Recommended Readings: Elaine Fuchs, Ph.D. Friday February 23rd, 2018

Friday Lectures

Friday, February 23rd, 2018  3:45 p.m.

Caspary Auditorium

Elaine Fuchs, Ph.D.

Rebecca C. Lancefield Professor and Head

Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development

The Rockefeller University

Stem Cells in Silence, Action, and Cancer

Recommended Readings:

Science News

David Nield. Our Skin Can ‘Remember’ Inflammation, And It Could Help Us Understand Psoriasis. (2017, Oct 21). ScienceAlert

Empirical Articles

Naik, Shruti; Larsen, Samantha B.; Gomez, Nicholas C.; et al. (2017). Inflammatory memory sensitizes skin epithelial stem cells to tissue damage. NATURE. 550 (7677): 475-+

Ge, Yejing; Gomez, Nicholas C.; Adam, Rene C.; et al. (2017). Stem Cell Lineage Infidelity Drives Wound Repair and Cancer. CELL. 169 (4): 636-650

Yang, Hanseul; Adam, Rene C.; Ge, Yejing; et al. (2017). Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices. CELL. 69 (3): 483-+  

Asare, Amma; Levorse, John; Fuchs, Elaine. (2017). Coupling organelle inheritance with mitosis to balance growth and differentiation. SCIENCE. 355 (6324): 493-+

Sendoel, Ataman; Dunn, Joshua G.; Rodriguez, Edwin H.; et al. (2017). Translation from unconventional 5 ‘ start sites drives tumour initiation. NATURE. 541 (7638)

Lay, Kenneth; Kume, Tsutomu; Fuchs, Elaine (2016). FOXC1 maintains the hair follicle stem cell niche and governs stem cell quiescence to preserve long-term tissue-regenerating potential. PNAS. 113 (11): E1506-E1515

Ouspenskaia, Tamara; Matos, Irina; Mertz, Aaron F.; et al. (2016). WNT-SHH Antagonism Specifies and Expands Stem Cells prior to Niche Formation. CELL. 164 (1-2): 156-169

Yang, Hanseul; Schramek, Daniel; Adam, Rene C.; et al. (2015). ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas. ELIFE. 4. # e10870

Review Papers

Gonzales, Kevin Andrew Uy; Fuchs, Elaine (2017). Skin and Its Regenerative Powers: An Alliance between Stem Cells and Their Niche.  DEVELOPMENTAL CELL. 43 (4): 387-401

Blanpain, Cedric; Fuchs, Elaine (2014). STEM CELL PLASTICITY Plasticity of epithelial stem cells in tissue regeneration. SCIENCE. 344 (6189): 1243-+

Hsu, Ya-Chieh; Li, Lishi; Fuchs, Elaine (2014). Emerging interactions between skin stem cells and their niches. NATURE MEDICINE. 20 (8): 847-856

Book Chapter

Fuchs, Elaine (2016). Epithelial Skin Biology: Three Decades of Developmental Biology, a Hundred Questions Answered and a Thousand New Ones to Address. ESSAYS ON DEVELOPMENTAL BIOLOGY, PT A  Book Series: Current Topics in Developmental Biology. 116: 357-+  


Recommended Readings: Gerald Crabtree, Ph.D. Friday February 16th, 2018

Friday Lectures

Friday, February 16th, 2018  3:45 p.m.

Caspary Auditorium

Gerald Crabtree, Ph.D.

David Korn Professor

Pathology and Developmental Biology

Stanford University

Chromatin regulation: Insights from new methods and the genomics of human disease

Recommended Readings:

Empirical Articles

Braun, Simon M. G.; Kirkland, Jacob G.; Chory, Emma J.; et al. (2017). Rapid and reversible epigenome editing by endogenous chromatin regulators. NATURE COMMUNICATIONS. 8

Stanton, Benjamin Z.; Hodges, Courtney; Calarco, Joseph P.; et al. (2017). Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. NATURE GENETICS. 49 (2): 282-288

Kadoch, Cigall; Williams, Robert T.; Calarco, Joseph P.; et al. (2017). Dynamics of BAF-Polycomb complex opposition on heterochromatin in normal and oncogenic states. NATURE GENETICS. 49 (2): 213-222

Miller, Erik L.; Hargreaves, Diana C.; Kadoch, Cigall; et al. (2017). TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24 (4): 344-+

Son, Esther Y.; Crabtree, Gerald R. (2014). The Role of BAF (mSWI/SNF) Complexes in Mammalian Neural Development. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS. 166 (3): 333-349

Hodges, Courtney; Crabtree, Gerald R. (2012). Dynamics of inherently bounded histone modification domains. PNAS. 109 (33): 13296-13301

Hathaway, Nathaniel A.; Bell, Oliver; Hodges, Courtney; et al. (2012). Dynamics and Memory of Heterochromatin in Living Cells. CELL. 149 (7): 1447-1460

Review Papers

Kadoch, Cigall; Crabtree, Gerald R. (2015). Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics. SCIENCE ADVANCES. 1 (5) 

Ho, Lena; Crabtree, Gerald R. (2010). Chromatin remodelling during development. NATURE. 463 (7280): 474-484

Book Chapter

Lessard, Julie A.; Crabtree, Gerald R. (2010). Chromatin Regulatory Mechanisms in Pluripotency. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. Book Series: Annual Review of Cell and Developmental Biology. 26: 503-532

Recommended Readings: Laura Landweber, Ph.D. Friday February 2nd, 2018

Friday Lectures

Friday, February 2nd, 2018  3:45 p.m.

Caspary Auditorium

Laura Landweber, Ph.D.


Biochemistry and Molecular Biophysics and Biological Sciences

Columbia University

RNA-programmed genome rearrangement and editing in the ciliate Oxytricha

Recommended Readings:

Science News

Greg Miller. This Bizarre Organism Builds Itself a New Genome Every Time It Has Sex. (2014, Sep 17). Wired

Empirical Articles

Khurana, Jaspreet S.; Clay, Derek M.; Moreira, Sandrine; et al.(2018). Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha. RNA. 24 (1): 18-29

Lindblad, Kelsi A.; Bracht, John R.; Williams, April E.; et al. (2017). Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 23 (8): 1200-1208

Chen, Xiao; Bracht, John R.; Goldman, Aaron David; et al. (2014). The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development. CELL. 158 (5): 1187-1198

Swart, Estienne C.; Bracht, John R.; Magrini, Vincent; et al. (2013). The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLOS BIOLOGY. 11 (1).

Goldman, Aaron David; Landweber, Laura F. (2012). Oxytricha as a modern analog of ancient genome evolution. TRENDS IN GENETICS. 28 (8): 382-388

Fang, Wenwen; Wang, Xing; Bracht, John R.; et al. (2012). Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement. CELL. 151 (6): 1243-1255

Nowacki, Mariusz; Haye, Joanna E.; Fang, Wenwen; et al. (2010). RNA-mediated epigenetic regulation of DNA copy number. PNAS. 107 (51): 22140-22144

Nowacki, Mariusz; Vijayan, Vikram; Zhou, Yi; et al. (2008). RNA-mediated epigenetic programming of a genome-rearrangement pathway. NATURE. 451 (7175): 153-U4

Review Papers

Bracht, John R.; Fang, Wenwen; Goldman, Aaron David; et al. (2013). Genomes on the Edge: Programmed Genome Instability in Ciliates. CELL. 152 (3): 406-416

Goldman, Aaron David; Landweber, Laura F. (2012). Oxytricha as a modern analog of ancient genome evolution. TRENDS IN GENETICS. 28 (8): 382-388

Book Chapter

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F. (2011). RNA-Mediated Epigenetic Programming of Genome Rearrangements. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. Book Series: Annual Review of Genomics and Human Genetics. 12: 367-389

Edited Books

Landweber, L. F. and Winfree, E., eds. (2003) Evolution as Computation. Springer Verlag.

Landweber, L. F. and Dobson, A. P., eds. (1999) Genetics and the Extinction of Species: DNA and the Conservation of Biodiversity. Princeton University Press. PLEASE REQUEST FROM MARKUS LIBRARY.

Landweber, L. and Baum, E., eds. (1998) DNA Based Computers II. American Mathematical Society. PLEASE REQUEST FROM MARKUS LIBRARY.


Write More Effective Data Management Plans:
Give NIH Reviewers What They Want to See
and Get More of the Funding You Need

Immediately Available 60-Minute Online Training:
All formats (CD, MP4, PDF Transcript) include training presentation handouts.

The NIH requires Data Sharing Plans for all grants seeking $500k or more in direct costs in any one year, or as required by the solicitation. The Data Management Plan is more than a component of your proposal; it’s a blueprint for how you’ll actually manage the data during the course of your funded work. Therefore, creating an effective Data Management Plan is an integral part of creating a winning proposal and getting the research money you need.

During this expert-led online training session, you’ll learn what counts as data, and understand exactly what funding agencies expect and require for your Data Management Plan to be successful. Your expert presenter, Michael Lesiecki, PhD, will explain how you should think about managing your data before you begin your proposed research to insure usability, long-run preservation and access. During this training, you’ll examine proven models and processes so you can improve your Data Management Plan and create the most competitive proposal possible.

5 Key Take-Aways:

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    regarding the release of sensitive or proprietary data.
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Recommended Readings: Edward H. Egelman, Ph.D. Friday January 19th, 2018

Friday Lectures

Friday, January 19, 2018  3:45 p.m.

Caspary Auditorium

Edward Egelman, Ph.D.

Harrison Distinguished Professor

Biochemistry and Molecular Genetics

University of Virginia Medical School

Cryo-EM of Protein and Nucleoprotein Polymers at Near-Atomic Resolution

Recommended Readings:

Science News

Kenny Walter. Virus Holds Key to Durable Material. (2017, Jul 20). Virus Holds Key to Durable Material. R&D Magazine

Empirical Articles

Egelman, Edward H. (2017). Cryo-EM of bacterial pili and archaeal flagellar filaments. CURRENT OPINION IN STRUCTURAL BIOLOGY. 46: 31-37

Wang, Fengbin; Burrage, Andrew M.; Postel, Sandra; et al. (2017). A structural model of flagellar filament switching across multiple bacterial species. NATURE COMMUNICATIONS. 8: 960

Wang, Fengbin; Coureuil, Mathieu; Osinski, Tomasz; et al. (2017). Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. STRUCTURE. 25 (9): 1423-+

Kasson, Peter; DiMaio, Frank; Yu, Xiong; et al. (2017). Model for a novel membrane envelope in a filamentous hyperthermophilic virus. ELIFE. 6  

Kolappan, Subramania; Coureuil, Mathieu; Yu, Xiong; et al. (2016). Structure of the Neisseria meningitidis Type IV pilus. NATURE COMMUNICATIONS. 7: 13015

Braun, Tatjana; Vos, Matthijn R.; Kalisman, Nir; et al. (2016). Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. PNAS. 113 (37): 10352-10357

Egelman, Edward H. (2016). The Current Revolution in Cryo-EM. BIOPHYSICAL JOURNAL. 110 (5): 1008-1012

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; et al. (2015). De novo protein structure determination from near-atomic-resolution cryo-EM maps. NATURE METHODS. 12 (4): 335-U84

DiMaio, Frank; Yu, Xiong; Rensen, Elena; et al. (2015). A virus that infects a hyperthermophile encapsidates A-form DNA. SCIENCE. 348 (6237): 914-917

Review Papers

Egelman, Edward H. (2015). Three-dimensional reconstruction of helical polymers. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 581: 54-58

Recommended Readings: Ruslan Medzhitov, Ph.D. Friday January 12th, 2018

Friday Lectures

Friday, January 12, 2018  3:45 p.m.

Caspary Auditorium

Ruslan Medzhitov, Ph.D.

Sterling Professor

Department of Immunobiology

Yale University

Evolutionary Perspectives on Health and Disease


Recommended Readings:

Science News

Ziba Kashef. May 8, 2017. Study pinpoints key pathway in inflammation and aging. YaleNews

Empirical Articles

Ip, W. K. Eddie; Hoshi, Namiko; Shouval, Dror S.; et al. (2017). Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages. SCIENCE. 356 (6337): 513-519

Kotas, Maya E.; Medzhitov, Ruslan (2015). Homeostasis, Inflammation, and Disease Susceptibility. CELL. (5): 816-827

Iwasaki, Akiko; Medzhitov, Ruslan (2015). Control of adaptive immunity by the innate immune system. NATURE IMMUNOLOGY. 16 (4): 343-353

Palm, Noah W.; Rosenstein, Rachel K.; Medzhitov, Ruslan (2012). Allergic host defences. NATURE. 484 (7395): 465-472

Review Papers

Medzhitov, Ruslan; Schneider, David S.; Soares, Miguel P. (2012). Disease Tolerance as a Defense Strategy. SCIENCE. 335 (6071): 936-941

Okin, Daniel; Medzhitov, Ruslan (2012). Evolution of Inflammatory Diseases. CURRENT BIOLOGY. 22 (17): R733-R740

Iwasaki, Akiko; Medzhitov, Ruslan (2010). Regulation of Adaptive Immunity by the Innate Immune System. SCIENCE. 327 (5963): 291-295

Recommended Readings: Joan A. Steitz, Ph.D. Friday January 5th, 2018

Friday Lectures

Friday, January 5, 2018  3:45 p.m.

Caspary Auditorium

Joan A. Steitz, Ph.D.

Sterling Professor

Molecular Biophysics and Biochemistry

Yale University

RNA Triple Helices in Cellular and Viral Biology


Recommended Readings:

Science News

Michael White. Oct 17, 2017. The Women Who Should Win the Nobel Prize—but Haven’t. PacificStandard

Empirical Articles

Brown, Jessica A.; Kinzig, Charles G.; DeGregorio, Suzanne J.; et al. (2016). Methyltransferase-like protein 16 binds the 3 ‘-terminal triple helix of MALAT1 long noncoding RNA. PNAS. 113 (49): 14013-14018

Brown, Jessica A.; Kinzig, Charles G.; Degregorio, Suzanne J.; et al. (2016). Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA. 22 (5): 743-749

Brown, Jessica A.; Bulkley, David; Wang, Jimin; et al. (2014). Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 21 (7): 633-640

Guo, Yang Eric; Riley, Kasandra J.; Iwasaki, Akiko; et al. (2014). Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. MOLECULAR CELL. 54 (1): 67-79

Brown, Jessica A.; Valenstein, Max L.; Yario, Therese A.; et al. (2012). Formation of triple-helical structures by the 3 ‘-end sequences of MALAT1 and MEN beta noncoding RNAs. PNAS. 109 (47): 19202-19207

Borah, Sumit; Darricarrere, Nicole; Darnell, Alicia; et al. (2011). A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS PATHOGENS. 7 (10)

Mitton-Fry, Rachel M.; DeGregorio, Suzanne J.; Wang, Jimin; et al. (2010). Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix. SCIENCE. 330 (6008): 1244-1247

Review Papers

Tycowski, Kazimierz T.; Guo, Yang Eric; Lee, Nara; et al. (2015). Viral noncoding RNAs: more surprises. GENES & DEVELOPMENT. 29 (6): 567-584

Cech, Thomas R.; Steitz, Joan A. (2014). The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones. CELL. 157 (1): 77-94

Recommended Readings: Rachel Wilson, Ph.D. Friday December 15th, 2017

Friday Lectures

Friday, December 15, 2017  3:45 p.m.

Caspary Auditorium

Rachel Wilson, Ph.D.

Martin Family Professor

Department of Neurobiology

Harvard Medical School

Neural Correlates of Orienting Behaviors and Latent Action Biases


Recommended Readings:

Empirical Articles

Azevedo, Anthony W.; Wilson, Rachel I. (2017). Active Mechanisms of Vibration Encoding and Frequency Filtering in Central Mechanosensory Neurons. NEURON. 96 (2): 446-+

Tobin, William F.; Wilson, Rachel I.; Lee, Wei-Chung Allen (2017). Wiring variations that enable and constrain neural computation in a sensory microcircuit. ELIFE. 6: e24838

Tuthill, John C.; Wilson, Rachel I. (2016). Parallel Transformation of Tactile Signals in Central Circuits of Drosophila. CELL. 164 (5): 1046-1059

Chang, Allison E. B.; Vaughan, Alex G.; Wilson, Rachel I. (2016). A Mechanosensory Circuit that Mixes Opponent Channels to Produce Selectivity for Complex Stimulus Features. NEURON. 92 (4): 888-901  

Jeanne, James M.; Wilson, Rachel I. (2015). Convergence, Divergence, and Reconvergence in a Feedforward Network Improves Neural Speed and Accuracy. NEURON. 88 (5)

Olsen, Shawn R.; Wilson, Rachel I. (2008). Lateral presynaptic inhibition mediates gain control in an olfactory circuit. NATURE. 452 (7190): 956-U3

Review Papers

Tuthill, John C.; Wilson, Rachel I. (2016). Mechanosensation and Adaptive Motor Control in Insects. CURRENT BIOLOGY. 26 (20): R1022-R1038

Olsen, Shawn R.; Wilson, Rachel I. (2008). Cracking neural circuits in a tiny brain: new approaches for understanding the neural circuitry of Drosophila. TRENDS IN NEUROSCIENCES. 31(10): 512-520

Book Chapter

Wilson, Rachel I. (2013). Early Olfactory Processing in Drosophila: Mechanisms and Principles. ANNUAL REVIEW OF NEUROSCIENCE. Book Series: Annual Review of Neuroscience. 36: 217-241





Recommended Readings: Thomas Walz, Ph.D. Monday December 11th, 2017

Monday Lectures

Monday, December 11, 2017  3:45 p.m.

Carson Family Auditorium

Thomas Walz, Ph.D.

Professor and Head

Laboratory of Molecular Electron Microscopy

The Rockefeller University

An Experimental Look at Hydrophobic Mismatch

Recommended Readings:

Empirical Articles

Mi, Wei; Li, Yanyan; Yoon, Sung Hwan; et al. (2017). Structural basis of MsbA-mediated lipopolysaccharide transport. NATURE. Volume: 549 (7671): 233-+

Saboe, Patrick O.; Rapisarda, Chiara; Kaptan, Shreyas; et al. (2017). Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0. BIOPHYSICAL JOURNAL. 112 (5): 953-965

Hite, Richard K.; Yuan, Peng; Li, Zongli; et al. (2015). Cryo-electron microscopy structure of the Slo2.2 Na+-activated K+ channel.  NATURE. 527 (7577): 198-+

Shen, Yue-xiao; Si, Wen; Erbakan, Mustafa; et al. (2015). Highly permeable artificial water channels that can self-assemble into two-dimensional arrays. PNAS. 112 (32):9810-9815

Gonen, T; Cheng, YF; Sliz, P; et al. (2005). Lipid-protein interactions in double-layered two-dimensional AQPO crystals. NATURE. 438 (7068): 633-638

Gonen, T; Sliz, P; Kistler, J; et al. (2004).  Aquaporin-0 membrane junctions reveal the structure of a closed water pore. NATURE. 429 (6988): 193-197


Review Paper

Hite, Richard K.; Raunser, Stefan; Walz, Thomas (2007). Revival of electron crystallography. CURRENT OPINION IN STRUCTURAL BIOLOGY. 17 (4): 389-395

Gonen, Tamir; Walz, Thomas (2006). The structure of acquaporins. QUARTERLY REVIEWS OF BIOPHYSICS. 39 (4): 361-396

Book Chapter

Schenk, Andreas D.; Hite, Richard K.; Engel, Andreas; et al. (2010). ELECTRON CRYSTALLOGRAPHY AND AQUAPORINS. METHODS IN ENZYMOLOGY. Book Series: Methods in Enzymology. 483: 91-119

Raunser, Stefan; Walz, Thomas (2009). Electron Crystallography as a Technique to Study the Structure on Membrane Proteins in a Lipidic Environment. ANNUAL REVIEW OF BIOPHYSICS. Book Series: Annual Review of Biophysics. 38: 89-105



Recommended Readings: Ivan E de Araujo, DPhil, Ph.D., Wednesday December 13th, 2017

Special Seminar Series

Wednesday, December 13, 2017  4:00 p.m.

Carson Family Auditorium

Ivan E de Araujo, DPhil, Ph.D.

Principal Investigator, The John B. Pierce Laboratory and Associate Professor

Department of Psychiatry and Cellular and Molecular Physiology

Yale University School of Medicine

The Gut-Brain Axis and Reward

Recommended Readings:

Science News

Radboud University. (2017, Sept 25). Do intestinal bacteria affect ADHD? Medical Xpress

Empirical Articles

Hankir, Mohammed K.; Seyfried, Florian; Hintschich, Constantin A.; et al. (2017). Gastric Bypass Surgery Recruits a Gut PPAR-alpha-Striatal D1R Pathway to Reduce Fat Appetite in Obese Rats. CELL METABOLISM. 25 (2): 335-344

Han, Wenfei; Tellez, Luis A.; Rangel, Miguel J., Jr.; et al. (2017). Integrated Control of Predatory Hunting by the Central Nucleus of the Amygdala. CELL. 168 (1-2): 311-+

Han, Wenfei; Tellez, Luis A.; Niu, Jingjing; et al. (2016). Striatal Dopamine Links Gastrointestinal Rerouting to Altered Sweet Appetite. CELL METABOLISM. 23 (1): 103-112

Sun, Xue; Kroemer, Nils B.; Veldhuizen, Maria G.; et al. (2015). Basolateral Amygdala Response to Food Cues in the Absence of Hunger Is Associated with Weight Gain Susceptibility. JOURNAL OF NEUROSCIENCE. 35 (20): 7964-7976

Tellez, Luis A.; Medina, Sara; Han, Wenfei; et al. (2013). A Gut Lipid Messenger Links Excess Dietary Fat to Dopamine Deficiency. SCIENCE. 341 (6147): 800-802

de Araujo, Ivan E.; Ferreira, Jozelia G.; Tellez, Luis A.; et al. (2012). The gut-brain dopamine axis: A regulatory system for caloric intake. PHYSIOLOGY & BEHAVIOR. 106 (3): 394-399

Book Chapter

de Araujo, Ivan E.; Ren, Xueying; Ferreira, Jozelia G. (2010). Metabolic Sensing in Brain Dopamine Systems. SENSORY AND METABOLIC CONTROL OF ENERGY BALANCE. Book Series: Results and Problems in Cell Differentiation. 52: 69-86