Characterization of visual pigments, oil droplets, lens and cornea in the whooping crane Grus americana.

Vision has been investigated in many species of birds, but few studies have considered the visual systems of large birds and the particular implications of large eyes and long-life spans on visual system capabilities. To address these issues we investigated the visual system of the whooping crane Grus americana (Gruiformes, Gruidae), which is one of only two North American crane species. It is a large, long-lived bird in which UV sensitivity might be reduced by chromatic aberration and entrance of UV radiation into the eye could be detrimental to retinal tissues. To investigate the whooping crane visual system we used microspectrophotometry to determine the absorbance spectra of retinal oil droplets and to investigate whether the ocular media (i.e. the lens and cornea) absorb UV radiation. In vitro expression and reconstitution was used to determine the absorbance spectra of rod and cone visual pigments. The rod visual pigments had wavelengths of peak absorbance (λmax) at 500 nm, whereas the cone visual pigment λmax values were determined to be 404 nm (SWS1), 450 nm (SWS2), 499 nm (RH2) and 561 nm (LWS), similar to other characterized bird visual pigment absorbance values. The oil droplet cut-off wavelength (λcut) values similarly fell within ranges recorded in other avian species: 576 nm (R-type), 522 nm (Y-type), 506 nm (P-type) and 448 nm (C-type). We confirm that G. americana has a violet-sensitive visual system; however, as a consequence of the λmax of the SWS1 visual pigment (404 nm), it might also have some UV sensitivity.

Opsin evolution in damselfish: convergence, reversal, and parallel evolution across tuning sites.

The visual system plays a role in nearly every aspect of an organism's life history, and there is a direct link between visual pigment phenotypes and opsin genotypes. In previous studies of African cichlid fishes, we found evidence for positive selection among some opsins, with sequence variation greatest for opsins producing the shortest and longest wavelength visual pigments. In this study, we examined opsin evolution in the closely related damselfish family (Pomacentridae), a group of reef fishes that are distributed widely and have a documented fossil record of at least 50 million years (MY). We found increased functional variation in the protein sequences of opsins at the short- and long-wavelength ends of the visual spectrum, in agreement with the African cichlids, despite an order of magnitude difference in the ages of the two radiations. We also reconstructed amino acid substitutions across opsin tuning sites. These reconstructions indicated multiple instances of parallel evolution, at least one definitive case of convergent evolution, and one evolutionary reversal. Our findings show that the amino acids at spectral tuning sites are labile evolutionarily, and that the same codons evolve repeatedly. These findings emphasize that the aquatic light environment can shape opsin sequence evolution. They further show that phylogenetic approaches can provide important insights into the mechanisms by which natural selection "tinkers" with phenotypes.

The eyes have it: regulatory and structural changes both underlie cichlid visual pigment diversity.

A major goal of evolutionary biology is to unravel the molecular genetic mechanisms that underlie functional diversification and adaptation. We investigated how changes in gene regulation and coding sequence contribute to sensory diversification in two replicate radiations of cichlid fishes. In the clear waters of Lake Malawi, differential opsin expression generates diverse visual systems, with sensitivities extending from the ultraviolet to the red regions of the spectrum. These sensitivities fall into three distinct clusters and are correlated with foraging habits. In the turbid waters of Lake Victoria, visual sensitivity is constrained to longer wavelengths, and opsin expression is correlated with ambient light. In addition to regulatory changes, we found that the opsins coding for the shortest- and longest-wavelength visual pigments have elevated numbers of potentially functional substitutions. Thus, we present a model of sensory evolution in which both molecular genetic mechanisms work in concert. Changes in gene expression generate large shifts in visual pigment sensitivity across the collective opsin spectral range, but changes in coding sequence appear to fine-tune visual pigment sensitivity at the short- and long-wavelength ends of this range, where differential opsin expression can no longer extend visual pigment sensitivity.

Parallel evolution of opsin gene expression in African cichlid fishes.

Phenotypic evolution may occur either through alterations to the structure of protein-coding genes or their expression. Evidence for which of these two mechanisms more commonly contribute to the evolution of a phenotype can be garnered from examples of parallel and convergent evolution. The visual system of East African cichlid fishes is an excellent system with which to address this question. Cichlid fishes from Lakes Malawi (LM) and Victoria together exhibit three diverse palettes of coexpressed opsins and several important protein-coding mutations that both shift spectral sensitivity. Here we assess both opsin expression and protein-coding diversity among cichlids from a third rift lake, Lake Tanganyika (LT). We found that Tanganyikan cichlids exhibit three palettes of coexpressed opsins that largely overlap the short-, middle-, and long-wavelength-sensitive palettes of LM cichlids. Bayesian phenotypic clustering and ancestral state reconstructions both support the parallel evolution of the short- and middle-wavelength palettes among cichlids from LT and LM. In each case, these transitions occurred from different ancestors that expressed the same long-wavelength palette. We also identified similar but distinct patterns of correlated evolution between opsin expression, diet, and lens transmittance among cichlids from LT and LM as well. In contrast to regulatory changes, we identified few functional or potentially functional mutations in the protein-coding sequences of three variable opsins, with the possible exception of the SWS1 (ultraviolet) opsin. These results underscore the important contribution that gene regulation can make to rapid phenotypic evolution and adaptation.

Intraspecific cone opsin expression variation in the cichlids of Lake Malawi.

The expression of cone opsin genes is a primary determinant of the characteristics of colour vision. Interspecific variation in opsin expression is common in African cichlids. It is correlated with foraging among cichlids from Lake Malawi, and with ambient light environment among cichlids from Lake Victoria. In this study, we tested whether gene expression varied within species such that it might be important in contributing to divergence. We hypothesized that light attenuation with depth would be correlated with predictable changes in gene expression in Lake Malawi, and that this variation would tune visual sensitivities to match the ambient light environment. We observed significant differences in cone opsin expression in three different comparisons among populations of the same species. Higher LWS expression was found in shallow versus deep Copadichromis eucinostomus. In Metriaclima zebra, individuals from Zimbawe Rock expressed significantly more SWS2B than those from Thumbi West Island, although these locales have similar ambient light environments. Finally, Tropheops gracilior from deeper water had significantly more variation in expression than their shallow counterparts. These results support that gene expression varies significantly between populations of the same species. Surprisingly, these results could not be explained by predicted visual performance as models predicted that differential expression patterns did not confer sensitivity advantages at different depths. This suggested that expression variation did not confer a local sensitivity advantage. Therefore, our findings were contrary to a primary requirement of the sensory bias hypothesis. As such, other explanations for intraspecific gene expression variation need to be tested.

Plasticity of opsin gene expression in cichlids from Lake Malawi.

Sensory systems play crucial roles in survival and reproduction. Therefore, sensory plasticity has important evolutionary implications. In this study, we examined retinal plasticity in five species of cichlid fish from Lake Malawi. We compared the cone opsin expression profiles of wild-caught fish to lab-reared F(1) that had been raised in a UV minus, reduced intensity light environment. All of the opsin genes that were expressed in wild-caught fish were also expressed in lab-reared individuals. However, we found statistically significant differences in relative opsin expression among all five species. The most consistent difference was in the SWS2B (violet) opsin, which was always expressed at higher levels in lab-reared individuals. Estimates of visual pigment quantum catch suggest that this change in expression would increase retinal sensitivity in the light environment of the lab. We also found that the magnitude of plasticity varied across species. These findings have important implications for understanding the genetic regulation of opsin expression and raise many interesting questions about how the cichlid visual system develops. They also suggest that sensory plasticity may have facilitated the ecological diversification of cichlids in Lake Malawi.

Surface-dependent expression in the platelet GPIb binding domain within human von Willebrand factor studied by atomic force microscopy.

Adsorption of plasma proteins such as von Willebrand factor (vWF) on thrombogenic surfaces can induce conformational changes in tertiary structure so that the prothrombotic functional epitopes are exposed for interactions with platelets, resulting in platelet adhesion and thrombus formation. Thus, understanding platelet binding following changes in the structure of vWF is critical in understanding the mechanisms of thrombogenesis. The present study examined the accessibility of platelet binding epitopes within vWF adsorbed on two different thrombogenic surfaces, a hydrophobic synthetic surface and collagen VI coated substrates, under physiological buffer conditions using atomic force microscopy (AFM) in combination with immunogold labeling. Our results demonstrated that the glycoprotein Ib (GPIb) binding domain in vWF undergoes changes when adsorbed on collagen VI compared to vWF on a hydrophobic synthetic surface. This study provides a basis for a novel approach to understand the molecular mechanisms of surface-induced thrombosis by directly examining the structure-function relationships of plasma proteins involved in the thrombus formation.

Using spectral data to reconstruct evolutionary changes in coloration: carotenoid color evolution in New World orioles.

Carotenoid-based colors are thought to play an important signaling role in many animal taxa. However, little is known about evolutionary changes in carotenoid coloration, especially among closely related species. We used a phylogenetic perspective to examine carotenoid color changes within New World orioles (genus Icterus). Oriole color was quantitatively measured using reflectance spectrometry. We found continuous variation from short- to long-wavelength carotenoid colors in extant orioles--perceived by humans as ranging from yellow to scarlet--suggesting that these carotenoid-based colors have evolved as a continuous character. Ancestral state reconstruction suggests that short- and long-wavelength carotenoid colors have evolved independently multiple times, likely from a middle-wavelength ancestor. Although color showed considerable lability, we found a significant amount of phylogenetic signal across the entire genus. This implies that while labile, the colors of closely related taxa tended to resemble each other more than would be expected due to chance. To our knowledge, this is the first study to use quantitative character states derived from reflectance spectra in ancestral state reconstruction. Reflectance spectra provide an unbiased quantitative description of color that allowed us to detect subtle changes among closely related taxa. Using these quantitative methods to score and reconstruct color changes among closely related taxa provides a better understanding of how elaborate animal colors evolve.

Peptide-conjugated glass slides for selective capture and purification of diagnostic cells: Applications in urine cytology.

Obtaining a clear view of the cells of interest in diagnostic cytology can be challenging when specimens are contaminated with blood or other obscuring cells. In this study, we present a powerful technique for the selective capture of diagnostic epithelial cells directly on a microscope slide, highlighting its applications in urine cytology and immunocytochemistry (ICC). Using phage-display biopanning, we identified and synthesized a series of peptides that bind with high affinity to urothelial cells but not blood cells. We developed methods for conjugating the peptides to glass slides, and we used these slides to selectively capture both normal and cancerous epithelial cells from urine contaminated with blood cells. Unlike non-selective microscope slides, the peptide-conjugated slides selectively retained the cells of interest, recovering up to 75% of urothelial cells, while up to 98% of blood cells were washed away. The slides are compatible with Papanicolaou and hematoxylin and eosin (H&E) staining for cytology preparations, as well as ICC for detecting membrane-associated and nuclear cancer markers. We successfully detected the expression of carcinoembryonic antigen and survivin, two commonly measured bladder cancer markers. In addition to bladder cancer diagnostics, this technology has broad applications for increasing the quality of sample preparations in slide-based diagnostic testing.

Targeted delivery of vancomycin to Staphylococcus epidermidis biofilms using a fibrinogen-derived peptide.

This study reports on the use of a fibrinogen-derived peptide for the specific targeting and delivery of vancomycin to Staphylococcus epidermidis biofilms. One method by which S. epidermidis initially adheres to biomaterials uses the plasma protein fibrinogen as an intermediary, where the S. epidermidis surface protein SdrG binds to a short amino acid sequence near the amino terminus of the Bß chain of fibrinogen. We mimicked this binding interaction and demonstrated the use of a synthetic fibrinogen-based ß6-20 peptide to target and deliver vancomycin to S. epidermidis in vitro. The ß6-20 peptide was synthesized and labeled with a Nanogold probe, and its targeting capabilities were examined through the use of scanning electron microscopy. The Nanogold component was then replaced by vancomycin, utilizing a flexible, variable length poly(ethylene glycol) linker between the peptide and antibiotic to create the targeted vancomycin products, ß6-20-PEG(x) -VAN. Initial binding to surface adherent S. epidermidis was increased in a concentration-dependent manner relative to vancomycin for all equivalent concentrations ≥4 µg/mL, with targeted vancomycin content up to 22.9 times that of vancomycin alone. Retention of the targeted antibiotics was measured after an additional 24-h incubation period, revealing levels 1.3 times that of vancomycin. The results demonstrate the improved targeting and retention of vancomycin within a biofilm due to the incorporation of a specific targeting motif.

Disruption of Staphylococcus epidermidis biofilm formation using a targeted cationic peptide.

This study reports the use of a targeted cationic peptide with the ability to disrupt Staphylococcus epidermidis biofilm formation. Complications due to nosocomial infections of implanted medical devices pose a significant health risk to patients, with Staphylococcus epidermidis often implicated in the case of blood-contacting biomaterials. S. epidermidis virulence relies mainly on its ability to form a biofilm, the main component of which is polysaccharide intercellular adhesin (PIA). We utilized the synthetic ß6-20 peptide, known to specifically bind S. epidermidis, in order to deliver a cationic polylysine peptide (G(3)K(6)) to the bacterial surface and disrupt the charge-charge interactions needed for PIA retention and biofilm stability. The effects of the ß6-20-G(3)K(6) peptide on biofilm formation were assessed using optical density, fluorescently labeled wheat germ agglutinin, nucleic acid stain (SYTO 9), and a metabolic assay (XTT, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt). Biofilms formed in the presence of ß6-20-G(3)K(6) peptide (100 µM) resulted in a 37.9% reduction in PIA content and a 17.5% reduction of adherent bacteria relative to biofilms grown in the absence of peptide. These studies demonstrate the targeting ability of the ß6-20 peptide towards biomaterial-adherent S. epidermidis, and highlight the potential for disrupting the early stages of biofilm formation.

The relationship between lens transmission and opsin gene expression in cichlids from Lake Malawi.

The lens plays an important role in regulating the wavelengths of light that reach the retina. However, the evolutionary relationship between lens transmission and retinal sensitivity remains cloudy at best. We examined the relationship between lens transmission and opsin gene expression in a group of rapidly radiating cichlids from East Africa. Lens transmission was bimodal, either cutting off around 360 or 400 nm, and appeared to be quite labile evolutionarily. We found a strong correlation between lens transmission and SWS1 (UV) opsin gene expression, suggesting that UV transmitting lenses are adaptive in cichlids. Species which expressed high levels of SWS2B (violet) opsin varied in their lens transmission while most species that expressed high levels of SWS2A (blue) opsin had UV blocking lenses. In no instance did lens transmission appear to limit retinal sensitivity. Finally, the strong correlation that we observe between SWS1 expression and lens transmission suggests that these two traits might be coupled genetically.

Gene duplication and differential gene expression play an important role in the diversification of visual pigments in fish.

Sensory systems provide crucial information about an organism's external environment and, thus, are often subject to strong natural selection. Because of the large variation in the intensity and spectral quality of light in aquatic environments, studies of sensory adaptation have focused on the visual systems of fish for over a half a century. Recently, the molecular genetic mechanisms that determine the spectral sensitivity of visual pigments have been characterized in several fishes including zebrafish, guppies, medaka, killifish, bream, and cichlids. The results of these studies suggest that teleost fish have incredibly diverse visual systems. In this paper, we review the role that opsin duplication and differential gene expression have played in the diversification of visual pigments. We compare our findings in cichlids to five other taxonomic groups and highlight the ways that their similarities and differences may provide new insights into the molecular genetic basis of sensory adaptation and diversification.

Correlated evolution of migration and sexual dichromatism in the New World orioles (icterus).

The evolution of sexual dimorphism has long been attributed to sexual selection, specifically as it would drive repeated gains of elaborate male traits. In contrast to this pattern, New World oriole species all exhibit elaborate male plumage, and the repeated gains of sexual dichromatism observed in the genus are due to losses of female elaboration. Interestingly, most sexually dichromatic orioles belong to migratory or temperate-breeding clades. Using character scoring and ancestral state reconstructions from two recent studies in Icterus, we tested a hypothesis of correlated evolution between migration and sexual dichromatism. We employed two discrete phylogenetic comparative approaches: the concentrated changes test and Pagel's discrete likelihood test. Our results show that the evolution of these traits is significantly correlated (CCT: uncorrected P < 0.05; ML: LRT = 12.470, P < 0.005). Indeed, our best model of character evolution suggests that gains of sexual dichromatism are 23 times more likely to occur in migratory taxa. This study demonstrates that a life-history trait with no direct relationship with sexual selection has a strong influence on the evolution of sexual dichromatism. We recommend that researchers further investigate the role of selection on elaborate female traits in the evolution of sexual dimorphism.