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  1. Article ; Online: Epigenetic Transgenerational Modifications Induced by Xenobiotic Exposure in Zebrafish

    Luis Terrazas-Salgado / Alejandra García-Gasca / Miguel Betancourt-Lozano / Raúl Llera-Herrera / Isabel Alvarado-Cruz / Beatriz Yáñez-Rivera

    Frontiers in Cell and Developmental Biology, Vol

    2022  Volume 10

    Abstract: Zebrafish (Danio rerio) is a well-established vertebrate model in ecotoxicology research that responds to a wide range of xenobiotics such as pesticides, drugs, and endocrine-disrupting compounds. The epigenome can interact with the environment and ... ...

    Abstract Zebrafish (Danio rerio) is a well-established vertebrate model in ecotoxicology research that responds to a wide range of xenobiotics such as pesticides, drugs, and endocrine-disrupting compounds. The epigenome can interact with the environment and transform internal and/or external signals into phenotypic responses through changes in gene transcription. Environmental exposures can also generate epigenetic variations in offspring even by indirect exposure. In this review, we address the advantages of using zebrafish as an experimental animal model to study transgenerational epigenetic processes upon exposure to xenobiotics. We focused mostly on DNA methylation, although studies on post-translational modifications of histones, and non-coding RNAs related to xenobiotic exposure in zebrafish are also discussed. A revision of the methods used to study epigenetic changes in zebrafish revealed the relevance and reproducibility for epigenetics-related research. PubMed and Google Scholar databases were consulted for original research articles published from 2013 to date, by using six keywords: zebrafish, epigenetics, exposure, parental, transgenerational, and F2. From 499 articles identified, 92 were considered, of which 14 were selected as included F2 and epigenetic mechanisms. Current knowledge regarding the effect of xenobiotics on DNA methylation, histone modifications, and changes in non-coding RNAs expressed in F2 is summarized, along with key experimental design considerations to characterize transgenerational effects.
    Keywords epigenetics ; Zebrafish ; xenobiotic ; transgenerational ; exposure ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: De novo transcriptome assembly for the rose spotted snapper Lutjanus guttatus and expression analysis of growth/atrophy‐related genes

    Escalante‐Rojas, Mauricio / Alejandra Garcia‐Gasca / Crisantema Hernández / Emyr Peña / Raúl Llera‐Herrera

    Aquaculture research. 2018 Apr., v. 49, no. 4

    2018  

    Abstract: The rose spotted snapper is an important fishery resource with potential for farming in several Latin American countries. Since transcriptomic information was not available for this species, we generated a reference transcriptome from eleven tissues ( ... ...

    Abstract The rose spotted snapper is an important fishery resource with potential for farming in several Latin American countries. Since transcriptomic information was not available for this species, we generated a reference transcriptome from eleven tissues (brain, heart, gonad, liver, gut, muscle, white skin, dark skin, and visceral fat) using Illumina HiSeq2000 platform. Transcriptome assembly and annotation were performed with Trinity and Trinotate respectively; 267,601 contigs were assembled, average contig length was 845 bp; 85,677 putative protein sequences were identified. Sixty‐six per cent of them showed a significant match to the SwissProt Database. From this assembly, we selected growth/atrophy‐related genes to investigate the effect of dietary protein source on gene expression. Pacap expression was measured in the brain; igf1, igf2 and ghr were measured in liver; and mtor, igf1, igf2, myod1, myod2, myogenin, foxo3a, foxo3b, murf1, mafbx, mstn1 and mstn2 were measured in muscle. A feeding trial with juveniles was performed, in which three diets were formulated, a fishmeal‐based diet (FM), a terrestrial animal protein diet (PPM) with porcine meat meal and poultry by‐products meal, and a vegetable diet (VEG) with a blend of soybean protein concentrate and corn gluten. A reduced expression of somatotropic and myogenic genes in fish fed the VEG diet was observed; however, expression of atrophy genes did not increase with this diet suggesting that atrophy mechanisms were not involved. These results indicate that protein from a vegetable source does not provide proper amino acid requirements to juvenile fish, decreasing expression of myogenic and other growth‐related genes.
    Keywords amino acid requirements ; amino acid sequences ; animal proteins ; atrophy ; brain ; corn gluten ; databases ; gene expression ; genes ; heart ; juveniles ; liver ; Lutjanus ; meat meal ; muscles ; myogenin ; pork ; protein concentrates ; protein sources ; snapper ; soy protein ; tissues ; transcriptome ; transcriptomics ; vegetables ; visceral fat
    Language English
    Dates of publication 2018-04
    Size p. 1709-1722.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1227359-4
    ISSN 1355-557X
    ISSN 1355-557X
    DOI 10.1111/are.13628
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 4230: Show issues

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  3. Article: Sex determination and differentiation genes in a functional hermaphrodite scallop, Nodipecten subnodosus

    Galindo-Torres, Pavel / Alejandra García-Gasca / Ana M. Ibarra / Cei Abreu-Goodger / Cristina Escobedo-Fregoso / Raúl Llera-Herrera

    Marine genomics. 2018 Feb., v. 37

    2018  

    Abstract: The lion-paw, Nodipecten subnodosus is one of three scallop species commercially exploited on the west coast of the Peninsula of Baja California. Because nothing is known about sex determination and sexual differentiation in hermaphrodite scallops, in ... ...

    Abstract The lion-paw, Nodipecten subnodosus is one of three scallop species commercially exploited on the west coast of the Peninsula of Baja California. Because nothing is known about sex determination and sexual differentiation in hermaphrodite scallops, in the present work, a global transcriptomic analysis was performed in two early developmental stages, settling eyed-larvae and spat, as well as in three tissues (undifferentiated gonad, digestive gland, and adductor muscle). Over 27 million Illumina paired-end reads were obtained through the MiSeq platform. After processing the reads a total of 243,774 transcripts were assembled with an N50 of 980 and an average length of 775nt. A total of 43,252 proteins were inferred and 36,103 transcripts had at least one homolog in the SwissProt database according to a blastx search. After differential expression analyses and GO annotations it was possible to identify several sex-related genes in the scallop, including one known to be involved in the sex determination pathway of the hermaphrodite model organism Caenorhabditis elegans, N. subnodosus-sex1 (Ns-sex1). Other interesting sex determination and differentiation genes were Ns-dmrta2, Ns-sox9, Ns-wnt4, Ns-doa, Ns-ovo, Ns-vir, among others. Most of these genes were mainly expressed in the testis region, suggesting their participation in male gonad region sex differentiation. These results represent the first available information on the genetics of sex determination and differentiation in a functional hermaphrodite scallop.
    Keywords Caenorhabditis elegans ; coasts ; databases ; developmental stages ; gene expression regulation ; genes ; hermaphroditism ; males ; models ; muscles ; Nodipecten subnodosus ; proteins ; scallops ; sex determination ; sexual development ; testes ; tissues ; transcriptomics ; Mexico
    Language English
    Dates of publication 2018-02
    Size p. 161-175.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2429626-0
    ISSN 1876-7478 ; 1874-7787
    ISSN (online) 1876-7478
    ISSN 1874-7787
    DOI 10.1016/j.margen.2017.11.004
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Identification of male gametogenesis expressed genes from the scallop Nodipecten subnodosus by suppressive subtraction hybridization and pyrosequencing.

    Raúl Llera-Herrera / Alejandra García-Gasca / Cei Abreu-Goodger / Arnaud Huvet / Ana M Ibarra

    PLoS ONE, Vol 8, Iss 9, p e

    2013  Volume 73176

    Abstract: Despite the great advances in sequencing technologies, genomic and transcriptomic information for marine non-model species with ecological, evolutionary, and economical interest is still scarce. In this work we aimed to identify genes expressed during ... ...

    Abstract Despite the great advances in sequencing technologies, genomic and transcriptomic information for marine non-model species with ecological, evolutionary, and economical interest is still scarce. In this work we aimed to identify genes expressed during spermatogenesis in the functional hermaphrodite scallop Nodipecten subnodosus (Mollusca: Bivalvia: Pectinidae), with the purpose of obtaining a panel of genes that would allow for the study of differentially transcribed genes between diploid and triploid scallops in the context of meiotic arrest and reproductive sterility. Because our aim was to isolate genes involved in meiosis and other testis maturation-related processes, we generated suppressive subtractive hybridization libraries of testis vs. inactive gonad. We obtained 352 and 177 ESTs by clone sequencing, and using pyrosequencing (454-Roche) we maximized the identified ESTs to 34,276 reads. A total of 1,153 genes from the testis library had a blastx hit and GO annotation, including genes specific for meiosis, spermatogenesis, sex-differentiation, and transposable elements. Some of the identified meiosis genes function in chromosome pairing (scp2, scp3), recombination and DNA repair (dmc1, rad51, ccnb1ip1/hei10), and meiotic checkpoints (rad1, hormad1, dtl/cdt2). Gene expression analyses in different gametogenic stages in both sexual regions of the gonad of meiosis genes confirmed that the expression was specific or increased towards the maturing testis. Spermatogenesis genes included known testis-specific ones (kelch-10, shippo1, adad1), with some of these known to be associated to sterility. Sex differentiation genes included one of the most conserved genes at the bottom of the sex-determination cascade (dmrt1). Transcript from transposable elements, reverse transcriptase, and transposases in this library evidenced that transposition is an active process during spermatogenesis in N. subnodosus. In relation to the inactive library, we identified 833 transcripts with functional annotation related to ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: A novel CHH gene from the Pacific white shrimp Litopenaeus vannamei was characterized and found highly expressed in gut and less in eyestalk and other extra-eyestalk tissues

    Ventura-López, Claudia / Ana M. Ibarra / Fabiola G. Arcos / Gracia Gómez-Anduro / Ilie S. Racotta / Raúl Llera-Herrera

    Gene. 2016 May 15, v. 582, no. 2

    2016  

    Abstract: The crustacean hyperglycemic hormone (CHH) family is an important group of neuropeptides involved in controlling growth, reproduction, and stress response in decapod species. In this study, a new gene containing 4 exons-3 introns flanked by canonical 5′- ... ...

    Abstract The crustacean hyperglycemic hormone (CHH) family is an important group of neuropeptides involved in controlling growth, reproduction, and stress response in decapod species. In this study, a new gene containing 4 exons-3 introns flanked by canonical 5′-GT-AG-3′ intron splice-site junctions was isolated from Litopenaeus vannamei. Two full length transcripts of this CHH were isolated from eyestalk and pericardial tissue of males and females using rapid amplification of cDNA ends (RACE). Transcripts sequences were 1578bp in length in males pericardial tissues and in males and females eyestalk with 100% identity, but the transcript isolated from females pericardial tissues was shorter (974bp). The differences in transcripts length is a result of two polyadenylation sites present in the 3'UTR resulting in two transcription termination signals. Transcript sequences encoded one unique protein that can be classified as type I CHH subfamily because of the 4 exons and 3 introns structure, although the CPRP region is not-well conserved and there is no amidation in the C-terminal of the deduced amino acid sequence. Furthermore, there is a glycine inserted in the mature peptide not at position 12 as in type II CHHs but after amino acid 31 and the phylogenetic analysis did not group the peptide within type I, but closer to type II CHHs. We demonstrated by endpoint-PCR, qPCR, and in situ hybridization (ISH), that this gene is expressed in neuroendocrine organs known to express CHHs in penaeid shrimp, including X-organ and optic nerve in eyestalk, supraesophageal ganglion (SoG), but it is also expressed in other organs as gill, gut, pericardial cavity, as well as in terminal ampoule or spermatophore and vas deferens of males.
    Keywords 3' untranslated regions ; amino acid sequences ; complementary DNA ; digestive system ; exons ; females ; ganglia ; gene expression ; genes ; glycine (amino acid) ; in situ hybridization ; introns ; Litopenaeus vannamei ; males ; nerve tissue ; neuropeptides ; pericardium ; phylogeny ; quantitative polymerase chain reaction ; rapid amplification of cDNA ends ; reproduction ; spermatophores ; stress response
    Language English
    Dates of publication 2016-0515
    Size p. 148-160.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2016.02.011
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 79/715: Show issues

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