Preface to the Second Edition

Jerlov, N. G.

doi:10.1016/s0422-9894(08)70792-x

Cited by 375 publications

(183 citation statements)

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“…Many fish, amphibians, birds, and mammals that live in these environments use rhodopsins with max s of Ϸ500 nm (12). In contrast, in deep water, the distribution of light is much narrower at Ϸ480 nm (18). Mature conger, mature eel, thornyhead, and coelacanth all live at the depths of 200-1,800 m (www.fishbase.org).…”

Section: Resultsmentioning

confidence: 99%

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

Yokoyama

Tada

Zhang

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

234

292

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Vertebrate ancestors appeared in a uniform, shallow water environment, but modern species flourish in highly variable niches. A striking array of phenotypes exhibited by contemporary animals is assumed to have evolved by accumulating a series of selectively advantageous mutations. However, the experimental test of such adaptive events at the molecular level is remarkably difficult. One testable phenotype, dim-light vision, is mediated by rhodopsins. Here, we engineered 11 ancestral rhodopsins and show that those in early ancestors absorbed light maximally ( max) at 500 nm, from which contemporary rhodopsins with variable maxs of 480 -525 nm evolved on at least 18 separate occasions. These highly environment-specific adaptations seem to have occurred largely by amino acid replacements at 12 sites, and most of those at the remaining 191 (Ϸ94%) sites have undergone neutral evolution. The comparison between these results and those inferred by commonly-used parsimony and Bayesian methods demonstrates that statistical tests of positive selection can be misleading without experimental support and that the molecular basis of spectral tuning in rhodopsins should be elucidated by mutagenesis analyses using ancestral pigments. molecular adaptation ͉ rhodopsin

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Section: Resultsmentioning

confidence: 99%

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

Yokoyama

Tada

Zhang

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

234

292

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“…It plays a very critical role to understand backscattering and absorption properties, photosynthesis and primary productivity models (Platt, 1986;Sathyendranath, 1989), heat budgets (Lewis, 1990;Morel, 1994), other biological processes in the water column, and to classify water types (Jerlov, 1976).…”

Section: Modelling Particulate Backscattering Coefficientmentioning

confidence: 99%

An optical model for deriving the spectral particulate backscattering coefficients in oceanic waters

Tiwari

Shanmugam

2013

Ocean Sci.

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Abstract. An optical model is developed based on the diffuse attenuation coefficient (K d ) to estimate particulate backscattering coefficients b bp (λ) in oceanic waters. A large in situ data set is used to establish robust relationships between b bp (530) and b bp (555) and K d (490) using an efficient nonlinear least-square method which uses the trust region algorithm with Bisquare weights scheme to adjust the coefficients. These relationships are obtained with good correlation coefficients (R 2 = 0.786 and 0.790), low root mean square error (RMSE = 0.00076 and 0.00072) and 95 % confidence bounds. The new model is tested with three independent data sets: the NOMAD SeaWiFS Match ups, OOXIX IOP algorithm workshop evaluation data set (Version 2.0w APLHA), and IOCCG simulated data set. Results show that the new model makes good retrievals of b bp at all key wavelengths (from 412-683 nm), with statistically significant improvements over other inversion models. Thus, the new model has the potential to improve our present knowledge of particulate matter and their optical variability in oceanic waters.

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“…Biological Significance of GPR and BPR Variation-The difference in photocycle rates between GPR and BPR and their different absorption maxima may be explained as an adaptation to the different light intensities in their respective marine environments based on measured spectral distributions of intensities of solar illumination at the ocean surface and at various depths (23). At solar radiation intensity of 1.5 watts⅐m Ϫ2 ⅐nm Ϫ1 at 525 nm (the absorption maximum of GPR) on the ocean surface under brightest conditions using a 95-nm half-bandwidth of GPR and 2 A 2 cross-sectional area, we calculate that 1 photon/proteorhodopsin molecule would be available for absorption for each ϳ150 ms. During this time, a population of GPR molecules reaches 98% recovery (Fig.…”

Section: Deep Ocean Proteorhodopsinbpr-mediated Proton Fluxes In E Cmentioning

confidence: 99%

Spectroscopic and Photochemical Characterization of a Deep Ocean Proteorhodopsin

Wang

Sineshchekov

Spudich

et al. 2003

Journal of Biological Chemistry

161

270

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A second group of proteorhodopsin-encoding genes (blue-absorbing proteorhodopsin, BPR) differing by 20 -30% in predicted primary structure from the first-discovered green-absorbing (GPR) group has been detected in picoplankton from Hawaiian deep sea water. Here we compare BPR and GPR absorption spectra, photochemical reactions, and proton transport activity. The photochemical reaction cycle of Hawaiian deep ocean BPR in cells is 10-fold slower than that of GPR with very low accumulation of a deprotonated Schiff base intermediate in cells and exhibits mechanistic differences, some of which are due to its glutamine residue rather than leucine at position 105. In contrast to GPR and other characterized microbial rhodopsins, spectral titrations of BPR indicate that a second titratable group, in addition to the retinylidene Schiff base counterion Asp-97, modulates the absorption spectrum near neutral pH. Mutant analysis confirms that Asp-97 and Glu-108 are proton acceptor and proton donor, respectively, in retinylidene Schiff base proton transfer reactions during the BPR photocycle as previously shown for GPR, but BPR contains an alternative acceptor evident in its D97N mutant, possibly the same as the second titratable group modulating the absorption spectrum. BPR, similar to GPR, carries out outward light-driven proton transport in Escherichia coli vesicles but with a reduced translocation rate attributable to its slower photocycle. In energized E. coli cells at physiological pH, the net effect of BPR photocycling is to generate proton currents dominated by a triggered proton influx, rather than efflux as observed with GPR-containing cells. Reversal of the proton current with the K ؉ -ionophore valinomycin supports that the influx is because of voltagegated channels in the E. coli cell membrane. These observations demonstrate diversity in photochemistry and mechanism among proteorhodopsins. Calculations of photon fluence rates at different ocean depths show that the difference in photocycle rates between GPR and BPR as well as their different absorption maxima may be explained as an adaptation to the different light intensities available in their respective marine environments. Finally, the results raise the possibility of regulatory (i.e. sensory) rather than energy harvesting functions of some members of the proteorhodopsin family.

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Preface to the Second Edition

Cited by 375 publications

References 0 publications

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

An optical model for deriving the spectral particulate backscattering coefficients in oceanic waters

Spectroscopic and Photochemical Characterization of a Deep Ocean Proteorhodopsin

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