• Animal Systematics, Evolution and Diversity
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• v.29 no.4
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• pp.272-278
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• 2013

Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI) and conservative nuclear rhodopsin (RHO). We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

• Proceedings of the Korea Information Processing Society Conference
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• 2007.05a
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• pp.285-288
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• 2007

There is substantial evidence from earlier researches that older adults have difficult seeing under low illumination and at night, even in the absence of ocular diseases. During human aging, there is a rampant decrease in rod/cone-meditated adaptation which is caused by delayed rhodopsin regeneration and pigment depletion. This calls for a need to develop appropriate visual gadgets to effectively aid the aging generation. Our research culminates its approach from Pattanaik's model by making extensions to temporal visual filtering, thereby simulating a reduction of visual response which comes with age. Our filtering model paves way and lays a foundation for future research to develop a more effective adaptation model that may be further used in developing visual content adaptation aids and guidelines in MPEG 21 environment. We demonstrate our visual model using a High Dynamic Range image and the experiment results are in conversant with the psychophysical data from previous vision researches.

• YAKHAK HOEJI
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• v.54 no.4
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• pp.300-308
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• 2010

Adrenoceptor has been considered to be an important target in psychiatric disorders. Based on x-ray structures of bovine rhodopsin, we established homology model of ${\alpha}_{2c}$-adrenoceptor (ADA2C_rat) and then analyzed docking from binding model of receptor-ligand complex with high-active compound No.29 in tricyclic isoxazole analogues (1-30). We observed that the N (1.907 $\AA$) and O (1.712 $\AA$) atoms of isoxazole ring on the docked ligand (No.29) formed H-bonding interaction with O-H of Ser5.32 and carmeron phenyl ring centroid of tricyclic isoxazole formed $\pi-\pi$ interaction at 3.342 $\AA$ distance with phenyl ring centroid of Phe6.52. According to predictions of blood-brain distribution (logBB) through penetration of blood-brain barrie (BBB) and polar surface area (PSA) of the ligands, the high-active compound No.29 has values of logBB=-0.203, PSA=67.50, respectively. These results suggest that the high-active compound No.29 is a novel anti-depressant with the characteristics such as dopamine and serotonin.

• Fisheries and Aquatic Sciences
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• v.10 no.1
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• pp.8-15
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• 2007

Rhodopsin, a dim-light receptor, is a model system for the study of G protein-coupled receptors that transduce extracellular signals into cells. To study the molecular mechanisms of visual systems in fish, the rod opsin gene of olive flounder Paralichthys olivaceus was characterized. The full-length P. olivaceus opsin gene was obtained by PCR amplification of genomic DNA, as well as cDNA synthesis. A comparison of clones obtained from both methods indicated that the olive flounder rod opsin gene lacks introns. Sequence analysis of the opsin gene indicated that it contains a 1,056-bp open reading frame encoding 352 amino acids. The deduced amino acid sequence contains features of typical rod opsins, such as sites for Schiff's base formation (K296) and its counterion (E113), disulfide formation (C110 and C187), and palmitoylation (C322 and C323). An opsin sequence alignment showed the highest similarity between P. olivaceus and Solea solea (95.1%), followed by Hippoglossus hippoglossus (94.5%). An opsin phylogenetic tree revealed a close relationship between olive flounder and teleost rod opsins.

• Development and Reproduction
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• v.23 no.2
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• pp.171-181
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• 2019

To produce healthy and stable seed production, we need to obtain information and understand vision that affects behavior of red spotted grouper. We examined their expression and retinal development during the juvenile development. Short-wavelength sensitive opsin (SWS2), a cone photoreceptor, began to be expressed from lens and ear vesicle formation stage and its expression increased until 10 days after hatching (dah). In case of middle-wavelength sensitive opsin (MWS), its expression was detected at 3 dah and reached the highest level at 21 dah. The expression of long-wavelength sensitive opsin (LWS) was first observed from 3 dah and their expression decreased thereafter. Rhodopsin, a rod photoreceptor, was found to be expressed from 2 dah and its expression reached the highest level at 50 dah. The outer nuclear layer (ONL), inner nuclear layer (INL) and ganglion cell layer began to differentiate at 2 dah, while choroid first appeared at 4 dah so that the eyes became black. These results indicate that the development of retina mostly completes around 4 dah. It seems that the development of the retina and the expression of the opsin genes are closely related to the behavior such as hunting prey, considering that the timing of the completion of the development of the retina, the timing of gene expression, and the timing of completion of yolk absorption are similar.

• Journal of Integrative Natural Science
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• v.5 no.1
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• pp.32-37
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• 2012

Chemokine receptor antagonists have potential applications in field of drug discovery. Although the chemokine receptors are G-protein-coupled receptors, their cognate ligands are small proteins (8 to 12 kDa), and so inhibiting the ligand/receptor interaction has been challenging. The application of structure-based in-silico methods to drug discovery is still considered a major challenge, especially when the x-ray structure of the target protein is unknown. Such is the case with human CCR2 and CCR5, the most important members of the chemokine receptor family and also a potential drug target. Herein, we review the success stories of combined receptor modeling/mutagenesis approach to probe the allosteric nature of chemokine receptor binding by small molecule antagonists for CCR2 and CCR5 using Rhodopsin as template. We also urged the importance of recently available ${\beta}2$-andrenergic receptor as an alternate template to guide mutagenesis. The results demonstrate the usefulness and robustness of in-silico 3D models. These models could also be useful for the design of novel and potent CCR2 and CCR5 antagonists using structure based drug design.

• Journal of Photoscience
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• v.9 no.2
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• pp.314-316
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• 2002

In halobacterial membrane, pharaonis phoborhodopsin (or pharaonis sensory rhdopsin II, psRII) forms a complex with its transducer pHtrII. Flash-photolyis of D75N mutant did not yield M-intermediate but an O-like intermediate is observed. We examined the interaction between D75N of ppR and t-Htr (truncated pHtrII). These formed a complex in the presence of n-dodecyl-$\beta$-D-maltoside, and the association accelerated the decay of the 0 of D75N from 15 to 56 s$\^$-1/. From the decay time constants under varying ratios of D75N and t-Htr, n, the molar ratio of D75N/t-Htr in the complex, and K$\_$D/, the dissociation constant, were estimated. The value of n was unity and K$\_$D/ was estimated to 146 nM. This K$\_$D/ value can be considered as the association between the photo-intermediate and t-Htr, which is deduced by the method of estimation. Previously we (Photochem. Photobiol. 74, 489-494 (2001)) reported K$\_$D/ of 15 $\mu$M for the interaction between the wild-type and t-Htr by means of the change of M-decay rates. Therefore, this value should be the K$\_$D/ value for the interaction between M of the wild-type and t-Htr.

• Journal of Photoscience
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• v.9 no.2
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• pp.106-109
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• 2002

Archaeal rhodopsins possess retinal molecule as their chromophores, and their light-energy and light-signal conversions are triggered by all-trans to 13-cis isomerization of the retinal chromophore. Relaxation through structural changes of protein then leads to functional processes, proton pump in bacteriorhodopsin (bR) and transducer activation in phoborhodopsin (pR). It is known that sensory rhodopsins can pump protons in the absence of their transducers. Thus, there should be common and specific features in their protein structural changes for function. In this paper, our r ecent studies on pR from Natronobacterium pharaonis (ppR) by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy are compared with those of bR. In particular, protein structural changes upon retinal photoisomerization are studied. Comparative investigation of ppR and bR revealed the similar structures of the polyene chain of the chromophore and water-containing hydrogen-bonding network, whereas the structural changes upon photoisomerization were more extended in ppR than in bR. Extended protein structural changes were clearly shown by the assignment of the C=O stretch of Asnl05. FTIR studies of a ppR mutant with the same retinal binding site as in bR revealed that the Schiff base region is important to determine their colors.

• Journal of Photoscience
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• v.9 no.2
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• pp.246-248
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• 2002

Light is a major environmental signal for entrainment of the circadian clock, but little is known about the phototransduction pathway triggered by light-activation of photoreceptive molecule(s) responsible for the phase shift of the clock in vertebrates. The chicken pineal gland and retina contain the autonomous circadian oscillators together with the photic entrainment pathway, and hence they provide useful experimental model for the clock system. We previously demonstrated the expression and light-dependent activation of rod-type transducin $\alpha$-subunit (Gtl$\alpha$) in the chicken pineal gland. It is unlikely, however, that the pineal Gt$_1$$\alpha$ plays a major role in the photic entrainment, because the light-induced phase shift is unaffected by bloking the signaling function of Gt$_1$$\alpha$. Here, we show the expression of G 11 $\alpha$, an $\alpha$-subunit of another heterotrimeric G-protein, in the chicken pineal gland and retina by cDNA cloning, Northern blot and Western blot analyses. GIl$\alpha$-immunoreactivity was colocalized with pinopsin in the chicken pineal cells and it was found predominantly at the outer segments of photoreceptor cells in the retinal sections, suggesting functional coupling of G11 $\alpha$ with opsins in the both the tissues. By coimmunoprecipitation experiments using the retina, we showed the light- and GTP-dependent interaction between rhodopsin and G11 $\alpha$. Upon ectopic expression of a Gq/ 11-coupled receptor in cultured pineal cells, pharmacological (non-photic) activation of endogenous G11 induced phase-dependent phase shifts of the melatonin rhythm in a manner very similar to the effect of light. These results suggested opsin-G11 pathway contributing to the photic entrainment of the circadian clock.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.2008-2014
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• 2011

Serotonin or 5-hydroxytryptamine subtype 2C ($5-HT_{2C}$) receptor belongs to class A amine subfamily of G-protein-coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (${\beta}$2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.