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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. Hybrid Breakdown in Cichlid Fish

    PubMed Central

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

    2015-01-01

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

  3. 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.

  4. Distant hybridization leads to different ploidy fishes.

    PubMed

    Liu, ShaoJun

    2010-04-01

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

  5. 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.

  6. 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…

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

    PubMed

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

    2005-03-07

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

  8. 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.

  9. Rapid genomic DNA changes in allotetraploid fish hybrids.

    PubMed

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

    2015-06-01

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

  10. Ancient hybridization fuels rapid cichlid fish adaptive radiations

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2016-01-01

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

  12. 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.

  13. 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

  14. 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.

  15. 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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

    Sanguedolce, Francesca; Bufo, Pantaleo

    2015-03-01

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

  18. Probabilistic assessment of uncertain adaptive hybrid composites

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

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

    PubMed

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

    2007-06-01

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

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

    PubMed

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

    2011-05-01

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

  1. 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.

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

    PubMed

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

    2016-04-01

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

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

    PubMed

    Kuo, P L; Guo, H R

    2001-05-01

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

  4. 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.

  5. 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.

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

    PubMed

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

    2012-12-28

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

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

    USGS Publications Warehouse

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

    1994-01-01

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

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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.

  16. 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.

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

    PubMed

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

    2015-01-01

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

  18. 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.

  19. 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.

  20. 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.

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

    PubMed Central

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. 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

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

    PubMed

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

    2017-03-01

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

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

    PubMed

    Zeller, Perrine; Ploux, Olivier; Méjean, Annick

    2016-03-01

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

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

    PubMed

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

    2016-02-23

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

  7. 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)

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

    PubMed

    Dolan, Michelle; Snover, Dale

    2005-05-01

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

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

    PubMed

    Albertson, R Craig; Kocher, Thomas D

    2005-03-01

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

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

    PubMed

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

    2011-12-02

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

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

    PubMed

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

    2007-01-01

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

  12. 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.

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

    PubMed

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

    2017-01-17

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

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

    PubMed Central

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

    2016-01-01

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

  15. 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...

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

    PubMed

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

    2003-02-01

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

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

    SciTech Connect

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

    1991-01-01

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

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

    PubMed

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

    1997-08-01

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

  19. 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.

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

    PubMed

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

    2017-02-27

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

  1. 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)

  2. 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

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

    PubMed

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

    2016-06-01

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

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

    SciTech Connect

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

    1995-11-01

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

  5. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. 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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-10-07

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

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

    PubMed

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

    2012-02-01

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

  11. 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.

  12. 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

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

    PubMed

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

    2014-01-01

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

  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. 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.

  16. 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.

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

    PubMed

    González, Graciela E; Poggio, Lidia

    2011-01-01

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

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

    PubMed

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

    2012-11-01

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

  19. 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.

  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.

  1. 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.

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

    PubMed Central

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

    2016-01-01

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

  3. 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.

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

    PubMed

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

    2015-03-01

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

  5. 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...

  6. 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

  7. 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.

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

    SciTech Connect

    United States. Bonneville Power Administration.

    1986-01-01

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

  9. 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.

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

    PubMed Central

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

    2013-01-01

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

  11. 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.

  12. 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.

  13. 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

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

    SciTech Connect

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

    1994-09-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    1999-01-01

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

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

    PubMed

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

    2008-11-01

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

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

    PubMed

    Ksiazczyk, T; Taciak, M; Zwierzykowski, Z

    2010-01-01

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

  20. 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

  1. 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.

  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. 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.

  4. 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.

  5. 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.

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

    PubMed

    Ueno, Ryohei

    2009-04-01

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

  7. 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.

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

    PubMed

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

    2009-11-16

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

  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. 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.

  11. 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.

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

    PubMed

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

    2007-02-01

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

  13. 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).

  14. 2008-09 National Rivers and Streams Assessment Fish Tissue Data Dictionary

    EPA Pesticide Factsheets

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

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

    SciTech Connect

    Pasch, R.W.

    1986-12-01

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

  16. 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...

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

    USGS Publications Warehouse

    Scribner, Kim T.; Avise, John C.

    1994-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  19. 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.

  20. 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

  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. 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.

  3. 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.

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2015-02-01

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

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

    PubMed

    Zanardi, Andrea; Barborini, Emanuele; Carbone, Roberta

    2013-01-01

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

  7. 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

  8. 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.

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

    PubMed

    Polidoro, Beth A; Morra, Matthew J

    2016-03-01

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

  10. 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.

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

    USGS Publications Warehouse

    Meador, Michael R.; Carlisle, Daren M.

    2009-01-01

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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. An integrative approach to assess ecological risks of surface water contamination for fish populations.

    PubMed

    Santos, Raphael; Joyeux, Aude; Besnard, Aurélien; Blanchard, Christophe; Halkett, Cédric; Bony, Sylvie; Sanchez, Wilfried; Devaux, Alain

    2017-01-01

    Contamination of aquatic ecosystems is considered as one of the main threats to global freshwater biodiversity. Within the European Water Framework Directive (EU-WFD) a particular attention is dedicated to assess ecological risks of surface water contamination and mitigation of chemical pressures on aquatic ecosystems. In this work, we evaluated ecological risks of surface water contamination for fish populations in four EU-WFD rivers through an integrative approach investigating three Lines of Evidence (chemical contamination, biomarker responses as early warning signals of contamination impacting individuals and ecological analyses as an indicator of fish community disturbances). This work illustrates through 4 case studies the complementary role of biomarkers, chemical and ecological analyses which, used in combination, provide fundamental information to understand impacts of chemical pressures that can affect fish population dynamics. We discuss the limitations of this approach and future improvements needed within the EU-WFD to assess ecological risk of river contamination for fish populations.

  17. 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).

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-02-14

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

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

    EPA Science Inventory

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

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

    PubMed

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

    2014-03-01

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

  2. 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.

  3. 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

  4. 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.

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

    PubMed

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

    2006-09-01

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

  6. 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.

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

    PubMed Central

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

    2014-01-01

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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    PubMed

    Heinrich, Luise; Krause, Torsten

    2016-08-26

    Ocean acidification (OA) describes a change in the ocean's carbonate chemistry. Whereas its chemical processes are largely understood, the biological and socioeconomic consequences particularly in relation to fisheries are less known. Norway is a major fishing nation worldwide and is potentially affected by OA. To improve the understanding of the socioeconomic consequences of OA, we conducted a risk assessment among the Norwegian counties using a modified version of a risk assessment framework introduced in the Intergovernmental Panel on Climate Change's "Special Report: Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation," which considers risk to be the sum of hazard, exposure, and vulnerability. Our results show that about 13 of 19 counties are likely to experience moderate to high risk from OA. We highlight that the success of integrated risk assessments highly depends on the availability of detailed environmental, economic, and societal data. In the case of Norway, modeling data regarding the progress of OA, improved information on potential biological impacts on a larger number of species, and statistical data on social variables are required. We conclude that although still in its infancy, integrated risk assessments are important prerequisites for any form of interdisciplinary research on OA and the development of successful response strategies. Integr Environ Assess Manag 2016;00:000-000. ©2016 SETAC.

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

    PubMed

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

    2007-11-21

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

  18. 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.

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

    PubMed

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

    2016-12-01

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

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

    PubMed

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

    2017-03-01

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

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

    PubMed

    Marescalchi, O; Scali, V

    2001-10-01

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

  4. 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.

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

    PubMed

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

    2012-09-01

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

  6. 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.

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

    PubMed

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

    2006-01-01

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

  8. 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.

  9. 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.

  10. 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

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

    SciTech Connect

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

    1995-12-31

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

  12. 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...

  13. 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...

  14. 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...

  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. 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

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

    PubMed

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

    2013-12-01

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

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

    PubMed Central

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

    2012-01-01

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

  19. 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.

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

    PubMed

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

    2017-02-20

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

  1. 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

  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. 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.

  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. 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

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

    PubMed

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

    2003-01-01

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

  7. 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

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

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Smith, David R.

    2015-01-01

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

  9. 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

  10. 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).

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

    USGS Publications Warehouse

    Meador, Michael R.

    2013-01-01

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

  12. Spatially explicit assessment of estuarine fish after Deepwater ...

    EPA Pesticide Factsheets

    Evaluating long- term contaminant effects on wildlife populations depends on spatial information about habitat quality, heterogeneity in contaminant exposure, and sensitivities and distributions of species integrated into a systems modeling approach. Rarely is this information readily available, making it difficult to determine the applicability of realistic models to quantify population- level risks. To evaluate the trade- offs between data demands and increased specificity of spatially explicit models for population- level risk assessments, we developed a model for a standard toxicity test species, the sheepshead minnow (Cyprinodon variegatus), exposed to oil contamination following the Deepwater Horizon oil spill and compared the output with various levels of model complexity to a standard risk quotient approach. The model uses habitat and fish occupancy data collected over five sampling periods throughout 2008–2010 in Pensacola and Choctawhatchee Bays, Florida, USA, to predict species distribution, field- collected and publically available data on oil distribution and concentration, and chronic toxicity data from laboratory assays applied to a matrix population model. The habitat suitability model established distribution of fish within Barataria Bay, Louisiana, USA, and the population model projected the dynamics of the species in the study area over a 5- yr period (October 2009–September 2014). Vital rates were modified according to estimated co

  13. 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.

  14. The use of tumors in wild populations of fish to assess ecosystem health

    USGS Publications Warehouse

    Baumann, Paul C.

    1992-01-01

    Evidence has linked toxicants in aquatic systems with cancer in fish and population level effects on species. Thus some types of tumors may be useful monitors of ecosystem health, at least as affected by genotoxins and promoters. However, tumors caused by purely genetic mechanisms or by virus would not be good indicators. Only neoplasms which have chemicals as a portion of their etiology (either as initiators or promoters) would be useful in assessing ecosystem health. Lesions which may fit these criteria include liver neoplasms (both biliary and hepatic) and skin lesions in a variety of primarily benthic fishes, and neural lesions in various drum species and in butterfly fish species. Two studies purporting to demonstrate a lack of tumors in fish from polluted areas have been reexamined and found either to have insufficient data on vulnerable species or to actually support a tumor-pollution linkage. Thus certain lesions in vulnerable species or species groups may serve as a mechanism to assess one facet of ecosystem health.

  15. Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization (LNA flow-FISH): A Method for Bacterial Small RNA Detection

    DTIC Science & Technology

    2012-01-10

    Friedrich, U. & Lenke, J. Improved Enumeration of Lactic Acid Bacteria in Mesophilic Dairy Starter Cultures by Using Multiplex Quantitative Real...messenger RNA using locked nucleic acid probes. Anal. Biochem. 390, 109-114 (2009). 13. Waters, L. & Storz, G. Regulatory RNAs in bacteria . Cell. 136, 615...Video Article Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization (LNA flow-FISH): a Method for Bacterial Small RNA Detection Kelly

  16. 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.

  17. 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

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

    PubMed

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

    2017-01-11

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

  19. 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…

  20. Predation risk assessment by olfactory and visual cues in a coral reef fish

    NASA Astrophysics Data System (ADS)

    McCormick, M. I.; Manassa, R.

    2008-03-01

    Assessment of predation risk is vital for the success of an individual. Primary cues for the assessment include visual and olfactory stimuli, but the relative importance of these sources of information for risk assessment has seldom been assessed for marine fishes. This study examined the importance of visual and chemical cues in assessing risk for the star goby, Asterropteryx semipunctatus. Visual and chemical cue intensities were used that were indicative of a high threat situation. The behavioural response elicited by both the visual cues of a predator (the rock cod, Cephalopholis boenak) and the chemical alarm cues from conspecifics were similar in magnitude, with responses including a decrease in feeding strikes and moves. A bobbing behaviour was exhibited when the predator was visible and not when only exposed to the chemical alarm cue. When visual and chemical cues were presented together they yielded a stronger antipredator response than when gobies were exposed solely to conspecific alarm cues. This suggests additivity of risk assessment information at the levels of threat used, however, the goby’s response is also likely to depend on the environmental and social context of the predator-prey encounter. This study highlights the importance of chemical cues in the assessment of predation risk for a coral reef fish.

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

    PubMed Central

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

    2009-01-01

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

  2. Composition of dioxin-like PCBs in fish: an application for risk assessment.

    PubMed

    Bhavsar, Satyendra P; Fletcher, Rachael; Hayton, Alan; Reiner, Eric J; Jackson, Donald A

    2007-05-01

    It is widely accepted that a congener-specific analysis of polychlorinated biphenyls (PCBs), rather than traditional Aroclor equivalent total PCB analysis, is required for risk assessment. This is based on the fact that environmental processes alter the original distribution of PCB congeners in Aroclors and that toxicity varies considerably among the congeners with dioxin-like PCBs (dl-PCBs) generally being among the most toxic. Using the largest known dl-PCB fish dataset, here we present a likely composition of dl-PCBs in fish. In contrast to common perception, we found that the dl-PCB composition is relatively constant (within approximately a factor of 2) regardless of fish species and total PCB level. The abundance of dl-PCBs expressed as a percentage of total PCB (25-75 quartile range) in fish is generally in the order of PCB-118 (3.0-6.2%) > PCB-105 (1.1-2.4%) > PCB-156 (0.39-0.75%) > PCB-167 (0.20-0.43%) > PCB-123 (0.11-0.26%) > PCB-157 (0.09-0.19%) = PCB-114 (0.08-0.18%) > PCB-189 (0.045-0.094%) > PCB-77 (0.018-0.093%) > PCB-126 (0.015-0.036%) > PCB-81 (0.002-0.007%) = PCB-169 (0.001-0.006%). The most toxic dl-PCB congeners PCB-126 and -169 contribute on average only 0.027 and 0.004% of total PCB, respectively. The statistically significant relationships presented between individual di-PCB and total-PCB concentrations can be used as a practical tool to estimate dl-PCBs for risk assessment purposes. A comparison of the dl-PCB pattern presented here with other studies suggests that this dl-PCB composition is applicable to fish from North America and perhaps from other geographical regions throughout the world.

  3. Assessing the efficacy of single-pass backpack electrofishing to characterize fish community structure

    USGS Publications Warehouse

    Meador, M.R.; McIntyre, J.P.; Pollock, K.H.

    2003-01-01

    Two-pass backpack electrofishing data collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program were analyzed to assess the efficacy of single-pass backpack electrofishing. A two-capture removal model was used to estimate, within 10 river basins across the United States, proportional fish species richness from one-pass electrofishing and probabilities of detection for individual fish species. Mean estimated species richness from first-pass sampling (ps1) ranged from 80.7% to 100% of estimated total species richness for each river basin, based on at least seven samples per basin. However, ps1 values for individual sites ranged from 40% to 100% of estimated total species richness. Additional species unique to the second pass were collected in 50.3% of the samples. Of these, cyprinids and centrarchids were collected most frequently. Proportional fish species richness estimated for the first pass increased significantly with decreasing stream width for 1 of the 10 river basins. When used to calculate probabilities of detection of individual fish species, the removal model failed 48% of the time because the number of individuals of a species was greater in the second pass than in the first pass. Single-pass backpack electrofishing data alone may make it difficult to determine whether characterized fish community structure data are real or spurious. The two-pass removal model can be used to assess the effectiveness of sampling species richness with a single electrofishing pass. However, the two-pass removal model may have limited utility to determine probabilities of detection of individual species and, thus, limit the ability to assess the effectiveness of single-pass sampling to characterize species relative abundances. Multiple-pass (at least three passes) backpack electrofishing at a large number of sites may not be cost-effective as part of a standardized sampling protocol for large-geographic-scale studies. However, multiple

  4. Assessing organic contaminants in fish: comparison of a nonlethal tissue sampling technique to mobile and stationary passive sampling devices.

    PubMed

    Heltsley, Rebecca M; Cope, W Gregory; Shea, Damian; Bringolf, Robert B; Kwak, Thomas J; Malindzak, Edward G

    2005-10-01

    As concerns mount over the human health risks associated with consumption of fish contaminated with persistent organic pollutants, there exists a need to better evaluate fish body burdens without lethally sampling many of the important commercial and sport species of interest. The aim of this study was to investigate two novel methods for estimating organic contaminants in fish that are a concern for both fish and human health. The removal of fish adipose fins, commonly done in mark-recapture studies with salmonid species, was evaluated as a nonlethal sampling technique to estimate concentrations of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) in flathead catfish (Pylodictis olivaris), relative to those found in muscle fillets of the same fish. We also assessed the efficacy of using poly(dimethylsiloxane) (PDMS) as a mobile passive sampling device (PSD) attached directly to wild flathead catfish for assessing location-specific exposure of the fish to waterborne contaminants. The results of this study have demonstrated for the first time that organic contaminant concentrations in adipose fin were highly correlated (R2 = 0.87) with muscle fillet concentrations, indicating that the adipose fin of certain fishes may be used to accurately estimate tissue concentrations without the need for lethal sampling. Moreover, mobile PSDs attached directly to fish and used here for the first time accurately estimated ultratrace concentrations of waterborne PCBs and OCPs without any apparent harm to the fish, indicating that there are no practical or physical barriers to the use of mobile passive samplers attached to aquatic organisms. Among the many practical implications of this research, two potential priority items include the analysis of organic contaminants in farm-raised and sport fish intended for human consumption, without the economic and population losses associated with lethally sampling fish to obtain tissues, and identifying specific areas

  5. 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

  6. 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.

  7. Assessing ecological risks to the fish community from residual coal fly ash in Watts Bar Reservoir, Tennessee

    DOE PAGES

    Rigg, David K.; Wacksman, Mitch N.; Iannuzzi, Jacqueline; ...

    2014-12-18

    For this research, extensive site-specific biological and environmental data were collected to support an evaluation of risks to the fish community in Watts Bar Reservoir from residual ash from the December 2008 Tennessee Valley Authority (TVA) Kingston ash release. This paper describes the approach used and results of the risk assessment for the fish community, which consists of multiple measurement endpoints (measures of exposure and effects) for fish. The lines of evidence included 1) comparing postspill annual fish community assessments with nearby prespill data and data from other TVA reservoirs, 2) evaluating possible effects of exposures of fish eggs andmore » larval fish to ash in controlled laboratory toxicity tests, 3) evaluating reproductive competence of field-exposed fish, 4) assessing individual fish health through physical examination, histopathology, and blood chemistry, 5) comparing fish tissue concentrations with literature-based critical body residues, and 6) comparing concentrations of ash-related contaminants in surface waters with US Environmental Protection Agency's (USEPA) Ambient Water Quality Standards for Fish and Aquatic Life. These measurement endpoints were treated as independent lines of evidence that were integrated into an overall weight-of-evidence estimate of risk to the fish community. Collectively, the data and analysis presented here indicate that ash and ash-related constituents pose negligible risks to the fish communities in Watts Bar Reservoir. This conclusion contradicts the predictions by some researchers immediately following the ash release of devastating effects on the aquatic ecology of Watts Bar Reservoir. The information presented in this article reaffirms the wisdom of carefully evaluating the evidence before predicting probable ecological effects of a major event such as the TVA Kingston ash release. Lastly, this study demonstrates that a thorough and detailed investigation using multiple measurement endpoints

  8. 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

  9. 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

  10. Rapid identification of Helicobacter pylori and assessment of clarithromycin susceptibility from clinical specimens using FISH

    PubMed Central

    Demiray‐Gürbüz, Ebru; Yılmaz, Özlem; Olivares, Asalia Z; Gönen, Can; Sarıoğlu, Sülen; Soytürk, Müjde; Tümer, Sait; Altungöz, Oğuz; Şimşek, İlkay

    2016-01-01

    Abstract Helicobacter pylori remains one of the most common bacterial infections worldwide. Clarithromycin resistance is the most important cause of H. pylori eradication failures. Effective antibiotic therapies in H. pylori infection must be rapidly adapted to local resistance patterns. We investigated the prevalence of clarithromycin resistance due to mutations in positions 2142 and 2143 of 23SrRNA gene of H. pylori by fluorescence in situ hybridisation (FISH), and compared with culture and antimicrobial susceptibility testing in 234 adult patients with dyspepsia who were enrolled. Antrum and corpus biopsy specimens were obtained for rapid urease test, histopathology and culture. Epsilometer test was used to assess clarithromycin susceptibility. H. pylori presence and clarithromycin susceptibility were determined by FISH in paraffin‐embedded biopsy specimens. We found that 164 (70.1%) patients were positive for H. pylori based on clinical criteria, 114 (69.5% CI 62.5–76.6%) were culture positive, and 137 (83.5% CI 77.8–89.2%) were FISH positive. Thus the sensitivity of FISH was significantly superior to that of culture. However specificity was not significantly different (91.4 versus 100.0%, respectively). The resistance rate to clarithromycin for both antrum and corpus was detected in H. pylori‐positive patients; 20.2% by FISH and 28.0% by E‐test.The concordance between E‐test and FISH was only 89.5% due to the presence of point mutations different from A2143G, A2142G or A2142C. We conclude that FISH is significantly more sensitive than culture and the E‐test for the detection of H. pylori and for rapid determinination of claritromycin susceptibility. The superior hybridisation efficiency of FISH is becoming an emerging molecular tool as a reliable, rapid and sensitive method for the detection and visualisation of H. pylori, especially when the management of H. pylori eradication therapy is necessary. This is particularly important for the

  11. Rapid identification of Helicobacter pylori and assessment of clarithromycin susceptibility from clinical specimens using FISH.

    PubMed

    Demiray-Gürbüz, Ebru; Yılmaz, Özlem; Olivares, Asalia Z; Gönen, Can; Sarıoğlu, Sülen; Soytürk, Müjde; Tümer, Sait; Altungöz, Oğuz; Şimşek, İlkay; Perez Perez, Guillermo I

    2017-01-01

    Helicobacter pylori remains one of the most common bacterial infections worldwide. Clarithromycin resistance is the most important cause of H. pylori eradication failures. Effective antibiotic therapies in H. pylori infection must be rapidly adapted to local resistance patterns. We investigated the prevalence of clarithromycin resistance due to mutations in positions 2142 and 2143 of 23SrRNA gene of H. pylori by fluorescence in situ hybridisation (FISH), and compared with culture and antimicrobial susceptibility testing in 234 adult patients with dyspepsia who were enrolled. Antrum and corpus biopsy specimens were obtained for rapid urease test, histopathology and culture. Epsilometer test was used to assess clarithromycin susceptibility. H. pylori presence and clarithromycin susceptibility were determined by FISH in paraffin-embedded biopsy specimens. We found that 164 (70.1%) patients were positive for H. pylori based on clinical criteria, 114 (69.5% CI 62.5-76.6%) were culture positive, and 137 (83.5% CI 77.8-89.2%) were FISH positive. Thus the sensitivity of FISH was significantly superior to that of culture. However specificity was not significantly different (91.4 versus 100.0%, respectively). The resistance rate to clarithromycin for both antrum and corpus was detected in H. pylori-positive patients; 20.2% by FISH and 28.0% by E-test.The concordance between E-test and FISH was only 89.5% due to the presence of point mutations different from A2143G, A2142G or A2142C. We conclude that FISH is significantly more sensitive than culture and the E-test for the detection of H. pylori and for rapid determinination of claritromycin susceptibility. The superior hybridisation efficiency of FISH is becoming an emerging molecular tool as a reliable, rapid and sensitive method for the detection and visualisation of H. pylori, especially when the management of H. pylori eradication therapy is necessary. This is particularly important for the treatment of patients with H

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Accurate assessment of HER2 gene status for invasive component of breast cancer by combination of immunohistochemistry and chromogenic In Situ hybridization.

    PubMed

    Nie, Xiu; He, Jun; Li, Yan; Pan, Dan-zhen; Pan, Hua-xiong; Weng, Mi-xia; Yang, Xiu-ping; Liu, Chun-ping; Huang, Tao

    2013-06-01

    The specimens of ductal carcinoma in situ (DCIS) with early invasion, and specimens collected by core needle biopsy (CNB) tend to contain limited amount of invasive component, so it is imperative to explore a new technique which can assess HER2 gene status accurately for the limited invasive cancer component in these specimens. Dual staining technique of combining immunohistochemistry (IHC) for myoepithelial cells and single or dual probe chromogenic in situ hybridization (CISH) for HER2 gene was performed on routinely processed paraffin sections from 20 cases diagnosed as having DCIS with invasive cancer. Among them, 10 had fluorescence in situ hybridization (FISH)-confirmed amplification of HER2 and 10 had FISH-confirmed non-amplification of HER2. We successfully detected HER2 genetic signals and myoepithelial IHC markers (SMM-HC or CK5/6) simultaneously on a single section in all 20 specimens. Myoepithelial markers and HER2 signals detected by dual staining assay were consistent with those by individual technique performed alone. HER2 gene amplification results determined by dual staining assay were 100% consistent with those of FISH. Dual staining technique which allows simultaneous detection of myoepithelial marker protein and cancerous HER2 gene is feasible, and it has potential to be used in clinical practice for effective determination of HER2 amplification in limited invasive component.

  17. A scoring system approach for the parasite predictive assessment of fish lots: a proof of concept with anisakids.

    PubMed

    Llarena-Reino, María; Abollo, Elvira; Pascual, Santiago

    2013-12-01

    A total of 982 individuals distributed in 11 lots belonging to 10 fish species from three Atlantic FAO fishing areas were sampled and examined to detect the presence of anisakid larvae in fish muscle. After hazard identification by genetic sequencing and exposure assessment by anatomic extent and demographic characterization of infection, all data were fitted for each fish species to a new proposed scoring schema of parasite prediction. In the absence of a criterion standard method for inspection and precise definition of the quantum satis for parasites in contaminated fish lots, the inspection rating scheme called SADE (Site of infection, Assurance of quality, Demography, Epidemiology) may help fish industries to precisely handle and to evaluate the likely outcome of infected fish lots after being diagnosed. For this purpose, a supporting flow diagram for decision was defined and suggested. This new performance assessment tool has the aim of staging fish lots, thus helping in planning manufacture, commercial, and research decisions during self-management programs. This novel scoring system provides an improved inspection format by implementing the occurrence stratification for parasites to guide Hazard Analysis and Critical Control Points (HACCP) programs for the uniform exchange of information among fish industries, administration and researchers, thus facilitating standardization and communication. In the future, this scoring version could be validated (in terms of classification and wording) for similar overall predictive purposes in other muscular parasites infecting seafood products.

  18. A comparative assessment of contaminants in fish from four resacas of the Texas, USA-Tamaulipas, Mexico border region.

    PubMed

    Mora, M A; Papoulias, D; Nava, I; Buckler, D R

    2001-07-01

    A recent survey of contaminant information for the Lower Rio Grande Valley (LRGV), Texas, has shown that little is known about contaminants and their impacts on biota of resacas (oxbows) along the US-Mexico border. In 1996, fish were collected from four resacas in the Texas-Tamaulipas border region to assess contaminant loadings and their impacts on fish and birds. Tissue residue concentrations in fish were analyzed and also compared to two histopathological bioindicators of unhealthy environmental conditions. Of the organochlorine insecticides measured, DDE was the most common and was present at relatively high concentrations (10 microg/g w/w) at some sites. DDE concentrations were nearly 20 times greater in fish from resacas in Texas than from resacas in Tamaulipas, although the limited sample sizes obtained precluded statistical comparisons. DDE concentrations in fish from the two Texas resacas were also greater than those reported in fish from nearby areas during the 1980s and 1990s. Most trace element concentrations were similar among resacas from Texas and Tamaulipas. Arsenic, however, was two to six times greater in fish from a downtown resaca in Matamoros than in fish from other resacas in Tamaulipas and Texas. The bioindicators, pigment accumulation, and macrophage aggregates (MAs), in general, reflected the contamination indicated by the tissue residues for each site. Overall, it appears that some resacas of the US-Mexico border region are contaminant sinks and could pose potential health or reproductive problems for fish and wildlife, and humans that consume fish from those sites.

  19. Next-Generation Assessment of Human Growth Factor Receptor 2 (ERBB2) Amplification Status: Clinical Validation in the Context of a Hybrid Capture-Based, Comprehensive Solid Tumor Genomic Profiling Assay.

    PubMed

    Ross, Dara S; Zehir, Ahmet; Cheng, Donavan T; Benayed, Ryma; Nafa, Khedoudja; Hechtman, Jaclyn F; Janjigian, Yelena Y; Weigelt, Britta; Razavi, Pedram; Hyman, David M; Baselga, José; Berger, Michael F; Ladanyi, Marc; Arcila, Maria E

    2017-03-01

    Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. Next-generation sequencing (NGS) is an attractive approach for up-front comprehensive assessment, including ERBB2 status, but the concordance with traditional methods of HER2 assessment is not well established. The Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay, a hybrid capture-based NGS assay interrogating the coding regions of 410 cancer-related genes, was performed on manually macrodissected unstained sections from formalin-fixed, paraffin-embedded breast (n = 213) and gastroesophageal (n = 39) tumors submitted for clinical mutation profiling. ERBB2 status was assessed using a custom bioinformatics pipeline, and NGS results were compared to IHC and FISH. NGS ERBB2 amplification calls had an overall concordance of 98.4% (248/252) with the combined IHC/FISH results in this validation set. Discrepancies occurred in the context of low tumor content and HER2 heterogeneity. ERBB2 amplification status can be reliably determined by hybridization capture-based NGS methods, allowing efficient concurrent testing for other potentially actionable genomic alterations, particularly in limited material.

  20. 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.

  1. 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.

  2. 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.

  3. Hybrid electric vehicle technology assessment : methodology, analytical issues, and interim results.

    SciTech Connect

    Plotkin, S.; Santini, D.; Vyas, A.; Anderson, J.; Wang, M.; Bharathan, D.; He, J.

    2002-03-13

    This report presents the results of the first phase of Argonne National Laboratory's (ANL's) examination of the costs and energy impacts of light-duty hybrid electric vehicles (HEVs). We call this research an HEV Technology Assessment, or HEVTA. HEVs are vehicles with drivetrains that combine electric drive components (electric motor, electricity storage) with a refuelable power plant (e.g., an internal combustion engine). The use of hybrid drivetrains is widely considered a key technology strategy in improving automotive fuel efficiency. Two hybrid vehicles--Toyota's Prius and Honda's Insight--have been introduced into the U.S. market, and all three auto industry participants in the Partnership for a New Generation of Vehicles (PNGV) have selected hybrid drivetrains for their prototype vehicles.

  4. 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.

  5. 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.

  6. 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

  7. Do national advisories serve local consumers: an assessment of mercury in economically important North Carolina fish.

    PubMed

    Petre, Sally Jane; Sackett, Dana K; Aday, D Derek

    2012-05-01

    Consumption of marine fish provides both benefits (lean protein, omega-3 fatty acids and essential nutrients) and risks (main source of mercury (Hg) exposure for humans). Mercury is a potent neurotoxin and the source of more fish advisories nationwide than any other toxicant. Despite the widespread nature of Hg, it is unknown whether local Hg contamination reflects national and regional levels often used as bases to inform consumers of potential fish consumption risk. Thus, the objectives of our study were to examine Hg levels of six commonly consumed marine species harvested locally off the North Carolina coast and to compare our results to published regional (Monterey Bay Aquarium's Seafood Watch List) and national (Environmental Protection Agency, EPA, and Food and Drug Administration, FDA) Hg averages, action levels, and guidelines. We found significant differences in Hg concentrations among collected species, and we identified correlations between Hg concentration and fish length and trophic levels. Collected mahi mahi and triggerfish were below the EPA fish tissue action level (0.3ppm). Wahoo and grouper exceeded the EPA action level but were below the FDA action level (1.0ppm). King mackerel had the highest Hg concentration among targeted species, exceeding both EPA and FDA action levels. Further, our local results were not always consistent with calculated averages from EPA and FDA databases for the same species, and although many of our findings were consistent with Monterey Bay Aquarium's Seafood Watch List (southeast region), recommendations based on Hg levels would conflict with recommendations they provide based on sustainability. We find regional and national averages are not always reflective of local Hg contamination and suggest local data may be needed to accurately assess consumer risk.

  8. 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.

  9. 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

  10. Assessing Fish and Motile Fauna around Offshore Windfarms Using Stereo Baited Video.

    PubMed

    Griffin, Ross A; Robinson, Gary J; West, Ashley; Gloyne-Phillips, Ian T; Unsworth, Richard K F

    2016-01-01

    There remains limited knowledge of how offshore windfarm developments influence fish assemblages, particularly at a local scale around the turbine structures. Considering the existing levels of anthropogenic pressures on coastal fish populations it is becoming increasingly important for developers and environmental regulators to gain a more comprehensive understanding of the factors influencing fish assemblages. Improving our ability to assess such fish populations in close proximity to structures will assist in increasing this knowledge. In the present study we provide the first trial use of Baited Remote Underwater Stereo-Video systems (stereo BRUVs) for the quantification of motile fauna in close proximity to offshore wind turbines. The study was conducted in the Irish Sea and finds the technique to be a viable means of assessing the motile fauna of such environments. The present study found a mixture of species including bottom dwellers, motile crustaceans and large predatory fish. The majority of taxa observed were found to be immature individuals with few adult individuals recorded. The most abundant species were the angular crab (Goneplax rhomboides) and the small-spotted catshark (Scyliorhinus canicula). Of note in this study was the generally low abundance and diversity of taxa recorded across all samples, we hypothesise that this reflects the generally poor state of the local fauna of the Irish Sea. The faunal assemblages sampled in close proximity to turbines were observed to alter with increasing distance from the structure, species more characteristic of hard bottom environments were in abundance at the turbines (e.g. Homarus gammarus, Cancer pagarus, Scyliorhinus spp.) and those further away more characteristic of soft bottoms (e.g. Norwegian Lobster). This study highlights the need for the environmental impacts of offshore renewables on motile fauna to be assessed using targeted and appropriate tools. Stereo BRUVs provide one of those tools, but like

  11. Assessing Fish and Motile Fauna around Offshore Windfarms Using Stereo Baited Video

    PubMed Central

    Griffin, Ross A.; Robinson, Gary J.; West, Ashley; Gloyne-Phillips, Ian T.; Unsworth, Richard K. F.

    2016-01-01

    There remains limited knowledge of how offshore windfarm developments influence fish assemblages, particularly at a local scale around the turbine structures. Considering the existing levels of anthropogenic pressures on coastal fish populations it is becoming increasingly important for developers and environmental regulators to gain a more comprehensive understanding of the factors influencing fish assemblages. Improving our ability to assess such fish populations in close proximity to structures will assist in increasing this knowledge. In the present study we provide the first trial use of Baited Remote Underwater Stereo-Video systems (stereo BRUVs) for the quantification of motile fauna in close proximity to offshore wind turbines. The study was conducted in the Irish Sea and finds the technique to be a viable means of assessing the motile fauna of such environments. The present study found a mixture of species including bottom dwellers, motile crustaceans and large predatory fish. The majority of taxa observed were found to be immature individuals with few adult individuals recorded. The most abundant species were the angular crab (Goneplax rhomboides) and the small-spotted catshark (Scyliorhinus canicula). Of note in this study was the generally low abundance and diversity of taxa recorded across all samples, we hypothesise that this reflects the generally poor state of the local fauna of the Irish Sea. The faunal assemblages sampled in close proximity to turbines were observed to alter with increasing distance from the structure, species more characteristic of hard bottom environments were in abundance at the turbines (e.g. Homarus gammarus, Cancer pagarus, Scyliorhinus spp.) and those further away more characteristic of soft bottoms (e.g. Norwegian Lobster). This study highlights the need for the environmental impacts of offshore renewables on motile fauna to be assessed using targeted and appropriate tools. Stereo BRUVs provide one of those tools, but like

  12. 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

  13. 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

  14. Process notebook for aquatic ecosystem simulation. [Evaluation of fish models for impact assessment

    SciTech Connect

    Swartzman, G.; Smith, E.; McKenzie, D.; Haar, B.; Fickeisen, D.

    1980-01-01

    This notebook contains a detailed comparison of 14 models of fish growth, energetics, population dynamics, and feeding. It is a basic document for the evaluation of thes models' usefulness for impact assessment. Model equations are categorized into 18 subprocesses comprising the major processes of consumption, predation, metabolic processes, growth, fecundity, and mortality. The model equations are compared in a standard notation and the equation rationales are considered and put into a historical framework with historical precedence charts. Model parameters are computed in standard units and data sources and techniques used for parameter estimation are identified. A translator compares standard notation with the notation used in the models. The major contribution of this work is that, for the first time, fish models are arrayed with their assumptions laid bare and their parameter values compared, allowing elucidation of model differeances and evaluaton of model behavior and data needs by using the process notebook as a base for further simulation comparison.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Nitrifying bacterial communities in an aquaculture wastewater treatment system using fluorescence in situ hybridization (FISH), 16S rRNA gene cloning, and phylogenetic analysis.

    PubMed

    Paungfoo, Chanyarat; Prasertsan, Poonsuk; Burrell, Paul C; Intrasungkha, Nugul; Blackall, Linda L

    2007-07-01

    Aquaculture, especially shrimp farming, has played a major role in the growth of Thailand's economy in recent years, as well as in many South East Asian countries. However, the nutrient discharges from these activities have caused adverse impacts on the quality of the receiving waterways. In particular nitrogenous compounds, which may accumulate in aquaculture ponds, can be toxic to aquatic animals and cause environmental problems such as eutrophication. The mineralization process is well known, but certain aspects of the microbial ecology of nitrifiers, the microorganisms that convert ammonia to nitrate, are poorly understood. A previously reported enrichment of nitrifying bacteria (ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB)) from a shrimp farm inoculated in a sequencing batch reactor (SBR) was studied by molecular methods. The initial identification and partial quantification of the nitrifying bacteria (AOB and NOB) were carried out by fluorescence in situ hybridization (FISH) using previously published 16S rRNA-targeting oligonucleotide probes. The two dominant bacterial groups detected by FISH were from the Cytophaga-Flavobacterium-Bacteroides and Proteobacteria (beta subdivision) phyla. Published FISH probes for Nitrobacter and Nitrospira did not hybridize to any of the bacterial cells. Therefore it is likely that new communities of NOBs, differing from previously reported ones, exist in the enrichments. Molecular genetic techniques (cloning, sequencing, and phylogenetic analysis) targeting the 16S rRNA genes from the nitrifying enrichments were performed to identify putative AOBs and NOBs.

  3. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH).

    PubMed

    Cortés-Gutiérrez, Elva I; Ortíz-Hernández, Brenda L; Dávila-Rodríguez, Martha I; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

    2013-02-19

    We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

  4. Assessing estuarine environmental quality using fish-based indices: performance evaluation under climatic instability.

    PubMed

    Martinho, F; Viegas, I; Dolbeth, M; Leitão, R; Cabral, H N; Pardal, M A

    2008-11-01

    The seasonal variation of five selected multimetric indices for the determination of the Ecological Quality Status (EQS) of transitional waters was evaluated, as well as the indices' responses to an extreme drought event that occurred in 2005. The database used regards the Mondego River estuary, which was sampled from June 2003 to August 2006 on a monthly basis. Among the selected indices (EBI-Deegan et al. [Deegan, L., Finn, J.T., Ayvazlan, S.G., Ryder-Kieffer, C.A., Buonaccoesi, J., 1997. Development and validation of an Estuarine Biotic Integrity Index. Estuaries 30(3), 601-617], EDI-Borja et al. [Borja, A., Franco, J., Valencia, V., Bald, J., Muxika, I., Belzunce, M.J., Solaun, O., 2004. Implementation of the European Water Framework Directive from the Basque Country (northern Spain): a methodological approach. Marine Pollution Bulletin 48(3-4), 209-218], EFCI-Harrison and Whitfield [Harrison, T.D., Whitfield, A.K., 2004. A multi-metric fish index to assess the environmental condition of estuaries. Journal of Fish Biology 65, 683-710], EBI-Breine et al. [Breine, J.J., Maes, J., Quataert, P., Van den Bergh, E., Simoens, I., Van Thuyne, G., Belpaire, C., 2007. A fish-based assessment tool for the ecological quality of the brackish Scheldt estuary in Flanders (Belgium). Hydrobiologia 575, 141-159] and TFCI - Coates et al. [Coates, S., Waugh, A., Anwar, A., Robson, M., 2007. Efficacy of a multi-metric fish index as an analysis tool for the transitional fish component of the Water Framework Directive. Marine Pollution Bulletin 55, 225-240]), the EBI by Breine et al. (2007) was the only that evidenced clear interannual and seasonal variations. The EQS by the several indices ranged from "Low" to "High", depending on the index considered, evidencing the high level of mismatch between indices. The results are discussed in the scope of the EU Water Framework Directive, regarding monitoring strategies, application of indices and EQS assessment.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Application of a regional procedure to assess the risk to fish from high sediment concentrations.

    PubMed

    Watts, Carol D; Naden, Pamela S; Cooper, David M; Gannon, Beate

    2003-10-01

    Periods of high suspended sediment concentration in rivers can affect the behaviour, health and habitat of freshwater fish. A simple regional model relating daily mean suspended sediment concentration in rivers to flow and percentage of cropped and urban land has been applied to the Lower Swale, UK. The model uses a GIS catchment coverage of hydrological response units (HRUs) of area 5-8 km2, each of which is assumed hydrologically independent and drains to an identified river reach. The sediment delivery properties of each HRU are a function of its land use characteristics determined from existing databases, and hydrological conditions determined from effective rainfall measurements. Daily mean suspended sediment concentrations for each river reach were derived by cumulating simulated HRU flows and sediment loads down successive reaches. A map of the modelled 10% quantile sediment concentrations is presented for both HRUs and river reaches. The map is substantially different from existing erosion risk maps because the delivery model is driven by flow in addition to land use, rather than by soil type. Frequency curves showing the exceedance probability of mean simulated sediment concentrations over 1-6-day durations have been derived using peaks-over-threshold techniques. Maps of the risk of harm to fish, based on the probability of 1- and 4-day sediment concentrations exceeding 80 mg l(-1), are presented. Such maps can be used to assess the impact of sediment on fish and for setting appropriate river water quality objectives.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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,

  16. Effects of the acute exposition to glyphosate-based herbicide on oxidative stress parameters and antioxidant responses in a hybrid Amazon fish surubim (Pseudoplatystoma sp).

    PubMed

    Sinhorin, Valéria Dornelles Gindri; Sinhorin, Adilson Paulo; Teixeira, Jhonnes Marcos dos Santos; Miléski, Kelly Márcia Lazarotto; Hansen, Paula Carine; Moreira, Paula Sueli Andrade; Kawashita, Nair Honda; Baviera, Amanda Martins; Loro, Vania Lúcia

    2014-08-01

    The aim of this study was to investigate the effects of acute glyphosate (active ingredient) exposure on the oxidative stress biomarkers and antioxidant defenses of a hybrid surubim (Pseudoplatystoma sp). The fish were exposed to different herbicide concentrations for 96 h. The thiobarbituric acid-reactive substances (TBARS), protein carbonyls and antioxidant responses were verified. The 15 mg a.pL(-1) of herbicide resulted in the death of 50% of the fish after 96 h. An increase in liver and muscle TBARS levels was observed when fish were exposed to the herbicide. The protein carbonyl content was also increased in the liver (4.5mg a.pL(-1) concentration) and brain (2.25 mg a.pL(-1) concentration). The antioxidant activities decreased in the liver and brain after exposure to herbicide. Levels of ascorbic acid in the liver (2.25 mg a.pL(-1) and 4.5 mg a.pL(-1) concentrations) and brain (2.25 mg a.pL(-1) concentration) were increased post-treatment. Levels of total thiols were increased in the liver and brain (2.25 mg L(-1) and 7.5mg a.pL(-1), respectively). Glyphosate exposure, at the tested concentrations affects surubim health by promoting changes that can affect their survival in natural environment. Some parameters as TBARS and protein carbonyl could be early biomarkers for Roundup exposure in this fish species.

  17. Preliminary Assessment of Plug-in Hybrid Electric Vehicles on Wind Energy Markets

    SciTech Connect

    Short, W.; Denholm, P.

    2006-04-01

    This report examines a measure that may potentially reduce oil use and also more than proportionately reduce carbon emissions from vehicles. The authors present a very preliminary analysis of plug-in hybrid electric vehicles (PHEVs) that can be charged from or discharged to the grid. These vehicles have the potential to reduce gasoline consumption and carbon emissions from vehicles, as well as improve the viability of renewable energy technologies with variable resource availability. This paper is an assessment of the synergisms between plug-in hybrid electric vehicles and wind energy. The authors examine two bounding cases that illuminate this potential synergism.

  18. Age-related aneuploidy analysis of human blood cells in vivo by fluorescence in situ hybridization (FISH).

    PubMed

    Mukherjee, A B; Alejandro, J; Payne, S; Thomas, S

    1996-09-18

    All prior studies on human age-related chromosomal analysis were done using only metaphase figures derived from lymphocyte cultures in vitro. However, we believe that this procedure may provide only partial information, since the chromosomal abnormalities probably hidden in non-dividing and/or terminally differentiated leukocytes will not be detected by this method. We, therefore, have attempted to analyze the nature and extent of chromosome-specific aneuploidy at interphase by fluorescence in situ hybridization (FISH) in differentiated myeloid cells in vivo derived from various age-group people. Our data from an analysis of 30,032 cells derived from 12 healthy donors indicate that there is an increase in the mean percentages of myeloid cells with chromosome-specific aneuploidy in the older groups as opposed to that of the younger groups. This increase is applicable to all the three cell types examined (promyelocytes, metamyelocytes and polymorphs). In both the younger and older females, the relatively higher mean frequencies of cells with aneuploidy were noted for chromosome nos. 4, 6 and the X, whereas the lowest mean frequencies of cells with aneuploidy were consistently observed for chromosome no. 3. In the younger and older male donors, similar to the female donors except the X chromosome the higher percentages of aneuploid cells were observed for chromosome nos. 4 and 6 whereas the lowest mean frequencies of aneuploid cells were noted for chromosome no. 3. Among the five autosomes studied, chromosome no. 3 consistently yielded the lowest frequency of aneuploidy in all the three cell types derived from both the younger and older groups of males and females. This could presumably mean that the maintenance of a very high frequency of cells with disomy for chromosome no. 3 might be more beneficial for the process of survival and/or differentiation of myeloid cells as compared to that of other autosomes such as chromosome nos. 4 and 6. Among the five autosomes

  19. Risk and toxicity assessments of heavy metals in sediments and fishes from the Yangtze River and Taihu Lake, China.

    PubMed

    Fu, Jie; Hu, Xin; Tao, Xiancong; Yu, Hongxia; Zhang, Xiaowei

    2013-11-01

    Heavy metal pollution is one of the most serous environmental issues globally. To evaluate the metal pollution in Jiangsu Province of China, the total concentrations of heavy metals in sediments and fishes from the Yangtze River and Taihu Lake were analyzed. Ecological risk of sediments and human health risk of fish consumption were assessed respectively. Furthermore, toxicity of samples on expression of the stress responsive genes was evaluated using microbial live cell-array method. The results showed that the heavy metals concentrations in sediments from the Yangtze River were much higher than those in sediments from the Taihu Lake. However, the fishes from the Taihu Lake had higher concentrations of heavy metals than fishes from the Yangtze River. Ecological risk evaluation showed that the heavy metal contaminants in sediments from the Yangtze River posed higher risk of adverse ecological effects, while sediments from the study areas of Taihu Lake were relatively safe. Health risk assessment suggested that the heavy metals in fishes of both Yangtze River and Taihu Lake might have risk of adverse health effects to human. The toxicity assessment indicated that the heavy metals in these sediments and fishes showed transcriptional effects on the selected 21 stress responsive genes, which were involved in the pathways of DNA damage response, chemical stress, and perturbations of electron transport. Together, this field investigation combined with chemical analysis, risk assessment and toxicity bioassay would provide useful information on the heavy metal pollution in Jiangsu Province.

  20. 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

  1. Genetic differentiation among distinct karyomorphs of the wolf fish Hoplias malabaricus species complex (Characiformes, Erythrinidae) and report of unusual hybridization with natural triploidy.

    PubMed

    Utsunomia, R; Alves, J C Pansonato; Paiva, L R S; Silva, G J Costa; Oliveira, C; Bertollo, L A C; Foresti, F

    2014-11-01

    In this study, genetic differentiation between karyomorphs A (2n = 42) and D (2n = 39/40) of the wolf fish Hoplias malabaricus, which is comprised of several cryptic species that present a wide variety of diploid chromosome numbers and sex chromosome systems, resulting in the identification of seven distinct karyomorphs (A-G), was investigated using a combination of molecular and cytogenetic tools. Deep sequence divergences for both karyomorphs were observed and indicate a long period of reproductive isolation between karyomorphs A and D. Additionally, one individual with 61 chromosomes was identified, which, as far as is known, is the first case of natural triploidy resulting from the hybridization between these highly differentiated karyomorphs of H. malabaricus. Molecular and cytogenetic analyses revealed that this allotriploid specimen carries two sets of maternal chromosomes from karyomorph D (2n = 40) and one set of chromosomes from karyomorph A (n = 21). Moreover, ribosomal sites and active nucleolus organizer regions from both parental contributors were found in the triploid hybrid. Considering the significant genetic distances between karyomorphs A and D, one of the primary reasons for the lack of recurrent reports of hybridization in the H. malabaricus species complex may be due to post-zygotic barriers, such as hybrid sterility or unviability.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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).

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

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

    PubMed Central

    Edgar, Graham J; Stuart-Smith, Rick D

    2014-01-01

    The assessment of patterns in macroecology, including those most relevant to global biodiversity conservation, has been hampered by a lack of quantitative data collected in a consistent manner over the global scale. Global analyses of species’ abundance data typically rely on records aggregated from multiple studies where different sampling methods and varying levels of taxonomic and spatial resolution have been applied. Here we describe the Reef Life Survey (RLS) reef fish dataset, which contains 134,759 abundance records, of 2,367 fish taxa, from 1,879 sites in coral and rocky reefs distributed worldwide. Data were systematically collected using standardized methods, offering new opportunities to assess broad-scale spatial patterns in community structure. The development of such a large dataset was made possible through contributions of investigators associated with science and conservation agencies worldwide, and the assistance of a team of over 100 recreational SCUBA divers, who undertook training in scientific techniques for underwater surveys and voluntarily contributed skills, expertise and their time to data collection. PMID:25977765

  15. Pharmaceutical Metabolism in Fish: Using a 3-D Hepatic In Vitro Model to Assess Clearance

    PubMed Central

    Baron, Matthew G.; Mintram, Kate S.; Owen, Stewart F.; Hetheridge, Malcolm J.; Moody, A. John; Purcell, Wendy M.; Jackson, Simon K.; Jha, Awadhesh N.

    2017-01-01

    At high internal doses, pharmaceuticals have the potential for inducing biological/pharmacological effects in fish. One particular concern for the environment is their potential to bioaccumulate and reach pharmacological levels; the study of these implications for environmental risk assessment has therefore gained increasing attention. To avoid unnecessary testing on animals, in vitro methods for assessment of xenobiotic metabolism could aid in the ecotoxicological evaluation. Here we report the use of a 3-D in vitro liver organoid culture system (spheroids) derived from rainbow trout to measure the metabolism of seven pharmaceuticals using a substrate depletion assay. Of the pharmaceuticals tested, propranolol, diclofenac and phenylbutazone were metabolised by trout liver spheroids; atenolol, metoprolol, diazepam and carbamazepine were not. Substrate depletion kinetics data was used to estimate intrinsic hepatic clearance by this spheroid model, which was similar for diclofenac and approximately 5 fold higher for propranolol when compared to trout liver microsomal fraction (S9) data. These results suggest that liver spheroids could be used as a relevant and metabolically competent in vitro model with which to measure the biotransformation of pharmaceuticals in fish; and propranolol acts as a reproducible positive control. PMID:28045944

  16. 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

  17. Revised Protocols for Sampling Algal, Invertebrate, and Fish Communities as Part of the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Moulton, Stephen R.; Kennen, Jonathan G.; Goldstein, Robert M.; Hambrook, Julie A.

    2002-01-01

    Algal, invertebrate, and fish communities are characterized as part of ecological studies in the U.S. Geological Survey.s National Water-Quality Assessment Program. Information from these ecological studies, together with chemical and physical data, provide an integrated assessment of water quality at local, regional, and national scales. Analysis and interpretation of water-quality data at these various geographic scales require accurate and consistent application of sampling protocols and sample-processing procedures. This report revises and unifies into a single document the algal, invertebrate, and fish community sampling protocols used in the National Water-Quality Assessment Program.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Risk assessment of N-nitrosodimethylamine formed endogenously after fish-with-vegetable meals.

    PubMed

    Zeilmaker, Marco J; Bakker, Martine I; Schothorst, Ronald; Slob, Wout

    2010-07-01

    The consumption of fish and nitrate-rich vegetables may lead to the formation of the genotoxic carcinogen N-nitrosodimethylamine (NDMA) in the stomach. To assess human cancer risk associated with this formation, a dynamic in vitro gastrointestinal model was used to simulate NDMA formation in the stomach after a fish + vegetable meal. The experimental results were combined with statistical modeling of Dutch food consumption data resulting in predicted exposures to endogenously formed NDMA in the population. The 95th percentile of the long-term exposure distribution was around 4 ng/kg-bw in young children and 0.4 ng/kg-bw in adults. By comparing this exposure with the Benchmark Dose Lower bound (BMDL) 10 for liver cancer in a chronic carcinogenicity study, a chronic margin of exposure (MOE) was calculated of 7000 and 73,000 for young children and adults. Furthermore, the long-term exposure distribution was combined with a dose-response analysis of the liver cancer incidence data to obtain a cancer risk distribution for the human population. The 95th percentile of that distribution was 6 x 10(-6) extra risk for 5-year-old children and 8 x 10(-7) for adults. The liver cancer data allowed for the analysis of the relationship between tumor incidence and time to tumor. For an extra risk of 10(-6), the decrease in time to tumor was conservatively estimated at 3.8 min in the rat, equivalent to 0.1 days in humans. We also combined acute exposure estimates with the BMDL10 from an acute carcinogenicity study for NDMA, resulting in an acute MOE of 110,000. We conclude that the combined consumption of fish and nitrate-rich vegetables appears to lead to marginal increases of additional cancer risk.

  5. 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.

  6. 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.

  7. Numerical assessment for a broadband and tuned noise using hybrid mufflers and a simulated annealing method

    NASA Astrophysics Data System (ADS)

    Chiu, Min-Chie

    2013-06-01

    A broadband noise hybridized with pure tones often occurs in practical engineering work. However, assessments of a muffler's optimal shape design that would simultaneously overcome a broadband noise hybridized with multiple tones within a constrained space were rarely addressed. In order to promote the best acoustical performance in mufflers, five kinds of the hybrid mufflers composed of a reactive unit, a dissipative unit, and Helmholtz resonator (HR) units will be proposed. Moreover, to strengthen the noise elimination at the pure tone, mufflers having parallel multiple-sectioned HRs or having multiple HR connections in series (muffler D and muffler E) will be also presented in the noise abatement. On the basis of the plane wave theory, the four-pole system matrix used to evaluate the acoustic performance of a multi-tone hybrid Helmholtz muffler will be presented. A numerical case for eliminating broadband noise hybridized with a pure tone emitted from a machine room using five kinds of mufflers (muffler A-E) will also be introduced. To find the best acoustical performance of a space-constrained muffler, a numerical assessment using a simulated annealing (SA) method is adopted. To verify the availability of the SA optimization, a numerical optimization of muffler A at a pure tone (280 Hz) is exemplified. Before the SA operation can be carried out, the accuracy of the mathematical model will be checked using the experimental data. The influences of the sound transmission loss (STL) with respect to N1-array HR and the STL with respect to one-array HR sectioned in N2 divisions have also been assessed. Also, the influence of the STL with respect to the design parameters such as the ratio of d1/d2, the diameter of the perforated hole (dH), the porosity (p%) of the perforated plate, and the outer diameter (d2) of the dissipative unit has been analyzed. Consequently, a successful approach in eliminating a broadband noise hybridized with a pure tone using optimally

  8. 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).

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Multibiomarker approach in fish to assess the impact of pollution in a large Brazilian river, Paraiba do Sul.

    PubMed

    Linde-Arias, Ana Rosa; Inácio, Alan F; Novo, Leonardo A; de Alburquerque, Carla; Moreira, Josino C

    2008-12-01

    This article examines the advantages of the use of biomarkers as environmental indicators by applying it to Paraiba do Sul watershed, one of the most important Brazilian water bodies, which is in a critical environmental situation. We use a multibiomarker approach in fish as an integrated strategy to assess the impact of pollution. It comprehends a general biomarker of fish health, the condition factor (CF), and specific biomarkers of contaminant exposure such as metallothionein (MT), acetylcholinesterase (AChE) activity and biliary polycyclic aromatic hydrocarbons (PAH) metabolites. Our results revealed different effects in the fish from diverse locations with varying degrees of pollution. Furthermore, fish located just upstream of the water-treatment plant of the metropolitan area of Rio de Janeiro has shown to be affected by metals. This study indicates the usefulness of integrating a set of biomarkers to define the effects of anthropogenic inputs in aquatic bodies under complex polluted situations.

  16. 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

  17. 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.

  18. 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.

  19. Accumulation of polychlorinated biphenyls in fish and assessment of dietary exposure: a study in Hyderabad City, India.

    PubMed

    Ahmed, M Noor; Sinha, Sukesh Narayan; Vemula, Sudershan Rao; Sivaperumal, P; Vasudev, K; Ashu, Shaik; Mendu, Vishnu Vardhana Rao; Bhatnagar, V

    2016-02-01

    The objective of this study is to determine the concentrations of polychlorinated biphenyls (PCBs) in different fish species collected from fish outlets in the south Indian city of Hyderabad. The samples of fish extracted by using Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) and concentrations of polychlorinated biphenyls (PCBs, 45 congeners) were determined by gas chromatography-microelectron capture detection (GC-μECD) method. The intake of individual PCB congeners through fish, toxicity equivalence factors (TEFs), hazardous quotient, quantitative assessment, and risk evaluations was estimated in the Indian population. Daily dietary intakes of PCBs at the 95th-percentile-measured concentrations were twice the values of the 50th-percentile-measured concentrations in all socio-economic groups. The dietary intakes of PCBs through fish consumption in middle-income group, low-income group, and industrial laborers (0.023 μg kg(-1) day(-1)), the high-income group (0.031 μg kg(-1) day(-1)), and slum dwellers (0.039 μg kg(-1) day(-1)) exceeded the reference dose. The observed estimated daily intakes (EDIs) of our study for all socio-economic sections (0.0087 μg/kg/day) crossed the cancer benchmark concentration of 0.0003 μg/kg/day. In slum dwellers, the ingestion of fish from freshwater and marine water results in the highest lifetime cancer risks of 4.7 in 100,000 and 7.8 in 100,000, respectively. Ultimately, the concentrations of PCBs were determined high in all of the fish species collected. Risk assessment showed that the fish were highly contaminated with PCBs and may pose health threats to consumers in the city of Hyderabad as well as a lifetime cancer risk.

  20. Effects of pulp and paper mill effluent on fish: a temporal assessment of fish health across sampling cycles.

    PubMed

    Barrett, Timothy J; Lowell, Richard B; Tingley, Maureen A; Munkittrick, Kelly R

    2010-02-01

    The Canadian environmental effects monitoring (EEM) program is a regulated, cyclical, industry-funded program designed to determine whether receiving water impacts exist when a mill is in compliance with its discharge limits. The results from three cycles of the fish monitoring program (1992 to 2004) are available from over 200 surveys of fish compared between sites located upstream and downstream of pulp and paper mill effluent outfalls. Previous meta-analyses have shown a national average response pattern across cycles characterized by an increase in endpoints measuring energy storage and growth and a decrease in a reproductive endpoint, consistent with a response of nutrient enrichment in combination with some form of metabolic disruption. Although the national average pattern of effects was temporally consistent, there was some variability in the magnitude of effects among cycles. Questions were raised as to whether the intercycle variability was due to changes in effluent quality or due, at least in part, to other factors. The present study compares responses over the first three cycles, and shows that the choice of sentinel species is likely to be a major contributing factor to the variability in observed effects. Subset analyses using studies from mills that used the same sentinel species across cycles reveal fairly uniform responses and little evidence of significant improvements in overall fish health from cycles one to three. However, a meta-analysis using 1991 data collected from 10 mills before the implementation of the EEM program and data from the same mills collected during cycles one to three of the program reveal significantly reduced effects on relative liver weight and potential improvements in other endpoints.

  1. 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.; Carins, V.W.; Hodson, P.V.; Nriagu, J.

    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.

  2. From fish chemical characterisation to the benefit-risk assessment--part A.

    PubMed

    Afonso, Cláudia; Lourenço, Helena Maria; Cardoso, Carlos; Bandarra, Narcisa Maria; Carvalho, Maria Luísa; Castro, Matilde; Nunes, Maria Leonor

    2013-04-15

    Proximate composition, fatty acid profile, cholesterol, α-tocoferol content and essential (K, Na, Cl, S, Mg, Ca, Zn, Cu, Fe, Mn, and Se) and contaminant element (Hg/MeHg, Cd, Pb, and As) levels in silver scabbardfish (Lepidopus caudatus), hake (Merluccius merluccius), and ray (Raja spp.) were investigated. Results showed that these species contain high protein, low cholesterol and energy levels, being its consumption recommended. Polyunsaturated fatty acids (PUFA) were the dominant group of the fatty acids, being 80% of the n-3 family. Attending to the dietary reference intakes (DRIs), these fish species are a good source of Se and the other minerals can give a relevant contribution to the DRIs in a balanced diet. More than one weekly meal of silver scabbardfish has to be avoided due to the organic mercury concentration. More accurate dietary recommendations require a probabilistic assessment, which will be the focus of this study's Part B.

  3. Toxicity assessment of the puffer fish Lagocephalus lagocephalus from the Tunisian coast.

    PubMed

    Saoudi, Mongi; Abdelmouleh, Abdelwaheb; Kammoun, Wassim; Ellouze, Feriel; Jamoussi, Kamel; El Feki, Abdelfattah

    2008-08-01

    This study was undertaken to assess the risk of poisoning due to consumption of the puffer fish Lagocephalus lagocephalus collected along the Tunisian coast. Wistar rats were daily intraperitoneally injected, for 10 days, with acidic extracts of liver or flesh (muscles + skin) of L. lagocephalus. Control rats received injections of NaCl (0.9%). No mortality and no evident signs of neurotoxicity were recorded in treated rats. Conversely, treatment led to: (1) diarrhoea and body and organ (liver, kidney) weights loss; (2) oxidative stress evidenced by an increase in lipid peroxidation (TBARS) and conversely a decrease in antioxidant enzyme activities (SOD, catalase, GSH-Px) in tissues (blood cells, liver, kidneys); (3) a decrease in alanine aminotransferase (ALT) and alkaline phosphatase (ALP) activities in blood plasma.

  4. 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.

  5. Turbo FISH: A Method for Rapid Single Molecule RNA FISH

    PubMed Central

    Shaffer, Sydney M.; Wu, Min-Tzu; Levesque, Marshall J.; Raj, Arjun

    2013-01-01

    Advances in RNA fluorescence in situ hybridization (RNA FISH) have allowed practitioners to detect individual RNA molecules in single cells via fluorescence microscopy, enabling highly accurate and sensitive quantification of gene expression. However, current methods typically employ hybridization times on the order of 2–16 hours, limiting its potential in applications like rapid diagnostics. We present here a set of conditions for RNA FISH (dubbed Turbo RNA FISH) that allow us to make accurate measurements with no more than 5 minutes of hybridization time and 3 minutes of washing, and show that hybridization times can go as low as 30 seconds while still producing quantifiable images. We further show that rapid hybridization is compatible with our recently developed iceFISH and SNP FISH variants of RNA FISH that enable chromosome and single base discrimination, respectively. Our method is simple and cost effective, and has the potential to dramatically increase the throughput and realm of applicability of RNA FISH. PMID:24066168

  6. 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)

  7. 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.

  8. Rapid assessment of the toxicity of oil sands process-affected waters using fish cell lines.

    PubMed

    Sansom, Bryan; Vo, Nguyen T K; Kavanagh, Richard; Hanner, Robert; Mackinnon, Michael; Dixon, D George; Lee, Lucy E J

    2013-01-01

    Rapid and reliable toxicity assessment of oil sands process-affected waters (OSPW) is needed to support oil sands reclamation projects. Conventional toxicity tests using whole animals are relatively slow, costly, and often subjective, while at the same time requiring the sacrifice of test organisms as is the case with lethal dosage/concentration assays. A nonlethal alternative, using fish cell lines, has been developed for its potential use in supporting oil sands reclamation planning and to help predict the viability of aquatic reclamation models such as end-pit lakes. This study employed six fish cell lines (WF-2, GFSk-S1, RTL-W1, RTgill-W1, FHML, FHMT) in 24 h viability assays for rapid fluorometric assessment of cellular integrity and functionality. Forty-nine test water samples collected from the surface of oil sands developments in the Athabasca Oil Sands deposit, north of Fort McMurray, Alberta, Canada, were evaluated in blind. Small subsample volumes (8 ml) were mixed with 2 ml of 5× concentrated exposure media and used for direct cell exposures. All cell line responses in terms of viability as measured by Alamar blue assay, correlated well with the naphthenic acids (NA) content in the samples (R (2) between 0.4519 and 0.6171; p<0.0001) when data comparisons were performed after the bioassays. NA or total acid-extractable organics group has been shown to be responsible for most of the acute toxicity of OSPW and our results further corroborate this. The multifish cell line bioassay provides a strong degree of reproducibility among tested cell lines and good relative sensitivity of the cell line bioassay as compared to available in vivo data that could lead to cost effective, high-throughput screening assays.

  9. 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...

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology

    PubMed Central

    Brown, A. R.; Gunnarsson, L.; Kristiansson, E.; Tyler, C. R.

    2014-01-01

    Fish represent the planet's most diverse group of vertebrates and they can be exposed to a wide range of pharmaceuticals. For practical reasons, extrapolation of pharmaceutical effects from ‘model’ species to other fish species is adopted in risk assessment. Here, we critically assess this approach. First, we show that between 65% and 86% of human drug targets are evolutionarily conserved in 12 diverse fish species. Focusing on nuclear steroid hormone receptors, we further show that the sequence of the ligand binding domain that plays a key role in drug potency is highly conserved, but there is variation between species. This variation for the oestrogen receptor, however, does not obviously account for observed differences in receptor activation. Taking the synthetic oestrogen ethinyloestradiol as a test case, and using life-table-response experiments, we demonstrate significant reductions in population growth in fathead minnow and medaka, but not zebrafish, for environmentally relevant exposures. This finding contrasts with zebrafish being ranked as more ecologically susceptible, according to two independent life-history analyses. We conclude that while most drug targets are conserved in fish, evolutionary divergence in drug-target activation, physiology, behaviour and ecological life history make it difficult to predict population-level effects. This justifies the conventional use of at least a 10× assessment factor in pharmaceutical risk assessment, to account for differences in species susceptibility. PMID:25405965

  20. 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

  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. 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

  3. 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.

  4. 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.

  5. 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.

  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. 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

  8. Effects of commonly used cooking practices on total mercury concentration in fish and their impact on exposure assessments.

    PubMed

    Morgan, J N; Berry, M R; Graves, R L

    1997-01-01

    The effects of cooking practices commonly used by Native Americans on total mercury concentrations in fish were investigated. A preparation factor relating mercury concentrations in fish as prepared for consumption to mercury concentration data as measured in typical environmental monitoring programs was calculated. Preparation factors are needed to provide risk assessors with a more accurate estimate of the actual amount of mercury ingested through consumption of contaminated fish. Data on fish preparation and consumption practices of two communities of Chippewa residing on the shores of Lake Superior in northern Wisconsin were used to select practices for study. The most commonly consumed species, walleye and lake trout, were selected. Whitefish livers were also selected for study. Commonly used cooking techniques including panfrying, deep-frying, baking, boiling, and smoking were duplicated in the laboratory. Total mercury concentrations were determined in fish portions before and after cooking and in a portion representative of that analyzed in programs to assess water quality (skin-on fillets). Total mercury was determined by microwave digestion-cold vapor atomic absorption spectroscopy. Mercury concentrations (wet weight basis) in panfried, baked, and boiled walleye fillets and deep-fried and baked whitefish livers ranged from 1.1 to 1.5 times higher than in corresponding raw portions. In lake trout, mercury concentrations were 1.5 to 2.0 times higher in cooked portions than in the raw portion. However, total mercury levels were constant before and after cooking, indicating the concentration effect is caused by weight (moisture and fat) loss. The addition of lemon juice to potentially release mercury from its bound state and promote volatilization did not exert any measurable influence on mercury concentrations in cooked walleye. In some cases mercury concentrations were increased with increased cooking times due to further loss of moisture and fat

  9. 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.

  10. 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

  11. A CO-FISH assay to assess sister chromatid segregation patterns in mitosis of mouse embryonic stem cells.

    PubMed

    Sauer, Stephan; Burkett, Sandra S; Lewandoski, Mark; Klar, Amar J S

    2013-05-01

    Sister chromatids contain identical DNA sequence but are chiral with respect to both their helical handedness and their replication history. Emerging evidence from various model organisms suggests that certain stem cells segregate sister chromatids nonrandomly to either maintain genome integrity or to bias cellular differentiation in asymmetric cell divisions. Conventional methods for tracing of old vs. newly synthesized DNA strands generally lack resolution for individual chromosomes and employ halogenated thymidine analogs with profound cytotoxic effects on rapidly dividing cells. Here, we present a modified chromosome orientation fluorescence in situ hybridization (CO-FISH) assay, where identification of individual chromosomes and their replication history is achieved in subsequent hybridization steps with chromosome-specific DNA probes and PNA telomere probes. Importantly, we tackle the issue of BrdU cytotoxicity and show that our method is compatible with normal mouse ES cell biology, unlike a recently published related protocol. Results from our CO-FISH assay show that mitotic segregation of mouse chromosome 7 is random in ES cells, which contrasts previously published results from our laboratory and settles a controversy. Our straightforward protocol represents a useful resource for future studies on chromatid segregation patterns of in vitro-cultured cells from distinct model organisms.

  12. 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.

  13. Spatially intensive sampling by electrofishing for assessing longitudinal discontinuities in fish distribution in a headwater stream

    USGS Publications Warehouse

    Le Pichon, Céline; Tales, Évelyne; Belliard, Jérôme; Torgersen, Christian E.

    2017-01-01

    Spatially intensive sampling by electrofishing is proposed as a method for quantifying spatial variation in fish assemblages at multiple scales along extensive stream sections in headwater catchments. We used this method to sample fish species at 10-m2 points spaced every 20 m throughout 5 km of a headwater stream in France. The spatially intensive sampling design provided information at a spatial resolution and extent that enabled exploration of spatial heterogeneity in fish assemblage structure and aquatic habitat at multiple scales with empirical variograms and wavelet analysis. These analyses were effective for detecting scales of periodicity, trends, and discontinuities in the distribution of species in relation to tributary junctions and obstacles to fish movement. This approach to sampling riverine fishes may be useful in fisheries research and management for evaluating stream fish responses to natural and altered habitats and for identifying sites for potential restoration.

  14. Technology assessments of advanced energy storage systems for electric and hybrid vehicles

    NASA Astrophysics Data System (ADS)

    1993-04-01

    Flywheels, hydropneumatic accumulators (in vehicles with a hydrostatic powertrain), and superconducting magnets were assessed as candidate technologies for recovering braking energy and averaging power demands in electric and hybrid vehicles. The technologies were also assessed for their suitability for fulfilling the entire energy storage requirement in vehicles. The scope of the technology assessments included the current state-of-the-art and developments anticipated within the next few years in the US and abroad. Key individuals and companies currently working on each technology contributed technical information to the study. Some of these individuals and companies are nearing the pre-production prototype stage with systems suitable for automobiles. Several have constructed systems using similar technology for other applications, including satellites and industrial equipment.

  15. Assessing population effects from entrainment of fish at a large volume water intake

    SciTech Connect

    Gray, R.H.; Page, T.L.; Neitzel, D.A.; Dauble, D.D.

    1986-01-01

    A method is described for estimating population effects from entrainment of juvenile chinook salmon (Oncorhynchus tshawytscha) at a steam electric generating station on the Columbia River that required cooperation between power plant operators and fishery biologists. The method involved sampling fish in the river and entrained fish (both marked recaptures and naturally occurring downstream migrants) within the intake, and estimating the 1) total number of fish entrained, 2) size of the natural population, and 3) percent of the natural population affected.

  16. 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.

  17. Determination and assessment of total mercury levels in local, frozen and canned fish in Lebanon.

    PubMed

    Obeid, Pierre J; El-Khoury, Bilal; Burger, Joanne; Aouad, Samer; Younis, Mira; Aoun, Amal; El-Nakat, John Hanna

    2011-01-01

    Fish is an important constituent of the Lebanese diet. However, very little attention in our area is given to bring awareness regarding the effect of the toxicity of mercury (Hg) mainly through fish consumption. This study aimed to report analytical data on total mercury levels in several fish species for the first time in thirty years and to also made individuals aware of the presence and danger from exposure to mercury through fish consumption. Fish samples were selected from local Lebanese markets and fisheries and included 94 samples of which were fresh, frozen, processed, and canned fish. All values were reported as microgram of mercury per gram of fish based on wet weight. The level of mercury ranged from 0.0190 to 0.5700 microg/g in fresh samples, 0.0059 to 0.0665 microg/g in frozen samples, and 0.0305 to 0.1190 microg/g in canned samples. The data clearly showed that higher levels of mercury were detected in local fresh fish as opposed to other types thus placing consumers at higher risk from mercury exposure. Moreover, the data revealed that Mallifa (yellowstripe barracuda/Sphyraena chrysotaenia), Sargous (white seabream/Diplodus sargus), Ghobbos (bogue/Boops boops), and shrimp (Penaeus sp.) were among the types containing the highest amounts of mercury. On the other hand, processed fish such as fish fillet, fish burger, small shrimp and crab are found to contain lower levels of mercury and are associated with lower exposure risks to mercury. Lebanese population should therefore, be aware to consume limited amounts of fresh local fish to minimize exposure to mercury.

  18. Development and assessment of indices to determine stream fish vulnerability to climate change and habitat alteration

    USGS Publications Warehouse

    Sievert, Nicholas A.; Paukert, Craig P.; Tsang, Yin-Phan; Infante, Dana M.

    2016-01-01

    Understanding the future impacts of climate and land use change are critical for long-term biodiversity conservation. We developed and compared two indices to assess the vulnerability of stream fish in Missouri, USA based on species environmental tolerances, rarity, range size, dispersal ability and on the average connectivity of the streams occupied by each species. These two indices differed in how environmental tolerance was classified (i.e., vulnerability to habitat alteration, changes in stream temperature, and changes to flow regimes). Environmental tolerance was classified based on measured species responses to habitat alteration, and extremes in stream temperatures and flow conditions for one index, while environmental tolerance for the second index was based on species’ traits. The indices were compared to determine if vulnerability scores differed by index or state listing status. We also evaluated the spatial distribution of species classified as vulnerable to habitat alteration, changes in stream temperature, and change in flow regimes. Vulnerability scores were calculated for all 133 species with the trait association index, while only 101 species were evaluated using the species response index, because 32 species lacked data to analyze for a response. Scores from the trait association index were greater than the species response index. This is likely due to the species response index's inability to evaluate many rare species, which generally had high vulnerability scores for the trait association index. The indices were consistent in classifying vulnerability to habitat alteration, but varied in their classification of vulnerability due to increases in stream temperature and alterations to flow regimes, likely because extremes in current climate may not fully capture future conditions and their influence on stream fish communities. Both indices showed higher mean vulnerability scores for listed species than unlisted species, which provided a coarse

  19. 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

  20. Effective assessment of tyre-road friction coefficient using a hybrid estimator

    NASA Astrophysics Data System (ADS)

    Ren, Hongbin; Chen, Sizhong; Shim, Taehyun; Wu, Zhicheng

    2014-08-01

    Vehicle stability and active safety control depend heavily on tyre forces available on each wheel of a vehicle. Since tyre forces are strongly affected by the tyre-road friction coefficient, it is crucial to optimise the use of the adhesion limits of the tyres. This study presents a hybrid method to identify the road friction limitation; it contributes significantly to active vehicle safety. A hybrid estimator is developed based on the three degrees-of-freedom vehicle model, which considers longitudinal, lateral and yaw motions. The proposed hybrid estimator includes two sub-estimators: one is the vehicle state information estimator using the unscented Kalman filter and another is the integrated road friction estimator. By connecting two sub-estimators simultaneously, the proposed algorithm can effectively estimate the road friction coefficient. The performance of the proposed estimation algorithm is validated in CarSim/Matlab co-simulation environment under three different road conditions (high-μ, low-μ and mixed-μ). Simulation results show that the proposed estimator can assess vehicle states and road friction coefficient with good accuracy.

  1. Comprehensive meiotic segregation analysis of a 4-breakpoint t(1;3;6) complex chromosome rearrangement using single sperm array comparative genomic hybridization and FISH.

    PubMed

    Hornak, Miroslav; Vozdova, Miluse; Musilova, Petra; Prinosilova, Petra; Oracova, Eva; Linkova, Vlasta; Vesela, Katerina; Rubes, Jiri

    2014-10-01

    Complex chromosomal rearrangements (CCR) represent rare structural chromosome abnormalities frequently associated with infertility. In this study, meiotic segregation in spermatozoa of an infertile normospermic carrier of a 4-breakpoint t(1;3;6) CCR was analysed. A newly developed array comparative genomic hybridization protocol was used, and all chromosomes in 50 single sperm cells were simultaneously examined. Three-colour FISH was used to analyse chromosome segregation in 1557 other single sperm cells. It was also used to measure an interchromosomal effect; sperm chromatin structure assay was used to measure chromatin integrity. A high-frequency of unbalanced spermatozoa (84%) was observed, mostly arising from the 3:3 symmetrical segregation mode. Array comparative genomic hybridization was used to detect additional aneuploidies in two out of 50 spermatozoa (4%) in chromosomes not involved in the complex chromosome rearrangement. Significantly increased rates of diploidy and XY disomy were found in the CCR carrier compared with the control group (P < 0.001). Defective condensation of sperm chromatin was also found in 22.7% of spermatozoa by sperm chromatin structure assay. The results indicate that the infertility in the man with CCR and normal spermatozoa was caused by a production of chromosomally unbalanced, XY disomic and diploid spermatozoa and spermatozoa with defective chromatin condensation.

  2. 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.

  3. 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

  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. Characterization of Saccharomyces uvarum (Beijerinck, 1898) and related hybrids: assessment of molecular markers that predict the parent and hybrid genomes and a proposal to name yeast hybrids.

    PubMed

    Nguyen, Huu-Vang; Boekhout, Teun

    2017-03-03

    The use of the nuclear-DNA re-association technique has led taxonomists to consider Saccharomyces uvarum a synonym of S. bayanus. The latter, however, is not a species but a hybrid harbouring S. eubayanus (Seu) and S. uvarum (Su) sub-genomes with a minor DNA contribution from S. cerevisiae (Sc). To recognize genetically pure lines of S. uvarum and putative interspecies hybrids among so-called S. bayanus strains present in public culture collections, we propose the use of four markers that were defined from the S. bayanus CBS 380T composite genome, namely SeuNTS2 (rDNA), ScMAL31, MTY1 and SuMEL1. S. carlsbergensis CBS 1513 was found similar to S. bayanus except that it carries the SeuMEL1 allele. Different marker combinations revealed that among 33 strains examined only few strains were similar to CBS 380T, but many pure S. uvarum lines and putative Su/Seu-related hybrids occurred. Our results demonstrated that these hybrids were erroneously considered authentic S. bayanus and therefore the varietal state "Saccharomyces bayanus var. uvarum comb. nov. Naumov" is not valid. Our markers constitute a tool to get insights into the genomic makeup of Saccharomyces interspecies hybrids. We also make a proposal to name those hybrids that may also be applicable to other fungal hybrids.

  6. 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.

  7. Quantum-dot-labeled DNA probes for fluorescence in situ hybridization (FISH) in the microorganism Escherichia coli.

    PubMed

    Wu, Sheng-Mei; Zhao, Xiang; Zhang, Zhi-Ling; Xie, Hai-Yan; Tian, Zhi-Quan; Peng, Jun; Lu, Zhe-Xue; Pang, Dai-Wen; Xie, Zhi-Xiong

    2006-05-12

    Semiconductor quantum dots (QDs) as a kind of nonisotopic biological labeling material have many unique fluorescent properties relative to conventional organic dyes and fluorescent proteins, such as composition- and size-dependent absorption and emission, a broad absorption spectrum, photostability, and single-dot sensitivity. These properties make them a promising stable and sensitive label, which can be used for long-term fluorescent tracking and subcellular location of genes and proteins. Here, a simple approach for the construction of QD-labeled DNA probes was developed by attaching thiol-ssDNA to QDs via a metal-thiol bond. The as-prepared QD-labeled DNA probes had high dispersivity, bioactivity, and specificity for hybridization. Based on such a kind of probe with a sequence complementary to multiple clone sites in plasmid pUC18, fluorescence in situ hybridization of the tiny bacterium Escherichia coli has been realized for the first time.

  8. 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

  9. 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.

  10. 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.

  11. An Indirect Cue of Predation Risk Counteracts Female Preference for Conspecifics in a Naturally Hybridizing Fish Xiphophorus birchmanni

    PubMed Central

    Willis, Pamela M.; Rosenthal, Gil G.; Ryan, Michael J.

    2012-01-01

    Mate choice is context dependent, but the importance of current context to interspecific mating and hybridization is largely unexplored. An important influence on mate choice is predation risk. We investigated how variation in an indirect cue of predation risk, distance to shelter, influences mate choice in the swordtail Xiphophorus birchmanni, a species which sometimes hybridizes with X. malinche in the wild. We conducted mate choice experiments to determine whether females attend to the distance to shelter and whether this cue of predation risk can counteract female preference for conspecifics. Females were sensitive to shelter distance independent of male presence. When conspecific and heterospecific X. malinche males were in equally risky habitats (i.e., equally distant from shelter), females associated primarily with conspecifics, suggesting an innate preference for conspecifics. However, when heterospecific males were in less risky habitat (i.e., closer to shelter) than conspecific males, females no longer exhibited a preference, suggesting that females calibrate their mate choices in response to predation risk. Our findings illustrate the potential for hybridization to arise, not necessarily through reproductive “mistakes”, but as one of many potential outcomes of a context-dependent mate choice strategy. PMID:22529936

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

    PubMed

    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.

  13. 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.

  14. 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/.

  15. 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).

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

    PubMed Central

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

    1987-01-01

    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 aquatic 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. PMID:3297660

  17. 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

  18. Disposable E-Tongue for the Assessment of Water Quality in Fish Tanks

    PubMed Central

    Chang, Chew-Cheen; Saad, Bahruddin; Surif, Misni; Ahmad, Mohd Noor; Shakaff, Ali Yeon Md

    2008-01-01

    A disposable screen-printed e-tongue based on sensor array and pattern recognition that is suitable for the assessment of water quality in fish tanks is described. The characteristics of sensors fabricated using two kinds of sensing materials, namely (i) lipids (referred to as Type 1), and (ii) alternative electroactive materials comprising liquid ion-exchangers and macrocyclic compounds (Type 2) were evaluated for their performance stability, sensitivity and reproducibility. The Type 2 e-tongue was found to have better sensing performance in terms of sensitivity and reproducibility and was thus used for application studies. By using a pattern recognition tool i.e. principal component analysis (PCA), the e-tongue was able to discriminate the changes in the water quality in tilapia and catfish tanks monitored over eight days. E-tongues coupled with partial least squares (PLS) was used for the quantitative analysis of nitrate and ammonium ions in catfish tank water and good agreement were found with the ion-chromatography method (relative error, ±1.04- 4.10 %). PMID:27879900

  19. 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.

  20. 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...

  1. Assessment of the St. Louis River AOC fish tumors and other deformities beneficial use impairment

    EPA Science Inventory

    The Fish Tumors and Other Deformities Beneficial Use Impairment (BUI) was listed as one of nine BUIs at the time the St. Louis River AOC was designated in 1987. At the time, no formal studies had been conducted to estimate the prevalence of either fish tumors or deformities. To a...

  2. Contents and risk assessment of heavy metals in marine invertebrates from Korean coastal fish markets.

    PubMed

    Mok, Jong Soo; Kwon, Ji Young; Son, Kwang Tae; Choi, Woo Seok; Kang, Sung Rim; Ha, Na Young; Jo, Mi Ra; Kim, Ji Hoe

    2014-06-01

    The concentrations of the heavy metals cadmium (Cd), mercury (Hg), lead (Pb), chromium, silver, nickel, copper, and zinc in the edible portions of 105 marine invertebrates representing 16 mollusk and crustacean species were accurately determined to evaluate their hazard for human consumption. The samples were collected in 2011 from major fish markets on the coast of Korea and analyzed for Hg using a direct Hg analyzer and for other metals using inductively coupled plasma mass spectrometry. Estimated dietary exposure (EDE) was determined, and a risk assessment was made of the heavy metals to provide information concerning consumer safety. The Cd concentrations, which were the highest for the three hazardous metals (Cd, Hg, and Pb), were significantly higher (P < 0.05) in the bivalves and crabs than in the gastropods and cephalopods. However, the concentrations of these metals in all samples were within the regulatory limits set by Korea and other countries. The EDE was compared with the provisional tolerable daily intake (PTDI) adopted by the Joint FAO/WHO Expert Committee on Food Additives or the U.S. Environmental Protection Agency. The EDE of Cd, Hg, and Pb for each class of marine invertebrate were 0.07 to 2.64, 0.01 to 0.43, and 0.001 to 0.16% of the PTDI, respectively. The total EDE of Cd, Hg, and Pb for marine invertebrates accounted for 4.03, 0.96, and 0.21%, respectively, of the PTDI. The EDE of other metals in each class of marine invertebrate was less than 2% of the PTDI. The hazard index is a reasonable parameter for assessing the risk of heavy metal consumption associated with contaminated food. In the present study, the hazard index for all of the species was less than 1.0, which indicates that the intake of heavy metals from consumption of these marine invertebrates does not represent an appreciable hazard to humans.

  3. 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.

  4. 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.

  5. Unveiling the neurotoxicity of methylmercury in fish (Diplodus sargus) through a regional morphometric analysis of brain and swimming behavior assessment.

    PubMed

    Puga, Sónia; Pereira, Patrícia; Pinto-Ribeiro, Filipa; O'Driscoll, Nelson J; Mann, Erin; Barata, Marisa; Pousão-Ferreira, Pedro; Canário, João; Almeida, Armando; Pacheco, Mário

    2016-11-01

    The current study aims to shed light on the neurotoxicity of MeHg in fish (white seabream - Diplodus sargus) by the combined assessment of: (i) MeHg toxicokinetics in the brain, (ii) brain morphometry (volume and number of neurons plus glial cells in specific brain regions) and (iii) fish swimming behavior (endpoints associated with the motor performance and the fear/anxiety-like status). Fish were surveyed for all the components after 7 (E7) and 14 (E14) days of dietary exposure to MeHg (8.7μgg(-1)), as well as after a post-exposure period of 28days (PE28). MeHg was accumulated in the brain of D. sargus after a short time (E7) and reached a maximum at the end of the exposure period (E14), suggesting an efficient transport of this toxicant into fish brain. Divalent inorganic Hg was also detected in fish brain along the experiment (indicating demethylation reactions), although levels were 100-200 times lower than MeHg, which pinpoints the organic counterpart as the great liable for the recorded effects. In this regard, a decreased number of cells in medial pallium and optic tectum, as well as an increased hypothalamic volume, occurred at E7. Such morphometric alterations were followed by an impairment of fish motor condition as evidenced by a decrease in the total swimming time, while the fear/anxiety-like status was not altered. Moreover, at E14 fish swam a greater distance, although no morphometric alterations were found in any of the brain areas, probably due to compensatory mechanisms. Additionally, although MeHg decreased almost two-fold in the brain during post-exposure, the levels were still high and led to a loss of cells in the optic tectum at PE28. This is an interesting result that highlights the optic tectum as particularly vulnerable to MeHg exposure in fish. Despite the morphometric alterations reported in the optic tectum at PE28, no significant changes were found in fish behavior. Globally, the effects of MeHg followed a multiphasic profile, where

  6. 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.

  7. Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes.

    PubMed

    Keller, I; Wagner, C E; Greuter, L; Mwaiko, S; Selz, O M; Sivasundar, A; Wittwer, S; Seehausen, O

    2013-06-01

    Adaptive radiations are an important source of biodiversity and are often characterized by many speciation events in very short succession. It has been proposed that the high speciation rates in these radiations may be fuelled by novel genetic combinations produced in episodes of hybridization among the young species. The role of such hybridization events in the evolutionary history of a group can be investigated by comparing the genealogical relationships inferred from different subsets of loci, but such studies have thus far often been hampered by shallow genetic divergences, especially in young adaptive radiations, and the lack of genome-scale molecular data. Here, we use a genome-wide sampling of SNPs identified within restriction site-associated DNA (RAD) tags to investigate the genomic consistency of patterns of shared ancestry and adaptive divergence among five sympatric cichlid species of two genera, Pundamilia and Mbipia, which form part of the massive adaptive radiation of cichlids in the East African Lake Victoria. Species pairs differ along several axes: male nuptial colouration, feeding ecology, depth distribution, as well as the morphological traits that distinguish the two genera and more subtle morphological differences. Using outlier scan approaches, we identify signals of divergent selection between all species pairs with a number of loci showing parallel patterns in replicated contrasts either between genera or between male colour types. We then create SNP subsets that we expect to be characterized to different extents by selection history and neutral processes and describe phylogenetic and population genetic patterns across these subsets. These analyses reveal very different evolutionary histories for different regions of the genome. To explain these results, we propose at least two intergeneric hybridization events (between Mbipia spp. and Pundamilia spp.) in the evolutionary history of these five species that would have lead to the evolution

  8. 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.

  9. A multi-criteria assessment of fishing gear impacts in demersal fisheries.

    PubMed

    Innes, James P; Pascoe, Sean

    2010-01-01

    Fishing gears have multiple impacts on the marine environment, and policies to reduce these impacts through modifying fishing gears are becoming common place. Different modifications result in different changes in the set of environmental impacts, and imply different sets of costs and benefits for different stakeholder groups. In this study, the analytic hierarchy process (AHP) is used to quantify the relative importance of the environmental impacts of fishing to different stakeholder groups. Forty eight individuals representing six different stakeholder groups (ecologists, biologists, economists, gear technologists, fishers and fisheries managers) were surveyed. As expected, fishers and gear technologists placed substantially greater importance on reducing discarding of commercial fish species than on habitat damage. Priorities of other stakeholder groups varied, but all placed greater priority on habitats than the commercial sector. The results suggest that management aimed at reducing environmental impacts of fishing broader than just discarding is appropriate, but such moves are likely to be opposed by the fishing industry. The derived weights also have a direct application to fisheries management, as they allow otherwise non-commensurate impacts to be aggregated into an overall impact to compare environmental benefits from alternative modifications of fishing gear.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  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. 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.

  18. 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

  19. A FISH-based method for assessment of HER-2 amplification status in breast cancer circulating tumor cells following CellSearch isolation

    PubMed Central

    Frithiof, Henrik; Aaltonen, Kristina; Rydén, Lisa

    2016-01-01

    Introduction Amplification of the HER-2/neu (HER-2) proto-oncogene occurs in 10%–15% of primary breast cancer, leading to an activated HER-2 receptor, augmenting growth of cancer cells. Tumor classification is determined in primary tumor tissue and metastatic biopsies. However, malignant cells tend to alter their phenotype during disease progression. Circulating tumor cell (CTC) analysis may serve as an alternative to repeated biopsies. The Food and Drug Administration-approved CellSearch system allows determination of the HER-2 protein, but not of the HER-2 gene. The aim of this study was to optimize a fluorescence in situ hybridization (FISH)-based method to quantitatively determine HER-2 amplification in breast cancer CTCs following CellSearch-based isolation and verify the method in patient samples. Methods Using healthy donor blood spiked with human epidermal growth factor receptor 2 (HER-2)-positive breast cancer cell lines, SKBr-3 and BT-474, and a corresponding negative control (the HER-2-negative MCF-7 cell line), an in vitro CTC model system was designed. Following isolation in the CellSearch system, CTC samples were further enriched and fixed on microscope slides. Immunocytochemical staining with cytokeratin and 4′,6-diamidino-2′-phenylindole dihydrochloride identified CTCs under a fluorescence microscope. A FISH-based procedure was optimized by applying the HER2 IQFISH pharmDx assay for assessment of HER-2 amplification status in breast cancer CTCs. Results A method for defining the presence of HER-2 amplification in single breast cancer CTCs after CellSearch isolation was established using cell lines as positive and negative controls. The method was validated in blood from breast cancer patients showing that one out of six patients acquired CTC HER-2 amplification during treatment against metastatic disease. Conclusion HER-2 amplification status of CTCs can be determined following CellSearch isolation and further enrichment. FISH is superior to

  20. [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

  1. Reduction of a large fish tissue analyte database: identifying and assessing data specific to a remediation site for risk assessment application.

    PubMed

    Tachovsky, J A; Urban, J D; Wikoff, D Staskal; Haws, L C; Harris, M A

    2010-07-01

    The Lower Passaic River (LPR) is one of the most heavily industrialized waterways in the US with both historical and continuing discharges of chemicals from point and non-point sources. Significant efforts have been initiated on behalf of public, private, and regulatory entities to restore this degraded urban river. Considerable attention has been devoted to characterizing environmental media with respect to human and ecological risk. As part of these efforts, a wealth of environmental data have been collected and analyzed for a variety of metals, pesticides, organic compounds, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), polychlorinated dibenzodioxins/furans (PCDD/Fs), and dioxin-like compounds. The objectives of the study described in this paper were two-fold: (1) to generate LPR-specific data for use in human health risk assessment by characterizing concentrations of contaminants in LPR fish tissue samples based on publicly available data using a methodical and transparent approach, and (2) using the resulting data, to calculate the contaminant concentrations in a "Representative Fish," which is a representation of proportional fish tissue concentrations calculated based upon consumption patterns of LPR anglers. The data reduction, processing, and analyses described provide a representative dataset for the conduct of a human health assessment associated with fish consumption from the LPR.

  2. 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.

  3. 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 ...

  4. Probabilistic assessment of risks of diethylhexyl phthalate (DEHP) in surface waters of China on reproduction of fish.

    PubMed

    Liu, Na; Wang, Yeyao; Yang, Qi; Lv, Yibing; Jin, Xiaowei; Giesy, John P; Johnson, Andrew C

    2016-06-01

    Diethylhexyl phthalate (DEHP) is considered to be an endocrine disruptor, which unlike other chemicals that have either non-specific (e.g., narcotics) or more generalized reactive modes of action, affect the Hypothalamic-pituitary-gonadal (HPG) axis and tend to have specific interactions with particular molecular targets within biochemical pathways. Responding to this challenge, a novel method for deriving predicted no-effect concentration (PNEC) and probabilistic ecological risk assessment (PERAs) for DEHP based on long-term exposure to potentially sensitive species with appropriate apical endpoints was development for protection of Chinese surface waters. PNECs based on potencies to cause lesions in reproductive tissues of fishes, which ranged from 0.04 to 0.20 μg DEHP L(-1), were significantly less than those derived based on other endpoints or other taxa, such as invertebrates. An assessment of risks posed by DEHP to aquatic organisms in surface waters of China showed that 88.17% and 78.85% of surface waters in China were predicted to pose risks to reproductive fitness of fishes with thresholds of protection for aquatic organisms based on 5% (HC5) and 10% (HC10), respectively. Assessment of risks of effects based on effects mediated by the HPG-axis should consider effects on chronic, non-lethal endpoints for specific taxa, especially for reproductive fitness of fishes.

  5. Assessing the toxic threat of selenium to fish and aquatic birds

    SciTech Connect

    Lemly, A.D.

    1996-12-31

    A procedure is given for evaluating the toxic threat of selenium to fish and wildlife. Toxic threat is expressed as hazard, and is based on the potential for food-chain bioaccumulation and reproductive impairment in fish and aquatic birds, which are the most sensitive biological responses for estimating ecosystem-level impacts of selenium contamination. Five degress of hazard are possible depending on the expected environmental concentrations of selenium, exposure of fish and aquatic birds to toxic concentrations, and resultant potential for reproductive impairment. A separate hazard score is given to each of five ecosystem components; water, sediments, benthic macroinvertebrates, fish eggs, and aquatic bird eggs. An example is given to illustrate how the procedure is applied to selenium data from a typical contaminant monitoring program.

  6. Assessment of ecosystem health based on fish assemblages in the Wei River basin, China.

    PubMed

    Wu, Wei; Xu, Zongxue; Yin, Xuwang; Zuo, Depeng

    2014-06-01

    In the Wei River basin, the ecosystem is gradually deteriorating due to the rapid growth of the population and the development of economies. It is thus important to assess the ecosystem health and take measures to restore the damaged ecosystem. In this study, an index of biotic integrity (IBI) for fish was developed to aid the conservation of the ecosystem based on a calibration data set. An index of water and habitat quality (IWHQ) was calculated based on environmental variables and habitat quality (QHEI) to identify the environmental degradation in the studied sites. The least degraded sites (IWHQ ≤ 2; W1, W5, W10, W12, W13, W14, and W16) were chosen as the reference sites. Six metrics that are sensitive to environmental degradation were utilized to differentiate the reference and the impaired sites using statistical methods. These metrics included the number of species (P1), the total biomass (P2), the number of Cobitidae species (P8), the proportion of species in the middle and low tiers (P10), the proportion of individuals that were classified as sensitive species (P25), and number of individuals in the sample (P39). A continuous scoring method was used to score the six metrics, and four classes were defined to characterize the ecosystem health of the Wei River basin. The fact that the overall IBI scores were negatively correlated with the index of environmental quality (IWHQ) based on the validation data set indicated that the index should be useful for biomonitoring and the conservation of biodiversity. According to the results, more than half of the sites were classified as poor or very poor. The ecosystem health in the Wei River was better than that in the Jing River and the Beiluo River, and this study will be a great reference for water resources management and ecosystem restoration in the Wei River basin.

  7. Safety Assessment of Two Hybrid Instrumentation Techniques in a Dental Student Endodontic Clinic: A Retrospective Study.

    PubMed

    Coelho, Marcelo Santos; Card, Steven John; Tawil, Peter Zahi

    2017-03-01

    The aim of this study was to retrospectively assess the safety potential of a hybrid technique combining nickel-titanium (NiTi) reciprocating and rotary instruments by third- and fourth-year dental students in the predoctoral endodontics clinic at one U.S. dental school. For the study, 3,194 root canal treatments performed by 317 dental students from 2012 through 2015 were evaluated for incidence of ledge creation and instrument separation. The hybrid reciprocating and rotary technique (RRT) consisted of a glide path creation with stainless steel hand files up to size 15/02, a crown down preparation with a NiTi reciprocating instrument, and an apical preparation with NiTi rotary instruments. The control was a traditional rotary and hand technique (RHT) that consisted of the same glide path procedure followed by a crown down preparation with NiTi rotary instruments and an apical preparation with NiTi hand instruments. The results showed that the RHT technique presented a rate of ledge creation of 1.4% per root and the RRT technique was 0.5% per root (p<0.05). Three stainless steel hand files separated: two in the RHT group and one in the RRT group. There was no separation of any NiTi file in any of the techniques. The use of the reciprocating and rotary technique for root canal instrumentation by these dental students provided good safety. This hybrid technique offered a low rate of ledge creation along with no NiTi instrument separation.

  8. Assessing the performance of hybrid CSP+PV plants in northern Chile

    NASA Astrophysics Data System (ADS)

    Starke, Allan; Cardemil, José M.; Escobar, Rodrigo; Colle, Sergio

    2016-05-01

    The electricity systems in Chile are characterized by a variable hourly demand in the central grid and an almost constant demand in the northern grid, which require different operation strategies for solar power plants depending on their location. Hybridizing a CSP plant with a PV plant can increase the whole plant capacity factor by allowing thermal energy to be stored while the PV plant is in production and thus help to achieve a fully dispatchable solar electricity production system. A thermal and economic analysis of hybrid CSP+PV plants is conducted considering a range of plant capacities based on a parabolic trough plant with the addition of a PV plant for the environmental conditions of Crucero in Northern Chile, which is a hotspot for solar energy development in the country. The study considers a parametric analysis and optimization of the storage and power block sizes for the CSP plant in terms of the levelized cost of energy (LCOE) for varying PV plant nominal capacity. The annual production of the plants are calculated by using the Transient System Simulation program (TRNSYS), which uses a new component library developed for that purpose. The results show good agreement with other software packages as well as with actual data from currently operating CSP plants. The adopted approach helps the proper assessment of the integration of different technologies, since it uses the well-kwon modular structure of the TRNSYS. Regarding the potential for the hybrid solar-solar plants in the Atacama Desert, the high level of irradiation available in Chile can provide a competitive electricity cost, allowing to investors the access to PPA contracts with mining companies in northern Chile. Additionally, the optimization analysis shows that the northern regions of Chile present an outstanding potential for the deployment of such projects.

  9. Assessing the impact of a downscaled climate change simulation on the fish fauna in an Inner-Alpine River.

    PubMed

    Matulla, C; Schmutz, S; Melcher, A; Gerersdorfer, T; Haas, P

    2007-12-01

    This study assesses the impact of a changing climate on fish fauna by comparing the past mean state of fish assemblage to a possible future mean state. It is based on (1) local scale observations along an Inner-Alpine river called Mur, (2) an IPCC emission scenario (IS92a), implemented by atmosphere-ocean global circulation model (AOGCM) ECHAM4/OPYC3, and (3) a model-chain that links climate research to hydrobiology. The Mur River is still in a near-natural condition and water temperature in summer is the most important aquatic ecological constraint for fish distribution. The methodological strategy is (1) to use downscaled air temperature and precipitation scenarios for the first half of the twenty-first century, (2) to establish a model that simulates water temperature by means of air temperature and flow rate in order to generate water temperature scenarios, and (3) to evaluate the impact on fish communities using an ecological model that is driven by water temperature. This methodology links the response of fish fauna to an IPCC emission scenario and is to our knowledge an unprecedented approach. The downscaled IS92a scenarios show increased mean air temperatures during the whole year and increased precipitation totals during summer, but reduced totals for the rest of the annual cycle. These changes result in scenarios of increased water temperatures, an altered annual cycle of flow rate, and, in turn, a 70 m displacement in elevation of fish communities towards the river's head. This would enhance stress on species that rely on low water temperatures and coerce cyprinid species into advancing against retreating salmonids. Hyporhithral river sectors would turn into epipotamal sectors. Grayling (Thymallus thymallus) and Danube salmon (Hucho hucho), presently characteristic for the Mur River, would be superceded by other species. Native brown trout (Salmo trutta), already now under pressure of competition, may be at risk of losing its habitat in favour of

  10. Assessing the use of existing data to compare plains fish assemblages collected from random and fixed sites in Colorado

    USGS Publications Warehouse

    Zuellig, Robert E.; Crockett, Harry J.

    2013-01-01

    The U.S. Geological Survey, in cooperation with Colorado Parks and Wildlife, assessed the potential use of combining recently (2007 to 2010) and formerly (1992 to 1996) collected data to compare plains fish assemblages sampled from random and fixed sites located in the South Platte and Arkansas River Basins in Colorado. The first step was to determine if fish assemblages collected between 1992 and 1996 were comparable to samples collected at the same sites between 2007 and 2010. If samples from the two time periods were comparable, then it was considered reasonable that the combined time-period data could be used to make comparisons between random and fixed sites. In contrast, if differences were found between the two time periods, then it was considered unreasonable to use these data to make comparisons between random and fixed sites. One-hundred samples collected during the 1990s and 2000s from 50 sites dispersed among 19 streams in both basins were compiled from a database maintained by Colorado Parks and Wildlife. Nonparametric multivariate two-way analysis of similarities was used to test for fish-assemblage differences between time periods while accounting for stream-to-stream differences. Results indicated relatively weak but significant time-period differences in fish assemblages. Weak time-period differences in this case possibly were related to changes in fish assemblages associated with environmental factors; however, it is difficult to separate other possible explanations such as limited replication of paired time-period samples in many of the streams or perhaps differences in sampling efficiency and effort between the time periods. Regardless, using the 1990s data to fill data gaps to compare random and fixed-site fish-assemblage data is ill advised based on the significant separation in fish assemblages between time periods and the inability to determine conclusive explanations for these results. These findings indicated that additional sampling will

  11. Toxicological assessment of spinosad: Implications for integrated control of Aedes aegypti using larvicides and larvivorous fish.

    PubMed

    Pereira, Boscolli Barbosa; Caixeta, Evelyn Siqueira; Freitas, Priscila Costa; Santos, Vanessa Santana Vieira; Limongi, Jean Ezequiel; de Campos Júnior, Edimar Olegário; Campos, Carlos Fernando; Souto, Henrique Nazareth; Rodrigues, Tamiris Sabrina; Morelli, Sandra

    2016-01-01

    Integration of larvivorous fish and biolarvicides at low concentrations to control of mosquito larvae in field situations may result in a safer and more effective tool. However, the usefulness of integrated approach depends upon survival and ecological fitness of fish employed. Thus, the aim of this study was to examine the genotoxic effects of combining different sublethal concentrations of spinosad, a naturally occurring neurotoxic insecticide, with male adult poecilid larvivorous guppy (Poecilia reticulata) and platy (Xiphophorus maculatus) fish on Aedes larvae mosquitos. Both fish species have been used for biological control of Aedes larvae in Brazil. Sublethal spinosad exposures were predetermined based on CL50-96hr. Nuclear abnormalities (NA) and micronucleus (MN) frequency in gill cells were measured after 14 d of exposure. Behavioral changes were monitored over 96 h. Although genotoxic effects were not markedly different from control, behavioral changes evaluated based upon the no-observable-effect concentration (NOEC) and lowest-observable-effect concentration (LOEC). Adverse effects were noted at concentrations of 12.6 mg/L (NOEC) and 25.3 mg/L (LOEC) spinosad. Therefore, these insecticide concentrations may be considered as being safe to these fish species and have important implications for integrated approach to control Aedes larvae using natural larvicides and larvivorous fish.

  12. Ilizarov hybrid external fixation for fractures of the distal radius: Part II. Internal fixation versus Ilizarov hybrid external fixation: Stability as assessed by cadaveric simulated motion testing.

    PubMed

    Dunning, C E; Lindsay, C S; Bicknell, R T; Johnson, J A; King, G J; Patterson, S D

    2001-03-01

    The in vitro stability of an Ilizarov hybrid external fixator was compared with that of a dorsal 3.5-mm AO T-plate in 8 unpaired, fresh-frozen upper extremities. A specially designed testing device that used computer-controlled pneumatic actuators was used to simulate active finger, wrist, and forearm motions by applying loads to relevant tendons. A comminuted extra-articular distal radius fracture was modelled using a dorsally based wedge osteotomy. Fracture stability was assessed using an electromagnetic tracking device to measure motion across the fracture site after randomized application of the plate and the hybrid fixator. During simulated finger and wrist motions with the forearm pronated or supinated, motion of the distal fragment with the hybrid fixator applied was comparable to or statistically less than with the AO plate applied. During simulated forearm rotation, the stability provided by the 2 fixation types was similar, although the plate allowed statistically less radial-ulnar deviation of the fragment. In this model of a 2-part extra-articular distal radius fracture, the clinically meaningful stability of the Ilizarov hybrid external fixator was comparable to that of the dorsal AO plate.

  13. Detection of Y chromosome sequences in a 45,X/46,XXq - patient by Southern blot analysis of PCR-amplified DNA and fluorescent in situ hybridization (FISH)

    SciTech Connect

    Kocova, M.; Siegel, S.F.; Wenger, S.L.

    1995-02-13

    In some cases of gonadal dysgenesis, cytogenetic analysis seems to be discordant with the phenotype of the patients. We have applied techniques such as Southern blot analysis and fluorescent in situ hybridization (FISH) to resolve the phenotype/genotype discrepancy in a patient with ambiguous genitalia in whom the peripheral blood karotype was 45,X. Gonadectomy at age 7 months showed the gonadal tissue to be prepubertal testis on the left side and a streak gonad on the right. The karyotype obtained from the left gonad was 45,X/46,XXq- and that from the right gonad was 45,X. Three different techniques, PCR amplification, FISH, and chromosome painting for X and Y chromosomes, confirmed the presence of Y chromosome sequences. Five different tissues were evaluated. The highest percentage of Y chromosome positive cells were detected in the left gonad, followed by the peripheral blood lymphocytes, skin fibroblasts, and buccal mucosa. No Y chromosomal material could be identified in the right gonad. Since the Xq- chromosome is present in the left gonad (testis), it is likely that the Xq- contains Y chromosomal material. Sophisticated analysis in this patient showed that she has at least 2 cell lines, one of which contains Y chromosomal material. These techniques elucidated the molecular basis of the genital ambiguity for this patient. When Y chromosome sequences are present in patients with Ullrich-Turner syndrome or gonadal dysgenesis, the risk for gonadal malignancy is significantly increased. Hence, molecular diagnostic methods to ascertain for the presence of Y chromosome sequences may expedite the evaluation of patients with the ambiguous genitalia. 21 refs., 4 figs., 2 tabs.

  14. Sperm cryopreservation of a live-bearing fish, Xiphophorus couchianus: male-to-male variation in post-thaw motility and production of F(1) hybrid offspring.

    PubMed

    Yang, Huiping; Hazlewood, Leona; Walter, Ronald B; Tiersch, Terrence R

    2009-03-01

    Fishes of the genus Xiphophorus are well-studied biomedical research models, and some species, such as X. couchianus, are currently listed as endangered in the wild. Sperm cryopreservation in these live-bearing fishes has begun recently. Thus far, live young have been produced with cryopreserved sperm only in one species (Xiphophorus helleri). In this study, the goal was to develop a practical protocol for sperm cryopreservation of Xiphophorus couchianus, and to produce live young with cryopreserved sperm. Sperm were collected by crushing of testis in Hanks' balanced salt solution at an osmolality of 500 mOsmol/kg (HBSS500), and were cryopreserved with 14% glycerol (v/v) as cryoprotectant at a cooling rate of 20 degrees C/min from 5 to -80 degrees C in 250-microL French straws. For artificial insemination, samples were thawed at 40 degrees C for 5 s in a water bath, washed once using fresh HBSS500 by centrifuging at 1000 g for 5 min at 4 degrees C, concentrated into approximately 5 microL, and injected into virgin females of Xiphophorus maculatus. The inseminated females were monitored for 90 days for subsequent discharge of live young. Results from 2006 and 2007 showed considerable male-to-male variation in post-thaw motility (from 1 to 70%). Offspring were produced by cryopreserved sperm in two tanks (of three) at 36 and 66 days after insemination in 2007. Paternity was confirmed via phenotypes (body color) and genotypes (microsatellite genetic marker) of the hybrid offspring. Overall, a practical protocol for sperm cryopreservation and artificial insemination is provided to preserve X. couchianus, which is an important biomedical research model, and also currently listed as an endangered species in the International Union for Conservation of Nature (IUCN) red list.

  15. A National Assessment of Promising Areas for Switchgrass, Hybrid Poplar, or Willow Energy Crop Production

    SciTech Connect

    Graham, R.L.; Walsh, M.E.

    1999-02-01

    The objective of this paper is to systematically assess the cropland acreage that could support energy crops and the expected farm gate and delivered prices of energy crops. The assessment is based on output from two modeling approaches: (1) the Oak Ridge County-Level Energy Crop (ORECCL) database (1996 version) and (2) the Oak Ridge Integrated Bioenergy Analysis System (ORIBAS). The former provides county-level estimates of suitable acres, yields, and farmgate prices of energy crops (switchgrass, hybrid poplar, willow) for all fifty states. The latter estimates delivered feedstock prices and quantities within a state at a fine resolution (1 km2) and considers the interplay between transportation costs, farmgate prices, cropland density, and facility demand. It can be used to look at any type of feedstock given the appropriate input parameters. For the purposes of this assessment, ORIBAS has been used to estimate farmgate and delivered switchgrass prices in 11 states (AL, FL, GA, IA, M N, MO, ND, NE, SC, SD, and TN). Because the potential for energy crop production can be considered from several perspectives, and is evolving as policies, economics and our basic understanding of energy crop yields and production costs change, this assessment should be viewed as a snapshot in time.

  16. Applications in environmental risk assessment of biochemical analysis on the Indian fresh water fish, Labeo rohita exposed to monocrotophos pesticide.

    PubMed

    Binukumari, S; Devi, K Anusiya; Vasanthi, J

    2016-10-01

    Pesticides are widely used in modern agriculture to aid in the production of high quality food. However, some pesticides have the potential to cause serious health and environmental damage. Repeated exposure to sub-lethal doses of pesticides can cause physiological and behavioral changes in fish that reduce populations such as abandonment of nests and broods, decreased immunity to disease and increased failure to avoid predators. Monocrotophos is one of the organophosphorus pesticide used in this study. The median lethal concentration (LC50) of Monocrotophos to fish L. rohita for 96h was found to be 45.1ppm. In sublethal concentration (1/10th of LC50 96h value, 4.51ppm) fishes were exposed for 24, 48, 72, 96h and 10, 20 and 30days. Organs of fishes were sacrificed and tested for biochemical analysis. A significant decrease in protein, carbohydrate and lipids were observed throughout the study period when compared to the control. It is essential for assessing the ecological risk of these pesticides.

  17. Relevance of cryptic fishes in biodiversity assessments: A case study at Buck Island Reef National Monument, St. Croix

    USGS Publications Warehouse

    Smith-Vaniz, W.F.; Jelks, H.L.; Rocha, L.A.

    2006-01-01

    Because cryptic fishes are difficult to accurately survey, they are undersampled components of coral reef habitats, and their ecological roles have been generally ignored. Fifty-eight enclosed stations were sampled in shoreline, nearshore reef, lagoon, backreef, forereef, and bank/shelf habitats with an ichthyocide (rotenone) at Buck Island Reef National Monument, St. Croix, U.S. Virgin Islands. Our samples included 55 families and 228 species, 60 previously unreported from St. Croix. Fish assemblages varied across habitat zones with the shoreline assemblage the most distinct. Only 8% of the species were present in all habitats. Multi-dimensional scaling plots of habitat characteristics and Bray-Curtis similarities of fish assemblages revealed similar patterns. Dominant and rare taxa are enumerated for each habitat sampled. Rotenone and visual census data are compared. While visual surveys accumulated more species per unit of effort, rotenone samples accumulated more species by area. Only 36% of the 228 species sampled with rotenone were visually detected, while 70% of the 115 species visually detected were also collected with rotenone. The use of rotenone is controversial but important for obtaining reasonably complete inventories of reef fishes. Misconceptions about rotenone and the advantages and limitations of alternative biodiversity assessment methods are discussed. ?? 2006 Rosenstiel School of Marine and Atmospheric Science of the University of Miami.

  18. Detection of {open_quotes}cryptic{close_quotes}karyotypic rearrangements in closely related primate species by fluorescence in situ hybridization (FISH) using human subtelomeric DNA probes

    SciTech Connect

    Youngblom, J.J.; Trask, B.J.; Friedman, C.

    1994-09-01

    Specific human subtelomeric DNA probes were used to reveal cryptic chromosomal rearrangements that cannot be detected by conventional high resolution cytogenetic techniques, or by chromosomal in situ suppression hybridization using whole chromosome paint analysis. Two cosmids containing different subtelomeric DNA sequences were derived from human chromosome 19 and designated as 7501 and 16432. Cosmid 7501 was hybridized to chromosomes from humans, chimpanzee, gorilla and orangutan. In humans, 7501 consistently labeled chromosomes 3q, 15q, and 19p. Additional chromosomes were labeled in different individuals, indicating a polymorphic distribution of this sequence in the human genome. In contrast, 7501 consistently and strongly labeled only the q arm terminus of chromosome 3 in both chimp and gorilla. The identification of the chromosome was made by two-color FISH analysis using human chromosome 4-specific paint and homologous to human chromosome 4. None of the human subjects showed labeling of chromosome 4 with 7501. This finding suggests that in the course of human evolution, subsequent to the divergence of humans and African apes, a cryptic translocation occurred between the ancestral human chromosome 4 and one or more of the other human chromosomes that now contain this DNA segment. In orangutan, 7501 labeled a single acrocentric chromosome pair, a distinctly different chromosome than that labeled in chimp and gorilla. Comparison of chromosome sites labeled with cosmid 16432 showed the distribution of signals on chromosome 1q arm is the same for humans and chimp, but different in the gorilla. Humans and chimps show distinct labeling on sites 1q terminus and 1q41-42. In gorilla, there is instead a large cluster of intense signal near the terminus of 1q that clearly does not extend all the way to the terminus. A paracentric inversion or an unequal cross-over event may account for the observed difference between these species.

  19. In vitro cytotoxicity assessment of two heavy metal salts in a fish cell line (RF).

    PubMed

    Goswami, Mukunda; Yadav, Kamalendra; Dubey, Akhilesh; Sharma, Bhagwati S; Konwar, Rituraj; Kumar, Ravindra; Nagpure, Naresh S; Lakra, Wazir S

    2014-01-01

    Labeo rohita (rohu) is one of most important of Indian major carps, which is highly ranked among the important freshwater aquaculture species in the world. Heavy metals are major risk factors for aquatic health, which are biomagnified through the food chain. The present study was carried out to investigate the effect of different divalent salts of two heavy metals, such as zinc (ZnCl(2), ZnSO(4) and ZnNO(3)) and cadmium (CdCl(2) and CdSO(4)), in an established fish cell line, RF developed from fin tissue of L. rohita. The RF cell line was used for assessment of heavy metal cytotoxicity through various endpoint assays, including maximum tolerated dose (MTD) determination, 3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyl tetrazolium bromide (MTT) assay, neutral red (NR) uptake assay, and Coomassie brilliant blue (CBB) assay. Results revealed that these heavy metal salts were cytotoxic to the RF cell line at varied concentrations. MTD values were found to be 1.563, 3.125, 6.25, 12.5 and 25 mg/L for CdCl(2), CdSO(4), ZnCl(2), Zn(NO(3))(2) and ZnSO(4), respectively. The half-maximal inhibitory concentration values calculated by MTT, NR and CB assay were 53.83 ± 7.02, 58.03 ± 9.12 and 79.20 ± 15.27 for ZnSO(4), 26.44 ± 7.01, 36.60 ± 7.82 and 155.6 ± 14.75 for Zn(NO(3))(2), 20.26 ± 17.95, 16.94 ± 7.05 and 87.54 ± 7.58 for ZnCl(2), 5.166 ± 0.57, 15 ± 1 and 41.80 ± 8.38 for CdSO(4) and 4.966 ± 0.56, 9.56 ± 1.73 and 20.93 ± 4.47 for CdCl(2). This study establishes the RF cell line as an in vitro tool for assessment and monitoring of heavy metal concentration in the aquatic environment.

  20. Life cycle assessment of greenhouse gas emissions from plug-in hybrid vehicles: implications for policy.

    PubMed

    Samaras, Constantine; Meisterling, Kyle

    2008-05-01

    Plug-in hybrid electric vehicles (PHEVs), which use electricity from the grid to power a portion of travel, could play a role in reducing greenhouse gas (GHG) emissions from the transport sector. However, meaningful GHG emissions reductions with PHEVs are conditional on low-carbon electricity sources. We assess life cycle GHG emissions from PHEVs and find that they reduce GHG emissions by 32% compared to conventional vehicles, but have small reductions compared to traditional hybrids. Batteries are an important component of PHEVs, and GHGs associated with lithium-ion battery materials and production account for 2-5% of life cycle emissions from PHEVs. We consider cellulosic ethanol use and various carbon intensities of electricity. The reduced liquid fuel requirements of PHEVs could leverage limited cellulosic ethanol resources. Electricity generation infrastructure is long-lived, and technology decisions within the next decade about electricity supplies in the power sector will affectthe potential for large GHG emissions reductions with PHEVs for several decades.

  1. Utility of selected non-coding chloroplast DNA sequences for lineage assessment of Musa interspecific hybrids.

    PubMed

    Swangpol, Sasivimon; Volkaert, Hugo; Sotto, Rachel C; Seelanan, Tosak

    2007-07-31

    Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Colla (A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

  2. Integrating Hybrid Life Cycle Assessment with Multiobjective Optimization: A Modeling Framework.

    PubMed

    Yue, Dajun; Pandya, Shyama; You, Fengqi

    2016-02-02

    By combining life cycle assessment (LCA) with multiobjective optimization (MOO), the life cycle optimization (LCO) framework holds the promise not only to evaluate the environmental impacts for a given product but also to compare different alternatives and identify both ecologically and economically better decisions. Despite the recent methodological developments in LCA, most LCO applications are developed upon process-based LCA, which results in system boundary truncation and underestimation of the true impact. In this study, we propose a comprehensive LCO framework that seamlessly integrates MOO with integrated hybrid LCA. It quantifies both direct and indirect environmental impacts and incorporates them into the decision making process in addition to the more traditional economic criteria. The proposed LCO framework is demonstrated through an application on sustainable design of a potential bioethanol supply chain in the UK. Results indicate that the proposed hybrid LCO framework identifies a considerable amount of indirect greenhouse gas emissions (up to 58.4%) that are essentially ignored in process-based LCO. Among the biomass feedstock options considered, using woody biomass for bioethanol production would be the most preferable choice from a climate perspective, while the mixed use of wheat and wheat straw as feedstocks would be the most cost-effective one.

  3. Assessment of pollution levels in fish and water of main basin, Lake Mariut.

    PubMed

    Amr, Hanaa M; El-Tawila, Mahmoud M; Ramadan, Mohamed H M

    2005-01-01

    Lake Mariut has suffered over the years from the untreated sewage, agricultural and industrial wastes dumped into it. Lake Mariut fish quality and quantity were adversely affected eventually being unfit for human consumption due to its poor water quality. The present study was carried out to evaluate the levels of metals in the fish caught from Lake Mariut main basin and its fitness for human consumption, and the water quality after the enforcement of the Egyptian Law for Environmental Protection (Law 4/1994). Fish and water samples were collected form Lake Mariut main basin through out the period from May to December 2000. The results showed that mercury was totally undetected in fish and water samples. The levels of Fe obtained were very low compared to previous studies. Fe and Cr contents in fish flesh were higher compared to their levels in water samples. Also Cu has shown a decrease in both fish and water samples. Zn and Cd contents in water samples have decreased compared with former studies. However, they have not changed in fish flesh. Pb content in both fish flesh and water samples has shown a great decrease compared to previous studies. The Cd and Pb mean values in fish flesh of the present study (0.81 and 0.14 mg/kg) exceeded the Egyptian Standards No. 2360/1993 value (should not exceed 0.1 mg/kg for each). The results also showed that the water quality has changed compared with previous studies. BOD has increased in north of Main Basin, east of Main Basin, South of Main Basin, and southwest of Main Basin; and deCreased in WTP effluent; and Qalaa Drain. There has been an increase in TSS, TVSS, and NO3 levels compared to pervious studies. There has been a decrease in TS, TDS, COD,hardness, and chloride levels. This decrease, especially in COD, may be attributed to the enforcement of the Egyptian Law 4/1994. The pH and alkalinity were in agreement with the values shown by previous studies except for east of Main Basin which showed higher values. The study

  4. Assessment of tolerant sunfish populations (Lepomis sp.) inhabiting selenium-laden coal ash effluents. 3. Serum chemistry and fish health indicators.

    PubMed

    Lohner, T W; Reash, R J; Willet, V E; Fletcher, J

    2001-11-01

    Sunfish were collected from fly ash discharge-receiving streams to assess the possible effects of exposure to elevated selenium. Concentrations of selenium, copper, and arsenic were statistically higher in fish tissue (liver) samples from effluent-exposed fish than in reference fish. Several biomarkers were indicative of metal exposure and effect. Plasma protein levels and cholesterol levels were significantly lower in exposed fish, indicating nutritional stress. Ion levels (i.e., K) increased with exposure to ash pond metals, indicating possible gill damage. Fish from the receiving streams also had increased serum glucose and osmolality indicating possible acute stress due to sampling. Fish health assessments revealed a lower incidence of fin erosion, kidney discoloration, urolithiasis or nephrocalcinosis, liver discoloration, and parasites in exposed fish and a higher incidence of skin, eye, and gill aberrations. Condition factors of exposed fish were correlated with biomarker response and were the same as or lower than those of reference fish, but not related to selenium levels. Although several serum biochemical indicators differed between the ash pond-receiving stream and reference sites, pollutant exposure was apparently not sufficient to cause functional damage to critical organ systems.

  5. A histology-based fish health assessment of the tigerfish, Hydrocynus vittatus from a DDT-affected area

    NASA Astrophysics Data System (ADS)

    McHugh, K. J.; Smit, N. J.; Van Vuren, J. H. J.; Van Dyk, J. C.; Bervoets, L.; Covaci, A.; Wepener, V.

    The Pongolapoort Dam (PPD) in the Phongola River, Kwa-Zulu Natal, South Africa and the surrounding area are classified as intermediate to low risk malaria areas and are continually being treated with DDT for malaria vector control. DDT is known as an endocrine disrupting chemical posing estrogenic and anti-androgenic properties and therefore might impact on the health of the 18 freshwater fish species found within this system. Of these species the tigerfish, Hydrocynus vittatus, is targeted by both recreational and local subsistence fishermen and was recently included in the South African threatened or protected species list. Their protected status and importance as a food source therefore emphasises the need for their health status elucidation. Previous research on H. vittatus in the Phongola floodplain highlighted DDT biomagnification in this species. Recent data show that the sum of the DDT levels in February 2009 (5403.9 ng/g lipid) and July 2009 (5537.4 ng/g lipid) is still comparable to the high levels found 30 years earlier. The aim of the current study was thus to determine the health status of H. vittatus in relation to DDT exposure by means of a histology-based fish health assessment protocol. Tigerfish were collected in February 2009 ( n = 30) and July 2009 ( n = 15) and gill, kidney and liver tissue were subjected to histological analyses. Mean Index values showed that the Kidney Index ( IK), Gill Index ( IG) and Fish Index ( IFISH) were higher in fish from the February survey while the Liver Index was higher in those collected during July. Liver alterations identified included intercellular oedema, granular degeneration, vacuolation, nuclear pleomorphism and lymphocyte infiltration. Kidney alterations included dilation of the glomerulus capillaries, vacuolation and hyaline droplet degeneration. Gill alterations identified included telangiectasia and hyperplasia of the secondary lamella, congestion, and rupture of pillar cells. Although histological

  6. Hybrid LCA model for assessing the embodied environmental impacts of buildings in South Korea

    SciTech Connect

    Jang, Minho; Hong, Taehoon; Ji, Changyoon

    2015-01-15

    The assessment of the embodied environmental impacts of buildings can help decision-makers plan environment-friendly buildings and reduce environmental impacts. For a more comprehensive assessment of the embodied environmental impacts of buildings, a hybrid life cycle assessment model was developed in this study. The developed model can assess the embodied environmental impacts (global warming, ozone layer depletion, acidification, eutrophication, photochemical ozone creation, abiotic depletion, and human toxicity) generated directly and indirectly in the material manufacturing, transportation, and construction phases. To demonstrate the application and validity of the developed model, the environmental impacts of an elementary school building were assessed using the developed model and compared with the results of a previous model used in a case study. The embodied environmental impacts from the previous model were lower than those from the developed model by 4.6–25.2%. Particularly, human toxicity potential (13 kg C{sub 6}H{sub 6} eq.) calculated by the previous model was much lower (1965 kg C{sub 6}H{sub 6} eq.) than what was calculated by the developed model. The results indicated that the developed model can quantify the embodied environmental impacts of buildings more comprehensively, and can be used by decision-makers as a tool for selecting environment-friendly buildings. - Highlights: • The model was developed to assess the embodied environmental impacts of buildings. • The model evaluates GWP, ODP, AP, EP, POCP, ADP, and HTP as environmental impacts. • The model presents more comprehensive results than the previous model by 4.6–100%. • The model can present the HTP of buildings, which the previous models cannot do. • Decision-makers can use the model for selecting environment-friendly buildings.

  7. A Vulnerability Assessment of Fish and Invertebrates to Climate Change on the Northeast U.S. Continental Shelf

    PubMed Central

    Hare, Jonathan A.; Morrison, Wendy E.; Nelson, Mark W.; Stachura, Megan M.; Teeters, Eric J.; Griffis, Roger B.; Alexander, Michael A.; Scott, James D.; Alade, Larry; Bell, Richard J.; Chute, Antonie S.; Curti, Kiersten L.; Curtis, Tobey H.; Kircheis, Daniel; Kocik, John F.; Lucey, Sean M.; McCandless, Camilla T.; Milke, Lisa M.; Richardson, David E.; Robillard, Eric; Walsh, Harvey J.; McManus, M. Conor; Marancik, Katrin E.; Griswold, Carolyn A.

    2016-01-01

    Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform

  8. A Vulnerability Assessment of Fish and Invertebrates to Climate Change on the Northeast U.S. Continental Shelf.

    PubMed

    Hare, Jonathan A; Morrison, Wendy E; Nelson, Mark W; Stachura, Megan M; Teeters, Eric J; Griffis, Roger B; Alexander, Michael A; Scott, James D; Alade, Larry; Bell, Richard J; Chute, Antonie S; Curti, Kiersten L; Curtis, Tobey H; Kircheis, Daniel; Kocik, John F; Lucey, Sean M; McCandless, Camilla T; Milke, Lisa M; Richardson, David E; Robillard, Eric; Walsh, Harvey J; McManus, M Conor; Marancik, Katrin E; Griswold, Carolyn A

    2016-01-01

    Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform

  9. Using ordination and clustering techniques to assess multimetric fish health response following a coal ash spill.

    PubMed

    Bevelhimer, Mark S; Adams, S Marshall; Fortner, Allison M; Greeley, Mark S; Brandt, Craig C

    2014-08-01

    The effect of coal ash exposure on fish health in freshwater communities is largely unknown. Given the large number of possible pathways of effects (e.g., toxicological effect of exposure to multiple metals, physical effects from ash exposure, and food web effects), measurement of only a few health metrics is not likely to give a complete picture. The authors measured a suite of 20 health metrics from 1100+ fish collected from 5 sites (3 affected and 2 reference) near a coal ash spill in east Tennessee over a 4.5-yr period. The metrics represented a wide range of physiological and energetic responses and were evaluated simultaneously using 2 multivariate techniques. Results from both hierarchical clustering and canonical discriminant analyses suggested that for most species × season combinations, the suite of fish health indicators varied more among years than between spill and reference sites within a year. In a few cases, spill sites from early years in the investigation stood alone or clustered together separate from reference sites and later year spill sites. Outlier groups of fish with relatively unique health profiles were most often from spill sites, suggesting that some response to the ash exposure may have occurred. Results from the 2 multivariate methods suggest that any change in the health status of fish at the spill sites was small and appears to have diminished since the first 2 to 3 yr after the spill.

  10. Histopathological assessment of liver and gonad pathology in continental slope fish from the northeast Atlantic Ocean.

    PubMed

    Feist, S W; Stentiford, G D; Kent, M L; Ribeiro Santos, A; Lorance, P

    2015-05-01

    The deep-sea environment is a sink for a wide variety of contaminants including heavy metals and organic compounds of anthropogenic origin. Life history traits of many deep-water fish species including longevity and high trophic position may predispose them to contaminant exposure and subsequent induction of pathological changes, including tumour formation. The lack of evidence for this hypothesis prompted this investigation in order to provide data on the presence of pathological changes in the liver and gonads of several deep-water fish species. Fish were obtained from the north east region of the Bay of Biscay (north east Atlantic Ocean) by trawling at depths between 700 and 1400 m. Liver and gonad samples were collected on board ship and fixed for histological processing and subsequent examination by light microscopy. Hepatocellular and nuclear pleomorphism and individual cases of ovotestis and foci of cellular alteration (FCA) were detected in black scabbardfish (Aphanopus carbo). Six cases of FCA were observed in orange roughy (Hoplostethus atlanticus) (n = 50) together with a single case of hepatocellular adenoma. A wide variety of inflammatory and degenerative lesions were found in all species examined. Deep-water fish display a range of pathologies similar to those seen in shelf-sea species used for international monitoring programmes including biological effects of contaminants. This study has confirmed the utility of health screening in deep-water fish for detecting evidence of prior exposure to contaminants and has also gained evidence of pathology potentially associated with exposure to algal toxins.

  11. Combining Turbine Blade-Strike and Life Cycle Models to Assess Mitigation Strategies for Fish Passing Dams

    SciTech Connect

    Ferguson, John W.; Ploskey, Gene R.; Leonardsson, Kjell; Zabel, Richard W.; Lundqvist, Hans

    2008-08-01

    Combining the two models produced a rapid, cost effective tool for assessing dam passage impacts to fish populations and prioritizing among mitigation strategies for conserving fish stocks in regulated rivers. Estimated mortality of juvenile and adult Atlantic salmon (Salmo salar) and sea trout (S. trutta) passing turbines at two dams in northern Sweden was significantly higher for Kaplan turbines compared to Francis turbines, and for adult fish compared to juveniles based on blade strike models. Mean probability of mortality ranged from 6.7% for salmon smolts passing Francis turbines to >100% for adult salmon passing Kaplan turbines. Life cycle modeling allowed benefits to be assessed for three alternatives that mitigated this mortality. Salmon population responses varied considerably among alternatives and rivers: growth rates improved as much as 17.9%, female escapements increased up to 669%, and more than 1,300 additional female salmon were produced in one case. Protecting both smolts and adults provided benefits, and in one river, mitigating turbine mortality alone was estimated to have met the production capacity of the available habitat.

  12. Assessment of hydraulic fish habitat condition using integrated toolkit: a case study of the Geum river basin, Republic of Korea.

    PubMed

    Park, Sangyoung; Kim, Jeongkon; Ko, Ick Hwan; Arthington, Angela; Jones, Gary; Yum, Kyung Taek

    2010-01-01

    Artificial changes of rivers, including construction and operation of dams, inevitably lead to physical and ecological changes throughout waterways and their floodplains. In this study, a conceptual model coupled with integrated numerical modeling is presented for hydraulic fish habitat assessment of the Geum River basin, Republic of Korea. Based on the major events which might have affected the ecological system, a conceptual model was formulated to guide desktop and field studies, modeling and scenario evaluations. The result of hydraulic fish habitat assessment indicated that the construction of the Daecheong Multipurpose Dam (DMD) in the Geum River basin has altered flow magnitudes and reduced the river's flow variability. Changes are evident in the magnitude of medium and small flows and the river experiences increased low flows during the dry season. Black shiner, an endangered fish species in Korea, was selected and analyzed to explore relationships between flow regime change by dams and changes to its preferred habitats. As a result, fewer sensitive riffle-benthic species were observed in the reaches downstream of DMD due to the reduction of suitable habitat conditions such as riffle-pool sequences. The proposed conceptual model and integrated toolkit would allow river managers to isolate the physical and biological effects associated with dam operation and could be useful for developing river management strategies.

  13. Trace element bioaccumulation in reef fish from New Caledonia: influence of trophic groups and risk assessment for consumers.

    PubMed

    Metian, Marc; Warnau, Michel; Chouvelon, Tiphaine; Pedraza, Fernando; Rodriguez y Baena, Alessia M; Bustamante, Paco

    2013-01-01

    Fourteen trace elements (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, V, and Zn) were analyzed in livers and muscles from 22 fish species from the New Caledonia lagoon, which is subjected to important chemical inputs due to intense land-based mining activities (New Caledonia is the third largest world producer of Ni). The results of this baseline research indicated that livers generally concentrated trace elements to a greater extent than muscles. Nevertheless, the overall trace element concentrations in both tissues were barely above the levels reported in fish and thus contamination at the local scale was poorly discriminated. Although these levels were low, preliminary risk assessment from a global health standpoint suggests that As would be an element potentially leading to exposure of concern for fish consumers. Based on the trace element concentrations in livers and the fish trophic preferences, some trends have been observed among trophic groups: Ag, Cu, Fe, Hg, and Zn concentrations were generally higher in liver of fish with the highest trophic position whereas Cd concentrations were lower in these groups. The use of the leopard coral grouper Plectropomus leopardus as a resident top predator allowed determining the geographical variations in contamination levels with significant differences for six out of the fourteen elements investigated. The sampling sites influenced by anthropogenic inputs were revealed by high Ag, Cd, Cu, Hg, and Pb concentrations. Such geographic differences also applied to Zn but surprisingly not for the typical elements associated with Ni mining, i.e., Co, Cr, Mn and Ni.

  14. Assessing distribution of migratory fishes and connectivity following complete and partial dam removals in a North Carolina River

    USGS Publications Warehouse

    Raabe, Joshua K.; Hightower, Joseph E.

    2014-01-01

    Fish, especially migratory species, are assumed to benefit from dam removals that restore connectivity and access to upstream habitat, but few studies have evaluated this assumption. Therefore, we assessed the movement of migratory fishes in the springs of 2008 through 2010 and surveyed available habitat in the Little River, North Carolina, a tributary to the Neuse River, after three complete dam removals and one partial (notched) dam removal. We tagged migratory fishes with PIT tags at a resistance-board weir located at a dam removal site (river kilometer [rkm] 3.7) and followed their movements with an array of PIT antennas. The river-wide distribution of fish following removals varied by species. For example, 24–31% of anadromous American Shad Alosa sapidissima, 45–49% of resident Gizzard Shad Dorosoma cepedianum, and 4–11% of nonnative Flathead CatfishPylodictis olivaris passed the dam removal site at rkm 56 in 2009 and 2010. No preremoval data were available for comparison, but reach connectivity appeared to increase as tagged individuals passed former dam sites and certain individuals moved extensively both upstream and downstream. However, 17–28% did not pass the partially removed dam at rkm 7.9, while 20–39% of those that passed remained downstream for more than a day before migrating upstream. Gizzard Shad required the deepest water to pass this notched structure, followed by American Shad then Flathead Catfish. Fish that passed the notched dam accessed more complex habitat (e.g., available substrate size-classes) in the middle and upper reaches. The results provide strong support for efforts to restore currently inaccessible habitat through complete removal of derelict dams.

  15. Effect of tannic acid-fish scale gelatin hydrolysate hybrid nanoparticles on intestinal barrier function and α-amylase activity.

    PubMed

    Wu, Shao-Jung; Ho, Yi-Cheng; Jiang, Shun-Zhou; Mi, Fwu-Long

    2015-07-01

    Practical application of tannic acid is limited because it readily binds proteins to form insoluble aggregates. In this study, tannic acid was self-assembled with fish scale gelatin hydrolysates (FSGH) to form stable colloidal complex nanoparticles. The nanoparticles prepared from 4 mg ml(-1) tannic acid and 4 mg ml(-1) FSGH had a mean particle size of 260.8 ± 3.6 nm, and showed a positive zeta potential (20.4 ± 0.4 mV). The nanoparticles acted as effective nano-biochelators and free radical scavengers because they provided a large number of adsorption sites for interaction with heavy metal ions and scavenging free radicals. The maximum adsorption capacity for Cu(2+) ions was 123.5 mg g(-1) and EC50 of DPPH radical scavenging activity was 21.6 ± 1.2 μg ml(-1). Hydroxyl radical scavenging effects of the nanoparticles were investigated by electron spin resonance spectroscopy. The copper-chelating capacity and free radical scavenging activity of the nanoparticles were associated with their capacity to inhibit Cu(2+) ion-induced barrier impairment and hyperpermeability of Caco-2 intestinal epithelial tight junction (TJ). However, α-amylase inhibitory activity of the nanoparticles was significantly lower than that of free tannic acid. The results suggest that the nanoparticles can ameliorate Cu(2+) ion induced intestinal epithelial TJ dysfunction without severely inhibiting the activity of the digestive enzymes.

  16. Hybrid life-cycle assessment of natural gas based fuel chains for transportation.

    PubMed

    Strømman, Anders Hammer; Solli, Christian; Hertwich, Edgar G

    2006-04-15

    This research compares the use of natural gas, methanol, and hydrogen as transportation fuels. These three fuel chains start with the extraction and processing of natural gas in the Norwegian North Sea and end with final use in Central Europe. The end use is passenger transportation with a sub-compact car that has an internal combustion engine for the natural gas case and a fuel cell for the methanol and hydrogen cases. The life cycle assessment is performed by combining a process based life-cycle inventory with economic input-output data. The analysis shows that the potential climate impacts are lowest for the hydrogen fuel scenario with CO2 deposition. The hydrogen fuel chain scenario has no significant environmental disadvantage compared to the other fuel chains. Detailed analysis shows that the construction of the car contributes significantly to most impact categories. Finally, it is shown how the application of a hybrid inventory model ensures a more complete inventory description compared to standard process-based life-cycle assessment. This is particularly significant for car construction which would have been significantly underestimated in this study using standard process life-cycle assessment alone.

  17. A radiation hybrid map of the European sea bass (Dicentrarchus labrax) based on 1581 markers: Synteny analysis with model fish genomes.

    PubMed

    Guyon, Richard; Senger, Fabrice; Rakotomanga, Michaelle; Sadequi, Naoual; Volckaert, Filip A M; Hitte, Christophe; Galibert, Francis

    2010-10-01

    The selective breeding of fish for aquaculture purposes requires the understanding of the genetic basis of traits such as growth, behaviour, resistance to pathogens and sex determinism. Access to well-developed genomic resources is a prerequisite to improve the knowledge of these traits. Having this aim in mind, a radiation hybrid (RH) panel of European sea bass (Dicentrarchus labrax) was constructed from splenocytes irradiated at 3000 rad, allowing the construction of a 1581 marker RH map. A total of 1440 gene markers providing ~4400 anchors with the genomes of three-spined stickleback, medaka, pufferfish and zebrafish, helped establish synteny relationships with these model species. The identification of Conserved Segments Ordered (CSO) between sea bass and model species allows the anticipation of the position of any sea bass gene from its location in model genomes. Synteny relationships between sea bass and gilthead seabream were addressed by mapping 37 orthologous markers. The sea bass genetic linkage map was integrated in the RH map through the mapping of 141 microsatellites. We are thus able to present the first complete gene map of sea bass. It will facilitate linkage studies and the identification of candidate genes and Quantitative Trait Loci (QTL). The RH map further positions sea bass as a genetic and evolutionary model of Perciformes and supports their ongoing aquaculture expansion.

  18. A screening-level assessment of lead, cadmium, and zinc in fish and crayfish from northeastern Oklahoma, USA

    USGS Publications Warehouse

    Schmitt, C.J.; Brumbaugh, W.G.; Linder, G.L.; Hinck, J.E.

    2006-01-01

    The objective of this study was to evaluate potential human and ecological risks associated with metals in fish and crayfish from mining in the Tri-States Mining District (TSMD). Crayfish (Orconectes spp.) and fish of six frequently consumed species (common carp, Cyprinus carpio; channel catfish, Ictalurus punctatus; flathead catfish, Pylodictis olivaris; largemouth bass, Micropterus salmoides; spotted bass, M. punctulatus; and white crappie, Pomoxis annularis) were collected in 2001-2002 from the Oklahoma waters of the Spring River (SR) and Neosho River (NR), which drain the TSMD. Samples from a mining-contaminated site in eastern Missouri and from reference sites were also analyzed. Individual fish were prepared for human consumption in the manner used locally by Native Americans (headed, eviscerated, and scaled) and analyzed for lead, cadmium, and zinc. Whole crayfish were analyzed as composite samples of 5-60 animals. Metals concentrations were typically higher in samples from sites most heavily affected by mining and lowest in reference samples. Within the TSMD, most metals concentrations were higher at sites on the SR than on the NR and were typically highest in common carp and crayfish than in other taxa. Higher concentrations and greater risk were associated with fish and crayfish from heavily contaminated SR tributaries than the SR or NR mainstems. Based on the results of this and previous studies, the human consumption of carp and crayfish could be restricted based on current criteria for lead, cadmium, and zinc, and the consumption of channel catfish could be restricted due to lead. Metals concentrations were uniformly low in Micropterus spp. and crappie and would not warrant restriction, however. Some risk to carnivorous avian wildlife from lead and zinc in TSMD fish and invertebrates was also indicated, as was risk to the fish themselves. Overall, the wildlife assessment is consistent with previously reported biological effects attributed to metals

  19. Potential Health Hazard Assessment in Terms of Some Heavy Metals Determined in Demersal Fishes Caught in Eastern Aegean Sea.

    PubMed

    Yabanli, Murat; Alparslan, Yunus

    2015-10-01

    A heavy metal risk assessment based on estimated daily intake (EDI) and target hazard quotient was made for children and adults. Five fish species captured from the eastern Aegean Sea were analyzed for Cr, Cu, Cd, Hg and Pb by inductively coupled plasma spectroscopy in muscle tissue of red mullet (Mullus barbatus), surmullet (Mullus surmuletus), sand steenbras (Lithognathus mormyrus), common two-banded seabream (Diplodus vulgaris) and common pandora (Pagellus erythinus). The ranges for mean metal concentration (mg/kg wet wt) in the five species were 0.27-0.39 Cr, 0.12-0.22 Cu, 0.09-0.10 Hg and 0.10-0.12 Pb. All means were identical for Cd at 0.03 mg/kg wet wt. The EDI values for each metal were ascertained not to exceed the tolerable daily intake amount. Fish did not contain sufficiently high levels of these metals to pose a carcinogenic risk.

  20. Assessing power of large river fish monitoring programs to detect population changes: the Missouri River sturgeon example

    USGS Publications Warehouse

    Wildhaber, M.L.; Holan, S.H.; Bryan, J.L.; Gladish, D.W.; Ellersieck, M.

    2011-01-01

    In 2003, the US Army Corps of Engineers initiated the Pallid Sturgeon Population Assessment Program (PSPAP) to monitor pallid sturgeon and the fish community of the Missouri River. The power analysis of PSPAP presented here was conducted to guide sampling design and effort decisions. The PSPAP sampling design has a nested structure with multiple gear subsamples within a river bend. Power analyses were based on a normal linear mixed model, using a mixed cell means approach, with variance estimates from the original data. It was found that, at current effort levels, at least 20 years for pallid and 10 years for shovelnose sturgeon is needed to detect a 5% annual decline. Modified bootstrap simulations suggest power estimates from the original data are conservative due to excessive zero fish counts. In general, the approach presented is applicable to a wide array of animal monitoring programs.

  1. Illustrated field guide for assessing external and internal anomalies in fish

    USGS Publications Warehouse

    Smith, Stephen B.; Donahue, Anne P.; Lipkin, Robin J.; Blazer, Vicki; Schmitt, Christopher J.; Goede, Ronald W.

    2002-01-01

    Procedures are described for processing fish for examination of external and internal anomalies and pathologies indicative of exposure to environmental contaminants and other peturbations. For the procedures described here, fish are captured (preferably by electrofishing) and held alive until processing (generally < 1 h). Fish are weighed, measured, and necropsied, and a scale sample is obtained from for age determination. Information is given for the collection and preservation of tissue samples for histopathological analysis. Photographs of most abnormalities are included along with normal conditions for easier identification of external (oral, head, eye, gill, opercula, and fin) and internal (liver, spleen, gonad, and kidney) anomalies. The report also includes recommendations for record keeping, sample labeling, and shipping records, equipment, supplies,and samples. A list of suggested equipment and supplies for field processing is included as are instructions for cleaning equipment.

  2. 78 FR 2868 - Draft Environmental Assessment for Rulemaking To Establish Minimum Sound Requirements for Hybrid...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-14

    ... require hybrid and electric passenger cars, light trucks, medium and heavy duty trucks and buses, low... Rulemaking To Establish Minimum Sound Requirements for Hybrid and Electric Vehicles AGENCY: National Highway... (FMVSS) setting minimum sound requirements for hybrid and electric vehicles. DATES: Comments must...

  3. Mercury content in commercial pelagic fish and its risk assessment in the Western Indian Ocean.

    PubMed

    Kojadinovic, Jessica; Potier, Michel; Le Corre, Matthieu; Cosson, Richard P; Bustamante, Paco

    2006-08-01

    As top predators of pelagic food webs, large fish naturally bioaccumulate mercury (Hg). Determining Hg burdens in commercialized fish is essential considering the concern about effects of contaminants on human health and the legal thresholds that are therefore set for local consumption and/or exportation. Total Hg levels were measured in the muscular tissue of 183 fish of five commercially important species from the tropical zone of the Western Indian Ocean. All individuals were measured and sexed in order to study the impregnation of Hg with size and sex within each species. Values of Hg found in this part of the Indian Ocean were comparable to Hg in muscular tissue of the same species studied in other areas. The highest Hg levels were noted in Swordfish (Xiphias gladius) caught in waters surrounding Reunion Island (3.97+/-2.67 microg g(-1) dry weight). Following the Swordfish, in decreasing order of Hg content, were the Yellowfin Tuna (Thunnus albacares) and the Skipjack (Katsuwonus pelamis), then the Common Dolphinfish (Coryphaena hippurus) and the Wahoo (Acanthocybium solandri). In the North of the Mozambique Channel, Swordfish had higher Hg levels than Yellowfin Tunas, and Dolphinfish exhibited intermediate Hg levels. The size of a fish was a determining factor of its Hg burden, as was the species. Differences in size-normalized Hg levels were observed between the two study zones for Swordfish and Common Dolphinfish. Sex, in contrast, did not influence Hg levels suggesting that females and males have similar feeding habits. The muscular Hg levels presented here suggest that consumers of fish originating from the Western Indian Ocean should limit themselves to one Swordfish based meal per week, or one fish meal a day if they choose to eat tuna or Common Dolphinfish.

  4. Fish Passage Assessment of an Advanced Hydropower Turbine and Conventional Turbine Using Blade-strike Modeling

    SciTech Connect

    Deng, Zhiqun; Carlson, Thomas J.; Dauble, Dennis D.; Ploskey, Gene R.

    2011-01-04

    In the Columbia and Snake River basins, several species of Pacific salmon were listed under the Endangered Species Act of 1973 due to significant declines of fish population. Dam operators and design engineers are thus faced with the task of making those hydroelectric facilities more ecologically friendly through changes in hydro-turbine design and operation. Public Utility District No. 2 of Grant County, Washington, applied for re-licensing from the U.S. Federal Energy Regulatory Commission to replace the 10 turbines at Wanapum Dam with advanced hydropower turbines that were designed to increase power generation and improve fish passage conditions. We applied both deterministic and stochastic blade-strike models to the newly installed turbine and an existing turbine. Modeled probabilities were compared to the results of a large-scale live fish survival study and a sensor fish study under the same operational parameters. Overall, injury rates predicted by the deterministic model were higher than experimental rates of injury while those predicted by the stochastic model were in close agreement with experiment results. Fish orientation at the time of entry into the plane of the leading edges of the turbine runner blades was an important factor contributing to uncertainty in modeled results. The advanced design turbine had slightly higher modeled injury rates than the existing turbine design; however, there was no statistical evidence that suggested significant differences in blade-strike injuries between the two turbines and the hypothesis that direct fish survival rate through the advanced hydropower turbine is equal or better than that through the conventional turbine could not be rejected.

  5. Assessment of impacts from water level fluctuations on fish in the Hanford Reach, Columbia River

    SciTech Connect

    Becker, C.D.; Fickeisen, D.H.; Montgomery, J.C.

    1981-05-01

    Observations on the effects of water level fluctuations in the Hanford Reach of the Columbia River, Washington, were made in 1976 and 1977. The two years provided contrasting flow regimes: high water and fluctuations of greater magnitude prevailed in 1976; low water and higher temperatures prevailed in 1977. Situations where fish and other aquatic organisms were destroyed by changing water levels were observed and evaluated each year in three study areas: Hanford, F-Area, and White Bluffs sloughs. Losses primarily were due to stranding, entrapment (with or without complete dewatering), and predation. Juvenile fish were more susceptible to entrapment and stranding than were adult fish. Estimates of actual losses were biased and conservative because relatively few fish could be found after each decline of water level and dewatering. The most valued species of fish affected by water level fluctuations at Hanford were the anadromus fall chinook salmon (Oncorhynchus tshawytscha) and the resident smallmouth bass (Micropterus dolomieui). Crucial periods for chinook salmon occurred during winter when incubating eggs were in the gravel of the main channel, and before and during seaward migration in the spring when fry were abundant in shoreline zones. The crucial period for smallmouth bass was during spring and early summer when adults were spawning in warmed sloughs and shoreline zones. Chinook salmon and smallmouth bass fry were vulnerable to stranding and entrapment, and smallmouth bass nests were susceptible to exposure and temperature changes resulting from repeated water level fluctuations. Thus, flow manipulation may be crucial to their survival. The extent to which other species of riverine fish were affected by water level fluctuations depended upon their use of shoreline zones for spawning and rearing young.

  6. Mercury in fish of the Madeira river (temporal and spatial assessment), Brazilian Amazon.

    PubMed

    Bastos, Wanderley R; Dórea, José G; Bernardi, José Vicente E; Lauthartte, Leidiane C; Mussy, Marilia H; Lacerda, Luiz D; Malm, Olaf

    2015-07-01

    The Madeira River is the largest tributary of the Amazon River Basin and one of the most impacted by artisanal gold-mining activities, deforestation for agricultural projects, and recent hydroelectric reservoirs. Total Hg (and methylmercury-MeHg) concentrations was determined in 3182 fish samples of 84 species from different trophic levels as a function of standard size. Species at the top of the trophic level (Piscivorous, Carnivorous) showed the highest mean total Hg concentrations (51-1242 µg/kg), Planctivorous and Omnivorous species showed intermediate total Hg concentrations (26-494 µg/kg), while Detritivorous and Herbivorous species showed the lowest range of mean total Hg concentrations (9-275 µg/kg). Significant correlations between fish size (standard length) and total Hg concentrations were seen for Planctivorous (r=0.474, p=0.0001), Piscivorous (r=0.459, p=0.0001), Detritivorous (r=0.227, p=0.0001), Carnivorous (r=0.212, p=0.0001), and Herbivorous (r=0.156, p=0.01), but not for the Omnivorous species (r=-0.064, p=0.0685). Moreover, fish trophic levels influenced the ratio of MeHg to total Hg (ranged from 70% to 92%). When adjusted for standard body length, significant increases in Hg concentrations in the last 10 years were species specific. Spatial differences, albeit significant for some species, were not consistent with time trends for environmental contamination from past alluvial gold mining activities. Fish-Hg bioaccumulation is species specific but fish feeding strategies are the predominant influence in the fish-Hg bioaccumulation pattern.

  7. Use of fish farms to assess river contamination: combining biomarker responses, active biomonitoring, and chemical analysis.

    PubMed

    Quesada-García, Alba; Valdehita, Ana; Torrent, Fernando; Villarroel, Morris; Hernando, M Dolores; Navas, José M

    2013-09-15

    Here we addressed the possible effects of trace levels of contaminants on fish by means of a combination of biomarker responses, active biomonitoring (ABM), and chemical analysis. In environmental studies, cytochromes P4501A (Cyp1A) and Cyp3A and related enzyme activities (7-ethoxyresorufin-O-deethylase, EROD, and benzyloxy-4-[trifluoromethyl]-coumarin-O-debenzyloxylase, BFCOD, respectively) are commonly used as biomarkers for evidencing exposure to a variety of contaminants. In a rainbow trout (Oncorhynchus mykiss) fish farm that is routinely sampled to obtain references regarding normal levels of such enzyme activities in freshwater fish, we observed a strong and punctual increase in these activities at the end of 2011. In order to shed light on the causes of this induction, we transferred some fish to a fish farm with controlled conditions and examined them using an active biomonitoring (ABM) approach. EROD activity showed a decrease of 80% from the original values after 7 days in the control farm, while BFCOD activity was also reduced after 15 days. Although not significant, a decrease in cyp1A and cyp3A mRNA levels was also observed. To determine the presence of pollutants, water and sediment samples from the river feeding the fish farm were analyzed by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF-MS). The screening study reflected a weak inflow of pollutants in the monitored area, which is located far from any industrial activity or densely populated cities. Trace levels of polyaromatic hydrocarbons (PAHs) and personal care products (the polycyclic musk fragrance HHCB, and triclosan) were detected in sediments, at concentrations ranging from 0.01 to 38 ng/g dry weight, and in water from 4 to 441 ng/L. The approach followed in this study proved useful as a biomonitoring technique for the early detection of trace contaminants.

  8. Using DNA Barcoding to Assess Caribbean Reef Fish Biodiversity: Expanding Taxonomic and Geographic Coverage

    PubMed Central

    Weigt, Lee A.; Baldwin, Carole C.; Driskell, Amy; Smith, David G.; Ormos, Andrea; Reyier, Eric A.

    2012-01-01

    This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding “coverages” for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness. PMID:22815912

  9. Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage.

    PubMed

    Weigt, Lee A; Baldwin, Carole C; Driskell, Amy; Smith, David G; Ormos, Andrea; Reyier, Eric A

    2012-01-01

    This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding "coverages" for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.

  10. Assessment of Dissolved Oxygen Mitigation at Hydropower Dams Using an Integrated Hydrodynamic/Water Quality/Fish Growth Model

    SciTech Connect

    Bevelhimer, Mark S; Coutant, Charles C

    2006-07-01

    Dissolved oxygen (DO) in rivers is a common environmental problem associated with hydropower projects. Approximately 40% of all FERC-licensed projects have requirements to monitor and/or mitigate downstream DO conditions. Most forms of mitigation for increasing DO in dam tailwaters are fairly expensive. One area of research of the Department of Energy's Hydropower Program is the development of advanced turbines that improve downstream water quality and have other environmental benefits. There is great interest in being able to predict the benefits of these modifications prior to committing to the cost of new equipment. In the case of turbine replacement or modification, there is a need for methods that allow us to accurately extrapolate the benefits derived from one or two turbines with better design to the replacement or modification of all turbines at a site. The main objective of our study was to demonstrate a modeling approach that integrates the effects of flow and water quality dynamics with fish bioenergetics to predict DO mitigation effectiveness over long river segments downstream of hydropower dams. We were particularly interested in demonstrating the incremental value of including a fish growth model as a measure of biological response. The models applied are a suite of tools (RMS4 modeling system) originally developed by the Tennessee Valley Authority for simulating hydrodynamics (ADYN model), water quality (RQUAL model), and fish growth (FISH model) as influenced by DO, temperature, and available food base. We parameterized a model for a 26-mile reach of the Caney Fork River (Tennessee) below Center Hill Dam to assess how improvements in DO at the dam discharge would affect water quality and fish growth throughout the river. We simulated different types of mitigation (i.e., at the turbine and in the reservoir forebay) and different levels of improvement. The model application successfully demonstrates how a modeling approach like this one can be used

  11. Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS▿ †

    PubMed Central

    Behrens, Sebastian; Lösekann, Tina; Pett-Ridge, Jennifer; Weber, Peter K.; Ng, Wing-On; Stevenson, Bradley S.; Hutcheon, Ian D.; Relman, David A.; Spormann, Alfred M.

    2008-01-01

    To examine phylogenetic identity and metabolic activity of individual cells in complex microbial communities, we developed a method which combines rRNA-based in situ hybridization with stable isotope imaging based on nanometer-scale secondary-ion mass spectrometry (NanoSIMS). Fluorine or bromine atoms were introduced into cells via 16S rRNA-targeted probes, which enabled phylogenetic identification of individual cells by NanoSIMS imaging. To overcome the natural fluorine and bromine backgrounds, we modified the current catalyzed reporter deposition fluorescence in situ hybridization (FISH) technique by using halogen-containing fluorescently labeled tyramides as substrates for the enzymatic tyramide deposition. Thereby, we obtained an enhanced element labeling of microbial cells by FISH (EL-FISH). The relative cellular abundance of fluorine or bromine after EL-FISH exceeded natural background concentrations by up to 180-fold and allowed us to distinguish target from non-target cells in NanoSIMS fluorine or bromine images. The method was optimized on single cells of axenic Escherichia coli and Vibrio cholerae cultures. EL-FISH/NanoSIMS was then applied to study interrelationships in a dual-species consortium consisting of a filamentous cyanobacterium and a heterotrophic alphaproteobacterium. We also evaluated the method on complex microbial aggregates obtained from human oral biofilms. In both samples, we found evidence for metabolic interactions by visualizing the fate of substrates labeled with 13C-carbon and 15N-nitrogen, while individual cells were identified simultaneously by halogen labeling via EL-FISH. Our novel approach will facilitate further studies of the ecophysiology of known and uncultured microorganisms in complex environments and communities. PMID:18359832

  12. State-of-the-art assessment of electric and hybrid vehicles

    NASA Technical Reports Server (NTRS)

    1978-01-01

    Data are presented that were obtained from the electric and hybrid vehicles tested, information collected from users of electric vehicles, and data and information on electric and hybrid vehicles obtained on a worldwide basis from manufacturers and available literature. The data given include: (1) information and data base (electric and hybrid vehicle systems descriptions, sources of vehicle data and information, and sources of component data); (2) electric vehicles (theoretical background, electric vehicle track tests, user experience, literature data, and summary of electric vehicle status); (3) electric vehicle components (tires, differentials, transmissions, traction motors, controllers, batteries, battery chargers, and component summary); and (4) hybrid vehicles (types of hybrid vehicles, operating modes, hybrid vehicles components, and hybrid vehicles performance characteristics).

  13. Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Walsh, Stephen Joseph; Meador, Michael R.

    1998-01-01

    Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

  14. Assessment of risk of PCDD/Fs and dioxin-like PCBs in marine and freshwater fish in Pearl River Delta, China.

    PubMed

    Wei, X; Leung, K S; Wong, M H; Giesy, J; Cai, Z W; Wong, Chris K C

    2011-01-01

    Fish consumption is known to be beneficial to human health. However since the age of industrialization, the released/disposed chemical pollutants into water systems make fish a source of various environmental toxicants to humans. In oceanic cities with heavy industrial activities, fish products contribute the greate