Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Identification of a novel FGFRL1 MicroRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies

MicroRNAs (miRNAs) are critical post-transcriptional regulators. Based on a previous genome-wide association (GWA) scan, we conducted a polymorphism in microRNAs' Target Sites (poly-miRTS)-centric multistage meta-analysis for lumbar spine (LS)-, total hip (HIP)-, and femoral neck (FN)-bone mineral density (BMD). In stage I, 41,102 poly-miRTSs were meta-analyzed in 7 cohorts with a genome-wide significance (GWS) α=0.05/41,102=1.22×10-6. By applying α=5×10-5 (suggestive significance), 11 poly-miRTSs were selected, with FGFRL1 rs4647940 and PRR5 rs3213550 as top signals for FN-BMD (P-value=7.67×10-6 and 1.58×10-5) in gender-combined sample. In stage II in silico replication (two cohorts), FGFRL1 rs4647940 was the only signal marginally replicated for FN-BMD (P-value=5.08×10-3) at α=0.10/11=9.09×10-3. PRR5 rs3213550 was also selected based on biological significance. In stage III de novo genotyping replication (two cohorts), FGFRL1 rs4647940 was the only signal significantly replicated for FN-BMD (P-value=7.55×10-6) at α=0.05/2=0.025 in gender-combined sample. Aggregating three stages, FGFRL1 rs4647940 was the single stage I-discovered and stages II- and III-replicated signal attaining GWS for FN-BMD (P-value=8.87×10-12). Dual-luciferase reporter assays demonstrated that FGFRL1 3' untranslated region harboring rs4647940 appears to be hsa-miR-140-5p's target site. In a zebrafish microinjection experiment, dre-miR-140-5p is shown to exert a dramatic impact on craniofacial skeleton formation. Taken together, we provided functional evidence for a novel FGFRL1 poly-miRTS rs4647940 in a previously known 4p16.3 locus, and experimental and clinical genetics studies have shown both FGFRL1 and hsa-miR-140-5p are important for bone formation. © The Author 2015. Published by Oxford University Press. All rights reserved.

Molecular genetics of Usher syndrome -inherited deafness and blindness

Usher syndrome (USH) is an inherited blindness and deafness disorder with variable vestibular dysfunction. The syndrome is divided into three subtypes according to the progression and severity of clinical symptoms. The gene mutated in Usher syndrome type 3 (USH3), clarin 1 (CLRN1), was identified in Finland in 2001 and two mutations were identified in Finnish patients at that time. Prior to this thesis study, the two CLRN1 gene mutations were the only USH mutations identified in Finnish USH patients. To further clarify the Finnish USH mutation spectrum, all nine USH genes were studied. Seven mutations were identified: one was a previously known mutation in CLRN1, four were novel mutations in myosin VIIa (MYO7A) and two were a novel and a previously known mutation in usherin (USH2A). Another aim of this thesis research was to further study the structure and function of the CLRN1 gene, and to clarify the effects of mutations on protein function. The search for new splice variants resulted in the identification of eight novel splice variants in addition to the three splice variants that were already known prior to this study. Studies of the possible promoter regions for these splice variants showed the most active region included the 1000 bases upstream of the translation start site in the first exon of the main three exon splice variant. The 232 aa CLRN1 protein encoded by the main (three-exon) splice variant was transported to the plasma membrane when expressed in cultured cells. Western blot studies suggested that CLRN1 forms dimers and multimers. The CLRN1 mutant proteins studied were retained in the endoplasmic reticulum (ER) and some of the USH3 mutations caused CLRN1 to be unstable. During this study, two novel CLRN1 sequence alterations were identified and their pathogenicity was studied with cell culture protein expression. Previous studies with mice had shown that Clrn1 is expressed in mouse cochlear hair cells and spiral ganglion cells, but the expression profile in mouse retina remained unknown. The Clrn1 knockout mice display cochlear cell disruption/death, but do not have a retinal phenotype. The zebrafish, Danio rerio, clrn1 was found to be expressed in hair cells associated with hearing and balance. Clrn1 expression was also found in the inner nuclear layer (INL), photoreceptor layer and retinal pigment epithelium layer (RPE) of the zebrafish retina. When Clrn1 production was knocked down with injected morpholino oligonucleotides (MO) targeting Clrn1 translation or correct splicing, the zebrafish larvae showed symptoms similar to USH3 patients. These larvae had balance/hearing problems and reduced response to visual stimuli. The knowledge this thesis research has provided about the mutations in USH genes and the Finnish USH mutation spectrum are important in USH patient diagnostics. The extended information about the structure and function of CLRN1 is a step further in exploring USH3 pathogenesis caused by mutated CLRN1 as well as a step in finding a cure for the disease.

Morphological Effects of G-Quadruplex Stabilization Using a Small Molecule in Zebrafish

Zebrafish (Danio rerio) embryos are transparent and advantageous for studying early developmental changes due to ex utero development, making them an appropriate model for studying gene expression changes as a result of molecular targeting. Zebrafish embryos were injected with a previously reported G-quadruplex selective ligand, and the phenotypic changes were recorded. We report marked discrepancies in the development of intersegmental vessels. In silico analysis determined that the putative G-quadruplex motif occur in the upstream promoter region of the Cdh5 (N-cadherin) gene. A real-time polymerase chain reaction-based investigation indicated that in zebrafish, CDH-2 (ZN-cad) was significantly downregulated in the ligand-treated embryos. Biophysical characterization of the interaction of the ligand with the G-quadruplex motif found in this promoter yielded strong binding and stabilization of the G-quadruplex with this ligand. Hence, we report for the first time the phenotypic impact of G-quadruplex targeting with a ligand in a vertebrate organism. This study has unveiled not only G-quadruplex targeting in non-human animal species but also the potential that G-quadruplexes can provide a ready tool for understanding the phenotypic effects of targeting certain important genes involved in differentiation and developmental processes in a living eukaryotic organism.

Dual Drug Conjugate Loaded Nanoparticles for the Treatment of Cancer

Two antineoplastic agents, Imatinib (IM) and 5-Fluorouracil (FU) were conjugated by hydrolysable linkers through an amide bond and entrapped in polymeric Human Serum Albumin (HSA) nanoparticles. The presence of dual drugs in a common carrier has the advantage of reaching the site of action simultaneously and acting at different phases of the cell cycle to arrest the growth of cancer cells before they develop chemoresistance. The study has demonstrated an enhanced anticancer activity of the conjugate, and conjugate loaded stealth HSA nanoparticles (NPs) in comparison to the free drug in A-549 human lung carcinoma cell line and Zebra fish embryos (Danio rerio). Hydrolysability of the conjugate has also been demonstrated with complete hydrolysis being observed after 12 h. In vivo pharmacodynamics study in terms of tumor volume and pharmacokinetics in mice for conjugate (IM-SC-FU) and conjugate loaded nanoparticles showed significant anti-cancer activity. The other parameters evaluated were particle size (86nm), Poly Dispersive Index (PDI) (0.209), zeta potential (-49mV), drug entrapment efficiency (96.73%) and drug loading efficiency (89%). Being in stealth mode gives the potential for the NPs to evade Reticulo-Endothelial system (RES), achieve passive targeting by Enhanced Permeation Retention (EPR) effect with controlled release of the therapeutic agent. As the conjugate cleaves into individual drugs in the tumor environment, this promises better suppression of cancer chemoresistance by delivering dual drugs with different modes of action at the same site, thereby synergistically inhibiting the growth of cancerous tissue.

The ontogeny of haematopoiesis in the marine teleost Leiostomus xanthurus and a comparison of the site of initial haematopoiesis with Opsanus tau

The ontogeny of haematopoiesis in the perciform fish, spot Leiostomus xanthurus, differed from that reported as the norm for fishes, as exemplified by the cypriniform zebrafish Danio rerio, and observed in the batrachoidiform oyster toadfish Opsanus tau. Erythropoiesis in spot was first evident in the head kidney of yolk-sac larvae 3 days after hatching (DAH). No embryonic intermediate cell mass (ICM) of primitive stem cells or blood islands on the yolk were apparent within embryos. Erythrocytes were first evident in circulation near the completion of yolk absorption, c. 5 DAH, when larvae were c. 20 mm notochord length (LN). Erythrocyte abundance increased rapidly with larval development for c. 14 to 16 DAH, then became highly variable following changes in cardiac chamber morphology and volume. Erythrocytic haemoglobin (Hb) was not detected within whole larvae until they were 12 DAH or c. 31 mm LN, well after yolk and oil-globule absorption. The Hb was not quantified until larvae were >47 DAH or >7 mm standard length. The delayed appearance of erythrocytes and Hb in spot was similar to that reported for other marine fishes with small embryos and larvae. In oyster toadfish, a marine teleost that exhibits large embryos and larvae, the ICM and Hb were first evident in two bilateral slips of erythropoietic tissue in the embryos, c. 5 days after fertilization. Soon thereafter, erythrocytes were evident in the heart, and peripheral and vitelline circulation. Initial haematopoiesis in oyster toadfish conformed with that described for zebrafish. While the genes that code for the development of haematopoiesis are conserved among vertebrates, gene expression lacks phylogenetic pattern among fishes and appears to conform more closely with phenotypic expression related to physiological and ecological influences of overall body size and environmental oxygen availability.

Mantenimiento en el laboratorio del pez cebra

El pez cebra (Danio rerio) se utiliza como organismo modelo en distintos campos como la biomedicina o la toxicogenómica. Las ventajas que ofrece frente a otros modelos animales, hace que se haya convertido en los últimos años en uno de los organismos modelo más utilizado en experimentación. La similitud de su desarrollo embrionario con el de otros vertebrados superiores o la semejanza de su genoma con la del ser humano lo han colocado en el punto de mira de las principales investigaciones. Pero disponer de ejemplares óptimos tanto de embriones como de adultos para su utilización en investigación, requiere de unos cuidados y de una atención adecuada. Para su mantenimiento se deberán tener en cuenta el tipo de instalaciones para su cría, la calidad del agua donde se encuentran, la alimentación que reciben o los procesos de reproducción utilizados. El objetivo de este estudio ha sido elaborar un protocolo de mantenimiento del pez cebra, que optimice los cuidados necesarios para que el número de embriones viables sea máximo y también poder mantener un número de ejemplares adultos en buenas condiciones.

Der Fischei-Test: Ein Toxizitätstest für ökotoxikologische Untersuchungen

Zebrafish (Danio rerio) embryos have been used to quantify the teratogenic potential of environmental samples and harmful substances respectively. The short spawning interval renders this species a good test organism in toxicological research. Due to the transparency of the eggs several lethal and non-lethal endpoints can be detected in parallel after 48 h of embryonic development. Zebrafishembryos have been shown to be sensitive to a number of environmental relevant contaminants, as well as to ex-tracts from polluted sediments

Flexible microimplants for in vivo sensing

The work in this thesis develops two types of microimplants for the application of cardiovascular in vivo biomedical sensing, one for short-term diagnosis and the other for long-term monitoring.

Despite advances in diagnosis and therapy, atherosclerotic cardiovascular disease remains the leading cause of morbidity and mortality in the Western world. Predicting metabolically active atherosclerotic plaques has remained an unmet clinical need. A stretchable impedance sensor manifested as a pair of quasi-concentric microelectrodes was developed to detect unstable intravascular. By integrating the impedance sensor with a cardiac catheter, high-resolution Electrochemical Impedance Spectroscopy (EIS) measurements can be conducted during cardiac catheterization. An inflatable silicone balloon is added to the sensor to secure a well-controlled contact with the plaque under test in vivo. By deploying the device to the explants of NZW rabbit aorta and live animals, distinct EIS measurements were observed for unstable atherosclerotic plaques that harbored active lipids and inflammatory cells.

On the other hand, zebrafish (Danio rerio) is an emerging genetic model for heart regenerative medicine. In humans, myocardial infarction results in the irreversible loss of cardiomyocytes. Zebrafish hearts can fully regenerate after two months with 20% ventricular resection. Long-term electrocardiogram (ECG) recording can characterize the heart regeneration in a functional dimension. A flexible microelectrode membrane was developed to be percutaneously implanted onto a zebrafish heart and record epicardial ECG signals from specific regions on it. Region-specific aberrant cardiac signals were obtained from injured and regenerated hearts. Following that, in order to achieve continuous and wireless recording from non-sedated and non-restricted small animal models, a wireless ECG recording system was designed for the microelectrode membrane, prototyped on a printed circuit board and demonstrated on a one-day-old neonatal mouse. Furthermore, a flexible and compact parylene C printed circuit membrane was used as the integration platform for the wireless ECG recording electronics. A substantially miniature wireless ECG recording system was achieved.

Estudo comparativo da sensibilidade de dois organismos expostos a efluentes líquidos.

Tendo em vista a multiplicidade das ações causada pela interação dos agentes químicos com possíveis danos a biota pelos efluentes, a estratégia mais eficiente é o uso integrado de análises físicas, químicas e ecotóxicológicas para avaliação e previsão do risco ambiental. Nesse sentido, ensaios ecotoxicológicos são importantes meios de monitoramento ambiental a fim de se preservar o meio aquático. Um dos objetivos principais do trabalho foi implementar o método de ensaio com Daphnia similis de acordo com a ABNT NBR 12713: 2009. Além disso, objetivou-se avaliar a sensibilidade relativa de dois organismos-testes (Daphnia similis e Danio rerio) a efluentes de diversas indústrias tais como: alimentícia, bebidas, farmacêutica, papel, petroquímica, efluente proveniente de decapagem de metais, e chorume proveniente de três aterros diferentes (São Paulo, Rio de Janeiro e Rio Grande do Sul) avaliando os resultados físico-químicos e os limites das legislações vigentes no Rio de Janeiro (NT 213, NT 202 e DZ 205). Dessa forma, pretende-se observar se os limites estabelecidos são suficientes para não conferir ecotoxicidade aguda ao corpo hídrico. Os efluentes tratados da indústria alimentícia, de bebidas, de papel e farmacêutica não apresentaram ecotoxicidade aguda nem a Daphnia similis nem ao Danio rerio. Já o ensaio com o efluente proveniente da decapagem de metais, apresentou-se muito tóxico aos dois organismos, sendo CL(I)50;48h igual 39,99% e CE(I)50;48h igual a 11,87%, respectivamente. Com relação aos efluentes da indústria petroquímica A, foi detectada ecotoxicidade mesmo estando todos os seus parâmetros analisados de acordo com as legislações vigentes. Já os efluentes provenientes de aterro sanitário, o chorume oriundo de aterro da região metropolitana de São Paulo, em geral, apresentou-se como sendo o mais tóxico dos três aterros sanitários. E o chorume tratado oriundo do aterro do Rio Grande do Sul, demonstrou-se ser o menos tóxico dos três, principalmente com relação à Daphnia similis. De modo geral, todos os efluentes que se encontraram dentro dos limites da legislação (DZ 205 e NT 202), não apresentaram ecotoxicidade aos organismos em estudo.

Cellular and molecular responses of zebrafish to legacy and emerging pollutants: the specific cases of PAHs and metal oxide nanoparticles

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Estudo experimental de wetlands construídos como unidade de polimento no tratamento de lixiviados de aterros sanitários.

A grande quantidade de resíduos sólidos gerados nas cidades é um desafio para o saneamento ambiental no Brasil. A fim de se reduzir os impactos gerados ao meio ambiente e à saúde pública, é necessário que haja um gerenciamento adequado, desde a coleta até a disposição final, desses resíduos sólidos urbanos. Os aterros sanitários permitem um maior controle ambiental, desde que sejam bem projetados e operados. A decomposição da matéria orgânica presente nesses resíduos, somada às águas das chuvas gera o lixiviado, líquido com alto potencial poluidor. Várias formas de tratamento são propostas com a finalidade de tornar o lixiviado menos poluente ao meio ambiente. Wetlands construídos tem se mostrado uma alternativa eficiente para a remoção de poluentes em lixiviados, além dos baixos custos operacionais e de implantação. O presente estudo investigou o uso de wetlands subsuperficiais em escala-piloto para o tratamento de um lixiviado prétratado. Os wetlands foram monitorados com a finalidade de se obter remoções de matéria orgânica e nitrogênio amoniacal. As maiores reduções percentuais de concentração de nitrogênio amoniacal, DQO e COD foram, 91%, 42% e 35%, respectivamente. As maiores reduções percentuais em carga de nitrogênio amoniacal e DQO foram, 67% e 50%, respectivamente. Os resultados dos ensaios de toxicidade realizados com os organismos Vibrio fischeri e Danio rerio revelaram que, a toxicidade do lixiviado foi reduzida ao ser tratado pelo wetland.

Avaliação de toxicidade de efluentes industriais utilizando organismos de três níveis tróficos.

O objetivo do estudo foi avaliar a qualidade de efluentes líquidos industriais, pela caracterização físico-química e ensaios ecotoxicológicos agudos com Danio rerio, Daphnia similis e Vibrio fischeri. Foram comparadas as sensibilidades dos organismos-teste aos variados tipos de efluentes (indústrias alimentícias, papeleiras, bebidas, petroquímicas e farmacêutica), sendo que estes organismos pertencem a três níveis tróficos diferentes. Além disso, foi implementado o método de ensaio com bactérias luminescentes, o Microtox, de acordo com a NBR 15411 (ABNT, 2006). Na maioria dos ensaios, os efluentes apresentaram parâmetros físico-químicos dentro dos limites permitidos pela legislação. Mesmo assim, algumas vezes foram observados efeitos nos organismos-teste. Foram utilizados efluentes tratados das ETEI, podendo ser avaliada a sensibilidade de cada organismo a cada efluente do estudo. Para a Indústria Alimentícia 1 foram realizadas coletas de efluente bruto e primário, que se mostraram tóxicos aos três organismos. Essa coleta também foi realizada para a Indústria Farmacêutica, na qual o efluente bruto foi tóxico aos três organismos e o efluente do tratamento primário, foi tóxico à Daphnia similis e à Vibrio fischeri. O efluente bruto da Indústria Alimentícia 2, da Indústria de Papel e Celulose 2 e da Indústria de Bebidas foram coletados e avaliados ecotoxicologicamente por meio do ensaio Microtox, demonstrando toxicidade aguda com baixos valores de CE(I)50 para todas as indústrias. Alguns parâmetros físicoquímicos das indústrias foram correlacionados com a toxicidade do efluente final para Daphnia similis, Danio rerio e Vibrio fischeri por meio da correlação de Spearman. O teste não paramétrico Mann-Whitney foi usado para comparar grupos de parâmetros físico-químicos que apresentaram presença ou ausência de toxicidade. Em alguns efluentes tratados das ETEI das Indústrias Alimentícia 1, Alimentícia 2, de Papel e Celulose 2 e Petroquímica 1, foram observadas respostas biológicas das bactérias aos efluentes, o efeito hormesis, que indica que a amostra não possui toxicidade aguda, mas é muito provável que apresente toxicidade crônica.

Remoção de amônia do lixiviado por arraste de ar e caracterização por fracionamento com membrana.

A proposta deste trabalho é estudar a tecnologia para a remoção de amônia do lixiviado através do processo físico-químico de arraste com ar e a sua caracterização por processos de fracionamento com membranas de MF e UF. Foram analisados no processo de arraste de ar os parâmetros pH, vazão de ar e tempo de operação. Foi verificada a remoção de nitrogênio amoniacal de 93,5% em um tempo de operação de 6 horas, com ajuste de pH igual a 11 e vazão de ar 100 L/h. Após a remoção do nitrogênio amoniacal, os lixiviados foram submetidos a processo de fracionamento com membranas de microfiltração (MF) e ultrafiltração (UF), sendo investigadas a remoção de amônia, a condutividade, DQO, COD, cloreto e pH. Obtiveram-se resultados praticamente constantes à medida que o lixiviado permeou nas membranas de MF e UF. Ademais, empregaram-se testes de toxicidade e ensaios de tratabilidade biológica com amostras de lixiviado bruto, lixiviado tratado (baixa concentração de amônia) e lixiviados fracionados com membranas de MF e UF. Nos ensaios de tratabilidade biológica os resultados mostraram que não houve uma remoção significativa de matéria orgânica e nos testes de toxicidade com organismos Danio rerio, embora tenha ocorrido uma redução na toxicidade na sequência dos experimentos, foi constatado que o lixiviado bruto, lixiviado tratado com remoção de amônia e fracionados com membranas de MF e UF mantiveram elevada toxicidade.

Construção e operação de wetland como polimento de lixiviado de aterro de resíduos sólidos urbanos.

O presente trabalho tem o objetivo de avaliar a metodologia de construção, de plantio, de manutenção, de operação e a eficiência de um sistema de tratamento por wetland construído como etapa de polimento da Estação de Tratamento de Lixiviado (ETC) de Aterro já encerrado de Resíduos Sólidos Urbanos na Região Metropolitana do Rio de Janeiro. Parte do efluente tratado por lodos ativados na ETC foi direcionado e tratado no wetland construído. Foi escolhido o projeto de Fluxo Horizontal Subsuperficial e a vegetação selecionada foi a taboa (Typha latifolia) que é nativa da área do aterro. Em média, foram feitas três amostragens mensais do afluente e do efluente do wetland, de maio a outubro de 2013. A eficiência do sistema foi avaliada por meio de parâmetros físico-químicos e de parâmetros coletivos específicos. A eficiência de remoção de Demanda Química de Oxigênio (DQO) foi de 60%, nitrogênio amoniacal de 67%, nitrito de 72% e nitrato de 57%. Outro parâmetro avaliado foi a toxicidade aguda, foram utilizados os organismos teste Danio rerio (peixe), a Daphnia similis (microcrustáceo) e a Aliivibrio fischeri (bactéria luminescente). Durante o período foram coletados diariamente as vazões de entrada e saída, a condutividade elétrica e o índice pluviométrico. Os resultados mostraram que o uso de wetland como etapa de polimento pode ser uma alternativa para o tratamento de lixiviado.