Recommended Readings: Daniel Kronauer, Ph.D., Friday September 15th, 2017

Friday Lectures

Friday, September 15, 2017  3:45 p.m.

Caspary Auditorium

Daniel Kronauer, Ph.D.

Stanley S. and Sydney R. Shuman Assistant Professor and Head

Laboratory of Social Evolution and Behavior

The Rockefeller University

Communication and Social Behavior in Ants

Recommended Readings:

News provided by NYU Langone Health (2017). Mutant Ants provide insights into social interaction.

Trible, Waring; Olivos-Cisneros, Leonora; McKenzie, Sean K.; et al. (2017). orco Mutagenesis Causes Loss of Antennal Lobe Glomeruli and Impaired Social Behavior in Ants. CELL. 170 (4): 727-+  

McKenzie, Sean K.; Fetter-Pruneda, Ingrid; Ruta, Vanessa; et al. (2016). Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication. PNAS. 113 (49): 14091-14096

Leonhardt, Sara Diana; Menzel, Florian; Nehring, Volker; et al. (2016). Ecology and Evolution of Communication in Social Insects. CELL. 164 (6): 1277-1287

Oxley, Peter R.; Ji, Lu; Fetter-Pruneda, Ingrid; et al. (2014). The Genome of the Clonal Raider Ant Cerapachys biroi. CURRENT BIOLOGY. 24 (4): 451-458  

Sumner, Seirian (2014). The importance of genomic novelty in social evolution. MOLECULAR ECOLOGY. 23 (1): 26-28


Recommended Readings: Jon Clardy, Ph.D. March 24, 2017

Friday Lectures

Friday, March 24, 2017   3:45 p.m.

Caspary Auditorium

Jon Clardy, Ph.D.

Hsien Wu and Daisy Yen Wu Professor,

Department of Biological Chemistry and Molecular Pharmacology

The Rockefeller University

Small Molecule Modulators of Multilateral Symbioses

Recommended Readings:

Pupo, Monica T.; Currie, Cameron R.; Clardy, Jon (2017). Microbial Symbionts of Insects are the Focus of the First International Cooperative Biodiversity Group (ICBG) in Brazil. JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY. 28 (3): 393-401

Ruzzini, Antonio C.; Clardy, Jon (2016). Gene Flow and Molecular Innovation in Bacteria. CURRENT BIOLOGY. 26(18)R859-R864

Cantley, Alexandra M.; Clardy, Jon (2015). Animals in a bacterial world: opportunities for chemical ecology.  NATURAL PRODUCT REPORTS. 32(7): 888-892

Sit, Clarissa S.; Ruzzini, Antonio C.; Van Arnam, Ethan B.; et al. (2015). Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112(43)13150-13154

Ramadhar, Timothy R.; Beemelmanns, Christine; Currie, Cameron R.; et al. (2014). Bacterial symbionts in agricultural systems provide a strategic source for antibiotic discover. JOURNAL OF ANTIBIOTICS. 67(1): 53-58

Crawford, Jason M.; Clardy, Jon (2011). Bacterial symbionts and natural products. CHEMICAL COMMUNICATIONS. 47(27): 7559-7566

Oh, Dong-Chan; Poulsen, Michael; Currie, Cameron R.; et al. (2009). Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis.  NATURE CHEMICAL BIOLOGY. 5(6) 391-393




Recommended Readings: Elly Tanaka, Ph.D. March 17, 2017

Friday Lectures

Friday, March 17, 2017   3:45 p.m.

Caspary Auditorium

Elly Tanaka, Ph.D.

Senior Scientist,

Research Institute of Molecular Pathology, Vienna, Austria

The Control of Growth, Signaling, and Patterning during Vertebrate Limb Regeneration

Recommended Readings:

Tanaka, Elly M. (2016). The Molecular and Cellular Choreography of Appendage on Regeneration. CELL. 165(7): 1598-1608

Tornini, Valerie A.; Puliafito, Alberto; Slota, Leslie A.; et al. (2016). Live Monitoring of Blastemal Cell Contributions during Appendage Regeneration. CURRENT BIOLOGY. 26(22): 2981-2991 

Sandoval-Guzman, Tatiana; Wang, Heng; Khattak, Shahryar; et al. (2014). Fundamental Differences in Dedifferentiation and Stem Cell Recruitment during Skeletal Muscle Regeneration in Two Salamander Species. CELL STEM CELL. 14(2): 174-187

Khattak, Shahryar; Schuez, Maritta; Richter, Tobias; et al. (2013). Germline Transgenic Methods for Tracking Cells and Testing Gene Function during Regeneration in the Axolotl. STEM CELL REPORTS. 1(1): 90-103

Simon, Andras; Tanaka, Elly M. (2013). Limb regeneration.  WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY. 2(2): 291-300

Recommended Readings: Frederick Cross Ph.D. Monday December 5, 2016

Monday Lectures

 December 5, 2016

4:00 p.m.  Carson Family Auditorium  CRC

Frederick Cross  Ph.D.

Professor,  Laboratory of Cell Cycle Genetics

The Rockefeller University

Evolution of Cell Cycle Control:

Branches and a Green Microbe

Recommended Readings:

Tulin, Frej; Cross, Frederick R.  Patching Holes in the Chlamydomonas Genome.  G3-GENES GENOMES GENETICS   6(7): 1899-1910   JUL 1 2016

Onishi, Masayuki; Pringle, John R.; Cross, Frederick R.   Evidence That an Unconventional Actin Can Provide Essential F-Actin Function and That a Surveillance System Monitors F-Actin Integrity in Chlamydomonas.  GENETICS    202(30): 977-+  MAR 2016

Tulin, Frej; Cross, Frederick R.   A Microbial Avenue to Cell Cycle Control in the Plant Superkingdom.   PLANT CELL   26(10): 4019-4038     OCT 2014

Cross, Frederick R.; Umen, James G.  The Chlamydomonas cell cycle   PLANT JOURNAL   82(3): 370-392   MAY 2015

Recommended Readings: Nicole King Ph.D. October 7 2016

Friday Lecture Series

Friday October 7, 2016   3:45 p.m.

The Fairfield Osborn Memorial Lecture

Caspary Auditorium

Nicole King

Professor, and HHMI Investigator

Dept.of Molecular and Cell Biology, Division of Genetics, Genomics and Development

University of California Berkeley

Bacteria as Master Regulators and Aphrodisiacs

Recommended Readings:

Anderson, Douglas P.; Whitney, Dustin S.; Hanson-Smith, Victor; et al.  Evolution of an ancient protein function involved in organized multicellularity in animals. ELIFE                   5: e10147    JAN 7 2016

Alegado, Rosanna A.; King, Nicole  Bacterial Influences on Animal OriginsCOLD SPRING HARBOR PERSPECTIVES IN BIOLOGY    6(11): a016162  NOV 2014

King, Nicole.  Evolutionary Transitions to Multicellular Life Principles and Mechanisms Forrward.  EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE: PRINCIPLES AND MECHANISMS   Book Series:Advances in Marine Genomics   Volume: 2   Pages: V-VI    2015

King, Nicole; Mueller, Susann.  Environmental microbiology: Revisiting the physiology of microorganisms on the single cell scale. CURRENT OPINION IN MICROBIOLOGY     Volume: 25   Pages: V-VI   Published: JUN 2015

Recommended Readings: Uri Alon Ph.D. October 28 2016

Friday Lecture Series

Friday  October 28  2016    3:45  p.m.

Caspary Auditorium

Uri Alon

Professor, Department of Molecular Cell Biology

Weizmann Institute of Science

Evolutionary Trade Offs and the Geometry of Phenotype Space

Recommended Readings:

Keren, Leeat; Hausser, Jean; Lotan-Pompan, Maya; et al. Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness. CELL    166(5):1282-+  AUG 25 2016

Korem, Yael; Szekely, Pablo; Hart, Yuval; et al. Geometry of the Gene Expression Space of Individual Cells. PLOS COMPUTATIONAL BIOLOGY    11(7):e1004224   JUL 2015

Tendler, Avichai; Mayo, Avraham; Alon, Uri  Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells. BMC SYSTEMS BIOLOGY  V 9: article number: 12   MAR 7 2015

Szekely, Pablo; Sheftel, Hila; Mayo, Avi; et al. Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems.  PLOS COMPUTATIONAL BIOLOGY.   9(8): e1003163    AUG 2013

Sheftel, Hila; Shoval, Oren; Mayo, Avi; et al. The geometry of the Pareto front in biological phenotype space. ECOLOGY AND EVOLUTION.   3(6):1471-1483    JUN 2013

Recommended Readings: Michael Levine Ph.D. Sept 30, 2016

Friday Lecture Series

Norton Zinder Lecture

Michael Levine, Ph.D.

Director, Lewis-Sigler Institute for Integrative Genomics, Princeton Univ.

Anthony B. Evnin Professor, Dept Molecular Biology, Princeton Univ.

Visualization and evolution of transcriptional enhancers

Recommended Readings:

Bothma, J.P., Garcia, H.G., Ng, S., Perry, M.W., Gregor, T., and Levine, M. (2015). Enhancer additivity and nonadditivity are determined by enhancer strength in the Drosophila embryo. eLife 4, 07956.

Farley, E.K., Olson, K.M., Zhang, W., Brandt, A.J., Rokhsar, D.S., and Levine, M. (2015). Suboptimization of developmental enhancers. Science 350, 325-328.

Fukaya, T., Lim, B., and Levine, M. 2016. Enhancer control of transcriptional bursting. Cell 166, 358-368.

Bothma, J., Garcia, H., Gavin, S., Esposito, E., Gregor, T., and Levine, M. (2014). Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. PNAS 111, 10598-10603.

Evans, Nicole C.; Swanson, Christina I.; Barolo, Scott.  Sparkling Insights into Enhancer Structure, Function, and Evolution.  TRANSCRIPTIONAL SWITCHES DURING DEVELOPMENT   Book Series: Current Topics in Developmental Biology .  98: 97-120   2012

Gordon, Kacy L.; Ruvinsky, Ilya.  Tempo and Mode in Evolution of Transcriptional Regulation.  PLOS GENETICS.   8(1): e1002432    2012

Recommended Readings: Li Zhao, Ph.D., March 2

Special Lecture Series
Wednesday, March 2, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Li Zhao, Ph.D.
Postdoctoral Researcher,
Department of Evolution and Ecology,
University of California Davis

Evolution of Genetic Novelties in Drosophila

Recommended Reading

Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., … & Ding, Y. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature Communications, 6(8212). doi:10.1038/ncomms9212

Zhao, L., Saelao, P., Jones, C. D., & Begun, D. J. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science, 343(6172), 769-772. doi: 10.1126/science.1248286.

Zhao, L., Wit, J., Svetec, N., & Begun, D. J. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS Genetics, 11(5), e1005184. doi: 10.1371/journal.pgen.1005184.

Recommended Readings: Neil H. Shubin, Ph.D. December 17

Special Seminar Series
Wednesday, December 17, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Neil H. Shubin, Ph.D.
Robert R. Bensley Distinguished Service Professor,
Senior Advisor to the President,
Department of Organismal Biology and Anatomy,
The University of Chicago

Organogenesis in Deep Time

Recommended Readings

Empirical Papers

Amemiya, C. T., Alföldi, J., Lee, A. P., Fan, S., Philippe, H., Maccallum, I., … Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311–316. doi:10.1038/nature12027

Dahn, R. D., Davis, M. C., Pappano, W. N., & Shubin, N. H. (2007). Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning. Nature, 445(7125), 311–314. doi:10.1038/nature05436

Davis, M. C., Dahn, R. D., & Shubin, N. H. (2007). An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature, 447(7143), 473–476. doi:10.1038/nature05838

Shubin, N. H., Daeschler, E. B., & Jenkins, F. a. (2006). The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature, 440(7085), 764–771. doi:10.1038/nature04637

Review Articles

Schneider, I., & Shubin, N. H. (2013). The origin of the tetrapod limb: from expeditions to enhancers. Trends in Genetics, 29(7), 419–426. doi:10.1016/j.tig.2013.01.012

Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty. Nature, 457(7231), 818–823. doi:10.1038/nature07891

Was the Cerebellum the Center of Evolutionary Change That Makes Us Human?

When we search for the seat of humanity, are we looking at the wrong part of the brain? Most neuroscientists assume that the neocortex, the brain’s distinctive folded outer layer, is the thing that makes us uniquely human. But a new study suggests that another part of the brain, the cerebellum, grew much faster in our ape ancestors.

Read more on this new research in Current Biology.