Research Topics
Genomes and Genes | Shozo YokoyamaSummaryAffiliation: Syracuse University Country: USA Publications
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Publications
Cloning and characterization of the pineal gland-specific opsin gene of marine lamprey (Petromyzon marinus)S Yokoyama
Syracuse University, Department of Biology, NY 13244, USA
Gene 202:89-93. 1997..These changes in P(Pm) might have been important in achieving marine lamprey-specific interaction between P(Pm) and other proteins in the pineal gland...- The spectral tuning in the short wavelength-sensitive type 2 pigmentsShozo Yokoyama
Department of Biology, Biological Research Laboratories, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
Gene 306:91-8. 2003.... - Molecular evolution of color vision in vertebratesShozo Yokoyama
Department of Biology, Biological Research Laboratories, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
Gene 300:69-78. 2002..These hypotheses can then be tested using the in vitro assay. This approach has been a powerful tool in elucidating not only the molecular bases of color vision, but the processes of adaptive evolution at the molecular level... - Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gekkoS Yokoyama
Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
Gene 276:117-25. 2001..The accelerated evolutionary rates reflect not only the transition from cones to rods in the retina but also the blue-shift in the absorption spectra of the gecko pigments... - Adaptive evolution of the African and Indonesian coelacanths to deep-sea environmentsS Yokoyama
Biological Research Laboratories, Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
Gene 261:35-42. 2000..Statistical analyses show that the adaptation of the coelacanths toward the deep-sea started as early as 200 million years ago... - Molecular evolution of color vision of zebra finchS Yokoyama
Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
Gene 259:17-24. 2000..Molecular evolutionary analyses suggest that specific amino acid replacements in the SWS1 and SWS2 pigments, resulting from accelerated evolution, must have been responsible for their functional divergences among the avian pigments... - Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1) and rhodopsin-like (RH2) pigmentsS Yokoyama
Department of Biology, Syracuse University, NY 13244 1220, USA
J Hered 91:215-20. 2000..Among these, D83N, E1220, M207L, and A292S are associated strongly with the adaptive blue shifts in the lambda max values of RH1 and RH2 pigments in vertebrates... 
The molecular genetics of red and green color vision in mammalsS Yokoyama
Department of Biology, Syracuse University, Syracuse, New York 13244, USA
Genetics 153:919-32. 1999..The additive effects of these amino acid changes fully explain the red-green color vision in a wide range of mammalian species, goldfish, American chameleon (Anolis carolinensis), and pigeon (Columba livia)...- Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae)S Yokoyama
Department of Biology, Syracuse University, Syracuse, NY 13244, USA
Proc Natl Acad Sci U S A 96:6279-84. 1999..The lambdamax values are shifted about 20 nm toward blue compared with those of the corresponding orthologous pigments. Mutagenesis experiments show that each of these coadapted changes is fully explained by two amino acid replacements... - The "five-sites" rule and the evolution of red and green color vision in mammalsS Yokoyama
Department of Biology, Syracuse University, New York 13244, USA
Mol Biol Evol 15:560-7. 1998..The inferred amino acid sequences of ancestral organisms suggest that the extant mammalian red and green pigments appear to have evolved from a single ancestral green-red hybrid pigment by directed amino acid substitutions... - Regeneration of ultraviolet pigments of vertebratesS Yokoyama
Department of Biology, Syracuse University, NY 13244, USA
FEBS Lett 423:155-8. 1998..The construction and functional assays of the ultraviolet or near-ultraviolet pigments from a wide range of vertebrate species will allow us to study the molecular bases of ultraviolet vision for the first time... - Molecular genetic basis of adaptive selection: examples from color vision in vertebratesS Yokoyama
Department of Biology, Syracuse University, New York, USA
Annu Rev Genet 31:315-36. 1997..The identification of potentially important amino acid changes using evolutionary biological means is an indispensable step in elucidating the molecular mechanisms that underlie the spectral tuning of visual pigments... - Tertiary structure and spectral tuning of UV and violet pigments in vertebratesShozo Yokoyama
Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
Gene 365:95-103. 2006..Both mutagenesis analyses of E113Q and quantum chemical calculations strongly suggest that unprotonated Schiff base-linked chromophore is responsible for detecting UV light... - Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminusShozo Yokoyama
Department of Biology, Emory University, Atlanta, GA, USA
Photochem Photobiol 83:236-41. 2007..We anticipate our analyses to be a starting point for viewing the spectral tuning of visual pigments as interactions between the retinal and key amino acids that are distributed throughout the entire pigment... - Molecular analysis of the evolutionary significance of ultraviolet vision in vertebratesYongsheng Shi
Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
Proc Natl Acad Sci U S A 100:8308-13. 2003..The use of UV vision is associated strongly with UV-dependent behaviors of organisms. When UV light is not available or is unimportant to organisms, the SWS1 gene can become nonfunctional, as exemplified by coelacanth and dolphin... - Elephants and human color-blind deuteranopes have identical sets of visual pigmentsShozo Yokoyama
Department of Biology, Emory University, Atlanta, Georgia 30322, USA
Genetics 170:335-44. 2005..During the day, therefore, elephants seem to have the dichromatic color vision of deuteranopes. During the night, however, they are likely to use RH1 and SWS1 pigments and detect light at 420-490 nm... - Evolutionary replacement of UV vision by violet vision in fishTakashi Tada
Department of Biology, Emory University, Atlanta, GA 30322, USA
Proc Natl Acad Sci U S A 106:17457-62. 2009.... - Evolutionary dynamics of rhodopsin type 2 opsins in vertebratesShozo Yokoyama
Department of Biology, Rollins Research Center, Emory University, USA
Mol Biol Evol 27:133-41. 2010..25 x 10(-9)/site/year, which increased to approximately 1 x 10(-9) to 3 x 10(-9)/site/year in euteleost lineages and to approximately 0.3 x 10(-9) to 0.5 x 10(-9)/site/year in coelacanth and tetrapods... - Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebratesShozo Yokoyama
Department of Biology, Emory University, Atlanta, GA 30322, USA
Genetics 179:2037-43. 2008..Our findings demonstrate that the evolutionary method should be used in elucidating the mechanisms of spectral tuning of four other pigment groups and, for that matter, functional differentiations of any other proteins... - The molecular basis of adaptive evolution of squirrelfish rhodopsinsShozo Yokoyama
Department of Biology, Emory University, Atlanta, Georgia, USA
Mol Biol Evol 21:2071-8. 2004.... - Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleonNaomi Takenaka
Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
Gene 399:26-32. 2007.... - Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebratesShozo Yokoyama
Department of Biology, Emory University, Atlanta, GA 30322, USA
Proc Natl Acad Sci U S A 105:13480-5. 2008.... - A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei)Shozo Yokoyama
Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
Gene 396:196-202. 2007..Moreover, the larger the individual effects of amino acid changes on the lambda(max)-shift are, the larger the synergistic effects tend to be generated, revealing a novel mechanism of spectral tuning of visual pigments... - Genetic basis of spectral tuning in the violet-sensitive visual pigment of African clawed frog, Xenopus laevisYusuke Takahashi
Department of Biology, Emory University, Atlanta, Georgia 30322, USA
Genetics 171:1153-60. 2005.... - Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebratesShozo Yokoyama
Department of Biology, Rollins Research Center, Emory University, USA
Mol Biol Evol 22:968-75. 2005.... 
Evolution of dim-light and color vision pigmentsShozo Yokoyama
Department of Biology, Emory University, Atlanta, Georgia 30322, USA
Annu Rev Genomics Hum Genet 9:259-82. 2008....- Mutagenesis and reconstitution of middle-to-long-wave-sensitive visual pigments of New World monkeys for testing the tuning effect of residues at sites 229 and 233Chihiro Hiramatsu
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimeitou 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
Vision Res 44:2225-31. 2004..These results preclude the necessity of examining exon 4, encoding the residues at sites 229 and 233, of M/LWS pigment genes for colour-vision typing of New World monkeys... - The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolutionSamir S Deeb
Department of Medicine, University of Washington, Seattle, USA
Mol Biol Evol 20:1642-9. 2003..Introns interrupt the coding sequences of the wallaby, mouse, and human MWS pigment sequences at the same corresponding nucleotide positions. However, the length of introns varies widely among these species... - Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteinsAhmet Altun
Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA, USA
Photochem Photobiol 84:845-54. 2008..We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants... - Evaluating adaptive evolutionShozo Yokoyama
Nat Genet 30:350-1. 2002 - Prediction of distant metastasis by using reverse transcriptase-polymerase chain reaction for epithelial and variant CD44 mRNA in the peripheral blood of patients with colorectal cancerShozo Yokoyama
Second Department of Surgery, Wakayama Medical University, School of Medicine 811-1 Kimiidera, Wakayama 641-8510, Japan
Arch Surg 137:1069-73. 2002..Molecular detection in the peripheral blood at surgical treatment suggests that systemic hematogenic tumor cell dissemination is an early event of distant metastasis...