L.C., London, S.E., Geschwind, D.H., White, S.A. 2004. Parallel FoxP1 and FoxP2 Expression in Songbird and Human Brain Predicts Functional Interaction. Journal of Neuroscience 24(13):3152-3163.

Haesler, S., Wada, K., Nshdejan, A., Morrisey, E.E., Lints, T., Jarvis, E.D., Scharff, C. 2004. FoxP2 Expression in Avian Vocal Learners and Non-Learners. Journal of Neuroscience 24(13):3164-3175.

Related Readings – Marie-Anne Felix Ph.D.

C. elegans in an Evolutionary Context


Wednesday, April 23, 2008 Welch Hall (2nd Floor)

3:45 pm Refreshments      4:00 pm Lecture

Recommended Review Article:

Braendle, C.; Millioz, J.; and Marie-Anne Felix. (2008)  Mechanisms and evolution of environmental reseponses in Caenorhabditis elegans. Current topics in Developmental Biology (2008):171-207

Related Articles:

Kiontke,K.; Barriere, A.; Kolotuev, I. et al.   (2007)  Trends, stasis, and drift in the evolution of nematode vulva development. .Current Biology  17:1925-1937

Cutter, A. D.; Felix, M.A.; Barriere, A. et al.   (2006)  Patterns of nucleiotide polumorphism distinguish temperate and tropical wild isolates of Caenorhabditis briggsae. Genetics  173(4):2021-2031

Felix, M.A. and A. Barriere. (2005)  Evolvability of cell specification mechanisms. Journal of Experimental Biology  304B(6):536-547

Felix, M.A.  (2004) Developmental biology of nematodes – what we learn from Caenorhabditis elegansNematogy: advances and perspectives 1:71-174

Delattre, M. and Marie-Anne Felix.  (2001)  Microevolutionary studies in nematodes: a beginning.  Bioessays  23(9):807-819