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Genomes and Genes | Linda Z HollandSummaryAffiliation: University of California Country: USA Publications
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Evolution of new characters after whole genome duplications: insights from amphioxusLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Semin Cell Dev Biol 24:101-9. 2013..In addition, while cis-regulatory changes are likely of primary importance in evolution of vertebrate-specific structures, changes in protein structure including alternative splicing are non-trivial...
Sequence and embryonic expression of the amphioxus engrailed gene (AmphiEn): the metameric pattern of transcription resembles that of its segment-polarity homolog in DrosophilaL Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093 0202, USA
Development 124:1723-32. 1997..If so, the protostomes and deuterostomes probably shared a common segmented ancestor...- Non-neural ectoderm is really neural: evolution of developmental patterning mechanisms in the non-neural ectoderm of chordates and the problem of sensory cell homologiesLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 0202 USA
J Exp Zool B Mol Dev Evol 304:304-23. 2005..Thus, similarities between the ectodermal sensory cells of any one species of tunicate and craniate hair cells may well represent convergent evolution rather than homology... - Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brainLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Brain Behav Evol 72:91-105. 2008..Their roles in modulating gene networks may turn out to rival gene duplication for facilitating the evolution of structures such as neural crest and the MHB... 
The amphioxus genome illuminates vertebrate origins and cephalochordate biologyLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
Genome Res 18:1100-11. 2008..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...- The Ciona intestinalis genome: when the constraints are offLinda Z Holland
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
Bioessays 25:529-32. 2003..With such a broadened database, comparative genomics can begin to ask pointed questions about the relationship between the evolution of genomes and the evolution of body plans... - A SINE in the genome of the cephalochordate amphioxus is an Alu elementLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla 92093 0202, USA
Int J Biol Sci 2:61-5. 2006..Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer... - The chordate amphioxus: an emerging model organism for developmental biologyL Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, 8750 Biological Grade, La Jolla, California 92093 0202, USA
Cell Mol Life Sci 61:2290-308. 2004..This relative structural and genomic simplicity in a vertebrate-like organism makes amphioxus ideal as a model organism for understanding mechanisms of vertebrate development... - Nuclear beta-catenin promotes non-neural ectoderm and posterior cell fates in amphioxus embryosLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093 0202, USA
Dev Dyn 233:1430-43. 2005.... - Heads or tails? Amphioxus and the evolution of anterior-posterior patterning in deuterostomesLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Dev Biol 241:209-28. 2002..Thus, roles for Wnt-signaling in dorso-ventral patterning of embryos may be a vertebrate innovation that arose in connection with the evolution of yolky eggs and gastrulation by extensive involution... - Chordate roots of the vertebrate nervous system: expanding the molecular toolkitLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093 0202, USA
Nat Rev Neurosci 10:736-46. 2009..Recent advances in genomics have provided insights into the elaboration of the molecular toolkit at the invertebrate-vertebrate transition that may have facilitated the evolution of these vertebrate characteristics... - Evolution of neural crest and placodes: amphioxus as a model for the ancestral vertebrate?L Z Holland
Scripps Institution of Oceanography, University of California San Diego, 92093 0202, USA
J Anat 199:85-98. 2001..In contrast, the origin of the other vertebrate placodes is very uncertain... - Sequence and developmental expression of AmphiTob, an amphioxus homolog of vertebrate Tob in the PC3/BTG1/Tob family of tumor suppressor genesN D Holland
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
Dev Dyn 210:11-8. 1997..During development, an intense and transitory transcription of AmphiTob may be an early event in cells exiting the cell cycle in preparation for differentiation... - Chordate origins of the vertebrate central nervous systemL Z Holland
Marine Biology Research Division Scripps Institution of Oceanography University of California at San Diego La Jolla, California, 92093 0202, USA
Curr Opin Neurobiol 9:596-602. 1999..In contrast, the telencephalon, a midbrain-hindbrain boundary region with organizer properties, and the definitive neural crest appear to be vertebrate innovations... - Analyses of gene function in amphioxus embryos by microinjection of mRNAs and morpholino oligonucleotidesLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
Methods Mol Biol 770:423-38. 2011..This chapter details methods for microinjection of amphioxus eggs with mRNAs or morpholino antisense oligonucleotides to analyze gene networks operating in early development... - Body-plan evolution in the Bilateria: early antero-posterior patterning and the deuterostome-protostome dichotomyL Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, 92093 0202, USA
Curr Opin Genet Dev 10:434-42. 2000..Comparisons with Drosophila and Cnidarians suggest a scheme for evolution of the Bilaterian body plan and emphasize the pressing need for similar studies in a wider variety of organisms, especially more basal protostomes... - Alternative splicing in development and function of chordate endocrine systems: a focus on Pax genesLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Integr Comp Biol 50:22-34. 2010.... - AmphiPax3/7, an amphioxus paired box gene: insights into chordate myogenesis, neurogenesis, and the possible evolutionary precursor of definitive vertebrate neural crestL Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093 0202, USA
Evol Dev 1:153-65. 1999.... - Retinoic acid and Wnt/beta-catenin have complementary roles in anterior/posterior patterning embryos of the basal chordate amphioxusTakayuki Onai
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Dev Biol 332:223-33. 2009..Although the two pathways may both influence such things as specification of neuronal identity, interactions between them in A/P patterning appear to be minimal... - Retinoic acid signaling targets Hox genes during the amphioxus gastrula stage: insights into early anterior-posterior patterning of the chordate body planDemian Koop
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Dev Biol 338:98-106. 2010.... - Expression of the AmphiTcf gene in amphioxus: insights into the evolution of the TCF/LEF gene family during vertebrate evolutionHsiu Chin Lin
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, USA
Dev Dyn 235:3396-403. 2006..Comparison of developmental expression for amphioxus AmphiTcf and vertebrate TCF/LEF genes indicates that this gene family has undergone extensive subfunctionalization and neofunctionalization during vertebrate evolution... - AmphiNk2-tin, an amphioxus homeobox gene expressed in myocardial progenitors: insights into evolution of the vertebrate heartNicholas D Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202, USA
Dev Biol 255:128-37. 2003.... - An amphioxus winged helix/forkhead gene, AmphiFoxD: insights into vertebrate neural crest evolutionJr Kai Yu
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093 0202, USA
Dev Dyn 225:289-97. 2002.... - AmphiFoxQ2, a novel winged helix/forkhead gene, exclusively marks the anterior end of the amphioxus embryoJr Kai Yu
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Dev Genes Evol 213:102-5. 2003..This is the first gene known that exclusively marks the anterior pole of chordate embryos. It may, therefore, play an important role in establishing and/or maintaining the anterior/posterior axis... - The amphioxus T-box gene, AmphiTbx15/18/22, illuminates the origins of chordate segmentationLaura Beaster-Jones
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 0202, USA
Evol Dev 8:119-29. 2006..This lends support to the hypothesis that the vertebrate head evolved from an ancestor possessing segmented cranial mesoderm... - Opposing Nodal/Vg1 and BMP signals mediate axial patterning in embryos of the basal chordate amphioxusTakayuki Onai
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Dev Biol 344:377-89. 2010.... - Developmental expression of the three iroquois genes of amphioxus (BfIrxA, BfIrxB, and BfIrxC) with special attention to the gastrula organizer and anteroposterior boundaries in the central nervous systemStacy L Kaltenbach
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Gene Expr Patterns 9:329-34. 2009.... - The retinoic acid signaling pathway regulates anterior/posterior patterning in the nerve cord and pharynx of amphioxus, a chordate lacking neural crestHector Escriva
Scripps Inst Oceanography, La Jolla, CA
Development 129:2905-16. 2002..Supplemental data available on-line.. - Characterization and developmental expression of the amphioxus homolog of Notch (AmphiNotch): evolutionary conservation of multiple expression domains in amphioxus and vertebratesL Z Holland
Marine Biology Research Division, University of California at San Diego, La Jolla, California 92093 0202, USA
Dev Biol 232:493-507. 2001.... - Amphioxus AmphiDelta: evolution of Delta protein structure, segmentation, and neurogenesisStacy L K Rasmussen
Division of Marine Biology Research, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Genesis 45:113-22. 2007.... - Expression of somite segmentation genes in amphioxus: a clock without a wavefront?Laura Beaster-Jones
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Dev Genes Evol 218:599-611. 2008.... - Axial patterning in cephalochordates and the evolution of the organizerJr Kai Yu
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92037 0202, USA
Nature 445:613-7. 2007..In light of recent phylogenetic analyses placing cephalochordates basally in the chordate lineage, we propose that separate signalling centres for patterning the D/V and A/P axes may be an ancestral chordate character... - Tail regression induced by elevated retinoic acid signaling in amphioxus larvae occurs by tissue remodeling, not cell deathDemian Koop
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, 92093, USA
Evol Dev 13:427-35. 2011..In contrast, however, the RA-induced closure of the amphioxus anus has parallels in the RA-induced caudal regression syndrome of mammals... - Cis-regulation of the amphioxus engrailed gene: insights into evolution of a muscle-specific enhancerLaura Beaster Jones
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 0202, USA
Mech Dev 124:532-42. 2007..intestinalis muscles, they express the transcription factors necessary to activate transcription from the amphioxus engrailed enhancer, suggesting that gene networks may not be completely disrupted if an individual component is lost... - The evolution of alternative splicing in the Pax family: the view from the Basal chordate amphioxusStephen Short
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093 0202, USA
J Mol Evol 66:605-20. 2008..Our results, together with previous studies of vertebrate Pax genes, support the theory that alternative splicing impacts functional motifs more than gene duplication followed by divergence... - An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer and mesoderm and later asymmetrical expression associated with left-right axis formationJr Kai Yu
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Evol Dev 4:418-25. 2002..These results suggest that amphioxus and vertebrate nodal genes play evolutionarily conserved roles in establishing Spemann's organizer, patterning the mesoderm rostrocaudally and setting up the asymmetrical left-right axis of the body... - AmphiFoxE4, an amphioxus winged helix/forkhead gene encoding a protein closely related to vertebrate thyroid transcription factor-2: expression during pharyngeal developmentJr-Kai Yu
Scripps Res Inst, La Jolla, CA
Evol Dev 4:9-15. 2002..Such a transfer could have provided part of the genetic program enabling the endostyle to separate from the pharyngeal endoderm and migrate away as the rudiment of the thyroid gland... - Characterization of amphioxus AmphiWnt8: insights into the evolution of patterning of the embryonic dorsoventral axisM Schubert
Scripps Institution of Oceanography, University of California at San Diego, La Jolla 92093 0202, USA
Evol Dev 2:85-92. 2000..Amphioxus AmphiWnt8 and its vertebrate Wnt8 homologs probably play comparable roles in the early dorsoventral patterning of the embryonic body axis... - Essential role of Dkk3 for head formation by inhibiting Wnt/β-catenin and Nodal/Vg1 signaling pathways in the basal chordate amphioxusTakayuki Onai
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 0202, USA
Evol Dev 14:338-50. 2012..We conclude that amphioxus Dkk3 regulates head formation by modulating both Wnt/β-catenin and Nodal signaling, and that these functions may have been partitioned among various vertebrate lineages during evolution of Dkk3 proteins... - Stage- and tissue-specific patterns of cell division in embryonic and larval tissues of amphioxus during normal developmentNicholas D Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA
Evol Dev 8:142-9. 2006..In sum, these stage- and tissue-specific changes in cell proliferation intensity illustrate how the requirements of embryonic and larval natural history can shape developmental programs... - The basal chordate amphioxus as a simple model for elucidating developmental mechanisms in vertebratesDemian Koop
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093 0202, USA
Birth Defects Res C Embryo Today 84:175-87. 2008..Thus, studies of amphioxus development can shed light on similar, but more complex, development of vertebrates. Such studies are especially interesting for their insights into the genetic basis of craniofacial birth defects in humans... - Three amphioxus Wnt genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) associated with the tail bud: the evolution of somitogenesis in chordatesM Schubert
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
Dev Biol 240:262-73. 2001..It is likely that presomitic mesoderm is a vertebrate innovation made possible by developmental interconversions between epithelium and mesenchyme that first became prominent at the dawn of vertebrate evolution... - A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxusM Schubert
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
Mol Biol Evol 17:1896-903. 2000..The tree topology suggested that in amphioxus, at least an AmphiWnt5 and an AmphiWnt10 have yet to be discovered... - Characterization of two amphioxus Wnt genes (AmphiWnt4 and AmphiWnt7b) with early expression in the developing central nervous systemM Schubert
Scripps Institution of Oceanography, University of California at San Diego, La Jolla 92093 0202, USA
Dev Dyn 217:205-15. 2000.... - Laboratory spawning and development of the Bahama lancelet, Asymmetron lucayanum (cephalochordata): fertilization through feeding larvaeNicholas D Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 93093, USA
Biol Bull 219:132-41. 2010..A better understanding of developmental diversity within the cephalochordates will require phylogenetic analyses based on nuclear genes and the genome sequence of an Asymmetron species... - A revised fate map for amphioxus and the evolution of axial patterning in chordatesLinda Z Holland
Scripps Institution of Oceanography, University of California San Diego, La Jolla CA 92093, USA
Integr Comp Biol 47:360-72. 2007.... - Amphioxus and the evolution of head segmentationLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla CA 92093 0202, USA Department of Anatomy, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
Integr Comp Biol 48:630-46. 2008..Although, bony vertebrates have lost the mesodermal head segments present in the shark and lamprey, their remnants persist in the muscles of the eye and jaw... - "Insights of early chordate genomics: endocrinology and development in amphioxus, tunicates and lampreys": introduction to the symposiumLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 0202, USA
Integr Comp Biol 50:17-21. 2010..To this end, we brought together researchers whose recent work on these organisms spans the gap from genomics to the evolution of body forms and functions as exemplified by endocrine systems and embryonic development... - Functional equivalency of amphioxus and vertebrate Pax258 transcription factors suggests that the activation of mid-hindbrain specific genes in vertebrates occurs via the recruitment of Pax regulatory elementsJana Krelová
Center for Integrated Genomics, Institute of Molecular Genetics, Flemingovo 2, 166 37 Praha 6, Czech Republic
Gene 282:143-50. 2002..Therefore, in amphioxus, AmphiPax2/5/8, although capable of performing all the necessary functions has not been recruited for a developmental mechanism which usually sets up MHB development in vertebrates... - The amphioxus genome and the evolution of the chordate karyotypeNicholas H Putnam
Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 453:1064-71. 2008..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution... - Expression of estrogen-receptor related receptors in amphioxus and zebrafish: implications for the evolution of posterior brain segmentation at the invertebrate-to-vertebrate transitionPierre Luc Bardet
Laboratoire de Biologie Moleculaire de la Cellule, CNRS UMR 5161, IFR128 Biosciences Lyon Gerland, Ecole Normale Superieure de Lyon, 46 allee d Italie, 69007 Lyon, France
Evol Dev 7:223-33. 2005.... - Tissue-specific expression of FoxD reporter constructs in amphioxus embryosJr-Kai Yu
CA Inst Technol, Pasadena
Dev Biol 274:452-61. 2004.... - Retinoic acid influences anteroposterior positioning of epidermal sensory neurons and their gene expression in a developing chordate (amphioxus)Michael Schubert
, Centre National de la Recherche Scientifique, , and Institut National de la Recherche Agronomique, , 69364 Lyon, France
Proc Natl Acad Sci U S A 101:10320-5. 2004.... - A Gbx homeobox gene in amphioxus: insights into ancestry of the ANTP class and evolution of the midbrain/hindbrain boundaryL Filipe C Castro
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Dev Biol 295:40-51. 2006..Comparison with hemichordates suggests that anterior Otx and posterior Gbx domains were probably overlapping in the ancestral deuterostome and came to abut at the MHB early in the chordate lineage before MHB organizer properties evolved... - Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxusMichael Schubert
CA Inst Technol, Pasadena
Development 132:61-73. 2005..This work highlights the potential of amphioxus, a genomically simple, vertebrate-like invertebrate chordate, as a paradigm for understanding gene hierarchies similar to the more complex ones of vertebrates... - A retinoic acid-Hox hierarchy controls both anterior/posterior patterning and neuronal specification in the developing central nervous system of the cephalochordate amphioxusMichael Schubert
, CNRS UMR5161/INRA UMR1237/ENS Lyon, IFR128 BioSciences Lyon-Gerland, , , 69364 Lyon Cedex 07, France
Dev Biol 296:190-202. 2006.... - Phylogenetic relationships of the Fox (Forkhead) gene family in the BilateriaFrancoise Mazet
School of Animal and Microbial Sciences, The University of Reading, P O Box 228 Whiteknights, RG6 6AJ Reading, UK
Gene 316:79-89. 2003..Our analyses suggest that the common ancestor of protostomes and deuterostomes had a minimum complement of 14 Fox genes... - Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but context specificity in vivoZbynek Kozmik
Institute of Molecular Genetics, Videnska 1083, 14220 Prague 4, Czech Republic
Dev Biol 306:143-59. 2007..g. in the control of mitosis, apoptosis, and cell/tissue motility)... - Developmental biology: a chordate with a differenceLinda Z Holland
Nature 447:153-5. 2007 - Differential mesodermal expression of two amphioxus MyoD family members (AmphiMRF1 and AmphiMRF2)Michael Schubert
U CA San Diego, La Jolla
Gene Expr Patterns 3:199-202. 2003..These two MRF genes of amphioxus have partly overlapping patterns of mesodermal expression and evidently duplicated independent of the diversification of the vertebrate MRF family... - Cephalochordate (amphioxus) embryos: procurement, culture, and basic methodsLinda Z Holland
CA Inst Technol, Pasadena
Methods Cell Biol 74:195-215. 2004 - A proposal to sequence the amphioxus genome submitted to the Joint Genome Institute of the US Department of EnergyJeremy J Gibson-Brown
Department of Biology, Washington University, St. Louis, Missouri 63130, USA
J Exp Zoolog B Mol Dev Evol 300:5-22. 2003