Surface mucous as a source of genomic DNA from Atlantic billfishes (Istiophoridae) and swordfish (Xiphiidae)

Procedures for sampling genomic DNA from live billfishes involve manual restraint and tissue excision that can be difficult to carry out and may produce stresses that affect fish survival. We examined the collection of surface mucous as a less invasive alternative method for sourcing genomic DNA by comparing it to autologous muscle tissue samples from Atlantic blue marlin (Makaira nigricans), white marlin (Tetrapturus albidus), sailfish (Istiophorus platypterus), and swordfish (Xiphias gladius). Purified DNA from mucous was comparable to muscle and was suitable for conventional polymerase chain reaction, random amplified polymorphic DNA analysis, and mitochondrial and nuclear locus sequencing. The nondestructive and less invasive characteristics of surface mucous collection may promote increased survival of released specimens and may be advantageous for other marine fish genetic studies, particularly those involving large live specimens destined for release.

Evolutionary associations between sand seatrout (Cynoscion arenarius) and silver seatrout (C. nothus) inferred from morphological characters, mitochondrial DNA, and microsatellite markers

The evolutionary associations between closely related fish species, both contemporary and historical, are frequently assessed by using molecular markers, such as microsatellites. Here, the presence and variability of microsatellite loci in two closely related species of marine fishes, sand seatrout (Cynoscion arenarius) and silver seatrout (C. nothus), are explored by using heterologous primers from red drum (Sciaenops ocellatus). Data from these loci are used in conjunction with morphological characters and mitochondrial DNA haplotypes to explore the extent of genetic exchange between species offshore of Galveston Bay, TX. Despite seasonal overlap in distribution, low genetic divergence at microsatellite loci, and similar life history parameters of C. arenarius and C. nothus, all three data sets indicated that hybridization between these species does not occur or occurs only rarely and that historical admixture in Galveston Bay after divergence between these species was unlikely. These results shed light upon the evolutionary history of these fishes and highlight the genetic properties of each species that are influenced by their life history and ecology.

Mitochondrial DNA markers to identify commercial spiny lobster species (Panulirus spp.) from the Pacific coast of Mexico: an application on phyllosoma larvae

Molecular markers based on mitochondrial DNA (mtDNA) are extensively used to study genetic relationships. mtDNA has been used in phylogenetic studies to understand the evolutionary history of species because it is maternally inherited and is not subject to genetic recombination (Gyllensten et al., 1991). The high mutation rate of mtDNA makes it a useful tool for differentiating between closely related species (Brown et al., 1979)—a tool that is especially important when significant variations occur between species, but not within species (Hill et al., 2001; Blair et al., 2006; Chow et al., 2006a).

Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers

Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John’s River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998−2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

Yellow (Perca flavescens) and Eurasian (P. fluviatilis) perch distinguished in fried fish samples by DNA analysis

DNA techniques are increasingly used as diagnostic tools in many fields and venues. In particular, a relatively new application is its use as a check for proper advertisement in markets and on restaurant menus. The identification of fish from markets and restaurants is a growing problem because economic practices often render it cost-effective to substitute one species for another. DNA sequences that are diagnostic for many commercially important fishes are now documented on public databases, such as the National Center for Biotechnology Information’s (NCBI) GenBank.1 It is now possible for most genetics laboratories to identify the species from which a tissue sample was taken without sequencing all the possible taxa it might represent.

Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starcevo Cris culture in Romania (Carcea, Gura Baciului and Negrilesti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelnita cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.

A key to selected rockfishes (Sebastes spp.) based on mitochondrial DNA restriction fragment analysis

Larval and juvenile rockfishes (Sebastes spp.) are difficult to identify using morphological characters. We developed a key based on sizes of restriction endonuclease fragments of the NADH dehydrogenase-3 and -4 (ND3/ND4) and 12S and 16S ribosomal RNA (12S/16S) mitochondrial regions. The key makes use of variation in the ND3/ND4 region. Restriction endonuclease Dde I variation can corroborate identifications, as can 12S/16S variation. The key, based on 71 species, includes most North American taxa, several Asian species, and Sebastolobus alascanus and Helicolenus hilgendorfi that are closely related to rockfishes. Fifty-eight of 71 rockfish species in our database can be distinguished unequivocally, using one to five restriction enzymes; identities of the remaining species are narrowed to small groups: 1) S. polyspinis, S. crameri, and S. ciliatus or variabilis (the two species could not be distinguished and were considered as a single species) ; 2) S. chlorostictus, S. eos, and S. rosenblatti; 3) S. entomelas and S. mystinus; 4)S. emphaeus, S. variegatus, and S. wilsoni; and 5) S. carnatus and S. chrysomelas.

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

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Efeito da p53 sobre a expressão e atividade da enzima de reparo de DNA Timina-DNA Glicosilase

O câncer de esôfago é uma malignidade altamente freqüente e letal. Uma característica específica das áreas de alta incidência de câncer de esôfago é a grande proporção de duplas mutações no gene TP53, sendo, ao menos uma delas, uma transição G para A em sítios CpG. Essas transições resultam de malpareamentos GT causados pela desaminação espontânea da 5-metilcitosina em ilhotas CpG. A enzima de reparo de DNA Timina-DNA Glicosilase (TDG) é responsável pelo primeiro passo na remoção da timina de malpareamentos GT em CpG. A alta proporção de mutações em sítios CpG em câncer de esôfago das áreas de alta incidência sugere que a via de reparo de DNA iniciada pela TDG pode estar prejudicada. A presença de duplas mutações, sendo ao menos uma delas em CpG, levantou a hipótese de que a primeira mutação no TP53 reduz a atividade da via de reparo iniciada pela TDG, que acarretaria a segunda mutação em sítios CpG. Dessa forma, o objetivo desse trabalho foi analisar o efeito da p53 sobre a expressão e atividade da TDG. Os resultados obtidos mostram que a expressão de TDG é regulada transcricionalmente pela p53 numa gama de linhagens celulares e é induzida pelo dano ao DNA, de forma p53-dependente. Além disto, os resultados apontam um possível papel da proteína p53 ativa na migração nuclear e atividade da TDG. Estes resultados ainda nos levam à conclusão de que o silenciamento de TDG aumenta a sensibilidade à morte celular induzida por MMS quando a p53 é encontrada na forma selvagem, mas não quando esta proteína é mutada, e de que o status mutacional de TP53 parece afetar a expressão de TDG em CEE primários. Juntos esses resultados sugerem que a p53 regula o reparo de DNA mediado pela TDG e que a inativação de p53 em células tumorais pode contribuir para a aquisição de um mutator phenotype.