Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs

BACKGROUND

Differences in morphology, ecology, and behavior through ontogeny can result in opposing selective pressures at different life stages. Most animals, however, transition through two or more distinct phenotypic phases, which is hypothesized to allow each life stage to adapt more freely to its ecological niche. How this applies to sensory systems, and in particular how sensory systems adapt across life stages at the molecular level, is not well understood. Here, we used whole-eye transcriptomes to investigate differences in gene expression between tadpole and juvenile southern leopard frogs (Lithobates sphenocephalus), which rely on vision in aquatic and terrestrial light environments, respectively. Because visual physiology changes with light levels, we also tested the effect of light and dark exposure.

RESULTS

We found 42% of genes were differentially expressed in the eyes of tadpoles versus juveniles and 5% for light/dark exposure. Analyses targeting a curated subset of visual genes revealed significant differential expression of genes that control aspects of visual function and development, including spectral sensitivity and lens composition. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results, consistent with adaptation to distinct light environments.

CONCLUSIONS

Overall, we identified extensive expression-level differences in the eyes of tadpoles and juveniles related to observed morphological and physiological changes through metamorphosis and corresponding adaptive shifts to improve vision in the distinct aquatic and terrestrial light environments these frogs inhabit during their life cycle. More broadly, these results suggest that decoupling of gene expression can mediate the opposing selection pressures experienced by organisms with complex life cycles that inhabit different environmental conditions throughout ontogeny.

Enhancing the evidential value of textile fibres Part 2: Application of a database-driven fibre comparison strategy to a cold-case investigation

This paper describes the involvement of our laboratory in a Western Australian 'cold-case' investigation that spanned 24 years. The investigation was widely considered to be the largest in Australian history. During the investigative phase, our laboratory was tasked with the collection of trace evidence of all types in connection with a sexual assault and two homicides that were suspected to be related. Textile fibres represented the vast majority of trace evidence recovered. A much greater quantity of fibres (>10,800) was collected than would be typical for a routine case, as fibres of any colour or type were potentially of investigative value. The investigation was unprecedented in its scale, and presented numerous challenges in terms of evidence recovery, analysis, interpretation, reporting, and provision of testimony. A textile fibre microspectrophotometric (MSP) database was developed specifically for the interpretation of data in connection with the investigation. The database currently contains over 25,000 normalised and first derivative spectra of casework, validation and reference textile fibres. A fibre comparison strategy was devised, involving the identification of preliminary fibre groups on the basis of corresponding/similar MSP spectra, and verification of these groups via brightfield and fluorescence comparison microscopy. A potential link to an automotive source was identified for one of the homicide victims during the investigative phase. After identification of a suspect, a total of 98 fibres recovered from victims and from a seized motor vehicle were found to correspond in properties to six different fibre types from known textile sources in connection with the suspect. A highly publicised criminal trial was held, and textile fibre evidence provided a major contribution to the trial findings, in which the accused was found guilty of two homicides.

Prediction of iron content in soil based on microspectrophotometry analysis

Soil is a very important type of trace evidence. The iron content of soil is of great significance in distinguishing soil types, discriminating among different soils, and tracing soils. However, conventional methods for analyzing the iron content of soil are expensive, laborious, and time-consuming. Previous studies have shown that the color of soil correlates well with its hematite content. This article thus deals with the indirect determination of iron content using soil color as a proxy. Soil color measurements were conducted using microspectrophotometry (MSP), and resulting data were transformed into chromaticity value (L*, a*, and b*). Predictions using the redness index in conjunction with a linear regression model were compared with those using the chromaticity value and a back propagation neural network (BPNN) model. The influences of different modeling conditions on the modeling accuracy were compared, and more accurate predictions were achieved when the iron content was higher than 2.13%. The BPNN model produced predictions with R² and RMSE values of 0.955 and 0.336%, which were better than the predictions of the linear regression model (R²: 0.859, RMSE, 1.07%). We thus demonstrated that MSP can be used for fast, accurate, and non-destructive measurements of soil color and prediction of its iron content. Although the results may not be as precise as conventional laboratory analysis, they still provide more information with acceptable accuracy, which should have promising applications in forensic applications.

The evaluation of evidence for microspectrophotometry data using functional data analysis

Microspectrophotometry data arise in the study of many forensically applicable situations. The situations here are those of ink and fibres. In a criminal investigation, data associated with a crime scene are compared with data associated with a person of interest. Methods based on the likelihood ratio are often used to evaluate such evidence. A technique known as functional data analysis for determining likelihood ratios using the full spectrum is described. It provides support comparing a proposition of common source with a proposition of different sources for data from the crime scene and from the person of interest. Data are available from ink, woollen and cotton fibres. The effectiveness of the method is assessed using false positive and false negative rates and Tippett plots in the comparison of data from known sources.

Vision in the snapping shrimp Alpheus heterochaelis

Snapping shrimp engage in heterospecific behavioral associations in which their partners, such as goby fish, help them avoid predators. It has been argued that snapping shrimp engage in these partnerships because their vision is impaired by their orbital hood, an extension of their carapace that covers their eyes. To examine this idea, we assessed the visual abilities of snapping shrimp. We found the big claw snapping shrimp, Alpheus heterochaelis, has spatial vision provided by compound eyes with reflecting superposition optics. These eyes view the world through an orbital hood that is 80-90% as transparent as seawater across visible wavelengths (400-700 nm). Through electroretinography and microspectrophotometry, we found the eyes of A. heterochaelis have a temporal sampling rate of >40 Hz and have at least two spectral classes of photoreceptors (λ_max=500 and 519 nm). From the results of optomotor behavioral experiments, we estimate the eyes of A. heterochaelis provide spatial vision with an angular resolution of ∼8 deg. We conclude that snapping shrimp have competent visual systems, suggesting the function and evolution of their behavioral associations should be re-assessed and that these animals may communicate visually with conspecifics and heterospecific partners.

Contribution of Human Hair in Solar UV Transmission in Skin: Implications for Melanoma Development

Melanoma is the deadliest type of skin cancer with its prevalence on the rise. Recently, the melanocyte stem cells in hair follicles have been identified as the possible origin of melanoma upon exposure to ultraviolet radiation (UVR) through skin. It is hypothesized that colourless vellus hair (predominant in childhood) can serve as an alternative pathway in transmitting these ultraviolet (UV) photons to the stem cells. To investigate this, we have used the CRAIC microspectrophotometer to investigate the optical properties of 'vellus-like' hairs and terminal hairs of different colours using UV-VIS-NIR light sources. It was found that the average attenuation coefficient of 'vellus-like' hair is significantly lower than that of terminal hair in the UVA (p < 0.0001) and UVB (p < 0.001) wavelength ranges. Next, the optical properties of hairs are applied to simulations for examining their influence on UV transmission into the skin. The results show that the presence of vellus hair would increase the solar UV transmission to the melanocyte stem cell layer significantly. The findings explain why children are particularly vulnerable to sun exposure and the positive correlation found between the incidence of melanoma in adults' bodies and the number of vellus hairs in these areas.

Extraneous fibre traces brought by river water - A case study

The fibre traces on a young victim found underwater were mostly single fibre traces besides small amounts of fibre collectives indistinguishable from his parents clothes (mainly wool). Most of those single fibre traces were blue-grey polyester fibres showing tiny differences among each other. They were unexpected according to known population fibre studies. One year after the victim's discovery experiments were conducted to evaluate the possible contamination with fibres from river water. A small amount of extraneous fibres were collected among which blue and grey-black cotton and man-made (mainly polyester) fibres. All man-made fibres were single fibre traces and small fibre collectives were only observed for cotton. These results confirmed the frequent occurrence of blue and grey-black cotton fibres as background, but also highlighted the possible contamination with single blue and grey-black man-made fibres from river water. No wool was found, strengthening the significance of the wool fibre collectives present on the victim.

Brilliant iridescence of Morpho butterfly wing scales is due to both a thin film lower lamina and a multilayered upper lamina

Butterflies belonging to the nymphalid subfamily, Morphinae, are famous for their brilliant blue wing coloration and iridescence. These striking optical phenomena are commonly explained as to originate from multilayer reflections by the ridges of the wing scales. Because the lower lamina of the scales of related nymphalid butterflies, the Nymphalinae, plays a dominant role in the wing coloration, by acting as a thin film reflector, we investigated single blue scales of three characteristic Morpho species: M. epistrophus, M. helenor and M. cypris. The experimental data obtained by spectrophotometry, scatterometry and scanning electron microscopy demonstrated that also in the Morpho genus the lower lamina of both the cover and ground scales acts as an optical thin film reflector, contributing importantly to the blue structural coloration of the wings. Melanin pigment has a contrast-enhancing function in a sub-class of ground scales.

Fluorescence characterisation and visual ecology of pseudocheilinid wrasses

BACKGROUND

Wrasses represent the second largest family of marine fishes and display a high diversity of complex colours linked to ecological functions. Recently, red autofluorescent body colouration has been reported in some of these fishes. However, little is known about the distribution of such fluorescent body patterns in wrasses or the animals' ability to perceive such colours.

RESULTS

Against this background, we (1) investigated long-wavelength emission autofluorescence in thirteen species of pseudocheilinid wrasses and (2) characterised the spectral absorbance of visual pigments in one of the examined species, the fairy wrasse Cirrhilabrus solorensis. Spectrophotometric analysis revealed that fluorescent body colouration is widespread and diverse within this clade, with considerable variation in both fluorescent pattern and maximum emission wavelength between species. Characterisation of visual pigments in retinal photoreceptors showed a single class of rod and three spectrally distinct cone photoreceptors, suggesting possible trichromacy.

CONCLUSION

Combining the emission characteristics of fluorescence body colouration and the spectral sensitivity data of retinal cells suggests that the visual system of C. solorensis is sensitive to pseudocheilinid fluorescence.

Spectral absorption of visual pigments in stomatopod larval photoreceptors

Larval stomatopod eyes appear to be much simpler versions of adult compound eyes, lacking most of the visual pigment diversity and photoreceptor specializations. Our understanding of the visual pigment diversity of larval stomatopods, however, is based on four species, which severely limits our understanding of stomatopod eye ontogeny. To investigate several poorly understood aspects of stomatopod larval eye function, we tested two hypotheses surrounding the spectral absorption of larval visual pigments. First, we examined a broad range of species to determine if stomatopod larvae generally express a single, spectral class of photoreceptor. Using microspectrophotometry (MSP) on larvae captured in the field, we found data which further support this long-standing hypothesis. MSP was also used to test whether larval species from the same geographical region express visual pigments with similar absorption spectra. Interestingly, despite occupation of the same geographical location, we did not find evidence to support our second hypothesis. Rather, there was significant variation in visual pigment absorption spectra among sympatric species. These data are important to further our understanding of larval photoreceptor spectral diversity, which is beneficial to ongoing investigations into the ontogeny, physiology, and molecular evolution of stomatopod eyes.

The analysis of colored acrylic, cotton, and wool textile fibers using micro-Raman spectroscopy. Part 2: comparison with the traditional methods of fiber examination

In the second part of this survey, the ability of micro-Raman spectroscopy to discriminate 180 fiber samples of blue, black, and red cottons, wools, and acrylics was compared to that gathered with the traditional methods for the examination of textile fibers in a forensic context (including light microscopy methods, UV-vis microspectrophotometry and thin-layer chromatography). This study shows that the Raman technique plays a complementary and useful role to obtain further discriminations after the application of light microscopy methods and UV-vis microspectrophotometry and assure the nondestructive nature of the analytical sequence. These additional discriminations were observed despite the lower discriminating powers of Raman data considered individually, compared to those of light microscopy and UV-vis MSP. This study also confirms that an instrument equipped with several laser lines is necessary for an efficient use as applied to the examination of textile fibers in a forensic setting.

Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins

In the last decade, protein allostery has experienced a major resurgence, boosted by the extension of the concept to systems of increasing complexity and by its exploitation for the development of drugs. Expansion of the field into new directions has not diminished the key role of hemoglobin as a test molecule for theory and experimental validation of allosteric models. Indeed, the diffusion of hemoglobins in all kingdoms of life and the variety of functions and of quaternary assemblies based on a common tertiary fold indicate that this superfamily of proteins is ideally suited for investigating the physical and molecular basis of allostery and firmly maintains its role as a main player in the field. This review is an attempt to briefly recollect common and different strategies adopted by metazoan hemoglobins, from monomeric molecules to giant complexes, exploiting homotropic and heterotropic allostery to increase their functional dynamic range. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

Role of tertiary structures on the Root effect in fish hemoglobins

Many fish hemoglobins exhibit a marked dependence of oxygen affinity and cooperativity on proton concentration, called Root effect. Both tertiary and quaternary effects have been evoked to explain the allosteric regulation brought about by protons in fish hemoglobins. However, no general rules have emerged so far. We carried out a complementary crystallographic and microspectroscopic characterization of ligand binding to crystals of deoxy-hemoglobin from the Antarctic fish Trematomus bernacchii (HbTb) at pH6.2 and pH8.4. At low pH ligation has negligible structural effects, correlating with low affinity and absence of cooperativity in oxygen binding. At high pH, ligation causes significant changes at the tertiary structural level, while preserving structural markers of the T state. These changes mainly consist in a marked displacement of the position of the switch region CD corner towards an R-like position. The functional data on T-state crystals validate the relevance of the crystallographic observations, revealing that, differently from mammalian Hbs, in HbTb a significant degree of cooperativity in oxygen binding is due to tertiary conformational changes, in the absence of the T-R quaternary transition. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.