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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. 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.

  3. Assessment of retrospective dose estimation, with fluorescence in situ hybridization (FISH), of six victims previously exposed to accidental ionizing radiation.

    PubMed

    Liu, Qing-Jie; Lu, Xue; Zhao, Xiao-Tao; Feng, Jiang-Bin; Lü, Yu-Min; Jiang, En-Hai; Zhang, Shu-Lan; Chen, De-Qing; Jia, Ting-Zhen; Liang, Li

    2014-01-01

    The present study aims to evaluate the use of the fluorescence in situ hybridization (FISH) translocation assay for retrospective dose estimation of acute accidental exposure to radiation in the past. Reciprocal translocation analysis by FISH with three whole-chromosome probes was performed on normal peripheral blood samples. Samples were irradiated with 0-5Gy (60)Co γ-rays in vitro, and dose-effect curves were established. FISH-based translocation analyses for six accident victims were then performed, and biological doses were estimated retrospectively by comparison with the dose-effect curves. Reconstructed doses by FISH were compared with estimated doses obtained by analysis of di-centrics performed soon after exposure, or with dose estimates from tooth-enamel electron paramagnetic resonance (EPR) data obtained at the same time as the FISH analysis. Follow-up FISH analyses for an adolescent victim were performed. Results showed that dose-effect curves established in the present study follow a linear-quadratic model, regardless of the background translocation frequency. Estimated doses according to two dose-effect curves for all six victims were similar. FISH dose estimations of three adult victims exposed to accidental radiation less than a decade prior to analysis (3, 6, or 7 years ago) were consistent with those estimated with tooth-enamel EPR measurements or analyses of di-centrics. Estimated doses of two other adult victims exposed to radiation over a decade prior to analysis (16 or 33 years ago) were underestimated and two to three times lower than the values obtained from analysis of di-centrics or tooth-enamel EPR. Follow-up analyses of the adolescent victim showed that doses estimated by FISH analysis decrease rapidly over time. Therefore, the accuracy of dose estimates by FISH is acceptable only when analysis is performed less than 7 years after exposure. Measurements carried out more than a decade after exposure through FISH analysis resulted in

  4. 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.

  5. 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…

  6. Reef fish hybridization: lessons learnt from butterflyfishes (genus Chaetodon)

    PubMed Central

    Montanari, Stefano R; van Herwerden, Lynne; Pratchett, Morgan S; Hobbs, Jean-Paul A; Fugedi, Anneli

    2012-01-01

    Natural hybridization is widespread among coral reef fishes. However, the ecological promoters and evolutionary consequences of reef fish hybridization have not been thoroughly evaluated. Butterflyfishes form a high number of hybrids and represent an appropriate group to investigate hybridization in reef fishes. This study provides a rare test of terrestrially derived hybridization theory in the marine environment by examining hybridization between Chaetodon trifasciatus and C. lunulatus at Christmas Island. Overlapping spatial and dietary ecologies enable heterospecific encounters. Nonassortative mating and local rarity of both parent species appear to permit heterospecific breeding pair formation. Microsatellite loci and mtDNA confirmed the status of hybrids, which displayed the lowest genetic diversity in the sample and used a reduced suite of resources, suggesting decreased adaptability. Maternal contribution to hybridization was unidirectional, and no introgression was detected, suggesting limited, localized evolutionary consequences of hybridization. Comparisons to other reef fish hybridization studies revealed that different evolutionary consequences emerge, despite being promoted by similar factors, possibly due to the magnitude of genetic distance between hybridizing species. This study highlights the need for further enquiry aimed at evaluating the importance and long-term consequences of reef fish hybridization. PMID:22423326

  7. Reef fish hybridization: lessons learnt from butterflyfishes (genus Chaetodon).

    PubMed

    Montanari, Stefano R; van Herwerden, Lynne; Pratchett, Morgan S; Hobbs, Jean-Paul A; Fugedi, Anneli

    2012-02-01

    Natural hybridization is widespread among coral reef fishes. However, the ecological promoters and evolutionary consequences of reef fish hybridization have not been thoroughly evaluated. Butterflyfishes form a high number of hybrids and represent an appropriate group to investigate hybridization in reef fishes. This study provides a rare test of terrestrially derived hybridization theory in the marine environment by examining hybridization between Chaetodon trifasciatus and C. lunulatus at Christmas Island. Overlapping spatial and dietary ecologies enable heterospecific encounters. Nonassortative mating and local rarity of both parent species appear to permit heterospecific breeding pair formation. Microsatellite loci and mtDNA confirmed the status of hybrids, which displayed the lowest genetic diversity in the sample and used a reduced suite of resources, suggesting decreased adaptability. Maternal contribution to hybridization was unidirectional, and no introgression was detected, suggesting limited, localized evolutionary consequences of hybridization.Comparisons to other reef fish hybridization studies revealed that different evolutionary consequences emerge, despite being promoted by similar factors, possibly due to the magnitude of genetic distance between hybridizing species. This study highlights the need for further enquiry aimed at evaluating the importance and long-term consequences of reef fish hybridization.

  8. Chromogenic in situ hybridization: a multicenter study comparing silver in situ hybridization with FISH.

    PubMed

    Bartlett, J M S; Campbell, Fiona M; Ibrahim, Merdol; Wencyk, Peter; Ellis, Ian; Kay, Elaine; Connolly, Yvonne; O'Grady, Anthony; Di Palma, Silvana; Starczynski, Jane; Morgan, John M; Jasani, Bharat; Miller, Keith

    2009-10-01

    Our purposes were to perform a robust assessment of a new HER2 chromogenic in situ hybridization test and report on concordance of silver in situ hybridization (SISH) data with fluorescence in situ hybridization (FISH) data and on intraobserver and interlaboratory scoring consistency. HER2 results were scored from 45 breast cancers in 7 laboratories using the Ventana (Tucson, AZ) INFORM HER-2 SISH assay and in 1 central laboratory using a standard FISH assay. Overall, 94.8% of cases were successfully analyzed by SISH across the 6 participating laboratories that reported data. Concordance for diagnosis of HER2 amplification by SISH compared with FISH was high (96.0% overall). Intraobserver variability (8.0%) and intersite variability (12.66%) of absolute HER2/chromosome 17 ratios appear to be tightly controlled across all 6 participating laboratories. The Ventana INFORM HER-2 SISH assay is robust and reproducible, shows good concordance with a standard FISH assay, and complies with requirements in national guidelines for performance of diagnostic tests.

  9. 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.

  10. Fluorescence in situ hybridization (FISH) in diagnostic and investigative neuropathology.

    PubMed

    Fuller, Christine E; Perry, Arie

    2002-01-01

    Over the last decade, fluorescence in situ hybridization (FISH) has emerged as a powerful clinical and research tool for the assessment of target DNA dosages within interphase nuclei. Detectable alterations include aneusomies, deletions, gene amplifications, and translocations, with primary advantages to the pathologist including its basis in morphology, its applicability to archival, formalin-fixed paraffin-embedded (FFPE) material, and its similarities to immunohistochemistry. Recent technical advances such as improved hybridization protocols, markedly expanded probe availability resulting from the human genome sequencing initiative, and the advent of high-throughput assays such as gene chip and tissue microarrays have greatly enhanced the applicability of FISH. In our lab, we currently utilize only a limited battery of DNA probes for routine diagnostic purposes, with determination of chromosome 1p and 19q dosage in oligodendroglial neoplasms representing the most common application. However, research applications are numerous and will likely translate into a growing list of clinically useful markers in the near future. In this review, we highlight the advantages and disadvantages of FISH and familiarize the reader with current applications in diagnostic and investigative neuropathology.

  11. 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.

  12. 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. PMID:26937625

  13. Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations

    PubMed Central

    Harbicht, Andrew; Wilson, Chris C; Fraser, Dylan J

    2014-01-01

    Current conservation practices exclude human-generated hybridized populations from protection, as the genetic effects of hybridization in the wild have been observed to be long-lasting based on neutral genetic markers and are considered potentially irreversible. Theory, however, predicts otherwise for genes under selection. We transplanted combinations of wild, domesticated and hybridized populations of a fish species to new environments. We then compared survival, phenotypic variation and plasticity to determine whether hybridization affects adaptive potential after multiple generations of selection in the wild. Although the fitness of our hybridized populations at the onset of hybridization cannot be assessed, our results suggest that within five to eleven generations, selection can remove introduced foreign genes from wild populations that have hybridized with domesticated conspecifics. The end result is hybridized populations that, in terms of survival, phenotypic plasticity, mean trait expression and overall general responses to environmental change, closely resemble neighbouring wild populations. These results have important implications for considering the potential conservation value of hybridized populations and illustrate the effectiveness of selection in a local environment. PMID:25558279

  14. 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.

  15. Environmental Assessment : Umatilla Fish Hatchery.

    SciTech Connect

    United States. Bonneville Power Administration. Office of Power and Resources Management.

    1987-02-01

    Environmental impacts of the fish hatchery expansion alternative are addressed. It is possible that numbers and species of fish produced could change through a future cooperative ODF and W/CTUIR hatchery master planning process. However, the environmental impacts of an expanded hatchery are expected to be basically the same as described in this document. The master plan includes the following information for the proposed Umatilla Fish Hatchery: rearing schedules and release sites and schedules; a detailed production profile that includes numbers of fish to be released and expected annual adult returns; harvest strategies for naturally and hatchery produced fish; proposed management policies and hatchery practices which will ensure that hatchery releases are coordinated with other fishery management agencies and tribes in the Columbia River Basin; and a proposal for biological monitoring and evaluation of the hatchery program. Development of the Umatilla Fish Hatchery, a joint agency effort, is designed to preserve and enhance summer steelhead and possibly spring and fall chinook salmon stocks of the Umatilla River. The hatchery would provide increased harvest opportunities to the commercial, ceremonial, and subsistence fisheries of the CTUIR and the regional sport fishery.

  16. Fluorescent in situ hybridization on comets: FISH comet.

    PubMed

    Shaposhnikov, Sergey; El Yamani, Naouale; Collins, Andrew R

    2015-01-01

    The DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. The comet assay, a sensitive method for monitoring DNA damage and repair, involves electrophoresis of nucleoids comprising supercoiled DNA attached to the nuclear matrix. Breaks in the DNA relax the supercoiling and allow DNA loops to expand, and on electrophoresis to move towards the anode, giving the appearance of a comet tail. We use fluorescent in situ hybridization (FISH) to investigate the structure of the chromatin within comet preparations and to study specific DNA sequences within comets. In this chapter we describe our FISH comets protocols, deal with some technical questions and outline the theory. FISH with comets should be useful to researchers interested in the structural organization of DNA and chromatin, the localization of DNA damage, and the kinetics of repair of damage. PMID:25827891

  17. HER2 in situ hybridization in gastric and gastroesophageal adenocarcinoma: comparison of automated dual ISH to FISH.

    PubMed

    Grin, Andrea; Brezden-Masley, Christine; Bauer, Sharon; Streutker, Catherine J

    2013-12-01

    Patients with gastric and gastroesophageal junction (GEJ) adenocarcinomas that are HER2 positive by immunohistochemistry (IHC) or in situ hybridization show a significant survival benefit with trastuzumab therapy. In situ hybridization is traditionally done by fluorescence in situ hybridization (FISH), despite some limitations. An alternative is the dual in situ hybridization (Dual ISH) technique that is fully automated and uses differentially labeled CEP17 and HER2 probes that can be read by light microscopy on 1 slide. The aim of this study was to assess the utility of Dual ISH in gastric/GEJ cancer and to compare the results with those obtained by IHC and FISH. Cases of gastric/GEJ adenocarcinoma were analyzed by IHC, FISH, and Dual ISH and the correlation between methods calculated. Results for 50 patients were available. There was a 98% (49/50) concordance rate between Dual ISH and FISH. One discrepant case was nonamplified by FISH but showed focal amplification by Dual ISH. Discrepancy was attributed to tumor heterogeneity, which was a frequent finding (78% of HER2-positive cases). There was excellent correlation between Dual ISH and FISH for assessment of HER2 amplification. Dual ISH was rapid, easy to interpret, and maintained cell morphology, which was valuable in identifying tumor heterogeneity.

  18. Extensive hybridization and tetrapolyploidy in spined loach fish.

    PubMed

    Saitoh, Kenji; Chen, Wei-Jen; Mayden, Richard L

    2010-09-01

    Hybridization and polyploidy are particular characteristics of biodiversity among cypriniform fish. To infer ancient parentage of the tetraploids found among Japanese Cobitis loaches, we compare mitochondrial and four nuclear loci from two tetraploids with several diploid populations of C. biwae, C. striata and related species. Mitochondrial gene tree showed monophyletic diploid C. striata and paraphyletic C. biwae relative to C. striata. On the contrary, nuclear sequence analysis recovered both monophyletic diploid C. biwae and C. striata. Disagreement in mitochondrial and nuclear gene trees indicates an ancient hybridization event and mitochondrial gene introgression. The tetraploid C. biwae includes both mitochondrial and nuclear sequences close to diploid C. biwae, indicating autotetraploidy. The tetraploid C. striata has nuclear alleles of both C. biwae and C. striata and mtDNA of C. biwae. It is an allotetraploid with C. biwae as the mother. Our analyses also reveal an onset of genome reshaping after the allotetraploidization. PMID:20416382

  19. 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.

  20. 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 Central

    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. PMID:26566289

  1. 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.

  2. DNA damage, repair and photoadaptation in a Xiphophorus fish hybrid.

    PubMed

    Mitchell, David L; Paniker, Lakshmi; Douki, Thierry

    2009-01-01

    Exposure to sunlight is responsible for most cutaneous malignant melanomas in the human population. It is very likely that DNA damage is an initial event in melanomagenesis, however, the role played by this damage is an open question. To this end, we used a hemipigmented F(1) hybrid of the fish genus Xiphophorus and HPLC tandem mass spectrometry to examine the effects of melanin on the induction and repair of the predominant UV-induced photoproducts formed in skin cell DNA. We found that heavily pigmented skin cells had about half the damage of nonpigmented cells and the relative induction of the major photoproducts was independent of the degree of pigmentation. The efficiency of photoenzymatic repair was the same in nonpigmented and pigmented areas of the fish. We found no evidence of residual damage at 10 days after the last exposure. Most striking was that repeated exposure to multiple doses of UVB caused a very significant photoadaptive response. Rather than an accumulation of damage after five doses of UVB we saw a significant reduction in the amount of damage induced after the final dose compared with the initial dose. The relevance of these observations is discussed in the context of melanoma susceptibility and UVB thresholds.

  3. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH).

    PubMed

    Vilas Boas, Diana; Almeida, Carina; Sillankorva, Sanna; Nicolau, Ana; Azeredo, Joana; Azevedo, Nuno F

    2016-01-01

    Bacteriophage-host interaction studies in biofilm structures are still challenging due to the technical limitations of traditional methods. The aim of this study was to provide a direct fluorescence in situ hybridization (FISH) method based on locked nucleic acid (LNA) probes, which targets the phage replication phase, allowing the study of population dynamics during infection. Bacteriophages specific for two biofilm-forming bacteria, Pseudomonas aeruginosa and Acinetobacter, were selected. Four LNA probes were designed and optimized for phage-specific detection and for bacterial counterstaining. To validate the method, LNA-FISH counts were compared with the traditional plaque forming unit (PFU) technique. To visualize the progression of phage infection within a biofilm, colony-biofilms were formed and infected with bacteriophages. A good correlation (r = 0.707) was observed between LNA-FISH and PFU techniques. In biofilm structures, LNA-FISH provided a good discrimination of the infected cells and also allowed the assessment of the spatial distribution of infected and non-infected populations. PMID:26813295

  4. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH).

    PubMed

    Vilas Boas, Diana; Almeida, Carina; Sillankorva, Sanna; Nicolau, Ana; Azeredo, Joana; Azevedo, Nuno F

    2016-01-01

    Bacteriophage-host interaction studies in biofilm structures are still challenging due to the technical limitations of traditional methods. The aim of this study was to provide a direct fluorescence in situ hybridization (FISH) method based on locked nucleic acid (LNA) probes, which targets the phage replication phase, allowing the study of population dynamics during infection. Bacteriophages specific for two biofilm-forming bacteria, Pseudomonas aeruginosa and Acinetobacter, were selected. Four LNA probes were designed and optimized for phage-specific detection and for bacterial counterstaining. To validate the method, LNA-FISH counts were compared with the traditional plaque forming unit (PFU) technique. To visualize the progression of phage infection within a biofilm, colony-biofilms were formed and infected with bacteriophages. A good correlation (r = 0.707) was observed between LNA-FISH and PFU techniques. In biofilm structures, LNA-FISH provided a good discrimination of the infected cells and also allowed the assessment of the spatial distribution of infected and non-infected populations.

  5. Liposarcoma or invasive lipomatosis in flower horn fish, hybrid cichlid: clinical, radiological, ultrasonographical and histopathological study.

    PubMed

    Rahmati-Holasoo, H; Shokrpoor, S; Tavakkoli, A; Vajhi, A; Ebrahimzadeh Mousavi, H

    2016-03-01

    Liposarcoma or invasive lipomatosis affecting three indoor aquarium fish (flower horn fish, hybrid cichlid) is characterized, by the presence of mature adipocytes of variable sizes and by an invasive behaviour, which affected internal organs and eyes of all cases. Detailed macroscopic, radiological, ultrasonographical and histopathological features are presented. All fish had bilateral exophthalmia with some masses around the eyes. Ultrasonography confirmed the presence of hyperechoic masses in the eyes. Histopathology of all cases described the presence of variable-sized adipose cells in the eyes. The suggested diagnosis is well-differentiated liposarcoma or invasive lipomatosis. This is the first report of liposarcoma or invasive lipomatosis in flower horn fish, hybrid cichlid.

  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. PMID:27391325

  7. 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

  8. 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.

  9. Detection of viral RNA by fluorescence in situ hybridization (FISH).

    PubMed

    Vyboh, Kishanda; Ajamian, Lara; Mouland, Andrew J

    2012-01-01

    localization using a method like this, abundant information has been gained on both viral and cellular RNA trafficking events. For instance, HIV-1 produces RNA in the nucleus of infected cells but the RNA is only translated in the cytoplasm. When one key viral protein is missing (Rev), FISH of the viral RNA has revealed that the block to viral replication is due to the retention of the HIV-1 genomic RNA in the nucleus. Here, we present the method for visual analysis of viral genomic RNA in situ. The method makes use of a labelled RNA probe. This probe is designed to be complementary to the viral genomic RNA. During the in vitro synthesis of the antisense RNA probe, the ribonucleotide that is modified with digoxigenin (DIG) is included in an in vitro transcription reaction. Once the probe has hybridized to the target mRNA in cells, subsequent antibody labelling steps (Figure 1) will reveal the localization of the mRNA as well as proteins of interest when performing FISH/IF. PMID:22588480

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. Suppression subtractive hybridization cDNA libraries to identify differentially expressed genes from contrasting fish habitats.

    PubMed

    Straub, Peter F; Higham, Mary L; Tanguy, Arnaud; Landau, Brenda J; Phoel, William C; Hales, L Stanton; Thwing, Theodore K M

    2004-01-01

    Suppression subtractive hybridization complementary DNA libraries identified differentially expressed genes in liver tissue of winter flounder collected from the highly impacted Raritan-Hudson estuary versus those from less industrialized estuaries farther south in New Jersey. Distinct transcript profiles emerged in the fish from these different habitats. A total of 251 clones from the forward (upregulated with anthropogenic impact) and reverse (downregulated with anthropogenic impact) subtracted libraries were sequenced. In the upregulated library immune response transcripts, including complement C-3, C-7, factor H, factor Bf/C2, differentially regulated trout protein 1, and the antimicrobial hepcidin, indicated the pollution-impacted fish were under a high viral or bacterial load. Transcripts for cytochrome P450 1A, P450 3A, and glutathione S-transferase, important components of phase I and II metabolism of xenobiotics, were found in the upregulated-with-pollution library. Vitellogenins I and II and egg envelope protein (zp) appeared to be downregulated. A homologue of the tumor suppressor p33(ING1) (down) and hepatocyte growth factor-like protein (up) may indicate liver damage or hepatocellular carcinoma or hepatoma. These expression patterns, confirmed by quantitative polymerase chain reaction, indicate that transcript analysis is a useful method for assessing the health of local habitats and the organisms therein. PMID:15546050

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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...

  17. 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...

  18. 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...

  19. 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 HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  20. 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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  2. Defining, assessing and promoting the welfare of farmed fish.

    PubMed

    Huntingford, F A; Kadri, S

    2014-04-01

    As currently practised, the culture of fish for food potentially raises concerns about the welfare of farmed fish, and this is a topic that has received considerable attention. As vertebrates, fish share a number of features with the birds and mammals that are more commonly farmed, so many welfare principles derived from consideration of these groups may also be applied to fish. However, fish have a long, separate evolutionary history and are also adapted to a very different, aquatic environment. For these reasons, they have a number of special features that are relevant to how welfare is defined, assessed and promoted and these are discussed. The various methods that are available to researchers for identifying and assessing good and bad welfare in fish are considered, including assessment of physical health and physiological, behavioural and genomic status. The subset of practical welfare indicators that can be used on working farms is also reviewed. Various aspects of intensive aquaculture that can potentially compromise fish welfare are outlined, as are some strategies available for mitigating such adverse effects. Finally, the paper ends by looking briefly to the future, identifying likely changes in aquaculture practices and how these might affect the welfare of farmed fish.

  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. 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.

  5. 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.

  6. 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.

  7. 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. PMID:24753154

  8. Fish stomach contents in benthic macroinvertebrate assemblage assessments.

    PubMed

    Tupinambás, T H; Pompeu, P S; Gandini, C V; Hughes, R M; Callisto, M

    2015-01-01

    The choice of sampling gears to assess benthic macroinvertebrate communities depends on environmental characteristics, study objectives, and cost effectiveness. Because of the high foraging capacity and diverse habitats and behaviors of benthophagous fishes, their stomach contents may offer a useful sampling tool in studies of benthic macroinvertebrates, especially in large, deep, fast rivers that are difficult to sample with traditional sediment sampling gear. Our objective was to compare the benthic macroinvertebrate communities sampled from sediments with those sampled from fish stomachs. We collected benthic macroinvertebrates and fish from three different habitat types (backwater, beach, riffle) in the wet season, drying season, and dry season along a single reach of the Grande River (Paraná River Basin, southeast Brazil). We sampled sediments through use of a Petersen dredge (total of 216 grabs) and used gill nets to sample fish (total of 36 samples). We analyzed the stomach contents of three commonly occurring benthophagous fish species (Eigenmannia virescens, Iheringichthys labrosus, Leporinus amblyrhynchus). Chironomids dominated in both sampling methods. Macroinvertebrate taxonomic composition and abundances from fish stomachs differed from those from sediment samples, but less so from riffles than from backwater and beach habitats. Macroinvertebrate taxa from E. virescens stomachs were more strongly correlated with sediment samples from all three habitats than were those from the other two species. The species accumulation curves and higher mean dispersion values, compared with with sediment samples suggest that E. virescens is more efficient than sediment samples and the other fish studied at collecting benthic taxa. We conclude that by analyzing the stomach contents of benthophagous fishes it is possible to assess important characteristics of benthic communities (dispersion, taxonomic composition and diversity). This is especially true for studies

  9. 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.

  10. 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.

  11. MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells

    PubMed Central

    Kleiner, Manuel; Wetzel, Silke; Liebeke, Manuel; Dubilier, Nicole

    2015-01-01

    Fluorescence in situ hybridization (FISH) has become a vital tool for environmental and medical microbiology and is commonly used for the identification, localization, and isolation of defined microbial taxa. However, fluorescence signal strength is often a limiting factor for targeting all members in a microbial community. Here, we present the application of a multilabeled FISH approach (MiL-FISH) that (i) enables the simultaneous targeting of up to seven microbial groups using combinatorial labeling of a single oligonucleotide probe, (ii) is applicable for the isolation of unfixed environmental microorganisms via fluorescence-activated cell sorting (FACS), and (iii) improves signal and imaging quality of tissue sections in acrylic resin for precise localization of individual microbial cells. We show the ability of MiL-FISH to distinguish between seven microbial groups using a mock community of marine organisms and its applicability for the localization of bacteria associated with animal tissue and their isolation from host tissues using FACS. To further increase the number of potential target organisms, a streamlined combinatorial labeling and spectral imaging-FISH (CLASI-FISH) concept with MiL-FISH probes is presented here. Through the combination of increased probe signal, the possibility of targeting hard-to-detect taxa and isolating these from an environmental sample, the identification and precise localization of microbiota in host tissues, and the simultaneous multilabeling of up to seven microbial groups, we show here that MiL-FISH is a multifaceted alternative to standard monolabeled FISH that can be used for a wide range of biological and medical applications. PMID:26475101

  12. 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

  13. 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

  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. Ultraviolet A does not induce melanomas in a Xiphophorus hybrid fish model

    PubMed Central

    Mitchell, David L.; Fernandez, André A.; Nairn, Rodney S.; Garcia, Rachel; Paniker, Lakshmi; Trono, David; Thames, Howard D.; Gimenez-Conti, Irma

    2010-01-01

    We examined the wavelength dependence of ultraviolet (UV) ra-diation (UVR)-induced melanoma in a Xiphophorus backcross hybrid model previously reported to be susceptible to melanoma induction by ultraviolet A (UVA) and visible light. Whereas ultraviolet B (UVB) irradiation of neonates yielded high frequencies of melanomas in pigmented fish, UVA irradiation resulted in melanoma frequencies that were not significantly different from unirradiated fish. Spontaneous and UV-induced melanoma frequencies correlated with the degree of pigmentation as expected from previous studies, and the histopathology phenotypes of the melanomas were not found in significantly different proportions in UV-treated and -untreated tumor-bearing fish. Our results support the conclusion that a brief early-life exposure to UVB radiation causes melanoma formation in this animal model. These data are consistent with an essential role for direct DNA damage, including cyclobutane dimers and (6-4) photoproducts, in the etiology of melanoma. PMID:20439744

  16. Ultraviolet A does not induce melanomas in a Xiphophorus hybrid fish model.

    PubMed

    Mitchell, David L; Fernandez, André A; Nairn, Rodney S; Garcia, Rachel; Paniker, Lakshmi; Trono, David; Thames, Howard D; Gimenez-Conti, Irma

    2010-05-18

    We examined the wavelength dependence of ultraviolet (UV) ra-diation (UVR)-induced melanoma in a Xiphophorus backcross hybrid model previously reported to be susceptible to melanoma induction by ultraviolet A (UVA) and visible light. Whereas ultraviolet B (UVB) irradiation of neonates yielded high frequencies of melanomas in pigmented fish, UVA irradiation resulted in melanoma frequencies that were not significantly different from unirradiated fish. Spontaneous and UV-induced melanoma frequencies correlated with the degree of pigmentation as expected from previous studies, and the histopathology phenotypes of the melanomas were not found in significantly different proportions in UV-treated and -untreated tumor-bearing fish. Our results support the conclusion that a brief early-life exposure to UVB radiation causes melanoma formation in this animal model. These data are consistent with an essential role for direct DNA damage, including cyclobutane dimers and (6-4) photoproducts, in the etiology of melanoma.

  17. 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)

  18. 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.

  19. Microfluidic fluorescence in situ hybridization and flow cytometry (µFlowFISH)

    PubMed Central

    Liu, Peng; Meagher, Robert J.; Light, Yooli Kim; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P.; Hazen, Terry C.; Singh, Anup K.

    2011-01-01

    We describe an integrated microfluidic device (µFlowFISH) capable of performing 16S rRNA fluorescence in situ hybridization (FISH) followed by flow cytometric detection for identifying bacteria in natural microbial communities. The device was used for detection of species involved in bioremediation of Cr(VI) and other metals in groundwater samples from a highly-contaminated environmental site (Hanford, WA, USA). The µFlowFISH seamlessly integrates two components: a hybridization chamber formed between two photopolymerized membranes, where cells and probes are electrophoretically loaded, incubated and washed; and a downstream cross structure for electrokinetically focusing cells into a single-file flow for flow cytometry analysis. The device is capable of analyzing a wide variety of bacteria including aerobic, facultative and anaerobic bacteria and was initially tested and validated using cultured microbes, including Escherichia coli, as well as two strains isolated from Hanford site: Desulfovibrio vulgaris strain RCH1, and Pseudomonas sp. strain RCH2 that are involved in Cr(VI) reduction and immobilization. Combined labeling and detection efficiencies of 74–97% were observed in experiments with simple mixtures of cultured cells confirmed specific labeling. Results obtained were in excellent agreement with those obtained by conventional flow cytometry confirming the accuracy of µFlowFISH. Finally, the device was used for analyzing water samples collected on different dates from the Hanford Site. We were able to monitor the numbers of Pseudomonas sp. with only 100–200 cells loaded into the microchip. The µFlowFISH approach provides an automated platform for quantitative detection of microbial cells from complex samples, and is ideally suited for analysis of precious samples with low cell numbers such as those found at extreme environmental niches, bioremediation sites, and the human microbiome. PMID:21755095

  20. 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

    2011-12-01

    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.

  1. 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.

  2. Disruptive sexual selection on male nuptial coloration in an experimental hybrid population of cichlid fish.

    PubMed

    Stelkens, Rike B; Pierotti, Michele E R; Joyce, Domino A; Smith, Alan M; van der Sluijs, Inke; Seehausen, Ole

    2008-09-12

    Theory suggests that genetic polymorphisms in female mating preferences may cause disruptive selection on male traits, facilitating phenotypic differentiation despite gene flow, as in reinforcement or other models of speciation with gene flow. Very little experimental data have been published to test the assumptions regarding the genetics of mate choice that such theory relies on. We generated a population segregating for female mating preferences and male colour dissociated from other species differences by breeding hybrids between species of the cichlid fish genus Pundamilia. We measured male mating success as a function of male colour. First, we demonstrate that non-hybrid females of both species use male nuptial coloration for choosing mates, but with inversed preferences. Second, we show that variation in female mating preferences in an F2 hybrid population generates a quadratic fitness function for male coloration suggestive of disruptive selection: intermediate males obtained fewer matings than males at either extreme of the colour range. If the genetics of female mate choice in Pundamilia are representative for those in other species of Lake Victoria cichlid fish, it may help explain the origin and maintenance of phenotypic diversity despite some gene flow.

  3. Disruptive sexual selection on male nuptial coloration in an experimental hybrid population of cichlid fish.

    PubMed

    Stelkens, Rike B; Pierotti, Michele E R; Joyce, Domino A; Smith, Alan M; van der Sluijs, Inke; Seehausen, Ole

    2008-09-12

    Theory suggests that genetic polymorphisms in female mating preferences may cause disruptive selection on male traits, facilitating phenotypic differentiation despite gene flow, as in reinforcement or other models of speciation with gene flow. Very little experimental data have been published to test the assumptions regarding the genetics of mate choice that such theory relies on. We generated a population segregating for female mating preferences and male colour dissociated from other species differences by breeding hybrids between species of the cichlid fish genus Pundamilia. We measured male mating success as a function of male colour. First, we demonstrate that non-hybrid females of both species use male nuptial coloration for choosing mates, but with inversed preferences. Second, we show that variation in female mating preferences in an F2 hybrid population generates a quadratic fitness function for male coloration suggestive of disruptive selection: intermediate males obtained fewer matings than males at either extreme of the colour range. If the genetics of female mate choice in Pundamilia are representative for those in other species of Lake Victoria cichlid fish, it may help explain the origin and maintenance of phenotypic diversity despite some gene flow. PMID:18522918

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

    PubMed

    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

  5. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples.

    PubMed

    Tischer, Karolin; Zeder, Michael; Klug, Rebecca; Pernthaler, Jakob; Schattenhofer, Martha; Harms, Hauke; Wendeberg, Annelie

    2012-12-01

    Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II. PMID:22425347

  8. Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples.

    PubMed

    Tischer, Karolin; Zeder, Michael; Klug, Rebecca; Pernthaler, Jakob; Schattenhofer, Martha; Harms, Hauke; Wendeberg, Annelie

    2012-12-01

    Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II.

  9. Fluorescence in situ hybridization (FISH) mapping of single copy genes on Trichomonas vaginalis chromosomes.

    PubMed

    Zubáčová, Zuzana; Krylov, Vladimír; Tachezy, Jan

    2011-04-01

    The highly repetitive nature of the Trichomonas vaginalis genome and massive expansion of various gene families has caused difficulties in genome assembly and has hampered genome mapping. Here, we adapted fluorescence in situ hybridization (FISH) for T. vaginalis, which is sensitive enough to detect single copy genes on metaphase chromosomes. Sensitivity of conventional FISH, which did not allow single copy gene detection in T. vaginalis, was increased by means of tyramide signal amplification. Two selected single copy genes, coding for serine palmitoyltransferase and tryptophanase, were mapped to chromosome I and II, respectively, and thus could be used as chromosome markers. This established protocol provides an amenable tool for the physical mapping of the T. vaginalis genome and other essential applications, such as development of genetic markers for T. vaginalis genotyping. PMID:21195113

  10. 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.

  11. 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

  12. Hybridization and contemporary evolution in an introduced cichlid fish from Lake Malawi National Park.

    PubMed

    Streelman, J Todd; Gmyrek, S L; Kidd, M R; Kidd, C; Robinson, R L; Hert, E; Ambali, A J; Kocher, T D

    2004-08-01

    Rapidly evolving systems offer the chance to observe genetic and phenotypic change in real time. We exploit a well-characterized introduction of cichlid fish into Lake Malawi National Park to document a short history of habitat colonization and the evolution of genes and colour pattern. In the early 1960s, a fish exporter introduced individuals of Cynotilapia afra to a single site (Mitande Point) of Thumbi West Island and, as late as 1983, the species was confined to this location. In 2001, C. afra had colonized the entire perimeter of Thumbi West. In July of that year, we sampled C. afra individuals from six sites around the island and scored variation in dorsal fin colour as well as allelic diversity at six microsatellite loci. We found that, in two decades, C. afra had diverged into genetically distinct, phenotypically different northern and southern populations. We observed a high proportion of hybrids between the introduced C. afra and the native Metriaclima zebra on the southern coast of Thumbi West, and speculate that hybridization is facilitated by low water clarity at these windward sites. The short history of C. afra at Thumbi West is a microcosm of contemporary evolutionary divergence and may provide the opportunity to study the process from start to finish in genetic detail. PMID:15245419

  13. Insertional translocation detected using FISH confirmation of array-comparative genomic hybridization (aCGH) results.

    PubMed

    Kang, Sung-Hae L; Shaw, Chad; Ou, Zhishuo; Eng, Patricia A; Cooper, M Lance; Pursley, Amber N; Sahoo, Trilochan; Bacino, Carlos A; Chinault, A Craig; Stankiewicz, Pawel; Patel, Ankita; Lupski, James R; Cheung, Sau Wai

    2010-05-01

    Insertional translocations (ITs) are rare events that require at least three breaks in the chromosomes involved and thus qualify as complex chromosomal rearrangements (CCR). In the current study, we identified 40 ITs from approximately 18,000 clinical cases (1:500) using array-comparative genomic hybridization (aCGH) in conjunction with fluorescence in situ hybridization (FISH) confirmation of the aCGH findings, and parental follow-up studies. Both submicroscopic and microscopically visible IT events were detected. They were divided into three major categories: (1) simple intrachromosomal and interchromosomal IT resulting in pure segmental trisomy, (2) complex IT involving more than one abnormality, (3) deletion inherited from a parent with a balanced IT resulting in pure segmental monosomy. Of the cases in which follow-up parental studies were available, over half showed inheritance from an apparently unaffected parent carrying the same unbalanced rearrangement detected in the propositi, thus decreasing the likelihood that these IT events are clinically relevant. Nevertheless, we identified six cases in which small submicroscopic events were detected involving known disease-associated genes/genomic segments and are likely to be pathogenic. We recommend that copy number gains detected by clinical aCGH analysis should be confirmed using FISH analysis whenever possible in order to determine the physical location of the duplicated segment. We hypothesize that the increased use of aCGH in the clinic will demonstrate that IT occurs more frequently than previously considered but can identify genomic rearrangements with unclear clinical significance.

  14. Insertional Translocation Detected Using FISH Confirmation of Array-Comparative Genomic Hybridization (aCGH) Results

    PubMed Central

    Kang, Sung-Hae L.; Shaw, Chad; Ou, Zhishuo; Eng, Patricia A.; Cooper, M. Lance; Pursley, Amber N.; Sahoo, Trilochan; Bacino, Carlos A.; Chinault, A. Craig; Stankiewicz, Pawel; Patel, Ankita; Lupski, James R.; Cheung, Sau Wai

    2013-01-01

    Insertional translocations (ITs) are rare events that require at least three breaks in the chromosomes involved and thus qualify as complex chromosomal rearrangements (CCR). In the current study, we identified 40 ITs from approximately 18,000 clinical cases (1:500) using array-comparative genomic hybridization (aCGH) in conjunction with fluorescence in situ hybridization (FISH) confirmation of the aCGH findings, and parental follow-up studies. Both submicroscopic and microscopically visible IT events were detected. They were divided into three major categories: (1) simple intrachromosomal and interchromosomal IT resulting in pure segmental trisomy, (2) complex IT involving more than one abnormality, (3) deletion inherited from a parent with a balanced IT resulting in pure segmental monosomy. Of the cases in which follow-up parental studies were available, over half showed inheritance from an apparently unaffected parent carrying the same unbalanced rearrangement detected in the propositi, thus decreasing the likelihood that these IT events are clinically relevant. Nevertheless, we identified six cases in which small submicroscopic events were detected involving known disease-associated genes/genomic segments and are likely to be pathogenic. We recommend that copy number gains detected by clinical aCGH analysis should be confirmed using FISH analysis whenever possible in order to determine the physical location of the duplicated segment. We hypothesize that the increased use of aCGH in the clinic will demonstrate that IT occurs more frequently than previously considered but can identify genomic rearrangements with unclear clinical significance. PMID:20340098

  15. 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.

  16. 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.

  17. Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH).

    PubMed

    Malic, Sladjana; Hill, Katja E; Hayes, Anthony; Percival, Steven L; Thomas, David W; Williams, David W

    2009-08-01

    Biofilms provide a reservoir of potentially infectious micro-organisms that are resistant to antimicrobial agents, and their importance in the failure of medical devices and chronic inflammatory conditions is increasingly being recognized. Particular research interest exists in the association of biofilms with wound infection and non-healing, i.e. chronic wounds. In this study, fluorescent in situ hybridization (FISH) was used in combination with confocal laser scanning microscopy (CLSM) to detect and characterize the spatial distribution of biofilm-forming bacteria which predominate within human chronic skin wounds (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sp. and Micrococcus sp.). In vitro biofilms were prepared using a constant-depth film fermenter and a reconstituted human epidermis model. In vivo biofilms were also studied using biopsy samples from non-infected chronic venous leg ulcers. The specificity of peptide nucleic acid (PNA) probes for the target organisms was confirmed using mixed preparations of planktonic bacteria and multiplex PNA probing. Identification and location of individual bacterial species within multi-species biofilms demonstrated that P. aeruginosa was predominant. CLSM revealed clustering of individual species within mixed-species biofilms. FISH analysis of archive chronic wound biopsy sections showed bacterial presence and allowed bacterial load to be determined. The application of this standardized procedure makes available an assay for identification of single- or multi-species bacterial populations in tissue biopsies. The technique provides a reliable tool to study bacterial biofilm formation and offers an approach to assess targeted biofilm disruption strategies in vivo. PMID:19477903

  18. Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH).

    PubMed

    Malic, Sladjana; Hill, Katja E; Hayes, Anthony; Percival, Steven L; Thomas, David W; Williams, David W

    2009-08-01

    Biofilms provide a reservoir of potentially infectious micro-organisms that are resistant to antimicrobial agents, and their importance in the failure of medical devices and chronic inflammatory conditions is increasingly being recognized. Particular research interest exists in the association of biofilms with wound infection and non-healing, i.e. chronic wounds. In this study, fluorescent in situ hybridization (FISH) was used in combination with confocal laser scanning microscopy (CLSM) to detect and characterize the spatial distribution of biofilm-forming bacteria which predominate within human chronic skin wounds (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sp. and Micrococcus sp.). In vitro biofilms were prepared using a constant-depth film fermenter and a reconstituted human epidermis model. In vivo biofilms were also studied using biopsy samples from non-infected chronic venous leg ulcers. The specificity of peptide nucleic acid (PNA) probes for the target organisms was confirmed using mixed preparations of planktonic bacteria and multiplex PNA probing. Identification and location of individual bacterial species within multi-species biofilms demonstrated that P. aeruginosa was predominant. CLSM revealed clustering of individual species within mixed-species biofilms. FISH analysis of archive chronic wound biopsy sections showed bacterial presence and allowed bacterial load to be determined. The application of this standardized procedure makes available an assay for identification of single- or multi-species bacterial populations in tissue biopsies. The technique provides a reliable tool to study bacterial biofilm formation and offers an approach to assess targeted biofilm disruption strategies in vivo.

  19. 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)

  20. 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

  1. Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH).

    PubMed

    Yamaguchi, Tsuyoshi; Fuchs, Bernhard Maximilian; Amann, Rudolf; Kawakami, Shuji; Kubota, Kengo; Hatamoto, Masashi; Yamaguchi, Takashi

    2015-09-01

    Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with rRNA-targeted oligonucleotide probes has significantly improved the identification of microorganisms in various environmental samples. However, one of the major constraints of CARD-FISH is the low probe penetration due to the high molecular weight of the horseradish peroxidase (HRP) label. Recently, this limitation has been overcome by a novel signal amplification approach termed in situ DNA-hybridization chain reaction (in situ DNA-HCR). In this study, we present an improved and accelerated in situ DNA-HCR protocol (quickHCR-FISH) with increased signal intensity, which was approximately 2 times higher than that of standard in situ DNA-HCR. In addition, the amplification time was only 15 min for the extension of amplifier probes from the initiator probe compared to 2h in the original protocol. The quickHCR-FISH was successfully tested for the quantification of marine bacteria with low rRNA contents in both seawater and sediment samples. It was possible to detect the same number of marine bacteria with quickHCR-FISH compared to CARD-FISH within only 3h. Thus, this newly developed protocol could be an attractive alternative to CARD-FISH for the detection and visualization of microorganisms in their environmental context.

  2. 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

  3. 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.

  4. 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

  5. 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

    2014-01-01

    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

  6. 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.

  7. The etiology of sunlight-induced melanoma in Xiphophorus hybrid fish.

    PubMed

    Mitchell, David; Paniker, Lakshmi; Sanchez, Guillermo; Trono, David; Nairn, Rodney

    2007-08-01

    In contrast to sunlight-induced squamous cell carcinoma the etiology of cutaneous malignant melanoma (CMM) is not well understood. In particular, the role that sunlight exposure and DNA damage play in the initiation of this deadly form of cancer is an open question. Early UV carcinogenesis studies in the Xiphophorus backcross hybrid fish model by Richard Setlow indicated that direct DNA damage caused by exposure to the UVB component of sunlight is necessary and sufficient for melanoma formation. Subsequent studies by Setlow suggested that monochromatic UVA radiation that is not directly absorbed by DNA was also sufficient for melanoma induction in Xiphophorus and was, indeed, primarily responsible for initiating human melanoma. These results had significant public health consequences, suggesting that although sunscreens may inhibit UVB-induced erythema they may actually increase exposure to the UVA wavelengths that cause cancer. An intensive worldwide public debate on sunscreen use and "abuse" ensued. Our data do not support a major role of free radical chemistry in melanoma induction. We find evidence that the direct damage caused by the absorption of UVB wavelengths by DNA (e.g., the cyclobutane pyrimidine dimer or CPD) is required for CMM formation and that the ability to repair these lesions plays a significant role in tumor susceptibility. Using the Xiphophorus backcross hybrid fish we are currently in the process of re-evaluating the wavelength- and DNA damage-dependence of UV-induced melanoma and the role nucleotide excision repair and the genes controlling DNA repair and the UV response play in melanoma resistance. From these studies we hope to define the effective solar wavelength boundaries of melanoma, identify the class of critical DNA damage and elucidate the role of DNA repair in tumor suppression.

  8. 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. PMID:24045124

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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. PMID:25447914

  14. 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.

  15. 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.

  16. 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.

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

    PubMed

    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

    2016-11-15

    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.

  18. 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.

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

    PubMed

    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

    2016-11-15

    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. PMID

  20. 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. PMID:27002811

  1. 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.

  2. 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...

  3. Multiplex fluorescence in situ hybridization (M-FISH) and confocal laser scanning microscopy (CLSM) to analyze multispecies oral biofilms.

    PubMed

    Karygianni, Lamprini; Hellwig, Elmar; Al-Ahmad, Ali

    2014-01-01

    Multiplex fluorescence in situ hybridization (M-FISH) constitutes a favorable microbiological method for the analysis of spatial distribution of highly variable phenotypes found in multispecies oral biofilms. The combined use of confocal laser scanning microscopy (CLSM) produces high-resolution three-dimensional (3D) images of individual bacteria in their natural environment. Here, we describe the application of M-FISH on early (Streptococcus spp., Actinomyces naeslundii) and late colonizers (Fusobacterium nucleatum, Veillonella spp.) of in situ-formed oral biofilms, the acquisition of CLSM images, as well as the qualitative and quantitative analysis of these digitally obtained and processed images.

  4. 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. PMID:27019847

  5. 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

  6. 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.

  7. Combined Use of Molecular Markers and High-Resolution Melting (HRM) to Assess Chromosome Dosage in Potato Hybrids.

    PubMed

    Villano, Clizia; Miraglia, Valeria; Iorizzo, Massimo; Aversano, Riccardo; Carputo, Domenico

    2016-03-01

    In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n = 2x = 24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of 5 interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding program or following transformation techniques. PMID:26663623

  8. 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

    2014-01-01

    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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Methods for sampling fish communities as part of the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Meador, M.R.; Cuffney, T.F.; Gurtz, M.E.

    1993-01-01

    Fish community structure is characterized in the U.S. Geological Survey's National Water-Quality Assessment Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. The objective of the National Water-Quality Assessment characterization of fish community structure is to relate fish community characteristics to physical, chemical, and other biological factors to assess water-quality conditions. To accomplish this, fish community structure is described at sites representing selected environmental settings. In addition, spatial and temporal patterns in fish community structure are examined at local, regional, and national levels. A representative sample of the fish community is collected by sampling a stream reach using two complementary methods. The primary collection method is electrofishing using backpack, towed, or boat-operated electrofishing gear; seining is a secondary technique. Other secondary techniques may be substituted after careful consideration of sampling efficiency and consultation with local fish ecologists. Before fish sampling is conducted, careful consideration must be given to collecting permits; protecting endangered, threatened, and special-concern species; and coordinating sampling efforts with other fish ecologists. After the sample is collected, individual fish are identified to species by ichthyologists. Length and weight measurements are taken, and the presence of external anomalies are recorded.

  14. 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

  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

    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.

  17. Interpretation of fish biomarker data for identification, classification, risk assessment and testing of endocrine disrupting chemicals.

    PubMed

    Dang, ZhiChao

    2016-01-01

    Chemical induced changes in fish biomarkers vitellogenin (VTG), secondary sex characteristics (SSC), and sex ratio indicate modes/mechanisms of action (MOAs) of EAS (estrogen, androgen and steroidogenesis) pathways. These biomarkers could be used for defining MOAs and the causal link between MOAs and adverse effects in fish for the identification of endocrine disrupting chemicals (EDCs). This paper compiled data sets of 150 chemicals for VTG, 57 chemicals for SSC and 38 chemicals for sex ratio in fathead minnow, medaka and zebrafish. It showed 1) changes in fish biomarkers can indicate the MOAs as anticipated; 2) in addition to EAS pathways, chemicals with non-EAS pathways induced changes in fish biomarkers; 3) responses of fish biomarkers did not always follow the anticipated patterns of EAS pathways. These responses may result from the interaction of chemical-induced multiple MOAs and confounding factors like fish diet, infection, culture conditions, general toxicity and stress response. The complex response of fish biomarkers to a chemical of interest requires EDC testing at multiple biological levels. Interpretation of fish biomarker data should be combined with relevant information at different biological levels, which is critical for defining chemical specific MOAs. The utility of fish biomarker data for identification, classification, PBT assessment, risk assessment, and testing of EDCs in the regulatory context was discussed. This paper emphasizes the importance of fish biomarker data in the regulatory context, a weight of evidence approach for the interpretation of fish biomarker data and the need for defining levels of evidence for the identification of EDCs.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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. PMID:25880597

  4. 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.

  5. Development and assessment of the CONTAIN hybrid flow solver

    SciTech Connect

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

    1997-06-20

    A new gravitational head formulation for the treatment of stratified flows has been developed for CONTAIN, a lumped-parameter code used primarily for the analysis of postulated accidents in nuclear power plants. This new hybrid formulation is discussed and compared in this paper with the old, average-density CONTAIN formulation. In addition, these formulations are assessed against experimental data from three large-scale experiments in which stratified conditions were observed. These are the NUPEC M-8-1, Surtsey ST-3, and the HDR E11.2 experiments.

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. [Hydroacoustic assessment of fish resources in reservoirs with different fishery management].

    PubMed

    Sun, Ming-Bo; Gu, Xiao-Hong; Zeng, Qing-Fei; Mao, Zhi-Gang; Gu, Xian-Kun

    2013-01-01

    By using Biosonics DT-X echosounder (208 kHz), a hydroacoustic investigation was conducted on the fish resources in three mesotrophic reservoirs (Daxi Reservoir, Shahe Reservoir, and Jinniushan Reservoir) with different fishery management in late autumn and early winter 2011, and a GIS model was constructed to assess the fish resource distribution in the reservoirs. No significant difference was observed in the average size of fish in the three reservoirs, but the distribution curves of fish target strength (TS) showed that the fish size distribution proportion was different, and had close correlation with fishery management. The fish density in Daxi Reservoir (averagely 0.0183 ind x m(-3)) had no significant difference with that in Shahe Reservoir (averagely 0.0124 ind x m(-3)), but the fish density in Jinniushan Reservoir (averagely 0.0085 ind x m(-3)) was significantly lower than that in Daxi and Shahe reservoirs. There was no significant correlation between the horizontal distribution of fish density and the water depth in the three reservoirs. The fish in the three reservoirs were in group distribution, and fish aggregation was found in Daxi and Shahe reservoirs. In the three reservoirs, the fish biomass was the highest in downstream, and there was a greater biomass near the dam, except in Shahe Reservoir which was affected by fish catch activity. Based on the raster data obtained from GIS fish distribution model and the surface water area of each grid, the total amount of fish resources with the TS > -60 dB in the Daxi, Shahe and Jinniushan reservoirs was estimated as about 480000, 610000 and 520000 individuals, and that with the TS > -40 dB was about 50400, 52900 and 90700 individuals, respectively.

  11. 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.

  12. Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species.

    PubMed

    Hasselman, Daniel J; Argo, Emily E; McBride, Meghan C; Bentzen, Paul; Schultz, Thomas F; Perez-Umphrey, Anna A; Palkovacs, Eric P

    2014-03-01

    Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry have received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites, we examined hybridization between sympatric populations of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to test whether the frequency of hybridization and pattern of introgression have been impacted by the construction of a dam that isolated formerly anadromous populations of both species in a landlocked freshwater reservoir. The frequency of hybridization and pattern of introgression differed markedly between anadromous and landlocked populations. The rangewide frequency of hybridization among anadromous populations was generally 0-8%, whereas all landlocked individuals were hybrids. Although neutral introgression was observed among anadromous hybrids, directional introgression leading to increased prevalence of alewife genotypes was detected among landlocked hybrids. We demonstrate that habitat alteration can lead to hybrid swarm formation between divergent species that naturally occur sympatrically, and provide empirical evidence that reinforcement does not always sustain reproductive isolation under such circumstances.

  13. 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. PMID:17108333

  14. 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.

  15. 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...

  16. Fluorescence in situ hybridizations (FISH) for the localization of viruses and endosymbiotic bacteria in plant and insect tissues.

    PubMed

    Kliot, Adi; Kontsedalov, Svetlana; Lebedev, Galina; Brumin, Marina; Cathrin, Pakkianathan Britto; Marubayashi, Julio Massaharu; Skaljac, Marisa; Belausov, Eduard; Czosnek, Henryk; Ghanim, Murad

    2014-02-24

    Fluorescence in situ hybridization (FISH) is a name given to a variety of techniques commonly used for visualizing gene transcripts in eukaryotic cells and can be further modified to visualize other components in the cell such as infection with viruses and bacteria. Spatial localization and visualization of viruses and bacteria during the infection process is an essential step that complements expression profiling experiments such as microarrays and RNAseq in response to different stimuli. Understanding the spatiotemporal infections with these agents complements biological experiments aimed at understanding their interaction with cellular components. Several techniques for visualizing viruses and bacteria such as reporter gene systems or immunohistochemical methods are time-consuming, and some are limited to work with model organisms and involve complex methodologies. FISH that targets RNA or DNA species in the cell is a relatively easy and fast method for studying spatiotemporal localization of genes and for diagnostic purposes. This method can be robust and relatively easy to implement when the protocols employ short hybridizing, commercially-purchased probes, which are not expensive. This is particularly robust when sample preparation, fixation, hybridization, and microscopic visualization do not involve complex steps. Here we describe a protocol for localization of bacteria and viruses in insect and plant tissues. The method is based on simple preparation, fixation, and hybridization of insect whole mounts and dissected organs or hand-made plant sections, with 20 base pairs short DNA probes conjugated to fluorescent dyes on their 5' or 3' ends. This protocol has been successfully applied to a number of insect and plant tissues, and can be used to analyze expression of mRNAs or other RNA or DNA species in the cell.

  17. Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries.

    PubMed

    Schramm, Andreas; Fuchs, Bernhard M; Nielsen, Jeppe L; Tonolla, Mauro; Stahl, David A

    2002-11-01

    A method is presented for fluorescence in situ hybridization (FISH) of 16S rRNA gene clones targeting in vivo transcribed plasmid inserts (Clone-FISH). Several different cloning approaches and treatments to generate target-rRNA in the clones were compared. Highest signal intensities of Clone-FISH were obtained using plasmids with a T7 RNA polymerase promoter and host cells with an IPTG-inducible T7 RNA polymerase. Combined IPTG-induction and chloramphenicol treatment of those clones resulted in FISH signals up to 2.8-fold higher than signals of FISH with probe EUB338 to cells of Escherichia coli. Probe dissociation curves for three oligonucleotide probes were compared for reference cells containing native (FISH) or cloned (Clone-FISH) target sequences. Melting behaviour and calculated T(d) values were virtually identical for clones and cells, providing a format to use 16S rRNA gene clones instead of pure cultures for probe validation and optimization of hybridization conditions. The optimized Clone-FISH protocol was also used to screen an environmental clone library for insert sequences of interest. In this application format, 13 out of 82 clones examined were identified to contain sulphate-reducing bacterial rRNA genes. In summary, Clone-FISH is a simple and fast technique, compatible with a wide variety of cloning vectors and hosts, that should have general utility for probe validation and screening of clone libraries. PMID:12460279

  18. 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.

  19. 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.

  20. 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. PMID:25465782

  1. 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

  2. Interpretation of fish biomarker data for identification, classification, risk assessment and testing of endocrine disrupting chemicals.

    PubMed

    Dang, ZhiChao

    2016-01-01

    Chemical induced changes in fish biomarkers vitellogenin (VTG), secondary sex characteristics (SSC), and sex ratio indicate modes/mechanisms of action (MOAs) of EAS (estrogen, androgen and steroidogenesis) pathways. These biomarkers could be used for defining MOAs and the causal link between MOAs and adverse effects in fish for the identification of endocrine disrupting chemicals (EDCs). This paper compiled data sets of 150 chemicals for VTG, 57 chemicals for SSC and 38 chemicals for sex ratio in fathead minnow, medaka and zebrafish. It showed 1) changes in fish biomarkers can indicate the MOAs as anticipated; 2) in addition to EAS pathways, chemicals with non-EAS pathways induced changes in fish biomarkers; 3) responses of fish biomarkers did not always follow the anticipated patterns of EAS pathways. These responses may result from the interaction of chemical-induced multiple MOAs and confounding factors like fish diet, infection, culture conditions, general toxicity and stress response. The complex response of fish biomarkers to a chemical of interest requires EDC testing at multiple biological levels. Interpretation of fish biomarker data should be combined with relevant information at different biological levels, which is critical for defining chemical specific MOAs. The utility of fish biomarker data for identification, classification, PBT assessment, risk assessment, and testing of EDCs in the regulatory context was discussed. This paper emphasizes the importance of fish biomarker data in the regulatory context, a weight of evidence approach for the interpretation of fish biomarker data and the need for defining levels of evidence for the identification of EDCs. PMID:27155823

  3. 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

  4. 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.

  5. 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.

  6. Combined DNA-RNA Fluorescent In situ Hybridization (FISH) to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells

    PubMed Central

    Barakat, Tahsin Stefan; Gribnau, Joost

    2014-01-01

    Fluorescent in situ hybridization (FISH) is a molecular technique which enables the detection of nucleic acids in cells. DNA FISH is often used in cytogenetics and cancer diagnostics, and can detect aberrations of the genome, which often has important clinical implications. RNA FISH can be used to detect RNA molecules in cells and has provided important insights in regulation of gene expression. Combining DNA and RNA FISH within the same cell is technically challenging, as conditions suitable for DNA FISH might be too harsh for fragile, single stranded RNA molecules. We here present an easily applicable protocol which enables the combined, simultaneous detection of Xist RNA and DNA encoded by the X chromosomes. This combined DNA-RNA FISH protocol can likely be applied to other systems where both RNA and DNA need to be detected. PMID:24961515

  7. 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.

  8. Towards a cellular multi-parameter analysis platform: fluorescence in situ hybridization (FISH) on microhole-array chips.

    PubMed

    Kurz, Christian M; Moosdijk, Stefan V D; Thielecke, Hagen; Velten, Thomas

    2011-01-01

    Highly-sensitive analysis systems based on cellular multi-parameter are needed in the diagnostics. Therefore we improved our previously developed chip platform for another additional analysis method, the fluorescence in situ hybridization. Fluorescence in situ hybridization (FISH) is a technique used in the diagnostics to determine the localization and the presence or absence of specific DNA sequence. To improve this labor- and cost-intensive method, we reduced the assay consumption by a factor of 5 compared to the standard protocol. Microhole chips were used for making the cells well addressable. The chips were fabricated by semiconductor technology on the basis of a Silicon wafer with a thin deposited silicon nitride layer (Si(3)N(4)). Human retina pigment epithelia (ARPE-19) cells were arrayed on 5-μm holes of a 35 × 35 microhole-array by a gently negative differential pressure of around 5 mbar. After 3 hours of incubation the cells were attached to the chip and the FISH protocol was applied to the positioned cells. A LabView software was developed to simplify the analysis. The software automatically counts the number of dots (positive labeled chromosome regions) as well as the distance between adjacent dots. Our developed platform reduces the assay consumption and the labor time. Furthermore, during the 3 hours of incubation non-invasive or minimal-invasive methods like Raman- and impedance-spectroscopy can be applied. PMID:22256298

  9. 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

  10. 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.

  11. Histopathological alterations of the heart in fish: proposal for a standardized assessment.

    PubMed

    Steinbach, Christoph; Kroupová, Hana Kocour; Wahli, Thomas; Klicnarová, Jana; Schmidt-Posthaus, Heike

    2016-03-30

    Histopathological alterations in the heart are often reported in fish as a result of exposure to a variety of chemical compounds. However, researchers presently lack a standardized method for the evaluation of histopathological alterations in the cardiovascular system of fish and the calculation of an 'organ index'. Therefore, we designed a method for a standardized assessment and evaluation of histopathological alterations in the heart of fish. As a model species, we used rainbow trout Oncorhynchus mykiss, but the protocol was also successfully applied to other fish species belonging to different taxonomic orders. To test the protocol, we re-evaluated sections of atenolol-exposed and unexposed rainbow trout obtained in a previous study. The results were in accordance with those previously published, demonstrating the applicability of the protocol. The protocol provides a universal method for the comparative evaluation of histopathological changes in the heart of fish. PMID:27025306

  12. Rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH) from colony and blood culture material

    PubMed Central

    Essig, A.; Hagen, R. M.; Riecker, M.; Jerke, K.; Ellison, D.; Poppert, S.

    2011-01-01

    Multi-drug-resistant strains of the Acinetobacter baumannii complex cause nosocomial infections. Rapid identification of Acinetobacter spp. is desirable in order to facilitate therapeutic or hygiene decisions. We evaluated a newly designed DNA probe that can be used under standard conditions in both a microwave oven and a slide chamber for the rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH). Using FISH, the new probe correctly identified 81/81 Acinetobacter spp. isolates and excluded 109/109 tested non-target organisms from agar culture. Furthermore, the new probe correctly identified 7/7 Acinetobacter spp. in 214 blood cultures determined to contain Gram-negative bacteria by Gram staining. Using either the microwave oven or slide chamber technique, the new probe was able to identify Acinetobacter spp. in 100% of the samples tested. FISH used in conjunction with our newly designed probe provides an easy, cheap, precise, and rapid method for the preliminary identification of Acinetobacter spp., especially in laboratories where more sophisticated methods like matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) are not available. PMID:24516735

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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. PMID:18951970

  20. 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.

  1. Assessment on dioxin-like compounds intake from various marine fish from Zhoushan Fishery, China.

    PubMed

    Wang, Xiangyong; Zhang, Hongxia; Zhang, Lei; Zhong, Kai; Shang, Xiaohong; Zhao, Yunfeng; Tong, Zhendong; Yu, Xinwei; Li, Jingguang; Wu, Yongning

    2015-01-01

    Sea fish consuming is an important intake source of dioxin-like compounds, especially for the coastal residents. To assess the intake levels of these contaminants from sea fish and to provide risk-based consumption advice, concentrations of 17 polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and 12 dioxin-like polychlorinated biphenyls (dl-PCBs) were measured in 32 commonly consumed fish species from Zhoushan Fishery, China. Due to the different accumulation influenced by fat content, feed habits and living zone in the sea area, the levels of PCDDs, PCDFs and dl-PCBs in different fish species varied significantly ranging from 0.002 to 0.078pg WHO-TEQ/g fresh weight, from 0.002 to 0.553pg WHO-TEQ/g fresh weight and from 0.003 to 2.059pg WHO-TEQ/g fresh weight, respectively. Based on mean fish consuming rate in China, the estimated maximum possible dioxin-like compounds intake through different fish species ranged from 0.26 to 65.61pgTEQkg(-1)bwmonth(-1). Bullet mackerel has the highest monthly intake level which was much higher than other fish species and very close to the provisional tolerable monthly intake (70pgTEQkg(-)(1)bwmonth(-)(1)) proposed by the Joint FAO/WHO Expert Committee on Food Additives. Hence, comparing to other fish species, the consumption of Bullet mackerel from Zhoushan Fishery should be cautious to reduce the potential health risk.

  2. 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).

  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. 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

  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. Assessing ecological water quality with macroinvertebrates and fish: a case study from a small Mediterranean river.

    PubMed

    Cheimonopoulou, Maria Th; Bobori, Dimitra C; Theocharopoulos, Ioannis; Lazaridou, Maria

    2011-02-01

    Biological elements, such as benthic macroinvertebrates and fish, have been used in assessing the ecological quality of rivers according to the requirements of the Water Framework Directive. However, the concurrent use of multiple organism groups provides a broader perspective for such evaluations, since each biological element may respond differently to certain environmental variables. In the present study, we assessed the ecological quality of a Greek river (RM4 type), during autumn 2003 and spring 2004 at 10 sites, with benthic macroinvertebrates and fish. Hydromorphological and physicochemical parameters, habitat structure, and riparian vegetation were also considered. Pollution sensitive macroinvertebrate taxa were more abundant at headwaters, which had good/excellent water quality according to the Hellenic Evaluation System (HES). The main river reaches possessed moderate water quality, while downstream sites were mainly characterised as having bad or poor water quality, dominated by pollution-tolerant macroinvertebrate taxa. Macroinvertebrates related strongly to local stressors as chemical degradation (ordination analysis CCA) and riparian quality impairment (bivariate analysis) while fish did not. Fish were absent from the severely impacted lower river reaches. Furthermore, external pathological signs were observed in fish caught at certain sites. A combined use of both macroinvertebrates and fish in biomonitoring programs is proposed for providing a safer assessment of local and regional habitat impairment.

  7. 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.

  8. Rapid detection of chromosome aneuploidies in uncultured amniocytes by using fluorescence in situ hybridization (FISH)

    PubMed Central

    Klinger, Katherine; Landes, Greg; Shook, Donna; Harvey, Robert; Lopez, Linda; Locke, Pat; Lerner, Terry; Osathanondh, Rapin; Leverone, Benjamin; Houseal, Timothy; Pavelka, Karen; Dackowski, William

    1992-01-01

    Herein we report the results of the first major prospective study directly comparing aneuploidy detection by fluorescence in situ hybridization of interphase nuclei with the results obtained by cytogenetic analysis. We constructed probes derived from specific subregions of human chromosomes 21, 18, 13, X, and Y that give a single copy–like signal when used in conjunction with suppression hybridization. A total of 526 independent amniotic fluid samples were analyzed in a blind fashion. All five probes were analyzed on 117 samples, while subsets of these five probes were used on the remaining samples (because of insufficient sample size), for a total of over 900 autosomal hybridization reactions and over 400 sex chromosome hybridization reactions. In this blind series, 21 of 21 abnormal samples were correctly identified. The remaining samples were correctly classified as disomic for these five chromosomes. The combination of chromosome-specific probe sets composed primarily of cosmid contigs and optimized hybridization/detection allowed accurate chromosome enumeration in uncultured human amniotic fluid cells, consistent with the results obtained by traditional cytogenetic analysis. Imagesp[60]-aFigure 1 PMID:1609805

  9. 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. PMID:24740479

  10. 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.

  11. 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.

  12. National rivers and streams assessment: fish tissue contaminants

    EPA Science Inventory

    Overview of the National Rivers and Streams Assessment (NRSA), a statistical survey of flowing waters in the U.S. Survey is designed to: assess the condition of the nation's rivers and streams; help build state and tribal capacity for monitoring and assessment; promote collabor...

  13. 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

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

    PubMed

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

    2015-07-01

    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

  16. 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.

  17. 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.

  18. Gill monogeneans of Nile tilapia (Oreochromis niloticus) and red hybrid tilapia (Oreochromis spp.) from the wild and fish farms in Perak, Malaysia: infection dynamics and spatial distribution.

    PubMed

    Lim, Shen-Yin; Ooi, Ai-Lin; Wong, Wey-Lim

    2016-01-01

    Tilapia is one of the commercially important fish in Malaysia as well as in other parts of the world. An understanding of monogenean infection dynamics in tilapia fish may assist us in searching for some intervention measures in reducing the loss of fish caused by parasitic diseases. The present study aimed (1) to compare infection level of monogeneans between the wild and cultured Oreochromis niloticus, and between the cultured O. niloticus and cultured red hybrid tilapia, and (2) to examine the spatial distribution of monogenean species over the gills of the different host species. From a total of 75 fish specimens, six species of monogeneans from two genera: Cichlidogyrus (C. halli, C. mbirizei, C. sclerosus, C. thurstonae, C. tilapiae) and Scutogyrus (S. longicornis) were identified. Data showed that the infection level of cultured O. niloticus was higher than that of the wild O. niloticus, however, the former was lower than that of the cultured red hybrid tilapia. Higher species richness of monogeneans was observed in the cultured red hybrid tilapia as compared to the others. Results for spatial distribution showed that the monogeneans have no preference on the left or right sides of the gills. However, C. halli, C. mbirizei, and C. tilapiae showed preferences on specific gill arches in the cultured O. niloticus and red hybrid tilapia. In general, the gill arch IV harboured the least number of monogeneans. The susceptibility of monogenean infection between the different types of tilapia is discussed. PMID:27652182

  19. Gill monogeneans of Nile tilapia (Oreochromis niloticus) and red hybrid tilapia (Oreochromis spp.) from the wild and fish farms in Perak, Malaysia: infection dynamics and spatial distribution.

    PubMed

    Lim, Shen-Yin; Ooi, Ai-Lin; Wong, Wey-Lim

    2016-01-01

    Tilapia is one of the commercially important fish in Malaysia as well as in other parts of the world. An understanding of monogenean infection dynamics in tilapia fish may assist us in searching for some intervention measures in reducing the loss of fish caused by parasitic diseases. The present study aimed (1) to compare infection level of monogeneans between the wild and cultured Oreochromis niloticus, and between the cultured O. niloticus and cultured red hybrid tilapia, and (2) to examine the spatial distribution of monogenean species over the gills of the different host species. From a total of 75 fish specimens, six species of monogeneans from two genera: Cichlidogyrus (C. halli, C. mbirizei, C. sclerosus, C. thurstonae, C. tilapiae) and Scutogyrus (S. longicornis) were identified. Data showed that the infection level of cultured O. niloticus was higher than that of the wild O. niloticus, however, the former was lower than that of the cultured red hybrid tilapia. Higher species richness of monogeneans was observed in the cultured red hybrid tilapia as compared to the others. Results for spatial distribution showed that the monogeneans have no preference on the left or right sides of the gills. However, C. halli, C. mbirizei, and C. tilapiae showed preferences on specific gill arches in the cultured O. niloticus and red hybrid tilapia. In general, the gill arch IV harboured the least number of monogeneans. The susceptibility of monogenean infection between the different types of tilapia is discussed.

  20. 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.

  1. Residual risk for cytogenetic abnormalities after prenatal diagnosis by interphase fluorescence in situ hybridization (FISH).

    PubMed

    Homer, Jeanne; Bhatt, Sucheta; Huang, Bing; Thangavelu, Maya

    2003-07-01

    Results from conventional cytogenetic studies on 21 609 amniotic fluid specimens were analyzed retrospectively to determine the residual risk for a cytogenetic abnormality if interphase FISH, capable of only detecting aneuploidy for chromosomes 13, 18, 21, X and Y, was performed and did not reveal an abnormality. Detection rates (the probability of detecting a cytogenetic abnormality when an abnormality is present) and residual risks (the likelihood of a cytogenetic abnormality, in view of normal interphase FISH results) were calculated for the four major clinical indications for prenatal diagnosis (advanced maternal age, abnormal maternal serum screen indicating increased risk for trisomy 18 or trisomy 21, abnormal maternal serum screen indicating increased risk for neural tube defects and ultrasound abnormality). Differences in detection rates were observed to depend on clinical indication and presence or absence of ultrasound abnormalities. The detection rate ranged from 18.2 to 82.6% depending on the clinical indication. The detection rates of abnormalities significant to the pregnancy being evaluated (i.e. abnormalities excluding familial balanced rearrangements and familial markers) were between 28.6 and 86.4%. The presence of ultrasound abnormalities increased the detection rate from 72.2 to 92.5% for advanced maternal age and from 78.6 to 91.3% for abnormal maternal serum screen, indicating increased risk for trisomy 18 or trisomy 21. With regard to residual risk, the risk for a clinically significant abnormality decreased from 0.9-10.1%, prior to the interphase FISH assay, to a residual risk of 0.6-1.5% following a normal interphase FISH result in the 4 groups studied. Providing patients with detection rates and residual risks, most relevant to their situation (clinical indication and presence or absence of ultrasound abnormality) during counseling, could help them better understand the advantages and limitations of interphase FISH in their prenatal

  2. 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.

  3. 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.

  4. QUANTITATIVE IMAGING AND STATISTICAL ANALYSIS OF FLUORESCENCE IN SITU HYBRIDIZATION (FISH) OF AUREOBASIDIUM PULLULANS. (R823845)

    EPA Science Inventory

    Abstract

    Image and multifactorial statistical analyses were used to evaluate the intensity of fluorescence signal from cells of three strains of A. pullulans and one strain of Rhodosporidium toruloides, as an outgroup, hybridized with either a universal o...

  5. Heavy metal bioaccumulation and health hazard assessment for three fish species from Nansi Lake, China.

    PubMed

    Li, Pengfei; Zhang, Jian; Xie, Huijun; Liu, Cui; Liang, Shuang; Ren, Yangang; Wang, Wenxing

    2015-04-01

    Metal accumulation in fish is a global public health concern, because the consumption of contaminated fish accounts for the primary exposure of humans to toxic metals. In this study, the concentrations of arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) in Crucian carp (Carassius auratus),Yellow catfish (Pelteobagrus fulvidraco), and Bighead carp (Hypophthalmichthys nobilis) from Nansi Lake of China were evaluated, and compared with the corresponding historical values in 2001 when the government started to govern water environment effectively. Bioaccumulation of heavy metal was highest in P.fulvidraco, followed by C.auratus and H.nobilis. The concentrations of Pb, As, Cd were much lower than the historical values, but Hg concentration was higher, suggesting that heavy metal pollution problem in fish from Nansi Lake still exists. Health hazard assessment showed no health risk from exposure to Pb, As, Cd, and Hg by consuming fish from this lake.

  6. Heavy metal bioaccumulation and health hazard assessment for three fish species from Nansi Lake, China.

    PubMed

    Li, Pengfei; Zhang, Jian; Xie, Huijun; Liu, Cui; Liang, Shuang; Ren, Yangang; Wang, Wenxing

    2015-04-01

    Metal accumulation in fish is a global public health concern, because the consumption of contaminated fish accounts for the primary exposure of humans to toxic metals. In this study, the concentrations of arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) in Crucian carp (Carassius auratus),Yellow catfish (Pelteobagrus fulvidraco), and Bighead carp (Hypophthalmichthys nobilis) from Nansi Lake of China were evaluated, and compared with the corresponding historical values in 2001 when the government started to govern water environment effectively. Bioaccumulation of heavy metal was highest in P.fulvidraco, followed by C.auratus and H.nobilis. The concentrations of Pb, As, Cd were much lower than the historical values, but Hg concentration was higher, suggesting that heavy metal pollution problem in fish from Nansi Lake still exists. Health hazard assessment showed no health risk from exposure to Pb, As, Cd, and Hg by consuming fish from this lake. PMID:25636438

  7. Assessment of fish health status in the Pechora River: effects of contamination.

    PubMed

    Lukin, A; Sharova, J; Belicheva, L; Camus, L

    2011-03-01

    The present study aimed to assess the ecological situation in the Pechora River Basin (east part of Sub-Arctic Russia) using histopathologies of fish and to relate fish health to environmental quality. This paper reports histopathological alterations of fish kidney, liver, and gills and their association with chemical contamination of the Pechora River. A variety of histopathological changes was found. Differences between studied species and sites of the Pechora River with regard to the type, prevalence, and severity of lesions were studied. The types of the lesions indicated that fish respond to both direct toxicant effects of contaminated water and sediment, and secondary stress effects caused by factors such as parasitism. The structural modifications found in this study are a result of acute damage associated with short-term exposure as much as chronic response due to long-term pollution.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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). PMID:26649068

  13. 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).

  14. Assessing RET/PTC in thyroid nodule fine-needle aspirates: the FISH point of view.

    PubMed

    Caria, Paola; Dettori, Tinuccia; Frau, Daniela V; Borghero, Angela; Cappai, Antonello; Riola, Alessia; Lai, Maria L; Boi, Francesco; Calò, Piergiorgio; Nicolosi, Angelo; Mariotti, Stefano; Vanni, Roberta

    2013-08-01

    RET/PTC rearrangement and BRAF(V600E) mutation are the two prevalent molecular alterations associated with papillary thyroid carcinoma (PTC), and their identification is increasingly being used as an adjunct to cytology in diagnosing PTC. However, there are caveats associated with the use of the molecular approach in fine-needle aspiration (FNA), particularly for RET/PTC, that should be taken into consideration. It has been claimed that a clonal or sporadic presence of this abnormality in follicular cells can distinguish between malignant and benign nodules. Nevertheless, the most commonly used PCR-based techniques lack the capacity to quantify the number of abnormal cells. Because fluorescence in situ hybridization (FISH) is the most sensitive method for detecting gene rearrangement in a single cell, we compared results from FISH and conventional RT-PCR obtained in FNA of a large cohort of consecutive patients with suspicious nodules and investigated the feasibility of setting a FISH-FNA threshold capable of distinguishing non-clonal from clonal molecular events. For this purpose, a home brew break-apart probe, able to recognize the physical breakage of RET, was designed. While a ≥3% FISH signal for broken RET was sufficient to distinguish nodules with abnormal follicular cells, only samples with a ≥6.8% break-apart FISH signal also exhibited positive RT-PCR results. On histological analysis, all nodules meeting the ≥6.8% threshold proved to be malignant. These data corroborate the power of FISH when compared with RT-PCR in quantifying the presence of RET/PTC in FNA and validate the RT-PCR efficiency in detecting clonal RET/PTC alterations.

  15. 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.

  16. Analysis of 5S rDNA organization and variation in polyploid hybrids from crosses of different fish subfamilies.

    PubMed

    Qin, Qinbo; He, Weiguo; Liu, Shaojun; Wang, Jing; Xiao, Jun; Liu, Yun

    2010-07-15

    In this article, sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) were conducted in red crucian carp (RCC), blunt snout bream (BSB), and their polyploid offspring. Three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) of RCC were characterized by distinct NTS types (designated NTS-I, II, and III for the 83, 220, and 357 bp monomers, respectively). In BSB, only one monomeric 5S rDNA was observed (designated class IV: 188 bp), which was characterized by one NTS type (designated NTS-IV: 68 bp). In the polyploid offspring, the tetraploid (4nRB) hybrids partially inherited 5S rDNA classes from their female parent (RCC); however, they also possessed a unique 5S rDNA sequence (designated class I-L: 203 bp) with a novel NTS sequence (designated NTS-I-L: 83 bp). The characteristic paternal 5S rDNA sequences (class IV) were not observed. The 5S rDNA of triploid (3nRB) hybrids was completely inherited from the parental species, and generally preserved the parental 5S rDNA structural organization. These results first revealed the influence of polyploidy on the organization and evolution of the multigene family of 5S rDNA of fish, and are also useful in clarifying aspects of vertebrate genome evolution.

  17. 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

    2016-01-01

    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. PMID:27583462

  18. Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon.

    PubMed

    Wu, Sheng-Mei; Tian, Zhi-Quan; Zhang, Zhi-Ling; Huang, Bi-Hai; Jiang, Peng; Xie, Zhi-Xiong; Pang, Dai-Wen

    2010-10-15

    Quantum dots (QDs) are inorganic fluorescent nanocrystals with excellent properties such as tunable emission spectra and photo-bleaching resistance compared with organic dyes, which make them appropriate for applications in molecular beacons. In this work, quantum dot-based molecular beacons (QD-based MBs) were fabricated to specifically detect β-lactamase genes located in pUC18 which were responsible for antibiotic resistance in bacteria Escherichia coli (E. coli) DH5α. QD-based MBs were constructed by conjugating mercaptoacetic acid-quantum dots (MAA-QDs) with black hole quencher 2 (BHQ2) labeled thiol DNA vial metal-thiol bonds. Two types of molecular beacons, double-strands beacons and hairpin beacons, were observed in product characterization by gel electrophoresis. Using QD-based MBs, one-step FISH in tiny bacteria DH5α was realized for the first time. QD-based MBs retained their bioactivity when hybridizing with complementary target DNA, which showed excellent advantages of eliminating background noise caused by adsorption of non-specific bioprobes and achieving clearer focus of genes in plasmids pUC18, and capability of bacterial cell penetration and signal specificity in one-step in situ hybridization.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Risk assessments of human exposure to bioaccessible phthalate esters through market fish consumption.

    PubMed

    Cheng, Zhang; Nie, Xiang-Ping; Wang, Hong-Sheng; Wong, Ming-Hung

    2013-07-01

    The bioaccessibility of phthalate esters in 20 fish species collected from Hong Kong market was evaluated using an in vitro gastrointestinal model. The ∑phthalate ester concentration detected in fresh water fish ranged from 1.66 to 3.14μg/g wet weight (ww) and in marine fish ranged from 1.57 to 7.10μg/g ww, respectively. di-2-Ethylhexyl phthalate (DEHP) and di-n-butyl phthalate (DBP) were the predominant compounds in both freshwater fish and marine fish. The digestible concentrations of phthalate esters ranged from 0.20 to 1.23μg/g ww (mean 0.35μg/g ww), and account for 2.44 to 45.5% (mean 16.8%) for raw concentrations of phthalate esters. In the present study, the accumulation ratio Rnn value of all phthalate esters was greater than 1 except for diisobutyl phthalate (DIBP), DBP and di-n-hexyl phthalate (DHP), suggesting that these phthalate esters could be accumulated during gastrointestinal digestion. Based on this health risk assessment, most of fish species were considered safe for consumption, however Hong Kong residents should take caution when consuming Mud carp and Bighead carp. PMID:23688402

  6. Risk assessments of human exposure to bioaccessible phthalate esters through market fish consumption.

    PubMed

    Cheng, Zhang; Nie, Xiang-Ping; Wang, Hong-Sheng; Wong, Ming-Hung

    2013-07-01

    The bioaccessibility of phthalate esters in 20 fish species collected from Hong Kong market was evaluated using an in vitro gastrointestinal model. The ∑phthalate ester concentration detected in fresh water fish ranged from 1.66 to 3.14μg/g wet weight (ww) and in marine fish ranged from 1.57 to 7.10μg/g ww, respectively. di-2-Ethylhexyl phthalate (DEHP) and di-n-butyl phthalate (DBP) were the predominant compounds in both freshwater fish and marine fish. The digestible concentrations of phthalate esters ranged from 0.20 to 1.23μg/g ww (mean 0.35μg/g ww), and account for 2.44 to 45.5% (mean 16.8%) for raw concentrations of phthalate esters. In the present study, the accumulation ratio Rnn value of all phthalate esters was greater than 1 except for diisobutyl phthalate (DIBP), DBP and di-n-hexyl phthalate (DHP), suggesting that these phthalate esters could be accumulated during gastrointestinal digestion. Based on this health risk assessment, most of fish species were considered safe for consumption, however Hong Kong residents should take caution when consuming Mud carp and Bighead carp.

  7. 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.

  8. 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

  9. 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...

  10. 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...

  11. THE USE OF SMALL FISH MODELS FOR TOXICITY ASSESSMENTS OF CHEMICAL CONTAINMENTS IN DRINKING WATER

    EPA Science Inventory

    This was an invited presentation. The first part described the results from a short-term carcinogenesis bioassay using medaka, a small aquarium fish. The second part described the development of a long-term multi-endpoint medaka bioassay which could be useful for assessing the ef...

  12. 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...

  13. 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. PMID:26267473

  14. 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

  15. 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.

  16. 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.

  17. Higher susceptibility to N-methyl-N'-nitro-N-nitrosoguanidine-induced tumorigenesis in an interstrain hybrid of the fish, Oryzias latipes (medaka).

    PubMed

    Hyodo-Taguchi, Y; Matsudaira, H

    1987-05-01

    Adult fish of an interstrain hybrid (F1) of inbred medaka, obtained from crosses between HO4C and HB32C, were exposed for 2 hr to an aqueous solution of the carcinogen N-methyl-N'-nitro-N-nitrosoguanidine at concentrations of 15, 20, 25, 30, and 35 ppm. Survival and neoplastic changes were examined over a 6-month period. A large variety of neoplasms were induced, including melanoma, papilloma, ovarian tumors, olfactory epithelioma, branchioblastoma and fibroma. More than 60% of the tumors were classified as melanoma on the basis of histological examinations. A markedly higher cumulative incidence of the melanoma with a dose-related response was demonstrated in the F1 hybrid fish compared to the parental strains. The latent period for melanoma development, however, remained unchanged in F1 compared to the parents. The variety of tumors induced in the F1 fish was greater than in the parental strains. The results indicate the usefulness of F1 hybrid fish in testing the carcinogenicity of certain water-soluble chemicals, due to their high sensitivity. PMID:3112060

  18. 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

  19. Mercury species of sediment and fish in freshwater fish ponds around the Pearl River Delta, PR China: human health risk assessment.

    PubMed

    Shao, Dingding; Liang, Peng; Kang, Yuan; Wang, Hongsheng; Cheng, Zhang; Wu, Shengchun; Shi, Jianbo; Lo, Samuel Chun Lap; Wang, Wenxiong; Wong, Ming H

    2011-04-01

    This study investigated total mercury (THg) and methylmercury (MeHg) concentrations in five species of freshwater fish and their associated fish pond sediments collected from 18 freshwater fish ponds around the Pearl River Delta (PRD). The concentrations of THg and MeHg in fish pond surface sediments were 33.1-386 ng g(-1) dry wt and 0.18-1.25 ng g(-1) dry wt, respectively. The age of ponds affected the surface sediment MeHg concentration. The vertical distribution of MeHg in sediment cores showed that MeHg concentrations decreased with increasing depth in the top 10 cm. In addition, a significant correlation was observed between %MeHg and DNA from Desulfovibrionacaea or Desulfobulbus (p<0.05) in sediment cores. Concentrations of THg and MeHg in fish muscles ranged from 7.43-76.7 to 5.93-76.1 ng g(-1) wet wt, respectively, with significant linear relationships (r=0.97, p<0.01, n=122) observed between THg and MeHg levels in fish. A significant correlation between THg concentrations in fish (herbivorous: r=0.71, p<0.05, n=7; carnivorous: r=0.77, p<0.05, n=11) and corresponding sediments was also obtained. Risk assessment indicated that the consumption of largemouth bass and mandarin fish would result in higher estimated daily intakes (EDIs) of MeHg than reference dose (RfD) for both adults and children.

  20. 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

  1. Characterization of Brazilian accessions of wild Arachis species of section Arachis (Fabaceae) using heterochromatin detection and fluorescence in situ hybridization (FISH)

    PubMed Central

    Custódio, Adriana Regina; Seijo, Guillermo; Valls, José Francisco Montenegro

    2013-01-01

    The cytogenetic characterization of Arachis species is useful for assessing the genomes present in this genus, for establishing the relationship among their representatives and for understanding the variability in the available germplasm. In this study, we used fluorescence in situ hybridization (FISH) to examine the distribution patterns of heterochromatin and rDNA genes in 12 Brazilian accessions of five species of the taxonomic section Arachis. The heterochromatic pattern varied considerably among the species: complements with centromeric bands in all of the chromosomes (A. hoehnei) and complements completely devoid of heterochromatin (A. gregoryi, A. magna) were observed. The number of 45S rDNA loci ranged from two (A. gregoryi) to eight (A. glandulifera), while the number of 5S rDNA loci was more conserved and varied from two (in most species) to four (A. hoehnei). In some species one pair of 5S rDNA loci was observed adjacent to 45S rDNA loci. The chromosomal markers revealed polymorphism in the three species with more than one accession (A. gregoryi, A. magna and A. valida) that were tested. The previous genome assignment for each of the species studied was confirmed, except for A. hoehnei. The intraspecific variability observed here suggests that an exhaustive cytogenetic and taxonomic analysis is still needed for some Arachis species. PMID:24130444

  2. 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

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

    PubMed

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

    2016-01-01

    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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

    2010-01-01

    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 annotated

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

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Smith, David

    2013-01-01

    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 4-8 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 8 fish could detect an increase of ∼ 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 ∼ 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 ∼ 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 by increased precision of composites for estimating mean

  11. 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

  12. 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

  13. 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). PMID:26445656

  14. Mekong River fish conservation zones in southern Laos: assessing effectiveness using local ecological knowledge.

    PubMed

    Baird, Ian G; Flaherty, Mark S; Baird, Ian G

    2005-09-01

    Small-scale fisheries are important in Laos, where rural people heavily depend upon Mekong River and tributary fish stocks for their livelihoods. Increasing pressures from human exploitation and habitat disturbance, however, have raised serious concerns about the potential depletion of various species. This has led to the establishment of large numbers of Fish Conservation Zones (FCZs) or "no-take" fish sanctuaries in southern Laos based on a "community-based fisheries co-management" framework. This study uses the local ecological knowledge (LEK) of fishers to assess the effectiveness of village-managed FCZs in enhancing fish stocks in the mainstream Mekong River in Khong District, Champasak Province. Focus group interviews about species that are believed to have benefited from different FCZs are compared with parameters such as FCZ area, age, depth, localized gradient, water velocity, and the presence of wetland forests nearby. The results suggest that no one aspect is likely to account for variations in fish stocks; rather, it is the interaction between numerous factors that has the largest impact. Secondly, the results indicate that microhabitat diversity and protection are critical for maintaining and enhancing Mekong fisheries. Deep-water pools are particularly important as dry season refuges for many fish species, and FCZ depth may be the single most important environmental factor affecting the success of FCZs in the Mekong River. FCZs have the most potential to benefit relatively sedentary species, but may also benefit highly migratory species, given the right conditions. This study shows that integrated approaches to stock assessment that employ LEK and scientific fisheries management have considerable potential for improving Mekong capture-fisheries management.

  15. 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

  16. 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.

  17. Risk assessment of heavy metals in water and two fish species from golf course ponds in Beijing, China.

    PubMed

    PuYang, Xuehua; Gao, Chenhao; Han, Liebao

    2015-04-01

    To assess the situation of heavy metals contamination, the concentrations of Cu, Zn, Pb, Cd, Cr, As and Hg in water and two fish species (crucian carp and grass carp) from six golf course ponds of Beijing were measured. Differences in metals concentrations in water and fish samples were observed among different sites, but below the relevant standards and safety values. Significant positive correlations were found between metals concentrations in water and fish samples, except for As in grass carp. Health risks to human via dietary intake of fish were then assessed based on the target hazard quotient and hazard index (HI). The HI in all fish samples were lower than 1, indicating the absence of health risks through consuming these fish.

  18. Risk assessment of heavy metals in water and two fish species from golf course ponds in Beijing, China.

    PubMed

    PuYang, Xuehua; Gao, Chenhao; Han, Liebao

    2015-04-01

    To assess the situation of heavy metals contamination, the concentrations of Cu, Zn, Pb, Cd, Cr, As and Hg in water and two fish species (crucian carp and grass carp) from six golf course ponds of Beijing were measured. Differences in metals concentrations in water and fish samples were observed among different sites, but below the relevant standards and safety values. Significant positive correlations were found between metals concentrations in water and fish samples, except for As in grass carp. Health risks to human via dietary intake of fish were then assessed based on the target hazard quotient and hazard index (HI). The HI in all fish samples were lower than 1, indicating the absence of health risks through consuming these fish. PMID:25636439

  19. 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.

  20. 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

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

    PubMed

    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

    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.

  2. [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

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

    PubMed

    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

  4. 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

  5. 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…

  6. 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

  7. 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

  8. 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. PMID:26047487

  9. 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 (p??s1) ranged from 80.7% to 100% of estimated total species richness for each river basin, based on at least seven samples per basin. However, p??s1 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

  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. 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; 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 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

  13. 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. PMID:25047482

  14. 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.

  15. 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.

  16. Mercury speciation in fish muscles from major Czech rivers and assessment of health risks.

    PubMed

    Sedláčková, Lenka; Kružíková, Kamila; Svobodová, Zdeňka

    2014-05-01

    The aim of this work was to determine the mercury and methylmercury content in muscle tissue of chub (Leuciscus cephalus L.), to assess the health risks of eating the fish and to determine the number of fish meat servings that are suitable for weekly consumption. Total mercury concentrations were determined using a single-purpose atomic absorption spectrophotometer AMA 254. Methylmercury concentrations were determined by gas chromatography. The location where the highest total mercury concentrations in fish muscle tissues were found was the Vltava - Vraňany (0.236±0.1001mg/kg(-1)), and the highest methylmercury concentration was found at the Labe - Obříství (0.231±0.1056mg/kg(-1)). The conclusion based on the data ascertained is that the locations from which the lowest number of fish meat servings can be eaten are the Vltava - Vraňany and the Labe - Obříství. The results of this study helped evaluate contamination levels of rivers that flow out of the Czech Republic.

  17. 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.

  18. Application of Biochemical and Physiological Indicators for Assessing Recovery of Fish Populations in a Disturbed Stream

    NASA Astrophysics Data System (ADS)

    Adams, S. Marshall; Ham, Kenneth D.

    2011-06-01

    Recovery dynamics in a previously disturbed stream were 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.

  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, 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.

  1. Mercury speciation in fish muscles from major Czech rivers and assessment of health risks.

    PubMed

    Sedláčková, Lenka; Kružíková, Kamila; Svobodová, Zdeňka

    2014-05-01

    The aim of this work was to determine the mercury and methylmercury content in muscle tissue of chub (Leuciscus cephalus L.), to assess the health risks of eating the fish and to determine the number of fish meat servings that are suitable for weekly consumption. Total mercury concentrations were determined using a single-purpose atomic absorption spectrophotometer AMA 254. Methylmercury concentrations were determined by gas chromatography. The location where the highest total mercury concentrations in fish muscle tissues were found was the Vltava - Vraňany (0.236±0.1001mg/kg(-1)), and the highest methylmercury concentration was found at the Labe - Obříství (0.231±0.1056mg/kg(-1)). The conclusion based on the data ascertained is that the locations from which the lowest number of fish meat servings can be eaten are the Vltava - Vraňany and the Labe - Obříství. The results of this study helped evaluate contamination levels of rivers that flow out of the Czech Republic. PMID:24360463

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Public health assessment of dioxin-contaminated fish at former US airbase, Bien Hoa, Vietnam.

    PubMed

    Durant, James T; Boivin, Thomas G; Pohl, Hana R; Sinks, Thomas H

    2015-01-01

    Ponds at the former US airbase at Ben Hoa, Vietnam are contaminated with Agent Orange. The ponds had been used for aquaculture, and in all likelihood, fish from those ponds have been sold to the public. We assessed human exposure to 2,3,7,8-tetrachloro-dibenzo-dioxin (2,3,7,8-TCDD) in fish samples from the ponds. For on-base tilapia, muscle concentrations 2,3,7,8-TCDD ranged from 1.4 to 32.7 pg/g. Fat concentrations ranged from 73.3 to 3990 pg/g. Estimated human exposure doses exceed international guidelines and exceed 2,3,7,8-TCDD's lowest adverse effect levels. The Bien Hoa fishponds are a completed human pathway for TCDD exposure.

  18. Toxicological assessment of fish (Clarias gariepinus) from bitumen-polluted River Oluwa, Nigeria.

    PubMed

    Ayandiran, T A; Dahunsi, S O

    2016-02-01

    Toxicological evaluation of Clarias gariepinus from bitumen-polluted River Oluwa, Nigeria, was carried out in furtherance of studies on the environmental impacts of the bitumen exploration in Ondo State, Nigeria. Samples were taken from three different (two polluted and one as control) sites. The effect of changes in monthly seasonal flow rate was assessed for the sites of study. Blood plasma clinical-chemical parameters (BCCPs) and histological changes/lesions in various organs were evaluated as markers of pollution in the fish blood using standard methods. The result of the physicochemical properties of water from the sampling points revealed some of the values conforming to approved standards while others showed deviation. Significant differences were found in the blood and histological endpoints between the control and the polluted sites as well as between the two seasons evaluated across the sites. The public health implications of consuming this fish are fully discussed. PMID:26725477

  19. Public health assessment of dioxin-contaminated fish at former US airbase, Bien Hoa, Vietnam.

    PubMed

    Durant, James T; Boivin, Thomas G; Pohl, Hana R; Sinks, Thomas H

    2015-01-01

    Ponds at the former US airbase at Ben Hoa, Vietnam are contaminated with Agent Orange. The ponds had been used for aquaculture, and in all likelihood, fish from those ponds have been sold to the public. We assessed human exposure to 2,3,7,8-tetrachloro-dibenzo-dioxin (2,3,7,8-TCDD) in fish samples from the ponds. For on-base tilapia, muscle concentrations 2,3,7,8-TCDD ranged from 1.4 to 32.7 pg/g. Fat concentrations ranged from 73.3 to 3990 pg/g. Estimated human exposure doses exceed international guidelines and exceed 2,3,7,8-TCDD's lowest adverse effect levels. The Bien Hoa fishponds are a completed human pathway for TCDD exposure. PMID:25087452

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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. PMID:26808475

  7. 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

  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. 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

  10. 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.

  11. 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.

  12. 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.

  13. Growth history and intrinsic factors influence risk assessment at a critical life transition for a fish

    NASA Astrophysics Data System (ADS)

    Lönnstedt, O. M.; McCormick, M. I.

    2011-09-01

    Making the appropriate decision in the face of predation risk dictates the fate of prey, and predation risk is highest at life history boundaries such as settlement. At the end of the larval phase, most coral reef fishes enter patches of reef containing novel predators. Since vision is often obscured in the complex surroundings, chemical information released from damaged conspecific is used to forewarn prey of an active predator. However, larvae enter the reef environment with their own feeding and growth histories, which will influence their motivation to feed and take risks. The present study explored the link between recent growth, feeding history, current performance and behavioural risk taking in newly settling stages of a coral reef damselfish ( Pomacentrus amboinensis). Older and larger juveniles in good body condition had a stronger response to chemical alarm cues of injured conspecifics; these fish spent a longer time in shelter and displayed a more dramatic decrease in foraging behaviour than fish in lower body condition. Feeding experiments supported these findings and emphasized the importance of body condition in affecting risk assessment. Evidently, larval growth history and body condition influences the likelihood of taking risks under the threat of predation immediately after settlement, thereby affecting the probability of survival in P. amboinensis.

  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. 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.

  16. 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

  17. 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.

  18. 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. PMID:27293767

  19. 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.

  20. 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

  1. 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,

  2. 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.

  3. Application of sensory and microbial analysis to assess quality of fish in Siliguri city of West Bengal, India.

    PubMed

    Jha, Prithwiraj; Roy, Rudra Prasad; Barat, S

    2010-09-01

    Sensory and certain microbial analyses were applied to assess the quality of raw fish sold at a market in Siliguri cityof West Bengal, India. In regular surveys undertaken during June to August 2008, a particular fish species was randomly selected, its source was noted and a sensory analysis, the quality index method (QIM) was applied to assess its quality Raw fish samples were also collected and a small quantity (about 1 g) of scales oran upper layer of the skin surface (forscale-less fish samples), gill, liverand a portion of gut with gut-contents were aseptically removed for enumeration of the total aerobic heterotrophic bacteria, Aeromonas spp., Pseudomonas spp., Salmonella spp. and coliform counts. Oreochromis mossambicus and Tenulosa ilisha recorded significantly higher QIM scores, compared to other species (p<0.05). Riverine fish, Lepidocephalichthys guntea and Channa punctatus scored the lowest QIM scores (0) while scores for Puntius ticto and Mystus vittatus and pond cultured species like Cirrhinus mrigala, Catla catla, Labeo rohita, Labeo bata and Cyprinus carpio were very marginal (p<0.05). Aeromonas spp., Salmonella spp. and total coliforms were recorded from all the studied species while Pseudomonas spp. was isolated from only seven species. Among the tissues examined, the lowest counts of total heterotrophic bacteria, Aeromonas spp., Pseudomonas spp., Salmonella spp. and total coliforms were recorded from the skin in every fish species. Highest counts of pathogenic bacteria (except Pseudomonas spp.) were recorded in Tenulosa ilisha for all the tissues except liver. Since fish are properly cooked in Bengali households, the risk of disease from fish consumption is relatively less. However, some tribes residing in the region are known to consume undercooked fish and proper cooking methods should be followed in view of the present findings to avoid health risks. Besides, utmost care should be taken while handling fish. PMID:21387907

  4. 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

  5. Immunotoxic effects of environmental toxicants in fish - how to assess them?

    PubMed

    Segner, Helmut; Wenger, Michael; Möller, Anja Maria; Köllner, Bernd; Casanova-Nakayama, Ayako

    2011-08-01

    Numerous environmental chemicals, both long-known toxicants such as persistent organic pollutants as well as emerging contaminants such as pharmaceuticals, are known to modulate immune parameters of wildlife species, what can have adverse consequences for the fitness of individuals including their capability to resist pathogen infections. Despite frequent field observations of impaired immunocompetence and increased disease incidence in contaminant-exposed wildlife populations, the potential relevance of immunotoxic effects for the ecological impact of chemicals is rarely considered in ecotoxicological risk assessment. A limiting factor in the assessment of immunotoxic effects might be the complexity of the immune system what makes it difficult (1) to select appropriate exposure and effect parameters out of the many immune parameters which could be measured, and (2) to evaluate the significance of the selected parameters for the overall fitness and immunocompetence of the organism. Here, we present - on the example of teleost fishes - a brief discussion of how to assess chemical impact on the immune system using parameters at different levels of complexity and integration: immune mediators, humoral immune effectors, cellular immune defenses, macroscopical and microscopical responses of lymphoid tissues and organs, and host resistance to pathogens. Importantly, adverse effects of chemicals on immunocompetence may be detectable only after immune system activation, e.g., after pathogen challenge, but not in the resting immune system of non-infected fish. Current limitations to further development and implementation of immunotoxicity assays and parameters in ecotoxicological risk assessment are not primarily due to technological constraints, but are related from insufficient knowledge of (1) possible modes of action in the immune system, (2) the importance of intra- and inter-species immune system variability for the response against chemical stressors, and (3

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  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. PMID:27644342

  13. 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.

  14. 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. PMID:27271815

  15. 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). PMID:27187161

  16. 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

  17. 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

  18. 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

  19. 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. PMID:25697818

  20. Applications of DNA barcoding to fish landings: authentication and diversity assessment

    PubMed Central

    Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

    2013-01-01

    Abstract DNA barcoding methodologies are being increasingly applied not only for scientific purposes but also for diverse real-life uses. Fisheries assessment is a potential niche for DNA barcoding, which serves for species authentication and may also be used for estimating within-population genetic diversity of exploited fish. Analysis of single-sequence barcodes has been proposed as a shortcut for measuring diversity in addition to the original purpose of species identification. Here we explore the relative utility of different mitochondrial sequences (12S rDNA, COI, cyt b, and D-Loop) for application as barcodes in fisheries sciences, using as case studies two marine and two freshwater catches of contrasting diversity levels. Ambiguous catch identification from COI and cyt b was observed. In some cases this could be attributed to duplicated names in databases, but in others it could be due to mitochondrial introgression between closely related species that may obscure species assignation from mtDNA. This last problem could be solved using a combination of mitochondrial and nuclear genes. We suggest to simultaneously analyze one conserved and one more polymorphic gene to identify species and assess diversity in fish catches. PMID:24453550

  1. 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.

  2. 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.

  3. Systematic global assessment of reef fish communities by the Reef Life Survey program.

    PubMed

    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

  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. Assessment and assortment: how fishes use local and global cues to choose which school to go to.

    PubMed

    Ward, Ashley J W; Hart, Paul J B; Krause, Jens

    2004-08-01

    Animals that live in groups are known preferentially to associate with phenotypically similar individuals. Despite this, groups of mixed phenotypic composition are the norm rather than the exception in several systems in the wild and this, combined with the large sizes of some animal groups, makes accurate global assessment by a choosing individual more difficult. In this study, we investigated the role of local and global information in mediating shoal-choice decisions in three-spined sticklebacks (Gasterosteus aculeatus) by manipulating the positions and phenotypes of stimulus fish in relation to a focal fish. Focal fish were able to assess globally mixed shoals composed of individuals of different body-length classes, preferring to associate with shoals where the majority phenotype matched their own. When local cues were manipulated this preference disappeared, although overall shoal composition remaining constant. Finally, if both stimulus shoals had the same overall composition but differed in their local cues, then the focus fish chose according to which local fish was of matching body length. These findings indicate that both local and global information play an important role in mediating assessment and shoal choice in fishes.

  6. A Hybrid Process Fidelity Assessment in a Home-based Randomized Clinical Trial

    PubMed Central

    WILDE, MARY H.; LIEBEL, DIANNE; FAIRBANKS, EILEEN; WILSON, PAULA; LASH, MARGARET; SHAH, SHIVANI; McDONALD, MARGARET V.; BRASCH, JUDITH; ZHANG, FENG; SCHEID, EILEEN; McMAHON, JAMES M.

    2016-01-01

    A process fidelity assessment was conducted as a nested study within a home-based randomized clinical trial teaching self-management to 101 long-term indwelling urinary catheter users in the treatment group. Our hybrid model combined external assessments (outside observations and tape recordings) with internal evaluation methods (through study nurse forms and notes) for a comprehensive process fidelity assessment. Barriers, patient-related issues, and nurse perspectives were identified demonstrating the complexity in home care intervention research. The complementary and synergistic approaches provided in depth information about the context of the delivery and the impact of the intervention on study outcomes. PMID:25894688

  7. Assessment of chromosomal aneuploidies in sperm of infertile males by using FISH technique.

    PubMed

    Andreescu, Nicoleta Ioana; Cosma, Mirela; Farcaş, Simona Sorina; Stoian, Monica; Amzăr, Daniela Georgiana; Puiu, Maria

    2016-01-01

    Reproductive failure is one of the most important issues for the population at age of procreation and approximately 15% of the couples who try to conceive a baby encounter reproductive difficulties. In this study, we used multicolor fluorescent in situ hybridization (FISH) probes for chromosomes 13, 18, 21, X and Y to evaluate the aneuploidy incidence in sperm cells. The study group included 35 males with infertility and oligoasthenoteratozoospermia (OAT) and 20 males with normal fertility and normal semen characteristics for which the conventional cytogenetic investigation using peripheral blood revealed a normal karyotype. The overall chromosome disomy and nulisomy in OAT group was higher than the one identified in the control group. By comparing the incidence of the disomy in the OAT group, the highest incidence was the sex chromosome disomy, followed by the disomy of chromosomes 13, 21 (equal values) and then 18. The nulisomy incidence in the OAT group was higher for sex chromosomes, followed by the nulisomy of autosomes 13, then 21 and 18. As in these days, for patients with OAT, intra-cytoplasmic sperm injection (ICSI) is frequently used, it is important to inform the patients if they might have an increased risk of aneuploidies in embryos. PMID:27151704

  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. 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

  10. 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.

  11. Simultaneous 16S and 18S rRNA fluorescence in situ hybridization (FISH) on LR White sections demonstrated in Vestimentifera (Siboglinidae) tubeworms.

    PubMed

    Schimak, Mario P; Toenshoff, Elena R; Bright, Monika

    2012-02-01

    Traditional morphological identification of invertebrate marine species is limited in early life history stages for many taxa. In this study, we demonstrate, by example of Vestimentiferan tubeworms (Siboglinidae, Polychaeta), that the simultaneous fluorescence in situ hybridization (FISH) of both eukaryotic host and bacterial symbiont cells is possible on a single semi-thin (1 μm) section. This allows the identification of host specimens to species level as well as offering visualization of bacteria distributed within the host tissue. Previously published 18S rRNA host-specific oligonucleotide probes for Riftia pachyptila, Tevnia jerichonana and a newly designed Oasisia alvinae probe, as well as a 16S rRNA probe targeting symbionts found in all host species, were applied. A number of standard fixation and hybridization parameters were tested and optimized for the best possible signal intensity and cellular resolution. Ethanol conserved samples embedded in LR White low viscosity resin yielded the best results with regard to both signal intensity and resolution. We show that extended storage times of specimens does not affect the quality of signals attained by FISH and use our protocol to identify morphologically unidentifiable tubeworm individuals from a small data set, conforming to previous findings in succession studies of the Siboglinidae family.

  12. Assessment of metal contamination in water, sediment, and tissues of Arius thalassinus fish from the Red Sea coast of Yemen and the potential human risk assessment.

    PubMed

    Saleh, Yousef S; Marie, Mohamed-Assem S

    2015-04-01

    Heavy metal pollution is one of the most serious environmental issues globally. To evaluate the metal pollution in the Red Sea coast of Hodeida, Yemen Republic, the concentrations of Fe, Cu, Ni, Pb, and Cd in water, sediment, and some vital organs of sea catfish, Arius thalassinus collected from polluted and unpolluted sites, were determined. The risk of these metals to humans through fish consumption was then assessed. The results showed that the concentration order of metals in water, sediment, and fish tissues were Fe > Cu > Ni > Pb > Cd. The levels of studied metals in water, sediment, and fish tissues were significantly higher in the polluted site than those of the unpolluted site, with few exceptions. Linear correlation incorporating paired variables (water-sediment, water-fish, and fish-fish) exhibited several significant correlations indicating a common metal pollution. The risk assessment performed revealed that fish consumption was safe for consumers. This field investigation provides a baseline data on metal pollution in this region.

  13. 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.

  14. Assessment of two nonnative poeciliid fishes for monitoring selenium exposure in the endangered desert pupfish

    USGS Publications Warehouse

    Saiki, Michael K.; Martin, Barbara A.; May, Thomas W.; Brumbaugh, William G.

    2012-01-01

    We assessed the suitability of two nonnative poeciliid fishes—western mosquitofish (Gambusia affinis) and sailfin mollies (Poecilia latipinna)—for monitoring selenium exposure in desert pupfish (Cyprinodon macularius). Our investigation was prompted by a need to avoid lethal take of an endangered species (pupfish) when sampling fish for chemical analysis. Total selenium (SeTot) concentrations in both poeciliids were highly correlated with SeTot concentrations in pupfish. However, mean SeTot concentrations varied among fish species, with higher concentrations measured in mosquitofish than in mollies and pupfish from one of three sampled agricultural drains. Moreover, regression equations describing the relationship of selenomethionine to SeTot differed between mosquitofish and pupfish, but not between mollies and pupfish. Because selenium accumulates in animals primarily through dietary exposure, we examined fish trophic relationships by measuring stable isotopes (δ13C and δ15N) and gut contents. According to δ13C measurements, the trophic pathway leading to mosquitofish was more carbon-depleted than trophic pathways leading to mollies and pupfish, suggesting that energy flow to mosquitofish originated from allochthonous sources (terrestrial vegetation, emergent macrophytes, or both), whereas energy flow to mollies and pupfish originated from autochthonous sources (filamentous algae, submerged macrophytes, or both). The δ15N measurements indicated that mosquitofish and mollies occupied similar trophic levels, whereas pupfish occupied a slightly higher trophic level. Analysis of gut contents showed that mosquitofish consumed mostly winged insects (an indication of terrestrial taxa), whereas mollies and pupfish consumed mostly organic detritus. Judging from our results, only mollies (not mosquitofish) are suitable for monitoring selenium exposure in pupfish.

  15. Assessing effects of water abstraction on fish assemblages in Mediterranean streams

    USGS Publications Warehouse

    Benejam, Lluis; Angermeier, Paul L.; Munne, Antoni; García-Berthou, Emili

    2010-01-01

    1. Water abstraction strongly affects streams in arid and semiarid ecosystems, particularly where there is a Mediterranean climate. Excessive abstraction reduces the availability of water for human uses downstream and impairs the capacity of streams to support native biota. 2. We investigated the flow regime and related variables in six river basins of the Iberian Peninsula and show that they have been strongly altered, with declining flows (autoregressive models) and groundwater levels during the 20th century. These streams had lower flows and more frequent droughts than predicted by the official hydrological model used in this region. Three of these rivers were sometimes dry, whereas there were predicted by the model to be permanently flowing. Meanwhile, there has been no decrease in annual precipitation. 3. We also investigated the fish assemblage of a stream in one of these river basins (Tordera) for 6 years and show that sites more affected by water abstraction display significant differences in four fish metrics (catch per unit effort, number of benthic species, number of intolerant species and proportional abundance of intolerant individuals) commonly used to assess the biotic condition of streams. 4. We discuss the utility of these metrics in assessing impacts of water abstraction and point out the need for detailed characterisation of the natural flow regime (and hence drought events) prior to the application of biotic indices in streams severely affected by water abstraction. In particular, in cases of artificially dry streams, it is more appropriate for regulatory agencies to assign index scores that reflect biotic degradation than to assign ‘missing’ scores, as is presently customary in assessments of Iberian streams.

  16. The development of a preliminary rock reef fish multimetric index for assessing thermal and urban impacts in a tropical bay.

    PubMed

    Teixeira-Neves, Tatiana Pires; Neves, Leonardo Mitrano; Araújo, Francisco Gerson

    2016-08-15

    We developed a multimetric index for assessing ecological conditions in rocky reefs areas to evaluate thermal and urban influences on fish community. Eight metrics were selected to assess thermal influence: (1) total number of species; (2) number of water column species; (3) number of transient species; (4) density of individuals with low resilience; (5) density of omnivores; (6) density of carnivores; (7) number of cryptic species; (8) density of herbivores. For urban influence, six metrics were selected: (1) total density; (2) ratio between the number of rare species and the total number of species; (3) density of individuals with heavy fishing pressure; (4) number of resident species; (5) number of cryptic species; (6) density of herbivores. This preliminary index succeed in discriminating control/impacted sites and proved to be an important tool to assess impacts that alter fish community and have potential to be used in tropical rock reef coastal areas.

  17. The development of a preliminary rock reef fish multimetric index for assessing thermal and urban impacts in a tropical bay.

    PubMed

    Teixeira-Neves, Tatiana Pires; Neves, Leonardo Mitrano; Araújo, Francisco Gerson

    2016-08-15

    We developed a multimetric index for assessing ecological conditions in rocky reefs areas to evaluate thermal and urban influences on fish community. Eight metrics were selected to assess thermal influence: (1) total number of species; (2) number of water column species; (3) number of transient species; (4) density of individuals with low resilience; (5) density of omnivores; (6) density of carnivores; (7) number of cryptic species; (8) density of herbivores. For urban influence, six metrics were selected: (1) total density; (2) ratio between the number of rare species and the total number of species; (3) density of individuals with heavy fishing pressure; (4) number of resident species; (5) number of cryptic species; (6) density of herbivores. This preliminary index succeed in discriminating control/impacted sites and proved to be an important tool to assess impacts that alter fish community and have potential to be used in tropical rock reef coastal areas. PMID:27293073

  18. Assessing impacts of land-applied manure from concentrated animal feeding operations on fish populations and communities.

    PubMed

    Leet, Jessica K; Lee, Linda S; Gall, Heather E; Goforth, Reuben R; Sassman, Stephen; Gordon, Denise A; Lazorchak, James M; Smith, Mark E; Jafvert, Chad T; Javfert, Chad T; Sepúlveda, Maria S

    2012-12-18

    Concentrated animal feeding operation (CAFO) manure is a cost-effective fertilizer. In the Midwest, networks of subsurface tile-drains expedite transport of animal hormones and nutrients from land-applied CAFO manure to adjacent waterways. The objective of this study was to evaluate impacts of land-applied CAFO manure on fish populations and communities. Water chemistry including hormone, pesticide, and nutrient concentrations was characterized from study sites along with fish assemblage structure, growth, and endocrine disruption assessed in selected fish species. Although most CAFO water samples had hormone concentrations <1 ng/L, equivalent concentrations for 17β-E2 and 17α-TB peaked at >30 ng/L each during the period of spawning, hatching, and development for resident fishes. CAFO sites had lower fish species richness, and fishes exhibited faster somatic growth and lower reproductive condition compared to individuals from the reference site. Fathead minnows (Pimephales promelas) exposed to CAFO ditchwater during early developmental stages exhibited significantly skewed sex ratios toward males. Maximum observed hormone concentrations were well above the lowest observable effect concentrations for these hormones; however, complexities at the field scale make it difficult to directly relate hormone concentration and impacts on fish. Complicating factors include the consistent presence of pesticides and nutrients, and the difference in temperature and stream architecture of the CAFO-impacted ditches compared to the reference site (e.g., channelization, bottom substrate, shallow pools, and riparian cover). PMID:23171355

  19. The technology assessment of LTA aircraft systems. [hybrid airships for passenger and cargo transportation

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The advantages of conventional small and large airships over heavier than air aircraft are reviewed and the need for developing hybrid aircraft for passenger and heavy charge transport is assessed. Performance requirements and estimated operating costs are discussed for rota-ships to be used for short distance transportation near large cities as well as for airlifting civil engineering machinery and supplies for the construction of power stations, dams, tunnels, and roads in remote areas or on isolated islands.

  20. Predation risk assessment by larval reef fishes during settlement-site selection

    NASA Astrophysics Data System (ADS)

    Dixson, D. L.

    2012-03-01

    Predation rates of marine species are often highest during the transition from the pelagic to the benthic life stage. Consequently, the ability to assess predation risk when selecting a settlement site can be critical to survival. In this study, pairwise choice trials were used to determine whether larvae of three species of anemonefish ( Amphiprion melanopus, A. percula and Premnas biaculeatus) are able to (1) assess the predation risk of potential anemone settlement sites through olfactory cues alone and (2) alter their settlement choices depending on the options available (host or non-host anemone). When predation risk was assessed with host and non-host anemone species independently, all species of anemonefish significantly chose the odor associated with the low-risk settlement option over the high-risk site. Most importantly, all species of anemonefish selected water with olfactory cues from their host anemone regardless of predation risk when paired against non-host anemone odor. These results demonstrate that larval reef fishes can use olfactory cues for complex risk assessment during settlement-site selection; however, locating the correct habitat is the most important factor when selecting a settlement site.

  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. Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives.

    PubMed

    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

  3. Determination of toxic elements (mercury, cadmium, lead, tin and arsenic) in fish and shellfish samples. Risk assessment for the consumers.

    PubMed

    Olmedo, P; Pla, A; Hernández, A F; Barbier, F; Ayouni, L; Gil, F

    2013-09-01

    Although fish intake has potential health benefits, the presence of metal contamination in seafood has raised public health concerns. In this study, levels of mercury, cadmium, lead, tin and arsenic have been determined in fresh, canned and frozen fish and shellfish products and compared with the maximum levels currently in force. In a further step, potential human health risks for the consumers were assessed. A total of 485 samples of the 43 most frequently consumed fish and shellfish species in Andalusia (Southern Spain) were analyzed for their toxic elements content. High mercury concentrations were found in some predatory species (blue shark, cat shark, swordfish and tuna), although they were below the regulatory maximum levels. In the case of cadmium, bivalve mollusks such as canned clams and mussels presented higher concentrations than fish, but almost none of the samples analyzed exceeded the maximum levels. Lead concentrations were almost negligible with the exception of frozen common sole, which showed median levels above the legal limit. Tin levels in canned products were far below the maximum regulatory limit, indicating that no significant tin was transferred from the can. Arsenic concentrations were higher in crustaceans such as fresh and frozen shrimps. The risk assessment performed indicated that fish and shellfish products were safe for the average consumer, although a potential risk cannot be dismissed for regular or excessive consumers of particular fish species, such as tuna, swordfish, blue shark and cat shark (for mercury) and common sole (for lead). PMID:23792415

  4. Determination of toxic elements (mercury, cadmium, lead, tin and arsenic) in fish and shellfish samples. Risk assessment for the consumers.

    PubMed

    Olmedo, P; Pla, A; Hernández, A F; Barbier, F; Ayouni, L; Gil, F

    2013-09-01

    Although fish intake has potential health benefits, the presence of metal contamination in seafood has raised public health concerns. In this study, levels of mercury, cadmium, lead, tin and arsenic have been determined in fresh, canned and frozen fish and shellfish products and compared with the maximum levels currently in force. In a further step, potential human health risks for the consumers were assessed. A total of 485 samples of the 43 most frequently consumed fish and shellfish species in Andalusia (Southern Spain) were analyzed for their toxic elements content. High mercury concentrations were found in some predatory species (blue shark, cat shark, swordfish and tuna), although they were below the regulatory maximum levels. In the case of cadmium, bivalve mollusks such as canned clams and mussels presented higher concentrations than fish, but almost none of the samples analyzed exceeded the maximum levels. Lead concentrations were almost negligible with the exception of frozen common sole, which showed median levels above the legal limit. Tin levels in canned products were far below the maximum regulatory limit, indicating that no significant tin was transferred from the can. Arsenic concentrations were higher in crustaceans such as fresh and frozen shrimps. The risk assessment performed indicated that fish and shellfish products were safe for the average consumer, although a potential risk cannot be dismissed for regular or excessive consumers of particular fish species, such as tuna, swordfish, blue shark and cat shark (for mercury) and common sole (for lead).

  5. Assessing trade-offs to inform ecosystem-based fisheries management of forage fish

    PubMed Central

    Shelton, Andrew Olaf; Samhouri, Jameal F.; Stier, Adrian C.; Levin, Philip S.

    2014-01-01

    Twenty-first century conservation is centered on negotiating trade-offs between the diverse needs of people and the needs of the other species constituting coupled human-natural ecosystems. Marine forage fishes, such as sardines, anchovies, and herring, are a nexus for such trade-offs because they are both central nodes in marine food webs and targeted by fisheries. An important example is Pacific herring, Clupea pallisii in the Northeast Pacific. Herring populations are subject to two distinct fisheries: one that harvests adults and one that harvests spawned eggs. We develop stochastic, age-structured models to assess the interaction between fisheries, herring populations, and the persistence of predators reliant on herring populations. We show that egg- and adult-fishing have asymmetric effects on herring population dynamics - herring stocks can withstand higher levels of egg harvest before becoming depleted. Second, ecosystem thresholds proposed to ensure the persistence of herring predators do not necessarily pose more stringent constraints on fisheries than conventional, fishery driven harvest guidelines. Our approach provides a general template to evaluate ecosystem trade-offs between stage-specific harvest practices in relation to environmental variability, the risk of fishery closures, and the risk of exceeding ecosystem thresholds intended to ensure conservation goals are met. PMID:25407879

  6. Behavioral assessment of acoustic parameters relevant to signal recognition and preference in a vocal fish.

    PubMed

    McKibben, J R; Bass, A H

    1998-12-01

    Acoustic signal recognition depends on the receiver's processing of the physical attributes of a sound. This study takes advantage of the simple communication sounds produced by plainfin midshipman fish to examine effects of signal variation on call recognition and preference. Nesting male midshipman generate both long duration (> 1 min) sinusoidal-like "hums" and short duration "grunts." The hums of neighboring males often overlap, creating beat waveforms. Presentation of humlike, single tone stimuli, but not grunts or noise, elicited robust attraction (phonotaxis) by gravid females. In two-choice tests, females differentiated and chose between acoustic signals that differed in duration, frequency, amplitude, and fine temporal content. Frequency preferences were temperature dependent, in accord with the known temperature dependence of hum fundamental frequency. Concurrent hums were simulated with two-tone beat stimuli, either presented from a single speaker or produced more naturally by interference between adjacent sources. Whereas certain single-source beats reduced stimulus attractiveness, beats which resolved into unmodulated tones at their sources did not affect preference. These results demonstrate that phonotactic assessment of stimulus relevance can be applied in a teleost fish, and that multiple signal parameters can affect receiver response in a vertebrate with relatively simple communication signals. PMID:9857511

  7. Probabilistic maturation reaction norms assessed from mark-recaptures of wild fish in their natural habitat.

    PubMed

    Olsen, Esben M; Serbezov, Dimitar; Vøllestad, Leif A

    2014-05-01

    Reaction norms are a valuable tool in evolutionary biology. Lately, the probabilistic maturation reaction norm approach, describing probabilities of maturing at combinations of age and body size, has been much applied for testing whether phenotypic changes in exploited populations of fish are mainly plastic or involving an evolutionary component. However, due to typical field data limitations, with imperfect knowledge about individual life histories, this demographic method still needs to be assessed. Using 13 years of direct mark-recapture observations on individual growth and maturation in an intensively sampled population of brown trout (Salmo trutta), we show that the probabilistic maturation reaction norm approach may perform well even if the assumption of equal survival of juvenile and maturing fish does not hold. Earlier studies have pointed out that growth effects may confound the interpretation of shifts in maturation reaction norms, because this method in its basic form deals with body size rather than growth. In our case, however, we found that juvenile body size, rather than annual growth, was more strongly associated with maturation. Viewed against earlier studies, our results also underscore the challenges of generalizing life-history patterns among species and populations. PMID:24967078

  8. Interrenal dysfunction in fish from contaminated sites: In vivo and in vitro assessment

    SciTech Connect

    Hontela, A.

    1998-01-01

    Cortisol, synthesized in the interrenal cells of teleost head kidney, has a major role in the physiologic response to physical and chemical stressors. Plasma levels of cortisol increase in physiologically competent fish acutely exposed to stressors such as cadmium or mercury. The effects of chronic low level exposures are less well understood. The author has diagnosed an endocrine impairment characterized by a reduced capacity to elevate plasma cortisol levels in response to an acute standardized capture stress in yellow perch (Perca flavescens) and in northern pike (Esox lucius) sampled at sites contaminated by mixtures of pollutants (heavy metals, polycyclic aromatic hydrocarbons, and polychlorinated biphenyls), by heavy metals, or by bleached kraft mill effluent. The studies with fish, as well as with amphibians at contaminated sites, demonstrated that low level chronic exposures impair secretion of corticosteroids. The author has developed new tests for assessment of the functional integrity of teleost and amphibian interrenal tissue using an adrenocorticotropic hormone (ACTH) challenge, in vivo and in vitro. The reduced ability to respond to ACTH indicates that the normal neuroendocrine response to stressors may be disrupted and that the ability to cope with biotic and abiotic stressors in the environment may be significantly reduced in the impaired animals.

  9. Assessing trade-offs to inform ecosystem-based fisheries management of forage fish.

    PubMed

    Shelton, Andrew Olaf; Samhouri, Jameal F; Stier, Adrian C; Levin, Philip S

    2014-11-19

    Twenty-first century conservation is centered on negotiating trade-offs between the diverse needs of people and the needs of the other species constituting coupled human-natural ecosystems. Marine forage fishes, such as sardines, anchovies, and herring, are a nexus for such trade-offs because they are both central nodes in marine food webs and targeted by fisheries. An important example is Pacific herring, Clupea pallisii in the Northeast Pacific. Herring populations are subject to two distinct fisheries: one that harvests adults and one that harvests spawned eggs. We develop stochastic, age-structured models to assess the interaction between fisheries, herring populations, and the persistence of predators reliant on herring populations. We show that egg- and adult-fishing have asymmetric effects on herring population dynamics--herring stocks can withstand higher levels of egg harvest before becoming depleted. Second, ecosystem thresholds proposed to ensure the persistence of herring predators do not necessarily pose more stringent constraints on fisheries than conventional, fishery driven harvest guidelines. Our approach provides a general template to evaluate ecosystem trade-offs between stage-specific harvest practices in relation to environmental variability, the risk of fishery closures, and the risk of exceeding ecosystem thresholds intended to ensure conservation goals are met.

  10. Replacing fish meal by food waste in feed pellets to culture lower trophic level fish containing acceptable levels of organochlorine pesticides: health risk assessments.

    PubMed

    Cheng, Zhang; Mo, Wing-Yin; Man, Yu-Bon; Nie, Xiang-Ping; Li, Kai-Bing; Wong, Ming-Hung

    2014-12-01

    The present study used food waste (collected from local hotels and restaurants) feed pellets in polyculture of low-trophic level fish [bighead (Aristichtys nobilis), grass carp (Ctenopharyngodon idellus), and mud carp (Cirrhina molitorella)] aiming at producing safe and quality products for local consumption. The results indicated that grass carp (hexachlorocyclohexanes (HCHs) <0.03; dichlorodiphenyltrichloroethanes (DDTs) 1.42-3.34 ng/g ww) and bighead carp (HCHs<0.03; DDTs 1.55-2.56 ng/g ww) fed with food waste feed pellets were relatively free of organochlorine pesticides (OCPs). The experimental ponds (water and sediment) were relatively free of OCPs, lowering the possibility of biomagnification of OCPs in the food chains within the ponds. The raw concentrations of OCPs extracted from the fish were not in the bioavailable form, which would ultimately reach bloodstream and exert adverse effects on human body. Health risk assessments based on digestible concentrations are commonly regarded as a more accurate method. The results of health risk assessments based on raw and digestible concentrations showed that the fish fed with food waste feed pellets were safe for consumption from the OCP perspective.

  11. Replacing fish meal by food waste in feed pellets to culture lower trophic level fish containing acceptable levels of organochlorine pesticides: health risk assessments.

    PubMed

    Cheng, Zhang; Mo, Wing-Yin; Man, Yu-Bon; Nie, Xiang-Ping; Li, Kai-Bing; Wong, Ming-Hung

    2014-12-01

    The present study used food waste (collected from local hotels and restaurants) feed pellets in polyculture of low-trophic level fish [bighead (Aristichtys nobilis), grass carp (Ctenopharyngodon idellus), and mud carp (Cirrhina molitorella)] aiming at producing safe and quality products for local consumption. The results indicated that grass carp (hexachlorocyclohexanes (HCHs) <0.03; dichlorodiphenyltrichloroethanes (DDTs) 1.42-3.34 ng/g ww) and bighead carp (HCHs<0.03; DDTs 1.55-2.56 ng/g ww) fed with food waste feed pellets were relatively free of organochlorine pesticides (OCPs). The experimental ponds (water and sediment) were relatively free of OCPs, lowering the possibility of biomagnification of OCPs in the food chains within the ponds. The raw concentrations of OCPs extracted from the fish were not in the bioavailable form, which would ultimately reach bloodstream and exert adverse effects on human body. Health risk assessments based on digestible concentrations are commonly regarded as a more accurate method. The results of health risk assessments based on raw and digestible concentrations showed that the fish fed with food waste feed pellets were safe for consumption from the OCP perspective. PMID:25080070

  12. Power to Detect Trends in Missouri River Fish Populations within the Habitat Assessment Monitoring Program

    USGS Publications Warehouse

    Bryan, Janice L.; Wildhaber, Mark L.; Gladish, Dan W.

    2010-01-01

    As with all large rivers in the United States, the Missouri River has been altered, with approximately one-third of the mainstem length impounded and one-third channelized. These physical alterations to the environment have affected the fish populations, but studies examining the effects of alterations have been localized and for short periods of time, thereby preventing generalization. In response to the U.S. Fish and Wildlife Service Biological Opinion, the U.S. Army Corps of Engineers (USACE) initiated monitoring of habitat improvements of the Missouri River in 2005. The goal of the Habitat Assessment Monitoring Program (HAMP) is to provide information on the response of target fish species to the USACE habitat creation on the Lower Missouri River. To determine the statistical power of the HAMP and in cooperation with USACE, a power analysis was conducted using a normal linear mixed model with variance component estimates based on the first complete year of data. At a level of 20/16 (20 bends with 16 subsamples in each bend), at least one species/month/gear model has the power to determine differences between treated and untreated bends. The trammel net in September had the most species models with adequate power at the 20/16 level and overall, the trammel net had the most species/month models with adequate power at the 20/16 level. However, using only one gear or gear/month combination would eliminate other species of interest, such as three chub species (Macrhybopsis meeki, Macrhybopsis aestivalis, and Macrhybopsis gelida), sand shiners (Notropis stramineus), pallid sturgeon (Scaphirhynchus albus), and juvenile sauger (Sander canadensis). Since gear types are selective in their species efficiency, the strength of the HAMP approach is using multiple gears that have statistical power to differentiate habitat treatment differences in different fish species within the Missouri River. As is often the case with sampling rare species like the pallid sturgeon, the

  13. Residual levels of DDTs and PAHs in freshwater and marine fish from Hong Kong markets and their health risk assessment.

    PubMed

    Cheung, K C; Leung, H M; Kong, K Y; Wong, M H

    2007-01-01

    Axial and ventral muscle from 10 each species of freshwater and marine fish purchased from markets in Hong Kong were analyzed for dichlorodiphenyltrichloroethane (total DDTs including DDE, DDD and DDT) and polycyclic aromatic hydrocarbons (PAHs). Among the 10 freshwater fish species, rice field eel (Monopterus albus) showed significantly higher levels of DDTs in both ventral (125 ng/g wet wt) and axial muscle (127 ng/g wet wt) than the other species. The highest concentration of PAHs was detected in catfish (Clarias fuscus), with 24.8 ng/g in ventral muscle and 9.1 ng/g in axial muscle. As to marine fish, snubnose pompano (Trachinotus blochii) showed significantly higher levels of DDT and its metabolites (1018 ng/g in ventral and 409 ng/g wet wt in axial tissues) than all other marine fish species. The overall concentrations of PAHs in marine fish species were 15.5-57.0 ng/g (axial muscle) and 18.1-118 ng/g wet wt (ventral muscle) where yellow seafin (Acanthopeyrus latus) and golden threadfin bream (Nemipterus virgatus) exhibited the highest concentrations of PAHs in the axial and ventral muscles, respectively. In general, results showed that levels of PAHs in Hong Kong market fish was low and do not expect to cause any concern for human consumption. However, the levels of DDTs in fish samples ranged from 1.10 to 1018 ng/g wet wt, and based on a fish consumption rate of 142.2g/day to calculate the screening value of 14.4 ng/g wet wt for human consumption (USEPA, 2000. Guidance for assessing chemical contaminant, data for use in fish advisories, vol. 1: fish sampling and analysis, third ed. EPA 823-R-95-007. Office of Water, Washington, DC), there were 9 out of 20 (45%) muscle samples of freshwater fish species and 14 out of 20 (70%) muscle samples of marine fish species had elevated levels of DDTs exceeded the screening value. It was also suggested to use ventral muscle for detecting concentrations of persistent organic pollutants in fish.

  14. 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.

  15. A Change in the Use of Regulatory Criteria for Assessing Potential Impacts of Sound on Fishes.

    PubMed

    Jacobs, Fred; Krebs, Justin; Popper, Arthur N

    2016-01-01

    The National Marine Fisheries Service (NMFS) currently uses interim criteria developed on the US West Coast to assess the potential onset of peak and cumulative effects of noise on fishes. Analyses performed for this project provided adequate support for the NMFS to use the peak criterion (i.e., area ensonified by 206 dB re 1 μPa peak sound pressure level [SPL(peak)]) for estimating the incidental take of Hudson River sturgeon. Application of the peak criterion (rather than the cumulative criterion) could have implications for future construction projects because estimates of take using SPL(peak) will generally be considerably lower than estimates of take based on the cumulative sound exposure level.

  16. Assessing Cumulative Thermal Stress in Fish During Chronic Exposure to High Temperature

    SciTech Connect

    Bevelhimer, M.S.; Bennett, W.R.

    1999-11-14

    As environmental laws become increasingly protective, and with possible future changes in global climate, thermal effects on aquatic resources are likely to receive increasing attention. Lethal temperatures for a variety of species have been determined for situations where temperatures rise rapidly resulting in lethal effects. However, less is known about the effects of chronic exposure to high (but not immediately lethal) temperatures and even less about stress accumulation during periods of fluctuating temperatures. In this paper we present a modeling framework for assessing cumulative thermal stress in fish. The model assumes that stress accumulation occurs above a threshold temperature at a rate depending on the degree to which the threshold is exceeded. The model also includes stress recovery (or alleviation) when temperatures drop below the threshold temperature as in systems with large daily variation. In addition to non-specific physiological stress, the model also simulates thermal effects on growth.

  17. Dynamic hybrid life cycle assessment of energy and carbon of multicrystalline silicon photovoltaic systems.

    PubMed

    Zhai, Pei; Williams, Eric D

    2010-10-15

    This paper advances the life cycle assessment (LCA) of photovoltaic systems by expanding the boundary of the included processes using hybrid LCA and accounting for the technology-driven dynamics of embodied energy and carbon emissions. Hybrid LCA is an extended method that combines bottom-up process-sum and top-down economic input-output (EIO) methods. In 2007, the embodied energy was 4354 MJ/m(2) and the energy payback time (EPBT) was 2.2 years for a multicrystalline silicon PV system under 1700 kWh/m(2)/yr of solar radiation. These results are higher than those of process-sum LCA by approximately 60%, indicating that processes excluded in process-sum LCA, such as transportation, are significant. Even though PV is a low-carbon technology, the difference between hybrid and process-sum results for 10% penetration of PV in the U.S. electrical grid is 0.13% of total current grid emissions. Extending LCA from the process-sum to hybrid analysis makes a significant difference. Dynamics are characterized through a retrospective analysis and future outlook for PV manufacturing from 2001 to 2011. During this decade, the embodied carbon fell substantially, from 60 g CO(2)/kWh in 2001 to 21 g/kWh in 2011, indicating that technological progress is realizing reductions in embodied environmental impacts as well as lower module price.

  18. Environmental Assessment of the US Department of Energy Electric and Hybrid Vehicle Program

    SciTech Connect

    Singh, M.K.; Bernard, M.J. III; Walsh, R.F

    1980-11-01

    This environmental assessment (EA) focuses on the long-term (1985-2000) impacts of the US Department of Energy (DOE) electric and hybrid vehicle (EHV) program. This program has been designed to accelerate the development of EHVs and to demonstrate their commercial feasibility as required by the Electric and Hybrid Vehicle Research, Development and Demonstration Act of 1976 (P.L. 94-413), as amended (P.L. 95-238). The overall goal of the program is the commercialization of: (1) electric vehicles (EVs) acceptable to broad segments of the personal and commercial vehicle markets, (2) hybrid vehicles (HVs) with range capabilities comparable to those of conventional vehicles (CVs), and (3) advanced EHVs completely competitive with CVs with respect to both cost and performance. Five major EHV projects have been established by DOE: market demonstration, vehicle evaluation and improvement, electric vehicle commercialization, hybrid vehicle commercialization, and advanced vehicle development. Conclusions are made as to the effects of EV and HV commercialization on the: consumption and importation of raw materials; petroleum and total energy consumption; ecosystems impact from the time of obtaining raw material through vehicle use and materials recycling; environmental impacts on air and water quality, land use, and noise; health and safety aspects; and socio-economic factors. (LCL)

  19. Assessing the tolerance of fish and fish populations to environmental stress: The problems and methods of monitoring

    USGS Publications Warehouse

    Wedemeyer, G.A.; McLeay, D.; Goodyear, C.P.

    1984-01-01

    Environmental stress is an inescapable aspect of life in the aquatic environment. The chemical and physical demands of life underwater impose somewhat rigorous constraints on aquatic species (Smith, 1982a). Superimposed on such demands may be the additional. physiological constraints of particular ecological niches. It is true that aquatic species are adapted to these conditions, but this does not imply the absence of energy drains (Lugo, 1978). For example, thermophilic fishes must still cope physiologically with the demands of high temperatures even though they are adapted to high temperatures per se.

  20. Rapid Discrimination of Haemophilus influenzae, H. parainfluenzae, and H. haemolyticus by Fluorescence In Situ Hybridization (FISH) and Two Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) Platforms

    PubMed Central

    Frickmann, Hagen; Christner, Martin; Donat, Martina; Berger, Anja; Essig, Andreas; Podbielski, Andreas; Hagen, Ralf Matthias; Poppert, Sven

    2013-01-01

    Background Due to considerable differences in pathogenicity, Haemophilus influenzae, H. parainfluenzae and H. haemolyticus have to be reliably discriminated in routine diagnostics. Retrospective analyses suggest frequent misidentifications of commensal H. haemolyticus as H. influenzae. In a multi-center approach, we assessed the suitability of fluorescence in situ hybridization (FISH) and matrix-assisted laser-desorption-ionization time-of-flight mass-spectrometry (MALDI-TOF-MS) for the identification of H. influenzae, H. parainfluenzae and H. haemolyticus to species level. Methodology A strain collection of 84 Haemophilus spp. comprising 50 H. influenzae, 25 H. parainfluenzae, 7 H. haemolyticus, and 2 H. parahaemolyticus including 77 clinical isolates was analyzed by FISH with newly designed DNA probes, and two different MALDI-TOF-MS systems (Bruker, Shimadzu) with and without prior formic acid extraction. Principal Findings Among the 84 Haemophilus strains analyzed, FISH led to 71 correct results (85%), 13 uninterpretable results (15%), and no misidentifications. Shimadzu MALDI-TOF-MS resulted in 59 correct identifications (70%), 19 uninterpretable results (23%), and 6 misidentifications (7%), using colony material applied directly. Bruker MALDI-TOF-MS with prior formic acid extraction led to 74 correct results (88%), 4 uninterpretable results (5%) and 6 misidentifications (7%). The Bruker MALDI-TOF-MS misidentifications could be resolved by the addition of a suitable H. haemolyticus reference spectrum to the system's database. In conclusion, no analyzed diagnostic procedure was free of errors. Diagnostic results have to be interpreted carefully and alternative tests should be applied in case of ambiguous test results on isolates from seriously ill patients. PMID:23646201

  1. Genome analysis of 7 Kengyilia (Triticeae Poaceae) species with FISH and GISH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome composition of and genetic relationships among seven Kengyilia species were assessed using a technique of sequential FISH (fluorescence in situ hybridization) and GISH (genomic in situ hybridization). Five of these 7 species, K. kokonorica, K. rigidula, K. hirsula, K. grandiglumis, and K. th...

  2. Detection of Escherichia coli O157 by Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA-FISH) and Comparison to a Standard Culture Method

    PubMed Central

    Almeida, C.; Sousa, J. M.; Rocha, R.; Cerqueira, L.; Fanning, S.; Azevedo, N. F.

    2013-01-01

    Despite the emergence of non-O157 Shiga toxin-producing Escherichia coli (STEC) infections, E. coli serotype O157 is still the most commonly identified STEC in the world. It causes high morbidity and mortality and has been responsible for a number of outbreaks in many parts of the world. Various methods have been developed to detect this particular serotype, but standard bacteriological methods remain the gold standard. Here, we propose a new peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the rapid detection of E. coli O157. Testing on 54 representative strains showed that the PNA probe is highly sensitive and specific to E. coli O157. The method then was optimized for detection in food samples. Ground beef and unpasteurized milk samples were artificially contaminated with E. coli O157 concentrations ranging from 1 × 10−2 to 1 × 102 CFU per 25 g or ml of food. Samples were then preenriched and analyzed by both the traditional bacteriological method (ISO 16654:2001) and PNA-FISH. The PNA-FISH method performed well in both types of food matrices with a detection limit of 1 CFU/25 g or ml of food samples. Tests on 60 food samples have shown a specificity value of 100% (95% confidence interval [CI], 82.83 to 100), a sensitivity of 97.22% (95% CI, 83.79 to 99.85%), and an accuracy of 98.33% (CI 95%, 83.41 to 99.91%). Results indicate that PNA-FISH performed as well as the traditional culture methods and can reduce the diagnosis time to 1 day. PMID:23934486

  3. Development of a fish assemblage tolerance index for the National Rivers and Streams Assessment

    EPA Science Inventory

    Whittier et al (Trans. Amer. Fish. Soc. 136:254-271) developed an assemblage tolerance index (ATI) for stream fishes in the western US based on quantitative tolerance values developed for individual fish and amphibian species. The ATI is conceptually similar to the Hilsenhoff Bi...

  4. Assessing the health condition profile in the freshwater fish Astyanax aeneus in Champoton River, Mexico.

    PubMed

    Trujillo-Jiménez, Patricia; Sedeño-Díaz, Jacinto Elías; López-López, Eugenia

    2014-01-01

    The use of biomarkers for monitoring aquatic environmental quality has gained considerable interest worldwide. The effects of the environmental conditions of Río Champotón, México, in the hotspot of Mesoamerica, were assessed in Astyanax aeneus, a native fish of the tropics of southwestern México. Pollution from agrochemical residues is a major problem in Río Champotón. Three study sites along the freshwater portion of the river were monitored in April, July, and November 2007 and February 2008. This study includes a water quality index, a set of biomarkers (hepatic glycogen levels and lipid peroxidation in liver, gills, and muscle) to assess the integrated biomarker response, and population bioindicators (gonadosomatic and hepatosomatic indices and Fulton's condition factor). Although the water quality index suggested low level of contamination in the Río Champotón, biomarkers indicated that A. aeneus is exposed to stressors that impair biological responses. The integrated biomarker response showed stress periods with higher biomarker response and recovery periods with decreasing biomarker values. The somatic indices did not indicate severe effects at the population level. This study illustrates the usefulness of lipid peroxidation evaluation in the assessment of aquatic health conditions and corroborates the suitability of A. aeneus as a sentinel species.

  5. The Alburnus benthopelagic fish species of the Western Balkan Peninsula: An assessment of their sustainable use.

    PubMed

    Simić, Vladica; Simić, Snežana; Paunović, Momir; Radojković, Nataša; Petrović, Ana; Talevski, Trajče; Milošević, Djuradj

    2016-01-01

    In this study, we aimed to assess the population status of bleak (Alburnus spp.) over the Western Balkan Peninsula in terms of its sustainable use. A second objective was to determine key factors important for fishery management planning. Two different basins, continental (the Danube Basin and the Sava River sub-basin) and marine (the Adriatic and the Aegean Sea Basins) were examined. A sustainability assessment and factor analysis were conducted using the adjusted ESHIPPOfishing model, extended with additional socio-economic sub-elements, and the categorical principal components analysis (CATPCA), respectively. The results of the assessment revealed the bleak populations in the Danube Basin and the Sava River sub-basin to be highly sustainable. The population characteristics with abiotic and biotic factors were responsible for this status, while the influence of socio-economic factors was insignificant. The sustainability status of the bleak populations of the Mediterranean basin varied, with the populations from Ohrid and Skadar Lakes showing a high and those from Prespa and Dojran Lakes a medium status. Socio-economic factors with traditional fishing were the most important for the Mediterranean bleak populations.

  6. Cichlid Fish Use Coloration as a Cue to Assess the Threat Status of Heterospecific Intruders.

    PubMed

    Lehtonen, Topi K; Sowersby, Will; Gagnon, Karine; Wong, Bob B M

    2015-10-01

    The ability to assess the threat posed by competitors, and to respond appropriately, is important for reducing the costs of aggression. In this respect, aggression directed toward heterospecifics is often just as significant as aggression among conspecifics. This is especially true for cichlid fish that share breeding grounds with heterospecifics. Indeed, cichlids are known to differentiate not only between conspecifics that pose different levels of threat but also between heterospecific territorial intruders by directing more aggression toward nonbreeding individuals. To assess whether the ability to make such distinctions could be based on color cues alone, we carried out a field study in which we experimentally presented Amphilophus sagittae cichlid pairs with model intruders of a sympatric congener, Amphilophus xiloaensis, in breeding versus nonbreeding coloration. Consistent with our prediction, we found that A. sagittae exhibited more aggression toward A. xiloaensis models of the latter color type. The results are, to our knowledge, the first to show that territory holders can, based on coloration alone, assess variation among individuals of a species other than their own in the threat posed to offspring survival.

  7. The Alburnus benthopelagic fish species of the Western Balkan Peninsula: An assessment of their sustainable use.

    PubMed

    Simić, Vladica; Simić, Snežana; Paunović, Momir; Radojković, Nataša; Petrović, Ana; Talevski, Trajče; Milošević, Djuradj

    2016-01-01

    In this study, we aimed to assess the population status of bleak (Alburnus spp.) over the Western Balkan Peninsula in terms of its sustainable use. A second objective was to determine key factors important for fishery management planning. Two different basins, continental (the Danube Basin and the Sava River sub-basin) and marine (the Adriatic and the Aegean Sea Basins) were examined. A sustainability assessment and factor analysis were conducted using the adjusted ESHIPPOfishing model, extended with additional socio-economic sub-elements, and the categorical principal components analysis (CATPCA), respectively. The results of the assessment revealed the bleak populations in the Danube Basin and the Sava River sub-basin to be highly sustainable. The population characteristics with abiotic and biotic factors were responsible for this status, while the influence of socio-economic factors was insignificant. The sustainability status of the bleak populations of the Mediterranean basin varied, with the populations from Ohrid and Skadar Lakes showing a high and those from Prespa and Dojran Lakes a medium status. Socio-economic factors with traditional fishing were the most important for the Mediterranean bleak populations. PMID:26216478

  8. Hybrid methodology for situation assessment model development within an air operations center domain

    NASA Astrophysics Data System (ADS)

    Ho, Stephen; Gonsalves, Paul; Call, Catherine

    2007-04-01

    Within the dynamic environment of an Air Operations Center (AOC), effective decision-making is highly dependent on timely and accurate situation assessment. In previous research efforts the capabilities and potential of a Bayesian belief network (BN) model-based approach to support situation assessment have been demonstrated. In our own prior research, we have presented and formalized a hybrid process for situation assessment model development that seeks to ameliorate specific concerns and drawbacks associated with using a BN-based model construct. Specifically, our hybrid methodology addresses the significant knowledge acquisition requirements and the associated subjective nature of using subject matter experts (SMEs) for model development. Our methodology consists of two distinct functional elements: an off-line mechanism for rapid construction of a Bayesian belief network (BN) library of situation assessment models tailored to different situations and derived from knowledge elicitation with SMEs; and an on-line machine-learning-based mechanism to learn, tune, or adapt BN model parameters and structure. The adaptation supports the ability to adjust the models over time to respond to novel situations not initially available or anticipated during initial model construction, thus ensuring that the models continue to meet the dynamic requirements of performing the situation assessment function within dynamic application environments such as an AOC. In this paper, we apply and demonstrate the hybrid approach within the specific context of an AOC-based air campaign monitoring scenario. We detail both the initial knowledge elicitation and subsequent machine learning phases of the model development process, as well as demonstrate model performance within an operational context.

  9. Assessment of sites of marrow and extramedullary hematopoiesis by hybrid imaging in primary myelofibrosis patients.

    PubMed

    Ojeda-Uribe, Mario; Morel, Olivier; Ungureanu, Constantin; Desterke, Christophe; Le Bousse-Kerdilès, Marie-Caroline; Boulahdour, Hatem

    2016-09-01

    We investigated noninvasive procedures by hybrid imaging to assess the sites of active or inactive hematopoiesis in patients with primary myelofibrosis (PMF). To this end, we used two radionuclides, technetium 99m ((99m) Tc) and indium 111-chloride ((111) In-Cl3 ), coupled with single-photon emission tomography/computed tomography (SPECT/CT). We studied five patients with PMF and one with secondary myelofibrosis (MF). The classical pattern of lower fixation of both tracers at the axial skeleton where the myelofibrotic process occurs and the reactivation of sites of active hematopoiesis at the distal skeleton were confirmed. Coupling both radionuclides to SPECT/CT imaging allowed for more precise visualization of the sites of extramedullary hematopoiesis as those observed in the spleen and liver. Splenic high uptake of (111) In-Cl3 coupled with SPECT/CT represents a pathognomonic feature of PMF. We conclude that, the hybrid imaging procedures that we studied might constitute an alternative noninvasive method for the screening of the whole-body marrow and, by this way, to assess the impact of targeted therapies in PMF patients in whom it is well known that the distribution of the hematopoietic active areas is disturbed. Hybrid imaging could also be useful for diagnostic purposes in cases of early PMF or in suspected cases of myelofibrosis secondary to polycythemia vera or essential thrombocythemia. PMID:27518041

  10. Factors in exposure assessment: Ethnic and socio-economic differences in fishing and consumption of fish caught along the Savannah River

    SciTech Connect

    Burger, J. |; Stephens, W.L.; Boring, C.S. |; Kuklinski, M.; Gibbons, J.W.; Gochfeld, M. |

    1999-06-01

    South Carolina has issued fish consumption advisories for the Savannah River based on mercury and radionuclide levels. The authors examine differences in fishing rates and fish consumption of 258 people interviewed while fishing along the Savannah River, as a function of age, education, ethnicity, employment history, and income, and test the assumption that the average consumption of fish is less than the recreational value of 19 kg/year assumed by risk assessors. Ethnicity and education contributed significantly to explaining variations in number of fish meals per month, serving size, and total quantity of fish consumed per year. Blacks fished more often, ate more fish meals of slightly larger serving sizes, and consumed more fish per year than did Whites. Although education and income were correlated, education contributed most significantly to behavior; people who did not graduate from high school ate fish more often, ate more fish per year, and ate more whole fish than people who graduated from high school. Computing consumption of fish for each person individually indicates that (1) people who eat fish more often also eat larger portions, (2) a substantial number of people consume more than the amount of fish used to compute risk to recreational fishermen, (3) some people consume more than the subsistence level default assumption (50 kg/year) and (4) Blacks consume more fish per year than Whites, putting them at greater risk from contaminants in fish. Overall, ethnicity, age, and education contributed to variations in fishing behavior and consumption.

  11. Assessment of freshwater fish assemblages and their habitats in the National Park Service system of the southeastern United States

    USGS Publications Warehouse

    Long, James M.; Nibbelink, Nathan P.; McAbee, Kevin T.; Stahli, Julie W.

    2012-01-01

    The southeast region of the United States contains the highest diversity of freshwater fish species in the country: approximately 662 species. Existing protected areas like units of the National Park Service (NPS) should reflect this biodiversity, but there has been no broad-scale assessment. We compiled several data sets identifying native freshwater fish species distributions in and surrounding NPS units and threats to those resources. Focusing on the 26 NPS units containing only freshwater fish species, we documented 288 species within NPS boundaries. The largest NPS units tended to have the most fish species and aquatic habitat but also the greatest amount of alteration. Increasing rates of urbanization, declines in percentage agriculture land cover, and increased density of road-stream crossings in surrounding watersheds were good predictors of nonindigenous species presence within NPS unit boundaries. These results help document the role of NPS units in conserving freshwater fish diversity and, in this region, suggest that measures aimed at controlling urbanization in the adjacent watersheds could affect the diversity of freshwater fish communities in these units.

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

    PubMed

    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. PMID:26872885

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

    PubMed

    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.

  14. Qualitative assessment of the impacts of proposed system operating strategies to resident fish within selected Columbia River Reservoirs

    SciTech Connect

    Shreffler, D.K.; Geist, D.R.; Mavros, W.V.

    1994-01-01

    The Bonneville Power Administration (BPA), Bureau of Reclamation (BOR), and US Army Corps of Engineers (COE) are presently conducting the System Operation Review (SOR) for the Columbia River basin. The SOR began in 1990 and is expected to provide an operating strategy that will take into consideration multiple uses of the Columbia River system including navigation, flood control, irrigation, power generation, fish migration, fish and wildlife habitat, recreation, water supply, and water quality. This report provides descriptions of each of the non-modeled reservoirs and other specified river reaches. The descriptions focus on the distinct management goals for resident fish: biodiversity, species-specific concerns, and sport fisheries. In addition, this report provides a qualitative assessment of impacts to the resident fish within these reservoirs and river reaches from the 7 alternative system operating strategies. In addition to this introduction, the report contains four more sections. Section 2.0 provides the methods that were used. Reservoir descriptions appear in Section 3.0, which is a synthesis of our literature review and interviews with resident fish experts. Section 4.0 contains a discussion of potential impacts to fish within each of these reservoirs and river reaches from the 7 proposed system operating strategies. The references cited are listed in Section 5.0.

  15. Risk assessment for human consumption of perfluorinated compound-contaminated freshwater and marine fish from Hong Kong and Xiamen.

    PubMed

    Zhao, Yin G; Wan, Hin T; Law, Alice Y S; Wei, Xi; Huang, Ye Q; Giesy, John P; Wong, Ming H; Wong, Chris K C

    2011-09-01

    Perfluorinated compounds (PFCs) are man-made fluoro-surfactants that are identified as global pollutants and can pose health risks to humans and wildlife. Two aspects of risk assessment were conducted in this study, including exposure and response. Exposure was estimated by using the concentrations of PFCs in fish and applying standard exposure factors. Among different PFCs, PFOS, PFOA, PFNA, PFDA, PFUdA and PFTrDA were detected. Total concentrations of PFC in fish ranged from 0.27-8.4 ng g(-1) to 0.37-8.7 ng g(-1) respectively in Hong Kong and Xiamen. The calculated hazard ratio (HR) of PFOS for all fish was less than 1.0. However, the HR for mandarin fish in Hong Kong and bighead carp, grass carp and tilapia in Xiamen, had HR values of approximately 0.5, indicating that frequent consumption of these 4 more contaminated fish species might pose an unacceptable risk to human health. Our data support the notion that the released/disposed chemical pollutants into water systems make fish a source of environmental toxicants to humans. The risks and potential effects of PFCs to health of coastal population in the Pearl River Delta are of concern. PMID:21705041

  16. Assessment of Hybrid Organic-Inorganic Antimony Sulfides for Earth-Abundant Photovoltaic Applications.

    PubMed

    Yang, Ruo Xi; Butler, Keith T; Walsh, Aron

    2015-12-17

    Hybrid organic-inorganic solar absorbers are currently the subject of intense interest; however, the highest-performing materials contain Pb. Here we assess the potential of three Sb-based semiconductors: (i) Sb2S3, (ii) Cs2Sb8S13, and (iii) (CH3NH3)2Sb8S13. While the crystal structure of Sb2S3 is composed of 1D chains, 2D layers are formed in the ternary cesium and hybrid methylammonium antimony sulfide compounds. In each case, a stereochemically active Sb 5s(2) lone pair is found, resulting in a distorted coordination environment for the Sb cations. The bandgap of the binary sulfide is found to increase, while the ionization potential also changes, upon transition to the more complex compounds. Based on the predicted electronic structure, device configurations are suggested to be suitable for photovoltaic applications. PMID:26624204

  17. Assessment of Hybrid Organic-Inorganic Antimony Sulfides for Earth-Abundant Photovoltaic Applications.

    PubMed

    Yang, Ruo Xi; Butler, Keith T; Walsh, Aron

    2015-12-17

    Hybrid organic-inorganic solar absorbers are currently the subject of intense interest; however, the highest-performing materials contain Pb. Here we assess the potential of three Sb-based semiconductors: (i) Sb2S3, (ii) Cs2Sb8S13, and (iii) (CH3NH3)2Sb8S13. While the crystal structure of Sb2S3 is composed of 1D chains, 2D layers are formed in the ternary cesium and hybrid methylammonium antimony sulfide compounds. In each case, a stereochemically active Sb 5s(2) lone pair is found, resulting in a distorted coordination environment for the Sb cations. The bandgap of the binary sulfide is found to increase, while the ionization potential also changes, upon transition to the more complex compounds. Based on the predicted electronic structure, device configurations are suggested to be suitable for photovoltaic applications.

  18. A size-based probabilistic assessment of PCB exposure from Lake Michigan fish consumption

    SciTech Connect

    Stow, C.A.; Qian, S.S.

    1998-08-01

    The state of Wisconsin has recently issued a fish consumption advisory that includes suggested consumption rates for Lake Michigan fish, based on fish size and PCB concentration. To evaluate the size-based exposure risk from Lake Michigan fish consumption, the authors estimated PCB exposure probabilities for five Lake Michigan fish species using two Bayesian models. The models confirm that very few individuals of any of the five species are likely to have PCB concentrations low enough to fall into the category in which consumption is unrestricted. Among smaller fish (<50 cm), brown trout have the highest PCB levels, while lake trout are the most contaminated among larger fish (>60 cm). Eating meals from multiple individuals of some species results in a high probability that at least one of the meals will exceed 1.9 mg/kg, the upper PCB concentration recommended for consumption in the advisory.

  19. USING A FISH INDEX TO ASSESS HABITAT QUALITY IN NARRAGANSETT BAY, RI: THE IMPORTANCE OF THE UPPER ESTUARY

    EPA Science Inventory

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

  20. The IUCN Red List of Threatened Species: an assessment of coral reef fishes in the US Pacific Islands

    NASA Astrophysics Data System (ADS)

    Zgliczynski, B. J.; Williams, I. D.; Schroeder, R. E.; Nadon, M. O.; Richards, B. L.; Sandin, S. A.

    2013-09-01

    Widespread declines among many coral reef fisheries have led scientists and managers to become increasingly concerned over the extinction risk facing some species. To aid in assessing the extinction risks facing coral reef fishes, large-scale censuses of the abundance and distribution of individual species are critically important. We use fisheries-independent data collected as part of the NOAA Pacific Reef Assessment and Monitoring Program from 2000 to 2009 to describe the range and density across the US Pacific of coral reef fishes included on The International Union for the Conservation of Nature's (IUCN) 2011 Red List of Threatened Species. Forty-five species, including sharks, rays, groupers, humphead wrasse ( Cheilinus undulatus), and bumphead parrotfish ( Bolbometopon muricatum), included on the IUCN List, were recorded in the US Pacific Islands. Most species were generally rare in the US Pacific with the exception of a few species, principally small groupers and reef sharks. The greatest diversity and densities of IUCN-listed fishes were recorded at remote and uninhabited islands of the Pacific Remote Island Areas; in general, lower densities were observed at reefs of inhabited islands. Our findings complement IUCN assessment efforts, emphasize the efficacy of large-scale assessment and monitoring efforts in providing quantitative data on reef fish assemblages, and highlight the importance of protecting populations at remote and uninhabited islands where some species included on the IUCN Red List of Threatened Species can be observed in abundance.

  1. AN ASSESSMENT OF FLYWHEEL HIGH POWER ENERGY STORAGE TECHNOLOGY FOR HYBRID VEHICLES

    SciTech Connect

    Hansen, James Gerald

    2012-02-01

    An assessment has been conducted for the DOE Vehicle Technologies Program to determine the state of the art of advanced flywheel high power energy storage systems to meet hybrid vehicle needs for high power energy storage and energy/power management. Flywheel systems can be implemented with either an electrical or a mechanical powertrain. The assessment elaborates upon flywheel rotor design issues of stress, materials and aspect ratio. Twelve organizations that produce flywheel systems submitted specifications for flywheel energy storage systems to meet minimum energy and power requirements for both light-duty and heavy-duty hybrid applications of interest to DOE. The most extensive experience operating flywheel high power energy storage systems in heavy-duty and light-duty hybrid vehicles is in Europe. Recent advances in Europe in a number of vehicle racing venues and also in road car advanced evaluations are discussed. As a frame of reference, nominal weight and specific power for non-energy storage components of Toyota hybrid electric vehicles are summarized. The most effective utilization of flywheels is in providing high power while providing just enough energy storage to accomplish the power assist mission effectively. Flywheels are shown to meet or exceed the USABC power related goals (discharge power, regenerative power, specific power, power density, weight and volume) for HEV and EV batteries and ultracapacitors. The greatest technical challenge facing the developer of vehicular flywheel systems remains the issue of safety and containment. Flywheel safety issues must be addressed during the design and testing phases to ensure that production flywheel systems can be operated with adequately low risk.

  2. A new fish-based multi-metric assessment index for cyprinid streams in the Iranian Caspian Sea Basin

    PubMed Central

    Mostafavi, Hossein; Schinegger, Rafaela; Melcher, Andreas; Moder, Karl; Mielach, Carina; Schmutz, Stefan

    2015-01-01

    A major issue for water resource management is the assessment of environmental degradation of lotic ecosystems. The overall aim of this study is to develop a multi-metric fish index for the cyprinid streams of the Caspian Sea Basin (MMICS) in Iran. As species diversity and composition as well as population structure in the studied streams are different to other regions, there is a substantial need to develop a new fish index. We sampled fish and environmental data of 102 sites in medium sized streams. We analysed human pressures at different spatial scales and determined applicable fish metrics showing a response to human pressures. In total, five structural and functional types of metrics (i.e. biodiversity, habitat, reproduction, trophic level and water quality sensitivity) were considered. In addition, we used 29 criteria describing major anthropogenic human pressures at sampling sites and generated a regional pressure index (RPI) that accounted for potential effects of multiple human pressures. For the MMICS development, we first defined reference sites (least disturbed) and secondly quantified differences of fish metrics between reference and impaired sites. We used a Generalised Linear Model (GLM) to describe metric responses to natural environmental differences in least disturbed conditions. By including impaired sites, the residual distributions of these models described the response range of each metric to human pressures, independently of natural environmental influence. Finally, seven fish metrics showed the best ability to discriminate between impaired and reference sites. The multi-metric fish index performed well in discriminating human pressure classes, giving a significant negative linear response to a gradient of the RPI. These methods can be used for further development of a standardised monitoring tool to assess the ecological status and trends in biological condition for streams of the whole country, considering its complex and diverse geology

  3. Automated quantification of FISH signals in urinary cells enables the assessment of chromosomal aberration patterns characteristic for bladder cancer.

    PubMed

    Köhler, Christina U; Martin, Laura; Bonberg, Nadine; Behrens, Thomas; Deix, Thomas; Braun, Katharina; Noldus, Joachim; Jöckel, Karl-Heinz; Erbel, Raimund; Sommerer, Florian; Tannapfel, Andrea; Harth, Volker; Käfferlein, Heiko U; Brüning, Thomas

    2014-06-13

    Targeting the centromeres of chromosomes 3, 7, 17 (CEP3, 7, 17) and the 9p21-locus (LSI9p21) for diagnosing bladder cancer (BC) is time- and cost-intensive and requires a manual investigation of the sample by a well-trained investigator thus overall limiting its use in clinical diagnostics and large-scaled epidemiological studies. Here we introduce a new computer-assisted FISH spot analysis tool enabling an automated, objective and quantitative assessment of FISH patterns in the urinary sediment. Utilizing a controllable microscope workstation, the microscope software Scan^R was programmed to allow automatic batch-scanning of up to 32 samples and identifying quadruple FISH signals in DAPI-scanned nuclei of urinary sediments. The assay allowed a time- and cost-efficient, automated and objective assessment of CEP3, 7 and 17 FISH signals and facilitated the quantification of nuclei harboring specific FISH patterns in all cells of the urinary sediment. To explore the diagnostic capability of the developed tool, we analyzed the abundance of 51 different FISH patterns in a pilot set of urine specimens from 14 patients with BC and 21 population controls (PC). Herein, the results of the fully automated approach yielded a high degree of conformity when compared to those obtained by an expert-guided re-evaluation of archived scans. The best cancer-identifying pattern was characterized by a concurrent gain of CEP3, 7 and 17. Overall, our automated analysis refines current FISH protocols and encourages its use to establish reliable diagnostic cutoffs in future large-scale studies with well-characterized specimens-collectives. PMID:24802410

  4. Survival rate of wine-related yeasts during alcoholic fermentation assessed by direct live/dead staining combined with fluorescence in situ hybridization.

    PubMed

    Branco, Patrícia; Monteiro, Margarida; Moura, Patrícia; Albergaria, Helena

    2012-08-01

    Real-time detection of microorganisms involved in complex microbial process, such as wine fermentations, and evaluation of their physiological state is crucial to predict whether or not those microbial species will be able to impact the final product. In the present work we used a direct live/dead staining (LDS) procedure combined with fluorescence in situ hybridization (FISH) to simultaneously assess the identity and viability of Saccharomyces cerevisiae (Sc) and Hanseniaspora guilliermondii (Hg) during fermentations performed with single and mixed cultures. The population evolution of both yeasts was determined by plating and by LDS combined with species-specific FISH-probes labeled with Fluorescein. Since the FISH method involves the permeabilization of the cell membrane prior to hybridization and that it may influence the free diffusion of PI in and out of the cells, we optimized the concentration of this dye (0.5 μg of PI per 10(6) cells) for minimal diffusion (less than 2%). Fluorescent cells were enumerated by hemocytometry and flow cytometry. Results showed that the survival rate of Sc during mixed cultures was high throughout the entire process (60% of viable cells at the 9th day), while Hg began to die off at the 2nd day, exhibited 98% of dead cells at the 3rd day (45 g/l of ethanol) and became completely unculturable at the 4th day. However, under single culture fermentation the survival rate and culturability of Hg decreased at a much slower pace, exhibiting at the 7th day (67 g/l of ethanol) 8.7×10(4) CFU/ml and 85% of dead cells. Thus, our work demonstrated that the LDS-FISH method is able to simultaneously assess the viability and identity of these wine-related yeast species during alcoholic fermentation in a fast and reliable way. In order to validate PI-staining as a viability marker during alcoholic fermentation, we evaluated the effect of ethanol on the membrane permeability of Sc and Hg cells, as well as their capacity to recover membrane

  5. Assessing Dispersal Patterns of Fish Propagules from an Effective Mediterranean Marine Protected Area

    PubMed Central

    Di Franco, Antonio; Coppini, Giovanni; Pujolar, José Martin; De Leo, Giulio A.; Gatto, Marino; Lyubartsev, Vladyslav; Melià, Paco; Zane, Lorenzo; Guidetti, Paolo

    2012-01-01

    Successfully enforced marine protected areas (MPAs) have been widely demonstrated to allow, within their boundaries, the recovery of exploited species and beyond their boundaries, the spillover of juvenile and adult fish. Little evidence is available about the so-called ‘recruitment subsidy’, the augmented production of propagules (i.e. eggs and larvae) due to the increased abundance of large-sized spawners hosted within effective MPAs. Once emitted, propagules can be locally retained and/or exported elsewhere. Patterns of propagule retention and/or export from MPAs have been little investigated, especially in the Mediterranean. This study investigated the potential for propagule production and retention/export from a Mediterranean MPA (Torre Guaceto, SW Adriatic Sea) using the white sea bream, Diplodus sargus sargus, as a model species. A multidisciplinary approach was used combining 1) spatial distribution patterns of individuals (post-settlers and adults) assessed through visual census within Torre Guaceto MPA and in northern and southern unprotected areas, 2) Lagrangian simulations of dispersal based on an oceanographic model of the region and data on early life-history traits of the species (spawning date, pelagic larval duration) and 3) a preliminary genetic study using microsatellite loci. Results show that the MPA hosts higher densities of larger-sized spawners than outside areas, potentially guaranteeing higher propagule production. Model simulations and field observation suggest that larval retention within and long-distance dispersal across MPA boundaries allow the replenishment of the MPA and of exploited populations up to 100 km down-current (southward) from the MPA. This pattern partially agrees with the high genetic homogeneity found in the entire study area (no differences in genetic composition and diversity indices), suggesting a high gene flow. By contributing to a better understanding of propagule dispersal patterns, these findings provide

  6. Apparent digestibility of Asian carp and common carp-derived fish meals in feeds for hybrid striped bass Morone saxatilis female x M. chrysops male and rainbow trout Oncorhynchus mykiss

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apparent digestibility coefficients (ADCs) of nutrients (crude protein, amino acids, crude lipid, fatty acids, and minerals) were determined for fish meals derived from menhaden, Asian carp (combination of silver and bighead carps), and common carp in feeds for hybrid striped bass and rainbow trout....

  7. Molecular detection of Helicobacter pylori in a large Mediterranean river, by direct viable count fluorescent in situ hybridization (DVC-FISH).

    PubMed

    Tirodimos, Ilias; Bobos, Mattheos; Kazakos, Evangelos; Haidich, Anna-Bettina; Dardavessis, Theodore; Kostopoulos, Ioannis; Arvanitidou, Malamatenia

    2014-12-01

    Although the precise route and mode of transmission of Helicobacter pylori are still unclear, molecular methods have been applied for the detection of H. pylori in environmental samples. In this study, we used the direct viable count fluorescent in situ hybridization (DVC-FISH) method to detect viable cells of H. pylori in the River Aliakmon, Greece. This is the longest river in Greece, and provides potable water in metropolitan areas. H. pylori showed positive detection for 23 out of 48 water samples (47.9%), while no seasonal variation was found and no correlation was observed between the presence of H. pylori and indicators of fecal contamination. Our findings strengthen the evidence that H. pylori is waterborne while its presence adds to the potential health hazards of the River Aliakmon.

  8. Use of automated monitoring to assess behavioral toxicology in fish: Linking behavior and physiology

    USGS Publications Warehouse

    Brewer, S.K.; DeLonay, A.J.; Beauvais, S.L.; Little, E.E.; Jones, S.B.

    1999-01-01

    We measured locomotory behaviors (distance traveled, speed, tortuosity of path, and rate of change in direction) with computer-assisted analysis in 30 day posthatch rainbow trout (Oncorhynchus mykiss) exposed to pesticides. We also examined cholinesterase inhibition as a potential endpoint linking physiology and behavior. Sublethal exposure to chemicals often causes changes in swimming behavior, reflecting alterations in sensory and motor systems. Swimming behavior also integrates functions of the nervous system. Rarely are the connections between physiology and behavior made. Although behavior is often suggested as a sensitive, early indicator of toxicity, behavioral toxicology has not been used to its full potential because conventional methods of behavioral assessment have relied on manual techniques, which are often time-consuming and difficult to quantify. This has severely limited the application and utility of behavioral procedures. Swimming behavior is particularly amenable to computerized assessment and automated monitoring. Locomotory responses are sensitive to toxicants and can be easily measured. We briefly discuss the use of behavior in toxicology and automated techniques used in behavioral toxicology. We also describe the system we used to determine locomotory behaviors of fish, and present data demonstrating the system's effectiveness in measuring alterations in response to chemical challenges. Lastly, we correlate behavioral and physiological endpoints.

  9. Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis.

    PubMed

    Laub, Brian G; Budy, Phaedra

    2015-08-01

    A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans.

  10. Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis.

    PubMed

    Laub, Brian G; Budy, Phaedra

    2015-08-01

    A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans. PMID:25627117

  11. Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis

    USGS Publications Warehouse

    Laub, P; Budy, Phaedra

    2015-01-01

    A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans.

  12. Hybrid Reynolds-Averaged/Large Eddy Simulation of a Cavity Flameholder; Assessment of Modeling Sensitivities

    NASA Technical Reports Server (NTRS)

    Baurle, R. A.

    2015-01-01

    Steady-state and scale-resolving simulations have been performed for flow in and around a model scramjet combustor flameholder. The cases simulated corresponded to those used to examine this flowfield experimentally using particle image velocimetry. A variety of turbulence models were used for the steady-state Reynolds-averaged simulations which included both linear and non-linear eddy viscosity models. The scale-resolving simulations used a hybrid Reynolds-averaged / large eddy simulation strategy that is designed to be a large eddy simulation everywhere except in the inner portion (log layer and below) of the boundary layer. Hence, this formulation can be regarded as a wall-modeled large eddy simulation. This effort was undertaken to formally assess the performance of the hybrid Reynolds-averaged / large eddy simulation modeling approach in a flowfield of interest to the scramjet research community. The numerical errors were quantified for both the steady-state and scale-resolving simulations prior to making any claims of predictive accuracy relative to the measurements. The steady-state Reynolds-averaged results showed a high degree of variability when comparing the predictions obtained from each turbulence model, with the non-linear eddy viscosity model (an explicit algebraic stress model) providing the most accurate prediction of the measured values. The hybrid Reynolds-averaged/large eddy simulation results were carefully scrutinized to ensure that even the coarsest grid had an acceptable level of resolution for large eddy simulation, and that the time-averaged statistics were acceptably accurate. The autocorrelation and its Fourier transform were the primary tools used for this assessment. The statistics extracted from the hybrid simulation strategy proved to be more accurate than the Reynolds-averaged results obtained using the linear eddy viscosity models. However, there was no predictive improvement noted over the results obtained from the explicit

  13. Risk assessment in a federal regulatory agency: an assessment of risk associated with the human consumption of some species of fish contaminated with polychlorinated biphenyls (PCBs).

    PubMed Central

    Cordle, F; Locke, R; Springer, J

    1982-01-01

    The problem of polychlorinated biphenyls (PCBs) became a national concern in 1971 when several accidental contaminations of foods were reported. Extensive efforts were undertaken by FDA to reduce the residues of PCBs in food. However, the PCB levels in several species of fresh-water fish have raised concern about the PCB residues from environmental contamination, and it is this concern which has prompted a reassessment of the human risk involved from consumption of such fish. The human epidemiology and animal toxicity of PCB exposure are reviewed, as well as risk assessment in general. Specific examples to risk assessment involving extrapolation of animal data to humans, based on several levels of human exposure to PCBs in fish, are presented. PMID:6814904

  14. Estimation of sport fish harvest for risk and hazard assessment of environmental contaminants

    SciTech Connect

    Poston, T.M.; Strenge, D.L.

    1989-01-01

    Consumption of contaminated fish flesh can be a significant route of human exposure to hazardous chemicals. Estimation of exposure resulting from the consumption of fish requires knowledge of fish consumption and contaminant levels in the edible portion of fish. Realistic figures of sport fish harvest are needed to estimate consumption. Estimates of freshwater sport fish harvest were developed from a review of 72 articles and reports. Descriptive statistics based on fishing pressure were derived from harvest data for four distinct groups of freshwater sport fish in three water types: streams, lakes, and reservoirs. Regression equations were developed to relate harvest to surface area fished where data bases were sufficiently large. Other aspects of estimating human exposure to contaminants in fish flesh that are discussed include use of bioaccumulation factors for trace metals and organic compounds. Using the bioaccumulation factor and the concentration of contaminants in water as variables in the exposure equation may also lead to less precise estimates of tissue concentration. For instance, muscle levels of contaminants may not increase proportionately with increases in water concentrations, leading to overestimation of risk. In addition, estimates of water concentration may be variable or expressed in a manner that does not truly represent biological availability of the contaminant. These factors are discussed. 45 refs., 1 fig., 7 tabs.

  15. A national statistical survey assessment of mercury concentrations in fillets of fish collected in the U.S. EPA national rivers and streams assessment of the continental USA.

    PubMed

    Wathen, John B; Lazorchak, James M; Olsen, Anthony R; Batt, Angela

    2015-03-01

    The U.S. EPA conducted a national statistical survey of fish fillet tissue with a sample size of 541 sites on boatable rivers =>5th order in 2008-2009. This is the first such study of mercury (Hg) in fish tissue from river sites focused on potential impacts to human health from fish consumption to also address wildlife impacts. Sample sites were identified as being urban or non-urban. All sample mercury concentrations were above the 3.33ugkg(-1) (ppb) quantitation limit, and an estimated 25.4% (±4.4%) of the 51663 river miles assessed exceeded the U.S. EPA 300ugkg(-1) fish-tissue based water quality criterion for mercury, representing 13144±181.8 river miles. Estimates of river miles exceeding comparable aquatic life thresholds (translated from fillet concentrations to whole fish equivalents) in avian species were similar to the number of river miles exceeding the human health threshold, whereas some mammalian species were more at risk than human from lower mercury concentrations. A comparison of means from the non-urban and urban data and among three ecoregions did not indicate a statistically significant difference in fish tissue Hg concentrations at p<0.05.

  16. A Preliminary Assessment of Barotrauma Injuries and Acclimation Studies for Three Fish Species

    SciTech Connect

    Brown, Richard S.; Walker, Ricardo W.; Stephenson, John R.

    2015-12-15

    Fish that pass hydro structures either through turbine passage, deep spill, or other deep pathways can experience rapid decreases in pressure that can result in barotrauma. In addition to morphology and physiology of the fish’s swim bladder, the severity of barotrauma is directly related to the volume of undissolved gas in fish prior to rapid decompression and the lowest pressure the fish experience as they pass hydro structures (termed the “nadir”). The volume of undissolved gas in fish is influenced by the depth of acclimation (the pressure at which the fish is neutrally buoyant); therefore, determining the depth where fish are neutrally buoyant is a critical precursor to determining the relationship between pressure changes and injury or mortality.

  17. Diterpenylquinone hybrids: synthesis and assessment of gastroprotective mechanisms of action in human cells.

    PubMed

    Theoduloz, Cristina; Bravo, Ivanna; Pertino, Mariano Walter; Schmeda-Hirschmann, Guillermo

    2013-09-10

    A modern approach in the search for new bioactive molecules is the synthesis of novel chemical entities combining molecules of different biosynthetic origin presenting biological effects as single compounds. Gastroprotective compounds from South American medicinal plants, namely quinones and diterpenes, were used as building blocks to obtain hybrid diterpenylquinones. Starting from the labdane diterpene junicedric acid and two isomers, as well as from three quinones, including lapachol, 18 hybrid molecules were synthesized. Six of them are described for the first time. The potential gastroprotective mechanisms of action of the compounds were assessed in dose-response experiments using human gastric epithelial cells (AGS) and human lung fibroblasts (MRC-5). The following studies were carried out: stimulation of cell proliferation, cytoprotection against sodium taurocholate (NaT)-induced damage, synthesis of PGE2 and total reduced sulfhydryl (GSH) content. The antioxidant capacity of the compounds was determined on the inhibition of the lipoperoxidation in human erythrocyte membranes. Hybrid compounds presented activities different from those shown by the starting compounds, supporting the potential of this approach in the search for new bioactive molecules. The effects might be modulated by selective modification in the terpene or quinone moieties of the new molecules. Structure-activity relationships are discussed.

  18. Diterpenylquinone hybrids: synthesis and assessment of gastroprotective mechanisms of action in human cells.

    PubMed

    Theoduloz, Cristina; Bravo, Ivanna; Pertino, Mariano Walter; Schmeda-Hirschmann, Guillermo

    2013-01-01

    A modern approach in the search for new bioactive molecules is the synthesis of novel chemical entities combining molecules of different biosynthetic origin presenting biological effects as single compounds. Gastroprotective compounds from South American medicinal plants, namely quinones and diterpenes, were used as building blocks to obtain hybrid diterpenylquinones. Starting from the labdane diterpene junicedric acid and two isomers, as well as from three quinones, including lapachol, 18 hybrid molecules were synthesized. Six of them are described for the first time. The potential gastroprotective mechanisms of action of the compounds were assessed in dose-response experiments using human gastric epithelial cells (AGS) and human lung fibroblasts (MRC-5). The following studies were carried out: stimulation of cell proliferation, cytoprotection against sodium taurocholate (NaT)-induced damage, synthesis of PGE2 and total reduced sulfhydryl (GSH) content. The antioxidant capacity of the compounds was determined on the inhibition of the lipoperoxidation in human erythrocyte membranes. Hybrid compounds presented activities different from those shown by the starting compounds, supporting the potential of this approach in the search for new bioactive molecules. The effects might be modulated by selective modification in the terpene or quinone moieties of the new molecules. Structure-activity relationships are discussed. PMID:24025455

  19. Hybrid ICA-Seed-Based Methods for fMRI Functional Connectivity Assessment: A Feasibility Study

    PubMed Central

    Kelly, Robert E.; Wang, Zhishun; Alexopoulos, George S.; Gunning, Faith M.; Murphy, Christopher F.; Morimoto, Sarah Shizuko; Kanellopoulos, Dora; Jia, Zhiru; Lim, Kelvin O.; Hoptman, Matthew J.

    2010-01-01

    Brain functional connectivity (FC) is often assessed from fMRI data using seed-based methods, such as those of detecting temporal correlation between a predefined region (seed) and all other regions in the brain; or using multivariate methods, such as independent component analysis (ICA). ICA is a useful data-driven tool, but reproducibility issues complicate group inferences based on FC maps derived with ICA. These reproducibility issues can be circumvented with hybrid methods that use information from ICA-derived spatial maps as seeds to produce seed-based FC maps. We report results from five experiments to demonstrate the potential advantages of hybrid ICA-seed-based FC methods, comparing results from regressing fMRI data against task-related a priori time courses, with “back-reconstruction” from a group ICA, and with five hybrid ICA-seed-based FC methods: ROI-based with (1) single-voxel, (2) few-voxel, and (3) many-voxel seed; and dual-regression-based with (4) single ICA map and (5) multiple ICA map seed. PMID:20689712

  20. Arsenic contamination in the freshwater fish ponds of Pearl River Delta: bioaccumulation and health risk assessment.

    PubMed

    Cheng, Zhang; Chen, Kun-Ci; Li, Kai-Bin; Nie, Xiang-Ping; Wu, Sheng Chun; Wong, Chris Kong-Chu; Wong, Ming-Hung

    2013-07-01

    This study investigated the extent of arsenic (As) contamination in five common species of freshwater fish (northern snakehead [Channa argus], mandrarin fish [Siniperca chuatsi], largemouth bass [Lepomis macrochirous], bighead carp [Aristichthys nobilis] and grass carp [Ctenopharyngodon idellus]) and their associated fish pond sediments collected from 18 freshwater fish ponds around the Pearl River Delta (PRD). The total As concentrations detected in fish muscle and sediment in freshwater ponds around the PRD were 0.05-3.01 mg kg(-1) wet weight (w. wt) and 8.41-22.76 mg kg(-1) dry weight (d. wt), respectively. In addition, the As content was positively correlated (p < 0.05) to total organic carbon (TOC) contents in sediments. Biota sediment accumulation factor (BSAF) showed that omnivorous fish and zooplankton accumulated higher concentrations of heavy metals from the sediment than carnivorous fish. In addition, feeding habits of fish also influence As accumulation in different fish species. In this study, two typical food chains of the aquaculture ponds were selected for investigation: (1) omnivorous food chain (zooplankton, grass carp and bighead carp) and (2) predatory food chain (zooplankton, mud carp and mandarin fish). Significant linear relationships were obtained between log As and δ (15)N. The slope of the regression (-0.066 and -0.078) of the log transformed As concentrations and δ (15)N values, as biomagnifications power, indicated there was no magnification or diminution of As from lower trophic levels (zooplankton) to fish in the aquaculture ponds. Consumption of largemouth bass, northern snakehead and bighead carp might impose health risks of Hong Kong residents consuming these fish to the local population, due to the fact that its cancer risk (CR) value exceeded the upper limit of the acceptable risk levels (10(-4)) stipulated by the USEPA.

  1. Arsenic contamination in the freshwater fish ponds of Pearl River Delta: bioaccumulation and health risk assessment.

    PubMed

    Cheng, Zhang; Chen, Kun-Ci; Li, Kai-Bin; Nie, Xiang-Ping; Wu, Sheng Chun; Wong, Chris Kong-Chu; Wong, Ming-Hung

    2013-07-01

    This study investigated the extent of arsenic (As) contamination in five common species of freshwater fish (northern snakehead [Channa argus], mandrarin fish [Siniperca chuatsi], largemouth bass [Lepomis macrochirous], bighead carp [Aristichthys nobilis] and grass carp [Ctenopharyngodon idellus]) and their associated fish pond sediments collected from 18 freshwater fish ponds around the Pearl River Delta (PRD). The total As concentrations detected in fish muscle and sediment in freshwater ponds around the PRD were 0.05-3.01 mg kg(-1) wet weight (w. wt) and 8.41-22.76 mg kg(-1) dry weight (d. wt), respectively. In addition, the As content was positively correlated (p < 0.05) to total organic carbon (TOC) contents in sediments. Biota sediment accumulation factor (BSAF) showed that omnivorous fish and zooplankton accumulated higher concentrations of heavy metals from the sediment than carnivorous fish. In addition, feeding habits of fish also influence As accumulation in different fish species. In this study, two typical food chains of the aquaculture ponds were selected for investigation: (1) omnivorous food chain (zooplankton, grass carp and bighead carp) and (2) predatory food chain (zooplankton, mud carp and mandarin fish). Significant linear relationships were obtained between log As and δ (15)N. The slope of the regression (-0.066 and -0.078) of the log transformed As concentrations and δ (15)N values, as biomagnifications power, indicated there was no magnification or diminution of As from lower trophic levels (zooplankton) to fish in the aquaculture ponds. Consumption of largemouth bass, northern snakehead and bighead carp might impose health risks of Hong Kong residents consuming these fish to the local population, due to the fact that its cancer risk (CR) value exceeded the upper limit of the acceptable risk levels (10(-4)) stipulated by the USEPA. PMID:23247527

  2. Hybrid Wing Body Aircraft System Noise Assessment with Propulsion Airframe Aeroacoustic Experiments

    NASA Technical Reports Server (NTRS)

    Thomas, Russell H.; Burley, Casey L.; Olson, Erik D.

    2010-01-01

    A system noise assessment of a hybrid wing body configuration was performed using NASA s best available aircraft models, engine model, and system noise assessment method. A propulsion airframe aeroacoustic effects experimental database for key noise sources and interaction effects was used to provide data directly in the noise assessment where prediction methods are inadequate. NASA engine and aircraft system models were created to define the hybrid wing body aircraft concept as a twin engine aircraft with a 7500 nautical mile mission. The engines were modeled as existing technology high bypass ratio turbofans. The baseline hybrid wing body aircraft was assessed at 22 dB cumulative below the FAA Stage 4 certification level. To determine the potential for noise reduction with relatively near term technologies, seven other configurations were assessed beginning with moving the engines two fan nozzle diameters upstream of the trailing edge and then adding technologies for reduction of the highest noise sources. Aft radiated noise was expected to be the most challenging to reduce and, therefore, the experimental database focused on jet nozzle and pylon configurations that could reduce jet noise through a combination of source reduction and shielding effectiveness. The best configuration for reduction of jet noise used state-of-the-art technology chevrons with a pylon above the engine in the crown position. This configuration resulted in jet source noise reduction, favorable azimuthal directivity, and noise source relocation upstream where it is more effectively shielded by the limited airframe surface, and additional fan noise attenuation from acoustic liner on the crown pylon internal surfaces. Vertical and elevon surfaces were also assessed to add shielding area. The elevon deflection above the trailing edge showed some small additional noise reduction whereas vertical surfaces resulted in a slight noise increase. With the effects of the configurations from the

  3. Assessment of Habitat, Fish Communities, and Streamflow Requirements for Habitat Protection, Ipswich River, Massachusetts, 1998-99

    USGS Publications Warehouse

    Armstrong, David S.; Richards, Todd A.; Parker, Gene W.

    2001-01-01

    The relations among stream habitat, fish communities, and hydrologic conditions were investigated in the Ipswich River Basin in northeastern Massachusetts. Data were assessed from 27 sites on the mainstem of the Ipswich River from July to September 1998 and from 10 sites on 5 major tributaries in July and August 1999. Habitat assessments made in 1998 determined that in a year with sustained streamflow for most of the summer, the Ipswich River contains diverse, high-quality aquatic habitat. Channel types are predominantly low gradient glides, pools, and impoundments, with a sandy streambed and a forest or shrub riparian zone. Features that provide fish habitat are located mostly along stream margins; these features include overhanging brush, undercut banks, exposed roots, and woody debris. These habitat features decrease in availability to aquatic communities with declining streamflows and generally become unavailable after streamflows drop to the point where the edge of water recedes from the stream banks.The mainstem and tributaries were sampled to determine fish species composition, relative abundance, and length frequency. Fish sampling indicates that the fish community in the Ipswich River is currently a warm-water fish community dominated by pond-type fish. However, historical temperature data, and survival of stocked trout in the mainstem Ipswich into late summer of 1998, indicate that the Ipswich River potentially could support cold-water fish species if adequate flows are maintained. Dominant fish species sampled in the mainstem Ipswich River were redfin pickerel (Esox americanus), American eel (Anguilla rostrata), and pumpkinseed (Lepomis gibbosus), which together represented 41, 22, and 10 percent, respectively, of 4,745 fish sampled. The fish communities of the mainstem and tributaries contained few fluvial-dependent or fluvial-specialist species (requiring flow), and were dominated by macrohabitat generalists (tolerant of low-flow, warm-water, and

  4. Assessment of asthmatic inflammation using hybrid fluorescence molecular tomography-x-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Ma, Xiaopeng; Prakash, Jaya; Ruscitti, Francesca; Glasl, Sarah; Stellari, Fabio Franco; Villetti, Gino; Ntziachristos, Vasilis

    2016-01-01

    Nuclear imaging plays a critical role in asthma research but is limited in its readings of biology due to the short-lived signals of radio-isotopes. We employed hybrid fluorescence molecular tomography (FMT) and x-ray computed tomography (XCT) for the assessment of asthmatic inflammation based on resolving cathepsin activity and matrix metalloproteinase activity in dust mite, ragweed, and Aspergillus species-challenged mice. The reconstructed multimodal fluorescence distribution showed good correspondence with ex vivo cryosection images and histological images, confirming FMT-XCT as an interesting alternative for asthma research.

  5. A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes (Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq)

    PubMed Central

    Recknagel, Hans; Elmer, Kathryn R.; Meyer, Axel

    2013-01-01

    Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F2 hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F2 offspring, we calculated a genome-wide mutation rate of 6.6 × 10−8 mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes. PMID:23316439

  6. Concentration and exposure assessment of mercury in commercial fish and other seafood marketed in Oman.

    PubMed

    Al-Mughairi, Sabra; Yesudhason, Poulose; Al-Busaidi, Moza; Al-Waili, Aaliah; Al-Rahbi, Waleed A K; Al-Mazrooei, Nashwa; Al-Habsi, Saoud H

    2013-07-01

    The results of this study present analytical data of the mercury levels in several fish and shellfish species to create awareness among individuals of the risks associated with consuming fish contaminated with mercury. Mercury concentrations varied from a mean of 0.02 mg/kg in Indian mackerel to 0.19 mg/kg in shark in both fresh and frozen fish, from 0.02 mg/kg in sardines to 0.18 mg/kg in skipjack tuna in canned fish, and from 0.02 mg/kg in Indian mackerel to 0.79 mg/kg in shark in dried fish. Shellfish contained a slightly higher amount of mercury than fresh or frozen fish with a mean of 0.09 mg/kg. Trophic position, followed by habitat, was the most important factors for variability in mercury concentrations in fish and shellfish. The maximum safe weekly intake (MSWI) values of mercury were significantly higher for herbivores than for carnivores. The MSWI value for total mercury in the case of consuming most (72%) fish species was more than 5 kg; however, the MSWI value was never more than 5 kg in most (66%) shellfish species. Risks were identified upon consumption of 120 g of dried shark when exceeding the provisional tolerable weekly intake threshold (1.6 μg/kg) for methylmercury. Therefore, fish-eating populations should reduce the quantity of dried shark to efficiently diminish the exposure to mercury. PMID:23701530

  7. Miller-Dieker syndrome associated with duplication of 17p13.3 confirmed by fluorescence in situ hybridization (FISH)

    SciTech Connect

    Li, S.; Tuck-Muller, C.M.; Martinez, J.E.

    1994-09-01

    Miller-Dieker syndrome is characterized by profound mental retardation, craniofacial abnormalities, and lissencephaly (smooth brain). Microscopic or submicroscopic deletions of the 17p13.3 region have been reported in Miller-Dieker patients. We report a patient with this syndrome in whom a duplication of the 17p13.3 region was detected by FISH. The 9-year-old female proband was referred because of features of Miller-Dieker syndrome: microcephaly, profound psychomotor retardation, seizures, characteristic facies, and lissencephaly shown by MRI studies. High-resolution G-banding failed to demonstrate an abnormality in chromosome 17. However, FISH analysis with the DNA probe (Oncor No. 5101) specific for Miller-Dieker region of chromosome 17p13.3 demonstrated duplication of this segment instead of the classic deletion. We know of no other report of Miller-Dieker syndrome associated with duplication of 17p13.3. The family study revealed normal chromosomes in both parents by cytogenetic and FISH analysis. Our investigation suggests that duplications, as well as deletions, of the 17p13.3 region are associated with the Miller-Dieker syndrome. The presence of deletions or duplications of the same chromosomal region in patients with features of Miller-Dieker syndrome suggests that its pathogenesis may be due to gene dosage effects.

  8. Bacterioplankton community structure in a maritime antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH).

    PubMed

    Pearce, D A

    2003-07-01

    The bacterioplankton community structure in Moss Lake, a maritime Antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on Signy Island in the South Orkney Islands. Bacterioplankton community structure was determined using a combination of direct counting of 4',6-diamidino-2-phenylindole (DAPI) stained cells, PCR amplification of 16S rRNA gene fragments, denaturing gradient gel electrophoresis (DGGE) and in situ hybridization with group-specific, fluorescently labeled oligonucleotide probes. Using PCR amplification of 16S rRNA gene fragments and DGGE, the bacterioplankton community composition was shown to be constant with vertical depth in the water column. Specific bacterioplankton species identified through cloning and sequencing the DGGE products obtained were Flavobacterium xinjiangensis (a Flavobacterium), Leptothrix discophora (a beta-Proteobacterium), and a number of uncultured groups: two beta-Proteobacteria, an unclassified Proteobacterium, three sequences from Actinobacteria, and a Cyanobacterium. Fluorescence in situ hybridization (FISH), however, demonstrated that there were minor but significant fluctuations in different groups of bacteria with vertical depth in the water column. It showed that the beta-Proteobacteria accounted for between 26.4 and 71.5%, the alpha-Proteobacteria 2.3-10.6%, the gamma-Proteobacteria 0-29.6%, and the Cytophaga-Flavobacterium group 1.8-23.5% of cells hybridizing to a universal probe. This study reports the first description of the community structure of an oligotrophic Antarctic freshwater lake as determined by PCR-dependent and PCR-independent molecular techniques. It also suggests that the bacterioplankton community of Moss Lake contains classes of bacteria known to be important in freshwater systems elsewhere in the world. PMID:12739078

  9. Exposure assessment of pregnant Portuguese women to methylmercury through the ingestion of fish: cross-sectional survey and biomarker validation.

    PubMed

    Nunes, Elisabete; Cavaco, Afonso; Carvalho, Cristina

    2014-01-01

    Methylmercury (MeHg) contamination is a critical public health problem in Portugal, where fish is an important component of the daily diet. The Portuguese are the third largest consumers in the world (after Japan and Iceland) but first in Europe. Prenatal exposure to MeHg is believed to be linked to fetal/child neurodevelopment and behavioral impairments due to the neurotoxicity of the compound. The objective of this study was to assess the exposure of pregnant Portuguese women to mercury (Hg) due to fish consumption, calculating the indices of risk and confirming exposure through analyses of a biomarker of exposure. The study consisted of a cross-sectional evaluation of 343 pregnant women recruited at their visit to two antenatal care units in Lisbon, Portugal. A food frequency questionnaire was used to estimate prenatal exposure. Total Hg levels in hair were analyzed by atomic absorption, in samples from 186 women. The average fish consumption was 3.1 meals per week. Median Hg level in the hair was 1.26 μg/g (range: 0.07-5.3 μg/g). The mean calculated risk index was 0.81; however, 28% of the pregnant women ingested levels above the provisional tolerable weekly intake (PTWI) level recommended by the World Health Organization (WHO; 1.6 mg/kg per body weight), indicating the possibility of risk due to MeHg exposure. Multiple linear regression analysis showed the risk index was reliably predicted from predatory fish species and number of fish meals consumed per week. Ingestion of black and silver scabbard fish as well as mixed predatory fish cooked in traditional dishes enhanced the toxicity risk. In conclusion, some exposure levels exceeded the reference value; therefore, nutritional counseling needs to be provided to populations at risk.

  10. Concentrations, bioaccumulation, and human health risk assessment of organochlorine pesticides and heavy metals in edible fish from Wuhan, China.

    PubMed

    Cui, Lili; Ge, Jing; Zhu, Yindi; Yang, Yuyi; Wang, Jun

    2015-10-01

    The objective of this study was to determine concentration and bioaccumulation of organochlorine pesticides and heavy metals in edible fish from Wuhan, China, in order to assess health risk to the human via fish consumption. Two edible fish species (Aristichthys nobilis and Hypophthalmichthys molitrix) were collected and analyzed for 11 organochlorine pesticides (OCPs) and eight heavy metals (HMs). Concentrations of ∑HCHs, ∑DDTs, and ∑OCPs in fish samples were in the range of 0.37-111.20, not detected (nd)-123.61, and 2.04-189.04 ng g(-1) (wet weight), respectively. Bioaccumulation factors (BAFs) of OCPs in bighead carp (A. nobilis) were higher than those in silver carp (H. molitrix). Concentrations of ∑HMs in bighead carp and silver carp were 352.48 and 345.20 mg kg(-1) (dw), respectively. Daily exposure of OCPs and HMs for consumers was estimated by comparing estimated daily intake (EDI) with different criteria. The results revealed that the EDIs in our study were all lower than those criteria. Target hazard quotient (THQ) and risk ratio (R) were used to evaluate non-carcinogenic and carcinogenic risks, respectively. As regard to non-carcinogenic effects of the contaminants, hazard quotients (THQ) of OCPs and HMs were both lower than 1.0, implying negligible non-carcinogenic risk via fish consumption in study area. Nevertheless, in view of carcinogenic effects of the contaminants, the total value of risk ratio (R) of OCPs was lower than the threshold of tolerable risk while the total value of risk ratio (R) of HMs was higher than the threshold of tolerable risk due to the high carcinogenic risk ratios of As and Cr, indicating high carcinogenic risks via fish consumption. The results demonstrated that HMs in edible fish from Wuhan, China, especially As and Cr required more attention than OCPs. PMID:26040264

  11. Assessing chronic fish health: An application to a case of an acute exposure to chemically treated crude oil.

    PubMed

    Mauduit, F; Domenici, P; Farrell, A P; Lacroix, C; Le Floch, S; Lemaire, P; Nicolas-Kopec, A; Whittington, M; Zambonino-Infante, J L; Claireaux, G

    2016-09-01

    Human alteration of marine ecosystems is substantial and growing. Yet, no adequate methodology exists that provides reliable predictions of how environmental degradation will affect these ecosystems at a relevant level of biological organization. The primary objective of this study was to develop a methodology to evaluate a fish's capacity to face a well-established environmental challenge, an exposure to chemically dispersed oil, and characterize the long-term consequences. Therefore, we applied high-throughput, non-lethal challenge tests to assess hypoxia tolerance, temperature susceptibility and maximal swimming speed as proxies for a fish's functional integrity. These whole animal challenge tests were implemented before (1 month) and after (1 month) juvenile European sea bass (Dicentrarchus labrax) had been acutely exposed (48h) to a mixture containing 0.08gL(-1) of weathered Arabian light crude oil plus 4% dispersant (Corexit© EC9500A), a realistic exposure concentration during an oil spill. In addition, experimental populations were then transferred into semi-natural tidal mesocosm ponds and correlates of Darwinian fitness (growth and survival) were monitored over a period of 4 months. Our results revealed that fish acutely exposed to chemically dispersed oil remained impaired in terms of their hypoxia tolerance and swimming performance, but not in temperature susceptibility for 1 month post-exposure. Nevertheless, these functional impairments had no subsequent ecological consequences under mildly selective environmental conditions since growth and survival were not impacted during the mesocosm pond study. Furthermore, the earlier effects on fish performance were presumably temporary because re-testing the fish 10 months post-exposure revealed no significant residual effects on hypoxia tolerance, temperature susceptibility and maximal swimming speed. We propose that the functional proxies and correlates of Darwinian fitness used here provide a useful

  12. Assessing chronic fish health: An application to a case of an acute exposure to chemically treated crude oil.

    PubMed

    Mauduit, F; Domenici, P; Farrell, A P; Lacroix, C; Le Floch, S; Lemaire, P; Nicolas-Kopec, A; Whittington, M; Zambonino-Infante, J L; Claireaux, G

    2016-09-01

    Human alteration of marine ecosystems is substantial and growing. Yet, no adequate methodology exists that provides reliable predictions of how environmental degradation will affect these ecosystems at a relevant level of biological organization. The primary objective of this study was to develop a methodology to evaluate a fish's capacity to face a well-established environmental challenge, an exposure to chemically dispersed oil, and characterize the long-term consequences. Therefore, we applied high-throughput, non-lethal challenge tests to assess hypoxia tolerance, temperature susceptibility and maximal swimming speed as proxies for a fish's functional integrity. These whole animal challenge tests were implemented before (1 month) and after (1 month) juvenile European sea bass (Dicentrarchus labrax) had been acutely exposed (48h) to a mixture containing 0.08gL(-1) of weathered Arabian light crude oil plus 4% dispersant (Corexit© EC9500A), a realistic exposure concentration during an oil spill. In addition, experimental populations were then transferred into semi-natural tidal mesocosm ponds and correlates of Darwinian fitness (growth and survival) were monitored over a period of 4 months. Our results revealed that fish acutely exposed to chemically dispersed oil remained impaired in terms of their hypoxia tolerance and swimming performance, but not in temperature susceptibility for 1 month post-exposure. Nevertheless, these functional impairments had no subsequent ecological consequences under mildly selective environmental conditions since growth and survival were not impacted during the mesocosm pond study. Furthermore, the earlier effects on fish performance were presumably temporary because re-testing the fish 10 months post-exposure revealed no significant residual effects on hypoxia tolerance, temperature susceptibility and maximal swimming speed. We propose that the functional proxies and correlates of Darwinian fitness used here provide a useful

  13. Assessment of general health of fishes collected at selected sites in the Great Lakes Basin In 2012

    USGS Publications Warehouse

    Mazik, Patricia M.; Braham, Ryan P.; Hahn, Cassidy M.; Blazer, Vicki

    2015-01-01

    The U. S. Fish and Wildlife Service received funding through the Great Lakes Restoration Initiative (GLRI) for an Early Warning Program to detect and identify emerging contaminants and to evaluate the effects of these contaminants on fish and wildlife. The U.S. Geological Survey (WV Cooperative Fish and Wildlife Research Unit and National Fish Health Research Laboratory, Leetown Science Center) developed and implemented a biological effects monitoring protocol to assist in this program. Fish collections and measurements of biomarkers of exposure in Fall 2010 and Spring 2011 occurred at individual sites within select Areas of Concern (AOCs). They provided an assessment of the utility of the suite of biomarkers and also identified sites for more in-depth analyses. Selected areas are characterized as areas with known emerging contaminants, sensitive or listed species, areas downstream from municipal wastewater discharges or receiving waters for industrial facilities, and/or areas susceptible to agricultural or urban contamination, or harbors or ports. The results of the 2010- 2011 studies were summarized in Blazer et al. 2014 a, b, c; Braham et al. in review and Blazer et al. in review.

  14. Refugia of marine fish in the northeast Atlantic during the last glacial maximum: concordant assessment from archaeozoology and palaeotemperature reconstructions

    NASA Astrophysics Data System (ADS)

    Kettle, A. J.; Morales-Muñiz, A.; Roselló-Izquierdo, E.; Heinrich, D.; Vøllestad, L. A.

    2011-03-01

    Archaeozoological finds of the remains of marine and amphihaline fish from the Last Glacial Maximum (LGM) ca. 21 ka ago show evidence of very different species ranges compared to the present. We have shown how an ecological niche model (ENM) based on palaeoclimatic reconstructions of sea surface temperature and bathymetry can be used to effectively predict the spatial range of marine fish during the LGM. The results indicate that the ranges of marine fish species now in northwestern Europe were displaced significantly southwards from the modern distribution, challenging an existing paradigm of marine glacial refugia. The model presents strong evidence that there was an invasion of important fish through the Straits of Gibraltar in glacial times, where they were exploited by Palaeolithic human populations around the western Mediterranean Sea. The ENM results are important for ongoing studies of molecular ecology that aim to assess marine glacial refugia from the genetic structure of living populations, and they pose questions about the genetic identity of vanished marine populations during the LGM. Economically, the approach may be used to understand how the ranges of exploited fish species may be displaced with the future climate warming. The research presents a challenge for future archaeozoological work to delimit the glacial refugia and to verify palaeoclimatic reconstructions based on deep-sea core records.

  15. Refugia of marine fish in the Northeast Atlantic during the Last Glacial Maximum: concordant assessment from archaeozoology and palaeotemperature reconstructions

    NASA Astrophysics Data System (ADS)

    Kettle, A. J.; Morales-Muñiz, A.; Roselló-Izquierdo, E.; Heinrich, D.; Vøllestad, L. A.

    2010-07-01

    Archaeozoological finds of the remains of marine and amphihaline fish from the Last Glacial Maximum (LGM) ca. 21 ka ago show evidence of very different species ranges compared to the present. We show how an ecological niche model (ENM) based on palaeoclimatic reconstructions of sea surface temperature and bathymetry can be used to effectively predict the spatial range of marine fish during the LGM. The results indicate that the ranges of marine fish species that are now in Northwestern Europe were almost completely displaced southward from the modern distribution. Significantly, there is strong evidence that there was an invasion of fish of current economic importance into the Western Mediterranean through the Straits of Gibraltar, where they were exploited by Palaeolithic human populations. There has been much recent interest in the marine glacial refugia to understand how the ranges of the economically important fish species will be displaced with the future climate warming. Recent ENM studies have suggested that species ranges may not have been displaced far southward during the coldest conditions of the LGM. However, archaeozoological evidence and LGM ocean temperature reconstructions indicate that there were large range changes, and certain marine species were able invade the Western Mediterranean. These findings are important for ongoing studies of molecular ecology that aim to assess marine glacial refugia from the genetic structure of living populations, and they pose questions about the genetic identity of vanished marine populations during the LGM. The research presents a challenge for future archaeozoological work to verify palaeoclimatic reconstructions and delimit the glacial refugia.

  16. Assessing the roles of environmental factors in coastal fish production in the northern Baltic Sea: a Bayesian network application.

    PubMed

    Uusitalo, Laura; Kuikka, Sakari; Kauppila, Pirkko; Söderkultalahti, Pirkko; Bäck, Saara

    2012-07-01

    Environmental conditions play a crucial role in the distribution and abundance of fish species in any area. Much research has been attributed to the requirements and tolerance limits of commercially exploited fish species. It is rare, however, that studies have been able to address the relative importance of potentially restrictive environmental factors; extensive enough to allow for estimation of the effect of several environmental factors through the fishes' life span. The coastline of Finland in the northern Baltic Sea offers a unique natural experimental setting that can be used to assess the relative importance of various environmental factors for the species occupying it. The area includes major variations in several crucial environmental factors: salinity, temperature regime, represented by winter ice duration, coastline characteristics, and eutrophic status. Furthermore, Finland has collected extensive and spatially representative data of water quality and environmental factors, as well as a long and extraordinarily spatially detailed data set of commercial catches of several fish species. In this article, we make an attempt to correlate the environmental data to the commercial catches of fish species, assuming that the commercial catches reflect, to some reasonable degree, the productivity of that species in that area (compared to other areas and combinations of environmental factors, not to other species). We use a Bayesian network approach to examine the sensitivity of the species to the environmental factors. PMID:21309077

  17. Fish acute toxicity syndromes and their use in the QSAR approach to hazard assessment

    SciTech Connect

    McKim, J.M.; Bradbury, S.P.; Niemi, G.J.

    1987-04-01

    Implementation of the Toxic Substances Control Act of 1977 creates the need to reliably establish testing priorities because laboratory resources are limited and the number of industrial chemicals requiring evaluation is overwhelming. The use of quantitative structure activity relationship (QSAR) models as rapid and predictive screening tools to select more potentially hazardous chemicals for in-depth laboratory evaluation has been proposed. Further implementation and refinement of quantitative structure-toxicity relationships in aqueous toxicology and hazard assessment requires the development of a mode-of-action database. With such a database, a qualitative structure-activity relationship can be formulated to assign the proper mode of action, and respective QSAR, to a given chemical structure. In this review, the development of fish acute toxicity syndromes (FATS), which are toxic-response sets based on various behavioral and physiological-biochemical measurements, and their projected use in the mode-of-action database are outlined. Using behavioral parameters monitored in the fathead minnow during acute toxicity testing, FATS associated with acetylcholinesterase (AChE) inhibitors and narcotics could be reliably predicted. However, compounds classified as oxidative phosphorylation uncouplers or stimulants could not be resolved. Refinement of this approach by using respiratory-cardiovascular responses in the rainbow trout, enabled FATS associated with AChE inhibitors, convulsants, narcotics, respiratory blockers, respiratory membrane irritants, and uncouplers to be correctly predicted.

  18. Fish liver and gill cells as cytogenotoxic indicators in assessment of water quality.

    PubMed

    Kaur, Rajbir; Dua, Anish

    2016-09-01

    The present study was aimed to evaluate the effect of municipal wastewater of Tung Dhab drain to freshwater fish Labeo rohita through genotoxicity assays. The idea is to explore and standardize procedures for assessment of toxic impact of pollutant at the cellular level in aquatic species. Hence, chronic, non-renewal toxicity tests were performed with sublethal concentrations (17.7, 26.6 and 35.4 %) of wastewater for exposure durations of 15, 30 and 60 days. Recovery experiments were also performed for duration of 60 days. Higher micronuclei (MN) and binuclei (BN) frequencies were recorded in fluorescently stained liver cells as compared to frequencies obtained for gill cells and erythrocytes. The induced frequencies of MN, BN and nuclear abnormalities (NA) were found in the following order: MN (liver cells) > BN (liver cells) > BN (gill cells) > MN (gill cells) > NA (erythrocytes) > MN (erythrocytes). The results pointed towards the mutagenic nature of water quality of Tung Dhab drain and recommend the incorporation of the liver and gill cells as biomarkers of cytotoxicity over erythrocytes in chronic experiments during water monitoring programs.

  19. Predictive models in hazard assessment of Great Lakes contaminants for fish

    USGS Publications Warehouse

    Passino, Dora R. May

    1986-01-01

    A hazard assessment scheme was developed and applied to predict potential harm to aquatic biota of nearly 500 organic compounds detected by gas chromatography/mass spectrometry (GC/MS) in Great Lakes fish. The frequency of occurrence and estimated concentrations of compounds found in lake trout (Salvelinus namaycush) and walleyes (Stizostedion vitreum vitreum) were compared with available manufacturing and discharge information. Bioconcentration potential of the compounds was estimated from available data or from calculations of quantitative structure-activity relationships (QSAR). Investigators at the National Fisheries Research Center-Great Lakes also measured the acute toxicity (48-h EC50's) of 35 representative compounds to Daphnia pulex and compared the results with acute toxicity values generated by QSAR. The QSAR-derived toxicities for several chemicals underestimated the actual acute toxicity by one or more orders of magnitude. A multiple regression of log EC50 on log water solubility and molecular volume proved to be a useful predictive model. Additional models providing insight into toxicity incorporate solvatochromic parameters that measure dipolarity/polarizability, hydrogen bond acceptor basicity, and hydrogen bond donor acidity of the solute (toxicant).

  20. Assessing juvenile native fish demographic responses to a steady flow experiment in a large regulated river

    USGS Publications Warehouse

    Finch, Colton G.; Pine, William E.; Yackulic, Charles B.; Dodrill, Michael J.; Yard, Michael D.; Gerig, Brandon S.; Coggins,, Lewis G.; Korman, Josh

    2016-01-01

    The Colorado River below Glen Canyon Dam, Arizona, is part of an adaptive management programme which optimizes dam operations to improve various resources in the downstream ecosystem within Grand Canyon. Understanding how populations of federally endangered humpback chub Gila cypha respond to these dam operations is a high priority. Here, we test hypotheses concerning temporal variation in juvenile humpback chub apparent survival rates and abundance by comparing estimates between hydropeaking and steady discharge regimes over a 3-year period (July 2009–July 2012). The most supported model ignored flow type (steady vs hydropeaking) and estimated a declining trend in daily apparent survival rate across years (99.90%, 99.79% and 99.67% for 2009, 2010 and 2011, respectively). Corresponding abundance of juvenile humpback chub increased temporally; open population model estimates ranged from 615 to 2802 individuals/km, and closed model estimates ranged from 94 to 1515 individuals/km. These changes in apparent survival and abundance may reflect broader trends, or simply represent inter-annual variation. Important findings include (i) juvenile humpback chub are currently surviving and recruiting in the mainstem Colorado River with increasing abundance; (ii) apparent survival does not benefit from steady fall discharges from Glen Canyon Dam; and (iii) direct assessment of demographic parameters for juvenile endangered fish are possible and can rapidly inform management actions in regulated rivers.

  1. A hierarchical spatial framework and database for the national river fish habitat condition assessment

    USGS Publications Warehouse

    Wang, L.; Infante, D.; Esselman, P.; Cooper, A.; Wu, D.; Taylor, W.; Beard, D.; Whelan, G.; Ostroff, A.

    2011-01-01

    Fisheries management programs, such as the National Fish Habitat Action Plan (NFHAP), urgently need a nationwide spatial framework and database for health assessment and policy development to protect and improve riverine systems. To meet this need, we developed a spatial framework and database using National Hydrography Dataset Plus (I-.100,000-scale); http://www.horizon-systems.com/nhdplus). This framework uses interconfluence river reaches and their local and network catchments as fundamental spatial river units and a series of ecological and political spatial descriptors as hierarchy structures to allow users to extract or analyze information at spatial scales that they define. This database consists of variables describing channel characteristics, network position/connectivity, climate, elevation, gradient, and size. It contains a series of catchment-natural and human-induced factors that are known to influence river characteristics. Our framework and database assembles all river reaches and their descriptors in one place for the first time for the conterminous United States. This framework and database provides users with the capability of adding data, conducting analyses, developing management scenarios and regulation, and tracking management progresses at a variety of spatial scales. This database provides the essential data needs for achieving the objectives of NFHAP and other management programs. The downloadable beta version database is available at http://ec2-184-73-40-15.compute-1.amazonaws.com/nfhap/main/.

  2. Are the Most Plastic Species the Most Abundant Ones? An Assessment Using a Fish Assemblage

    PubMed Central

    Vidal, Nicolás; Zaldúa, Natalia; D'Anatro, Alejandro; Naya, Daniel E.

    2014-01-01

    Few studies have evaluated phenotypic plasticity at the community level, considering, for example, plastic responses in an entire species assemblage. In addition, none of these studies have addressed the relationship between phenotypic plasticity and community structure. Within this context, here we assessed the magnitude of seasonal changes in digestive traits (seasonal flexibility), and of changes during short-term fasting (flexibility during fasting), occurring in an entire fish assemblage, comprising ten species, four trophic levels, and a 37-fold range in body mass. In addition, we analyzed the relationship between estimates of digestive flexibility and three basic assemblage structure attributes, i.e., species trophic position, body size, and relative abundance. We found that: (1) Seasonal digestive flexibility was not related with species trophic position or with body size; (2) Digestive flexibility during fasting tended to be inversely correlated with body size, as expected from scaling relationships; (3) Digestive flexibility, both seasonal and during fasting, was positively correlated with species relative abundance. In conclusion, the present study identified two trends in digestive flexibility in relation to assemblage structure, which represents an encouraging departure point in the search of general patterns in phenotypic plasticity at the local community scale. PMID:24651865

  3. Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding.

    PubMed

    Knebelsberger, Thomas; Dunz, Andreas R; Neumann, Dirk; Geiger, Matthias F

    2015-05-01

    This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour-Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.

  4. Assessing reproductive status in elasmobranch fishes using steroid hormones extracted from skeletal muscle tissue

    PubMed Central

    Prohaska, Bianca K.; Tsang, Paul C. W.; Driggers, William B.; Hoffmayer, Eric R.; Wheeler, Carolyn R.; Brown, A. Christine; Sulikowski, James A.

    2013-01-01

    Elasmobranch fishes (sharks, skates, and rays) are particularly susceptible to anthropogenic threats, making a thorough understanding of their life history characteristics essential for proper management. Historically, elasmobranch reproductive data have been collected by lethal sampling, an approach that is problematic for threatened and endangered species. However, recent studies have demonstrated that non-lethal approaches can be as effective as lethal ones for assessment of the reproductive status of an animal. For example, plasma has been used to examine concentrations of steroid hormones. Additionally, skeletal muscle tissue, which can be obtained non-lethally and with minimal stress, can also be used to quantify concentrations of steroid hormones. Skeletal muscle progesterone, testosterone, and estradiol concentrations were determined to be statistically significant indicators of reproductive status in the oviparous Leucoraja erinacea, the yolk-dependent viviparous Squalus acanthias, and the yolk-sac placental viviparous Rhizoprionodon terraenovae. The results of the present study demonstrate that steroid hormones present in non-lethally harvested skeletal muscle tissue can be used as reliable indicators of reproductive status in elasmobranchs. PMID:27293612

  5. Survey design for lakes and reservoirs in the United States to assess contaminants in fish tissue

    EPA Science Inventory

    The National Lake Fish Tissue Study (NLFTS) was the first survey of fish contamination in lakes and reservoirs in the 48 conterminous states based on probability survey design. This study included the largest set (268) of persistent, bioaccumulative, and toxic (PBT) chemicals ev...

  6. The Application of Traits-Based Assessment Approaches to Estimate the Effects of Hydroelectric Turbine Passage on Fish Populations

    SciTech Connect

    Cada, Glenn F; Schweizer, Peter E

    2012-04-01

    ) found useful turbine passage survival data for only 30 species. Tests of advanced hydropower turbines have been limited to seven species - Chinook and coho salmon, rainbow trout, alewife, eel, smallmouth bass, and white sturgeon. We are investigating possible approaches for extending experimental results from the few tested fish species to predict turbine passage survival of other, untested species (Cada and Richmond 2011). In this report, we define the causes of injury and mortality to fish tested in laboratory and field studies, based on fish body shape and size, internal and external morphology, and physiology. We have begun to group the large numbers of unstudied species into a small number of categories, e.g., based on phylogenetic relationships or ecological similarities (guilds), so that subsequent studies of a few representative species (potentially including species-specific Biological Index Testing) would yield useful information about the overall fish community. This initial effort focused on modifying approaches that are used in the environmental toxicology field to estimate the toxicity of substances to untested species. Such techniques as the development of species sensitivity distributions (SSDs) and Interspecies Correlation Estimation (ICE) models rely on a considerable amount of data to establish the species-toxicity relationships that can be extended to other organisms. There are far fewer studies of turbine passage stresses from which to derive the turbine passage equivalent of LC{sub 50} values. Whereas the SSD and ICE approaches are useful analogues to predicting turbine passage injury and mortality, too few data are available to support their application without some form of modification or simplification. In this report we explore the potential application of a newer, related technique, the Traits-Based Assessment (TBA), to the prediction of downstream passage mortality at hydropower projects.

  7. Assessing a dual-frequency identification sonars' fish-counting accuracy, precision, and turbid river range capability.

    PubMed

    Maxwell, Suzanne L; Gove, Nancy E

    2007-12-01

    Accurately assessing migrating salmon populations in turbid rivers with hydroacoustics is challenging. Using single, dual, or split-beam sonars, difficulties occur fitting acoustic beams between the river's narrow boundaries, distinguishing fish from nonfish echoes, and resolving individual fish at high densities. To address these issues, the fish-counting capability of a dual-frequency identification sonar (DIDSON), which produces high resolution, video-like images, was assessed. In a clear river, fish counts generated from a DIDSON, an echo counter, split-beam sonar, and video were compared to visual counts from a tower, a method frequently used to ground-truth sonars. The DIDSON and tower counts were very similar and showed the strongest agreement and least variability compared to the other methods. In a highly turbid river, the DIDSON's maximum detection range for a 10.16 cm spherical target was 17 m, less than absorption and wave spreading losses predict, and 26 m in clear water. Unlike tower and video methods, the DIDSON was not limited by surface disturbances or turbidity. DIDSON advantages over other sonars include: better target resolution; wider viewing angle; better coverage of the water column; accurate direction of travel; and simpler to aim and operate.

  8. Computer-aided lung nodule detection and assessment by using a hybrid PET/CT scanner

    NASA Astrophysics Data System (ADS)

    Franquiz, Juan; Vaddadi, Sulohita; Soler, George

    2004-04-01

    In this study we present an automatic algorithm for the detection and functional assessment of lung nodules on three-dimensional slices derived from a hybrid PET/CT scanner. In addition to differentiate malignant from benign lesions, the algorithm was mainly designed for assessing the response of lung cancer to therapy. The automated algorithm involves three major steps. First, the lung region is segmented from low resolution multislice CT images. Once the lung is segmented on CT images, a search of seed pixels with maximum activity of 18FDG is undertaken into the lung regions of the electronically registered PET images. A 3D growing algorithm identified the lesion pixels around the maximum 18FDG activity seed pixels. In the third step, the total activity (Bq), concentration (Bq/ml), metabolically active volume (ml) and standard uptake values (SUV) were calculated for lesions on PET images. A threshold and filtering method was applied to high resolution CT scans to determine the CT volume of these lesions identified on PET images. All PET images were corrected for attenuation and partial volume effect and cross calibrated with a standard activity measured in a dose calibrator. Studies were performed using a hybrid PET/CT Discovery LS (GE Medical Systems). The feasibility and robustness of the automatic algorithm was demonstrated in studies with a lung-chest phantom and by retrospective analysis of clinical studies.

  9. Phenotypic consequences of a mosaic marker chromosome identified by fluorescence in situ hybridization (FISH) as being derived from chromosome 16

    SciTech Connect

    Ray, J.H.; Zhou, X.; Pletcher, B.A.

    1994-09-01

    De novo marker chromosomes are detected in 1 in 2500 amniotic fluid samples and are associated with a 10-15% risk for phenotypic abnormality. FISH can be utilized as a research tool to identify the origins of marker chromosomes. The phenotypic consequences of a marker chromosome derived from the short arm of chromosome 16 are described. A 26-year-old woman underwent amniocentesis at 28 weeks gestation because of a prenatally diagnosed tetralogy of Fallot. Follow-up ultrasounds also showed ventriculomegaly and cleft lip and palate. 32 of 45 cells had the karyotype 47,XY,+mar; the remaining cells were 46,XY. The de novo marker chromosome was C-band positive and non-satellited and failed to stain with distamycin A/DAPI. At birth the ultrasound findings were confirmed and dysmorphic features and cryptorchidism were noted. Although a newborn blood sample contained only normal cells, mosaicism was confirmed in 2 skin biopsies. FISH using whole-chromosome painting and alpha-satellite DNA probes showed that the marker chromosome had originated from chromosome 16. As proximal 16q is distamycin A/DAPI positive, the marker is apparently derived from proximal 16p. At 15 months of age, this child is hypotonic, globally delayed and is gavage-fed. His physical examination is significant for microbrachycephaly, a round face, sparse scalp hair, ocular hypertelorism, exotropia, a flat, wide nasal bridge and tip, mild micrognathia, and tapered fingers with lymphedema of hands and feet. Inguinal hernias have been repaired. His features are consistent with those described for patients trisomic for most or all of the short arm of chromosome 16. Marker chromosomes derived from the short arm of chromosome 16 appear to have phenotypic consequences. As the origin of more marker chromosomes are identified using FISH, their karyotype/phenotype correlations will become more apparent, which will permit more accurate genetic counseling.

  10. Assessment of the health status of wild fish inhabiting a cotton basin heavily impacted by pesticides in Benin (West Africa).

    PubMed

    Agbohessi, Prudencio T; Imorou Toko, Ibrahim; Ouédraogo, Alfred; Jauniaux, Thierry; Mandiki, S N M; Kestemont, Patrick

    2015-02-15

    , vacuolation and melano-macrophagic centers. The histopathology of the liver revealed the presence of necrosis, hypertrophic hepatocytes, foci of vacuolation, glycogen depletion and hemosiderin. An assessment of the general health of the fish indicated that all of the sampled fish from the polluted sites were in poorer health compared with those from the reference site but that the African catfish appeared much more affected than the Guinean tilapia, regardless of the sex and season. In conclusion, the overall results indicated that agricultural pesticides significantly impair the endocrine regulation of fish living in the Beninese cotton basin and that this would most likely be one of the causes of the severe damage observed in the liver and gonads and the reduced health condition.

  11. Real-time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers.

    PubMed

    Godinho, Raquel; López-Bao, José Vicente; Castro, Diana; Llaneza, Luís; Lopes, Susana; Silva, Pedro; Ferrand, Nuno

    2015-03-01

    Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.

  12. Real-time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers.

    PubMed

    Godinho, Raquel; López-Bao, José Vicente; Castro, Diana; Llaneza, Luís; Lopes, Susana; Silva, Pedro; Ferrand, Nuno

    2015-03-01

    Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations. PMID:25132482

  13. [A Case of Xp.11.2 Traslocational Renal Cell Carcinoma Diagnosed by Fluorescence in Situ Hybridization (FISH)].

    PubMed

    Iinuma, Koji; Kojima, Keitaro; Okamoto, Kiyohisa; Yuhara, Kazuya

    2016-08-01

    A 72-year-old woman was referred to our hospital with complaints of macro-hematuria. The radiographic evaluation including computed tomography (CT) and magnetic resonance imaging (MRI) suggested it to be renal cell carcinoma (RCC) in her right kidney. She underwent laparoscopic nephrectomy. We diagnosed her with renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion, based on pathological findings and break apart of transcription factor E3 (TFE3)by fluorescence in situ hybridization. She was free of recurrence at 8 months postoperatively. PMID:27624107

  14. A retrospective on hydroacoustic assessment of fish passage in Alaskan rivers

    NASA Astrophysics Data System (ADS)

    Burwen, Debby; Fleischman, Steve; Maxwell, Suzanne; Pfisterer, Carl

    2005-04-01

    The Alaska Department of Fish and Game (ADFG) has enumerated fish stocks in rivers for over 30 years using a variety of acoustic technologies including single-, dual-, and split-beam sonar. Most recently, ADFG has evaluated a relatively new sonar technology at several sites in Alaska to determine its applicability to counting migrating fish in rivers. The new system, called a Dual frequency IDentification SONar (DIDSON), is a high-definition imaging sonar designed and manufactured by the University of Washington's Applied Physics Lab for military applications such as diver detection and underwater mine identification. Results from experiments conducted in 2002-2004 indicate that DIDSON provides significant improvements in our ability to detect, track, and determine the direction of travel of migrating fish in rivers. One of the most powerful uses of the DIDSON has been to combine its camera-like images of fish swimming behavior with corresponding split-beam data. These linked datasets have allowed us to evaluate the effects of fish orientation and swimming behavior on echo shape parameters that have proven useful in the classification of certain fish species.

  15. Assessment of elemental contaminants in water and fish samples from Aba river.

    PubMed

    Alinnor, I J

    2005-03-01

    The elemental contaminants in water and fish samples from Aba river were studied. The elements studied were Zn, Ni, As, Hg, Co and Mn. Three water samples and three samples of different fish species were collected from different locations in the river. The water and fish samples were analysed for elemental contaminants using Atomic Absorption Spectrophotometer (AAS). The elemental toxicants Zn and Mn were identified in appreciable amounts in fresh fish species namely, Lates niloticus and Oriochronis niloticus, of mean values 8.012 ppm and 0.861 ppm, respectively. The analysis also shows arsenic concentration of mean value 0.01 ppm in Lates niloticus. The analysis of frozen fish samples purchased from the Waterside market located near the river shows Ni and Hg levels of mean values 0.83 ppm and 0.02 ppm, respectively. The levels of elemental contaminants As, Zn, Hg and Mn from the water samples have mean values 0.082 ppm, 11.284 ppm, 0.201 ppm and 1.024 ppm, respectively. There are five industries that discharge waste products into Aba river. In view of this, there is a need to determine the level of pollution of the river, since the inhabitants depend on the river for their drinking water, fishing and other domestic uses. This study is aimed at determining the level of heavy metal toxicants in fish and water samples from the river. The effect of these elemental contaminants and the associated health hazards were examined.

  16. Comparative assessment of genetic and morphological variation at an extensive hybrid zone between two wild cats in southern Brazil.

    PubMed

    Trigo, Tatiane C; Tirelli, Flávia P; de Freitas, Thales R O; Eizirik, Eduardo

    2014-01-01

    Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species.

  17. Comparative Assessment of Genetic and Morphological Variation at an Extensive Hybrid Zone between Two Wild Cats in Southern Brazil

    PubMed Central

    Trigo, Tatiane C.; Tirelli, Flávia P.; de Freitas, Thales R. O.; Eizirik, Eduardo

    2014-01-01

    Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species. PMID:25250657

  18. Assessing genetic diversity of Brazilian reef fishes by chromosomal and DNA markers.

    PubMed

    Galetti, Pedro Manoel; Molina, Wagner Franco; Affonso, Paulo Roberto A M; Aguilar, Cecília Teixeira

    2006-01-01

    Little is known on genetics of Brazilian coral reef fish and most of this information is limited to chromosome characterization of major representative species. The diploid chromosome number in marine fish varies from 2n= 22-26 to 2n = 240-260. Despite of this apparent diversity, most studied marine species have a diploid complement with 48 acrocentric chromosomes. This latter trend is mostly observed among Perciformes, an important major taxon of coral reef fishes. Studies in the families Pomacentridae, Pomacanthidae and Chaetodontidae, for example, have shown a common karyotype pattern entirely formed by 48 uniarmed chromosomes. However, rare numerical and structural chromosome polymorphisms and cryptic chromosome rearrangements involving heterochromatin segments and/or nucleolar organizing sites have been reported among such fishes. Although new chromosome forms can contribute to the establishment of genetically isolated populations, their role in reef fish speciation at marine realm still is an open question. More recently, genomic DNA analyses using RAPD and microsatellites, and sequencing and RFLP of mitochondrial DNA have increasingly been used in Atlantic reef fish species. Genetic homogeneity over wide geographical ranges has been reported for different fish groups, in contrast to several cases of population substructuring related to environmental constraints or evolutionary history. Amazonas outflow and upwelling on the Southeastern coast of Brazil are believed to be strong barriers to dispersal of some reef species. Moreover, it is suggested that the pattern of speciation and population structure at South Atlantic is quite distinctive from Pacific Ocean, even when comparing closely related taxa. Further genetic studies are strongly encouraged in Brazilian reef fishes in order to provide a reliable scenario of the genetic structure in this important and diverse fish group.

  19. Assessing effects of stocked trout on nongame fish assemblages in southern Appalachian Mountain streams

    USGS Publications Warehouse

    Weaver, D.; Kwak, Thomas J.

    2013-01-01

    Fisheries managers are faced with the challenge of balancing the management of recreational fisheries with that of conserving native species and preserving ecological integrity. The negative effects that nonnative trout species exert on native trout are well documented and include alteration of competitive interactions, habitat use, and production. However, the effects that nonnative trout may exert on nongame fish assemblages are poorly understood. Our objectives were to quantify the effects of trout stocking on native nongame fish assemblages intensively on one newly stocked river, the North Toe River, North Carolina, and extensively on other southern Appalachian Mountain streams that are annually stocked with trout. In the intensive study, we adopted a before-after, control-impact (BACI) experimental design to detect short-term effects on the nongame fish assemblage and found no significant differences in fish density, species richness, species diversity, or fish microhabitat use associated with trout stocking. We observed differences in fish microhabitat use between years, however, which suggests there is a response to environmental changes, such as the flow regime, which influence available habitat. In the extensive study, we sampled paired stocked and unstocked stream reaches to detect long-term effects from trout stocking; however, we detected no differences in nongame fish density, species richness, species diversity, or population size structure between paired sites. Our results revealed high inherent system variation caused by natural and anthropogenic factors that appear to overwhelm any acute or chronic effect of stocked trout. Furthermore, hatchery-reared trout may be poor competitors in a natural setting and exert a minimal or undetectable impact on native fish assemblages in these streams. These findings provide quantitative results necessary to assist agencies in strategic planning and decision making associated with trout fisheries, stream

  20. Organochlorine pesticides in fish from Taihu Lake, China, and associated human health risk assessment.

    PubMed

    Wang, Deqing; Yu, Yingxin; Zhang, Xinyu; Zhang, Dongping; Zhang, Shaohuan; Wu, Minghong

    2013-12-01

    Because contaminants and nutrients always coexist in fish, the risk from contaminants and the benefit from nutrients, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are also concomitant via fish consumption. To investigate the risk and benefit via fish consumption, concentrations of dichlorodiphenyltrichloroethane and its metabolites (DDTs), and hexachlorocyclohexanes (HCHs) in the whole- and portion-muscles of fish from Taihu Lake, China, were measured. Based on the contaminant data and nutrients from our previous study, and the associated risk and benefit via fish consumption were estimated. The concentrations of DDTs and HCHs in the whole-muscles ranged from 7.8 × 10² to 3.4×10³ pg g⁻¹ ww, and from 67.3 to 300 pg g⁻¹ ww, respectively. Of DDTs and HCHs measured, p,p'-DDE and β-HCH were respectively the most abundant pesticides. The composition profiles of DDTs and HCHs suggested that the pesticides were mainly historical residues. The benefit-risk quotient (BRQ) of EPA+DHA vs. POPs (persistent organic pollutants including data of DDTs, HCHs, and those of polychlorinated biphenyls and polybrominated diphenyl ethers cited from our previous study) via consumption of fish from Taihu Lake was calculated. As a result, to achieve the recommended EPA+DHA intake of 250 mg d⁻¹ for a healthy adult, the consumption of most fish species from the lake can cause cancer and non-cancer risks. However, the fish consumption at the rates of 44.9 g d⁻¹ by Chinese would not lead to the risks for most of the species. The results also suggested that the risk of consuming silver carp was generally lower than other fish species, and those of dorsal muscles were lower than ventral and tail muscles.

  1. Empirical assessment of fish introductions in a subtropical wetland: An evaluation of contrasting views

    USGS Publications Warehouse

    Trexler, J.C.; Loftus, W.F.; Jordan, F.; Lorenz, J.J.; Chick, J.H.; Kobza, Robert M.

    2000-01-01

    We summarized data from eight quantitative fish surveys conducted in southern Florida to evaluate the distribution and relative abundance of introduced fishes across a variety of habitats. These surveys encompassed marsh and canal habitats throughout most of the Everglades region, including the mangrove fringe of Florida Bay. Two studies provided systematically collected density information over a 20-year period, and documented the first local appearance of four introduced fishes based on their repeated absence in prior surveys. Those species displayed a pattern of rapid population growth followed by decline, then persistence at lower densities. Estuarine areas in the southern Everglades, characterized by natural tidal creeks surrounded by mangrove-dominated marshes, and canals held the largest introduced-fish populations. Introduced fishes were also common, at times exceeding 50% of the fish community, in solution holes that serve as dry-season refuges in short-hydroperiod rockland habitats of the eastern Everglades. Wet prairies and alligator ponds distant from canals generally held few individuals of introduced fishes. These patterns suggest that the introduced fishes in southern Florida at present may not be well-adapted to persist in freshwater marshes of the Everglades, possibly because of an interaction of periodic cold-temperature stress and hydrologic fluctuation. Our analyses indicated low densities of these fishes in central or northern Everglades wet-prairie communities, and, in the absence of experimental data, little evidence of biotic effects in this spatially extensive habitat. There is no guarantee that this condition will be maintained, especially under the cumulative effects of future invasions or environmental change.

  2. Assessment of Committed Effective Dose due to consumption of Red Sea coral reef fishes collected from the local market (Sudan).

    PubMed

    Hassona, Rifaat K; Sam, A K; Osman, O I; Sirelkhatim, D A; LaRosa, J

    2008-04-15

    An assessment of Committed Effective Dose (CED) due to consumption of Red Sea fish containing (210)Po and (137)Cs was performed for 23 different marine fish samples collected from the local market at Port Sudan. The fish were classified according to their feeding habits into three categories: carnivores, herbivores, and omnivores. Measured activity concentrations of (210)Po were found in the ranges 0.25-6.42 (carnivores), 0.7-5 (omnivores) and 1.5-3.8 (herbivores) Bq/kg fresh weight. In the same study, activity concentrations of Cs-137 were determined to be in the ranges 0.1-0.46 (carnivores), 0.09-0.35 (omnivores) and 0.09-0.32 (herbivores) Bq/kg fresh weight, which were several times lower than those of (210)Po. Appropriate conversion factors were used to derive the CED, which was found to be 0.012, 0.01 and 0.01 (microSv/yr) in carnivores, omnivores and herbivores, respectively, for (137)Cs. This contributes about 0.4% of the total dose exclusively by ingestion of fish. For (210)Po, it was found to be 3.47, 4.81 and 4.14 (microSv/yr) in carnivores, omnivores and herbivores, respectively, which represents 99.6% of the total dose (exclusively by ingestion of fish). The results of CED calculations suggest that the dose received by the Sudanese population from the consumption of marine fish is rather small and that the contribution of (137)Cs is negligible compared to (210)Po.

  3. Exposure and effects assessment of persistent organohalogen contaminants in arctic wildlife and fish.

    PubMed

    Letcher, Robert J; Bustnes, Jan Ove; Dietz, Rune; Jenssen, Bjørn M; Jørgensen, Even H; Sonne, Christian; Verreault, Jonathan; Vijayan, Mathilakath M; Gabrielsen, Geir W

    2010-07-01

    Persistent organic pollutants (POPs) encompass an array of anthropogenic organic and elemental substances and their degradation and metabolic byproducts that have been found in the tissues of exposed animals, especially POPs categorized as organohalogen contaminants (OHCs). OHCs have been of concern in the circumpolar arctic for decades. For example, as a consequence of bioaccumulation and in some cases biomagnification of legacy (e.g., chlorinated PCBs, DDTs and CHLs) and emerging (e.g., brominated flame retardants (BFRs) and in particular polybrominated diphenyl ethers (PBDEs) and perfluorinated compounds (PFCs) including perfluorooctane sulfonate (PFOS) and perfluorooctanic acid (PFOA) found in Arctic biota and humans. Of high concern are the potential biological effects of these contaminants in exposed Arctic wildlife and fish. As concluded in the last review in 2004 for the Arctic Monitoring and Assessment Program (AMAP) on the effects of POPs in Arctic wildlife, prior to 1997, biological effects data were minimal and insufficient at any level of biological organization. The present review summarizes recent studies on biological effects in relation to OHC exposure, and attempts to assess known tissue/body compartment concentration data in the context of possible threshold levels of effects to evaluate the risks. This review concentrates mainly on post-2002, new OHC effects data in Arctic wildlife and fish, and is largely based on recently available effects data for populations of several top trophic level species, including seabirds (e.g., glaucous gull (Larus hyperboreus)), polar bears (Ursus maritimus), polar (Arctic) fox (Vulpes lagopus), and Arctic charr (Salvelinus alpinus), as well as semi-captive studies on sled dogs (Canis familiaris). Regardless, there remains a dearth of data on true contaminant exposure, cause-effect relationships with respect to these contaminant exposures in Arctic wildlife and fish. Indications of exposure effects are largely

  4. [Evaluation of peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method in the identifi cation of Candida species isolated from blood cultures].

    PubMed

    Aydemir, Gonca; Koç, Ayşe Nedret; Atalay, Mustafa Altay

    2016-04-01

    In recent years, increased number of patients who are hospitalized in intensive care units, received immunosuppressive therapy and treated with broad-spectrum antibiotics that can lead an increase in the incidence of systemic candidiasis. In these patients, the most common clinical manifestation is candidemia. Since the identification of Candida species isolated from blood cultures is time consuming by conventional (morphological and biochemical) methods, rapid, reliable and accurate methods are needed. For this purpose novel systems have been developed to identify the agent directly. The aim of this study was to evaluate the peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method for the identification of Candida species by comparing with the conventional methods. A total of 50 patients who were admitted to Erciyes University Medical Faculty Hospital clinics and followed with prediagnosis of systemic fungal infections whose blood cultures were positive for the yeasts between July 2011 and July 2012 were included in the study. The conventional identification of Candida isolates was performed by considering macroscopic and microscopic morphology, germ tube test, cycloheximide sensitivity, urease activity and carbohydrate assimilation patterns with API 20C AUX (bioMerieux, France) test. PNA FISH method was conducted by the use of a commercial kit namely Yeast Traffic Light(®) PNA FISH (AdvanDx, USA). According to morphological and biochemical characteristics (conventional methods), 19 (38%) out of 50 Candida isolates were identified as C.albicans, 12 (24%) as C.glabrata, five (10%) as C.parapsilosis, five (10%) as C.kefyr, four (8%) as C.krusei, two (4%) as C.guilliermondii, two (4%) as C.tropicalis and one (2%) as C.lusitaniae. On the other hand, 24 (48%) of the isolates were identified as C.albicans/C.parapsilosis (with green fluorescence), 16 (32%) as C.glabrata/C.krusei (with red fluorescence) and one (%2) as C.tropicalis (with yellow

  5. [Evaluation of peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method in the identifi cation of Candida species isolated from blood cultures].

    PubMed

    Aydemir, Gonca; Koç, Ayşe Nedret; Atalay, Mustafa Altay

    2016-04-01

    In recent years, increased number of patients who are hospitalized in intensive care units, received immunosuppressive therapy and treated with broad-spectrum antibiotics that can lead an increase in the incidence of systemic candidiasis. In these patients, the most common clinical manifestation is candidemia. Since the identification of Candida species isolated from blood cultures is time consuming by conventional (morphological and biochemical) methods, rapid, reliable and accurate methods are needed. For this purpose novel systems have been developed to identify the agent directly. The aim of this study was to evaluate the peptide nucleic acid fluorescent in situ hybridization (PNA FISH) method for the identification of Candida species by comparing with the conventional methods. A total of 50 patients who were admitted to Erciyes University Medical Faculty Hospital clinics and followed with prediagnosis of systemic fungal infections whose blood cultures were positive for the yeasts between July 2011 and July 2012 were included in the study. The conventional identification of Candida isolates was performed by considering macroscopic and microscopic morphology, germ tube test, cycloheximide sensitivity, urease activity and carbohydrate assimilation patterns with API 20C AUX (bioMerieux, France) test. PNA FISH method was conducted by the use of a commercial kit namely Yeast Traffic Light(®) PNA FISH (AdvanDx, USA). According to morphological and biochemical characteristics (conventional methods), 19 (38%) out of 50 Candida isolates were identified as C.albicans, 12 (24%) as C.glabrata, five (10%) as C.parapsilosis, five (10%) as C.kefyr, four (8%) as C.krusei, two (4%) as C.guilliermondii, two (4%) as C.tropicalis and one (2%) as C.lusitaniae. On the other hand, 24 (48%) of the isolates were identified as C.albicans/C.parapsilosis (with green fluorescence), 16 (32%) as C.glabrata/C.krusei (with red fluorescence) and one (%2) as C.tropicalis (with yellow

  6. Population-level assessments should be emphasized over community/ecosystem-level assessments. Environmental Sciences Division Publication No. 1535. [Concerning the impact of power plants on fish populations

    SciTech Connect

    Van Winkle, W

    1980-01-01

    Arguments are presented in favor of emphasizing population-level assessments over community/ecosystem-level assessments. The two approaches are compared on each of four issues: (1) the nature of entrainment/impingement impacts; (2) the ability to forecast reliably for a single fish population as contrasted to the ability to forecast for an aquatic community or ecosystem; (3) practical considerations involving money, manpower, time, and the need to make decisions; and (4) the nature of societal and economic concerns. The conclusion on each of these four issues is that population-level assessments provide the optimal approach for evaluating the effects of entrainment and impingement mortality.

  7. Results of EPA’s Assessment of Fish Tissue from U.S. Rivers for Selenium with Implications for Aquatic Life and Human Health

    EPA Science Inventory

    EPA’s Office of Water and Office of Research and Development collaborated to conduct the first statistically based survey of contaminants in fish fillets from U.S. rivers. This national fish survey was conducted under the framework of EPA’s National Rivers and Streams Assessment ...