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Sample records for hybridization fish assessment

  1. Fluorescent in situ hybridization (FISH) assessment of chromosome copy number in sperm

    SciTech Connect

    Sheu, M.; Sigman, M.; Mark, H.F.L.

    1994-09-01

    Approximately 15% of all recognized pregnancies end in spontaneous abortions. The overall frequency of chromosome abnormalities in spontaneous abortions is approximately 50%. Thus aneuploidy is a significant cause of fetal wastage. In addition, structural and numerical abnormalities of chromosomes can also lead to birth defects, developmental delay, mental retardation and infertility. Conventional cytogenetic analysis via GTG- and other banding techniques is a powerful tool in the elucidation of the nature of chromosomal abnormalities. Fluorescent in situ hybridization (FISH) enables detection of numerical chromosomal abnormalities, especially trisomies, in intact cells. Using FISH and commercially available biotin-labeled probes, we have initiated a prospective study to assess specific chromosome copy number of preparations of unstained smears from men referred for a male infertility evaluation as well as smears from normal control males chosen randomly from the sample of sperm donors. A total of approximately 19,000 sperm nuclei have been examined thus far. Of those suitable for analysis, 7382 (38.75%) were normal possessing one copy of chromosome 8, 155 (0.81%) were disomic, and 15 (0.079%) had more than two copies of chromosome 8. Comparisons with data available in the literature will be discussed. Work is ongoing to increase the efficiency of hybridization using both reported and previously untried pretreatment and fixation protocols. We have also initiated studies using multicolor FISH with various chromosome enumeration probes. The assay described here is a potentially powerful tool for detecting rare events such as spontaneous germ cell aneuploidy, aneuploidy detected in semen from men with carcinoma in situ of the testis and aneuploidy induced by potential environmental genotoxicants. It can also be utilized for segregation analysis and for correlating chromosome copy number with germ cell morphology.

  2. An approach for quantitative assessment of fluorescence in situ hybridization (FISH) signals for applied human molecular cytogenetics.

    PubMed

    Iourov, Ivan Y; Soloviev, Ilia V; Vorsanova, Svetlana G; Monakhov, Viktor V; Yurov, Yuri B

    2005-03-01

    A number of applied molecular cytogenetic studies require the quantitative assessment of fluorescence in situ hybridization (FISH) signals (for example, interphase FISH analysis of aneuploidy by chromosome enumeration DNA probes; analysis of somatic pairing of homologous chromosomes in interphase nuclei; identification of chromosomal heteromorphism after FISH with satellite DNA probes for differentiation of parental origin of homologous chromosome, etc.). We have performed a pilot study to develop a simple technique for quantitative assessment of FISH signals by means of the digital capturing of microscopic images and the intensity measuring of hybridization signals using Scion Image software, commonly used for quantification of electrophoresis gels. We have tested this approach by quantitative analysis of FISH signals after application of chromosome-specific DNA probes for aneuploidy scoring in interphase nuclei in cells of different human tissues. This approach allowed us to exclude or confirm a low-level mosaic form of aneuploidy by quantification of FISH signals (for example, discrimination of pseudo-monosomy and artifact signals due to over-position of hybridization signals). Quantification of FISH signals was also used for analysis of somatic pairing of homologous chromosomes in nuclei of postmortem brain tissues after FISH with "classical" satellite DNA probes for chromosomes 1, 9, and 16. This approach has shown a relatively high efficiency for the quantitative registration of chromosomal heteromorphism due to variations of centromeric alphoid DNA in homologous parental chromosomes. We propose this approach to be efficient and to be considered as a useful tool in addition to visual FISH signal analysis for applied molecular cytogenetic studies.

  3. Hybrid Breakdown in Cichlid Fish

    PubMed Central

    Stelkens, Rike Bahati; Schmid, Corinne; Seehausen, Ole

    2015-01-01

    Studies from a wide diversity of taxa have shown a negative relationship between genetic compatibility and the divergence time of hybridizing genomes. Theory predicts the main breakdown of fitness to happen after the F1 hybrid generation, when heterosis subsides and recessive allelic (Dobzhansky-Muller) incompatibilities are increasingly unmasked. We measured the fitness of F2 hybrids of African haplochromine cichlid fish bred from species pairs spanning several thousand to several million years divergence time. F2 hybrids consistently showed the lowest viability compared to F1 hybrids and non-hybrid crosses (crosses within the grandparental species), in agreement with hybrid breakdown. Especially the short- and long-term survival (2 weeks to 6 months) of F2 hybrids was significantly reduced. Overall, F2 hybrids showed a fitness reduction of 21% compared to F1 hybrids, and a reduction of 43% compared to the grandparental, non-hybrid crosses. We further observed a decrease of F2 hybrid viability with the genetic distance between grandparental lineages, suggesting an important role for negative epistatic interactions in cichlid fish postzygotic isolation. The estimated time window for successful production of F2 hybrids resulting from our data is consistent with the estimated divergence time between the multiple ancestral lineages that presumably hybridized in three major adaptive radiations of African cichlids. PMID:25996870

  4. Assessment of chromosomal abnormalities in sperm of infertile men using sperm karyotyping and multicolour fluorescence in situ hybridization (FISH)

    SciTech Connect

    Moosani, N.; Martin, R.H.

    1994-09-01

    Individuals with male factor infertility resulting from idiopathic oligo-, astheno- or teratozoospermia are frequently offered IVF in an attempt to increase their chances of having a child. A concern remains whether these infertile males have an elevated risk of transmitting chromosomal abnormalities to their offspring. Sperm chromosomal complements from these men were assayed using the human sperm/hamster oocyte fusion system and fluorescence in situ hybridization (FISH) on sperm nuclei. For each of 5 infertile patients, 100 sperm karyotypes were analyzed and multicolour FISH analysis was performed on a minimum of 10,000 sperm nuclei for each chromosome-specific DNA probe for chromosomes 1 (pUC1.77), 12 (D12Z3), X (XC) and Y (DYZ3). As a group, the infertile patients showed increased frequencies of both numerical ({chi}{sup 2}=17.26, {proportional_to} <0.001) and total abnormalities ({chi}{sup 2}=7.78, {proportional_to} <0.01) relative to control donors when assessed by sperm karyotypes. Analysis of sperm nuclei by FISH indicated a significant increase in the frequency of disomy for chromosome 1 in three of the five patients as compared to control donors ({chi}{sup 2}>8.35, {proportional_to} <0.005). In addition, the frequency of XY disomy was significantly higher in four of the five patients studied by FISH ({chi}{sup 2}>10.58, {proportional_to}<0.005), suggesting that mis-segregation caused by the failure of the XY bivalent to pair may play a role in idiopathic male infertility.

  5. Distant hybridization leads to different ploidy fishes.

    PubMed

    Liu, ShaoJun

    2010-04-01

    Distant hybridization makes it possible to transfer the genome of one species to another, which results in changes in phenotypes and genotypes of the progenies. This study shows that distant hybridization or the combination of this method with gynogenesis or androgenesis lead to different ploidy fishes with genetic variation, including fertile tetraploid hybrids, sterile triploid hybrids, fertile diploid hybrids, fertile diploid gynogenetic fish, and their derived progenies. The formations of the different ploidy fishes depend on the genetic relationship between the parents. In this study, several types of distant hybridization, including red crucian carp (Carassius auratus red var.) (2n=100, abbreviated as RCC) (female) x common carp (Cyprinus carpio L.) (2n=100, abbreviated as CC) (male), and RCC (2n=100) (female) x blunt snout bream (Megalobrama amblycephala) (2n=48, abbreviated as BSB) (male) are described. In the distant hybridization of RCC (female) x CC (male), bisexual fertile F(3)-F(18) allotetraploid hybrids (4n=200, abbreviated as 4nAT) were formed. The diploid hybrid eggs and diploid sperm generated by the females and males of 4nAT developed into diploid gynogenetic hybrids and diploid androgenetic hybrids, respectively, by gynogenesis and androgenesis, without treatment for doubling the chromosome. Improved tetraploid hybrids and improved diploid fishes with genetic variation were derived from the gynogenetic hybrid line. The improved diploid fishes included the high-body RCC and high-body goldfish. The formation of the tetraploid hybrids was related to the occurrence of unreduced gametes generated from the diploid hybrids, which involved in premeiotic endoreduplication, endomitosis, or fusion of germ cells. The sterile triploid hybrids (3n=150) were produced on a large scale by crossing the males of tetraploid hybrids with females of diploid fish (2n=100). In another distant hybridization of RCC (female) x BSB (male), different ploidy fishes were

  6. Hybrid seine for full fish community collections

    USGS Publications Warehouse

    McKenna, James E.; Waldt, Emily M.; Abbett, Ross; David, Anthony; Snyder, James

    2013-01-01

    Seines are simple and effective fish collection gears, but the net mesh size influences how well the catch represents the fish communities. We designed and tested a hybrid seine with a dual-mesh bag (1/4″ and 1/8″) and compared the fish assemblage collected by each mesh. The fine-mesh net retained three times as many fish and collected more species (as many as eight), including representatives of several rare species, than did the coarser mesh. The dual-mesh bag permitted us to compare both sizes and species retained by each layer and to develop species-specific abundance correction factors, which allowed comparison of catches with the coarse-mesh seine used for earlier collections. The results indicate that a hybrid seine with coarse-mesh wings and a fine-mesh bag would enhance future studies of fish communities, especially when small-bodied fishes or early life stages are the research focus.

  7. FISH-ing for Genes: Modeling Fluorescence "in situ" Hybridization

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton Buck

    2006-01-01

    Teaching methods of genetic analysis such as fluorescence in situ hybridization (FISH) can be an important part of instructional units in biology, microbiology, and biotechnology. Experience, however, indicates that these topics are difficult for many students. The authors of this article describe how they created an activity that effectively…

  8. FISH-ing for Genes: Modeling Fluorescence "in situ" Hybridization

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton Buck

    2006-01-01

    Teaching methods of genetic analysis such as fluorescence in situ hybridization (FISH) can be an important part of instructional units in biology, microbiology, and biotechnology. Experience, however, indicates that these topics are difficult for many students. The authors of this article describe how they created an activity that effectively…

  9. Increased incidence of micronuclei assessed with the micronucleus assay and the fluorescence in situ hybridization (FISH) technique in peripheral blood lymphocytes of nurses exposed to nitrous oxide.

    PubMed

    Lewińska, D; Stepnik, M; Krajewski, W; Arkusz, J; Stańczyk, M; Wrońska-Nofer, T

    2005-03-07

    It has been postulated that exposure to nitrous oxide and halogenated anaesthetics is associated with various adverse health effects such as neurological and reproductive abnormalities or impairment of hepatic functions. In spite of the quite well known genotoxic effects of exposure to nitrous oxide in vivo, the mechanisms of these effects are still not clear. The aim of this study was to assess the frequency of micronuclei and to identify the type of chromosomal damage (clastogenic or aneugenic) in peripheral blood lymphocytes of operating-room nurses exposed to nitrous oxide. The study group comprised 46 women working at departments where the concentration of nitrous oxide ranged from 14 to 2308 mg/m3. The control population was composed of 28 women employed in the same hospitals but in non-surgical departments. The clastogenic/aneugenic effect of nitrous oxide was evaluated in lymphocytes using the standard micronucleus (MN) assay in combination with the fluorescence in situ hybridization (FISH) technique with pancentromeric probes. The results show a significant increase of the MN frequency in lymphocytes of exposed nurses compared with the control group (4.36+/-2.23 versus 9.02+/-4.67). The multiple regression analysis revealed a statistically significant relationship (p=0.0009) between MN frequency and exposure status, indicating that the level of exposure was the main factor affecting chromosomal damage. As assessed by FISH analysis, the overall frequencies of centromere-positive MN in the control and exposed groups were 43 and 49%, respectively. The increase observed in the exposed group may suggest a slight, statistically insignificant pro-aneugenic effect of exposure to nitrous oxide.

  10. Marine genetic swamping: hybrids replace an obligately estuarine fish.

    PubMed

    Roberts, David G; Gray, Charles A; West, Ronald J; Ayre, David J

    2010-02-01

    Populations of obligately estuarine taxa are potentially small and isolated and may lack genetic variation and display regional differentiation as a result of drift and inbreeding. Hybridization with a wide-ranging marine congener should introduce genetic variation and reduce the effects of inbreeding depression and genetic drift. However, high levels of hybridization can cause demographic and genetic swamping. In southeastern Australia hybridization occurs between obligately estuarine Black bream (Acanthopagrus butcheri) and migratory marine Yellowfin bream (Acanthopagrus australis). Here, we surveyed genetic variation at eight microsatellite loci and the mitochondrial control region of juvenile fish from five coastal lagoons (including temporal replication in two lagoons) (total n = 970) to determine the frequency and persistence of hybridization, and its likely consequence for the estuarine restricted A. butcheri. Of 688 juvenile fish genotyped 95% were either A. australis (347) or hybrids (309); only 5% (32) were A. butcheri. Most hybrids were later generation hybrids or A. butcheri backcrosses, which are likely multi-generational residents within lagoons. Far greater proportions of hybrid juveniles were found within two lagoons that are generally closed to the ocean (>90% hybrid fish within generally closed lagoons vs. 12-27% in permanently or intermittently open lagoons). In both lagoons, this was consistent across multiple cohorts of fish [79-97% hybrid fish (n = 282)]. Hybridization and introgression represent a major threat to the persistence of A. butcheri and have yet to be investigated for large numbers of estuarine taxa.

  11. Methods for assessing fish populations

    Treesearch

    Kevin L. Pope; Steve E. Lochmann; Michael K. Young

    2010-01-01

    Fisheries managers are likely to assess fish populations at some point during the fisheries management process. Managers that follow the fisheries management process (see Chapter 5) might find their knowledge base insufficient during the steps of problem identification or management action and must assess a population before appropriate actions can be taken. Managers...

  12. International, collaborative assessment of limitations of chromosome-specific probes (CSP) and fluorescent in situ hybridization (FISH): Analysis of expected detections in 73,000 prenatal cases

    SciTech Connect

    Evans, M.I.; Henry, G.P.; Miller, W.A.

    1994-09-01

    FISH and CSP have been proposed to reduce karyotyping need. The purpose of this study was to assess the potential efficacy of CSP-FISH using currently available probes (13, 18, 21, X, & Y) in large, prenatal diagnostic centers. Results (1990-1993) from 7 centers in 4 countries were divided by those expected to be detectable by currently available probes, and those which would be missed assuming 10% probe efficacy. 72,994 karyotypes included 699 trisomy 21`s, 352 trisomy 18`s, 136 trisomy 13`s, 358 sex chromosome aneuploidies, 70 triploidies, and 855 others (translocations, inversions, deletions, markers). Of 2,613 abnormalities, 1,745 would be detectable (66.8%). [Detroit 55.7%, Stockholm 68.3%, Boston 52.6%, Denver 61.3%, Muenster 77.0%, London 84.5%, Philadelphia 69.4%]. Centers with high proportions of referrals for ultrasound anomalies had the highest CSP-FISH positives secondary to increased T 18 & 13. We conclude: (1) 73,000 karyotypes show relatively consistent incidences of the common trisomies, sex chromosome abnormalities, and other chromosome abnormalities among the centers. (2) The proportion expected detectable by FISH-CSP technology varies from 52.6% to 84.5%, averaging 66.8%. (3) 1/3 of the karyotypic abnormalities would be missed, and therefore, replacement of complete karyotyping with FISH would have unacceptably high false-negative rates for routine evaluation. (4) FISH-CSP, while useful when positive for anomalies, is not sufficient when negative to obviate the need for a complete karyotype.

  13. Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish.

    PubMed

    Selz, O M; Thommen, R; Maan, M E; Seehausen, O

    2014-02-01

    Hybrid speciation is constrained by the homogenizing effects of gene flow from the parental species. In the absence of post-mating isolation due to structural changes in the genome, or temporal or spatial premating isolation, another form of reproductive isolation would be needed for homoploid hybrid speciation to occur. Here, we investigate the potential of behavioural mate choice to generate assortative mating among hybrids and parental species. We made three-first-generation hybrid crosses between different species of African cichlid fish. In three-way mate-choice experiments, we allowed hybrid and nonhybrid females to mate with either hybrid or nonhybrid males. We found that hybrids generally mated nonrandomly and that hybridization can lead to the expression of new combinations of traits and preferences that behaviourally isolate hybrids from both parental species. Specifically, we find that the phenotypic distinctiveness of hybrids predicts the symmetry and extent of their reproductive isolation. Our data suggest that behavioural mate choice among hybrids may facilitate the establishment of isolated hybrid populations, even in proximity to one or both parental species. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  14. Ancient hybridization and genomic stabilization in a swordtail fish.

    PubMed

    Schumer, Molly; Cui, Rongfeng; Powell, Daniel L; Rosenthal, Gil G; Andolfatto, Peter

    2016-06-01

    A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human-Neanderthal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome. © 2016 John Wiley & Sons Ltd.

  15. The chromosomal constitution of fish hybrid lineage revealed by 5S rDNA FISH.

    PubMed

    Zhang, Chun; Ye, Lihai; Chen, Yiyi; Xiao, Jun; Wu, Yanhong; Tao, Min; Xiao, Yamei; Liu, Shaojun

    2015-12-03

    The establishment of the bisexual fertile fish hybrid lineage including the allodiploid and allotetraploid hybrids, from interspecific hybridization of red crucian carp (Carassius auratus red var. 2n = 100, 2n = AA) (♀) × common carp (Cyprinus carpio L. 2n = 100, 2n = BB) (♂), provided a good platform to investigate genetic relationship between the parents and their hybrid progenies. The chromosomal inheritance of diploid and allotetraploid hybrid progenies in successive generations, was studied by applying 5S rDNA fluorescence in situ hybridization. Signals of 5S rDNA distinguished the chromosomal constitution of common carp (B-genome) from red crucian carp (A-genome), in which two strong signals were observed on the first submetacentric chromosome, while no major signal was found in common carp. After fish hybridization, one strong signal of 5S rDNA was detected in the same locus on the chromosome of diploid hybrids. As expected, two strong signals were observed in 4nF3 tetraploid hybrids offspring and it is worth mentioning that two strong signals were detected in a separating bivalent of a primary spermatocyte in 4nF3. Furthermore, the mitosis of heterozygous chromosomes was shown normal and stable with blastular tissue histological studies. We revealed that 5S rDNA signal can be applied to discern A-genome from B-genome, and that 5S rDNA bearing chromosomes can be stably passed down in successive generations. Our work provided a significant method in fish breeding and this is important for studies in fish evolutionary biology.

  16. Fluorescence in situ hybridization (FISH) using snap frozen buffy coat.

    PubMed

    Min, Hun Jung; Lee, Jinkyoung; Choi, Jung Eun; Shin, Su; Lee, Dong Soon

    2007-01-01

    We report the successful application of interphase fluorescent in situ hybridization (FISH) using extracted nuclei from snap frozen buffy coat stored for the purpose of molecular analysis. Included in this study were 30 frozen buffy coat specimens, ranging from <1 day to 3 yr old. Thawing of the buffy coat at 37 degrees C was followed by lysing erythrocytes with lysing solution (LYSE S III DIFF, Coulter Corp.). Cells were fixed and slides were prepared according to manufacturer's FISH protocol. All specimens from the 30 frozen-thawed buffy coats were suitable for FISH evaluation, and signal intensities were not significantly related to the age of specimens. In conclusion, interphase FISH is feasible using frozen-thawed buffy coat; the technique will be useful for retrospective molecular cytogenetic analysis of hematologic malignancies.

  17. Rapid genomic DNA changes in allotetraploid fish hybrids.

    PubMed

    Wang, J; Ye, L H; Liu, Q Z; Peng, L Y; Liu, W; Yi, X G; Wang, Y D; Xiao, J; Xu, K; Hu, F Z; Ren, L; Tao, M; Zhang, C; Liu, Y; Hong, Y H; Liu, S J

    2015-06-01

    Rapid genomic change has been demonstrated in several allopolyploid plant systems; however, few studies focused on animals. We addressed this issue using an allotetraploid lineage (4nAT) of freshwater fish originally derived from the interspecific hybridization of red crucian carp (Carassius auratus red var., ♀, 2n=100) × common carp (Cyprinus carpio L., ♂, 2n=100). We constructed a bacterial artificial chromosome (BAC) library from allotetraploid hybrids in the 20th generation (F20) and sequenced 14 BAC clones representing a total of 592.126 kb, identified 11 functional genes and estimated the guanine-cytosine content (37.10%) and the proportion of repetitive elements (17.46%). The analysis of intron evolution using nine orthologous genes across a number of selected fish species detected a gain of 39 introns and a loss of 30 introns in the 4nAT lineage. A comparative study based on seven functional genes among 4nAT, diploid F1 hybrids (2nF1) (first generation of hybrids) and their original parents revealed that both hybrid types (2nF1 and 4nAT) not only inherited genomic DNA from their parents, but also demonstrated rapid genomic DNA changes (homoeologous recombination, parental DNA fragments loss and formation of novel genes). However, 4nAT presented more genomic variations compared with their parents than 2nF1. Interestingly, novel gene fragments were found for the iqca1 gene in both hybrid types. This study provided a preliminary genomic characterization of allotetraploid F20 hybrids and revealed evolutionary and functional genomic significance of allopolyploid animals.

  18. San Juanico Hybrid System Technical and Institutional Assessment: Preprint

    SciTech Connect

    Corbus, D.; Newcomb, C.; Yewdall, Z.

    2004-07-01

    San Juanico is a fishing village of approximately 120 homes in the Municipality of Comondu, Baja California. In April, 1999, a hybrid power system was installed in San Juanico to provide 24-hour power, which was not previously available. Before the installation of the hybrid power system, a field study was conducted to characterize the electrical usage and institutional and social framework of San Juanico. One year after the installation of the hybrid power system a''post-electrification'' study was performed to document the changes that had occurred after the installation. In December of 2003, NREL visited the site to conduct a technical assessment of the system.

  19. Ancient hybridization fuels rapid cichlid fish adaptive radiations

    PubMed Central

    Meier, Joana I.; Marques, David A.; Mwaiko, Salome; Wagner, Catherine E.; Excoffier, Laurent; Seehausen, Ole

    2017-01-01

    Understanding why some evolutionary lineages generate exceptionally high species diversity is an important goal in evolutionary biology. Haplochromine cichlid fishes of Africa's Lake Victoria region encompass >700 diverse species that all evolved in the last 150,000 years. How this ‘Lake Victoria Region Superflock' could evolve on such rapid timescales is an enduring question. Here, we demonstrate that hybridization between two divergent lineages facilitated this process by providing genetic variation that subsequently became recombined and sorted into many new species. Notably, the hybridization event generated exceptional allelic variation at an opsin gene known to be involved in adaptation and speciation. More generally, differentiation between new species is accentuated around variants that were fixed differences between the parental lineages, and that now appear in many new combinations in the radiation species. We conclude that hybridization between divergent lineages, when coincident with ecological opportunity, may facilitate rapid and extensive adaptive radiation. PMID:28186104

  20. Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models.

    PubMed

    Fontenete, Sílvia; Guimarães, Nuno; Wengel, Jesper; Azevedo, Nuno Filipe

    2016-01-01

    The thermodynamics and kinetics of DNA hybridization, i.e. the process of self-assembly of one, two or more complementary nucleic acid strands, has been studied for many years. The appearance of the nearest-neighbor model led to several theoretical and experimental papers on DNA thermodynamics that provide reasonably accurate thermodynamic information on nucleic acid duplexes and allow estimation of the melting temperature. Because there are no thermodynamic models specifically developed to predict the hybridization temperature of a probe used in a fluorescence in situ hybridization (FISH) procedure, the melting temperature is used as a reference, together with corrections for certain compounds that are used during FISH. However, the quantitative relation between melting and experimental FISH temperatures is poorly described. In this review, various models used to predict the melting temperature for rRNA targets, for DNA oligonucleotides and for nucleic acid mimics (chemically modified oligonucleotides), will be addressed in detail, together with a critical assessment of how this information should be used in FISH.

  1. Introgressive hybridization as a promoter of genome reshuffling in natural homoploid fish hybrids (Cyprinidae, Leuciscinae)

    PubMed Central

    Pereira, C S A; Aboim, M A; Ráb, P; Collares-Pereira, M J

    2014-01-01

    Understanding the mechanisms underlying diversification and speciation by introgressive hybridization is currently one of the major challenges in evolutionary biology. Here, the analysis of hybridization between two pairs of Iberian Leuciscinae provided new data on independent hybrid zones involving Achondrostoma oligolepis (AOL) and Pseudochondrostoma duriense (PDU), and confirmed the occurrence of hybrids between AOL and Pseudochondrostoma polylepis (PPO). A multilevel survey combining morphological, genetic and cytogenomic markers on a vast population screening successfully sorted the selected fishes as admixed. Results were similar in both AOL × PDU and AOL × PPO systems. Overall, hybrid morphotypes, cytogenomic data and genetic profiling indicated preferential backcrossing and suggested AOL as a major genomic contributor. Moreover, results implied AOL as more permissive to introgression than PDU or PPO. Although PDU- and PPO-like individuals appeared more resilient to genome modifications, AOL appeared to be more involved and affected by the ongoing hybridization events, as chromosomal translocations were only found in AOL-like individuals. All hybrids analysed evidenced extensive ribosomal DNA (rDNA) polymorphism that was not found in parental species, but usually seen falling within the range of possible parental combinations. Yet, transgressive phenotypes that cannot be explained by normal recombination, including more rDNA clusters than expected or the occurrence of syntenic rDNAs, were also detected. Present results proved rapid genomic evolution providing the genetic novelty for species to persist. In addition, although the ultimate consequences of such apparently extensive and recurrent events remain unknown, modern genome-wide methodologies are of great promise towards answering questions concerning the causes, dynamics and impacts of hybridization. PMID:24220087

  2. Introgressive hybridization as a promoter of genome reshuffling in natural homoploid fish hybrids (Cyprinidae, Leuciscinae).

    PubMed

    Pereira, C S A; Aboim, M A; Ráb, P; Collares-Pereira, M J

    2014-03-01

    Understanding the mechanisms underlying diversification and speciation by introgressive hybridization is currently one of the major challenges in evolutionary biology. Here, the analysis of hybridization between two pairs of Iberian Leuciscinae provided new data on independent hybrid zones involving Achondrostoma oligolepis (AOL) and Pseudochondrostoma duriense (PDU), and confirmed the occurrence of hybrids between AOL and Pseudochondrostoma polylepis (PPO). A multilevel survey combining morphological, genetic and cytogenomic markers on a vast population screening successfully sorted the selected fishes as admixed. Results were similar in both AOL × PDU and AOL × PPO systems. Overall, hybrid morphotypes, cytogenomic data and genetic profiling indicated preferential backcrossing and suggested AOL as a major genomic contributor. Moreover, results implied AOL as more permissive to introgression than PDU or PPO. Although PDU- and PPO-like individuals appeared more resilient to genome modifications, AOL appeared to be more involved and affected by the ongoing hybridization events, as chromosomal translocations were only found in AOL-like individuals. All hybrids analysed evidenced extensive ribosomal DNA (rDNA) polymorphism that was not found in parental species, but usually seen falling within the range of possible parental combinations. Yet, transgressive phenotypes that cannot be explained by normal recombination, including more rDNA clusters than expected or the occurrence of syntenic rDNAs, were also detected. Present results proved rapid genomic evolution providing the genetic novelty for species to persist. In addition, although the ultimate consequences of such apparently extensive and recurrent events remain unknown, modern genome-wide methodologies are of great promise towards answering questions concerning the causes, dynamics and impacts of hybridization.

  3. Lake Ontario benthic prey fish assessment, 2015

    USGS Publications Warehouse

    Weidel, Brian C.; Walsh, M.G.; Holden, J. P.; Connerton, M.J.

    2016-01-01

    Benthic prey fishes are a critical component of the Lake Ontario food web, serving as energy vectors from benthic invertebrates to native and introduced piscivores. Since the late 1970’s, Lake Ontario benthic prey fish status was primarily assessed using bottom trawl observations confined to the lake’s south shore, in waters from 8 – 150 m (26 – 492 ft). In 2015, the Benthic Prey Fish Survey was cooperatively adjusted and expanded to address resource management information needs including lake-wide benthic prey fish population dynamics. Effort increased from 55 bottom trawl sites to 135 trawl sites collected in depths from 8 - 225m (26 – 738 ft). The spatial coverage of sampling was also expanded and occurred in all major lake basins. The resulting distribution of tow depths more closely matched the available lake depth distribution. The additional effort illustrated how previous surveys were underestimating lake-wide Deepwater Sculpin, Myoxocephalus thompsonii, abundance by not sampling in areas of highest density. We also found species richness was greater in the new sampling sites relative to the historic sites with 11 new fish species caught in the new sites including juvenile Round Whitefish, Prosopium cylindraceum, and Mottled sculpin, Cottus bairdii. Species-specific assessments found Slimy Sculpin, Cottus cognatus abundance increased slightly in 2015 relative to 2014, while Deepwater Sculpin and Round Goby, Neogobius melanostomus, dramatically increased in 2015, relative to 2014. The cooperative, lake-wide Benthic Prey Fish Survey expanded our understanding of benthic fish population dynamics and habitat use in Lake Ontario. This survey’s data and interpretations influence international resource management decision making, such as informing the Deepwater Sculpin conservation status and assessing the balance between sport fish consumption and prey fish populations. Additionally a significant Lake Ontario event occurred in May 2015 when a single

  4. Assessment of HER2 Status Using Immunohistochemistry (IHC) and Fluorescence In Situ Hybridization (FISH) Techniques in Mucinous Epithelial Ovarian Cancer: A Comprehensive Comparison between ToGA Biopsy Method and ToGA Surgical Specimen Method.

    PubMed

    Chao, Wan-Ru; Lee, Ming-Yung; Ruan, Alexandra; Sheng, Huang Pin; Hsu, Jeng-Dong; Han, Chih-Ping; Koo, Chiew-Loon

    2015-01-01

    We aimed to compare the assay performance characteristics of HER2 status in mucinous epithelial ovarian cancer (EOC) by ToGA (Trastuzumab for Gastric Cancer) biopsy versus ToGA surgical specimen methods. Forty-nine tissue microarray (TMA) samples of mucinous EOC from Asian women were analyzed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) tests using ToGA trial HER2 scoring methods. The overall concordance between IHC and FISH by the ToGA surgical specimen method is 97.56% and by the ToGA biopsy specimen method is 97.14%. The agreements of HER2 IHC results under both biopsy and surgical specimen methods were nearly perfect (weighted kappa = 0.845). Additionally, the percentage of Her2 FISH amplification showed increasing trend with increasing HER2 IHC ordinals (negative, equivocal, positive) by both TOGA biopsy (P<0.001) and surgical specimen method (P<0.001). After excluding equivocal cases, the sensitivity (100%), PPV (88.89%) and NPV (100%) of HER2 IHC were unchanged under either surgical specimen method or biopsy method. However, the specificity (96.97%) and accuracy (97.56%) of HER2 IHC was slightly higher under the surgical specimen method than those (specificity 96.30%, accuracy 97.14%) under the biopsy method. Of the total 49 cases, the number (n = 14) of HER2 IHC equivocal results under the ToGA biopsy method was 1.75-fold higher than those (n = 8) under the ToGA surgical specimen method (28.57% vs. 16.32%). Therefore, compared to ToGA surgery specimen method, the ToGA biopsy method caused more equivocal IHC cases to be referred to FISH testing and did not increase the detection rates of Her2 FISH amplification.

  5. Mitochondrial Genome Variation after Hybridization and Differences in the First and Second Generation Hybrids of Bream Fishes

    PubMed Central

    Zhang, Wei-Zhuo; Xiong, Xue-Mei; Zhang, Xiu-Jie; Wan, Shi-Ming; Guan, Ning-Nan; Nie, Chun-Hong; Zhao, Bo-Wen; Hsiao, Chung-Der; Wang, Wei-Min; Gao, Ze-Xia

    2016-01-01

    Hybridization plays an important role in fish breeding. Bream fishes contribute a lot to aquaculture in China due to their economically valuable characteristics and the present study included five bream species, Megalobrama amblycephala, Megalobrama skolkovii, Megalobrama pellegrini, Megalobrama terminalis and Parabramis pekinensis. As maternal inheritance of mitochondrial genome (mitogenome) involves species specific regulation, we aimed to investigate in which way the inheritance of mitogenome is affected by hybridization in these fish species. With complete mitogenomes of 7 hybrid groups of bream species being firstly reported in the present study, a comparative analysis of 17 mitogenomes was conducted, including representatives of these 5 bream species, 6 first generation hybrids and 6 second generation hybrids. The results showed that these 17 mitogenomes shared the same gene arrangement, and had similar gene size and base composition. According to the phylogenetic analyses, all mitogenomes of the hybrids were consistent with a maternal inheritance. However, a certain number of variable sites were detected in all F1 hybrid groups compared to their female parents, especially in the group of M. terminalis (♀) × M. amblycephala (♂) (MT×MA), with a total of 86 variable sites between MT×MA and its female parent. Among the mitogenomes genes, the protein-coding gene nd5 displayed the highest variability. The number of variation sites was found to be related to phylogenetic relationship of the parents: the closer they are, the lower amount of variation sites their hybrids have. The second generation hybrids showed less mitogenome variation than that of first generation hybrids. The non-synonymous and synonymous substitution rates (dN/dS) were calculated between all the hybrids with their own female parents and the results indicated that most PCGs were under negative selection. PMID:27391325

  6. Mitochondrial Genome Variation after Hybridization and Differences in the First and Second Generation Hybrids of Bream Fishes.

    PubMed

    Zhang, Wei-Zhuo; Xiong, Xue-Mei; Zhang, Xiu-Jie; Wan, Shi-Ming; Guan, Ning-Nan; Nie, Chun-Hong; Zhao, Bo-Wen; Hsiao, Chung-Der; Wang, Wei-Min; Gao, Ze-Xia

    2016-01-01

    Hybridization plays an important role in fish breeding. Bream fishes contribute a lot to aquaculture in China due to their economically valuable characteristics and the present study included five bream species, Megalobrama amblycephala, Megalobrama skolkovii, Megalobrama pellegrini, Megalobrama terminalis and Parabramis pekinensis. As maternal inheritance of mitochondrial genome (mitogenome) involves species specific regulation, we aimed to investigate in which way the inheritance of mitogenome is affected by hybridization in these fish species. With complete mitogenomes of 7 hybrid groups of bream species being firstly reported in the present study, a comparative analysis of 17 mitogenomes was conducted, including representatives of these 5 bream species, 6 first generation hybrids and 6 second generation hybrids. The results showed that these 17 mitogenomes shared the same gene arrangement, and had similar gene size and base composition. According to the phylogenetic analyses, all mitogenomes of the hybrids were consistent with a maternal inheritance. However, a certain number of variable sites were detected in all F1 hybrid groups compared to their female parents, especially in the group of M. terminalis (♀) × M. amblycephala (♂) (MT×MA), with a total of 86 variable sites between MT×MA and its female parent. Among the mitogenomes genes, the protein-coding gene nd5 displayed the highest variability. The number of variation sites was found to be related to phylogenetic relationship of the parents: the closer they are, the lower amount of variation sites their hybrids have. The second generation hybrids showed less mitogenome variation than that of first generation hybrids. The non-synonymous and synonymous substitution rates (dN/dS) were calculated between all the hybrids with their own female parents and the results indicated that most PCGs were under negative selection.

  7. Effect of graded fingerlings on hybrid catfish food fish size distribution

    USDA-ARS?s Scientific Manuscript database

    It is not unusual to have both 0.5 lb and 5 lb fish harvested from a single-batch hybrid catfish production pond at the end of the growing season. When that happens, farmers may be docked for fish that are either larger or smaller than the processor’s preferred size range. This study was conducted t...

  8. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... automated scanning microscope, image analysis system, and customized software applications for FISH assays...

  9. Reassociation and hybridization properties of DNAs from several species of fish

    USGS Publications Warehouse

    Gharrett, A.J.; Simon, R.C.; McIntyre, J.D.

    1977-01-01

    Reassociation and hybridization properties from spectrophotometric studies of DNAs from 10 species of fish indicate:1. Great diversity in the amounts of repeated sequences in the genomes of different species - more specialized fish had less redundancy.2. Large differences in the complexities of the DNAs - more specialized fish had less information.3. Little homology between sequences of remotely related species but substantial homology between sequences of closely related species.

  10. Role of fluorescence in situ hybridization (FISH) in sequencing the tomato genome

    USDA-ARS?s Scientific Manuscript database

    Chromosomes at various stages of the cell cycle can be used for localization of DNA probes via Fluorescence in situ hybridization (FISH). While mitotic metaphase chromosomes are demonstrably too short and compact for this purpose, long pachytene chromosomes are ideal. BACs that hybridize to euchrom...

  11. Active Fish Tracking Sonar (AFTS) for Assessing Fish Behavior

    SciTech Connect

    Hedgepeth, J; Johnson, Gary E. ); Skalski, John R.; Burczynski, J

    2002-11-01

    Active fish tracking sonars (AFTS) were used in 2001 to study fish movement in response to intake occlusion plates at The Dalles Dam on the Columbia River. AFTS provides three-dimensional fish tracks by aligning the axis of a split-beam transducer with a fish target. High-speed stepper motors move the transducer so that a tracked target remains on-axis. Occlusion plates with lateral extensions covered the top half of the turbine intakes to produce a fish friendly near-dam environment. Two AFTS were positioned at the center of Main Unit 1, one each for monitoring installed and removed plate conditions. A regression analysis showed that occlusion plates had pronounced effects on fish movement along the dam. The plates appeared to inhibit movement toward the spillway, movement toward the dam (especially in front of the turbine intake), and movement downward toward the turbines. Fish fate (as opposed to movement directions from regression slopes) into particular areas was determined using Markov-chain analysis. The sluiceway (a safer passage route above the turbine intake) zone of influence was larger with the occlusion plates installed, contrary to the regression results. In addition, the probability of passage out the near turbine and bottom sides of the sample volume was about 50% lower with occlusion plates installed.

  12. Preparation of Amniocytes for Interphase Fluorescence In Situ Hybridization (FISH).

    PubMed

    Schwartz, Stuart

    2015-04-01

    FISH has been used to detect and clarify deletions and/or other structural rearrangements, and also has applications in interphase analysis. This unit describes preparation of uncultured amniotic fluid cells for FISH analysis. Cells are swollen, and then slides are prepared by standard methods. The cells are then fixed and permeabilized for subsequent FISH. An alternate protocol describes attachment of amniocytes to a glass or plastic surface followed by hypotonic swelling, fixation, and permeabilization for subsequent FISH. Interphase FISH analysis of amniotic fluid cells is also described. Copyright © 2015 John Wiley & Sons, Inc.

  13. HER2 assessment by silver in situ hybridization: where are we now?

    PubMed

    Sanguedolce, Francesca; Bufo, Pantaleo

    2015-03-01

    HER2 testing in breast and gastric cancer is critical not only as a prognostic tool but also as a predictive marker for response to the humanized monoclonal antibody trastuzumab. Currently, HER2 status is assessed on histological and cytological specimens by conventional validated methods such as immunohistochemistry and FISH, while bright-field in situ hybridization techniques, such as silver in situ hybridization and chromogenic in situ hybridization, may offer performance benefits over FISH. The major points are first, technical issues, advantages and disadvantages relevant to each methods, and their clinical implications and second, the well-known genetic heterogeneity of HER2, and the occurrence of polysomy of chromosome 17. This review aims to summarize the growing body of literature on the accuracy of bright-field in situ techniques, notably silver in situ hybridization, in assessing HER2 status, and to discuss the role of such methods in pathology practice.

  14. The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance.

    PubMed

    Liu, Shaojun; Qin, Qinbo; Xiao, Jun; Lu, Wenting; Shen, Jiamin; Li, Wei; Liu, Jifang; Duan, Wei; Zhang, Chun; Tao, Min; Zhao, Rurong; Yan, Jinpeng; Liu, Yun

    2007-06-01

    This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp x blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (female symbol) x blunt snout bream (BSB) (male symbol) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.

  15. Current and historical hybridization with differential introgression among three species of cyprinid fishes (genus Cyprinella).

    PubMed

    Broughton, Richard E; Vedala, Krishna C; Crowl, Tessa M; Ritterhouse, Lauren L

    2011-05-01

    Hybridization is common among freshwater fishes, particular among the Cyprinidae. We used two mitochondrial genes and one nuclear gene to characterize hybridization among two species pairs of Cyprinella in southwestern North America. Genalogical patterns revealed that C. lutrensis and C. venusta are currently hybridizing in several localities producing apparent F(1), F(2) and backcross generations, yet there was no evidence for introgression outside of local hybrid zones. Alternatively, mitochondrial haplotypes from C. lutrensis appear to have introgressed into a C. lepida population in the Nueces River completely replacing the native C. lepida haplotype. There was no evidence of introgression of nuclear DNA and there does not appear to be ongoing hybridization. The population of C. lepida from the nearby Frio River exhibits no evidence of hybridization with C. lutrensis. Thus, contact between C. lutrensis and C. venusta results in the formation of localized hybrid swarms, while contact between C. lutrensis and C. lepida has resulted in complete mitochondrial introgression in the Nueces River or no apparent hybridization in the Frio River. The three different outcomes of contact between these species illustrate the variable nature of interspecific reproductive interactions and provide an excellent system in which to better understand the factors influencing hybridization among freshwater fishes.

  16. Micro fluorescence in situ hybridizationFISH) for spatially multiplexed analysis of a cell monolayer.

    PubMed

    Huber, D; Autebert, J; Kaigala, G V

    2016-04-01

    We here present a micrometer-scale implementation of fluorescence in situ hybridization that we term μFISH. This μFISH implementation makes use of a non-contact scanning probe technology, namely, a microfluidic probe (MFP) that hydrodynamically shapes nanoliter volumes of liquid on a surface with micrometer resolution. By confining FISH probes at the tip of this microfabricated scanning probe, we locally exposed approximately 1000 selected MCF-7 cells of a monolayer to perform incubation of probes - the rate-limiting step in conventional FISH. This method is compatible with the standard workflow of conventional FISH, allows re-budgeting of the sample for various tests, and results in a ~ 15-fold reduction in probe consumption. The continuous flow of probes and shaping liquid on these selected cells resulted in a 120-fold reduction of the hybridization time compared with the standard protocol (3 min vs. 6 h) and efficient rinsing, thereby shortening the total FISH assay time for centromeric probes. We further demonstrated spatially multiplexed μFISH, enabling the use of spectrally equivalent probes for detailed and real-time analysis of a cell monolayer, which paves the way towards rapid and automated multiplexed FISH on standard cytological supports.

  17. Influence of Environment and Mitochondrial Heritage on the Ecological Characteristics of Fish in a Hybrid Zone

    PubMed Central

    Stolzenberg, Nicolas; Nguyen The, Bénédicte; Salducci, Marie Dominique; Cavalli, Laurent

    2009-01-01

    Background Ecological characteristics (growth, morphology, reproduction) arise from the interaction between environmental factors and genetics. Genetic analysis of individuals' life history traits might be used to improve our understanding of mechanisms that form and maintain a hybrid zone. Methodology/Principal Findings A fish hybrid zone was used to characterize the process of natural selection. Data were collected during two reproductive periods (2001 and 2002) and 1117 individuals (nase, Chondrostama nasus nasus, sofie C. toxostoma toxostoma and hybrids) were sampled. Reproductive dates of the two parental species overlapped at sympatric sites. The nase had an earlier reproductive period than the sofie; males had longer reproductive periods for both species. Hybridisation between female nase and male sofie was the most likely. Hybrids had a reproductive period similar to the inherited parental mitochondrial type. Growth and reproductive information from different environments has been synthesised following a bayesian approach of the von Bertalanffy model. Hybrid life history traits appear to link with maternal heritage. Hybrid size from the age of two and size at first maturity appeared to be closer to the size of the maternal origin species (nase or sofie). Median growth rates for hybrids were similar and intermediate between those of the parental species. We observed variable life history traits for hybrids and pure forms in the different parts of the hybrid zone. Geometrical analysis of the hybrid fish shape gave evidence of two main morphologies with a link to maternal heritage. Conclusions/Significance Selective mating seemed to be the underlying process which, with mitochondrial heritage, could explain the evolution of the studied hybrid zone. More generally, we showed the importance of studies on hybrid zones and specifically the study of individuals' ecological characteristics, to improve our understanding of speciation. PMID:19536286

  18. Salmonellae in fish feces analyzed by in situ hybridization and quantitative polymerase chain reaction.

    PubMed

    Sha, Qiong; Forstner, Michael R J; Bonner, Timothy H; Hahn, Dittmar

    2013-09-01

    The potential of fish to transfer salmonellae from heterogeneous aquatic biofilms into feces was assessed in controlled aquarium studies with Suckermouth Catfish Hypostomus plecostomus and with biofilms inoculated with salmonellae. Neither the presence of catfish nor inoculation with salmonellae had detectable effects on the abundance of the microbial community. Densities of the microbial community were about 10(5) cells/mL in the water during a 1-week period, whereas densities of the microbial community increased 10-fold (10(6) to 10(7) cells/mg) in catfish feces during the same period. Salmonellae were detected by both quantitative polymerase chain reaction (qPCR) and situ hybridization in water samples immediately after inoculation, in numbers of about 10(4) cells/mL, representing up to 20% of the cells of the microbial community. Numbers decreased by three orders of magnitude within the first 3 d of the study, which represented only 0.01% of the community, and became undetectable after day 5. In catfish feces, numbers of Salmonella initially increased to up to 6% of the cells of the community but then declined. These results suggest that Salmonella are not biomagnified during gut passage, and thus, fish only provide a means for the translocation of this pathogen.

  19. Probabilistic assessment of uncertain adaptive hybrid composites

    NASA Technical Reports Server (NTRS)

    Shiao, Michael C.; Singhal, Surendra N.; Chamis, Christos C.

    1994-01-01

    Adaptive composite structures using actuation materials, such as piezoelectric fibers, were assessed probabilistically utilizing intraply hybrid composite mechanics in conjunction with probabilistic composite structural analysis. Uncertainties associated with the actuation material as well as the uncertainties in the regular (traditional) composite material properties were quantified and considered in the assessment. Static and buckling analyses were performed for rectangular panels with various boundary conditions and different control arrangements. The probability density functions of the structural behavior, such as maximum displacement and critical buckling load, were computationally simulated. The results of the assessment indicate that improved design and reliability can be achieved with actuation material.

  20. Magnetic-activated cell sorting (MACS) significantly decreases the hybridization efficiency of fluorescence in situ hybridization (FISH).

    PubMed

    Kuo, P L; Guo, H R

    2001-05-01

    Fetal cells were enriched from maternal blood using density gradient centrifugation of Histopaque followed by magnetic-activated cell sorting (MACS) to select CD71-positive cells. For each specimen, cells partially purified by Histopaque were split into equal portions, and each portion was subjected to purification by MACS in parallel. Cells before and after MACS were subjected to dual-color fluorescence in situ hybridization (FISH) analysis with X- and Y-chromosome-specific probes. We found that the hybridization rates were decreased by approximately 10% after MACS based on duplicated analysis for each sample.

  1. ASSESSING FISH TISSUE CONTAMINATION ON A REGIONAL SCALE

    EPA Science Inventory

    The selection of target fish species for assessing the extent of fish tissue contaminants is a critical consideration in regional stream surveys such as the Environmental Monitoring and Assessment Program (EMAP). The ideal species would be widely distributed and common, bioaccumu...

  2. A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes.

    PubMed

    Wang, Dan Ohtan; Matsuno, Hitomi; Ikeda, Shuji; Nakamura, Akiko; Yanagisawa, Hiroyuki; Hayashi, Yasunori; Okamoto, Akimitsu

    2012-01-01

    Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO-FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO-FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO-FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO-FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution.

  3. LARGE RIVER ASSESSMENT METHODS FOR BENTHIC MACROINVERTEBRATES AND FISH

    EPA Science Inventory

    Multiple projects are currently underway to increase our understanding of the varying results of different sampling methods and designs used for the biological assessment and monitoring of large (boatable) rivers. Studies include methods used to assess fish, benthic macroinverte...

  4. LARGE RIVER ASSESSMENT METHODS FOR BENTHIC MACROINVERTEBRATES AND FISH

    EPA Science Inventory

    Multiple projects are currently underway to increase our understanding of the varying results of different sampling methods and designs used for the biological assessment and monitoring of large (boatable) rivers. Studies include methods used to assess fish, benthic macroinverte...

  5. DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) in buccal cells.

    PubMed

    Cortés-Gutiérrez, E I; Dávila-Rodríguez, M I; Fernández, J L; López-Fernández, C; Gosálvez, J

    2012-12-28

    DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) is a recently developed technique that allows cell-by-cell detection and quantification of DNA breakage in the whole genome or within specific DNA sequences. The present investigation was conducted to adapt the methodology of DBD-FISH to the visualization and evaluation of DNA damage in buccal epithelial cells. DBD-FISH revealed that DNA damage increased significantly according to H2O2 concentration (r2=0.91). In conclusion, the DBD-FISH technique is easy to apply in buccal cells and provides prompt results that are easy to interpret. Future studies are needed to investigate the potential applicability of a buccal cell DBD-FISH model to human biomonitoring and nutritional work.

  6. Equivocal ALK fluorescence in-situ hybridization (FISH) cases may benefit from ancillary ALK FISH probe testing.

    PubMed

    Selinger, Christina; Cooper, Wendy; Lum, Trina; McNeil, Catriona; Morey, Adrienne; Waring, Paul; Amanuel, Benhur; Millward, Michael; Peverall, Joanne; Van Vliet, Chris; Christie, Michael; Tran, Yen; Diakos, Connie; Pavlakis, Nick; Gill, Anthony J; O'Toole, Sandra

    2015-11-01

    Accurate assessment of anaplastic lymphoma kinase (ALK) gene rearrangement in non-small-cell lung cancers (NSCLCs) is critical to identify patients who are likely to respond to crizotinib. The aim of this study was to evaluate the ALK/EML4 TriCheck FISH probe in a series of NSCLCs enriched for tumours with equivocal ALK status. ALK FISH was prospectively performed on 45 NSCLCs with the ALK/EML4 TriCheck probe (ZytoVision) and the Vysis ALK break-apart probe (Abbott Molecular). ALK immunohistochemistry was performed with 5A4 and D5F3 antibodies. Fourteen cases had equivocal ALK status, based on borderline or focal FISH positivity, an atypical FISH pattern, or discrepancy between ALK FISH and immunohistochemistry. Four of the 14 equivocal cases showed discordance between the two FISH probes. All other cases were concordant. The TriCheck probe showed that, of 31 unequivocal cases, 15 were ALK-rearranged, and 60% of these had EML4 as the translocation partner. Within the group of 14 equivocal cases, 12 showed rearrangement with the Tricheck probe; only one of these showed EML4 rearrangement. Of the six equivocal cases that received crizotinib, four showed clinical benefit. The ALK/EML4 TriCheck FISH probe may be useful for the detection of ALK rearrangements, especially in borderline or atypical cases, where an additional unique ALK FISH probe may provide further confirmation of rearrangement. © 2015 John Wiley & Sons Ltd.

  7. Cytonuclear genetics of experimental fish hybrid zones inside Biosphere 2

    USGS Publications Warehouse

    Scribner, K.T.; Avise, John C.

    1994-01-01

    Two species of mosquitofish (family Poeciliidae) known to hybridize in nature were introduced into freshwater habitats inside Biosphere 2, and their population genetics were monitored after 2 years. Within four to six generations, nuclear and cytoplasmic markers characteristic of Gambusia holbrooki had risen greatly in frequency, although some Gambusia affinis alleles and haplotypes were retained primarily in recombinant genotypes, indicative of introgressive hybridization. The temporal cytonuclear dynamics proved similar to population genetic changes observed in replicated experimental hybrid populations outside of Biosphere 2, thus indicating strong directional selection favoring G. holbrooki genotypes across the range of environments monitored. When interpreted in the context of species-specific population demographies observed previously, results suggest that the extremely rapid evolution in these zones of secondary contact is attributable primarily to species differences in life-history traits.

  8. Confirmation of hybridity using GISH and determination of 18S rDNA copy number using FISH in interspecific F(1) hybrids of Tecoma (Bignoniaceae).

    PubMed

    Contreras, Ryan N; Ruter, John M; Conner, Joann; Zeng, Yajuan; Ozias-Akins, Peggy

    2012-06-01

    Interspecific hybridization in Tecoma Juss. was conducted to develop novel forms for the nursery industry. We report fertile hybrids from the cross T. garrocha Hieron. (pistillate parent) × T. stans (L.) Juss. ex Kunth. Leaf morphology of the F(1) hybrids of T. garrocha × T. stans was intermediate between the parents. GISH also confirmed hybridity. The F(1) hybrids were successfully backcrossed to both parents and self-pollinated to produce BC and F(2) progeny. Tecoma garrocha , T. stans, and T. guarume A. DC. 'Tangelo' were self-fertile. The F(1) hybrids also were crossed with T. capensis (Thunb.) Lindl. and T. guarume 'Tangelo', resulting in three-species hybrids. FISH conducted on F(1) hybrids identified four copies of the 18S internal transcribed spacer region. Further analysis using FISH has the potential to provide information on the evolution of Bignoniaceae and the potential role of polyploidy.

  9. Effectiveness of fishing gears to assess fish assemblage size structure in small lake ecosystems

    Treesearch

    T. A. Clement; K. Pangle; D. G. Uzarski; B. A. Murry

    2014-01-01

    Measurement of fish body-size distributions is increasingly used as a management tool to assess fishery status. However, the effects of gear selection on observed fish size structure has not received sufficient attention. Four different gear types (experimental gill nets, fine mesh bag seine, and two different sized mesh trap nets), which are commonly employed in the...

  10. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  11. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  12. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology...

  13. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology...

  14. Inconsistent phylogeographic pattern between a sperm dependent fish and its host: in situ hybridization vs dispersal.

    PubMed

    Vergilino, Roland; Leung, Christelle; Angers, Bernard

    2016-09-06

    Co-dispersal of sperm-dependent hybrids and their sexual relatives is expected to result in consistent spatial patterns between assemblages of hybrids and genetic structure of parental species. However, local hybridization events may blur this signal as assemblages could be organized under different connectivity constraints. This study aims at testing the hypothesis of local hybridization events by comparing the assemblage of hybrid fish Chrosomus eos-neogaeus to the genetic diversity of one of its parental species, Chrosomus eos. An extensive survey performed on a total of 132 sites located in two regions of Southern Quebec (West-Qc and East-Qc) revealed a distinct organization of hybrid lineages. One of the six hybrid lineages detected in West-Qc is widespread throughout this region resulting in a low α-diversity (1.38) and β-diversity (4.35). On the other hand, 36 hybrid lineages were detected in East-Qc and displayed narrow geographic distributions leading to a high α-diversity (2.30) and β-diversity (15.68). In addition, the C. eos multilocus haplotype of several of these hybrids is assigned to their respective sympatric C. eos population. Finally, contrasting with hybrids, the paternal species C. eos displayed a higher ρST in West-Qc (0.2300) than in East-Qc (0.0734). The unusually high diversity of hybrid lineages in East-Qc as well as the spatial organization and the close genetic relationship with C. eos sympatric populations support the hypothesis that multiple hybridization events occurred in situ. These findings coupled to the near absence of the maternal species Chrosomus neogeaus suggest that the decline of this species could be the trigger event at the origin of the high rates of spontaneous hybridization in this region.

  15. Water quality in hybrid catfish ponds after partial fish harvest

    USDA-ARS?s Scientific Manuscript database

    Intensification of United States catfish aquaculture involves hybrid catfish ('channel catfish Ictalurus punctatus x ' blue catfish I. furcatus) grown in ponds with abundant aeration and high feeding rates. High feeding rates cause water quality deterioration because most of the nitrogen, phosphorus...

  16. Nondestructive spectroscopic and imaging techniques for quality evaluation and assessment of fish and fish products.

    PubMed

    He, Hong-Ju; Wu, Di; Sun, Da-Wen

    2015-01-01

    Nowadays, people have increasingly realized the importance of acquiring high quality and nutritional values of fish and fish products in their daily diet. Quality evaluation and assessment are always expected and conducted by using rapid and nondestructive methods in order to satisfy both producers and consumers. During the past two decades, spectroscopic and imaging techniques have been developed to nondestructively estimate and measure quality attributes of fish and fish products. Among these noninvasive methods, visible/near-infrared (VIS/NIR) spectroscopy, computer/machine vision, and hyperspectral imaging have been regarded as powerful and effective analytical tools for fish quality analysis and control. VIS/NIR spectroscopy has been widely applied to determine intrinsic quality characteristics of fish samples, such as moisture, protein, fat, and salt. Computer/machine vision on the other hand mainly focuses on the estimation of external features like color, weight, size, and surface defects. Recently, by incorporating both spectroscopy and imaging techniques in one system, hyperspectral imaging cannot only measure the contents of different quality attributes simultaneously, but also obtain the spatial distribution of such attributes when the quality of fish samples are evaluated and measured. This paper systematically reviews the research advances of these three nondestructive optical techniques in the application of fish quality evaluation and determination and discuss future trends in the developments of nondestructive technologies for further quality characterization in fish and fish products.

  17. Telomere analysis of platyhelminths and acanthocephalans by FISH and Southern hybridization.

    PubMed

    Bombarová, Marta; Vítková, Magda; Spakulová, Marta; Koubková, Bozena

    2009-11-01

    We examined the composition of telomeres in chromosomes of parasitic worms, representatives of the flatworm groups Monogenea and Cestoda (Platyhelminthes), and thorny-headed worms (Syndermata: Acanthocephala) by fluorescence in situ hybridization (FISH) with different telomeric repeat probes. Our results show that the (TTAGGG)n sequence, supposed to be the ancestral telomeric repeat motif of Metazoa, is conserved in Monogenea (Paradiplozoon homoion) and Cestoda (Caryophyllaeus laticeps, Caryophyllaeides fennica, and Nippotaenia mogurndae) but not in Acanthocephala (Pomphorhynchus laevis and Pomphorhynchus tereticollis). In the Pomphorhynchus species, no hybridization signals were obtained with the "nematode" (TTAGGC)n, "arthropod" (TTAGG)n, and bdelloid (TGTGGG)n telomeric probes using FISH with their chromosomes and Southern hybridization with P. laevis DNA. Therefore, we suggest that parasitic Acanthocephala have evolved yet unknown telomeric repeat motifs or different mechanisms of telomere maintenance.

  18. Hybrid vehicle potential assessment. Volume 7: Hybrid vehicle review

    NASA Technical Reports Server (NTRS)

    Leschly, K. O.

    1979-01-01

    Review of hybrid vehicles built during the past ten years or planned to be built in the near future is presented. An attempt is made to classify and analyze these vehicles to get an overall picture of their key characteristics. The review includes onroad hybrid passenger cars, trucks, vans, and buses.

  19. Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes.

    PubMed

    Wallis, Graham P; Cameron-Christie, Sophia R; Kennedy, Hannah L; Palmer, Gemma; Sanders, Tessa R; Winter, David J

    2017-06-01

    Classification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNA alone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here, we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater. We test the hypothesis that freshwater fish phylogenies should, on average, show more discordance because of their higher propensity for hybridization in the past. In keeping with this idea, concordance between mitochondrial and nuclear gene trees (as measured by proportion of components shared) is on average 50% higher in marine fishes. We discuss why this difference almost certainly results from introgression caused by greater historical hybridization among lineages in freshwater groups, and further emphasize the need to use multiple nuclear genes, and identify conflict among them, in estimation of species phylogeny. © 2017 John Wiley & Sons Ltd.

  20. Ocean warming, a rapid distributional shift, and the hybridization of a coastal fish species.

    PubMed

    Potts, Warren M; Henriques, Romina; Santos, Carmen V; Munnik, Kate; Ansorge, Isabelle; Dufois, Francois; Booth, Anthony J; Kirchner, Carola; Sauer, Warwick H H; Shaw, Paul W

    2014-09-01

    Despite increasing awareness of large-scale climate-driven distribution shifts in the marine environment, no study has linked rapid ocean warming to a shift in distribution and consequent hybridization of a marine fish species. This study describes rapid warming (0.8 °C per decade) in the coastal waters of the Angola-Benguela Frontal Zone over the last three decades and a concomitant shift by a temperature sensitive coastal fish species (Argyrosomus coronus) southward from Angola into Namibia. In this context, rapid shifts in distribution across Economic Exclusive Zones will complicate the management of fishes, particularly when there is a lack of congruence in the fisheries policy between nations. Evidence for recent hybridization between A. coronus and a congener, A. inodorus, indicate that the rapid shift in distribution of A. coronus has placed adults of the two species in contact during their spawning events. Ocean warming may therefore revert established species isolation mechanisms and alter the evolutionary history of fishes. While the consequences of the hybridization on the production of the resource remain unclear, this will most likely introduce additional layers of complexity to their management.

  1. Automictic reproduction in interspecific hybrids of poeciliid fish.

    PubMed

    Lampert, Kathrin P; Lamatsch, Dunja K; Fischer, Petra; Epplen, Jörg T; Nanda, Indrajit; Schmid, Michael; Schartl, Manfred

    2007-11-20

    Automixis, the process whereby the fusion of meiotic products restores the diploid state of the egg, is a common mode of reproduction in plants but has also been described in invertebrate animals. In vertebrates, however, automixis has so far only been discussed as one of several explanations for isolated cases of facultative parthenogenesis. Analyzing oocyte formation in F1 hybrids derived from Poecilia mexicana limantouri and P. latipinna crosses (the cross that led to the formation of the gynogenetic Poecilia formosa), we found molecular evidence for automictic oocyte production. The mechanism involves the random fusion of meiotic products after the second meiotic division. The fertilization of diploid oocytes gives rise to fully viable triploid offspring. Although the automictic production of diploid oocytes as seen in these F1 hybrids clearly represents a preadaptation to parthenogenetic reproduction, it is also a powerful intrinsic postzygotic isolation mechanism because the resulting next generation triploids were always sterile. The mechanism described here can explain facultative parthenogenesis, as well as varying ploidy levels reported in different animal groups. Most importantly, at least some of the reported cases of triploidy in humans can now be traced back to automixis.

  2. SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK FOR ENDANGERED FISHES

    EPA Science Inventory

    Rainbow trout, fathead minnows, and sheepshead minnows were tested as surrogate species to assess contaminant risk for 17 endangered fishes and one toad species. Acute toxicity tests were conducted with carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin in accord...

  3. SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK FOR ENDANGERED FISHES

    EPA Science Inventory

    Rainbow trout, fathead minnows, and sheepshead minnows were tested as surrogate species to assess contaminant risk for 17 endangered fishes and one toad species. Acute toxicity tests were conducted with carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin in accord...

  4. Fully automated fluorescent in situ hybridization (FISH) staining and digital analysis of HER2 in breast cancer: a validation study.

    PubMed

    van der Logt, Elise M J; Kuperus, Deborah A J; van Setten, Jan W; van den Heuvel, Marius C; Boers, James E; Schuuring, Ed; Kibbelaar, Robby E

    2015-01-01

    HER2 assessment is routinely used to select patients with invasive breast cancer that might benefit from HER2-targeted therapy. The aim of this study was to validate a fully automated in situ hybridization (ISH) procedure that combines the automated Leica HER2 fluorescent ISH system for Bond with supervised automated analysis with the Visia imaging D-Sight digital imaging platform. HER2 assessment was performed on 328 formalin-fixed/paraffin-embedded invasive breast cancer tumors on tissue microarrays (TMA) and 100 (50 selected IHC 2+ and 50 random IHC scores) full-sized slides of resections/biopsies obtained for diagnostic purposes previously. For digital analysis slides were pre-screened at 20x and 100x magnification for all fluorescent signals and supervised-automated scoring was performed on at least two pictures (in total at least 20 nuclei were counted) with the D-Sight HER2 FISH analysis module by two observers independently. Results were compared to data obtained previously with the manual Abbott FISH test. The overall agreement with Abbott FISH data among TMA samples and 50 selected IHC 2+ cases was 98.8% (κ = 0.94) and 93.8% (κ = 0.88), respectively. The results of 50 additionally tested unselected IHC cases were concordant with previously obtained IHC and/or FISH data. The combination of the Leica FISH system with the D-Sight digital imaging platform is a feasible method for HER2 assessment in routine clinical practice for patients with invasive breast cancer.

  5. itFISH: Enhanced Staining by Iterative Fluorescent In Situ Hybridization.

    PubMed

    Row, Richard H; Martin, Benjamin L

    2017-03-20

    Fluorescent in situ hybridization (FISH) is an important tool for zebrafish research, particularly when observing the expression of two different genes in the same embryo. Peroxidase-catalyzed deposition of tyramide-conjugated dyes is a widely used and cost-effective approach to performing FISH. A major limitation of the technique is that it does not work well for weakly expressed genes. Here we present a method adapted from planarian research for use in zebrafish that provides a dramatic enhancement of weak staining. By iterating the antibody staining and development steps, a strong signal can be obtained from probes that were previously too weak to detect.

  6. A Winner Determination Algorithm for Combinatorial Auctions Based on Hybrid Artificial Fish Swarm Algorithm

    NASA Astrophysics Data System (ADS)

    Zheng, Genrang; Lin, ZhengChun

    The problem of winner determination in combinatorial auctions is a hotspot electronic business, and a NP hard problem. A Hybrid Artificial Fish Swarm Algorithm(HAFSA), which is combined with First Suite Heuristic Algorithm (FSHA) and Artificial Fish Swarm Algorithm (AFSA), is proposed to solve the problem after probing it base on the theories of AFSA. Experiment results show that the HAFSA is a rapidly and efficient algorithm for The problem of winner determining. Compared with Ant colony Optimization Algorithm, it has a good performance with broad and prosperous application.

  7. Multiplex Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA-FISH) for Diagnosis of Bacterial Vaginosis.

    PubMed

    Machado, Antonio; Cerca, Nuno

    2017-01-01

    Fluorescence in situ hybridization (FISH) is a molecular method used to identify and quantify microorganisms in a wide range of samples. This technique combines the simplicity of microscopic observation and the specificity of DNA/rRNA hybridization, allowing detection of selected bacterial species and morphologic visualization. Here, we describe a quantitative molecular diagnosis of bacterial vaginosis, based on the classical Nugent score. Our probes are able to differentiate Lactobacillus spp. and Gardnerella vaginalis from the other undefined bacterial species considered in the Nugent score.

  8. Hybridization of reef fishes at the Indo-Pacific biogeographic barrier: a case study

    NASA Astrophysics Data System (ADS)

    Marie, A. D.; van Herwerden, L.; Choat, J. H.; Hobbs, J.-P. A.

    2007-12-01

    Hybridization is recognized as an important source of genetic variation. In some reef fishes, including the Acanthuridae, hybridization has been detected due to intermediate colouration. This study used a molecular genetic approach to investigate hybridization in two Acanthurid species: Acanthurus leucosternon and Acanthurus nigricans, which have Indian and Pacific Ocean distributions respectively and are sympatric in the eastern Indian Ocean. In this area a putatitve hybrid, Acanthurus cf. leucosternon has been recognized based on intermediate colouration and restriction to the sympatric region of otherwise allopatric putative parental species. This study aimed to test this hypothesis using genetic tools. The three species were sampled from Cocos (Keeling) and Christmas Islands, the biogeographic boundary where many Indian and Pacific Ocean biota meet. Representatives from allopatric populations of both parental species and outgroups were also sampled. Mitochondrial COI and intron 1 of the nuclear ribosomal protein S7 were sequenced from 13 and 30 specimens respectively. Although sample sizes in this study are relatively small and more genetic data, including an extended phylogeographic sampling, is required to further evaluate these findings, the COI results support hybrid origins of Acanthurus cf. leucosternon, but S7 data are inconclusive due to the possibility of incomplete lineage sorting . The fourfold more abundant Acanthurus nigricans is most often the maternal parent. Inter-fertile hybrids apparently backcross with rare Acanthurus leucosternon males, transferring Acanthurus nigricans mitochondria to this species. These results suggest that Acanthurus leucosternon may eventually be lost from these islands, due to their relative rarity and introgressive hybridization.

  9. Does interspecies hybridization affect the host specificity of parasites in cyprinid fish?

    PubMed

    Simková, Andrea; Dávidová, Martina; Papoušek, Ivo; Vetešník, Lukáš

    2013-04-12

    Host specificity varies among parasite species. Some parasites are strictly host-specific, others show a specificity for congeneric or non-congeneric phylogenetically related host species, whilst some others are non-specific (generalists). Two cyprinids, Cyprinus carpio and Carassius gibelio, plus their respective hybrids were investigated for metazoan parasites. The aim of this study was to analyze whether interspecies hybridization affects host specificity. The different degrees of host specificity within a phylogenetic framework were taken into consideration (i.e. strict specialist, intermediate specialist, and intermediate generalist). Fish were collected during harvesting the pond and identified using meristic traits and molecular markers. Metazoan parasite species were collected. Host specificity of parasites was determined using the following classification: strict specialist, intermediate specialist, intermediate generalist and generalist. Parasite species richness was compared between parental species and their hybrids. The effect of host species on abundance of parasites differing in host specificity was tested. Hybrids harbored more different parasite species but their total parasite abundance was lower in comparison with parental species. Interspecies hybridization affected the host specificity of ecto- and endoparasites. Parasite species exhibiting different degrees of host specificity for C. carpio and C. gibelio were also present in hybrids. The abundance of strict specialists of C. carpio was significantly higher in parental species than in hybrids. Intermediate generalists parasitizing C. carpio and C. gibelio as two phylogenetically closely related host species preferentially infected C. gibelio when compared to C. carpio, based on prevalence and maximum intensity of infection. Hybrids were less infected by intermediate generalists when compared to C. gibelio. This finding does not support strict co-adaptation between host and parasite genotypes

  10. Does interspecies hybridization affect the host specificity of parasites in cyprinid fish?

    PubMed Central

    2013-01-01

    Background Host specificity varies among parasite species. Some parasites are strictly host-specific, others show a specificity for congeneric or non-congeneric phylogenetically related host species, whilst some others are non-specific (generalists). Two cyprinids, Cyprinus carpio and Carassius gibelio, plus their respective hybrids were investigated for metazoan parasites. The aim of this study was to analyze whether interspecies hybridization affects host specificity. The different degrees of host specificity within a phylogenetic framework were taken into consideration (i.e. strict specialist, intermediate specialist, and intermediate generalist). Methods Fish were collected during harvesting the pond and identified using meristic traits and molecular markers. Metazoan parasite species were collected. Host specificity of parasites was determined using the following classification: strict specialist, intermediate specialist, intermediate generalist and generalist. Parasite species richness was compared between parental species and their hybrids. The effect of host species on abundance of parasites differing in host specificity was tested. Results Hybrids harbored more different parasite species but their total parasite abundance was lower in comparison with parental species. Interspecies hybridization affected the host specificity of ecto- and endoparasites. Parasite species exhibiting different degrees of host specificity for C. carpio and C. gibelio were also present in hybrids. The abundance of strict specialists of C. carpio was significantly higher in parental species than in hybrids. Intermediate generalists parasitizing C. carpio and C. gibelio as two phylogenetically closely related host species preferentially infected C. gibelio when compared to C. carpio, based on prevalence and maximum intensity of infection. Hybrids were less infected by intermediate generalists when compared to C. gibelio. Conclusions This finding does not support strict co

  11. Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish

    PubMed Central

    2009-01-01

    Background Transgressive segregation describes the occurrence of novel phenotypes in hybrids with extreme trait values not observed in either parental species. A previously experimentally untested prediction is that the amount of transgression increases with the genetic distance between hybridizing species. This follows from QTL studies suggesting that transgression is most commonly due to complementary gene action or epistasis, which become more frequent at larger genetic distances. This is because the number of QTLs fixed for alleles with opposing signs in different species should increase with time since speciation provided that speciation is not driven by disruptive selection. We measured the amount of transgression occurring in hybrids of cichlid fish bred from species pairs with gradually increasing genetic distances and varying phenotypic similarity. Transgression in multi-trait shape phenotypes was quantified using landmark-based geometric morphometric methods. Results We found that genetic distance explained 52% and 78% of the variation in transgression frequency in F1 and F2 hybrids, respectively. Confirming theoretical predictions, transgression when measured in F2 hybrids, increased linearly with genetic distance between hybridizing species. Phenotypic similarity of species on the other hand was not related to the amount of transgression. Conclusion The commonness and ease with which novel phenotypes are produced in cichlid hybrids between unrelated species has important implications for the interaction of hybridization with adaptation and speciation. Hybridization may generate new genotypes with adaptive potential that did not reside as standing genetic variation in either parental population, potentially enhancing a population's responsiveness to selection. Our results make it conceivable that hybridization contributed to the rapid rates of phenotypic evolution in the large and rapid adaptive radiations of haplochromine cichlids. PMID:19961584

  12. Limited variability in upper thermal tolerance among pure and hybrid populations of a cold-water fish

    PubMed Central

    Wells, Zachery R. R.; McDonnell, Laura H.; Chapman, Lauren J.; Fraser, Dylan J.

    2016-01-01

    As climate warming threatens the persistence of many species and populations, it is important to forecast their responses to warming thermal regimes. Climate warming often traps populations in smaller habitat fragments, not only changing biotic parameters, but potentially decreasing adaptive potential by decreasing genetic variability. We examined the ability of six genetically distinct and different-sized populations of a cold-water fish (brook trout, Salvelinus fontinalis) to tolerate acute thermal warming and whether this tolerance could be altered by hybridizing populations. Critical thermal maximum (CTmax) assays were conducted on juveniles from each population to assess thermal tolerance, and the agitation temperature was recorded for assessing behavioural changes to elevated temperatures. An additional metric, which we have called the ‘CTmax–agitation window’ (CTmax minus agitation temperature), was also assessed. The CTmax differed between five out of 15 population pairs, although the maximal CTmax difference was only 0.68°C (29.11–29.79°C). Hybridization between one large population and two small populations yielded no obvious heterosis in mean CTmax, and no differences in agitation temperature or CTmax–agitation window were detected among pure populations or hybrids. Summer variation in temperature within each stream was negatively correlated with mean CTmax and mean CTmax–agitation window, although the maximal difference was small. Despite being one of the most phenotypically divergent and plastic north temperate freshwater fishes, our results suggest that limited variability exists in CTmax among populations of brook trout, regardless of their population size, standing genetic variation and differing natural thermal regimes (temperature variation, minimum and maximum). This study highlights the level to which thermal tolerance is conserved between isolated populations of a vertebrate species, in the face of climate warming. PMID:27990291

  13. Yeasts identification in microfluidic devices using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH).

    PubMed

    Ferreira, André M; Cruz-Moreira, Daniela; Cerqueira, Laura; Miranda, João M; Azevedo, Nuno F

    2017-03-01

    Peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) is a highly specific molecular method widely used for microbial identification. Nonetheless, and due to the detection limit of this technique, a time-consuming pre-enrichment step is typically required before identification. In here we have developed a lab-on-a-chip device to concentrate cell suspensions and speed up the identification process in yeasts. The PNA-FISH protocol was optimized to target Saccharomyces cerevisiae, a common yeast that is very relevant for several types of food industries. Then, several coin-sized microfluidic devices with different geometries were developed. Using Computational fluid dynamics (CFD), we modeled the hydrodynamics inside the microchannels and selected the most promising options. SU-8 structures were fabricated based on the selected designs and used to produce polydimethylsiloxane-based microchips by soft lithography. As a result, an integrated approach combining microfluidics and PNA-FISH for the rapid identification of S. cerevisiae was achieved. To improve fluid flow inside microchannels and the PNA-FISH labeling, oxygen plasma treatment was applied to the microfluidic devices and a new methodology to introduce the cell suspension and solutions into the microchannels was devised. A strong PNA-FISH signal was observed in cells trapped inside the microchannels, proving that the proposed methodology works as intended. The microfluidic designs and PNA-FISH procedure described in here should be easily adaptable for detection of other microorganisms of similar size.

  14. Fluorescence In Situ Hybridization (FISH) Assays for Diagnosing Malaria in Endemic Areas

    PubMed Central

    Shah, Jyotsna; Mark, Olivia; Weltman, Helena; Barcelo, Nicolas; Lo, Wai; Wronska, Danuta; Kakkilaya, Srinivas; Rao, Aravinda; Bhat, Shalia T.; Sinha, Ruchi; Omar, Sabah; Moro, Manuel; Gilman, Robert H.; Harris, Nick

    2015-01-01

    Malaria is a responsible for approximately 600 thousand deaths worldwide every year. Appropriate and timely treatment of malaria can prevent deaths but is dependent on accurate and rapid diagnosis of the infection. Currently, microscopic examination of the Giemsa stained blood smears is the method of choice for diagnosing malaria. Although it has limited sensitivity and specificity in field conditions, it still remains the gold standard for the diagnosis of malaria. Here, we report the development of a fluorescence in situ hybridization (FISH) based method for detecting malaria infection in blood smears and describe the use of an LED light source that makes the method suitable for use in resource-limited malaria endemic countries. The Plasmodium Genus (P-Genus) FISH assay has a Plasmodium genus specific probe that detects all five species of Plasmodium known to cause the disease in humans. The P. falciparum (PF) FISH assay and P. vivax (PV) FISH assay detect and differentiate between P. falciparum and P. vivax respectively from other Plasmodium species. The FISH assays are more sensitive than Giemsa. The sensitivities of P-Genus, PF and PV FISH assays were found to be 98.2%, 94.5% and 98.3%, respectively compared to 89.9%, 83.3% and 87.9% for the detection of Plasmodium, P. falciparum and P. vivax by Giemsa staining respectively. PMID:26333092

  15. Design of Hybrid Solar and Wind Energy Harvester for Fishing Boat

    NASA Astrophysics Data System (ADS)

    Banjarnahor, D. A.; Hanifan, M.; Budi, E. M.

    2017-07-01

    In southern beach of West Java, Indonesia, there are many villagers live as fishermen. They use small boats for fishing, in one to three days. Therefore, they need a fish preservation system. Fortunately, the area has high potential of solar and wind energy. This paper presents the design of a hybrid solar and wind energy harvester to power a refrigerator in the fishing boat. The refrigerator should keep the fish in 2 - 4 °C. The energy needed is 720 Wh daily. In the area, the daily average wind velocity is 4.27 m/s and the sun irradiation is 672 W/m2. The design combined two 100W solar panels and a 300W wind turbine. The testing showed that the solar panels can harvest 815 - 817 Wh of energy, while the wind turbine can harvest 43 - 62 Wh of energy daily. Therefore, the system can fulfil the energy requirement in fishing boat, although the solar panels were more dominant. To install the wind turbine on the fishing-boat, a computational design had been conducted. The boat hydrostatic dimension was measured to determine its stability condition. To reach a stable equilibrium condition, the wind turbine should be installed no more than 1.7 m of height.

  16. Detection of VHSV IVb within the gonads of Great Lakes fish using in situ hybridization.

    PubMed

    Al-Hussinee, L; Lumsden, J S

    2011-05-24

    Viral haemorrhagic septicaemia virus (VHSV) genotype IVb was recently detected as the cause of numerous mortality events in Great Lakes fish. In situ hybridization was used to examine the gonads from 13 fish, including freshwater drum Aplodinotus grunniens and muskellunge Esox masquinongy that were infected naturally, as well as rainbow trout Oncorhynchus mykiss and fathead minnows Pimphales promelas, which were experimentally infected. Although the ovaries and testes of fish infected by VHSV IVb had few lesions, viral RNA was present in the ovaries of the rainbow trout and fathead minnow and was abundant in the gonads of muskellunge and in the ovaries of freshwater drum. Viral RNA was present mainly surrounding yolk vacuoles/granules or adjacent to the germinal vesicle, with lesser amounts found within the germinal vesicle, in the mesovarium and/or tunica albuginea and blood vessels of the ovary. Viral RNA was also found in and surrounding primary and secondary spermatocytes of the muskellunge.

  17. Simultaneous specific in planta visualization of root-colonizing fungi using fluorescence in situ hybridization (FISH).

    PubMed

    Vági, Pál; Knapp, Dániel G; Kósa, Annamária; Seress, Diána; Horváth, Áron N; Kovács, Gábor M

    2014-05-01

    In planta detection of mutualistic, endophytic, and pathogenic fungi commonly colonizing roots and other plant organs is not a routine task. We aimed to use fluorescence in situ hybridization (FISH) for simultaneous specific detection of different fungi colonizing the same tissue. We have adapted ribosomal RNA (rRNA) FISH for visualization of common mycorrhizal (arbuscular- and ectomycorrhiza) and endophytic fungi within roots of different plant species. Beside general probes, we designed and used specific ones hybridizing to the large subunit of rRNA with fluorescent dyes chosen to avoid or reduce the interference with the autofluorescence of plant tissues. We report here an optimized efficient protocol of rRNA FISH and the use of both epifluorescence and confocal laser scanning microscopy for simultaneous specific differential detection of those fungi colonizing the same root. The method could be applied for the characterization of other plant-fungal interactions, too. In planta FISH with specific probes labeled with appropriate fluorescent dyes could be used not only in basic research but to detect plant colonizing pathogenic fungi in their latent life-period.

  18. Risk stratification of plasma cell neoplasm: insights from plasma cell-specific cytoplasmic immunoglobulin fluorescence in situ hybridization (cIg FISH) vs. conventional FISH.

    PubMed

    Dong, Henry; Yang, Hai-Su; Jagannath, Sundar; Stephenson, Christine F; Brenholz, Pauline; Mazumder, Amitabha; Chari, Ajai

    2012-10-01

    We directly compared the results of routine fluorescence in situ hybridization (FISH) and plasma cell-specific cytoplasmic immunoglobulin (cIg) FISH from 75 paired samples for myeloma risk stratification. CIg FISH improves test specificity and sensitivity and tends to eliminate borderline results. It proves that most plasma cells (PCs) consistently carry the abnormality in myelomas with an IGH translocation, whereas routine FISH detects these cells only at variably low levels. Routine cytogenetic analysis of plasma cell neoplasms (PCNs) has a low sensitivity. Conventional fluorescence in situ hybridization (FISH) is not plasma cell (PC) specific and results are diluted by other cells in the sample. Although PC-specific FISH testing has been recommended for multiple myeloma (MM) risk stratification, eg, by combining cytoplasmic immunoglobulin (cIg) staining with FISH, the benefits of cIg FISH have never been directly demonstrated in a controlled study. Seventy-five samples from patients with PCNs were analyzed by concomitant conventional FISH and cIg FISH with probes for t(4;14), t(11;14), t(14;16), -13, 17p-, and +3. The results were compared for their reliability, specificity, and consistency. Apart from marginally improving detection threshold in samples with low PC burden, cIg FISH identified more abnormal cases (50 vs. 47 cases) and more chromosome abnormalities (113 vs. 103 events) than did conventional FISH. It differentiated del(13q) in myelodysplasia from MM. Remarkably, cIg FISH consistently identified a high percentage of abnormal PCs in all cases. It detected IGH translocation in 78% to 100% of PCs in all but 2 positive cases, whereas conventional FISH detected 0% to 46% in these cases (median, 91% vs. 9%). The abnormal cells found in patients with 17p- were 19% to 96% by cIg FISH vs. 0% to 13% by conventional FISH (median, 54% vs. 9%). Cases with insufficient PCs for cIg FISH had only normal conventional FISH results. CIg FISH improves reliability of

  19. An assessment of fish assemblage structure in a large river

    USGS Publications Warehouse

    Kiraly, Ian A.; Coghlan, S.M.; Zydlewski, Joseph; Hayes, D.

    2015-01-01

    The Penobscot River drains the largest watershed in Maine and once provided spawning and rearing habitats to 11 species of diadromous fishes. The construction of dams blocked migrations of these fishes and likely changed the structure and function of fish assemblages throughout the river. The proposed removal of two main-stem dams, improved upstream fish passage at a third dam, and construction of a fish bypass on a dam obstructing a major tributary is anticipated to increase passage of and improve habitat connectivity for both diadromous and resident fishes. We captured 61 837 fish of 35 species in the Penobscot River and major tributaries, through 114 km of boat electrofishing. Patterns of fish assemblage structure did not change considerably during our sampling; relatively few species contributed to seasonal and annual variability within the main-stem river, including smallmouth bass Micropterus dolomieu, white sucker Catostomus commersonii, pumpkinseed Lepomis gibbosus, and golden shiner Notemigonus crysoleucas. However, distinct fish assemblages were present among river sections bounded by dams. Many diadromous species were restricted to tidal waters downriver of the Veazie Dam; Fundulus species were also abundant within the tidal river section. Smallmouth bass and pumpkinseed were most prevalent within the Veazie Dam impoundment and the free-flowing river section immediately upriver, suggesting the importance of both types of habitat that supports multiple life stages of these species. Further upriver, brown bullhead Ameiurus nebulosus, yellow perch Perca flavescens, chain pickerel Esox niger, and cyprinid species were more prevalent than within any other river section. Our findings describe baseline spatial patterns of fish assemblages in the Penobscot River in relation to dams with which to compare assessments after dam removal occurs.

  20. Assessing upstream fish passage connectivity with network analysis.

    PubMed

    McKay, S Kyle; Schramski, John R; Conyngham, Jock N; Fischenich, J Craig

    2013-09-01

    Hydrologic connectivity is critical to the structure, function, and dynamic process of river ecosystems. Dams, road crossings, and water diversions impact connectivity by altering flow regimes, behavioral cues, local geomorphology, and nutrient cycling. This longitudinal fragmentation of river ecosystems also increases genetic and reproductive isolation of aquatic biota such as migratory fishes. The cumulative effects on fish passage of many structures along a river are often substantial, even when individual barriers have negligible impact. Habitat connectivity can be improved through dam removal or other means of fish passage improvement (e.g., ladders, bypasses, culvert improvement). Environmental managers require techniques for comparing alternative fish passage restoration actions at alternative or multiple locations. Herein, we examined a graph-theoretic algorithm for assessing upstream habitat connectivity to investigate both basic and applied fish passage connectivity problems. First, we used hypothetical watershed configurations to assess general alterations to upstream fish passage connectivity with changes in watershed network topology (e.g., linear vs. highly dendritic) and the quantity, location, and passability of each barrier. Our hypothetical network modeling indicates that locations of dams with limited passage efficiency near the watershed outlet create a strong fragmentation signal but are not individually sufficient to disconnect the system. Furthermore, there exists a threshold in the number of dams beyond which connectivity declines precipitously, regardless of watershed topology and dam configuration. Watersheds with highly branched configurations are shown to be less susceptible to disconnection as measured by this metric. Second, we applied the model to prioritize barrier improvement in the mainstem of the Truckee River, Nevada, USA. The Truckee River application demonstrates the ability of the algorithm to address conditions common in fish

  1. The complete mitochondrial genome of Channa argus, Channa maculata and hybrid snakehead fish [Channa maculata (♀) × Channa argus (♂)].

    PubMed

    Zhu, Shu-Ren; Ma, Ke-Yi; Xing, Zhi-Jun; Xie, Nan; Wang, Yu-Xi; Wang, Qun; Li, Jia-Le

    2013-06-01

    We sequenced and characterized the complete mitochondrial genome of Channa argus, Channa maculata and their hybrid [C. maculata (♀) and C. argus (♂)]. All the three mitochondrial genomes contained the typical complement of 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 control region. The entire mitochondrial DNA (mtDNA) molecule of C. maculata was 16,559 bp long while the complete mtDNA molecule of C. argus and hybrid snakehead fish was 16,558 bp long. This is the first report on the complete mitogenome sequence of C. maculata and hybrid snakehead fish.

  2. Genetic architecture sets limits on transgressive segregation in hybrid cichlid fishes.

    PubMed

    Albertson, R Craig; Kocher, Thomas D

    2005-03-01

    The role of hybridization in the evolution of animal species is poorly understood. Transgressive segregation is a mechanism through which hybridization can generate diversity and ultimately lead to speciation. In this report we investigated the capacity of hybridization to generate novel (transgressive) phenotypes in the taxonomically diverse cichlid fishes. We generated a large F2 hybrid population by crossing two closely related cichlid species from Lake Malawi in Africa with differently shaped heads. Our morphometric analysis focused on two traits with different selective histories. The cichlid lower jaw (mandible) has evolved in response to strong directional selection, and does not segregate beyond the parental phenotype. The cichlid neurocranium (skull) has likely diverged in response to forces other than consistent directional selection (e.g., stabilizing selection), and exhibits marked transgressive segregation in our F2 population. We show that the genetic architecture of the cichlid jaw limits transgression, whereas the genetic basis of skull shape is permissive of transgressive segregation. These data suggest that natural selection, acting through the genome, will limit the degree of diversity that may be achieved via hybridization. Results are discussed in the context of the broader question of how phenotypic diversity may be achieved in rapidly evolving systems.

  3. Detection of a complex translocation using fluorescent in situ hybridization (FISH)

    SciTech Connect

    Rosen, B.A.; Abuelo, D.N.; Mark, H.F.

    1994-09-01

    The use of fluorescent in situ hybridization (FISH) allowed the detection of a complex 3-way translocation in a patient with multiple congenital malformations and mental retardation. The patient was a 10-year-old girl with mental retardation, seizures, repaired cleft palate, esotropia, epicanthal folds, broad nasal bridge, upward slanting palpebral fissures, single transverse palmar crease, brachydactyly, hypoplastic nails, ectrodactyly between the third and fourth right toes, and hypoplasia of the left third toe. Chromosome analysis performed at birth was reported as normal. We performed high resolution banding analysis which revealed an apparently balanced translocation between chromosomes 2 and 9. However, because of her multiple abnormalities, further studies were ordered. Fluorescent in situ hybridization (FISH) using chromosome painting probes revealed a karyotype of 46,XX,t(2;8;9) (2pter{yields}q31::8q21.2{yields}8qter; 8pter{yields}q21.2::2q31{yields}q34::9q34{yields}qter; 9pter{yields}q34::2q34{yields}qter). The 3-way translocation appears to be de novo, as neither parent is a translocation carrier. This case illustrates the importance of using FISH to further investigate cases of apparently balanced translocations in the presence of phenotypic abnormalities and/or mental retardation.

  4. Detection of Helicobacter pylori in raw bovine milk by fluorescence in situ hybridization (FISH).

    PubMed

    Angelidis, Apostolos S; Tirodimos, Ilias; Bobos, Mattheos; Kalamaki, Mary S; Papageorgiou, Demetrios K; Arvanitidou, Malamatenia

    2011-12-02

    The transmission pathways of Helicobacter pylori in humans have not been fully elucidated. Research in the last decade has proposed that foodborne transmission, among others, may be a plausible route of human infection. Owing to the organism's fastidious growth characteristics and its ability to convert to viable, yet unculturable states upon exposure to stress conditions, the detection of H. pylori in foods via culture-dependent methods has been proven to be laborious, difficult and in most cases unsuccessful. Hence, nucleic acid-based methods have been proposed as alternative methods but, to date, only PCR-based methods have been reported in the literature. In the current study, fluorescence in situ hybridization (FISH) was used for the detection of H. pylori in raw, bulk-tank bovine milk. After repeated milk centrifugation and washing steps, the bacterial flora of raw milk was subjected to fixation and permeabilization and H. pylori detection was conducted by FISH after hybridization with an H. pylori-specific 16S rRNA-directed fluorescent oligonucleotide probe. Using this protocol, H. pylori was detected in four out of the twenty (20%) raw milk samples examined. The data presented in this manuscript indicate that FISH can serve as an alternative molecular method for screening raw bovine milk for the presence of H. pylori.

  5. Detection of airborne Legionella while showering using liquid impingement and fluorescent in situ hybridization (FISH).

    PubMed

    Deloge-Abarkan, Magali; Ha, Thi-Lan; Robine, Enric; Zmirou-Navier, Denis; Mathieu, Laurence

    2007-01-01

    Aerosols of water contaminated with Legionella bacteria constitute the only mode of exposure for humans. However, the prevention strategy against this pathogenic bacteria risk is managed through the survey of water contamination. No relationship linked the Legionella bacteria water concentration and their airborne abundance. Therefore, new approaches in the field of the metrological aspects of Legionella bioaerosols are required. This study was aimed at testing the main principles for bioaerosol collection (solid impaction, liquid impingement and filtration) and the in situ hybridization (FISH) method, both in laboratory and field assays, with the intention of applying such methodologies for airborne Legionella bacteria detection while showering. An aerosolization chamber was developed to generate controlled and reproducible L. pneumophila aerosols. This tool allowed the identification of the liquid impingement method as the most appropriate one for collecting airborne Legionella bacteria. The culturable fraction of airborne L. pneumophila recovered with the liquid impingement principle was 4 and 700 times higher compared to the impaction and filtration techniques, respectively. Moreover, the concentrations of airborne L. pneumophila in the impinger fluid were on average 7.0 x 10(5) FISH-cells m(-3) air with the fluorescent in situ hybridization (FISH) method versus 9.0 x 10(4) CFU m(-3) air with the culture method. These results, recorded under well-controlled conditions, were confirmed during the field experiments performed on aerosols generated by hot water showers in health institutions. This new approach may provide a more accurate characterization of aerobiocontamination by Legionella bacteria.

  6. Intragenus (Campylomormyrus) and intergenus hybrids in mormyrid fish: Physiological and histological investigations of the electric organ ontogeny.

    PubMed

    Kirschbaum, Frank; Nguyen, Linh; Baumgartner, Stephanie; Chi, Hiu Wan Linda; Wolfart, Rene; Elarbani, Khouloud; Eppenstein, Hari; Korniienko, Yevheniia; Guido-Böhm, Lilian; Mamonekene, Victor; Vater, Marianne; Tiedemann, Ralph

    2017-01-17

    African weakly electric mormyrid fish show a high diversity of their electric organ discharge (EOD) both across and within genera. Thanks to a recently developed technique of artificial reproduction in mormyrid fish, we were able to perform hybridizations between different genera and within one genus (Campylomormyrus). The hybrids of intergenus hybridizations exhibited different degrees of reduced survival related to the phylogenetic distance of the parent species: hybrids of the crosses between C. rhynchophorus and its sister genus Gnathonemus survived and developed normally. Hybrids between C. rhynchophorus and a Mormyrus species (a more basal clade compared to Campylomormyrus s) survived up to 42days and developed many malformations, e.g., at the level of the unpaired fins. Hybrids between C. numenius and Hippopotamyrus pictus (a derived clade, only distantly related to Campylomormyrus) only survived for two days during embryological development. Eight different hybrid combinations among five Campylomormyrus species (C. tamandua, C. compressirostris, C. tshokwe, C. rhynchophorus, C. numenius) were performed. The aim of the hybridizations was to combine species with (1) either caudal or rostral position of the main stalk innervating the electrocytes in the electric organ and (2) short, median or long duration of their EOD. The hybrids, though they are still juveniles, show very interesting features concerning electrocyte geometry as well as EOD form and duration: the caudal position of the stalk is prevailing over the rostral position, and the penetration of the stalk is dominant over the non-penetrating feature (in the Campylomormyrus hybrids); in the hybrid between C. rhynchophorus and Gnathonemus petersii it is the opposite. When crossing species with long and short EODs, it is always the long duration EOD that is expressed in the hybrids. The F1-Hybrids of the cross C. tamandua×C. compressirostris are fertile: viable F2-fish could be obtained with artificial

  7. Surface Enhanced Raman Scattering Based in Situ Hybridization Strategy for Telomere Length Assessment.

    PubMed

    Zong, Shenfei; Chen, Chen; Wang, Zhuyuan; Zhang, Yizhi; Cui, Yiping

    2016-02-23

    Assessing telomere length is of vital importance since telomere length is closely related with several fatal diseases such as atherosclerosis and cancer. Here, we present a strategy to assess/measure telomere length, that is, surface enhanced Raman scattering (SERS) based in situ hybridization (SISH). The SISH method uses two kinds of SERS nanoprobes to hybridize in situ with telomeres and centromeres, respectively. The telomere specific SERS nanoprobe is called the Telo-probe, while the centromere specific SERS nanoprobe is called the Centro-probe. They are composed of metal nanoparticles (NPs), Raman reporter molecules and specially designed DNA strands. With longer telomeres, more Telo-probes will hybridize with them, resulting in a stronger SERS signal. To exclude possible influence of the SERS intensity by external factors (such as the nanoprobe concentration, the cell number or different batches of nanoprobes), centromeres are used as the inner control, which can be recognized by Centro-probes. Telomere length is evaluated using a redefined telomere-to-centromere ratio (T/C ratio). The calculation method for T/C ratio in SISH method is more reliable than that in fluorescent in situ hybridization (FISH). In addition, unlike FISH method, the SISH method is insensitive to autofluorescence. Moreover, SISH method can be used to analyze single telomeres. These features make SISH an excellent alternative strategy for telomere length measurement.

  8. Water quality and plankton communities in hybrid catfish (female channel catfish, Ictalurus punctatus x male blue catfish, I. furcatus) ponds after partial fish harvest

    USDA-ARS?s Scientific Manuscript database

    Twelve, 0.4-ha ponds were stocked with 10,000 hybrid catfish fingerlings in March 2015. Six ponds were partially harvested in August to remove fish larger than ~ 0.57 kg. All remaining fish were removed in October and November. Partial harvest of faster-growing fish removed ~26% of fish initially st...

  9. Comparison of immunohistochemical and fluorescence in situ hybridization assessment of HER-2 status in routine practice.

    PubMed

    Dolan, Michelle; Snover, Dale

    2005-05-01

    Because HER-2 expression in invasive carcinoma of the breast has well-documented ramifications for treatment and prognosis, accurate assessment of HER-2 status is critical. Comparative studies have shown high concordance rates between immunohistochemical analysis and fluorescence in situ hybridization (FISH) in cases with immunohistochemical scores of 0 or 1+ (negative) and 3+ (strongly positive) and low concordance rates among cases with immunohistochemical scores of 2+. The present study was performed to determine concordance rates in a setting more representative of routine clinical practice, in which multiple pathologists submit specimens to a single cytogenetics referral laboratory. We found a higher rate of discordance between immunohistochemical analysis and FISH (approximately 92%) in the groups with immunohistochemical scores of 2+ than reported in other studies. These results strongly support the practice of performing FISH in all cases with immunohistochemical scores of 2+, particularly in routine practice, in which interobserver variability in immunohistochemical scoring among multiple pathologists is likely to be high.

  10. Development of a fluorescence in situ hybridization (FISH) method for rapid detection of Ulva prolifera

    NASA Astrophysics Data System (ADS)

    Zhang, Qing-Chun; Liu, Qing; Kang, Zhen-Jun; Yu, Ren-Cheng; Yan, Tian; Zhou, Ming-Jiang

    2015-09-01

    Large-scale green tides have occurred consecutively since 2007 in the Yellow Sea (YS), China. The dominant causative species of the green tides has been identified as Ulva prolifera. The origin of green tides in the YS has been traced back to the Subei Shoal based on the results of remote-sensing, numerical simulations and field investigations. However, it is difficult to study the early development of green tides in the Subei Shoal because of the mixture of multiple green algae and the morphological diversity of U. prolifera when under variable environmental conditions. In this study, a rapid and accurate fluorescence in situ hybridization (FISH) method was developed to detect U. prolifera from the community of green algae targeting the 5S rDNA spacer region of U. prolifera. Two specific probes, 5S-1 and 5S-2, were designed based on the sequences of the 5S rDNA spacer regions of U. prolifera, Ulva linza and Ulva flexuosa. Specificity of the FISH method was tested using the six species of green algae commonly occurring in the Subei Shoal, including U. prolifera, U. linza, U. flexuosa, Ulva compressa, Ulva pertusa and Blidingia sp. The results showed that only U. prolifera could be labeled with both probes. Probe 5S-1, which showed a much higher labeling efficiency on U. prolifera, was ultimately selected as the probe for the FISH detection. The sample preparation method was optimized, particularly for the mature green algae, by the addition of cellulase and proteinase K in the pre-hybridization solution. Labeling efficiency with the probe 5S-1 reached 96% on average under the optimized conditions. The successful development of the FISH method has been applied to qualitative and quantitative analysis of field samples collected from the YS, and the results indicate a potential use in future green algae studies.

  11. The Fish Bowl: A Strategy for Assessing Independent Reading.

    ERIC Educational Resources Information Center

    Katz, Claudia Anne; Kuby, Sue Ann

    2001-01-01

    Explains Fish Bowl, an activity for upper elementary and middle school students to share what they read and a method for teachers to assess student understanding of a book. Discusses benefits of reading aloud a summary of the book, reading a passage from the book, asking appropriate questions, and answering questions. (LRW)

  12. The Fish Bowl: A Strategy for Assessing Independent Reading.

    ERIC Educational Resources Information Center

    Katz, Claudia Anne; Kuby, Sue Ann

    2001-01-01

    Explains Fish Bowl, an activity for upper elementary and middle school students to share what they read and a method for teachers to assess student understanding of a book. Discusses benefits of reading aloud a summary of the book, reading a passage from the book, asking appropriate questions, and answering questions. (LRW)

  13. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

    PubMed Central

    Schumer, Molly; Cui, Rongfeng; Powell, Daniel L; Dresner, Rebecca; Rosenthal, Gil G; Andolfatto, Peter

    2014-01-01

    Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species. DOI: http://dx.doi.org/10.7554/eLife.02535.001 PMID:24898754

  14. Reef Fish Survey Techniques: Assessing the Potential for Standardizing Methodologies

    PubMed Central

    Caldwell, Zachary R.; Zgliczynski, Brian J.; Williams, Gareth J.; Sandin, Stuart A.

    2016-01-01

    Dramatic changes in populations of fishes living on coral reefs have been documented globally and, in response, the research community has initiated efforts to assess and monitor reef fish assemblages. A variety of visual census techniques are employed, however results are often incomparable due to differential methodological performance. Although comparability of data may promote improved assessment of fish populations, and thus management of often critically important nearshore fisheries, to date no standardized and agreed-upon survey method has emerged. This study describes the use of methods across the research community and identifies potential drivers of method selection. An online survey was distributed to researchers from academic, governmental, and non-governmental organizations internationally. Although many methods were identified, 89% of survey-based projects employed one of three methods–belt transect, stationary point count, and some variation of the timed swim method. The selection of survey method was independent of the research design (i.e., assessment goal) and region of study, but was related to the researcher’s home institution. While some researchers expressed willingness to modify their current survey protocols to more standardized protocols (76%), their willingness decreased when methodologies were tied to long-term datasets spanning five or more years. Willingness to modify current methodologies was also less common among academic researchers than resource managers. By understanding both the current application of methods and the reported motivations for method selection, we hope to focus discussions towards increasing the comparability of quantitative reef fish survey data. PMID:27111085

  15. Revisiting Psychoacoustic Methods for the Assessment of Fish Hearing.

    PubMed

    Bhandiwad, Ashwin A; Sisneros, Joseph A

    2016-01-01

    Behavioral methods have been critical in the study of auditory perception and discrimination in fishes. In this chapter, we review some of the common methods used in fish psychoacoustics. We discuss associative methods, such as operant, avoidance, and classical conditioning, and their use in constructing audiograms, measuring frequency selectivity, and auditory stream segregation. We also discuss the measurement of innate behavioral responses, such as the acoustic startle response (ASR), prepulse inhibition (PPI), and phonotaxis, and their use in the assessment of fish hearing to determine auditory thresholds and in the testing of mechanisms for sound source localization. For each psychoacoustic method, we provide examples of their use and discuss the parameters and situations where such methods can be best utilized. In the case of the ASR, we show how this method can be used to construct and compare audiograms between two species of larval fishes, the three-spined stickleback (Gasterosteus aculeatus) and the zebrafish (Danio rerio). We also discuss considerations for experimental design with respect to stimulus presentation and threshold criteria and how these techniques can be used in future studies to investigate auditory perception in fishes.

  16. Somatic hybrids Solanum nigrum (+) S. tuberosum: morphological assessment and verification of hybridity.

    PubMed

    Szczerbakowa, A; Maciejewska, U; Zimnoch-Guzowska, E; Wielgat, B

    2003-02-01

    Somatic hybrids between the cultivated potato diploid hybrid clone, ZEL-1136, and hexaploid non-tuber-bearing wild species Solanum nigrum L. exhibiting resistance to Phytophthora infestans were regenerated after PEG-mediated fusion of mesophyll protoplasts. The objective was to transfer the late-blight resistance genes from the wild species into plants of the cultivated potato clone. From a total of 59 regenerants, 40 clones survived and have been maintained in vitro on hormone-free MS/2 medium. Thirty-two somatic hybrids were identified by their intermediate morphology (leaves of nigrum type and flowers of tuberosum type) and verified by flow cytometry and random amplified polymorphic DNA (RAPD) patterns. The RAPD analysis of nuclear DNA confirmed the hybrid nature of 29 clones. Flow cytometry revealed a wide range of ploidy in the generated hybrids, from nearly the tetra- to decaploid level. Most of the hybrid clones were stable in vitro, grew vigorously in soil, and set flowers and parthenocarpic berries. However, all of the flowering hybrids were male-sterile. Nine hybrid clones produced tuber-like structures in soil. The most vigorous flowering somatic hybrids were selected for assessment of the late-blight resistance.

  17. Fluorescence in situ hybridization (FISH): an increasingly demanded tool for biomarker research and personalized medicine

    PubMed Central

    2014-01-01

    Extensive studies of the genetic aberrations related to human diseases conducted over the last two decades have identified recurrent genomic abnormalities as potential driving factors underlying a variety of cancers. Over the time, a series of cutting-edge high-throughput genetic tests, such as microarrays and next-generation sequencing, have been developed and incorporated into routine clinical practice. Although it is a classical low-throughput cytogenetic test, fluorescence in situ hybridization (FISH) does not show signs of fading; on the contrary, it plays an increasingly important role in detecting specific biomarkers in solid and hematologic neoplasms and has therefore become an indispensable part of the rapidly developing field of personalized medicine. In this article, we have summarized the recent advances in FISH application for both de novo discovery and routine detection of chromosomal rearrangements, amplifications, and deletions that are associated with the pathogenesis of various hematopoietic and non-hematopoietic malignancies. In addition, we have reviewed the recent developments in FISH methodology as well. PMID:24499728

  18. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset.

    PubMed

    Dornburg, Alex; Townsend, Jeffrey P; Brooks, Willa; Spriggs, Elizabeth; Eytan, Ron I; Moore, Jon A; Wainwright, Peter C; Lemmon, Alan; Lemmon, Emily Moriarty; Near, Thomas J

    2017-05-01

    Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. A simple protocol for attenuating the auto-fluorescence of cyanobacteria for optimized fluorescence in situ hybridization (FISH) imaging.

    PubMed

    Zeller, Perrine; Ploux, Olivier; Méjean, Annick

    2016-03-01

    Cyanobacteria contain pigments, which generate auto-fluorescence that interferes with fluorescence in situ hybridization (FISH) imaging of cyanobacteria. We describe simple chemical treatments using CuSO4 or H2O2 that significantly reduce the auto-fluorescence of Microcystis strains. These protocols were successfully applied in FISH experiments using 16S rRNA specific probes and filamentous cyanobacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae - Saccharinae).

    PubMed

    Besse, P; McIntyre, C L; Burner, D M; Almeida, C G

    1997-08-01

    The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum x Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum x Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.

  1. Improving the assessment of instream flow needs for fish populations

    SciTech Connect

    Sale, M.J. ); Otto, R.G. and Associates, Arlington, VA )

    1991-01-01

    Instream flow requirements are one of the most frequent and most costly environmental issues that must be addressed in developing hydroelectric projects. Existing assessment methods for determining instream flow requirements have been criticized for not including all the biological response mechanisms that regulate fishery resources. A new project has been initiated to study the biological responses of fish populations to altered stream flows and to develop improved ways of managing instream flows. 21 refs., 3 figs.

  2. Critical assessment of regulatory standards and tests for fish vaccines.

    PubMed

    Midtlyng, P J

    2005-01-01

    Within the European Economic Area (EU member states plus Norway, Iceland and Liechtenstein), veterinary vaccines must comply with EU regulations and relevant monographs of the European Pharmacopoeia. Since 1996, three European monographs specific for fish have been adopted; concerning oil-adjuvanted, injectable vaccine for salmonids against furunculosis, as well as bacterins against classical vibriosis (Listonella anguillarum) or cold-water vibriosis (Vibrio salmonicida) in salmonids. The regulatory requirements laid down in these monographs include the use of seronegative fish for in vivo safety testing; conduct of vaccination trials in which experimental challenge is administered by injection, and minimum relative protection to be achieved at a given level of control mortality. Several aspects of these requirements are being questioned. This concerns the relevance of injection challenge methods as opposed to waterborne challenge; the validity of relative protection assessed at 60 % control mortality (RPS6) as compared to protection calculated at the endpoint of mortality (RPSendpoint), and poor test power due to low numbers of fish per treatment group. There is a strong need for future efforts to refine the methods for documentation and testing of fish vaccines, and to assure their suitability for the intended purpose.

  3. Behavioral assay for assessing effects of pollutants on fish chemoreception

    SciTech Connect

    Lemly, A.D.; Smith, R.J.

    1986-04-01

    Behavioral assays are sensitive to sublethal levels of pollution but they usually require highly trained personnel and long observation periods. We describe a system that combines the sensitivity of a behavioral assay with commercially available automated monitoring equipment. The observation system consists of a special aquarium coupled to a recirculating water system, and an Opto-Varimex-Aqua activity tracking meter (Columbus Instruments, Columbus, Ohio) interfaced to a microcomputer. The tracking meter forms an intersecting, planar grid of light beams which, when interrupted by fish movements, is translated into a digitized signal and fed to the computer. The assay is based on the response of fish to natural chemical stimuli such as food odors or pheromones. When these stimulus solutions are injected into the water circulation the response of the fish is monitored by the computer system, which is capable of discriminating and quantifying changes in eight parameters. Normal responses to stimuli are compared with the response of fish that have been exposed to pollutants. We have successfully used this technique to examine effects of reduced pH on the response of fathead minnows, Pimephales promelas, to chemical feeding stimuli. The system should be easily adapted to any laboratory concerned with testing for effects of toxic substances, and will identify effects of pollution that have thus far been difficult or impossible to assess.

  4. Ocular tumors in hybrid fish of the genus Xiphophorus exposed to n-methyl-n-nitrosourea (mnu)

    SciTech Connect

    Grist, E.; Setlow, R.B.; Woodhead, A.D.

    1995-11-01

    The authors investigated the potential of hybrid fish, genus Xiphophorus, as a useful experimental animal model for human retinoblastoma, a neuroepithelial tumor. These fish have been valuable for over 60 years in studies of induction of neoplasia by chemical and physical carcinogens. There is extensive homology between the human and fish Rb genes. Some of the pigmented and non pigmented fish from the first backcross generation developed unilateral ocular tumors after treatment with MNU. The yield of growths, at 4-6 mo, among 1,200 fish increased with the product of the concentration times treatment time times number of treatments. A preliminary dose response curve was concave upwards rising from a control value of 0/185 to 15% at high doses. A few growths have been examined histologically. They were protruberant meduloepitheliomas, originating from the same stem cells that give rise to human retinoblastoma.

  5. Trade-off between morphological convergence and opportunistic diet behavior in fish hybrid zone

    PubMed Central

    Corse, Emmanuel; Costedoat, Caroline; Pech, Nicolas; Chappaz, Rémi; Grey, Jonathan; Gilles, André

    2009-01-01

    Background The invasive Chondrostoma nasus nasus has colonized part of the distribution area of the protected endemic species Chondrostoma toxostoma toxostoma. This hybrid zone is a complex system where multiple effects such as inter-species competition, bi-directional introgression, strong environmental pressure and so on are combined. Why do sympatric Chondrostoma fish present a unidirectional change in body shape? Is this the result of inter-species interactions and/or a response to environmental effects or the result of trade-offs? Studies focusing on the understanding of a trade-off between multiple parameters are still rare. Although this has previously been done for Cichlid species flock and for Darwin finches, where mouth or beak morphology were coupled to diet and genetic identification, no similar studies have been done for a fish hybrid zone in a river. We tested the correlation between morphology (body and mouth morphology), diet (stable carbon and nitrogen isotopes) and genomic combinations in different allopatric and sympatric populations for a global data set of 1330 specimens. To separate the species interaction effect from the environmental effect in sympatry, we distinguished two data sets: the first one was obtained from a highly regulated part of the river and the second was obtained from specimens coming from the less regulated part. Results The distribution of the hybrid combinations was different in the two part of the sympatric zone, whereas all the specimens presented similar overall changes in body shape and in mouth morphology. Sympatric specimens were also characterized by a larger diet behavior variance than reference populations, characteristic of an opportunistic diet. No correlation was established between the body shape (or mouth deformation) and the stable isotope signature. Conclusion The Durance River is an untamed Mediterranean river despite the presence of numerous dams that split the river from upstream to downstream. The

  6. Assessment of the potential of hybrid vehicles: Summary

    NASA Technical Reports Server (NTRS)

    Surber, F. T.

    1980-01-01

    The potential of hybrid vehicles as a replacement of the conventional gasoline or diesel fueled internal combustion engine vehicle within the next 20 to 30 years, was assessed. Hybrid vehicle designs and applications which are technically and economically viable were studied to determine if reductions in petroleum usage were large enough to warrant major expenditures of research and development funds. Critical technical areas where research and development can be most usefully concentrated were identified.

  7. Fluorescence in-situ hybridization (FISH) as a tool for visualization and enumeration of Campylobacter in broiler ceca

    USDA-ARS?s Scientific Manuscript database

    Food-borne human pathogens are typically detected and enumerated by either cultural methods or PCR-based approaches. Fluorescence in-situ hybridization (FISH) is a standard microscopy tool for microbial ecology but has not been widely used for food safety applications despite important advantages o...

  8. Determination of the ruminant origin of bone particles using fluorescence in situ hybridization (FISH)

    PubMed Central

    Lecrenier, M. C.; Ledoux, Q.; Berben, G.; Fumière, O.; Saegerman, C.; Baeten, V.; Veys, P.

    2014-01-01

    Molecular biology techniques such as PCR constitute powerful tools for the determination of the taxonomic origin of bones. DNA degradation and contamination by exogenous DNA, however, jeopardise bone identification. Despite the vast array of techniques used to decontaminate bone fragments, the isolation and determination of bone DNA content are still problematic. Within the framework of the eradication of transmissible spongiform encephalopathies (including BSE, commonly known as “mad cow disease”), a fluorescence in situ hybridization (FISH) protocol was developed. Results from the described study showed that this method can be applied directly to bones without a demineralisation step and that it allows the identification of bovine and ruminant bones even after severe processing. The results also showed that the method is independent of exogenous contamination and that it is therefore entirely appropriate for this application. PMID:25034259

  9. Determination of the ruminant origin of bone particles using fluorescence in situ hybridization (FISH).

    PubMed

    Lecrenier, M C; Ledoux, Q; Berben, G; Fumière, O; Saegerman, C; Baeten, V; Veys, P

    2014-07-17

    Molecular biology techniques such as PCR constitute powerful tools for the determination of the taxonomic origin of bones. DNA degradation and contamination by exogenous DNA, however, jeopardise bone identification. Despite the vast array of techniques used to decontaminate bone fragments, the isolation and determination of bone DNA content are still problematic. Within the framework of the eradication of transmissible spongiform encephalopathies (including BSE, commonly known as "mad cow disease"), a fluorescence in situ hybridization (FISH) protocol was developed. Results from the described study showed that this method can be applied directly to bones without a demineralisation step and that it allows the identification of bovine and ruminant bones even after severe processing. The results also showed that the method is independent of exogenous contamination and that it is therefore entirely appropriate for this application.

  10. Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

    PubMed Central

    Ronander, Elena; Bengtsson, Dominique C.; Joergensen, Louise; Jensen, Anja T. R.; Arnot, David E.

    2012-01-01

    Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes. The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE1. Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System2 (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription and regulation of a variety of genes expressed during the different stages of the P. falciparum life cycle and is adaptable to other malaria parasite species and other organisms and cell types. PMID:23070076

  11. Analysis of single-cell gene transcription by RNA fluorescent in situ hybridization (FISH).

    PubMed

    Ronander, Elena; Bengtsson, Dominique C; Joergensen, Louise; Jensen, Anja T R; Arnot, David E

    2012-10-07

    Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes. The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE(1). Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System(2) (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription and regulation of a variety of genes expressed during the different stages of the P. falciparum life cycle and is adaptable to other malaria parasite species and other organisms and cell types.

  12. Capture antibody targeted fluorescence in situ hybridization (CAT-FISH): dual labeling allows for increased specificity in complex samples.

    PubMed

    Stroot, Joyce M; Leach, Kelly M; Stroot, Peter G; Lim, Daniel V

    2012-02-01

    Pathogen detection using biosensors is commonly limited due to the need for sensitivity and specificity in detecting targets within mixed populations. These issues were addressed through development of a dual labeling method that allows for both liquid-phase fluorescence in situ hybridization (FISH) and capture antibody targeted detection (CAT-FISH). CAT-FISH was developed using Escherichia coli O157:H7 and Staphylococcus aureus as representative bacteria, and processing techniques were evaluated with regard to FISH intensities and antibody recognition. The alternative fixative solution, methacarn, proved to be superior to standard solid-phase paraformaldehyde fixation procedures, allowing both FISH labeling and antibody recognition. CAT-FISH treated cells were successfully labeled with FISH probes, captured by immunomagnetic separation using fluorescent cytometric array beads, and detected using a cytometric array biosensor. CAT-FISH treated cells were detectable with LODs comparable to the standard antibody-based technique, (~10(3)cells/ml in PBS), and the technique was also successfully applied to two complex matrices. Although immunomagnetic capture and detection using cytometric arrays were demonstrated, CAT-FISH is readily applicable to any antibody-based fluorescence detection platform, and further optimization for sensitivity is possible via inclusion of fluorescently tagged antibodies. Since the confidence level needed for positive identification of a detected target is often paramount, CAT-FISH was developed to allow two separate levels of specificity, namely nucleic acid and protein signatures. With proper selection of FISH probes and capture antibodies, CAT-FISH may be used to provide rapid detection of target pathogens from within complex matrices with high levels of confidence.

  13. Fish Passage Assessment: Big Canyon Creek Watershed, Technical Report 2004.

    SciTech Connect

    Christian, Richard

    2004-02-01

    This report presents the results of the fish passage assessment as outlined as part of the Protect and Restore the Big Canyon Creek Watershed project as detailed in the CY2003 Statement of Work (SOW). As part of the Northwest Power Planning Council's Columbia Basin Fish and Wildlife Program (FWP), this project is one of Bonneville Power Administration's (BPA) many efforts at off-site mitigation for damage to salmon and steelhead runs, their migration, and wildlife habitat caused by the construction and operation of federal hydroelectric dams on the Columbia River and its tributaries. The proposed restoration activities within the Big Canyon Creek watershed follow the watershed restoration approach mandated by the Fisheries and Watershed Program. Nez Perce Tribal Fisheries/Watershed Program vision focuses on protecting, restoring, and enhancing watersheds and treaty resources within the ceded territory of the Nez Perce Tribe under the Treaty of 1855 with the United States Federal Government. The program uses a holistic approach, which encompasses entire watersheds, ridge top to ridge top, emphasizing all cultural aspects. We strive toward maximizing historic ecosystem productive health, for the restoration of anadromous and resident fish populations. The Nez Perce Tribal Fisheries/Watershed Program (NPTFWP) sponsors the Protect and Restore the Big Canyon Creek Watershed project. The NPTFWP has the authority to allocate funds under the provisions set forth in their contract with BPA. In the state of Idaho vast numbers of relatively small obstructions, such as road culverts, block thousands of miles of habitat suitable for a variety of fish species. To date, most agencies and land managers have not had sufficient, quantifiable data to adequately address these barrier sites. The ultimate objective of this comprehensive inventory and assessment was to identify all barrier crossings within the watershed. The barriers were then prioritized according to the amount of

  14. Electric and hybrid vehicle systems assessment seminar: proceedings

    SciTech Connect

    Not Available

    1984-03-15

    The following twenty papers are included in these proceedings: (1) electric and hybrid vehicle assessment overview, (2) electric and hybrid vehicle systems considerations, (3) advanced vehicle assessment, (4) hybrid vehicle assessment, (5) battery optimization considerations, (6) alkaline battery technology, (7) lead-acid batteries, (8) nickel-iron batteries, (9) zinc-chloride batteries, (10) zinc-bromine batteries, (11) sodium-sulfur batteries, (12) system/battery design interaction for a lithium-method sulfide van battery, (13) iorn-air batteries, (14) aluminium-air cells, (15) fuel cell overview, (16) variable-reluctance motor drives, (17) electric vehicle design, (18) advanced electric vehicle powertrain program, (19) Eaton ac drivetrains, and (20) JET Propulsion Laboratory ac power system. (MOW)

  15. Introgressive Hybridization and the Evolution of Lake-Adapted Catostomid Fishes

    PubMed Central

    Dowling, Thomas E.; Markle, Douglas F.; Tranah, Greg J.; Carson, Evan W.; Wagman, David W.; May, Bernard P.

    2016-01-01

    Hybridization has been identified as a significant factor in the evolution of plants as groups of interbreeding species retain their phenotypic integrity despite gene exchange among forms. Recent studies have identified similar interactions in animals; however, the role of hybridization in the evolution of animals has been contested. Here we examine patterns of gene flow among four species of catostomid fishes from the Klamath and Rogue rivers using molecular and morphological traits. Catostomus rimiculus from the Rogue and Klamath basins represent a monophyletic group for nuclear and morphological traits; however, the Klamath form shares mtDNA lineages with other Klamath Basin species (C. snyderi, Chasmistes brevirostris, Deltistes luxatus). Within other Klamath Basin taxa, D. luxatus was largely fixed for alternate nuclear alleles relative to C. rimiculus, while Ch. brevirostris and C. snyderi exhibited a mixture of these alleles. Deltistes luxatus was the only Klamath Basin species that exhibited consistent covariation of nuclear and mitochondrial traits and was the primary source of mismatched mtDNA in Ch. brevirostris and C. snyderi, suggesting asymmetrical introgression into the latter species. In Upper Klamath Lake, D. luxatus spawning was more likely to overlap spatially and temporally with C. snyderi and Ch. brevirostris than either of those two with each other. The latter two species could not be distinguished with any molecular markers but were morphologically diagnosable in Upper Klamath Lake, where they were largely spatially and temporally segregated during spawning. We examine parallel evolution and syngameon hypotheses and conclude that observed patterns are most easily explained by introgressive hybridization among Klamath Basin catostomids. PMID:26959681

  16. Chromosomal aneusomy in sputum, as detected by Fluorescence In Situ Hybridization (FISH) predicts lung cancer incidence

    PubMed Central

    Varella-Garcia, Marileila; Schulte, Aline P.; Wolf, Holly J.; Feser, William J; Zeng, Chan; Braudrick, Sarah; Yin, Xiang; Hirsch, Fred R.; Kennedy, Timothy C.; Keith, Robert L.; Barón, Anna E.; Belinsky, Steven A.; Miller, York E.; Byers, Tim; Franklin, Wilbur A.

    2009-01-01

    Lung cancer is usually disseminated at diagnosis making prognosis poor. Smokers are at high risk for lung cancer and are targets for prevention and early detection strategies. Sputum is a potential source for lung cancer biomarkers, but no test is currently available with sufficient sensitivity and specificity for clinical screening utility. Chromosomal aneusomy (CA) was measured in sputum samples collected prospectively from 100 incident lung cancer cases and 96 controls matched on age, gender, and date of collection. The CA-FISH assay was performed using a four-target DNA FISH probe including EGFR, MYC, 5p15 and CEP6. Sensitivity for a positive CA-FISH assay (abnormal for ≥ 2 of the 4 markers) was substantially higher for samples collected within 18 months (76%) than >18 months before lung cancer diagnosis (31%). Specificity for a positive FISH by this same definition was 85%. Among subjects providing sputum sample within 18 months before diagnosis, sensitivity was higher for squamous cell cancers (94%) than for other histologic types (69%). The adjusted odds ratios for specimens collected within 18 months of cancer diagnosis were higher using the CA-FISH assay (OR=27.2, 95% CI 7.8 to 94.1) than previous studies assessing cytologic atypia (OR=2.3, CI 0.8 to 6.4) or gene promoter methylation (OR=6.5; CI 1.2 to 35.5). In conclusion, chromosomal aneusomy in sputum is a promising biomarker for prediction of lung cancer risk. Evaluation of the 4-DNA targets was more effective than any single marker and had highest sensitivity for samples collected ≤ 18 months to lung cancer diagnosis and patients diagnosed with squamous cell carcinoma. PMID:20332298

  17. Bioelectrical impedance analysis: A new tool for assessing fish condition

    USGS Publications Warehouse

    Hartman, Kyle J.; Margraf, F. Joseph; Hafs, Andrew W.; Cox, M. Keith

    2015-01-01

    Bioelectrical impedance analysis (BIA) is commonly used in human health and nutrition fields but has only recently been considered as a potential tool for assessing fish condition. Once BIA is calibrated, it estimates fat/moisture levels and energy content without the need to kill fish. Despite the promise held by BIA, published studies have been divided on whether BIA can provide accurate estimates of body composition in fish. In cases where BIA was not successful, the models lacked the range of fat levels or sample sizes we determined were needed for model success (range of dry fat levels of 29%, n = 60, yielding an R2 of 0.8). Reduced range of fat levels requires an increased sample size to achieve that benchmark; therefore, standardization of methods is needed. Here we discuss standardized methods based on a decade of research, identify sources of error, discuss where BIA is headed, and suggest areas for future research.

  18. Multimodality imaging assessment for Thoraflex hybrid total arch replacement.

    PubMed

    Wong, Randolph Hl; Ho, Jacky Yk; Underwood, Malcolm J

    2016-06-01

    Conventionally, aortic pathologies involving the ascending, arch, and descending thoracic aorta are treated by a staged operation. The Thoraflex device is a composite 4-branched graft with a distal endovascular stent, which allows one-stage treatment of these pathologies. We describe our multimodality hybrid approach for total arch replacement using the Thoraflex device with the adjunct of intraoperative 3-dimensional transesophageal echocardiography, Endo-EYE endoscopy, and on-table aortography in a hybrid operating room. These multimodality assessments can ascertain adequate sealing of a distal aortic tear and proper opening of the endograft, and provide on-table functional assessment of false lumen hemodynamics. Early results are promising.

  19. Assessing the impact of fishing in shallow rocky reefs: a multivariate approach to ecosystem management.

    PubMed

    Sangil, Carlos; Martín-García, Laura; Clemente, Sabrina

    2013-11-15

    In this paper we develop a tool to assess the impact of fishing on ecosystem functioning in shallow rocky reefs. The relationships between biological parameters (fishes, sea urchins, seaweeds), and fishing activities (fish traps, boats, land-based fishing, spearfishing) were tested in La Palma island (Canary Islands). Data from fishing activities and biological parameters were analyzed using principal component analyses. We produced two models using the first component of these analyses. This component was interpreted as a new variable that described the fishing pressure and the conservation status at each studied site. Subsequently the scores on the first axis were mapped using universal kriging methods and the models obtained were extrapolated across the whole island to display the expected fishing pressure and conservation status more widely. The fishing pressure and conservation status models were spatially related; zones where fishing pressure was high coincided with zones in the unhealthiest ecological state. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Karyotype of Zea luxurians and Z. mays subsp. mays using FISH/DAPI, and analysis of meiotic behavior of hybrids.

    PubMed

    González, Graciela E; Poggio, Lidia

    2011-01-01

    The karyotypes of Zea luxurians and a race of maize from northwestern Argentina are described and compared using 4′,6-diamidino-2-phenylindole (DAPI) banding and fluorescent in situ hybridization (FISH) to localize the 180 bp knobs. The meiotic behavior of the F₁ artificial hybrids Z. luxurians × maize is also analyzed to determine the genomic relationships between both species. Neocentromere activity at knobs in the meiosis of the hybrids is particularly discussed. The meiotic behavior and the high pollen sterility of the hybrid revealed genetical and (or) chromosomal divergences, leading to postzygotic reproductive isolation among their parents. Here, we propose that maize shows lower genomic affinity to Z. luxurians than to other species of the genus with 2n = 20.

  1. Chromogenic in situ hybridization (CISH) to detect HER2 gene amplification in breast and gastric cancer: comparison with immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).

    PubMed

    Kiyose, Shinichiro; Igarashi, Hisaki; Nagura, Kiyoko; Kamo, Takaharu; Kawane, Kazunori; Mori, Hiroki; Ozawa, Takachika; Maeda, Matsuyoshi; Konno, Keisuke; Hoshino, Hideaki; Konno, Hiroyuki; Ogura, Hiroyuki; Shinmura, Kazuya; Hattori, Naohiko; Sugimura, Haruhiko

    2012-11-01

    The chromogenic in situ hybridization (CISH) assay, designed to detect the amplification of the HER2 gene in formalin-fixed, paraffin-embedded (FFPE) breast cancer (BC) and gastric cancer (GC) tissue specimens, was evaluated in 125 FFPE BC cases and 198 FFPE GC cases for which the HER2 status had been predetermined using immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). In the 125 BC cases and the 198 gastric cases, we found a very good concordance (98.4% and 99.0%, respectively) between CISH and FISH. In particular, we evaluated the polysomy cases, as these cases often have ambiguous treatment options in clinical practice. The polysomy of chromosome 17 was defined as the presence of three or more CEP17 signals in at least 10% of the tumor cells. In the 50 BC cases and 54 GC cases displaying chromosome 17 polysomy, the concordance between FISH and CISH was 98.0% and 98.1%, respectively. These results indicate that CISH could provide an accurate and practical alternative to FISH for the clinical diagnosis of HER2 gene amplification in FFPE BC and FFPE GC samples.

  2. Preconceptual design and assessment of a Tokamak Hybrid Reactor

    SciTech Connect

    Teofilo, V.L.; Leonard, B.R. Jr.; Aase, D.T.

    1980-09-01

    The preconceptual design of a commercial Tokamak Hybrid Reactor (THR) power plant has been performed. The tokamak fusion driver for this hybrid is operated in the ignition mode. The D-T fusion plasma, which produces 1140 MW of power, has a major radius of 5.4 m and a minor radius of 1.0 m with an elongation of 2.0. Double null poloidal divertors are assumed for impurity control. The confining toroidal field is maintained by D-shaped Nb/sub 3/Sn superconducting magnets with a maximum field of 12T at the coil. Three blankets with four associated fuel cycle alternatives have been combined with the ignited tokamak fusion driver. The engineering, material, and balance of plant design requirements for the THR are briefly described. Estimates of the capital, operating and maintenance, and fuel cycle costs have been made for the various driver/blanket combinations and an assessment of the market penetrability of hybrid systems is presented. An analysis has been made of the nonproliferation aspects of the hybrid and its associated fuel cycles relative to fission reactors. The current and required level of technology for both the fusion and fission components of the hybrid system has been reviewed. Licensing hybrid systems is also considered.

  3. Identification of intracellular bacteria in adenoid and tonsil tissue specimens: the efficiency of culture versus fluorescent in situ hybridization (FISH).

    PubMed

    Stępińska, M; Olszewska-Sosińska, O; Lau-Dworak, M; Zielnik-Jurkiewicz, B; Trafny, E A

    2014-01-01

    Monocyte/macrophage cells from human nasopharyngeal lymphoid tissue can be a source of bacteria responsible for human chronic and recurrent upper respiratory tract infection. Detection and characterization of pathogens surviving intracellularly could be a key element in bacteriological diagnosis of the infections as well as in the study on interactions between bacteria and their host. The present study was undertaken to assess the possibility of isolation of viable bacteria from the cells expressing monocyte/macrophage marker CD14 in nasopharyngeal lymphoid tissue. Overall, 74 adenotonsillectomy specimens (adenoids and tonsils) from 37 children with adenoid hypertrophy and recurrent infections as well as 15 specimens from nine children with adenoid hypertrophy, which do not suffer from upper respiratory tract infections (the control group), were studied. The suitability of immunomagnetic separation for extraction of CD14(+) cells from lymphoid tissue and for further isolation of the intracellular pathogens has been shown. The coexistence of living pathogens including Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pyogenes with the bacteria representing normal nasopharyngeal microbiota inside CD14(+) cells was demonstrated. Twenty-four strains of these pathogens from 32.4 % of the lysates of CD14(+) cells were isolated. Concurrently, the fluorescent in situ hybridization (FISH) with a universal EUB388, and the species-specific probes demonstrated twice more often the persistence of these bacterial species in the lysates of CD14(+) cells than conventional culture. Although the FISH technique appears to be more sensitive than traditional culture in the intracellular bacteria identification, the doubts on whether the bacteria are alive, and therefore, pathogenic would still exist without the strain cultivation.

  4. Application of Fluorescence In Situ Hybridization (FISH) Technique for the Detection of Genetic Aberration in Medical Science.

    PubMed

    Ratan, Zubair Ahmed; Zaman, Sojib Bin; Mehta, Varshil; Haidere, Mohammad Faisal; Runa, Nusrat Jahan; Akter, Nasrin

    2017-06-09

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technique, which is considered as a new advent in the field of cytology. Initially, it was developed as a physical mapping tool to delineate genes within chromosomes. The accuracy and versatility of FISH were subsequently capitalized upon in biological and medical research. This visually appealing technique provides an intermediate degree of resolution between DNA analysis and chromosomal investigations. FISH consists of a hybridizing DNA probe, which can be labeled directly or indirectly. In the case of direct labeling, fluorescent nucleotides are used, while indirect labeling is incorporated with reporter molecules that are subsequently detected by fluorescent antibodies or other affinity molecules. FISH is applied to detect genetic abnormalities that include different characteristic gene fusions or the presence of an abnormal number of chromosomes in a cell or loss of a chromosomal region or a whole chromosome. It is also applied in different research applications, such as gene mapping or the identification of novel oncogenes. This article reviews the concept of FISH, its application, and its advantages in medical science.

  5. Models for U.S Fish Stock Assessment

    NASA Astrophysics Data System (ADS)

    Bynes, K.

    2016-02-01

    A stock assessment is a statistical summary of fish population that provides past and current information about the population, and forecasts the status of the stock. The NOAA Fisheries' Species Information System (SIS) collects data pertaining to the stock assessments that are completed throughout the U.S. The system was standardized by categorizing statistical models used in stock assessments across the U.S. The categories of the statistical models were Statistical Catch-at-Age (SCAA), Statistical Catch-at-Length (SCAL), Biomass Dynamics, Index, Virtual Population Analysis (VPA), Equilibrium, and Unknown. An analytical summary was performed on the categories of approaches used to evaluate stock assessments. It was hypothesized the size and age based models would become more frequent over time, and approaches would differ by science center. By conducting linear regressions, it was determined the frequency of size and age based models did increase with time; thus, the alternative hypothesis was supported. The frequency at which age based models are conducted have a direct positive relationship with time. The frequency at which size based models are used to assess stocks have an inverse relationship with time which neither fails to reject null hypothesis. Also, the approaches differed based on science center rejecting the null hypothesis. SCAA was overall the most frequent approach used across science centers to evaluate stock assessments. The northern regions rely heavily on SCAA and Index approaches to evaluate stocks, while the southern regions are more likely to use a variety of approaches.

  6. Responses to crizotinib in patients with ALK-positive lung adenocarcinoma who tested immunohistochemistry (IHC)-positive and fluorescence in situ hybridization (FISH)-negative

    PubMed Central

    Yang, Lin; Mu, Xinlin; Wang, Yan; Zhao, Xinming; Li, Junling; Lin, Dongmei

    2016-01-01

    Although the Ventana immunohistochemistry (IHC) platform for detecting anaplastic lymphoma kinase gene (ALK) (D5F3) expression was recently approved by the US Food and Drugs Administration (FDA), fluorescence in situ hybridization (FISH) is still the “gold-standard” method recommended by the US National Comprehensive Cancer Network (NCCN) guideline for NSCLC. We evaluated 6 ALK-positive lung adenocarcinoma patients who tested Ventana IHC-positive and FISH-negative and assessed their clinical responses to the ALK tyrosine kinase inhibitor (TKI) crizotinib. Histologic and cytologic specimens from the 6 patients were stained with Ventana anti-ALK(D5F3) rabbit monoclonal primary antibody using the OptiView™ DAB IHC detection kit and OptiView™ amplification kit on a Ventana BenchMark XT processor. In addition, they were also tested by FISH, qRT-PCR, next-generation sequencing (NGS), and RNAscope ISH analysis. All patients received crizotinib treatment and their follow-up clinical data were recorded. The objective response rate achieved with crizotinib therapy was 66.7% (4/6 partial responses and 2/6 stable disease). One patient in whom a new fusion type (EML4->EXOC6B->ALK fusion) was identified obtained a partial response. These findings indicate that patients with ALK-positive lung adenocarcinoma who test Ventana IHC-positive and FISH-negative may still respond to crizotinib therapy. PMID:27418132

  7. Assessing the impact of policy changes in the Icelandic cod fishery using a hybrid simulation model.

    PubMed

    Sigurðardóttir, Sigríður; Johansson, Björn; Margeirsson, Sveinn; Viðarsson, Jónas R

    2014-01-01

    Most of the Icelandic cod is caught in bottom trawlers or longliners. These two fishing methods are fundamentally different and have different economic, environmental, and even social effects. In this paper we present a hybrid-simulation framework to assess the impact of changing the ratio between cod quota allocated to vessels with longlines and vessels with bottom trawls. It makes use of conventional bioeconomic models and discrete event modelling and provides a framework for simulating life cycle assessment (LCA) for a cod fishery. The model consists of two submodels, a system dynamics model describing the biological aspect of the fishery and a discrete event model for fishing activities. The model was run multiple times for different quota allocation scenarios and results are presented where different scenarios are presented in the three dimensions of sustainability: environmental, social, and economic. The optimal allocation strategy depends on weighing the three different factors. The results were encouraging first-steps towards a useful modelling method but the study would benefit greatly from better data on fishing activities.

  8. Assessing the Impact of Policy Changes in the Icelandic Cod Fishery Using a Hybrid Simulation Model

    PubMed Central

    Sigurðardóttir, Sigríður; Johansson, Björn; Margeirsson, Sveinn; Viðarsson, Jónas R.

    2014-01-01

    Most of the Icelandic cod is caught in bottom trawlers or longliners. These two fishing methods are fundamentally different and have different economic, environmental, and even social effects. In this paper we present a hybrid-simulation framework to assess the impact of changing the ratio between cod quota allocated to vessels with longlines and vessels with bottom trawls. It makes use of conventional bioeconomic models and discrete event modelling and provides a framework for simulating life cycle assessment (LCA) for a cod fishery. The model consists of two submodels, a system dynamics model describing the biological aspect of the fishery and a discrete event model for fishing activities. The model was run multiple times for different quota allocation scenarios and results are presented where different scenarios are presented in the three dimensions of sustainability: environmental, social, and economic. The optimal allocation strategy depends on weighing the three different factors. The results were encouraging first-steps towards a useful modelling method but the study would benefit greatly from better data on fishing activities. PMID:24778597

  9. Genetic assessment of ornamental fish species from North East India.

    PubMed

    Dhar, Bishal; Ghosh, Sankar Kumar

    2015-01-25

    Ornamental fishes are traded with multiple names from various parts around the world, including North East India. Most are collected from the wild, due to lack of species-specific culture or breeding, and therefore, such unmanaged collection of the wild and endemic species could lead to severe threats to biodiversity. Despite many regulatory policies, trade of threatened species, including the IUCN listed species have been largely uncontrolled, due to species identification problems arising from the utilization of multiple trade names. So, the development of species-specific DNA marker is indispensable where DNA Barcoding is proved to be helpful in species identification. Here, we investigated, through DNA Barcoding and morphological assessment, the identification of 128 ornamental fish specimens exported from NE India from different exporters. The generated sequences were subjected to similarity match in BOLD-IDS as well as BLASTN, and analysed using MEGA5.2 for species identification through Neighbour-Joining (NJ) clustering, and K2P distance based approach. The analysis revealed straightforward identification of 84 specimens into 35 species, while 44 specimens were difficult to distinguish based on CO1 barcode alone. However, these cases were resolved through morphology, NJ and distanced based method and found to be belonging to 16 species. Among the 51 identified species, 14 species represented multiple trade names; 17 species belonged to threatened category. Species-level identification through DNA Barcoding along with traditional morphotaxonomy reflects its efficacy in regulating ornamental fish trade and therefore, appeals for their conservation in nature. The use of trade names rather than the zoological name created the passage for trafficking of the threatened species and demands immediate attention for sustaining wildlife conservation. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Food wastes as fish feeds for polyculture of low-trophic-level fish: bioaccumulation and health risk assessments of heavy metals in the cultured fish.

    PubMed

    Cheng, Zhang; Lam, Cheung-Lung; Mo, Wing-Yin; Nie, Xiang-Ping; Choi, Wai-Ming; Man, Yu-Bon; Wong, Ming-Hung

    2016-04-01

    The major purpose of this study was to use different types of food wastes which serve as the major sources of protein to replace the fish meal used in fish feeds to produce quality fish. Two types of food waste-based feed pellets FW A (with cereals) and FW B (with cereals and meat products) and the commercial feed Jinfeng® were used to culture fingerlings of three low-trophic-level fish species: bighead carp, grass carp, and mud carp (in the ratio of 1:3:1) for 1 year period in the Sha Tau Kok Organic Farm in Hong Kong. Heavy metal concentrations in all of the fish species fed with food waste pellets and commercial pellets in Sha Tau Kok fish ponds were all below the local and international maximum permissible levels in food. Health risk assessments indicated that human consumption of the fish fed with food waste feed pellets was safe for the Hong Kong residents. The present results revealed that recycling of food waste for cultivating low-trophic-level fish (mainly herbivores and detritus feeders) is feasible, and at the same time will ease the disposal pressure of food waste, a common problem of densely populated cities like Hong Kong.

  11. Enhancing fish Underwater Visual Census to move forward assessment of fish assemblages: An application in three Mediterranean Marine Protected Areas.

    PubMed

    Prato, Giulia; Thiriet, Pierre; Di Franco, Antonio; Francour, Patrice

    2017-01-01

    Monitoring fish assemblages is needed to assess whether Marine Protected Areas (MPAs) are meeting their conservation and fisheries management goals, as it allows one to track the progress of recovery of exploited species and associated communities. Underwater Visual Census techniques (UVC) are used to monitor fish assemblages in MPAs. UVCs should be adapted to fish abundance, body-size and behaviour, which can strongly affect fish detectability. In Mediterranean subtidal habitats, however, UVC strip transects of one surface area (25x5 m2) are commonly used to survey the whole fish assemblage, from large shy fish to small crypto-benthic fish. Most high trophic level predators (HTLPs) are large shy fish which rarely swim close to divers and, consequently, their abundance may be under-estimated with commonly used transects. Here, we propose an improvement to traditional transect surveys to better account for differences in behaviour among and within species. First, we compared the effectiveness of combining two transect surface areas (large: 35x20 m2; medium: 25x5 m2) in quantifying large, shy fish within and outside Mediterranean MPAs. We identified species-specific body-size thresholds defining a smaller and a larger size class better sampled by medium and large transects respectively. Combining large and medium transects provided more accurate biomass and species richness estimates for large, shy species than using medium transects alone. We thus combined the new approach with two other transect surface areas commonly used to survey crypto-benthic (10x1 m2) and necto-benthic (25x5 m2) species in order to assess how effectively MPAs protection the whole fish assemblage. We verified that MPAs offer significant protection for HTLPs, their response in terms of biomass and density increase in MPAs was always higher in magnitude than other functional groups. Inside MPAs, the contribution of HTLP reached >25% of total fish biomass, against < 2% outside MPAs. Surveys with

  12. Enhancing fish Underwater Visual Census to move forward assessment of fish assemblages: An application in three Mediterranean Marine Protected Areas

    PubMed Central

    Thiriet, Pierre; Di Franco, Antonio; Francour, Patrice

    2017-01-01

    Monitoring fish assemblages is needed to assess whether Marine Protected Areas (MPAs) are meeting their conservation and fisheries management goals, as it allows one to track the progress of recovery of exploited species and associated communities. Underwater Visual Census techniques (UVC) are used to monitor fish assemblages in MPAs. UVCs should be adapted to fish abundance, body-size and behaviour, which can strongly affect fish detectability. In Mediterranean subtidal habitats, however, UVC strip transects of one surface area (25x5 m2) are commonly used to survey the whole fish assemblage, from large shy fish to small crypto-benthic fish. Most high trophic level predators (HTLPs) are large shy fish which rarely swim close to divers and, consequently, their abundance may be under-estimated with commonly used transects. Here, we propose an improvement to traditional transect surveys to better account for differences in behaviour among and within species. First, we compared the effectiveness of combining two transect surface areas (large: 35x20 m2; medium: 25x5 m2) in quantifying large, shy fish within and outside Mediterranean MPAs. We identified species-specific body-size thresholds defining a smaller and a larger size class better sampled by medium and large transects respectively. Combining large and medium transects provided more accurate biomass and species richness estimates for large, shy species than using medium transects alone. We thus combined the new approach with two other transect surface areas commonly used to survey crypto-benthic (10x1 m2) and necto-benthic (25x5 m2) species in order to assess how effectively MPAs protection the whole fish assemblage. We verified that MPAs offer significant protection for HTLPs, their response in terms of biomass and density increase in MPAs was always higher in magnitude than other functional groups. Inside MPAs, the contribution of HTLP reached >25% of total fish biomass, against < 2% outside MPAs. Surveys with

  13. Assessing potential health risks to fish and humans using mercury concentrations in inland fish from across western Canada and the United States

    USGS Publications Warehouse

    Lepak, Jesse M; Hooten, Mevin B.; Eagles-Smith, Collin A.; Tate, Michael T.; Lutz, Michelle A.; Ackerman, Joshua T.; Willacker, James J.; Jackson, Allyson K.; Evers, David C.; Wiener, James G.; Pritz, Colleen Flanagan; Davis, Jay

    2016-01-01

    Fish represent high quality protein and nutrient sources, but Hg contamination is ubiquitous in aquatic ecosystems and can pose health risks to fish and their consumers. Potential health risks posed to fish and humans by Hg contamination in fish were assessed in western Canada and the United States. A large compilation of inland fish Hg concentrations was evaluated in terms of potential health risk to the fish themselves, health risk to predatory fish that consume Hg contaminated fish, and to humans that consume Hg contaminated fish. The probability that a fish collected from a given location would exceed a Hg concentration benchmark relevant to a health risk was calculated. These exceedance probabilities and their associated uncertainties were characterized for fish of multiple size classes at multiple health-relevant benchmarks. The approach was novel and allowed for the assessment of the potential for deleterious health effects in fish and humans associated with Hg contamination in fish across this broad study area. Exceedance probabilities were relatively common at low Hg concentration benchmarks, particularly for fish in larger size classes. Specifically, median exceedances for the largest size classes of fish evaluated at the lowest Hg concentration benchmarks were 0.73 (potential health risks to fish themselves), 0.90 (potential health risk to predatory fish that consume Hg contaminated fish), and 0.97 (potential for restricted fish consumption by humans), but diminished to essentially zero at the highest benchmarks and smallest fish size classes. Exceedances of benchmarks are likely to have deleterious health effects on fish and limit recommended amounts of fish humans consume in western Canada and the United States. Results presented here are not intended to subvert or replace local fish Hg data or consumption advice, but provide a basis for identifying areas of potential health risk and developing more focused future research and monitoring efforts.

  14. Hybrid vehicle assessment. Phase 1: Petroleum savings analysis

    NASA Technical Reports Server (NTRS)

    Levin, R.; Liddle, S.; Deshpande, G.; Trummel, M.; Vivian, H. C.

    1984-01-01

    The results of a comprehensive analysis of near term electric hybrid vehicles are presented, with emphasis on their potential to save significant amounts of petroleum on a national scale in the 1990s. Performance requirements and expected annual usage patterns of these vehicles are first modeled. The projected U.S. fleet composition is estimated, and conceptual hybrid vehicle designs are conceived and analyzed for petroleum use when driven in the expected annual patterns. These petroleum consumption estimates are then compared to similar estimates for projected 1990 conventional vehicles having the same performance and driven in the same patterns. Results are presented in the form of three utility functions and comparisons of sevral conceptual designs are made. The Hybrid Vehicle (HV) design and assessment techniques are discussed and a general method is explained for selecting the optimum energy management strategy for any vehicle mission battery combination. Conclusions and recommendations are presented, and development recommendations are identified.

  15. Chromosome orientation fluorescence in situ hybridization (CO-FISH) to study sister chromatid segregation in vivo

    PubMed Central

    Falconer, Ester; Chavez, Elizabeth; Henderson, Alexander; Lansdorp, Peter M.

    2013-01-01

    Previously, assays for sister chromatid segregation patterns relied on incorporation of BrdU and indirect methods to infer segregation patterns after two cell divisions. Here we describe a method to differentially label sister chromatids of murine cells and directly assay sister chromatid segregation patterns following one cell division in vitro and in vivo by adaptation of the well-established CO-FISH (chromosome orientation fluorescent in situ hybridization) technique. 5-bromo-2′-deoxyuridine (BrdU) is incorporated into newly-formed DNA strands, followed by photolysis and exonuclease digestion to create single-stranded sister chromatids containing parental template DNA only. Such single-stranded sister chromatids are differentially labeled using unidirectional probes to major satellite sequences coupled to fluorescent markers. Differentially-labeled sister chromatids in post-mitotic cells are visualized using fluorescence microscopy and sister chromatid segregation patterns can be directly assayed after one cell division. This procedure requires four days for in vivo mouse tissues, and two days for in vitro cultured cells. PMID:20595964

  16. Development of a fluorescent in situ hybridization (FISH) technique for visualizing CGMMV in plant tissues.

    PubMed

    Shargil, D; Zemach, H; Belausov, E; Lachman, O; Kamenetsky, R; Dombrovsky, A

    2015-10-01

    Cucumber green mottle mosaic virus (CGMMV), which belongs to the genus Tobamovirus, is a major pathogen of cucurbit crops grown indoors and in open fields. Currently, immunology (e.g., ELISA) and molecular amplification techniques (e.g., RT-PCR) are employed extensively for virus detection in plant tissues and commercial seed lots diagnostics. In this study, a fluorescent in situ hybridization (FISH) technique, using oligonucleotides whose 5'-terminals were labeled with red cyanine 3 (Cy3) or green fluorescein isothiocyanate (FITC), was developed for the visualization of the pathogen in situ. This simple and reliable method allows detection and localization of CGMMV in the vegetative and reproductive tissues of cucumber and melon. When this technique was applied in male flowers, anther tissues were found to be infected; whereas the pollen grains were found to be virus-free. These results have meaningful epidemiological implications for the management of CGMMV, particularly with regard to virus transfer via seed and the role of insects as CGMMV vectors.

  17. Hybrid mechanosensing system to generate the polarity needed for migration in fish keratocytes

    PubMed Central

    Okimura, Chika; Iwadate, Yoshiaki

    2016-01-01

    ABSTRACT Crawling cells can generate polarity for migration in response to forces applied from the substratum. Such reaction varies according to cell type: there are both fast- and slow-crawling cells. In response to periodic stretching of the elastic substratum, the intracellular stress fibers in slow-crawling cells, such as fibroblasts, rearrange themselves perpendicular to the direction of stretching, with the result that the shape of the cells extends in that direction; whereas fast-crawling cells, such as neutrophil-like differentiated HL-60 cells and Dictyostelium cells, which have no stress fibers, migrate perpendicular to the stretching direction. Fish epidermal keratocytes are another type of fast-crawling cell. However, they have stress fibers in the cell body, which gives them a typical slow-crawling cell structure. In response to periodic stretching of the elastic substratum, intact keratocytes rearrange their stress fibers perpendicular to the direction of stretching in the same way as fibroblasts and migrate parallel to the stretching direction, while blebbistatin-treated stress fiber-less keratocytes migrate perpendicular to the stretching direction, in the same way as seen in HL-60 cells and Dictyostelium cells. Our results indicate that keratocytes have a hybrid mechanosensing system that comprises elements of both fast- and slow-crawling cells, to generate the polarity needed for migration. PMID:27124267

  18. Production of F1 interspecies hybrid offspring with cryopreserved sperm from a live-bearing fish, the swordtail Xiphophorus helleri.

    PubMed

    Yang, Huiping; Hazlewood, Leona; Heater, Sheila J; Guerrero, Paula A; Walter, Ronald B; Tiersch, Terrence R

    2007-03-01

    Despite study of sperm cryopreservation in more than 200 fish species, production of broods from cryopreserved sperm in live-bearing fish has not been demonstrated. This has not been due to a lack of effort, but instead is a result of the unique morphology, biology, and biochemistry of reproduction in viviparous fishes. For example, sperm of Xiphophorus helleri have a cylindrical nucleus, can swim for days after being activated, have glycolytic capabilities, and can reside in the female reproduction tract for months before fertilization. These traits are not found in fishes with external fertilization. The long-standing research use of the genus Xiphophorus has led to development of over 60 pedigreed lines among the 26 species maintained around the world. These species and lines serve as contemporary models in medical research, although they must be maintained as live populations. Previous attempts at establishing sperm cryopreservation protocols for Xiphophorus have not produced live young. To address this we have been studying the parameters surrounding cryobiology of Xiphophorus sperm and applying this information to an improved understanding of internal fertilization and reproduction. Here we report the first successful fertilization and offspring production by cryopreserved sperm in any live-bearing fish. This claim is supported by our use of artificial insemination between two species that yield distinct hybrid offspring to verify paternity via cryopreserved sperm. We provide a practical approach for preservation of valuable genetic resources from live-bearing fish species, a group that is rapidly being lost due to destruction of native habitats.

  19. Fluorescence in situ hybridization techniques (FISH) to detect changes in CYP19a gene expression of Japanese medaka (Oryzias latipes)

    SciTech Connect

    Park, June-Woo; Tompsett, Amber; Zhang, Xiaowei; Newsted, John L.; Jones, Paul D.; Au, Doris; Kong, Richard; Wu, Rudolf S.S.; Giesy, John P. Hecker, Markus

    2008-10-15

    The aim of this study was to develop a sensitive in situ hybridization methodology using fluorescence-labeled riboprobes (FISH) that allows for the evaluation of gene expression profiles simultaneously in multiple target tissues of whole fish sections of Japanese medaka (Oryzias latipes). To date FISH methods have been limited in their application due to autofluorescence of tissues, fixatives or other components of the hybridization procedure. An optimized FISH method, based on confocal fluorescence microscopy was developed to reduce the autofluorescence signal. Because of its tissue- and gender-specific expression and relevance in studies of endocrine disruption, gonadal aromatase (CYP19a) was used as a model gene. The in situ hybridization (ISH) system was validated in a test exposure with the aromatase inhibitor fadrozole. The optimized FISH method revealed tissue-specific expression of the CYP19a gene. Furthermore, the assay could differentiate the abundance of CYP19a mRNA among cell types. Expression of CYP19a was primarily associated with early stage oocytes, and expression gradually decreased with increasing maturation. No expression of CYP19a mRNA was observed in other tissues such as brain, liver, or testes. Fadrozole (100 {mu}g/L) caused up-regulation of CYP19a expression, a trend that was confirmed by RT-PCR analysis on excised tissues. In a combination approach with gonad histology, it could be shown that the increase in CYP19a expression as measured by RT-PCR on a whole tissue basis was due to a combination of both increases in numbers of CYP19a-containing cells and an increase in the amount of CYP19a mRNA present in the cells.

  20. Assessing patterns of fish demographics and habitat in stream networks

    EPA Science Inventory

    Effective habitat restoration planning requires correctly anticipating demographic responses to altered habitats. New applications of Passive Integrated Transponder (PIT) tag technology to fish-habitat research have provided critical insights into fish movement, growth, and surv...

  1. Assessing patterns of fish demographics and habitat in stream networks

    EPA Science Inventory

    Effective habitat restoration planning requires correctly anticipating demographic responses to altered habitats. New applications of Passive Integrated Transponder (PIT) tag technology to fish-habitat research have provided critical insights into fish movement, growth, and surv...

  2. Microbiological Quality Assessment of Frozen Fish and Fish Processing Materials from Bangladesh

    PubMed Central

    Sanjee, Sohana Al; Karim, Md. Ekramul

    2016-01-01

    The present study aims at the microbiological analysis of export oriented frozen fishes, namely, Jew fish, Tongue Sole fish, Cuttle fish, Ribbon fish, Queen fish, and fish processing water and ice from a view of public health safety and international trade. Microbiological analysis includes the determination of total viable aerobic count by standard plate count method and enumeration of total coliforms and fecal coliforms by most probable number method. The presence of specific fish pathogens such as Salmonella spp. and Vibrio cholerae were also investigated. The TVAC of all the samples was estimated below 5 × 105 cfu/g whereas the total coliforms and fecal coliforms count were found below 100 MPN/g and 10 MPN/g, respectively, which meet the acceptable limit specified by International Commission of Microbiological Specification for Food. The microbiological analysis of water and ice also complies with the specifications having TVAC < 20 cfu/mL, and total coliforms and fecal coliforms count were below the limit detection of the MPN method. Specific fish pathogens such as Salmonella sp. and V. cholerae were found absent in all the samples under the investigation. From this study, it can be concluded that the investigated frozen fishes were eligible for export purpose and also safe for human consumption. PMID:27019847

  3. Microbiological Quality Assessment of Frozen Fish and Fish Processing Materials from Bangladesh.

    PubMed

    Sanjee, Sohana Al; Karim, Md Ekramul

    2016-01-01

    The present study aims at the microbiological analysis of export oriented frozen fishes, namely, Jew fish, Tongue Sole fish, Cuttle fish, Ribbon fish, Queen fish, and fish processing water and ice from a view of public health safety and international trade. Microbiological analysis includes the determination of total viable aerobic count by standard plate count method and enumeration of total coliforms and fecal coliforms by most probable number method. The presence of specific fish pathogens such as Salmonella spp. and Vibrio cholerae were also investigated. The TVAC of all the samples was estimated below 5 × 10(5) cfu/g whereas the total coliforms and fecal coliforms count were found below 100 MPN/g and 10 MPN/g, respectively, which meet the acceptable limit specified by International Commission of Microbiological Specification for Food. The microbiological analysis of water and ice also complies with the specifications having TVAC < 20 cfu/mL, and total coliforms and fecal coliforms count were below the limit detection of the MPN method. Specific fish pathogens such as Salmonella sp. and V. cholerae were found absent in all the samples under the investigation. From this study, it can be concluded that the investigated frozen fishes were eligible for export purpose and also safe for human consumption.

  4. Concurrent assessment of fish and habitat in warmwater streams in Wyoming

    USGS Publications Warehouse

    Quist, M.C.; Hubert, W.A.; Rahel, F.J.

    2006-01-01

    Fisheries research and management in North America have focused largely on sport fishes, but native non-game fishes have attracted increased attention due to their declines. The Warmwater Stream Assessment (WSA) was developed to evaluate simultaneously both fish and habitat in Wyoming streams by a process that includes three major components: (1) stream-reach selection and accumulation of existing information, (2) fish and habitat sampling and (3) summarisation and evaluation of fish and habitat information. Fish are sampled by electric fishing or seining and habitat is measured at reach and channel-unit (i.e. pool, run, riffle, side channel, or backwater) scales. Fish and habitat data are subsequently summarised using a data-matrix approach. Hierarchical decision trees are used to assess critical habitat requirements for each fish species expected or found in the reach. Combined measurements of available habitat and the ecology of individual species contribute to the evaluation of the observed fish assemblage. The WSA incorporates knowledge of the fish assemblage and habitat features to enable inferences of factors likely influencing both the fish assemblage and their habitat. The WSA was developed for warmwater streams in Wyoming, but its philosophy, process and conceptual basis may be applied to environmental assessments in other geographical areas. ?? 2006 Blackwell Publishing Ltd.

  5. VOXMAT: Hybrid Computational Phantom for Dose Assessment

    SciTech Connect

    Akkurt, Hatice; Eckerman, Keith F

    2007-01-01

    The Oak Ridge National Laboratory (ORNL) computational phantoms have been the standard for assessing the radiation dose due to internal and external exposure over the past three decades. In these phantoms, the body surface and each organ are approximated by mathematical equations; hence, some of the organs are not necessarily realistic in their shape. Over the past two decades, these phantoms have been revised and updated: some of the missing internal organs have been added and the locations of the existing organs have been revised (e.g., thyroid). In the original phantom, only three elemental compositions were used to describe all body tissues. Recently, the compositions of the organs have been updated based on ICRP-89 standards. During the past decade, phantoms based on CT scans were developed for use in dose assessment. Although their shapes are realistic, some computational challenges are noted; including increased computational times and increased memory requirements. For good spatial resolution, more than several million voxels are used to represent the human body. Moreover, when CT scans are obtained, the subject is in a supine position with arms at the side. In some occupational exposure cases, it is necessary to evaluate the dose with the arms and legs in different positions. It will be very difficult and inefficient to reposition the voxels defining the arms and legs to simulate these exposure geometries. In this paper, a new approach for computational phantom development is presented. This approach utilizes the combination of a mathematical phantom and a voxelized phantom for the representation of the anatomy.

  6. Assessing the applicability of FISH-based prematurely condensed dicentric chromosome assay in triage biodosimetry.

    PubMed

    Suto, Yumiko; Gotoh, Takaya; Noda, Takashi; Akiyama, Miho; Owaki, Makiko; Darroudi, Firouz; Hirai, Momoki

    2015-03-01

    The dicentric chromosome assay (DCA) has been regarded as the gold standard of radiation biodosimetry. The assay, however, requires a 2-d peripheral blood lymphocyte culture before starting metaphase chromosome analyses to estimate biological doses. Other biological assays also have drawbacks with respect to the time needed to obtain dose estimates for rapid decision on the correct line of medical treatment. Therefore, alternative technologies that suit requirements for triage biodosimetry are needed. Radiation-induced DNA double strand breaks in G0 lymphocytes can be detected as interphase chromosome aberrations by the cell fusion-mediated premature chromosome condensation (PCC) method. The method, in combination with fluorescence in situ hybridization (FISH) techniques, has been proposed in early studies as a powerful tool for obtaining biological dose estimates without 2-d lymphocyte culture procedures. The present work assesses the applicability of FISH-based PCC techniques using pan-centromeric and telomeric peptide nucleic acid (PNA) probes in triage mode biodosimetry and demonstrates that an improved rapid procedure of the prematurely condensed dicentric chromosome (PCDC) assay has the potential for evaluating exposed radiation doses in as short as 6 h after the collection of peripheral blood specimens.

  7. Preparation of Cells from Formalin-Fixed, Paraffin-Embedded Tissue for Use in Fluorescence In Situ Hybridization (FISH) Experiments.

    PubMed

    Weremowicz, Stanislawa

    2015-01-20

    Numerical and structural chromosome abnormalities can be accurately detected in cells from archived tissues using fluorescence in situ hybridization (FISH). This unit describes two common approaches to performing FISH in formalin-fixed, paraffin-embedded tissue. The first approach utilizes 4 to 6 μm tissue sections in cases for which preserving tissue morphology is necessary, and the second involves extraction of intact nuclei from 50-μm tissue sections. To interpret FISH results using 4 to 6 μm sections, an adequate number of nuclei must be evaluated to perform statistical analysis. Evaluation of 30 to 50 nuclei from the single-cell suspension generally gives an interpretable result. Copyright © 2015 John Wiley & Sons, Inc.

  8. Application of ELN cosmid probes using fluorescence in situ hybridization (FISH) towards a clinical diagnostic test for Williams syndrome

    SciTech Connect

    Lowery, M.; Brothman, L.; Leonard, C.

    1994-09-01

    Williams syndrome (WS) is characterized by mental deficiency, gregarious personalities, dysmorphic facies, supravalvular aortic stenosis (SVAS), and idiopathic infantile hypercalcemia. Expression of the phenotype is variable. Deletions including an elastin allele (ELN) are thought to be the basis of the connective tissue and vascular abnormalities in WS patients. Patients with WS are hemizygous for ELN, exhibiting a submicroscopic deletion at 7q11.23 detected by FISH. To substantiate the hemizygosity hypothesis and define molecular cytogenetics in patients with familial and sporadic WS, a series of 71 patients were evaluated. EBV-transformed lymphocytes from 48 selected patients were cultured and harvested according to cytogenetic protocol. Cosmids containing ELN were biotinylated and hybridized to metaphase cells by routine procedures. In addition, an alpha-satellite probe for chromosome 7 was included in hybridizations as an internal control. Thirty-one of these 48 patients (65%) showed a deletion in one ELN allele by FISH. Negative patients were shown to be non-affected family members or patients in the {open_quotes}uncertain{close_quotes} category (expressing some, but not all features characteristic of WS). The FISH data were consistent with molecular analyses of ELN deletions. Twenty-three additional patients were referred to confirm or rule out a diagnosis of WS. Nine patients (39%) showed a deletion of ELN by FISH. Correlations between phenotype and FISH results are in progress. These results suggest that a rapid, accurate diagnostic technique for WS using FISH can be implemented in the cytogenetics laboratory as a routine clinical service. Identification of the deletion in patients suspected of having WS will facilitate classification of these patients and improve clinical management.

  9. Localization of single- and low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH).

    PubMed Central

    Peterson, D G; Lapitan, N L; Stack, S M

    1999-01-01

    Fluorescence in situ hybridization (FISH) is a powerful means by which single- and low-copy DNA sequences can be localized on chromosomes. Compared to the mitotic metaphase chromosomes that are normally used in FISH, synaptonemal complex (SC) spreads (hypotonically spread pachytene chromosomes) have several advantages. SC spreads (1) are comparatively free of debris that can interfere with probe penetration, (2) have relatively decondensed chromatin that is highly accessible to probes, and (3) are about ten times longer than their metaphase counterparts, which permits FISH mapping at higher resolution. To investigate the use of plant SC spreads as substrates for single-copy FISH, we probed spreads of tomato SCs with two single-copy sequences and one low-copy sequence (ca. 14 kb each) that are associated with restriction fragment length polymorphism (RFLP) markers on SC 11. Individual SCs were identified on the basis of relative length, arm ratio, and differential staining patterns after combined propidium iodide (PI) and 4', 6-diamidino-2-phenylindole (DAPI) staining. In this first report of single-copy FISH to SC spreads, the probe sequences were unambiguously mapped on the long arm of tomato SC 11. Coupled with data from earlier studies, we determined the distance in micrometers, the number of base pairs, and the rates of crossing over between these three FISH markers. We also observed that the order of two of the FISH markers is reversed in relation to their order on the molecular linkage map. SC-FISH mapping permits superimposition of markers from molecular linkage maps directly on pachytene chromosomes and thereby contributes to our understanding of the relationship between chromosome structure, gene activity, and recombination. PMID:10224272

  10. HER2 Gene Amplification Testing by Fluorescent In Situ Hybridization (FISH): Comparison of the ASCO-College of American Pathologists Guidelines With FISH Scores Used for Enrollment in Breast Cancer International Research Group Clinical Trials

    PubMed Central

    Sauter, Guido; Buyse, Marc; Fourmanoir, Hélène; Quinaux, Emmanuel; Tsao-Wei, Denice D.; Eiermann, Wolfgang; Robert, Nicholas; Pienkowski, Tadeusz; Crown, John; Martin, Miguel; Valero, Vicente; Mackey, John R.; Bee, Valerie; Ma, Yanling; Villalobos, Ivonne; Campeau, Anaamika; Mirlacher, Martina; Lindsay, Mary-Ann; Slamon, Dennis J.

    2016-01-01

    Purpose ASCO and the College of American Pathologists (ASCO-CAP) recently recommended further changes to the evaluation of human epidermal growth factor receptor 2 gene (HER2) amplification by fluorescent in situ hybridization (FISH). We retrospectively assessed the impact of these new guidelines by using annotated Breast Cancer International Research Group (BCIRG) -005, BCIRG-006, and BCIRG-007 clinical trials data for which we have detailed outcomes. Patients and Methods The HER2 FISH status of BCIRG-005/006/007 patients with breast cancers was re-evaluated according to current ASCO-CAP guidelines, which designates five different groups according to HER2 FISH ratio and average HER2 gene copy number per tumor cell: group 1 (in situ hybridization [ISH]–positive): HER2-to-chromosome 17 centromere ratio ≥ 2.0, average HER2 copies ≥ 4.0; group 2 (ISH-positive): ratio ≥ 2.0, copies < 4.0; group 3 (ISH-positive): ratio < 2.0, copies ≥ 6.0; group 4 (ISH-equivocal): ratio < 2.0, copies ≥ 4.0 and < 6.0; and group 5 (ISH-negative): ratio < 2.0, copies < 4.0. We assessed correlations with HER2 protein, clinical outcomes by disease-free survival (DFS) and overall survival (OS) and benefit from trastuzumab therapy (hazard ratio [HR]). Results Among 10,468 patients with breast cancers who were successfully screened for trial entry, 40.8% were in ASCO-CAP ISH group 1, 0.7% in group 2; 0.5% in group 3, 4.1% in group 4, and 53.9% in group 5. Distributions were similar in screened compared with accrued subpopulations. Among accrued patients, FISH group 1 breast cancers were strongly correlated with immunohistochemistry 3+ status (P < .0001), whereas groups 2, 3, 4, and 5 were not; however, groups 2, 4 and, 5 were strongly correlated with immunohistochemistry 0/1+ status (all P < .0001), whereas group 3 was not. Among patients accrued to BCIRG-005, group 4 was not associated with significantly worse DFS or OS compared with group 5. Among patients accrued to BCIRG-006

  11. Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects

    PubMed Central

    Edwards, C. B.; Friedlander, A. M.; Green, A. G.; Hardt, M. J.; Sala, E.; Sweatman, H. P.; Williams, I. D.; Zgliczynski, B.; Sandin, S. A.; Smith, J. E.

    2014-01-01

    On coral reefs, herbivorous fishes consume benthic primary producers and regulate competition between fleshy algae and reef-building corals. Many of these species are also important fishery targets, yet little is known about their global status. Using a large-scale synthesis of peer-reviewed and unpublished data, we examine variability in abundance and biomass of herbivorous reef fishes and explore evidence for fishing impacts globally and within regions. We show that biomass is more than twice as high in locations not accessible to fisheries relative to fisheries-accessible locations. Although there are large biogeographic differences in total biomass, the effects of fishing are consistent in nearly all regions. We also show that exposure to fishing alters the structure of the herbivore community by disproportionately reducing biomass of large-bodied functional groups (scraper/excavators, browsers, grazer/detritivores), while increasing biomass and abundance of territorial algal-farming damselfishes (Pomacentridae). The browser functional group that consumes macroalgae and can help to prevent coral–macroalgal phase shifts appears to be most susceptible to fishing. This fishing down the herbivore guild probably alters the effectiveness of these fishes in regulating algal abundance on reefs. Finally, data from remote and unfished locations provide important baselines for setting management and conservation targets for this important group of fishes. PMID:24258715

  12. Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects.

    PubMed

    Edwards, C B; Friedlander, A M; Green, A G; Hardt, M J; Sala, E; Sweatman, H P; Williams, I D; Zgliczynski, B; Sandin, S A; Smith, J E

    2014-01-07

    On coral reefs, herbivorous fishes consume benthic primary producers and regulate competition between fleshy algae and reef-building corals. Many of these species are also important fishery targets, yet little is known about their global status. Using a large-scale synthesis of peer-reviewed and unpublished data, we examine variability in abundance and biomass of herbivorous reef fishes and explore evidence for fishing impacts globally and within regions. We show that biomass is more than twice as high in locations not accessible to fisheries relative to fisheries-accessible locations. Although there are large biogeographic differences in total biomass, the effects of fishing are consistent in nearly all regions. We also show that exposure to fishing alters the structure of the herbivore community by disproportionately reducing biomass of large-bodied functional groups (scraper/excavators, browsers, grazer/detritivores), while increasing biomass and abundance of territorial algal-farming damselfishes (Pomacentridae). The browser functional group that consumes macroalgae and can help to prevent coral-macroalgal phase shifts appears to be most susceptible to fishing. This fishing down the herbivore guild probably alters the effectiveness of these fishes in regulating algal abundance on reefs. Finally, data from remote and unfished locations provide important baselines for setting management and conservation targets for this important group of fishes.

  13. Variability of ribosomal DNA sites in Festuca pratensis, Lolium perenne, and their intergeneric hybrids, revealed by FISH and GISH.

    PubMed

    Ksiazczyk, T; Taciak, M; Zwierzykowski, Z

    2010-01-01

    This study focuses on the variability of chromosomal location and number of ribosomal DNA (rDNA) sites in some diploid and autotetraploid Festuca pratensis and Lolium perenne cultivars, as well as on identification of rDNA-bearing chromosomes in their triploid and tetraploid F. pratensis × L. perenne hybrids. The rDNA loci were mapped using fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes, and the origin of parental genomes was verified by genomic in situ hybridization (GISH) with L. perenne genomic DNA as a probe, and F. pratensis genomic DNA as a block. FISH detected variation in the number and chromosomal location of both 5S and 45S rDNA sites. In F. pratensis mostly additional signals of 5S rDNA loci occurred, as compared with standard F. pratensis karyotypes. Losses of 45S rDNA loci were more frequent in L. perenne cultivars and intergeneric hybrids. Comparison of the F. pratensis and L. perenne genomes approved a higher number of rDNA sites as well as variation in chromosomal rDNA location in L. perenne. A greater instability of F. pratensis-genome-like and L. perenne-genome-like chromosomes in tetraploid hybrids was revealed, indicating gains and losses of rDNA loci, respectively. Our data indicate that the rDNA loci physically mapped on chromosomes 2 and 3 in F. pratensis and on chromosome 3 in L. perenne are useful markers for these chromosomes in intergeneric Festuca × Lolium hybrids.

  14. Environmental Assessment : Tumwater Dam and Dryden Dam Fish Passage Projects.

    SciTech Connect

    United States. Bonneville Power Administration.

    1986-01-01

    Existing fish passage facilities at Tumwater Dam and Dryden Dam currently do not effectively pass the anadromous fish runs in the Wenatchee River. At Tumwater Dam, the proposed action includes the construction of a new fish ladder which will improve water flow characteristics and, subsequently, fish passage. In order to improve fish passage at Dryden Dam, a new fish ladder will be constructed to replace the existing ladder and another ladder will be constructed. The proposed action will supplement mitigation of adverse hydroelectric impacts to the fisheries of the Columbia River basin. The proposal to fund the Tumwater Dam and Dryden Dam Fish Passage facilities does not appear to constitute a major Federal action significantly affecting the quality of the human environment and would not require an environmental impact statement.

  15. Peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) assay for specific detection of Mycobacterium immunogenum and DNA-FISH assay for analysis of pseudomonads in metalworking fluids and sputum.

    PubMed

    Selvaraju, Suresh B; Kapoor, Renuka; Yadav, Jagjit S

    2008-01-01

    Specific and rapid detection and quantification of mycobacteria in contaminated metalworking fluid (MWF) are problematic due to complexity of the matrix and heavy background co-occurring microflora. Furthermore, cross-reactivity among neighboring species of Mycobacterium makes species differentiation difficult for this genus. Here, we report for the first time a species-specific peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) method for Mycobacterium immunogenum, a non-tuberculous Mycobacterium species prevalent in MWF and implicated in occupational lung disease hypersensitivity pneumonitis and pseudo-outbreaks. A novel species-specific 14-bp PNA probe was designed for M. immunogenum based on its 16S rRNA gene sequence and was validated for specificity, by testing against a panel of other phylogenetically closely related rapidly growing mycobacteria and representative species of gram-positive, gram-negative, and acid fast organisms. In addition, a DNA-FISH protocol was optimized for co-detection of Pseudomonas, the most predominantly co-occurring genus in contaminated MWF. Reliable quantification for both the test organisms was achieved at or above a cell density of 10(3)cellsml(-1), a recognized minimum limit for microscopic quantification. The mycobacterial PNA-FISH assay was successfully adapted to human sputum demonstrating its potential for clinical diagnostic applications in addition to industrial MWF monitoring, to assess MWF-associated exposures and pseudo-outbreaks.

  16. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    PubMed Central

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-01-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent–offspring relationships in natural populations, with over 99.6% accuracy in parent–offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28–96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. PMID:25360247

  17. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).

    PubMed

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-06-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.

  18. Fluorescence in situ hybridization (FISH) analysis of melanocytic nevi and melanomas: sensitivity, specificity, and lack of association with sentinel node status.

    PubMed

    Fang, Yuqiang; Dusza, Stephen; Jhanwar, Suresh; Busam, Klaus J

    2012-10-01

    A 4-color fluorescence in situ hybridization (FISH) assay, using probes to chromosomes 11q, 6p, 6q, and 6 cent, has recently been proposed as an ancillary tool for the diagnosis of melanoma. The authors report herein their experience with this assay. To determine the sensitivity and specificity of the assay for histopathologically unequivocal cases, they analyzed 50 melanocytic nevi, 50 primary melanomas, and 15 metastatic melanomas. Of 50 melanocytic nevi, 47 were FISH negative on initial readout (test sensitivity, 94%); 49 were FISH negative after correction for tetraploidy (test specificity, 98%). Of 50 primary melanomas, 41 were FISH positive (test sensitivity, 82%). Of 15 metastatic lesions, 13 were FISH positive (test sensitivity, 85%). Of the 9 FISH-negative melanomas, 6 metastasized. The tumors of the 5 patients who had survived thick primary melanoma for more than 5 years without recurrence were all FISH positive. Half of the patients whose primary melanoma was tested by FISH had undergone sentinel lymph node (SLN) biopsy. When the authors compared the FISH results of those 25 melanomas with the SLN status, no statistically significant correlation was found. These findings document limitations of the current FISH assay. A rare nevus may be FISH positive. Some primary metastasizing melanomas are FISH negative. Even metastatic melanomas can be FISH negative. Awareness of the limitations in test sensitivity and specificity of the FISH assay is important to avoid an erroneous diagnosis by overreliance on cytogenetic findings. Correlation with clinical and histopathological findings is paramount for accurate diagnosis.

  19. Technical Note: Determination of the metabolically active fraction of benthic foraminifera by means of Fluorescent In Situ Hybridization (FISH)

    NASA Astrophysics Data System (ADS)

    Borrelli, C.; Sabbatini, A.; Luna, G. M.; Nardelli, M. P.; Sbaffi, T.; Morigi, C.; Danovaro, R.; Negri, A.

    2011-08-01

    Benthic foraminifera are an important component of the marine biota, but protocols for investigating their viability and metabolism are still extremely limited. Classical studies on benthic foraminifera have been based on direct counting under light microscopy. Typically, these organisms are stained with Rose Bengal, which binds proteins and other macromolecules, but does not allow discrimination between viable and recently dead organisms. The fluorescent in situ hybridization technique (FISH) represents a new and useful approach to identify living cells possessing an active metabolism. Our work is the first test of the suitability of the FISH technique, based on fluorescent probes targeting the 18S rRNA, to detect live benthic foraminifera. The protocol was applied on Ammonia group and Miliolids, as well as on agglutinated polythalamous (i.e., Leptohalysis scottii and Eggerella scabra) and soft-shelled monothalamous (i.e., Psammophaga sp. and saccamminid morphotypes) taxa. The results from FISH analyses were compared with those obtained, on the same specimens assayed with FISH, from microscopic analysis of the cytoplasm colour, presence of pigments and pseudopodial activity. Our results indicate that FISH targets only metabolically active foraminifera, and allows discerning from low to high cellular activity, validating the hypothesis that the intensity of the fluorescent signal emitted by the probe is dependent upon the physiological status of cells. These findings support the usefulness of this molecular approach as a key tool for obtaining information on the physiology of living foraminifera, both in field and experimental settings.

  20. Hybrid vehicle assessment. Phase I. Petroleum savings analysis

    SciTech Connect

    Levin, R.; Liddle, S.; Deshpande, G.; Trummel, M.; Vivian, H.

    1984-03-01

    This report presents the results of a comprehensive analysis of near-term electric-hybrid vehicles. Its purpose was to estimate their potential to save significant amounts of petroleum on a national scale in the 1990s. Performance requirements and expected annual usage patterns of these vehicles were first modeled. The projected US fleet composition was estimated, and conceptual hybrid vehicle designs were conceived and analyzed for petroleum use when driven in the expected annual patterns. These petroleum consumption estimates were then compared to similar estimates for projected 1990 conventional vehicles having the same performance and driven in the same patterns. Results are presented in the form of three utility functions and comparisons of several conceptual designs are made. The Hybrid Vehicle (HV) design and assessment techniques are discussed and a general method is explained for selecting the optimum energy management strategy for any vehicle-mission-battery combination. A discussion of lessons learned during the construction and test of the General Electric Hybrid Test Vehicle is also presented. Conclusions and recommendations are presented, and development recommendations are identified.

  1. Prenatal aneupioidy detection by fluorencence in situ hybridization (FISH) in 1,068 second trimester pregnancies with fetal ultrasound abnormalities

    SciTech Connect

    Ward, B.E.; Wright, M.; Lytle, C. |

    1994-09-01

    One indication for rapid prenatal aneuploidy detection in uncultured amniocytes by FISH is the identification of fetal abnormalities by ultrasound. We analyzed 1,068 consecutive specimens from second trimester pregnancies with fetal ultrasound abnormalities referred for FISH plus cytogenetics. These specimens are a subset (14.7%) of the most recent 7,240 clinical referrals for these combined analyses. Hybridization with specific probes for chromosomes 21, 18, 13, X and Y were used to detect common aneuploidies. As defined by previously described criteria, specimens were reported as informative disomic, informative trisomic, or uninformative within two days of receipt. The rate of informative results from acceptable specimens was 90.1%. The vast majority of uninformative results was due to maternal cell contamination which precluded analysis. Within the informative group there were no false positives, false negatives nor reports of incorrect gender. Of the 1,068 tested specimens with ultrasound abnormalities, 135 (12.5%) were cytogenetically diagnosed as aneuploid. Prior to the cytogenetic analysis, a total of 107 aneuploidies were correctly identified by FISH. The remaining 26 aneuploidies generated an uninformative FISH result. The overall FISH detection rate for aneuploidy (including informative and uninformative results) was 79%. Other unbalanced chromosome abnormalities were present in 2.1% of specimens and 0.7% had balanced chromosome abnormalities. The inclusive total cytogenetic abnormality rate was 15.4%, of which 85% were potentially detectable by our FISH protocol. This clinical experience demonstrates that aneuploidy detection by FISH on uncultured amniocytes can provide accurate and rapid identification of aneuploidies, especially when such abnormalities are suspected following the diagnosis of fetal anomalies by ultrasound examination.

  2. Preliminary assessment of factors influencing riverine fish communities in Massachusetts.

    USGS Publications Warehouse

    Armstrong, David S.; Richards, Todd A.; Brandt, Sara L.

    2010-01-01

    The U.S. Geological Survey, in cooperation with the Massachusetts Department of Conservation and Recreation (MDCR), Massachusetts Department of Environmental Protection (MDEP), and the Massachusetts Department of Fish and Game (MDFG), conducted a preliminary investigation of fish communities in small- to medium-sized Massachusetts streams. The objective of this investigation was to determine relations between fish-community characteristics and anthropogenic alteration, including flow alteration and impervious cover, relative to the effect of physical basin and land-cover (environmental) characteristics. Fish data were obtained for 756 fish-sampling sites from the Massachusetts Division of Fisheries and Wildlife fish-community database. A review of the literature was used to select a set of fish metrics responsive to flow alteration. Fish metrics tested include two fish-community metrics (fluvial-fish relative abundance and fluvial-fish species richness), and five indicator species metrics (relative abundance of brook trout, blacknose dace, fallfish, white sucker, and redfin pickerel). Streamflows were simulated for each fish-sampling site using the Sustainable Yield Estimator application (SYE). Daily streamflows and the SYE water-use database were used to determine a set of indicators of flow alteration, including percent alteration of August median flow, water-use intensity, and withdrawal and return-flow fraction. The contributing areas to the fish-sampling sites were delineated and used with a Geographic Information System (GIS) to determine a set of environmental characteristics, including elevation, basin slope, percent sand and gravel, percent wetland, and percent open water, and a set of anthropogenic-alteration variables, including impervious cover and dam density. Two analytical techniques, quantile regression and generalized linear modeling, were applied to determine the association between fish-response variables and the selected environmental and

  3. Assessment of dietary fish consumption in pregnancy: comparing one-, four- and thirty-six-item questionnaires.

    PubMed

    Oken, Emily; Guthrie, Lauren B; Bloomingdale, Arienne; Gillman, Matthew W; Olsen, Sjurdur F; Amarasiriwardena, Chitra J; Platek, Deborah N; Bellinger, David C; Wright, Robert O

    2014-09-01

    Fish consumption influences a number of health outcomes. Few studies have directly compared dietary assessment methods to determine the best approach to estimating intakes of fish and its component nutrients, including DHA, and toxicants, including methylmercury. Our objective was to compare three methods of assessing fish intake. We assessed 30 d fish intake using three approaches: (i) a single question on total fish consumption; (ii) a brief comprehensive FFQ that included four questions about fish; and (iii) a focused FFQ with thirty-six questions about different finfish and shellfish. Obstetrics practices in Boston, MA, USA. Fifty-nine pregnant women who consumed ≤2 monthly fish servings. Estimated intakes of fish, DHA and Hg were lowest with the one-question screener and highest with the thirty-six-item fish questionnaire. Estimated intake of DHA with the thirty-six-item questionnaire was 4·4-fold higher (97 v. 22 mg/d), and intake of Hg was 3·8-fold higher (1·6 v. 0·42 μg/d), compared with the one-question screener. Plasma DHA concentration was correlated with fish intake assessed with the one-question screener (Spearman r = 0·27, P = 0·04), but not with the four-item FFQ (r = 0·08, P = 0·54) or the thirty-six-item fish questionnaire (r = 0·01, P = 0·93). In contrast, blood and hair Hg concentrations were similarly correlated with fish and Hg intakes regardless of the assessment method (r = 0·35 to 0·52). A longer questionnaire provides no advantage over shorter questionnaires in ranking intakes of fish, DHA and Hg compared with biomarkers, but estimates of absolute intakes can vary by as much as fourfold across methods.

  4. Clinical significance of detecting circulating tumor cells in colorectal cancer using subtraction enrichment and immunostaining-fluorescence in situ hybridization (SE-iFISH)

    PubMed Central

    Shen, Zhen; Jing, Yan; Lu, Haibo; Li, Heng; Yang, Xiaoye; Cui, Xiangbin; Li, Yuqing; Lou, Zheng; Liu, Peng; Zhang, Cun; Zhang, Wei

    2017-01-01

    Circulating tumor cells (CTC) are useful in early detection of colorectal cancer. This study described a newly developed platform, integrated subtraction enrichment and immunostaining-fluorescence in situ hybridization (SE-iFISH), to assess CTCs in colorectal cancer. CTCs were detected by SE-iFISH in 40 of 44 preoperative colorectal cancer patients, and yielded a sensitivity of 90.9%, which was significantly higher than CellSearch system (90.9% vs. 43.2%, P=0.033). No significant association was found between tumor stage, survival and preoperative CTC number. CTCs were detected in 10 colorectal cancer patients one week after surgery; seven patients with decreased CTC numbers (compared with preoperative CTC number) were free of recurrence; whereas two of the three patients with increased CTC numbers had tumor recurrence. Moreover, CTCs were detected in 34 colorectal cancer patients three months after surgery; patients with CTC<2 at three months after surgery had significantly longer Progression Free Survival than those with CTC>=2 (P=0.019); patients with decreased CTC number (compared with preoperative CTC number) had significantly longer Progression Free Survival than those with increased CTC number (P=0.003). In conclusion, CTCs could be detected in various stages of colorectal cancer using SE-iFISH. Dynamic monitoring of CTC numbers could predict recurrence and prognosis. PMID:28423493

  5. Do scientists and fishermen collect the same size fish? Possible implications for exposure assessment.

    PubMed

    Burger, Joanna; Gochfeld, Michael; Burke, Sean; Jeitner, Christian W; Jewett, Stephen; Snigaroff, Daniel; Snigaroff, Ronald; Stamm, Tim; Harper, Shawn; Hoberg, Max; Chenelot, Heloise; Patrick, Robert; Volz, Conrad D; Weston, James

    2006-05-01

    research/commercial trawler operated under charter to the National Oceanographic and Atmospheric Administration (NOAA). The fish selected for sampling, including those caught commercially in the Bering Sea, represented different trophic levels, and are species regularly caught by Aleuts while fishing near their villages. Not all fish were caught by all three groups. There were no significant differences in length and weight for five species of fish caught by Aleuts, scientists, and fisheries trawls, and for an additional 3 species caught only by the Aleut and scientist teams. There were small, but significant, differences in the sizes of rock greenling (Hexagrammos lagocephalus) and red Irish lord (Hemilepidotus hemilepidotus) caught by the scientist and Aleut fishermen. No scientists caught rock greenling using poles; those speared by the divers were significantly smaller than those caught by the Aleuts. Further, there were no differences in the percent of males in the samples as a function of fishing method or type of fishermen, except for rockfish and red Irish lord. These data suggest that if scientists collect fish in the same manner as subsistence fishermen (in this case, using fishing rods from boats), they can collect the same-sized fish. The implications for exposure and risk assessment are that scientists should either engage subsistence and recreational fishermen to collect fish for analysis, or mimic their fishing methods to ensure that the fish collected are similar in size and weight to those being caught and consumed by these groups. Further, total length, standard length, and weight were highly correlated for all species of fish, suggesting that risk assessors could rely on recreational and commercial fishermen to measure total lengths for the purpose of correlating mercury levels with known size/mercury level relationships. Our data generally demonstrate that the scientists and trawlers can collect the same size fish as those caught by Aleuts, making

  6. Fish pass assessment by remote control: a novel framework for quantifying the hydraulics at fish pass entrances

    NASA Astrophysics Data System (ADS)

    Kriechbaumer, Thomas; Blackburn, Kim; Gill, Andrew; Breckon, Toby; Everard, Nick; Wright, Ros; Rivas Casado, Monica

    2014-05-01

    Fragmentation of aquatic habitats can lead to the extinction of migratory fish species with severe negative consequences at the ecosystem level and thus opposes the target of good ecological status of rivers defined in the EU Water Framework Directive (WFD). In the UK, the implementation of the EU WFD requires investments in fish pass facilities of estimated 532 million GBP (i.e. 639 million Euros) until 2027 to ensure fish passage at around 3,000 barriers considered critical. Hundreds of passes have been installed in the past. However, monitoring studies of fish passes around the world indicate that on average less than half of the fish attempting to pass such facilities are actually successful. There is a need for frameworks that allow the rapid identification of facilities that are biologically effective and those that require enhancement. Although there are many environmental characteristics that can affect fish passage success, past research suggests that variations in hydrodynamic conditions, reflected in water velocities, velocity gradients and turbulences, are the major cues that fish use to seek migration pathways in rivers. This paper presents the first steps taken in the development of a framework for the rapid field-based quantification of the hydraulic conditions downstream of fish passes and the assessment of the attractivity of fish passes for salmonids and coarse fish in UK rivers. For this purpose, a small-sized remote control platform carrying an acoustic Doppler current profiler (ADCP), a GPS unit, a stereo camera and an inertial measurement unit has been developed. The large amount of data on water velocities and depths measured by the ADCP within relatively short time is used to quantify the spatial and temporal distribution of water velocities. By matching these hydraulic features with known preferences of migratory fish, it is attempted to identify likely migration routes and aggregation areas at barriers as well as hydraulic features that

  7. Contribution of conservation genetics in assessing neotropical freshwater fish biodiversity.

    PubMed

    Piorski, N M; Sanches, A; Carvalho-Costa, L F; Hatanaka, T; Carrillo-Avila, M; Freitas, P D; Galetti, P M

    2008-11-01

    Human activities have a considerable impact on hydrographic systems and fish fauna. The present review on conservation genetics of neotropical freshwater fish reveals that DNA analyses have been promoting increased knowledge on the genetic structure of fish species and their response to environmental changes. This knowledge is fundamental to the management of wild fish populations and the establishment of Evolutionary Significant Units capable of conserving genetic integrity. While population structuring can occur even in long-distance migratory fish, isolated populations can show reduced genetic variation and be at greater risk of extinction. Phylogeography and phylogeny have been powerful tools in understanding the evolution of fish populations, species and communities in distinct neotropic environments. Captive fish can be used to introduce new individuals and genes into the wild and their benefits and disadvantages can be monitored through genetic analysis. Understanding how fish biodiversity in neotropical freshwaters is generated and maintained is highly important, as these habitats are transformed by human development and fish communities are increasingly exploited as food sources to sustain a growing human population.

  8. Application of a fluorescence in situ hybridization (FISH) method to study green tides in the Yellow Sea

    NASA Astrophysics Data System (ADS)

    Zhang, Qing-Chun; Liu, Qing; Yu, Ren-Cheng; Kang, Zhen-Jun; Guo, Wei; Ding, Yue-Min; Chen, Jian-Hua; Wang, Yun-Feng; Li, Yan; Yan, Tian; Zhou, Ming-Jiang

    2015-09-01

    Massive green tides of Ulva prolifera have been recorded consecutively since 2007 in the Yellow Sea (YS). It has been proposed that the floating green algae in the YS are originally from the culture rafts of Porphyra yezoensis in the Subei Shoal. However, there is still much debate about this, mainly due to the difficulty in rapid and accurate identification of U. prolifera. In this study, a developed fluorescence in situ hybridization (FISH) method was adopted to identify U. prolifera and assess its relative abundance in the green algal community. Using this method, several processes related to the formation of green tides were studied, including: (1) variation of the relative abundance of U. prolifera in the green algal community attached to Porphyra rafts in the Subei Shoal; (2) contribution of the microscopic propagules in seawater to the U. prolifera population attached to the rafts; and (3) variation of the proportion of U. prolifera in the floating green algae in the YS. U. prolifera were detected in the green algae attached to Porphyra rafts from March to May 2012, where its relative abundance increased rapidly from 10% at the end of April to 40-60% in mid-May. Microscopic propagules of U. prolifera, which could be detected from seawater and sediment, contributed significantly to the dramatic increase of the attached U. prolifera on the Porphyra rafts. After the attached green algae were removed from the rafts, U. prolifera rapidly demonstrated dominance in the floating green algal community, and the proportion of U. prolifera increased gradually from south to north. Our conceptual model is that the germination of U. prolifera microscopic propagules on Porphyra rafts promotes the proliferation of attached U. prolifera on the rafts, which release more microscopic propagules into seawater and sediments after they became mature. This positive feedback enhances the dominance of U. prolifera in the attached green algal community in late May, which leads to the

  9. Visualization of sporopollenin-containing pathogenic green micro-alga Prototheca wickerhamii by fluorescent in situ hybridization (FISH).

    PubMed

    Ueno, Ryohei

    2009-04-01

    Fluorescent in situ hybridization (FISH) using taxon-specific, rRNA-targeted oligonucleotide probes is one of the most powerful tools for the rapid identification of harmful microorganisms. However, eukaryotic algal cells do not always allow FISH probes to permeate over their cell walls. Members of the pathogenic micro-algal genus Prototheca are characterized by their distinctive cell-wall component, sporopollenin, an extremely tough biopolymer that resists acid and alkaline hydrolysis, enzyme attack, and acetolysis. To our knowledge, there has been no report of the successful permeation by the oligonucleotide probes over the cell walls of unicellular green micro-algae, which contain sporopollenin. The DNA probes passed through the cell wall of Prototheca wickerhamii after treating the algal cells with cetyltrimethylammonium bromide (CTAB). Most cells in the middle logarithmic growth phase culture fluoresced when hybridized with the rRNA-targeted universal probe for eukaryotes, though individual cells included in this culture differed in the level of cell-wall vulnerability to attack by the polysaccharide-degrading enzyme, thus reflecting the different stages of the life cycle. This is the first report regarding the visualization of sporopollenin-containing, green micro-algal cells by FISH.

  10. Identification and characterization of marker chromosomes, de novo rearrangements and microdeletions in 100 cases with fluorescence in situ hybridization (FISH)

    SciTech Connect

    Anderson, S.M.; Liu, Y.; Papenhausen, P.R.

    1994-09-01

    Results of molecular cytogenetic analysis are presented for 100 cases in which fluorescence in situ hybridization (FISH) was used as an adjunct to standard cytogenetics. Commercially available centromeric, telomeric, chromosome painting and unique sequence probes were used. Cases were from a 12-month period (June 1993-May 1994) and included examples of sex chromosome abnormalities (8), duplications (5), de novo translocations (6), satellited (12) and non-satellited (7) markers, and microdeletion syndromes (62). Satellited marker chromosomes were evaluated using a combination of DAPI/Distamycin A staining, hybridization with a classical satellite probe for chromosome 15 and hybridization with alpha-satellite probes for chromosomes 13, 14, 21 and 22. Markers positive for the chromosome 15 probe were further evaluated using unique sequence probes for the Prader-Willi/Angelman region. Microdeletion analysis was performed for Prader-Willi/Angelman (49) and DiGeorge/VCF (13) syndromes. Seven cases evaluated for Prader-Willi/Angelman syndrome demonstrated evidence of a deletion within this region. Uniparental disomy analysis was available in cases where a deletion was not detected by FISH, yet follow-up was clinically indicated. Two cases evaluated for DiGeorge/VCF syndrome demonstrated molecular evidence of a deletion. Included in our analysis is an example of familial DiGeorge syndrome.

  11. Environmental assessment, K Pool fish rearing, Hanford Site, Richland, Washington

    SciTech Connect

    1996-12-01

    The US Department of Energy (DOE) has a need to respond to a request to lease facilities at the Hanford Site 100-KE and 100-KW filter plant pools (K Pools) for fish rearing activities. These fish rearing activities would be: (1) business ventures with public and private funds and (2) long-term enhancement and supplementation programs for game fish populations in the Columbia River Basin. The proposed action is to enter into a use permit or lease agreement with the YIN or other parties who would rear fish in the 100-K Area Pools. The proposed action would include necessary piping, pump, and electrical upgrades of the facility; cleaning and preparation of the pools; water withdrawal from the Columbia River, and any necessary water or wastewater treatment; and introduction, rearing and release of fish. Future commercial operations may be included.

  12. Quantitative assessment of brain volumes in fish: comparison of methodologies.

    PubMed

    Ullmann, Jeremy F P; Cowin, Gary; Collin, Shaun P

    2010-01-01

    When correlating brain areas with behavioral and environmental characteristics, a variety of techniques are employed. In fishes (elasmobranchs and teleosts), 2 methods, histology and the idealized ellipsoid and/or half-ellipsoid technique, are primarily used to calculate the volume of a brain area and therefore its relationship to social or ecological complexity. In this study on a perciform teleost, we have quantitatively compared brain volumes obtained using the conventional techniques of histology and approximating brain volume to an idealized ellipsoid (or half ellipsoid) and magnetic resonance imaging, an established clinical tool typically used for assessing brain volume in other vertebrates. Our results indicate that, when compared to brain volumes measured using magnetic resonance imaging of brain regions in situ, variations in brain shape and histological artifacts can lead to significant differences in brain volume, especially in the telencephalon and optic tecta. Consequently, in comparative studies of brain volumes, we advise caution when using the histological and/or ellipsoid methods to make correlations between brain area size and environmental, behavioral and social characteristics and, when possible, we propose the use of magnetic resonance imaging. Copyright © 2010 S. Karger AG, Basel.

  13. In situ DNA hybridized chain reaction (FISH-HCR) as a better method for quantification of bacteria and archaea within marine sediment

    NASA Astrophysics Data System (ADS)

    Buongiorno, J.; Lloyd, K. G.; Shumaker, A.; Schippers, A.; Webster, G.; Weightman, A.; Turner, S.

    2015-12-01

    Nearly 75% of the Earth's surface is covered by marine sediment that is home to an estimated 2.9 x 1029 microbial cells. A substantial impediment to understanding the abundance and distribution of cells within marine sediment is the lack of a consistent and reliable method for their taxon-specific quantification. Catalyzed reporter fluorescent in situ hybridization (CARD-FISH) provides taxon-specific enumeration, but this process requires passing a large enzyme through cell membranes, decreasing its precision relative to general cell counts using a small DNA stain. In 2015, Yamaguchi et al. developed FISH hybridization chain reaction (FISH-HCR) as an in situ whole cell detection method for environmental microorganisms. FISH-HCR amplifies the fluorescent signal, as does CARD-FISH, but it allows for milder cell permeation methods that might prevent yield loss. To compare FISH-HCR to CARD-FISH, we examined bacteria and archaea cell counts within two sediment cores, Lille Belt (~78 meters deep) and Landsort Deep (90 meters deep), which were retrieved from the Baltic Sea Basin during IODP Expedition 347. Preliminary analysis shows that CARD-FISH counts are below the quantification limit for most depths across both cores. By contrast, quantification of cells was possible with FISH-HCR in all examined depths. When quantification with CARD-FISH was above the limit of detection, counts with FISH-HCR were up to 11 fold higher for Bacteria and 3 fold higher for Archaea from the same sediment sample. Further, FISH-HCR counts follow the trends of on board counts nicely, indicating that FISH-HCR may better reflect the cellular abundance within marine sediment than other quantification methods, including qPCR. Using FISH-HCR, we found that archaeal cell counts were on average greater than bacterial cell counts, but within the same order of magnitude.

  14. A feasibility assessment of automated FISH image and signal analysis to assist cervical cancer detection

    NASA Astrophysics Data System (ADS)

    Wang, Xingwei; Li, Yuhua; Liu, Hong; Li, Shibo; Zhang, Roy R.; Zheng, Bin

    2012-02-01

    Fluorescence in situ hybridization (FISH) technology provides a promising molecular imaging tool to detect cervical cancer. Since manual FISH analysis is difficult, time-consuming, and inconsistent, the automated FISH image scanning systems have been developed. Due to limited focal depth of scanned microscopic image, a FISH-probed specimen needs to be scanned in multiple layers that generate huge image data. To improve diagnostic efficiency of using automated FISH image analysis, we developed a computer-aided detection (CAD) scheme. In this experiment, four pap-smear specimen slides were scanned by a dual-detector fluorescence image scanning system that acquired two spectrum images simultaneously, which represent images of interphase cells and FISH-probed chromosome X. During image scanning, once detecting a cell signal, system captured nine image slides by automatically adjusting optical focus. Based on the sharpness index and maximum intensity measurement, cells and FISH signals distributed in 3-D space were projected into a 2-D con-focal image. CAD scheme was applied to each con-focal image to detect analyzable interphase cells using an adaptive multiple-threshold algorithm and detect FISH-probed signals using a top-hat transform. The ratio of abnormal cells was calculated to detect positive cases. In four scanned specimen slides, CAD generated 1676 con-focal images that depicted analyzable cells. FISH-probed signals were independently detected by our CAD algorithm and an observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in detecting/counting FISH signal spots. The study demonstrated the feasibility of applying automated FISH image and signal analysis to assist cyto-geneticists in detecting cervical cancers.

  15. A Hybrid Method for Image Segmentation Based on Artificial Fish Swarm Algorithm and Fuzzy c-Means Clustering.

    PubMed

    Ma, Li; Li, Yang; Fan, Suohai; Fan, Runzhu

    2015-01-01

    Image segmentation plays an important role in medical image processing. Fuzzy c-means (FCM) clustering is one of the popular clustering algorithms for medical image segmentation. However, FCM has the problems of depending on initial clustering centers, falling into local optimal solution easily, and sensitivity to noise disturbance. To solve these problems, this paper proposes a hybrid artificial fish swarm algorithm (HAFSA). The proposed algorithm combines artificial fish swarm algorithm (AFSA) with FCM whose advantages of global optimization searching and parallel computing ability of AFSA are utilized to find a superior result. Meanwhile, Metropolis criterion and noise reduction mechanism are introduced to AFSA for enhancing the convergence rate and antinoise ability. The artificial grid graph and Magnetic Resonance Imaging (MRI) are used in the experiments, and the experimental results show that the proposed algorithm has stronger antinoise ability and higher precision. A number of evaluation indicators also demonstrate that the effect of HAFSA is more excellent than FCM and suppressed FCM (SFCM).

  16. Development and assessment of the CONTAIN hybrid flow solver

    SciTech Connect

    Murata, K.K.; Stamps, D.W.

    1996-11-01

    A new gravitational head formulation for the treatment of stratified conditions has been developed for CONTAIN 1.2, a control volume code used primarily for the analyses of postulated accidents in nuclear power plants. The new CONTAIN formulation of gravitational heads, termed the hybrid formulation, is described. This method of calculating stratified conditions is compared with the old, average-density formulation used in code versions prior to CONTAIN 1.2. Both formulations are assessed in this report with experimental data from three large-scale experiments in which stratified conditions formed by injection of a buoyant gas were observed. In general, the hybrid formulation gives a substantially higher degree of stratification than the old formulation. For stable, fully developed stratifications, the hybrid formulation also gives much better agreement with the measured degree of stratification than the old formulation. In addition, the predicted degree of stratification is robust and not sensitive to nodalization, provided a set of nodalization guidelines are followed. However, for stratification behavior controlled by special physics not modeled in CONTAIN, such as momentum convection, plume entrainment, or bulk molecular diffusion, one should not expect good agreement with experiment unless special measures to accommodate the missing physics are taken.

  17. Complete mitochondrial genome of the hybridized fish (Oncorhynchus mykiss ♀ × Atlantic salmon ♂).

    PubMed

    Wang, Fenghua; He, Enpeng; Li, Yanhong; Cai, Xiaodi; Ma, Wen

    2016-11-01

    In this study, 16 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of the hybridized fish (Oncorhynchus mykiss ♀ × Atlantic salmon ♂) in order to characterize and compare their mitochondrial genomes. The total length of the mitochondrial genome is 16,658 bp and deposited in the GenBank with accession numbers KP218514. The organization of the mitochondrial genomes contained 37 genes (13 protein-coding genes, two ribosomal RNA, and 22 transfer RNAs) and a major non-coding control region which was similar to those reported mitochondrial genomes. Most genes were encoded on the H-strand, except for the ND6 and eight tRNA genes, encoding on the L-strand. Similarity and divergence analysis also showed that hybrid offspring were genetically closer to mother parent than father parent. These results indicate that, despite hybridization, the mitochondrial genomes of these hybrids remain maternally inherited.

  18. Population cage experiments with a vertebrate: The temporal demography and cytonuclear genetics of hybridization on Gambusia fishes

    USGS Publications Warehouse

    Scribner, Kim T.; Avise, John C.

    1994-01-01

    The dynamics of mitochondrial and multilocus nuclear genotypic frequencies were monitored for 2 yr in experimental populations established with equal numbers of two poeciliid fishes (Gambusia affinis and Gambusia holbrooki) that hybridize naturally in the southeastern United States. In replicated "small-pool" populations (experiment I), 1018 sampled individuals at six time periods revealed an initial flush of hybridization, followed by a rapid decline in frequencies of G. affinis nuclear and mitochondrial alleles over 64 wk. Decay of gametic and cytonuclear disequilibria differed from expectations under random mating as well as under a model of assortative mating involving empirically estimated mating propensities. In two replicate "large-pond" populations (experiment II), 841 sampled individuals across four reproductive cohorts revealed lower initial frequencies of F1 hybrids than in experiment I, but again G. holbrooki alleles achieved high frequencies over four generations (72 wk). Thus, evolution within experimental Gambusia hybrid populations can be extremely rapid, resulting in consistent loss of G. affinis nuclear and cytoplasmic alleles. Concordance in results between experiments and across genetic markers suggests strong directional selection favoring G. holbrooki genotypes. Results are interpreted in light of previous reports of genotype-specific differences in life-history traits, reproductive ecology, patterns of recruitment, and size-specific mortality, and in the context of patterns of introgression previously studied indirectly from spatial observations on cytonuclear genotypes in natural Gambusia populations.

  19. Public awareness of mercury in fish: analysis of public awareness and assessment of fish consumption in vermont.

    PubMed

    Damsky, William E; Duncan, Elizabeth; Flanagan, Noreen; Fromhold, Karen; Dung, Hyunh; Meyer, Russell; Sax, Jordan; Delaney, Thomas; Bress, William; Hoffman-Contois, Razelle; Carney, Jan K

    2009-11-16

    Exposure to mercury from environmental sources, such as fish consumption, poses potential health risks to the public. The state of Vermont has developed educational brochures and posters displaying safe fish consumption guidelines in order to educate the public regarding mercury exposure through fish. In this study, a group of medical students from the University of Vermont College of Medicine, in partnership with the Vermont Department of Health, conducted a study in Chittenden County, Vermont in order to assess both fish consumption practices and overall awareness of such safe eating guidelines and mercury advisories. A total of 166 Vermont residents were surveyed during a six week period. The results of this survey suggest that in Chittenden county of Vermont, these educational efforts are markedly successful, with 48% of respondents being specifically aware of the safe eating guidelines. Further, these results suggest that 61% of those respondents that reported low monthly canned tuna consumption had a decreased their consumption in response to the safe eating guidelines. last, a series of specific, yet widely applicable recommendations are presented for future public educational efforts regarding mercury exposure through fish consumption.

  20. Optimization of a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the detection of bacteria and disclosure of a formamide effect.

    PubMed

    Santos, Rita S; Guimarães, Nuno; Madureira, Pedro; Azevedo, Nuno F

    2014-10-10

    Despite the fact that fluorescence in situ hybridization (FISH) is a well-established technique to identify microorganisms, there is a lack of understanding concerning the interaction of the different factors affecting the obtained fluorescence. In here, we used flow cytometry to study the influence of three essential factors in hybridization - temperature, time and formamide concentration - in an effort to optimize the performance of a Peptide Nucleic Acid (PNA) probe targeting bacteria (EUB338). The PNA-FISH optimization was performed with bacteria representing different families employing response surface methodology. Surprisingly, the optimum concentration of formamide varied according to the bacterium tested. While hybridization on the bacteria possessing the thickest peptidoglycan was more successful at nearly 50% (v/v) formamide, hybridization on all other microorganisms appeared to improve with much lower formamide concentrations. Gram staining and transmission electron microscopy allowed us to confirm that the overall effect of formamide concentration on the fluorescence intensity is a balance between a harmful effect on the bacterial cell envelope, affecting cellular integrity, and the beneficial denaturant effect in the hybridization process. We also conclude that microorganisms belonging to different families will require different hybridization parameters for the same FISH probe, meaning that an optimum universal PNA-FISH procedure is non-existent for these situations.

  1. An autosomal locus controls sex reversal in interspecific XY hybrids of the medaka fishes.

    PubMed

    Kato, M; Takehana, Y; Fukuda, Y; Naruse, K; Sakaizumi, M; Hamaguchi, S

    2011-12-01

    Although the two medaka species Oryzias latipes and O. curvinotus share the sex-determining gene Dmy, XY sex reversal occurs in interspecific hybridization between O. latipes females of the Hd-rR inbred strain and O. curvinotus males. In this Hd-rR-curvinotus mating, all XX and XY hybrids developed as females. In this study, we used another O. latipes inbred strain (HNI) for the mating, and found that 23% of XY hybrids developed as males, although all XX and the remaining XY hybrids developed as females. Linkage analysis using 236 XY hybrid males obtained from (Hd-rR × HNI) F(1) females showed that a single major locus, Hybrid maleless (Hml), on autosomal linkage group 17, contributed to the strain difference in the XY sex reversal. Furthermore, we found that crossing females of a different O. latipes inbred strain, HO4C, did not cause XY sex reversal in the interspecific hybrids, and that the XY hybrids from (Hd-rR × HO4C) F(1) females showed a 1:1 sex ratio. XY hybrid males had the HO4C allele at sequence-tagged site loci around the Hml locus whereas XY females had the Hd-rR allele, confirming the strong contribution of this locus to XY sex reversal. Reverse transcriptase PCR analysis showed a reduced expression of Dmy(curvinotus) in XY fry of the Hd-rR-curvinotus hybrids at hatching. These results suggest that the Hd-rR allele at the Hml locus interfere with the function of Dmy(curvinotus) on a hybrid background, thus resulting in XY sex reversal.

  2. DNA Barcoding and Microsatellites Help Species Delimitation and Hybrid Identification in Endangered Galaxiid Fishes

    PubMed Central

    Vanhaecke, Delphine; Garcia de Leaniz, Carlos; Gajardo, Gonzalo; Young, Kyle; Sanzana, Jose; Orellana, Gabriel; Fowler, Daniel; Howes, Paul; Monzon-Arguello, Catalina; Consuegra, Sofia

    2012-01-01

    The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty. PMID:22412956

  3. Fish Alternatives in Environmental Risk Assessment: Overview of the Current Landscape

    EPA Science Inventory

    The need for alternative testing strategies has recently expanded into the realm of environmental risk assessment leading to the development of new alternatives to standard aquatic vertebrate testing such as the OECD 203 acute fish toxicity test. The fish embryo test (FET) is one...

  4. Fish Alternatives in Environmental Risk Assessment: Overview of the Current Landscape

    EPA Science Inventory

    The need for alternative testing strategies has recently expanded into the realm of environmental risk assessment leading to the development of new alternatives to standard aquatic vertebrate testing such as the OECD 203 acute fish toxicity test. The fish embryo test (FET) is one...

  5. Automation of ALK gene rearrangement testing with fluorescence in situ hybridization (FISH): a feasibility study.

    PubMed

    Zwaenepoel, Karen; Merkle, Dennis; Cabillic, Florian; Berg, Erica; Belaud-Rotureau, Marc-Antoine; Grazioli, Vittorio; Herelle, Olga; Hummel, Michael; Le Calve, Michele; Lenze, Dido; Mende, Stefanie; Pauwels, Patrick; Quilichini, Benoit; Repetti, Elena

    2015-02-01

    In the past several years we have observed a significant increase in our understanding of molecular mechanisms that drive lung cancer. Specifically in the non-small cell lung cancer sub-types, ALK gene rearrangements represent a sub-group of tumors that are targetable by the tyrosine kinase inhibitor Crizotinib, resulting in significant reductions in tumor burden. Phase II and III clinical trials were performed using an ALK break-apart FISH probe kit, making FISH the gold standard for identifying ALK rearrangements in patients. FISH is often considered a labor and cost intensive molecular technique, and in this study we aimed to demonstrate feasibility for automation of ALK FISH testing, to improve laboratory workflow and ease of testing. This involved automation of the pre-treatment steps of the ALK assay using various protocols on the VP 2000 instrument, and facilitating automated scanning of the fluorescent FISH specimens for simplified enumeration on various backend scanning and analysis systems. The results indicated that ALK FISH can be automated. Significantly, both the Ikoniscope and BioView system of automated FISH scanning and analysis systems provided a robust analysis algorithm to define ALK rearrangements. In addition, the BioView system facilitated consultation of difficult cases via the internet.

  6. microFIND(®) approach to fluorescent in situ hybridization (FISH).

    PubMed

    Zanardi, Andrea; Barborini, Emanuele; Carbone, Roberta

    2013-01-01

    FISH technology has gained increasing attention in the management of cancer disease, either for predictive or prognostic indications. Molecular cytogenetics has greatly improved diagnostic capability of classical cytogenetics analysis of metaphase-based chromosome for the identification of genetic aberrations. The availability of a large number of fluorescent probes, each specific for different genetic lesions, together with a robust protocol for interphase FISH, provide the pathologist with the essential tools for an accurate evaluation of patient's disease. Hemato-oncological and many of the solid tumors have been comprehensively characterized by peculiar genetic defects and are now routinely evaluated by interphase FISH. Despite the reliability of the method, which has undergone only minor changes since the 1970s, FISH assay is still hampered by reagents cost, preventing its adoption in large-scale oncological screening. In this chapter we describe a major improvement of interphase FISH assay for cytological samples through the description of the miniaturized device microFIND(®) that offers, besides reduction of cost per assay, a completely novel vision to the FISH technology, thanks to the perspective of full automation of FISH assay using a dedicated robotic platform for microFIND(®) handling, (not presently described in the chapter).

  7. Commercial fish species of inland waters: a model for sustainability assessment and management.

    PubMed

    Simić, Vladica M; Simić, Snežana B; Stojković Piperac, Milica; Petrović, Ana; Milošević, Djuradj

    2014-11-01

    The permanent increase in the exploitation of commercial fish species has led to the need for developing practical and effective tools for the sustainability assessment and management of the target fish populations. The aim of this study was to formulate an ESHIPPOfishing model which would provide a reliable assessment of commercial fish population sustainability and indicate the conservation priorities. The existing ESHIPPO model was modified by introducing a new Index of local sustainability of fish populations (ILSFP) which enables the selection of "keystone populations" and "keystone habitats/ecosystems" within the basin being investigated. We employed a self-organizing map (SOM) in order to visualize the spatial distribution of the keystone populations and keystone habitats/ecosystems for each fish species. Based on the ILSFP values, environmental specialization (ES) of a fish species and local environmental factors (HIPPO factors), the model estimates the degree of sustainability (DS) of commercial fish populations in the freshwater ecosystems of the western Balkan Peninsula. The results indicate a low degree of sustainability for the majority of commercial fish species of the Middle Danube Basin, especially Acipenser ruthenus and Hucho hucho. The ESHIPPOfishing model presents a cost effective conservation approach, formulated to be applicable to any kind of river basin. The application of the ESHIPPOfishing model provides a comprehensive insight into the viability of target fish populations, which would not only further improve the selection of conservation priorities, but also facilitate the management of aquatic ecosystems.

  8. Exposure assessment for trace elements from consumption of marine fish in Southeast Asia.

    PubMed

    Agusa, Tetsuro; Kunito, Takashi; Sudaryanto, Agus; Monirith, In; Kan-Atireklap, Supawat; Iwata, Hisato; Ismail, Ahmad; Sanguansin, Joompol; Muchtar, Muswerry; Tana, Touch Seang; Tanabe, Shinsuke

    2007-02-01

    Concentrations of 20 trace elements were determined in muscle and liver of 34 species of marine fish collected from coastal areas of Cambodia, Indonesia, Malaysia and Thailand. Large regional difference was observed in the levels of trace elements in liver of one fish family (Carangidae): the highest mean concentration was observed in fish from the Malaysian coastal waters for V, Cr, Zn, Pb and Bi and those from the Java Sea side of Indonesia for Sn and Hg. To assess the health risk to the Southeast Asian populations from consumption of fish, intake rates of trace elements were estimated. Some marine fish showed Hg levels higher than the guideline values by U.S. Environmental Protection Agency and Joint FAO/WHO Expert Committee on Food Additives (JECFA). This suggests that consumption of these fish may be hazardous to the people.

  9. Action spectrum for melanoma induction in hybrid fish of the genus Xiphophorus

    SciTech Connect

    Setlow, R.B.

    1997-03-01

    Cutaneous malignant melanoma (CMM) is a complicated disease that is dependent on a number of factors that influence its incidence in ways that are quantitatively uncertain. The incidence of CMM increases with proximity to the Equator -- an observation in line with the conclusion that sun exposure is the most important etiologic agent. However, the latitude effect does not implicate UVB because the intensities of all spectral regions increase toward the Equator. An understanding of the useful public health measures to lower the incidence of CMM would benefit greatly if the spectral region of sunlight implicated in melanoma incidence were known. Such knowledge requires animal models to evaluate the incidence as a function of wavelength. There are marsupial models, a transgenic mouse model, and a fish model. To date, only the fish model has been employed to obtain an action spectrum. The paper describes a fish model, implications of the fish spectrum, and epidemiological data.

  10. 2008-09 National Rivers and Streams Assessment Fish Tissue Data Dictionary

    EPA Pesticide Factsheets

    The Office of Science and Technology (OST) is providing the fish tissue results from the 2008-09 National Rivers and Streams Assessment (NRSA). This document includes the “data dictionary” for Mercury, Selenium, PBDEs, PCBs, Pesticides and PFCs.

  11. SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK FOR ENDANGERED FISHES, INCLUDING INTERSPECIES TOXICITY CORRELATIONS

    EPA Science Inventory

    Rainbow trout, fathead minnows, and sheepshead minnows were tested as surrogate species to assess contaminant risk for 17 endangered fishes and one toad species. Acute toxicity tests were conducted with carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin in accorda...

  12. Assessment of fish passage technology applicable to John Sevier detention dam

    SciTech Connect

    Pasch, R.W.

    1986-12-01

    This report provides an assessment of existing technologies and developments in fish passage technology applicable to moving sauger and paddlefish upstream and downstream of the John Sevier detention dam. (ACR)

  13. SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK FOR ENDANGERED FISHES, INCLUDING INTERSPECIES TOXICITY CORRELATIONS

    EPA Science Inventory

    Rainbow trout, fathead minnows, and sheepshead minnows were tested as surrogate species to assess contaminant risk for 17 endangered fishes and one toad species. Acute toxicity tests were conducted with carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin in accorda...

  14. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: Fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

    SciTech Connect

    Worley, K.C.; Lindsay, E.A.; McCabe, E.R.B.

    1995-07-17

    Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosome deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available. 17 refs., 2 figs.

  15. IFNa of triploid hybrid of gold fish and allotetraploid is an antiviral cytokine against SVCV and GCRV.

    PubMed

    Yan, Jun; Peng, Lingzhi; Li, Yang; Fan, Hui; Tian, Yu; Liu, Shaojun; Feng, Hao

    2016-07-01

    Triploid hybrid of gold fish (Carassius auratus red var., ♀, 2n = 100) and allotetroploid (♂, 2n = 100) displays much improved disease resistance than its parents. In this paper, one of the type I IFNs of triploid hybrid (3nIFNa) has been cloned and characterized. The full-length cDNA of 3nIFNa consists of 740 nucleotides and the predicted 3nIFNa protein contains 183 amino acids. The mRNA transcription of 3nIFNa was detected in all the selected tissues of triploid hybrid and was obviously enhanced after SVCV or GCRV infection. bcIFNa was detected in both whole cell lysate and supernatant media of HEK293T cells transfected with plasmids expressing bcIFNa. It is interesting that the pre-matured 3nIFNa is modified with N-linked glycosylation, which is located within the N-terminal signal peptide. EPC cells showed much-decreased cytopathic effect when treated with 3nIFNa-containing media or transfected with plasmid expressing 3nIFNa at 24 h before SVCV or GCRV infection; and the virus titers in these cells were much lower than those of the control EPC cells. All the above data support the conclusion that 3nIFNa is a secreted cytokine functioning in host innate immune response against virus invasion. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae.

    PubMed

    Davis, Brian W; Raudsepp, Terje; Pearks Wilkerson, Alison J; Agarwala, Richa; Schäffer, Alejandro A; Houck, Marlys; Chowdhary, Bhanu P; Murphy, William J

    2009-04-01

    We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2662 markers, translating to an estimated average intermarker distance of 939 kilobases (kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence.

  17. A High-Resolution Cat Radiation Hybrid and Integrated FISH Mapping Resource for Phylogenomic Studies across Felidae

    PubMed Central

    Davis, Brian W.; Raudsepp, Terje; Wilkerson, Alison J. Pearks; Agarwala, Richa; Schäffer, Alejandro A.; Houck, Marlys; Ryder, Oliver A.; Chowdhdary, Bhanu P.; Murphy, William J.

    2008-01-01

    We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2,662 markers, translating to an estimated average intermarker distance of 939 kilobases (Kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 Kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC-clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence. PMID:18951970

  18. Using posts to an online social network to assess fishing effort

    USGS Publications Warehouse

    Martin, Dustin R.; Chizinski, Christopher J.; Eskridge, Kent M.; Pope, Kevin L

    2014-01-01

    Fisheries management has evolved from reservoir to watershed management, creating a need to simultaneously gather information within and across interacting reservoirs. However, costs to gather information on the fishing effort on multiple reservoirs using traditional creel methodology are often prohibitive. Angler posts about reservoirs online provide a unique medium to test hypotheses on the distribution of fishing pressure. We show that the activity on an online fishing social network is related to fishing effort and can be used to facilitate management goals. We searched the Nebraska Fish and Game Association Fishing Forum for all references from April 2009 to December 2010 to 19 reservoirs that comprise the Salt Valley regional fishery in southeastern Nebraska. The number of posts was positively related to monthly fishing effort on a regional scale, with individual reservoirs having the most annual posts also having the most annual fishing effort. Furthermore, this relationship held temporally. Online fishing social networks provide the potential to assess effort on larger spatial scales than currently feasible.

  19. Climate Change Vulnerability of Native and Alien Freshwater Fishes of California: A Systematic Assessment Approach

    PubMed Central

    Moyle, Peter B.; Kiernan, Joseph D.; Crain, Patrick K.; Quiñones, Rebecca M.

    2013-01-01

    Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California’s native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (<22°C) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It

  20. Climate change vulnerability of native and alien freshwater fishes of California: a systematic assessment approach.

    PubMed

    Moyle, Peter B; Kiernan, Joseph D; Crain, Patrick K; Quiñones, Rebecca M

    2013-01-01

    Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California's native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (<22°C) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It

  1. Assessing environmental correlates of fish movement on a coral reef

    NASA Astrophysics Data System (ADS)

    Currey, Leanne M.; Heupel, Michelle R.; Simpfendorfer, Colin A.; Williams, Ashley J.

    2015-12-01

    Variation in dispersal and movement patterns of coral reef fishes is likely linked to changes in environmental conditions. Monitoring in situ environmental parameters on coral reefs in conjunction with the movements of fishes can help explain the relationship between exploited populations and their environment. Sixty adult Lethrinus miniatus were acoustically tagged and monitored along a coral reef slope for up to 1 yr. Individuals occurred more often on the reef slope during days of cooler temperatures, suggesting a thermal tolerance threshold may exist. Results indicate that individuals responded to elevated temperatures by moving away from the reef slope to deeper adjacent habitats, thus shifting their position in the water column to remain at a preferred temperature. Space use within the water column (vertical activity space) was not influenced by environmental parameters or fish size, but this result was possibly influenced by use of deeper habitat outside the acoustic array that was not monitored. With elevation of ocean temperature, L. miniatus may need to adapt to warmer waters or disperse into cooler habitats, by either shifting their distribution deeper or towards higher latitudes. Identifying key environmental drivers that affect the distribution of reef fishes is important, and may allow managers to predict the effect of these changes on exploited species.

  2. Tools for assessing climate impacts on fish and wildlife

    Treesearch

    Chad B. Wilsey; Joshua J. Lawler; Edwin P. Maurer; Donald McKenzie; Patricia A. Townsend; Richard Gwozdz; James A. Freund; Keala Hagmann; Karen M. Hutten

    2013-01-01

    Climate change is already affecting many fish and wildlife populations. Managing these populations requires an understanding of the nature, magnitude, and distribution of current and future climate impacts. Scientists and managers have at their disposal a wide array of models for projecting climate impacts that can be used to build such an understanding. Here, we...

  3. Determination of the metabolically active fraction of benthic foraminifera by means of Fluorescent in situ Hybridization (FISH)

    NASA Astrophysics Data System (ADS)

    Borrelli, C.; Sabbatini, A.; Luna, G. M.; Morigi, C.; Danovaro, R.; Negri, A.

    2010-10-01

    Benthic foraminifera are an important component of the marine living biota, but protocols for investigating their viability and metabolism are still extremely limited. Classical studies on benthic foraminifera have been based on direct counting under light microscopy. Typically these organisms are stained with Rose Bengal, which binds proteins and other macromolecules, but this approach does not allow discriminating between viable and recently dead organisms. The fluorescent in situ hybridization technique (FISH) represents a potentially useful approach identifying living cells with active metabolism cells. In this work, we tested for the first time the suitability of the FISH technique based on fluorescent probes targeting the 18S rRNA, to detect these live benthic protists. The protocol was applied on the genus Ammonia, on the Miliolidae group and an attempt was made also with agglutinated species (i.e., Leptohalysis scottii and Eggerella scabra). In addition microscopic analysis of the cytoplasm colour, presence of pigments and, sometimes, those of pseudopodial activity where conducted. The results of the present study indicate that FISH targeted only live and metabolically active foraminifera. These results allowed to identify as "live", cells improperly classified as "dead" by means of the classical technique (Type I error) and vice versa to identify as dead the foraminifera without rRNA, but stained using Rose Bengal (Type II error). In addition, the comparative FISH analysis of starved and actively growing cells demonstrated that individuals with active metabolism were stained more intensively than starved cells. This finding supports the hypothesis that the physiological status of cells can be directly related with the intensity of the fluorescent signal emitted by the fluorescent probe. We conclude that the use of molecular approaches could represent a key tool for acquiring crucial information on living foraminifera specimens and for investigating their

  4. Hybrid life-cycle assessment of algal biofuel production.

    PubMed

    Malik, Arunima; Lenzen, Manfred; Ralph, Peter J; Tamburic, Bojan

    2015-05-01

    The objective of this work is to establish whether algal bio-crude production is environmentally, economically and socially sustainable. To this end, an economic multi-regional input-output model of Australia was complemented with engineering process data on algal bio-crude production. This model was used to undertake hybrid life-cycle assessment for measuring the direct, as well as indirect impacts of producing bio-crude. Overall, the supply chain of bio-crude is more sustainable than that of conventional crude oil. The results indicate that producing 1 million tonnes of bio-crude will generate almost 13,000 new jobs and 4 billion dollars' worth of economic stimulus. Furthermore, bio-crude production will offer carbon sequestration opportunities as the production process is net carbon-negative.

  5. Fish as bioindicators in aquatic environmental pollution assessment: A case study in Lake Victoria wetlands, Uganda

    NASA Astrophysics Data System (ADS)

    Naigaga, I.; Kaiser, H.; Muller, W. J.; Ojok, L.; Mbabazi, D.; Magezi, G.; Muhumuza, E.

    Growing human population and industrialization have led to the pollution of most aquatic ecosystems and consequent deterioration in environmental water quality. Indicator organisms are needed to improve assessment programmes on the ecological impacts of anthropogenic activities on the aquatic environment. Fish have been widely documented as useful indicators of environmental water quality because of their differential sensitivity to pollution. This study investigated the environmental water quality of selected wetland ecosystems using fish as biological indicators. Fish community structure in relation to water quality was assessed in five wetlands along the shoreline of Lake Victoria from August 2006 to June 2008. Four urban wetlands were variedly impacted by anthropogenic activities while one rural wetland was less impacted, and served as a reference site. Fish species diversity, abundance and richness were assessed, and canonical correspondence analysis (CCA) was used to evaluate the relationship between the fish communities and environmental variables. Results revealed that urban effluent impacted negatively on water quality and consequently the fish community structure. A total of 29 fish species were recorded throughout the study with the lowest number of 15 species recorded in the most impacted site. Shannon diversity and Margalef species richness indices were highest at the references site and lowest at the most impacted site. Wetland haplochromis species dominated the reference site, while oreochromis species dominated the most impacted site. The inshore locations registered higher species diversity and low species richness than the offshore locations. Low dissolved oxygen, pH, secchi depth and high electrical conductivity, total phosphorous, and total nitrogen were strongly associated with the effluent-impacted sites and greatly influenced the fish community structure. This study recommends the use of fish as valuable biological indicators in aquatic

  6. An ecological risk assessment of pesticides and fish kills in the Sixaola watershed, Costa Rica.

    PubMed

    Polidoro, Beth A; Morra, Matthew J

    2016-03-01

    Along the southeastern coast of Costa Rica, a variety of pesticides are intensively applied to produce export-quality plantains and bananas. In this region, and in other agricultural areas, fish kills are often documented by local residents and/or in the national news. This study examines principal exposure pathways, measured environmental concentrations, and selected toxicity thresholds of the three most prevalent pesticides (chlorpyrifos, terbufos, and difenoconazole) to construct a deterministic risk assessment for fish mortality. Comparisons of observed pesticide concentrations, along with estimated biological effects and observations during actual fish kills, highlight gaps in knowledge in correlating pesticide environmental concentration and toxicity in tropical environments. Observations of fish kill events and measured pesticide concentrations in the field, along with other water quality indicators, suggest that a number of environmental conditions can interact to cause fish mortality and that current species toxicity datasets may not be applicable for estimating toxicological or other synergistic effects, especially in tropical environments.

  7. Combining telephone surveys and fishing catches self-report: the French sea bass recreational fishery assessment.

    PubMed

    Rocklin, Delphine; Levrel, Harold; Drogou, Mickaël; Herfaut, Johanna; Veron, Gérard

    2014-01-01

    Fisheries statistics are known to be underestimated, since they are mainly based on information about commercial fisheries. However, various types of fishing activities exist and evaluating them is necessary for implementing effective management plans. This paper assesses the characteristics and catches of the French European sea bass recreational fishery along the Atlantic coasts, through the combination of large-scale telephone surveys and fishing diaries study. Our results demonstrated that half of the total catches (mainly small fish) were released at sea and that the mean length of a kept sea bass was 46.6 cm. We highlighted different patterns of fishing methods and type of gear used. Catches from boats were greater than from the shore, both in abundance and biomass, considering mean values per fishing trip as well as CPUE. Spearfishers caught the highest biomass of sea bass per fishing trip, but the fishing rod with lure was the most effective type of gear in terms of CPUE. Longlines had the highest CPUE value in abundance but not in biomass: they caught numerous but small sea bass. Handlines were less effective, catching few sea bass in both abundance and biomass. We estimated that the annual total recreational sea bass catches was 3,173 tonnes of which 2,345 tonnes were kept. Since the annual commercial catches landings were evaluated at 5,160 tonnes, recreational landings represent 30% of the total fishing catches on the Atlantic coasts of France. Using fishers' self-reports was a valuable way to obtain new information on data-poor fisheries. Our results underline the importance of evaluating recreational fishing as a part of the total amount of fisheries catches. More studies are critically needed to assess overall fish resources caught in order to develop effective fishery management tools.

  8. Combining Telephone Surveys and Fishing Catches Self-Report: The French Sea Bass Recreational Fishery Assessment

    PubMed Central

    Rocklin, Delphine; Levrel, Harold; Drogou, Mickaël; Herfaut, Johanna; Veron, Gérard

    2014-01-01

    Fisheries statistics are known to be underestimated, since they are mainly based on information about commercial fisheries. However, various types of fishing activities exist and evaluating them is necessary for implementing effective management plans. This paper assesses the characteristics and catches of the French European sea bass recreational fishery along the Atlantic coasts, through the combination of large-scale telephone surveys and fishing diaries study. Our results demonstrated that half of the total catches (mainly small fish) were released at sea and that the mean length of a kept sea bass was 46.6 cm. We highlighted different patterns of fishing methods and type of gear used. Catches from boats were greater than from the shore, both in abundance and biomass, considering mean values per fishing trip as well as CPUE. Spearfishers caught the highest biomass of sea bass per fishing trip, but the fishing rod with lure was the most effective type of gear in terms of CPUE. Longlines had the highest CPUE value in abundance but not in biomass: they caught numerous but small sea bass. Handlines were less effective, catching few sea bass in both abundance and biomass. We estimated that the annual total recreational sea bass catches was 3,173 tonnes of which 2,345 tonnes were kept. Since the annual commercial catches landings were evaluated at 5,160 tonnes, recreational landings represent 30% of the total fishing catches on the Atlantic coasts of France. Using fishers' self-reports was a valuable way to obtain new information on data-poor fisheries. Our results underline the importance of evaluating recreational fishing as a part of the total amount of fisheries catches. More studies are critically needed to assess overall fish resources caught in order to develop effective fishery management tools. PMID:24489885

  9. Evaluation of generalized habitat criteria for assessing impacts of altered flow regimes on warmwater fishes

    USGS Publications Warehouse

    Bowen, Z.H.; Freeman, Mary C.; Bovee, K.D.

    1998-01-01

    Assessing potential effects of flow regulation on southeastern warmwater fish assemblages is problematic because of high species richness and our poor knowledge of habitat requirements for most species. A previous attempt to reduce the complexity of describing habitat requirements for diverse assemblages defined five 'key habitat' types based on quantitative descriptions of depth, velocity, substrate, and cover for assessing the effects of streamflow alteration on fish communities. Our study investigated relationships between availability and temporal stability of key habitats and fish abundances at regulated and unregulated sites in the Tallapoosa River system. Fish assemblage characteristics at seven sites were quantified based on 1,400 electrofishing samples collected during 1994 and 1995. Simulations were used to model availability and temporal stability of key habitats at regulated and unregulated sites, Associations between fish assemblages and availability or stability of key habitats were identified using correlation analysis. We found that hydropeaking dam operation reduced the average length of time that shallow-water habitats were stable during the spring and summer and also reduced year-to-year variation in the stability of shallow-water habitats compared to unregulated sites. Within-site comparisons of fish and habitat variables indicated that differences in fish abundances correlated with differences in the availability and temporal stability of shallow-water habitats. Additionally, groups of stream fishes defined by taxonomy or differences in orientation to the substrate and feeding mode responded similarly to changes in key habitat availability. These findings demonstrate that the temporal and spatial availability of key habitats could serve as a useful measure of the potential effects of flow alteration on lotic fish assemblages, and suggest that both short-term temporal stability of key habitats as well as annual variation in key habitat

  10. Kootenai River Resident Fish Assessment, FY2008 KTOI Progress Report.

    SciTech Connect

    Holderman, Charles

    2009-06-26

    The overarching goal of project 1994-049-00 is to recover a productive, healthy and biologically diverse Kootenai River ecosystem, with emphasis on native fish species rehabilitation. It is especially designed to aid the recovery of important fish stocks, i.e. white sturgeon, burbot, bull trout, kokanee and several other salmonids important to the Kootenai Tribe of Idaho and regional sport-fisheries. The objectives of the project have been to address factors limiting key fish species within an ecosystem perspective. Major objectives include: establishment of a comprehensive and thorough biomonitoring program, investigate ecosystem--level in-river productivity, test the feasibility of a large-scale Kootenai River nutrient addition experiment (completed), to evaluate and rehabilitate key Kootenai River tributaries important to the health of the lower Kootenai River ecosystem, to provide funding for Canadian implementation of nutrient addition and monitoring in the Kootenai River ecosystem (Kootenay Lake) due to lost system productivity created by construction and operation of Libby Dam, mitigate the cost of monitoring nutrient additions in Arrow Lakes due to lost system productivity created by the Libby-Arrow water swap, provide written summaries of all research and activities of the project, and, hold a yearly workshop to convene with other agencies and institutions to discuss management, research, and monitoring strategies for this project and to provide a forum to coordinate and disseminate data with other projects involved in the Kootenai River basin.

  11. Using industry ROV videos to assess fish associations with subsea pipelines

    NASA Astrophysics Data System (ADS)

    McLean, D. L.; Partridge, J. C.; Bond, T.; Birt, M. J.; Bornt, K. R.; Langlois, T. J.

    2017-06-01

    Remote Operated Vehicles are routinely used to undertake inspection and maintenance activities of underwater pipelines in north-west Australia. In doing so, many terabytes of geo-referenced underwater video are collected at depths, and on a scale usually unobtainable for ecological research. We assessed fish diversity and abundance from existing ROV videos collected along 2-3 km sections of two pipelines in north-west Australia, one at 60-80 m water depth and the other at 120-130 m. A total of 5962 individual fish from 92 species and 42 families were observed. Both pipelines were characterised by a high abundance of commercially important fishes including: snappers (Lutjanidae) and groupers (Epinephelidae). The presence of thousands of unidentifiable larval fish, in addition to juveniles, sub-adults and adults suggests that the pipelines may be enhancing, rather than simply attracting, fish stocks. The prevalence and high complexity of sponges on the shallower pipeline and of deepwater corals on the deeper pipeline had a strong positive correlation with the fish abundance. These habitats likely offer a significant food source and refuge for fish, but also for invertebrates upon which fish feed. A greater diversity on the shallower pipeline, and a higher abundance of fishes on both pipelines, were associated with unsupported pipeline sections (spans) and many species appeared to be utilising pipeline spans as refuges. This study is a first look at the potential value of subsea pipelines for fishes on the north-west shelf. While the results suggest that these sections of pipeline appear to offer significant habitat that supports diverse and important commercially fished species, further work, including off-pipeline surveys on the natural seafloor, are required to determine conclusively the ecological value of pipelines and thereby inform discussions regarding the ecological implications of pipeline decommissioning.

  12. Assessing changes in amphibian population dynamics following experimental manipulations of introduced fish.

    PubMed

    Pope, Karen L

    2008-12-01

    Sport-fish introductions are now recognized as an important cause of amphibian decline, but few researchers have quantified the demographic responses of amphibians to current options in fisheries management designed to minimize effects on sensitive amphibians. Demographic analyses with mark-recapture data allow researchers to assess the relative importance of survival, local recruitment, and migration to changes in population densities. I conducted a 4-year, replicated whole-lake experiment in the Klamath Mountains of northern California (U.S.A.) to quantify changes in population density, survival, population growth rate, and recruitment of the Cascades frog (Rana cascadae) in response to manipulations of non-native fish populations. I compared responses of the frogs in lakes where fish were removed, in lakes in their naturally fish-free state, and in lakes where fish remained that were either stocked annually or no longer being stocked. Within 3 years of fish removals from 3 lakes, frog densities increased by a factor of 13.6. The survival of young adult frogs increased from 59% to 94%, and realized population growth and recruitment rates at the fish-removal lakes were more than twice as high as the rates for fish-free reference lakes and lakes that contained fish. Population growth in the fish-removal lakes was likely due to better on-site recruitment of frogs to later life stages rather than increased immigration. The effects on R. cascadae of suspending stocking were ambiguous and suggested no direct benefit to amphibians. With amphibians declining worldwide, these results show that active restoration can slow or reverse the decline of species affected by fish stocking within a short time frame.

  13. Predictive models for fish assemblages in eastern USA streams: implications for assessing biodiversity

    USGS Publications Warehouse

    Meador, Michael R.; Carlisle, Daren M.

    2009-01-01

    Management and conservation of aquatic systems require the ability to assess biological conditions and identify changes in biodiversity. Predictive models for fish assemblages were constructed to assess biological condition and changes in biodiversity for streams sampled in the eastern United States as part of the U.S. Geological Survey's National Water Quality Assessment Program. Separate predictive models were developed for northern and southern regions. Reference sites were designated using land cover and local professional judgment. Taxonomic completeness was quantified based on the ratio of the number of observed native fish species expected to occur to the number of expected native fish species. Models for both regions accurately predicted fish species composition at reference sites with relatively high precision and low bias. In general, species that occurred less frequently than expected (decreasers) tended to prefer riffle areas and larger substrates, such as gravel and cobble, whereas increaser species (occurring more frequently than expected) tended to prefer pools, backwater areas, and vegetated and sand substrates. In the north, the percentage of species identified as increasers and the percentage identified as decreasers were equal, whereas in the south nearly two-thirds of the species examined were identified as decreasers. Predictive models of fish species can provide a standardized indicator for consistent assessments of biological condition at varying spatial scales and critical information for an improved understanding of fish species that are potentially at risk of loss with changing water quality conditions.

  14. Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using fluorescence in situ hybridization (FISH).

    PubMed

    Urzì, Clara; La Cono, Violetta; Stackebrandt, Erko

    2004-07-01

    Bacteria of the family of Geodermatophilaceae are actively involved in the decay processes [Urzì, C. and Realini, M. (1998) Int Biodeterior Biodegrad 42: 45-54; Urzì, C., Salamone, P., Schumann, P., and Stackebrandt, E. (2000) Int J Syst Evol Microbiol 50: 529-536] of stone monuments. Characterization of isolates includes phenotypic, chemotaxonomic and genetic analysis often requiring long-term procedures. The use of specific probes for members of Geodermatophilaceae family could be useful for the easy detection of those strains colonizing rock surfaces and involved in the biodeterioration. Two 16S rRNA-targeted oligonucleotide probes were designed for the specific detection of members of the family Geodermatophilaceae using fluorescence in situ hybridization (FISH); one probe specific for members of the two genera Geodermatophilus/Blastococcus and the second for members of the genus Modestobacter.

  15. Distribution characteristics of ammonia-oxidizing bacteria in the Typha latifolia constructed wetlands using fluorescent in situ hybridization (FISH).

    PubMed

    Yan, Li; Inamori, Ryuhei; Gui, Ping; Xu, Kai-qin; Kong, Hai-nan; Matsumura, Masatoshi; Inamori, Yuhei

    2005-01-01

    A molecular biology method, fluorescent in situ hybridization (FISH), in which the pre-treatment was improved in allusion to the media of the constructed wetlands (CW), e.g. the soil and the grit, was used to investigate the vertical distribution characteristics of ammonia-oxidizing bacteria (AOB) quantity and the relation with oxidation-reduction potential (ORP) in the Typha latifolia constructed wetlands under three different loadings in summer from May to September. Results showed that the quantity of the AOB decreased in the Typha latifolia CW with the increase of vertical depth. However, the AOB quantity was 2-4 times the quantity of the control in the root area. Additionally, ORP in the rhizosphere was found to be higher than other areas, which showed that Typha latifolia CW was in an aerobic state in summer when using simulated non-point sewage at the rural area of Taihu Lake in China and small town combined sewage.

  16. Clinical methods for the assessment of the effects of environmental stress on fish health

    USGS Publications Warehouse

    Wedemeyer, Gary A.; Yasutake, William T.

    1977-01-01

    Clinical methods are presented for biological monitoring of hatchery and native fish populations to assess the effects of environmental stress on fish health. The choice of methods is based on the experience of the authors and the judgment of colleagues at fishery laboratories of the U.S. Fish and Wildlife Service. Detailed analysis methods, together with guidelines for sample collection and for the interpretation of results, are given for tests on blood (cell counts, chloride, cholesterol, clotting time, cortisol, glucose, hematocrit, hemoglobin, lactic acid, methemoglobin, osmolality, and total protein); water (ammonia and nitrite content); and liver and muscle (glycogen content).

  17. Hybrid striped bass feeds based on fish oil, beef tallow, and eicosapentaenoic acid/docosahexaenoic acid supplements: Insight regarding fish oil sparing and demand for -3 long-chain polyunsaturated fatty acids.

    PubMed

    Bowzer, J; Jackson, C; Trushenski, J

    2016-03-01

    Previous research suggests that saturated (SFA) and monounsaturated fatty acid (MUFA) rich lipids, including beef tallow, can make utilization or diet-to-tissue transfer of long-chain polyunsaturated fatty acids (LC-PUFA) more efficient. We hypothesized that using beef tallow as an alternative to fish oil may effectively reduce the LC-PUFA demand of hybrid striped bass × and allow for greater fish oil sparing. Accordingly, we evaluated growth performance and tissue fatty acid profiles of juvenile fish (23.7 ± 0.3 g) fed diets containing menhaden fish oil (considered an ideal source of LC-PUFA for this taxon), beef tallow (BEEF ONLY), or beef tallow amended with purified sources of eicosapentaenoic acid (EPA) and/or docosahexaenoic acid (DHA) to achieve levels corresponding to 50 or 100% of those observed in the FISH ONLY feed. Diets were randomly assigned to quadruplicate tanks of fish ( = 4; 10 fish/tank), and fish were fed assigned diets to apparent satiation once daily for 10 wk. Survival (98-100%) was equivalent among treatments, but weight gain (117-180%), specific growth rate (1.1-1.5% BW/d), feed intake (1.4-1.8% BW/d), thermal growth coefficient (0.50-0.70), and feed conversion ratio (FCR; 1.1-1.4, DM basis) varied. Except for FCR, no differences were observed between the FISH ONLY and BEEF ONLY treatments, but performance was generally numerically superior among fish fed the diets containing beef tallow supplemented with DHA at the 100% or both EPA and DHA at the 50% or 100% level. Tissue fatty acid composition was significantly distorted in favor among fish fed the beef tallow-based feeds; however, profile distortion was most overt in peripheral tissues. Results suggest that beef tallow may be used as a primary lipid source in practical diets for hybrid striped bass, but performance may be improved by supplementation with LC-PUFA, particularly DHA. Furthermore, our results suggest that -3 LC-PUFA requirements reported for hybrid striped bass may not be

  18. Fish Health Study Ashtabula River Natural Resource Damage Assessment

    USGS Publications Warehouse

    Blazer, V.S.; Iwanowicz, L.R.; Baumann, P.C.

    2006-01-01

    INTRODUCTION The Ashtabula River is located in northeast Ohio, flowing into Lake Erie at Ashtabula, Ohio. Tributaries include Fields Brook, Hubbard Run, Strong Brook, and Ashtabula Creek. The bottom sediments, bank soils and biota of Fields Brook have been severely contaminated by unregulated discharges of hazardous substances. Hazardous substances have migrated downstream from Fields Brook to the Ashtabula River and Harbor, contaminating bottom sediments, fish and wildlife. There are presently more than 1,000,000 cubic yards of contaminated sediment in the Ashtabula River and Harbor, much of which originated from Fields Brook. Contaminants include polychlorinated biphenyls (PCBs), chlorinated benzenes, chlorinated ethenes, hexachlorobutadiene, polyaromatic hydrocarbons (PAHs), other organic chemicals, heavy metals and low level radionuclides. A Preassessment Screen, using existing data, was completed for the Ashtabula River and Harbor on May 18, 2001. Among the findings was that the fish community at Ashtabula contained approximately 45 percent fewer species and 52 percent fewer individuals than the Ohio EPA designated reference area, Conneaut Creek. The Ashtabula River and Conneaut Creek are similar in many respects, with the exception of the presence of contamination at Ashtabula. The difference in the fish communities between the two sites is believed to be at least partially a result of the hazardous substance contamination at Ashtabula. In order to investigate this matter further, the Trustees elected to conduct a study of the status and health of the aquatic biological communities of the Ashtabula River and Conneaut Creek in 2002-2004. The following document contains brief method descriptions (more detail available in attached Appendix A) and a summary of the data used to evaluate the health status of brown bullheads (Ameiurus nebulosus) and largemouth bass (Micropterus salmoides) collected from the above sites.

  19. Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids.

    PubMed

    Shen, Yingjia; Catchen, Julian; Garcia, Tzintzuni; Amores, Angel; Beldorth, Ion; Wagner, Jonathan; Zhang, Ziping; Postlethwait, John; Warren, Wes; Schartl, Manfred; Walter, Ronald B

    2012-01-01

    Variations in gene expression are essential for the evolution of novel phenotypes and for speciation. Studying allelic specific gene expression (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms of genetic variation. Using Xiphophorus interspecies hybrid fishes and high-throughput next generation sequencing technology, we were able to assess variations between two closely related vertebrate species, Xiphophorus maculatus and Xiphophorus couchianus, and their F(1) interspecies hybrids. We constructed transcriptome-wide SNP polymorphism sets between two highly inbred X. maculatus lines (JP 163 A and B), and between X. maculatus and a second species, X. couchianus. The X. maculatus JP 163 A and B parental lines have been separated in the laboratory for ≈70 years and we were able to identify SNPs at a resolution of 1 SNP per 49 kb of transcriptome. In contrast, SNP polymorphisms between X. couchianus and X. maculatus species, which diverged ≈5-10 million years ago, were identified about every 700 bp. Using 6524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F(1) interspecies hybrids. We developed an in silico X. couchianus transcriptome by replacing 90,788 SNP bases for X. maculatus transcriptome with the consensus X. couchianus SNP bases and provide evidence that this procedure overcomes read mapping biases. Employment of the in silico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F(1) interspecies hybrids. Overall, these results show that Xiphophorus is a tractable vertebrate experimental model to investigate how genetic variations that occur during speciation may affect gene interactions and the regulation of gene expression. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Feasibility of using fluorescence in situ hybridization (FISH) to detect early gene changes in sputum cells from uranium miners

    SciTech Connect

    Neft, R.E.; Rogers, J.L.; Belinsky, S.A.

    1995-12-01

    Epidemiological studies have shown that combined exposure to radon progeny and tobacco smoke produce a greater than additive or synergistic increase in lung cancer risk. Lung cancer results from multiple genetic changes over a long period of time. An early change that occurs in lung cancer is trisomy 7 which is found in 50% of non-small cell lung cancer and in the far margins of resected lung tumors. The 80% mortality associated with lung cancer is in part related to the high proportion of patients who present with an advanced, unresectable tumor. Therefore, early detection of patients at risk for tumor development is critical to improve treatment of this disease. Currently, it is difficult to detect lung cancer early while it is still amendable by surgery. Saccomanno, G. has shown that premalignant cytologic changes in sputum cells collected from uranium miners can be detected by a skilled, highly trained cytopathologist. A more objective alternative for identifying premalignant cells in sputum may be to determine whether an early genetic change such as trisomy 7 is present in these cells. Fluorescence in situ hybridization (FISH) can be used to identify cells with trisomy 7. The results of this investigation indicate that FISH may prove to be an accurate, efficient method to test at-risk individuals for genetic alterations in bronchial epithelial cells from sputum.

  1. Complex structural rearrangement of chromosomes 13, 19 and 20 detected cytogenetically and by fluorescence in situ hybridization (FISH)

    SciTech Connect

    Al-Nassar, K.E.; Murthy, S.K.; Verghese, L.

    1994-09-01

    Complex chromosomal rearrangements (CCRs) are rare. To date, 72 CCRs have been reported. We report here a case of CCR in a 10 year old boy and his mother involving chromosomes 13, 19 and 20, detected by G-,C- and Ag-NOR banding and by fluorescence in situ hybridization (FISH) technique. Father and other sibs were found to be chromosomally normal. The patient presented with clinical features having obesity, micropenis, slow learning and IQ=70. Mother was clinically normal. Karyotype of the patient and mother showed apparently balanced chromosomal rearrangements involving chromosomes 13, 19 and 20. The karyotypes were interpreted as: 45,XY,-19,der(13),der(20),t(13;19)(13p11.2)::(19q13.2{r_arrow}19pter),t(19;20)(19q13.3{r_arrow}19qter::20qter) in the patient and 45,XX,-19,t(13;19),t(19;20) involving the same breakpoints in the mother. C-banding showed dicentric der(13). FISH using alpha-satellite DNA probes for 13/21 showed the presence of centromeric region of 13 in the der(13). Deletion of 13p11.2{r_arrow}pter was confirmed by negative Ag-NOR staining in der(13).

  2. Spatial assessment of wolf-dog hybridization in a single breeding period

    PubMed Central

    Pacheco, C.; López-Bao, J. V.; García, E. J.; Lema, F. J.; Llaneza, L.; Palacios, V.; Godinho, R.

    2017-01-01

    Understanding the dynamics of wolf-dog hybridization and delineating evidence-based conservation strategies requires information on the spatial extent of wolf-dog hybridization in real-time, which remains largely unknown. We collected 332 wolf-like scats over ca. 5,000km2 in the NW Iberian Peninsula to evaluate wolf-dog hybridization at population level in a single breeding/pup-rearing season. Mitochondrial DNA (MtDNA) and 18 ancestry informative markers were used for species and individual identification, and to detect wolf-dog hybrids. Genetic relatedness was assessed between hybrids and wolves. We identified 130 genotypes, including 67 wolves and 7 hybrids. Three of the hybrids were backcrosses to dog whereas the others were backcrosses to wolf, the latter accounting for a 5.6% rate of introgression into the wolf population. Our results show a previously undocumented scenario of multiple and widespread wolf-dog hybridization events at the population level. However, there is a clear maintenance of wolf genetic identity, as evidenced by the sharp genetic identification of pure individuals, suggesting the resilience of wolf populations to a small amount of hybridization. We consider that real-time population level assessments of hybridization provide a new perspective into the debate on wolf conservation, with particular focus on current management guidelines applied in wolf-dog hybridization events. PMID:28195213

  3. Spatial assessment of wolf-dog hybridization in a single breeding period.

    PubMed

    Pacheco, C; López-Bao, J V; García, E J; Lema, F J; Llaneza, L; Palacios, V; Godinho, R

    2017-02-14

    Understanding the dynamics of wolf-dog hybridization and delineating evidence-based conservation strategies requires information on the spatial extent of wolf-dog hybridization in real-time, which remains largely unknown. We collected 332 wolf-like scats over ca. 5,000km(2) in the NW Iberian Peninsula to evaluate wolf-dog hybridization at population level in a single breeding/pup-rearing season. Mitochondrial DNA (MtDNA) and 18 ancestry informative markers were used for species and individual identification, and to detect wolf-dog hybrids. Genetic relatedness was assessed between hybrids and wolves. We identified 130 genotypes, including 67 wolves and 7 hybrids. Three of the hybrids were backcrosses to dog whereas the others were backcrosses to wolf, the latter accounting for a 5.6% rate of introgression into the wolf population. Our results show a previously undocumented scenario of multiple and widespread wolf-dog hybridization events at the population level. However, there is a clear maintenance of wolf genetic identity, as evidenced by the sharp genetic identification of pure individuals, suggesting the resilience of wolf populations to a small amount of hybridization. We consider that real-time population level assessments of hybridization provide a new perspective into the debate on wolf conservation, with particular focus on current management guidelines applied in wolf-dog hybridization events.

  4. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management.

    PubMed

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-03-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

  5. A quantitative health assessment index for rapid evaluation of fish condition in the field

    SciTech Connect

    Adams, S.M. ); Brown, A.M. ); Goede, R.W. )

    1993-01-01

    The health assessment index (HAI) is an extension and refinement of a previously published field necropsy system. The HAI is a quantitative index that allows statistical comparisons of fish health among data sets. Index variables are assigned numerical values based on the degree of severity or damage incurred by an organ or tissue from environmental stressors. This approach has been used to evaluate the general health status of fish populations in a wide range of reservoir types in the Tennessee River basin (North Carolina, Tennessee, Alabama, Kentucky), in Hartwell Reservoir (Georgia, South Carolina) that is contaminated by polychlorinated biphenyls, and in the Pigeon River (Tennessee, North Carolina) that receives effluents from a bleaches kraft mill. The ability of the HAI to accurately characterize the health of fish in these systems was evaluated by comparing this index to other types of fish health measures (contaminant, bioindicator, and reproductive analysis) made at the same time as the HAI. In all cases, the HAI demonstrated the same pattern of fish health status between sites as did each of the other more sophisticated health assessment methods. The HAI has proven to be a simple and inexpensive means of rapidly assessing general fish health in field situations. 29 refs., 5 tabs.

  6. Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

    PubMed Central

    Laugen, Ane T; Engelhard, Georg H; Whitlock, Rebecca; Arlinghaus, Robert; Dankel, Dorothy J; Dunlop, Erin S; Eikeset, Anne M; Enberg, Katja; Jørgensen, Christian; Matsumura, Shuichi; Nusslé, Sébastien; Urbach, Davnah; Baulier, Loїc; Boukal, David S; Ernande, Bruno; Johnston, Fiona D; Mollet, Fabian; Pardoe, Heidi; Therkildsen, Nina O; Uusi-Heikkilä, Silva; Vainikka, Anssi; Heino, Mikko; Rijnsdorp, Adriaan D; Dieckmann, Ulf

    2014-01-01

    Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries. PMID:26430388

  7. Observation and Quantification of Telomere and Repetitive Sequences Using Fluorescence In Situ Hybridization (FISH) with PNA Probes in Caenorhabditis elegans.

    PubMed

    Seo, Beomseok; Lee, Junho

    2016-08-04

    Telomere is a ribonucleoprotein structure that protects chromosomal ends from aberrant fusion and degradation. Telomere length is maintained by telomerase or an alternative pathway, known as alternative lengthening of telomeres (ALT)(1). Recently, C. elegans has emerged as a multicellular model organism for the study of telomere and ALT(2). Visualization of repetitive sequences in the genome is critical in understanding the biology of telomeres. While telomere length can be measured by telomere restriction fragment assay or quantitative PCR, these methods only provide the averaged telomere length. On the contrary, fluorescence in situ hybridization (FISH) can provide the information of the individual telomeres in cells. Here, we provide protocols and representative results of the method to determine telomere length of C. elegans by fluorescent in situ hybridization. This method provides a simple, but powerful, in situ procedure that does not cause noticeable damage to morphology. By using fluorescently labeled peptide nucleic acid (PNA) and digoxigenin-dUTP-labeled probe, we were able to visualize two different repetitive sequences: telomere repeats and template of ALT (TALT) in C. elegans embryos and gonads.

  8. Large-scale assessment of Mediterranean marine protected areas effects on fish assemblages.

    PubMed

    Guidetti, Paolo; Baiata, Pasquale; Ballesteros, Enric; Di Franco, Antonio; Hereu, Bernat; Macpherson, Enrique; Micheli, Fiorenza; Pais, Antonio; Panzalis, Pieraugusto; Rosenberg, Andrew A; Zabala, Mikel; Sala, Enric

    2014-01-01

    Marine protected areas (MPAs) were acknowledged globally as effective tools to mitigate the threats to oceans caused by fishing. Several studies assessed the effectiveness of individual MPAs in protecting fish assemblages, but regional assessments of multiple MPAs are scarce. Moreover, empirical evidence on the role of MPAs in contrasting the propagation of non-indigenous-species (NIS) and thermophilic species (ThS) is missing. We simultaneously investigated here the role of MPAs in reversing the effects of overfishing and in limiting the spread of NIS and ThS. The Mediterranean Sea was selected as study area as it is a region where 1) MPAs are numerous, 2) fishing has affected species and ecosystems, and 3) the arrival of NIS and the northward expansion of ThS took place. Fish surveys were done in well-enforced no-take MPAs (HP), partially-protected MPAs (IP) and fished areas (F) at 30 locations across the Mediterranean. Significantly higher fish biomass was found in HP compared to IP MPAs and F. Along a recovery trajectory from F to HP MPAs, IP were similar to F, showing that just well enforced MPAs triggers an effective recovery. Within HP MPAs, trophic structure of fish assemblages resembled a top-heavy biomass pyramid. Although the functional structure of fish assemblages was consistent among HP MPAs, species driving the recovery in HP MPAs differed among locations: this suggests that the recovery trajectories in HP MPAs are likely to be functionally similar (i.e., represented by predictable changes in trophic groups, especially fish predators), but the specific composition of the resulting assemblages may depend on local conditions. Our study did not show any effect of MPAs on NIS and ThS. These results may help provide more robust expectations, at proper regional scale, about the effects of new MPAs that may be established in the Mediterranean Sea and other ecoregions worldwide.

  9. Probabilistic framework for assessing the arsenic exposure risk from cooked fish consumption.

    PubMed

    Ling, Min-Pei; Wu, Chiu-Hua; Chen, Szu-Chieh; Chen, Wei-Yu; Chio, Chia-Pin; Cheng, Yi-Hsien; Liao, Chung-Min

    2014-12-01

    Geogenic arsenic (As) contamination of groundwater is a major ecological and human health problem in southwestern and northeastern coastal areas of Taiwan. Here, we present a probabilistic framework for assessing the human health risks from consuming raw and cooked fish that were cultured in groundwater As-contaminated ponds in Taiwan by linking a physiologically based pharmacokinetics model and a Weibull dose-response model. Results indicate that As levels in baked, fried, and grilled fish were higher than those of raw fish. Frying resulted in the greatest increase in As concentration, followed by grilling, with baking affecting the As concentration the least. Simulation results show that, following consumption of baked As-contaminated fish, the health risk to humans is <10(-6) excess bladder cancer risk level for lifetime exposure; as the incidence ratios of liver and lung cancers are generally acceptable at risk ranging from 10(-6) to 10(-4), the consumption of baked As-contaminated fish is unlikely to pose a significant risk to human health. However, contaminated fish cooked by frying resulted in significant health risks, showing the highest cumulative incidence ratios of liver cancer. We also show that males have higher cumulative incidence ratio of liver cancer than females. We found that although cooking resulted in an increase for As levels in As-contaminated fish, the risk to human health of consuming baked fish is nevertheless acceptable. We suggest the adoption of baking as a cooking method and warn against frying As-contaminated fish. We conclude that the concentration of contaminants after cooking should be taken into consideration when assessing the risk to human health.

  10. Mercury contamination in fish from gold mining areas in Indonesia and human health risk assessment.

    PubMed

    Castilhos, Zuleica C; Rodrigues-Filho, Saulo; Rodrigues, Ana Paula C; Villas-Bôas, Roberto C; Siegel, Shefa; Veiga, Marcello M; Beinhoff, Christian

    2006-09-01

    This study investigates the effects on fish and assesses human health hazards from mercury released in two gold mining areas in Indonesia: Tatelu (North Sulawesi Province) and Galangan (Katingan District, Central Kalimatan Province). In Tatelu, 154 fish specimens of 10 freshwater species were collected, as well as five marine species from the fish market. The mean concentration of total mercury in muscles of freshwater fish from this area was 0.58+/-0.44 microg/g, with more than 45% of fish having Hg levels above the WHO guideline for human consumption of 0.5 microg/g. In Galangan, where 263 fish specimens of 25 species were collected, the total mercury in muscles averaged 0.25+/-0.69 microg/g. Excluding data from flooded open pits in sub-area P4, mean Hg levels in fish from Galangan were 2 to 4 times lower than 0.5 microg/g, while fewer than 10% of fish from Galangan exceeded WHO guidelines. The Hazard Quotient (HQ) was applied to both areas to determine the threat of MeHg exposure for communities in both areas. The HQ is a risk assessment indicator which defines the ratio of exposure level to a single substance in relation to a reference dose. Samples from Tatelu (excluding marine species) had an HQ above one, while those from Galangan resulted in values of 2.4 for the whole area and 9.9 for sub-area P4, pointing to potentially harmful fish consumption for the local population. By using the single-compartment model to estimate mercury levels in blood and hair from daily intake dose, sub-area P4 showed the highest levels, higher than the upper limit guideline for pregnant women, but still lower than threshold levels associated with observed clinical effects.

  11. Large-Scale Assessment of Mediterranean Marine Protected Areas Effects on Fish Assemblages

    PubMed Central

    Guidetti, Paolo; Baiata, Pasquale; Ballesteros, Enric; Di Franco, Antonio; Hereu, Bernat; Macpherson, Enrique; Micheli, Fiorenza; Pais, Antonio; Panzalis, Pieraugusto; Rosenberg, Andrew A.; Zabala, Mikel; Sala, Enric

    2014-01-01

    Marine protected areas (MPAs) were acknowledged globally as effective tools to mitigate the threats to oceans caused by fishing. Several studies assessed the effectiveness of individual MPAs in protecting fish assemblages, but regional assessments of multiple MPAs are scarce. Moreover, empirical evidence on the role of MPAs in contrasting the propagation of non-indigenous-species (NIS) and thermophilic species (ThS) is missing. We simultaneously investigated here the role of MPAs in reversing the effects of overfishing and in limiting the spread of NIS and ThS. The Mediterranean Sea was selected as study area as it is a region where 1) MPAs are numerous, 2) fishing has affected species and ecosystems, and 3) the arrival of NIS and the northward expansion of ThS took place. Fish surveys were done in well-enforced no-take MPAs (HP), partially-protected MPAs (IP) and fished areas (F) at 30 locations across the Mediterranean. Significantly higher fish biomass was found in HP compared to IP MPAs and F. Along a recovery trajectory from F to HP MPAs, IP were similar to F, showing that just well enforced MPAs triggers an effective recovery. Within HP MPAs, trophic structure of fish assemblages resembled a top-heavy biomass pyramid. Although the functional structure of fish assemblages was consistent among HP MPAs, species driving the recovery in HP MPAs differed among locations: this suggests that the recovery trajectories in HP MPAs are likely to be functionally similar (i.e., represented by predictable changes in trophic groups, especially fish predators), but the specific composition of the resulting assemblages may depend on local conditions. Our study did not show any effect of MPAs on NIS and ThS. These results may help provide more robust expectations, at proper regional scale, about the effects of new MPAs that may be established in the Mediterranean Sea and other ecoregions worldwide. PMID:24740479

  12. Development of a spatially distributed model of fish population density for habitat assessment of rivers

    NASA Astrophysics Data System (ADS)

    Sui, Pengzhe; Iwasaki, Akito; Ryo, Masahiro; Saavedra, Oliver; Yoshimura, Chihiro

    2013-04-01

    Flow conditions play an important role in sustaining biodiversity of river ecosystem. However, their relations to freshwater fishes, especially to fish population density, have not been clearly described. This study, therefore, aimed to propose a new methodology to quantitatively link habitat conditions, including flow conditions and other physical conditions, to population density of fish species. We developed a basin-scale fish distribution model by integrating the concept of habitat suitability assessment with a distributed hydrological model (DHM) in order to estimate fish population density with particular attention to flow conditions. Generalized linear model (GLM) was employed to evaluate the relationship between population density of fish species and major environmental factors. The target basin was Sagami River in central Japan, where the river reach was divided into 10 sections by estuary, confluences of tributaries, and river-crossing structures (dams, weirs). The DHM was employed to simulate river discharge from 1998 to 2005, which was used to calculate 10 flow indices including mean discharge, 25th and 75th percentile discharge, duration of low and high flows, number of floods. In addition, 5 water quality parameters and 13 other physical conditions (such as basin area, river width, mean diameter of riverbed material, and number of river-crossing structures upstream and downstream) of each river section were considered as environmental variables. In case of Sagami River, 10 habitat variables among them were then selected based on their correlations to avoid multicollinearity. Finally, the best GLM was developed for each species based on Akaike's information criterion. As results, population densities of 16 fish species in Sagami River were modelled, and correlation coefficients between observed and calculated population densities for 10 species were more than 0.70. The key habitat factors for population density varied among fish species. Minimum

  13. Comparative assessment of Vibrio virulence in marine fish larvae.

    PubMed

    Rønneseth, A; Castillo, D; D'Alvise, P; Tønnesen, Ø; Haugland, G; Grotkjaer, T; Engell-Sørensen, K; Nørremark, L; Bergh, Ø; Wergeland, H I; Gram, L

    2017-10-01

    Vibrionaceae infections are a major obstacle for marine larviculture; however, little is known about virulence differences of Vibrio strains. The virulence of Vibrio strains, mostly isolated from vibriosis outbreaks in farmed fish, was tested in larval challenge trials with cod (Gadus morhua), turbot (Scophthalmus maximus) and halibut (Hippoglossus hippoglossus) using a multiwell dish assays with single-egg/larvae cultures. The strains differed significantly in virulence as some caused a high mortality of larva reaching 100% mortality after a few days, while others had no or only marginal effects on survival. Some Vibrio strains were pathogenic in all of the larva species, while some caused disease only in one of the species. Twenty-nine of the Vibrio anguillarum strains increased the mortality of larvae from at least one fish species; however, pathogenicity of the strains differed markedly. Other Vibrio species had no or less pronounced effects on larval mortalities. Iron uptake has been related to V. anguillarum virulence; however, the presence or absence of the plasmid pJM1 encoding anguibactin did not correlate with virulence. The genomes of V. anguillarum were compared (D. Castillo, P.W. D'Alvise, M. Middelboe & L. Gram, unpublished data) and most of the high-virulent strains had acquired virulence genes from other pathogenic Vibrio. © 2017 John Wiley & Sons Ltd.

  14. Assessing niche width of endothermic fish from genes to ecosystem

    PubMed Central

    Madigan, Daniel J.; Carlisle, Aaron B.; Gardner, Luke D.; Jayasundara, Nishad; Micheli, Fiorenza; Schaefer, Kurt M.; Fuller, Daniel W.; Block, Barbara A.

    2015-01-01

    Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization. PMID:26100889

  15. Reagent and labor cost optimization through automation of fluorescence in situ hybridization (FISH) with the VP 2000: an Italian case study.

    PubMed

    Zanatta, Lucia; Valori, Laura; Cappelletto, Eleonora; Pozzebon, Maria Elena; Pavan, Elisabetta; Dei Tos, Angelo Paolo; Merkle, Dennis

    2015-02-01

    In the modern molecular diagnostic laboratory, cost considerations are of paramount importance. Automation of complex molecular assays not only allows a laboratory to accommodate higher test volumes and throughput but also has a considerable impact on the cost of testing from the perspective of reagent costs, as well as hands-on time for skilled laboratory personnel. The following study tracked the cost of labor (hands-on time) and reagents for fluorescence in situ hybridization (FISH) testing in a routine, high-volume pathology and cytogenetics laboratory in Treviso, Italy, over a 2-y period (2011-2013). The laboratory automated FISH testing with the VP 2000 Processor, a deparaffinization, pretreatment, and special staining instrument produced by Abbott Molecular, and compared hands-on time and reagent costs to manual FISH testing. The results indicated significant cost and time saving when automating FISH with VP 2000 when more than six FISH tests were run per week. At 12 FISH assays per week, an approximate total cost reduction of 55% was observed. When running 46 FISH specimens per week, the cost saving increased to 89% versus manual testing. The results demonstrate that the VP 2000 processor can significantly reduce the cost of FISH testing in diagnostic laboratories. © 2014 Society for Laboratory Automation and Screening.

  16. IFNa2 of triploid hybrid of gold fish and allotetraploid is an intracellular antiviral cytokine against SVCV and GCRV.

    PubMed

    Yan, Jun; Peng, Lingzhi; Chi, Mengdie; Xiao, Jun; Li, Jun; Liu, Shaojun; Feng, Hao

    2017-03-01

    Sterile triploid hybrids (3n = 150) of gold fish (Carassius auratus red var., ♀, 2n = 100) and allotetroploid (♂, 2n = 100) display obviously improved disease resistance and much enhanced growth rate than their parents, which have been cultured widely in China. In this paper, one of the type I IFNs of triploid hybrid (3nIFNa2) has been cloned and characterized. The full-length cDNA of 3nIFNa2 gene consists of 715 nucleotides and the predicted 3nIFNa2 contains 183 amino acids. The transcription of 3nIFNa2 gene was detected in all the examined tissues of triploid hybrid and the mRNA level of 3nIFNa2 was obviously enhanced in response to SVCV and GCRV infection. 3nIFNa2 has been detected in the whole cell lysate of HEK293T cells transfected with plasmids expressing 3nIFNa2 but not in the supernatant media. EPC cells transfected with plasmid expressing 3nIFNa2 at 24 h before SVCV and GCRV infection showed obviously decreased cytopathic effect; and the virus titers in the supernatant media were much lower than those of the control cells. Glycosidase digestion analysis demonstrates that 3nIFNa2 is modified with N-linked glycosylation, which occurs on the asparagine (N) of residue 177 of this cytokine. The un-glycosylated mutant 3nIFNa2-N177Q shows the similar antiviral ability as that of 3nIFNa2, which suggests that the N-linked glycosylation does not contribute directly to its antiviral property. All the above data support the conclusion that 3nIFNa2 is an intracellular cytokine functioning importantly in host antiviral innate immunity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. New DAPI and FISH findings on egg maturation processes in related hybridogenetic and parthenogenetic Bacillus hybrids (Insecta, Phasmatodea).

    PubMed

    Marescalchi, O; Scali, V

    2001-10-01

    Bacillus stick insects have proved adequate for studying a wide array of reproductive modes: sexual, parthenogenetic, hybridogenetic, androgenetic. Hybridogenetic strains (B. rossius-grandii) were thought to discard the paternal "grandii" haploset during first meiotic division and keep the "rossius" hemiclone, whereas the clonal B. whitei (=rossius/grandii) would maintain its hybrid structure by fusing back two nonsister nuclei-each derived from previously segregated heterospecific complements-by the end of the 2(nd) meiotic division. New investigations on laid eggs and ovariole squashes, either DAPI stained or FISH labeled, revealed that in hybridogens the "grandii" set is excluded from the germ line prior to meiosis and that a DNA extra-synthesis should occur to produce hemiclonal eggs after two cytologically normal meiotic divisions. On the other hand, in B. whitei eggs no genome segregation appears to occur and an intrameiotic DNA extra-synthesis must take place to produce 2n tetrachromatidic oocytes I; these divide twice and give unreduced clonal eggs. The new findings bring hybridogenetic oogenesis of Bacillus to be coincident with that of the known hemiclonal organisms and point to an independent onset of B. whitei from hemiclonal strains. In addition, B. whitei gains a closer resemblance to B. lynceorum owing to the sharing of a cytologically identical egg maturation mechanism, of the same maternal ancestor and of peculiar chromosomal features. It is here suggested that B. lynceorum originated from the incorporation of an "atticus" genome into a B. whitei egg, according to a pathway of repeated hybridization often occurred with other polyploid hybrids.

  18. Replacing fish meal by food waste to produce lower trophic level fish containing acceptable levels of polycyclic aromatic hydrocarbons: Health risk assessments.

    PubMed

    Cheng, Zhang; Mo, Wing-Yin; Lam, Cheung-Lung; Choi, Wai-Ming; Wong, Ming-Hung

    2015-08-01

    This study aimed at using different types of food wastes (mainly containing cereal [food waste A] and meat meal [food waste B]) as major sources of protein to replace the fish meal used in fish feeds to produce quality fish. The traditional fish farming model used to culture low trophic level fish included: bighead, (Hypophthalmichthys nobilis), grass carp, (Ctenopharyngodon idellus), and mud carp, (Cirrhinus molitorella) of omnivorous chain. The results indicated that grass carp and bighead carp fed with food waste feeds were relatively free of PAHs. The results of health risk assessment showed that the fish fed with food waste feeds were safe for consumption from the PAHs perspective. Copyright © 2015. Published by Elsevier B.V.

  19. DEVELOPMENT OF A FISH INDEX OF BIOTIC INTEGRITY FOR ASSESSING WADEABLE STREAMS IN WEST VIRGINIA

    EPA Science Inventory

    We used Environmental Monitoring Assessment Program (EMAP) data from the Mid-Atlantic Highlands Assessment (MAHA) to develop an Index of Biotic Integrity (IBI) for West Virginia (WV). Standard techniques were used to evaluate a candidate pool of 58 fish assemblage metrics. Resp...

  20. DEVELOPMENT OF A FISH INDEX OF BIOTIC INTEGRITY FOR ASSESSING WADEABLE STREAMS IN WEST VIRGINIA

    EPA Science Inventory

    We used Environmental Monitoring Assessment Program (EMAP) data from the Mid-Atlantic Highlands Assessment (MAHA) to develop an Index of Biotic Integrity (IBI) for West Virginia (WV). Standard techniques were used to evaluate a candidate pool of 58 fish assemblage metrics. Resp...

  1. Fishes, mussels, crayfishes, and aquatic habitats of the Hoosier-Shawnee ecological assessment area

    Treesearch

    M. Burr Brooks; Justin T. Sipiorski; Matthew R. Thomas; Kevin S. Cummings; Christopher A. Taylor

    2004-01-01

    The Hoosier-Shawnee Ecological Assessment Area, part of the Coastal Plain and Interior Low Plateau physiographic provinces, includes 194 native fish species, 76 native mussel species, and 34 native crayfish species. Five of the subregions (e.g., Mississippi Embayment) that make up the assessment area were recently ranked as either globally or bioregionally outstanding...

  2. Residual levels of rare earth elements in freshwater and marine fish and their health risk assessment from Shandong, China.

    PubMed

    Yang, Luping; Wang, Xining; Nie, Hongqian; Shao, Lijun; Wang, Guoling; Liu, Yongjun

    2016-06-15

    The total concentrations of rare earth elements (ΣREE) were quantified in 251 samples from 10 common species of freshwater and marine fish in seventeen cities of Shandong, China. ΣREE obtained from the freshwater fish ranged from 34.0 to 37.9ngg(-1) (wet weight) and marine fish from 12.7 to 37.6ngg(-1). The ratio of LREE to HREE was 13.7:1 and 10:1 for freshwater and marine fish, respectively. This suggests that freshwater fish exhibit greater REE concentrations than marine fish and the biological effects of LREE are higher than HREE. Results revealed a similar REE distribution pattern between those fish and coastal sediments, abiding the "abundance law". The health risk assessment demonstrated the EDIs of REEs in fish were significantly lower than the ADI, indicating that the consumption of these fish presents little risk to human health.

  3. Risk-benefit evaluation of fish from Chinese markets: nutrients and contaminants in 24 fish species from five big cities and related assessment for human health.

    PubMed

    Du, Zhen-Yu; Zhang, Jian; Wang, Chunrong; Li, Lixiang; Man, Qingqing; Lundebye, Anne-Katrine; Frøyland, Livar

    2012-02-01

    The risks and benefits of fish from markets in Chinese cities have not previously been fully evaluated. In the present study, 24 common fish species with more than 400 individual samples were collected from markets from five big Chinese cities in 2007. The main nutrients and contaminants were measured and the risk-benefit was evaluated based on recommended nutrient intakes and risk level criteria set by relevant authorities. The comprehensive effects of nutrients and contaminants in marine oily fish were also evaluated using the data of two related human dietary intervention trials performed in dyslipidemic Chinese men and women in 2008 and 2010, respectively. The results showed that concentrations of contaminants analyzed including DDT, PCB(7), arsenic and cadmium were much lower than their corresponding maximum limits with the exception of the mercury concentration in common carp. Concentrations of POPs and n-3 LCPUFA, mainly EPA and DHA, were positively associated with the lipid content of the fish. With a daily intake of 80-100g marine oily fish, the persistent organic pollutants in fish would not counteract the beneficial effects of n-3 LCPUFA in reducing cardiovascular disease (CVD) risk markers. Marine oily fish provided more effective protection against CVD than lean fish, particularly for the dyslipidemic populations. The risk-benefit assessment based on the present daily aquatic product intake in Chinese urban residents (44.9 and 62.3g for the average values for all cities and big cities, respectively) indicated that fish, particularly marine oily fish, can be regularly consumed to achieve optimal nutritional benefits from n-3 LCPUFA, without causing significant contaminant-related health risks. However, the potential health threat from contaminants in fish should still be emphasized for the populations consuming large quantities of fish, particularly wild fish.

  4. Statistical assessment of fish behavior from split-beam hydro-acoustic sampling

    SciTech Connect

    McKinstry, Craig A.; Simmons, Mary Ann; Simmons, Carver S.; Johnson, Robert L.

    2005-04-01

    Statistical methods are presented for using echo-traces from split-beam hydro-acoustic sampling to assess fish behavior in response to a stimulus. The data presented are from a study designed to assess the response of free-ranging, lake-resident fish, primarily kokanee (Oncorhynchus nerka) and rainbow trout (Oncorhynchus mykiss) to high intensity strobe lights, and was conducted at Grand Coulee Dam on the Columbia River in Northern Washington State. The lights were deployed immediately upstream from the turbine intakes, in a region exposed to daily alternating periods of high and low flows. The study design included five down-looking split-beam transducers positioned in a line at incremental distances upstream from the strobe lights, and treatments applied in randomized pseudo-replicate blocks. Statistical methods included the use of odds-ratios from fitted loglinear models. Fish-track velocity vectors were modeled using circular probability distributions. Both analyses are depicted graphically. Study results suggest large increases of fish activity in the presence of the strobe lights, most notably at night and during periods of low flow. The lights also induced notable bimodality in the angular distributions of the fish track velocity vectors. Statistical summaries are presented along with interpretations on fish behavior.

  5. Some potentials and limits of the leucocrit test as a fish health assessment method

    USGS Publications Warehouse

    Wedemeyer, G.A.; Gould, R.W.; Yasutake, W.T.

    1983-01-01

    The sensitivity of the leucocrit as a stress tolerance and fish health assessment method was evaluated by subjecting juvenile coho salmon, Oncorhynchus kisutch, or steelhead trout, Salmo gairdneri, to standardized crowding, handling, temperature and disease challenges. The leucocrit was a sensitive indicator of the physiological stress resulting from crowding at population densities of 0·2–0·4 kg l−1, and to the stress of handling and to temperature changes. It was relatively insensitive to physiological sampling procedures which supports its continued development as a stress assessment method.In the case of fish diseases, subclinical or active Renibacterium salmoninarum and Yersinia ruckeriinfections had essentially no effect on leucocrit values. In contrast, active Aeromonas salmonicidainfections significantly depressed the leucocrit. However, no change was seen during the subclinical (incubation) phase prior to the development of an epizootic. Thus, the potential of the leucocrit as a fish health assessment method appears limited.

  6. The State of In Vitro Science for Use in Bioaccumulation Assessments for Fish

    SciTech Connect

    Weisbrod, Anne V.; Sahi, Jasminder; Segner, Helmut; James, Margaret O.; Nichols, John W.; Schultz, Irvin R.; Erhardt, Susan; Cowan-Ellsberry, Christina; Bonnell, Mark; Hoeger, Birgit

    2009-01-01

    Through the concerted evaluations of thousands of commercial substances for the qualities of persistence, bioaccumulation, and toxicity as a result of the United Nations Environment Program’s Stockholm Convention, it has become apparent that fewer empirical data are available on bioaccumulation than other endpoints and that bioaccumulation models were not designed to accommodate all chemical classes. Due to the number of chemicals that may require further assessment, in vivo testing is cost prohibitive and discouraged due to the large number of animals needed. Although in vitro systems are less developed and characterized for fish, multiple high-throughput in vitro assays have been used to explore the dietary uptake and elimination of pharmaceuticals and other xenobiotics by mammals. While similar processes determine bioaccumulation in mammalian species, a review of methods to measure chemical bioavailability in fish screening systems, such as chemical biotransformation or metabolism in tissue slices, perfused tissues, fish embryos, primary and immortalized cell lines, and subcellular fractions, suggest quantitative and qualitative differences between fish and mammals exist. Using in vitro data in assessments for whole organisms or populations requires certain considerations and assumptions to scale data from a test tube to a fish, and across fish species. Also, different models may incorporate the predominant site of metabolism, such as the liver, and significant presystemic metabolism by the gill or gastrointestinal system to help accurately convert in vitro data into representative whole-animal metabolism and subsequent bioaccumulation potential. The development of animal alternative tests for fish bioaccumulation assessment is framed in the context of in vitro data requirements for regulatory assessments in Europe and Canada.

  7. Diagnosis of a constitutional five-chromosome rearrangement by fluorescent in situ hybridization (FISH)

    SciTech Connect

    Tsien, F.; Shapira, E.; Carvalho, T.

    1994-09-01

    Complex chromosomal rearrangements are structural rearrangements involving at least three chromosomes and three or more chromosome breakpoints. Such karyotypes are often acquired during cancer multi-step development and in chromosome instability syndromes. However, extremely rare constitutional forms have been reported, most of which are incompatible with life. We present a 2-year-old female with de novo complex rearrangement consisting of five chromosomes and nine breakpoints. Clinical evaluation at two years of age revealed a weight of 5 kg, length of 66 cm, and had circumference of 38 cm, all below the 5th percentile, microcephaly, trigonocephaly, epicanthal folds, inguinal hernia, left clubfoot, hypertonicity, and developmental delay. The neurological examination revealed chorea-acanthocytosis and psychomotor delay. Cultured lymphocytes and fibroblasts revealed a karyotype consisting of five derivative chromosomes. The metaphases were further analyzed by FISH using chromosome-specific libraries and telomeric probes in order to delineate the composition of the rearranged chromosomes; FISH results demonstrated a karyotype of: 46,XX,1pter{r_arrow}1q25::1q42.1{r_arrow}1qter, 2pter{r_arrow}q32.3::1q32.3{r_arrow}2q41::2q37.3{r_arrow}2qter, 7qter{r_arrow}7q21.2::6q22.3{r_arrow}6qter::1q31{r_arrow}1q32.3::6p23{r_arrow}6q22.3, 7pter{r_arrow}7q21.1::6p23{r_arrow}6pter, 2q33{r_arrow}2q37, 1::9p21{r_arrow}9qter. This analysis demonstrates the usefulness of FISH in characterizing complex chromosome rearrangements otherwise difficult to correctly interpret using classical cytogenetics alone.

  8. Local hybrid functionals: an assessment for thermochemical kinetics.

    PubMed

    Kaupp, Martin; Bahmann, Hilke; Arbuznikov, Alexei V

    2007-11-21

    Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b(tau(W)(r)tau(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.

  9. Local hybrid functionals: An assessment for thermochemical kinetics

    SciTech Connect

    Kaupp, Martin; Bahmann, Hilke; Arbuznikov, Alexei V.

    2007-11-21

    Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b({tau}{sub W}(r)/{tau}(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.

  10. Assessing the natural and anthropogenic influences on basin-wide fish species richness.

    PubMed

    Cheng, Su-Ting; Herricks, Edwin E; Tsai, Wen-Ping; Chang, Fi-John

    2016-12-01

    Theory predicts that the number of fish species increases with river size in natural free-flowing rivers, but the relationship is lost under intensive exploitation of water resources associated with dams and/or landscape developments. In this paper, we aim to identify orthomorphic issues that disrupt theoretical species patterns based on a multi-year, basin-wide assessment in the Danshuei River Watershed of Taiwan. We hypothesize that multiple human-induced modifications fragment habitat areas leading to decreases of local fish species richness. We integrally relate natural and anthropogenic influences on fish species richness by a multiple linear regression model that is driven by a combination of factors including river network structure controls, water quality alterations of habitat, and disruption of channel connectivity with major discontinuities in habitat caused by dams. We found that stream order is a major forcing factor representing natural influence on fish species richness. In addition to stream order, we identified dams, dissolved oxygen deficiency (DO), and excessive total phosphorus (TP) as major anthropogenic influences on the richness of fish species. Our results showed that anthropogenic influences were operating at various spatial scales that inherently regulate the physical, chemical, and biological condition of fish habitats. Moreover, our probability-based risk assessment revealed causes of species richness reduction and opportunities for mitigation. Risks of species richness reduction caused by dams were determined by the position of dams and the contribution of tributaries in the drainage network. Risks associated with TP and DO were higher in human-activity-intensified downstream reaches. Our methodology provides a structural framework for assessing changes in basin-wide fish species richness under the mixed natural and human-modified river network and habitat conditions. Based on our analysis results, we recommend that a focus on landscape

  11. A moving target--incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations.

    PubMed

    Cooke, Steven J; Martins, Eduardo G; Struthers, Daniel P; Gutowsky, Lee F G; Power, Michael; Doka, Susan E; Dettmers, John M; Crook, David A; Lucas, Martyn C; Holbrook, Christopher M; Krueger, Charles C

    2016-04-01

    Freshwater fish move vertically and horizontally through the aquatic landscape for a variety of reasons, such as to find and exploit patchy resources or to locate essential habitats (e.g., for spawning). Inherent challenges exist with the assessment of fish populations because they are moving targets. We submit that quantifying and describing the spatial ecology of fish and their habitat is an important component of freshwater fishery assessment and management. With a growing number of tools available for studying the spatial ecology of fishes (e.g., telemetry, population genetics, hydroacoustics, otolith microchemistry, stable isotope analysis), new knowledge can now be generated and incorporated into biological assessment and fishery management. For example, knowing when, where, and how to deploy assessment gears is essential to inform, refine, or calibrate assessment protocols. Such information is also useful for quantifying or avoiding bycatch of imperiled species. Knowledge of habitat connectivity and usage can identify critically important migration corridors and habitats and can be used to improve our understanding of variables that influence spatial structuring of fish populations. Similarly, demographic processes are partly driven by the behavior of fish and mediated by environmental drivers. Information on these processes is critical to the development and application of realistic population dynamics models. Collectively, biological assessment, when informed by knowledge of spatial ecology, can provide managers with the ability to understand how and when fish and their habitats may be exposed to different threats. Naturally, this knowledge helps to better evaluate or develop strategies to protect the long-term viability of fishery production. Failure to understand the spatial ecology of fishes and to incorporate spatiotemporal data can bias population assessments and forecasts and potentially lead to ineffective or counterproductive management actions.

  12. A moving target—incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations

    USGS Publications Warehouse

    Cooke, Steven J.; Martins, Eduardo G; Struthers, Daniel P; Gutowsky, Lee F G; Powers, Michael H.; Doka, Susan E; Dettmers, John M.; Crook, David A; Lucas, Martyn C.; Holbrook, Christopher; Krueger, Charles C.

    2016-01-01

    Freshwater fish move vertically and horizontally through the aquatic landscape for a variety of reasons, such as to find and exploit patchy resources or to locate essential habitats (e.g., for spawning). Inherent challenges exist with the assessment of fish populations because they are moving targets. We submit that quantifying and describing the spatial ecology of fish and their habitat is an important component of freshwater fishery assessment and management. With a growing number of tools available for studying the spatial ecology of fishes (e.g., telemetry, population genetics, hydroacoustics, otolith microchemistry, stable isotope analysis), new knowledge can now be generated and incorporated into biological assessment and fishery management. For example, knowing when, where, and how to deploy assessment gears is essential to inform, refine, or calibrate assessment protocols. Such information is also useful for quantifying or avoiding bycatch of imperiled species. Knowledge of habitat connectivity and usage can identify critically important migration corridors and habitats and can be used to improve our understanding of variables that influence spatial structuring of fish populations. Similarly, demographic processes are partly driven by the behavior of fish and mediated by environmental drivers. Information on these processes is critical to the development and application of realistic population dynamics models. Collectively, biological assessment, when informed by knowledge of spatial ecology, can provide managers with the ability to understand how and when fish and their habitats may be exposed to different threats. Naturally, this knowledge helps to better evaluate or develop strategies to protect the long-term viability of fishery production. Failure to understand the spatial ecology of fishes and to incorporate spatiotemporal data can bias population assessments and forecasts and potentially lead to ineffective or counterproductive management actions.

  13. Fishing in acid waters: A vulnerability assessment of the Norwegian fishing industry in the face of increasing ocean acidification.

    PubMed

    Heinrich, Luise; Krause, Torsten

    2017-07-01

    Ocean acidification (OA) describes a change in the ocean's carbonate chemistry. Whereas its chemical processes are largely understood, the biological and socioeconomic consequences particularly in relation to fisheries are less known. Norway is a major fishing nation worldwide and is potentially affected by OA. To improve the understanding of the socioeconomic consequences of OA, we conducted a risk assessment among the Norwegian counties using a modified version of a risk assessment framework introduced in the Intergovernmental Panel on Climate Change's "Special Report: Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation," which considers risk to be the sum of hazard, exposure, and vulnerability. Our results show that about 13 of 19 counties are likely to experience moderate to high risk from OA. We highlight that the success of integrated risk assessments highly depends on the availability of detailed environmental, economic, and societal data. In the case of Norway, modeling data regarding the progress of OA, improved information on potential biological impacts on a larger number of species, and statistical data on social variables are required. We conclude that although still in its infancy, integrated risk assessments are important prerequisites for any form of interdisciplinary research on OA and the development of successful response strategies. Integr Environ Assess Manag 2017;13:778-789. ©2016 SETAC. © 2016 SETAC.

  14. Dealing with uncertainty when assessing fish passage through culvert road crossings

    USGS Publications Warehouse

    Anderson, Gregory B.; Freeman, Mary C.; Freeman, Byron J.; Straight, Carrie A.; Hagler, Megan M.; Peterson, James T.

    2012-01-01

    Assessing the passage of aquatic organisms through culvert road crossings has become increasingly common in efforts to restore stream habitat. Several federal and state agencies and local stakeholders have adopted assessment approaches based on literature-derived criteria for culvert impassability. However, criteria differ and are typically specific to larger-bodied fishes. In an analysis to prioritize culverts for remediation to benefit imperiled, small-bodied fishes in the Upper Coosa River system in the southeastern United States, we assessed the sensitivity of prioritization to the use of differing but plausible criteria for culvert impassability. Using measurements at 256 road crossings, we assessed culvert impassability using four alternative criteria sets represented in Bayesian belief networks. Two criteria sets scored culverts as either passable or impassable based on alternative thresholds of culvert characteristics (outlet elevation, baseflow water velocity). Two additional criteria sets incorporated uncertainty concerning ability of small-bodied fishes to pass through culverts and estimated a probability of culvert impassability. To prioritize culverts for remediation, we combined estimated culvert impassability with culvert position in the stream network relative to other barriers to compute prospective gain in connected stream habitat for the target fish species. Although four culverts ranked highly for remediation regardless of which criteria were used to assess impassability, other culverts differed widely in priority depending on criteria. Our results emphasize the value of explicitly incorporating uncertainty into criteria underlying remediation decisions. Comparing outcomes among alternative, plausible criteria may also help to identify research most needed to narrow management uncertainty.

  15. Dealing With Uncertainty When Assessing Fish Passage Through Culvert Road Crossings

    NASA Astrophysics Data System (ADS)

    Anderson, Gregory B.; Freeman, Mary C.; Freeman, Byron J.; Straight, Carrie A.; Hagler, Megan M.; Peterson, James T.

    2012-09-01

    Assessing the passage of aquatic organisms through culvert road crossings has become increasingly common in efforts to restore stream habitat. Several federal and state agencies and local stakeholders have adopted assessment approaches based on literature-derived criteria for culvert impassability. However, criteria differ and are typically specific to larger-bodied fishes. In an analysis to prioritize culverts for remediation to benefit imperiled, small-bodied fishes in the Upper Coosa River system in the southeastern United States, we assessed the sensitivity of prioritization to the use of differing but plausible criteria for culvert impassability. Using measurements at 256 road crossings, we assessed culvert impassability using four alternative criteria sets represented in Bayesian belief networks. Two criteria sets scored culverts as either passable or impassable based on alternative thresholds of culvert characteristics (outlet elevation, baseflow water velocity). Two additional criteria sets incorporated uncertainty concerning ability of small-bodied fishes to pass through culverts and estimated a probability of culvert impassability. To prioritize culverts for remediation, we combined estimated culvert impassability with culvert position in the stream network relative to other barriers to compute prospective gain in connected stream habitat for the target fish species. Although four culverts ranked highly for remediation regardless of which criteria were used to assess impassability, other culverts differed widely in priority depending on criteria. Our results emphasize the value of explicitly incorporating uncertainty into criteria underlying remediation decisions. Comparing outcomes among alternative, plausible criteria may also help to identify research most needed to narrow management uncertainty.

  16. Dealing with uncertainty when assessing fish passage through culvert road crossings.

    PubMed

    Anderson, Gregory B; Freeman, Mary C; Freeman, Byron J; Straight, Carrie A; Hagler, Megan M; Peterson, James T

    2012-09-01

    Assessing the passage of aquatic organisms through culvert road crossings has become increasingly common in efforts to restore stream habitat. Several federal and state agencies and local stakeholders have adopted assessment approaches based on literature-derived criteria for culvert impassability. However, criteria differ and are typically specific to larger-bodied fishes. In an analysis to prioritize culverts for remediation to benefit imperiled, small-bodied fishes in the Upper Coosa River system in the southeastern United States, we assessed the sensitivity of prioritization to the use of differing but plausible criteria for culvert impassability. Using measurements at 256 road crossings, we assessed culvert impassability using four alternative criteria sets represented in Bayesian belief networks. Two criteria sets scored culverts as either passable or impassable based on alternative thresholds of culvert characteristics (outlet elevation, baseflow water velocity). Two additional criteria sets incorporated uncertainty concerning ability of small-bodied fishes to pass through culverts and estimated a probability of culvert impassability. To prioritize culverts for remediation, we combined estimated culvert impassability with culvert position in the stream network relative to other barriers to compute prospective gain in connected stream habitat for the target fish species. Although four culverts ranked highly for remediation regardless of which criteria were used to assess impassability, other culverts differed widely in priority depending on criteria. Our results emphasize the value of explicitly incorporating uncertainty into criteria underlying remediation decisions. Comparing outcomes among alternative, plausible criteria may also help to identify research most needed to narrow management uncertainty.

  17. Assessing the potential for fish predation to impact zebra mussels (Dreissena polymorpha): Insight from bioenergetics models

    USGS Publications Warehouse

    Eggleton, M.A.; Miranda, L.E.; Kirk, J.P.

    2004-01-01

    Rates of annual food consumption and biomass were modeled for several fish species across representative rivers and lakes in eastern North America. Results were combined to assess the relative potential of fish predation to impact zebra mussels (Dreissena polymorpha). Predicted annual food consumption by fishes in southern waters was over 100% greater than that in northern systems because of warmer annual water temperatures and presumed increases in metabolic demand. Although generally increasing with latitude, biomasses of several key zebra mussel fish predators did not change significantly across latitudes. Biomasses of some less abundant fish predators did increase significantly with latitude, but increases were not of the magnitude to offset predicted decreases in food consumption. Our results generally support the premise that fishes in rivers and lakes of the southern United States (U.S.) have inherently greater potential to impact zebra mussels by predation. Our simulations may provide a partial explanation of why zebra mussel invasions have not been as rapid and widespread in southern U.S. waters compared to the Great Lakes region. ?? Blackwell Munksgaard, 2004.

  18. Assessing Potential Conservation and Restoration Areas of Freshwater Fish Fauna in the Indian River Basins

    NASA Astrophysics Data System (ADS)

    Bhatt, Jay P.; Manish, Kumar; Mehta, Rajender; Pandit, Maharaj K.

    2016-05-01

    Conservation efforts globally are skewed toward terrestrial ecosystems. To date, conservation of aquatic ecosystems, in particular fish fauna, is largely neglected. We provide a country-wide assessment of Indian river ecosystems in order to identify and prioritize areas for protection and restoration of freshwater fish fauna. Using various biodiversity and anthropogenic attributes, coupled with tools of ecological modeling, we delineated areas for fish fauna conservation and restoration in the 20 major river basins of India. To do this, we used prioritization analyses and reserve selection algorithms to derive conservation value index (CVI) and vulnerability index (VI) of the river basins. CVI was estimated using endemicity, rarity, conservation value, and taxonomic singularity, while VI was estimated using a disturbance index derived from percent geographic area of the basin under human settlements, human population density, predominant land use, and total number of exotic fish species in each basin. The two indices, CVI and VI, were converted into geo-referenced maps, and each map was super-imposed onto species richness and forest cover maps, respectively. After superimposition, areas with high CVI and low VI shade intensities were delineated for conservation, while areas with high CVI and high VI shade intensities were demarcated for restoration. In view of the importance of freshwater fish for human livelihoods and consumption, and ecosystems of India's rivers, we call for urgent attention to the conservation of their fish fauna along with restoration of their degraded habitats.

  19. Large-scale polymorphism near the ends of several human chromosomes analyzed by using fluorescence in situ hybridization (FISH)

    SciTech Connect

    Trask, B.J.; Friedman, C.; Giorgi, D.

    1994-09-01

    We have discovered a large DNA segment that is polymorphically present at the ends of several human chromosomes. The segment, f7501, was originally derived form a human chromosome 19-specific cosmid library. FISH was used to determine the cosmid`s chromosomal distribution on 44 unrelated humans and several closely related primates. The human subjects represent a diversity of reproductively isolated ethnic populations. FISH analysis revealed that sequences highly homologous to the cosmid`s insert are present on both homologs at 3q, 15q,. and 19p in almost all individuals (88, 85, and 87 of 88 homologs, respectively). Other chromosomes sites were labeled much more rarely in the sampled individuals. For example, 56 of the 88 analyzed chromosomes 11 were labeled (18+/+, 6-/-, and 20+/- individuals). In contrast, 2q was labeled on only 1/88 sampled chromosomes. The termini of 2q, 5q, 6p, 6q, 7p, 8p, 9p, 9q, 11p, 12q, 16p, 19q, and 20q and an interstitial site at 2q13-14 were labeled in at least one individual of the set. EcoR1-fragments derived from the cosmid showed the same hybridization pattern as the entire cosmid, indicating that at least 40 kbp is shared by these chromosome ends. Ethnic differences in the allele frequency of these polymorphic variants was observed. For example, signals were observed on 8/10 and 7/10 of the chromosomes 7p and 16q, respectively, derived form Biakan Pygmies, but these sites were infrequently labeled in non-Pygmy human populations (2/68, respectively). This region has undergone significant changes in chromosome location during human evolution. Strong signal was seen on chimpanzee and gorilla chromosome 3, which is homologous to human chromosome 4, a chromosome unlabeled in any of the humans we have analyzed.

  20. Microphthalmia with linear skin defects (MLS) syndrome evaluated by prenatal karyotyping, FISH and array comparative genomic hybridization.

    PubMed

    Cain, Colyn Cargile; Saul, Daniel; Attanasio, Lisa; Oehler, Erin; Hamosh, Ada; Blakemore, Karin; Stetten, Gail

    2007-04-01

    To explore the utility of comparative genomic hybridization to BAC arrays (array CGH) for prenatal diagnosis of microphthalmia and linear skin defects syndrome. We used karyotype analysis, FISH and array CGH to investigate an X;Y translocation. Replication studies were done on cultured amniocytes and lymphoblasts. We describe a severe case of MLS syndrome that presented prenatally with multiple anomalies including cystic hygroma, microphthalmia, intrauterine growth restriction and a complex congenital heart defect. Cytogenetic analysis of amniocytes revealed an unbalanced de novo translocation between chromosomes X and Y [karyotype 46,X,der(X)t(X;Y)(p22.3;q11.2).ish der(X)(DXZ1+,DMD+,KAL-,STS-,SRY-),22q11.2 (Tuple1 x 2)]. MLS diagnosis was made at birth and the prenatal karyotype was confirmed. Replication studies showed the derivative X chromosome was the inactive X. Array CGH confirmed the X and Y imbalances seen in the karyotype and also showed twelve BACs in the MLS region were deleted as a result of the translocation. FISH with BAC clones verified the array findings and placed the X breakpoint in Xp22.2, resulting in the amended karyotype, 46,X,der(X)t(X;Y)(p22.2;q11.2).ish der(X)(DXZ1+,DMD+,KAL-,STS-,SRY-),22q11.2(Tuple1 x 2) arr cgh Xp22.33p22.2(LLNOYCO3M15D10 -->GS1-590J6)x 1,Yq11.222q23(RP11-20H21-->RP11-79J10)x 1. The sensitivity of array CGH was valuable in detecting monosomy of the MLS critical region. Array CGH should be considered for the prenatal diagnosis of this syndrome. Copyright (c) 2007 John Wiley & Sons, Ltd.

  1. Male infertility and copy number variants (CNVs) in the dog: a two-pronged approach using Computer Assisted Sperm Analysis (CASA) and Fluorescent In Situ Hybridization (FISH)

    PubMed Central

    2013-01-01

    Background Infertility affects ~10-15% of couples trying to have children, in which the rate of male fertility problems is approximately at 30-50%. Copy number variations (CNVs) are DNA sequences greater than or equal to 1 kb in length sharing a high level of similarity, and present at a variable number of copies in the genome; in our study, we used the canine species as an animal model to detect CNVs responsible for male infertility. We aim to identify CNVs associated with male infertility in the dog genome with a two-pronged approach: we performed a sperm analysis using the CASA system and a cytogenetic-targeted analysis on genes involved in male gonad development and spermatogenesis with fluorescence in situ hybridization (FISH), using dog-specific clones. This analysis was carried out to evaluate possible correlations between CNVs on targeted genes and spermatogenesis impairments or infertility factors. Results We identified two genomic regions hybridized by BACs CH82-321J09 and CH82-509B23 showing duplication patterns in all samples except for an azoospermic dog. These two regions harbor two important genes for spermatogenesis: DNM2 and TEKT1. The genomic region encompassed by the BAC clone CH82-324I01 showed a single-copy pattern in all samples except for one dog, assessed with low-quality sperm, displaying a marked duplication pattern. This genomic region harbors SOX8, a key gene for testis development. Conclusion We present the first study involving functional and genetic analyses in male infertility. We set up an extremely reliable analysis on dog sperm cells with a highly consistent statistical significance, and we succeeded in conducting FISH experiments on sperm cells using BAC clones as probes. We found copy number differences in infertile compared with fertile dogs for genomic regions encompassing TEKT1, DNM2, and SOX8, suggesting those genes could have a role if deleted or duplicated with respect to the reference copy number in fertility biology

  2. Use of a fish health condition profile in assessing the health and condition of juvenile Chinook salmon

    USGS Publications Warehouse

    Novotny, J.F.; Beeman, J.W.

    1990-01-01

    The fish health condition profile, a simplified system for assessing fish health and condition, was originally developed for fish hatcheries and feral trout populations in Utah. We evaluated the method during routine health assessments of juvenile fall chinook salmon (Oncorhynchus tshawytscha) reared in net pens in the Columbia River in 1986 and 1987. The procedure yielded a thorough assessment of the condition offish held under various rearing conditions. This assessment was generally consistent with results of regular diagnostic examinations completed by certified fish health pathologists. The simplicity and availability of the system to most field biologists make it useful for monitoring fish in culture facilities as well as fish from wild stocks. This system may provide the framework for developing a more comprehensive smolt condition index that could be used to evaluate the general condition of juvenile anadromous salmonids before release or during out-migration.

  3. Comparison of HER2 gene amplification assessed by fluorescence in situ hybridization and HER2 protein expression assessed by immunohistochemistry in gastric cancer.

    PubMed

    Yano, Tomonori; Doi, Toshihiko; Ohtsu, Atsushi; Boku, Narikazu; Hashizume, Kaoru; Nakanishi, Mamoru; Ochiai, Atsushi

    2006-01-01

    A monoclonal antibody to HER2 protein is widely used in the treatment of patients with HER2-overexpressing breast cancer and has also been found to exhibit antitumor activity in human gastric cancer cells that overexpress HER2. The purpose of this study was to evaluate the frequency of HER2 overexpression and concordance between the results for protein expression and gene amplification in both surgical and biopsy specimens of gastric cancer as assessed with two commercial kits, one for immunohistochemistry (IHC) and the other for fluorescence in situ hybridization (FISH). The specimens consisted of formalin-fixed, paraffin-embedded sections of biopsy specimens and surgically resected tumors from 200 cases of invasive gastric cancer that had been treated surgically at the National Cancer Center Hospital East. The lesions were analyzed with the IHC kit, and expression was graded by the United States Food and Drug Administration (FDA)-approved grading system. Gene amplification was evaluated by FISH. IHC revealed HER2 overexpression in 46 of the 200 (23%) cases. The FISH assay was technically successful in 199 cases (99.5%), and gene amplification was observed in 54 cases (27.1%). The concordance rate between the results obtained by IHC and FISH was 86.9%. The concordance rate between the findings in the surgically resected tumors and the 200 pre-treatment biopsy specimens was 88.7%. HER2 expression can be assessed in gastric cancer with a commercial kit as previously reported in breast cancer. Even small biopsy specimens were found to be suitable for evaluating gastric cancer for HER2 overexpression.

  4. A membrane assisted hybrid bioreactor for the post treatment of an anaerobic effluent from a fish canning factory.

    PubMed

    Oyanedel, V; Garrido, J M; Lema, J M; Méndez, R

    2003-01-01

    An innovative membrane assisted hybrid bioreactor was used to treat a mixture of two streams produced in a fish canning factory: a highly loaded stream that had previously been treated in an anaerobic contact reactor, and a second stream with a relatively low COD and N concentration. Experiments were carried out during two experimental stages: an aerobic stage, which is focused in the study on the aerobic oxidation of ammonia and COD and a nitrification-denitrification stage in which the study was mainly focused on the removal of nitrogen. Results of the aerobic period pointed out that it was feasible to achieve ammonia and COD removals of around 99% at OLR of 6.5 kg COD/m3 x d and NLR of 1.8 kg N-NH4+/m3 x d. Specific nitrifying activities of up to 0.78 g N-NH4+/g protein x d and 0.25 g N-NH4+/g VSS x d, were recorded for the attached and suspended biomass, respectively. Around 50-60% of the nitrifying capacity of the reactor was a result of the nitrifying capacity of the biofilm. During the nitrification-denitrification stage 76% of nitrogen removal was attained at an NLR of 0.8 kg N-NH4+/m3 x d. The biofilm nitrifying activity was not affected by the operating conditions of the system, as a result of the preferential consumption of COD by suspended biomass in the reactor. Thus, the combination of a hybrid system, with both suspended and attached biomass, and an ultrafiltration membrane module might be an alternative for treating wastewaters in compact biological systems. The intrinsic characteristics of the system made it feasible to operate at high OLR without problems related with the settling properties of the sludge or the drop in the nitrogen conversion. There were no solids in the effluent as a result of the use of the membrane filtration module.

  5. Assessment of fish consumption and mercury exposure among pregnant women in Jamaica and Trinidad & Tobago.

    PubMed

    Ricketts, Phylicia; Basu, Niladri; Fletcher, Horace; Voutchkov, Mitko; Bassaw, Bharat

    2016-12-01

    Fish is an essential and traditional element in the diet of most Caribbean people. However it also contains methylmercury which can have severe effects on fetal neurodevelopment. The objective of this study was to assess the fish intake of a selected group of pregnant women from Jamaica and Trinidad & Tobago and evaluate prenatal mercury exposure, using the placenta as a biomarker. Food frequency questionnaires and placental samples were obtained from participating parturients at the time of delivery at the University Hospital of the West Indies in Kingston, Jamaica (N = 100, from November 2012 to March 2013) and the Mt Hope Women's hospital in St Joseph, Trinidad & Tobago (N = 30, in June 2015). The participants were asked to identify the species of fish and the frequency of consumption. Placental samples were analysed for mercury using cold vapour atomic absorption. The fish consumption preferences for pregnant women, varies based on the marine fish catch production of each country. The main fish species that contributed to the highest estimated methylmercury exposure in Jamaica and Trinidad & Tobago were cod and shark, respectively. There was a weak association between maternal fish intake and placental mercury concentrations. The mean placental mercury concentrations in Jamaica and Trinidad & Tobago were 0.74 ± 0.5 μg/kg and 1.46 ± 0.6 μg/kg, wet weight respectively. The results from this study showed an influence of Caribbean fish intake preferences on mercury exposure and thus a recommendation for continuous bio-monitoring for public health purposes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Assessment of fish health in Ashumet and Johns Ponds adjacent to the Massachusetts Military Reservation

    SciTech Connect

    Greeley, M.S. Jr.; Adams, S.M.; Hinton, D.E.

    1995-12-31

    Ashumet and Johns Ponds are located adjacent to the Massachusetts Military Reservation (MMR) on Cape Cod, and lie in or near the paths of several plumes of groundwater contamination flowing from the MMR. This study had the objective of documenting the present status of fish in both ponds in efforts to establish base-line conditions for any future biological monitoring activities and to determine whether evidence exists for current contaminant impacts. This objective was addressed through three complimentary approaches, including the determination of Health Assessment Index (HAI) scores for fish sampled from Ashumet and Johns Ponds and several reference ponds in the area, measurement of various biochemical and physiological indicators in fish tissues and fluids and histopathological examinations of fish organs. For each of the three primary fish species examined in this study, largemouth bass, brown bullhead catfish, and yellow perch, many similarities were noted in the physiological, biochemical and histopathological condition of fish in all the study ponds. However, mean HAIs tended to be slightly higher (indicative of poorer health) in Ashumet and Johns Ponds, due in part to pathologies related to a higher incidence of parasitic infection at these sites. The most striking differences between the ponds were very high prevalences of oral and body surface papillomas in brown bullhead catfish from Johns Pond (59%) and Ashumet Pond (34%). Although pesticides, PCBs, and other chemical contaminants were present in fish from all of ponds, there was no obvious relationship between chemical body burdens and the responses of any of the measured indicator parameters, nor was there any conclusive evidence of current impacts on fish from the contaminant plumes.

  7. A protocol for identifying suitable biomarkers to assess fish health: A systematic review

    PubMed Central

    2017-01-01

    Background Biomarkers have been used extensively to provide the connection between external levels of contaminant exposure, internal levels of tissue contamination, and early adverse effects in organisms. Objectives To present a three-step protocol for identifying suitable biomarkers to assess fish health in coastal and marine ecosystems, using Gladstone Harbour (Australia) as a case study. Methods Prior to applying our protocol, clear working definitions for biomarkers were developed to ensure consistency with the global literature on fish health assessment. First, contaminants of concern were identified based on the presence of point and diffuse sources of pollution and available monitoring data for the ecosystem of interest. Second, suitable fish species were identified using fisheries dependent and independent data, and prioritised based on potential pathways of exposure to the contaminants of concern. Finally, a systematic and critical literature review was conducted on the use of biomarkers to assess the health of fish exposed to the contaminants of concern. Results/Discussion We present clear working definitions for bioaccumulation markers, biomarkers of exposure, biomarkers of effect and biomarkers of susceptibility. Based on emission and concentration information, seven metals were identified as contaminants of concern for Gladstone Harbour. Twenty out of 232 fish species were abundant enough to be potentially suitable for biomarker studies; five of these were prioritised based on potential pathways of exposure and susceptibility to metals. The literature search on biomarkers yielded 5,035 articles, of which 151met the inclusion criteria. Based on our review, the most suitable biomarkers include bioaccumulation markers, biomarkers of exposure (CYP1A, EROD, SOD, LPOX, HSP, MT, DNA strand breaks, micronuclei, apoptosis), and biomarkers of effect (histopathology, TAG:ST). Conclusion Our protocol outlines a clear pathway to identify suitable biomarkers to

  8. Length-based assessment of coral reef fish populations in the main and northwestern Hawaiian islands.

    PubMed

    Nadon, Marc O; Ault, Jerald S; Williams, Ivor D; Smith, Steven G; DiNardo, Gerard T

    2015-01-01

    The coral reef fish community of Hawaii is composed of hundreds of species, supports a multimillion dollar fishing and tourism industry, and is of great cultural importance to the local population. However, a major stock assessment of Hawaiian coral reef fish populations has not yet been conducted. Here we used the robust indicator variable "average length in the exploited phase of the population ([Formula: see text])", estimated from size composition data from commercial fisheries trip reports and fishery-independent diver surveys, to evaluate exploitation rates for 19 Hawaiian reef fishes. By and large, the average lengths obtained from diver surveys agreed well with those from commercial data. We used the estimated exploitation rates coupled with life history parameters synthesized from the literature to parameterize a numerical population model and generate stock sustainability metrics such as spawning potential ratios (SPR). We found good agreement between predicted average lengths in an unfished population (from our population model) and those observed from diver surveys in the largely unexploited Northwestern Hawaiian Islands. Of 19 exploited reef fish species assessed in the main Hawaiian Islands, 9 had SPRs close to or below the 30% overfishing threshold. In general, longer-lived species such as surgeonfishes, the redlip parrotfish (Scarus rubroviolaceus), and the gray snapper (Aprion virescens) had the lowest SPRs, while short-lived species such as goatfishes and jacks, as well as two invasive species (Lutjanus kasmira and Cephalopholis argus), had SPRs above the 30% threshold.

  9. Length-Based Assessment of Coral Reef Fish Populations in the Main and Northwestern Hawaiian Islands

    PubMed Central

    Nadon, Marc O.; Ault, Jerald S.; Williams, Ivor D.; Smith, Steven G.; DiNardo, Gerard T.

    2015-01-01

    The coral reef fish community of Hawaii is composed of hundreds of species, supports a multimillion dollar fishing and tourism industry, and is of great cultural importance to the local population. However, a major stock assessment of Hawaiian coral reef fish populations has not yet been conducted. Here we used the robust indicator variable “average length in the exploited phase of the population (L¯)”, estimated from size composition data from commercial fisheries trip reports and fishery-independent diver surveys, to evaluate exploitation rates for 19 Hawaiian reef fishes. By and large, the average lengths obtained from diver surveys agreed well with those from commercial data. We used the estimated exploitation rates coupled with life history parameters synthesized from the literature to parameterize a numerical population model and generate stock sustainability metrics such as spawning potential ratios (SPR). We found good agreement between predicted average lengths in an unfished population (from our population model) and those observed from diver surveys in the largely unexploited Northwestern Hawaiian Islands. Of 19 exploited reef fish species assessed in the main Hawaiian Islands, 9 had SPRs close to or below the 30% overfishing threshold. In general, longer-lived species such as surgeonfishes, the redlip parrotfish (Scarus rubroviolaceus), and the gray snapper (Aprion virescens) had the lowest SPRs, while short-lived species such as goatfishes and jacks, as well as two invasive species (Lutjanus kasmira and Cephalopholis argus), had SPRs above the 30% threshold. PMID:26267473

  10. Probabilistic risk assessment of exposure to leucomalachite green residues from fish products.

    PubMed

    Chu, Yung-Lin; Chimeddulam, Dalaijamts; Sheen, Lee-Yan; Wu, Kuen-Yuh

    2013-12-01

    To assess the potential risk of human exposure to carcinogenic leucomalachite green (LMG) due to fish consumption, the probabilistic risk assessment was conducted for adolescent, adult and senior adult consumers in Taiwan. The residues of LMG with the mean concentration of 13.378±20.56 μg kg(-1) (BFDA, 2009) in fish was converted into dose, considering fish intake reported for three consumer groups by NAHSIT (1993-1996) and body weight of an average individual of the group. The lifetime average and high 95th percentile dietary intakes of LMG from fish consumption for Taiwanese consumers were estimated at up to 0.0135 and 0.0451 μg kg-bw(-1) day(-1), respectively. Human equivalent dose (HED) of 2.875 mg kg-bw(-1) day(-1) obtained from a lower-bound benchmark dose (BMDL10) in mice by interspecies extrapolation was linearly extrapolated to oral cancer slope factor (CSF) of 0.035 (mgkg-bw(-1)day(-1))(-1) for humans. Although, the assumptions and methods are different, the results of lifetime cancer risk varying from 3×10(-7) to 1.6×10(-6) were comparable to those of margin of exposures (MOEs) varying from 410,000 to 4,800,000. In conclusions, Taiwanese fish consumers with the 95th percentile LADD of LMG have greater risk of liver cancer and need to an action of risk management in Taiwan.

  11. Comparison of nine different methods to assess fish communities in lentic flood-plain habitats.

    PubMed

    Mueller, M; Pander, J; Knott, J; Geist, J

    2017-07-01

    This study compares the effectiveness and representativeness of electrofishing, snorkelling, seining, baited lift netting, multi-mesh gillnetting, baited fish traps, fyke netting, angling and longline fishing, considering three typical lentic flood-plain habitats at different times of day. Electrofishing was by far the most effective method yielding highest species richness, species trait representation and catch per unit of effort (CPUE), followed by seining. For single species like dace Leuciscus leuciscus, European ruffe Gymnocephalus cernua, common bream Abramis brama and silver bream Blicca bjoerkna, seining was more effective than electrofishing. With both methods, some species were more consistently caught during night, dusk or dawn than during daylight. All other methods tested cannot be generally recommended for fish community assessments in shallow backwaters due to their low representativeness of species inventory and generally low CPUE. Based on these results, electrofishing of 30 m transect replicates at different times of day for monitoring the fish community in shallow backwaters, can be recommended, enabling the maximum possible comparability to adjacent river habitats. Seining should be considered as an alternative if accessibility of habitats is restricted or electrofishing is prohibited. The 25 species detected in the backwaters also suggest that these habitats contribute a large proportion of fish diversity and should be included in standard assessments of river ecological status. © 2017 The Fisheries Society of the British Isles.

  12. Discriminating Multi-Species Populations in Biofilms with Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA FISH)

    PubMed Central

    Almeida, Carina; Azevedo, Nuno F.; Santos, Sílvio; Keevil, Charles W.; Vieira, Maria J.

    2011-01-01

    Background Our current understanding of biofilms indicates that these structures are typically composed of many different microbial species. However, the lack of reliable techniques for the discrimination of each population has meant that studies focusing on multi-species biofilms are scarce and typically generate qualitative rather than quantitative data. Methodology/Principal Findings We employ peptide nucleic acid fluorescence in situ hybridization (PNA FISH) methods to quantify and visualize mixed biofilm populations. As a case study, we present the characterization of Salmonella enterica/Listeria monocytogenes/Escherichia coli single, dual and tri-species biofilms in seven different support materials. Ex-situ, we were able to monitor quantitatively the populations of ∼56 mixed species biofilms up to 48 h, regardless of the support material. In situ, a correct quantification remained more elusive, but a qualitative understanding of biofilm structure and composition is clearly possible by confocal laser scanning microscopy (CLSM) at least up to 192 h. Combining the data obtained from PNA FISH/CLSM with data from other established techniques and from calculated microbial parameters, we were able to develop a model for this tri-species biofilm. The higher growth rate and exopolymer production ability of E. coli probably led this microorganism to outcompete the other two [average cell numbers (cells/cm2) for 48 h biofilm: E. coli 2,1×108 (±2,4×107); L. monocytogenes 6,8×107 (±9,4×106); and S. enterica 1,4×106 (±4,1×105)]. This overgrowth was confirmed by CSLM, with two well-defined layers being easily identified: the top one with E. coli, and the bottom one with mixed regions of L. monocytogenes and S. enterica. Significance While PNA FISH has been described previously for the qualitative study of biofilm populations, the present investigation demonstrates that it can also be used for the accurate quantification and spatial distribution of species in

  13. Combining fluorescent in situ hybridization data with ISS staging improves risk assessment in myeloma: an International Myeloma Working Group collaborative project

    PubMed Central

    Avet-Loiseau, H; Durie, BGM; Cavo, M; Attal, M; Gutierrez, N; Haessler, J; Goldschmidt, H; Hajek, R; Lee, JH; Sezer, O; Barlogie, B; Crowley, J; Fonseca, R; Testoni, N; Ross, F; Rajkumar, SV; Sonneveld, P; Lahuerta, J; Moreau, P; Morgan, G

    2014-01-01

    The combination of serum β2-microglobulin and albumin levels has been shown to be highly prognostic in myeloma as the International Staging System (ISS). The aim of this study was to assess the independent contributions of ISS stage and cytogenetic abnormalities in predicting outcomes. A retrospective analysis of international studies looking at both ISS and cytogenetic abnormalities was performed in order to assess the potential role of combining ISS stage and cytogenetics to predict survival. This international effort used the International Myeloma Working Group database of 12 137 patients treated worldwide for myeloma at diagnosis, of whom 2309 had cytogenetic studies and 5387 had analyses by fluorescent in situ hybridization (iFISH). Comprehensive analyses used 2642 patients with sufficient iFISH data available. Using the comprehensive iFISH data, combining both t(4;14) and deletion (17p), along with ISS stage, significantly improved the prognostic assessment in terms of progression-free survival and overall survival. The additional impact of patient age and use of high-dose therapy was also demonstrated. In conclusion, the combination of iFISH data with ISS staging significantly improves risk assessment in myeloma. PMID:23032723

  14. Combining fluorescent in situ hybridization data with ISS staging improves risk assessment in myeloma: an International Myeloma Working Group collaborative project.

    PubMed

    Avet-Loiseau, H; Durie, B G M; Cavo, M; Attal, M; Gutierrez, N; Haessler, J; Goldschmidt, H; Hajek, R; Lee, J H; Sezer, O; Barlogie, B; Crowley, J; Fonseca, R; Testoni, N; Ross, F; Rajkumar, S V; Sonneveld, P; Lahuerta, J; Moreau, P; Morgan, G

    2013-03-01

    The combination of serum β2-microglobulin and albumin levels has been shown to be highly prognostic in myeloma as the International Staging System (ISS). The aim of this study was to assess the independent contributions of ISS stage and cytogenetic abnormalities in predicting outcomes. A retrospective analysis of international studies looking at both ISS and cytogenetic abnormalities was performed in order to assess the potential role of combining ISS stage and cytogenetics to predict survival. This international effort used the International Myeloma Working Group database of 12 137 patients treated worldwide for myeloma at diagnosis, of whom 2309 had cytogenetic studies and 5387 had analyses by fluorescent in situ hybridization (iFISH). Comprehensive analyses used 2642 patients with sufficient iFISH data available. Using the comprehensive iFISH data, combining both t(4;14) and deletion (17p), along with ISS stage, significantly improved the prognostic assessment in terms of progression-free survival and overall survival. The additional impact of patient age and use of high-dose therapy was also demonstrated. In conclusion, the combination of iFISH data with ISS staging significantly improves risk assessment in myeloma.

  15. Comparison of in situ hybridization methods for the assessment of HER-2/neu gene amplification status in breast cancer using a tissue microarray

    PubMed Central

    Malicka-Durczak, Anna; Korski, Konstanty; Ibbs, Matthew

    2012-01-01

    Background This project compared HER-2/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool. Materials and methods A TMA was constructed using 121 breast cancer specimens, 6 cores from each specimen. Demonstration and assessment of HER-2/neu gene status was by FISH (Vysis Path) and CISH (DAKO Duo CISH). Results The 121 breast cancer specimens were divided into 3 groups by HER-2 status, as determined by immunohistochemistry. In the HER-2 negative group no amplification was observed in 36 out of 40 cases. 3 cases showed amplification by both methods and one by CISH alone. The equivocal HER-2 group showed no amplification in 30 out of 41 cases and amplification in 9 cases. One case was FISH negative CISH positive and one was discarded. In the HER-2 positive group, amplification was confirmed in 37 of the 40 cases by both methods. 3 cases were unsuitable for assessment. Conclusions This study indicated that CISH is a sensitive alternative to FISH in detecting HER2 gene amplification and may replace FISH in HER2 testing. Good agreement was observed between methods (98.5% – 119 out of 121 cases). Furthermore, as only 4 out of 121 cases were unsuitable for assessment (no signal or missing TMA cores) – it may be feasible to use TMA in diagnostics. PMID:24377000

  16. USE OF SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK TO ENDANGERED AND THREATENED FISHES

    EPA Science Inventory

    Surrogate species used in toxicity assessments must be carefully selected in order to be protective of listed species. At present, the rainbow trout is considered to be an acceptable surrogate for coldwater fishes. Similarly, the fathead minnow is considered to be an acceptable s...

  17. USE OF SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK TO ENDANGERED AND THREATENED FISHES

    EPA Science Inventory

    Surrogate species used in toxicity assessments must be carefully selected in order to be protective of listed species. At present, the rainbow trout is considered to be an acceptable surrogate for coldwater fishes. Similarly, the fathead minnow is considered to be an acceptable s...

  18. USING A FISH INDEX TO ASSESS HABITAT QUALITY IN NARRAGANSETT BAY, RHODE ISLAND

    EPA Science Inventory

    We developed an estuarine index of biotic integrity to assess habitat quality in Narragansett Bay, Rhode Island. Fish were collected at 18 fixed stations with a 61-m x 3.05-m beach seine once per month in July and August from 1988 to 1999. Stations were designated high or low qua...

  19. DETAILED ENDOCRINE ASSESSMENTS IN WILD FISH DOWNSTREAM OF PULP AND PAPER MILLS IN NORTHERN ALBERTA, CANADA

    EPA Science Inventory

    2001. Detailed Endocrine Assessments in Wild Fish Downstream of Pulp and Paper Mills in Northern Alberta, Canada (Abstract). In: Environmental Sciences in the 21st Century: Paradigms, Opportunities, and Challenges: Abstract Book: SETAC 21st Annual Meeting, 12-16 November 2000, N...

  20. GENETIC DIVERSITY OF STREAM FISH IN THE MID-ATLANTIC INTEGRATED ASSESSMENT AREA

    EPA Science Inventory

    In this report, we describe the results of research to assess the genetics of three stream fish species in the Mid-Atlantic region. This research had three specific goals. First, we sought to examine the utility of genetic analysis for purposes of taxonomic identification. Bioa...

  1. Assessing Changes in Amphibian Population Dynamics Following Experimental Manipulations of Introduced Fish

    Treesearch

    Karen L. Pope

    2008-01-01

    Sport-fish introductions are now recognized as an important cause of amphibian decline, but few researchers have quantified the demographic responses of amphibians to current options in fisheries management designed to minimize effects on sensitive amphibians. Demographic analyses with mark–recapture data allow researchers to assess the relative importance of...

  2. In prostate cancer needle biopsies, detections of PTEN loss by fluorescence in situ hybridization (FISH) and by immunohistochemistry (IHC) are concordant and show consistent association with upgrading.

    PubMed

    Picanço-Albuquerque, C G; Morais, C L; Carvalho, F L F; Peskoe, S B; Hicks, J L; Ludkovski, O; Vidotto, T; Fedor, H; Humphreys, E; Han, M; Platz, E A; De Marzo, A M; Berman, D M; Lotan, T L; Squire, J A

    2016-05-01

    The prognostic value of phosphatase and tensin homolog (PTEN) loss in prostate cancer has primarily been evaluated by either fluorescence in situ hybridization (FISH) or immunohistochemistry (IHC). Previously, we found that PTEN loss by IHC was associated with increased risk of upgrading from biopsy (Gleason 3 + 3) to prostatectomy (Gleason 7+). Now, using an evaluable subset of 111 patients with adjacent biopsy sections, we analyzed the association between PTEN deletion in cancer and the odds of upgrading by a highly sensitive and specific four-color FISH assay. We also compared the concordance of PTEN loss by IHC and PTEN deletion by FISH. PTEN deletion was found in 27 % (12/45) of upgraded cases compared with 11 % (7/66) of controls (P = 0.03). Cancers with PTEN deletions were more likely to be upgraded than those without deletions (adjusting for age odds ratio = 3.40, 95 % confidence interval 1.14-10.11). With respect to concordance, of 93 biopsies with PTEN protein detected by IHC, 89 (96 %) had no PTEN deletion by FISH, and of 18 biopsies without PTEN protein by IHC, 15 had homozygous or hemizygous PTEN deletion by FISH. Only 4 biopsies of the 93 (4 %) with PTEN protein intact had PTEN deletion by FISH. When the regions of uncertainty in these biopsies were systematically studied by FISH, intra-tumoral variation of PTEN deletion was found, which could account for variation in immunoreactivity. Thus, FISH provides a different approach to determining PTEN loss when IHC is uncertain. Both FISH and IHC are concordant, showing consistent positive associations between PTEN loss and upgrading.

  3. Assessing connectivity in salmonid fishes with DNA microsatellite markers

    Treesearch

    Helen Neville; Jason Dunham; Mary Peacock

    2006-01-01

    Connectivity is a key consideration for the management and conservation of any species, but empirical characterizations of connectivity can be extremely challenging. Assessments of connectivity require biologically realistic classifications of landscape structure (Kotliar and Wiens 1990), and an understanding of how landscape structure affects migration, dispersal, and...

  4. Systems Engineering Technology Readiness Assessment of Hybrid-Electric Technologies for Tactical Wheeled Vehicles

    DTIC Science & Technology

    2014-09-01

    ENGINEERING TECHNOLOGY READINESS ASSESSMENT OF HYBRID-ELECTRIC TECHNOLOGIES FOR TACTICAL WHEELED VEHICLES by Eddie E. McCown September 2014 Thesis...REPORT DATE September 2014 3. REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE SYSTEMS ENGINEERING TECHNOLOGY READINESS ASSESSMENT OF...HYBRID-ELECTRIC TECHNOLOGIES FOR TACTICAL WHEELED VEHICLES 5. FUNDING NUMBERS 6. AUTHOR(S) Eddie E. McCown 7. PERFORMING ORGANIZATION NAME(S) AND

  5. Assessment of dam effects on streams and fish assemblages of the conterminous USA.

    PubMed

    Cooper, Arthur R; Infante, Dana M; Daniel, Wesley M; Wehrly, Kevin E; Wang, Lizhu; Brenden, Travis O

    2017-02-20

    Despite the prevalence of damming as a global disturbance to river habitats, detailed reach-based assessments of the ecological effects of dams are lacking, particularly across large spatial extents. Using data from nearly 50,000 large dams, we assessed stream network fragmentation and flow alteration by large dams for streams of the conterminous USA. We developed 21 dam metrics characterizing a diversity of dam influences operating at both localized (e.g., distances-to-dams) and landscape scales (e.g., cumulative reservoir storage throughout stream networks) for every stream reach in the study region. We further evaluated how dams have affected stream fish assemblages within large ecoregions using more than 37,000 stream fish samples. Streams have been severely fragmented by large dams, with the number of stream segments increasing by 801% compared to free-flowing streams in the absence of dams and a staggering 79% of stream length is disconnected from their outlet (i.e., oceans and Great Lakes). Flow alteration metrics demonstrate a landscape-scale disturbance of dams, resulting in total upstream reservoir storage volumes exceeding estimated annual discharge volumes of many of the nation's largest rivers. Further, we show large-scale changes in fish assemblages with dams. Species adapted to lentic habitats increase with dams across the conterminous USA, while rheophils, lithophils, and intolerant fishes decrease with dams. Overall, fragmentation and flow alteration by dams have affected fish assemblages as much or more than other anthropogenic stressors, with dam effects generally increasing with stream size. Dam-induced stream fragmentation and flow alteration are critical natural resource issues. This study emphasizes the importance of considering dams as a landscape-scale disturbance to river habitats along with the need to assess differential effects that dams may have on river habitats and the fishes they support. Together, these insights are essential for

  6. CONTAMINATION OF FISH IN STREAMS OF THE MID-ATLANTIC REGION: AN APPROACH TO REGIONAL INDICATOR SELECTION AND WILDLIFE ASSESSMENT

    EPA Science Inventory

    The extent of contamination of fish in the Mid-Atlantic Region was evaluated as part of the U.S. Environmental Protection Agency's Monitoring and Assessment Program's regional assessment in 1993 through 1994. Fish assemblages from wadeable streams were dominated by small, short-...

  7. Three sympatric karyomorphs in the fish Astyanax fasciatus (Teleostei, Characidae) do not seem to hybridize in natural populations

    PubMed Central

    Ferreira-Neto, Maressa; Artoni, Roberto Ferreira; Vicari, Marcelo Ricardo; Moreira-Filho, Orlando; Camacho, Juan Pedro Martínez; Bakkali, Mohammed; de Oliveira, Claudio; Foresti, Fausto

    2012-01-01

    Abstract Ninety individuals of the characid fish Astyanax fasciatus (Cuvier, 1819) were collected at Água da Madalena stream (Botucatu, São Paulo, Brazil) and analyzed for diploid chromosome number 2n and karyotype composition as well as for the chromosomal location of the 5S and 18S ribosomal DNA (rDNA). Whereas no chromosome differences were associated with sex, three different karyomorphs with diploid chromosome numbers 2n=46, 2n=48 and 2n=50 were found. No intermediate 2n numbers were discovered. The 2n=50 karyomorph showed some differences in 18S rDNA location compared to the two other karyomorphs. Finally, all specimens with the 2n=46 karyomorph showed the presence of a partly heterochromatic macro supernumerary chromosome, which was absent in all individuals with the two other karyomorphs. All these results suggest that indviduals of the three different karyomorphs are not likely to hybridize in the examined populations. Our findings strongly suggest the presence of three separate species (sensu biological species concept) easily diagnosed on the basis of differences in the diploid chromosome numbers and other chromosomal markers. PMID:24260650

  8. Fluorescent in situ hybridization (FISH) and high resolution karyotype analysis reveal a novel inversion duplication of 10q

    SciTech Connect

    Czarnecki, P.; Dyke, D.L. Van; Dowling, P.K.

    1994-09-01

    A white male born with dysmorphic features, including upslanting palpebral fissures, bilateral simian creases, posteriorly rotated ears, bitemporal narrowing, frontal bossing, camptodactyly and head circumference and weight less than the 5th percentile was found to have a de novo add(10)(q26.1). High resolution karyotype analysis revealed a novel chromosomal abnormality: 46,XY,inv dup(10)(q26.3-q25.1). Fluorescent in situ hybridization using a chromosome 10-specific painting probe (Oncor, Inc.) confirmed that the extra material was derived from chromosome 10. Duplication of 10q24 or 10q25 is associated with characteristic craniofacial malformations, minor malformations of the hands and feet, major malformations of the heart, skeleton, and kidneys and severe mental retardation. Our patient, currently 7 months old, has many of the skeletal and craniofacial manifestations of other patients, but is developmentally normal at this early age. This is the first FISH confirmation of a 10q duplication and demonstrates the utility of this technology in addition to karyotype analysis. Molecular studies to determine the parental origin and extent of the duplication are in progress, since the apparent lack of developmental delay was unexpected. Identification of the origin of duplicated material will help assist in genetic counseling by further delineating new genetic syndromes.

  9. Techno-economic assessment of a hybrid solar receiver and combustor

    NASA Astrophysics Data System (ADS)

    Lim, Jin Han; Nathan, Graham; Dally, Bassam; Chinnici, Alfonso

    2016-05-01

    A techno-economic analysis is performed to compare two different configurations of hybrid solar thermal systems with fossil fuel backup to provide continuous electricity output. The assessment compares a Hybrid Solar Receiver Combustor (HSRC), in which the functions of a solar cavity receiver and a combustor are integrated into a single device with a reference conventional solar thermal system using a regular solar cavity receiver with a backup boiler, termed the Solar Gas Hybrid (SGH). The benefits of the integration is assessed by varying the size of the storage capacity and heliostat field while maintaining the same overall thermal input to the power block.

  10. Cell fusion as the formation mechanism of unreduced gametes in the gynogenetic diploid hybrid fish

    PubMed Central

    Wang, Jing; Liu, Qingfeng; Luo, Kaikun; Chen, Xuan; Xiao, Jun; Zhang, Chun; Tao, Min; Zhao, Rurong; Liu, Shaojun

    2016-01-01

    The gynogenetic diploid hybrid clone line (GDH) derived from red crucian carp (♀ RCC) × common carp (♂ CC) possesses the unusual reproductive trait of producing unreduced diploid eggs. To identify the mechanism underlying this phenomenon, we examined the structure, in vivo developmental process and in vitro dynamic development of the GDH gonad. In summary, compared with RCC and CC, GDH showed certain special straits. First, a high frequency (84.7%) of germ cell fusion occurred in gonadal tissue culture in vitro as observed by time-lapse microscopy. Second, microstructural and ultrastructural observation showed numerous binucleated and multinucleated germ cells in the gonad, providing evidence of germ cell fusion in vivo. By contrast, in the diploid RCC and CC ovaries, neither cell fusion nor multinucleated cells were observed during the development of gonads. Third, the ovary of GDH remained at stage I for 10 months, whereas those of RCC and CC remained at that stage for 2 months, indicating that the GDH germ cells underwent abnormal development before meiosis. This report is the first to demonstrate that cell fusion facilitates the formation of unreduced gametes in vertebrates, which is a valuable finding for both evolutionary biology and reproductive biology. PMID:27530321

  11. Detection of Inter-chromosomal Stable Aberrations by Multiple Fluorescence In Situ Hybridization (mFISH) and Spectral Karyotyping (SKY) in Irradiated Mice.

    PubMed

    Pathak, Rupak; Koturbash, Igor; Hauer-Jensen, Martin

    2017-01-11

    Ionizing radiation (IR) induces numerous stable and unstable chromosomal aberrations. Unstable aberrations, where chromosome morphology is substantially compromised, can easily be identified by conventional chromosome staining techniques. However, detection of stable aberrations, which involve exchange or translocation of genetic materials without considerable modification in the chromosome morphology, requires sophisticated chromosome painting techniques that rely on in situ hybridization of fluorescently labeled DNA probes, a chromosome painting technique popularly known as fluorescence in situ hybridization (FISH). FISH probes can be specific for whole chromosome/s or precise sub-region on chromosome/s. The method not only allows visualization of stable aberrations, but it can also allow detection of the chromosome/s or specific DNA sequence/s involved in a particular aberration formation. A variety of chromosome painting techniques are available in cytogenetics; here two highly sensitive methods, multiple fluorescence in situ hybridization (mFISH) and spectral karyotyping (SKY), are discussed to identify inter-chromosomal stable aberrations that form in the bone marrow cells of mice after exposure to total body irradiation. Although both techniques rely on fluorescent labeled DNA probes, the method of detection and the process of image acquisition of the fluorescent signals are different. These two techniques have been used in various research areas, such as radiation biology, cancer cytogenetics, retrospective radiation biodosimetry, clinical cytogenetics, evolutionary cytogenetics, and comparative cytogenetics.

  12. Towards Integration of Environmental and Health Impact Assessments for Wild Capture Fishing and Farmed Fish with Particular Reference to Public Health and Occupational Health Dimensions

    PubMed Central

    Watterson, Andrew; Little, David; Young, James A.; Boyd, Kathleen; Azim, Ekram; Murray, Francis

    2008-01-01

    The paper offers a review and commentary, with particular reference to the production of fish from wild capture fisheries and aquaculture, on neglected aspects of health impact assessments which are viewed by a range of international and national health bodies and development agencies as valuable and necessary project tools. Assessments sometimes include environmental health impact assessments but rarely include specific occupational health and safety impact assessments especially integrated into a wider public health assessment. This is in contrast to the extensive application of environmental impact assessments to fishing and the comparatively large body of research now generated on the public health effects of eating fish. The value of expanding and applying the broader assessments would be considerable because in 2004 the United Nations Food and Agriculture Organization reports there were 41,408,000 people in the total ‘fishing’ sector including 11,289,000 in aquaculture. The paper explores some of the complex interactions that occur with regard to fishing activities and proposes the wider adoption of health impact assessment tools in these neglected sectors through an integrated public health impact assessment tool. PMID:19190356

  13. A hybrid method for assessment of soil pollutants spatial distribution

    NASA Astrophysics Data System (ADS)

    Tarasov, D. A.; Medvedev, A. N.; Sergeev, A. P.; Shichkin, A. V.; Buevich, A. G.

    2017-07-01

    The authors propose a hybrid method to predict the distribution of topsoil pollutants (Cu and Cr). The method combines artificial neural networks and kriging. Corresponding computer models were built and tested on real data on example of subarctic regions of Russia. The network structure selection was based on the minimization of the Root-mean-square error between real and predicted concentrations. The constructed models show that the prognostic accuracy of the artificial neural network is higher than in case of the geostatistical (kriging) and deterministic methods. The conclusion is that hybridization of models (artificial neural network and kriging) provides the improvement of the total predictive accuracy.

  14. The 2014 FDA assessment of commercial fish: practical considerations for improved dietary guidance.

    PubMed

    McGuire, Jennifer; Kaplan, Jason; Lapolla, John; Kleiner, Rima

    2016-07-13

    The U.S. Food and Drug Administration (FDA) recently released its report: A Quantitative Assessment of the Net Effects on Fetal Neurodevelopment from Eating Commercial Fish (As Measured by IQ and also by Early Age Verbal Development in Children). By evaluating the benefits and potential concerns of eating fish during pregnancy and breastfeeding, the analysis suggests that pregnant women consuming two seafood meals (8-12 oz) per week could provide their child with an additional 3.3 IQ points by age 9. Recent insights from behavioral economics research indicate that other factors, such as concerns about price and methylmercury (MeHg) exposure, appear to reduce fish consumption in many individuals.To assess the net effects of eating commercial fish during pregnancy, we compared the consumption of select fish species necessary to achieve IQ benefits with the amount necessary to have adverse developmental effects due to MeHg exposure. For the species or market types evaluated, the number of servings necessary to reach MeHg exposure to observe an adverse effect was at least twice that the amount estimated to achieve peak developmental benefit. We then reported average costs of fresh and canned or pouched fish, and calculated the cost per week for pregnant women to achieve maximum IQ benefits for their gestating child. Canned light tuna was the least expensive option at $1.83 per week to achieve maximum IQ benefit.Due to their relatively low cost, canned and pouched fish products eaten with enough regularity are likely to provide peak cognitive benefits. Because of its popularity, canned and pouched tuna could provide some of the largest cognitive benefits from fish consumption in the U.S. Future FDA consumer advice and related educational initiatives could benefit from a broader perspective that highlights the importance of affordable and accessible fish choices. These observations underscore the importance of clear public health messaging that address both health

  15. Non-Hodgkin Lymphoma (NHL) subtypes defined by common translocations: utility of fluorescence in situ hybridization (FISH) in a case-control study

    PubMed Central

    Chang, Cindy M.; Schroeder, Jane C.; Huang, Wen-Yi; Dunphy, Cherie H.; Baric, Ralph S.; Olshan, Andrew F.; Dorsey, Kathleen C.; Dent, Georgette A.; Cerhan, James R.; Lynch, Charles F.; Rothman, Nathaniel; Cantor, Kenneth P.; Blair, Aaron

    2009-01-01

    We used fluorescence in situ hybridization (FISH) assays to identify t(14;18) translocations in archival paraffin-embedded tumor sections from non-Hodgkin lymphoma (NHL) cases enrolled in a population-based study. t(14;18) was identified in 54% of 152 cases, including 39% of diffuse large cell lymphomas (26 of 66 cases) and 84% of follicular lymphomas (36 of 43 cases). Eighty-seven percent of t(14;18)-positive cases and 57% of t(14;18)-negative cases expressed bcl-2. FISH assays detected twice as many t(14;18)-positive follicular lymphomas as PCR assays. Overall, study findings support the use of FISH assays to detect t(14;18) in archival tumor samples for epidemiologic studies of NHL subtypes. PMID:19505720

  16. Biodiversity Assessment of the Fishes of Saba Bank Atoll, Netherlands Antilles

    PubMed Central

    Williams, Jeffrey T.; Carpenter, Kent E.; Van Tassell, James L.; Hoetjes, Paul; Toller, Wes; Etnoyer, Peter; Smith, Michael

    2010-01-01

    Biodiversity surveys were conducted on Saba Bank, Netherlands Antilles, to assess ichthyofaunal richness and to compare with published surveys of other Caribbean localities. The primary objective was to estimate the total species richness of the Saba Bank ichthyofauna. A variety of sampling techniques was utilized to survey the fish species of both the visually accessible megafauna and the camouflaged and small-sized species comprising the cryptic ichthyofauna. Based on results presented herein, the number of species known on Saba Bank is increased from 42 previously known species to 270 species. Expected species-accumulation curves demonstrate that the current estimate of species richness of fishes for Saba Bank under represents the actual richness, and our knowledge of the ichthyofauna has not plateaued. The total expected fish-species richness may be somewhere between 320 and 411 species. The Saba Bank ichthyofaunal assemblage is compared to fish assemblages found elsewhere in the Caribbean. Despite the absence of shallow or emergent shore habitats like mangroves, Saba Bank ranks as having the eighth highest ichthyofaunal richness of surveyed localities in the Greater Caribbean. Some degree of habitat heterogeneity was evident. Fore-reef, patch-reef, and lagoonal habitats were sampled. Fish assemblages were significantly different between habitats. Species richness was highest on the fore reef, but 11 species were found only at lagoonal sites. A comprehensive, annotated list of the fishes currently known to occur on Saba Bank, Netherland Antilles, is provided and color photographs of freshly collected specimens are presented for 165 of the listed species of Saba Bank fishes to facilitate identification and taxonomic comparison with similar taxa at other localities. Coloration of some species is shown for the first time. Preliminary analysis indicates that at least six undescribed new species were collected during the survey and these are indicated in the

  17. Biodiversity assessment of the fishes of Saba Bank atoll, Netherlands Antilles.

    PubMed

    Williams, Jeffrey T; Carpenter, Kent E; Van Tassell, James L; Hoetjes, Paul; Toller, Wes; Etnoyer, Peter; Smith, Michael

    2010-05-21

    Biodiversity surveys were conducted on Saba Bank, Netherlands Antilles, to assess ichthyofaunal richness and to compare with published surveys of other Caribbean localities. The primary objective was to estimate the total species richness of the Saba Bank ichthyofauna. A variety of sampling techniques was utilized to survey the fish species of both the visually accessible megafauna and the camouflaged and small-sized species comprising the cryptic ichthyofauna.Based on results presented herein, the number of species known on Saba Bank is increased from 42 previously known species to 270 species. Expected species-accumulation curves demonstrate that the current estimate of species richness of fishes for Saba Bank under represents the actual richness, and our knowledge of the ichthyofauna has not plateaued. The total expected fish-species richness may be somewhere between 320 and 411 species.The Saba Bank ichthyofaunal assemblage is compared to fish assemblages found elsewhere in the Caribbean. Despite the absence of shallow or emergent shore habitats like mangroves, Saba Bank ranks as having the eighth highest ichthyofaunal richness of surveyed localities in the Greater Caribbean. Some degree of habitat heterogeneity was evident. Fore-reef, patch-reef, and lagoonal habitats were sampled. Fish assemblages were significantly different between habitats. Species richness was highest on the fore reef, but 11 species were found only at lagoonal sites.A comprehensive, annotated list of the fishes currently known to occur on Saba Bank, Netherland Antilles, is provided and color photographs of freshly collected specimens are presented for 165 of the listed species of Saba Bank fishes to facilitate identification and taxonomic comparison with similar taxa at other localities. Coloration of some species is shown for the first time. Preliminary analysis indicates that at least six undescribed new species were collected during the survey and these are indicated in the annotated

  18. FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry

    PubMed Central

    Arrigucci, Riccardo; Bushkin, Yuri; Radford, Felix; Lakehal, Karim; Vir, Pooja; Pine, Richard; Martin, December; Sugarman, Jeffrey; Zhao, Yanlin; Yap, George S; Lardizabal, Alfred A; Tyagi, Sanjay; Gennaro, Maria Laura

    2017-01-01

    We describe a flow-cytometry-based protocol for intracellular mRNA measurements in nonadherent mammalian cells using fluorescence in situ hybridization (FISH) probes. The method, which we call FISH-Flow, allows for high-throughput multiparametric measurements of gene expression, a task that was not feasible with earlier, microscopy-based approaches. The FISH-Flow protocol involves cell fixation, permeabilization and hybridization with a set of fluorescently labeled oligonucleotide probes. In this protocol, surface and intracellular protein markers can also be stained with fluorescently labeled antibodies for simultaneous protein and mRNA measurement. Moreover, a semiautomated, single-tube version of the protocol can be performed with a commercially available cell-wash device that reduces cell loss, operator time and interoperator variability. It takes ~30 h to perform this protocol. An example of FISH-Flow measurements of cytokine mRNA induction by ex vivo stimulation of primed T cells with specific antigens is described. PMID:28518171

  19. Assessing risks to fish populations near a proposed disposal facility for used nuclear fuel

    SciTech Connect

    Hart, D.; Miesenheimer, P.; Hull, R.

    1995-12-31

    The concept of used nuclear fuel disposal in the Canadian Shield is currently undergoing a federal environmental assessment review process. As part of this review, potential risks to brook trout populations in the vicinity of such an underground repository were considered. Chemical fate, transport and exposure models have been utilized to estimate the dose rates from released radionuclides and other fuel constituents, and these likely will not be sufficient to harm fish in nearby streams. However, other stressors such as habitat alteration (e.g., loss of upwelling) and/or fishing pressure associated with increased public access could have significant population impacts if the site is located in a pristine northern region. Population models are utilized to explore the risks of local population reduction for different combinations of fishing pressure and habitat degradation.

  20. Development of automated brightfield double In Situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) for breast carcinomas and an assay performance comparison to manual dual color HER2 fluorescence In Situ hybridization (FISH)

    PubMed Central

    Nitta, Hiroaki; Hauss-Wegrzyniak, Beatrice; Lehrkamp, Megan; Murillo, Adrian E; Gaire, Fabien; Farrell, Michael; Walk, Eric; Penault-Llorca, Frederique; Kurosumi, Masafumi; Dietel, Manfred; Wang, Lin; Loftus, Margaret; Pettay, James; Tubbs, Raymond R; Grogan, Thomas M

    2008-01-01

    Background Human epidermal growth factor receptor 2 (HER2) fluorescence in situ hybridization (FISH) is a quantitative assay for selecting breast cancer patients for trastuzumab therapy. However, current HER2 FISH procedures are labor intensive, manual methods that require skilled technologists and specialized fluorescence microscopy. Furthermore, FISH slides cannot be archived for long term storage and review. Our objective was to develop an automated brightfield double in situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) and test the assay performance with dual color HER2 FISH evaluated breast carcinomas. Methods The BDISH assay was developed with the nick translated dinitrophenyl (DNP)-labeled HER2 DNA probe and DNP-labeled CEN 17 oligoprobe on the Ventana BenchMark® XT slide processing system. Detection of HER2 and CEN 17 signals was accomplished with the silver acetate, hydroquinone, and H2O2 reaction with horseradish peroxidase (HRP) and the fast red and naphthol phosphate reaction with alkaline phosphatise (AP), respectively. The BDISH specificity was optimized with formalin-fixed, paraffin-embedded xenograft tumors, MCF7 (non-amplified HER2 gene) and BT-474 (amplified HER2 gene). Then, the BDISH performance was evaluated with 94 routinely processed breast cancer tissues. Interpretation of HER2 and CEN 17 BDISH slides was conducted by 4 observers using a conventional brightfield microscope without oil immersion objectives. Results Sequential hybridization and signal detection for HER2 and CEN 17 ISH demonstrated both DNA targets in the same cells. HER2 signals were visualized as discrete black metallic silver dots while CEN 17 signals were detected as slightly larger red dots. Our study demonstrated a high consensus concordance between HER2 FISH and BDISH results of clinical breast carcinoma cases based on the historical scoring method (98.9%, Simple Kappa = 0.9736, 95% CI = 0.9222 – 1.0000) and the ASCO

  1. Exploratory assessment of fish consumption among Asian-origin sportfishers on the St. Lawrence River in the Montreal region

    SciTech Connect

    Shatenstein, B. |; Kosatsky, T.; Tapia, M.; Nadon, S.; Leclerc, B.S.

    1999-02-01

    An exploratory survey was undertaken in the fall 1995 open-water fishing seasons with nine Bangladeshi and nine Vietnamese-origin sportfishers. A 70-item instrument assessing sportfishing practices and fish consumption habits was administered by dietitians in participants` homes. Two 24-h diet recalls and a fish consumption calendar permitted the assessment of fish intake in the overall dietary context. Annually, Bangladeshi fishers consumed 46.8 {+-} 25.6 sportfish meals, and Vietnamese fishers ate 40.7 {+-} 35.1 meals. Consumption of sportfish taken from the St. Lawrence River has the potential both for dietary benefit and for hazardous chemical exposure.

  2. Nutrient enrichment and fish nutrient tolerance: Assessing biologically relevant nutrient criteria

    USGS Publications Warehouse

    Meador, Michael R.

    2013-01-01

    Relationships between nutrient concentrations and fish nutrient tolerance were assessed relative to established nutrient criteria. Fish community, nitrate plus nitrite (nitrate), and total phosphorus (TP) data were collected during summer low-flow periods in 2003 and 2004 at stream sites along a nutrient-enrichment gradient in an agricultural basin in Indiana and Ohio and an urban basin in the Atlanta, Georgia, area. Tolerance indicator values for nitrate and TP were assigned for each species and averaged separately for fish communities at each site (TIVo). Models were used to predict fish species expected to occur at a site under minimally disturbed conditions and average tolerance indicator values were determined for nitrate and TP separately for expected communities (TIVe). In both areas, tolerance scores (TIVo/TIVe) for nitrate increased significantly with increased nitrate concentrations whereas no significant relationships were detected between TP tolerance scores and TP concentrations. A 0% increase in the tolerance score (TIVo/TIVe = 1) for nitrate corresponded to a nitrate concentration of 0.19 mg/l (compared with a USEPA summer nitrate criterion of 0.17 mg/l) in the urban area and 0.31 mg/l (compared with a USEPA summer nitrate criterion of 0.86 mg/l) in the agricultural area. Fish nutrient tolerance values offer the ability to evaluate nutrient enrichment based on a quantitative approach that can provide insights into biologically relevant nutrient criteria.

  3. Threshold-dependent sample sizes for selenium assessment with stream fish tissue.

    PubMed

    Hitt, Nathaniel P; Smith, David R

    2015-01-01

    Natural resource managers are developing assessments of selenium (Se) contamination in freshwater ecosystems based on fish tissue concentrations. We evaluated the effects of sample size (i.e., number of fish per site) on the probability of correctly detecting mean whole-body Se values above a range of potential management thresholds. We modeled Se concentrations as gamma distributions with shape and scale parameters fitting an empirical mean-to-variance relationship in data from southwestern West Virginia, USA (63 collections, 382 individuals). We used parametric bootstrapping techniques to calculate statistical power as the probability of detecting true mean concentrations up to 3 mg Se/kg above management thresholds ranging from 4 to 8 mg Se/kg. Sample sizes required to achieve 80% power varied as a function of management thresholds and Type I error tolerance (α). Higher thresholds required more samples than lower thresholds because populations were more heterogeneous at higher mean Se levels. For instance, to assess a management threshold of 4 mg Se/kg, a sample of eight fish could detect an increase of approximately 1 mg Se/kg with 80% power (given α=0.05), but this sample size would be unable to detect such an increase from a management threshold of 8 mg Se/kg with more than a coin-flip probability. Increasing α decreased sample size requirements to detect above-threshold mean Se concentrations with 80% power. For instance, at an α-level of 0.05, an 8-fish sample could detect an increase of approximately 2 units above a threshold of 8 mg Se/kg with 80% power, but when α was relaxed to 0.2, this sample size was more sensitive to increasing mean Se concentrations, allowing detection of an increase of approximately 1.2 units with equivalent power. Combining individuals into 2- and 4-fish composite samples for laboratory analysis did not decrease power because the reduced number of laboratory samples was compensated for by increased precision of composites

  4. Assessment of fish abundance and species composition at selected sites in South Dakota: an overview

    USGS Publications Warehouse

    Harwood, Alison

    2010-01-01

    The U.S. Geological Survey (USGS) conducted surveys of streams throughout the State of South Dakota during 2008-09 as part of the U.S. Environmental Protection Agency?s (USEPA) National Rivers and Streams Assessment (NRSA) Program. During 2008-09, as part of the stream assessment, the USGS completed surveys of fish populations and species composition at 64 sites. Fish were inventoried at 60 of the 64 sites, but not at four of the sites because water was too low to sustain fish or specific conductivity was too high to electroshock effectively. Four of the sites were surveyed in 2000-04 during the USEPA's Environmental Monitoring and Assessment Program-West (EMAP-West) project. Two wadeable sites and two boatable sites were revisited for quality-assurance/quality-control requirements. During the study, both wadeable and boatable streams were sampled using electrofishing equipment and methods. Of the 64 sites, 62 were wadeable and 2 were boatable. Procedures for sampling wadeable streams differed slightly from procedures for boatable streams. Backpack electrofishing equipment was used for wadeable streams, whereas boat electrofishing equipment was used for boatable streams. Wadeable streams also were fished in an opposite direction than boatable streams. Several species of fish were collected during the NRSA. Species diversity ranged from 0-11 species in wadeable streams and from 6-26 species in boatable streams. Many common species were sampled during the study. The most frequently sampled fish was the sand shiner (Notropis stramineus), with 609 individuals sampled. In contrast, only one heritage species, the skipjack herring (Alosa chrysochloris), was identified during 2008-09. Common anomalies found in fish caught were parasitic lesions, "black spot disease," and tumors. When comparing the fish sampling results for the four sites visited in both 2000-04 and in 2008-09, more individuals and species were collected during 2008-09 than in 2000-04 at two sites, whereas

  5. Threshold-dependent sample sizes for selenium assessment with stream fish tissue

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Smith, David R.

    2015-01-01

    Natural resource managers are developing assessments of selenium (Se) contamination in freshwater ecosystems based on fish tissue concentrations. We evaluated the effects of sample size (i.e., number of fish per site) on the probability of correctly detecting mean whole-body Se values above a range of potential management thresholds. We modeled Se concentrations as gamma distributions with shape and scale parameters fitting an empirical mean-to-variance relationship in data from southwestern West Virginia, USA (63 collections, 382 individuals). We used parametric bootstrapping techniques to calculate statistical power as the probability of detecting true mean concentrations up to 3 mg Se/kg above management thresholds ranging from 4 to 8 mg Se/kg. Sample sizes required to achieve 80% power varied as a function of management thresholds and Type I error tolerance (α). Higher thresholds required more samples than lower thresholds because populations were more heterogeneous at higher mean Se levels. For instance, to assess a management threshold of 4 mg Se/kg, a sample of eight fish could detect an increase of approximately 1 mg Se/kg with 80% power (given α = 0.05), but this sample size would be unable to detect such an increase from a management threshold of 8 mg Se/kg with more than a coin-flip probability. Increasing α decreased sample size requirements to detect above-threshold mean Se concentrations with 80% power. For instance, at an α-level of 0.05, an 8-fish sample could detect an increase of approximately 2 units above a threshold of 8 mg Se/kg with 80% power, but when α was relaxed to 0.2, this sample size was more sensitive to increasing mean Se concentrations, allowing detection of an increase of approximately 1.2 units with equivalent power. Combining individuals into 2- and 4-fish composite samples for laboratory analysis did not decrease power because the reduced number of laboratory samples was compensated for by increased

  6. Indices for assessing coral reef fish biodiversity: the need for a change in habits.

    PubMed

    Loiseau, Nicolas; Gaertner, Jean-Claude

    2015-09-01

    We present the first representative and quantified overview of the indices used worldwide for assessing the biodiversity of coral reef fishes. On this basis, we discuss the suitability and drawbacks of the indices most widely used in the assessment of coral fish biodiversity. An extensive and systematic survey of the literature focused on coral reef fish biodiversity was conducted from 1990 up to the present. We found that the multicomponent aspect of biodiversity, which is considered as a key feature of biodiversity for numerous terrestrial and marine ecosystems, has been poorly taken into account in coral reef fish studies. Species richness is still strongly dominant while other diversity components, such as functional diversity, are underestimated even when functional information is available. We also demonstrate that the reason for choosing particular indices is often unclear, mainly based on empirical rationales and/or the reproduction of widespread habits, but generally with no clear relevance with regard to the aims of the studies. As a result, the most widely used indices (species richness, Shannon, etc.) would appear to be poorly suited to meeting the main challenges facing the monitoring of coral reef fish biodiversity in the future. Our results clearly show that coral reef scientists should rather take advantage of the multicomponent aspect of biodiversity. To facilitate this approach, we propose general guidelines to serve as a basis for the selection of indices that provide complementary and relevant information for monitoring the response of coral reef fish biodiversity in the face of structuring factors (natural or anthropic). The aim of these guidelines was to achieve a better match between the properties of the selected indices and the context of each study (e.g. expected effect of the main structuring factors, nature of data available).

  7. A fish-based index of biotic integrity to assess intermittent headwater streams in Wisconsin, USA.

    PubMed

    Lyons, John

    2006-11-01

    I developed a fish-based index of biotic integrity (IBI) to assess environmental quality in intermittent headwater streams in Wisconsin, USA. Backpack electrofishing and habitat surveys were conducted four times on 102 small (watershed area 1.7-41.5 km(2)), cool or warmwater (maximum daily mean water temperature > or = 22 C), headwater streams in spring and late summer/fall 2000 and 2001. Despite seasonal and annual changes in stream flow and habitat volume, there were few significant temporal trends in fish attributes. Analysis of 36 least-impacted streams indicated that fish were too scarce to calculate an IBI at stations with watershed areas less than 4 km(2) or at stations with watershed areas from 4-10 km(2) if stream gradient exceeded 10 m/km (1% slope). For streams with sufficient fish, potential fish attributes (metrics) were not related to watershed size or gradient. Seven metrics distinguished among streams with low, agricultural, and urban human impacts: numbers of native, minnow (Cyprinidae), headwater-specialist, and intolerant (to environmental degradation) species; catches of all fish excluding species tolerant of environmental degradation and of brook stickleback (Culaea inconstans) per 100 m stream length; and percentage of total individuals with deformities, eroded fins, lesions, or tumors. These metrics were used in the final IBI, which ranged from 0 (worst) to 100 (best). The IBI accurately assessed the environmental quality of 16 randomly chosen streams not used in index development. Temporal variation in IBI scores in the absence of changes in environmental quality was not related to season, year, or type of human impact and was similar in magnitude to variation reported for other IBI's.

  8. Assessing Historical Fish Community Composition Using Surveys, Historical Collection Data, and Species Distribution Models

    PubMed Central

    Labay, Ben; Cohen, Adam E.; Sissel, Blake; Hendrickson, Dean A.; Martin, F. Douglas; Sarkar, Sahotra

    2011-01-01

    Accurate establishment of baseline conditions is critical to successful management and habitat restoration. We demonstrate the ability to robustly estimate historical fish community composition and assess the current status of the urbanized Barton Creek watershed in central Texas, U.S.A. Fish species were surveyed in 2008 and the resulting data compared to three sources of fish occurrence information: (i) historical records from a museum specimen database and literature searches; (ii) a nearly identical survey conducted 15 years earlier; and (iii) a modeled historical community constructed with species distribution models (SDMs). This holistic approach, and especially the application of SDMs, allowed us to discover that the fish community in Barton Creek was more diverse than the historical data and survey methods alone indicated. Sixteen native species with high modeled probability of occurrence within the watershed were not found in the 2008 survey, seven of these were not found in either survey or in any of the historical collection records. Our approach allowed us to more rigorously establish the true baseline for the pre-development fish fauna and then to more accurately assess trends and develop hypotheses regarding factors driving current fish community composition to better inform management decisions and future restoration efforts. Smaller, urbanized freshwater systems, like Barton Creek, typically have a relatively poor historical biodiversity inventory coupled with long histories of alteration, and thus there is a propensity for land managers and researchers to apply inaccurate baseline standards. Our methods provide a way around that limitation by using SDMs derived from larger and richer biodiversity databases of a broader geographic scope. Broadly applied, we propose that this technique has potential to overcome limitations of popular bioassessment metrics (e.g., IBI) to become a versatile and robust management tool for determining status of

  9. Assessment of insect and bird damage on grain sorghum hybrids

    USDA-ARS?s Scientific Manuscript database

    Thirty seven commercial grain sorghum hybrids were evaluated for insect and bird damage in 2014. All insect and bird damage on sorghum plants were monitored throughout the season. The key pest damage was rated at pre-harvest. An outbreak of sugarcane aphid occurred in southern Georgia in 2014 for...

  10. Spatially explicit assessment of estuarine fish after Deepwater ...

    EPA Pesticide Factsheets

    Evaluating long- term contaminant effects on wildlife populations depends on spatial information about habitat quality, heterogeneity in contaminant exposure, and sensitivities and distributions of species integrated into a systems modeling approach. Rarely is this information readily available, making it difficult to determine the applicability of realistic models to quantify population- level risks. To evaluate the trade- offs between data demands and increased specificity of spatially explicit models for population- level risk assessments, we developed a model for a standard toxicity test species, the sheepshead minnow (Cyprinodon variegatus), exposed to oil contamination following the Deepwater Horizon oil spill and compared the output with various levels of model complexity to a standard risk quotient approach. The model uses habitat and fish occupancy data collected over five sampling periods throughout 2008–2010 in Pensacola and Choctawhatchee Bays, Florida, USA, to predict species distribution, field- collected and publically available data on oil distribution and concentration, and chronic toxicity data from laboratory assays applied to a matrix population model. The habitat suitability model established distribution of fish within Barataria Bay, Louisiana, USA, and the population model projected the dynamics of the species in the study area over a 5- yr period (October 2009–September 2014). Vital rates were modified according to estimated co

  11. Assessment of the St. Louis River AOC fish tumors and other ...

    EPA Pesticide Factsheets

    The Fish Tumors and Other Deformities Beneficial Use Impairment (BUI) was listed as one of nine BUIs at the time the St. Louis River AOC was designated in 1987. At the time, no formal studies had been conducted to estimate the prevalence of either fish tumors or deformities. To assess the current status of fish tumors and deformities in the AOC, adult white suckers (Catostomus commersonii) were sampled during the spawning period in May during 2011, 2013 and 2015. We measured each fish, determined its sex and age (sagittal otolith), sampled dorsal muscle tissue for carbon and nitrogen stable isotope ratios to determine river versus lake residency, and conducted a necropsy-based assessment to document grossly visible abnormalities. Pieces of any observable abnormalities were preserved for subsequent histological analyses. A total of 622 white sucker were surveyed from 2011 through 2015. Of these, 27 (4.3%) white suckers had skin neoplasms, all of which were papillomas. A total of 29 (4.7%) of the white suckers had liver neoplasms. Sex and age were significantly associated with skin neoplasia incidence, whereas only age was significantly associated with liver neoplasia incidence. Neither neoplasia type was significantly associated with habitat use, indicating that neoplasia incidence did not change with increasing feeding in the AOC relative to Lake Superior. Further, there was not a significant difference in skin or liver neoplasia incidence between migratory whit

  12. The use of tumors in wild populations of fish to assess ecosystem health

    USGS Publications Warehouse

    Baumann, Paul C.

    1992-01-01

    Evidence has linked toxicants in aquatic systems with cancer in fish and population level effects on species. Thus some types of tumors may be useful monitors of ecosystem health, at least as affected by genotoxins and promoters. However, tumors caused by purely genetic mechanisms or by virus would not be good indicators. Only neoplasms which have chemicals as a portion of their etiology (either as initiators or promoters) would be useful in assessing ecosystem health. Lesions which may fit these criteria include liver neoplasms (both biliary and hepatic) and skin lesions in a variety of primarily benthic fishes, and neural lesions in various drum species and in butterfly fish species. Two studies purporting to demonstrate a lack of tumors in fish from polluted areas have been reexamined and found either to have insufficient data on vulnerable species or to actually support a tumor-pollution linkage. Thus certain lesions in vulnerable species or species groups may serve as a mechanism to assess one facet of ecosystem health.

  13. An integrative approach to assess ecological risks of surface water contamination for fish populations.

    PubMed

    Santos, Raphael; Joyeux, Aude; Besnard, Aurélien; Blanchard, Christophe; Halkett, Cédric; Bony, Sylvie; Sanchez, Wilfried; Devaux, Alain

    2017-01-01

    Contamination of aquatic ecosystems is considered as one of the main threats to global freshwater biodiversity. Within the European Water Framework Directive (EU-WFD) a particular attention is dedicated to assess ecological risks of surface water contamination and mitigation of chemical pressures on aquatic ecosystems. In this work, we evaluated ecological risks of surface water contamination for fish populations in four EU-WFD rivers through an integrative approach investigating three Lines of Evidence (chemical contamination, biomarker responses as early warning signals of contamination impacting individuals and ecological analyses as an indicator of fish community disturbances). This work illustrates through 4 case studies the complementary role of biomarkers, chemical and ecological analyses which, used in combination, provide fundamental information to understand impacts of chemical pressures that can affect fish population dynamics. We discuss the limitations of this approach and future improvements needed within the EU-WFD to assess ecological risk of river contamination for fish populations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Assessment of the St. Louis River AOC fish tumors and other ...

    EPA Pesticide Factsheets

    The Fish Tumors and Other Deformities Beneficial Use Impairment (BUI) was listed as one of nine BUIs at the time the St. Louis River AOC was designated in 1987. At the time, no formal studies had been conducted to estimate the prevalence of either fish tumors or deformities. To assess the current status of fish tumors and deformities in the AOC, adult white suckers (Catostomus commersonii) were sampled during the spawning period in May during 2011, 2013 and 2015. We measured each fish, determined its sex and age (sagittal otolith), sampled dorsal muscle tissue for carbon and nitrogen stable isotope ratios to determine river versus lake residency, and conducted a necropsy-based assessment to document grossly visible abnormalities. Pieces of any observable abnormalities were preserved for subsequent histological analyses. A total of 622 white sucker were surveyed from 2011 through 2015. Of these, 27 (4.3%) white suckers had skin neoplasms, all of which were papillomas. A total of 29 (4.7%) of the white suckers had liver neoplasms. Sex and age were significantly associated with skin neoplasia incidence, whereas only age was significantly associated with liver neoplasia incidence. Neither neoplasia type was significantly associated with habitat use, indicating that neoplasia incidence did not change with increasing feeding in the AOC relative to Lake Superior. Further, there was not a significant difference in skin or liver neoplasia incidence between migratory whit

  15. [Rapid ecological assessment of tropical fish communities in a gold mine area of Costa Rica].

    PubMed

    Espinoza Mendiola, Mario

    2008-12-01

    Gold mining impacts have generated a great concern regarding aquatic systems and habitat fragmentation. Anthropogenic disturbances on the structure and heterogeneity of a system can have an important effect on aquatic community stability. Ecological rapid assessments (1996, 2002, and 2007) were employed to determine the structure, composition and distribution of tropical fish communities in several rivers and smaller creeks from a gold mining area in Cerro Crucitas, Costa Rica. In addition, species composition and relative abundance were related with habitat structure. A total of 35 species were registered, among which sardine Astyanax aeneus (Characidae) and livebearer Alfaro cultratus (Poeciliidae) were the most abundant fish (71%). The highest species richness was observed in Caño Crucitas (s=19) and Minas Creek (s=18). Significant differences in fish communities structure and composition from Infiernillo river and Minas creek were observed (lamda = 0.0, F(132, 66) = 2.24, p < 0.001). Presence and/or absence of certain species such as Dormitor gobiomorus, Rhamdia nicaraguensis, Parachromis loiseillei and Atractosteus tropicus explained most of the spatial variation among sites. Habitat structure also contributed to explain differences among sites (lamda = 0.004, F(60.183) = 5.52, p < 0.001). Substratum (soft and hard bottom types) and habitat attributes (elevation, width and depth) explained most of the variability observed in Infiernillo River, Caño Crucitas and Tamagá Creek. In addition, a significant association between fish species and habitat structure was observed. This study reveals a high complexity in tropical fish communities that inhabit a gold mine area. Furthermore, it highlights the importance of habitat heterogeneity in fish community dynamics. The loss and degradation of aquatic systems in Cerro Crucitas can have a strong negative effect on fish community structure and composition of local species. A better understanding of the use of specific

  16. Mercury concentration in meconium and risk assessment of fish consumption among pregnant women in Taiwan.

    PubMed

    Jiang, Chuen-Bin; Yeh, Ching-Ying; Lee, Hung-Chang; Chen, Ming-Jun; Hung, Fang-Yu; Fang, Sheng-Shiung; Chien, Ling-Chu

    2010-01-01

    Meconium is a matrix that can be obtained easily and noninvasively and is useful for detecting antenatal fetal exposure to environmental toxins. Taiwan is an island with high fish consumption, and many pregnant women would like to enjoy the benefits of fish without jeopardizing their health or that of their child. The aim of this study is to assess the mercury concentration in meconium in relation to the health risk of mercury exposure. A total of 198 mother-infant pairs residing in the city of HsinChu were recruited for the study between January 2007 and June 2007. The average mean concentration of mercury in meconium was 79.2+/-7.3 ng g(-1) dry wt We use the Monte Carlo technique to assess the uncertainty in risk assessment and the impact of these uncertainties on the estimation of expected risk of mercury intake from fish in mothers. Based on the FAO/WHO's tolerable daily intake of methylmercury (0.23 microg kg(-1)d(-1)), we found that 17.3% and 14.0% of the daily mercury exposure estimated exceeded the reference dose for foreign-born and Taiwan-born mothers, respectively. We found that the mercury concentration in meconium was much higher than in other studies, except for one study done in Tagum in the Philippines where mercury is used in gold mining. This may be because Asia is the largest emitter of anthropogenic mercury, accounting for 53% of worldwide emissions. Sensitivity analysis suggests that mercury concentration in fish and the rate of ingesting fish may be the key parameters for governments offering risk management guidance to protect the health of mothers and unborn babies.

  17. Multi-Ecosystem Assessment of Mercury Bioaccumulation in Fishes: Habitat, Landscape, and Biogeochemical Drivers of Fish Mercury

    NASA Astrophysics Data System (ADS)

    Eagles-Smith, C.; Ackerman, J.; Herring, G.; Willacker, J.; Flanagan, C.

    2014-12-01

    Mercury (Hg) is a globally distributed contaminant that threatens ecosystem health across aquatic environments. The complexity of the Hg cycle and its primary drivers, coupled with dynamic food web processes that govern biomagnification, result in marked spatial variability in Hg bioaccumulation across aquatic ecosystems. However, it is unclear if patterns of bioaccumulation are consistent in magnitude and direction across ecosystem types. We synthesized data from several studies spanning more than 200 individual sites, comprising four distinct ecosystem classifications (estuaries, sub-alpine lakes, rivers, and managed wetlands). Within each ecosystem, we compared fish Hg concentrations among replicated sub-habitats and also evaluated the influence of land use, landscape composition, and biogeochemical drivers on fish Hg concentrations. We found substantial variability in fish Hg concentrations among adjacent sub-habitats within ecosystems. In estuarine environments, fish Hg concentrations were 7.4x higher in seasonal-saline wetlands than adjacent tidal wetland habitats. In riverine alcoves, preliminary data suggest that fish Hg concentrations were 1.5x higher than in fishes from paired mainstem river habitat. Among managed wetland habitats, fish Hg concentrations in rice fields were 2x higher than those in managed seasonal wetlands that were subjected to identical wetting and drying patterns. Across ecosystems, dissolved organic carbon (DOC) concentrations in surface waters were consistently correlated with fish Hg concentrations, highlighting its importance in Hg methylation and transport processes. Yet, the strength and direction of the relationships varied among habitat types. For example, fish Hg concentrations were positively correlated with DOC concentrations in riverine environments, whereas we found a negative correlation in alpine lakes. Instead, the most important determinant of fish Hg concentrations in alpine lakes was conifer tree density within a

  18. Comparison of high resolution chromosome banding and fluorescence in situ hybridization (FISH) for the laboratory evaluation of Prader-Willi syndrome and Angelman syndrome

    SciTech Connect

    Delach, J.A.; Rosengren, S.S.; Kaplan, L.; Greenstein, R.M.; Cassidy, S.B.; Benn, P.A.

    1994-08-01

    The development of probes containing segments of DNA from chromosome region 15q11-q13 provides the opportunity to confirm the diagnosis of Prader-Willi syndrome (PWS) and Angelman syndrome (AS) by fluorescence in situ hybridization (FISH). We have evaluated FISH studies and high resolution chromosome banding studies in 14 patients referred to confirm or rule out AS. In four patients (three from the PWS category and 1 from the AS group) chromosome analysis suggested that a deletion was present but FISH failed to confirm the finding. In one AS group patient, FISH identified a deletion not detectable by high resolution banding. Review of the clinical findings in the discrepant cases suggested that FISH results were correct and high resolution findings were erroneous. Studies with a chromosome 15 alpha satellite probe (D15Z) on both normal and abnormal individuals suggested that incorrect interpretation of chromosome banding may occasionally be attributable to alpha satellite polymorphism but other variation of 15q11-q13 chromosome bands also contributes to misinterpretation. We conclude that patients who have been reported to have a cytogenetic deletion of 15q11-q13 and who have clinical findings inconsistent with PWS and AS should be re-evaluated by molecular genetic techniques. 31 refs., 3 figs., 2 tabs.

  19. mRNA-targeted Fluorescent in Situ Hybridization (FISH) of Gram-negative Bacteria Without Template Amplification or Tyramide Signal Amplification

    SciTech Connect

    Coleman, James R.; Culley, David E.; Chrisler, William B.; Brockman, Fred J.

    2007-12-01

    Technologies are needed to study gene expression at the level of individual cells within a population or microbial community. Fluorescent in situ hybridization (FISH) supplies high-resolution spatial information and has been widely applied to study microbial communities at the rRNA level. While mRNA-targeted FISH has been popular for studying gene expression in eukaryotic cells, very little success has been achieved with prokaryotes. At present, detection of specific mRNAs in individual prokaryotic cells requires the use of in situ-RT-PCR or tyramide signal amplification (TSA). In this study we used DNA oligonucleotide probes labeled with a single near-infrared dye in FISH assays to detect multicopy plasmid-based and endogenous mRNA molecules in Escherichia coli and Shewanella oneidensis MR-1. We took advantage of the fact there is much less background signal produced by biological materials and support matrices in the near-infrared spectrum and thus long camera exposure times could be used. In addition, we demonstrate that a combination of probes targeting both rRNA and mRNA could be successfully employed within the same FISH assay. These results, as well as ongoing R&D improvements in NIR and infrared dyes, indicate the FISH approach we demonstrated could be applied in certain environmental settings to monitor gene expression in mixed populations.

  20. Hierarchical behaviour, habitat use and species size differences shape evolutionary outcomes of hybridization in a coral reef fish.

    PubMed

    Gainsford, A; van Herwerden, L; Jones, G P

    2015-01-01

    Hybridization is an important evolutionary process, with ecological and behavioural factors influencing gene exchange between hybrids and parent species. Patterns of hybridization in anemonefishes may result from living in highly specialized habitats and breeding status regulated by size-based hierarchal social groups. Here, morphological, ecological and genetic analyses in Kimbe Bay, Papua New Guinea, examine the hybrid status of Amphiprion leucokranos, a nominal species and presumed hybrid between Amphiprion sandaracinos and Amphiprion chrysopterus. We test the hypothesis that habitat use and relative size differences of the parent species and hybrids determine the patterns of gene exchange. There is strong evidence that A. leucokranos is a hybrid of smaller A. sandaracinos and larger A. chrysopterus, where A. chrysopterus is exclusively the mother to each hybrid, based on mtDNA cytochrome b and multiple nDNA microsatellite loci. Overlap in habitat, depth and host anemone use was found, with hybrids intermediate to parents and cohabitation in over 25% of anemones sampled. Hybrids, intermediate in body size, colour and pattern, were classified 55% of the time as morphologically first-generation hybrids relative to parents, whereas 45% of hybrids were more A. sandaracinos-like, suggesting backcrossing. Unidirectional introgression of A. chrysopterus mtDNA into A. sandaracinos via hybrid backcrosses was found, with larger female hybrids and small male A. sandaracinos mating. Potential nDNA introgression was also evident through distinct intermediate hybrid genotypes penetrating both parent species. Findings support the hypothesis that anemonefish hierarchical behaviour, habitat use and species-specific size differences determine how hybrids form and the evolutionary consequences of hybridization.

  1. Rat karyotyping by fluorescence in situ hybridization (FISH): Localization of oncogene c-raf to 4q42, retinoblastoma antioncogene to 15q12, and mitochondrial D-loop-like sequences to the Y chromosome

    SciTech Connect

    Zullo, S. |; Upender, M.

    1995-02-10

    Fluorescence in situ hybridization (FISH) has been used to karyotype the rat genome with long interspersed repetitive elements (LINEs). Two-color FISH experiments were used to localize the rat c-raf oncogene to 4q42 and the rat retinoblastoma anti-oncogene to 15q12. In addition, sequences similar to the rat mitochondrial origin of replication (D-loop-like sequences) have been found to be concentrated among repetitive element sequences on the Y chromosome. This report extends hybridization-based karyotype technology to the rat, thus facilitating the application of FISH to rat gene mapping. 13 refs., 1 fig.

  2. Using Tournament Angler Data to Rapidly Assess the Invasion Status of Alien Sport Fishes (Micropterus spp.) in Southern Africa.

    PubMed

    Hargrove, John S; Weyl, Olaf L F; Allen, Micheal S; Deacon, Neil R

    2015-01-01

    Fishes are one of the most commonly introduced aquatic taxa worldwide, and invasive fish species pose threats to biodiversity and ecosystem function in recipient waters. Considerable research efforts have focused on predicting the invasibility of different fish taxa; however, accurate records detailing the establishment and spread of invasive fishes are lacking for large numbers of fish around the globe. In response to these data limitations, a low-cost method of cataloging and quantifying the temporal and spatial status of fish invasions was explored. Specifically, angler catch data derived from competitive bass angling tournaments was used to document the distribution of 66 non-native populations of black bass (Micropterus spp.) in southern Africa. Additionally, catch data from standardized tournament events were used to assess the abundance and growth of non-native bass populations in southern Africa relative to their native distribution (southern and eastern United States). Differences in metrics of catch per unit effort (average number of fish retained per angler per day), daily bag weights (the average weight of fish retained per angler), and average fish weight were assessed using catch data from 14,890 angler days of tournament fishing (11,045 days from South Africa and Zimbabwe; 3,845 days from the United States). No significant differences were found between catch rates, average daily bag weight, or the average fish weight between countries, suggesting that bass populations in southern Africa reach comparable sizes and numbers relative to waters in their native distribution. Given the minimal cost associated with data collection (i.e. records are collected by tournament organizers), the standardized nature of the events, and consistent bias (i.e. selection for the biggest fish in a population), the use of angler catch data represents a novel approach to infer the status and distribution of invasive sport fish.

  3. Using Tournament Angler Data to Rapidly Assess the Invasion Status of Alien Sport Fishes (Micropterus spp.) in Southern Africa

    PubMed Central

    Hargrove, John S.; Weyl, Olaf L. F.; Allen, Micheal S.; Deacon, Neil R.

    2015-01-01

    Fishes are one of the most commonly introduced aquatic taxa worldwide, and invasive fish species pose threats to biodiversity and ecosystem function in recipient waters. Considerable research efforts have focused on predicting the invasibility of different fish taxa; however, accurate records detailing the establishment and spread of invasive fishes are lacking for large numbers of fish around the globe. In response to these data limitations, a low-cost method of cataloging and quantifying the temporal and spatial status of fish invasions was explored. Specifically, angler catch data derived from competitive bass angling tournaments was used to document the distribution of 66 non-native populations of black bass (Micropterus spp.) in southern Africa. Additionally, catch data from standardized tournament events were used to assess the abundance and growth of non-native bass populations in southern Africa relative to their native distribution (southern and eastern United States). Differences in metrics of catch per unit effort (average number of fish retained per angler per day), daily bag weights (the average weight of fish retained per angler), and average fish weight were assessed using catch data from 14,890 angler days of tournament fishing (11,045 days from South Africa and Zimbabwe; 3,845 days from the United States). No significant differences were found between catch rates, average daily bag weight, or the average fish weight between countries, suggesting that bass populations in southern Africa reach comparable sizes and numbers relative to waters in their native distribution. Given the minimal cost associated with data collection (i.e. records are collected by tournament organizers), the standardized nature of the events, and consistent bias (i.e. selection for the biggest fish in a population), the use of angler catch data represents a novel approach to infer the status and distribution of invasive sport fish. PMID:26047487

  4. Assessing organic contaminants in fish: comparison of a nonlethal tissue sampling technique to mobile and stationary passive sampling devices.

    PubMed

    Heltsley, Rebecca M; Cope, W Gregory; Shea, Damian; Bringolf, Robert B; Kwak, Thomas J; Malindzak, Edward G

    2005-10-01

    As concerns mount over the human health risks associated with consumption of fish contaminated with persistent organic pollutants, there exists a need to better evaluate fish body burdens without lethally sampling many of the important commercial and sport species of interest. The aim of this study was to investigate two novel methods for estimating organic contaminants in fish that are a concern for both fish and human health. The removal of fish adipose fins, commonly done in mark-recapture studies with salmonid species, was evaluated as a nonlethal sampling technique to estimate concentrations of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) in flathead catfish (Pylodictis olivaris), relative to those found in muscle fillets of the same fish. We also assessed the efficacy of using poly(dimethylsiloxane) (PDMS) as a mobile passive sampling device (PSD) attached directly to wild flathead catfish for assessing location-specific exposure of the fish to waterborne contaminants. The results of this study have demonstrated for the first time that organic contaminant concentrations in adipose fin were highly correlated (R2 = 0.87) with muscle fillet concentrations, indicating that the adipose fin of certain fishes may be used to accurately estimate tissue concentrations without the need for lethal sampling. Moreover, mobile PSDs attached directly to fish and used here for the first time accurately estimated ultratrace concentrations of waterborne PCBs and OCPs without any apparent harm to the fish, indicating that there are no practical or physical barriers to the use of mobile passive samplers attached to aquatic organisms. Among the many practical implications of this research, two potential priority items include the analysis of organic contaminants in farm-raised and sport fish intended for human consumption, without the economic and population losses associated with lethally sampling fish to obtain tissues, and identifying specific areas

  5. [Variant Philadelphia chromosome identified by interphase fluorescence in situ hybridization (FISH) without evidence on G-banded karyotyping and metaphase FISH].

    PubMed

    Kim, Mi Kyung; Mun, Yeung Chul; Seong, Chu Myong; Chung, Wha Soon; Huh, Jungwon

    2010-12-01

    A variant Philadelphia chromosome (Ph) is generated from translocation of one or more partner chromosomes in addition to chromosomes 9 and 22. We have described the cases of 2 patients bearing variant Ph detected by interphase FISH but not detected by G-banded karyotyping and metaphase FISH. FISH was performed using BCR/ABL dual color dual fusion translocation probes (Abbott Molecular, USA). A 52-year-old man was diagnosed with acute leukemia of mixed phenotype. G-banded karyotyping showed 46,XY,t(9;22)(q34;q11.2)[12]/47,idem,+der(22)t(9;22)[5]/46,XY[3]. Interphase FISH revealed nuc ish(ABL1,BCR) × 3(ABL1 con BCR × 2)[329/450]/(ABL1,BCR) × 4(ABL1 con BCR × 3)[5/450]/(AL1,BCR) × 3(ABL1 con BCR × 1)[44/450]. Metaphase FISH showed ish (9;22)(ABL1+,BCR1+;BCR+,ABL+)[22]/der(22)(BCR+,ABL1+)[3]. The other case was that of a 31-yr-old male patient diagnosed with CML in the blastic phase. G-banded karyotyping of all 20 metaphase cells showed 47,XYYc,dup(1)(q21q32),del(7)(p11.2),t(9;22)(q34;q11.2). Interphase FISH revealed nuc ish(ABL1,BCR) × 3(ABL1 con BCR × 2)[254/600]/(ABL1,BCR) × 3(ABL1 con BCR × 1)[191/600]. Metaphase FISH showed ish t(9;22)(ABL1+,BCR+;BCR+,ABL1+)[16]. These results suggest that typical t(9;22) and variant Ph may coexist in the same patient, and interphase FISH may facilitate the detection of the variant Ph that cannot be detected by G-banded karyotyping alone.

  6. Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration.

    PubMed

    Rocha, Rui; Santos, Rita S; Madureira, Pedro; Almeida, Carina; Azevedo, Nuno F

    2016-05-20

    Fluorescence in situ hybridization (FISH) is a molecular technique widely used for the detection and characterization of microbial populations. FISH is affected by a wide variety of abiotic and biotic variables and the way they interact with each other. This is translated into a wide variability of FISH procedures found in the literature. The aim of this work is to systematically study the effects of pH, dextran sulfate and probe concentration in the FISH protocol, using a general peptide nucleic acid (PNA) probe for the Eubacteria domain. For this, response surface methodology was used to optimize these 3 PNA-FISH parameters for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). The obtained results show that a probe concentration higher than 300nM is favorable for both groups. Interestingly, a clear distinction between the two groups regarding the optimal pH and dextran sulfate concentration was found: a high pH (approx. 10), combined with lower dextran sulfate concentration (approx. 2% [w/v]) for Gram-negative species and near-neutral pH (approx. 8), together with higher dextran sulfate concentrations (approx. 10% [w/v]) for Gram-positive species. This behavior seems to result from an interplay between pH and dextran sulfate and their ability to influence probe concentration and diffusion towards the rRNA target. This study shows that, for an optimum hybridization protocol, dextran sulfate and pH should be adjusted according to the target bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Occurrence and human dietary assessment of fluoroquinolones antibiotics in cultured fish around Tai Lake, China.

    PubMed

    Song, Chao; Zhang, Cong; Kamira, Barry; Qiu, Liping; Fan, Limin; Wu, Wei; Meng, Shunlong; Hu, Gengdong; Chen, Jiazhang

    2017-06-06

    Fluoroquinolone antibiotics are widely used in the production of aquatic products and considered to be a significant contributing factor to the burden of both natural and aquaculture environments. However, the main types of fluoroquinolones present in aquaculture systems have not been determined. The objectives of the present study were to explore the occurrence of residual fluoroquinolone antibiotics in fish muscle tissues sampled from across the entire aquaculture season in the Tai Lake basin in China and to assess the dietary risks associated with the upcoming vendible fish in the last month of the aquaculture season. Fluoroquinolones were detected in 95.69% of all fish samples, and the concentrations ranged from the limit of quantification (LOQ) to 47 108.00 μg · kg(-1) . Enrofloxacin contributed the most among the 9 fluoroquinolone antibiotics tested. Of the 4 fish species studied, enrofloxacin was present in bream at significant (p < 0.05) concentrations in August, with an average value of 321.45 μg · kg(-1) , while enrofloxacin concentrations peaked in crab and shrimp in September, with average values of 6949.60 and 460.82 μg · kg(-1) , respectively. However, different patterns were observed in perch, suggesting that other categories of antibiotics may be used in the production of this fish. Dietary risk assessment showed that the residual levels and estimated daily intake in bream, perch, and shrimp were far below the maximum residual level and acceptable daily intake. However, the average residual level in crab exceeded the maximum residual level, and the estimated daily intake value accounted for 78.49% of the acceptable daily intake, indicating potential consumption risk. In summary, the present study aims to guide the production and consumption of aquatic products. Environ Toxicol Chem 2017;9999:1-7. © 2017 SETAC. © 2017 SETAC.

  8. Composition of dioxin-like PCBs in fish: an application for risk assessment.

    PubMed

    Bhavsar, Satyendra P; Fletcher, Rachael; Hayton, Alan; Reiner, Eric J; Jackson, Donald A

    2007-05-01

    It is widely accepted that a congener-specific analysis of polychlorinated biphenyls (PCBs), rather than traditional Aroclor equivalent total PCB analysis, is required for risk assessment. This is based on the fact that environmental processes alter the original distribution of PCB congeners in Aroclors and that toxicity varies considerably among the congeners with dioxin-like PCBs (dl-PCBs) generally being among the most toxic. Using the largest known dl-PCB fish dataset, here we present a likely composition of dl-PCBs in fish. In contrast to common perception, we found that the dl-PCB composition is relatively constant (within approximately a factor of 2) regardless of fish species and total PCB level. The abundance of dl-PCBs expressed as a percentage of total PCB (25-75 quartile range) in fish is generally in the order of PCB-118 (3.0-6.2%) > PCB-105 (1.1-2.4%) > PCB-156 (0.39-0.75%) > PCB-167 (0.20-0.43%) > PCB-123 (0.11-0.26%) > PCB-157 (0.09-0.19%) = PCB-114 (0.08-0.18%) > PCB-189 (0.045-0.094%) > PCB-77 (0.018-0.093%) > PCB-126 (0.015-0.036%) > PCB-81 (0.002-0.007%) = PCB-169 (0.001-0.006%). The most toxic dl-PCB congeners PCB-126 and -169 contribute on average only 0.027 and 0.004% of total PCB, respectively. The statistically significant relationships presented between individual di-PCB and total-PCB concentrations can be used as a practical tool to estimate dl-PCBs for risk assessment purposes. A comparison of the dl-PCB pattern presented here with other studies suggests that this dl-PCB composition is applicable to fish from North America and perhaps from other geographical regions throughout the world.

  9. Assessing ecological risks to the fish community from residual coal fly ash in Watts Bar Reservoir, Tennessee

    DOE PAGES

    Rigg, David K.; Wacksman, Mitch N.; Iannuzzi, Jacqueline; ...

    2014-12-18

    For this research, extensive site-specific biological and environmental data were collected to support an evaluation of risks to the fish community in Watts Bar Reservoir from residual ash from the December 2008 Tennessee Valley Authority (TVA) Kingston ash release. This paper describes the approach used and results of the risk assessment for the fish community, which consists of multiple measurement endpoints (measures of exposure and effects) for fish. The lines of evidence included 1) comparing postspill annual fish community assessments with nearby prespill data and data from other TVA reservoirs, 2) evaluating possible effects of exposures of fish eggs andmore » larval fish to ash in controlled laboratory toxicity tests, 3) evaluating reproductive competence of field-exposed fish, 4) assessing individual fish health through physical examination, histopathology, and blood chemistry, 5) comparing fish tissue concentrations with literature-based critical body residues, and 6) comparing concentrations of ash-related contaminants in surface waters with US Environmental Protection Agency's (USEPA) Ambient Water Quality Standards for Fish and Aquatic Life. These measurement endpoints were treated as independent lines of evidence that were integrated into an overall weight-of-evidence estimate of risk to the fish community. Collectively, the data and analysis presented here indicate that ash and ash-related constituents pose negligible risks to the fish communities in Watts Bar Reservoir. This conclusion contradicts the predictions by some researchers immediately following the ash release of devastating effects on the aquatic ecology of Watts Bar Reservoir. The information presented in this article reaffirms the wisdom of carefully evaluating the evidence before predicting probable ecological effects of a major event such as the TVA Kingston ash release. Lastly, this study demonstrates that a thorough and detailed investigation using multiple measurement endpoints

  10. Assessing ecological risks to the fish community from residual coal fly ash in Watts Bar Reservoir, Tennessee

    SciTech Connect

    Rigg, David K.; Wacksman, Mitch N.; Iannuzzi, Jacqueline; Baker, Tyler F.; Adams, Marshall; Greeley, Jr., Mark Stephen

    2014-12-18

    For this research, extensive site-specific biological and environmental data were collected to support an evaluation of risks to the fish community in Watts Bar Reservoir from residual ash from the December 2008 Tennessee Valley Authority (TVA) Kingston ash release. This paper describes the approach used and results of the risk assessment for the fish community, which consists of multiple measurement endpoints (measures of exposure and effects) for fish. The lines of evidence included 1) comparing postspill annual fish community assessments with nearby prespill data and data from other TVA reservoirs, 2) evaluating possible effects of exposures of fish eggs and larval fish to ash in controlled laboratory toxicity tests, 3) evaluating reproductive competence of field-exposed fish, 4) assessing individual fish health through physical examination, histopathology, and blood chemistry, 5) comparing fish tissue concentrations with literature-based critical body residues, and 6) comparing concentrations of ash-related contaminants in surface waters with US Environmental Protection Agency's (USEPA) Ambient Water Quality Standards for Fish and Aquatic Life. These measurement endpoints were treated as independent lines of evidence that were integrated into an overall weight-of-evidence estimate of risk to the fish community. Collectively, the data and analysis presented here indicate that ash and ash-related constituents pose negligible risks to the fish communities in Watts Bar Reservoir. This conclusion contradicts the predictions by some researchers immediately following the ash release of devastating effects on the aquatic ecology of Watts Bar Reservoir. The information presented in this article reaffirms the wisdom of carefully evaluating the evidence before predicting probable ecological effects of a major event such as the TVA Kingston ash release. Lastly, this study demonstrates that a thorough and detailed investigation using multiple measurement endpoints is needed

  11. Assessing ecological risks to the fish community from residual coal fly ash in Watts Bar Reservoir, Tennessee.

    PubMed

    Rigg, David K; Wacksman, Mitch N; Iannuzzi, Jacqueline; Baker, Tyler F; Adams, Marshall; Greeley, Mark S

    2015-01-01

    Extensive site-specific biological and environmental data were collected to support an evaluation of risks to the fish community in Watts Bar Reservoir from residual ash from the December 2008 Tennessee Valley Authority (TVA) Kingston ash release. This article describes the approach used and results of the risk assessment for the fish community, which consists of multiple measurement endpoints (measures of exposure and effects) for fish. The lines of evidence included 1) comparing postspill annual fish community assessments with nearby prespill data and data from other TVA reservoirs, 2) evaluating possible effects of exposures of fish eggs and larval fish to ash in controlled laboratory toxicity tests, 3) evaluating reproductive competence of field-exposed fish, 4) assessing individual fish health through physical examination, histopathology, and blood chemistry, 5) comparing fish tissue concentrations with literature-based critical body residues, and 6) comparing concentrations of ash-related contaminants in surface waters with US Environmental Protection Agency's (USEPA) Ambient Water Quality Standards for Fish and Aquatic Life. These measurement endpoints were treated as independent lines of evidence that were integrated into an overall weight-of-evidence estimate of risk to the fish community. Collectively, the data and analysis presented here indicate that ash and ash-related constituents pose negligible risks to the fish communities in Watts Bar Reservoir. This conclusion contradicts the predictions by some researchers immediately following the ash release of devastating effects on the aquatic ecology of Watts Bar Reservoir. The information presented in this article reaffirms the wisdom of carefully evaluating the evidence before predicting probable ecological effects of a major event such as the TVA Kingston ash release. This study demonstrates that a thorough and detailed investigation using multiple measurement endpoints is needed to properly evaluate

  12. Predation risk assessment by olfactory and visual cues in a coral reef fish

    NASA Astrophysics Data System (ADS)

    McCormick, M. I.; Manassa, R.

    2008-03-01

    Assessment of predation risk is vital for the success of an individual. Primary cues for the assessment include visual and olfactory stimuli, but the relative importance of these sources of information for risk assessment has seldom been assessed for marine fishes. This study examined the importance of visual and chemical cues in assessing risk for the star goby, Asterropteryx semipunctatus. Visual and chemical cue intensities were used that were indicative of a high threat situation. The behavioural response elicited by both the visual cues of a predator (the rock cod, Cephalopholis boenak) and the chemical alarm cues from conspecifics were similar in magnitude, with responses including a decrease in feeding strikes and moves. A bobbing behaviour was exhibited when the predator was visible and not when only exposed to the chemical alarm cue. When visual and chemical cues were presented together they yielded a stronger antipredator response than when gobies were exposed solely to conspecific alarm cues. This suggests additivity of risk assessment information at the levels of threat used, however, the goby’s response is also likely to depend on the environmental and social context of the predator-prey encounter. This study highlights the importance of chemical cues in the assessment of predation risk for a coral reef fish.

  13. Rapid identification of Helicobacter pylori and assessment of clarithromycin susceptibility from clinical specimens using FISH.

    PubMed

    Demiray-Gürbüz, Ebru; Yılmaz, Özlem; Olivares, Asalia Z; Gönen, Can; Sarıoğlu, Sülen; Soytürk, Müjde; Tümer, Sait; Altungöz, Oğuz; Şimşek, İlkay; Perez Perez, Guillermo I

    2017-01-01

    Helicobacter pylori remains one of the most common bacterial infections worldwide. Clarithromycin resistance is the most important cause of H. pylori eradication failures. Effective antibiotic therapies in H. pylori infection must be rapidly adapted to local resistance patterns. We investigated the prevalence of clarithromycin resistance due to mutations in positions 2142 and 2143 of 23SrRNA gene of H. pylori by fluorescence in situ hybridisation (FISH), and compared with culture and antimicrobial susceptibility testing in 234 adult patients with dyspepsia who were enrolled. Antrum and corpus biopsy specimens were obtained for rapid urease test, histopathology and culture. Epsilometer test was used to assess clarithromycin susceptibility. H. pylori presence and clarithromycin susceptibility were determined by FISH in paraffin-embedded biopsy specimens. We found that 164 (70.1%) patients were positive for H. pylori based on clinical criteria, 114 (69.5% CI 62.5-76.6%) were culture positive, and 137 (83.5% CI 77.8-89.2%) were FISH positive. Thus the sensitivity of FISH was significantly superior to that of culture. However specificity was not significantly different (91.4 versus 100.0%, respectively). The resistance rate to clarithromycin for both antrum and corpus was detected in H. pylori-positive patients; 20.2% by FISH and 28.0% by E-test.The concordance between E-test and FISH was only 89.5% due to the presence of point mutations different from A2143G, A2142G or A2142C. We conclude that FISH is significantly more sensitive than culture and the E-test for the detection of H. pylori and for rapid determinination of claritromycin susceptibility. The superior hybridisation efficiency of FISH is becoming an emerging molecular tool as a reliable, rapid and sensitive method for the detection and visualisation of H. pylori, especially when the management of H. pylori eradication therapy is necessary. This is particularly important for the treatment of patients with H

  14. Rapid identification of Helicobacter pylori and assessment of clarithromycin susceptibility from clinical specimens using FISH

    PubMed Central

    Demiray‐Gürbüz, Ebru; Yılmaz, Özlem; Olivares, Asalia Z; Gönen, Can; Sarıoğlu, Sülen; Soytürk, Müjde; Tümer, Sait; Altungöz, Oğuz; Şimşek, İlkay

    2016-01-01

    Abstract Helicobacter pylori remains one of the most common bacterial infections worldwide. Clarithromycin resistance is the most important cause of H. pylori eradication failures. Effective antibiotic therapies in H. pylori infection must be rapidly adapted to local resistance patterns. We investigated the prevalence of clarithromycin resistance due to mutations in positions 2142 and 2143 of 23SrRNA gene of H. pylori by fluorescence in situ hybridisation (FISH), and compared with culture and antimicrobial susceptibility testing in 234 adult patients with dyspepsia who were enrolled. Antrum and corpus biopsy specimens were obtained for rapid urease test, histopathology and culture. Epsilometer test was used to assess clarithromycin susceptibility. H. pylori presence and clarithromycin susceptibility were determined by FISH in paraffin‐embedded biopsy specimens. We found that 164 (70.1%) patients were positive for H. pylori based on clinical criteria, 114 (69.5% CI 62.5–76.6%) were culture positive, and 137 (83.5% CI 77.8–89.2%) were FISH positive. Thus the sensitivity of FISH was significantly superior to that of culture. However specificity was not significantly different (91.4 versus 100.0%, respectively). The resistance rate to clarithromycin for both antrum and corpus was detected in H. pylori‐positive patients; 20.2% by FISH and 28.0% by E‐test.The concordance between E‐test and FISH was only 89.5% due to the presence of point mutations different from A2143G, A2142G or A2142C. We conclude that FISH is significantly more sensitive than culture and the E‐test for the detection of H. pylori and for rapid determinination of claritromycin susceptibility. The superior hybridisation efficiency of FISH is becoming an emerging molecular tool as a reliable, rapid and sensitive method for the detection and visualisation of H. pylori, especially when the management of H. pylori eradication therapy is necessary. This is particularly important for the

  15. Assessing the efficacy of single-pass backpack electrofishing to characterize fish community structure

    USGS Publications Warehouse

    Meador, M.R.; McIntyre, J.P.; Pollock, K.H.

    2003-01-01

    Two-pass backpack electrofishing data collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program were analyzed to assess the efficacy of single-pass backpack electrofishing. A two-capture removal model was used to estimate, within 10 river basins across the United States, proportional fish species richness from one-pass electrofishing and probabilities of detection for individual fish species. Mean estimated species richness from first-pass sampling (ps1) ranged from 80.7% to 100% of estimated total species richness for each river basin, based on at least seven samples per basin. However, ps1 values for individual sites ranged from 40% to 100% of estimated total species richness. Additional species unique to the second pass were collected in 50.3% of the samples. Of these, cyprinids and centrarchids were collected most frequently. Proportional fish species richness estimated for the first pass increased significantly with decreasing stream width for 1 of the 10 river basins. When used to calculate probabilities of detection of individual fish species, the removal model failed 48% of the time because the number of individuals of a species was greater in the second pass than in the first pass. Single-pass backpack electrofishing data alone may make it difficult to determine whether characterized fish community structure data are real or spurious. The two-pass removal model can be used to assess the effectiveness of sampling species richness with a single electrofishing pass. However, the two-pass removal model may have limited utility to determine probabilities of detection of individual species and, thus, limit the ability to assess the effectiveness of single-pass sampling to characterize species relative abundances. Multiple-pass (at least three passes) backpack electrofishing at a large number of sites may not be cost-effective as part of a standardized sampling protocol for large-geographic-scale studies. However, multiple

  16. First among Equals: Hybridization of Cognitive Diagnostic Assessment and Evidence-Centered Game Design

    ERIC Educational Resources Information Center

    Leighton, Jacqueline P.; Chu, Man-Wai

    2016-01-01

    The objective of the present article is to explore differences and similarities between cognitive diagnostic assessment (CDA) and evidence-centered game design (ECgD) in the service of intentional hybridization. Although some testing specialists might argue that both are essentially the same given their origins in principled assessment design and…

  17. First among Equals: Hybridization of Cognitive Diagnostic Assessment and Evidence-Centered Game Design

    ERIC Educational Resources Information Center

    Leighton, Jacqueline P.; Chu, Man-Wai

    2016-01-01

    The objective of the present article is to explore differences and similarities between cognitive diagnostic assessment (CDA) and evidence-centered game design (ECgD) in the service of intentional hybridization. Although some testing specialists might argue that both are essentially the same given their origins in principled assessment design and…

  18. Accurate assessment of HER2 gene status for invasive component of breast cancer by combination of immunohistochemistry and chromogenic In Situ hybridization.

    PubMed

    Nie, Xiu; He, Jun; Li, Yan; Pan, Dan-zhen; Pan, Hua-xiong; Weng, Mi-xia; Yang, Xiu-ping; Liu, Chun-ping; Huang, Tao

    2013-06-01

    The specimens of ductal carcinoma in situ (DCIS) with early invasion, and specimens collected by core needle biopsy (CNB) tend to contain limited amount of invasive component, so it is imperative to explore a new technique which can assess HER2 gene status accurately for the limited invasive cancer component in these specimens. Dual staining technique of combining immunohistochemistry (IHC) for myoepithelial cells and single or dual probe chromogenic in situ hybridization (CISH) for HER2 gene was performed on routinely processed paraffin sections from 20 cases diagnosed as having DCIS with invasive cancer. Among them, 10 had fluorescence in situ hybridization (FISH)-confirmed amplification of HER2 and 10 had FISH-confirmed non-amplification of HER2. We successfully detected HER2 genetic signals and myoepithelial IHC markers (SMM-HC or CK5/6) simultaneously on a single section in all 20 specimens. Myoepithelial markers and HER2 signals detected by dual staining assay were consistent with those by individual technique performed alone. HER2 gene amplification results determined by dual staining assay were 100% consistent with those of FISH. Dual staining technique which allows simultaneous detection of myoepithelial marker protein and cancerous HER2 gene is feasible, and it has potential to be used in clinical practice for effective determination of HER2 amplification in limited invasive component.

  19. Bioaccumulation of trace metals in farmed fish from South China and potential risk assessment.

    PubMed

    Qiu, Yao-Wen; Lin, Duan; Liu, Jing-Qin; Zeng, Eddy Y

    2011-03-01

    Concentrations of trace metals were determined in water, sediment, fish feed and two species of farmed fish, pompano and snapper, collected from Daya Bay and Hailing Bay of South China in July 2007 and January 2008. Total average concentrations of Cu, Pb, Zn, Cd, Cr, Hg and As were 1.6, 2.7, 27.3, 0.025, 0.62, 0.18 and 0.59 μg/g dry wt in pompano and 1.5, 2.6, 23.6, 0.020, 0.55, 0.22 and 0.53 μg/g dry wt in snapper. In general, the concentrations of all target metals except Hg were positively correlated with lipid contents whereas negative correlations were observed between the metal concentrations and fish body weights. Model calculation indicated that dietary uptake of Zn and Cd predominate their accumulation in snapper, accounting for 99.9% and 98.2% of the total inputs. Risk assessments suggested that potential ecological and human health risk may be present due to elevated Pb concentrations in sediment and farmed fish.

  20. Application of Biochemical and Physiological Indicators for Assessing Recovery of Fish Populations in a Disturbed Stream

    SciTech Connect

    Adams, S. M.; Ham, Kenneth D.

    2011-06-01

    Recovery dynamics in a previously disturbed streamwere investigated to determine the influence of a series of remedial actions on stream recovery and to evaluate the potential application of bioindicators as an environmental management tool. A suite of bioindicators, representing five different functional response groups, were measured annually for a sentinel fish species over a 15 year period during which a variety of remedial and pollution abatement actions were implemented. Trends in biochemical, physiological, condition, growth, bioenergetic, and nutritional responses demonstrated that the health status of a sentinel fish species in the disturbed stream approached that of fish in the reference stream by the end of the study. Two major remedial actions, dechlorination and water flow management, had large effects on stream recovery resulting in an improvement in the bioenergetic, disease, nutritional, and organ condition status of the sentinel fish species. A subset of bioindicators responded rather dramatically to temporal trends affecting all sites, but some indicators showed little response to disturbance or to restoration activities. In assessing recovery of aquatic systems, application of appropriate integrative structural indices along with a variety of sensitive functional bioindicators should be used to understand the mechanistic basis of stress and recovery and to reduce the risk of false positives. Understanding the mechanistic processes involved between stressors, stress responses of biota, and the recovery dynamics of aquatic systems reduces the uncertainty involved in environmental management and regulatory decisions resulting in an increased ability to predict the consequences of restoration and remedial actions for aquatic systems.

  1. Trace metal levels in water, fish, and sediment from River Nile, Egypt: potential health risks assessment.

    PubMed

    Dahshan, Hesham; Abd-Elall, Amr Mohamed Mohamed; Megahed, Ayman Mohamed

    2013-01-01

    The purposes of this study were to describe the impact of metal pollution on the main economic fish species Tilapia nilotica and to assess the potential health risk from consuming this contaminated fish in Egypt. Trace metals, including Ag, Al, Cd, Bo, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, St, V, Zn, and As, were determined in water, Tilapia nilotica, and sediments from the River Nile, Domiate branch, Egypt. Metal concentrations in fish of Al, Cd, Co, Fe, Mn, Pb, V, and Zn (mg/kg dry weight [dw]) and concentrations in sediment of Cd, Co, Cr, Cu, Mn, Ni, Pb, V, and Zn (mg/kg dw) were above the International Atomic Energy Agency (IAEA-407) levels. However, trace metals in river water were still at permissible levels for Egyptian standards. The hazard index (HI) of estimated metal mixtures for intake of Tilapia nilotica (23.37) demonstrated that intake resulted in higher noncarcinogenic risk. In conclusion, the overall problem of metal contamination in fish collected from the River Nile was more serious than postulated to occur in an industrialized and densely populated area. In the light of known risks to public health, environmental protection laws are needed in Egypt.

  2. Ecological risk assessment of the fish community of the Clinch River/Poplar Creek system

    SciTech Connect

    Suter, G.; Barnthouse, L.; Efroymson, R.; Jaeger, H.; Beauchamp, J.

    1995-12-31

    The CERCLA remedial investigation for the Clinch River/Poplar Creek included the fish community as an endpoint. The assessment endpoint was defined as a 20% reduction in the species richness or abundance of the fish community in the Poplar Creek embayment or in any of three reaches of the Clinch River. Screening of chemicals in water against benchmarks determined that Ag, Cd, Cu, Hg, Ni, Zn, PCBs, and bis(2-ethylhexyl)phthalate were contaminants of potential ecological concern (COPECs). Comparison of the distributions of COPEC concentrations with the distributions of literature toxicity values indicated that none of the COPECs was routinely toxic but episodic concentrations (< 10% of the distribution) of some COPECs were in the toxic range. Aqueous toxicity tests gave unclear results except for regularly high lethality to fish embryos in Poplar Creek. Bioindicators analysis found elevated histopathologies and disrupted reproductive indicators in Centrarchids from Poplar Creek, but their implications for the community are unclear. Body burdens of PCBs in some channel catfish exceeded levels associated with sublethal effects on that species in the laboratory. Electrofishing and gill netting found that the fish community of Poplar Creek had low species number and abundance, but habitat quality was also low. These mixed results present a challenge to ecological risk characterization based on weight-of-evidence. The process of weighing the evidence will be presented.

  3. Application of Biochemical and Physiological Indicators for Assessing Recovery of Fish Populations in a Disturbed Stream

    SciTech Connect

    Adams, Marshall; Ham, Kenneth

    2011-01-01

    Recovery dynamics in a previously disturbed streamwere investigated to determine the influence of a series of remedial actions on stream recovery and to evaluate the potential application of bioindicators as an environmental management tool. A suite of bioindicators, representing five different functional response groups, were measured annually for a sentinel fish species over a 15 year period during which a variety of remedial and pollution abatement actions were implemented. Trends in biochemical, physiological, condition, growth, bioenergetic, and nutritional responses demonstrated that the health status of a sentinel fish species in the disturbed stream approached that of fish in the reference stream by the end of the study. Two major remedial actions, dechlorination and water flow management, had large effects on stream recovery resulting in an improvement in the bioenergetic, disease, nutritional, and organ condition status of the sentinel fish species. A subset of bioindicators responded rather dramatically to temporal trends affecting all sites, but some indicators showed little response to disturbance or to restoration activities. In assessing recovery of aquatic systems, application of appropriate integrative structural indices along with a variety of sensitive functional bioindicators should be used to understand the mechanistic basis of stress and recovery and to reduce the risk of false positives. Understanding the mechanistic processes involved between stressors, stress responses of biota, and the recovery dynamics of aquatic systems reduces the uncertainty involved in environmental management and regulatory decisions resulting in an increased ability to predict the consequences of restoration and remedial actions for aquatic systems.

  4. [A fish-based biotic integrity index selection for rivers in Hechi Prefecture, Guangxi and their environmental quality assessment].

    PubMed

    Liu, Kai; Zhou, Wei; Li, Feng-Lian; Lan, Jia-Hu

    2010-10-01

    This study aims to develop a multi-metric, fish-based Index of Biological Integrity (IBI) for assessing the environmental quality of rivers in Hechi Prefecture, Guangxi Province, South China. Data on fish assemblage were collected via electrofishing We screened 21 candidate metrics representing attributes of fish assemblage. Among these, six metrics were finally selected for the IBI. It was shown that the fish-based biological integrity was good in Xiaohuanjiang River , fair in Hongshuihe, Longjiang and Dahuanjiang Rivers, but poor in Diaojiang River. The results of assessment were consistent with the actual situation of human disturbance. The assessment system constructed by this study could be used or used for reference in the area around Hechi. Biotic integrity assessment was an important means of water environment quality monitoring. To enable the biotic integrity assessment more scientific and more objective, much more research work is required to focus on the relationship between biotic integrity and environmental factors.

  5. Nitrifying bacterial communities in an aquaculture wastewater treatment system using fluorescence in situ hybridization (FISH), 16S rRNA gene cloning, and phylogenetic analysis.

    PubMed

    Paungfoo, Chanyarat; Prasertsan, Poonsuk; Burrell, Paul C; Intrasungkha, Nugul; Blackall, Linda L

    2007-07-01

    Aquaculture, especially shrimp farming, has played a major role in the growth of Thailand's economy in recent years, as well as in many South East Asian countries. However, the nutrient discharges from these activities have caused adverse impacts on the quality of the receiving waterways. In particular nitrogenous compounds, which may accumulate in aquaculture ponds, can be toxic to aquatic animals and cause environmental problems such as eutrophication. The mineralization process is well known, but certain aspects of the microbial ecology of nitrifiers, the microorganisms that convert ammonia to nitrate, are poorly understood. A previously reported enrichment of nitrifying bacteria (ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB)) from a shrimp farm inoculated in a sequencing batch reactor (SBR) was studied by molecular methods. The initial identification and partial quantification of the nitrifying bacteria (AOB and NOB) were carried out by fluorescence in situ hybridization (FISH) using previously published 16S rRNA-targeting oligonucleotide probes. The two dominant bacterial groups detected by FISH were from the Cytophaga-Flavobacterium-Bacteroides and Proteobacteria (beta subdivision) phyla. Published FISH probes for Nitrobacter and Nitrospira did not hybridize to any of the bacterial cells. Therefore it is likely that new communities of NOBs, differing from previously reported ones, exist in the enrichments. Molecular genetic techniques (cloning, sequencing, and phylogenetic analysis) targeting the 16S rRNA genes from the nitrifying enrichments were performed to identify putative AOBs and NOBs.

  6. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH)

    PubMed Central

    Cortés-Gutiérrez, Elva I.; Ortíz-Hernández, Brenda L.; Dávila-Rodríguez, Martha I.; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

    2013-01-01

    We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1. PMID:23429197

  7. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH).

    PubMed

    Cortés-Gutiérrez, Elva I; Ortíz-Hernández, Brenda L; Dávila-Rodríguez, Martha I; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

    2013-02-19

    We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

  8. Asexual Reproduction Does Not Apparently Increase the Rate of Chromosomal Evolution: Karyotype Stability in Diploid and Triploid Clonal Hybrid Fish (Cobitis, Cypriniformes, Teleostei).

    PubMed

    Majtánová, Zuzana; Choleva, Lukáš; Symonová, Radka; Ráb, Petr; Kotusz, Jan; Pekárik, Ladislav; Janko, Karel

    2016-01-01

    Interspecific hybridization, polyploidization and transitions from sexuality to asexuality considerably affect organismal genomes. Especially the last mentioned process has been assumed to play a significant role in the initiation of chromosomal rearrangements, causing increased rates of karyotype evolution. We used cytogenetic analysis and molecular dating of cladogenetic events to compare the rate of changes of chromosome morphology and karyotype in asexually and sexually reproducing counterparts in European spined loach fish (Cobitis). We studied metaphases of three sexually reproducing species and their diploid and polyploid hybrid clones of different age of origin. The material includes artificial F1 hybrid strains, representatives of lineage originated in Holocene epoch, and also individuals of an oldest known age to date (roughly 0.37 MYA). Thereafter we applied GISH technique as a marker to differentiate parental chromosomal sets in hybrids. Although the sexual species accumulated remarkable chromosomal rearrangements after their speciation, we observed no differences in chromosome numbers and/or morphology among karyotypes of asexual hybrids. These hybrids possess chromosome sets originating from respective parental species with no cytogenetically detectable recombinations, suggesting their integrity even in a long term. The switch to asexual reproduction thus did not provoke any significant acceleration of the rate of chromosomal evolution in Cobitis. Asexual animals described in other case studies reproduce ameiotically, while Cobitis hybrids described here produce eggs likely through modified meiosis. Therefore, our findings indicate that the effect of asexuality on the rate of chromosomal change may be context-dependent rather than universal and related to particular type of asexual reproduction.

  9. Asexual Reproduction Does Not Apparently Increase the Rate of Chromosomal Evolution: Karyotype Stability in Diploid and Triploid Clonal Hybrid Fish (Cobitis, Cypriniformes, Teleostei)

    PubMed Central

    Majtánová, Zuzana; Choleva, Lukáš; Symonová, Radka; Ráb, Petr; Kotusz, Jan; Pekárik, Ladislav; Janko, Karel

    2016-01-01

    Interspecific hybridization, polyploidization and transitions from sexuality to asexuality considerably affect organismal genomes. Especially the last mentioned process has been assumed to play a significant role in the initiation of chromosomal rearrangements, causing increased rates of karyotype evolution. We used cytogenetic analysis and molecular dating of cladogenetic events to compare the rate of changes of chromosome morphology and karyotype in asexually and sexually reproducing counterparts in European spined loach fish (Cobitis). We studied metaphases of three sexually reproducing species and their diploid and polyploid hybrid clones of different age of origin. The material includes artificial F1 hybrid strains, representatives of lineage originated in Holocene epoch, and also individuals of an oldest known age to date (roughly 0.37 MYA). Thereafter we applied GISH technique as a marker to differentiate parental chromosomal sets in hybrids. Although the sexual species accumulated remarkable chromosomal rearrangements after their speciation, we observed no differences in chromosome numbers and/or morphology among karyotypes of asexual hybrids. These hybrids possess chromosome sets originating from respective parental species with no cytogenetically detectable recombinations, suggesting their integrity even in a long term. The switch to asexual reproduction thus did not provoke any significant acceleration of the rate of chromosomal evolution in Cobitis. Asexual animals described in other case studies reproduce ameiotically, while Cobitis hybrids described here produce eggs likely through modified meiosis. Therefore, our findings indicate that the effect of asexuality on the rate of chromosomal change may be context-dependent rather than universal and related to particular type of asexual reproduction. PMID:26808475

  10. Discovery and validation of gene-linked diagnostic SNP markers for assessing hybridization between Largemouth bass (Micropterus salmoides) and Florida bass (M. floridanus).

    PubMed

    Li, Chao; Gowan, Spencer; Anil, Ammu; Beck, Benjamin H; Thongda, Wilawan; Kucuktas, Huseyin; Kaltenboeck, Ludmilla; Peatman, Eric

    2015-03-01

    Efforts to improve recreational fisheries have included widespread stocking of Micropterus floridanus outside its native range of peninsular Florida. Hybridization of Florida bass (M. floridanus) with largemouth bass (Micropterus salmoides) has now dramatically expanded beyond a naturally occurring intergrade zone in the southeast U.S. In recent years, there has been growing interest in protecting the genetic integrity of native basses and assessing the impact and nature of M. salmoides/M. floridanus introgression from the standpoint of hatchery and sport-fishery managers, fish biologists, ecologists and evolutionary biologists. Here, we conducted RNA-seq-based sequencing of the transcriptomes of M. salmoides, M. floridanus and their F1 hybrid and identified a set of 3674 SNP markers with fixed-allelic differences from 2112 unique genes. We then developed a subset of 25 of these markers into a single diagnostic multiplex assay and validated its capacity for assessing integrity and hybridization in hatchery and wild populations of largemouth and Florida bass. The availability of this resource, high-quality transcriptomes and a large set of gene-linked SNPs, should greatly facilitate functional and population genomics studies in these key species and allow the identification of traits and processes under selection during introgressive hybridization.

  11. Assessing karyotype precision by microarray-based comparative genomic hybridization in the myelodysplastic/myeloproliferative syndromes

    PubMed Central

    2010-01-01

    Background Recent genome-wide microarray-based research investigations have revealed a high frequency of submicroscopic copy number alterations (CNAs) in the myelodysplastic syndromes (MDS), suggesting microarray-based comparative genomic hybridization (aCGH) has the potential to detect new clinically relevant genomic markers in a diagnostic laboratory. Results We performed an exploratory study on 30 cases of MDS, myeloproliferative neoplasia (MPN) or evolving acute myeloid leukemia (AML) (% bone marrow blasts ≤ 30%, range 0-30%, median, 8%) by aCGH, using a genome-wide bacterial artificial chromosome (BAC) microarray. The sample data were compared to corresponding cytogenetics, fluorescence in situ hybridization (FISH), and clinical-pathological findings. Previously unidentified imbalances, in particular those considered submicroscopic aberrations (< 10 Mb), were confirmed by FISH analysis. CNAs identified by aCGH were concordant with the cytogenetic/FISH results in 25/30 (83%) of the samples tested. aCGH revealed new CNAs in 14/30 (47%) patients, including 28 submicroscopic or hidden aberrations verified by FISH studies. Cryptic 344-kb RUNX1 deletions were found in three patients at time of AML transformation. Other hidden CNAs involved 3q26.2/EVI1, 5q22/APC, 5q32/TCERG1,12p13.1/EMP1, 12q21.3/KITLG, and 17q11.2/NF1. Gains of CCND2/12p13.32 were detected in two patients. aCGH failed to detect a balanced translocation (n = 1) and low-level clonality (n = 4) in five karyotypically aberrant samples, revealing clinically important assay limitations. Conclusions The detection of previously known and unknown genomic alterations suggests that aCGH has considerable promise for identification of both recurring microscopic and submicroscopic genomic imbalances that contribute to myeloid disease pathogenesis and progression. These findings suggest that development of higher-resolution microarray platforms could improve karyotyping in clinical practice. PMID:21078186

  12. A comparative assessment of contaminants in fish from four resacas of the Texas, USA-Tamaulipas, Mexico border region.

    PubMed

    Mora, M A; Papoulias, D; Nava, I; Buckler, D R

    2001-07-01

    A recent survey of contaminant information for the Lower Rio Grande Valley (LRGV), Texas, has shown that little is known about contaminants and their impacts on biota of resacas (oxbows) along the US-Mexico border. In 1996, fish were collected from four resacas in the Texas-Tamaulipas border region to assess contaminant loadings and their impacts on fish and birds. Tissue residue concentrations in fish were analyzed and also compared to two histopathological bioindicators of unhealthy environmental conditions. Of the organochlorine insecticides measured, DDE was the most common and was present at relatively high concentrations (10 microg/g w/w) at some sites. DDE concentrations were nearly 20 times greater in fish from resacas in Texas than from resacas in Tamaulipas, although the limited sample sizes obtained precluded statistical comparisons. DDE concentrations in fish from the two Texas resacas were also greater than those reported in fish from nearby areas during the 1980s and 1990s. Most trace element concentrations were similar among resacas from Texas and Tamaulipas. Arsenic, however, was two to six times greater in fish from a downtown resaca in Matamoros than in fish from other resacas in Tamaulipas and Texas. The bioindicators, pigment accumulation, and macrophage aggregates (MAs), in general, reflected the contamination indicated by the tissue residues for each site. Overall, it appears that some resacas of the US-Mexico border region are contaminant sinks and could pose potential health or reproductive problems for fish and wildlife, and humans that consume fish from those sites.

  13. A scoring system approach for the parasite predictive assessment of fish lots: a proof of concept with anisakids.

    PubMed

    Llarena-Reino, María; Abollo, Elvira; Pascual, Santiago

    2013-12-01

    A total of 982 individuals distributed in 11 lots belonging to 10 fish species from three Atlantic FAO fishing areas were sampled and examined to detect the presence of anisakid larvae in fish muscle. After hazard identification by genetic sequencing and exposure assessment by anatomic extent and demographic characterization of infection, all data were fitted for each fish species to a new proposed scoring schema of parasite prediction. In the absence of a criterion standard method for inspection and precise definition of the quantum satis for parasites in contaminated fish lots, the inspection rating scheme called SADE (Site of infection, Assurance of quality, Demography, Epidemiology) may help fish industries to precisely handle and to evaluate the likely outcome of infected fish lots after being diagnosed. For this purpose, a supporting flow diagram for decision was defined and suggested. This new performance assessment tool has the aim of staging fish lots, thus helping in planning manufacture, commercial, and research decisions during self-management programs. This novel scoring system provides an improved inspection format by implementing the occurrence stratification for parasites to guide Hazard Analysis and Critical Control Points (HACCP) programs for the uniform exchange of information among fish industries, administration and researchers, thus facilitating standardization and communication. In the future, this scoring version could be validated (in terms of classification and wording) for similar overall predictive purposes in other muscular parasites infecting seafood products.

  14. Assessment of Present Anadromous Fish Production Facilities in the Columbia River Basin, US Fish and Wildlife Hatcheries, Final Report.

    SciTech Connect

    Delarm, Michael R.; Smith, Robert Z.

    1990-07-01

    The goal of this report is to document current production practices for hatcheries which rear anadromous fish in the Columbia River Basin and to identify those facilities where production can be increased. A total of 85 hatchery and satellite facilities operated by the Idaho Department of Fish and Game, Oregon Department of Fish and Game, US Fish and Wildlife Service, Washington Department of Wildlife, and Washington Department of Fisheries were evaluated. The years 1985 to 1987 were used in this evaluation. During those years, releases averaged 143,306,596 smolts weighing 7,693,589 pounds. A total of 48 hatchery or satellite facilities were identified as having expansion capability. They were estimated to have the potential for increasing production by an 84,448,000 smolts weighing 4,853,306 pounds. 2 refs., 25 tabs.

  15. Assessment of Present Anadromous Fish Production Facilities in the Columbia River Basin, Washington Department of Fish Hatcheries, Final Report.

    SciTech Connect

    Delarm, Michael R.; Smith, Robert Z.

    1990-07-01

    The goal of this report is to document current production practices for hatcheries which rear anadromous fish in the Columbia River Basin and to identify those facilities where production can be increased. A total of 85 hatchery and satellite facilities operated by the Idaho Department of Fish and Game, Oregon Department of Fish and Game, US Fish and Wildlife Service, Washington Department of Wildlife, and Washington Department of Fisheries were evaluated. The years 1985 to 1987 were used in this evaluation. During those years, releases averaged 143,306,596 smolts weighing 7,693,589 pounds. A total of 48 hatchery or satellite facilities were identified as having expansion capability. They were estimated to have the potential for increasing production by an 84,448,000 smolts weighing 4,853,306 pounds. 2 refs., 25 figs.

  16. Assessing connectivity of estuarine fishes based on stable isotope ratio analysis

    NASA Astrophysics Data System (ADS)

    Herzka, Sharon Z.

    2005-07-01

    Assessing connectivity is fundamental to understanding the population dynamics of fishes. I propose that isotopic analyses can greatly contribute to studies of connectivity in estuarine fishes due to the high diversity of isotopic signatures found among estuarine habitats and the fact that variations in isotopic composition at the base of a food web are reflected in the tissues of consumers. Isotopic analysis can be used for identifying nursery habitats and estimating their contribution to adult populations. If movement to a new habitat is accompanied by a shift to foods of distinct isotopic composition, recent immigrants and residents can be distinguished based on their isotopic ratios. Movement patterns thus can be reconstructed based on information obtained from individuals. A key consideration is the rate of isotopic turnover, which determines the length of time that an immigrant to a given habitat will be distinguishable from a longtime resident. A literature survey indicated that few studies have measured turnover rates in fishes and that these have focused on larvae and juveniles. These studies reveal that biomass gain is the primary process driving turnover rates, while metabolic turnover is either minimal or undetectable. Using a simple dilution model and biomass-specific growth rates, I estimated that young fishes with fast growth rates will reflect the isotopic composition of a new diet within days or weeks. Older or slower-growing individuals may take years or never fully equilibrate. Future studies should evaluate the factors that influence turnover rates in fishes during various stages of the life cycle and in different tissues, as well as explore the potential for combining stable isotope and otolith microstructure analyses to examine the relationship between demographic parameters, movement and connectivity.

  17. Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

    PubMed Central

    Civade, Raphaël; Dejean, Tony; Valentini, Alice; Roset, Nicolas; Raymond, Jean-Claude; Bonin, Aurélie; Taberlet, Pierre; Pont, Didier

    2016-01-01

    In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site. PMID:27359116

  18. Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System.

    PubMed

    Civade, Raphaël; Dejean, Tony; Valentini, Alice; Roset, Nicolas; Raymond, Jean-Claude; Bonin, Aurélie; Taberlet, Pierre; Pont, Didier

    2016-01-01

    In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.

  19. Do national advisories serve local consumers: an assessment of mercury in economically important North Carolina fish.

    PubMed

    Petre, Sally Jane; Sackett, Dana K; Aday, D Derek

    2012-05-01

    Consumption of marine fish provides both benefits (lean protein, omega-3 fatty acids and essential nutrients) and risks (main source of mercury (Hg) exposure for humans). Mercury is a potent neurotoxin and the source of more fish advisories nationwide than any other toxicant. Despite the widespread nature of Hg, it is unknown whether local Hg contamination reflects national and regional levels often used as bases to inform consumers of potential fish consumption risk. Thus, the objectives of our study were to examine Hg levels of six commonly consumed marine species harvested locally off the North Carolina coast and to compare our results to published regional (Monterey Bay Aquarium's Seafood Watch List) and national (Environmental Protection Agency, EPA, and Food and Drug Administration, FDA) Hg averages, action levels, and guidelines. We found significant differences in Hg concentrations among collected species, and we identified correlations between Hg concentration and fish length and trophic levels. Collected mahi mahi and triggerfish were below the EPA fish tissue action level (0.3ppm). Wahoo and grouper exceeded the EPA action level but were below the FDA action level (1.0ppm). King mackerel had the highest Hg concentration among targeted species, exceeding both EPA and FDA action levels. Further, our local results were not always consistent with calculated averages from EPA and FDA databases for the same species, and although many of our findings were consistent with Monterey Bay Aquarium's Seafood Watch List (southeast region), recommendations based on Hg levels would conflict with recommendations they provide based on sustainability. We find regional and national averages are not always reflective of local Hg contamination and suggest local data may be needed to accurately assess consumer risk.

  20. Hybrid electric vehicle technology assessment : methodology, analytical issues, and interim results.

    SciTech Connect

    Plotkin, S.; Santini, D.; Vyas, A.; Anderson, J.; Wang, M.; Bharathan, D.; He, J.

    2002-03-13

    This report presents the results of the first phase of Argonne National Laboratory's (ANL's) examination of the costs and energy impacts of light-duty hybrid electric vehicles (HEVs). We call this research an HEV Technology Assessment, or HEVTA. HEVs are vehicles with drivetrains that combine electric drive components (electric motor, electricity storage) with a refuelable power plant (e.g., an internal combustion engine). The use of hybrid drivetrains is widely considered a key technology strategy in improving automotive fuel efficiency. Two hybrid vehicles--Toyota's Prius and Honda's Insight--have been introduced into the U.S. market, and all three auto industry participants in the Partnership for a New Generation of Vehicles (PNGV) have selected hybrid drivetrains for their prototype vehicles.

  1. Contamination of fish in UK fresh water systems: risk assessment for human consumption.

    PubMed

    Rose, Martin; Fernandes, Alwyn; Mortimer, David; Baskaran, Christina

    2015-03-01

    There is growing evidence that more people in the UK are consuming fish taken from inland waterways. This may be partly due to the increased numbers of migrants from Eastern Europe where this is part of traditional culture and partly because of a desire to try new foods encouraged by celebrity chefs. Fish can bioaccumulate environmental contaminants and so could contribute a significant amount to dietary exposure to these chemicals. This study examined the changing habits of anglers and consumers and characterised a range of existing and emerging contaminants in freshwater fish species with a view to determining current levels of occurrence and possible risk from consumption. The project was conducted in two stages. The first stage included (a) a study that identified freshwater systems that are contaminated either by anthropogenic activity or as a result of the geology of the area; and (b) socioeconomic research to assess the consumption habits of the public, particularly anglers, with respect to fish and shellfish from unmanaged inland waterways. Based on the outcome from the first stage, specific rivers and other inland waterways were chosen for investigation, along with the range of contaminants to be included in the analytical programme. Predicted contamination levels and prevalence of anglers were among the factors taken into consideration. The second stage of the project involved sampling and analysis of fish taken from selected locations on the chosen waterways. A range of fish species from a variety of inland water habitats were obtained. These were analysed for the following contaminants: heavy metals, chlorinated dioxins (PCDD/Fs), polybrominated biphenyls (PBBs), polychlorinated biphenyls (PCBs), brominated dioxins (PBDD/Fs), polychlorinated naphthalenes (PCNs), polybrominated diphenylethers (PBDEs), OC pesticides, organotin compounds and organo-fluorine compounds. Legal limits for contaminants apply only to food traded commercially, but some samples

  2. Arsenic Speciation in Fish Products and Seafood as a Prerequisite for Proper Risk Assessment

    PubMed Central

    Orletti, Roberta; Chessa, Giannina; Carloni, Cristiano; Griffoni, Francesco; Palombo, Paolo; Velieri, Francesco

    2015-01-01

    The Boi Cerbus lagoon, facing a mining and industrial site in Sardinia (Italy), is an important fishing area for the local population. Previous studies showed high concentrations of total arsenic (Astot) in fish, molluscs and crustaceans sampled in the lagoon, and a possible exceeding of the provisional tolerable weekly intake set by the Joint FAO/WHO Expert Committee on Food Additives by some local consumer groups. However, the percentage of inorganic As (Asinorg) should be known for a correct assessment of potential risk, as its toxicity is much higher than that of the organic forms. Eighty samples of 14 different species of fish, molluscs and crustaceans, sampled in the Boi Cerbus lagoon in 3 different seasons (winter, spring and summer), were analysed for Astot by inductively coupled plasma mass spectrometry (ICP-MS) and Asinorg by high performance liquid chromatography-ICP-MS. All the data obtained from the analysis were statistically processed to evaluate significant differences based on season, taxon and habitat, in preparation for a subsequent risk assessment. PMID:27800381

  3. Assessing possible effects of fish-culture systems on fish swimming: the role of stability in turbulent flows.

    PubMed

    Webb, Paul W; Cotel, Aline J

    2011-06-01

    Fish are cultured in ponds, recirculating systems, raceways, and cages. Turbulence is associated with one or more of mechanisms to facilitate food accessibility, maintain adequate levels of oxygen, remove carbon dioxide, urinary and fecal wastes, as well as from locomotion of fishes themselves. Turbulence has been shown to have positive and negative effects on fish swimming, feeding, and energetics, usually with negative impacts at very low and at high levels, and least effects and sometimes positive effects at intermediate levels. Differences in responses of fishes with varying levels of turbulence are related to the size of eddies relative to the size of a fish (larvae, juveniles, and adults). Impacts on locomotor functions are associated with eddy diameters of the order of 0.5-1L, where L is the total length of a fish. Negative locomotor impacts of turbulence are associated with eddies challenging stability, while positive effects promote drafting and station holding with reduced locomotor motions. Deployment of control surfaces increases with the level of turbulence up to a threshold where control is overwhelmed. The design of culture facilities is expected to affect levels of turbulence and may be engineered to provide optimal levels facilitating high growth.

  4. SCREENING AND TESTING FOR ENDOCRINE DISRUPTION IN FISH - BIOMARKERS AS "SIGNPOSTS," NOT "TRAFFIC LIGHTS," IN RISK ASSESSMENT

    EPA Science Inventory

    Biomarkers provide important tools for addressing the impacts of endocrine disrupting chemicals (EDCs) in fish. Presently, biomarkers are best used as mechanistic "signposts" rather than as "red traffic lights" in the environmental risk assessment of EDCs. In field studies, bio...

  5. Ecological risk assessment of substances with suspected estrogenic activity using standard laboratory fish tests

    SciTech Connect

    Gimeno, S.; Bowmer, C.T.

    1999-07-01

    The assessment of risks to the aquatic environment in the European Union is generally based on a comparison of Predicted Environmental Concentrations (PEC) with Predicted No Effect Concentrations (PNEC) for surrogate, or representative, organisms of the receiving waters. Such risk assessments are required for new and priority existing chemicals, pesticides, and, in the near future, biocides; they are dependent on robust in vivo test data. Current strategies for ecological risk assessment were not designed to assess the risk of endocrine disrupters. The selection of suitable fish species and practical in vivo end points for determining endocrine disruption in fish are discussed, including the adaptation of some existing guidelines. This paper is partly based on a series of experiments conducted at the laboratory to look at the effects of a model alkylphenol (4-tert-pentylphenol), an industrial chemical intermediate, acting as a pseudo-estrogen on an all-male population of the common carp, Cyprinus carpio. Exposure to the test substance occurred at critical life stages for endocrine disruption. Biochemical parameters as well as histological parameters were applied, and their suitability to be used in ecological risk assessment is discussed.

  6. Using fish communities to assess streams in Romania: Initial development of an index of biotic integrity

    USGS Publications Warehouse

    Angermeier, P.L.; Davideanu, G.

    2004-01-01

    Multimetric biotic indices increasingly are used to complement physicochemical data in assessments of stream quality. We initiated development of multimetric indices, based on fish communities, to assess biotic integrity of streams in two physiographic regions of central Romania. Unlike previous efforts to develop such indices for European streams, our metrics and scoring criteria were selected largely on the basis of empirical relations in the regions of interest. We categorised 54 fish species with respect to ten natural-history attributes, then used this information to compute 32 candidate metrics of five types (taxonomic, tolerance, abundance, reproductive, and feeding) for each of 35 sites. We assessed the utility of candidate metrics for detecting anthropogenic impact based on three criteria: (a) range of values taken, (b) relation to a site-quality index (SQI), which incorporated information on hydrologic alteration, channel alteration, land-use intensity, and water chemistry, and (c) metric redundancy. We chose seven metrics from each region to include in preliminary multimetric indices (PMIs). Both PMIs included taxonomic, tolerance, and feeding metrics, but only two metrics were common to both PMIs. Although we could not validate our PMIs, their strong association with the SQI in each region suggests that such indices would be valuable tools for assessing stream quality and could provide more comprehensive assessments than the traditional approaches based solely on water chemistry.

  7. Assessment of a long-range corrected hybrid functional

    SciTech Connect

    Vydrov, Oleg A.; Scuseria, Gustavo E.

    2006-12-21

    Common approximate exchange-correlation functionals suffer from self-interaction error, and as a result, their corresponding potentials have incorrect asymptotic behavior. The exact asymptote can be imposed by introducing range separation into the exchange component and replacing the long-range portion of the approximate exchange by the Hartree-Fock counterpart. The authors show that this long-range correction works particularly well in combination with the short-range variant of the Perdew-Burke-Ernzerhof (PBE) exchange functional. This long-range-corrected hybrid, here denoted LC-{omega}PBE, is remarkably accurate for a broad range of molecular properties, such as thermochemistry, barrier heights of chemical reactions, bond lengths, and most notably, description of processes involving long-range charge transfer.

  8. Direct viable count combined with fluorescence in situ hybridization (DVC-FISH) for specific enumeration of viable escherichia coli in cow manure.

    PubMed

    Wu, Shengjin; Ueno, Daisuke; Inoue, Koichi; Someya, Takashi

    2009-01-01

    A direct viable count procedure combined with fluorescence in situ hybridization (DVC-FISH) was developed for the specific detection and enumeration of viable Escherichia coli in cow manure. The DVC method was performed by trapping bacterial cells, extracted from cow manure samples, onto Nucleopore filters followed by incubation on a DVC medium containing yeast extract and four gyrase inhibitors. E. coli cells were identified by using the probe ES445. The DVC method efficiently promoted the elongation of E. coli cells and allowed for the recognition of individual cell division events, by observing microcolonies. Cell recovery by DVC-FISH together with bacterial extraction, was 53% with an inoculum of 10(7) to 10(10) cells g(-1) dry weight, when the manure samples were inoculated with a fresh culture of E. coli and determinations were made immediately. An examination of the survival of E. coli in a cow manure microcosm showed that an increasing fraction of E. coli became non-culturable but were still detectable by DVC-FISH. All these results suggest that DVC-FISH is useful for enumerating viable, even non-culturable, E. coli in cow manure.

  9. A multi-scale GIS and hydrodynamic modelling approach to fish passage assessment: Clarence and Shoalhaven Rivers, NSW Australia

    NASA Astrophysics Data System (ADS)

    Bonetti, Rita M.; Reinfelds, Ivars V.; Butler, Gavin L.; Walsh, Chris T.; Broderick, Tony J.; Chisholm, Laurie A.

    2016-05-01

    Natural barriers such as waterfalls, cascades, rapids and riffles limit the dispersal and in-stream range of migratory fish, yet little is known of the interplay between these gradient dependent landforms, their hydraulic characteristics and flow rates that facilitate fish passage. The resurgence of dam construction in numerous river basins world-wide provides impetus to the development of robust techniques for assessment of the effects of downstream flow regime changes on natural fish passage barriers and associated consequences as to the length of rivers available to migratory species. This paper outlines a multi-scale technique for quantifying the relative magnitude of natural fish passage barriers in river systems and flow rates that facilitate passage by fish. First, a GIS-based approach is used to quantify channel gradients for the length of river or reach under investigation from a high resolution DEM, setting the magnitude of identified passage barriers in a longer context (tens to hundreds of km). Second, LiDAR, topographic and bathymetric survey-based hydrodynamic modelling is used to assess flow rates that can be regarded as facilitating passage across specific barriers identified by the river to reach scale gradient analysis. Examples of multi-scale approaches to fish passage assessment for flood-flow and low-flow passage issues are provided from the Clarence and Shoalhaven Rivers, NSW, Australia. In these river systems, passive acoustic telemetry data on actual movements and migrations by Australian bass (Macquaria novemaculeata) provide a means of validating modelled assessments of flow rates associated with successful fish passage across natural barriers. Analysis of actual fish movements across passage barriers in these river systems indicates that two dimensional hydraulic modelling can usefully quantify flow rates associated with the facilitation of fish passage across natural barriers by a majority of individual fishes for use in management

  10. Assessing Fish and Motile Fauna around Offshore Windfarms Using Stereo Baited Video.

    PubMed

    Griffin, Ross A; Robinson, Gary J; West, Ashley; Gloyne-Phillips, Ian T; Unsworth, Richard K F

    2016-01-01

    There remains limited knowledge of how offshore windfarm developments influence fish assemblages, particularly at a local scale around the turbine structures. Considering the existing levels of anthropogenic pressures on coastal fish populations it is becoming increasingly important for developers and environmental regulators to gain a more comprehensive understanding of the factors influencing fish assemblages. Improving our ability to assess such fish populations in close proximity to structures will assist in increasing this knowledge. In the present study we provide the first trial use of Baited Remote Underwater Stereo-Video systems (stereo BRUVs) for the quantification of motile fauna in close proximity to offshore wind turbines. The study was conducted in the Irish Sea and finds the technique to be a viable means of assessing the motile fauna of such environments. The present study found a mixture of species including bottom dwellers, motile crustaceans and large predatory fish. The majority of taxa observed were found to be immature individuals with few adult individuals recorded. The most abundant species were the angular crab (Goneplax rhomboides) and the small-spotted catshark (Scyliorhinus canicula). Of note in this study was the generally low abundance and diversity of taxa recorded across all samples, we hypothesise that this reflects the generally poor state of the local fauna of the Irish Sea. The faunal assemblages sampled in close proximity to turbines were observed to alter with increasing distance from the structure, species more characteristic of hard bottom environments were in abundance at the turbines (e.g. Homarus gammarus, Cancer pagarus, Scyliorhinus spp.) and those further away more characteristic of soft bottoms (e.g. Norwegian Lobster). This study highlights the need for the environmental impacts of offshore renewables on motile fauna to be assessed using targeted and appropriate tools. Stereo BRUVs provide one of those tools, but like

  11. Assessing Fish and Motile Fauna around Offshore Windfarms Using Stereo Baited Video

    PubMed Central

    Griffin, Ross A.; Robinson, Gary J.; West, Ashley; Gloyne-Phillips, Ian T.; Unsworth, Richard K. F.

    2016-01-01

    There remains limited knowledge of how offshore windfarm developments influence fish assemblages, particularly at a local scale around the turbine structures. Considering the existing levels of anthropogenic pressures on coastal fish populations it is becoming increasingly important for developers and environmental regulators to gain a more comprehensive understanding of the factors influencing fish assemblages. Improving our ability to assess such fish populations in close proximity to structures will assist in increasing this knowledge. In the present study we provide the first trial use of Baited Remote Underwater Stereo-Video systems (stereo BRUVs) for the quantification of motile fauna in close proximity to offshore wind turbines. The study was conducted in the Irish Sea and finds the technique to be a viable means of assessing the motile fauna of such environments. The present study found a mixture of species including bottom dwellers, motile crustaceans and large predatory fish. The majority of taxa observed were found to be immature individuals with few adult individuals recorded. The most abundant species were the angular crab (Goneplax rhomboides) and the small-spotted catshark (Scyliorhinus canicula). Of note in this study was the generally low abundance and diversity of taxa recorded across all samples, we hypothesise that this reflects the generally poor state of the local fauna of the Irish Sea. The faunal assemblages sampled in close proximity to turbines were observed to alter with increasing distance from the structure, species more characteristic of hard bottom environments were in abundance at the turbines (e.g. Homarus gammarus, Cancer pagarus, Scyliorhinus spp.) and those further away more characteristic of soft bottoms (e.g. Norwegian Lobster). This study highlights the need for the environmental impacts of offshore renewables on motile fauna to be assessed using targeted and appropriate tools. Stereo BRUVs provide one of those tools, but like

  12. Process notebook for aquatic ecosystem simulation. [Evaluation of fish models for impact assessment

    SciTech Connect

    Swartzman, G.; Smith, E.; McKenzie, D.; Haar, B.; Fickeisen, D.

    1980-01-01

    This notebook contains a detailed comparison of 14 models of fish growth, energetics, population dynamics, and feeding. It is a basic document for the evaluation of thes models' usefulness for impact assessment. Model equations are categorized into 18 subprocesses comprising the major processes of consumption, predation, metabolic processes, growth, fecundity, and mortality. The model equations are compared in a standard notation and the equation rationales are considered and put into a historical framework with historical precedence charts. Model parameters are computed in standard units and data sources and techniques used for parameter estimation are identified. A translator compares standard notation with the notation used in the models. The major contribution of this work is that, for the first time, fish models are arrayed with their assumptions laid bare and their parameter values compared, allowing elucidation of model differeances and evaluaton of model behavior and data needs by using the process notebook as a base for further simulation comparison.

  13. Age-related aneuploidy analysis of human blood cells in vivo by fluorescence in situ hybridization (FISH).

    PubMed

    Mukherjee, A B; Alejandro, J; Payne, S; Thomas, S

    1996-09-18

    All prior studies on human age-related chromosomal analysis were done using only metaphase figures derived from lymphocyte cultures in vitro. However, we believe that this procedure may provide only partial information, since the chromosomal abnormalities probably hidden in non-dividing and/or terminally differentiated leukocytes will not be detected by this method. We, therefore, have attempted to analyze the nature and extent of chromosome-specific aneuploidy at interphase by fluorescence in situ hybridization (FISH) in differentiated myeloid cells in vivo derived from various age-group people. Our data from an analysis of 30,032 cells derived from 12 healthy donors indicate that there is an increase in the mean percentages of myeloid cells with chromosome-specific aneuploidy in the older groups as opposed to that of the younger groups. This increase is applicable to all the three cell types examined (promyelocytes, metamyelocytes and polymorphs). In both the younger and older females, the relatively higher mean frequencies of cells with aneuploidy were noted for chromosome nos. 4, 6 and the X, whereas the lowest mean frequencies of cells with aneuploidy were consistently observed for chromosome no. 3. In the younger and older male donors, similar to the female donors except the X chromosome the higher percentages of aneuploid cells were observed for chromosome nos. 4 and 6 whereas the lowest mean frequencies of aneuploid cells were noted for chromosome no. 3. Among the five autosomes studied, chromosome no. 3 consistently yielded the lowest frequency of aneuploidy in all the three cell types derived from both the younger and older groups of males and females. This could presumably mean that the maintenance of a very high frequency of cells with disomy for chromosome no. 3 might be more beneficial for the process of survival and/or differentiation of myeloid cells as compared to that of other autosomes such as chromosome nos. 4 and 6. Among the five autosomes

  14. Using otolith microchemistry and shape to assess the habitat value of oil structures for reef fish.

    PubMed

    Fowler, Ashley M; Macreadie, Peter I; Bishop, David P; Booth, David J

    2015-05-01

    Over 7500 oil and gas structures (e.g. oil platforms) are installed in offshore waters worldwide and many will require decommissioning within the next two decades. The decision to remove such structures or turn them into reefs (i.e. 'rigs-to-reefs') hinges on the habitat value they provide, yet this can rarely be determined because the residency of mobile species is difficult to establish. Here, we test a novel solution to this problem for reef fishes; the use of otolith (earstone) properties to identify oil structures of residence. We compare the otolith microchemistry and otolith shape of a site-attached coral reef fish (Pseudanthias rubrizonatus) among four oil structures (depth 82-135 m, separated by 9.7-84.2 km) on Australia's North West Shelf to determine if populations developed distinct otolith properties during their residency. Microchemical signatures obtained from the otolith edge using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) differed among oil structures, driven by elements Sr, Ba and Mn, and to a lesser extent Mg and Fe. A combination of microchemical data from the otolith edge and elliptical Fourier (shape) descriptors allowed allocation of individuals to their 'home' structure with moderate accuracy (overall allocation accuracy: 63.3%, range: 45.5-78.1%), despite lower allocation accuracies for each otolith property in isolation (microchemistry: 47.5%, otolith shape: 45%). Site-specific microchemical signatures were also stable enough through time to distinguish populations during 3 separate time periods, suggesting that residence histories could be recreated by targeting previous growth zones in the otolith. Our results indicate that reef fish can develop unique otolith properties during their residency on oil structures which may be useful for assessing the habitat value of individual structures. The approach outlined here may also be useful for determining the residency of reef fish on artificial reefs, which would

  15. Genetic differentiation among distinct karyomorphs of the wolf fish Hoplias malabaricus species complex (Characiformes, Erythrinidae) and report of unusual hybridization with natural triploidy.

    PubMed

    Utsunomia, R; Alves, J C Pansonato; Paiva, L R S; Silva, G J Costa; Oliveira, C; Bertollo, L A C; Foresti, F

    2014-11-01

    In this study, genetic differentiation between karyomorphs A (2n = 42) and D (2n = 39/40) of the wolf fish Hoplias malabaricus, which is comprised of several cryptic species that present a wide variety of diploid chromosome numbers and sex chromosome systems, resulting in the identification of seven distinct karyomorphs (A-G), was investigated using a combination of molecular and cytogenetic tools. Deep sequence divergences for both karyomorphs were observed and indicate a long period of reproductive isolation between karyomorphs A and D. Additionally, one individual with 61 chromosomes was identified, which, as far as is known, is the first case of natural triploidy resulting from the hybridization between these highly differentiated karyomorphs of H. malabaricus. Molecular and cytogenetic analyses revealed that this allotriploid specimen carries two sets of maternal chromosomes from karyomorph D (2n = 40) and one set of chromosomes from karyomorph A (n = 21). Moreover, ribosomal sites and active nucleolus organizer regions from both parental contributors were found in the triploid hybrid. Considering the significant genetic distances between karyomorphs A and D, one of the primary reasons for the lack of recurrent reports of hybridization in the H. malabaricus species complex may be due to post-zygotic barriers, such as hybrid sterility or unviability.

  16. Concentrations of heavy metals in marine wild fishes captured from the southern sea of Korea and associated health risk assessments

    NASA Astrophysics Data System (ADS)

    Hwang, Dong-Woon; Kim, Seong-Soo; Kim, Seong-Gil; Kim, Dong-Sun; Kim, Tae-Hoon

    2017-07-01

    Concentrations of heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) were determined in edible parts (muscle) of 34 marine wild fish caught from the southern sea of Korea in 2007 and 2008 in order to understand the accumulation pattern of heavy metals in wild fish and to assess the potential health risk posed by fish consumption. The highest concentrations in the muscle of 17 pelagic and 17 demersal fishes were Zn and As, respectively, while the lowest concentration in both fishes was Cd. The mean concentrations of all metals except As in wild fish were much lower than the regulatory limits for fish and fishery products applied in a number of countries. Unlike other metals, As concentration in wild fish of this study region was relatively higher than that found in other country. Estimated daily intake (EDI) of the metals was in the range of 0.05% to 22.5% of the provisional maximum tolerable daily intakes (PMTDI). Similarly, the target hazard quotient (THQ) was below 1.0 for each metal. These results imply that the consumption of the investigated wild fish do not cause significant adverse health effects.

  17. Assessment of Student Learning in a Hybrid PBL Capstone Seminar

    ERIC Educational Resources Information Center

    Levia, Del F., Jr.; Quiring, Steven M.

    2008-01-01

    Assessment is a key component of the learning process. In order to maximize student learning, instructors need to provide students with appropriate, explicit and timely assessment. Despite the potential benefits of problem-based learning, some instructors may be reluctant to adopt this approach because it will require them to modify their current…

  18. Assessing Fishing and Marine Biodiversity Changes Using Fishers' Perceptions: The Spanish Mediterranean and Gulf of Cadiz Case Study

    PubMed Central

    Coll, Marta; Carreras, Marta; Ciércoles, Cristina; Cornax, Maria-José; Gorelli, Giulia; Morote, Elvira; Sáez, Raquel

    2014-01-01

    Background The expansion of fishing activities has intensively transformed marine ecosystems worldwide. However, available time series do not frequently cover historical periods. Methodology Fishers' perceptions were used to complement data and characterise changes in fishing activity and exploited ecosystems in the Spanish Mediterranean Sea and Gulf of Cadiz. Fishers' interviews were conducted in 27 fishing harbours of the area, and included 64 fishers from ages between 20 to >70 years old to capture the experiences and memories of various generations. Results are discussed in comparison with available independent information using stock assessments and international convention lists. Principal Findings According to fishers, fishing activity substantially evolved in the area with time, expanding towards deeper grounds and towards areas more distant from the coast. The maximum amount of catch ever caught and the weight of the largest species ever captured inversely declined with time. Fishers (70%) cited specific fishing grounds where depletion occurred. They documented ecological changes of marine biodiversity during the last half of the century: 94% reported the decline of commercially important fish and invertebrates and 61% listed species that could have been extirpated, with frequent mentions to cartilaginous fish. Declines and extirpations were in line with available quantitative evaluations from stock assessments and international conventions, and were likely linked to fishing impacts. Conversely, half of interviewed fishers claimed that several species had proliferated, such as cephalopods, jellyfish, and small-sized fish. These changes were likely related to trophic cascades due to fishing and due to climate change effects. The species composition of depletions, local extinctions and proliferations showed differences by region suggesting that regional dynamics are important when analysing biodiversity changes. Conclusions/Significance Using fishers

  19. Assessing fishing and marine biodiversity changes using fishers' perceptions: the Spanish Mediterranean and Gulf of Cadiz case study.

    PubMed

    Coll, Marta; Carreras, Marta; Ciércoles, Cristina; Cornax, Maria-José; Gorelli, Giulia; Morote, Elvira; Sáez, Raquel

    2014-01-01

    The expansion of fishing activities has intensively transformed marine ecosystems worldwide. However, available time series do not frequently cover historical periods. Fishers' perceptions were used to complement data and characterise changes in fishing activity and exploited ecosystems in the Spanish Mediterranean Sea and Gulf of Cadiz. Fishers' interviews were conducted in 27 fishing harbours of the area, and included 64 fishers from ages between 20 to >70 years old to capture the experiences and memories of various generations. Results are discussed in comparison with available independent information using stock assessments and international convention lists. According to fishers, fishing activity substantially evolved in the area with time, expanding towards deeper grounds and towards areas more distant from the coast. The maximum amount of catch ever caught and the weight of the largest species ever captured inversely declined with time. Fishers (70%) cited specific fishing grounds where depletion occurred. They documented ecological changes of marine biodiversity during the last half of the century: 94% reported the decline of commercially important fish and invertebrates and 61% listed species that could have been extirpated, with frequent mentions to cartilaginous fish. Declines and extirpations were in line with available quantitative evaluations from stock assessments and international conventions, and were likely linked to fishing impacts. Conversely, half of interviewed fishers claimed that several species had proliferated, such as cephalopods, jellyfish, and small-sized fish. These changes were likely related to trophic cascades due to fishing and due to climate change effects. The species composition of depletions, local extinctions and proliferations showed differences by region suggesting that regional dynamics are important when analysing biodiversity changes. Using fishers' perceptions, fishing and ecological changes in the study area were

  20. Assessing estuarine environmental quality using fish-based indices: performance evaluation under climatic instability.

    PubMed

    Martinho, F; Viegas, I; Dolbeth, M; Leitão, R; Cabral, H N; Pardal, M A

    2008-11-01

    The seasonal variation of five selected multimetric indices for the determination of the Ecological Quality Status (EQS) of transitional waters was evaluated, as well as the indices' responses to an extreme drought event that occurred in 2005. The database used regards the Mondego River estuary, which was sampled from June 2003 to August 2006 on a monthly basis. Among the selected indices (EBI-Deegan et al. [Deegan, L., Finn, J.T., Ayvazlan, S.G., Ryder-Kieffer, C.A., Buonaccoesi, J., 1997. Development and validation of an Estuarine Biotic Integrity Index. Estuaries 30(3), 601-617], EDI-Borja et al. [Borja, A., Franco, J., Valencia, V., Bald, J., Muxika, I., Belzunce, M.J., Solaun, O., 2004. Implementation of the European Water Framework Directive from the Basque Country (northern Spain): a methodological approach. Marine Pollution Bulletin 48(3-4), 209-218], EFCI-Harrison and Whitfield [Harrison, T.D., Whitfield, A.K., 2004. A multi-metric fish index to assess the environmental condition of estuaries. Journal of Fish Biology 65, 683-710], EBI-Breine et al. [Breine, J.J., Maes, J., Quataert, P., Van den Bergh, E., Simoens, I., Van Thuyne, G., Belpaire, C., 2007. A fish-based assessment tool for the ecological quality of the brackish Scheldt estuary in Flanders (Belgium). Hydrobiologia 575, 141-159] and TFCI - Coates et al. [Coates, S., Waugh, A., Anwar, A., Robson, M., 2007. Efficacy of a multi-metric fish index as an analysis tool for the transitional fish component of the Water Framework Directive. Marine Pollution Bulletin 55, 225-240]), the EBI by Breine et al. (2007) was the only that evidenced clear interannual and seasonal variations. The EQS by the several indices ranged from "Low" to "High", depending on the index considered, evidencing the high level of mismatch between indices. The results are discussed in the scope of the EU Water Framework Directive, regarding monitoring strategies, application of indices and EQS assessment.

  1. Assessment of genetic purity in rice (Oryza sativa L.) hybrids using microsatellite markers.

    PubMed

    Bora, Anjana; Choudhury, Partha Ray; Pande, Veena; Mandal, Asit B

    2016-06-01

    The objective of the present study is to detect genetic impurity in the seed lots of CMS lines, restorers and hybrids and to identify signature markers to differentiate parents and hybrids through DNA-based assays. Furthermore, attempts have been made to find out an alternative to Grow-Out-Test, which is very tedious, time consuming and used conventionally for seed genetic purity testing since beginning of quality seed multiplication chain. Fifty-one rice-specific sequence tagged microsatellite (STMS) primer pairs distributed throughout the rice genome were employed for fingerprinting of eight rice hybrids and their parental lines with a view to assess variation within parental lines and to test the genetic purity of the commercial seed lots. Among those, 51 markers, 28 microsatellite markers showed polymorphism (54.90 %). A total of 98 alleles were obtained with an average of 1.92 alleles per primer pair and number of alleles amplified for each primer pair ranged from 1 to 4. A set of markers were identified to differentiate parental lines of the hybrids and which emphasizes the immense scope of those molecular markers for their use in the unambiguous identification of hybrid, which would be of great benefit to farmers that depend on the hybrids.

  2. Hybrid Airships for Lift: A New Lift Paradigm and a Pragmatic Assessment of the Vehicle’s Key Operational Challenges

    DTIC Science & Technology

    2011-12-01

    required lift for flight, Hybrid Airships use a combination of buoyant lift (provided by a gas such as Helium), aerodynamic lift (generated by airflow...AIR FORCE FELLOWS AIR UNIVERSITY HYBRID AIRSHIPS FOR LIFT: A NEW LIFT PARADIGM AND A PRAGMATIC ASSESSMENT OF THE...00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Hybrid Airships for Lift: A New Lift Paradigm And A Pragmatic Assessment Of The Vehicle’s Key

  3. Assessment of Technologies for Noncryogenic Hybrid Electric Propulsion

    NASA Technical Reports Server (NTRS)

    Dever, Timothy P.; Duffy, Kirsten P.; Provenza, Andrew J.; Loyselle, Patricia L.; Choi, Benjamin B.; Morrison, Carlos R.; Lowe, Angela M.

    2015-01-01

    The Subsonic Fixed Wing Project of NASA's Fundamental Aeronautics Program is researching aircraft propulsion technologies that will lower noise, emissions, and fuel burn. One promising technology is noncryogenic electric propulsion, which could be either hybrid electric propulsion or turboelectric propulsion. Reducing dependence on the turbine engine would certainly reduce emissions. However, the weight of the electricmotor- related components that would have to be added would adversely impact the benefits of the smaller turbine engine. Therefore, research needs to be done to improve component efficiencies and reduce component weights. This study projects technology improvements expected in the next 15 and 30 years, including motor-related technologies, power electronics, and energy-storage-related technologies. Motor efficiency and power density could be increased through the use of better conductors, insulators, magnets, bearings, structural materials, and thermal management. Energy storage could be accomplished through batteries, flywheels, or supercapacitors, all of which expect significant energy density growth over the next few decades. A first-order approximation of the cumulative effect of each technology improvement shows that motor power density could be improved from 3 hp/lb, the state of the art, to 8 hp/lb in 15 years and 16 hp/lb in 30 years.

  4. Microbiological assessment along the fish production chain of the Norwegian pelagic fisheries sector--Results from a spot sampling programme.

    PubMed

    Svanevik, Cecilie Smith; Roiha, Irja Sunde; Levsen, Arne; Lunestad, Bjørn Tore

    2015-10-01

    Microbes play an important role in the degradation of fish products, thus better knowledge of the microbiological conditions throughout the fish production chain may help to optimise product quality and resource utilisation. This paper presents the results of a ten-year spot sampling programme (2005-2014) of the commercially most important pelagic fish species harvested in Norway. Fish-, surface-, and storage water samples were collected from fishing vessels and processing factories. Totally 1,181 samples were assessed with respect to microbiological quality, hygiene and food safety. We introduce a quality and safety assessment scheme for fresh pelagic fish recommending limits for heterotrophic plate counts (HPC), thermos tolerant coliforms, enterococci and Listeria monocytogenes. According to the scheme, in 25 of 41 samplings, sub-optimal conditions were found with respect to quality, whereas in 21 and 9 samplings, samples were not in compliance concerning hygiene and food safety, respectively. The present study has revealed that the quality of pelagic fish can be optimised by improving the hygiene conditions at some critical points at an early phase of the production chain. Thus, the proposed assessment scheme may provide a useful tool for the industry to optimise quality and maintain consumer safety of pelagic fishery products.

  5. Application of a regional procedure to assess the risk to fish from high sediment concentrations.

    PubMed

    Watts, Carol D; Naden, Pamela S; Cooper, David M; Gannon, Beate

    2003-10-01

    Periods of high suspended sediment concentration in rivers can affect the behaviour, health and habitat of freshwater fish. A simple regional model relating daily mean suspended sediment concentration in rivers to flow and percentage of cropped and urban land has been applied to the Lower Swale, UK. The model uses a GIS catchment coverage of hydrological response units (HRUs) of area 5-8 km2, each of which is assumed hydrologically independent and drains to an identified river reach. The sediment delivery properties of each HRU are a function of its land use characteristics determined from existing databases, and hydrological conditions determined from effective rainfall measurements. Daily mean suspended sediment concentrations for each river reach were derived by cumulating simulated HRU flows and sediment loads down successive reaches. A map of the modelled 10% quantile sediment concentrations is presented for both HRUs and river reaches. The map is substantially different from existing erosion risk maps because the delivery model is driven by flow in addition to land use, rather than by soil type. Frequency curves showing the exceedance probability of mean simulated sediment concentrations over 1-6-day durations have been derived using peaks-over-threshold techniques. Maps of the risk of harm to fish, based on the probability of 1- and 4-day sediment concentrations exceeding 80 mg l(-1), are presented. Such maps can be used to assess the impact of sediment on fish and for setting appropriate river water quality objectives.

  6. Comparative toxicology for risk assessment of marine fishes and crustaceans. [Cyprinodon variegatus

    SciTech Connect

    Suter, G.W. II; Rosen, A.E. )

    1988-05-01

    The goal of this study was to collect data on the effects of chemicals on marine fishes and crustaceans and to evaluate the predictive power of the data for assessing risks to marine resources. The data sets consisted of acute median lethal concentrations (LC{sub 50s}) and chronic maximum acceptable toxicant concentrations (MATCs). They were analyzed with regression models and simple comparisons. The conclusions include the following: (1) the variability found in the marine data was comparable to that found in freshwater data; (2) the standard marine test fish Cyprinodon variegatus appears to be representative of marine fishes; (3) the responses of marine crustaceans are so highly diverse that the concept of a representative crustacean is questionable; (4) mysid and penaeid shrimp appear to be particularly sensitive to toxic chemicals. These conclusions are subject to the constraints of the existing limited data base and should be confirmed by a systematic study of the relative sensitivity of marine organisms to chemicals with diverse modes of action.

  7. [Measurement and preliminary human health risk assessment of representative organochlorines in farmed Mandarin fish].

    PubMed

    Wang, Ying; Qiu, Yan-Ling; Fei, Yong; Li, Li; Zhu, Zhi-Liang; Zhao, Jian-Fu; Yao, En-Qin; Yao, Yu-Xin

    2011-08-01

    Concentrations of representative organochlorines (OCs), including organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in a batch of farmed mandarin fish from a cultivation pond in Wujiang City, Jiangsu Province, were determined with GC-ECD. Meanwhile, a preliminary human health risk assessment was conducted. Results showed that, the concentrations of dichlorodiphenyltrichloroethanes (DDTs), hexachlorocyclohexanes (HCHs), hexachlorobenzene (HCB) and PCBs in the farmed mandarin fish were in the range of 1.3-4.57 ng/g, 0.13-1.24 ng/g, 0.07-0.44 ng/g and 0-5.22 ng/g, respectively, with an average value of 2.96, 0.40, 1.27 and 0.7 ng/g, respectively. These values were far below the corresponding residue limits set by China's Ministry of Health and the U.S. Food and Drug Administration, and at the low end of the global pollution bar. Referring to the reference values given by USEPA Integrated Risk Information System, calculated non-carcinogenic hazard ratios (HRs) of DDTs, HCB and PCBs were all <1 and carcinogenic HRs of DDTs, HCHs, HCB and PCBs were all >1. The results indicated that DDTs, HCHs and HCB in farmed mandarin fish did not have negative human health influence, but existed potential carcinogenic risk to humans. Compared to rural residents, urban residents were more vulnerable to DDTs, HCHs, HCB and PCBs threats.

  8. Hybridization leads to sensory repertoire expansion in a gynogenetic fish, the Amazon molly (poecilia formosa): a test of the hybrid-sensory expansion hypothesis.

    PubMed

    Sandkam, Benjamin A; Joy, Jeffrey B; Watson, Corey T; Gonzalez-Bendiksen, Pablo; Gabor, Caitlin R; Breden, Felix

    2013-01-01

    Expansions in sensory systems usually require processes such as gene duplication and divergence, and thus evolve slowly. We evaluate a novel mechanism leading to rapid sensory repertoire expansion: hybrid-sensory expansion (HSE). HSE occurs when two species with differently tuned sensory systems form a hybrid, bringing together alleles from each of the parental species. In one generation, a sensory repertoire is created that is the sum of the variance between parental species. The Amazon molly presents a unique opportunity to test the HSE hypothesis in a "frozen" hybrid. We compared opsin sequences of the Amazon molly, Poecilia formosa, to those of the parental species. Both parental species are homozygous at the RH2-1 locus and each of the four long wavelength sensitive loci, while P. formosa possess two different alleles at these loci; one matching each parental allele. Gene expression analysis showed P. formosa use the expanded opsin repertoire that was the result of HSE. Additionally, behavioral tests revealed P. formosa respond to colored stimuli in a manner similar or intermediate to the parental species P. mexicana and P. latipinna. Together these results strongly support the HSE hypothesis. Hybrid-sensory repertoire expansion is likely important in other hybrid species and in other sensory systems.

  9. Rapid detection of clarithromycin-resistant Helicobacter pylori in patients with dyspepsia by fluorescent in situ hybridization (FISH) compared with the E-test.

    PubMed

    Moosavian, Mojtaba; Tajbakhsh, Saeid; Samarbaf-Zadeh, Ali Reza

    2007-01-01

    Clarithromycin is the antibiotic of choice for treatment of H.pylori-related dyspepsia, but unfortunately, resistance to clarithromycin is not rare. Detection of resistant strains takes 2 to 4 days by conventional methods. In this report, we applied the FISH technique for rapid detection of H.pylori in biopsies of dyspeptic patients. Gastric biopsies from 50 patients suffering from dyspepsia were tested in this study. Part of each biopsy specimen was cultured and the remainder was fixed in liquid nitrogen. After mounting of frozen sections on microscopic slides, they were hybridized with oligonucleotide probes for detection of clarithromycin-resistant H.pylori. The slides were visualized under a fluorescent microscope. Susceptibility of cultured strains of H. pylori to clarithromycin was also determined by the E-test and the results were compared. Twenty-five of 50 biopsy specimens examined by FISH were positive for H.pylori. FISH showed that 17 strains (68%) were susceptible to clarithromycin and 6 strains (24%) were resistant. Bacteria isolated following culture of 2 biopsy specimens had a mixture of both clarithromycin-susceptible and resistant strains (8%). There was no discrepancy between the E-test and FISH technique for detection of resistant strains of H.pylori. FISH is a rapid technique for detection of H.pylori in clinical samples. Moreover, strains susceptible to clarithromycin can be detected quickly. Therefore, this method is suitable for determination of susceptibility of H.pylori to clarithromycin, especially when a quick decision is necessary for treating dyspeptic patients.

  10. Proposed best modeling practices for assessing the effects of ecosystem restoration on fish

    USGS Publications Warehouse

    Rose, Kenneth A; Sable, Shaye; DeAngelis, Donald L.; Yurek, Simeon; Trexler, Joel C.; Graf, William L.; Reed, Denise J.

    2015-01-01

    Large-scale aquatic ecosystem restoration is increasing and is often controversial because of the economic costs involved, with the focus of the controversies gravitating to the modeling of fish responses. We present a scheme for best practices in selecting, implementing, interpreting, and reporting of fish modeling designed to assess the effects of restoration actions on fish populations and aquatic food webs. Previous best practice schemes that tended to be more general are summarized, and they form the foundation for our scheme that is specifically tailored for fish and restoration. We then present a 31-step scheme, with supporting text and narrative for each step, which goes from understanding how the results will be used through post-auditing to ensure the approach is used effectively in subsequent applications. We also describe 13 concepts that need to be considered in parallel to these best practice steps. Examples of these concepts include: life cycles and strategies; variability and uncertainty; nonequilibrium theory; biological, temporal, and spatial scaling; explicit versus implicit representation of processes; and model validation. These concepts are often not considered or not explicitly stated and casual treatment of them leads to mis-communication and mis-understandings, which in turn, often underlie the resulting controversies. We illustrate a subset of these steps, and their associated concepts, using the three case studies of Glen Canyon Dam on the Colorado River, the wetlands of coastal Louisiana, and the Everglades. Use of our proposed scheme will require investment of additional time and effort (and dollars) to be done effectively. We argue that such an investment is well worth it and will more than pay back in the long run in effective and efficient restoration actions and likely avoided controversies and legal proceedings.

  11. Assessment of faecal glucocorticoid metabolite excretion in captive female fishing cats (Prionailurus viverinus) in Thailand

    PubMed Central

    Khonmee, Jaruwan; Vorawattanatham, Narathip; Pinyopummin, Anuchai; Thitaram, Chatchote; Somgird, Chaleamchat; Punyapornwithaya, Veerasak; Brown, Janine L.

    2016-01-01

    There is little information on the endocrinology of fishing cats (Prionailurus viverinus), an endangered species in Southeast Asia, especially that pertaining to adrenal function. This study characterized faecal glucocorticoid metabolites in female fishing cats housed at Chiang Mai Night Safari to investigate seasonal and age relationships in hormone patterns. Faecal samples were collected 3 days/week for 1 year from seven females ranging in age from 4.5 to 9.6 years. A corticosterone enzyme immunoassay was validated for fishing cats by showing increases (∼60%) in faecal glucocorticoid immunoactivity above pre-treatment baseline levels within 1–2 days after an adrenocorticotrophic hormone injection. Faecal glucocorticoid metabolite concentrations were not related to age (P > 0.05), but there was a seasonal effect, with concentrations being higher (P < 0.05) during the winter (1.54 ± 0.04 µg/g) and rainy season (1.43 ± 0.04 µg/g) compared with the summer (1.22 ± 0.05 µg/g). Significant relationships were found between faecal glucocorticoids and rainfall (positive) and day length (negative), but not a temperature–humidity index. This is the first study to assess adrenal steroidogenic activity in female fishing cats, and we found that glucocorticoid metabolite production was influenced by seasonal factors, but not by age. We conclude that weather patterns should be taken into consideration in future studies of glucocorticoid activity in this endangered species, especially those studies aimed at improving captive management to create self-sustaining and healthy populations. PMID:27293767

  12. Assessment of faecal glucocorticoid metabolite excretion in captive female fishing cats (Prionailurus viverinus) in Thailand.

    PubMed

    Khonmee, Jaruwan; Vorawattanatham, Narathip; Pinyopummin, Anuchai; Thitaram, Chatchote; Somgird, Chaleamchat; Punyapornwithaya, Veerasak; Brown, Janine L

    2016-01-01

    There is little information on the endocrinology of fishing cats (Prionailurus viverinus), an endangered species in Southeast Asia, especially that pertaining to adrenal function. This study characterized faecal glucocorticoid metabolites in female fishing cats housed at Chiang Mai Night Safari to investigate seasonal and age relationships in hormone patterns. Faecal samples were collected 3 days/week for 1 year from seven females ranging in age from 4.5 to 9.6 years. A corticosterone enzyme immunoassay was validated for fishing cats by showing increases (∼60%) in faecal glucocorticoid immunoactivity above pre-treatment baseline levels within 1-2 days after an adrenocorticotrophic hormone injection. Faecal glucocorticoid metabolite concentrations were not related to age (P > 0.05), but there was a seasonal effect, with concentrations being higher (P < 0.05) during the winter (1.54 ± 0.04 µg/g) and rainy season (1.43 ± 0.04 µg/g) compared with the summer (1.22 ± 0.05 µg/g). Significant relationships were found between faecal glucocorticoids and rainfall (positive) and day length (negative), but not a temperature-humidity index. This is the first study to assess adrenal steroidogenic activity in female fishing cats, and we found that glucocorticoid metabolite production was influenced by seasonal factors, but not by age. We conclude that weather patterns should be taken into consideration in future studies of glucocorticoid activity in this endangered species, especially those studies aimed at improving captive management to create self-sustaining and healthy populations.

  13. Screening level fish community risk assessment of chemical warfare agents in the Baltic Sea.

    PubMed

    Sanderson, Hans; Fauser, Patrik; Thomsen, Marianne; Sørensen, Peter B

    2008-06-15

    Chemical warfare agents (CWAs) have been disposed of in various fashions over the past decades. Significant amounts (approximately 11,000 tonnes) have been dumped in the Baltic Sea east of the island Bornholm following the disarmament of Germany after World War II, causing concerns over potential environmental risks. Absence of risk based on assumptions of extremely low solubility of CWAs cannot alone dismiss these concerns. Existing and modelled fate and effects data were used in the analysis to assess the fish community risk level. The most realistic and also conservative assessment result is the scenario describing 70 m water depth for the most realistic dump-site area with a focus on chronic toxicity, at 0-20 cm above the sediment, yielding a total mixture toxic unit (TU) of 0.62. Triphenylarsine is the CWA with the highest realistic risk profile at 0.2 TU for the fish community followed by Adamsite (0.17), Clark I (0.086) and Yperite (0.083) TU. Adamsite is more persistent and constitutes a potential risk for a longer period than triphenylarsine. The seawater volume potentially at risk is <4 m above sediment and <58 km down current of dump sites. Further risk assessment of dumped CWAs in the Baltic Sea is warranted.

  14. Designing long-term fish community assessments in connecting channels: Lessons from the Saint Marys River

    USGS Publications Warehouse

    Schaeffer, Jeff; Rogers, Mark W.; Fielder, David G.; Godby, Neal; Bowen, Anjanette K.; O'Connor, Lisa; Parrish, Josh; Greenwood, Susan; Chong, Stephen; Wright, Greg

    2014-01-01

    Long-term surveys are useful in understanding trends in connecting channel fish communities; a gill net assessment in the Saint Marys River performed periodically since 1975 is the most comprehensive connecting channels sampling program within the Laurentian Great Lakes. We assessed efficiency of that survey, with intent to inform development of assessments at other connecting channels. We evaluated trends in community composition, effort versus estimates of species richness, ability to detect abundance changes for four species, and effects of subsampling yellow perch catches on size and age-structure metrics. Efficiency analysis revealed low power to detect changes in species abundance, whereas reduced effort could be considered to index species richness. Subsampling simulations indicated that subsampling would have allowed reliable estimates of yellow perch (Perca flavescens) population structure, while greatly reducing the number of fish that were assigned ages. Analyses of statistical power and efficiency of current sampling protocols are useful for managers collecting and using these types of data as well as for the development of new monitoring programs. Our approach provides insight into whether survey goals and objectives were being attained and can help evaluate ability of surveys to answer novel questions that arise as management strategies are refined.

  15. Sequential female assessment drives complex sexual selection on bower shape in a cichlid fish.

    PubMed

    Young, Kyle A; Genner, Martin J; Haesler, Marcel P; Joyce, Domino A

    2010-08-01

    In many animals, sexual selection on male traits results from female mate choice decisions made during a sequence of courtship behaviors. We use a bower-building cichlid fish, Nyassachromis cf. microcephalus, to show how applying standard selection analysis to data on sequential female assessment provides new insights into sexual selection by mate choice. We first show that the cumulative selection differentials confirm previous results suggesting female choice favors males holding large volcano-shaped sand bowers. The sequential assessment analysis reveals these cumulative differentials are the result of selection acting on different bower dimensions during the courtship sequence; females choose to follow males courting from tall bowers, but choose to engage in premating circling with males holding bowers with large diameter platforms. The approach we present extends standard selection analysis by partitioning the variances of increasingly accurate estimates of male reproductive fitness and is applicable to systems in which sequential female assessment drives sexual selection on male traits.

  16. Use of In Vitro Absorption, Distribution, Metabolism, and Excretion (ADME) Data in Bioaccumulation Assessments for Fish

    SciTech Connect

    Nichols, John W.; Erhardt, Susan; Dyer, Scott; James, Margaret O.; Moore, Margo; Plotzke, Kathleen; Segner, Helmut; Schultz, Irvin R.; Thomas, Karluss; Vasiluk, Luba; Weisbrod, Anne V.

    2007-11-01

    A scientific workshop was held in 2006 to discuss the use of in vitro Absorption, Distribution, Metabolism, and Excretion (ADME) data in chemical bioaccumulation assessments for fish. Computer-based (in silico) modeling tools are widely used to estimate chemical bioaccumulation. These in silico methods have inherent limitations that result in inaccurate estimates for many compounds. Based on a review of the science workshop participants concluded that two factors, absorption and metabolism, represent the greatest sources of uncertainty in current bioaccumulation models. Both factors can be investigated experimentally using in vitro test systems.

  17. Hybrid Probabilistic and Possibilistic Safety Assessment: Methodology and Application

    NASA Astrophysics Data System (ADS)

    Kato, Kazuyuki; Amano, Osamu; Ueda, Hiroyoshi; Ikeda, Takao; Yoshida, Hideji; Takase, Hiroyasu

    This paper presents a unified methodology to handle variability and ignorance by using probabilistic and possibilistic techniques respectively. The methodology has been applied to the safety assessment of geological disposal of high-level radioactive waste. Uncertainties associated with scenarios, models and parameters were defined in terms of fuzzy membership functions derived through a series of interviews to the experts, while variability was formulated by means of probability density functions (pdfs) based on available data sets. The exercise demonstrated the applicability of the new methodology and, in particular, its advantage in quantifying uncertainties based on expert opinion and in providing information on the dependence of assessment results on the level of conservatism. In addition, it was shown that sensitivity analysis can identify key parameters contributing to uncertainties associated with results of the overall assessment. The information mentioned above can be utilized to support decision-making and to guide the process of disposal system development and optimization of protection against potential exposure.

  18. Efficient hybrid density functional calculations in solids: assessment of the Heyd-Scuseria-Ernzerhof screened Coulomb hybrid functional.

    PubMed

    Heyd, Jochen; Scuseria, Gustavo E

    2004-07-15

    The present work introduces an efficient screening technique to take advantage of the fast spatial decay of the short range Hartree-Fock (HF) exchange used in the Heyd-Scuseria-Ernzerhof (HSE) screened Coulomb hybrid density functional. The screened HF exchange decay properties and screening efficiency are compared with traditional hybrid functional calculations on solids. The HSE functional is then assessed using 21 metallic, semiconducting, and insulating solids. The examined properties include lattice constants, bulk moduli, and band gaps. The results obtained with HSE exhibit significantly smaller errors than pure density functional theory (DFT) calculations. For structural properties, the errors produced by HSE are up to 50% smaller than the errors of the local density approximation, PBE, and TPSS functionals used for comparison. When predicting band gaps of semiconductors, we found smaller errors with HSE, resulting in a mean absolute error of 0.2 eV (1.3 eV error for all pure DFT functionals). In addition, we present timing results which show the computational time requirements of HSE to be only a factor of 2-4 higher than pure DFT functionals. These results make HSE an attractive choice for calculations of all types of solids. (c) 2004 American Institute of Physics.

  19. Assessment of injury to fish and wildlife resources in the Grand Calumet River and Indiana Harbor Area of Concern, USA

    USGS Publications Warehouse

    MacDonald, D.D.; Ingersoll, C.G.; Smorong, D.E.; Lindskoog, R.A.; Sparks, D.W.; Smith, J.R.; Simon, T.P.; Hanacek, M.A.

    2002-01-01

    This article is the second in a series of three that describes the results of a Natural Resource Damage Assessment (NRDA) conducted in the Grand Calumet River and Indiana Harbor Area of Concern (IHAOC). The assessment area is located in northwest Indiana and was divided into nine reaches to facilitate the assessment. This component of the NRDA was undertaken to determine if fish and wildlife resources have been injured due to exposure to contaminants that are associated with discharges of oil or releases of other hazardous substances. To support this assessment, information was compiled on the chemical composition of sediment and tissues; on the toxicity of whole sediments, pore water, and elutriates to fish; on the status of fish communities; and on fish health. The data on each of these indicators were compared to regionally relevant benchmarks to assess the presence and extent of injury to fish and wildlife resources. The results of this assessment indicate that injury to fish and wildlife resources has occurred throughout the assessment area, with up to five distinct lines of evidence demonstrating injury within the various reaches. Based on the frequency of exceedance of the benchmarks for assessing sediment and tissue chemistry data, total polychlorinated biphenyls is the primary bioaccumulative contaminant of concern in the assessment area. It is important to note, however, that this assessment was restricted by the availability of published bioaccumulation-based sediment quality guidelines, tissue residue guidelines, and other benchmarks of sediment quality conditions. The availability of chemistry data for tissues also restricted this assessment in certain reaches of the assessment area. Furthermore, insufficient information was located to facilitate identification of the substances that are causing or substantially contributing to effects on fish (i.e., sediment toxicity, impaired fish health, or impaired fish community structure). Therefore, substances

  20. Methylmercury Concentration in Fish and Risk-Benefit Assessment of Fish Intake among Pregnant versus Infertile Women in Taiwan.

    PubMed

    Hsi, Hsing-Cheng; Hsu, You-Wen; Chang, Tien-Chin; Chien, Ling-Chu

    2016-01-01

    This study examined methylmercury (MeHg) concentrations in fish, the daily MeHg exposure dose, and the risk-benefit of MeHg, ω-3 polyunsaturated fatty acid (ω-3 PUFA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA) related to fish intake among pregnant and infertile women in Taiwan. The measured MeHg concentrations in fish did not exceed the Codex guideline level of 1 mg/kg. Swordfish (0.28 ± 0.23 mg/kg) and tuna (0.14 ± 0.13 mg/kg) had the highest MeHg concentrations. The MeHg concentration in the hair of infertile women (1.82 ± 0.14 mg/kg) was significantly greater than that of pregnant women (1.24 ± 0.18 mg/kg). In addition, 80% of infertile women and 68% of pregnant women had MeHg concentrations in hair that exceeded the USEPA reference dose (1 mg/kg). The MeHg concentrations in hair were significantly and positively correlated with the estimated daily MeHg exposure dose. Based on the risk-benefit evaluation results, this paper recommends consumption of fish species with a low MeHg concentration and high concentrations of DHA + EPA and ω-3 PUFA (e.g., salmon, mackerel, and greater amberjack).

  1. Methylmercury Concentration in Fish and Risk-Benefit Assessment of Fish Intake among Pregnant versus Infertile Women in Taiwan

    PubMed Central

    Hsi, Hsing-Cheng; Hsu, You-Wen; Chang, Tien-Chin; Chien, Ling-Chu

    2016-01-01

    This study examined methylmercury (MeHg) concentrations in fish, the daily MeHg exposure dose, and the risk–benefit of MeHg, ω-3 polyunsaturated fatty acid (ω-3 PUFA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA) related to fish intake among pregnant and infertile women in Taiwan. The measured MeHg concentrations in fish did not exceed the Codex guideline level of 1 mg/kg. Swordfish (0.28 ± 0.23 mg/kg) and tuna (0.14 ± 0.13 mg/kg) had the highest MeHg concentrations. The MeHg concentration in the hair of infertile women (1.82 ± 0.14 mg/kg) was significantly greater than that of pregnant women (1.24 ± 0.18 mg/kg). In addition, 80% of infertile women and 68% of pregnant women had MeHg concentrations in hair that exceeded the USEPA reference dose (1 mg/kg). The MeHg concentrations in hair were significantly and positively correlated with the estimated daily MeHg exposure dose. Based on the risk–benefit evaluation results, this paper recommends consumption of fish species with a low MeHg concentration and high concentrations of DHA + EPA and ω-3 PUFA (e.g., salmon, mackerel, and greater amberjack). PMID:27187161

  2. Ontogenetic shifts in fishes between vegetated and unvegetated tidepools: assessing the effect of physical structure on fish habitat selection.

    PubMed

    Oliveira, R R de S; Macieira, R M; Giarrizzo, T

    2016-07-01

    The aim of this study of tidepool fishes was analyse variation in their use of intertidal habitats (rocky shore, mangrove and salt marsh). Specimens were collected during wet and dry periods from 18 tidepools in the three habitats. A total of 7690 specimens, belonging to 19 families and 30 species, was captured. The fish assemblage in rocky shore pools was clearly distinct from that of vegetated habitats (mangrove and salt marshes). The rocky shore fauna was dominated by permanent resident species, whereas pools in mangrove and salt marsh habitats were inhabited primarily by opportunistic and transient species. Habitat segregation by ontogenetic stage (e.g. smaller individuals in mangroves, intermediate size classes in salt marsh and sub-adults/adults on rocky shores) indicates age-related migration in response to the physical structure of these habitats and to the natural history of each fish species. These findings are important for the development of effective conservation and management plans for intertidal fishes. © 2016 The Fisheries Society of the British Isles.

  3. Using Hybrid Assessments to Develop Civic Competency in History

    ERIC Educational Resources Information Center

    Maddox, Lamont E.; Saye, John W.

    2017-01-01

    This article addresses the problem of how to best design authentic writing assessments in history that support learners in demonstrating the types of higher order thinking skills needed for effective citizenship. Recent research has primarily focused on curriculum interventions intended to build disciplinary literacies through various types of…

  4. Risk and toxicity assessments of heavy metals in sediments and fishes from the Yangtze River and Taihu Lake, China.

    PubMed

    Fu, Jie; Hu, Xin; Tao, Xiancong; Yu, Hongxia; Zhang, Xiaowei

    2013-11-01

    Heavy metal pollution is one of the most serous environmental issues globally. To evaluate the metal pollution in Jiangsu Province of China, the total concentrations of heavy metals in sediments and fishes from the Yangtze River and Taihu Lake were analyzed. Ecological risk of sediments and human health risk of fish consumption were assessed respectively. Furthermore, toxicity of samples on expression of the stress responsive genes was evaluated using microbial live cell-array method. The results showed that the heavy metals concentrations in sediments from the Yangtze River were much higher than those in sediments from the Taihu Lake. However, the fishes from the Taihu Lake had higher concentrations of heavy metals than fishes from the Yangtze River. Ecological risk evaluation showed that the heavy metal contaminants in sediments from the Yangtze River posed higher risk of adverse ecological effects, while sediments from the study areas of Taihu Lake were relatively safe. Health risk assessment suggested that the heavy metals in fishes of both Yangtze River and Taihu Lake might have risk of adverse health effects to human. The toxicity assessment indicated that the heavy metals in these sediments and fishes showed transcriptional effects on the selected 21 stress responsive genes, which were involved in the pathways of DNA damage response, chemical stress, and perturbations of electron transport. Together, this field investigation combined with chemical analysis, risk assessment and toxicity bioassay would provide useful information on the heavy metal pollution in Jiangsu Province. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Preliminary Assessment of Plug-in Hybrid Electric Vehicles on Wind Energy Markets

    SciTech Connect

    Short, W.; Denholm, P.

    2006-04-01

    This report examines a measure that may potentially reduce oil use and also more than proportionately reduce carbon emissions from vehicles. The authors present a very preliminary analysis of plug-in hybrid electric vehicles (PHEVs) that can be charged from or discharged to the grid. These vehicles have the potential to reduce gasoline consumption and carbon emissions from vehicles, as well as improve the viability of renewable energy technologies with variable resource availability. This paper is an assessment of the synergisms between plug-in hybrid electric vehicles and wind energy. The authors examine two bounding cases that illuminate this potential synergism.

  6. Online Assessment of Human-Robot Interaction for Hybrid Control of Walking

    PubMed Central

    del-Ama, Antonio J.; Moreno, Juan C.; Gil-Agudo, Àngel; de-los-Reyes, Ana; Pons, José L.

    2012-01-01

    Restoration of walking ability of Spinal Cord Injury subjects can be achieved by different approaches, as the use of robotic exoskeletons or electrical stimulation of the user’s muscles. The combined (hybrid) approach has the potential to provide a solution to the drawback of each approach. Specific challenges must be addressed with specific sensory systems and control strategies. In this paper we present a system and a procedure to estimate muscle fatigue from online physical interaction assessment to provide hybrid control of walking, regarding the performances of the muscles under stimulation. PMID:22368465

  7. Online assessment of human-robot interaction for hybrid control of walking.

    PubMed

    del-Ama, Antonio J; Moreno, Juan C; Gil-Agudo, Angel; de-los-Reyes, Ana; Pons, José L

    2012-01-01

    Restoration of walking ability of Spinal Cord Injury subjects can be achieved by different approaches, as the use of robotic exoskeletons or electrical stimulation of the user's muscles. The combined (hybrid) approach has the potential to provide a solution to the drawback of each approach. Specific challenges must be addressed with specific sensory systems and control strategies. In this paper we present a system and a procedure to estimate muscle fatigue from online physical interaction assessment to provide hybrid control of walking, regarding the performances of the muscles under stimulation.

  8. Linking hydrologic, physical and chemical habitat environments for the potential assessment of fish community rehabilitation in a developing city

    NASA Astrophysics Data System (ADS)

    Zhao, C. S.; Yang, S. T.; Liu, C. M.; Dou, T. W.; Yang, Z. L.; Yang, Z. Y.; Liu, X. L.; Xiang, H.; Nie, S. Y.; Zhang, J. L.; Mitrovic, S. M.; Yu, Q.; Lim, R. P.

    2015-04-01

    Aquatic ecological rehabilitation is increasingly attracting considerable public and research attention. An effective method that requires less data and expertise would help in the assessment of rehabilitation potential and in the monitoring of rehabilitation activities as complicated theories and excessive data requirements on assemblage information make many current assessment models expensive and limit their wide use. This paper presents an assessment model for restoration potential which successfully links hydrologic, physical and chemical habitat factors to fish assemblage attributes drawn from monitoring datasets on hydrology, water quality and fish assemblages at a total of 144 sites, where 5084 fish were sampled and tested. In this model three newly developed sub-models, integrated habitat index (IHSI), integrated ecological niche breadth (INB) and integrated ecological niche overlap (INO), are established to study spatial heterogeneity of the restoration potential of fish assemblages based on gradient methods of habitat suitability index and ecological niche models. To reduce uncertainties in the model, as many fish species as possible, including important native fish, were selected as dominant species with monitoring occurring over several seasons to comprehensively select key habitat factors. Furthermore, a detrended correspondence analysis (DCA) was employed prior to a canonical correspondence analysis (CCA) of the data to avoid the "arc effect" in the selection of key habitat factors. Application of the model to data collected at Jinan City, China proved effective reveals that three lower potential regions that should be targeted in future aquatic ecosystem rehabilitation programs. They were well validated by the distribution of two habitat parameters: river width and transparency. River width positively influenced and transparency negatively influenced fish assemblages. The model can be applied for monitoring the effects of fish assemblage restoration

  9. Fish products available in Polish market--assessment of the nutritive value and human exposure to dioxins and other contaminants.

    PubMed

    Usydus, Zygmunt; Szlinder-Richert, Joanna; Polak-Juszczak, Lucyna; Komar, Katarzyna; Adamczyk, Maria; Malesa-Ciecwierz, Małgorzata; Ruczynska, Wiesława

    2009-03-01

    Chemical analyses were performed on one hundred and twenty of the most popular varieties of fish products (smoked fish, salted fish, and marinated fish) of the fish market in Poland. The contents of the nutritive substances of fish products (protein, micro- and macronutrients, vitamins A(1), D(3), E, and fatty acids) and the chosen contaminant (toxic metals--mercury, cadmium, lead, arsenic; dioxin/furans--PCDDFs; dioxin-like PCB--dl-PCBs; seven congeners of polybrominated diphenyl ethers--PBDEs; organochlorine pesticides--SigmaDDT, HCB, SigmaHCH and marker polychlorinated biphenyls--PCB(7)) levels were determined. It was confirmed that fish products are a good source of digestible proteins, iodine, selenium, and vitamin D(3). The fundamental nutritive benefit of processed fish lies in its highly beneficial fatty acid composition, which is what imparts them healthy nutritive qualities. The high content of long-chain polyunsaturated fatty acids (LC-PUFAs), which is not noted in other food products, is particularly important. The majority of contaminants studied were present in low levels. The possible threats, particularly in the case of pregnant/nursing women and young children, can pose the levels of dioxin/furans (PCDD/Fs) and dioxin-like (dl-PCBs) in smoked Baltic salmon and smoked sprat, elevated in a relation to particular requirements concerning the content of sum of PCDD/Fs and dl-PCBs in fish (8pg WHO-TEQg(-1)). The health benefits and risks stemming from consumption of fish products were determined according to the Provisional Tolerable Weekly Intake (PTWI) for chosen contaminants (Cd, Hg, As, PCDD/Fs+dl-PCB) and the quantity of ingredients that render a fish diet healthy based on data from the EFSA Journal [EFSA (European Food Safety Authority), 2005. Opinion of the scientific panel on contaminants in the food chain on a request from the European Parliament related to the safety assessment of wild and farmed fish. EFSA J. 236, 1-118]. In regard of high

  10. Assessing the feasibility of native fish reintroductions: a framework applied to threatened bull trout

    USGS Publications Warehouse

    Dunham, Jason B.; Gallo, Kirsten; Shively, Dan; Allen, Chris; Goehring, Brad

    2011-01-01

    Translocations to recover native fishes have resulted in mixed success. One reason for the failure of these actions is inadequate assessments of their feasibility prior to implementation. Here, we provide a framework developed to assess the feasibility of one type of translocation-reintroduction. The framework was founded on two simple components of feasibility: the potential for recipient habitats to support a reintroduction and the potential of available donor populations to support a reintroduction. Within each component, we developed a series of key questions. The final assessment was based on a scoring system that incorporated consideration of uncertainty in available information. The result was a simple yet transparent system for assessing reintroduction feasibility that can be rapidly applied in practice. We applied this assessment framework to the potential reintroduction of threatened bull trout Salvelinus confluentus into the Clackamas River, Oregon. In this case, the assessment suggested that the degree of feasibility for reintroduction was high based on the potential of recipient habitats and available donor populations. The assessment did not provide a comprehensive treatment of all possible factors that would drive an actual decision to implement a reintroduction,

  11. Assessing water quality at large geographic scales: Relations among land use, water physicochemistry, riparian condition, and fish community structure

    USGS Publications Warehouse

    Meador, M.R.; Goldstein, R.M.

    2003-01-01

    Data collected from 172 sites in 20 major river basins between 1993 and 1995 as part of the US Geological Survey's National Water-Quality Assessment Program were analyzed to assess relations among basinwide land use (agriculture, forest, urban, range), water physicochemistry, riparian condition, and fish community structure. A multimetric approach was used to develop regionally referenced indices of fish community and riparian condition. Across large geographic areas, decreased riparian condition was associated with water-quality constituents indicative of nonpoint source inputs-total nitrogen and suspended sediment and basin-wide urban land use. Decreased fish community condition was associated with increases in total dissolved solids and rangeland use and decreases in riparian condition and agricultural land use. Fish community condition was relatively high even in areas where agricultural land use was relatively high (>50% of the basin). Although agricultural land use can have deleterious effects on fish communities, the results of this study suggest that other factors also may be important, including practices that regulate the delivery of nutrients, suspended sediments, and total dissolved solids into streams. Across large geographic scales, measures of water physicochemistry may be better indicators of fish community condition than basinwide land use. Whereas numerous studies have indicated that riparian restorations are successful in specific cases, this analysis suggests the universal importance of riparian zones to the maintenance and restoration of diverse fish communities in streams.

  12. Mercury concentrations in fish from three major lakes in north Mississippi: Spatial and temporal differences and human health risk assessment.

    PubMed

    Wolff, Stacy; Brown, Garry; Chen, Jingjing; Meals, Keith; Thornton, Cammi; Brewer, Steve; Cizdziel, James V; Willett, Kristine L

    2016-01-01

    The goal of this study was to compare total mercury (Hg) concentrations in fish muscle tissue and assess consumption health risks of fish collected from three north Mississippi lakes (Sardis, Enid, and Grenada) that are extensively used for fishing and recreation. Largemouth bass (LMB; n = 64), channel catfish (CC; n = 72), and white crappie (WC; n = 100), which represent a range of trophic levels, were collected during spring 2013 and 2014. Creel data estimated that anglers harvested approximately 370,000 kg of WC, 27,000 kg of CC, and 15,000 kg of LMB from the lakes annually. Median Hg wet weight concentrations were highest in LMB (443 ng/g), followed by CC (211 ng/g) and WC (192 ng/g). Fish-Hg concentrations were lower than those reported in fish >10 years ago. There were significant differences between lakes consistent across species. Grenada length-normalized fish-Hg concentrations were higher than those from Enid and Sardis. Because existing consumption advisories for CC are length based, the lack of relationship between length and Hg concentration indicated that the recommendations may not be sufficiently protective. Further, five different risk assessment paradigms yielded hazard quotient (HQ) values suggesting that existing fish consumption advisories may be insufficient to protect adults and especially children from exposure to Hg.

  13. Biological assessments of Appalachian streams based on predictive models for fish, macroinvertebrate, and diatom assemblages

    USGS Publications Warehouse

    Carlisle, D.M.; Hawkins, C.P.; Meador, M.R.; Potapova, M.; Falcone, J.

    2008-01-01

    We developed empirical models for fish, macroinvertebrate, and diatom assemblages to assess the biological condition of 268 streams sampled from 1993 to 2002 in 7 major river basins in the Appalachian region of the USA. These models estimate the expected taxonomic composition at each site based on observed variation in taxonomic composition at reference sites. The index, O/E, is the ratio of the number of predicted taxa that were observed (O) to that expected (E) to occur at a site and is a measure of taxonomic completeness. We compared how O/E for each assemblage varied among major landuse settings and whether impaired assemblages were associated with particular physicochemical conditions. We also examined concordance among assemblages in their response to stress. Biological, chemical, and physical data were collected following consistent protocols. We used land-cover criteria, published data, and topographic maps to classify sites by major landuse setting. Fish, macroinvertebrate, and diatom assemblages had been sampled at 73, 108, and 52, respectively, of the least disturbed sites used to establish reference conditions. The models accounted for a substantial portion of the natural variation in taxonomic composition across sites that was associated with biogeographic, climatic, and basin-scale factors and generally were unbiased across the range of environmental gradients observed in the region. Assessments at nonreference sites showed that impairment of fish and macroinvertebrate assemblages was most strongly associated with agriculture and urban land uses, whereas impairment of diatom assemblages was most strongly associated with mining in the basin. Concordance in assessments among assemblages was not strong. Assessments based on 2 assemblages differed in 28 to 57% of cases, and assessments were never concordant for cases where all 3 assemblages were sampled. Furthermore, only 1/2 of these cases would have been assessed as ecologically impaired had only 1

  14. Dual color fluorescence in situ hybridization (FISH) assays for detecting Mycobacterium tuberculosis and Mycobacterium avium complexes and related pathogens in cultures.

    PubMed

    Shah, Jyotsna; Weltman, Helena; Narciso, Patricia; Murphy, Christina; Poruri, Akhila; Baliga, Shrikala; Sharon, Leesha; York, Mary; Cunningham, Gail; Miller, Steve; Caviedes, Luz; Gilman, Robert; Desmond, Edward; Ramasamy, Ranjan

    2017-01-01

    Two rapid dual color fluorescence in situ hybridization (FISH) assays were evaluated for detecting M. tuberculosis and related pathogens in cultures. The MN Genus-MTBC FISH assay uses an orange fluorescent probe specific for the Mycobacterium tuberculosis complex (MTBC) and a green fluorescent probe specific for the Mycobacterium and Nocardia genera (MN Genus) to detect and distinguish MTBC from other Mycobacteria and Nocardia. A complementary MTBC-MAC FISH assay uses green and orange fluorescent probes specific for the MTBC and M. avium complex (MAC) respectively to identify and differentiate the two species complexes. The assays are performed on acid-fast staining bacteria from liquid or solid cultures in less than two hours. Forty-three of 44 reference mycobacterial isolates were correctly identified by the MN Genus-specific probe as Mycobacterium species, with six of these correctly identified as MTBC with the MTBC-specific probe and 14 correctly as MAC by the MAC-specific probe. Of the 25 reference isolates of clinically relevant pathogens of other genera tested, only four isolates representing two species of Corynebacterium gave a positive signal with the MN Genus probe. None of these 25 isolates were detected by the MTBC and MAC specific probes. A total of 248 cultures of clinical mycobacterial isolates originating in India, Peru and the USA were also tested by FISH assays. DNA sequence of a part of the 23S ribosomal RNA gene amplified by PCR was obtained from 243 of the 248 clinical isolates. All 243 were confirmed by DNA sequencing as Mycobacterium species, with 157 and 50 of these identified as belonging to the MTBC and the MAC, respectively. The accuracy of the MN Genus-, MTBC-and MAC -specific probes in identifying these 243 cultures in relation to their DNA sequence-based identification was 100%. All ten isolates of Nocardia, (three reference strains and seven clinical isolates) tested were detected by the MN Genus-specific probe but not the MTBC- or

  15. Total and inorganic arsenic in fish, seafood and seaweeds--exposure assessment.

    PubMed

    Mania, Monika; Rebeniak, Małgorzata; Szynal, Tomasz; Wojciechowska-Mazurek, Maria; Starska, Krystyna; Ledzion, Ewa; Postupolski, Jacek

    2015-01-01

    According to the European Food Safety Authority (EFSA), fish, seafood and seaweeds are foodstuffs that significantly contribute to dietary arsenic intake. With the exception of some algal species, the dominant compounds of arsenic in such food products are the less toxic organic forms. Both the Joint FAO/WHO Expert Committee on Food Additives (JECFA) and EFSA recommend that speciation studies be performed to determine the different chemical forms in which arsenic is present in food due to the differences in their toxicity. Knowing such compositions can thus enable a complete exposure assessment to be made. Determination of total and inorganic arsenic contents in fish, their products, seafood and seaweeds present on the Polish market. This was then followed by an exposure assessment of consumers to inorganic arsenic in these foodstuffs. Total and inorganic arsenic was determined in 55 samples of fish, their products, seafood as well as seaweeds available on the market. The analytical method was hydride generation atomic absorption spectrometry (HGAAS), after dry ashing of samples and reduction of arsenic to arsenic hydride using sodium borohydride. In order to isolate only the inorganic forms of arsenic prior to mineralisation, samples were subjected to concentrated HCl hydrolysis, followed by reduction with hydrobromic acid and hydrazine sulphate after which triple chloroform extractions and triple 1M HCl re-extractions were performed. Exposure of adults was estimated in relation to the Benchmark Dose Lower Confidence Limit (BMDL0.5) as set by the Joint FAO/WHO Expert Committee on Food Additives (JECFA) that resulted in a 0.5% increase in lung cancer (3.0 μg/kg body weight (b.w.) per day). Mean total arsenic content from all investigated fish samples was 0.46 mg/kg (90th percentile 0.94 mg/kg), whilst the inorganic arsenic content never exceeded the detection limit of the analytical method used (0.025 mg/kg). In fish products, mean total arsenic concentration was

  16. A framework for assessing the feasibility of native fish conservation translocations: Applications to threatened bull trout

    USGS Publications Warehouse

    Galloway, Benjamin T.; Muhlfeld, Clint C.; Guy, Christopher S.; Downs, Christopher C.; Fredenberg, Wade A.

    2016-01-01

    There is an urgent need to consider more aggressive and direct interventions for the conservation of freshwater fishes that are threatened by invasive species, habitat loss, and climate change. Conservation introduction (moving a species outside its indigenous range to other areas where conditions are predicted to be more suitable) is one type of translocation strategy that fisheries managers can use to establish new conservation populations in areas of refugia. To date, however, there are few examples of successful conservation-based introductions. Many attempts fail to establish new populations—in part because environmental factors that might influence success are inadequately evaluated before the translocation is implemented. We developed a framework to assess the feasibility of rescuing threatened fish populations through translocation into historically unoccupied stream and lake habitats. The suitability of potential introduction sites was evaluated based on four major components: the recipient habitat, recipient community, donor population, and future threats. Specific questions were then developed to evaluate each major component. The final assessment was based on a scoring system that addressed each question by using criteria developed from characteristics representative of highly suitable habitats and populations. This framework was used to evaluate the proposed within-drainage translocation of three Bull Trout Salvelinus confluentus populations in Glacier National Park, Montana. Our results indicated that within-drainage translocation is a feasible strategy for conserving locally adapted populations of Bull Trout through the creation of new areas of refugia in Glacier National Park. The framework provides a flexible platform that can help managers make informed decisions for moving threatened fishes into new areas of refugia for conservation and recovery programs.

  17. Influencing factors on the functional level of haemophilic patients assessed by FISH.

    PubMed

    Kachooei, A R; Badiei, Z; Zandinezhad, M E; Ebrahimzadeh, M H; Mazloumi, S M; Omidi-Kashani, F; Moradi, A; Mahdavian-Naghashzargar, R; Razi, S

    2014-03-01

    Joint destruction in early adulthood brings the patients to the orthopaedic clinics. If a haemophilic patient becomes disabled, it shows a number of factors such as timely diagnosis, availability of appropriate treatment depending on the country, access and affordability to treatments and equally importantly the responsibility of the patient in managing self care by remaining compliant by prescribed treatment regimen. We assessed the functional level by functional independence score in haemophilia (FISH). Overall, 104 patients with haemophilia A and 29 with haemophilia B were evaluated. We assessed the function of the patients by FISH. We divided the sum scores into weak (FISH score 8-16), moderate (17-24), and good (25-32). For evaluating the level of functional deficit in a 2 × 2 table, we categorized the weak and moderate levels into Disordered Group and the good level into Not-Disordered Group. The average age was 26.9 ± 14.24. Each 1 year increase in age can increase 1.07 fold the possibility of being placed in Disordered Function Group. Severe haemophilia can increase 7.34 fold, presence of inhibitor can increase 9.75 fold and home self-care increases 3.89 fold the possibility of being placed in Disordered Function Group. To decrease the burden of the cost on patient, family and the government, education plays the most important role. We suggest that we send a trained team of physician and nurses to the deprived villages and cities instead of waiting for the patient to refer to our Care Center.

  18. Progress and recent advances in fabrication and utilization of hypoxanthine biosensors for meat and fish quality assessment: a review.

    PubMed

    Lawal, Abdulazeez T; Adeloju, Samuel B

    2012-10-15

    This review provides an update on the research conducted on the fabrication and utilization of hypoxanthine (Hx) biosensors published over the past four decades. In particular, the review focuses on progress made in the development and use of Hx biosensors for the assessment of fish and meat quality which has dominated research in this area. The various fish and meat freshness indexes that have been proposed over this period are highlighted. Furthermore, recent developments and future advances in the use of screen-printed electrodes and nanomaterials for achieving improved performances for the reliable determination of Hx in fish and meat are discussed.

  19. Health risk assessment from mercury levels in bycatch fish species from the coasts of Guerrero, Mexico (Eastern Pacific).

    PubMed

    Spanopoulos-Zarco, P; Ruelas-Inzunza, J; Meza-Montenegro, M; Osuna-Sánchez, K; Amezcua-Martínez, F

    2014-09-01

    With the aim of determining Hg distribution in muscle and liver of bycatch fish from Guerrero state in the Eastern Pacific Ocean and assess the potential risk to consumer, Hg was quantified in 14 species of bycatch fish. For the majority of fish the order of Hg levels was liver > muscle. The highest concentration corresponded to the liver of Isopisthus remifer (2.05 µg g(-1)) and the lowest (0.02 µg g(-1)) was detected in muscle of Prionotus sp. The highest hazard quotient (0.75) was found in the Mexican milkfish Micropogonias ectenes; considering all the individuals, mean hazard quotient was 0.336.

  20. 3D-catFISH: a system for automated quantitative three-dimensional compartmental analysis of temporal gene transcription activity imaged by fluorescence in situ hybridization.

    PubMed

    Chawla, Monica K; Lin, Gang; Olson, Kathy; Vazdarjanova, Almira; Burke, Sara N; McNaughton, Bruce L; Worley, Paul F; Guzowski, John F; Roysam, Badrinath; Barnes, Carol A

    2004-10-15

    Fluorescence in situ hybridization (FISH) of neural activity-regulated, immediate-early gene (IEG) expression provides a method of functional brain imaging with cellular resolution. This enables the identification, in one brain, of which specific principal neurons were active during each of two distinct behavioral epochs. The unprecedented potential of this differential method for large-scale analysis of functional neural circuits is limited, however, by the time-intensive nature of manual image analysis. A comprehensive software tool for processing three-dimensional, multi-spectral confocal image stacks is described which supports the automation of this analysis. Nuclei counterstained with conventional DNA dyes and FISH signals indicating the sub-cellular distribution of specific, IEG RNA species are imaged using different spectral channels. The DNA channel data are segmented into individual nuclei by a three-dimensional multi-step algorithm that corrects for depth-dependent attenuation, non-isotropic voxels, and imaging noise. Intra-nuclear and cytoplasmic FISH signals are associated spatially with the nuclear segmentation results to generate a detailed tabular/database and graphic representation. Here we present a comprehensive validation of data generated by the automated software against manual quantification by human experts on hippocampal and parietal cortical regions (96.5% concordance with multi-expert consensus). The high degree of reliability and accuracy suggests that the software will generalize well to multiple brain areas and eventually to large-scale brain analysis.

  1. Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives

    PubMed Central

    Iwata-Otsubo, Aiko; Radke, Brittany; Findley, Seth; Abernathy, Brian; Vallejos, C. Eduardo; Jackson, Scott A.

    2016-01-01

    Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species. PMID:26865698

  2. Life cycle assessment on microalgal biodiesel production using a hybrid cultivation system.

    PubMed

    Adesanya, Victoria O; Cadena, Erasmo; Scott, Stuart A; Smith, Alison G

    2014-07-01

    A life cycle assessment (LCA) was performed on a putative biodiesel production plant in which the freshwater alga Chlorella vulgaris, was grown using an existing system similar to a published commercial-scale hybrid cultivation. The hybrid system couples airlift tubular photobioreactors with raceway ponds in a two-stage process for high biomass growth and lipid accumulation. The results show that microalgal biodiesel production would have a significantly lower environmental impact than fossil-derived diesel. Based on the functional unit of 1 ton of biodiesel produced, the hybrid cultivation system and hypothetical downstream process (base case) would have 42% and 38% savings in global warming potential (GWP) and fossil-energy requirements (FER) when compared to fossil-derived diesel, respectively. Sensitivity analysis was performed to identify the most influential process parameters on the LCA results. The maximum reduction in GWP and FER was observed under mixotrophic growth conditions with savings of 76% and 75% when compared to conventional diesel, respectively.

  3. Parasitological assessment in the hybrid surubim (Pseudoplatystoma reticulatum x P. corruscans), with uncommon occurrence of Monogenea parasites.

    PubMed

    Jerônimo, Gabriela Tomas; Pádua, Santiago Benites de; Ventura, Arlene Sobrinho; Gonçalves, Eduardo Luis Tavares; Ishikawa, Márcia Mayumi; Martins, Maurício Laterça

    2016-06-14

    This study evaluated the parasite fauna of farmed hybrid surubim (Pseudoplatystoma reticulatum x P. corruscans) and the host-parasite-environment relationship in two fish farms located in Mato Grosso do Sul, Central Brazil, South America. A total of 120 hybrids from two different farms, 60 in each season (30 in the hot and 30 in cold season) were examined during a year. Water quality was weekly measured to evaluate the interaction among environmental conditions and parasitism. Histopathology was used to observe the effects of the parasites and environment on the fish gills. The ciliate protozoan Ichthyophthirius multifiliis and the monogeneans (Ameloblastella sp., Amphocleithrium paraguayensis, Vancleaveus ciccinus, V. fungulus and V. janacauensis) were the most prevalent parasites detected in both seasons in both farms, with prevalence above 80%. It was stated that parasites did not cause important damage in the health status of the hybrid surubim. These results might be related to general good management practices and environmental quality implemented by the fish farmers. The presence of uncommon monogenean parasites to this hybrid compared to their parents causing an environmental and ecological concern is here discussed.

  4. Assessment of fish assemblages and minimum sampling effort required to determine botic integrity of large rivers in southern Idaho, 2002

    USGS Publications Warehouse

    Maret, Terry R.; Ott, D.S.

    2004-01-01

    width was determined to be sufficient for collecting an adequate number of fish to estimate species richness and evaluate biotic integrity. At most sites, about 250 fish were needed to effectively represent 95 percent of the species present. Fifty-three percent of the sites assessed, using an IBI developed specifically for large Idaho rivers, received scores of less than 50, indicating poor biotic integrity.

  5. Systematic global assessment of reef fish communities by the Reef Life Survey program

    PubMed Central

    Edgar, Graham J; Stuart-Smith, Rick D

    2014-01-01

    The assessment of patterns in macroecology, including those most relevant to global biodiversity conservation, has been hampered by a lack of quantitative data collected in a consistent manner over the global scale. Global analyses of species’ abundance data typically rely on records aggregated from multiple studies where different sampling methods and varying levels of taxonomic and spatial resolution have been applied. Here we describe the Reef Life Survey (RLS) reef fish dataset, which contains 134,759 abundance records, of 2,367 fish taxa, from 1,879 sites in coral and rocky reefs distributed worldwide. Data were systematically collected using standardized methods, offering new opportunities to assess broad-scale spatial patterns in community structure. The development of such a large dataset was made possible through contributions of investigators associated with science and conservation agencies worldwide, and the assistance of a team of over 100 recreational SCUBA divers, who undertook training in scientific techniques for underwater surveys and voluntarily contributed skills, expertise and their time to data collection. PMID:25977765

  6. Comparative assessment of water quality parameters of mariculture for fish production in Hong Kong Waters.

    PubMed

    Leung, H M; Leung, S K S; Au, C K; Cheung, K C; Wong, Y K; Leung, A O W; Yung, K K L

    2015-05-15

    The objective of the study is to evaluate the effect of fish cultivation on water quality in fish culture zone (FCZ) and analysed by Principle Component Analysis (PCA). 120 surface water samples were collected from Hong Kong Waters (60 samples in Victoria Harbour and another 60 in Ma Wan FCZ). Significant difference was found in dissolved oxygen (MW: 59.6%; VH: 81.3%), and Escherichia coli (MW: 465 CFU/100 ml; VH: 162.5 CFU/100 ml). Three principle components are responsible for water quality variations in the studying sites. The first component included E. coli (0.625) and dissolved oxygen (0.701). The second included E. coli (0.387) and ammonical-nitrogen (0.571). The third included E. coli (0.194) and ammonical-nitrogen (0.287). This framework provides information to assess the relative contribution of eco-aquaculture to nutrient loads and the subsequent risk of eutrophication. To conclude, a rigorous monitoring of water quality is necessary to assess point and nonpoint source pollution. Besides, appropriate remediation techniques should be used to combat water pollution and achieve sustainability.

  7. Arsenic concentration in rice, fish, meat and vegetables in Cambodia: a preliminary risk assessment.

    PubMed

    Wang, Hong-Sheng; Sthiannopkao, Suthipong; Chen, Zhuo-Jia; Man, Yu-Bon; Du, Jun; Xing, Guang-Hua; Kim, Kyoung-Woong; Mohamed Yasin, Mohamed Salleh; Hashim, Jamal Hisham; Wong, Ming-Hung

    2013-12-01

    To assess arsenic contaminations and its possible adverse health effects, food samples were collected from Kandal, Kratie and Kampong Cham in Cambodia. The highest and the lowest concentrations were observed in fish (mean 2,832 ng g(-1), ww) collected from Kandal province and cattle stomach (1.86 ± 1.10 ng g(-1), ww) collected from Kratie, respectively. The daily intake of arsenic via food consumption was 604, 9.70 and 136 μg day(-1) in Kandal, Kratie and Kampong Cham, respectively. The arsenic dietary intake in Kandal ranked No. 1 among all the 17 compared countries or regions. Fish consumption contributed the greatest proportion of total arsenic daily intake in Kandal (about 63.0 %) and Kampong Cham (about 69.8 %). It is revealed to be a much more important exposure pathway than drinking water for residents in Kampong Cham. The results of risk assessment suggested that the residents in Cambodia, particularly for people in Kandal province, suffer high public health risks due to consuming arsenic-contaminated food.

  8. Pharmaceutical Metabolism in Fish: Using a 3-D Hepatic In Vitro Model to Assess Clearance

    PubMed Central

    Baron, Matthew G.; Mintram, Kate S.; Owen, Stewart F.; Hetheridge, Malcolm J.; Moody, A. John; Purcell, Wendy M.; Jackson, Simon K.; Jha, Awadhesh N.

    2017-01-01

    At high internal doses, pharmaceuticals have the potential for inducing biological/pharmacological effects in fish. One particular concern for the environment is their potential to bioaccumulate and reach pharmacological levels; the study of these implications for environmental risk assessment has therefore gained increasing attention. To avoid unnecessary testing on animals, in vitro methods for assessment of xenobiotic metabolism could aid in the ecotoxicological evaluation. Here we report the use of a 3-D in vitro liver organoid culture system (spheroids) derived from rainbow trout to measure the metabolism of seven pharmaceuticals using a substrate depletion assay. Of the pharmaceuticals tested, propranolol, diclofenac and phenylbutazone were metabolised by trout liver spheroids; atenolol, metoprolol, diazepam and carbamazepine were not. Substrate depletion kinetics data was used to estimate intrinsic hepatic clearance by this spheroid model, which was similar for diclofenac and approximately 5 fold higher for propranolol when compared to trout liver microsomal fraction (S9) data. These results suggest that liver spheroids could be used as a relevant and metabolically competent in vitro model with which to measure the biotransformation of pharmaceuticals in fish; and propranolol acts as a reproducible positive control. PMID:28045944

  9. Fish cell lines as a tool for the ecotoxicity assessment and ranking of engineered nanomaterials.

    PubMed

    Bermejo-Nogales, A; Fernández-Cruz, M L; Navas, J M

    2017-09-28

    Risk assessment of engineered nanomaterials (ENMs) is being hindered by the sheer production volume of these materials. In this regard, the grouping and ranking of ENMs appears as a promising strategy. Here we sought to evaluate the usefulness of in vitro systems based on fish cell lines for ranking a set of ENMs on the basis of their cytotoxicity. We used the topminnow (Poeciliopsis lucida) liver cell line (PLHC-1) and the rainbow trout (Oncorhynchus mykiss) fibroblast-like gonadal cell line (RTG-2). ENMs were obtained from the EU Joint Research Centre repository. The size frequency distribution of ENM suspensions in cell culture media was characterized. Cytotoxicity was evaluated after 24 h of exposure. PLHC-1 cells exhibited higher sensitivity to the ENMs than RTG-2 cells. ZnO-NM was found to exert toxicity mainly by altering lysosome function and metabolic activity, while multi-walled carbon nanotubes (MWCNTs) caused plasma membrane disruption at high concentrations. The hazard ranking for toxicity (ZnO-NM > MWCNT ≥ CeO2-NM = SiO2-NM) was inversely related to the ranking in size detected in culture medium. Our findings reveal the suitability of fish cell lines for establishing hazard rankings of ENMs in the framework of integrated approaches to testing and assessment. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. The Applicability of Oxidative Stress Biomarkers in Assessing Chromium Induced Toxicity in the Fish Labeo rohita

    PubMed Central

    Khare, Ankur; Dange, Swati

    2014-01-01

    The evaluation of metal's toxicity in freshwater is one of the imperative areas of research and there is an emergent concern on the development of techniques for detecting toxic effects in aquatic animals. Oxidative stress biomarkers are very useful in assessing the health of aquatic life and more in depth studies are necessary to establish an exact cause effect relationship. Therefore, to study the effectiveness of this approach, a laboratory study was conducted in the fish Labeo rohita as a function of hexavalent chromium and the toxicity indices using a battery of oxidative stress biomarkers such as catalase (CAT), superoxide dismutase (SOD), and glutathione reductase (GR) in the liver, muscle, gills, and brain have been studied along with biometric parameters, behavioral changes, and Cr bioaccumulation. A significant increased HSI was observed in contrast to CF which reduced significantly. SOD, CAT, and GR activity increased significantly in all the tissues of treated fishes. The bioaccumulation of Cr was highest in liver followed by gills, muscle, and brain. This study highlights the significance of using a set of integrated biomarker and advocate to include these parameters in National Water Quality Monitoring Program in areas potentially polluted with metals to assess the health of the ecosystem. PMID:25302308

  11. Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes

    PubMed Central

    Breen, Matthew; Jouquand, Sophie; Renier, Corinne; Mellersh, Cathryn S.; Hitte, Christophe; Holmes, Nigel G.; Chéron, Angélique; Suter, Nicola; Vignaux, Françoise; Bristow, Anna E.; Priat, Catherine; McCann, E.; André, Catherine; Boundy, Sam; Gitsham, Paul; Thomas, Rachael; Bridge, Wendy L.; Spriggs, Helen F.; Ryder, Ed J.; Curson, Alistair; Sampson, Jeff; Ostrander, Elaine A.; Binns, Matthew M.; Galibert, Francis

    2001-01-01

    We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest. PMID:11591656

  12. Analysis of chromosomal polymorphism in barley (Hordeum vulgare L. ssp. vulgare) and between H. vulgare and H. chilense using three-color fluorescence in situ hybridization (FISH).

    PubMed

    Szakács, É; Kruppa, K; Molnár-Láng, M

    2013-11-01

    The aim of the present work was to study chromosomal polymorphism within cultivated barley (Hordeum vulgare ssp. vulgare) using three-color fluorescence in situ hybridization (FISH). The physical distribution of the most frequently used, highly repetitive DNA sequences (GAA)7 specific for pericentromeric heterochromatic regions, the ribosomal DNA clone pTa71, specific for the 45S rDNA, and the barley-specific telomere-associated sequence HvT01, was investigated to reveal genetic diversity in metaphase spreads of ten barley genotypes with diverse geographical origin, growth habit and row number. A wild relative of barley, Hordeum chilense was also studied in order to compare the polymorphism between and within Hordeum species. Significant differences in the hybridization patterns of all three DNA probes could be detected between the two related species, but only probes pTa71 and HvT01 showed variation in the intensity and/or position of hybridization sites among genotypes of H. vulgare ssp. vulgare. The extent of polymorphism was less than that earlier reported for molecular markers and was restricted to the long chromosome arms, with differences between the chromosomes. 1H and 3H proved to be the most variable chromosomes and 4H and 6H the most conserved.

  13. Heavy metals and arsenic concentrations in ten fish species from the Šalek lakes (Slovenia): assessment of potential human health risk due to fish consumption.

    PubMed

    Al Sayegh Petkovšek, Samar; Mazej Grudnik, Zdenka; Pokorny, Boštjan

    2012-05-01

    The study, which measured the concentrations of Hg, Pb, Cd, Zn and As in various fish tissues (muscle, gill and liver) of 10 fish species (Abramis brama danubii, Alburnus alburnus alburnus, Barbus meridionalis petenyi, Carassius auratius gibelio, Cyprinus carpio, Lepomis gibossus, Leuciscius cephalus cephalus, Perca fluviatilis fluviatilis, Rutilus rutilus, Scardinus erythrophtlalmus erythrophtlalmus) collected in the Šalek lakes, is the first survey regarding metal concentrations in fish species with samples originating from Slovene lakes, while only a limited number of such studies have been carried out in southeastern Europe. Since these lakes are situated in the close vicinity of the largest Slovene thermal power plant, the study provides an insight into the potential impact of increased levels of metals in the environment as well as an estimate of the contamination of fish tissues with metals. Furthermore, it was possible to compare the results obtained with those from other studies regarding metal levels in freshwater fish species. The mean metal concentrations of different tissues irrespective of species varied in the following ranges: Zn 4.31-199 mg/kg ww, Pb 0.01-0.48 mg/kg ww, As 0.02-0.44 mg/kg ww, Hg <0.01-0.31 mg/kg ww, Cd < 0.01-0.19 mg/kg ww. In general, higher contents of Hg were found in muscles and livers than in gills and higher contents of As in gills and livers than in muscles, respectively. The accumulation of Pb and Zn was most pronounced in gills. The result obtained regarding metal concentrations in fish revealed that the ecosystems of the Šalek lakes are not polluted with Hg and Pb, slightly loaded with As and Cd and moderately polluted with Zn. In addition, the potential human health risk due to fish consumption was assessed. This showed that the estimated weekly intakes for all metals were far below provisional permissible tolerable weekly intakes determined by WHO/FAO. The consumption of fish from the Šalek lakes, therefore

  14. Revised Protocols for Sampling Algal, Invertebrate, and Fish Communities as Part of the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Moulton, Stephen R.; Kennen, Jonathan G.; Goldstein, Robert M.; Hambrook, Julie A.

    2002-01-01

    Algal, invertebrate, and fish communities are characterized as part of ecological studies in the U.S. Geological Survey.s National Water-Quality Assessment Program. Information from these ecological studies, together with chemical and physical data, provide an integrated assessment of water quality at local, regional, and national scales. Analysis and interpretation of water-quality data at these various geographic scales require accurate and consistent application of sampling protocols and sample-processing procedures. This report revises and unifies into a single document the algal, invertebrate, and fish community sampling protocols used in the National Water-Quality Assessment Program.

  15. A comparative assessment of contaminants in fish from four resacas of the Texas, USA-Tamaulipas, Mexico border region

    USGS Publications Warehouse

    Mora, Miguel A.; Papoulias, Diana M.; Nava, Ismael; Buckler, Denny R.

    2001-01-01

    A recent survey of contaminant information for the Lower Rio Grande Valley (LRGV), Texas, has shown that little is known about contaminants and their impacts on biota of resacas (oxbows) along the US-Mexico border. In 1996, fish were collected from four resacas in the Texas- Tamaulipas border region to assess contaminant loadings and their impacts on fish and birds. Tissue residue concentrations in fish were analyzed and also compared to two histopathological bioindicators of unhealthy environmental conditions. Of the organochlorine insecticides measured, DDE was the most common and was present at relatively high concentrations (10 ??g/g w/w) at some sites. DDE concentrations were nearly 20 times greater in fish from resacas in Texas than from resacas in Tamaulipas, although the limited sample sizes obtained precluded statistical comparisons. DDE concentrations in fish from the two Texas resacas were also greater than those reported in fish from nearby areas during the 1980s and 1990s. Most trace element concentrations were similar among resacas from Texas and Tamaulipas. Arsenic, however, was two to six times greater in fish from a downtown resaca in Matamoros than in fish from other resacas in Tamaulipas and Texas. The bioindicators, pigment accumulation, and macrophage aggregates (MAs), in general, reflected the contamination indicated by the tissue residues for each site. Overall, it appears that some resacas of the US-Mexico border region are contaminant sinks and could pose potential health or reproductive problems for fish and wildlife, and humans that consume fish from those sites. Published by Elsevier Science Ltd.

  16. Turbo FISH: A Method for Rapid Single Molecule RNA FISH

    PubMed Central

    Shaffer, Sydney M.; Wu, Min-Tzu; Levesque, Marshall J.; Raj, Arjun

    2013-01-01

    Advances in RNA fluorescence in situ hybridization (RNA FISH) have allowed practitioners to detect individual RNA molecules in single cells via fluorescence microscopy, enabling highly accurate and sensitive quantification of gene expression. However, current methods typically employ hybridization times on the order of 2–16 hours, limiting its potential in applications like rapid diagnostics. We present here a set of conditions for RNA FISH (dubbed Turbo RNA FISH) that allow us to make accurate measurements with no more than 5 minutes of hybridization time and 3 minutes of washing, and show that hybridization times can go as low as 30 seconds while still producing quantifiable images. We further show that rapid hybridization is compatible with our recently developed iceFISH and SNP FISH variants of RNA FISH that enable chromosome and single base discrimination, respectively. Our method is simple and cost effective, and has the potential to dramatically increase the throughput and realm of applicability of RNA FISH. PMID:24066168

  17. Assessing HER2 amplification by IHC, FISH, and real-time polymerase chain reaction analysis (real-time PCR) following LCM in formalin-fixed paraffin embedded tissue from 40 women with ovarian cancer.

    PubMed

    Hillig, Thore; Thode, Jørgen; Breinholt, Marie F; Franzmann, Maria-Benedicte; Pedersen, Carsten; Lund, Flemming; Mygind, Henrik; Sölétormos, György; Rudnicki, Martin

    2012-12-01

    We compare HER2 receptor amplification analysis by immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and real-time polymerase chain reaction (real-time PCR) DNA copy-number assay following laser capture microdissection (LCM) in formalin-fixed paraffin embedded tissue from 40 women with verified ovarian cancer. We speculate that LCM should result in a more accurate assessment of HER2 amplification in our real-time PCR assay compared with IHC and FISH. HER2 overexpression measured by IHC, FISH, or real-time PCR was found in 5.0%, 5.0%, and 22.5%, respectively. HER2 negative results measured by IHC, FISH, or real-time PCR were found in 95%, 92.5%, and 60.0%, respectively. Analysis failed for IHC, FISH, or real-time PCR in 0%, 2.5%, or 17.5% of cases. Concordance between IHC and FISH, IHC and real-time PCR, or FISH and real-time PCR were 89.7%, 72.7%, or 78.1%, respectively. Only few ovarian cancer patients were HER2 overexpressed measured by IHC or FISH and thus could be eligible for antibody-based therapy with trastuzumab (Herceptin). Interestingly, we find an increased number of HER2 positive patients by real-time PCR analysis on microdissected cancer cells, suggesting a number of HER2 positive patients not detected by current methods. Thus, the concept of quantitative measurement of HER2 on microdissected cancer cells should be explored further.

  18. Effects of the acute exposition to glyphosate-based herbicide on oxidative stress parameters and antioxidant responses in a hybrid Amazon fish surubim (Pseudoplatystoma sp).

    PubMed

    Sinhorin, Valéria Dornelles Gindri; Sinhorin, Adilson Paulo; Teixeira, Jhonnes Marcos dos Santos; Miléski, Kelly Márcia Lazarotto; Hansen, Paula Carine; Moreira, Paula Sueli Andrade; Kawashita, Nair Honda; Baviera, Amanda Martins; Loro, Vania Lúcia

    2014-08-01

    The aim of this study was to investigate the effects of acute glyphosate (active ingredient) exposure on the oxidative stress biomarkers and antioxidant defenses of a hybrid surubim (Pseudoplatystoma sp). The fish were exposed to different herbicide concentrations for 96 h. The thiobarbituric acid-reactive substances (TBARS), protein carbonyls and antioxidant responses were verified. The 15 mg a.pL(-1) of herbicide resulted in the death of 50% of the fish after 96 h. An increase in liver and muscle TBARS levels was observed when fish were exposed to the herbicide. The protein carbonyl content was also increased in the liver (4.5mg a.pL(-1) concentration) and brain (2.25 mg a.pL(-1) concentration). The antioxidant activities decreased in the liver and brain after exposure to herbicide. Levels of ascorbic acid in the liver (2.25 mg a.pL(-1) and 4.5 mg a.pL(-1) concentrations) and brain (2.25 mg a.pL(-1) concentration) were increased post-treatment. Levels of total thiols were increased in the liver and brain (2.25 mg L(-1) and 7.5mg a.pL(-1), respectively). Glyphosate exposure, at the tested concentrations affects surubim health by promoting changes that can affect their survival in natural environment. Some parameters as TBARS and protein carbonyl could be early biomarkers for Roundup exposure in this fish species. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Fluorescent in situ hybridization (FISH) in the differential diagnosis of ground-glass opacities in the lung.

    PubMed

    Bettio, Daniela; Venci, Anna; Cariboni, Umberto; Di Rocco, Mariagrazia; Infante, Maurizio

    2011-03-01

    Computed tomographic (CT) screening for lung cancer has increased the detection rate of nodules manifesting as ground-glass opacities (GGOs). The natural history of this new entity it is not well known nor is the factors that influence the growth, progression and malignant potential. This genetic study was performed in order to identify molecular markers with possible diagnostic and prognostic significance to differentiate lesions with malignant or benign profiles. Ten pure GGO fresh samples and 5 specimens of normal lung tissue were cytogenetically investigated using a direct method and short-term cultures, and molecular analysis was performed using the 4-target FISH LAVysion kit for the detection of non-small cell lung cancer (NSCLC). Interestingly, all the karyotypes turned out to be normal both with the direct method and cultured cells, while in 3 out of 10 GGOs FISH analysis was abnormal for all the targets and in 2 cases only c-MYC amplification was observed. Karyotypes and FISH performed on the normal tissue samples gave normal results. Two of three FISH positive patients died, one had a relapse of the disease and at the last follow-up showed lung and bone metastases. Despite the small sample due to the rarity of pure GGOs, these preliminary results indicate that interphase FISH analyses are more informative than metaphase studies and might contribute clinically relevant information about the nature of these lesions. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  20. Assessing the techno-economics of modular hybrid solar thermal systems

    NASA Astrophysics Data System (ADS)

    Lim, Jin Han; Chinnici, Alfonso; Dally, Bassam; Nathan, Graham

    2017-06-01

    A techno-economic assessment was performed on modular hybrid solar thermal (in particular, solar power tower) systems with combustion from natural gas as backup to provide a continuous supply of electricity. Two different configurations were compared, i.e. a Hybrid Solar Receiver Combustor (HSRC), in which the functions of a solar cavity receiver and a combustor are integrated into a single device, and a Solar Gas Hybrid (SGH), which is a reference hybrid solar thermal system with a standalone solar-only cavity receiver and a backup boile