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For many species, vision contributes to a number of fitness-related tasks, including mating and the detection of prey and predators. Selection on the visual system should therefore be strong, especially when ecological or genomic changes open new avenues for evolutionary changes. Visual system proteins are thus attractive systems for molecular evolutionary analyses. This thesis presents a collection of evolutionary studies on two gene families, opsins and crystallins. Opsin proteins determine the wavelengths of light detected by the retina, while crystallin proteins contribute to lens transparency and refractory power. My studies focus on teleost fishes, because teleost visual ecology is exceptionally diverse and because gene duplication is common in this group. In Chapter One, I outline the relevance of protein variation to organismal evolution and describe the analytical methods employed throughout this thesis. Chapter Two considers the long-wavelength sensitive (LWS) opsins of the guppy (Poecilia reticulata). The guppy is shown to possess multiple LWS opsins that have accumulated differences at functionally important amino acid sites since duplicating. Chapter Three focuses on the guppy’s main predator, the pike cichlid Crenicichla frenata, which is shown to have a greater capacity for short-wavelength vision than previously believed. However, this cichlid possesses three fewer opsins than closely-related African cichlids, a difference partly due to duplication of a green-sensitive (RH2) opsin in African cichlids. In Chapter Four, this RH2 duplication event is studied in greater depth; variation in selective constraint is documented following gene duplication and between species from different lakes. Some of the analytical methods employed in Chapter Four were newly developed, as detailed in Chapter Five, where a test for functional divergence among clades is evaluated and then improved upon through the presentation of a new null model that better accommodates among-site variation in selection. In Chapter Six, phylogenetic relationships within the βγ lens crystallin superfamily are clarified, and the functionally distinct γN family is shown to have evolved conservatively compared to other crystallin families. The thesis concludes with suggestions for future directions for evolutionary research on opsins and crystallins, and summarizes recent work that has built on these studies.

For many species, vision contributes to a number of fitness-related tasks, including mating and the detection of prey and predators. Selection on the visual system should therefore be strong, especially when ecological or genomic changes open new avenues for evolutionary changes. Visual system proteins are thus attractive systems for molecular evolutionary analyses. This thesis presents a collection of evolutionary studies on two gene families, opsins and crystallins. Opsin proteins determine the wavelengths of light detected by the retina, while crystallin proteins contribute to lens transparency and refractory power. My studies focus on teleost fishes, because teleost visual ecology is exceptionally diverse and because gene duplication is common in this group. In Chapter One, I outline the relevance of protein variation to organismal evolution and describe the analytical methods employed throughout this thesis. Chapter Two considers the long-wavelength sensitive (LWS) opsins of the guppy (Poecilia reticulata). The guppy is shown to possess multiple LWS opsins that have accumulated differences at functionally important amino acid sites since duplicating. Chapter Three focuses on the guppy’s main predator, the pike cichlid Crenicichla frenata, which is shown to have a greater capacity for short-wavelength vision than previously believed. However, this cichlid possesses three fewer opsins than closely-related African cichlids, a difference partly due to duplication of a green-sensitive (RH2) opsin in African cichlids. In Chapter Four, this RH2 duplication event is studied in greater depth; variation in selective constraint is documented following gene duplication and between species from different lakes. Some of the analytical methods employed in Chapter Four were newly developed, as detailed in Chapter Five, where a test for functional divergence among clades is evaluated and then improved upon through the presentation of a new null model that better accommodates among-site variation in selection. In Chapter Six, phylogenetic relationships within the βγ lens crystallin superfamily are clarified, and the functionally distinct γN family is shown to have evolved conservatively compared to other crystallin families. The thesis concludes with suggestions for future directions for evolutionary research on opsins and crystallins, and summarizes recent work that has built on these studies.

Guppies exhibit color based sexual dimorphism and females generally prefer the most colorful males. It has also recently been found that guppies possess a large opsin repertoire. As opsins are the receptors responsible for color vision, this ten gene repertoire might have contributed to the evolution of extravagant male coloration in this species. My study starts by characterizing the opsin repertoire of Jenynsia onca, a noncolorful relative of the guppy belonging to the family Anablepidae (sister group to Poeciliidae, of which the guppy is a member). A PCR based survey indicated that J. onca had a very similar opsin repertoire to the guppy; J. onca had nine genes including orthologs of all but one of the guppy opsins. To gain further insight into the origin of the guppy repertoire, a bioinformatics based survey of ray-finned fish opsins was undertaken. This revealed that large opsin repertoires are common in ray-finned fish and are the product of gene duplication events, spanning the age of the taxon Teleostei. Given that the large opsin repertoire of the guppy did not appear to be perfectly correlated with the evolution of color based sexual selection in this lineage, I turned to investigating the expression of this opsin repertoire. In situ hybridization was used to characterize the pattern of opsin expression across the surface of the retina of adult male and female guppies. In situ hybridization demonstrated that most opsin genes had distinct expression profiles. These expression patterns also indicated that sensitivity and discrimination in the dorsal retina might differ from the ventral retina; the ventral retina appears to be tuned to middle-wavelength light (green), while the dorsal retina is predicted to have exceptional wavelength discriminatory ability and broad spectral sensitivity. This expression data was then used to evaluate models of sexual selection in the context of the predicted visual capacity of the guppy. / Graduate

In the 1980s, it was widely accepted that new neurons are continuously generated in the dentate gyrus of the mammalian hippocampus. Since its acceptance, researchers have employed various techniques and behavioral paradigms to study the proliferation, differentiation, and functional role of adult-born neurons. This literature thesis aims to discuss how optogenetics is able to overcome the limitations of past techniques and provide the field with new insights into the functional role of neurogenesis. We will review the current knowledge on both adult hippocampal neurogenesis and optogenetics, present representative studies using optogenetics to investigate neurogenesis and discuss potential limitations and concerns involved in using optogenetics.

The positive effect of photobiomodulation in wound healing has previously been reported, however there is a considerable lack of knowledge regarding the molecular mechanisms involved, and no consensus on light parameters. Cytochrome c oxidase (CCO) is established as the main photoreceptor in cells, but light also induces nitric oxide (NO), production of reactive oxygen species (ROS) and activation of ion channels. Emerging new molecular targets include the GPCRs opsins (OPNs) and the circadian clock transcription factors, cryptochromes (CRYs). Localisation of OPN1-SW, OPN3, OPN5, CRY1 and CRY2 was seen in female facial and abdominal human skin. Furthermore, expression of these photoreceptors was retained in primary epidermal keratinocytes and dermal fibroblasts in culture; both cell types expressed OPN1-SW, OPN3, CRY1 and CRY2, at the mRNA and protein level. OPN2 was only expressed in cultured dermal fibroblasts, while in line with in situ expression, OPN5 was only expressed in cultured keratinocytes. The photoreceptor-expressing cultured epidermal keratinocytes demonstrated a dose- and wavelength- dependent response in both metabolic activity and cell migration in a scratch-wound assay. Specifically, low dose (2 J/cm2) blue light (447 nm) increased metabolic activity, but it did not impact keratinocyte migration. In contrast, high dose (30 J/cm2) blue light had no effect on metabolism, but inhibited migration of epidermal keratinocytes. Red light (655 nm) at 30 J/cm2 stimulated metabolic activity but did not modulate migration, while a higher dose of 60 J/cm2 had no effect on keratinocyte metabolic activity. In order to study OPN3 and CRY1 function, they were silenced in keratinocytes using siRNA; additionally 8 μM KL001 was used to stabilize CRY1. KL001 inhibited migration, and induced KRT1 and KRT10, an effect which was abrogated by knockdown of OPN3. Interestingly, knockdown of OPN3 upregulated CRY1 expression, while KL001 upregulated OPN3 expression, indicating a regulation by OPN3 of the molecular epidermal clock. Low levels of blue light increased early differentiation of epidermal keratinocytes, which was mediated by OPN3 and circadian clock mechanisms. However, low levels of blue light decreased keratinocyte DNA synthesis, which was mediated by circadian clock independently of OPN3. Translation of parameters ex vivo showed increasing re-epithelialisation and induction of OPN3 and CRY1 expression following exposure to 2 J/cm2 of blue light; however high doses of blue light inhibited re-epithelialisation. Red light, also increased re-epithelialisation, but had no effect on OPN3 or CRY1 expression. In conclusion, photoreceptors are expressed in human skin and they mediate DNA synthesis, migration and differentiation of epidermal keratinocytes. Furthermore, low dose of blue light interacts with OPN3 to induce epidermal differentiation, through the regulation of the circadian clock. A better understanding of the molecular mechanisms behind the photobiomodulation response in vitro will help to develop light based therapies for human wound healing. Interestingly, selected light parameters translated to human ex vivo skin showed a beneficial effect of low doses of blue (2 J/cm2) and red (30 J/cm2) light in re-epithelialisation. / Marie Curie ... the CLaSSiC project

yes / Photobiomodulation is reported to positively influence hair regrowth, wound healing, skin rejuvenation, and psoriasis. Despite rapid translation of this science to commercial therapeutic solutions, significant gaps in our understanding of the underlying processes remain. The aim of this review was to seek greater clarity and rationality specifically for the selection of optical parameters for studies on hair regrowth and wound healing. Our investigation of 90 reports published between 1985-2015 revealed major inconsistencies in optical parameters selected for clinical applications. Moreover, poorly understood photoreceptors expressed in skin such as cytochrome c oxidase, cryptochromes, opsins, may trigger different molecular mechanisms. All this could explain the plethora of reported physiological effects of light. To derive parameters for optimal clinical efficacy of photobiomodulation, we recommend a more rational approach, underpinning clinical studies with research of molecular targets and pathways using well-defined biological model systems enabling easy translation of optical parameters from in vitro to in vivo. Furthermore, special attention needs to be paid when conducting studies for hair regrowth, aiming for double-blind, placebo-controlled randomized clinical trials as the gold standard for quantifying hair growth. / European Marie-Curie Actions Programme, Grant agreement no.: 607886

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Serpentes habitam grande diversidade de habitats na maior parte do planeta. Tamanha variedade ambiental implica o desempenho de distintos nichos ecológicos e padrões comportamentais, muitas vezes relacionados a diferentes adaptações de seus sistemas visuais. Não apenas a dispersão destes animais oferece oportunidades privilegiadas de investigação, os diversos e particulares históricos evolutivos neste grupo demarcam transições ambientais convenientes para esclarecer a influência da cena visual sobre a organização de sistemas visuais, comportamentos e a filogenia. A análise comparativa da retina destes animais traz informações a respeito de adaptações comportamentais e ecológicas relativas ao ambiente e padrões circadianos de atividade. Neste trabalho foi realizada a análise dos genes de fotopigmentos visuais e da morfologia dos fotorreceptores de duas espécies de serpentes da família Viperidae, Bothrops jararaca e Crotalus durissus terrificus. Três indivíduos de cada espécie foram obtidos junto ao laboratório de Herpetologia do Instituto Butantan. O RNA total foi extraído a partir de retinas homogeneizadas e convertido em cDNA por meio da reação de transcriptase reversa. Os genes de interesse foram amplificados com uso de primers específicos por meio de reação em cadeia de polimerase (PCR). Após purificação dos produtos de PCR foi realizado o sequenciamento dos genes de opsinas visuais expressos nas retinas das duas espécies, lws, rh1 e sws1. Cada opsina, maximamente sensível a uma banda espectral específica e presente em diferentes populações de fotorreceptores da retina, teve o seu pico de absorção estimado com base na estrutura proteica revelada. Adicionalmente, foi conduzida análise dos tipos celulares de células fotorreceptoras da retina das duas espécies de viperídeos, por meio da técnica de imunohistoquímica, visando caracterização morfológica dos fotorreceptores em que estão compreendidas cada classe de opsina. Os resultados obtidos apontam para os mesmos grupos morfológicos de fotorreceptores e a mesma sensibilidade espectral dos respectivos pigmentos visuais, das duas espécies analisadas: cones simples e cones duplos com o fotopigmento LWS, e pico de sensibilidade espectral (max) estimado em ~555nm; cones simples com o fotopigmento SWS1, e max estimado em ~360nm; e bastonetes, com o fotopigmento RH1, com max de ~500nm. Desta forma conclui-se similaridade do nicho ecológico e do histórico natural das duas espécies, que apontam para adaptações ao habito noturno. Isto demonstra o sucesso evolutivo e a versatilidade proporcionada pela disposição de retina duplex dominada por bastonetes. Em B. jararaca e C. d. terrificus, serpentes da subfamília Crotalinae, estas características de organização do sistema visual são somadas à capacidade de detecção de comprimentos de onda infravermelhos, o que aponta para similaridades em relação a serpentes do grupo Henophidia, consideradas evolutivamente mais primitivas, e consagra novamente a vantagens obtidas na manutenção deste padrão sensorial / Serpents inhabit a great diversity of habitats around the planet. Such environmental variability implies the performance of distinct ecological niches and behavior patterns that are related to different visual system adaptations. The diversity of environments inhabited by snakes and their evolutionary history provides a privileged investigative opportunity on the adaptive organization of the visual systems, specific behaviors and phylogeny. The comparative analysis of the retina of those animals provide many information concerning behavior and ecological adaptations related to their respective environment and circadian rhythm patterns. In this study, we performed genetic analysis of the opsin genes and morphological analysis of the photoreceptors of two snakes from the Viperidae family, Bothrops jararaca and Crotalus durissus terrificus. Three subjects of each species were collected at the Butantan Institute. Total RNA was extracted from homogenized retinas, and mRNA was converted to cDNA by reverse transcriptase reaction. The opsin genes lws, rh1 and sws1 were amplified by polymerase chain reactions (PCR), using specific primers. Each opsin is expressed in a different photoreceptor population and is maximally responsive to a determined spectral absorption peak (max) that was inferred according to the protein structure. Additionally, photorreceptor cell populations were analyzed using immunohistochemistry technique. Results point out to the same morphological cell populations and the same absorption peak in their respective opsins in the two species: double and single cones with the LWS photopigment and estimated max at ~555nm; single cones with the SWS1 photopigment and max at ~360nm; and rods with the rhodopsin RH1 photopigment and max at ~500nm. In this way, great similarity of ecological niche and natural history was concluded for both species, which present adaptations to the nocturnal habit. This should demonstrate the great evolutionary success and versatility attained by the rod-domminated duplex retina. In B. jararaca and C. d. terrificus, snakes from the Crotalinae subfamily, those retinal features are summed to the capability of infra-red detection, which point out to similarity with snakes from the basal Henophidia group

A visão de cores em vertebrados necessita de pelo menos duas classes de cones, (fotorreceptores presentes na retina) e a existência de um substrato neural para que os fótons de luz sejam comparados, processados e posteriormente resultar na sensação da cor. Primatas do Velho Mundo, incluindo humanos, apresentam visão de cor tricromata, enquanto que primatas do Novo Mundo apresentam um polimorfismo nos genes dos pigmentos visuais e, entre os primatas, são os únicos que podem apresentar indivíduos com visão dicromata ou tricromata. O polimorfismo encontrado em primatas do Novo Mundo ocorre devido à variabilidade dos genes que expressam as opsinas responsáveis por absorver comprimentos de onda médios ou longos. Os estudos genéticos das opsinas são essenciais para compreensão do processamento e da sensação de cores nesses animais, e podem ajudar a entender a evolução da visão de cores nos Primatas. O objetivo deste trabalho é caracterizar a diversidade dos pigmentos visuais (LWS/MWS e SWS1) das espécies de primatas do Novo Mundo através de análises genéticas e descrever a sequência de aminoácidos observados para estimar o pico de sensibilidade espectral das opsinas. Foram coletadas amostras de sangue, fezes e/ou pelo de seis gêneros de primatas provenientes de diferentes regiões do Brasil (Pará, Rio de Janeiro, Rio Grande do Norte e São Paulo) e pertencentes às espécies Cebus apella, Callithrix jacchus, Alouatta clamitans, Alouatta caraya, Lagothrix lagothricha, Ateles belzebuth e Brachyteles arachnoides e posteriormente foram analisados os genes que expressam as opsinas nesses indivíduos. As sequências de aminoácidos encontradas nas posições importantes do gene SWS1 (52, 86, 93, 114 e 118) foram diferentes para algumas espécies. No gene SWS1 as espécies C. apella, L. lagotricha, A. belzebuth e B. arachnoides apresentam a sequência de aminoácidos LLPAT e as espécies C. jacchus, A. caraya e A. clamitans apresentaram a sequência de aminoácidos LLPGT. Foi descoberto que variações de aminoácidos na posição 50 do gene SWS1 em primatas do Novo Mundo podem ser importantes na determinação do pico de absorção espectral dos pigmentos expressos por este gene. Os genes LWS e MWS de indivíduos da espécie C. jacchus foram estudados e os aminoácidos localizados nas posições 180, 277 e 285 das opsinas foram identificados. Os resultados dos alelos encontrados nesses grupos tiveram cinco combinações diferentes (SFT, SYA, SYT, AYA e AYT), os alelos AYA e SYA foram descritos pela primeira vez neste grupo e a partir do resultado genético foi inferido o pico de absorção espectral da opsina. Este trabalho preencheu algumas lacunas da bibliografia e trouxe novas informações a respeito da diversidade genética dos pigmentos visuais em primatas do Novo Mundo / Color vision in vertebrates requires the presence of at least two different classes of cones in the retina, and a neural substrate capable to compare the activation of the different photoreceptors, which ultimately leads to color perception. Old World Monkeys (OWM), including humans, have trichromatic color vision, whereas New World Monkeys (NWM) have visual pigment genes polymorphism and among primates, are the only group with dichromatic or trichromatic individuals in the same species. This polymorphism in NWM occurs due to the variability of genes that express the opsins responsible for absorbing medium or long wavelengths. The genetic studies of color vision are fundamental for the comprehension of color perception in these animals and it could help to understand the color vision evolution in Primates. The aim of this work is to characterize the visual pigment diversity (LWS/MWS and SWS1) in NWM species by genetic analysis and estimate the opsin spectral absorption peak, based on the amino acid sequence. Blood, feces and hair were collected from six primate genres from different regions of Brazil (Pará, Rio de Janeiro, Rio Grande do Norte and São Paulo): Cebus apella, Callithrix jacchus, Alouatta clamitans, Alouatta caraya, Lagothrix lagothricha, Ateles belzebuth and Brachyteles arachnoides. The amino acid sequences found in important positions of the SWS1 gene (52, 86, 93, 114 and 118) were different among some species. In C. apella, L. lagotricha, A. belzebuth and B. arachnoides was found the amino acid sequence LLPAT. In C. jacchus, A. caraya and A. clamitans the amino acid sequence was LLPGT. It was observed in previous studies that residue 50 of the SWS1 gene in the New World primates is important to determining the spectral absorption peak of the visual pigments expressed by this gene. The LWS and MWS genes of C. jacchus have been studied and the amino acids located at positions 180, 277 and 285 have been identified. Five different combinations were found among the individuals analyzed: SFT, SYA, SYT, AYA and AYT. Two alleles, AYA and SYA, were described for the first time in this species. The present study filled some gaps in the literature and brought new information on the genetic diversity of visual pigments in New World primates