Recommended Readings: Christopher Chang, Ph.D. Wednesday March 6, 2019

Special Seminar Series

Wednesday, March 6, 2019  4:00 p.m.

Carson Family Auditorium

Christopher Chang, Ph.D.

Chair Professor

Department of Chemistry and Molecular and Cell Biology

University of California, Berkeley

Deciphering Transition Metal Signaling with Activity-Based Sensing

 

Recommended Readings:

Empirical Articles

Su TA, Shihadih DS, Cao W, Detomasi TC, Heffern MC, Jia S, Stahl A, Chang CJ. (2018). A Modular Ionophore Platform for Liver-Directed Copper Supplementation in Cells and Animals. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 140 (42): 13764–13774

Xiao, T.; Ackerman, C. M.; Carroll, E. C.; Jia, S.; et al. (2018). Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system. NATURE CHEMICAL BIOLOGY. 14: 655-663

Smith, P. T.; Benke, B. P.; Cao, Z.; Kim, et al. (2018). Iron Porphyrins Embedded into a Supramolecular Porous Organic Cage for Electrochemical CO2 Reduction in Water. ANGEWANDTE CHEMIE INTERNATIONAL EDITION. 57: 9684-9688

Aron, Allegra T.; Loehr, Morten O.; Bogena, Jana; et al. (2016). An Endoperoxide Reactivity-Based FRET Probe for Ratiometric Fluorescence Imaging of Labile Iron Pools in Living Cells. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138 (43): 14338-14346

Dodani, Sheel C.; Firl, Alana; Chan, Jefferson; et al. (2014). Copper is an endogenous modulator of neural circuit spontaneous activity. PNAS. 11 (46): 16280-16285

Dodani, Sheel C.; Domaille, Dylan W.; Nam, Christine I.; et al. (2011). Calcium-dependent copper redistributions in neuronal cells revealed by a fluorescent copper sensor and X-ray fluorescence microscopy. PNAS. 108 (15): 5980-5985

Review Papers

Chang CJ. (2017). Bioinorganic Life and Neural Activity: Toward a Chemistry of Consciousness? ACCOUNTS OF CHEMICAL RESEARCH. 50 (3): 535-538

Ackerman, Cheri M.; Lee, Sumin; Chang, Christopher J. (2017). Analytical Methods for Imaging Metals in Biology: From Transition Metal Metabolism to Transition Metal Signaling. ANALYTICAL CHEMISTRY. 89 (1): 22-41

Cotruvo, Joseph A., Jr.; Aron, Allegra T.; Ramos-Torres, Karla M. et al. (2015). Synthetic fluorescent probes for studying copper in biological systems. CHEMICAL SOCIETY REVIEWS. 44 (13): 4400-4414

 

Recommended Readings: Howard C. Hang, Ph.D. Monday February 25, 2019

Monday Lectures

Monday, February 25, 2019  4:00 p.m.

Carson Family Auditorium

Howard C. Hang Ph.D.

Richard E. Salomon Family Associate Professor and Head

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

Microbiota Modulation of Host Immunity, the SagA continues

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

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

Pedicord, Virginia A.; Lockhart, Ainsley A. K.; Rangan, Kavita J.; et al. (2016). Exploiting a host-commensal interaction to promote intestinal barrier function and enteric pathogen tolerance. SCIENCE IMMUNOLOGY. 1 (3)    

Review Paper

Rangan, Kavita J.; Hang, Howard C. (2017). Biochemical Mechanisms of Pathogen Restriction by Intestinal Bacteria. TRENDS IN BIOCHEMICAL SCIENCES. 42 (11): 887-898

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: Jodi Nunnari, Ph.D. Friday February 15, 2019

Friday Lectures

Friday, February 15, 2019  3:45 p.m

Caspary Auditorium

Jodi Nunnari Ph.D.

Professor and Chair

Department of Molecular and Cellular Biology

University of California

Natural Products as Probes of the Pain Pathway: From Physiology to Atomic Structure

Recommended Readings:

Empirical Articles

Mallat, A.; Uchiyama, L. F.; Lewis, S. C.; et al. (2018). Discovery and characterization of selective small molecule inhibitors of the mammalian mitochondrial division dynamin, DRP1. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 499  (3): 556-562

Lewis, Samantha C.; Uchiyama, Lauren F.; Nunnari, Jodi. (2016). ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells. SCIENCE. 353 (6296)

Labbe, Katherine; Murley, Andrew; Nunnari, Jodi. (2014). Determinants and Functions of Mitochondrial Behavior. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 357-391

Review Papers

Murley, Andrew; Nunnari, Jodi. (2016). The Emerging Network of Mitochondria-Organelle Contacts. MOLECULAR CELL. 61 (5): 648-653

Friedman, Jonathan R.; Nunnari, Jodi. (2014). Mitochondrial form and function. NATURE. 505 (7483): 335-343

Nunnari, Jodi; Suomalainen, Anu. (2012). Mitochondria: In Sickness and in Health. CELL. 148 (6): 1145-1159

Book Chapter

Labbe, Katherine; Murley, Andrew; Nunnari, Jodi. (2014). Determinants and Functions of Mitochondrial Behavior. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 357-391

Recommended Readings: David Keays, Ph.D. Monday March 4, 2019

Special Seminar Series

Monday, March 4, 2019  4:00 p.m.

Carson Family Auditorium

David Keays, Ph.D.

Group Leader

Research Institute of Molecular Pathology – Vienna, Austria

The Mysterious Magnetoreceptors

 

Recommended Readings:

Empirical Articles

Landler, Lukas; Keays, David A. (2018). Cryptochrome: The magnetosensor with a sinister side? PLOS BIOLOGY. 16 (10)

Engels, Svenja; Treiber, Christoph Daniel; Salzer, Marion Claudia; et al. (2018). Lidocaine is a nocebo treatment for trigeminally mediated magnetic orientation in birds. JOURNAL OF THE ROYAL SOCIETY INTERFACE. 15 (145)

Nimpf, Simon; Malkemper, Erich Pascal; Lauwers, Mattias; et al. (2017). Subcellular analysis of pigeon hair cells implicates vesicular trafficking in cuticulosome formation and maintenance. ELIFE. 6

Nimpf, Simon; Keays, David A. (2017). Is magnetogenetics the new optogenetics? EMBO JOURNAL. 36 (12): 1643-1646

Nordmann, Gregory C.; Hochstoeger, Tobias; Keays, David A. (2017). Unsolved mysteries: Magnetoreception-A sense without a receptor. PLOS BIOLOGY. 15 (10)

Edelman, Nathaniel B.; Fritz, Tanja; Nimpf, Simon; et al. (2015). No evidence for intracellular magnetite in putative vertebrate magnetoreceptors identified by magnetic screening. PNAS. 112 (1): 262-267

Lauwers, Mattias; Pichler, Paul; Edelman, Nathaniel Bernard; et al. (2013). An Iron-Rich Organelle in the Cuticular Plate of Avian Hair Cells. CURRENT BIOLOGY. 23 (10): 924-929

Treiber, Christoph Daniel; Salzer, Marion Claudia; Riegler, Johannes; et al. (2012). Clusters of iron-rich cells in the upper beak of pigeons are macrophages not magnetosensitive neurons. NATURE. 484 (7394): 367-U102

 

Recommended Readings: David Julius, Ph.D. Friday February 8, 2019

Friday Lectures

Friday, February 8, 2019  3:45 p.m

Caspary Auditorium

David Julius Ph.D.

Morris Herzstein Chair in Molecular Biology and Medicine

Professor and Chair of Physiology

University of California

Natural Products as Probes of the Pain Pathway: From Physiology to Atomic Structure

Recommended Readings:

Empirical Articles

Gao, Yuan; Cao, Erhu; Julius, David; et al. (2016). TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. NATURE. 534 (7607): 347-+

Paulsen, Candice E.; Armache, Jean-Paul; Gao, Yuan; et al. (2015). Structure of the TRPA1 ion channel suggests regulatory mechanisms. NATURE. 520 (7548): 511-+

Liao, Maofu; Cao, Erhu; Julius, David; et al. (2013). Structure of the TRPV1 ion channel determined by electron cryo-microscopy. NATURE. 504 (7478): 107-+

Cavanaugh, Daniel J.; Chesler, Alexander T.; Jackson, Alexander C.; et al. (2011). Trpv1 Reporter Mice Reveal Highly Restricted Brain Distribution and Functional Expression in Arteriolar Smooth Muscle Cells. JOURNAL OF NEUROSCIENCE. 31 (13): 5067-5077

Cordero-Morales, Julio F.; Gracheva, Elena O.; Julius, David. (2011). Cytoplasmic ankyrin repeats of transient receptor potential A1 (TRPA1) dictate sensitivity to thermal and chemical stimuli. PNAS. 108 (46): E1184-E1191

Cavanaugh, Daniel J.; Chesler, Alexander T.; Braz, Joao M.; et al. (2011). Restriction of Transient Receptor Potential Vanilloid-1 to the Peptidergic Subset of Primary Afferent Neurons Follows Its Developmental Downregulation in Nonpeptidergic Neurons. JOURNAL OF NEUROSCIENCE. 31 (28): 10119-10127

Review Papers

Bohlen, Christopher J.; Julius, David (2012). Receptor-targeting mechanisms of pain-causing toxins: How ow? TOXICON. 60 (3): 254-264

Basbaum, Allan I.; Bautista, Diana M.; Scherrer, Gregory; et al. (2009). Cellular and Molecular Mechanisms of Pain. CELL. 139 (2): 267-284

Book Chapter

Julius, David. (2013). TRP Channels and Pain. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 29: 355-384

 

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