Recommended Readings: David Artis, Ph.D. Monday, Oct. 14, 2013


Regulation of Barrier Immunity

 David Artis, Ph.D.

Associate Professor of Microbiology

 Perelman School of Medicine

University of Pennsylvania

Monday, October 14, 2013

4:00 p.m., Carson Family Auditorium

Recommended Review:

Saenz, Steven A.; Taylor, Betsy C.; Artis, David. 2008.  Welcome to the neighborhood: epithelial cell-derived cytokines license innate and adaptive immune responses at mucosal sites .   IMMUNOLOGICAL REVIEWS  226: 172-190  

Artis, David.  2008.  Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut.  NATURE REVIEWS IMMUNOLOGY   8(6):411-420   DOI: 10.1038/nri2316

Recommended Readings:

Saenz, Steven A.; Siracusa, Mark C.; Monticelli, Laurel A.; et al. 2013. IL-25 simultaneously elicits distinct populations of innate lymphoid cells and multipotent progenitor type 2 (MPPtype2) cells .    JOURNAL OF EXPERIMENTAL MEDICINE.  210(9): 1823-1837   DOI: 10.1084/jem.20122332

Philip, Naomi H.; Artis, David. 2013. New friendships and old feuds: relationships between innate lymphoid cells and microbial communities.   IMMUNOLOGY AND CELL BIOLOGY.   91(3):225-231   DOI: 10.1038/icb.2013.2

Tomasello, Elena; Bedoui, Sammy.  2013. Intestinal innate immune cells in gut homeostasis and immunosurveillance.   IMMUNOLOGY AND CELL BIOLOGY   91(3): 201-203   DOI: 10.1038/icb.2012.85

Goto, Yoshiyuki; Ivanov, Ivaylo I.  2013.  Intestinal epithelial cells as mediators of the commensal-host immune crosstalk.   IMMUNOLOGY AND CELL BIOLOGY.  91(3):204-214   DOI: 10.1038/icb.2012.80

Monticelli, Laurel A.; Sonnenberg, Gregory F.; Artis, David. 2012.   Innate lymphoid cells: critical regulators of allergic inflammation and tissue repair in the lung.   CURRENT OPINION IN IMMUNOLOGY   24(3):284-289   DOI: 10.1016/j.coi.2012.03.012

Artis, D.; Grencis, R. K.  2008. The intestinal epithelium: sensors to effectors in nematode infection.  MUCOSAL IMMUNOLOGY .  1(4): 252-264   DOI: 10.1038/mi.2008.21


Recommended Readings: Jian Xu, Ph.D. September 30, 2013

Epigenetics of Genetic Switches: Micro and Macro Views
Jian Xu, Ph.D.
Division of Hematology/Oncology
Boston Children’s Hospital, HHMI
Harvard Medical School
4:00 p.m., Carson Family Auditorium

Recommended Readings:

Review Papers

Bauer, D. E., Kamran, S. C., & Orkin, S. H. (2012). Reawakening fetal hemoglobin: prospects for new therapies for the β-globin disorders. Blood,120(15), 2945-2953. doi: 10.1182/blood-2012-06-292078

McGrath, K., & Palis, J. (2008). Ontogeny of erythropoiesis in the mammalian embryo. Current topics in developmental biology, 82(07), 1–22. doi:10.1016/S0070-2153(07)00001-4

Sankaran, V. G., Xu, J., & Orkin, S. H. (2010). Advances in the understanding of haemoglobin switching. British journal of haematology, 149(2), 181–194. doi:10.1111/j.1365-2141.2010.08105.x

Thein, S. L., Menzel, S., Lathrop, M., & Garner, C. (2009). Control of fetal hemoglobin: new insights emerging from genomics and clinical implications. Human molecular genetics, 18(R2), R216–223. doi:10.1093/hmg/ddp401

Empirical Articles

Jawaid, K., Wahlberg, K., Thein, S. L., & Best, S. (2010). Binding patterns of BCL11A in the globin and GATA1 loci and characterization of the BCL11A fetal hemoglobin locus. Blood cells, molecules & diseases, 45(2), 140–146. doi:10.1016/j.bcmd.2010.05.006

Sankaran, V. G., Menne, T. F., Xu, J., Akie, T. E., Lettre, G., Van Handel, B., … Orkin, S. H. (2008). Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science, 322(5909), 1839–1842. doi:10.1126/science.1165409

Sankaran, V. G., Xu, J., Ragoczy, T., Ippolito, G. C., Walkley, C. R., Maika, S. D., … Orkin, S. H. (2009). Developmental and species-divergent globin switching are driven by BCL11A. Nature, 460(7259), 1093–1097. doi:10.1038/nature08243

Xu, J., Bauer, D. E., Kerenyi, M. a, Vo, T. D., Hou, S., Hsu, Y.-J., … Orkin, S. H. (2013). Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A. Proceedings of the National Academy of Sciences of the United States of America, 110(16), 6518–6523. doi:10.1073/pnas.1303976110

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

Landmark CDC Report Details Threat of ‘Postantibiotic Era’

The Centers for Disease Control and Prevention (CDC) released its “landmark” report today on the rising and lethal threat of antibiotic resistance, titled Antibiotic Resistance Threats in the United States, 2013.

The report describes a complex problem and the steps that must be taken to prevent catastrophic consequences.

In it, experts describe “what happens when the microbes can outsmart our best antibiotics,” explained CDC Director Tom Frieden, MD, MPH, at a press conference. He elaborated by describing his hope that the report will prioritize pathogens and propel action to curb antibiotic resistance.

Recommended Readings: Frederick Cross Ph.D. September 23, 2013

Monday Lecture Series
A Fast Route to Cell Cycle Control in the Plant Superkingdom
Frederick Cross, Ph.D.
Professor, Laboratory of Cell Cycle Genetics
The Rockefeller University
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

Bloom, J., & Cross, F. R. (2007). Multiple levels of cyclin specificity in cell-cycle control. Nature Reviews Molecular and Cell Biology, 8(2), 1491–1560. doi:10.1038/nrm2105

Cross, F. R., Buchler, N. E., & Skotheim, J. M. (2011). Evolution of networks and sequences in eukaryotic cell cycle control. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 366(1584), 3532–3544. doi:10.1098/rstb.2011.0078

Harris, E. (2001). Chlamydomonas as a model organism. Annual Review of Plant Biology, 52, 363–406. doi:10.1146/annurev.arplant.52.1.363

Empirical Papers

Bisova, K., Krylov, D. M., & Umen, J. G. (2005). Genome-wide annotation and expression profiling of cell cycle regulatory genes in Chlamydomonas reinhardtii. Plant Physiology, 137, 475–491. doi:10.1104/pp.104.054155.G1-S-G2-M

Fang, S.-C., de los Reyes, C., & Umen, J. G. (2006). Cell size checkpoint control by the retinoblastoma tumor suppressor pathway. PLoS Genetics, 2(10), e167. doi:10.1371/journal.pgen.0020167

Koff, a, Cross, F., Fisher, a, Schumacher, J., Leguellec, K., Philippe, M., & Roberts, J. M. (1991). Human cyclin E, a new cyclin that interacts with two members of the CDC2 gene family. Cell, 66(6), 1217–1228.

Olson, B. J. S. C., Oberholzer, M., Li, Y., Zones, J. M., Kohli, H. S., Bisova, K., … Umen, J. G. (2010). Regulation of the Chlamydomonas cell cycle by a stable, chromatin-associated retinoblastoma tumor suppressor complex. The Plant Cell, 22(10), 3331–3347. doi:10.1105/tpc.110.076067

Richardson, H. E., Wittenberg, C., Cross, F., & Reed, S. I. (1989). An essential G1 function for cyclin-like proteins in yeast. Cell, 59(6), 1127–1133.

Recommended Readings: Benjamin Judkewitz Ph.D. Monday September 16, 2013

Monday Seminar   September 16, 2013

Deep Tissue Fluorescence Imaging With Time-reversed Light

Benjamin Judkewitz, Ph.D.

Sir Henry Wellcome Postdoctoral Fellow

Departments of Bioengineering and Electrical Engineering

California Institute of Technology

4:00 p.m. Carson Family Auditorium

Recommended Readings:

Judkewitz, Benjamin; Wang, Ying Min; Horstmeyer, Roarke; et al.  2013.  Speckle-scale focusing in the diffusive regime with time reversal of variance-encoded light (TROVE).  NATURE PHOTONICS  7(4):300-305   DOI: 10.1038/NPHOTON.2013.31  

Wang, Ying Min; Judkewitz, Benjamin; DiMarzio, Charles A.; et al. 2012. Deep-tissue focal fluorescence imaging with digitally time-reversed ultrasound-encoded light.   NATURE COMMUNICATIONS   3(Article 928):   DOI: 10.1038/ncomms1925

Suzuki, Yuta; Xu, Xiao; Lai, Puxiang; et al   2012.  Energy enhancement in time-reversed ultrasonically encoded optical focusing using a photorefractive polymer.   JOURNAL OF BIOMEDICAL OPTICS   17(8): Article Number: 080507   DOI: 10.1117/1.JBO.17.8.080507  

Makale, Milan; McElroy, Michele; O’Brien, Peter; et al.  2009.  Extended-working-distance multiphoton micromanipulation microscope for deep-penetration imaging in live mice and tissue.   JOURNAL OF BIOMEDICAL OPTICS   14(2): Article Number 024032   DOI:10.1117/1.3103783  

Lai, Puxiang; Xu, Xiao; Liu, Honglin; et al.  2012.  Time-reversed ultrasonically encoded optical focusing in biological tissue.   JOURNAL OF BIOMEDICAL OPTICS   17(3): Article Number 030506   DOI: 10.1117/1.JBO.17.3.030506  

Liu, Honglin; Xu, Xiao; Wang, Lihong V.  2011. Focusing light into turbid media: time-reversed ultrasonically encoded (TRUE) focusing. Book Editor(s): Oraevsky, AA; Wang, LV.   Conference on Photons Plus Ultrasound – Imaging and Sensing  Location: San Francisco, CA Date: JAN 23-25,  Proceedings of SPIE   7899:Article Number 78991A   DOI: 10.1117/12.876956