MBL Catalyst Magazine, Winter 2013-2014

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cat.winter.14sm MBL Catalyst, Volume 9, Number 1, Winter 2013-14
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Pp. 2-3: Introduction

Acorn worm group at MBL

Pani AM, Mullarkey EE, Aronowicz, J, Assimacopoulos, S, Grove EA, and Lowe CJ (2012) Ancient deuterostome origins of vertebrate brain signalling centres. Nature 483: 289-294.

Rottinger E and Lowe CJ (2012) Evolutionary crossroads in developmental biology: hemichordates. Development 139: doi: 10.1242/dev.066712.

Lowe CJ et al (2006) Dorsoventral patterning in hemichordates: Insights into early chordate evolution. PLoS Biology 4:e291.

Lowe CJ, Tagawa K, Humphreys T, Kirschner M, and Gerhart J (2004) Hemichordate embryos: procurement, culture, and basic methods. Meth. Cell Biol. 74: 171-194.

Marine animal genomics

Ryan JF et al (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342: DOI: 10.1126/science.1242592

Smith JJ et (2013) Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics 45: 415-421.

Srivastava M [et al]… Rokhsar DS (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466: 720-6.

Hellsten U [et al]… Rokhsar DS (2010) The genome of the Western clawed frog Xenopus tropicalis. Science 328: 633-636.

Chapman JA [et al]… Rokhsar DS, and Steele RE (2010) The dynamic genome of hydra. Nature 464: 592-596.

Cameron RA and Rast JP (2008) Biological Bulletin Virtual Symposium: genomics of large marine metazoans. Biol. Bull. 214: 203-204.

Putnam NH [et al]… Rokhsar DS (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064-1071.

Putnam NH [et al]… Rokhsar DS (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science: 317:86-94.

Sodergren E et al (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314: 941–952.

Dehal P [et al]…Rokhsar S (2003) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298: 2157-2167.

Aparacio S [et al]…Rokhsar DS and Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-13010.

Pp. 4-5: In Pursuit of a Genome

Marx V (2013) Next generation sequencing: The genome jigsaw. Nature 501: 263-268.

Albertin CB [et al] … Ragsdale CW (2012) Cephaloped genomics: A plan of strategies and organization. Stand. Genomic Sci. 7: 1 doi:10.4056/sigs.3136559

Sidebar: selected references

Mäthger LM [et al]…Hanlon RT (2013) Bright white scattering from protein spheres in color changing, flexible cuttlefish skin. Advanced Functional Materials. doi: 10.1002/adfm.201203705

Wardill TJ, Gonzalez-Bellido PT, Crook RJ and Hanlon RT (2012) Neural control of dynamic structural coloration in squid iridophores. Proc. Roy. Soc. B. doi: 10.1098/rspb.2012.1374

Song Y and Brady ST (2013) Analysis of microtubules in isolated axoplasm from the squid giant axon. Methods Cell Biol. 115:125-37.

Morfini GA [et al]…Brady ST (2013) Inhibition of fast axonal transport by pathogenic SOD1 involves activation of p38 MAP kinase. PLoS One 8(6):e65235. doi: 10.1371/journal.pone.0065235

Song Y [et al]…Horwich AL and Brady ST (2012) Molecular chaperone Hsp110 rescues a vesicle transport defect produced by an ALS-associated mutant SOD1 protein in squid axoplasm. PNAS 110: 5428-33.

2012 Albert Lasker Basic Medical Research Award to Michael Sheetz, James Spudich and Ronald Vale: Lasker Foundation Award Description.

Vale RD (2012) How lucky can one be? A perspective from a young scientist at the right place at the right time. Nature Medicine 18: 1-3.

Moreno H [et al]…Llinás RR (2011) Synaptic transmission block by presynaptic injection of oligomeric amyloid beta. PNAS 106: 5901-5906.

Moreno H [et al]…Llinás RR (2011) Blocking effects of human tau on squid giant synapse transmission and its prevention by T-817 MA. Front. Synaptic Neurosci. 3: doi:  10.3389/fnsyn.2011.00003

Hodgkin AL (1963) The ionic basis of nervous conduction. Nobel Lecture: http://www.nobelprize.org/nobel_prizes/medicine/laureates/1963/hodgkin-lecture.html

Pp. 6-7: News and Notes

University of Chicago, MBL Announce Lillie Research Innovation Awards, Scholarship Program

Scientists Discover Thriving Colonies of Microbes in Ocean “Plastisphere”
Zettler ER, Mincer TJ and Zettler LA (2013) Life in the “Plastisphere”: Microbial Communities on Plastic Marine Debris. Environ. Sci. Technol. 47: 7137–7146.

Built for Efficiency, Not Speed: Scientists Discover New Propulsive Mechanism in Jellyfish
Gemmell BJ, Costello JH, Colin SP et al (2013) Passive energy recapture in jellyfish contributes to propulsive advantage over other metazoans. PNAS 110: 17904-17909.

Long-Term Tundra Warming Study Provides Insight Into Ecosystem’s Resiliency
Sistla SA et al (2013) Long-term warming restructures Arctic tundra without changing net soil carbon storage. Nature doi: 10.1038/nature12129.

MBL Researchers Find Zinc’s Crucial Pathway to the Brain
Chowanadisai W, Graham DM, Keen CL, Rucker RB, Messerli MA (2013) Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12). PNAS 110: 9903-9908.

Pp. 8-9: The Balancing Acts of a Fish

Clapp, Cornelia M. The lateral line system of Batrachus tau. Doctoral Dissertation, University of Chicago, May 1896. Reprinted in the Journal of Morphology, November 1898.

Watkins D, Cooperstein SJ, Dixit PK, Lazarow A (1968) Insulin secretion from toadfish islet tissue stimulated by pyridine nucleotides. Science 162: 283-4.

Boyle R, Mensinger AF, Yoshida K, Usui S, Intravaia A, Tricas T, Highstein SM (2001) Neural readaptation to Earth’s gravity following return from space. J Neurophysiol. 86: 2118-22.

Rabbitt RD, Boyle R and Highstein SM (2010) Mechanical amplification by hair cells in the semicircular canals. PNAS 107: 3864-9.

Radford C and Mensinger AF. Anterior lateral line nerve encoding to tones and play back vocalisations in free swimming oyster toadfish, Opsanus tau.  J. Exp. Biol.  Submitted June 2013, in revision.

Mensinger AF (2013) Disruptive communication: Stealth signaling in the toadfish. J Exp Biol. doi: 10.1242/​jeb.090316.

Palmer LM, Deffenbaugh M and Mensinger AF (2005) Sensitivity of the anterior lateral line to natural stimuli in the oyster toadfish, Opsanus tau (Linnaeus).  J.  Exp. Biol. 208: 3441-3450.

Palmer LM, Giuffrida BA and Mensinger AF (2003) Neural recordings from the lateral line in free swimming toadfish, Opsanus tauBiol. Bull. 205: 216-218.

Mensinger AF and Deffenbaugh M (2002) Acoustical neural telemetry from free-swimming fish.  Bioacoustics 12: 333-334.

Pp. 10-11: Regeneration Revolution

Seifert AW, Kiama SG, Seifert MG, Goheen JR, Palmer TM, Maden M (2012) Skin shedding and tissue regeneration in African spiny mice (Acomys). Nature 489: 561-5. doi: 10.1038/nature11499.

Morgan, Thomas Hunt. Regeneration (New York: The Macmillan Company, 1901).

Reddien PW, Bermange AL, Murfitt KJ, Jennings JR and Sánchez Alvarado A (2005) Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic perturbation in planarians Developmental Cell. 8:635-649.

Gurley KA, Rink JC and Sánchez Alvarado A (2007) ß-Catenin defines head versus tail identity during planarian regeneration and homeostasis. Science 319: 323-327.

Eisenhoffer GT, Kang H and Sánchez Alvarado A (2008) Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell 3: 327-339.

Rink JC, Gurley KA, Elliott SA, and Sánchez Alvarado A (2009) Planarian Hh signaling regulates regeneration polarity and links Hh pathway evolution to cilia. Science, 326: 1406-10.

Pp. 12-13: The Collector’s Net

Hill AW …. Remsen D (2009) Location, location, location: utilizing pipelines and services to more effectively georeference the world’s biodiversity data BMC Bioinformatics 10 Suppl 14:S3. doi: 10.1186/1471-2105-10-S14-S3.

Leary PR, Remsen DP, Norton CN, Patterson DJ, Sarkar IN (2007) uBioRSS: tracking taxonomic literature using RSS. Bioinformatics 23: 1434-6.

Patterson DJ, Remsen D, Marino WA, Norton C (2006) Taxonomic indexing–extending the role of taxonomy. Syst Biol 55: 367-73.

Smith, Ralph Ingram. Keys to marine invertebrates of the Woods Hole region : a manual for the identification of the more common marine invertebrates (Woods Hole, Mass.: Systematics-Ecology Program, Marine Biological Laboratory, 1964).

Page 15: Cool Tool: Transcriptomes

Brown CT (January 2014) The Dead Sea scrolls and an open marine transcriptomes project. informaticsblogs.com

Brown CT (December 2013) Announcing the Khmer-protocols project. Living in an Ivory Basement (blog).

Page 16: A Chaos of Delight

Hodgkin AL. The ionic basis of nervous conduction. Nobel Lecture, 1963.

Kandel ER.  The molecular biology of memory storage: A dialog between genes and synapses. Nobel Lecture, 2000.

Hunt Tim. Protein synthesis, proteolysis, and cell cycle transitions. Nobel Lecture, 2001.

Vale RD (2012) How lucky can one be? A perspective from a young scientist at the right place at the right time. Nature Medicine 18: 1-3.

Thomas, Lewis. “The MBL,” in The Lives of a Cell: Notes of a Biology Watcher (New York: Viking Press, 1974).

Isaac Newton quote: Brewster, Sir David. Memoirs of the Life, Writings, and Discoveries of Sir Isaac Newton (Volume II. Ch. 27), 1855.

Charles Darwin quote (at end of page):  http://darwinbeagle.blogspot.com/2007/02/28th-february-1832.html

P. 17: From the Mermaid’s Purse

Schneider I and Shubin NH (2013) The origin of the tetrapod limb: from expeditions to enhancers. Trends in Genetics 29: 419-426.

Freitas R, Zhang GJ, Cohn MJ (2007) Biphasic Hoxd Gene Expression in Shark Paired Fins Reveals an Ancient Origin of the Distal Limb Domain. PLoS ONE doi: 10.1371/journal.pone.0000754