Recommended Readings: Tom Muir, Ph.D. Friday January 25, 2019

Friday Lectures

Friday, January 25, 2019  3:45 p.m

Caspary Auditorium

Tom Muir Ph.D.

Professor of Chemistry and Chair

Department of Chemistry

Princeton University

Painting Chromatin with Synthetic Protein Chemistry

 

Recommended Readings:

Empirical Articles

Nacev, B.A., Feng, L., Bagert, J.D. Lemiesz, A., et al. (2019). The expanding landscape of ‘oncohistone’ mutations in human cancers. NATURE, in press

Wojcik, Felix; Dann, Geoffrey P.; Beh, Leslie Y.; et al. (2018). Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. NATURE COMMUNICATIONS. 9

Lu, Chao; Jain, Siddhant U.; Hoelper, Dominik; et al. (2016). Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. SCIENCE. 352 (6287): 844-849

Nguyen, Uyen T. T.; Bittoval, Lenka; Mueller, Manuel M.; et al. (2014). Accelerated chromatin biochemistry using DNA-barcoded nucteosome libraries. NATURE METHODS. 11 (8): 834-840

Fierz, Beat; Kilic, Sinan; Hieb, Aaron R.; et al. (2012). Stability of Nucleosomes Containing Homogenously Ubiquitylated H2A and H2B Prepared Using Semisynthesis. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 134 (48): 19548-19551

Review Paper

David, Yael; Muir, Tom W. (2017). Emerging Chemistry Strategies for Engineering Native Chromatin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 139 (27): 9090-9096

Mueller, Manuel M.; Muir, Tom W. (2015). Histones: At the Crossroads of Peptide and Protein Chemistry. CHEMICAL REVIEWS. 115 (6): 2296-2349

Chatterjee, Champak; Muir, Tom W. (2010). Chemical Approaches for Studying Histone Modifications. JOURNAL OF BIOLOGICAL CHEMISTRY. 285 (15): 11045-11050

Book Chapter

Holt, Matthew; Muir, Tom (2015). Application of the Protein Semisynthesis Strategy to the Generation of Modified Chromatin. ANNUAL REVIEW OF BIOCHEMISTRY. 84: 265-290

McGinty, Robert K.; Chatterjee, Champak; Muir, Tom W. (2009). Semisynthesis of Ubiquitylated Proteins. METHODS IN ENZYMOLOGY: NON-NATURAL AMINO ACIDS. 462: 225-243

Recommended Readings: David Baker, Ph.D. Friday January 11, 2019

Friday Lectures

Friday, January 11, 2018  3:45 p.m

Caspary Auditorium

David Baker Ph.D.

Professor of Biochemistry and Director of the Institute for Protein Design

University of Washington

The Coming of Age of De Novo Protein Design

 

Recommended Readings:

Science News

Scientists program proteins to pair exactly. December 19, 2018. Science Daily

Empirical Articles

Shen, Hao; Fallas, Jorge A.; Lynch, Eric; et al. (2018). De novo design of self-assembling helical protein filaments. SCIENCE. 362 (6415): 705-709

Marcos, Enrique; Chidyausiku, Tamuka M.; McShan, Andrew C.; et al. (2018). De novo design of a non-local beta-sheet protein with high stability and accuracy. NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 25 (11): 1028-1030

Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William; et al. (2018). De novo design of a fluorescence-activating beta-barrel. NATURE. 561 (7724): 485-+

Lu, Peilong; Min, Duyoung; DiMaio, Frank; et al. (2018). Accurate computational design of multipass transmembrane proteins. SCIENCE. 359 (6379): 1042-1046

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple; et al. (2017). Comprehensive computational design of ordered peptide macrocycles. SCIENCE. 358 (6369): 1461-1466

Review Paper

Huang, Po-Ssu; Boyken, Scott E.; Baker, David. (2016). The coming of age of de novo protein design. NATURE. 537 (7620): 320-327

Fleishman, Sarel J.; Baker, David. (2012). Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution. CELL. 149 (2): 262-273

Book Chapter

Thyme, Summer; Baker, David. (2014). Redesigning the Specificity of Protein-DNA Interactions with Rosetta. HOMING ENDONUCLEASES: METHODS AND PROTOCOLS. 1123: 265-282

Whitehead, Timothy A.; Baker, David; Fleishman, Sarel J. (2013). Computational Design of Novel Protein Binders and Experimental Affinity Maturation. METHODS IN PROTEIN DESIGN. 523: 1-19

 Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.; et al. (2011). Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules. METHODS IN ENZYMOLOGY. 487: 545-574

 

Recommended Readings: Jue Chen, Ph.D., Monday December 10, 2018

Monday Lectures

Monday, December 10, 2018  4:00 p.m.

Carson Family Auditorium

Jue Chen, Ph.D.

William E. Ford Professor and Head

Laboratory of Membrane Biology and Biophysics

The Rockefeller University

CFTR, the Odd ABC Transporter Responsible for Cystic Fibrosis

 

Recommended Readings:

Empirical Articles

Kim, Youngjin; Chen, Jue. (2018). Molecular structure of human P-glycoprotein in the ATP-bound, outward-facing conformation. SCIENCE. 359 (6378): 915-919

Zhang, Zhe; Liu, Fangyu; Chen, Jue. (2017). Conformational Changes of CFTR upon Phosphorylation and ATP Binding. CELL. 170 (3): 483-+

Liu, Fangyu; Zhang, Zhe; Csanady, Laszlo; et al. (2017). Molecular Structure of the Human CFTR Ion Channel. CELL. 169 (1): 85-+

Zhang, Zhe; Chen, Jue. (2016). Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator. CELL. 167 (6): 1586-+

Oldham, Michael L.; Davidson, Amy L.; Chen, Jue. (2008). Structural insights into ABC transporter mechanism. CURRENT OPINION IN STRUCTURAL BIOLOGY. 18 (6): 726-733

Review Paper

Davidson, Amy L.; Dassa, Elie; Orelle, Cedric; et al. (2008). Structure, function, and evolution of bacterial ATP-binding cassette systems. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 72 (2): 317-364

 

Recommended Readings: Alexander Rudensky, Ph.D. Friday December 7, 2018

Friday Lectures

Friday, December 7, 2018  3:45 p.m

Caspary Auditorium

Alexander Rudensky Ph.D.

Tri-institutional Professor and Chair

Immunology Program

Memorial Sloan Kettering Cancer Center

Faces and Functions of Regulatory T Cells

 

Recommended Readings:

Empirical Articles

Fan, Xiying; Moltedo, Bruno; Mendoza, Alejandra; et al. (2018). CD49b defines functionally mature Treg cells that survey skin and vascular tissues. JOURNAL OF EXPERIMENTAL MEDICINE. 215 (11): 2796-2814  

Levine, Andrew G.; Medoza, Alejandra; Hemmers, Saskia; et al. (2017). Stability and function of regulatory T cells expressing the transcription factor T-bet. NATURE. 546 (7658): 421-+

Plitas, George; Konopacki, Catherine; Wu, Kenmin; et al. (2016). Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. IMMUNITY. 45 (5): 1122-1134

Chinen, Takatoshi; Kannan, Arun K.; Levine, Andrew G.; et al. (2016). An essential role for the IL-2 receptor in T-reg cell function. NATURE IMMUNOLOGY. 17 (11): 1322-1333

By: Feng, Yongqiang; Arvey, Aaron; Chinen, Takatoshi; et al. (2014). Control of the Inheritance of Regulatory T Cell Identity by a cis Element in the Foxp3 Locus. CELL. 158 (4): 749-763

Zheng, Ye; Josefowicz, Steven; Chaudhry, Ashutosh; et al. (2010). Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. NATURE. 463 (7282): 808-U120  

Review Paper

Li, Ming O.; Rudensky, Alexander Y. (2016). T cell receptor signalling in the control of regulatory T cell differentiation and function. NATURE REVIEWS IMMUNOLOGY. 16 (4): 220-233

Fan, Xiying; Rudensky, Alexander Y. (2016). Hallmarks of Tissue-Resident Lymphocytes. CELL. 164 (6): 1198-1211

Rudensky, Alexander Y. (2011). Regulatory T cells and Foxp3. IMMUNOLOGICAL REVIEWS. 241: 260-268

Book Chapter

Josefowicz, Steven Z.; Lu, Li-Fan; Rudensky, Alexander Y. (2012). Regulatory T Cells: Mechanisms of Differentiation and Function. ANNUAL REVIEW OF IMMUNOLOGY. 30: 531-564

 

Recommended Readings: Molly Przeworski, Ph.D. Friday November 30, 2018

Friday Lectures

Friday, November 30, 2018  3:45 p.m

Caspary Auditorium

Molly Przeworski Ph.D.

Professor

Department of Biological Sciences and Systems Biology

Columbia University

An Evolutionary Perspective on Meiotic Recombination in Vertebrates

 

Recommended Readings:

Science News

Hakhamanesh Mostafavi, Joe Pickrell and Molly Przeworski. Evolutionary geneticists spot natural selection happening now in people. September 11, 2017. The Conversation

Empirical Articles

Schumer, Molly; Xu, Chenling; Powell, Daniel L.; et al. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. SCIENCE. 360 (6389): 656-659  

Baker, Zachary; Schumer, Molly; Haba, Yuki; et al. (2017). Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. ELIFE. 6

Singhal, Sonal; Leffler, Ellen M.; Sannareddy, Keerthi; et al. (2015). Stable recombination hotspots in birds. SCIENCE. 350 (6263): 928-932

Auton, Adam; Fledel-Alon, Adi; Pfeifer, Susanne; et al. (2012). A Fine-Scale Chimpanzee Genetic Map from Population Sequencing. SCIENCE. 336 (6078): 193-198

Segurel, Laure; Leffler, Ellen Miranda; Przeworski, Molly. (2011). The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans. PLOS BIOLOGY. 9 (12)

Fledel-Alon, Adi; Leffler, Ellen Miranda; Guan, Yongtao; et al. (2011). Variation in Human Recombination Rates and Its Genetic Determinants. PLOS ONE.

Review Paper

Sella, Guy; Petrov, Dmitri A.; Przeworski, Molly; et al. (2009). Pervasive Natural Selection in the Drosophila Genome?. PLOS GENETICS. 5 (6)

Coop, Graham; Przeworski, Molly. (2007). An evolutionary view of human recombination. NATURE REVIEWS GENETICS. 8 (1): 23-34  

Book Chapter

Segurel, Laure; Wyman, Minyoung J.; Przeworski, Molly. (2014). Determinants of Mutation Rate Variation in the Human Germline. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 15: 47-70

Recommended Readings: Anna Wedell, M.D., Ph.D., Friday November 2, 2018

Friday Lectures

Friday, November 2, 2018  3:45 p.m.

Caspary Auditorium

Anna Wedell, M.D., Ph.D.

Professor

Department of Molecular Medicine and Surgery

Karolinska Institute

 

Clinical Whole Genome Sequencing Sheds Light on Novel Metabolic Pathways in the Brain

 

Recommended Readings:

Empirical Articles

Baric, Ivo; Staufner, Christian; Augoustides-Savvopoulou, Persephone; et al. (2017). Consensus recommendations for the diagnosis, treatment and follow-up of inherited methylation disorders. JOURNAL OF INHERITED METABOLIC DISEASE. 40 (1): 5-20

Siibak, Triinu; Clemente, Paula; Bratic, Ana; et al. (2017). A multi-systemic mitochondrial disorder due to a dominant p.Y955H disease variant in DNA polymerase gamma.  26 (13): 2515-2525

Dahlin, Maria; Martin, Daniel A.; Hedlund, Zandra; et al. (2015). The ketogenic diet compensates for AGC1 deficiency and improves myelination. EPILEPSIA. 56 (11): e176-e181

Brownstein, Catherine A.; Beggs, Alan H.; Homer, Nils; et al. (2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. GENOME BIOLOGY. (15) 3

Stranneheim, Henrik; Engvall, Martin; Naess, Karin; et al. (2014). Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism. BMC GENOMICS. 15

Gidlof, Sebastian; Falhammar, Henrik; Thilen, Astrid; et al. (2013). One hundred years of congenital adrenal hyperplasia in Sweden: a retrospective, population-based cohort study. LANCET DIABETES & ENDOCRINOLOGY. 1 (1): 35-42

Bjursell, Magnus K.; Blom, Henk J.; Cayuela, Jordi Asin; et al. (2011). Adenosine Kinase Deficiency Disrupts the Methionine Cycle and Causes Hypermethioninemia, Encephalopathy, and Abnormal Liver Function. AMERICAN JOURNAL OF HUMAN GENETICS. 89 (4): 507-515

Wibom, Rolf; Lasorsa, Francesco M.; Tohonen, Virpi; et al. (2009). AGC1 Deficiency Associated with Global Cerebral Hypomyelination.  NEW ENGLAND JOURNAL OF MEDICINE. 361 (5): 489-495

Recommended Readings: Mary E. Hatten, Ph.D., Monday November 12, 2018

Monday Lectures

Monday, November 12, 2018  4:00 p.m.

Carson Family Auditorium

Mary E. Hatten, Ph.D.

Frederick P. Rose Professor and Head

Laboratory of Developmental Neurobiology

The Rockefeller University

Neuronal Migration and the Formation of the Cerebellar Circuitry

Recommended Readings:

Science News

Florian Rosado. Insights Into Autism From The Protein Modulator ASTN2. . RELIAWIRE

Empirical Articles

Behesti, Hourinaz; Fore, Taylor R.; Wu, Peter; et al. (2018). ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins. PNAS. 115 (41): E9717-E9726

Govek, Eve-Ellen; Hatten, Mary E.; Van Aelst, Linda. (2011). The Role of Rho GTPase Proteins in CNS Neuronal Migration. DEVELOPMENTAL NEUROBIOLOGY. 71 (6): 528-553

Wilson, Perrin M.; Fryer, Robert H.; Fang, Yin; et al. (2010). Astn2, A Novel Member of the Astrotactin Gene Family, Regulates the Trafficking of ASTN1 during Glial-Guided Neuronal Migration. JOURNAL OF NEUROSCIENCE. 30 (25): 8529-8540

Solecki, David J.; Trivedi, Niraj; Govek, Eve-Ellen; et al. (2009). Myosin II Motors and F-Actin Dynamics Drive the Coordinated Movement of the Centrosome and Soma during CNS Glial-Guided Neuronal Migration. NEURON. 63 (1): 63-80

Review Paper

Hatten, Mary E.; Roussel, Martine F. (2011). Development and cancer of the cerebellum. TRENDS IN NEUROSCIENCES. 34 (3): 134-142

Book Chapter

Roussel, Martine F.; Hatten, Mary E. (2011). CEREBELLUM: Development and Medulloblastoma. CANCER AND DEVELOPMENT. 94: 235-282

Recommended Readings: Susan T. Fiske, Ph.D. Friday October 26, 2018

Friday Lectures

Friday, October 26, 2018  3:45 p.m.

Caspary Auditorium

Susan T. Fiske Ph.D.

Eugene Higgins Professor

Department of Psychology

Princeton University

Navigating the Social World: Universal Dimensions of Evaluation 

Recommended Readings:

Science News

Susan T. Fiske . A Call to Change Science’s Culture of Shaming. October 31, 2016. Association for Phychological Science

Empirical Articles

Fiske ST. (2018). Stereotype Content: Warmth and Competence Endure. CURRENT DIRECTIONS IN PSYCHOLOGICAL SCIENCE. 27(2) 67–73

Cikara, Mina; Eberhardt, Jennifer L.; Fiske, Susan T. (2011). From Agents to Objects: Sexist Attitudes and Neural Responses to Sexualized Targets. JOURNAL OF COGNITIVE NEUROSCIENCE. 23 (3): 540-551

Cikara, Mina; Farnsworth, Rachel A.; Harris, Lasana T.; et al. (2010). On the wrong side of the trolley track: neural correlates of relative social valuation. SOCIAL COGNITIVE AND AFFECTIVE NEUROSCIENCE. 5 (4): 404-413

Harris, Lasana T.; McClure, Samuel M.; van den Bos, Wouter; et al. (2007). Regions of the MPFC differentially tuned to social and nonsocial affective evaluation. COGNITIVE AFFECTIVE & BEHAVIORAL NEUROSCIENCE. 7 (4): 309-316

Harris, Lasana T.; Fiske, Susan T. (2007). Social groups that elicit disgust are differentially processed in mPFC. SOCIAL COGNITIVE AND AFFECTIVE NEUROSCIENCE. 2 (1): 45-51

Fiske ST, Cuddy AJ, Glick P, Xu J. (2002). A model of  (often mixed) stereotype content:  Competence and warmth respectively follow from perceived status and competition. JOURNAL OF PERSONALITY AND SOCIAL PSYCHOLOGY. 82: 878-902

Review Paper

Fiske, Susan T.; Borgida, Eugene. (2008). Providing Expert Knowledge in an Adversarial Context: Social Cognitive Science in Employment Discrimination Cases.  ANNUAL REVIEW OF LAW AND SOCIAL SCIENCE. 4: 123-148

Fiske, Susan T.; Cuddy, Amy J. C.; Glick, Peter. (2007). Universal dimensions of social cognition: warmth and competence.  TRENDS IN COGNITIVE SCIENCES. 11 (2): 77-83

Book Chapter

Cuddy, Amy J. C.; Fiske, Susan T.; Glick, Peter. (2008). Warmth and competence as universal dimensions of social perception: The stereotype content model and the BIAS.  ADVANCES IN EXPERIMENTAL SOCIAL PSYCHOLOGY-BOOK. 40: 61-149. PLEASE REQUEST FROM MARKUS LIBRARY.

Books

Borgida, E., & Fiske, S. T. (Eds.). (2008). Beyond common sense: Psychological science in the courtroom. London: Wiley-Blackwell. PLEASE REQUEST FROM MARKUS LIBRARY.

Fiske, S. T., & Taylor, S. E. (1984, 1991, 2008, 2013). Social cognition: From brains to culture. London: Sage. PLEASE REQUEST FROM MARKUS LIBRARY.

Recommended Readings: Howard C. Hang, Ph.D. Friday October 19, 2018

Friday Lectures

Friday, October 19, 2018  3:45 p.m.

Caspary Auditorium

Howard C. Hang Ph.D.

Richard E. Salomon Family Associate Professor and Head

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

Chemical Dissection of Host-Microbe Interactions

Recommended Readings:

Empirical Articles

Liu W, Zhou Y, Peng T, Zhou P, Ding X, Li Z, Zhong H, Xu Y, Chen S, Hang HC, Shao F. (2018). Nε-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function. NATURE MICROBIOLOGY. 3 (9): 996-1009

Thinon, Emmanuelle; Fernandez, Joseph P.; Molina, Henrik; et al. (2018). Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites. JOURNAL OF PROTEOME RESEARCH. 17 (5): 1907-1922

Westcott N, Fernandez JP, Molina H, Hang HC. (2017). Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress. NATURE CHEMICAL BIOLOGY. 13 (3): 302-308

Peng T, Hang HC. (2016). Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138 (43): 14423-14433

Rangan, Kavita J.; Pedicord, Virginia A.; Wang, Yen-Chih; et al. (2016). A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. SCIENCE. 353 (6306): 1434-1437

Percher, Avital; Ramakrishnan, Srinivasan; Thinon, Emmanuelle; et al. (2016). Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation. PNAS. 113 (16): 4302-7

Review Paper

Peng, Tao; Thinon, Emmanuelle; Hang, Howard C. (2016). Proteomic analysis of fatty-acylated proteins. CURRENT OPINION IN CHEMICAL BIOLOGY. 30: 77-86

Westcott, Nathan P.; Hang, Howard C. (2014). Chemical reporters for exploring ADP-ribosylation and AMPylation at the host-pathogen interface.  CURRENT OPINION IN CHEMICAL BIOLOGY. 23: 56-62

Grammel, Markus; Hang, Howard C. (2013). Chemical reporters for biological discovery. NATURE CHEMICAL BIOLOGY. 9 (8): 475-484

Recommended Readings: Titia de Lange, Ph.D., Monday October 15, 2018

Monday Lectures

Monday, October 15, 2018  4:00 p.m.

Carson Family Auditorium

Titia de Lange, Ph.D.

Leon Hess Professor and Head

Laboratory of Cell Biology and Genetics

The Rockefeller University

 

Understanding DSB Repair: How Telomeres Gave Us a Break(through)

 

Recommended Readings:

Science News

Scientists discover a mechanism of drug resistance in breast and ovarian cancer. July 18, 2018. ScienceDaily 

Empirical Articles

Mirman Z, Lottersberger F, Takai H, Kibe T. et al. (2018). 53BP1-RIF1-shieldin counteracts DSB resection through CST- and Polα-dependent fill-in. NATURE. 560 (7716): 112-116

Gong, Yi; Handa, Naofumi; Kowalczykowski, Stephen C.; et al. (2017). PHF11 promotes DSB resection, ATR signaling, and HR. GENES AND DEVELOPMENT. 31 (1): 46-58

Doksani, Ylli; de Lange, Titia. (2016). Telomere-Internal Double-Strand Breaks Are Repaired by Homologous Recombination and PARP1/Lig3-Dependent End-Joining. CELL REPORTS. 17 (6)1646-1656

Lottersberger, Francisca; Karssemeijer, Roos Anna; Dimitrova, Nadya; et al. (2015). 53BP1 and the LINC Complex Promote Microtubule-Dependent DSB Mobility and DNA Repair. CELL. 163 (4):  880-893 

Doksani Y, de Lange T. (2014). The role of double-strand break repair pathways at functional and dysfunctional telomeres. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 6 (12)

Zimmermann, Michal; Lottersberger, Francisca; Buonomo, Sara B.; et al. (2013). 53BP1 Regulates DSB Repair Using Rif1 to Control 5 ‘ End Resection. SCIENCE. 339 (6120): 700-704

Lottersberger, Francisca; Bothmer, Anne; Robbiani, Davide F.; et al. (2013). Role of 53BP1 oligomerization in regulating double-strand break repair. PNAS. 110 (6): 2146-2151

Review Papers

Maciejowski, John; de lange, Titia. (2017). Telomeres in cancer: tumour suppression and genome instability. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 18 (3): 175-186

Zimmerman, Michal; de Lange, Titia. (2014). 53BP1: pro choice in DNA repair. TRENDS IN CELL BIOLOGY. 24 (2)108-117