Recommended Readings: Ali H. Brivanlou, Ph.D. Monday November 20th, 2017

Monday Lectures

Monday, November 20, 2017  3:45 p.m.

Carson Family Auditorium

Ali H. Brivanlou, Ph.D.

Robert and Harriet Heilbrunnand Professor and Head

Laboratory of Stem Cell Biology and Molecular Embryology

The Rockefeller University

 

Self-organization of Spatial Patterns in Artificial Human Embryos and Organoids

Recommended Readings:

News

Patrick Monahan.

Empirical Articles

Deglincerti, Alessia; Croft, Gist F.; Pietila, Lauren N.; et al. (2016). Self-organization of the in vitro attached human embryo. NATURE.  533 (7602): 251-+

Etoc, Fred; Metzger, Jakob; Ruzo, Albert; et al. (2016). A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization. DEVELOPMENTAL CELL. 39 (3): 302-315  

Haremaki, Tomomi; Deglincerti, Alessia; Brivanlou, Ali H. (2015). Huntingtin is required for ciliogenesis and neurogenesis during early Xenopus development. DEVELOPMENTAL BIOLOGY. 408 (2): 305-315

Warmflash, Aryeh; Sorre, Benoit; Etoc, Fred; et al. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. NATURE METHODS. 11 (8): 847-854

Bedzhov, Ivan; Leung, Chuen Yan; Bialecka, Monika; et al. (2014). In vitro culture of mouse blastocysts beyond the implantation stages. NATURE PROTOCOLS.  9 (12): 2732-2739

Review Paper

Simunovic, Mijo; Brivanlou, Ali H. (2017). Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis.  DEVELOPMENT. 144 (6): 976-985

Clevers, Hans (2016). Modeling Development and Disease with Organoids. CELL. 165 (7): 1586-1597

 

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: Gregory M. Alushin, Ph.D. Monday November 13th, 2017

Monday Lectures

Monday, November 13, 2017  3:45 p.m.

Carson Family Auditorium

Gregory M. Alushin, Ph.D.

Assistant Professor and Head

Laboratory of Structural Biophysics and Mechanobiology

The Rockefeller University

Cytoskeletal Structural Plasticity in Force Generation and Mechanosensation

Recommended Readings:

Empirical Articles

Omabegho T, Gurel PS, Cheng CY, Kim LY, Ruijgrok PV, Das R, Alushin GM, Bryant Z. (2017). Controllable molecular motors engineered from myosin and RNA. NATURE NANOTECHNOLOGY. PLEASE REQUEST FROM MARKUS LIBRARY.

Swaminathan V, Alushin GM, Waterman CM. (2017). Mechanosensation: A Catch Bond That Only Hooks One Way. CURRENT BIOLOGY. 27 (21):R1158–R1160

Kim, Laura Y.; Thompson, Peter M.; Lee, Hyunna T.; et al. (2016). The Structural Basis of Actin Organization by Vinculin and Metavinculin. JOURNAL OF MOLECULAR BIOLOGY.  428 (1): 10-25

Skau, Colleen T.; Fischer, Robert S.; Gurel, Pinar; et al. (2016). FMN2 Makes Perinuclear Actin to Protect Nuclei during Confined Migration and Promote Metastasis. CELL. 167 (6):1571-+

Review Papers

Thomas DG, Robinson DN. (2017). The fifth sense: Mechanosensory regulation of alpha-actinin-4 and its relevance for cancer metastasis. SEMINARS IN CELL AND DEVELOPMENTAL BIOLOGY. PLEASE REQUEST FROM MARKUS LIBRARY.

Mishra, Mithilesh; Huang, Junqi; Balasubramanian, Mohan K. (2014). The yeast actin cytoskeleton. FEMS MICROBIOLOGY REVIEWS. 38 (2): 213-227

Book Chapter

Luo, Tianzhi; Robinson, Douglas N. (2011). The Role of the Actin Cytoskeleton in Mechanosensation. MECHANOSENSITIVITY AND MECHANOTRANSDUCTION. Mechanosensitivity in Cells and Tissues. 4: 25-65

 

Recommended Readings: Sten Linnarsson, Ph.D. Friday November 10th, 2017

Friday Lectures

Friday, November 10, 2017  3:45 p.m.

Caspary Auditorium

Sten Linnarsson, Ph.D.

Professor

Department of Medical Biochemistry and Biophysics

Karolinska Institute

Unraveling Brain Development using Single-cell Technologies

Recommended Readings:

News

Ed Yong. Oct 14, 2016. A Google Maps for the Human Body. The Atlantic

Empirical Articles

Cervo, Pia Rivetti di Val; Romanov, Roman A.; Spigolon, Giada; et al. (2017). Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model. NATURE. 35 (5): 444-+

La Manno, Gioele; Gyllborg, Daniel; Codeluppi, Simone; et al. (2016). Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. CELL. 167 (2): 566-+  

Marques, Sueli; Zeisel, Amit; Codeluppi, Simone; et al. (2016). Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. SCIENCE. 352 (6291): 1326-1329

Zeisel, Amit; Munoz-Manchado, Ana B.; Codeluppi, Simone; et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. SCIENCE. 347 (6226): 1138-1142

Islam, Saiful; Zeisel, Amit; Joost, Simon; et al. (2014). Quantitative single-cell RNA-seq with unique molecular identifiers.  NATURE METHODS. 11 (2): 163-+

Review Paper

Shapiro, Ehud; Biezuner, Tamir; Linnarsson, Sten (2013). Single-cell sequencing-based technologies will revolutionize whole-organism science.  NATURE REVIEWS GENETICS. 14 (9): 618-630

 

 

 

Recommended Readings: Seth Darst, Ph.D. Monday November 6th, 2017

Monday Lectures

Monday, November 6, 2017  3:45 p.m.

Carson Family Auditorium

Seth Darst, Ph.D.

Jack Fishman Professor and Head

Laboratory of Molecular Biophysics

The Rockefeller University

Promoter Melting by Bacterial RNA Polymerase – One Step at a Time

Recommended Readings:

Feklistov, Andrey; Bae, Brian; Hauver, Jesse; et al. (2017). RNA polymerase motions during promoter melting. SCIENCE. 356 (6340): 863-866

Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine; et al. (2017). Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. ELIFE. 6

Chen, James; Wassarman, Karen M.; Feng, Shili; et al. (2017). 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. MOLECULAR CELL. 68 (2): 388-+

Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka; et al. (2015). Structure of a bacterial RNA polymerase holoenzyme open promoter complex. ELIFE. 4

Davis, Elizabeth; Chen, James; Leon, Katherine; et al. (2015). Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD.  NUCLEIC ACIDS RESEARCH. 43 (1): 433-445

Chen, Jie; Darst, Seth A.; Thirumalai, D. (2010). Promoter melting triggered by bacterial RNA polymerase occurs in three steps. PNAS. 107 (28): 12523-12528

 

Recommended Readings: Sohail Tavazoie, M.D., Ph.D. Friday November 3rd, 2017

Friday Lectures

Friday, November 3, 2017  3:45 p.m.

Caspary Auditorium

Sohail Tavazoie, M.D., Ph.D.,

Leon Hess Associate Professor and Head

Elizabeth and Vincent Meyer Laboratory of Systems Cancer Biology

The Rockefeller University

Small RNA Regulation of Cancer Metastasis: Molecular Mechanisms and Therapeutic Application

Recommended Readings:

Kingham, T. Peter; Nguyen, Hoang C. B.; Zheng, Jian; et al. (2017). MicroRNA-203 predicts human survival after resection of colorectal liver metastasis.  ONCOTARGET. 8 (12): 18821-18831

Sengelaub, Caitlin A.; Navrazhina, Kristina; Ross, Jason B.; et al. (2016). PTPRN2 and PLCb1 promote metastatic breast cancer cell migration through PI(4,5)P-2-dependent actin remodeling. EMBO JOURNAL. 35 (1): 62-76  

Goodarzi, Hani; Nguyen, Hoang C. B.; Zhang, Steven; et al. (2016). Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. CELL. 165 (6): 1416-1427

Lee, Hyeseung; Goodarzi, Hani; Tavazoie, Sohail F.; et al. (2016). TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer. CANCER RESEARCH. 76 (17): 4994-5005

Alarcon, Claudio R.; Lee, Hyeseung; Goodarzi, Hani; et al. (2015). N-6-methyladenosine marks primary microRNAs for processing. NATURE. 519 (7544): 482-+

Loo, Jia Min; Scherl, Alexis; Alexander Nguyen; et al. (2015). Extracellular Metabolic Energetics Can Promote Cancer Progression. CELL. 160 (3): 393-406

Pencheva, Nora; Tavazoie, Sohail F. (2013). Control of metastatic progression by microRNA regulatory networks. NATURE CELL BIOLOGY. 15 (6) : 546-554