Byrappa Venkatesh

Summary

Country: Singapore

Publications

  1. pmc Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii)
    Yue Ying Tan
    Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
    PLoS ONE 7:e47174. 2012
  2. pmc Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus
    Alison P Lee
    Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
    PLoS ONE 6:e20088. 2011
  3. pmc Tissue sampling methods and standards for vertebrate genomics
    Pamela By Wong
    Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
    Gigascience 1:8. 2012
  4. pmc Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216
    Byrappa Venkatesh
    Comparative Genomics Lab, Institute of Molecular and Cell Biology, A STAR, Biopolis, Singapore
    Mol Biol Evol 30:62-5. 2013
  5. pmc Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates
    Sandra Dos Santos
    Universite Paris Diderot, Sorbonne Paris Cité, Unité Biologie Fonctionnelle et Adaptative BFA, EAC4413 CNRS, Paris, France
    BMC Evol Biol 11:332. 2011
  6. pmc Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii ) in zebrafish and mice
    Ryan B MacDonald
    Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
    BMC Evol Biol 10:157. 2010
  7. pmc Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleosts
    Wei Ping Yu
    Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng 308433, Singapore
    BMC Evol Biol 7:49. 2007
  8. pmc Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions
    Tomas A Larsson
    Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden
    BMC Evol Biol 8:184. 2008
  9. ncbi request reprint Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
    Bioessays 27:100-7. 2005
  10. ncbi request reprint Fugu genome does not contain mitochondrial pseudogenes
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
    Genomics 87:307-10. 2006

Detail Information

Publications64

  1. pmc Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii)
    Yue Ying Tan
    Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
    PLoS ONE 7:e47174. 2012
    ..These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole genome sequencing...
  2. pmc Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus
    Alison P Lee
    Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
    PLoS ONE 6:e20088. 2011
    ..Other approaches such as sequence comparison between multiple mammals are required to identify and characterize such enhancers...
  3. pmc Tissue sampling methods and standards for vertebrate genomics
    Pamela By Wong
    Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
    Gigascience 1:8. 2012
    ..Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota...
  4. pmc Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216
    Byrappa Venkatesh
    Comparative Genomics Lab, Institute of Molecular and Cell Biology, A STAR, Biopolis, Singapore
    Mol Biol Evol 30:62-5. 2013
    ..Analyses of the coelacanth and lamprey genomes support this hypothesis. Our study highlights the importance of basal vertebrates as critical reference genomes...
  5. pmc Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates
    Sandra Dos Santos
    Universite Paris Diderot, Sorbonne Paris Cité, Unité Biologie Fonctionnelle et Adaptative BFA, EAC4413 CNRS, Paris, France
    BMC Evol Biol 11:332. 2011
    ..To have a better insight into this process we used new genomic resources and tools to characterize the ancestral environment before the duplication occurred...
  6. pmc Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii ) in zebrafish and mice
    Ryan B MacDonald
    Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
    BMC Evol Biol 10:157. 2010
    ..We then conducted a comparative study of the sequence and enhancer activity of CmURE2 with that of orthologous regulatory sequences from zebrafish and mouse...
  7. pmc Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleosts
    Wei Ping Yu
    Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng 308433, Singapore
    BMC Evol Biol 7:49. 2007
    ..To gain further insight into the evolutionary history of protocadherin clusters, we have sequenced and analyzed protocadherin clusters from the compact genome of the pufferfish, Fugu rubripes...
  8. pmc Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions
    Tomas A Larsson
    Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden
    BMC Evol Biol 8:184. 2008
    ..These correspond to Homo sapiens chromosomes 4, 5, 8 and 10...
  9. ncbi request reprint Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
    Bioessays 27:100-7. 2005
    ..The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents...
  10. ncbi request reprint Fugu genome does not contain mitochondrial pseudogenes
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
    Genomics 87:307-10. 2006
    ..Shotgun sequences of whole genomes often include some mitochondrial sequences. Therefore, any Numts identified in shotgun-sequence assemblies should be verified by Southern hybridization or PCR amplification...
  11. pmc Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, Singapore
    PLoS Biol 5:e101. 2007
    ..This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes...
  12. ncbi request reprint Ancient noncoding elements conserved in the human genome
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
    Science 314:1892. 2006
    ..The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression...
  13. pmc Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes
    Pai Chung Gwee
    Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, 138673 Singapore
    BMC Evol Biol 9:47. 2009
    ..We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the amphioxus (Branchiostoma floridae)...
  14. pmc Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes
    Vydianathan Ravi
    Institute of Molecular and Cell Biology, ASTAR, Biopolis, Singapore 138673
    Proc Natl Acad Sci U S A 106:16327-32. 2009
    ....
  15. pmc Elephant shark genome provides unique insights into gnathostome evolution
    Byrappa Venkatesh
    1 Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A STAR, Biopolis, Singapore 138673 2 Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
    Nature 505:174-9. 2014
    ..It thus presents a new model for understanding the origin of adaptive immunity. ..
  16. pmc Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences
    Vydianathan Ravi
    Institute of Molecular and Cell Biology, Agency for Science Technology and Research ASTAR, Biopolis, Singapore, Singapore
    PLoS Genet 9:e1003177. 2013
    ..In summary, our study reveals that the pleiotropic functions of Pax6 in vertebrates are served by a divergent family of Pax6 genes, forged by ancient duplication events and by independent, lineage-specific gene losses...
  17. pmc Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters
    Alison P Lee
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
    Proc Natl Acad Sci U S A 103:6994-9. 2006
    ..We propose that the regulatory elements spread across large regions on either side of Hox clusters are a major evolutionary constraint that has maintained the exceptionally long syntenic blocks at the HoxA and HoxD loci...
  18. pmc Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum)
    Tarang K Mehta
    Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
    Proc Natl Acad Sci U S A 110:16044-9. 2013
    ..Such a relationship suggests that the first two rounds of genome duplication may have occurred independently in the lamprey and gnathostome lineages. ..
  19. pmc Identification and comparative analysis of the protocadherin cluster in a reptile, the green anole lizard
    Xiao Juan Jiang
    Gene Regulation Laboratory, National Neuroscience Institute, Singapore, Singapore
    PLoS ONE 4:e7614. 2009
    ..In this study, we report the identification and comparative analysis of the protocadherin cluster in a reptile, the green anole lizard (Anolis carolinensis)...
  20. doi request reprint Evolution of the Cdk-activator Speedy/RINGO in vertebrates
    Sangeeta Chauhan
    Institute of Molecular and Cell Biology IMCB, A STAR Agency for Science, Technology and Research, Singapore, Republic of Singapore
    Cell Mol Life Sci 69:3835-50. 2012
    ..Despite the interspecies variation, Speedy is conserved among most species examined. Our results provide a complete picture of the Speedy gene family and its evolution...
  21. ncbi request reprint STAT4 is a target of the hematopoietic zinc-finger transcription factor Ikaros in T cells
    Wai Ho Yap
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
    FEBS Lett 579:4470-8. 2005
    ..Transactivation, electrophoretic mobility shift assay and RNA interference-mediated gene knockdown experiments revealed that Ik is involved in the regulation of STAT4 in human T cells...
  22. doi request reprint Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes
    Alison P Lee
    Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, Singapore
    Mol Biol Evol 28:1205-15. 2011
    ..Transgenic zebrafish assay of some human CNE enhancers that have been lost in teleosts has indicated instances of conservation or changes in trans-acting factors between mammals and fishes...
  23. doi request reprint Rapidly evolving fish genomes and teleost diversity
    Vydianathan Ravi
    Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore, Singapore
    Curr Opin Genet Dev 18:544-50. 2008
    ..The divergence of CNEs seems to have been initiated in basal ray-finned fishes before the WGD. The fast evolving singleton and duplicated genes as well as the divergent CNEs might have contributed to the diversity of teleost fishes...
  24. doi request reprint Characterization of a hypoxia-response element in the Epo locus of the pufferfish, Takifugu rubripes
    Rashmi P Kulkarni
    Institute of Molecular and Cell Biology, A STAR, Biopolis, 138673, Singapore
    Mar Genomics 3:63-70. 2010
    ..Our investigations also revealed that the Epo locus has experienced extensive rearrangements during vertebrate evolution...
  25. ncbi request reprint Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon)
    Yong Hwee Loh
    Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Biopolis, Singapore
    Mol Biol Evol 25:526-35. 2008
    ..Our findings indicate that overall very little intron turnover has occurred in pufferfishes and mammals during recent evolution and that intron gain is an extremely rare event in vertebrate evolution...
  26. ncbi request reprint Genetic basis of tetrodotoxin resistance in pufferfishes
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
    Curr Biol 15:2069-72. 2005
    ..4b is similar to that in the saxitoxin- and TTX-resistant Na+ channels of softshell clams . Besides helping to deter predators, TTX resistance enables pufferfishes to selectively feed on TTX-bearing organisms...
  27. ncbi request reprint Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu
    Wei Ping Yu
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore, 117609 Singapore
    Trends Genet 19:180-3. 2003
    ....
  28. doi request reprint Phylogenetic and evolutionary relationships and developmental expression patterns of the zebrafish twist gene family
    Gare Hoon Yeo
    Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
    Dev Genes Evol 219:289-300. 2009
    ..We also observed minimal expression overlap among the four twist genes, suggesting that despite their significant peptide similarity, their regulatory controls have diverged considerably, with minimal functional redundancy between them...
  29. ncbi request reprint The regulation of retina specific expression of rhodopsin gene in vertebrates
    Tao Zhang
    Institute of Molecular and Cell Biology, 117609 Singapore, Singapore
    Gene 313:189-200. 2003
    ..Our investigation suggests that the regulation of retinal specific expression is conserved in the pufferfish, frog and mouse and that the ancestral intron-containing rhodopsin gene has been displaced by an intronless copy in teleosts...
  30. pmc Sequence and organization of coelacanth neurohypophysial hormone genes: evolutionary history of the vertebrate neurohypophysial hormone gene locus
    Pai Chung Gwee
    Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, 138673, Singapore
    BMC Evol Biol 8:93. 2008
    ..The coelacanths occupy a unique phylogenetic position close to the divergence of the mammalian and ray-finned fish lineages...
  31. pmc TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
    Alison P Lee
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
    BMC Genomics 8:441. 2007
    ..To this end, we have used a comparative genomics approach to identify putative cis-regulatory elements associated with TF-encoding genes in vertebrates...
  32. ncbi request reprint Characterization of the platelet-derived growth factor receptor alpha and c-kit genes in the pufferfish Fugu rubripes
    Hawys Williams
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore, Singapore 117609
    DNA Seq 13:263-70. 2002
    ..The Fugu PDGFR alpha gene is transcribed from two promoters giving rise to alternate transcripts...
  33. ncbi request reprint Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes
    Alan Christoffels
    Institute of Molecular and Cell Biology, Singapore
    Mol Biol Evol 21:1146-51. 2004
    ..These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts...
  34. ncbi request reprint Identification and analysis of additional copies of the platelet-derived growth factor receptor and colony stimulating factor 1 receptor genes in fugu
    Hawys Williams
    Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore
    Gene 295:255-64. 2002
    ..These results are discussed in the context of the proposed teleost lineage-specific whole genome duplication hypothesis...
  35. ncbi request reprint cDNA cloning of Runx family genes from the pufferfish (Fugu rubripes)
    Cherry Ee Lin Ng
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
    Gene 399:162-73. 2007
    ..The similarities and differences between the Runx family genes of fugu and mammals will improve our understanding of the functions of these proteins...
  36. ncbi request reprint Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences
    Patrick Gilligan
    Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore
    Gene 294:35-44. 2002
    ..This study confirms the utility of the Fugu as a supplementary tool to uncover and confirm novel genes and putative gene regulatory regions in the human genome...
  37. ncbi request reprint Cloning and expression of the reverse transcriptase component of pufferfish (Fugu rubripes) telomerase
    Wai Ho Yap
    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
    Gene 353:207-17. 2005
    ..The level of expression was found to be higher in actively dividing cells and reduced at quiescence, suggesting cell cycle regulation of TERT and possibly telomerase activity, in this cell line...
  38. pmc Runx Family Genes in a Cartilaginous Fish, the Elephant Shark (Callorhinchus milii)
    Giselle Sek Suan Nah
    Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
    PLoS ONE 9:e93816. 2014
    ..In summary, our analysis reveals that the genomic organization and expression profiles of Runx genes were already complex in the common ancestor of jawed vertebrates. ..
  39. pmc Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history
    L Filipe C Castro
    CIMAR Associate Laboratory, Interdisciplinary Centre of Marine and Environmental Research CIIMAR, University of Porto, Porto, Portugal, Institute of Biomedical Sciences Abel Salazar ICBAS, University of Porto, Porto, Portugal, Development and Evolution of Vertebrates, CNRS UPMC UMR 7150, Station Biologique, Roscoff, France, Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, Singapore
    Proc Biol Sci 281:20132669. 2014
    ..Significantly, the absence of the gastric genes predicts that reinvention of the stomach in agastric lineages would be highly improbable, in line with Dollo's principle...
  40. ncbi request reprint Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines
    Jens E Ruhe
    Institute of Medical Biology, Singapore, Singapore
    Cancer Res 67:11368-76. 2007
    ..Our data therefore provide extensive system information for the design and interpretation of cell line-based cancer research, and may stimulate further investigations into broader clinical applications of current cancer therapeutics...
  41. ncbi request reprint Evolution of the neuropeptide Y family: new genes by chromosome duplications in early vertebrates and in teleost fishes
    Gorel Sundstrom
    Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden
    Gen Comp Endocrinol 155:705-16. 2008
    ..Our study shows that when sequence comparisons give ambiguous results, chromosomal location can serve as a useful criterion to identify orthologs. This strategy may help to resolve relationships in several families of short peptides...
  42. pmc Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes
    Yong Hwee Loh
    Institute of Molecular and Cell Biology, Singapore 117609
    Genome Res 14:1248-57. 2004
    ....
  43. ncbi request reprint Application of comparative genomics to the analysis of vertebrate regulatory elements
    Patrick Gilligan
    Institute of Molecular and Cell Biology, 30, Medical Drive, Singapore 117609
    Brief Funct Genomic Proteomic 3:7-11. 2004
    ..There is need for high throughput assay systems to analyse the function of predicted vertebrate gene regulatory regions...
  44. pmc Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates
    Henner Brinkmann
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    Proc Natl Acad Sci U S A 101:4900-5. 2004
    ..These results are supported by high bootstrap values, Bayesian posterior probabilities, and likelihood ratio tests...
  45. ncbi request reprint Origin and diversity of the SOX transcription factor gene family: genome-wide analysis in Fugu rubripes
    Peter Koopman
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
    Gene 328:177-86. 2004
    ....
  46. ncbi request reprint Evolution and diversity of fish genomes
    Byrappa Venkatesh
    Institute of Molecular and Cell Biology 30, Medical Drive, Singapore 117609, Singapore
    Curr Opin Genet Dev 13:588-92. 2003
    ..Fish genomes seem to be 'plastic' in comparison with other vertebrate genomes because genetic changes, such as polyploidization, gene duplications, gain of spliceosomal introns and speciation, are more frequent in fishes...
  47. pmc Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis
    Esther G L Koh
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
    Proc Natl Acad Sci U S A 100:1084-8. 2003
    ....
  48. ncbi request reprint Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    Samuel Aparicio
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
    Science 297:1301-10. 2002
    ..Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order...
  49. ncbi request reprint Novel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce loci
    Brett S Abrahams
    Centre for Molecular Medicine and Therapeutics, British Columbia Research Institute for Children s and Women s Health, and Department of Medical Genetics, University of British Columbia, 980 West 28 th Avenue, Vancouver, British Columbia, V5Z 4H4, Canada
    Genomics 80:45-53. 2002
    ..A high degree of conservation across NR2E1 combined with a lack of interspersed repeats suggests that an array of regulatory elements embedded within the gene is required for proper gene expression...
  50. pmc Variation in sequence and organization of splicing regulatory elements in vertebrate genes
    Gene Yeo
    Departments of Biology and Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue 68 223, Cambridge, MA 02139 4307, USA
    Proc Natl Acad Sci U S A 101:15700-5. 2004
    ....
  51. ncbi request reprint A compact cartilaginous fish model genome
    Byrappa Venkatesh
    Curr Biol 15:R82-3. 2005
  52. pmc A genetic linkage map for the tiger pufferfish, Takifugu rubripes
    Wataru Kai
    Fisheries Laboratory, The University of Tokyo, Maisaka, Shizuoka, Japan
    Genetics 171:227-38. 2005
    ....
  53. ncbi request reprint The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths
    Jun G Inoue
    Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
    Gene 349:227-35. 2005
    ....
  54. pmc Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster
    Wei Ping Yu
    Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore
    Proc Natl Acad Sci U S A 105:3819-24. 2008
    ..The small and "stable" genome of the elephant shark is a valuable reference for understanding the evolution of vertebrate genomes...
  55. ncbi request reprint Comparative genomics of the Hlx homeobox gene and protein: conservation of structure and expression from fish to mammals
    Michael D Bates
    Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
    Gene 352:45-56. 2005
    ..These results suggest that the function of Hlx and the mechanisms regulating its expression are highly conserved in mammals, birds, amphibians and fish...
  56. ncbi request reprint Comparative genomics of the human and Fugu voltage-gated calcium channel alpha1-subunit gene family reveals greater diversity in Fugu
    Esther Wong
    Ion Channel and Transporter Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, S308433, Singapore
    Gene 366:117-27. 2006
    ..These results indicate that Fugu, a lower vertebrate, has more extensive channel heterogeneity compared to human...
  57. ncbi request reprint Ray-fin fish tetraploidization gave rise to pufferfish duplicates of NPY and PYY, but zebrafish NPY duplicate was lost
    Gorel Sundstrom
    Department of Neuroscience, Uppsala University, Sweden
    Ann N Y Acad Sci 1040:476-8. 2005
    ..The two fugu NPY genes are predominantly expressed in brain. The two PYY genes are expressed in a broad range of tissues including brain and gonads. Thus, the NPY system appears to be more complex in teleosts than in tetrapods...
  58. ncbi request reprint The RIN family of Ras effectors
    Joanne M Bliss
    Department of Biological Chemistry, University of California Los Angeles School of Medicine, Los Angeles, California, USA
    Methods Enzymol 407:335-44. 2006
    ..In this chapter, we summarize our assays and approaches for evaluating the biochemistry and biology of RIN1...
  59. ncbi request reprint Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization of Fugu 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenic Xenopus
    Tara Stapleton
    Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive N W, T2N 4N1, Calgary, AB, Canada
    FEBS Lett 556:59-63. 2004
    ....
  60. ncbi request reprint The 350-fold compacted Fugu parkin gene is structurally and functionally similar to human Parkin
    Wei Ping Yu
    Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
    Gene 346:97-104. 2005
    ..Conceivably, the compact locus of fuparkin could serve as a useful model to understand the transcriptional regulation of huParkin...
  61. ncbi request reprint Pufferfish and zebrafish have five distinct NPY receptor subtypes, but have lost appetite receptors Y1 and Y5
    Tomas A Larsson
    Department of Neuroscience, Uppsala University, Sweden
    Ann N Y Acad Sci 1040:375-7. 2005
    ..These results reveal interesting differences in the NPY system of teleosts and mammals that may have arisen in the genetic turmoil involving the basal ray-fin fish tetraploidization...
  62. ncbi request reprint Erythropoietin gene from a teleost fish, Fugu rubripes
    Chih Fong Chou
    Institute of Molecular and Cell Biology, 30 Medical Dr, Singapore 117609
    Blood 104:1498-503. 2004
    ..Transient transfection studies in a fish hepatoma cell line (PLHC-1) and a human hepatoma cell line (HepG2) suggest that although the Fugu Epo promoter many not be hypoxia inducible, the gene may be regulated by hypoxia...
  63. pmc Conserved regulation of the lymphocyte-specific expression of lck in the Fugu and mammals
    Sydney Brenner
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, USA
    Proc Natl Acad Sci U S A 99:2936-41. 2002
    ..The short promoter of the Fugu lck isolated by us offers a powerful tool for labeling T cells, targeting expression, and manipulating T cell activity in fishes as well as in mammals...
  64. ncbi request reprint Biochemical implications of sequence comparisons of the cystic fibrosis transmembrane conductance regulator
    Agnes L C Tan
    Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, Republic of Singapore
    Arch Biochem Biophys 401:215-22. 2002
    ..Major adaptations in fishes include variations in the postulated ion sensor (111)PDNKE, and the absence of a proline residue in the R domain with consequent higher chloride efflux...