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Journal of the Royal Society, Interface Oct 2015Vision is the primary sensory modality of birds, and its importance is evident in the sophistication of their visual systems. Coloured oil droplets in the cone...
Vision is the primary sensory modality of birds, and its importance is evident in the sophistication of their visual systems. Coloured oil droplets in the cone photoreceptors represent an adaptation in the avian retina, acting as long-pass colour filters. However, we currently lack understanding of how the optical properties and morphology of component structures (e.g. oil droplet, mitochondrial ellipsoid and outer segment) of the cone photoreceptor influence the transmission of light into the outer segment and the ultimate effect they have on receptor sensitivity. In this study, we use data from microspectrophotometry, digital holographic microscopy and electron microscopy to inform electromagnetic models of avian cone photoreceptors to quantitatively investigate the integrated optical function of the cell. We find that pigmented oil droplets primarily function as spectral filters, not light collection devices, although the mitochondrial ellipsoid improves optical coupling between the inner segment and oil droplet. In contrast, unpigmented droplets found in violet-sensitive cones double sensitivity at its peak relative to other cone types. Oil droplets and ellipsoids both narrow the angular sensitivity of single cone photoreceptors, but not as strongly as those in human cones.
Topics: Animals; Chickens; Color; Electromagnetic Radiation; Humans; Light; Microscopy, Electron, Scanning; Microspectrophotometry; Models, Biological; Models, Statistical; Oils; Optics and Photonics; Refractometry; Retina; Retinal Cone Photoreceptor Cells; Vision, Ocular
PubMed: 26423439
DOI: 10.1098/rsif.2015.0591 -
Molecular Biology and Evolution Apr 2024Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are...
Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.
Topics: Humans; Animals; Opsins; Retinal Pigments; Anura; Gene Duplication; Microspectrophotometry
PubMed: 38573520
DOI: 10.1093/molbev/msae049 -
Journal of the Royal Society, Interface Aug 2013Cephalopods (e.g. octopus, squid and cuttlefish) dynamically tune the colour and brightness of their skin for camouflage and communication using specialized skin cells...
Cephalopods (e.g. octopus, squid and cuttlefish) dynamically tune the colour and brightness of their skin for camouflage and communication using specialized skin cells called iridocytes. We use high-resolution microspectrophotometry to investigate individual tunable Bragg structures (consisting of alternating reflectin protein-containing, high-refractive index lamellae and low-refractive index inter-lamellar spaces) in live and chemically fixed iridocytes of the California market squid, Doryteuthis opalescens. This subcellular, single-stack microspectrophotometry allows for spectral normalization, permitting use of a transfer-matrix model of Bragg reflectance to calculate all the parameters of the Bragg stack-the refractive indices, dimensions and numbers of the lamellae and inter-lamellar spaces. Results of the fitting analyses show that eight or nine pairs of low- and high-index layers typically contribute to the observed reflectivity in live cells, whereas six or seven pairs of low- and high-index layers typically contribute to the reflectivity in chemically fixed cells. The reflectin-containing, high-index lamellae of live cells have a refractive index proportional to the peak reflectivity, with an average of 1.405 ± 0.012 and a maximum around 1.44, while the reflectin-containing lamellae in fixed tissue have a refractive index of 1.413 ± 0.015 suggesting a slight increase of refractive index in the process of fixation. As expected, incremental changes in refractive index contribute to the greatest incremental changes in reflectivity for those Bragg stacks with the most layers. The excursions in dimensions required to tune the measured reflected wavelength from 675 (red) to 425 nm (blue) are a decrease from ca 150 to 80 nm for the high-index lamellae and from ca 120 to 50 nm for the low-index inter-lamellar spaces. Fixation-induced dimensional changes also are quantified, leading us to suggest that further microspectrophotometric analyses of this iridocyte system can be used as a model system to quantify the effects of various methods of tissue fixation. The microspectrophotometry technique described can be expected to provide deeper insights into the molecular and physical mechanisms governing other biophotonically active cells and structures.
Topics: Animals; Decapodiformes; Refractometry; Skin; Skin Pigmentation
PubMed: 23740489
DOI: 10.1098/rsif.2013.0386 -
The Journal of Physiology Jun 19771. A dual system of visual pigments having absorbance maxima in the green and blue respectively has been found in the retinas of geckos both by single cell...
1. A dual system of visual pigments having absorbance maxima in the green and blue respectively has been found in the retinas of geckos both by single cell microspectrophotometry and by the method of extraction. Microspectrophotometry has shown the system to be present in four species of geckos representing four genera. Along with previous work with extracts (Crescitelli, 1972) this indicates a fundamental property in this family of lizards. No other photopigments have been detected.2. For Gekko gekko, the species most intensively studied, the two pigments have absorbance maxima at 521 and 467 nm respectively. Both are based on vitamin A(1) and both are characterized by absorbance spectra that nearly conform to the Dartnall nomogram.3. In situ, the 521-pigment is not temperature-sensitive, and has virtually the same absorbance spectrum at 23 degrees C as at 5 degrees C. On extraction into digitonin solution, however, the absorbance spectrum of the pigment becomes temperature-dependent and, though identical when measured at low temperature (2-5 degrees C) with the constant in situ curve, is displaced to shorter wave-lengths at higher temperatures (10-25 degrees C). Thus the extract spectrum is relevant to the in situ spectrum only at low temperature (and in the presence of chloride ions).4. Unlike the rhodopsins of several vertebrates, the gecko 521-pigment displays no evidence of a meta-III stage in the sequence of products following photic bleaching, even at low temperatures. This is true for the pigment in situ as well as in the extracted condition.
Topics: Animals; Digitonin; Lizards; Retinal Pigments; Spectrophotometry; Temperature
PubMed: 874921
DOI: 10.1113/jphysiol.1977.sp011872 -
The Journal of Neuroscience : the... Feb 1997Retinas of adult teleost fish can regenerate after injury. Two important issues regarding this phenomenon are the assembly of the regenerated retina and the neuronal...
Retinas of adult teleost fish can regenerate after injury. Two important issues regarding this phenomenon are the assembly of the regenerated retina and the neuronal images of the visual scene that the regenerated retina produces. Here we report experiments in which the visual pigment content of photoreceptors derived from native and regenerated sunfish retinas was determined by microspectrophotometry. In native retina, there is an apparently perfect correspondence between cone morphology and visual pigment content; all rods contain a middle-wavelength pigment, all single cones contain a different middle-wavelength pigment, and all double cone members contain a long-wavelength pigment. The visual pigments in regenerated rods and double cones were the same as in native retina; however, triple cones, a morphology never observed in native retina, contained the long-wavelength pigment. Moreover, although approximately 60% of regenerated single cones contained the expected middle-wavelength pigment, all other single cones contained the long-wavelength pigment. This mismatch between morphology of regenerated single cones and their visual pigment assignment indicated the following: (1) There is a degree of independence between the mechanisms that establish cone morphology and pigment content during regeneration, which suggests that cone photoreceptor regeneration is not a straightforward recapitulation of the normal cone photoreceptor developmental plan. (2) Although anomalous, the long-wavelength single cones may enable regenerated retina to restore the native spectral sampling of the visual scene.
Topics: Animals; Nerve Regeneration; Perciformes; Photoreceptor Cells; Pigment Epithelium of Eye; Retina
PubMed: 8994046
DOI: 10.1523/JNEUROSCI.17-03-00917.1997 -
PloS One 2014The mesopelagic zone is a visual scene continuum in which organisms have developed various strategies to optimize photon capture. Here, we used light microscopy,...
The mesopelagic zone is a visual scene continuum in which organisms have developed various strategies to optimize photon capture. Here, we used light microscopy, stereology-assisted retinal topographic mapping, spectrophotometry and microspectrophotometry to investigate the visual ecology of deep-sea bioluminescent sharks [four etmopterid species (Etmopterus lucifer, E. splendidus, E. spinax and Trigonognathus kabeyai) and one dalatiid species (Squaliolus aliae)]. We highlighted a novel structure, a translucent area present in the upper eye orbit of Etmopteridae, which might be part of a reference system for counterillumination adjustment or acts as a spectral filter for camouflage breaking, as well as several ocular specialisations such as aphakic gaps and semicircular tapeta previously unknown in elasmobranchs. All species showed pure rod hexagonal mosaics with a high topographic diversity. Retinal specialisations, formed by shallow cell density gradients, may aid in prey detection and reflect lifestyle differences; pelagic species display areae centrales while benthopelagic and benthic species display wide and narrow horizontal streaks, respectively. One species (E. lucifer) displays two areae within its horizontal streak that likely allows detection of conspecifics' elongated bioluminescent flank markings. Ganglion cell topography reveals less variation with all species showing a temporal area for acute frontal binocular vision. This area is dorsally extended in T. kabeyai, allowing this species to adjust the strike of its peculiar jaws in the ventro-frontal visual field. Etmopterus lucifer showed an additional nasal area matching a high rod density area. Peak spectral sensitivities of the rod visual pigments (λmax) fall within the range 484-491 nm, allowing these sharks to detect a high proportion of photons present in their habitat. Comparisons with previously published data reveal ocular differences between bioluminescent and non-bioluminescent deep-sea sharks. In particular, bioluminescent sharks possess higher rod densities, which might provide them with improved temporal resolution particularly useful for bioluminescent communication during social interactions.
Topics: Animals; Luminescence; Pigmentation; Retinal Rod Photoreceptor Cells; Sharks
PubMed: 25099504
DOI: 10.1371/journal.pone.0104213 -
Integrative and Comparative Biology Sep 2018Most stomatopod crustaceans have complex retinas in their compound eyes, with up to 16 spectral types of photoreceptors, but members of the superfamily Squilloidea have...
Most stomatopod crustaceans have complex retinas in their compound eyes, with up to 16 spectral types of photoreceptors, but members of the superfamily Squilloidea have much simpler retinas, thought to contain a single photoreceptor spectral class. In the Atlantic stomatopod Squilla empusa, microspectrophotometry shows that all photoreceptors absorb light maximally at 517 nm, indicating that a single visual pigment is present in all photoreceptors in the retina. However, six distinct, but partial, long wavelength sensitive (LWS) opsin transcripts, which encode the protein component of the visual pigment, have been previously isolated through RT-PCR. In order to investigate the spectral and functional differences among S. empusa's opsins, we used RT-PCR to complete the 3' end of sequences for five of the six expressed opsins. The extended sequences spanned from the first transmembrane (TM1) helix to the 3' end of the coding region. Using homology-based modeling, we predicted the three-dimensional structure of the amino acid translation of the S. empusa opsins. Based on these analyses, S. empusa LWS opsins share a high sequence identity in TM regions and in amino acids within 15 Å of the chromophore-binding lysine on TM helix 7 (TM7), suggesting that these opsins produce spectrally similar visual pigments in agreement with previous results. However, we propose that these spectrally similar opsins differ functionally, as there are non-conservative amino acid substitutions found in intracellular loop 2 (ICL2) and TM5/ICL3, which are critical regions for G-protein binding, and substitutions in extracellular regions suggest different chromophore attachment affinities. In situ hybridization of two of the opsins (Se5 and Se6) revealed strong co-expression in all photoreceptors in both midband and peripheral regions of the retina as well as in selected ocular and cerebral ganglion neuropils. These data suggest the expression of multiple opsins-likely spectrally identical, but functionally different-in multiple types of neuronal cells in S. empusa. This suggests that the multiple opsins characteristic of other stomatopod species may have similar functional specialization.
Topics: Amino Acid Sequence; Animals; Arthropod Proteins; Crustacea; Eye; Gene Expression; Gene Expression Profiling; Opsins; Sequence Alignment
PubMed: 29697793
DOI: 10.1093/icb/icy007 -
Annals of Botany Apr 2007Consensus higher-level molecular phylogenies present a compelling case that an ancient divergence separates eukaryotic green algae into two major monophyletic lineages,...
BACKGROUND AND AIMS
Consensus higher-level molecular phylogenies present a compelling case that an ancient divergence separates eukaryotic green algae into two major monophyletic lineages, Chlorophyta and Streptophyta, and a residuum of green algae, which have been referred to prasinophytes or micromonadophytes. Nuclear DNA content estimates have been published for less than 1% of the described green algal members of Chlorophyta, which includes multicellular green marine algae and freshwater flagellates (e.g. Chlamydomonas and Volvox). The present investigation summarizes the state of our knowledge and adds substantially to our database of C-values, especially for the streptophyte charophycean lineage which is the sister group of the land plants. A recent list of 2C nuclear DNA contents for isolates and species of green algae is expanded by 72 to 157.
METHODS
The DNA-localizing fluorochrome DAPI (4',6-diamidino-2-phenylindole) and red blood cell (chicken erythrocytes) standard were used to estimate 2C values with static microspectrophotometry.
KEY RESULTS
In Chlorophyta, including Chlorophyceae, Prasinophyceae, Trebouxiophyceae and Ulvophyceae, 2C DNA estimates range from 0.01 to 5.8 pg. Nuclear DNA content variation trends are noted and discussed for specific problematic taxon pairs, including Ulotrichales-Ulvales, and Cladophorales-Siphonocladales. For Streptophyta, 2C nuclear DNA contents range from 0.2 to 6.4 pg, excluding the highly polyploid Charales and Desmidiales, which have genome sizes of up to 14.8 and 46.8 pg, respectively. Nuclear DNA content data for Streptophyta superimposed on a contemporary molecular phylogeny indicate that early diverging lineages, including some members of Chlorokybales, Coleochaetales and Klebsormidiales, have genomes as small as 0.1-0.5 pg. It is proposed that the streptophyte ancestral nuclear genome common to both the charophyte and the embryophyte lineages can be characterized as 1C = 0.2 pg and 1n = 6.
CONCLUSIONS
These data will help pre-screen candidate species for the on-going construction of bacterial artificial chromosome nuclear genome libraries for land plant ancestors. Data for the prasinophyte Mesostigma are of particular interest as this alga reportedly most closely resembles the 'ancestral green flagellate'. Both mechanistic and ecological processes are discussed that could have produced the observed C-value increase of >100-fold in the charophyte green algae whereas the ancestral genome was conserved in the embryophytes.
Topics: Cell Nucleus; Chlorophyta; DNA, Algal; Microspectrophotometry; Phylogeny
PubMed: 17272304
DOI: 10.1093/aob/mcl294 -
Proceedings of the National Academy of... Jan 2017Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as a...
Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as a testbed to study directional light emission. DNA-guided nanoparticle colloidal crystallization allows for the formation of micrometer-scale single-crystal body-centered cubic gold nanoparticle superlattices, with dye molecules coupled to the DNA strands that link the particles together, in the form of a rhombic dodecahedron. Encapsulation in silica allows one to create robust architectures with the plasmonically active particles and dye molecules fixed in space. At the micrometer scale, the anisotropic rhombic dodecahedron crystal habit couples with photonic modes to give directional light emission. At the nanoscale, the interaction between the dye dipoles and surface plasmons can be finely tuned by coupling the dye molecules to specific sites of the DNA particle-linker strands, thereby modulating dye-nanoparticle distance (three different positions are studied). The ability to control dye position with subnanometer precision allows one to systematically tune plasmon-excition interaction strength and decay lifetime, the results of which have been supported by electrodynamics calculations that span length scales from nanometers to micrometers. The unique ability to control surface plasmon/exciton interactions within such superlattice microcavities will catalyze studies involving quantum optics, plasmon laser physics, strong coupling, and nonlinear phenomena.
Topics: Coloring Agents; Computer Simulation; Crystallization; DNA; Gold; Metal Nanoparticles; Microspectrophotometry; Models, Molecular; Nanotechnology; Optical Phenomena; Silicon Dioxide
PubMed: 28053232
DOI: 10.1073/pnas.1619802114 -
PloS One 2012Although molecular classification brings interesting insights into breast cancer taxonomy, its implementation in daily clinical care is questionable because of its...
Although molecular classification brings interesting insights into breast cancer taxonomy, its implementation in daily clinical care is questionable because of its expense and the information supplied in a single sample allocation is not sufficiently reliable. New approaches, based on a panel of small molecules derived from the global or targeted analysis of metabolic profiles of cells, have found a correlation between activation of de novo lipogenesis and poorer prognosis and shorter disease-free survival for many tumors. We hypothesized that the lipid content of breast cancer cells might be a useful indirect measure of a variety of functions coupled to breast cancer progression. Raman microspectroscopy was used to characterize metabolism of breast cancer cells with different degrees of malignancy. Raman spectra from MDA-MB-435, MDA-MB-468, MDA-MB-231, SKBR3, MCF7 and MCF10A cells were acquired with an InVia Raman microscope (Renishaw) with a backscattered configuration. We used Principal Component Analysis and Partial Least Squares Discriminant Analyses to assess the different profiling of the lipid composition of breast cancer cells. Characteristic bands related to lipid content were found at 3014, 2935, 2890 and 2845 cm(-1), and related to lipid and protein content at 2940 cm(-1). A classificatory model was generated which segregated metastatic cells and non-metastatic cells without basal-like phenotype with a sensitivity of 90% and a specificity of 82.1%. Moreover, expression of SREBP-1c and ABCA1 genes validated the assignation of the lipid phenotype of breast cancer cells. Indeed, changes in fatty acid unsaturation were related with the epithelial-to-mesenchymal transition phenotype. Raman microspectroscopy is a promising technique for characterizing and classifying the malignant phenotype of breast cancer cells on the basis of their lipid profiling. The algorithm for the discrimination of metastatic ability is a first step towards stratifying breast cancer cells using this rapid and reagent-free tool.
Topics: Breast Neoplasms; Cell Line, Tumor; Discriminant Analysis; Epithelial Cells; Epithelial-Mesenchymal Transition; Fatty Acids; Female; Gene Expression Regulation, Neoplastic; Humans; Least-Squares Analysis; Lipid Metabolism; Microspectrophotometry; Neoplasm Metastasis; Phenotype; Principal Component Analysis; Spectrum Analysis, Raman
PubMed: 23082122
DOI: 10.1371/journal.pone.0046456