Non-model model organisms

BMC Biology

Volumn 15, Issue 1, 2017, Pages

  Russell, James J ^a   Theriot, Julie A ^a   Sood, Pranidhi ^b   Marshall, Wallace F ^b   Landweber, Laura F ^c   Fritz Laylin, Lillian ^d   Polka, Jessica K ^e   Oliferenko, Snezhana ^f,g   Gerbich, Therese ^h   Gladfelter, Amy ^h   Umen, James ⁱ   Bezanilla, Magdalena ^d   Lancaster, Madeline A ^j   He, Shuonan ^k   Gibson, Matthew C ^k,l   Goldstein, Bob ^h   Tanaka, Elly M ^m   Hu, Chi Kuo ^a   Brunet, Anne ^a  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

^d UNIVERSITY OF MASSACHUSETTS   (United States)

^e WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^f THE FRANCIS CRICK INSTITUTE   (United Kingdom)

^g KING'S COLLEGE LONDON   (United Kingdom)

^h UNIVERSITY OF NORTH CAROLINA   (United States)

ⁱ DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^j MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^k STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^l UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^m RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ANIMAL MODEL; BIOLOGY; EUKARYOTE; PLANT;

ANIMALS; BIOLOGY; EUKARYOTA; MODELS, ANIMAL; PLANTS;

EID: 85021381312     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/s12915-017-0391-5     Document Type: Article

References (328)

1. Nelson DM, Tréguer P, Brzezinski MA, Leynaert A, Quéguiner B. Production and dissolution of biogenic silica in the ocean: Revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Global Biogeochem Cycles. 1995;9(3):359-72.
2. Round FE, Crawford RM, Mann DG. Diatoms: Biology and Morphology of the Genera. UK: Cambridge University Press; 1990.
3. Tomas CR, Hasle GR. Identifying marine phytoplankton. USA: Academic Press; 1997.
4. Gambino M. Secretive Victorian Artists Made These Intricate Patterns Out of Algae. http://www.smithsonianmag.com/arts-culture/secretive-victorian-artists-made-these-intricate-patterns-out-of-algae-180952720/. Accessed 27 Jan 2017.
5. Simpson TL, Volcani BE, editors. Silicon and Siliceous Structures in Biological Systems. New York, NY: Springer New York; 1981.
6. Belcher AM, Wu XH, Christensen RJ, Hansma PK, Stucky GD, Morse DE. Control of crystal phase switching and orientation by soluble mollusc- shell proteins. Nature. 1996;381(6577):56-8.
7. Aizenberg J. Skeleton of Euplectella sp.: Structural Hierarchy from the Nanoscale to the Macroscale. Science. 2005;309(5732):275-8.
8. Crawford SA, Higgins MJ, Mulvaney P, Wetherbee R. Nanostructure of the diatom frustule as revealed by atomic force and scanning electron microscopy. J Phycol. 2001;37(4):543-54.
9. Kröger N, Lorenz S, Brunner E, Sumper M. Self-assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis. Science. 2002;298(5593):584-6.
10. Tesson B, Hildebrand M, Brzezinski M, Stucky G, Morse D. Extensive and Intimate Association of the Cytoskeleton with Forming Silica in Diatoms: Control over Patterning on the Meso- and Micro-Scale. PLoS One. 2010;5(12), e14300.
11. Cohn SA, Nash J, Pickett-Heaps JD. The effect of drugs on diatom valve morphogenesis. Protoplasma. 1989;149(2-3):130-43.
12. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 2004;306(5693):79-86.
13. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Maheswari U, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008;456:239-44.
14. Pseudo-nitzschia multiseries CLN-47. http://genome.jgi.doe.gov/Psemu1/Psemu1.home.html. Accessed 27 Jan 2017.
15. Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, et al. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature. 2017;541(7638):536-40.
16. Miyahara M, Aoi M, Inoue-Kashino N, Kashino Y, Ifuku K. Highly Efficient Transformation of the Diatom Phaeodactylum tricornutum by Multi-Pulse Electroporation. Biosci Biotechnol Biochem. 2013;77(4):874-6.
17. Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips APR, Noddings CM, et al. Designer diatom episomes delivered by bacterial conjugation. Nat Commun. 2015;6:6925.
18. Scheffel A, Poulsen N, Shian S, Kröger N. Nanopatterned protein microrings from a diatom that direct silica morphogenesis. Proc Natl Acad Sci U S A. 2011;108(8):3175-80.
19. Hopes A, Nekrasov V, Kamoun S, Mock T. Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. Plant Methods. 2016;12(1):49.
20. Nymark M, Sharma AK, Sparstad T, Bones AM, Winge P. A CRISPR/Cas9 system adapted for gene editing in marine algae. Sci Rep. 2016;6(1):24951.
21. Kadono T, Miyagawa-Yamaguchi A, Kira N, Tomaru Y, Okami T, Yoshimatsu T, et al. Characterization of marine diatom-infecting virus promoters in the model diatom Phaeodactylum tricornutum. Sci Rep. 2015;5:1-13.
22. Gröger P, Poulsen N, Klemm J, Kröger N, Schlierf M. Establishing super-resolution imaging for proteins in diatom biosilica. Sci Rep. 2016;6:36824.
23. Stonik V, Stonik I. Low-Molecular-Weight Metabolites from Diatoms: Structures, Biological Roles and Biosynthesis. Mar Drugs. 2015;13(6):3672-709.
24. Martin-Belmonte F, Perez-Moreno M. Epithelial cell polarity, stem cells and cancer. Nat Rev Cancer. 2011;12(1):23-38.
25. Morgan TH. Regeneration of proportionate structures in Stentor. Biol Bull. 1901;2(6):311-28.
26. de Terra N. Evidence for cortical control of macronuclear behavior inStentor. J Cell Physiol. 1971;78(3):377-85.
27. Tartar V. The biology of Stentor. Pergamon: Elsevier; 1961.
28. Tartar V. Extreme alteration of the nucleocytoplasmic ration in Stentor coeruleus. J Protozool. 1963;10:445-61.
29. Whitson GL. The effects of actinomycin D and ribonuclease on oral regeneration in Stentor coeruleus. J Exp Zool. 1965;160(2):207-14.
30. Burchill BR. Synthesis of RNA and protein in relation to oral regeneration in the ciliateStentor coeruleus. J Exp Zool. 1968;167(4):427-38.
31. James EA. Regeneration and division in Stentor coeruleus: the effects of microinjected and externally applied actinomycin D and puromycin. Dev Biol. 1967;16(6):577-93.
32. Younger KB, Banerjee S, Kelleher JK, Winston M, Margulis L. Evidence that the Synchronized Production of New Basal Bodies is not Associated with Dna synthesis in Stentor coeruleus. J Cell Sci. 1972;11(2):621-37.
33. Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, et al. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Curr Biol. 2017;27(4):569-75.
34. Ellwood LC, Cowden RR. RNA metabolism during regeneration in Stentor coeruleus. Cytologia (Tokyo). 1966;31(1):80-8.
35. Randall JT, Jackson SF. Fine structure and function in Stentor polymorphous. J Biophys Biochem Cytol. 1958;4(6):807-30.
36. Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF. The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor morphogenesis. PLoS Biol. 2014;12(5), e1001861.
37. Yu F-X, Guan K-L. The Hippo pathway: regulators and regulations. Genes Dev. 2013;27(4):355-71.
38. Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, et al. The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development. Cell. 2014;158(5):1187-98.
39. Prescott DM. The DNA, of ciliated protozoa. Microbiol Rev. 1994;58(2):233-67.
40. Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, et al. The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLoS Biol. 2013;11(1), e1001473.
41. Gottschling DE, Zakian VA. Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA. Cell. 1986;47(2):195-205.
42. Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA, Schultz SC. Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell. 1998;95(7):963-74.
43. Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, Herrick G, et al. Characterization and Taxonomic Validity of the Ciliate Oxytricha trifallax (Class Spirotrichea) Based on Multiple Gene Sequences: Limitations in Identifying Genera Solely by Morphology. Protist. 2012;163(4):643-57.
44. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature. 2008;451(7175):153-8.
45. Lindblad KA, Bracht JR, Williams AE, Landweber L. Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 2017;rna.058511.116.
46. Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell. 2012;151(6):1243-55.
47. Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, Landweber LF. A functional role for transposases in a large eukaryotic genome. Science. 2009;324(1996):935-8.
48. Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, Landweber LF, et al. Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes. Nucleic Acids Res. 2011;39(17):7529-47.
49. Nowacki M, Landweber LF. Epigenetic inheritance in ciliates. Curr Opin Microbiol. 2009;12(6):638-43.
50. Bracht JR, Wang X, Shetty K, Chen X, Uttarotai GJ, Callihan EC, et al. Chromosome fusions triggered by noncoding RNA. RNA Biol. 2017;14(5):620-31.
51. Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, et al. The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility. Cell. 2010;140(5):631-42.
52. Fulton C. Naegleria: A Research Partner For Cell and Developmental Biology. J Eukaryot Microbiol. 1993;40(4):520-32.
53. Fulton C. Amebo-flagellates as research partners : the laboratory biology of naegleria and tetramitus. In: Prescott DM, editor. Methods Cell Physiol. 1970;4:341-476.
54. Fulton C, Dingle AD. Basal bodies, but not centrioles, in Naegleria. J Cell Biol. 1971;51(3):826-36.
55. Chung S, Cho J, Cheon H, Paik S, Lee J. Cloning and characterization of a divergent alpha-tubulin that is expressed specifically in dividing amebae of Naegleria gruberi. Gene. 2002;293(1-2):77-86.
56. King CA, Cooper L, Preston TM. Cell-substrate interactions during amoeboid locomotion ofNaegleria gruberi with special reference to alterations in temperature and electrolyte concentration of the medium. Protoplasma. 1983;118(1):10-8.
57. Lieber AD, Yehudai-Resheff S, Barnhart EL, Theriot JA, Keren K. Membrane tension in rapidly moving cells is determined by cytoskeletal forces. Curr Biol. 2013;23(15):1409-17.
58. Buenemann M, Levine H, Rappel W-J, Sander LM. The role of cell contraction and adhesion in dictyostelium motility. Biophys J. 2010;99(1):50-8.
59. Butler KL, Ambravaneswaran V, Agrawal N, Bilodeau M, Toner M, Tompkins RG, et al. Burn injury reduces neutrophil directional migration speed in microfluidic devices. PLoS One. 2010;5(7): e11921.
60. Euteneuer U, Schliwa M. Persistent, directional motility of cells and cytoplasmic fragments in the absence of microtubules. Nature. 1984;310(5972):58-61.
61. Dziezanowski MA, DeStefano MJ, Rabinovitch M. Effect of antitubulins on spontaneous and chemotactic migration of neutrophils under agarose. J Cell Sci. 1980;42:379-88.
62. Paluch EK, Raz E. The role and regulation of blebs in cell migration. Curr Opin Cell Biol. 2013;25:582-90.
63. Lämmermann T, Sixt M. Mechanical modes of "amoeboid" cell migration. Curr Opin Cell Biol. 2009;21:636-44.
64. Rodriguez MA, LeClaire LL, Roberts TM. Preparing to move: assembly of the MSP amoeboid motility apparatus during spermiogenesis in Ascaris. Cell Motil Cytoskeleton. 2005;60(4):191-9.
65. Bergert M, Chandradoss SD, Desai R, Paluch E. Cell mechanics control rapid transitions between blebs and lamellipodia during migration. Proc Natl Acad Sci U S A. 2012;109(36):14434-9.
66. Yoshida K, Soldati T. Dissection of amoeboid movement into two mechanically distinct modes. J Cell Sci. 2006;119(Pt 18):3833-44.
67. Fulton C, Dingle AD. Appearance of the flagellate phenotype in populations of Naegleria amebae. Dev Biol. 1967;15(2):165-91.
68. Fulton C, Walsh C. Cell differentiation and flagellar elongation in Naegleria gruberi. Dependence on transcription and translation. J Cell Biol. 1980;85(2):346-60.
69. Dingle AD, Fulton C. Development of the flagellar apparatus of Naegleria. J Cell Biol. 1966;31(1):43-54.
70. Fritz-Laylin LK, Fulton C. Naegleria: a classic model for de novo basal body assembly. Cilia. 2016;5(1):10.
71. Fritz-Laylin LK, Assaf ZJ, Chen S, Cande WZ. Naegleria gruberi de novo basal body assembly occurs via stepwise incorporation of conserved proteins. Eukaryot Cell. 2010;9(6):860-5.
72. Lai EY, Walsh C, Wardell D, Fulton C. Programmed appearance of translatable flagellar tubulin mRNA during cell differentiation in Naegleria. Cell. 1979;17(4):867-78.
73. Levy YY, Lai EY, Remillard SP, Fulton C. Centrin is synthesized and assembled into basal bodies during Naegleria differentiation. Cell Motil Cytoskeleton. 1998;40(3):249-60.
74. Fritz-Laylin LK, Cande WZ. Ancestral centriole and flagella proteins identified by analysis of Naegleria differentiation. J Cell Sci. 2010;123(Pt 23):4024-31.
75. Khodjakov A, Rieder CL, Sluder G, Cassels G, Sibon O, Wang C-L. De novo formation of centrosomes in vertebrate cells arrested during S phase. J Cell Biol. 2002;158(7):1171-81.
76. La Terra S, English CN, Hergert P, McEwen BF, Sluder G, Khodjakov A. The de novo centriole assembly pathway in HeLa cells: Cell cycle progression and centriole assembly/maturation. J Cell Biol. 2005;168(5):713-22.
77. Uetake Y, Lončarek J, Nordberg JJ, English CN, La Terra S, Khodjakov A, et al. Cell cycle progression and de novo centriole assembly after centrosomal removal in untransformed human cells. J Cell Biol. 2007;176(2):173-82.
78. Fritz-Laylin LK, Levy YY, Levitan E, Chen S, Cande WZ, Lai EY, et al. Rapid centriole assembly in N aegleria reveals conserved roles for both de novo and mentored assembly. Cytoskeleton. 2016;73(3):109-16.
79. Müller B, Groscurth S, Menzel M, Rüping BA, Twyman RM, Prüfer D, et al. Molecular and ultrastructural analysis of forisome subunits reveals the principles of forisome assembly. Ann Bot. 2014;113(7):1121-37.
80. Knoblauch M, Stubenrauch M, Van Bel AJE, Peters WS. Forisome performance in artificial sieve tubes. Plant, Cell Environ. 2012;35(8):1419-27.
81. Upadhyaya A, Baraban M, Wong J, Matsudaira P, van Oudenaarden A, Mahadevan L. Power-limited contraction dynamics of Vorticella convallaria: an ultrafast biological spring. Biophys J. 2008;94(1):265-72.
82. Raymann K, Bobay L-M, Doak TG, Lynch M, Gribaldo S. A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3 (Bethesda). 2013;3:505-16.
83. Sonneborn TM. Gene and cytoplasm. Proc Natl Acad Sci U S A. 1943;29(11):329-38.
84. Dippell RV. The Fine Structure of Kappa in Killer Stock 51 of Paramecium aurelia; preliminary observations. J Biophys Biochem Cytol. 1958;4(1):125-8.
85. Mueller JA. Vitally stained kappa in Paramecium aurelia. J Exp Zool. 1965;160(3):369-72.
86. Quackenbush RL, Burbach JA. Cloning and expression of DNA sequences associated with the killer trait of Paramecium tetraurelia stock 47. Proc Natl Acad Sci U S A. 1983;80(1):250-4.
87. Heruth DP, Pond FR, Dilts JA, Quackenbush RL. Characterization of genetic determinants for R body synthesis and assembly in Caedibacter taeniospiralis 47 and 116. J Bacteriol. 1994;176(12):3559-67.
88. Kanabrocki JA, Quackenbush RL, Pond FR. Organization and expression of genetic determinants for synthesis and assembly of type 51 R bodies. J Bacteriol. 1986;168(1):40-8.
89. Polka JK, Silver PA. A Tunable Protein Piston That Breaks Membranes to Release Encapsulated Cargo. ACS Synth Biol. 2016;5(4):303-11.
90. Drechsler H, McAinsh AD. Exotic mitotic mechanisms. Open Biol. 2012;2(12):120140.
91. Makarova M, Oliferenko S. Mixing and matching nuclear envelope remodeling and spindle assembly strategies in the evolution of mitosis. Curr Opin Cell Biol. 2016;41:43-50.
92. Oliferenko S, Chew TG, Balasubramanian MK. Positioning cytokinesis. Genes and Dev. 2009;23:660-74.
93. Ungricht R, Kutay U. Mechanisms and functions of nuclear envelope remodelling. Nat Rev Mol Cell Biol. 2017;18(4):229-45.
94. Zhang D, Oliferenko S. Remodeling the nuclear membrane during closed mitosis. Curr Opin Cell Biol. 2013;25:1-7.
95. Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, et al. Comparative functional genomics of the fission yeasts. Science. 2011;332(6032):930-6.
96. Yam C, He Y, Zhang D, Chiam KH, Oliferenko S. Divergent strategies for controlling the nuclear membrane satisfy geometric constraints during nuclear division. Curr Biol. 2011;21(15):1314-9.
97. Aoki K, Hayashi H, Furuya K, Sato M, Takagi T, Osumi M, et al. Breakage of the nuclear envelope by an extending mitotic nucleus occurs during anaphase in Schizosaccharomyces japonicus. Genes Cells. 2011;16(9):911-26.
98. Makarova M, Gu Y, Chen JS, Beckley JR, Gould KL, Oliferenko S. Temporal Regulation of Lipin Activity Diverged to Account for Differences in Mitotic Programs. Curr Biol. 2016;26(2):237-43.
99. Fujita I, Nishihara Y, Tanaka M, Tsujii H, Chikashige Y, Watanabe Y, et al. Telomere-nuclear envelope dissociation promoted by rap1 phosphorylation ensures faithful chromosome segregation. Curr Biol. 2012;22(20):1932-7.
100. Hediger F, Neumann FR, Van Houwe G, Dubrana K, Gasser SM. Live imaging of telomeres: yKu and Sir proteins define redundant telomere-anchoring pathways in yeast. Curr Biol. 2002;12(24):2076-89.
101. Yam C, Gu Y, Oliferenko S. Partitioning and remodeling of the Schizosaccharomyces japonicus mitotic nucleus require chromosome tethers. Curr Biol. 2013;23(22):2303-10.
102. Lemaitre JM, Géraud G, Méchali M. Dynamics of the genome during early Xenopus laevis development: Karyomeres as independent units of replication. J Cell Biol. 1998;142(5):1159-66.
103. Abrams EW, Zhang H, Marlow FL, Kapp L, Lu S, Mullins MC. Dynamic assembly of brambleberry mediates nuclear envelope fusion during early development. Cell. 2012;150(3):521-32.
104. Ulbert S, Antonin W, Platani M, Mattaj IW. The inner nuclear membrane protein Lem2 is critical for normal nuclear envelope morphology. FEBS Lett. 2006;580(27):6435-41.
105. Barkan R, Zahand AJ, Sharabi K, Lamm AT, Feinstein N, Haithcock E, et al. Ce-emerin and LEM-2: essential roles in Caenorhabditis elegans development, muscle function, and mitosis. Mol Biol Cell. 2012;23(4):543-52.
106. Gonzalez Y, Saito A, Sazer S. Fission yeast Lem2 and Man1 perform fundamental functions of the animal cell nuclear lamina. Nucleus. 2012;3(1):60-76.
107. Gu Y, Yam C, Oliferenko S. Rewiring of cellular division site selection in evolution of fission yeasts. Curr Biol. 2015;25(9):1187-94.
108. Gu Y, Oliferenko S. Comparative biology of cell division in the fission yeast clade. Curr Opin Microbiol. 2015;28:18-25.
109. Huang J, Chew TG, Gu Y, Palani S, Kamnev A, Martin DS, et al. Curvature-induced expulsion of actomyosin bundles during cytokinetic ring contraction. Elife. 2016;5:e21383.
110. Furuya K, Niki H. Isolation of heterothallic haploid and auxotrophic mutants of Schizosaccharomyces japonicus. Yeast. 2009;26(4):221-33.
111. Aoki K, Nakajima R, Furuya K, Niki H. Novel episomal vectors and a highly efficient transformation procedure for the fission yeast Schizosaccharomyces japonicus. Yeast. 2010;27(12):1049-60.
112. Furuya K, Niki H. Hyphal differentiation induced via a DNA damage checkpoint-dependent pathway engaged in crosstalk with nutrient stress signaling in Schizosaccharomyces japonicus. Curr Genet. 2012;58(5-6):291-303.
113. Okamoto S, Furuya K, Nozaki S, Aoki K, Niki H. Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus. Eukaryot Cell. 2013;12(9):1235-43.
114. Bulder CJEA. On respiratory deficiency in yeasts. The Netherlands: TU Left; 1963.
115. Upadhyay U, Srivastava S, Khatri I, Nanda JS, Subramanian S, Arora A, et al. Ablation of RNAi and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB. Mol Biol Cell. 2017; doi: 10.1091/mbc.E16-07-0485.
116. Chen YE, Tropini C, Jonas K, Tsokos CG, Huang KC, Laub MT. Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium. Proc Natl Acad Sci U S A. 2011;108(3):1052-7.
117. Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, et al. Global analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function. Cell. 2007;131(1):174-87.
118. Dietrich FS, Voegeli S, Kuo S, Philippsen P. Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications. G3 (Bethesda). 2013;3:1225-39.
119. Schmitz HP, Philippsen P. Evolution of multinucleated Ashbya gossypii hyphae from a budding yeast-like ancestor. Fungal Biol. 2011;115(6):557-68.
120. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004;304(5668):304-7.
121. Wright MC, Philippsen P. Replicative transformation of the filamentous fungus Ashbya gossypii with plasmids containing Saccharomyces cerevisiae ARS elements. Gene. 1991;109(1):99-105.
122. Steiner S, Wendland J, Wright MC, Philippsen P. Homologous recombination as the main mechanism for DNA integration and cause of rearrangements in the filamentous ascomycete Ashbya gossypii. Genetics. 1995;140(3):973-87.
123. Wendland J, Ayad-Durieux Y, Knechtle P, Rebischung C, Philippsen P. PCR-based gene targeting in the filamentous fungus Ashbya gossypii. Gene. 2000;242(1-2):381-91.
124. Wendland J, Walther A. Ashbya gossypii: a model for fungal developmental biology. Nat Rev Microbiol. 2005;3(5):421-9.
125. Lee CH, Zhang H, Baker AE, Occhipinti P, Borsuk ME, Gladfelter AS. Protein aggregation behavior regulates cyclin transcript localization and cell-cycle control. Dev Cell. 2013;25(6):572-84.
126. Zhang H, Elbaum-Garfinkle S, Langdon EM, Taylor N, Occhipinti P, Bridges AA, et al. RNA Controls PolyQ Protein Phase Transitions. Mol Cell. 2015;60(2):220-30.
127. Lee CH, Occhipinti P, Gladfelter AS. PolyQ-dependent RNA-protein assemblies control symmetry breaking. J Cell Biol. 2015;208(5):533-44.
128. Szathmáry E, Smith JM. The major evolutionary transitions. Nature. 1995;374:227-32.
129. Bonner JT. The origins of multicellularity. Integr Biol. 1998;1(1):27-36.
130. King N. The unicellular ancestry of animal development. Dev Cell. 2004;7:313-25.
131. Grosberg RK, Strathmann RR. The Evolution of Multicellularity: A Minor Major Transition? Annu Rev Ecol Evol Syst. 2007;38:621-54.
132. Matt G, Umen J. Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation. Dev Biol. 2016;419:99-113.
133. Herron MD, Hackett JD, Aylward FO, Michod RE. Triassic origin and early radiation of multicellular volvocine algae. Proc Natl Acad Sci U S A. 2009;106(9):3254-8.
134. Harris EH. Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol. 2001;52:363-406.
135. Umen JG, Olson BJSC. Genomics of Volvocine Algae. Adv Bot Res. 2012;64:185-243.
136. Starr RC. Control of differentiation in Volvox. Soc Dev Biol. 1970;29:59-100.
137. Kirk DL. Volvox: molecular-genetic origins of multicellularity and cellular differentiation. UK: Cambridge University Press; 1998.
138. van Leeuwenhoek A. Part of a letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs. Philos Trans R Soc Lond. 1700;22(260-276):509-18.
139. Kirk DL. A twelve-step program for evolving multicellularity and a division of labor. BioEssays. 2005;27:299-310.
140. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007;318(5848):245-50.
141. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, et al. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science. 2010;329(5988):223-6.
142. Hanschen ER, Marriage TN, Ferris PJ, Hamaji T, Toyoda A, Fujiyama A, et al. The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nat Commun. 2016;7:11370.
143. Nishii I, Miller SM. Volvox: simple steps to developmental complexity? Curr Opin Plant Biol. 2010;13:646-53.
144. Huskey R, Griffin B, Cecil P, Callahan A. A Preliminary Genetic Investigation of Volvox Carteri. Genetics. 1979;91(2):229-44.
145. Umen JG. Evolution of sex and mating loci: An expanded view from Volvocine algae. Curr Opin Microbiol. 2011;14:634-41.
146. Miller SM, Schmitt R, Kirk DL. Jordan, an active Volvox transposable element similar to higher plant transposons. Plant Cell. 1993;5(9):1125-38.
147. Ueki N, Nishii I. Idaten is a new cold-inducible transposon of Volvox carteri that can be used for tagging developmentally important genes. Genetics. 2008;180(3):1343-53.
148. Ishida K. Vectorette PCR-primed transposon display using the Jordan transposon in Volvox carteri: an efficient tool that analyzes more than 300 Jordan-derived PCR Fragments to retrieve tagged genes. Protist. 2008;159(1):5-19.
149. Geng S, De Hoff P, Umen JG, Callahan A, Gruber H. Evolution of Sexes from an Ancestral Mating-Type Specification Pathway. PLoS Biol. 2014;12(7):e1001904.
150. Schiedlmeier B, Schmitt R, Müller W, Kirk MM, Gruber H, Mages W, et al. Nuclear transformation of Volvox carteri. Proc Natl Acad Sci U S A. 1994;91(11):5080-4.
151. Jakobiak T, Mages W, Scharf B, Babinger P, Stark K, Schmitt R. The bacterial paromomycin resistance gene, aphH, as a dominant selectable marker in Volvox carteri. Protist. 2004;155:381-93.
152. Hallmann A, Sumper M. The Chlorella hexose/H+ symporter is a useful selectable marker and biochemical reagent when expressed in Volvox. Proc Natl Acad Sci U S A. 1996;93(2):669-73.
153. Ishida K. Sexual pheromone induces diffusion of the pheromone-homologous polypeptide in the extracellular matrix of Volvox carteri. Eukaryot Cell. 2007;6(11):2157-62.
154. Pappas V, Miller SM. Functional analysis of the Volvox carteri asymmetric division protein GlsA. Mech Dev. 2009;126(10):842-51.
155. Ebnet E, Fischer M, Deininger W, Hegemann P. Volvoxrhodopsin, a Light-Regulated Sensory Photoreceptor of the Spheroidal Green Alga Volvox carteri. Plant Cell. 1999;11:1473-84.
156. Cheng Q, Hallmann A, Edwards L, Miller SM. Characterization of a heat-shock-inducible hsp70 gene of the green alga Volvox carteri. Gene. 2006;371(1):112-20.
157. Baek K, Kim DH, Jeong J, Sim SJ, Melis A, Kim J-S, et al. DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins. Sci Rep. 2016;6:30620.
158. Shin S-E, Lim J-M, Koh HG, Kim EK, Kang NK, Jeon S, et al. CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii. Sci Rep. 2016;6:27810.
159. Höhn S, Honerkamp-Smith AR, Haas PA, Trong PK, Goldstein RE. Dynamics of a Volvox embryo turning itself inside out. Phys Rev Lett. 2015;114(17):178101.
160. Kodama Y. Time gating of chloroplast autofluorescence allows clearer fluorescence imaging in planta. PLoS One. 2016;11(3):e0152484.
161. Kirk MM, Ransick A, McRae SE, Kirk DL. The relationship between cell size and cell fate in Volvox carteri. J Cell Biol. 1993;123(1):191-208.
162. Nakazawa A, Nishii I. Amidic and acetonic cryoprotectants improve cryopreservation of volvocine green algae. Cryo Lett. 2012;33(3):202-13.
163. Chlamydomonas Center Meeting Announcements. http://www.chlamycollection.org/category/meetings/. Accessed 15 Mar 2017.
164. Volvox 2017 http://www.volvox2017.org/. Accessed 15 Mar 2017.
165. Cove DJ, Schild A, Ashton NW, Hartmann E. Genetic and physiological studies of light on the development of the moss Physcomitrella patens. Photochem Photobiol. 1978;27(2):249-54.
166. Harrison CJ, Roeder AHK, Meyerowitz EM, Langdale JA. Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens. Curr Biol. 2009;19(6):461-71.
167. Bascom CS, Wu S-Z, Nelson K, Oakey J, Bezanilla M. Long-Term Growth of Moss in Microfluidic Devices Enables Subcellular Studies in Development. Plant Physiol. 2016;172(1):28-37.
168. Schaefer D, Zryd JP, Knight CD, Cove DJ. Stable transformation of the moss Physcomitrella patens. MGG Mol Gen Genet. 1991;226(3):418-24.
169. Kammerer W, Cove DJ. Genetic analysis of the effects of re-transformation of transgenic lines of the moss Physcomitrella patens. Mol Gen Genet. 1996;250(3):380-2.
170. Schaefer DG, Zryd J-P. Efficient gene targeting in the moss Physcomitrella patens. Plant J. 1997;11(6):1195-206.
171. Strepp R, Scholz S, Kruse S, Speth V, Reski R. Plant nuclear gene knockout reveals a role in plastid division for the homolog of the bacterial cell division protein FtsZ, an ancestral tubulin. Proc Natl Acad Sci U S A. 1998;95(8):4368-73.
172. Sakakibara K, Nishiyama T, Sumikawa N, Kofuji R, Murata T, Hasebe M. Involvement of auxin and a homeodomain-leucine zipper I gene in rhizoid development of the moss Physcomitrella patens. Development. 2003;130(20):4835-46.
173. Perroud PF, Cove DJ, Quatrano RS, Mcdaniel SF. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines. New Phytol. 2011;191(1):301-6.
174. Collonnier C, Epert A, Mara K, Maclot F, Guyon-Debast A, Charlot F, et al. CRISPR-Cas9-mediated efficient directed mutagenesis and RAD51-dependent and RAD51-independent gene targeting in the moss Physcomitrella patens. Plant Biotechnol J. 2016;15(1):122-31.
175. Lopez-Obando M, Hoffmann B, Géry C, Guyon-Debast A, Téoulé E, Rameau C, et al. Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens. G3 (Bethesda). 2016;6(11):3647-53.
176. Bezanilla M, Perroud PF, Pan A, Klueh P, Quatrano RS. An RNAi system in Physcomitrella patens with an internal marker for silencing allows for rapid identification of loss of function phenotypes. Plant Biol. 2005;7(3):251-7.
177. Bezanilla M, Pan A, Quatrano RS. RNA interference in the moss Physcomitrella patens. Plant Physiol. 2003;133:470-4.
178. Nakaoka Y, Miki T, Fujioka R, Uehara R, Tomioka A, Obuse C, et al. An inducible RNA interference system in Physcomitrella patens reveals a dominant role of augmin in phragmoplast microtubule generation. Plant Cell. 2012;24(4):1478-93.
179. Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, et al. Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR), a regulator of ABA responses unique to basal land plants and required for desiccation tolerance. Plant Cell. 2016;28(6):1310-27.
180. Herculano-Houzel S. The human brain in numbers: a linearly scaled-up primate brain. Front Hum Neurosci. 2009;3:31.
181. DeFelipe J. The evolution of the brain, the human nature of cortical circuits, and intellectual creativity. Front Neuroanat. 2011;5:29.
182. Ballesteros Yáñez I, Muñoz A, Contreras J, Gonzalez J, Rodriguez-Veiga E, DeFelipe J. Double bouquet cell in the human cerebral cortex and a comparison with other mammals. J Comp Neurol. 2005;486(4):344-60.
183. Raghanti MA, Spocter MA, Stimpson CD, Erwin JM, Bonar CJ, Allman JM, et al. Species-specific distributions of tyrosine hydroxylase-immunoreactive neurons in the prefrontal cortex of anthropoid primates. Neuroscience. 2009;158(4):1551-9.
184. Benavides-Piccione R, Ballesteros-Yáñez I, DeFelipe J, Yuste R. Cortical area and species differences in dendritic spine morphology. J Neurocytol. 2002;31(3-5 SPEC. ISS):337-46.
185. Mahmood S, Ahmad W, Hassan MJ. Autosomal recessive primary microcephaly (MCPH): clinical manifestations, genetic heterogeneity and mutation continuum. Orphanet J Rare Dis. 2011;6(1):39.
186. LaFerla FM, Green KN. Animal models of Alzheimer disease. Cold Spring Harb Perspect Med. 2012;2(11):a006320.
187. Friedman RA. A dry pipeline for psychiatric drugs. The New York Times. 2013. http://www.nytimes.com/2013/08/20/health/a-dry-pipeline-for-psychiatric-drugs.html. Accessed 15 Mar 2017.
188. Zhang S-C, Wernig M, Duncan ID, Brüstle O, Thomson JA. In vitro differentiation of transplantable neural precursors from human embryonic stem cells. Nat Biotechnol. 2001;19(12):1129-33.
189. Shi Y, Kirwan P, Smith J, Robinson HPC, Livesey FJ. Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses. Nat Neurosci. 2012;15(3):477-86. S1.
190. Chambers SM, Fasano CA, Papapetrou EP, Tomishima M, Sadelain M, Studer L. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol. 2009;27(3):275-80.
191. Eiraku M, Watanabe K, Matsuo-Takasaki M, Kawada M, Yonemura S, Matsumura M, et al. Self-Organized Formation of Polarized Cortical Tissues from ESCs and Its Active Manipulation by Extrinsic Signals. Cell Stem Cell. 2008;3(5):519-32.
192. Lancaster MA, Renner M, Martin C-A, Wenzel D, Bicknell LS, Hurles ME, et al. Cerebral organoids model human brain development and microcephaly. Nature. 2012;501(1):373-9.
193. Kadoshima T, Sakaguchi H, Nakano T, Soen M, Ando S, Eiraku M, et al. Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex. Proc Natl Acad Sci U S A. 2013;110(50):20284-9.
194. Paşca AM, Sloan SA, Clarke LE, Tian Y, Makinson CD, Huber N, et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat Methods. 2015;12(7):671-8.
195. Kelava I, Lancaster MA. Stem Cell Models of Human Brain Development. Cell Stem Cell. 2016;18:736-48.
196. Otani T, Marchetto MC, Gage FH, Simons BD, Livesey FJ. 2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size. Cell Stem Cell. 2016;18(4):467-80.
197. Mora-Bermúdez F, Badsha F, Kanton S, Camp JG, Vernot B, Köhler K, et al. Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. Elife. 2016;5.
198. Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, et al. FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell. 2015;162(2):375-90.
199. Bershteyn M, Nowakowski TJ, Pollen AA, Di Lullo E, Nene A, Wynshaw-Boris A, et al. Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia. Cell Stem Cell. 2017;20(4):435-49.e4.
200. Qian X, Nguyen HN, Song MM, Hadiono C, Ogden SC, Hammack C, et al. Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure. Cell. 2016;165(5):1238-54.
201. Cugola FR, Fernandes IR, Russo FB, Freitas BC, Dias JLM, Guimarães KP, et al. The Brazilian Zika virus strain causes birth defects in experimental models. Nature. 2016;534(7606):267-71.
202. Lenhoff SG, Lenhoff HM, Trembley A. Hydra and the birth of experimental biology, 1744: Abraham Trembley's Mémoires concerning the polyps. Pacific Grove: Boxwood Press; 1986.
203. Haeckel E. Art forms from the ocean: the radiolarian atlas of 1862, Munich; London: Prestel; 2005.
204. Hyman LH. The invertebrates. 1st ed. McGraw-Hill publications in the zoological sciences. New York: McGraw-Hill; 1940.
205. Muscatine L, Lenhoff HM. Coelenterate biology: reviews and new perspectives. New York: Academic Press; 1974.
206. Stephenson TA. The British sea anemones. 1935.
207. Wells S, Pyle RM, Collins NM, IUCN Conservation Monitoring Centre., International Union for Conservation of Nature and Natural Resources., International Union for Conservation of Nature and Natural Resources. Species Survival Commission. The IUCN invertebrate red data book. Gland: IUCN; 1983.
208. Hand C, Uhlinger KR. The Culture, Sexual and Asexual Reproduction, and Growth of the Sea Anemone Nematostella vectensis. Biol Bull. 1992;182(2):169-76.
209. Bridge D, Cunningham CW, DeSalle R, Buss LW. Class-level relationships in the phylum Cnidaria: molecular and morphological evidence. Mol Biol Evol. 1995;12(4):679-89.
210. Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol. 2013;13:5.
211. Brusca RC, Brusca GJ. Invertebrates. Sunderland, Mass: Sinauer Associates; 1990.
212. Bridge D, Cunningham CW, Schierwater B, DeSalle R, Buss LW. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc Natl Acad Sci U S A. 1992;89(18):8750-3.
213. Marques AC, Collins AG. Cladistic analysis of Medusozoa and cnidarian evolution. Invertebr Biol. 2004;123(1):23-42.
214. Darling JA, Reitzel AR, Burton PM, Mazza ME, Ryan JF, Sullivan JC, et al. Rising starlet: the starlet sea anemone, Nematostella vectensis. Bioessays. 2005;27(2):211-21.
215. Collins AG. Phylogeny of Medusozoa and the evolution of cnidarian life cycles. J Evol Biol. 2002;15(3):418-32. Blackwell Science Ltd.
216. Loya Y, Sakai K. Bidirectional sex change in mushroom stony corals. Proc Biol Sci. 2008;275(1649):2335-43.
217. Schlesinger A, Kramarsky-Winter E, Rosenfeld H, Armoza-Zvoloni R, Loya Y. Sexual plasticity and self-fertilization in the sea anemone Aiptasia diaphana. PLoS One. 2010;5(7):e11874.
218. Fritzenwanker JH, Technau U. Induction of gametogenesis in the basal cnidarian Nematostella vectensis(Anthozoa). Dev Genes Evol. 2002;212(2):99-103.
219. Genikhovich G, Technau U. Induction of spawning in the starlet sea anemone Nematostella vectensis, in vitro fertilization of gametes, and dejellying of zygotes. Cold Spring Harb Protoc. 2009;2009(9):pdb prot5281.
220. Fritzenwanker JH, Genikhovich G, Kraus Y, Technau U. Early development and axis specification in the sea anemone Nematostella vectensis. Dev Biol. 2007;310(2):264-79.
221. Fritz AE, Ikmi A, Seidel C, Paulson A, Gibson MC. Mechanisms of tentacle morphogenesis in the sea anemone Nematostella vectensis. Development. 2013;140(10):2212-23.
222. Hand C, Uhlinger KR. Asexual Reproduction by Transverse Fission and Some Anomalies in the Sea Anemone Nematostella vectensis. Invertebr Biol. 1995;114(1):9-18.
223. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007;317(5834):86-94.
224. Sullivan JC, Finnerty JR. A surprising abundance of human disease genes in a simple "basal" animal, the starlet sea anemone (Nematostella vectensis). Genome. 2007;50(7):689-92.
225. Sullivan JC, Reitzel AM, Finnerty JR. A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis. Genome Inf. 2006;17(1):219-29.
226. Sullivan JC, Ryan JF, Watson JA, Webb J, Mullikin JC, Rokhsar D, et al. StellaBase: the Nematostella vectensis Genomics Database. Nucleic Acids Res. 2006;34(Database issue):D495-9.
227. Layden MJ, Rottinger E, Wolenski FS, Gilmore TD, Martindale MQ. Microinjection of mRNA or morpholinos for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nat Protoc. 2013;8(5):924-34.
228. Renfer E, Amon-Hassenzahl A, Steinmetz PR, Technau U. A muscle-specific transgenic reporter line of the sea anemone, Nematostella vectensis. Proc Natl Acad Sci U S A. 2010;107(1):104-8.
229. Nakanishi N, Renfer E, Technau U, Rentzsch F. Nervous systems of the sea anemone Nematostella vectensis are generated by ectoderm and endoderm and shaped by distinct mechanisms. Development. 2012;139(2):347-57.
230. Layden MJ, Johnston H, Amiel AR, Havrilak J, Steinworth B, Chock T, et al. MAPK signaling is necessary for neurogenesis in Nematostella vectensis. BMC Biol. 2016;14:61.
231. Schwaiger M, Schonauer A, Rendeiro AF, Pribitzer C, Schauer A, Gilles AF, et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 2014;24(4):639-50.
232. Ikmi A, McKinney SA, Delventhal KM, Gibson MC. TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis. Nat Commun. 2014;5:5486.
233. Kraus Y, Aman A, Technau U, Genikhovich G. Pre-bilaterian origin of the blastoporal axial organizer. Nat Commun. 2016;7:11694.
234. Kusserow A, Pang K, Sturm C, Hrouda M, Lentfer J, Schmidt HA, et al. Unexpected complexity of the Wnt gene family in a sea anemone. Nature. 2005;433(7022):156-60.
235. Leclere L, Rentzsch F. RGM regulates BMP-mediated secondary axis formation in the sea anemone Nematostella vectensis. Cell Rep. 2014;9(5):1921-30.
236. Hudry B, Thomas-Chollier M, Volovik Y, Duffraisse M, Dard A, Frank D, et al. Molecular insights into the origin of the Hox-TALE patterning system. Elife. 2014;3:e01939.
237. Magie CR, Daly M, Martindale MQ. Gastrulation in the cnidarian Nematostella vectensis occurs via invagination not ingression. Dev Biol. 2007;305(2):483-97.
238. Martindale MQ, Pang K, Finnerty JR. Investigating the origins of triploblasty: "mesodermal" gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum, Cnidaria; class, Anthozoa). Development. 2004;131(10):2463-74.
239. Layden MJ, Boekhout M, Martindale MQ. Nematostella vectensis achaete-scute homolog NvashA regulates embryonic ectodermal neurogenesis and represents an ancient component of the metazoan neural specification pathway. Development. 2012;139(5):1013-22.
240. Richards GS, Rentzsch F. Regulation of Nematostella neural progenitors by SoxB, Notch and bHLH genes. Development. 2015;142(19):3332-42.
241. Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, et al. The genome of Aiptasia, a sea anemone model for coral symbiosis. Proc Natl Acad Sci U S A. 2015;112(38):11893-8.
242. Yasuoka Y, Shinzato C, Satoh N. The Mesoderm-Forming Gene brachyury Regulates Ectoderm-Endoderm Demarcation in the Coral Acropora digitifera. Curr Biol. 2016;26(21):2885-92.
243. Plickert G, Frank U, Muller WA. Hydractinia, a pioneering model for stem cell biology and reprogramming somatic cells to pluripotency. Int J Dev Biol. 2012;56(6-8):519-34.
244. Houliston E, Momose T, Manuel M. Clytia hemisphaerica: a jellyfish cousin joins the laboratory. Trends Genet. 2010;26(4):159-67.
245. Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 1997;387:489-93.
246. Gabriel WN, McNuff R, Patel SK, Gregory TR, Jeck WR, Jones CD, et al. The tardigrade Hypsibius dujardini, a new model for studying the evolution of development. Dev Biol. 2007;312(2):545-59.
247. Altiero T, Rebecchi L. Rearing tardigrades: Results and problems. Zool Anz. 2001;240(3-4):217-21.
248. Blaxter M, Elsworth B, Daub J. DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades. Proc Biol Sci. 2004;271(Suppl):S189-92.
249. Gabriel WN, Goldstein B. Segmental expression of Pax3/7 and Engrailed homologs in tardigrade development. Dev Genes Evol. 2007;217(6):421-33.
250. Tenlen JR, McCaskill S, Goldstein B. RNA interference can be used to disrupt gene function in tardigrades. Dev Genes Evol. 2013;223(3):171-81.
251. Smith FW, Boothby TC, Giovannini I, Rebecchi L, Jockusch EL, Goldstein B. The Compact Body Plan of Tardigrades Evolved by the Loss of a Large Body Region. Curr Biol. 2016;26(2):224-9.
252. Maderspacher F. Zoology: The Walking Heads. Curr Biol. 2016;26(5):R194-7.
253. Watanabe M. Anhydrobiosis in invertebrates. Appl Entomol Zool. 2006;41(1):15-31.
254. Møbjerg N, Halberg KA, Jørgensen A, Persson D, Bjørn M, Ramløv H, et al. Survival in extreme environments - on the current knowledge of adaptations in tardigrades. Acta Physiol. 2011;202(3):409-20.
255. Jönsson KI, Rabbow E, Schill RO, Harms-Ringdahl M, Rettberg P. Tardigrades survive exposure to space in low Earth orbit. Curr Biol. 2008;18(17):R729-31.
256. Rebecchi L, Altiero T, Guidetti R, Cesari M, Bertolani R, Negroni M, et al. Tardigrade Resistance to Space Effects: First Results of Experiments on the LIFE-TARSE Mission on FOTON-M3 (September 2007). Astrobiology. 2009;9(6):581-91.
257. Boothby T, Tapia H, Brozena AH, Piszkiewicz S, Smith AE, Giovannini I. Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Mol Cell. 2017;65(6):In Press.
258. Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, et al. Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nat Commun. 2016;7:12808.
259. Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, et al. Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. bioRxiv. 2017;112664. https://doi.org/10.1101/112664.
260. Goldstein B, King N. The Future of Cell Biology: Emerging Model Organisms. Trends Cell Biol. 2016;26(11):818-24.
261. Stocum DL. The urodele limb regeneration blastema: a self-organizing system. I. Morphogenesis and differentiation of autografted whole and fractional blastemas. Dev Biol. 1968;18(5):457-80.
262. Iten LE, Bryant SV. Regeneration from different levels along the tail of the newt, Notophthalmus viridescens. J Exp Zool. 1976;196(3):293-306.
263. Dunis DA, Namenwirth M. The role of grafted skin in the regeneration of X-irradiated axolotl limbs. Dev Biol. 1977;56(1):97-109.
264. Sobkow L, Epperlein HH, Herklotz S, Straube WL, Tanaka EM. A germline GFP transgenic axolotl and its use to track cell fate: Dual origin of the fin mesenchyme during development and the fate of blood cells during regeneration. Dev Biol. 2006;290(2):386-97.
265. Khattak S, Schuez M, Richter T, Knapp D, Haigo SL, Sandoval-Guzmán T, et al. Germline transgenic methods for tracking cells and testing gene function during regeneration in the axolotl. Stem Cell Reports. 2013;1(1):90-103.
266. Whited JL, Lehoczky JA, Tabin CJ. Inducible genetic system for the axolotl. Proc Natl Acad Sci U S A. 2012;109(34):13662-7.
267. Flowers GP, Timberlake AT, McLean KC, Monaghan JR, Crews CM. Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease. Development. 2014;141(10):2165-71.
268. Fei JF, Schuez M, Tazaki A, Taniguchi Y, Roensch K, Tanaka EM. CRISPR-mediated genomic deletion of Sox2 in the axolotl shows a requirement in spinal cord neural stem cell amplification during tail regeneration. Stem Cell Rep. 2014;3(3):444-59.
269. Roy S, Gardiner DM, Bryant SV. Vaccinia as a Tool for Functional Analysis in Regenerating Limbs: Ectopic Expression of Shh. Dev Biol. 2000;218(2):199-205.
270. Whited JL, Tsai SL, Beier KT, White JN, Piekarski N, Hanken J, et al. Pseudotyped retroviruses for infecting axolotl in vivo and in vitro. Development. 2013;140(5):1137-46.
271. Khattak S, Sandoval-Guzmán T, Stanke N, Protze S, Tanaka EM, Lindemann D. Foamy virus for efficient gene transfer in regeneration studies. BMC Dev Biol. 2013;13(1):1-9.
272. Nacu E, Gromberg E, Oliveira CR, Drechsel D, Tanaka EM. FGF8 and SHH substitute for anterior-posterior tissue interactions to induce limb regeneration. Nature. 2016;1(7603):1-16.
273. Echeverri K, Tanaka EM. Electroporation as a tool to study in vivo spinal cord regeneration. Dev Dyn. 2003;226(2):418-25.
274. Hayashi T, Sakamoto K, Sakuma T, Yokotani N, Inoue T, Kawaguchi E, et al. Transcription activator-like effector nucleases efficiently disrupt the target gene in Iberian ribbed newts (Pleurodeles waltl), an experimental model animal for regeneration. Dev Growth Differ. 2014;56(1):115-21.
275. Maki N, Suetsugu-Maki R, Sano S, Nakamura K, Nishimura O, Tarui H, et al. Oocyte-type linker histone B4 is required for transdifferentiation of somatic cells in vivo. FASEB J. 2010;24(9):3462-7.
276. Kumar A, Godwin JW, Gates PB, Garza-Garcia AA, Brockes JP. Molecular Basis for the Nerve Dependence of Limb Regeneration in an Adult Vertebrate. Science. 2007;318(5851):772-7.
277. Wang H, Lööf S, Borg P, Nader GA, Blau HM, Simon A. Turning terminally differentiated skeletal muscle cells into regenerative progenitors. Nat Commun. 2015;6:7916.
278. Sandoval-Guzmán T, Wang H, Khattak S, Schuez M, Roensch K, Nacu E, et al. Fundamental differences in dedifferentiation and stem cell recruitment during skeletal muscle regeneration in two salamander species. Cell Stem Cell. 2014;14(2):174-87.
279. Butlera PG, Wanamaker Jr AD, Scoursea JD, Richardson CA, Reynolds AP. Variability of marine climate on the North Icelandic Shelf in a 1357-year proxy archive based on growth increments in the bivalve Arctica islandica. Palaeogeogr Palaeoclimatol Palaeoecol. 2013;373:141-51.
280. Helfand SL, Rogina B. Genetics of aging in the fruit fly, Drosophila melanogaster. Annu Rev Genet. 2003;37:329-48.
281. Olsen A, Vantipalli MC, Lithgow GJ. Using Caenorhabditis elegans as a model for aging and age-related diseases. Ann NY Acad Sci. 2006;1067:120-8.
282. Kaeberlein M, Burtner CR, Kennedy BK. Recent developments in yeast aging. PLoS Genet. 2007;3(5), e84.
283. Weyand CM, Goronzy JJ. Aging of the Immune System. Mechanisms and Therapeutic Targets. Ann Am Thorac Soc. 2016;13(Supplement_5):S422-8.
284. Monti D, Ostan R, Borelli V, Castellani G, Franceschi C. Inflammaging and human longevity in the omics era. Mech Ageing Dev. 2016;
285. Miller RA, Harper JM, Dysko RC, Durkee SJ, Austad SN. Longer life spans and delayed maturation in wild-derived mice. Exp Biol Med. 2002;227(7):500-8.
286. Gerhard GS, Kauffman EJ, Wang X, Stewart R, Moore JL, Kasales CJ, et al. Life spans and senescent phenotypes in two strains of Zebrafish (Danio rerio). Exp Gerontol. 2002;37(8-9):1055-68.
287. Valenzano DR, Sharp S, Brunet A. Transposon-Mediated Transgenesis in the Short-Lived African Killifish Nothobranchius furzeri, a Vertebrate Model for Aging. G3. 2011;1(7):531-8.
288. Valenzano DR, Benayoun BA, Singh PP, Zhang E, Etter PD, Hu CK, et al. The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell. 2015;163(6):1539-54.
289. Reichwald K, Petzold A, Koch P, Downie BR, Hartmann N, Pietsch S, et al. Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish. Cell. 2015;163(6):1527-38.
290. Valdesalici S, Cellerino A. Extremely short lifespan in the annual fish Nothobranchius furzeri. Proc Biol Sci. 2003;270(Suppl):S189-91.
291. Kirschner J, Weber D, Neuschl C, Franke A, Bottger M, Zielke L, et al. Mapping of quantitative trait loci controlling lifespan in the short-lived fish Nothobranchius furzeri--a new vertebrate model for age research. Aging Cell. 2012;11(2):252-61.
292. Valenzano DR, Kirschner J, Kamber RA, Zhang E, Weber D, Cellerino A, et al. Mapping loci associated with tail color and sex determination in the short-lived fish Nothobranchius furzeri. Genetics. 2009;183(4):1385-95.
293. Harel I, Valenzano DR, Brunet A. Efficient genome engineering approaches for the short-lived African turquoise killifish. Nat Protoc. 2016;11(10):2010-28.
294. Polacik M, Blazek R, Reichard M. Laboratory breeding of the short-lived annual killifish Nothobranchius furzeri. Nat Protoc. 2016;11(8):1396-413.
295. Di Cicco E, Tozzini ET, Rossi G, Cellerino A. The short-lived annual fish Nothobranchius furzeri shows a typical teleost aging process reinforced by high incidence of age-dependent neoplasias. Exp Gerontol. 2011;46(4):249-56.
296. Valenzano DR, Terzibasi E, Cattaneo A, Domenici L, Cellerino A. Temperature affects longevity and age-related locomotor and cognitive decay in the short-lived fish Nothobranchius furzeri. Aging Cell. 2006;5(3):275-8.
297. Wendler S, Hartmann N, Hoppe B, Englert C. Age-dependent decline in fin regenerative capacity in the short-lived fish Nothobranchius furzeri. Aging Cell. 2015;14(5):857-66.
298. Bartakova V, Reichard M, Janko K, Polacik M, Blazek R, Reichwald K, et al. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique. BMC Evol Biol. 2013;13:196.
299. Furness AI. The evolution of an annual life cycle in killifish: adaptation to ephemeral aquatic environments through embryonic diapause. Biol Rev Camb Philos Soc. 2016;91(3):796-812.
300. Polacik M, Blazek R, Rezucha R, Vrtilek M, Terzibasi Tozzini E, Reichard M. Alternative intrapopulation life-history strategies and their trade-offs in an African annual fish. J Evol Biol. 2014;27(5):854-65.
301. Parle R. Two new Nothos from Rhodesia. AKA Kill Notes. 1970;3(6):15-21.
302. Harel I, Brunet A. The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane. Cold Spring Harb Symp Quant Biol. 2015;80:275-9.
303. Kim Y, Nam HG, Valenzano DR. The short-lived African turquoise killifish: an emerging experimental model for ageing. Dis Model Mech. 2016;9(2):115-29.
304. Platzer M, Englert C. Nothobranchius furzeri: A Model for Aging Research and More. Trends Genet. 2016;32(9):543-52.
305. Cellerino A, Valenzano DR, Reichard M. From the bush to the bench: the annual Nothobranchius fishes as a new model system in biology. Biol Rev Camb Philos Soc. 2016;91(2):511-33.
306. Stanford African Turquoise Killifish Genome Browser. http://africanturquoisekillifishbrowser.org/. Accessed 3 Mar 2017.
307. FLI Nothobranchius furzeri Genome Browser. http://nfingb.leibniz-fli.de/.
308. Baumgart M, Groth M, Priebe S, Savino A, Testa G, Dix A, et al. RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis. Aging Cell. 2014;13(6):965-74.
309. Baumgart M, Groth M, Priebe S, Appelt J, Guthke R, Platzer M, et al. Age-dependent regulation of tumor-related microRNAs in the brain of the annual fish Nothobranchius furzeri. Mech Ageing Dev. 2012;133(5):226-33.
310. D'Angelo L, De Girolamo P, Lucini C, Terzibasi ET, Baumgart M, Castaldo L, et al. Brain-derived neurotrophic factor: mRNA expression and protein distribution in the brain of the teleost Nothobranchius furzeri. J Comp Neurol. 2014;522(5):1004-30.
311. Ng'oma E, Groth M, Ripa R, Platzer M, Cellerino A. Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci. BMC Genomics. 2014;15:754.
312. Petzold A, Reichwald K, Groth M, Taudien S, Hartmann N, Priebe S, et al. The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels. BMC Genomics. 2013;14:185.
313. Baumgart M, Priebe S, Groth M, Hartmann N, Menzel U, Pandolfini L, et al. Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan. Cell Syst. 2016;2(2):122-32.
314. NCBI Reference Genome--Nothobranchius furzeri. https://www.ncbi.nlm.nih.gov/genome/2642.
315. Meenakumari KJ, Krishna A. Delayed embryonic development in the Indian short-nosed fruit bat, Cynopterus sphinx. Zool. 2005;108(2):131-40.
316. Bleier WJ. Early embryology and implantation in the California leaf-nosed bat, Macrotus californicus. Anat Rec. 1975;182(2):237-53.
317. Frezal L, Felix MA. C. elegans outside the Petri dish. Elife. 2015;4, e05849.
318. Fielenbach N, Antebi A. C. elegans dauer formation and the molecular basis of plasticity. Genes Dev. 2008;22(16):2149-65.
319. Murphy CT. The search for DAF-16/FOXO transcriptional targets: approaches and discoveries. Exp Gerontol. 2006;41(10):910-21.
320. Zhao X, Bergland AO, Behrman EL, Gregory BD, Petrov DA, Schmidt PS. Global Transcriptional Profiling of Diapause and Climatic Adaptation in Drosophila melanogaster. Mol Biol Evol. 2016;33(3):707-20.
321. Kucerova L, Kubrak OI, Bengtsson JM, Strnad H, Nylin S, Theopold U, et al. Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster. BMC Genomics. 2016;17:50.
322. Klass M, Hirsh D. Non-ageing developmental variant of Caenorhabditis elegans. Nature. 1976;260(5551):523-5.
323. Roux AE, Langhans K, Huynh W, Kenyon C. Reversible Age-Related Phenotypes Induced during Larval Quiescence in C. elegans. Cell Metab. 2016;23(6):1113-26.
324. Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76(3):667-84.
325. Vogt A, Goldman AD, Mochizuki K, Landweber LF. Transposon Domestication versus Mutualism in Ciliate Genome Rearrangements. PLoS Genetics. 2013;9(8), e1003659.
326. Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, et al. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol. 2009;7(1), e20.
327. Jekely G, Paps J, Nielsen C. The phylogenetic position of ctenophores and the origin(s) of nervous systems. Evodevo. 2015;6:1.
328. Goss RJ. Principles of Regeneration. USA: Elsevier Books; 1969.