1,721,344 research outputs found
A clockwork fish: Age prediction using DNA methylation‐based biomarkers in the European seabass
No full text11 pages, 4 figures, 3 tables, supporting information https://dx.doi.org/10.1111/1755-0998.13111.-- All data related to this publication are publicly available: mapped reads and methylation values of each CpG for each sample can be found in https://doi.org/10.5061/dryad.m0cfxpnz4 Anastasiadi & Piferrer, 2019)Age‐related changes in DNA methylation do occur. Taking advantage of this, mammalian and avian epigenetic clocks have been constructed to predict age. In fish, studies on age‐related DNA methylation changes are scarce and no epigenetic clocks have been constructed. However, in fisheries and population dynamics studies there is a need for accurate estimation of age, something that is often impossible for some economically important species with the currently available methods. Here, we used the European sea bass, a marine fish the age of which can be determined with accuracy, to construct a piscine epigenetic clock, the first one in a cold‐blooded vertebrate. We used targeted bisulfite sequencing to amplify 48 CpGs from four genes in muscle samples and applied penalized regressions to predict age. We thus developed an age predictor in fish that is highly accurate (0.824) and precise (2.149 years). In juvenile fish, accelerated growth due to elevated temperatures had no effect on age prediction, indicating that the clock is able to predict the chronological age independently of environmentally‐driven perturbations. An epigenetic clock developed using muscle samples accurately predicted age in samples of testis but not ovaries, possibly reflecting the reproductive biology of fish. In conclusion, we report the development of the first piscine epigenetic clock, paving the way for similar studies in other species. Piscine epigenetic clocks should be of great utility for fisheries management and conservation purposes, where age determination is of crucialD.A. was supported by a PhD scholarship from the Spanish Government (BES–2011–044860). Research was supported by Spanish Ministry of Economy and Competitiveness “Epimark” (ref. AGL2016-78710-R) to F.P.With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI
Triploidía y ginogénesis en el rodaballo (Scophthalmus maximus). Inducción, verificación y efectos sobre el crecimiento y la reproducción
No full textMemoria de tesis doctoral presentada por Rosa María Cal Rodríguez para obtener el título de Doctora en Ciencias Biológicas por la Universidade de Vigo (UVIGO), realizada bajo la dirección del Dr. Francesc Piferrer Circuns del Institut de Ciències del Mar (ICM-CSIC).-- 201 pagesEn la acuicultura, el control de la reproducción de las especies en cautividad permite su domesticación y la aplicación de la tecnología adecuada para su mejora genética. En los sistemas actuales de producción del rodaballo (Scophthalmus maximus L.), los métodos utilizados para el control de la reproducción son ya habituales e incluyen la manipulación del fotoperiodo, la criopreservación del esperma, la inducción hormonal a la maduración y la aplicación de técnicas de mejora genética tradicional, tales como la selección fenotípica asistida en programas de cruzamientos. Estos métodos se ejercen sobre individuos adultos y permiten decidir "cuando" y "con quien" ha de efectuarse la reproducción. [...]Peer Reviewe
Density effects during sex differentiation in zebrafish (Danio rerio)
No full textTrabajo final presentado por Guillermo Gambús Gubern para obtener el grado, realizado bajo la dirección del Dr. Francesc Piferrer del Institut de Ciències del Mar (ICM-CSIC).-- 24 pagesSexual determination in some fish is still unknown and it has been studied that abiotic factors such as temperature, density, pH and hypoxia have an influence in this process. Based on previous experiments, we analysed density factor in domesticated zebrafish (AB strain), which has a masculinizing effect in a population, subjected to high density treatments. Six different were set up for the experiment, combining low (16 fish/L) and high (66 fish/L) densities in order to determine which period(s) were more sensitive to this factor during zebrafish sexual development having a masculinizing effect, because there were not studies looking for the critical periods. Experiment had a duration from one until 90 days post fertilization, dpf. The results obtained showed that high density treatments had significant differences with low density treatments, having a masculinizing effect. Treatments that spanned (7–18 dpf) and (7–45 dpf) obtained the same percentage of males, making the period (7–18 dpf) the most sensitive during sexual differentiation and having a masculinizing effect, affecting negatively in the growth (body weight and standard length) of this fish speciesPeer Reviewe
Intrinsic and environmental influences on DNA methylation and gene expression in fish
No full textEpigenetic mechanisms, influenced by intrinsic and environmental factors are crucial for the regulation of gene expression and, ultimately, the phenotype. The European sea bass is used as a model to study these influences on DNA methylation and the phenotype during early development and later in life. We identify loci altered with age, suggestive of the existence of a piscine epigenetic clock. We show that moderate early developmental temperature increases are associated with genome-wide changes in DNA methylation and with parent-specific responses of genes involved in sexual development. Furthermore, we highlight a genome-wide inverse relationship of gene expression with the DNA methylation of the first intron. Lastly, we provide one of the first empirical demonstrations in support of the neural crest cell deficit hypothesis to explain Darwin’s domestication syndrome. Together, these results constitute the most integrative analysis of DNA methylation patterns in a fish species under intrinsic and ecologically relevant contexts.Els mecanismes epigenètics són crucials per a la regulació de l'expressió gènica. El llobarro s’utilitza com a model per estudiar aquestes influències sobre la metilació de l'ADN i el fenotip durant el desenvolupament primerenc. S’identifiquen loci alterats amb l'edat, suggeridors de l’existència d’un rellotge epigenètic en peixos. Mostrem que augments moderats de la temperatura a l’inici del desenvolupament s'associen amb canvis en la metilació de l'ADN en tot el genoma i amb les respostes de gens implicats en el sistema de desenvolupament sexual. D'altra banda, destaquem una relació inversa de l'expressió gènica amb la metilació de l'ADN del primer intró. Finalment, oferim una de les primeres demostracions en suport de la hipòtesi del dèficit de cèl·lules de la cresta neural per a explicar la síndrome de domesticació de Darwin. En conjunt, aquests resultats constitueixen l'anàlisi més integradora de la metilació de l'ADN en un peix sota contextos intrínsics i ecològicament pertinents.Programa de doctorat en Biomedicin
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Els mecanismes de regulació i els efectes de la temperatura en la diferenciació sexual del llobarro
No full textMemòria de tesi doctoral presentada per Laia Navarro Martín per optar al grau de Doctora en Biologia per la Universitat de Barcelona (UB), realitzada sota la direcció del Dr. Francesc Piferrer i Circuns de l'Institut de Ciències del Mar (ICM-CSIC).-- 326 pagesThis Thesis has been carried out in the Group of Biology of the Reproduction (GBR) of the Department of Renewable Marine Resources at the Institute of Marine Sciences (ICM-CSIC) of Barcelona and under the tuition of the department of Physiology of the University of Barcelona during the period 2003-2008. The results obtained in these studies are not only important in sea bass, but also some of them can be generalized to other fish and vertebrates. The aim of this Thesis was to study sea bass sex differentiation at different levels: at endocrine level, analysing the influence of different steroids and agonists and antagonists compounds of the ovarian and testicular differentiation pathways; at expression level of some genes that are required for the necessities of the gonads to differentiate towards ovaries or testes; and also through mechanisms of epigenetic regulation, such as methylation, that may be responsible for the complex process of developing a bipotential tissue, like the undifferentiated gonad, into a ovary or testis. In non-mammalian vertebrates like some fishes, amphibians and reptiles, the mechanism by which the temperature can affect sex differentiation, and consequently the proportion of sexes, remains unknown. The results obtained in this thesis allow to propose an hypotheses about how temperature can be influencing sex differentiation and which mechanism can be responsible for that. In the present thesis, the sea bass has been used as model specie. However, and although these studies have broadened our knowledge in this field, the obtained results have posed new questions that can be resolved in future experiments. [...]Laia Navarro Martín was supported by a FPI fellowship (BES-2003-0006) from the Spanish Ministry of Education and SciencePeer Reviewe
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Inducción de la triploidía y la ginogénesis en la lubina (Dicentrarchus labrax L.): Efectos sobre el crecimiento y la fisiología reproductiva
No full textMemoria de tesis doctoral presentada por Alicia Felip Edo para obtener el título de Doctora por la Universitat de València (UV), realizada bajo la dirección del Dr. Françesc Piferrer Circuns del Institut de Ciències del Mar (ICM-CSIC) y de la Dra. Silvia Zanuy Doste del Instituto de Acuicultura de Torre de la Sal (IATS-CSIC)Peer Reviewe
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