Recommended Readings: Vamsi Mootha, M.D. Friday November 17th, 2017

Friday Lectures

Friday, November 17, 2017  3:45 p.m.

Caspary Auditorium

Vamsi Mootha, M.D.

Professor

Systems Biology and Medicine

Harvard Medical School and Massachusetts General Hospital

Genome-scale Approaches to Mitochondrial Disease

Recommended Readings:

Science News

Howard Hughes Medical Institute. (2017, May 8). Low oxygen reverses mitochondrial disease in mice. ScienceDaily

Empirical Articles

Ferrari, Michele; Jain, Isha H.; Goldberger, Olga; et al. (2017). Hypoxia treatment reverses neurodegenerative disease in a mouse model of Leigh syndrome. PNAS. 114 (21): E4241-E4250

Jain, Isha H.; Zazzeron, Luca; Goli, Rahul; et al. (2016). Hypoxia as a therapy for mitochondrial disease. SCIENCE. 352 (6281): 54-61  

Titov, Denis V.; Cracan, Valentin; Goodman, Russell P.; et al. (2016). Complementation of mitochondrial electron transport chain by manipulation of the NAD(+)/NADH ratio. SCIENCE. 352 (6282): 231-235

Calvo, Sarah E.; Clauser, Karl R.; Mootha, Vamsi K. (2016). MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins.  NUCLEIC ACIDS RESEARCH. 44 (D1): D1251-D1257

Lake, Nicole J.; Bird, Matthew J.; Isohanni, Pirjo; et al. (2015). Leigh Syndrome: Neuropathology and Pathogenesis. JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY. 74 (6): 482-492  

Lieber, Daniel S.; Calvo, Sarah E.; Shanahan, Kristy; et al. (2013). Targeted exome sequencing of suspected mitochondrial disorders. NEUROLOGY. 80 (19): 1762-1770

Calvo, Sarah E.; Compton, Alison G.; Hershman, Steven G.; et al. (2012). Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing. SCIENCE TRANSLATIONAL MEDICINE. 4 (118)

Calvo, S; Jain, M; Xie, XH; et al. (2006). Systematic identification of human mitochondrial disease genes through integrative genomics. NATURE GENETICS. 38 (5): 576-582

Review Papers

Kamer, Kimberli J.; Mootha, Vamsi K. (2015). The molecular era of the mitochondrial calcium uniporter.  NATURE REVIEWS MOLECULAR CELL BIOLOGY. 16 (9): 545-553

Vafai, Scott B.; Mootha, Vamsi K. (2012). Mitochondrial disorders as windows into an ancient organelle. NATURE. 491 (7424): 374-383

Book Chapter

Calvo, Sarah E.; Mootha, Vamsi K. (2010). The Mitochondrial Proteome and Human Disease. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. Book Series: Annual Review of Genomics and Human Genetics. 11: 25-44

 

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: Luciano Marraffini, Ph.D., Friday October 20th, 2017

Friday Lectures

Friday, October 20, 2017  3:45 p.m.

Caspary Auditorium

Luciano Marraffini, Ph.D.

Associate Professor and Head

Laboratory of Bacteriology

The Rockefeller University

CRISPR-Cas, Acquired Immunity in Prokaryotes

 

Recommended Readings:

Niewoehner, Ole; Garcia-Doval, Carmela; Rostol, Jakob T.; et al. (2017). Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers.  NATURE. 548 (7669): 543-+

Modell, Joshua W.; Jiang, Wenyan; Marraffini, Luciano A. (2017). CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity. NATURE. 544 (7648): 101-+  

Marraffini, Luciano A. (2017). Sensing danger. PNAS. 114 (1): 15-16

Heler, Robert; Wright, Addison V.; Vucelja, Marija; et al. (2017). Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. MOLECULAR CELL. 65 (1): 168-175

Marraffini, Luciano A. (2015). CRISPR-Cas immunity in prokaryotes. NATURE. 526 (7571): 55-61

McGinn, Jon; Marraffini, Luciano A. (2016). CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration. MOLECULAR CELL. 64 (3): 616-623

Barrangou, Rodolphe; Marraffini, Luciano A. (2014). CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity. MOLECULAR CELL. 54 (2): 234-244

Cong, Le; Ran, F. Ann; Cox, David; et al. (2013). Multiplex Genome Engineering Using CRISPR/Cas Systems.  SCIENCE. 339 (6121): 819-823

 

 

Recommended Readings: Anja Groth, Ph.D., Friday October 13th, 2017

Friday Lectures

Friday, October 13, 2017  3:45 p.m.

Caspary Auditorium

Anja Groth, Ph.D.

Professor and Group Leader

Biotech Research and Innovation Centre (BRIC)

 University of Copenhagen

Chromatin Replication and Epigenome Maintenance

 

Recommended Readings:

Hammond, Colin M.; Stromme, Caroline B.; Huang, Hongda; et al. (2017). Histone chaperone networks shaping chromatin function. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 18 (3): 141-158

Saredi, Giulia; Huang, Hongda; Hammond, Colin M.; et al. (2016). H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex. NATURE. 534 (7609): 714-+   

Alabert, Constance; Barth, Teresa K.; Reveron-Gomez, Nazaret; et al. (2015). Two distinct modes for propagation of histone PTMs across the cell cycle. GENES & DEVELOPMENT 29 (6): 585-590

Huang, Hongda; Stromme, Caroline B.; Saredi, Giulia; et al. (2015). A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 22 (8): 618-626

Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; et al. (2014). Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.  NATURE CELL BIOLOGY. 16 (3): 281-+

Alabert, Constance; Groth, Anja (2012). Chromatin replication and epigenome maintenance. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 13 (3): 153-167

 

 

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: Thomas P. Sakmar, M.D., Monday May 22th, 2017

Monday Lectures

Monday, May 22, 2017  3:45 p.m.

Carson Family Auditorium

Thomas P. Sakmar, M.D.

Richard M. and Isabel P. Furlaud Professor and Head,

Laboratory of Chemical Biology and Signal Transduction

The Rockefeller University

Uveal Melanoma: Case History of a Mutant GPCR

Recommended Readings:

https://medicalxpress.com/news/2017-04-newly-chemical-reaction-eye-vision.html

Chua V, Lapadula D, Randolph C, Benovic JL, Wedegaertner PB, Aplin AE. (2017). Dysregulated GPCR Signaling and Therapeutic Options in Uveal Melanoma. MOLECULAR CANCER RESEARCH. 15(5):501-506

Moore, Amanda R.; Ceraudo, Emilie; Sher, Jessica J.; et al. (2016). Recurrent activating mutations of G-protein-coupled receptor CYSLTR2 in uveal melanoma. NATURE GENETICS. 48(6): 675-+

Shoushtari, Alexander N.; Carvajal, Richard D. (2014). GNAQ and GNA11 mutations in uveal melanoma. MELANOMA RESEARCH. 24(6): 525-534. PLEASE REQUEST FROM MARKUS LIBRARY.

Harbour, J. William (2012). The genetics of uveal melanoma: an emerging framework for targeted therapy. PIGMENT CELL & MELANOMA RESEARCH. 25(2)

Periole, Xavier; Knepp, Adam M.; Sakmar, Thomas P.; et al. (2012). Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 134(26): 10959-10965

 

 

Recommended Readings: Bing Ren, Ph.D., Friday May 19th, 2017

Friday Lectures

Friday, May 19, 2017  3:45 p.m.

Caspary Auditorium

Bing Ren, Ph.D.

Professor of Cellular and Molecular Medicine and Director of the Center for Epigenomics

University of California, San Diego

Organization and Regulation of the Human Genome

Recommended Readings:

https://www.bcm.edu/news/genetics/nih-funds-effort-map-genome-folding

https://www.bcm.edu/news/genome-sequencing/scientist-assemble-genome-of-zika-virus

Schmitt, Anthony D.; Hu, Ming; Ren, Bing (2016). Genome-wide mapping and analysis of chromosome architecture. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 17(12): 743-755

Dixon, Jesse R.; Gorkin, David U.; Ren, Bing (2016). Chromatin Domains: The Unit of Chromosome Organization. MOLECULAR CELL. 62(5): 668-680

Zuin, Jessica; Dixon, Jesse R.; van der Reijden, Michael I. J. A.; et al. (2014). Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 111(3): 996-1001

Smallwood, Andrea; Ren, Bing (2013). Genome organization and long-range regulation of gene expression by enhancers. CURRENT OPINION IN CELL BIOLOGY. 25(3): 387-394

Dunham, Ian; Kundaje, Anshul; Aldred, Shelley F.; et al. (2012). An integrated encyclopedia of DNA elements in the human genome. NATURE. 489(7414): 57-74

 

Recommended Readings: Peter Campbell, Ph.D. March 31, 2017

Friday Lectures

Friday, March 31, 2017   3:45 p.m.

Caspary Auditorium

Peter Campbell, Ph.D.

Head of Cancer Genetics and Genomics,

The Wellcome Trust Sanger Institute

Interrogating the Architecture of Cancer Genomes

Recommended Readings:

The Past, Present and Future of Genome Sequencing

Forbes, Simon A.; Beare, David; Gunasekaran, Prasad; et al. (2015). COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. NUCLEIC ACIDS RESEARCH. 43(D1): D805-D811

Martincorena, Inigo; Campbell, Peter J. (2015). Somatic mutation in cancer and normal cellsSCIENCE.  349(6255): 1483-1489

Alioto, Tyler S.; Buchhalter, Ivo; Derdak, Sophia; et al. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencingNATURE COMMUNICATIONS. 6(10001)

Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C.; et al. (2013). Signatures of mutational processes in human cancer. NATURE. 500(7463): 415-+

Yates, Lucy R.; Campbell, Peter J. (2012). Evolution of the cancer genome. NATURE REVIEWS GENETICS. 13(11): 795-806  

 

 

Recommended Readings: Stuart H. Orkin M.D. January 6 2017

Friday Lectures

Friday, January 6,  3:45 p.m.

Caspary Auditorium

Stuart H. Orkin   M.D.

David G. Nathan Distinguished Professor of Pediatrics, Dana Farber Institute

The Human Fetal Globin Switch:

A Paradigm for Disease-related Common Genetic Variation in Regulatory Elements

Recommended Readings:

Bauer, Daniel E.; Kamran, Sophia C.; Lessard, Samuel; et al.  An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level.  SCIENCE  342(6155): 253-257    OCT 11 2013  

Galarneau, Genevieve; Palmer, Cameron D.; Sankaran, Vijay G.; et al.  Fine-mapping at three loci known to affect fetal hemoglobin levels explains additional genetic variation.  NATURE GENETICS   42(12): 1049-1051   DEC 2010

Menzel, Stephan; Thein, Swee Lay.   Genetic architecture of hemoglobin F control. CURRENT OPINION IN HEMATOLOGY   16(3): 179-186   MAY 2009  PLEASE REQUEST FROM MARKUS LIBRARY

He, Yunyan; Lin, Weixiong; Luo, Jianming.  Influences of Genetic Variation on Fetal Hemoglobin. PEDIATRIC HEMATOLOGY AND ONCOLOGY   Volume: 28   Issue: 8   Pages: 708-717   Published:  NOV 2011   PLEASE REQUEST FROM MARKUS LIBRARY.

Orkin, Stuart H.  Recent advances in globin research using genome-wide association studies and gene editing. Annals of the New York Academy of Sciences   1368 : 5-10    2016

Recommended Readings: Maria Barna Ph.D. Friday December 9, 2016

Friday Lectures

Friday, December 9, 2016   3:45 p.m.

Caspary Auditorium

Maria Barna, Ph.D.

Assistant Professor,

Departments of Developmental Biology and Genetics at Stanford University

Specialized Ribosomes:

A New Frontier in Gene Regulation, Organismal Biology, & Evolution

Recommended Readings:

Xue, Shifeng; Barna, Maria.   Specialized ribosomes: a new frontier in gene regulation and organismal biology.  NATURE REVIEWS MOLECULAR CELL BIOLOGY    13( 6):355-369     JUN 2012

Amunts, Alexey; Brown, Alan; Bai, Xiao-chen; et al.  Structure of the Yeast Mitochondrial Large Ribosomal Subunit.  SCIENCE   343(6178):1485-1489      MAR 28 2014

Xue, Shifeng; Tian, Siqi; Fujii, Kotaro; et al.  RNA regulons in Hox 5 ‘ UTRs confer ribosome specificity to gene regulation. NATURE   517(7532):33-U55   JAN 1 2015

Wu, XQ; Iyengar, P; RajBhandary, UL.   Ribosome-initiator tRNA complex as an intermediate in translation initiation in Escherichia coli revealed by use of mutant initiator tRNAs and specialized ribosomes. EMBO JOURNAL    15(17):4734-4739  SEP 2 1996

Shi, Zhen; Barna, Maria   Trransiating the Genome in Time and Space: Specialized Ribosomes, RNA. Regulons, and RNA-Binding Proteins. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 31   Book Series: Annual Review of Cell and Developmental Biology   V. 31: 31-+    2015

Yadav, Anupama; Radhakrishnan, Aparna; Panda, Anshuman; et al. The Modular Adaptive Ribosome.   PLOS ONE   11(11): Article Number: e0166021    NOV 3 2016