Genomes and Genes
Experts and Doctors on zebrafish in Baltimore, Maryland, United States
Locale: Baltimore, Maryland, United States
- Carten J, Bradford M, Farber S. Visualizing digestive organ morphology and function using differential fatty acid metabolism in live zebrafish. Dev Biol. 2011;360:276-85 pubmed publisher..Because this labeling technique can be used to investigate digestive organ morphology and function, we foresee its application in diverse studies of organ development and physiology. ..
- Hong E, Santhakumar K, Akitake C, Ahn S, Thisse C, Thisse B, et al. Cholinergic left-right asymmetry in the habenulo-interpeduncular pathway. Proc Natl Acad Sci U S A. 2013;110:21171-6 pubmed publisher..Our studies of the newly identified cholinergic gene locus resolve the neurotransmitter identity of the zebrafish habenular nuclei and reveal functional asymmetry in a major cholinergic neuromodulatory pathway of the vertebrate brain. ..
- Castelino C, Ball G. A role for norepinephrine in the regulation of context-dependent ZENK expression in male zebra finches (Taeniopygia guttata). Eur J Neurosci. 2005;21:1962-72 pubmed
- Du S, Dienhart M. Zebrafish tiggy-winkle hedgehog promoter directs notochord and floor plate green fluorescence protein expression in transgenic zebrafish embryos. Dev Dyn. 2001;222:655-66 pubmed..Together, these data indicated that the 5.2-kb twhh promoter contains regulatory elements for tissue-specific expression of twhh in the floor plate, pectoral fin bud, branchial arches, retina, and Kupffer's vesicle. ..
- Zaghloul N, Katsanis N. Zebrafish assays of ciliopathies. Methods Cell Biol. 2011;105:257-72 pubmed publisher..The techniques presented here provide a basic toolkit for in vivo investigation of both the biological and genetic mechanisms underlying a growing class of human diseases. ..
- Farber S, Olson E, Clark J, Halpern M. Characterization of Ca2+-dependent phospholipase A2 activity during zebrafish embryogenesis. J Biol Chem. 1999;274:19338-46 pubmed..Biol. Chem. 269, 18239-18249). By using a quenched BODIPY-labeled phosphatidylcholine that fluoresces only upon cleavage by PLA2, lipase activity was visualized in the cells of living embryos where it localized to perinuclear membranes. ..
- Noren D, Chou W, Lee S, Qutub A, Warmflash A, Wagner D, et al. Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses. Sci Signal. 2016;9:ra20 pubmed publisher..Ca(2+) signaling patterns associated with proliferation and migration were detected during angiogenesis in developing zebrafish. ..
- Kazeto Y, Goto Kazeto R, Trant J. Membrane-bound progestin receptors in channel catfish and zebrafish ovary: changes in gene expression associated with the reproductive cycles and hormonal reagents. Gen Comp Endocrinol. 2005;142:204-11 pubmed
- Joshi B, Robalino J, Schott E, Jagus R. Yeast "knockout-and-rescue" system for identification of eIF4E-family members possessing eIF4E-activity. Biotechniques. 2002;33:392-3, 395-6, 398 passim pubmed
- Leslie E, Liu H, Carlson J, Shaffer J, Feingold E, WEHBY G, et al. A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3. Am J Hum Genet. 2016;98:744-54 pubmed publisher..This finding advances our understanding of the genetic basis of craniofacial development and might ultimately lead to improvements in recurrence risk prediction, treatment, and prognosis. ..
- Ahmed H, Vasta G. Unlike mammalian GRIFIN, the zebrafish homologue (DrGRIFIN) represents a functional carbohydrate-binding galectin. Biochem Biophys Res Commun. 2008;371:350-5 pubmed publisher..Therefore, DrGRIFIN is a bona fide galectin family member that in addition to its carbohydrate-binding properties, may also function as a crystallin. ..
- Pisharath H, Rhee J, Swanson M, Leach S, Parsons M. Targeted ablation of beta cells in the embryonic zebrafish pancreas using E. coli nitroreductase. Mech Dev. 2007;124:218-29 pubmed
- Gorkin D, Lee D, Reed X, Fletez Brant C, Bessling S, Loftus S, et al. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res. 2012;22:2290-301 pubmed publisher..This study provides deep insight into the regulation of gene expression in melanocytes and demonstrates a powerful approach to the investigation of regulatory sequences that can be applied to other cell types...
- Miyares R, Stein C, Renisch B, Anderson J, Hammerschmidt M, Farber S. Long-chain Acyl-CoA synthetase 4A regulates Smad activity and dorsoventral patterning in the zebrafish embryo. Dev Cell. 2013;27:635-47 pubmed publisher..Our results reveal a critical role for Acsl4a in modulating Bmp-Smad activity and provide a potential avenue for LC-PUFAs to influence a variety of developmental processes. ..
- Carroll K, Esain V, Garnaas M, Cortes M, Dovey M, Nissim S, et al. Estrogen defines the dorsal-ventral limit of VEGF regulation to specify the location of the hemogenic endothelial niche. Dev Cell. 2014;29:437-53 pubmed publisher..Together, these data suggest that yolk-derived E2 sets the ventral boundary of hemogenic vascular niche specification by antagonizing the dorsal-ventral regulatory limits of VEGF. ..
- Zaghloul N, Liu Y, Gerdes J, Gascue C, Oh E, Leitch C, et al. Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome. Proc Natl Acad Sci U S A. 2010;107:10602-7 pubmed publisher..Importantly, superimposition of these results to human genetics data suggests a previously underappreciated complexity in disease architecture that might be shared among diverse clinical phenotypes. ..
- Cadet J. Amphetamine recapitulates developmental programs in the zebrafish. Genome Biol. 2009;10:231 pubmed publisher..Addictive drugs hijack the human brain's 'reward' systems. A zebrafish model of addiction has recently been used to query changes in gene expression during this process. ..
- Abraham E, Palevitch O, Ijiri S, Du S, Gothilf Y, Zohar Y. Early development of forebrain gonadotrophin-releasing hormone (GnRH) neurones and the role of GnRH as an autocrine migration factor. J Neuroendocrinol. 2008;20:394-405 pubmed publisher..Moreover we show, in vivo, that GnRH3 is an important factor regulating GnRH3 fibre pathfinding and neurone localisation in an autocrine fashion. ..
- Fisher S, Amacher S, Halpern M. Loss of cerebum function ventralizes the zebrafish embryo. Development. 1997;124:1301-11 pubmed..Analysis of the cerebum phenotype provides genetic evidence for the existence of ventralizing signals in the zebrafish gastrula and for antagonists of those signals. ..
- Tan X, Rotllant J, Li H, De Deyne P, DeDeyne P, Du S. SmyD1, a histone methyltransferase, is required for myofibril organization and muscle contraction in zebrafish embryos. Proc Natl Acad Sci U S A. 2006;103:2713-8 pubmed..Together, these data indicate that SmyD1a and SmyD1b are histone methyltransferases and play a critical role in myofibril organization during myofiber maturation. ..
- Kuan Y, Yu H, Moens C, Halpern M. Neuropilin asymmetry mediates a left-right difference in habenular connectivity. Development. 2007;134:857-65 pubmed..The results indicate that Sema3D acts in concert with Nrp1a to guide neurons on the left side of the brain to innervate the target nucleus differently than those on the right side. ..
- Gamse J, Kuan Y, Macurak M, Brösamle C, Thisse B, Thisse C, et al. Directional asymmetry of the zebrafish epithalamus guides dorsoventral innervation of the midbrain target. Development. 2005;132:4869-81 pubmed..The results demonstrate that laterality of the dorsal forebrain influences the formation of midbrain connections and their molecular properties. ..
- Xu C, Wu G, Zohar Y, Du S. Analysis of myostatin gene structure, expression and function in zebrafish. J Exp Biol. 2003;206:4067-79 pubmed..Together, these data demonstrate that Myostatin plays an inhibitory role in hyperplastic muscle growth in zebrafish. ..
- Steven C, Lehnen N, Kight K, Ijiri S, Klenke U, Harris W, et al. Molecular characterization of the GnRH system in zebrafish (Danio rerio): cloning of chicken GnRH-II, adult brain expression patterns and pituitary content of salmon GnRH and chicken GnRH-II. Gen Comp Endocrinol. 2003;133:27-37 pubmed
- Goto Kazeto R, Kight K, Zohar Y, Place A, Trant J. Localization and expression of aromatase mRNA in adult zebrafish. Gen Comp Endocrinol. 2004;139:72-84 pubmed..The differential expression of the aromatase genes, particularly CYP19A2 in the brain, suggests that the two aromatase genes play different roles in the reproductive behavior and/or physiology of bony fish. ..
- Stine Z, McGaughey D, Bessling S, Li S, McCallion A. Steroid hormone modulation of RET through two estrogen responsive enhancers in breast cancer. Hum Mol Genet. 2011;20:3746-56 pubmed publisher..Taken collectively, these data suggest that RET transcription in breast cancer cells is modulated by E2 via ESR1 acting on multiple elements collectively. ..
- Gamse J, Thisse C, Thisse B, Halpern M. The parapineal mediates left-right asymmetry in the zebrafish diencephalon. Development. 2003;130:1059-68 pubmed..The left-sided parapineal therefore influences the left-right identity of adjacent brain nuclei, indicating that laterality of the dorsal diencephalon arises in a step-wise fashion. ..
- Haga Y, Dominique V, Du S. Analyzing notochord segmentation and intervertebral disc formation using the twhh:gfp transgenic zebrafish model. Transgenic Res. 2009;18:669-83 pubmed publisher..These studies demonstrate that the twhh:gfp transgenic zebrafish is a useful model for studying vertebral segmentation and disc formation, and moreover, that RA signaling may play a role in this process...
- Du S, Dienhart M. Gli2 mediation of hedgehog signals in slow muscle induction in zebrafish. Differentiation. 2001;67:84-91 pubmed
- Xu J, Gao J, Li J, Xue L, Clark K, Ekker S, et al. Functional analysis of slow myosin heavy chain 1 and myomesin-3 in sarcomere organization in zebrafish embryonic slow muscles. J Genet Genomics. 2012;39:69-80 pubmed publisher..Together, these studies indicate that myosin thick filaments are required for M-line organization and M-line localization of myomesin-3. In contrast, myomesin-3 is dispensable for sarcomere organization in slow muscles...
- Provost E, Wehner K, Zhong X, Ashar F, Nguyen E, Green R, et al. Ribosomal biogenesis genes play an essential and p53-independent role in zebrafish pancreas development. Development. 2012;139:3232-41 pubmed publisher..The pancreatic phenotypes observed in rpl3- and pes-deficient embryos were also independent of p53. Together, these data suggest novel p53-independent roles for ribosomal biogenesis genes in zebrafish pancreas development. ..
- Davison J, Akitake C, Goll M, Rhee J, Gosse N, Baier H, et al. Transactivation from Gal4-VP16 transgenic insertions for tissue-specific cell labeling and ablation in zebrafish. Dev Biol. 2007;304:811-24 pubmed
- Xie J, Fisher S. Twisted gastrulation enhances BMP signaling through chordin dependent and independent mechanisms. Development. 2005;132:383-91 pubmed
- Lodh S, Hostelley T, Leitch C, O Hare E, Zaghloul N. Differential effects on Î²-cell mass by disruption of Bardet-Biedl syndrome or Alstrom syndrome genes. Hum Mol Genet. 2016;25:57-68 pubmed publisher..Taken together, these findings implicate discrepant production and maintenance of Î²-cells in the differential susceptibility to diabetes found between these two genetic syndromes. ..
- Esni F, Ghosh B, Biankin A, Lin J, Albert M, Yu X, et al. Notch inhibits Ptf1 function and acinar cell differentiation in developing mouse and zebrafish pancreas. Development. 2004;131:4213-24 pubmed..These results define a normal inhibitory role for Notch in the regulation of exocrine pancreatic differentiation. ..
- Otteson D, Tsujikawa M, Gunatilaka T, Malicki J, Zack D. Genomic organization of zebrafish cone-rod homeobox gene and exclusion as a candidate gene for retinal degeneration in niezerka and mikre oko. Mol Vis. 2005;11:986-95 pubmed..Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines. ..
- Li H, Randall W, Du S. skNAC (skeletal Naca), a muscle-specific isoform of Naca (nascent polypeptide-associated complex alpha), is required for myofibril organization. FASEB J. 2009;23:1988-2000 pubmed publisher..Western blot analysis revealed that myosin protein levels were significantly reduced. Collectively, these results demonstrate that skNAC plays a vital role in myofibril assembly and function during muscle cell differentiation. ..
- McGaughey D, McCallion A. Efficient discovery of ASCL1 regulatory sequences through transgene pooling. Genomics. 2010;95:363-9 pubmed publisher..These data demonstrate the utility of this approach and its potential for further adaptation and higher throughput application. ..
- Parsons M, Pisharath H, Yusuff S, Moore J, Siekmann A, Lawson N, et al. Notch-responsive cells initiate the secondary transition in larval zebrafish pancreas. Mech Dev. 2009;126:898-912 pubmed publisher..We also show that Notch-responsive cells persist in the adult pancreas and possess the classical characteristics of centroacinar cells, a cell type believed to be a multipotent progenitor cell in adult mammalian pancreas. ..
- Abraham E, Palevitch O, Gothilf Y, Zohar Y. The zebrafish as a model system for forebrain GnRH neuronal development. Gen Comp Endocrinol. 2009;164:151-60 pubmed publisher..We also discuss the potential use of this line to study regulation of GnRH3 system development. ..
- McGaughey D, Stine Z, Huynh J, Vinton R, McCallion A. Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend. BMC Genomics. 2009;10:8 pubmed publisher..Our data combined with the ENCODE data suggests that this may represent a genome wide trend. ..
- Facchin L, Burgess H, Siddiqi M, Granato M, Halpern M. Determining the function of zebrafish epithalamic asymmetry. Philos Trans R Soc Lond B Biol Sci. 2009;364:1021-32 pubmed publisher..We discuss these findings with respect to previous studies and recent work linking the habenular region with control of the motivation/reward pathway of the vertebrate brain. ..
- Saltis M, Criscitiello M, Ohta Y, Keefe M, Trede N, Goitsuka R, et al. Evolutionarily conserved and divergent regions of the autoimmune regulator (Aire) gene: a comparative analysis. Immunogenetics. 2008;60:105-14 pubmed publisher..These findings reveal a very rapid evolution of certain regions of aire during vertebrate evolution and support the existence of an aire-dependent mechanism of T cell tolerance dating back at least to the emergence of bony fish...
- Fisher S, Jagadeeswaran P, Halpern M. Radiographic analysis of zebrafish skeletal defects. Dev Biol. 2003;264:64-76 pubmed..Radiography is a practical screening tool to detect subtle skeletal abnormalities in the adult zebrafish. The identification of chihuahua demonstrates that mutant phenotypes analogous to human skeletal dysplasias will be discovered. ..
- Du S, Gao J, Anyangwe V. Muscle-specific expression of myogenin in zebrafish embryos is controlled by multiple regulatory elements in the promoter. Comp Biochem Physiol B Biochem Mol Biol. 2003;134:123-34 pubmed..In addition, because these regulatory elements control myogenin expression in mouse and human embryos, these data suggest that the regulatory mechanism controlling myogenin expression might be conserved during evolution. ..
- Ahmed H, Du S, O Leary N, Vasta G. Biochemical and molecular characterization of galectins from zebrafish (Danio rerio): notochord-specific expression of a prototype galectin during early embryogenesis. Glycobiology. 2004;14:219-32 pubmed..The distinct temporal and spatial patterns of expression of members of the zebrafish galectin repertoire suggest that each may play distinct biological roles during early embryogenesis. ..
- Rotllant J, Liu D, Yan Y, Postlethwait J, Westerfield M, Du S. Sparc (Osteonectin) functions in morphogenesis of the pharyngeal skeleton and inner ear. Matrix Biol. 2008;27:561-72 pubmed publisher..A comparison of the phenotypes of Sparc knockdown and known zebrafish mutants with similar defects places Sparc downstream of sox9 in the genetic network that regulates development of the pharyngeal skeleton and inner ear of vertebrates...
- Burzynski G, Reed X, Taher L, Stine Z, Matsui T, Ovcharenko I, et al. Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. Genome Res. 2012;22:2278-89 pubmed publisher..This study represents a critical step toward the dissection of regulatory control in specific neuronal subtypes. ..
- Bord L, Wheeler J, Paek M, Saleh M, Lyons Warren A, Ross C, et al. Primate disrupted-in-schizophrenia-1 (DISC1): high divergence of a gene for major mental illnesses in recent evolutionary history. Neurosci Res. 2006;56:286-93 pubmed
- Deasey S, Grichenko O, Du S, Nurminskaya M. Characterization of the transglutaminase gene family in zebrafish and in vivo analysis of transglutaminase-dependent bone mineralization. Amino Acids. 2012;42:1065-75 pubmed publisher..This is the first in vivo demonstration of the crucial requirement for the TG-catalyzed cross-linking activity in bone mineralization. ..
- Roberson S, Halpern M. Convergence of signaling pathways underlying habenular formation and axonal outgrowth in zebrafish. Development. 2017;144:2652-2662 pubmed publisher..The results define a signaling network underlying the generation of dHb neurons and connectivity with their midbrain target. ..
- Garner J, Joshi B, Jagus R. Characterization of rainbow trout and zebrafish eukaryotic initiation factor 2alpha and its response to endoplasmic reticulum stress and IPNV infection. Dev Comp Immunol. 2003;27:217-31 pubmed..Overall these data are consistent with the premise that fish are able to regulate protein synthesis in response to cellular stresses through phosphorylation of eIF2alpha...
- Miller Bertoglio V, Carmany Rampey A, Fürthauer M, Gonzalez E, Thisse C, Thisse B, et al. Maternal and zygotic activity of the zebrafish ogon locus antagonizes BMP signaling. Dev Biol. 1999;214:72-86 pubmed..The results suggest that ogo encodes an as yet unidentified dorsalizing factor that mediates dorsoventral patterning by directly or indirectly antagonizing BMP activity. ..
- Lin J, Biankin A, Horb M, Ghosh B, Prasad N, Yee N, et al. Differential requirement for ptf1a in endocrine and exocrine lineages of developing zebrafish pancreas. Dev Biol. 2004;270:474-86 pubmed..Together, these findings suggest the presence of distinct ptf1a-dependent and ptf1a-independent precursor populations in developing zebrafish pancreas. ..
- Chalasani K, Brewster R. N-cadherin-mediated cell adhesion restricts cell proliferation in the dorsal neural tube. Mol Biol Cell. 2011;22:1505-15 pubmed publisher..In addition, these findings are the first to demonstrate a requirement for cadherins in synchronizing cell-cycle exit and differentiation and a reciprocal interaction between AJs and Hh signaling. ..
- Wang Y, Rovira M, Yusuff S, Parsons M. Genetic inducible fate mapping in larval zebrafish reveals origins of adult insulin-producing β-cells. Development. 2011;138:609-17 pubmed publisher..As pancreas organogenesis continues, the ventral bud derived PNCs align along the duct, remain multipotent and later in development differentiate to form secondary islets, ducts and CACs. ..
- Bernick E, Zhang P, Du S. Knockdown and overexpression of Unc-45b result in defective myofibril organization in skeletal muscles of zebrafish embryos. BMC Cell Biol. 2010;11:70 pubmed publisher..Collectively, these studies indicate that the expression levels of Unc-45b must be precisely regulated to ensure normal myofibril organization. Loss or overexpression of Unc-45b leads to defective myofibril organization. ..
- Fisher S, Grice E, Vinton R, Bessling S, McCallion A. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science. 2006;312:276-9 pubmed..The majority of human RET noncoding sequences also directed ret-specific expression in zebrafish. Thus, vast amounts of functional sequence information may exist that would not be detected by sequence similarity approaches. ..
- Hama K, Provost E, Baranowski T, Rubinstein A, Anderson J, Leach S, et al. In vivo imaging of zebrafish digestive organ function using multiple quenched fluorescent reporters. Am J Physiol Gastrointest Liver Physiol. 2009;296:G445-53 pubmed publisher..Thus the multiple fluorescent reporter-based methodology facilitates the rapid analysis of digestive organ function in live zebrafish larvae. ..
- Brösamle C, Halpern M. Nogo-Nogo receptor signalling in PNS axon outgrowth and pathfinding. Mol Cell Neurosci. 2009;40:401-9 pubmed publisher..We propose that localized Nogo expression defines inhibitory territories that through repulsion restrict axon growth to permissive regions. ..
- Hong E, Brewster R. N-cadherin is required for the polarized cell behaviors that drive neurulation in the zebrafish. Development. 2006;133:3895-905 pubmed
- Du S, Li H, Bian Y, Zhong Y. Heat-shock protein 90alpha1 is required for organized myofibril assembly in skeletal muscles of zebrafish embryos. Proc Natl Acad Sci U S A. 2008;105:554-9 pubmed publisher..These results indicate that Hsp90alpha1 plays an important role in muscle development, likely through facilitating myosin folding and assembly into organized myofibril filaments...
- Rovira M, Huang W, Yusuff S, Shim J, FERRANTE A, Liu J, et al. Chemical screen identifies FDA-approved drugs and target pathways that induce precocious pancreatic endocrine differentiation. Proc Natl Acad Sci U S A. 2011;108:19264-9 pubmed publisher..Using pharmacological approaches, we have identified and characterized two unique pathways in ?-cell differentiation in the zebrafish, including down-regulation of GTP production and retinoic acid biosynthesis. ..
- Rattner A, Chen J, Nathans J. Proteolytic shedding of the extracellular domain of photoreceptor cadherin. Implications for outer segment assembly. J Biol Chem. 2004;279:42202-10 pubmed