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: Sean F. Brady, Ph.D., Friday October 27th, 2017

Friday Lectures

Friday, October 27, 2017  3:45 p.m.

Caspary Auditorium

Sean F. Brady, Ph.D.

Evnin Associate Professor and Head

Laboratory of Genetically Encoded Small Molecules

The Rockefeller University

Watch your step, there is new chemistry everywhere

Recommended Readings:

Cohen LJ, Han S, Huang YH, Brady SF. (2017). Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library.  ACS Infect Dis.  In Press doi: 10.1021/acsinfecdis.7b00081

Fierer, Noah (2017). Embracing the unknown: disentangling the complexities of the soil microbiome. NATURE REVIEWS MICROBIOLOGY. 15 (10): 579-590

Chu, John; Vila-Farres, Xavier; Inoyama, Daigo; et al. (2016). Discovery of MRSA active antibiotics using primary sequence from the human microbiome.  NATURE CHEMICAL BIOLOGY. 12 (12): 1004-+

O’Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.; et al. (2016). Spatial scale drives patterns in soil bacterial diversity.  ENVIRONMENTAL MICROBIOLOGY. 18 (6): 2039-2051

Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin; et al. (2015). Minimum Information about a Biosynthetic Gene cluster. NATURE CHEMICAL BIOLOGY. (11) 9: 625-631

Owen, Jeremy G.; Reddy, Boojala Vijay B.; Ternei, Melinda A.; et al. (2013). Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. PNAS. 110 (29): 11797-11802  

 

Recommended Readings: Sean F. Brady Ph.D. May 10, 2010

Monday Seminar Series

Culture Independent Approaches for the

Discvoery of New Bacterial Metabolites

Sean F. Bady  Ph.D.,

Laboratory of Geneticall Encoded Small Molecules

Howard Hughes Medical Institute, The Rockefeller University

May 10, 2010

3:45 p.m.-5:00 p.m.  Welch Hall Level two

 

Recommended Articles:

 Simon, C;  Daniel, R.   2009.  Achievements and new knowledge unraveled by metagenomic approaches.  APPLIED MICROBIOLOGY AND BIOTECHNOLOGY    85(2): 265-276     Request from Markus Library.

 McAlpine, J. B.    2009.  Advances in the Understanding and Use of the Genomic Base of Microbial Secondary Metabolite Biosynthesis for the Discovery of New Natural Products.   JOURNAL OF NATURAL PRODUCTS,   72(3, Sp. Iss. SI): 566-572      Request from Markus Library.   

 Brady S.F; Simmons L;  Kim J.H. et al.   2009.  Metagenomic approaches to natural products from free-living and symbiotic organisms .   NATURAL PRODUCT REPORTS.    26(11): 1488-1503    Request from Markus Library.

 King, R. W.; Bauer, J. D.; Brady, S.F.    2009.  An Environmental DNA-Derived Type II Polyketide Biosynthetic Pathway Encodes the Biosynthesis of the Pentacyclic Polyketide ErdacinANGEWANDTE CHEMIE-INTERNATIONAL EDITION     48( 34): 6257-6261    

 Banik, J J; Brady, S. F.    2008.  Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary .  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.     105(45):17273-17277    

 Sharma P;  Kumari, H;  Kumar, M; Verna, M;  KUmariu K;  Malhotra, S;  Kurana, J; Lal, R.  2008.   From bacterial genomics to metagenomics: concept, tools and recent advances.   Indian Journal of Microbiology.  48(2);173-194.  Requesst from Markus Library.

  Brady SF, Bauer JD, Clarke-Pearson MF, et al.   2007. Natural products from isnA-containing biosynthetic gene clusters recovered from the genomes of cultured and uncultured bacteria.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.   129( 40): 12102-+    

 

 

 

 

Related Readings – Dominique Frueh Ph.D.

Dynamic Communication in Nonribosomal Peptide Synthetases:

The T-TE Di-domain of Enterobactin Synthetase

Monday, March 31, 2008

Welch Hall    Markus Library Level Two     4 p.m.     Refreshments at 3:45 p.m.

Recommended Review Article:

Donadio, S.; Monciardini, P; and m. Sosio. (2007). Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics.   Natural Products Reports. 24(5): 1073-1109

Related Articles:

Wilkinson, B. and J. Micklefield. (2007). Mining and engineering natural-product biosynthetic pathways.   Nature Chemical Biology   3(7):379-386

Tang, G.L.; YQ. Cheng; and B. Shen. (2007). Chain initiation in the leinamycin-producing hybrid nonribosomal peptide/polyketide synthetase from Streptomyces atroolivaceus S-140 – Discrete, monofunctional adenylation enzyme and peptidyl carrier protein that directly load D-Alanine.  Journal of Biological Chemistry  282(28):20273-20282

Zhou, Z.; Lai, J. R.; and Walsh, C.T. (2006). Interdomain communication between the thiolation and thioesterase domains of EntF explored by combinatorial mutagenesis and selection.  Chemistry & Biology   13(8):869-879

Doekel, S. (2000). Dipeptide formation on engineered hybrid peptide synthetases. Chemistry & Biology  7(6):373-384

Samuel, S.A. (2006) The thioesterase domain of the fengycin biosynthesis cluster: a structural base for the macrocyclization of a non-ribosomal lipopeptide. Journal of Molecular Biology  359:876-889

Shawreid, C.A. (1999). Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E-coli EntF catalyzes both elongation and cyclolactonization. Chemistry & Biology 6(6):385-400