Application of genetic markers to provide species identification and define stock structure: Analyses of selected marine fishes of the Mid -Atlantic Bight

Molecular markers and techniques were employed to develop a genetic key for the forensic identification of 16 species of Chesapeake Bay sportfishes and to investigate the stock structure of one of those species, the weakfish Cynoscion regalis. Regions within the ATP synthetase 6 (ATPase 6), Cytochrome b , cytochrome c oxidase I, NADH dehydrogenase 4 (ND4), and 12S/16S ribosomal RNA mitochondrial genes were amplified using the polymerase chain reaction (PCR) and digested with a bank of restriction endonucleases to find a genetic marker that exhibited complete interspecific differentiation and low intraspecific variation. Complete separation of all sixteen species was accomplished by restriction fragment length polymorphism (RFLP) analysis of an approximately 1495 bp region of the 12S/16S ribosomal RNA mitochondrial genes with the single endonuclease Rsa I. Ten species exhibiting a single digestion pattern and the remaining six were dimorphic. Analyses of four microsatellite loci and two nuclear intron regions were used to investigate the genetic basis of population structure of weakfish collected at five locations along the U.S. East Coast. Microsatellite mean expected heterozygosities ranged from a low of 8.5% for the SOCO14 marker to a high of 92.8% for the CNE612 locus. Mean expected heterozygosities for the CRESIA1 and RP2 intron regions were 5.1% and 24.0%, respectively. None of the sample genotype distributions differed significantly from Hardy-Weinberg expectations, and pairwise FST values were consistently low (0.000--0.087 for microsatellite loci, 0.000--0.050 for intron regions). Analyses of molecular variance (AMOVA) and exact F permutation tests of sample heterogeneity were nonsignificant for all loci. Evaluation of some individuals in the Georgia 1997 sample exhibiting unusually small allele sizes using the previously developed genetic key based on the 12S/16S rRNA marker revealed that two other species of Cynoscion , the sand seatrout C. arenarius and the silver seatrout C. nothus, had been inadvertently included in the sample of YOY weakfish. Based on data from the mitochondrial marker and the SOC050 microsatellite locus, a number of the Georgia 1997 fish were identified as hybrid offspring of weakfish and sand seatrout crosses

Discrimination Of Nine Crassostrea Oyster Species Based Upon Restriction Fragment-Length Polymorphism Analysis Of Nuclear And Mitochondrial Dna Markers

A molecular genetic identification key for nine species of Crassostrea oysters was developed based on restriction fragment-length polymorphism (RFLP) analyses of nuclear and mitochondrial DNA markers. Seven of nine species were unambiguosly differentiated based on digestion of the ITS-1 nuclear marker with Hae III an Hinf I. Individual species exhibited one or two RFLP patterns for each restriction endonuclease, and only C. madrasensis and C. iredalei were indistinguishable electrophoretically. All nine species were unambiguosly differentiated based on digestion of the COI mitochondrial marker with Dde I and Hae III. Species exhibited one or two RFLP patterns for each restriction endonuclease, and species pairs unresolved by the first restriction enzyme were completely resolved with the second. The resulting key distinguishes among many Indo-Pacific Crassostrea oysters that overlap across some or all on their ranges, and establish as an expandable framework for future additions of other species to the key

Genetic Diversity In U.S. Hatchery Stocks Of Crassostrea Ariakensis (Fujita, 1913) And Comparison With Natural Populations In Asia

Although several different U.S. hatchery stocks of the Asian Suminoe oyster Crassosirea ariakensis were used in laboratory and field trials assessing performance, and in comparative studies with the native oyster Crassostrea virginica, the genetic composition of these hatchery stocks has not yet been examined comprehensively. Using eight microsatellite markers we investigated the genetic variability among five hatchery stocks and compared the genetic makeup of these stocks with 8 wild populations from Asia. Results showed significant genetic differentiation among the 5 hatchery stocks that was 6-fold larger than that observed among wild populations. A significant reduction in genetic diversity was observed in hatchery stocks compared with wild source populations, indicating a genetic bottleneck. Two long-established stocks showed significant decreases in both allelic diversity and heterozygosity compared with the wild Japanese source population, whereas three recently established stocks showed less severe reductions in allelic diversity and a nonsignificant change in levels of heterozygosity compared with their source Chinese populations. These microsatellite markers also proved useful for assignment of hatchery individuals back to their source stocks with a high degree of confidence. Although assignment of wild individuals back to their population of origin proved less reliable, approximately 70% of wild individuals could be assigned either to their source population or to geographically proximal populations. Our results suggest that results obtained from experiments that used hatchery animals of a single C. ariakensis stock for biological and ecological studies should be interpreted cautiously, because they may not always accurately reflect the behavior of wild populations or of other hatchery stocks

Evaluating Recruitment Contribution Of A Selectively Bred Aquaculture Line Of The Oyster, Crassostrea Virginica Used In Restoration Efforts

Severe over-fishing, habitat degradation, and recent disease impacts have devastated the eastern oyster (Crassostrea virginica) fisherey in the Chesapeake Bay. Several restoration efforts are in progress, including the unconventional approach of seeding reefs with an aquaculture strain selected for disease resistance and fast growth in hopes of mitigating the negative effects of diseases and low census numbers. Supplementation of four sites (The Great Wicomico, Lynnhaven, York and Elizabeth Rivers) examined in this study totaled approximatedly 18,500,000 aquaculture oysters from 2002 to 2006. We collected locally recruited offspring (n = 6517) from 2002 to 2006 at these sites to determine if reproduction by the transplanted oysters produced detectable contributions to recruitment by examining the frequency of a composite mitochondrial haplotype that occurs at high frequencies in this aquaculture strain but is rare in wild Chesapeake Bay oysters. The estimated frequency of this haplotype in locally recruited oysters (average 1.4%, SD = 0.9) was compared with the average frequencies found in the hatchery produced (35%, SD = 12.8) and wild (1.2%, SD = 0.9) oysters, but we were unable to refute the null-hypothesis that population supplementation made no contribution to recruitment. We discuss five nonmutually exclusive explanations for the limited impact of supplementation, including unequal sex-ratio, predation, flushing, relative scale, and aquaculture selection. We argue that predation, relative scale and aquaculture selection are the likely reasons for the limited contribution made by aquaculture oysters used for population supplementation

Conserved Role of unc-79 in Ethanol Responses in Lightweight Mutant Mice

The mechanisms by which ethanol and inhaled anesthetics influence the nervous system are poorly understood. Here we describe the positional cloning and characterization of a new mouse mutation isolated in an N-ethyl-N-nitrosourea (ENU) forward mutagenesis screen for animals with enhanced locomotor activity. This allele, Lightweight (Lwt), disrupts the homolog of the Caenorhabditis elegans (C. elegans) unc-79 gene. While Lwt/Lwt homozygotes are perinatal lethal, Lightweight heterozygotes are dramatically hypersensitive to acute ethanol exposure. Experiments in C. elegans demonstrate a conserved hypersensitivity to ethanol in unc-79 mutants and extend this observation to the related unc-80 mutant and nca-1;nca-2 double mutants. Lightweight heterozygotes also exhibit an altered response to the anesthetic isoflurane, reminiscent of unc-79 invertebrate mutant phenotypes. Consistent with our initial mapping results, Lightweight heterozygotes are mildly hyperactive when exposed to a novel environment and are smaller than wild-type animals. In addition, Lightweight heterozygotes exhibit increased food consumption yet have a leaner body composition. Interestingly, Lightweight heterozygotes voluntarily consume more ethanol than wild-type littermates. The acute hypersensitivity to and increased voluntary consumption of ethanol observed in Lightweight heterozygous mice in combination with the observed hypersensitivity to ethanol in C. elegans unc-79, unc-80, and nca-1;nca-2 double mutants suggests a novel conserved pathway that might influence alcohol-related behaviors in humans

Cytokine Plasma Levels: Reliable Predictors for Radiation Pneumonitis?

BACKGROUND: Radiotherapy (RT) is the primary treatment modality for inoperable, locally advanced non-small-cell lung cancer (NSCLC), but even with highly conformal treatment planning, radiation pneumonitis (RP) remains the most serious, dose-limiting complication. Previous clinical reports proposed that cytokine plasma levels measured during RT allow to estimate the individual risk of patients to develop RP. The identification of such cytokine risk profiles would facilitate tailoring radiotherapy to maximize treatment efficacy and to minimize radiation toxicity. However, cytokines are produced not only in normal lung tissue after irradiation, but are also over-expressed in tumour cells of NSCLC specimens. This tumour-derived cytokine production may influence circulating plasma levels in NSCLC patients. The aim of the present study was to investigate the prognostic value of TNF-alpha, IL-1beta, IL-6 and TGF-beta1 plasma levels to predict radiation pneumonitis and to evaluate the impact of tumour-derived cytokine production on circulating plasma levels in patients irradiated for NSCLC. METHODOLOGY/PRINCIPAL FINDINGS: In 52 NSCLC patients (stage I-III) cytokine plasma levels were investigated by ELISA before and weekly during RT, during follow-up (1/3/6/9 months after RT), and at the onset of RP. Tumour biopsies were immunohistochemically stained for IL-6 and TGF-beta1, and immunoreactivity was quantified (grade 1-4). RP was evaluated according to LENT-SOMA scale. Tumour response was assessed according to RECIST criteria by chest-CT during follow-up. In our clinical study 21 out of 52 patients developed RP (grade I/II/III/IV: 11/3/6/1 patients). Unexpectedly, cytokine plasma levels measured before and during RT did not correlate with RP incidence. In most patients IL-6 and TGF-beta1 plasma levels were already elevated before RT and correlated significantly with the IL-6 and TGF-beta1 production in corresponding tumour biopsies. Moreover, IL-6 and TGF-beta1 plasma levels measured during follow-up were significantly associated with the individual tumour responses of these patients. CONCLUSIONS/SIGNIFICANCE: The results of this study did not confirm that cytokine plasma levels, neither their absolute nor any relative values, may identify patients at risk for RP. In contrast, the clear correlations of IL-6 and TGF-beta1 plasma levels with the cytokine production in corresponding tumour biopsies and with the individual tumour responses suggest that the tumour is the major source of circulating cytokines in patients receiving RT for advanced NSCLC

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

Peer reviewe

THEMIS: A Parameter Estimation Framework for the Event Horizon Telescope

The Event Horizon Telescope (EHT) provides the unprecedented ability to directly resolve the structure and dynamics of black hole emission regions on scales smaller than their horizons. This has the potential to critically probe the mechanisms by which black holes accrete and launch outflows, and the structure of supermassive black hole spacetimes. However, accessing this information is a formidable analysis challenge for two reasons. First, the EHT natively produces a variety of data types that encode information about the image structure in nontrivial ways; these are subject to a variety of systematic effects associated with very long baseline interferometry and are supplemented by a wide variety of auxiliary data on the primary EHT targets from decades of other observations. Second, models of the emission regions and their interaction with the black hole are complex, highly uncertain, and computationally expensive to construct. As a result, the scientific utilization of EHT observations requires a flexible, extensible, and powerful analysis framework. We present such a framework, Themis, which defines a set of interfaces between models, data, and sampling algorithms that facilitates future development. We describe the design and currently existing components of Themis, how Themis has been validated thus far, and present additional analyses made possible by Themis that illustrate its capabilities. Importantly, we demonstrate that Themis is able to reproduce prior EHT analyses, extend these, and do so in a computationally efficient manner that can efficiently exploit modern high-performance computing facilities. Themis has already been used extensively in the scientific analysis and interpretation of the first EHT observations of M87

Monitoring the Morphology of M87* in 2009–2017 with the Event Horizon Telescope

The Event Horizon Telescope (EHT) has recently delivered the first resolved images of M87*, the supermassive black hole in the center of the M87 galaxy. These images were produced using 230 GHz observations performed in 2017 April. Additional observations are required to investigate the persistence of the primary image feature—a ring with azimuthal brightness asymmetry—and to quantify the image variability on event horizon scales. To address this need, we analyze M87* data collected with prototype EHT arrays in 2009, 2011, 2012, and 2013. While these observations do not contain enough information to produce images, they are sufficient to constrain simple geometric models. We develop a modeling approach based on the framework utilized for the 2017 EHT data analysis and validate our procedures using synthetic data. Applying the same approach to the observational data sets, we find the M87* morphology in 2009–2017 to be consistent with a persistent asymmetric ring of ~40 μas diameter. The position angle of the peak intensity varies in time. In particular, we find a significant difference between the position angle measured in 2013 and 2017. These variations are in broad agreement with predictions of a subset of general relativistic magnetohydrodynamic simulations. We show that quantifying the variability across multiple observational epochs has the potential to constrain the physical properties of the source, such as the accretion state or the black hole spin