Near-reef elemental signals in the otoliths of settling Pomacentrus amboinensis (Pomacentridae)

NASA Astrophysics Data System (ADS)

Sih, Tiffany L.; Kingsford, Michael J.

2016-03-01

Settlement is a key life history transition for coral reef fishes, and how long a fish spends close to a reef prior to settlement is poorly understood. We used laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and otolith microstructure analysis (daily increments and settlement marks) to determine the length of time larval fish spend near a reef prior to settlement. The otoliths of Pomacentrus amboinensis collected from four neighbouring reefs in the southern Great Barrier Reef showed clear and consistent differences in their elemental signatures prior to and following settlement. Elevated Ba:Ca near settlement and post-settlement was found in fish from all four reefs. However, there was individual variation in elemental profiles, with an increased otolith Ba-to-Ca ratio (near-reef signature) at settlement in 33 % of fish, and up to 8 d prior to settlement in others. Increment widths, often used as a proxy for growth, decreased approaching the settlement mark for all fish, providing further evidence for a "search phase" in larvae. We demonstrated experimentally that otoliths of fish kept in reefal or inter-reefal waters had different elemental chemistry. There were differences in the elemental composition of water samples within the study area, but no consistent trends with distance from reefs. There was poor discrimination of multi-element signatures among fish from different reefs during their pre-settlement phases. However, discrimination improved in the settlement and post-settlement phases of otoliths, indicating that reef waters and perhaps stage of ontogeny affected otolith chemistry. This study demonstrated clear near-reef elemental signatures in fish around settlement. We suggest these differences are due to a combination of water chemistry and physiological influences (e.g., growth). Combining LA-ICP-MS with otolith microstructure analysis can provide high-resolution information on the early life history of reef fishes. Further, a near-reef "search phase" prior to settlement may be common in reef fishes.

Use of Standing Gold Nanorods for Detection of Malachite Green and Crystal Violet in Fish by SERS.

PubMed

Chen, Xiaowei; Nguyen, Trang H D; Gu, Liqun; Lin, Mengshi

2017-07-01

With growing consumption of aquaculture products, there is increasing demand on rapid and sensitive techniques that can detect prohibited substances in the seafood products. This study aimed to develop a novel surface-enhanced Raman spectroscopy (SERS) method coupled with simplified extraction protocol and novel gold nanorod (AuNR) substrates to detect banned aquaculture substances (malachite green [MG] and crystal violet [CV]) and their mixture (1:1) in aqueous solution and fish samples. Multivariate statistical tools such as principal component analysis (PCA) and partial least squares regression (PLSR) were used in data analysis. PCA results demonstrate that SERS can distinguish MG, CV and their mixture (1:1) in aqueous solution and in fish samples. The detection limit of SERS coupled with standing AuNR substrates is 1 ppb for both MG and CV in fish samples. A good linear relationship between the actual concentration and predicted concentration of analytes based on PLSR models with R 2 values from 0.87 to 0.99 were obtained, indicating satisfactory quantification results of this method. These results demonstrate that the SERS method coupled with AuNR substrates can be used for rapid and accurate detection of MG and CV in fish samples. © 2017 Institute of Food Technologists®.

Comparison of an enzyme-linked immunosorbent assay (ELISA) to gas chromatography (GC) - measurement of polychlorinated biphenyls (PCBs) in selected US fish extracts

USGS Publications Warehouse

Zajicek, J.L.; Tillitt, D.E.; Schwartz, T.R.; Schmitt, C.J.; Harrison, R.O.

2000-01-01

The analysis of PCBs in fish tissues by immunoassay methods was evaluated using fish collected from a US monitoring program, the National Contaminant Biomonitoring Program of the US Department of Interior, Fish and Wildlife Service. Selected composite whole fish samples, which represented widely varying concentrations and sources of PCBs, were extracted and subjected to congener PCB analysis by gas chromatography (GC) and total PCB analysis using an ELISA (ePCBs) calibrated against technical Aroclor 1248. PCB congener patterns in these fishes were different from the patterns found in commercial Aroclors or their combinations as demonstrated by principal component analysis of normalized GC congener data. The sum of the PCB congeners measured by GC (total-PCBs) ranged from 37 to 4600 ng/g (wet weight). Concentrations of PCBs as determined by the ELISA method were positively correlated with total-PCBs and the ePCBs/total-PCBs ratios for individual samples ranged from 1 to 6. Ratios of ePCBs/total-PCBs for dilutions of Aroclors 1242, 1254, and 1260 and for matrix spikes range from 0.6 for 1242 to 2.5 for 1254 and 1260. These results suggest that higher chlorinated PCB congeners have higher affinity for the anti-PCB antibodies. Partial least squares with latent variable analysis of GC and ELISA data of selected Aroclors and fish samples also support the conclusion that ELISA derived PCB concentrations are dependent on the degree on chlorination.

Identification of hydrologic indicators related to fish diversity and abundance: A data mining approach for fish community analysis

NASA Astrophysics Data System (ADS)

Yang, Yi-Chen E.; Cai, Ximing; Herricks, Edwin E.

2008-04-01

This paper develops a new approach to identify hydrologic indicators related to fish community and generate a quantitative function between an ecological target index and the identified hydrologic indicators. The approach is based on genetic programming (GP), a data mining method. Using the Shannon Index (a fish community diversity index) or the number of individuals (total abundance) of a fish community, as an ecological target, the GP identified the most ecologically relevant hydrologic indicators (ERHIs) from 32 indicators of hydrologic alteration, for the case study site, the upper Illinois River. Robustness analysis showed that different GP runs found a similar set of ERHIs; each of the identified ERHI from different GP runs had a consistent relationship with the target index. By comparing the GP results with those from principal component analysis and autecology matrix, the three approaches identified a small number (six) of common ERHIs. Particularly, the timing of low flow (Dmin) seems to be more relevant to the diversity of the fish community, while the magnitude of the low flow (Qb) is more relevant to the total fish abundance; large rising rates result in a significant improvement of fish diversity, which is counterintuitive and against previous findings. The quantitative function developed by GP was further used to construct an indicator impact matrix (IIM), which was demonstrated as a potentially useful tool for streamflow restoration design.

Fish Assemblage Response to a Small Dam Removal in the Eightmile River System, Connecticut, USA

NASA Astrophysics Data System (ADS)

Poulos, Helen M.; Miller, Kate E.; Kraczkowski, Michelle L.; Welchel, Adam W.; Heineman, Ross; Chernoff, Barry

2014-11-01

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

Community structure and biogeography of shore fishes in the Gulf of Aqaba, Red Sea

NASA Astrophysics Data System (ADS)

Khalaf, Maroof A.; Kochzius, Marc

2002-02-01

Shore fish community structure off the Jordanian Red Sea coast was determined on fringing coral reefs and in a seagrass-dominated bay at 6 m and 12 m depths. A total of 198 fish species belonging to 121 genera and 43 families was recorded. Labridae and Pomacentridae dominated the ichthyofauna in terms of species richness and Pomacentridae were most abundant. Neither diversity nor species richness was correlated to depth. The abundance of fishes was higher at the deep reef slope, due to schooling planktivorous fishes. At 12 m depth abundance of fishes at the seagrass-dominated site was higher than on the coral reefs. Multivariate analysis demonstrated a strong influence on the fish assemblages by depth and benthic habitat. Fish species richness was positively correlated with hard substrate cover and habitat diversity. Abundance of corallivores was positively linked with live hard coral cover. The assemblages of fishes were different on the shallow reef slope, deep reef slope and seagrass meadows. An analysis of the fish fauna showed that the Gulf of Aqaba harbours a higher species richness than previously reported. The comparison with fish communities on other reefs around the Arabian Peninsula and Indian Ocean supported the recognition of an Arabian subprovince within the Indian Ocean. The affinity of the Arabian Gulf ichthyofauna to the Red Sea is not clear.

Fish assemblage response to a small dam removal in the Eightmile River system, Connecticut, USA.

PubMed

Poulos, Helen M; Miller, Kate E; Kraczkowski, Michelle L; Welchel, Adam W; Heineman, Ross; Chernoff, Barry

2014-11-01

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

Integration of Fish and Wildlife Data with Geobased and Remotely Sensed Land Use/land Cover Data: a Demonstration Using Sites in Pennsylvania. [Berwick and Lancaster

NASA Technical Reports Server (NTRS)

Cushwa, C. T.; Laroche, G.; Dubrock, C. W.

1982-01-01

The U.S. Fish and Wildlife Service developed a statewide fish and wildlife data base for the Pennsylvania Game Commission that includes 125 categories of information on each of the 844 species. This species data base is integrated with geobased and remotely-sensed land use/land cover data from two sites in Pennsylvania. One site is an energy development project; the other is a high-energy use area. Analyses using the combined animal and land use data bases can be demonstrated for a variety of land use/land cover types at both sites. The ability to make "what if" analysis prior to project implementation is presented.

MYC immunohistochemical and cytogenetic analysis are required for identification of clinically relevant aggressive B cell lymphoma subtypes.

PubMed

Raess, Philipp W; Moore, Stephen R; Cascio, Michael J; Dunlap, Jennifer; Fan, Guang; Gatter, Ken; Olson, Susan B; Braziel, Rita M

2018-06-01

Accurate subclassification of aggressive B cell lymphomas (ABCLs) requires integration of morphologic, immunohistochemical (IHC), and cytogenetic information. Optimal strategies have not been well defined for diagnosis of high grade B cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBLwR) and double expressor lymphomas with MYC and BCL2 protein overexpression. One hundred and eighty seven ABCLs were investigated with complete IHC and FISH analysis. Morphologic and IHC analysis was insufficient to identify clinically relevant HGBLwR. Approximately, 75% of cases classified as HGBLwR showed conventional DLBCL morphologic features. Fourteen percent of MYC-rearranged cases were negative by IHC. Conversely, 60% of cases positive for MYC by IHC did not demonstrate a MYC rearrangement. Analysis by FISH without MYC and BCL2 IHC would miss 41 cases of double expressor lymphoma. Complete IHC and FISH analysis is recommended in the evaluation of all ABCLs.

Evaluation of HER-2/neu status in breast cancer specimens using immunohistochemistry (IHC) & fluorescence in-situ hybridization (FISH) assay.

PubMed

Goud, Kalal Iravathy; Dayakar, Seetha; Vijayalaxmi, Kolanupaka; Babu, Saidam Jangu; Reddy, P Vijay Anand

2012-03-01

Fluorescence in situ hybridization (FISH) is increasingly being recognized as the most accurate and predictive test for HER 2/neu gene amplification and response to therapy in breast cancer. In the present study we investigated HER-2/neu gene amplification by FISH in breast carcinoma tissue specimens and compared the results with that of immunohistochemical (IHC) analysis. A total of 90 breast carcinoma tissue samples were used for immunohistochemical (IHC) and FISH analysis. IHC was performed by using mouse monoclonal antibody to the intracellular domain of HER-2/neu protein. Each slide was scored in a blinded fashion by two pathologists according to the manufacturer's recommended criteria. FISH analysis was performed on paraffin embedded breast tumour tissue sections. The polysomy for centromere 17 (Spec green signal) was read as green signals less than 4 as moderate polysomy, and more than 4 as highly polysomy. Thirty of the 90 patients had negative results by IHC and FISH. Of the 28 patients with the score of 2+ by IHC, 20 were FISH positive for HER-2/neu gene amplification, three were FISH negative and five patients showed equivocal (1.8-2.2) results by FISH. These five cases were retested for IHC and FISH on different paraffin embedded tissue blocks, and all five were found positive for HER-2/neu gene amplification. Twenty five patients with the score of 3+ by IHC were FISH positive for HER-2/neu gene amplification (>2.2). Seven cases with the score of 3+ by IHC were FISH negative for HER-2/neu gene amplification (>2.2), and showed polysomy of chromosome number 17 high polysomy > 4. Our results indicated that HER-2/neu status by FISH should be performed in all cases of breast tumour with a 2+ score by IHC. Cases demonstrating a 3+ score by IHC may be subjected to FISH to rule out polysomy of chromosome 17 which could be falsely interpreted as HER-2/neu overexpression by IHC analysis. There is also a need for establishing a clinically validated cut-off value for HER-2/neu FISH amplification against IHC which may be further compared and calibrated.

Evolutionary Origins for Social Vocalization in a Vertebrate Hindbrain–Spinal Compartment

PubMed Central

Bass, Andrew H.; Gilland, Edwin H.; Baker, Robert

2008-01-01

The macroevolutionary events leading to neural innovations for social communication, such as vocalization, are essentially unexplored. Many fish vocalize during female courtship and territorial defense, as do amphibians, birds, and mammals. Here, we map the neural circuitry for vocalization in larval fish and show that the vocal network develops in a segment-like region across the most caudal hindbrain and rostral spinal cord. Taxonomic analysis demonstrates a highly conserved pattern between fish and all major lineages of vocal tetrapods. We propose that the vocal basis for acoustic communication among vertebrates evolved from an ancestrally shared developmental compartment already present in the early fishes. PMID:18635807

Sensory Cells of the Fish Ear: A Hairy Enigma

NASA Technical Reports Server (NTRS)

Popper, A. N.; Saidel, W. M.

1995-01-01

Analysis of the structure of the ears in teleost fishes has led to the tentative suggestion that otolithic endorgans may function differently, in different species. Recently, evidence has demonstrated different 'types' of sensory hair cells can be found in the ears of teleost fishes, and individual hair cell types are found in discrete regions of individual sensory, epithelia. The presence of multiple hair cell types in fishes provides strong support to the hypothesis of regional differences in the responses of individual otolithic sensory epithelia. The finding of hair cell types in fishes that closely resemble those found in amniote vestibular endorgans also suggests that hair cell heterogeneity arose earlier in the evolution of the vertebrate ear than previously thought.

Immunological cross-reactivity between four distant parvalbumins-Impact on allergen detection and diagnostics.

PubMed

Sharp, Michael F; Stephen, Juan N; Kraft, Lukas; Weiss, Thomas; Kamath, Sandip D; Lopata, Andreas L

2015-02-01

Fish are the largest and most diverse group of vertebrates. Fish are also a part of the eight food groups that cause the majority of IgE mediated food reactions. Detection tools for fish allergens are however limited due to the great diversity of fish species, despite fish allergy and its major allergen parvalbumin being well documented. The most commonly studied fish are frequently consumed in North America and Europe. However, much less is known about fish allergens in the Australasian region although fish is widely consumed in this region. A comprehensive phylogenetic analysis was performed of known parvalbumin amino acid sequences to determine possible candidate antigens for new cross-reactive antibodies to be used to detect most fish parvalbumins. Polyclonal rabbit antibodies were raised against parvalbumins from frequently consumed barramundi (Lates calcarifer), basa (Pangasius bocourti), pilchard (Sardinops sagax) and Atlantic salmon (Salmo salar). These were evaluated for cross-reactivity against a panel of 45 fish extracts (raw, heated and canned fish). Anti-barramundi parvalbumin proved to be the most cross-reactive antibody, detecting 87.5% of the 40 species analyzed, followed by anti-pilchard and anti-basa antibody. In contrast the anti-salmon antibody was very specific and only reacted to salmonidae and a few other fish. All analyzed fish species, except mahi mahi, swordfish, yellowfin tuna and all 5 canned fish had parvalbumin detected in raw extracts. However antibody reactivity to many fish was heat liable or susceptible to denaturation, demonstrating that some parvalbumins have most likely conformational epitopes, which lose antibody reactivity after heat treatment. We have demonstrated the generation of highly cross-reactive anti-parvalbumin antibodies that could be used for the detection of allergenic fish parvalbumin in contaminated food products. This cross-reactivity study thus shows processing of fish, especially canning, can have on impact on antibody recognition by ELISA, possibly similar to IgE-binding in vivo. Copyright © 2014 Elsevier Ltd. All rights reserved.

Opportunism or aquatic specialization? Evidence of freshwater fish exploitation at Ohalo II- A waterlogged Upper Paleolithic site

PubMed Central

Dayan, Tamar; Goren, Menachem; Nadel, Dani; Hershkovitz, Israel

2018-01-01

Analysis of ca. 17,000 fish remains recovered from the late Upper Paleolithic/early Epi-Paleolithic (LGM; 23,000 BP) waterlogged site of Ohalo II (Rift Valley, Israel) provides new insights into the role of wetland habitats and the fish inhabiting them during the evolution of economic strategies prior to the agricultural evolution. Of the current 19 native fish species in Lake Kinneret (Sea of Galilee), eight species were identified at Ohalo II, belonging to two freshwater families: Cyprinidae (carps) and Cichlidae (St. Peter fish). Employing a large set of quantitative and qualitative criteria (NISP, species richness, diversity, skeletal element representation, fragmentation, color, spatial distribution, etc.), we demonstrate that the inhabitants of Ohalo II used their knowledge of the breeding behavior of different species of fish, for year-round intensive exploitation. PMID:29912923

Opportunism or aquatic specialization? Evidence of freshwater fish exploitation at Ohalo II- A waterlogged Upper Paleolithic site.

PubMed

Zohar, Irit; Dayan, Tamar; Goren, Menachem; Nadel, Dani; Hershkovitz, Israel

2018-01-01

Analysis of ca. 17,000 fish remains recovered from the late Upper Paleolithic/early Epi-Paleolithic (LGM; 23,000 BP) waterlogged site of Ohalo II (Rift Valley, Israel) provides new insights into the role of wetland habitats and the fish inhabiting them during the evolution of economic strategies prior to the agricultural evolution. Of the current 19 native fish species in Lake Kinneret (Sea of Galilee), eight species were identified at Ohalo II, belonging to two freshwater families: Cyprinidae (carps) and Cichlidae (St. Peter fish). Employing a large set of quantitative and qualitative criteria (NISP, species richness, diversity, skeletal element representation, fragmentation, color, spatial distribution, etc.), we demonstrate that the inhabitants of Ohalo II used their knowledge of the breeding behavior of different species of fish, for year-round intensive exploitation.

3D tooth microwear texture analysis in fishes as a test of dietary hypotheses of durophagy

NASA Astrophysics Data System (ADS)

Purnell, Mark A.; Darras, Laurent P. G.

2016-03-01

An understanding of how extinct animals functioned underpins our understanding of past evolutionary events, including adaptive radiations, and the role of functional innovation and adaptation as drivers of both micro- and macroevolution. Yet analysis of function in extinct animals is fraught with difficulty. Hypotheses that interpret molariform teeth in fishes as evidence of durophagous (shell-crushing) diets provide a good example of the particular problems inherent in the methods of functional morphology. This is because the assumed close coupling of form and function upon which the approach is based is weakened by, among other things, behavioural flexibility and the absence of a clear one to one relationship between structures and functions. Here we show that ISO 25178-2 standard parameters for surface texture, derived from analysis of worn surfaces of molariform teeth of fishes, vary significantly between species that differ in the amount of hard-shelled prey they consume. Two populations of the Sheepshead Seabream (Archosargus probatocephalus) were studied. This fish is not a dietary specialist, and one of the populations is known to consume more vegetation and less hard-shelled prey than the other; this is reflected in significant differences in their microwear textures. The Archosargus populations differ significantly in their microwear from the specialist shell-crusher Anarhichas lupus (the Atlantic Wolffish). Multivariate analysis of these three groups of fishes lends further support to the relationship between diet and tooth microwear, and provides robust validation of the approach. Application of the multivariate models derived from microwear texture in Archosargus and Anarhichas to a third fish species—the cichlid Astatoreochromis alluaudi—successfully separates wild caught fish that ate hard-shelled prey from lab-raised fish that did not. This cross-taxon validation demonstrates that quantitative analysis of tooth microwear texture can differentiate between fishes with different diets even when they range widely in size, habitat, and in the structure of their trophic apparatus. The approach thus has great potential as an additional tool for dietary analysis in extant fishes, and for testing dietary hypotheses in ancient and extinct species.

The role of immunohistochemical analysis in the evaluation of EML4-ALK gene rearrangement in lung cancer.

PubMed

Sullivan, Harold C; Fisher, Kevin E; Hoffa, Anne L; Wang, Jason; Saxe, Debra; Siddiqui, Momin T; Cohen, Cynthia

2015-04-01

Among the mutations described in non-small cell lung carcinoma is a rearrangement resulting from an inversion within chromosome 2p leading to the formation of a fusion gene, echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK). Fluorescence in situ hybridization (FISH) is the gold standard for the detection of ALK gene rearrangements. However, molecular methods are not readily available in all pathology laboratories. Immunohistochemistry (IHC) using an antibody directed against the EML4-ALK fusion protein provides a widely available alternative method of detection. We assessed whether IHC is a comparable and cost-effective alternative to FISH analysis for the detection of ALK gene rearrangements. A total of 110 non-small cell lung carcinoma cases (63 surgical/biopsy and 47 cytology specimens), previously tested for ALK gene rearrangements by FISH [7 (6.4%) positive for the rearrangement], were probed for the EML4-ALK fusion protein using a monoclonal EML4-ALK antibody, clone 5A4. Cells were considered to stain positive for ALK if >5% of cells showed cytoplasmic staining of at least grade 1 intensity (scale: 0 to 3). A cost analysis was performed using ALK IHC as a screening test. The sensitivity and specificity of the EML4-ALK IHC stain compared with ALK FISH analysis were 100% and 96%, respectively. All 7 FISH-positive cases stained positive by IHC, whereas 4 FISH-negative cases demonstrated positive staining. One of the 4 FISH-negative, IHC-positive cases harbored an EML4-ALK rearrangement by RT-PCR yielding 3 false-positive results overall. The κ agreement between IHC and FISH methods is 0.76 (substantial/excellent). The potential savings of implementing the ALK IHC as a screening method would be $10,418.21. Sensitivity of the EML4-ALK IHC stain is excellent (100%) but due to its suboptimal specificity, IHC cannot reliably supplant FISH analysis for the detection of ALK gene rearrangements. IHC shows promise as a screening tool to prevent unnecessary costly FISH analysis.

Evaluation of a Fast and Simple Sample Preparation Method for Polybrominated Diphenyl Ether (PBDE) Flame Retardants and Dichlorodiphenyltrichloroethane (DDT) Pesticides in Fish for Analysis by ELISA Compared with GC-MS/MS.

PubMed

Sapozhnikova, Yelena; Simons, Tawana; Lehotay, Steven J

2015-05-13

A simple, fast, and cost-effective sample preparation method, previously developed and validated for the analysis of organic contaminants in fish using low-pressure gas chromatography-tandem mass spectrometry (LPGC-MS/MS), was evaluated for the analysis of polybrominated diphenyl ethers (PBDEs) and dichlorodiphenyltrichloroethane (DDT) pesticides using enzyme-linked immunosorbent assay (ELISA). The sample preparation technique was based on the quick, easy, cheap, rugged, effective, and safe (QuEChERS) approach with filter-vial dispersive solid phase extraction (d-SPE). Incurred PBDEs and DDTs were analyzed in three types of fish with 3-10% lipid content: Pacific croaker, salmon, and National Institute of Standards and Technology (NIST) Standard Reference Material 1947 (Lake Michigan fish tissue). LPGC-MS/MS and ELISA results were in agreement: 108-111 and 65-82% accuracy ELISA versus LPGC-MS/MS results for PBDEs and DDTs, respectively. Similar detection limits were achieved for ELISA and LPGC-MS/MS. Matrix effects (MEs) were significant (e.g., -60%) for PBDE measurement in ELISA, but not a factor in the case of DDT pesticides. This study demonstrated that the sample preparation method can be adopted for semiquantitative screening analysis of fish samples by commercial kits for PBDEs and DDTs.

[AFM fishing of proteins under impulse electric field].

PubMed

Ivanov, Yu D; Pleshakova, T O; Malsagova, K A; Kaysheva, A L; Kopylov, A T; Izotov, A A; Tatur, V Yu; Vesnin, S G; Ivanova, N D; Ziborov, V S; Archakov, A I

2016-05-01

A combination of (atomic force microscopy)-based fishing (AFM-fishing) and mass spectrometry allows to capture protein molecules from solutions, concentrate and visualize them on an atomically flat surface of the AFM chip and identify by subsequent mass spectrometric analysis. In order to increase the AFM-fishing efficiency we have applied pulsed voltage with the rise time of the front of about 1 ns to the AFM chip. The AFM-chip was made using a conductive material, highly oriented pyrolytic graphite (HOPG). The increased efficiency of AFM-fishing has been demonstrated using detection of cytochrome b5 protein. Selection of the stimulating pulse with a rise time of 1 ns, corresponding to the GHz frequency range, by the effect of intrinsic emission from water observed in this frequency range during water injection into the cell.

Size-dependent social attraction and repulsion explains the decision of Atlantic cod Gadus morhua to enter baited pots.

PubMed

Anders, N; Fernö, A; Humborstad, O-B; Løkkeborg, S; Rieucau, G; Utne-Palm, A C

2017-12-01

The present study tested whether the presence of already retained fishes inside baited fish pots acted as a social attraction and affected the entrance probability of Atlantic cod Gadus morhua in a fjord in northern Norway. Video analysis revealed that the probability of an entrance initially increased with the presence of low numbers of fishes inside the pot, but subsequently decreased at a critical number of caught fishes. The critical number was dependent on the size of the G. morhua attempting to enter. This demonstrates that social attraction and repulsion play a role in G. morhua pot fishing and has important implications for the capture efficiency of fisheries executed with pots. © 2017 The Fisheries Society of the British Isles.

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

PubMed

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

2006-05-01

Recreational and subsistence fishing plays a major role in the lives of many people, although most Americans obtain their fish from supermarkets or other commercial sources. Fish consumption has generally increased in recent years, largely because of the nutritional benefits. Recent concerns about contaminants in fish have prompted federal and state agencies to analyze fish (especially freshwater fish targeted by recreational anglers) for contaminants, such as mercury and polychlorinated biphenyls (PCBs), and to issue fish consumption advisories to help reduce the public health risks, where warranted. Scientists engaged in environmental sampling collect fish by a variety of means, and analyze the contaminants in those fish. Risk assessors use these levels as the basis for their advisories. Two assumptions of this methodology are that scientists collect the same size (and types) of fish that fishermen catch, and that, for some contaminants (such as methylmercury and PCBs), levels increase with the size and age of the fish. While many studies demonstrate a positive relationship between size and mercury levels in a wide range of different species of fish, the assumption that scientists collect the same size fish as fishermen has not been examined. The assumption that scientists collect the same size fish as those caught (and eaten) by recreationalists or subsistence fishermen is extremely important because contaminant levels are different in different size fish. In this article, we test the null hypothesis that there are no differences in the sizes of fish collected by Aleut fishermen, scientists (including divers), and commercial trawlers in the Bering Sea from Adak to Kiska. Aleut fishermen caught fish using rod-and-reel (fishing rods, hook, and fresh bait) from boats, as they would in their Aleutian villages. The scientists collected fish using rod-and-reel, as well as by scuba divers using spears up to 90 ft depths. A fisheries biologist collected fish from a research/commercial trawler operated under charter to the National Oceanographic and Atmospheric Administration (NOAA). The fish selected for sampling, including those caught commercially in the Bering Sea, represented different trophic levels, and are species regularly caught by Aleuts while fishing near their villages. Not all fish were caught by all three groups. There were no significant differences in length and weight for five species of fish caught by Aleuts, scientists, and fisheries trawls, and for an additional 3 species caught only by the Aleut and scientist teams. There were small, but significant, differences in the sizes of rock greenling (Hexagrammos lagocephalus) and red Irish lord (Hemilepidotus hemilepidotus) caught by the scientist and Aleut fishermen. No scientists caught rock greenling using poles; those speared by the divers were significantly smaller than those caught by the Aleuts. Further, there were no differences in the percent of males in the samples as a function of fishing method or type of fishermen, except for rockfish and red Irish lord. These data suggest that if scientists collect fish in the same manner as subsistence fishermen (in this case, using fishing rods from boats), they can collect the same-sized fish. The implications for exposure and risk assessment are that scientists should either engage subsistence and recreational fishermen to collect fish for analysis, or mimic their fishing methods to ensure that the fish collected are similar in size and weight to those being caught and consumed by these groups. Further, total length, standard length, and weight were highly correlated for all species of fish, suggesting that risk assessors could rely on recreational and commercial fishermen to measure total lengths for the purpose of correlating mercury levels with known size/mercury level relationships. Our data generally demonstrate that the scientists and trawlers can collect the same size fish as those caught by Aleuts, making contaminant analysis, and subsequent contaminant analysis, representative of the risks to fish consumers.

Optimizing fish sampling for fish - mercury bioaccumulation factors

USGS Publications Warehouse

Scudder Eikenberry, Barbara C.; Riva-Murray, Karen; Knightes, Christopher D.; Journey, Celeste A.; Chasar, Lia C.; Brigham, Mark E.; Bradley, Paul M.

2015-01-01

Fish Bioaccumulation Factors (BAFs; ratios of mercury (Hg) in fish (Hgfish) and water (Hgwater)) are used to develop Total Maximum Daily Load and water quality criteria for Hg-impaired waters. Both applications require representative Hgfish estimates and, thus, are sensitive to sampling and data-treatment methods. Data collected by fixed protocol from 11 streams in 5 states distributed across the US were used to assess the effects of Hgfish normalization/standardization methods and fish sample numbers on BAF estimates. Fish length, followed by weight, was most correlated to adult top-predator Hgfish. Site-specific BAFs based on length-normalized and standardized Hgfish estimates demonstrated up to 50% less variability than those based on non-normalized Hgfish. Permutation analysis indicated that length-normalized and standardized Hgfish estimates based on at least 8 trout or 5 bass resulted in mean Hgfish coefficients of variation less than 20%. These results are intended to support regulatory mercury monitoring and load-reduction program improvements.

Evaluation of HER-2/neu status in breast cancer specimens using immunohistochemistry (IHC) & fluorescence in-situ hybridization (FISH) assay

PubMed Central

Goud, Kalal Iravathy; Dayakar, Seetha; Vijayalaxmi, Kolanupaka; Babu, Saidam Jangu; Vijay, Anand Reddy P.

2012-01-01

Background & objectives: Fluorescence in situ hybridization (FISH) is increasingly being recognized as the most accurate and predictive test for HER2/neu gene amplification and response to therapy in breast cancer. In the present study we investigated HER-2/neu gene amplification by FISH in breast carcinoma tissue specimens and compared the results with that of immunohistochemical (IHC) analysis. Methods: A total of 90 breast carcinoma tissue samples were used for immunohistochemical (IHC) and FISH analysis. IHC was performed by using mouse monoclonal antibody to the intracellular domain of HER-2/neu protein. Each slide was scored in a blinded fashion by two pathologists according to the manufacturer's recommended criteria. FISH analysis was performed on paraffin embedded breast tumour tissue sections. The polysomy for centromere 17 (Spec green signal) was read as green signals less than 4 as moderate polysomy, and more than 4 as highly polysomy. Results: Thirty of the 90 patients had negative results by IHC and FISH. Of the 28 patients with the score of 2+ by IHC, 20 were FISH positive for HER-2/neu gene amplification, three were FISH negative and five patients showed equivocal (1.8-2.2) results by FISH. These five cases were retested for IHC and FISH on different paraffin embedded tissue blocks, and all five were found positive for HER-2/neu gene amplification. Twenty five patients with the score of 3+ by IHC were FISH positive for HER-2/neu gene amplification (>2.2). Seven cases with the score of 3+ by IHC were FISH negative for HER-2/neu gene amplification (>2.2), and showed polysomy of chromosome number 17 high polysomy > 4. Interpretation & conclusions: Our results indicated that HER-2/neu status by FISH should be performed in all cases of breast tumour with a 2+ score by IHC. Cases demonstrating a 3+ score by IHC may be subjected to FISH to rule out polysomy of chromosome 17 which could be falsely interpreted as HER-2/neu overexpression by IHC analysis. There is also a need for establishing a clinically validated cut-off value for HER-2/neu FISH amplification against IHC which may be further compared and calibrated. PMID:22561616

Comparative analysis of EPA and DHA in fish oil nutritional capsules by GC-MS.

PubMed

Yi, Tao; Li, Shuk-Man; Fan, Jia-Yi; Fan, Lan-Lan; Zhang, Zhi-Feng; Luo, Pei; Zhang, Xiao-Jun; Wang, Jian-Gang; Zhu, Lin; Zhao, Zhong-Zhen; Chen, Hu-Biao

2014-12-13

Fish oil is a popular nutritional product consumed in Hong Kong. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are the two main bioactive components responsible for the health benefits of fish oil. Market survey in Hong Kong demonstrated that various fish oil capsules with different origins and prices are sold simultaneously. However, these capsules are labelled with same ingredient levels, namely EPA 180 mg/g and DHA 120 mg/g. This situation makes the consumers very confused. To evaluate the quality of various fish oil capsules, a comparative analysis of the contents of EPA and DHA in fish oil is crucial. A gas chromatography-mass spectrometry (GC-MS) method was developed for identification and determination of EPA and DHA in fish oil capsules. A comprehensive validation of the developed method was conducted. Ten batches of fish oil capsules samples purchased from drugstores of Hong Kong were analyzed by using the developed method. The present method presented good sensitivity, precision and accuracy. The limits of detection (LOD) for EPA and DHA were 0.08 ng and 0.21 ng, respectively. The relative standard deviation (RSD) values of EPA and DHA for repeatability tests were both less than 1.05%; and the recovery for accuracy test of EPA and DHA were 100.50% and 103.83%, respectively. In ten fish oil samples, the contents of EPA ranged from 39.52 mg/g to 509.16 mg/g, and the contents of DHA ranged from 35.14 mg/g to 645.70 mg/g. The present method is suitable for the quantitative analysis of EPA and DHA in fish oil capsules. There is a significant variation in the contents of the quantified components in fish oil samples, and there is not a linear relationship between price and contents of EPA and DHA. Strict supervision of the labelling of the fish oil capsules is urgently needed.

What Happens to the Fish's Achievement in a Little Pond? A Simultaneous Analysis of Class-Average Achievement Effects on Achievement and Academic Self-Concept

ERIC Educational Resources Information Center

Stäbler, Franziska; Dumont, Hanna; Becker, Michael; Baumert, Jürgen

2017-01-01

Empirical studies have demonstrated that students who are taught in a group of students with higher average achievement benefit in terms of their achievement. However, there is also evidence showing that being surrounded by high-achieving students has a negative effect on students' academic self-concept, also known as the big-fish--little-pond…

New hosts and genetic diversity of Flavobacterium columnare isolated from Brazilian native species and Nile tilapia.

PubMed

Barony, G M; Tavares, G C; Assis, G B N; Luz, R K; Figueiredo, H C P; Leal, C A G

2015-11-17

Flavobacterium columnare is responsible for disease outbreaks in freshwater fish farms. Several Brazilian native fish have been commercially exploited or studied for aquaculture purposes, including Amazon catfish Leiarius marmoratus × Pseudoplatystoma fasciatum and pacamã Lophiosilurus alexandri. This study aimed to identify the aetiology of disease outbreaks in Amazon catfish and pacamã hatcheries and to address the genetic diversity of F. columnare isolates obtained from diseased fish. Two outbreaks in Amazon catfish and pacamã hatcheries took place in 2010 and 2011. Four F. columnare strains were isolated from these fish and identified by PCR. The disease was successfully reproduced under experimental conditions for both fish species, fulfilling Koch's postulates. The genomovar of these 4 isolates and of an additional 11 isolates from Nile tilapia Oreochromis niloticus was determined by 16S rRNA restriction fragment length polymorphism PCR. The genetic diversity was evaluated by phylogenetic analysis of the 16S rRNA gene and repetitive extragenic palindromic PCR (REP-PCR). Most isolates (n = 13) belonged to genomovar II; the remaining 2 isolates (both from Nile tilapia) were assigned to genomovar I. Phylogenetic analysis and REP-PCR were able to demonstrate intragenomovar diversity. This is the first report of columnaris in Brazilian native Amazon catfish and pacamã. The Brazilian F. columnare isolates showed moderate diversity, and REP-PCR was demonstrated to be a feasible method to evaluate genetic variability in this bacterium.

Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway.

PubMed

Hagey, Lee R; Møller, Peter R; Hofmann, Alan F; Krasowski, Matthew D

2010-01-01

Bile salts are the major end metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates.

Fatty acid composition of freshwater wild fish in subalpine lakes: a comparative study.

PubMed

Vasconi, Mauro; Caprino, Fabio; Bellagamba, Federica; Busetto, Maria Letizia; Bernardi, Cristian; Puzzi, Cesare; Moretti, Vittorio Maria

2015-03-01

In this study, the proximate and fatty acid compositions of the muscle tissue of 186 samples of fish belonging to fifteen species of freshwater fish harvested in subalpine lakes (bleak, shad, crucian carp, whitefish, common carp, pike, black bullhead, burbot, perch, Italian roach, roach, rudd, wels catfish, chub and tench) were investigated. Most of the fish demonstrated a lipid content in the fillet lower than 2.0 g 100 g(-1) wet weight (range 0.6-9.7). A strong relationship between feeding behavior and fatty acid composition of the muscle lipids was observed. Planktivorous fish showed the lowest amounts of n-3 fatty acids (p < 0.05), but the highest monounsaturated fatty acid (MUFA) contents, in particular 18:1n-9. Conversely, carnivorous fish showed the highest amounts of saturated fatty acids and n-3 fatty acids (p < 0.05), but the lowest MUFA contents. Omnivorous fish showed substantial proportions of n-3 fatty acids and the highest contents of n-6 fatty acids. Principal component analysis showed a distinct separation between fish species according to their feeding habits and demonstrated that the most contributing trophic markers were 18:1n-9, 18:3n-3, 22:6n-3 and 20:4n-6. The quantitative amounts n-3 polyunsaturated fatty acid in muscle tissues varied depending on the fish species, the lipid content and the feeding habits. Some species were very lean, and therefore would be poor choices for human consumption to meet dietary n-3 fatty acid requirements. Nevertheless, the more frequently consumed and appreciated fish, shad and whitefish, had EPA and DHA contents in the range 900-1,000 mg 100 g(-1) fresh fillet.

Changes in fish diversity and community structure in the central and southern Yellow Sea from 2003 to 2015

NASA Astrophysics Data System (ADS)

Chen, Yunlong; Shan, Xiujuan; Jin, Xianshi; Johannessen, Arne; Yang, Tao; Dai, Fangqun

2017-07-01

The central and southern Yellow Sea is an important overwintering ground for many fish species in the Bohai Sea and Yellow Sea. For better understanding the status of the fish community after years of heavy exploitation, variations in fish community structure and diversity were analyzed using data from bottom trawls during 2003-2015. Five fish assemblage indices all showed fluctuations without clear trends from 2003 to 2015, yet there were strong positive and significant correlations (P < 0.05) among them. The top-five dominant species accounted for a high weight percentage (49.7%-82.1%) in the annual fish catch. Multivariate analysis showed that two year groups could be pooled for the fish community: Group I consisted of the years 2006, 2007, 2008 and 2015, while Group II consisted of the years 2003, 2004, 2005, 2009, 2010 and 2014; the groups aggregated with 63.71% similarity, indicating a high level of similarity among all years. The multivariate dispersion values were 1.455 and 0.818 for Groups I and II, respectively, indicating greater variances in fish assemblage structure in Group I than that in Group II. Similarity of percentage analysis demonstrated that the average similarities for Group I and Group II were 71.58% and 67.51%, respectively. Size-spectra analysis revealed no consistent trend in the intercept and slope (P > 0.05); there were also no significant differences between the slope of the size-spectra and fishing effort. The catch per unit effort and mean individual weight analyses of the whole fish assemblage both showed a significantly decreasing trend over time. Overall, the results showed that the fish community structure in the central and southern Yellow Sea was relatively stable from 2003 to 2015 and the study could be used as a reference for supporting ecosystem-based fishery management.

The role of maintenance thalidomide therapy in multiple myeloma: MRC Myeloma IX results and meta-analysis.

PubMed

Morgan, Gareth J; Gregory, Walter M; Davies, Faith E; Bell, Sue E; Szubert, Alexander J; Brown, Julia M; Coy, Nuria N; Cook, Gordon; Russell, Nigel H; Rudin, Claudius; Roddie, Huw; Drayson, Mark T; Owen, Roger G; Ross, Fiona M; Jackson, Graham H; Child, J Anthony

2012-01-05

Thalidomide maintenance has the potential to modulate residual multiple myeloma (MM) after an initial response. This trial compared the effect of thalidomide maintenance and no maintenance on progression-free survival (PFS) and overall survival (OS) in MM patients. After intensive or nonintensive induction therapy, 820 newly diagnosed MM patients were randomized to open-label thalidomide maintenance until progression, or no maintenance. Interphase FISH (iFISH) analysis was performed at study entry. Median PFS was significantly longer with thalidomide maintenance (log-rank P < .001). Median OS was similar between regimens (log-rank P = .40). Patients with favorable iFISH showed improved PFS (P = .004) and a trend toward a late survival benefit. Patients with adverse iFISH receiving thalidomide showed no significant PFS benefit and worse OS (P = .009). Effective relapse therapy enhanced survival after progression, translating into a significant OS benefit. Meta-analysis of this and other studies show a significant late OS benefit (P < .001, 7-year difference hazard ratio = 12.3; 95% confidence interval, 5.5-19.0). Thalidomide maintenance significantly improves PFS and can be associated with improved OS. iFISH testing is important in assessing the clinical impact of maintenance therapy. Overview analysis demonstrated that thalidomide maintenance was associated with a significant late OS benefit. This trial was registered at www.isrctn.org as #ISRCTN68454111.

Application of ERTS-1 imagery to the harvest model of the US Menhaden fishery

NASA Technical Reports Server (NTRS)

Maughan, P. M.; Marmelstein, A. D.; Temple, O. R.

1973-01-01

Preliminary results of an experiment to demonstrate the utility of ERTS-1 imagery for providing significant information to the harvest model of the menhaden industry are reported. Fisheries and related environmental data were obtained discontinuously throughout the 1973 menhaden (a surface schooling, coastal species) fishing season in Mississippi Sound. The unexpected complexity of the physical environment in Mississippi Sound precluded simplistic analysis of fish/environment relationships. Preliminary indications are that an association does exist between fish availability and differences in water transparency (turbidity) within the Sound. A clearer relationship is developing between major turbid features, imaged by ERTS-1 and location of successful fishing attempts. On all occasions where relatively cloudfree ERTS-1 overflight days coincided with fishery activity, overlays of catch location of ERTS-1 images show an association of school position with interfaces between imaged turbid features. Analysis is currently underway to determine persistence of such associations in an attempt to define minimum satellite return time necessary to maintain continuity of associations.

Comparative Analysis of Lipid Content and Fatty Acid Composition of Commercially Important Fish and Shellfish from Sri Lanka and Japan.

PubMed

Devadason, Chandravathany; Jayasinghe, Chamila; Sivakanesan, Ramiah; Senarath, Samanthika; Beppu, Fumiaki; Gotoh, Naohiro

2016-01-01

Sri Lanka is surrounded by the Indian Ocean, allowing plenty of fishes to be caught. Moreover, these fishes represent one of the undocumented fish resources in the world and their detailed lipid profiles have not been previously examined. In this study, the lipid content and fatty acid composition of 50 commercially important fishes from the Indian Ocean (Sri Lanka) and the Pacific Ocean (Japan) were compared. The total lipid content and fatty acid composition, including eicosapentaenoic acid (C20:5n-3, EPA) and docosahexaenoic acid (C22:6n-3, DHA), differed significantly among species. Fish from the Pacific Ocean had higher proportions of fatty acids, including EPA and DHA. Herrings and mackerels from both oceanic areas demonstrated high levels of EPA and DHA, and n-3/n-6 ratio. Brackish and freshwater fishes from both groups showed low levels of PUFAs. Fish from the Indian Ocean were high in n-6 fatty acids. Monounsaturated fatty acid levels were high in omnivorous fish from the Pacific Ocean, and saturated fatty acid levels were high in fish from the Indian Ocean. The results of this study will be of value in determining the dietary usefulness of fish caught in Sri Lanka.

Seasonal influence on the hematological parameters in cultured Nile tilapia from southern Brazil.

PubMed

Jerônimo, G T; Laffitte, L V; Speck, G M; Martins, M L

2011-08-01

This study evaluated seasonality in hematological parameters of Nile tilapia cultured in the state of Santa Catarina, southern Brazil. A total of 240 fish were examined during four seasons between April 2007 and March 2008 in three different fish farms. After being anesthetised in a benzocaine solution, blood samples were withdrawn into syringes containing a drop of 10% EDTA for hematological analysis. The results were compared between fish farms and seasons, which are well delimited in southern Brazil. In a traditional fish farm in Joinville in the summer, there was an increase in the percentage of hematocrit and in the red blood cell count. The highest values of total leukocytes were found in fish from fee-fishing in Blumenau in the autumn while the lowest values occurred in those from swine consorted system in Ituporanga in the summer. Thrombocytosis was observed in the autumn, and lymphocytosis was found in both the autumn and winter in tilapia from all fish farms investigated. Neutrophilia was only observed in winter and autumn in fish from Blumenau and Ituporanga. This work demonstrated the influence of seasonality and the handling characteristics of each fish farm on certain hematological parameters in Nile tilapia.

Genome-wide association meta-analysis of fish and EPA+DHA consumption in 17 US and European cohorts.

PubMed

Mozaffarian, Dariush; Dashti, Hassan S; Wojczynski, Mary K; Chu, Audrey Y; Nettleton, Jennifer A; Männistö, Satu; Kristiansson, Kati; Reedik, Mägi; Lahti, Jari; Houston, Denise K; Cornelis, Marilyn C; van Rooij, Frank J A; Dimitriou, Maria; Kanoni, Stavroula; Mikkilä, Vera; Steffen, Lyn M; de Oliveira Otto, Marcia C; Qi, Lu; Psaty, Bruce; Djousse, Luc; Rotter, Jerome I; Harald, Kennet; Perola, Markus; Rissanen, Harri; Jula, Antti; Krista, Fischer; Mihailov, Evelin; Feitosa, Mary F; Ngwa, Julius S; Xue, Luting; Jacques, Paul F; Perälä, Mia-Maria; Palotie, Aarno; Liu, Yongmei; Nalls, Nike A; Ferrucci, Luigi; Hernandez, Dena; Manichaikul, Ani; Tsai, Michael Y; Kiefte-de Jong, Jessica C; Hofman, Albert; Uitterlinden, André G; Rallidis, Loukianos; Ridker, Paul M; Rose, Lynda M; Buring, Julie E; Lehtimäki, Terho; Kähönen, Mika; Viikari, Jorma; Lemaitre, Rozenn; Salomaa, Veikko; Knekt, Paul; Metspalu, Andres; Borecki, Ingrid B; Cupples, L Adrienne; Eriksson, Johan G; Kritchevsky, Stephen B; Bandinelli, Stefania; Siscovick, David; Franco, Oscar H; Deloukas, Panos; Dedoussis, George; Chasman, Daniel I; Raitakari, Olli; Tanaka, Toshiko

2017-01-01

Regular fish and omega-3 consumption may have several health benefits and are recommended by major dietary guidelines. Yet, their intakes remain remarkably variable both within and across populations, which could partly owe to genetic influences. To identify common genetic variants that influence fish and dietary eicosapentaenoic acid plus docosahexaenoic acid (EPA+DHA) consumption. We conducted genome-wide association (GWA) meta-analysis of fish (n = 86,467) and EPA+DHA (n = 62,265) consumption in 17 cohorts of European descent from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Nutrition Working Group. Results from cohort-specific GWA analyses (additive model) for fish and EPA+DHA consumption were adjusted for age, sex, energy intake, and population stratification, and meta-analyzed separately using fixed-effect meta-analysis with inverse variance weights (METAL software). Additionally, heritability was estimated in 2 cohorts. Heritability estimates for fish and EPA+DHA consumption ranged from 0.13-0.24 and 0.12-0.22, respectively. A significant GWA for fish intake was observed for rs9502823 on chromosome 6: each copy of the minor allele (FreqA = 0.015) was associated with 0.029 servings/day (~1 serving/month) lower fish consumption (P = 1.96x10-8). No significant association was observed for EPA+DHA, although rs7206790 in the obesity-associated FTO gene was among top hits (P = 8.18x10-7). Post-hoc calculations demonstrated 95% statistical power to detect a genetic variant associated with effect size of 0.05% for fish and 0.08% for EPA+DHA. These novel findings suggest that non-genetic personal and environmental factors are principal determinants of the remarkable variation in fish consumption, representing modifiable targets for increasing intakes among all individuals. Genes underlying the signal at rs72838923 and mechanisms for the association warrant further investigation.

Genome-wide association meta-analysis of fish and EPA+DHA consumption in 17 US and European cohorts

PubMed Central

Dashti, Hassan S; Wojczynski, Mary K; Chu, Audrey Y; Nettleton, Jennifer A; Männistö, Satu; Kristiansson, Kati; Reedik, Mägi; Lahti, Jari; Houston, Denise K; Cornelis, Marilyn C; van Rooij, Frank J. A; Dimitriou, Maria; Kanoni, Stavroula; Mikkilä, Vera; Steffen, Lyn M; de Oliveira Otto, Marcia C; Qi, Lu; Psaty, Bruce; Djousse, Luc; Rotter, Jerome I; Harald, Kennet; Perola, Markus; Rissanen, Harri; Jula, Antti; Krista, Fischer; Mihailov, Evelin; Feitosa, Mary F; Ngwa, Julius S; Xue, Luting; Jacques, Paul F; Perälä, Mia-Maria; Palotie, Aarno; Liu, Yongmei; Nalls, Nike A; Ferrucci, Luigi; Hernandez, Dena; Manichaikul, Ani; Tsai, Michael Y; Kiefte-de Jong, Jessica C; Hofman, Albert; Uitterlinden, André G; Rallidis, Loukianos; Ridker, Paul M; Rose, Lynda M; Buring, Julie E; Lehtimäki, Terho; Kähönen, Mika; Viikari, Jorma; Lemaitre, Rozenn; Salomaa, Veikko; Knekt, Paul; Metspalu, Andres; Borecki, Ingrid B; Cupples, L. Adrienne; Eriksson, Johan G; Kritchevsky, Stephen B; Bandinelli, Stefania; Siscovick, David; Franco, Oscar H; Deloukas, Panos; Dedoussis, George; Chasman, Daniel I; Raitakari, Olli; Tanaka, Toshiko

2017-01-01

Background Regular fish and omega-3 consumption may have several health benefits and are recommended by major dietary guidelines. Yet, their intakes remain remarkably variable both within and across populations, which could partly owe to genetic influences. Objective To identify common genetic variants that influence fish and dietary eicosapentaenoic acid plus docosahexaenoic acid (EPA+DHA) consumption. Design We conducted genome-wide association (GWA) meta-analysis of fish (n = 86,467) and EPA+DHA (n = 62,265) consumption in 17 cohorts of European descent from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Nutrition Working Group. Results from cohort-specific GWA analyses (additive model) for fish and EPA+DHA consumption were adjusted for age, sex, energy intake, and population stratification, and meta-analyzed separately using fixed-effect meta-analysis with inverse variance weights (METAL software). Additionally, heritability was estimated in 2 cohorts. Results Heritability estimates for fish and EPA+DHA consumption ranged from 0.13–0.24 and 0.12–0.22, respectively. A significant GWA for fish intake was observed for rs9502823 on chromosome 6: each copy of the minor allele (FreqA = 0.015) was associated with 0.029 servings/day (~1 serving/month) lower fish consumption (P = 1.96x10-8). No significant association was observed for EPA+DHA, although rs7206790 in the obesity-associated FTO gene was among top hits (P = 8.18x10-7). Post-hoc calculations demonstrated 95% statistical power to detect a genetic variant associated with effect size of 0.05% for fish and 0.08% for EPA+DHA. Conclusions These novel findings suggest that non-genetic personal and environmental factors are principal determinants of the remarkable variation in fish consumption, representing modifiable targets for increasing intakes among all individuals. Genes underlying the signal at rs72838923 and mechanisms for the association warrant further investigation. PMID:29236708

Concurrent environmental stressors and jellyfish stings impair caged European sea bass (Dicentrarchus labrax) physiological performances

PubMed Central

Bosch-Belmar, Mar; Giomi, Folco; Rinaldi, Alessandro; Mandich, Alberta; Fuentes, Verónica; Mirto, Simone; Sarà, Gianluca; Piraino, Stefano

2016-01-01

The increasing frequency of jellyfish outbreaks in coastal areas has led to multiple ecological and socio-economic issues, including mass mortalities of farmed fish. We investigated the sensitivity of the European sea bass (Dicentrarchus labrax), a widely cultured fish in the Mediterranean Sea, to the combined stressors of temperature, hypoxia and stings from the jellyfish Pelagia noctiluca, through measurement of oxygen consumption rates (MO2), critical oxygen levels (PO2crit), and histological analysis of tissue damage. Higher levels of MO2, PO2crit and gill damage in treated fish demonstrated that the synergy of environmental and biotic stressors dramatically impair farmed fish metabolic performances and increase their health vulnerability. As a corollary, in the current scenario of ocean warming, these findings suggest that the combined effects of recurrent hypoxic events and jellyfish blooms in coastal areas might also threaten wild fish populations. PMID:27301314

Ciguatera fish poisoning in Hong Kong--a 10-year perspective on the class of ciguatoxins.

PubMed

Wong, Chun-Kwan; Hung, Patricia; Lo, Janice Y C

2014-08-01

The present study used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to investigate retrospectively ciguatoxin (CTX)-positive samples as determined by mouse bioassay (MBA) in the past 10 years in Hong Kong. The results showed that Pacific CTXs (P-CTX-1, -2 and -3) were the most commonly observed toxins found in the samples, indicating Pacific Ocean areas as the most important origin of ciguatera fish poisoning. Clinical diagnosis from ciguatera patients also revealed the predominance of neurological illnesses in most cases, supporting intoxication of Pacific origin. This study demonstrated the ability of laboratory analysis to identify and quantify Pacific CTXs in suspected fish samples, so as to support the clinical diagnosis of ciguatera. Comparative analysis (Student's t-test and Spearman's rank correlation analysis) on the two CTX detection methods showed approximate linearity for overall P-CTXs (P-CTX-1, -2 and -3)/P-CTX-1 alone as derived by LC-MS/MS and total toxicity levels (P-CTX-1 equivalent) as determined by MBA. The LC-MS/MS method coupled with the rapid extraction method could allow the detection of trace amount of CTXs at levels below the clinically relevant limit, 0.1 ppb P-CTX-1 in fish flesh. For practical application, the adoption of a two-tiered approach for testing, chemical analysis by LC-MS/MS for toxic fish screening, coupled with biological assay by MBA for final toxicity confirmation, was proposed for first-line screening of CTX in potentially contaminated fish samples in the market, with an aim to minimizing the use of laboratory mice and at the same time providing reasonably effective means for routine analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular prey identification in Central European piscivores.

PubMed

Thalinger, Bettina; Oehm, Johannes; Mayr, Hannes; Obwexer, Armin; Zeisler, Christiane; Traugott, Michael

2016-01-01

Diet analysis is an important aspect when investigating the ecology of fish-eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time-consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two-step multiplex PCR system, comprised of six assays, allowing for rapid, sensitive and specific detection of fish DNA in dietary samples. This approach encompasses 78 fish and lamprey species native to Central European freshwaters and enables the identification of 31 species, six genera, two families, two orders and two fish family clusters. All targeted taxa were successfully amplified from 25 template molecules, and each assay was specific when tested against a wide range of invertebrates and vertebrates inhabiting aquatic environments. The applicability of the multiplex PCR system was evaluated in a feeding trial, wherein it outperformed morphological prey analysis regarding species-specific prey identification in faeces of Eurasian otters. Additionally, a wide spectrum of fish species was detected in field-collected faecal samples and regurgitated pellets of Common Kingfishers and Great Cormorants, demonstrating the broad applicability of the approach. In conclusion, this multiplex PCR system provides an efficient, easy to use and cost-effective tool for assessing the trophic ecology of piscivores in Central Europe. Furthermore, the multiplex PCRs and the primers described therein will be applicable wherever DNA of the targeted fish species needs to be detected at high sensitivity and specificity. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Detection of clonal aberrations by cytogenetic analysis after different culture methods and by FISH in 129 patients with Chronic Lymphocytic Leukemia.

PubMed

Jenderny, Jutta; Goldmann, Claudia; Thede, Rebekka; Ebrecht, Monika; Korioth, Frank

2014-01-01

There are only a few cytogenetic analysis (CA) studies that directly compare the novel cultivation technique using immunostimulatory CpG-oligonucleotide DSP30/interleukin-2 (DSP30/IL2) with other culture methods. Therefore, parallel cultures of peripheral blood of 129 chronic lymphocytic leukemia (CLL) patients were set up in unstimulated cultures, in the presence of pokeweed medium (PWM), and with DSP30/IL2. Furthermore, CA results were compared with data obtained by FISH. Clonal aberrations were observed by CA in 6% of the cases in unstimulated cultures, in 27% of the cases with PWM, and in 40% of the cases with DSP30/IL2. Some clonal aberrations were detected by CA only with one culture method. Using 3 different culture methods, clonal aberrations were detected in 41% of the cases by CA and in 71% of the cases by FISH. Altogether, 78% of the cases exhibited clonal aberrations discovered by CA and FISH. Also, CA detected clonal aberrations not targeted by FISH in 7% of the cases, and FISH identified clonal aberrations not detected by CA in 36% of the cases. Our study demonstrates that the combined use of CA with different culture methods together with FISH increases our knowledge of the genetic complexity and heterogeneity in CLL pathogenesis. © 2014 S. Karger AG, Basel.

Ornamental marine species culture in the coral triangle: seahorse demonstration project in the Spermonde Islands, Sulawesi, Indonesia.

PubMed

Williams, Susan L; Janetski, Noel; Abbott, Jessica; Blankenhorn, Sven; Cheng, Brian; Crafton, R Eliot; Hameed, Sarah O; Rapi, Saipul; Trockel, Dale

2014-12-01

Ornamental marine species ('OMS') provide valuable income for developing nations in the Indo-Pacific Coral Triangle, from which most of the specimens are exported. OMS culture can help diversify livelihoods in the region, in support of management and conservation efforts to reduce destructive fishing and collection practices that threaten coral reef and seagrass ecosystems. Adoption of OMS culture depends on demonstrating its success as a livelihood, yet few studies of OMS culture exist in the region. We present a case study of a land-based culture project for an endangered seahorse (Hippocampus barbouri) in the Spermonde Islands, Sulawesi, Indonesia. The business model demonstrated that culturing can increase family income by seven times. A Strengths Weaknesses Opportunities Threats (SWOT) analysis indicated good collaboration among diverse stakeholders and opportunities for culturing non-endangered species and for offshoot projects, but complicated permitting was an issue as were threats of market flooding and production declines. The OMS international market is strong, Indonesian exporters expressed great interest in cultured product, and Indonesia is the largest exporting country for H. barbouri. Yet, a comparison of Indonesia ornamental marine fish exports to fish abundance in a single local market indicated that OMS culture cannot replace fishing livelihoods. Nevertheless, seahorse and other OMS culture can play a role in management and conservation by supplementing and diversifying the fishing and collecting livelihoods in the developing nations that provide the majority of the global OMS.

Ornamental Marine Species Culture in the Coral Triangle: Seahorse Demonstration Project in the Spermonde Islands, Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Williams, Susan L.; Janetski, Noel; Abbott, Jessica; Blankenhorn, Sven; Cheng, Brian; Crafton, R. Eliot; Hameed, Sarah O.; Rapi, Saipul; Trockel, Dale

2014-12-01

Ornamental marine species (`OMS') provide valuable income for developing nations in the Indo-Pacific Coral Triangle, from which most of the specimens are exported. OMS culture can help diversify livelihoods in the region, in support of management and conservation efforts to reduce destructive fishing and collection practices that threaten coral reef and seagrass ecosystems. Adoption of OMS culture depends on demonstrating its success as a livelihood, yet few studies of OMS culture exist in the region. We present a case study of a land-based culture project for an endangered seahorse ( Hippocampus barbouri) in the Spermonde Islands, Sulawesi, Indonesia. The business model demonstrated that culturing can increase family income by seven times. A Strengths Weaknesses Opportunities Threats (SWOT) analysis indicated good collaboration among diverse stakeholders and opportunities for culturing non-endangered species and for offshoot projects, but complicated permitting was an issue as were threats of market flooding and production declines. The OMS international market is strong, Indonesian exporters expressed great interest in cultured product, and Indonesia is the largest exporting country for H. barbouri. Yet, a comparison of Indonesia ornamental marine fish exports to fish abundance in a single local market indicated that OMS culture cannot replace fishing livelihoods. Nevertheless, seahorse and other OMS culture can play a role in management and conservation by supplementing and diversifying the fishing and collecting livelihoods in the developing nations that provide the majority of the global OMS.

A comparison of techniques for preparing fish fillet for ICP-AES multielemental analysis and the microwave digestion of whole fish.

PubMed

Moeller, A; Ambrose, R F; Que Hee, S S

2001-01-01

Four catfish fillet homogenate treatments before multielemental metal analysis by simultaneous inductively coupled plasma/atomic emission spectroscopy were compared in triplicate. These treatments were: nitric acid wet-ashing by Parr bomb digestion; nitric acid wet-ashing by microwave digestion; tetramethylammonium hydroxide/nitric acid wet digestion; and dry-ashing. The tetramethylammonium hydroxide/nitric acid method was imprecise (coefficients of variation > 20%). The dry-ashing method was fast and sensitive but had low recoveries of 50% for spiked Pb and Al and was not as precise as the Parr bomb or microwave treatments. The Parr bomb method was the most precise method but was less sensitive than the microwave method which had nearly the same precision. The microwave method was then adapted to homogenates of small whole fish < or = 3 cm in length. The whole fish homogenate required more vigorous digestion conditions, and addition of more acid after the evaporative step because of the presence of less oxidizable and acid-soluble components than fillet. The whole fish homogenate was also more heterogeneous than catfish fillet. A quality assurance protocol to demonstrate homogenate uniformity is essential. The use of a non-specialized microwave oven system allowed precise results for fillet and whole fish homogenates.

The Novel Application of Non-Lethal Citizen Science Tissue Sampling in Recreational Fisheries.

PubMed

Williams, Samuel M; Holmes, Bonnie J; Pepperell, Julian G

2015-01-01

Increasing fishing pressure and uncertainty surrounding recreational fishing catch and effort data promoted the development of alternative methods for conducting fisheries research. A pilot investigation was undertaken to engage the Australian game fishing community and promote the non-lethal collection of tissue samples from the black marlin Istiompax indica, a valuable recreational-only species in Australian waters, for the purpose of future genetic research. Recruitment of recreational anglers was achieved by publicizing the project in magazines, local newspapers, social media, blogs, websites and direct communication workshops at game fishing tournaments. The Game Fishing Association of Australia and the Queensland Game Fishing Association were also engaged to advertise the project and recruit participants with a focus on those anglers already involved in the tag-and-release of marlin. Participants of the program took small tissue samples using non-lethal methods which were stored for future genetic analysis. The program resulted in 165 samples from 49 participants across the known distribution of I. indica within Australian waters which was a sufficient number to facilitate a downstream population genetic analysis. The project demonstrated the potential for the development of citizen science sampling programs to collect tissue samples using non-lethal methods in order to achieve targeted research objects in recreationally caught species.

Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging.

PubMed

Valm, Alex M; Mark Welch, Jessica L; Rieken, Christopher W; Hasegawa, Yuko; Sogin, Mitchell L; Oldenbourg, Rudolf; Dewhirst, Floyd E; Borisy, Gary G

2011-03-08

Microbes in nature frequently function as members of complex multitaxon communities, but the structural organization of these communities at the micrometer level is poorly understood because of limitations in labeling and imaging technology. We report here a combinatorial labeling strategy coupled with spectral image acquisition and analysis that greatly expands the number of fluorescent signatures distinguishable in a single image. As an imaging proof of principle, we first demonstrated visualization of Escherichia coli labeled by fluorescence in situ hybridization (FISH) with 28 different binary combinations of eight fluorophores. As a biological proof of principle, we then applied this Combinatorial Labeling and Spectral Imaging FISH (CLASI-FISH) strategy using genus- and family-specific probes to visualize simultaneously and differentiate 15 different phylotypes in an artificial mixture of laboratory-grown microbes. We then illustrated the utility of our method for the structural analysis of a natural microbial community, namely, human dental plaque, a microbial biofilm. We demonstrate that 15 taxa in the plaque community can be imaged simultaneously and analyzed and that this community was dominated by early colonizers, including species of Streptococcus, Prevotella, Actinomyces, and Veillonella. Proximity analysis was used to determine the frequency of inter- and intrataxon cell-to-cell associations which revealed statistically significant intertaxon pairings. Cells of the genera Prevotella and Actinomyces showed the most interspecies associations, suggesting a central role for these genera in establishing and maintaining biofilm complexity. The results provide an initial systems-level structural analysis of biofilm organization.

The contribution of nearshore fish aggregating devices (FADs) to food security and livelihoods in Solomon Islands.

PubMed

Albert, Joelle A; Beare, Doug; Schwarz, Anne-Maree; Albert, Simon; Warren, Regon; Teri, James; Siota, Faye; Andrew, Neil L

2014-01-01

Fish aggregating devices, or FADs, are used widely in developing countries to concentrate pelagic fish, making them easier to catch. Nearshore FADs anchored close to the coast allow access for rural communities, but despite their popularity among policy makers, there is a dearth of empirical analysis of their contributions to the supply of fish and to fisheries management. In this paper we demonstrate that nearshore FADs increased the supply of fish to four communities in Solomon Islands. Estimated total annual fish catch ranged from 4300 to 12,000 kg across the study villages, with nearshore FADs contributing up to 45% of the catch. While it is clear that FADs increased the supply of fish, FAD catch rates were not consistently higher than other fishing grounds. Villages with limited access to diverse or productive fishing grounds seemingly utilized FADs to better effect. Villagers believed FADs increased household income and nutrition, as well as providing a source of fish for community events. FADs were also perceived to increase intra-household conflict and reduce fishers' participation in community activities. FADs need to be placed within a broader rural development context and treated as another component in the diversified livelihoods of rural people; as with other livelihood options they bring trade-offs and risks.

The Contribution of Nearshore Fish Aggregating Devices (FADs) to Food Security and Livelihoods in Solomon Islands

PubMed Central

Albert, Joelle A.; Beare, Doug; Schwarz, Anne-Maree; Albert, Simon; Warren, Regon; Teri, James; Siota, Faye; Andrew, Neil L.

2014-01-01

Fish aggregating devices, or FADs, are used widely in developing countries to concentrate pelagic fish, making them easier to catch. Nearshore FADs anchored close to the coast allow access for rural communities, but despite their popularity among policy makers, there is a dearth of empirical analysis of their contributions to the supply of fish and to fisheries management. In this paper we demonstrate that nearshore FADs increased the supply of fish to four communities in Solomon Islands. Estimated total annual fish catch ranged from 4300 to 12 000 kg across the study villages, with nearshore FADs contributing up to 45% of the catch. While it is clear that FADs increased the supply of fish, FAD catch rates were not consistently higher than other fishing grounds. Villages with limited access to diverse or productive fishing grounds seemingly utilized FADs to better effect. Villagers believed FADs increased household income and nutrition, as well as providing a source of fish for community events. FADs were also perceived to increase intra-household conflict and reduce fishers' participation in community activities. FADs need to be placed within a broader rural development context and treated as another component in the diversified livelihoods of rural people; as with other livelihood options they bring trade-offs and risks. PMID:25513808

Coral reef grazer-benthos dynamics complicated by invasive algae in a small marine reserve

PubMed Central

Stamoulis, Kostantinos A.; Friedlander, Alan M.; Meyer, Carl G.; Fernandez-Silva, Iria; Toonen, Robert J.

2017-01-01

Blooms of alien invasive marine algae have become common, greatly altering the health and stability of nearshore marine ecosystems. Concurrently, herbivorous fishes have been severely overfished in many locations worldwide, contributing to increases in macroalgal cover. We used a multi-pronged, interdisciplinary approach to test if higher biomass of herbivorous fishes inside a no-take marine reserve makes this area more resistant to invasive algal overgrowth. Over a two year time period, we (1) compared fish biomass and algal cover between two fished and one unfished patch reef in Hawai’i, (2) used acoustic telemetry to determine fidelity of herbivorous fishes to the unfished reef, and (3) used metabarcoding and next-generation sequencing to determine diet composition of herbivorous fishes. Herbivore fish biomass was significantly higher in the marine reserve compared to adjacent fished reefs, whereas invasive algal cover differed by species. Herbivorous fish movements were largely confined to the unfished patch reef where they were captured. Diet analysis indicated that the consumption of invasive algae varied among fish species, with a high prevalence of comparatively rare native algal species. Together these findings demonstrate that the contribution of herbivores to coral reef resilience, via resistance to invasive algae invasion, is complex and species-specific. PMID:28276458

FISH-BOL and seafood identification: geographically dispersed case studies reveal systemic market substitution across Canada.

PubMed

Hanner, Robert; Becker, Sven; Ivanova, Natalia V; Steinke, Dirk

2011-10-01

The Fish Barcode of Life campaign involves a broad international collaboration among scientists working to advance the identification of fishes using DNA barcodes. With over 25% of the world's known ichthyofauna currently profiled, forensic identification of seafood products is now feasible and is becoming routine. Driven by growing consumer interest in the food supply, investigative reporters from five different media establishments procured seafood samples (n = 254) from numerous retail establishments located among five Canadian metropolitan areas between 2008 and 2010. The specimens were sent to the Canadian Centre for DNA Barcoding for analysis. By integrating the results from these individual case studies in a summary analysis, we provide a broad perspective on seafood substitution across Canada. Barcodes were recovered from 93% of the samples (n = 236), and identified using the Barcode of Life Data Systems "species identification" engine ( www.barcodinglife.org ). A 99% sequence similarity threshold was employed as a conservative matching criterion for specimen identification to the species level. Comparing these results against the Canadian Food Inspection Agency's "Fish List" a guideline to interpreting "false, misleading or deceptive" names (as per s 27 of the Fish Inspection regulations) demonstrated that 41% of the samples were mislabeled. Most samples were readily identified; however, this was not true in all cases because some samples had no close match. Others were ambiguous due to limited barcode resolution (or imperfect taxonomy) observed within a few closely related species complexes. The latter cases did not significantly impact the results because even the partial resolution achieved was sufficient to demonstrate mislabeling. This work highlights the functional utility of barcoding for the identification of diverse market samples. It also demonstrates how barcoding serves as a bridge linking scientific nomenclature with approved market names, potentially empowering regulatory bodies to enforce labeling standards. By synchronizing taxonomic effort with sequencing effort and database curation, barcoding provides a molecular identification resource of service to applied forensics.

The myelin proteolipid DMα in fishes.

PubMed

Brösamle, Christian

2010-05-01

Vertebrate myelin membranes are compacted and held in close apposition by three structural proteins of myelin, myelin basic protein, myelin protein zero (MPZ) and myelin proteolipid protein (PLP1/DMalpha). PLP1/DMalpha is considered to function as a scaffolding protein and play a role in intracellular trafficking in oligodendrocytes. In humans, point mutations, duplications or deletions of PLP1 are associated with Pelizaeus-Merzbacher disease and spastic paraplegia Type 2. PLP1 is highly conserved between mammals, but less so in lower vertebrates. This has led some researchers to question whether certain fish species express PLP1 orthologues at all, and to suggest that the function of PLP1/DMalpha in the central nervous system (CNS) may have been taken over by MPZ. Here, we review the evidence for the conservation of orthologues of PLP1/DMalpha in actinopterygian fishes and provide a comparison of currently available sequence data across 17 fish species. Our analysis demonstrates that orthologues of PLP1/DMalpha have been retained and are functionally expressed in many, if not all, extant species of bony fish. Many of the amino acids that, when mutated, are associated with severe CNS pathology are conserved in teleosts, demonstrating conservation of essential functions and justifying the development of novel disease models in species such as the zebrafish.

Tracing the biotransformation of polychlorinated biphenyls (PCBs) in common carp (Cryprinus carpio): Enantiomeric fraction and compound-specific stable carbon isotope analyses.

PubMed

Tang, Bin; Luo, Xiao-Jun; Zeng, Yan-Hong; Sun, Run-Xia; Chen, Hua-Shan; Li, Zong-Rui; Mai, Bi-Xian

2016-09-01

Metabolites of polychlorinated biphenyls (PCBs) in fish are difficult to detect in vivo due to the complexity of biometabolism. In the present study, atropisomeric fraction analysis of chiral PCB congeners and compound-specific isotopic analysis (CSIA) were applied to trace the biotransformation of PCBs in fish by exposure of common carp (Cryprinus carpio) to the commercial PCB mixture Aroclor 1242. Stereoselective elimination of the chiral PCB congeners 91, 95, and 136 was observed, indicating a stereoselective biotransformation process. The δ(13)C values of PCBs 5/8, 18, and 20/33 in fish were increased compared with those in the spiked food, while PCBs 47/48 and 49 showed significant heavy isotope depletion. These results suggested a significant biotransformation of the corresponding individual PCB congeners although the potential PCB metabolites, hydroxylated PCBs (OH-PCBs) and methylsulfone PCBs (MeSO2-PCBs), were not detected in the fish tissue samples throughout this experiment. The results of the present study demonstrated that a combination of chiral analysis and CSIA is a promising new approach for investigating the biotransformation of PCBs in biota. Copyright © 2016 Elsevier Ltd. All rights reserved.

Predictive value of sperm-FISH analysis on the outcome of preimplantation genetic diagnosis (PGD) for a pericentric inversion inv5(p15.3q11.2) carrier.

PubMed

Bernicot, I; Dechanet, C; Mace, A; Hedon, B; Hamamah, S; Pellestor, F; Anahory, T

2010-07-01

Pericentric inversions (PIs) are structural chromosomal abnormalities, potentially associated with infertility or multiple miscarriages. More rarely, at meiosis, odd numbers of genetic recombinations within the inversion loop produce recombinant gametes which may lead to aneusomy of recombination in the offspring. We report a FISH segregation analysis of an inv5(p15.3q11.2) carrier, both in sperm and blastomeres. In sperm, we directly evaluated the proportion of recombinant gametes and compared the results with chromosomal abnormalities found in blastomeres collected from embryos obtained following a preimplantation genetic diagnosis (PGD) procedure. A total of 7006 sperm nuclei were analyzed. The size of the inverted segment represented 27% of the total length of chromosome 5. The frequencies of balanced chromosomes (normal or inverted), recombinant chromosomes and unbalanced combinations were 97.1, 0.17 and 2.73%, respectively. Of six embryos, PGD FISH analysis revealed that one was a balanced embryo, whereas five were unbalanced and there were no recombinants. This study demonstrated the value of sperm-FISH analysis in providing reproductive genetic counseling for PI carriers. Our study also highlights the clinical relevance of performing PGD instead of prenatal diagnosis.

Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH

PubMed Central

Komosa, Martin; Root, Heather; Meyn, M. Stephen

2015-01-01

Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells. PMID:25662602

Detection of ALK rearrangements in malignant pleural effusion cell blocks from patients with advanced non-small cell lung cancer: a comparison of Ventana immunohistochemistry and fluorescence in situ hybridization.

PubMed

Wang, Weiya; Tang, Yuan; Li, Jinnan; Jiang, Lili; Jiang, Yong; Su, Xueying

2015-02-01

Surgical resections or tumor biopsies are often not available for patients with late-stage non-small cell lung cancer (NSCLC). Cytological specimens, such as malignant pleural effusion (MPE) cell blocks, are critical for molecular testing. Currently, diagnostic methods to identify anaplastic lymphoma kinase (ALK) rearrangements include fluorescence in situ hybridization (FISH), real-time reverse transcriptase-polymerase chain reaction (RT-PCR), and immunohistochemistry (IHC). In the current study, the authors compared Ventana ALK IHC assays and ALK FISH to detect ALK rearrangements in MPE cell blocks from patients with advanced NSCLC. The ALK IHC assay and ALK FISH were performed on 63 MPE cell blocks. RT-PCR analysis was performed as additional validation in cases in which a discrepancy was observed between the IHC assay and FISH results. The Ventana ALK IHC assay was found to be informative for all 63 samples, and 8 cases were positive. Fifty-eight cases were interpretable for FISH detection, and 6 were positive. The concordance between IHC and FISH was 100% among the 58 cases. Of the 5 uninterpretable ALK FISH cases, 2 cases and 3 cases, respectively, were ALK IHC positive and negative. One of the 2 ALK IHC-positive cases also demonstrated a positive result in the RT-PCR assay and the patient benefited from crizotinib treatment. MPE cell blocks can be used successfully for the detection of ALK rearrangement when tumor tissue is not available. The Ventana ALK IHC assay is an effective screening method for ALK rearrangement in MPE cell blocks from patients with advanced NSCLC, demonstrating high agreement with FISH results. © 2014 American Cancer Society.

Development of software and modification of Q-FISH protocol for estimation of individual telomere length in immunopathology.

PubMed

Barkovskaya, M Sh; Bogomolov, A G; Knauer, N Yu; Rubtsov, N B; Kozlov, V A

2017-04-01

Telomere length is an important indicator of proliferative cell history and potential. Decreasing telomere length in the cells of an immune system can indicate immune aging in immune-mediated and chronic inflammatory diseases. Quantitative fluorescent in situ hybridization (Q-FISH) of a labeled (C 3 TA[Formula: see text] peptide nucleic acid probe onto fixed metaphase cells followed by digital image microscopy allows the evaluation of telomere length in the arms of individual chromosomes. Computer-assisted analysis of microscopic images can provide quantitative information on the number of telomeric repeats in individual telomeres. We developed new software to estimate telomere length. The MeTeLen software contains new options that can be used to solve some Q-FISH and microscopy problems, including correction of irregular light effects and elimination of background fluorescence. The identification and description of chromosomes and chromosome regions are essential to the Q-FISH technique. To improve the quality of cytogenetic analysis after Q-FISH, we optimized the temperature and time of DNA-denaturation to get better DAPI-banding of metaphase chromosomes. MeTeLen was tested by comparing telomere length estimations for sister chromatids, background fluorescence estimations, and correction of nonuniform light effects. The application of the developed software for analysis of telomere length in patients with rheumatoid arthritis was demonstrated.

Comparison of lipid content and Fatty Acid composition in the edible meat of wild and cultured freshwater and marine fish and shrimps from china.

PubMed

Li, Guipu; Sinclair, Andrew J; Li, Duo

2011-03-09

The lipid content and fatty acid composition in the edible meat of twenty-nine species of wild and cultured freshwater and marine fish and shrimps were investigated. Both the lipid content and fatty acid composition of the species were specified due to their unique food habits and trophic levels. Most of the marine fish demonstrated higher lipid content than the freshwater fish, whereas shrimps had the lowest lipid content. All the marine fish and shrimps had much higher total n-3 PUFA than n-6 PUFA, while most of the freshwater fish and shrimps demonstrated much lower total n-3 PUFA than n-6 PUFA. This may be the biggest difference in fatty acid composition between marine and freshwater species. The cultured freshwater fish demonstrated higher percentages of total PUFA, total n-3 PUFA, and EPA + DHA than the wild freshwater fish. Two freshwater fish, including bighead carp and silver carp, are comparable to the marine fish as sources of n-3 PUFA.

Modulation of stress related protein genes in the bass (Epinephelus guaza) caught from the Gulf of Suez, the Red Sea, Egypt.

PubMed

Abdel-Gawad, Fagr Kh; Khalil, Wagdy K B

2013-10-01

Impact of chemical pollution on expression of stress protein genes in the bass Epinephelus guaga collected from several locations including Suez Oil Production Port (Floating port), Atakah Fishing Port, Adabiya Port and Tawfik Port in Suez Governorate, Egypt, was investigated. In the current study, levels of polycyclic aromatic hydrocarbons (PAHs) in water and fish samples collected from Suez Gulf were assessed. In addition, gills and liver tissues of caught bass fish were used to address the interaction between pollution status and the expression of stress-related genes (Hsp70a, Hsp70b, Hsp47, MT and CYP1A). Our analysis demonstrated that levels of PAHs in Floating and Tawfik ports were higher than those found in the Atakah Fishing Port and the Adabiya Port. In addition, MDA and PC contents were significantly higher in gills and liver tissues collected from Floating and Tawfik ports than those collected from Adabiya and Atakah ports. In correlation to the above results, all fish collected from the Floating and Tawfik ports presented a significant increase in Hsp-, MT- and CYP1A-mRNAs. On the other hand, fish samples collected from the Atakah Fishing and Adabiya ports showed no induction of the stress-related genes transcription in such tissues. In conclusion, the current research demonstrates that remarkable increase in PAH contaminants levels in Floating and Tawfik ports are correlated with the levels stress protein-related genes transcription in E. guaga gills and liver tissues. Copyright © 2013 Elsevier Inc. All rights reserved.

Fish protein hydrolysates: application in deep-fried food and food safety analysis.

PubMed

He, Shan; Franco, Christopher; Zhang, Wei

2015-01-01

Four different processes (enzymatic, microwave-intensified enzymatic, chemical, and microwave-intensified chemical) were used to produce fish protein hydrolysates (FPH) from Yellowtail Kingfish for food applications. In this study, the production yield and oil-binding capacity of FPH produced from different processes were evaluated. Microwave intensification significantly increased the production yields of enzymatic process from 42% to 63%. It also increased the production yields of chemical process from 87% to 98%. The chemical process and microwave-intensified chemical process produced the FPH with low oil-binding capacity (8.66 g oil/g FPH and 6.25 g oil/g FPH), whereas the microwave-intensified enzymatic process produced FPH with the highest oil-binding capacity (16.4 g oil/g FPH). The FPH from the 4 processes were applied in the formulation of deep-fried battered fish and deep-fried fish cakes. The fat uptake of deep-fried battered fish can be reduced significantly from about 7% to about 4.5% by replacing 1% (w/w) batter powder with FPH, and the fat uptake of deep-fried fish cakes can be significantly reduced from about 11% to about 1% by replacing 1% (w/w) fish mince with FPH. Food safety tests of the FPH produced by these processes demonstrated that the maximum proportion of FPH that can be safely used in food formulation is 10%, due to its high content of histamine. This study demonstrates the value of FPH to the food industry and bridges the theoretical studies with the commercial applications of FPH. © 2015 Institute of Food Technologists®

3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines.

PubMed

Kocanova, Silvia; Goiffon, Isabelle; Bystricky, Kerstin

2018-06-01

Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines. Copyright © 2018 Elsevier Inc. All rights reserved.

Evidence for fish dispersal from spatial analysis of stream network topology

USGS Publications Warehouse

Hitt, N.P.; Angermeier, P.L.

2008-01-01

Developing spatially explicit conservation strategies for stream fishes requires an understanding of the spatial structure of dispersal within stream networks. We explored spatial patterns of stream fish dispersal by evaluating how the size and proximity of connected streams (i.e., stream network topology) explained variation in fish assemblage structure and how this relationship varied with local stream size. We used data from the US Environmental Protection Agency's Environmental Monitoring and Assessment Program in wadeable streams of the Mid-Atlantic Highlands region (n = 308 sites). We quantified stream network topology with a continuous analysis based on the rate of downstream flow accumulation from sites and with a discrete analysis based on the presence of mainstem river confluences (i.e., basin area >250 km2) within 20 fluvial km (fkm) from sites. Continuous variation in stream network topology was related to local species richness within a distance of ???10 fkm, suggesting an influence of fish dispersal within this spatial grain. This effect was explained largely by catostomid species, cyprinid species, and riverine species, but was not explained by zoogeographic regions, ecoregions, sampling period, or spatial autocorrelation. Sites near mainstem river confluences supported greater species richness and abundance of catostomid, cyprinid, and ictalurid fishes than did sites >20 fkm from such confluences. Assemblages at sites on the smallest streams were not related to stream network topology, consistent with the hypothesis that local stream size regulates the influence of regional dispersal. These results demonstrate that the size and proximity of connected streams influence the spatial distribution of fish and suggest that these influences can be incorporated into the designs of stream bioassessments and reserves to enhance management efficacy. ?? 2008 by The North American Benthological Society.

Radiocarbon reservoir between charred seeds and fish bone in Neolithic sites, northeastern Qinghai-Tibetan Plateau

NASA Astrophysics Data System (ADS)

Zhou, A.; Dong, G.; Ren, L.

2017-12-01

Many efforts have been done to understand the reservoir effect of Qinghai Lake, yet no agreement has been reached. Five archaeological sites, located around the junction between the estuary of Rivers and Qinghai Lake, are the earliest Neolithic Age sites in the Qinghai- Tibetan Plateau (QTP), which is critical for understanding patterns of prehistoric human inhabitation in the high plateau extreme environments. This study compares radiocarbon dates of fish bones and terrestrial plant remains uncovered from the same archaeological strata to see whether there was reservoir effect reference to reliable data. Results demonstrate that there were reservoir effects ranging from 300 to 600 years back to 3600 years ago, nevertheless, no reservoir was observed of the modern fish. Besides, stable isotopic analysis illustrated that modern fish consumed similar food to those of millennias ago.

Fish oil alleviated high-fat diet-induced non-alcoholic fatty liver disease via regulating hepatic lipids metabolism and metaflammation: a transcriptomic study.

PubMed

Yuan, Fahu; Wang, Hualin; Tian, Yu; Li, Qi; He, Lei; Li, Na; Liu, Zhiguo

2016-02-01

Intake of fish oil rich in n-3 polyunsaturated fatty acids (PUFAs) is believed to be beneficial against development of non-alcoholic fatty liver disease (NAFLD). However, the underlying mechanisms remain unclear. This study was to gain further understanding of the potential mechanisms of the protective effects of fish oil against NAFLD. Ten male Sprague-Dawley rats were fed a control diet (CON), a Western style high-fat and high-cholesterol diet (WD), or a WD diet containing fish oil (FOH) for 16 weeks respectively. The development of liver steatosis and fibrosis were verified by histological and biochemical examination. Hepatic transcriptome were extracted for RNA-seq analysis, and particular results were confirmed by real-time polymerase chain reaction (PCR). The consumption of fish oil significantly ameliorated WD-induced dyslipidemia, transaminase elevation, hepatic steatosis, inflammatory infiltration, and fibrosis. Hepatic RNA-Seq analysis showed that long-term intake of fish oil restored the expression of circadian clock-related genes per2 and per3, which were reduced in WD fed animals. Fish oil consumption also corrected the expression levels of genes involved in fatty acid and cholesterol metabolism, such as Srebf1, Fasn, Scd1, Insig2, Cd36, Cyp7a1, Abcg5, Abcg8 and Pcsk9. Moreover, the expression levels of pro-inflammation genes Mcp1, Socs2, Sema4a, and Cd44 in the FOH group were lower than that of WD group, implying that fish oil protects the liver against WD-induced hepatic inflammation. The present study demonstrates fish oil protects against WD-induced NALFD via improving lipid metabolism and ameliorating hepatic inflammation. Our findings add to the current understanding on the benefits of n-3 PUFAs against NAFLD.

Immunostimulatory oligonucleotide-induced metaphase cytogenetics detect chromosomal aberrations in 80% of CLL patients: A study of 132 CLL cases with correlation to FISH, IgVH status, and CD38 expression.

PubMed

Dicker, Frank; Schnittger, Susanne; Haferlach, Torsten; Kern, Wolfgang; Schoch, Claudia

2006-11-01

Compared with fluorescence in situ hybridization (FISH), conventional metaphase cytogenetics play only a minor prognostic role in chronic lymphocytic leukemia (CLL) so far, due to technical problems resulting from limited proliferation of CLL cells in vitro. Here, we present a simple method for in vitro stimulation of CLL cells that overcomes this limitation. In our unselected patient population, 125 of 132 cases could be successfully stimulated for metaphase generation by culture with the immunostimulatory CpG-oligonucleotide DSP30 plus interleukin 2. Of 125 cases, 101 showed chromosomal aberrations. The aberration rate is comparable to the rate detected by parallel interphase FISH. In 47 patients, conventional cytogenetics detected additional aberrations not detected by FISH analysis. A complex aberrant karyotype, defined as one having at least 3 aberrations, was detected in 30 of 125 patients, compared with only one such case as defined by FISH. Conventional cytogenetics frequently detected balanced and unbalanced translocations. A significant correlation of the poor-prognosis unmutated IgV(H) status with unbalanced translocations and of the likewise poor-prognosis CD38 expression to balanced translocations and complex aberrant karyotype was found. We demonstrate that FISH analysis underestimates the complexity of chromosomal aberrations in CLL. Therefore, conventional cytogenetics may define subgroups of patients with high risk of progression.

An Integrated Ecological Modeling System for Assessing ...

EPA Pesticide Factsheets

We demonstrate a novel, spatially explicit assessment of the current condition of aquatic ecosystem services, with limited sensitivity analysis for the atmospheric contaminant mercury. The Integrated Ecological Modeling System (IEMS) forecasts water quality and quantity, habitat suitability for aquatic biota, fish biomasses, population densities, productivities, and contamination by methylmercury across headwater watersheds. We applied this IEMS to the Coal River Basin (CRB), West Virginia (USA), an 8-digit hydrologic unit watershed, by simulating a network of 97 stream segments using the SWAT watershed model, a watershed mercury loading model, the WASP water quality model, the PiSCES fish community estimation model, a fish habitat suitability model, the BASS fish community and bioaccumulation model, and an ecoservices post-processer. Model application was facilitated by automated data retrieval and model setup and updated model wrappers and interfaces for data transfers between these models from a prior study. This companion study evaluates baseline predictions of ecoservices provided for 1990 – 2010 for the population of streams in the CRB and serves as a foundation for future model development. Published in the journal, Ecological Modeling. Highlights: • Demonstrate a spatially-explicit IEMS for multiple scales. • Design a flexible IEMS for

Oral immunization of Carassius auratus with modified recombinant A-layer proteins entrapped in alginate beads.

PubMed

Maurice, Sarah; Nussinovitch, Amos; Jaffe, Nicole; Shoseyov, Oded; Gertler, Arieh

2004-12-09

This study was focused on the utilization of a recombinant expression system to produce a unique modified subunit vaccine possessing a self-contained delivery system which could potentially improve the uptake and delivery of vaccine products as well their immunogenic potential. For this purpose the A-layer protein (At-R) associated with the fish pathogen atypical Aeromonas salmonicida was cloned and modified by the genetic fusion of the protein transduction domain (MTS) derived from Kaposi fibroblast growth factor (At-MTS). The potential for these proteins to be employed as antigens for oral immunization of goldfish was examined by encapsulation of At-R, At-MTS and the control, BSA, into biodegradable alginate gel macrospheres which were fed to goldfish in place of standard pellet fish feed. The bead physical properties were modified only in the presence of At-R and the temporal release of proteins was significantly less when At-MTS was employed. Western blot analysis of serum samples collected from fish following intubation with the recombinant proteins determined that the rate of protein uptake from the digestive tract into the blood system improved considerably when MTS was fused to At-R. Experimental fish were fed one of three protein-alginate formulae on a schedule of 3 days/week or 5 days/month for a period of 2 months. After 1 month, animals fed on the 5-day protocol demonstrated increased serum antibody titers while following an additional month of feeding this level decreased and titers were found to be higher in fish maintained on the 3-day regime. Fish fed At-MTS maintained the highest titer at the end of 2-month period. To determine whether the diminished antibody titers were a result of oral tolerance fish were injected intraperitoneally with the At-R antigen. Only experimental groups which had been fed At-R or At-MTS demonstrated increased antibody titers which paralleled a typical secondary humoral response. In spite of the presence of an increased titer to A-protein, vaccinated fish did not demonstrate resistance to infection with atypical A. salmonicida.

Model-free information-theoretic approach to infer leadership in pairs of zebrafish.

PubMed

Butail, Sachit; Mwaffo, Violet; Porfiri, Maurizio

2016-04-01

Collective behavior affords several advantages to fish in avoiding predators, foraging, mating, and swimming. Although fish schools have been traditionally considered egalitarian superorganisms, a number of empirical observations suggest the emergence of leadership in gregarious groups. Detecting and classifying leader-follower relationships is central to elucidate the behavioral and physiological causes of leadership and understand its consequences. Here, we demonstrate an information-theoretic approach to infer leadership from positional data of fish swimming. In this framework, we measure social interactions between fish pairs through the mathematical construct of transfer entropy, which quantifies the predictive power of a time series to anticipate another, possibly coupled, time series. We focus on the zebrafish model organism, which is rapidly emerging as a species of choice in preclinical research for its genetic similarity to humans and reduced neurobiological complexity with respect to mammals. To overcome experimental confounds and generate test data sets on which we can thoroughly assess our approach, we adapt and calibrate a data-driven stochastic model of zebrafish motion for the simulation of a coupled dynamical system of zebrafish pairs. In this synthetic data set, the extent and direction of the coupling between the fish are systematically varied across a wide parameter range to demonstrate the accuracy and reliability of transfer entropy in inferring leadership. Our approach is expected to aid in the analysis of collective behavior, providing a data-driven perspective to understand social interactions.

Model-free information-theoretic approach to infer leadership in pairs of zebrafish

NASA Astrophysics Data System (ADS)

Butail, Sachit; Mwaffo, Violet; Porfiri, Maurizio

2016-04-01

Collective behavior affords several advantages to fish in avoiding predators, foraging, mating, and swimming. Although fish schools have been traditionally considered egalitarian superorganisms, a number of empirical observations suggest the emergence of leadership in gregarious groups. Detecting and classifying leader-follower relationships is central to elucidate the behavioral and physiological causes of leadership and understand its consequences. Here, we demonstrate an information-theoretic approach to infer leadership from positional data of fish swimming. In this framework, we measure social interactions between fish pairs through the mathematical construct of transfer entropy, which quantifies the predictive power of a time series to anticipate another, possibly coupled, time series. We focus on the zebrafish model organism, which is rapidly emerging as a species of choice in preclinical research for its genetic similarity to humans and reduced neurobiological complexity with respect to mammals. To overcome experimental confounds and generate test data sets on which we can thoroughly assess our approach, we adapt and calibrate a data-driven stochastic model of zebrafish motion for the simulation of a coupled dynamical system of zebrafish pairs. In this synthetic data set, the extent and direction of the coupling between the fish are systematically varied across a wide parameter range to demonstrate the accuracy and reliability of transfer entropy in inferring leadership. Our approach is expected to aid in the analysis of collective behavior, providing a data-driven perspective to understand social interactions.

Physicochemical properties and characterization of chitosan synthesized from fish scales, crab and shrimp shells.

PubMed

Kumari, Suneeta; Kumar Annamareddy, Sri Hari; Abanti, Sahoo; Kumar Rath, Pradip

2017-11-01

Chitosan is derived from different starting materials such as fish scales, shrimp and crab shells by the process of deacetylation of chitin, which is carried out using 40% KOH at 90°C for 6h. Prepared chitosan was characterized by Fourier transforms infrared spectroscopy, X-ray powder diffraction, Scanning electron microscope and Thermogravimetric analysis. Futher the physicochemical properties of chitosan like Fat binding capacity (FBC), water binding capacity (WBC), solubility, average molecular weight, ash content, moisture and degree of deacetylation of chitosan were also studied. Crystalline index (%) values of commercial, shrimp, crab and fish chitosan were found to be 96, 82, 88 and 84% respectively. The presence of amino group was confirmed from the FTIR spectra of chitosan synthesized. TGA results demonstrated the lower thermal stability of chitosan. Relatively smother surface and nano-fiber structures were observed from SEM analysis. The degree of deacetylation of chitosan from different sources such as shells of fish, shrimp and crab were found to be 75%, 78%, and 70% respectively. In a similar way the WBC and FBC of fish, shrimp and crab shells were found to be 492, 358 and 138% and 226, 246 and 138% respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Extinction, survival or recovery of large predatory fishes

PubMed Central

Myers, Ransom A.; Worm, Boris

2005-01-01

Large predatory fishes have long played an important role in marine ecosystems and fisheries. Overexploitation, however, is gradually diminishing this role. Recent estimates indicate that exploitation has depleted large predatory fish communities worldwide by at least 90% over the past 50–100 years. We demonstrate that these declines are general, independent of methodology, and even higher for sensitive species such as sharks. We also attempt to predict the future prospects of large predatory fishes. (i) An analysis of maximum reproductive rates predicts the collapse and extinction of sensitive species under current levels of fishing mortality. Sensitive species occur in marine habitats worldwide and have to be considered in most management situations. (ii) We show that to ensure the survival of sensitive species in the northwest Atlantic fishing mortality has to be reduced by 40–80%. (iii) We show that rapid recovery of community biomass and diversity usually occurs when fishing mortality is reduced. However, recovery is more variable for single species, often because of the influence of species interactions. We conclude that management of multi-species fisheries needs to be tailored to the most sensitive, rather than the more robust species. This requires reductions in fishing effort, reduction in bycatch mortality and protection of key areas to initiate recovery of severely depleted communities. PMID:15713586

Extinction, survival or recovery of large predatory fishes.

PubMed

Myers, Ransom A; Worm, Boris

2005-01-29

Large predatory fishes have long played an important role in marine ecosystems and fisheries. Overexploitation, however, is gradually diminishing this role. Recent estimates indicate that exploitation has depleted large predatory fish communities worldwide by at least 90% over the past 50-100 years. We demonstrate that these declines are general, independent of methodology, and even higher for sensitive species such as sharks. We also attempt to predict the future prospects of large predatory fishes. (i) An analysis of maximum reproductive rates predicts the collapse and extinction of sensitive species under current levels of fishing mortality. Sensitive species occur in marine habitats worldwide and have to be considered in most management situations. (ii) We show that to ensure the survival of sensitive species in the northwest Atlantic fishing mortality has to be reduced by 40-80%. (iii) We show that rapid recovery of community biomass and diversity usually occurs when fishing mortality is reduced. However, recovery is more variable for single species, often because of the influence of species interactions. We conclude that management of multi-species fisheries needs to be tailored to the most sensitive, rather than the more robust species. This requires reductions in fishing effort, reduction in bycatch mortality and protection of key areas to initiate recovery of severely depleted communities.

Structure and variation of the mitochondrial genome of fishes.

PubMed

Satoh, Takashi P; Miya, Masaki; Mabuchi, Kohji; Nishida, Mutsumi

2016-09-07

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.

Factors influencing riverine fish assemblages in Massachusetts

USGS Publications Warehouse

Armstrong, David S.; Richards, Todd A.; Levin, Sara B.

2011-01-01

The U.S. Geological Survey, in cooperation with the Massachusetts Department of Conservation and Recreation, Massachusetts Department of Environmental Protection, and the Massachusetts Department of Fish and Game, conducted an investigation of fish assemblages in small- to medium-sized Massachusetts streams. The objective of this study was to determine relations between fish-assemblage characteristics and anthropogenic factors, including impervious cover and estimated flow alteration, relative to the effects of environmental factors, including physical-basin characteristics and land use. The results of this investigation supersede those of a preliminary analysis published in 2010. Fish data were obtained for 669 fish-sampling sites from the Massachusetts Division of Fisheries and Wildlife fish-community database. A review of the literature was used to select fish metrics - species richness, abundance of individual species, and abundances of species grouped on life history traits - responsive to flow alteration. The contributing areas to the fish-sampling sites were delineated and used with a geographic information system to determine a set of environmental and anthropogenic factors that were tested for use as explanatory variables in regression models. Reported and estimated withdrawals and return flows were used together with simulated unaltered streamflows to estimate altered streamflows and indicators of flow alteration for each fish-sampling site. Altered streamflows and indicators of flow alteration were calculated on the basis of methods developed in a previous U.S. Geological Survey study in which unaltered daily streamflows were simulated for a 44-year period (water years 1961-2004), and streamflow alterations were estimated by use of water-withdrawal and wastewater-return data previously reported to the State for the 2000-04 period and estimated domestic-well withdrawals and septic-system discharges. A variable selection process, conducted using principal components analysis and Spearman rank correlation, was used to select a set of 15 non-redundant environmental and anthropogenic factors to test for use as explanatory variables in the regression analyses. Twenty-one fish species were used in a multivariate analysis of fish-assemblage patterns. Results of nonmetric multidimensional scaling and hierarchical cluster analysis were used to group fish species into fluvial and macrohabitat generalist habitat-use classes. Two analytical techniques, quantile regression and generalized linear modeling, were applied to characterize the association between fish-response variables and environmental and anthropogenic explanatory variables. Quantile regression demonstrated that as percent impervious cover and an indicator of percent alteration of August median flow from groundwater withdrawals increase, the relative abundance and species richness of fluvial fish decrease. The quantile regression plots indicate that (1) as many as seven fluvial fish species are expected in streams with little flow alteration or impervious cover, (2) no more than four fluvial fish species are expected in streams where flow alterations from groundwater withdrawals exceed 50 percent of the August median flow or the percent area of impervious cover exceeds 15 percent, and (3) few fluvial fish remain at high rates of withdrawal (approaching 100 percent) or high rates of impervious cover (between 25 and 30 percent). Three generalized linear models (GLMs) were developed to quantify the response of fluvial fish to multiple environmental and anthropogenic variables. All variables in the GLM equations were demonstrated to be significant (p less than 0.05, with most less than 0.01). Variables in the fluvial-fish relative-abundance model were channel slope, estimated percent alteration of August median flow from groundwater withdrawals, percent wetland in a 240-meter buffer strip, and percent impervious cover. Variables in the fluvial-fish species-richness model were drainage area, channel slope, total undammed reach length, percent wetland in a 240-meter buffer strip, and percent impervious cover. Variables in the brook trout relativeabundance model were drainage area, percent open water, and percent impervious cover. The variability explained by the GLM models, as measured by the pseudo R2, ranged from 18.2 to 34.6, and correlations between observed and predicted values ranged from 0.50 to 0.60. Results of GLM models indicated that, keeping all other variables the same, a one-unit (1 percent) increase in the percent depletion of August median flow would result in a 0.9-percent decrease in the relative abundance (in counts per hour) of fluvial fish. The results of GLM models also indicated that a unit increase in impervious cover (1 percent) resulted in a 3.7-percent decrease in the relative abundance of fluvial fish, a 5.4-percent decrease in fluvial-fish species richness, and an 8.7-percent decrease in brook trout relative abundance.

Effects of freezing on white perch Morone americana (Gmelin, 1789): Implications for multivariate morphometrics

USGS Publications Warehouse

Kocovsky, Patrick

2016-01-01

This study tested the hypothesis that duration of freezing differentially affects whole-body morphometrics of a derived teleost. Whole-body morphometrics are frequently analyzed to test hypotheses of different species, or stocks within a species, of fishes. Specimens used for morphometric analyses are typically fixed or preserved prior to analysis, yet little research has been done on how fixation or preservation methods or duration of preservation of specimens might affect outcomes of multivariate statistical analyses of differences in shape. To determine whether whole-body morphometrics changed as a result of freezing, 23 whole-body morphometrics of age-1 white perch (Morone americana) from western Lake Erie (n = 211) were analyzed immediately after capture, after being held on ice overnight, and after freezing for 100 or 200 days. Discriminant function analysis revealed that all four groups differed significantly from one another (P < 0.0001). The first canonical axis reflected long-axis morphometrics, where there was a clear pattern of positive translation along this axis with duration of preservation. Re-classification analysis demonstrated fish were typically assigned to their original preservation class except for fish frozen 100 days, which assigned mostly to frozen 200 days. Morphometric comparisons using frozen fish must be done on fish frozen for identical periods of time to avoid biases related to the length of time they were frozen. Similar experiments should be conducted on other species and also using formalin- and alcohol-preserved specimens.

Dual phylogenetic staining protocol for simultaneous analysis of yeast and bacteria in artworks

NASA Astrophysics Data System (ADS)

González-Pérez, Marina; Brinco, Catarina; Vieira, Ricardo; Rosado, Tânia; Mauran, Guilhem; Pereira, António; Candeias, António; Caldeira, Ana Teresa

2017-02-01

The detection and analysis of metabolically active microorganisms are useful to determine those directly involved in the biodeterioration of cultural heritage (CH). Fluorescence in situ hybridization with oligonucleotide probes targeted at rRNA (RNA-FISH) has demonstrated to be a powerful tool for signaling them. However, more efforts are required for the technique to become a vital tool for the analysis of CH's microbiological communities. Simultaneous analysis of microorganisms belonging to different kingdoms, by RNA-FISH in-suspension approach, could represent an important progress: it could open the door for the future use of the technique to analyze the microbial communities by flow cytometry, which has shown to be a potent tool in environmental microbiology. Thus, in this work, various already implemented in-suspension RNA-FISH protocols for ex situ analysis of yeast and bacteria were investigated and adapted for allowing the simultaneous detection of these types of microorganisms. A deep investigation of the factors that can affect the results was carried out, focusing particular attention on the selection of the fluorochromes used for labelling the probe set. The resultant protocol, involving the use of EUK516-6-FAM/EUB338-Cy3 probes combination, was validated using artificial consortia and gave positive preliminary results when applied in samples from a real case study: the Paleolithic archaeological site of Escoural Cave (Alentejo, Portugal). This approach represents the first dual-staining RNA-FISH in-suspension protocol developed and applied for the simultaneous investigation of CH biodeteriogenic agents belonging to different kingdoms.

Development of an NPM1/MLF1 D-FISH probe set for the detection of t(3;5)(q25;q35) identified in patients with acute myeloid leukemia.

PubMed

Aypar, Umut; Knudson, Ryan A; Pearce, Kathryn E; Wiktor, Anne E; Ketterling, Rhett P

2014-09-01

The t(3;5)(q25;q35) NPM1/MLF1 fusion has an incidence of approximately 0.5% in acute myeloid leukemia (AML) and has an intermediate prognosis at diagnosis. We have developed a dual-color, dual-fusion fluorescence in situ hybridization (D-FISH) assay to detect fusion of the MLF1 and NPM1 genes. A blinded investigation was performed using 25 normal bone marrow specimens and 26 bone marrow samples from patients with one or more metaphases with a t(3;5)(q21-q25;q31-q35) or a der(5)t(3;5)(q21-q25;q31-q35) previously identified by chromosome analysis. Once unblinded, the results indicate our D-FISH method identified NPM1/MLF1 fusion in 15 of the 26 fully evaluated patient samples. Excluding three samples with a single abnormal t(3;5) metaphase, 15 of 17 (88%) patient samples with a balanced t(3;5) demonstrated NPM1/MLF1 fusion, and 0 of 6 patient samples with a der(5)t(3;5) demonstrated NPM1/MLF1 fusion, suggesting only the balanced form of this 3;5 translocation as observed by karyotype is associated with NPM1/MLF1 fusion. Overall, the FISH results demonstrated five different outcomes (NPM1/MLF1 fusion, MLF1 disruption, MLF1 duplication, NPM1 deletion, and normal), indicating significant molecular heterogeneity when the 3;5 translocation is identified. The development of this sensitive D-FISH strategy for the detection of NPM1/MLF1 fusion adds to the AML FISH testing repertoire and is effective in the detection of this translocation at diagnosis as well as monitoring residual disease in AML patients. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet

PubMed Central

Meyer, Christopher P.; Mills, Suzanne C.

2015-01-01

Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators’ diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. PMID:26137428

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet.

PubMed

Leray, Matthieu; Meyer, Christopher P; Mills, Suzanne C

2015-01-01

Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.

Climate change and fishing: a century of shifting distribution in North Sea cod

PubMed Central

Engelhard, Georg H; Righton, David A; Pinnegar, John K

2014-01-01

Globally, spatial distributions of fish stocks are shifting but although the role of climate change in range shifts is increasingly appreciated, little remains known of the likely additional impact that high levels of fishing pressure might have on distribution. For North Sea cod, we show for the first time and in great spatial detail how the stock has shifted its distribution over the past 100 years. We digitized extensive historical fisheries data from paper charts in UK government archives and combined these with contemporary data to a time-series spanning 1913–2012 (excluding both World Wars). New analysis of old data revealed that the current distribution pattern of cod – mostly in the deeper, northern- and north-easternmost parts of the North Sea – is almost opposite to that during most of the Twentieth Century – mainly concentrated in the west, off England and Scotland. Statistical analysis revealed that the deepening, northward shift is likely attributable to warming; however, the eastward shift is best explained by fishing pressure, suggestive of significant depletion of the stock from its previous stronghold, off the coasts of England and Scotland. These spatial patterns were confirmed for the most recent 3½ decades by data from fisheries-independent surveys, which go back to the 1970s. Our results demonstrate the fundamental importance of both climate change and fishing pressure for our understanding of changing distributions of commercially exploited fish. PMID:24375860

Transcriptomic and physiological responses to fishmeal substitution with plant proteins in formulated feed in farmed Atlantic salmon (Salmo salar)

PubMed Central

2012-01-01

Background Aquaculture of piscivorous fish is in continual expansion resulting in a global requirement to reduce the dependence on wild caught fish for generation of fishmeal and fish oil. Plant proteins represent a suitable protein alternative to fish meal and are increasingly being used in fish feed. In this study, we examined the transcriptional response of Atlantic salmon (Salmo salar) to a high marine protein (MP) or low fishmeal, higher plant protein replacement diet (PP), formulated to the same nutritional specification within previously determined acceptable maximum levels of individual plant feed materials. Results After 77 days of feeding the fish in both groups doubled in weight, however neither growth performance, feed efficiency, condition factor nor organ indices were significantly different. Assessment of histopathological changes in the heart, intestine or liver did not reveal any negative effects of the PP diet. Transcriptomic analysis was performed in mid intestine, liver and skeletal muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The dietary comparison revealed large alteration in gene expression in all the tissues studied between fish on the two diets. Gene ontology analysis showed, in the mid intestine of fish fed PP, higher expression of genes involved in enteritis, protein and energy metabolism, mitochondrial activity/kinases and transport, and a lower expression of genes involved in cell proliferation and apoptosis compared to fish fed MP. The liver of fish fed PP showed a lower expression of immune response genes but a higher expression of cell proliferation and apoptosis processes that may lead to cell reorganization in this tissue. The skeletal muscle of fish fed PP vs MP was characterized by a suppression of processes including immune response, energy and protein metabolism, cell proliferation and apoptosis which may reflect a more energy efficient tissue. Conclusions The PP diet resulted in significant effects on transcription in all the 3 tissues studied. Despite of these alterations, we demonstrated that high level of plant derived proteins in a salmon diet allowed fish to grow with equal efficiency as those on a high marine protein diet, and with no difference in biometric quality parameters. PMID:22853566

Transcriptomic and physiological responses to fishmeal substitution with plant proteins in formulated feed in farmed Atlantic salmon (Salmo salar).

PubMed

Tacchi, Luca; Secombes, Christopher J; Bickerdike, Ralph; Adler, Michael A; Venegas, Claudia; Takle, Harald; Martin, Samuel A M

2012-08-01

Aquaculture of piscivorous fish is in continual expansion resulting in a global requirement to reduce the dependence on wild caught fish for generation of fishmeal and fish oil. Plant proteins represent a suitable protein alternative to fish meal and are increasingly being used in fish feed. In this study, we examined the transcriptional response of Atlantic salmon (Salmo salar) to a high marine protein (MP) or low fishmeal, higher plant protein replacement diet (PP), formulated to the same nutritional specification within previously determined acceptable maximum levels of individual plant feed materials. After 77 days of feeding the fish in both groups doubled in weight, however neither growth performance, feed efficiency, condition factor nor organ indices were significantly different. Assessment of histopathological changes in the heart, intestine or liver did not reveal any negative effects of the PP diet. Transcriptomic analysis was performed in mid intestine, liver and skeletal muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The dietary comparison revealed large alteration in gene expression in all the tissues studied between fish on the two diets. Gene ontology analysis showed, in the mid intestine of fish fed PP, higher expression of genes involved in enteritis, protein and energy metabolism, mitochondrial activity/kinases and transport, and a lower expression of genes involved in cell proliferation and apoptosis compared to fish fed MP. The liver of fish fed PP showed a lower expression of immune response genes but a higher expression of cell proliferation and apoptosis processes that may lead to cell reorganization in this tissue. The skeletal muscle of fish fed PP vs MP was characterized by a suppression of processes including immune response, energy and protein metabolism, cell proliferation and apoptosis which may reflect a more energy efficient tissue. The PP diet resulted in significant effects on transcription in all the 3 tissues studied. Despite of these alterations, we demonstrated that high level of plant derived proteins in a salmon diet allowed fish to grow with equal efficiency as those on a high marine protein diet, and with no difference in biometric quality parameters.

An interactive governance and fish chain approach to fisheries rebuilding: a case study of the Northern Gulf cod in eastern Canada.

PubMed

Khan, Ahmed; Chuenpagdee, Ratana

2014-09-01

Rebuilding collapsed fisheries is a multifaceted problem, requiring a holistic governance approach rather than technical management fixes. Using the Northern Gulf cod case study in eastern Canada, we illustrate how a "fish chain" framework, drawn from the interactive governance perspective, is particularly helpful in analyzing rebuilding challenges. The analysis demonstrates that factors limiting rebuilding exist along the entire fish chain, i.e., the pre-harvest, harvest, and post-harvest stages. These challenges are embedded in both the ecological and social systems associated with the Northern Gulf cod fisheries, as well as in the governing systems. A comparative analysis of the pre- and post-collapse of the cod fisheries also reveals governance opportunities in rebuilding, which lie in policy interventions such as integrated and ecosystem-based management, livelihood transitional programs, and cross-scale institutional arrangements. Lessons from the Northern Gulf cod case study, especially the missed opportunities to explore alternative governing options during the transition, are valuable for rebuilding other collapsed fisheries.

A watershed-based spatially-explicit demonstration of an integrated environmental modeling framework for ecosystem services in the Coal River Basin (WV, USA)

Treesearch

John M. Johnston; Mahion C. Barber; Kurt Wolfe; Mike Galvin; Mike Cyterski; Rajbir Parmar; Luis Suarez

2016-01-01

We demonstrate a spatially-explicit regional assessment of current condition of aquatic ecoservices in the Coal River Basin (CRB), with limited sensitivity analysis for the atmospheric contaminant mercury. The integrated modeling framework (IMF) forecasts water quality and quantity, habitat suitability for aquatic biota, fish biomasses, population densities, ...

Optimum swimming pathways of fish spawning migrations in rivers

USGS Publications Warehouse

McElroy, Brandon; DeLonay, Aaron; Jacobson, Robert

2012-01-01

Fishes that swim upstream in rivers to spawn must navigate complex fluvial velocity fields to arrive at their ultimate locations. One hypothesis with substantial implications is that fish traverse pathways that minimize their energy expenditure during migration. Here we present the methodological and theoretical developments necessary to test this and similar hypotheses. First, a cost function is derived for upstream migration that relates work done by a fish to swimming drag. The energetic cost scales with the cube of a fish's relative velocity integrated along its path. By normalizing to the energy requirements of holding a position in the slowest waters at the path's origin, a cost function is derived that depends only on the physical environment and not on specifics of individual fish. Then, as an example, we demonstrate the analysis of a migration pathway of a telemetrically tracked pallid sturgeon (Scaphirhynchus albus) in the Missouri River (USA). The actual pathway cost is lower than 105 random paths through the surveyed reach and is consistent with the optimization hypothesis. The implication—subject to more extensive validation—is that reproductive success in managed rivers could be increased through manipulation of reservoir releases or channel morphology to increase abundance of lower-cost migration pathways.

Invasive lionfish harbor a different external bacterial community than native Bahamian fishes

NASA Astrophysics Data System (ADS)

Stevens, J. L.; Olson, J. B.

2013-12-01

The introduction and subsequent spread of lionfish into the Atlantic Ocean and Caribbean Sea has become a worldwide conservation issue. These highly successful invaders may also be capable of introducing non-native microorganisms to the invaded regions. This study compared the bacterial communities associated with lionfish external tissue to those of native Bahamian fishes and ambient water. Terminal restriction fragment length polymorphism analyses demonstrated that lionfish bacterial communities were significantly different than those associated with three native Bahamian fishes. Additionally, all fishes harbored distinct bacterial communities from the ambient bacterioplankton. Analysis of bacterial clone libraries from invasive lionfish and native squirrelfish indicated that lionfish communities were more diverse than those associated with squirrelfish, yet did not contain known fish pathogens. Using microscopy and molecular genetic approaches, lionfish eggs were examined for the presence of bacteria to evaluate the capacity for vertical transmission. Eggs removed from the ovaries of gravid females were free of bacteria, suggesting that lionfish likely acquire bacteria from the environment. This study was the first examination of bacterial communities associated with the invasive lionfish and indicated that they support different communities of environmentally derived bacteria than Caribbean reef fishes.

Microbial and nutritional aspects on the production of live feeds in a fish farming industry.

PubMed

De Donno, A; Lugoli, F; Bagordo, F; Vilella, S; Campa, A; Grassi, T; Guido, M

2010-03-01

Aquaculture is an enterprise in constant development, in particular relating to its effect on the environment and also the quality of its products. It represents a valid alternative to traditional fishing, facing the increasing demand for fish products. To guarantee to the consumer a product of high nutritional, organoleptic and hygienic quality, it is fundamental to monitor every phase of the fish farming industry, isolating the potential risk points. For this reason there has been a rapid evolution of productive technique, particularly in the technology, artificial reproduction and feed sectors. The aim of this research has been the monitoring of the evolution of certain microbial and nutritional quality indexes (total microbial counts and lipid analysis on suspensions of Rotifers and Artemia, used as live feed) in the larval phase of the productive cycle of the farm raised fish, in an intensive system. The study has shown an increment in the total microbial counts in the fish farming industry within the production of Rotifers and Artemia, more evident in the suspensions of Rotifers. In addition the study has demonstrated that the maintenance phase, in the enrichment protocol, can reduce the EPA and DHA content. The results confirm the importance of microbial and nutritional control of the live feeds before they get supplied to fish larvae.

Interphase cytogenetics of prostatic carcinoma in fine needle aspirate smears of radical prostatectomy specimens: A practical screening tool?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, R.Y.; Troncoso, P.; El-Naggar, A.K.

1994-09-01

Identification of chromosomal aberrations that may be used for diagnostic or prognostic evaluation of prostatic adenocarcinoma has been the subject of great interest. In a previous study, we applied the fluorescence in situ hybridization (FISH) method on paraffin-embedded material to show that trisomy 7 was associated with the progression of human prostate cancer. In this study, we attempted to assess the utility of the FISH technique in detecting aneuploidy in fine needle aspirate (FNA) smears of prostatic tissues and to compare FISH results with that of DNA flow cytometry (FCM). Paired samples of normal and tumor FNA smears were obtainedmore » from 10 radical prostatectomy specimens. Dual-color chromosomes 7 and 9-specific centromeric DNA probes were used for FISH. FISH analysis demonstrated increased frequencies of trisomy 7 cells in all 10 tumors studied when compared with the paired normals. In contrast, 6 of 10 tumors were determined to be diploid by FCM. Our results show that FNA of radical prostatectomy specimens is a practical method for obtaining suitable material for both FISH and FCM analyses of prostate carcinoma. Thus, interphase FISH may be a practical screening tool to determine aneuploidy in FNA smears of prostatic carcinoma.« less

Characterization of microbiota in Arapaima gigas intestine and isolation of potential probiotic bacteria.

PubMed

do Vale Pereira, G; da Cunha, D G; Pedreira Mourino, J L; Rodiles, A; Jaramillo-Torres, A; Merrifield, D L

2017-11-01

The aim of this study was to determine the intestinal microbiota of pirarucu (Arapaima gigas) in different growth stages (adult and fingerlings) and to isolate and identify potential probiotic bacteria. High-throughput sequencing analysis of the intestinal contents revealed that the majority of sequences belonged to the Proteobacteria, Fusobacteria and Firmicutes phyla. At the genus level, the greatest number of sequences belonged to Bradyrhizobium in adult fish, while Cetobacterium was the most abundant in juvenile fish. Twenty-three lactic-acid bacteria (LABs) were isolated on MRS agar from healthy juvenile fish. The isolates were tested in vitro for probiotic properties. Two isolates (identified as strains of Lactococcus lactis subsp. lactis and Enterococcus faecium) displayed antagonism against all 10 pathogens tested, were nonhaemolytic and maintained good viability for at least 3 weeks when supplemented to fish diets. The presence of a number of antibiotic resistance genes (ARGs), conferring resistance to erythromycin, tetracycline and chloramphenicol, was investigated by PCR. The absence of ARGs investigated the potential to antagonize pathogens, and favourable growth and survival characteristics indicate that these autochthonous isolates have the potential to be considered probiotics, which will be studied in future in vivo experiments. This study has demonstrated, for the first time, the normal microbiota in the A. gigas intestine during different life stages and the presence of LAB strains. It also demonstrated LAB antibiotic resistance and antagonistic behaviour against pathogens isolated from the same fish. © 2017 The Society for Applied Microbiology.

A stitch in time saves nine: external quality assessment rounds demonstrate improved quality of biomarker analysis in lung cancer

PubMed Central

Keppens, Cleo; Tack, Véronique; Hart, Nils ‘t; Tembuyser, Lien; Ryska, Ales; Pauwels, Patrick; Zwaenepoel, Karen; Schuuring, Ed; Cabillic, Florian; Tornillo, Luigi; Warth, Arne; Weichert, Wilko; Dequeker, Elisabeth

2018-01-01

Biomarker analysis has become routine practice in the treatment of non-small cell lung cancer (NSCLC). To ensure high quality testing, participation to external quality assessment (EQA) schemes is essential. This article provides a longitudinal overview of the EQA performance for EGFR, ALK, and ROS1 analyses in NSCLC between 2012 and 2015. The four scheme years were organized by the European Society of Pathology according to the ISO 17043 standard. Participants were asked to analyze the provided tissue using their routine procedures. Analysis scores improved for individual laboratories upon participation to more EQA schemes, except for ROS1 immunohistochemistry (IHC). For EGFR analysis, scheme error rates were 18.8%, 14.1% and 7.5% in 2013, 2014 and 2015 respectively. For ALK testing, error rates decreased between 2012 and 2015 by 5.2%, 3.2% and 11.8% for the fluorescence in situ hybridization (FISH), FISH digital, and IHC subschemes, respectively. In contrast, for ROS1 error rates increased between 2014 and 2015 for FISH and IHC by 3.2% and 9.3%. Technical failures decreased over the years for all three markers. Results show that EQA contributes to an ameliorated performance for most predictive biomarkers in NSCLC. Room for improvement is still present, especially for ROS1 analysis. PMID:29755669

A reliable DNA barcode reference library for the identification of the North European shelf fish fauna.

PubMed

Knebelsberger, Thomas; Landi, Monica; Neumann, Hermann; Kloppmann, Matthias; Sell, Anne F; Campbell, Patrick D; Laakmann, Silke; Raupach, Michael J; Carvalho, Gary R; Costa, Filipe O

2014-09-01

Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within-species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51-fold higher than those within species. The validation of the sequence library by applying BOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of the DNA barcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two-thirds of the typical fish species recorded for the North Sea. © 2014 John Wiley & Sons Ltd.

Environmental Influences on the Fish Assemblage of the Humber Estuary, U.K.

NASA Astrophysics Data System (ADS)

Marshall, S.; Elliott, M.

1998-02-01

Salinity, temperature, turbidity and dissolved oxygen were measured in conjunction with a series of fish samples taken by a 2 m beam trawl from 14 sites throughout the Humber estuary, U.K., over the period April 1992 to November 1994. Sediment type was not measured as the literature indicates that the area is homogeneous. The influences of environmental factors and the characteristics of the fish assemblage were analysed using a range of multivariate techniques, including two-way indicator species analysis, canonical correspondence analysis, principal components analysis and Spearman rank correlation. The analyses indicate that salinity is the dominant factor influencing the distribution of the species, with temperature also having a major influence. Of the species examined, whiting (Merlangius merlangus), sole (Solea solea), flounder (Pleuronectes flesus), sprat (Sprattus sprattus) and herring (Clupea harengus) showed a correlation in distribution to temperature, sole, plaice (Pleuronectes platessa), pogge (Agonus cataphractus) and stickleback (Gasterosteus aculeatus) to salinity, and whiting, flounder, pogge and stickleback to dissolved oxygen. Only cod (Gadus morhua) showed a correlation with tidal state, while whiting, pogge and stickleback were correlated to depth. Unlike in some other estuaries, turbidity did not influence the composition of the fish assemblage. Temperature and salinity fluctuations appear to influence different aspects of the community, with temperature proving to be the best predictor of total abundance, while salinity influenced the species richness and total biomass. The analyses demonstrate the most important variables with regard to environmental-biotic interactions, although they also indicate that the variables measured do not account for all of the observed variation in fish biomass and abundance.

Augmentation of French grunt diet description using combined visual and DNA-based analyses

USGS Publications Warehouse

Hargrove, John S.; Parkyn, Daryl C.; Murie, Debra J.; Demopoulos, Amanda W.J.; Austin, James D.

2012-01-01

Trophic linkages within a coral-reef ecosystem may be difficult to discern in fish species that reside on, but do not forage on, coral reefs. Furthermore, dietary analysis of fish can be difficult in situations where prey is thoroughly macerated, resulting in many visually unrecognisable food items. The present study examined whether the inclusion of a DNA-based method could improve the identification of prey consumed by French grunt, Haemulon flavolineatum, a reef fish that possesses pharyngeal teeth and forages on soft-bodied prey items. Visual analysis indicated that crustaceans were most abundant numerically (38.9%), followed by sipunculans (31.0%) and polychaete worms (5.2%), with a substantial number of unidentified prey (12.7%). For the subset of prey with both visual and molecular data, there was a marked reduction in the number of unidentified sipunculans (visual – 31.1%, combined &ndash 4.4%), unidentified crustaceans (visual &ndash 15.6%, combined &ndash 6.7%), and unidentified taxa (visual &ndash 11.1%, combined &ndash 0.0%). Utilising results from both methodologies resulted in an increased number of prey placed at the family level (visual &ndash 6, combined &ndash 33) and species level (visual &ndash 0, combined &ndash 4). Although more costly than visual analysis alone, our study demonstrated the feasibility of DNA-based identification of visually unidentifiable prey in the stomach contents of fish.

Diet × genotype interactions in hepatic cholesterol and lipoprotein metabolism in Atlantic salmon (Salmo salar) in response to replacement of dietary fish oil with vegetable oil.

PubMed

Morais, Sofia; Pratoomyot, Jarunan; Torstensen, Bente E; Taggart, John B; Guy, Derrick R; Bell, J Gordon; Tocher, Douglas R

2011-11-01

The present study investigates the effects of genotype on responses to alternative feeds in Atlantic salmon. Microarray analysis of the liver transcriptome of two family groups, lean or fat, fed a diet containing either a fish oil (FO) or a vegetable oil (VO) blend indicated that pathways of cholesterol and lipoprotein metabolism might be differentially affected by the diet depending on the genetic background of the fish, and this was further investigated by real-time quantitative PCR, plasma and lipoprotein biochemical analysis. Results indicate a reduction in VLDL and LDL levels, with no changes in HDL, when FO is replaced by VO in the lean family group, whereas in fat fish fed FO, levels of apoB-containing lipoproteins were low and comparable with those fed VO in both family groups. Significantly lower levels of plasma TAG and LDL-TAG were measured in the fat group that was independent of diet, whereas plasma cholesterol was significantly higher in fish fed the FO diet in both groups. Hepatic expression of genes involved in cholesterol homeostasis, β-oxidation and lipoprotein metabolism showed relatively subtle changes. A significantly lower expression of genes considered anti-atherogenic in mammals (ATP-binding cassette transporter A1, apoAI, scavenger receptor class B type 1, lipoprotein lipase (LPL)b (TC67836) and LPLc (TC84899)) was found in lean fish, compared with fat fish, when fed VO. Furthermore, the lean family group appeared to show a greater response to diet composition in the cholesterol biosynthesis pathway, mediated by sterol-responsive element-binding protein 2. Finally, the presence of three different transcripts for LPL, with differential patterns of nutritional regulation, was demonstrated.

Typology of historical sources and the reconstruction of long-term historical changes of riverine fish: a case study of the Austrian Danube and northern Russian rivers

PubMed Central

Haidvogl, Gertrud; Lajus, Dmitry; Pont, Didier; Schmid, Martin; Jungwirth, Mathias; Lajus, Julia

2014-01-01

Historical data are widely used in river ecology to define reference conditions or to investigate the evolution of aquatic systems. Most studies rely on printed documents from the 19th century, thus missing pre-industrial states and human impacts. This article discusses historical sources that can be used to reconstruct the development of riverine fish communities from the Late Middle Ages until the mid-20th century. Based on the studies of the Austrian Danube and northern Russian rivers, we propose a classification scheme of printed and archival sources and describe their fish ecological contents. Five types of sources were identified using the origin of sources as the first criterion: (i) early scientific surveys, (ii) fishery sources, (iii) fish trading sources, (iv) fish consumption sources and (v) cultural representations of fish. Except for early scientific surveys, all these sources were produced within economic and administrative contexts. They did not aim to report about historical fish communities, but do contain information about commercial fish and their exploitation. All historical data need further analysis for a fish ecological interpretation. Three case studies from the investigated Austrian and Russian rivers demonstrate the use of different source types and underline the necessity for a combination of different sources and a methodology combining different disciplinary approaches. Using a large variety of historical sources to reconstruct the development of past fish ecological conditions can support future river management by going beyond the usual approach of static historical reference conditions. PMID:25284959

The Impact of Marine Protected Areas on Reef-Wide Population Structure and Fishing-Induced Phenotypes in Coral-Reef Fishes

NASA Astrophysics Data System (ADS)

Fidler, Robert Young, III

Overfishing and destructive fishing practices threaten the sustainability of fisheries worldwide. In addition to reducing population sizes, anthropogenic fishing effort is highly size-selective, preferentially removing the largest individuals from harvested stocks. Intensive, size-selective mortality induces widespread phenotypic shifts toward the predominance of smaller and earlier-maturing individuals. Fish that reach sexual maturity at smaller size and younger age produce fewer, smaller, and less viable larvae, severely reducing the reproductive capacity of exploited populations. These directional phenotypic alterations, collectively known as "fisheries-induced evolution" (FIE) are among the primary causes of the loss of harvestable fish biomass. Marine protected areas (MPAs) are one of the most widely utilized components of fisheries management programs around the world, and have been proposed as a potential mechanism by which the impacts of FIE may be mitigated. The ability of MPAs to buffer exploited populations against fishing pressure, however, remains debated due to inconsistent results across studies. Additionally, empirical evidence of phenotypic shifts in fishes within MPAs is lacking. This investigation addresses both of these issues by: (1) using a categorical meta-analysis of MPAs to standardize and quantify the magnitude of MPA impacts across studies; and (2) conducting a direct comparison of life-history phenotypes known to be influenced by FIE in six reef-fish species inside and outside of MPAs. The Philippines was used as a model system for analyses due to the country's significance in global marine biodiversity and reliance on MPAs as a fishery management tool. The quantitative impact of Philippine MPAs was assessed using a "reef-wide" meta-analysis. This analysis used pooled visual census data from 39 matched pairs of MPAs and fished reefs surveyed twice over a mean period of 3 years. In 17 of these MPAs, two additional surveys were conducted using size-specific fish counts, allowing for spatiotemporal comparisons of abundance and demographic structure of fish populations across protected and fished areas. Results of the meta-analysis revealed that: (1) although fish density was higher inside MPAs than in fished reefs at each sampling period, reef-wide density often increased or remained stable over time; and (2) increases in large-bodied fish were evident reef-wide between survey periods, indicating that positive demographic shifts occurred simultaneously in both MPAs and adjacent areas. Increases in large-bodied fish were observed across a range of taxa, but were most prominent in families directly targeted by fishermen. These results suggest that over relatively few years of protection, Philippine MPAs promoted beneficial shifts in population structure throughout entire reef systems, rather than simply maintaining stable populations within their borders. Relationships between MPA age and shifts in fish density or demographic structure were rare, but may have been precluded by the relatively short period between replicate surveys. Although increases in fish density inside MPAs were occasionally associated with MPA size, there were no significant relationships between the size of MPAs and reef-wide increases in fish density. The reef-wide framework of MPA assessment used in this study has the advantage of treating MPAs and fished reefs as an integrated system, thus revealing trends that would be indistinguishable in traditional spatial comparisons between MPAs and fished reefs. The impact of MPAs on fishing-induced life-history traits was assessed by comparing growth and maturation patterns exhibited by six reef-fish species inside and outside five MPAs and adjacent, fished reefs in Zambales, Luzon, Philippines. This analysis demonstrated considerable variation in terminal body-sizes (Linf) and growth rates (K) between conspecifics in MPAs and fished reefs. Three of the four experimental species directly targeted for food in the region (Acanthurus nigrofuscus, Ctenochaetus striatus, and Parupeneus multifasciatus) exhibited greater Linf, lower K, or both characteristics inside at least one MPA compared to populations in adjacent, fished reefs. Life-history shifts were concentrated in the oldest and largest MPAs, but occurred at least once in each of the five MPAs that were examined. A fourth species harvested for food (Ctenochaetus binotatus), as well as a species targeted for the aquarium trade (Zebrasoma scopas) and a non-target species (Plectroglyphidodon lacrymatus) did not exhibit differential phenotypes between MPAs and fished reefs. The relatively high frequency of alterations to life-history characteristics across MPAs in harvested species suggests that observed changes in the density and size-structure of harvested fish populations inside MPAs are likely driven by spatial disparities in fishing pressure, and are the result of phenotypic changes rather than increased longevity.

Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

PubMed

Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

2016-04-30

Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Proteomic sensitivity to dietary manipulations in rainbow trout.

PubMed

Martin, S A M; Vilhelmsson, O; Médale, F; Watt, P; Kaushik, S; Houlihan, D F

2003-09-23

Changes in dietary protein sources due to substitution of fish meal by other protein sources can have metabolic consequences in farmed fish. A proteomics approach was used to study the protein profiles of livers of rainbow trout that have been fed two diets containing different proportions of plant ingredients. Both diets control (C) and soy (S) contained fish meal and plant ingredients and synthetic amino acids, but diet S had a greater proportion of soybean meal. A feeding trial was performed for 12 weeks at the end of which, growth and protein metabolism parameters were measured. Protein growth rates were not different in fish fed different diets; however, protein consumption and protein synthesis rates were higher in the fish fed the diet S. Fish fed diet S had lower efficiency of retention of synthesised protein. Ammonia excretion was increased as well as the activities of hepatic glutamate dehydrogenase and aspartate amino transferase (ASAT). No differences were found in free amino acid pools in either liver or muscle between diets. Protein extraction followed by high-resolution two-dimensional electrophoresis, coupled with gel image analysis, allowed identification and expression of hundreds of protein. Individual proteins of interest were then subjected to further analysis leading to protein identification by trypsin digest fingerprinting. During this study, approximately 800 liver proteins were analysed for expression pattern, of which 33 were found to be differentially expressed between diets C and S. Seventeen proteins were positively identified after database searching. Proteins were identified from diverse metabolic pathways, demonstrating the complex nature of gene expression responses to dietary manipulation revealed by proteomic characterisation.

Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing.

PubMed

Jorge, Paulo H; Mastrochirico-Filho, Vito A; Hata, Milene E; Mendes, Natália J; Ariede, Raquel B; de Freitas, Milena Vieira; Vera, Manuel; Porto-Foresti, Fábio; Hashimoto, Diogo T

2018-01-01

The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme.

Climate change and fishing: a century of shifting distribution in North Sea cod.

PubMed

Engelhard, Georg H; Righton, David A; Pinnegar, John K

2014-08-01

Globally, spatial distributions of fish stocks are shifting but although the role of climate change in range shifts is increasingly appreciated, little remains known of the likely additional impact that high levels of fishing pressure might have on distribution. For North Sea cod, we show for the first time and in great spatial detail how the stock has shifted its distribution over the past 100 years. We digitized extensive historical fisheries data from paper charts in UK government archives and combined these with contemporary data to a time-series spanning 1913-2012 (excluding both World Wars). New analysis of old data revealed that the current distribution pattern of cod - mostly in the deeper, northern- and north-easternmost parts of the North Sea - is almost opposite to that during most of the Twentieth Century - mainly concentrated in the west, off England and Scotland. Statistical analysis revealed that the deepening, northward shift is likely attributable to warming; however, the eastward shift is best explained by fishing pressure, suggestive of significant depletion of the stock from its previous stronghold, off the coasts of England and Scotland. These spatial patterns were confirmed for the most recent 3 1/2 decades by data from fisheries-independent surveys, which go back to the 1970s. Our results demonstrate the fundamental importance of both climate change and fishing pressure for our understanding of changing distributions of commercially exploited fish. © 2013 Crown copyright. Global Change Biology published by John Wiley & Sons Ltd. This article is published with the permission of the Controller of HMSO and the Queen's Printer for Scotland.

Marine Fish Proteins and Peptides for Cosmeceuticals: A Review

PubMed Central

Venkatesan, Jayachandran; Anil, Sukumaran; Kim, Se-Kwon; Shim, Min Suk

2017-01-01

Marine fish provide a rich source of bioactive compounds such as proteins and peptides. The bioactive proteins and peptides derived from marine fish have gained enormous interest in nutraceutical, pharmaceutical, and cosmeceutical industries due to their broad spectrum of bioactivities, including antioxidant, antimicrobial, and anti-aging activities. Recently, the development of cosmeceuticals using marine fish-derived proteins and peptides obtained from chemical or enzymatical hydrolysis of fish processing by-products has increased rapidly owing to their activities in antioxidation and tissue regeneration. Marine fish-derived collagen has been utilized for the development of cosmeceutical products due to its abilities in skin repair and tissue regeneration. Marine fish-derived peptides have also been utilized for various cosmeceutical applications due to their antioxidant, antimicrobial, and matrix metalloproteinase inhibitory activities. In addition, marine fish-derived proteins and hydrolysates demonstrated efficient anti-photoaging activity. The present review highlights and presents an overview of the current status of the isolation and applications of marine fish-derived proteins and peptides. This review also demonstrates that marine fish-derived proteins and peptides have high potential for biocompatible and effective cosmeceuticals. PMID:28524092

Understanding spearfishing in a coral reef fishery: Fishers' opportunities, constraints, and decision-making.

PubMed

Pavlowich, Tyler; Kapuscinski, Anne R

2017-01-01

Social and ecological systems come together during the act of fishing. However, we often lack a deep understanding of the fishing process, despite its importance for understanding and managing fisheries. A quantitative, mechanistic understanding of the opportunities fishers encounter, the constraints they face, and how they make decisions within the context of opportunities and constraints will enhance the design of fisheries management strategies to meet linked ecological and social objectives and will improve scientific capacity to predict impacts of different strategies. We examined the case of spearfishing in a Caribbean coral reef fishery. We mounted cameras on fishers' spearguns to observe the fish they encountered, what limited their ability to catch fish, and how they made decisions about which fish to target. We observed spearfishers who dove with and without the assistance of compressed air, and compared the fishing process of each method using content analysis of videos and decision models of fishers' targeting selections. Compressor divers encountered more fish, took less time to catch each fish, and had a higher rate of successful pursuits. We also analyzed differences among taxa in this multispecies fishery, because some taxa are known to be ecologically or economically more valuable than others. Parrotfish are ecologically indispensable for healthy coral reefs, and they were encountered and captured more frequently than any other taxon. Fishers made decisions about which fish to target based on a fish's market value, proximity to the fisher, and taxon. The information uncovered on fishers' opportunities, constraints, and decision making has implications for managing this fishery and others. Moreover, it demonstrates the value of pursuing an improved understanding of the fishing process from the perspective of the fishers.

Hypoxia alters testicular functions of marine medaka through microRNAs regulation.

PubMed

Tse, Anna Chung-Kwan; Li, Jing-Woei; Wang, Simon Yuan; Chan, Ting-Fung; Lai, Keng Po; Wu, Rudolf Shiu-Sun

2016-11-01

Hypoxia is a global environmental concern and poses a significant threat to aquatic ecosystems, including the sustainability of natural fish populations. The deleterious effects of hypoxia on fish reproductive fitness, as mediated by disruption of sex hormones and gene expression along the Brain-Pituitary-Gonad axis, have been well documented. Recently, we further demonstrated that the observed disruption of steroidogenesis in the ovary of marine medaka Oryzias melastigma is mediated through microRNAs (miRNAs). More importantly, we reported the transgenerational epigenetic effect of hypoxia on the male reproductive impairment of marine medaka. This study attempts to elucidate the function of miRNAs and its potential role in the transgenerational effect of hypoxia in the male medaka testis, using small RNA sequencing. A total of 558 miRNAs were found in the testis, of which 9 were significant upregulated and 5 were downregulated by hypoxia. Bioinformatics analysis further revealed that among the 2885 genes targeted by the hypoxia-responsive miRNAs, many are closely related to stress response, cell cycle, epigenetic modification, sugar metabolism and cell motion. Furthermore, the integrated analysis of transcriptome data and the result of target gene prediction demonstrated 108 genes and 65 genes were concordantly upregulated and downregulated, respectively. In which, euchromatic histone-lysine N-methyltransferase 2, the epigenetic regulator of transgenerational reproductive impairment caused by hypoxia, is found to be targeted by miR-125-5p. The present findings not only reveal that miRNAs are crucial downstream mediators of hypoxic stress in fish male gonad, but also shed light on the underlying epigenetic mechanism for the reproductive impairments of hypoxia on male fish, including the observed transgenerational effects. Copyright © 2016 Elsevier B.V. All rights reserved.

Intraguild Predation Dynamics in a Lake Ecosystem Based on a Coupled Hydrodynamic-Ecological Model: The Example of Lake Kinneret (Israel).

PubMed

Makler-Pick, Vardit; Hipsey, Matthew R; Zohary, Tamar; Carmel, Yohay; Gal, Gideon

2017-03-29

The food web of Lake Kinneret contains intraguild predation (IGP). Predatory invertebrates and planktivorous fish both feed on herbivorous zooplankton, while the planktivorous fish also feed on the predatory invertebrates. In this study, a complex mechanistic hydrodynamic-ecological model, coupled to a bioenergetics-based fish population model (DYCD-FISH), was employed with the aim of revealing IGP dynamics. The results indicate that the predation pressure of predatory zooplankton on herbivorous zooplankton varies widely, depending on the season. At the time of its annual peak, it is 10-20 times higher than the fish predation pressure. When the number of fish was significantly higher, as occurs in the lake after atypical meteorological years, the effect was a shift from a bottom-up controlled ecosystem, to the top-down control of planktivorous fish and a significant reduction of predatory and herbivorous zooplankton biomass. Yet, seasonally, the decrease in predatory-zooplankton biomass was followed by a decrease in their predation pressure on herbivorous zooplankton, leading to an increase of herbivorous zooplankton biomass to an extent similar to the base level. The analysis demonstrates the emergence of non-equilibrium IGP dynamics due to intra-annual and inter-annual changes in the physico-chemical characteristics of the lake, and suggests that IGP dynamics should be considered in food web models in order to more accurately capture mass transfer and trophic interactions.

PERIODIC AIR-BREATHING BEHAVIOUR IN A PRIMITIVE FISH REVEALED BY SPECTRAL ANALYSIS

PubMed

Hedrick; Katz; Jones

1994-12-01

The ventilatory patterns of air-breathing fish are commonly described as 'arrhythmic' or 'irregular' because the variable periods of breath-holding are punctuated by seemingly unpredictable air-breathing events (see Shelton et al. 1986). This apparent arrhythmicity contrasts with the perceived periodism or regularity in the gill ventilation patterns of some fish and with lung ventilation in birds and mammals. In this sense, periodism refers to behaviour that occurs with a definite, recurring interval (Bendat and Piersol, 1986). The characterisation of aerial ventilation patterns in fish as 'aperiodic' has been generally accepted on the basis of qualitative examination and it remains to be validated with rigorous testing. The bowfin, Amia calva (L.), is a primitive air-breathing fish that makes intermittent excursions to the air­water interface to gulp air, which is transferred to its well-vascularized gas bladder. Its phylogenetic position as the only extant member of the sister lineage of modern teleosts affords a unique opportunity to examine the evolution of aerial ventilation and provides a model for the examination of ventilatory patterns in primitive fishes. To establish whether Amia calva exhibit a particular pattern of air-breathing, we examined time series records of aerial ventilations from undisturbed fish over long periods (8 h). These records were the same as those used to calculate average ventilation intervals under a variety of experimental conditions (Hedrick and Jones, 1993). Their study also reported the occurrence of two distinct breath types. Type I breaths were characterised by an exhalation followed by an inhalation, whereas type II breaths were characterised by inhalation only. It was also hypothesized that the type I breaths were employed to meet oxygen demands, whereas the type II breaths were used to regulate gas bladder volume. However, they did not investigate the potential presence of a periodic ventilatory pattern. We now report the results of just such an analysis of ventilatory pattern that demonstrates a clear periodism to air-breathing in a primitive fish.

Improving non-native fish larvae detection based on temporal habitat use.

EPA Science Inventory

As part of the development of an early detection monitoring strategy for non-native fishes, larval fish surveys have been conducted since 2012 in the St. Louis River estuary. Survey data demonstrates considerable variability in fish abundance and species assemblages across habit...

Acoustical monitoring of fish behavior in a tank

NASA Astrophysics Data System (ADS)

Conti, Stephan G.; Maurer, Benjamin D.; Roux, Philippe; Fauvel, Christian; Demer, David A.; Waters, Kendall R.

2004-10-01

In recent publications, it has been demonstrated that the total scattering cross section of fish moving in a tank can be estimated from ensembles of reverberation time series. However, the reproducibility of these measurements is influenced by parameters such as the motion or the behavior of the fish. In this work, we propose to observe acoustically the behavior of fish in a tank, and to measure their average speed. The total scattering cross section of live fish (sardines, sea bass and bocaccio) in a tank was measured repeatedly over multiple days. The species used in this study have different behaviors, which are reflected in the acoustical measurements. Depending on the behavior of the fish, such as the average displacement between two acoustic pings or the aggregation type, the total scattering cross section is different. Correlation between the acoustical measurements and the day and night behavior of the fish is demonstrated. Interpretation of such measurements can lead to monitoring acoustically and nonintrusively the behavior of fish in tanks.

The evolution of aryl hydrocarbon signaling proteins: diversity of ARNT isoforms among fish species.

PubMed

Powell, W H; Hahn, M E

2000-01-01

The aryl hydrocarbon receptor nuclear translocator (ARNT) mediates aryl hydrocarbon signaling and toxicity by dimerizing with the ligand-activated aryl hydrocarbon receptor (AHR), forming a complex that binds specific DNA elements and alters transcription of target genes. Two genes encode different forms of ARNT in rodents: ARNT1, which is widely expressed, and ARNT2, which exhibits a very restricted expression pattern. In an effort to characterize aryl hydrocarbon signaling mechanisms in fishes, we previously isolated an ARNT cDNA from Fundulus heteroclitus and discovered that this species expresses ARNT2 ubiquitously. This situation differs not only from mammals, but also from rainbow trout, which expresses a divergent ARNT gene that we hypothesized was peculiar to salmonids (rtARNTa/b). In this communication, we examine the ARNT sequences of multiple fish species, including a newly isolated cDNA from scup (Stenotomus chrysops). Our phylogenetic analysis demonstrates that zebrafish ARNT, like the Fundulus protein, is an ARNT2. Contrary to expectations, the scup ARNT is closely related to the rainbow trout protein, demonstrating that the existence of this ARNT isoform predates the divergence of salmonids from the other teleosts. Thus, different species of fish express distinct and highly conserved isoforms of ARNT. The number, type, and expression pattern of ARNT proteins may contribute to interspecies differences in aryl hydrocarbon toxicity, possibly through distinct interactions with additional PAS-family proteins.

Histologic, immunologic and endocrine biomarkers indicate contaminant effects in fishes of the Ashtabula River.

PubMed

Iwanowicz, Luke R; Blazer, Vicki S; Hitt, Nathaniel P; McCormick, Stephen D; DeVault, David S; Ottinger, Christopher A

2012-01-01

The use of fish as sentinels of aquatic ecosystem health is a biologically relevant approach to environmental monitoring and assessment. We examined the health of the Ashtabula River using histologic, immunologic, and endocrine biomarkers in brown bullhead (BB; Ameiurus nebulosus) and largemouth bass (Micropterus salmoides) and compared fish collected from a reference site (Conneaut Creek). Seasonal analysis was necessary to distinguish differences in fish between the two rivers. Overall BB from the Ashtabula River had a lower condition factor and significantly more macrophage aggregates than those from the reference site. Reduced bactericidal and cytotoxic-cell activity was observed in anterior kidney leukocytes from both BB and largemouth bass from the Ashtabula River. Lower plasma thyroxine and triiodo-L-thyronine in both species in the Ashtabula River indicated disruption of the thyroid axis. Differences in physiological biomarker responses were supported by body burden chemical concentrations when data were analyzed on a seasonal basis. The use of two fish species added a level of rigor that demonstrated biological effects were not exclusive to a single species. The results provide strong evidence that contaminants have affected fish in the Ashtabula River, a Great Lakes Area of Concern, and provide a baseline by which to evaluate remediation activities.

Histologic, immunologic and endocrine biomarkers indicate contaminant effects in fishes of the Ashtabula River

USGS Publications Warehouse

Iwanowicz, L.R.; Blazer, V.S.; Hitt, N.P.; McCormick, S.D.; Devault, D.S.; Ottinger, C.A.

2012-01-01

The use of fish as sentinels of aquatic ecosystem health is a biologically relevant approach to environmental monitoring and assessment. We examined the health of the Ashtabula River using histologic, immunologic, and endocrine biomarkers in brown bullhead (BB; Ameiurus nebulosus) and largemouth bass (Micropterus salmoides) and compared fish collected from a reference site (Conneaut Creek). Seasonal analysis was necessary to distinguish differences in fish between the two rivers. Overall BB from the Ashtabula River had a lower condition factor and significantly more macrophage aggregates than those from the reference site. Reduced bactericidal and cytotoxic-cell activity was observed in anterior kidney leukocytes from both BB and largemouth bass from the Ashtabula River. Lower plasma thyroxine and triiodo-L-thyronine in both species in the Ashtabula River indicated disruption of the thyroid axis. Differences in physiological biomarker responses were supported by body burden chemical concentrations when data were analyzed on a seasonal basis. The use of two fish species added a level of rigor that demonstrated biological effects were not exclusive to a single species. The results provide strong evidence that contaminants have affected fish in the Ashtabula River, a Great Lakes Area of Concern, and provide a baseline by which to evaluate remediation activities.

Visual receptive field properties of cells in the optic tectum of the archer fish.

PubMed

Ben-Tov, Mor; Kopilevich, Ivgeny; Donchin, Opher; Ben-Shahar, Ohad; Giladi, Chen; Segev, Ronen

2013-08-01

The archer fish is well known for its extreme visual behavior in shooting water jets at prey hanging on vegetation above water. This fish is a promising model in the study of visual system function because it can be trained to respond to artificial targets and thus to provide valuable psychophysical data. Although much behavioral data have indeed been collected over the past two decades, little is known about the functional organization of the main visual area supporting this visual behavior, namely, the fish optic tectum. In this article we focus on a fundamental aspect of this functional organization and provide a detailed analysis of receptive field properties of cells in the archer fish optic tectum. Using extracellular measurements to record activities of single cells, we first measure their retinotectal mapping. We then determine their receptive field properties such as size, selectivity for stimulus direction and orientation, tuning for spatial frequency, and tuning for temporal frequency. Finally, on the basis of all these measurements, we demonstrate that optic tectum cells can be classified into three categories: orientation-tuned cells, direction-tuned cells, and direction-agnostic cells. Our results provide an essential basis for future investigations of information processing in the archer fish visual system.

Linking Fossil Fish Cyclicity and Paleoenvironmental Proxies in the mid-Devonian

NASA Astrophysics Data System (ADS)

Grogan, D.; Whiteside, J. H.; Trewin, N. H.; Johnson, J. E.

2009-12-01

The significant radiation of fishes throughout the Devonian, combined with the abundance of well-preserved fossil fish assemblages from this period, provides for a high-resolution record of prevalent fish taxa in the Orcadian basin of North Scotland. In addition to their ability to serve as a lake-level and lake-chemistry proxy, the waxing and waning of dominant fish taxa exhibit a pronounced cyclicity, suggesting they respond to broader climate rhythms. Recent studies of mid-Devonian lacustrine sedimentary sequences have quantitatively demonstrated the presence of Milankovitch cyclicity in geochemical and gamma ray proxy records. Spectral analysis of gamma ray data show a strong obliquity peak usually associated with ice-house conditions; this obliquity signal is unexpected as tropical latitudes in the mid-Devonian are traditionally thought to have been in a greenhouse climate. Geochemical data include the measurement of bulk carbon and nitrogen stable isotopes, molecule-specific carbon isotopes of plant biomarkers, and depth ranks from eight sections of the Caithness Flagstone Group of the Orcadian Basin. Evidence for orbital forcing of climate change paired with the fossil fish record provides a unique opportunity to establish an astronomically calibrated timescale for the mid-Devonian, as well as to make a quantitative assessment of the validity of a greenhouse climate existing in the mid-Devonian.

Design and fabrication of thin microvascularised polymer matrices inspired from secondary lamellae of fish gills

NASA Astrophysics Data System (ADS)

Kumar, Prasoon; Gandhi, Prasanna S.; Majumder, Mainak

2016-04-01

Gills are one of the most primitive gas, solute exchange organs available in fishes. They facilitate exchange of gases, solutes and ions with a surrounding water medium through their functional unit called secondary lamella. These lamellae through their extraordinary morphometric features and peculiar arrangement in gills, achieve remarkable mass transport properties. Therefore, in the current study, modeling and simulation of convection-diffusion transport through a two dimensional model of secondary lamella and theoretical analysis of morphometric features of fish gills were carried out. Such study suggested an evolutionary conservation of parametric ratios across fishes of different weights. Further, we have also fabricated a thin microvascularised PDMS matrices mimicking secondary lamella by use of micro-technologies like electrospinning. In addition, we have also demonstrated the fluid flow by capillary action through these thin microvascularised PDMS matrices. Eventually, we also illustrated the application of these thin microvascularied PDMS matrices in solute exchange process under capillary flow conditions. Thus, our study suggested that fish gills have optimized parameteric ratios, at multiple length scale, throughout an evolution to achieve an organ with enhanced mass transport capabilities. Thus, these defined parametric ratios could be exploited to design and develop efficient, scaled-up gas/solute exchange microdevices. We also proposed an inexpensive and scalable method of fabrication of thin microvascularised polymer matrices and demonstrated its solute exchange capabilities under capillary flow conditions. Thus, mimicking the microstructures of secondary lamella will enable fabrication of microvascularised thin polymer systems through micro manufacturing technologies for potential applications in filtration, self-healing/cooling materials and bioengineering.

Skeletal stiffening in an amphibious fish out of water is a response to increased body weight.

PubMed

Turko, Andy J; Kültz, Dietmar; Fudge, Douglas; Croll, Roger P; Smith, Frank M; Stoyek, Matthew R; Wright, Patricia A

2017-10-15

Terrestrial animals must support their bodies against gravity, while aquatic animals are effectively weightless because of buoyant support from water. Given this evolutionary history of minimal gravitational loading of fishes in water, it has been hypothesized that weight-responsive musculoskeletal systems evolved during the tetrapod invasion of land and are thus absent in fishes. Amphibious fishes, however, experience increased effective weight when out of water - are these fishes responsive to gravitational loading? Contrary to the tetrapod-origin hypothesis, we found that terrestrial acclimation reversibly increased gill arch stiffness (∼60% increase) in the amphibious fish Kryptolebias marmoratus when loaded normally by gravity, but not under simulated microgravity. Quantitative proteomics analysis revealed that this change in mechanical properties occurred via increased abundance of proteins responsible for bone mineralization in other fishes as well as in tetrapods. Type X collagen, associated with endochondral bone growth, increased in abundance almost ninefold after terrestrial acclimation. Collagen isoforms known to promote extracellular matrix cross-linking and cause tissue stiffening, such as types IX and XII collagen, also increased in abundance. Finally, more densely packed collagen fibrils in both gill arches and filaments were observed microscopically in terrestrially acclimated fish. Our results demonstrate that the mechanical properties of the fish musculoskeletal system can be fine-tuned in response to changes in effective body weight using biochemical pathways similar to those in mammals, suggesting that weight sensing is an ancestral vertebrate trait rather than a tetrapod innovation. © 2017. Published by The Company of Biologists Ltd.

Assessment of cytology based molecular analysis to guide targeted therapy in advanced non-small-cell lung cancer.

PubMed

Li, Wenbin; Zhang, Zhihui; Guo, Lei; Qiu, Tian; Ling, Yun; Cao, Jian; Guo, Huiqin; Zhao, Huan; Li, Lin; Ying, Jianming

2016-02-16

To investigate the use of molecular testing on cytological specimens in selecting advanced non-small cell lung cancer (NSCLC) patients who are adequate for targeted treatment, a total of 137 NSCLC cases were analyzed by fluorescence in situ hybridization (FISH) for anaplastic lymphoma kinase (ALK) rearrangements, and Epidermal growth factor receptor (EGFR), kirsten rat sarcoma viral oncogene homolog (KRAS) mutations were evaluated by quantitative real-time PCR (qRT-PCR) platform combining amplification refractory mutation system (ARMS) primers and TaqMan probes. Cytological specimens included 91 fine-needle aspirates, 5 fibreoptic bronchoscopic derived samples and 41 pleural effusions. Among 137 NSCLCs analyzed for ALK FISH, 16 (11.7%, of 137) were detected to harbor ALK rearrangement. FISH positive cases were all defined as adenocarcinoma (ADC) histologic subtype and the FNA samples showed the highest ALK positive rate (13.2%, 12/91). Of the 9 ALK FISH positive patients who received crizotinib treatment, 8 (88.9%) patients exhibited tumor regression. In addition, 60 (44.8%, of 134) cases were found to harbor EGFR mutations and 22 patients with EGFR sensitive mutations who received gefitinib or erlotinib treatment showed a median PFS of 16.0 months. Mutations of KRAS occurred in 8 (6.0%, of 134) cases and this was mutually exclusive from EGFR mutation. Our results demonstrated that ALK FISH and EGFR, KRAS mutational analysis on cytological specimens are sensitive methods for screening advanced stage NSCLC patients who are adequate for targeted treatment.

Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA).

PubMed

Salimi, Nima; Loh, Kar Hoe; Kaur Dhillon, Sarinder; Chong, Ving Ching

2016-01-01

Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies.

Levels of polychlorinated biphenyls in fish and shellfish from the Adriatic Sea.

PubMed

Sagratini, G; Buccioni, M; Ciccarelli, C; Conti, P; Cristalli, G; Giardinà, D; Lambertucci, C; Marucci, G; Volpini, R; Vittori, S

2008-01-01

Levels of 18 polychlorinated biphenyl (PCB) congeners were determined by gas chromatography-mass spectrometry (GC-MS) in some marine species, living both in the coastal area and in deeper seawater. In some species analysis was performed separately in edible parts (fillets) and in viscera. The existence and degree of bioaccumulation was assessed studying individual species of very different size, with the smaller being younger. Furthermore, with a multivariate statistical analysis, a correlation between PCB congeners and the feeding habits and habitat of the fish was demonstrated. The results show that fat from edible parts (fish fillets) had total PCB levels in the range 22.6-601.9 µg kg⁻¹ (with 601.9 µg kg⁻¹ in anchovies), while fat from viscera showed much higher concentrations (407.3-916.6 µg kg⁻¹). Bioaccumulation was confirmed, comparing PCB levels between younger and older individual hake, squid, and horned octopus. The total PCB concentration ratio (older/younger individuals) ranges from 2.11 (squid = 292.1/137.8 µg kg⁻¹) to 3.46 (hake = 546.0/158.0 µg kg⁻¹).

Potential aquaculture probiont Lactococcus lactis TW34 produces nisin Z and inhibits the fish pathogen Lactococcus garvieae.

PubMed

Sequeiros, Cynthia; Garcés, Marisa E; Vallejo, Marisol; Marguet, Emilio R; Olivera, Nelda L

2015-04-01

Bacteriocin-producing Lactococcus lactis TW34 was isolated from marine fish. TW34 bacteriocin inhibited the growth of the fish pathogen Lactococcus garvieae at 5 AU/ml (minimum inhibitory concentration), whereas the minimum bactericidal concentration was 10 AU/ml. Addition of TW34 bacteriocin to L. garvieae cultures resulted in a decrease of six orders of magnitude of viable cells counts demonstrating a bactericidal mode of action. The direct detection of the bacteriocin activity by Tricine-SDS-PAGE showed an active peptide with a molecular mass ca. 4.5 kDa. The analysis by MALDI-TOF-MS detected a strong signal at m/z 2,351.2 that corresponded to the nisin leader peptide mass without the initiating methionine, whose sequence STKDFNLDLVSVSKKDSGASPR was confirmed by MS/MS. Sequence analysis of nisin structural gene confirmed that L. lactis TW34 was a nisin Z producer. This nisin Z-producing strain with probiotic properties might be considered as an alternative in the prevention of lactococcosis, a global disease in aquaculture systems.

Analysis of the African coelacanth genome sheds light on tetrapod evolution

PubMed Central

Amemiya, Chris T.; Alföldi, Jessica; Lee, Alison P.; Fan, Shaohua; Philippe, Hervé; MacCallum, Iain; Braasch, Ingo; Manousaki, Tereza; Schneider, Igor; Rohner, Nicolas; Organ, Chris; Chalopin, Domitille; Smith, Jeramiah J.; Robinson, Mark; Dorrington, Rosemary A.; Gerdol, Marco; Aken, Bronwen; Biscotti, Maria Assunta; Barucca, Marco; Baurain, Denis; Berlin, Aaron M.; Blatch, Gregory L.; Buonocore, Francesco; Burmester, Thorsten; Campbell, Michael S.; Canapa, Adriana; Cannon, John P.; Christoffels, Alan; De Moro, Gianluca; Edkins, Adrienne L.; Fan, Lin; Fausto, Anna Maria; Feiner, Nathalie; Forconi, Mariko; Gamieldien, Junaid; Gnerre, Sante; Gnirke, Andreas; Goldstone, Jared V.; Haerty, Wilfried; Hahn, Mark E.; Hesse, Uljana; Hoffmann, Steve; Johnson, Jeremy; Karchner, Sibel I.; Kuraku, Shigehiro; Lara, Marcia; Levin, Joshua Z.; Litman, Gary W.; Mauceli, Evan; Miyake, Tsutomu; Mueller, M. Gail; Nelson, David R.; Nitsche, Anne; Olmo, Ettore; Ota, Tatsuya; Pallavicini, Alberto; Panji, Sumir; Picone, Barbara; Ponting, Chris P.; Prohaska, Sonja J.; Przybylski, Dariusz; Saha, Nil Ratan; Ravi, Vydianathan; Ribeiro, Filipe J.; Sauka-Spengler, Tatjana; Scapigliati, Giuseppe; Searle, Stephen M. J.; Sharpe, Ted; Simakov, Oleg; Stadler, Peter F.; Stegeman, John J.; Sumiyama, Kenta; Tabbaa, Diana; Tafer, Hakim; Turner-Maier, Jason; van Heusden, Peter; White, Simon; Williams, Louise; Yandell, Mark; Brinkmann, Henner; Volff, Jean-Nicolas; Tabin, Clifford J.; Shubin, Neil; Schartl, Manfred; Jaffe, David; Postlethwait, John H.; Venkatesh, Byrappa; Di Palma, Federica; Lander, Eric S.; Meyer, Axel; Lindblad-Toh, Kerstin

2013-01-01

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution. PMID:23598338

Detection of clonal evolution in hematopoietic malignancies by combining comparative genomic hybridization and single nucleotide polymorphism arrays.

PubMed

Hartmann, Luise; Stephenson, Christine F; Verkamp, Stephanie R; Johnson, Krystal R; Burnworth, Bettina; Hammock, Kelle; Brodersen, Lisa Eidenschink; de Baca, Monica E; Wells, Denise A; Loken, Michael R; Zehentner, Barbara K

2014-12-01

Array comparative genomic hybridization (aCGH) has become a powerful tool for analyzing hematopoietic neoplasms and identifying genome-wide copy number changes in a single assay. aCGH also has superior resolution compared with fluorescence in situ hybridization (FISH) or conventional cytogenetics. Integration of single nucleotide polymorphism (SNP) probes with microarray analysis allows additional identification of acquired uniparental disomy, a copy neutral aberration with known potential to contribute to tumor pathogenesis. However, a limitation of microarray analysis has been the inability to detect clonal heterogeneity in a sample. This study comprised 16 samples (acute myeloid leukemia, myelodysplastic syndrome, chronic lymphocytic leukemia, plasma cell neoplasm) with complex cytogenetic features and evidence of clonal evolution. We used an integrated manual peak reassignment approach combining analysis of aCGH and SNP microarray data for characterization of subclonal abnormalities. We compared array findings with results obtained from conventional cytogenetic and FISH studies. Clonal heterogeneity was detected in 13 of 16 samples by microarray on the basis of log2 values. Use of the manual peak reassignment analysis approach improved resolution of the sample's clonal composition and genetic heterogeneity in 10 of 13 (77%) patients. Moreover, in 3 patients, clonal disease progression was revealed by array analysis that was not evident by cytogenetic or FISH studies. Genetic abnormalities originating from separate clonal subpopulations can be identified and further characterized by combining aCGH and SNP hybridization results from 1 integrated microarray chip by use of the manual peak reassignment technique. Its clinical utility in comparison to conventional cytogenetic or FISH studies is demonstrated. © 2014 American Association for Clinical Chemistry.

Repeatability of standard metabolic rate (SMR) in a small fish, the spined loach (Cobitis taenia).

PubMed

Maciak, Sebastian; Konarzewski, Marek

2010-10-01

Significant repeatability of a trait of interest is an essential assumption for undertaking studies of phenotypic variability. It is especially important in studies on highly variable traits, such as metabolic rates. Recent publications suggest that resting/basal metabolic rate of homeotherms is repeatable across wide range of species. In contrast, studies on the consistency of standard metabolic rate (SMR) in ectotherms, particularly fish, are scarce. Here we present a comprehensive analysis of several important technical aspects of body mass-corrected SMR measurements and its repeatability in a small (average weight approximately 3g) fish, the spined loach (Cobitis taenia). First we demonstrated that release of oxygen from the walls of metabolic chambers exposed to hypoxic conditions did not confound SMR measurements. Next, using principle of propagation of measurement uncertainties we demonstrated that in aquatic systems, measurement error is significantly higher in open than closed respirometry setups. The measurement error for SMR of a small fish determined in a closed aquatic system is comparable to that obtainable using top-notch open-flow systems used for air-breathing terrestrial animals. Using a closed respirometer we demonstrated that body mass-corrected SMR in spined loaches was repeatable under both normoxia and hypoxia over a 5-month period (Pearson correlation r=0.68 and r=0.73, respectively) as well as across both conditions (intraclass correlation coefficient tau=0.30). In these analyses we accounted for possible effect of oxygen consumption of the oxygen electrode on repeatability of SMR. Significant SMR consistency was accompanied by significant repeatability of body mass (intraclass correlation coefficient tau=0.86). To our knowledge, this is the first study showing long-term repeatability of body mass and SMR in a small fish, and is consistent with the existence of heritable variation of these two traits. 2010 Elsevier Inc. All rights reserved.

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 is needed to properly evaluate ecological effects.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 is needed to properly evaluate ecological effects.« less

Detecting conservation benefits of marine reserves on remote reefs of the northern GBR

PubMed Central

Bozec, Yves-Marie; Dempsey, Alexandra; Ortiz, Juan Carlos; Robbins, William D.; Renaud, Philip G.; Mumby, Peter J.

2017-01-01

The Great Barrier Reef Marine Park (GBRMP) is the largest network of marine reserves in the world, yet little is known of the efficacy of no-fishing zones in the relatively lightly-exploited remote parts of the system (i.e., northern regions). Here, we find that the detection of reserve effects is challenging and that heterogeneity in benthic habitat composition, specifically branching coral cover, is one of the strongest driving forces of fish assemblages. As expected, the biomass of targeted fish species was generally greater (up to 5-fold) in no-take zones than in fished zones, but we found no differences between the two forms of no-take zone: ‘no-take’ versus ‘no-entry’. Strong effects of zoning were detected in the remote Far-North inshore reefs and more central outer reefs, but surprisingly fishing effects were absent in the less remote southern locations. Moreover, the biomass of highly targeted species was nearly 2-fold greater in fished areas of the Far-North than in any reserve (no-take or no-entry) further south. Despite high spatial variability in fish biomass, our results suggest that fishing pressure is greater in southern areas and that poaching within reserves may be common. Our results also suggest that fishers ‘fish the line’ as stock sizes in exploited areas decreased near larger no-take zones. Interestingly, an analysis of zoning effects on small, non-targeted fishes appeared to suggest a top-down effect from mesopredators, but was instead explained by variability in benthic composition. Thus, we demonstrate the importance of including appropriate covariates when testing for evidence of trophic cascades and reserve successes or failures. PMID:29117191

Understanding spearfishing in a coral reef fishery: Fishers’ opportunities, constraints, and decision-making

PubMed Central

Pavlowich, Tyler; Kapuscinski, Anne R.

2017-01-01

Social and ecological systems come together during the act of fishing. However, we often lack a deep understanding of the fishing process, despite its importance for understanding and managing fisheries. A quantitative, mechanistic understanding of the opportunities fishers encounter, the constraints they face, and how they make decisions within the context of opportunities and constraints will enhance the design of fisheries management strategies to meet linked ecological and social objectives and will improve scientific capacity to predict impacts of different strategies. We examined the case of spearfishing in a Caribbean coral reef fishery. We mounted cameras on fishers’ spearguns to observe the fish they encountered, what limited their ability to catch fish, and how they made decisions about which fish to target. We observed spearfishers who dove with and without the assistance of compressed air, and compared the fishing process of each method using content analysis of videos and decision models of fishers’ targeting selections. Compressor divers encountered more fish, took less time to catch each fish, and had a higher rate of successful pursuits. We also analyzed differences among taxa in this multispecies fishery, because some taxa are known to be ecologically or economically more valuable than others. Parrotfish are ecologically indispensable for healthy coral reefs, and they were encountered and captured more frequently than any other taxon. Fishers made decisions about which fish to target based on a fish’s market value, proximity to the fisher, and taxon. The information uncovered on fishers’ opportunities, constraints, and decision making has implications for managing this fishery and others. Moreover, it demonstrates the value of pursuing an improved understanding of the fishing process from the perspective of the fishers. PMID:28750077

[Niche and interspecific association of the dominant fish in the south coastal waters of Wenzhou, China].

PubMed

Dong, Jing Rui; Shui, Bo Nian; Hu, Cheng Ye; Shui, Yu Yue; DU, Xiao; Tian, Kuo

2017-05-18

The studies about the niche and interspecific association in China were mainly focused on the plants, birds and marine animals, and seldom on fish. Based on the fishery resources survey in spring (May) and autumn (September) in 2015, the associations among major fish species in south coastal waters of Wenzhou were investigated. The methods including niche breadth, niche overlap, variance ratio (VR), Χ 2 -test, association coefficient (AC), percentage of co-occurrence (PC) and point correlation coefficients (Ф) were used. The results showed that 47 fish species were identified, including 9 orders, 27 families and 41 genera. Four species were dominant species and 9 were important species, which together accounted for 17%. The niche breadth cluster analysis demonstrated two clearly identifiable ecological niches. The first one referred to wide niche that included Harpodon nehereus, Collichthys lucidus, Engraulis japonicas, Pampus echinogaster, Argyrosomus argentatus, Polynemus sextarius, Decapterus maruadsi and Trichiurus haumela, and the second one was narrow niche that included Muraenesox cinereus, Amblychaeturichthys hexanema, Cunoglossus robustus, Pseudosciaena polyactis and Ilisha elongate. The niche overlap value of the main fish was 0-0.90, indicating that there was difference in the resource utilization among the species. The ecological niche widths of C. robustus and M. cinereus were narrow, and the overlap values were high. This indicated that there was competition between these two species. The VR analysis revealed significant positive correlation among the main fish species. In view of the advantages of Ф value, which could reduce the impact of the analysis results of Χ 2 -test, AC and PC to the interspecific association, the Ф value method was selected in this study, and the association of 63 couples were positive. Both the interspecific association and ecological niche had different degrees of correlation with the stability of community structure and community succession.

Comparative analysis of Edwardsiella isolates from fish in the eastern United States identifies two distinct genetic taxa amongst organisms phenotypically classified as E. tarda

USGS Publications Warehouse

Griffin, Matt J.; Quiniou, Sylvie M.; Cody, Theresa; Tabuchi, Maki; Ware, Cynthia; Cipriano, Rocco C.; Mauel, Michael J.; Soto, Esteban

2013-01-01

Edwardsiella tarda, a Gram-negative member of the family Enterobacteriaceae, has been implicated in significant losses in aquaculture facilities worldwide. Here, we assessed the intra-specific variability of E. tarda isolates from 4 different fish species in the eastern United States. Repetitive sequence mediated PCR (rep-PCR) using 4 different primer sets (ERIC I & II, ERIC II, BOX, and GTG5) and multi-locus sequence analysis of 16S SSU rDNA, groEl, gyrA, gyrB, pho, pgi, pgm, and rpoA gene fragments identified two distinct genotypes of E. tarda (DNA group I; DNA group II). Isolates that fell into DNA group II demonstrated more similarity to E. ictaluri than DNA group I, which contained the reference E. tarda strain (ATCC #15947). Conventional PCR analysis using published E. tarda-specific primer sets yielded variable results, with several primer sets producing no observable amplification of target DNA from some isolates. Fluorometric determination of G + C content demonstrated 56.4% G + C content for DNA group I, 60.2% for DNA group II, and 58.4% for E. ictaluri. Surprisingly, these isolates were indistinguishable using conventional biochemical techniques, with all isolates demonstrating phenotypic characteristics consistent with E. tarda. Analysis using two commercial test kits identified multiple phenotypes, although no single metabolic characteristic could reliably discriminate between genetic groups. Additionally, anti-microbial susceptibility and fatty acid profiles did not demonstrate remarkable differences between groups. The significant genetic variation (<90% similarity at gyrA, gyrB, pho, phi and pgm; <40% similarity by rep-PCR) between these groups suggests organisms from DNA group II may represent an unrecognized, genetically distinct taxa of Edwardsiella that is phenotypically indistinguishable from E. tarda.

Investigating phenology of larval fishes in St. Louis River estuary shallow water habitats

EPA Science Inventory

As part of the development of an early detection monitoring strategy for non-native fishes, larval fish surveys have been conducted since 2012 in the St. Louis River estuary. Survey data demonstrates there is considerable variability in fish abundance and species assemblages acro...

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

PubMed

Sato, Yukuto; Miya, Masaki; Fukunaga, Tsukasa; Sado, Tetsuya; Iwasaki, Wataru

2018-06-01

Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies. MitoFish, MitoAnnotator, and MiFish pipeline constitute a key platform for studies of fish evolution, ecology, and conservation, and are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed April 7th, 2018).

Fish gelatin thin film standards for biological application of PIXE

NASA Astrophysics Data System (ADS)

Manuel, Jack E.; Rout, Bibhudutta; Szilasi, Szabolcs Z.; Bohara, Gyanendra; Deaton, James; Luyombya, Henry; Briski, Karen P.; Glass, Gary A.

2014-08-01

There exists a critical need to understand the flow and accumulation of metallic ions, both naturally occurring and those introduced to biological systems. In this paper the results of fabricating thin film elemental biological standards containing nearly any combination of trace elements in a protein matrix are presented. Because it is capable of high elemental sensitivity, particle induced X-ray emission spectrometry (PIXE) is an excellent candidate for in situ analysis of biological tissues. Additionally, the utilization of microbeam PIXE allows the determination of elemental concentrations in and around biological cells. However, obtaining elemental reference standards with the same matrix constituents as brain tissue is difficult. An excellent choice for simulating brain-like tissue is Norland® photoengraving glue which is derived from fish skin. Fish glue is water soluble, liquid at room temperature, and resistant to dilute acid. It can also be formed into a thin membrane which dries into a durable, self-supporting film. Elements of interest are introduced to the fish glue in precise volumetric additions of well quantified atomic absorption standard solutions. In this study GeoPIXE analysis package is used to quantify elements intrinsic to the fish glue as well as trace amounts of manganese added to the sample. Elastic (non-Rutherford) backscattered spectroscopy (EBS) and the 1.734 MeV proton-on-carbon 12C(p,p)12C resonance is used for a normalization scheme of the PIXE spectra to account for any discrepancies in X-ray production arising from thickness variation of the prepared standards. It is demonstrated that greater additions of the atomic absorption standard cause a viscosity reduction of the liquid fish glue resulting in thinner films but the film thickness can be monitored by using simultaneous PIXE and EBS proton data acquisition.

Transcriptome-wide identification, molecular evolution and expression analysis of Toll-like receptor family in a Tibet fish, Gymnocypris przewalskii.

PubMed

Tong, Chao; Lin, Yaqiu; Zhang, Cunfang; Shi, Jianquan; Qi, Hongfang; Zhao, Kai

2015-10-01

Toll-like receptors (TLR) are key components of innate immunity that play significant roles in immune defense against pathogens invasion. Recent frequent outbreaks of the "white spot disease" caused by parasitic infection in farmed Tibetan fishes had resulted in great economic losses. However, to our knowledge, the roles of TLRs in mediating immune response to parasitic infection in Tibetan fishes remain to be determined. Here, we performed data-mining on a widely-farmed Tibetan fish (Gymnocypris przewalskii or Gp) transcriptome to determine the genetic variation and expression pattern of TLRs. We totally obtained 14 GpTLRs and identified 5 with a complete coding sequence. Phylogenetic analysis verified their identities and supported the classification of TLRs into six families as in other vertebrates. The TLR family motifs, such as leucine rich repeat (LRR) and Toll/interleukin (IL)-1 receptor (TIR) domain, are conserved in GpTLR1-5. Selective pressure test demonstrated that all known GpTLRs are under purifying selection, except GpTLR4 underwent positive selection. Further, site model analysis suggested that 11 positively selected sites are found in LRR domain of GpTLR4. Three positively selected sites are located on outside surface of TLR4 3D structure, indicating that function of GpTLR4 may be affected. Tissue specific expression analysis showed all GpTLRs are present in gill, head-kidney and spleen but the relative abundance varied among tissues. In response to parasite Ichthyophthirius multifiliis infection, 5 GpTLR (GpTLR1, -2, -4, -9 and -20) expressions were induced. Intriguingly, GpTLR4 was significantly up-regulated in gills, while GpTLR19 and GpTLR21 unexpectedly showed no any change. In summary, these results revealed the first genomic resources of TLR family and several parasitic infection responsive TLRs in Tibetan fish. These findings provide key information for future studies aiming to understand the molecular mechanisms underlying the immune response to pathogen invasion in Tibetan fishes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fish as bioreactors: transgene expression of human coagulation factor VII in fish embryos.

PubMed

Hwang, Gyulin; Müller, Ferenc; Rahman, M Aziz; Williams, Darren W; Murdock, Paul J; Pasi, K John; Goldspink, Geoffrey; Farahmand, Hamid; Maclean, Norman

2004-01-01

A plasmid containing human coagulation factor VII (hFVII) complementary DNA regulated by a cytomegalovirus promoter was microinjected into fertilized eggs of zebrafish, African catfish, and tilapia. The active form of hFVll was detected in the fish embryos by various assays. This positive expression of human therapeutic protein in fish embryos demonstrates the possibility of exploitation of transgenic fish as bioreactors.

WAGR(O?) syndrome and congenital ptosis caused by an unbalanced t(11;15)(p13;p11.2)dn demonstrating a 7 megabase deletion by FISH.

PubMed

Lennon, P A; Scott, D A; Lonsdorf, D; Wargowski, D S; Kirkpatrick, S; Patel, A; Cheung, S W

2006-06-01

Aniridia usually occurs in isolation, but may also occur as part of the WAGR contiguous gene deletion syndrome, which includes Wilms tumor, aniridia, genitourinary abnormalities, and mental retardation. The aniridia and predisposition for Wilms tumor seen in WAGR are caused by haploinsufficiency for PAX 6 and WT1, respectively. We present a female infant with aniridia, bilateral ptosis, bilateral posterior capsular cataracts, nystagmus, left-sided glaucoma, microcephaly, mild unilateral hydronephrosis, poor linear growth, and gross motor delay consistent with a clinical diagnosis of WAGR syndrome. In addition, weight-for-height ratio at 12 months is at the 94th centile, raising the possibility of a diagnosis of WAGRO (WAGR + Obesity). Chromosome analysis revealed a translocation (11;15)(p13;p11.2) which has not been previously associated with a diagnosis of WAGR. Subsequent clinical WAGR fluorescent in situ hybridization (FISH) analysis demonstrated a deletion of 11p13 including PAX6 and WT1. A complete FISH-mapping of the breakpoints on chromosome 11 revealed a 7 Mb deletion within 11p13-11p14. The patient is examined in light of other reported patients with deletions and/or translocations involving the regions between 11p12 --> 11p14 including patients with WAGR + obesity (WAGRO) as well as with other reported patients with aniridia and congenital ptosis. Copyright 2006 Wiley-Liss, Inc.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota.

PubMed

Jami, Mansooreh; Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J

2015-06-01

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated biosynthetic genes, one-fourth of them harbours more than four. This study demonstrates the significant diversity of Actinobacteria in the fish gut microbiota and it's potential to produce biologically active compounds. Copyright © 2015 Elsevier GmbH. All rights reserved.

A Markov chain analysis of the movements of juvenile salmonids, including sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006-09

USGS Publications Warehouse

Adams, Noah S.; Hatton, Tyson W.

2012-01-01

Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting 3-D results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish in the forebay. This report is the second report published in 2012 that uses this analytical method. The first report included only fish released as part of the annual studies conducted at McNary Dam. This second report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant County Public Utility Districts at mid-Columbia River dams. The studies conducted in the mid-Columbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width was different between studies. Additionally, no passive integrated transponder tags were implanted in sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To facilitate comparison among species in this report, we combined JBS and turbine passage for yearling Chinook salmon, steelhead, and subyearling Chinook salmon even though we were able to differentiate between passage through the JBS or turbines for these three species. Information on passage proportions through the JBS and turbines can be found in the first report. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, within the powerhouse region, passage proportions among the three powerhouse areas were often greater in the southern and middle areas of the powerhouse compared to the northern area of the powerhouse for yearling and subyearling Chinook salmon. The opposite generally was observed for steelhead. The results of this analysis also allowed us to confirm and quantify the extent of milling behavior that was observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the spillway before passing the dam. In comparison, greater than 0.20 of the Chinook salmon passed within each of the powerhouse areas. Less milling behavior was observed for all species for fish that first approached the spillway. Compared to the powerhouse areas, a higher proportion of fish, regardless of species, passed the spillway areas and fewer transitioned to adjoining areas in the powerhouse. In addition to quantifying what had been previously speculated about the behavior of fish in the forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and passage can be influenced by changes to the operations and structure of McNary Dam. For example, the addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been reported showing that TSWs increased passage through non-turbine routes and the fish-track videos indicated, in general, how fish behaved before passing the TSWs. However, the analysis presented in this report allowed us to better understand how fish transitioned across the face of the dam before passing the TSWs and resulted in a quantitative way to measure the effect of moving the location of the TSWs from year to year. Installation of the TSWs in bays 22 and 20 clearly increased passage proportions through the southern one-third of the spillway area for all species, most significantly for steelhead. When the TSWs were moved to bays 19 and 20 in 2008, overall passage through the southern one-third of the spillway remained higher than 2006, but decreased from what was observed in 2007. Shifting the TSWs to the north decreased the proportion of fish passing through the TSWs and increased the number of fish that transitioned to adjoining areas before passing the dam. Perhaps the most interesting new information to come out of the two-step Markov chain analysis relates to how the performance of the TSWs was influenced by their proximity to the powerhouse. During 2007, the highest proportion of fish passing through TSW 22 was for fish that transitioned from the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW 20 after coming from the powerhouse area. Instead, the proportion of fish that passed TSW 20 after coming from the northern part of the spillway was twice as high as the proportion of fish that passed through TSW 20 after coming from the powerhouse. During 2008, the TSW in bay 22 was moved to bay 19, leaving the TSW in bay 20 as the one closest to the powerhouse. As was the case when a TSW was located in bay 22, the proportion of fish passing through TSW 20 after coming from the powerhouse was higher than the proportion of fish passing TSW 20 after coming from the northern part of the spillway. Passage proportions for fish passing through TSW 19, the farthest north of the two TSWs during 2008, was higher for fish that came from the northern part of the spillway compared to the proportion of fish that passed through TSW 19 after coming from the powerhouse. The Markov chain analysis provided a mathematical way to characterize fish behavior in the forebay of McNary Dam and helped refine our understanding of how fish movements were influenced by operational and structural changes at the dam. The numerical information used to quantify the behavior of fish also can be used to construct simulations to examine how proposed fish passage structures might influence passage of juvenile salmonids. To demonstrate this, we used the results of the Markov chain analysis to examine how a virtual fish collector located in the center of the powerhouse might influence passage of juvenile salmonids at McNary Dam.

Fish embryo toxicity test: identification of compounds with weak toxicity and analysis of behavioral effects to improve prediction of acute toxicity for neurotoxic compounds.

PubMed

Klüver, Nils; König, Maria; Ortmann, Julia; Massei, Riccardo; Paschke, Albrecht; Kühne, Ralph; Scholz, Stefan

2015-06-02

The fish embryo toxicity test has been proposed as an alternative for the acute fish toxicity test, but concerns have been raised for its predictivity given that a few compounds have been shown to exhibit a weak acute toxicity in the fish embryo. In order to better define the applicability domain and improve the predictive capacity of the fish embryo test, we performed a systematic analysis of existing fish embryo and acute fish toxicity data. A correlation analysis of a total of 153 compounds identified 28 compounds with a weaker or no toxicity in the fish embryo test. Eleven of these compounds exhibited a neurotoxic mode of action. We selected a subset of eight compounds with weaker or no embryo toxicity (cyanazine, picloram, aldicarb, azinphos-methyl, dieldrin, diquat dibromide, endosulfan, and esfenvalerate) to study toxicokinetics and a neurotoxic mode of action as potential reasons for the deviating fish embryo toxicity. Published fish embryo LC50 values were confirmed by experimental analysis of zebrafish embryo LC50 according to OECD guideline 236. Except for diquat dibromide, internal concentration analysis did not indicate a potential relation of the low sensitivity of fish embryos to a limited uptake of the compounds. Analysis of locomotor activity of diquat dibromide and the neurotoxic compounds in 98 hpf embryos (exposed for 96 h) indicated a specific effect on behavior (embryonic movement) for the neurotoxic compounds. The EC50s of behavior for neurotoxic compounds were close to the acute fish toxicity LC50. Our data provided the first evidence that the applicability domain of the fish embryo test (LC50s determination) may exclude neurotoxic compounds. However, neurotoxic compounds could be identified by changes in embryonic locomotion. Although a quantitative prediction of acute fish toxicity LC50 using behavioral assays in fish embryos may not yet be possible, the identification of neurotoxicity could trigger the conduction of a conventional fish acute toxicity test or application of assessment factors while considering the very good fish embryo-acute fish toxicity correlation for other compounds.

Immunoproteomic analysis of the antibody response obtained in tilapia following immunization with a Streptococcus iniae vaccine

USDA-ARS?s Scientific Manuscript database

Streptococcus iniae is one of the most economically important Gram-positive pathogens in cultured fish species worldwide. Research has shown that vaccination is a tool that can be used in the prevention of streptococcal disease. The USDA-ARS patented S. iniae vaccine has been demonstrated to be ef...

Detection of fish antigens aerosolized during fish processing using newly developed immunoassays.

PubMed

Lopata, Andreas L; Jeebhay, Mohamed F; Reese, Gerald; Fernandes, Joshua; Swoboda, Ines; Robins, Thomas G; Lehrer, Samuel B

2005-09-01

Aerosolization of fish proteins during seafood processing has been identified as a potential route for allergic sensitization and occupational asthma among workers involved in high-risk activities. The aim of this study was to develop immunological assays for the quantification of aerosolized fish antigens in a fish-processing factory. Polyclonal antibodies to the main fish species processed in the factory (anchovy and pilchard) were generated in rabbits and compared by ELISA inhibition assay and immunoblotting. These antisera were utilized to develop ELISA assays for the detection of fish antigens. The ELISA inhibition assays were evaluated by analyzing environmental air samples collected from three areas in a fish-processing factory: pilchard canning, fish meal production and lobster processing. By immunoblotting, the rabbit polyclonal antibodies demonstrated IgG antibody binding patterns comparable with IgE antibodies of fish-sensitized patients, particularly in regard to the major fish allergens parvalbumins. The sensitivity of the fish-specific ELISA assays developed was 0.5 microg/ml. The ELISA inhibition assays were able to differentiate between the two different fish species of interest but did not recognize a crustacean species. Notable differences in exposure levels to canned pilchard and anchovy antigens were demonstrated in the three different working areas of the factory, with assays having a detection limit as low as 105 ng/m(3). These ELISA-based assays are sensitive and specific to quantify differential exposure levels to fish antigens produced during fish processing, making it possible to investigate exposure-disease response relationships among workers in this industry. Copyright (c) 2005 S. Karger AG, Basel.

Puffy Skin Disease Is an Emerging Transmissible Condition in Rainbow Trout Oncorhynchus mykiss Walbaum

PubMed Central

Cano, Irene; Verner-Jeffreys, David W.; van Aerle, Ronny; Paley, Richard K.; Peeler, Edmund J.; Green, Matthew; Rimmer, Georgina S. E.; Savage, Jacqueline; Joiner, Claire L.; Bayley, Amanda E.; Mewett, Jason; Hulland, Jonathan; Feist, Stephen W.

2016-01-01

The transmission of puffy skin disease (PSD) to rainbow trout Oncorhynchus mykiss Walbaum was tested in the laboratory by conducting co-habitation challenges with puffy skin (PS)-affected fish (Trojans) collected from the field. Two separate challenges were conducted using Trojans sourced from two different sites and diploid (first trial) or triploid (second trial) naïve fish. PSD-specific clinical signs were observed in both groups of naïve fish, with 66% of the fish sampled during the challenges showing signs of varying severity. The first clinical features of PSD were presented as white oval skin patches on one or both flanks 15–21 days post-challenge (dpc). The extent of the lesions ranged from 10 to 90% of the body surface, depending on the severity of the lesion. Both the severity and number of affected fish increased during the challenge. Macroscopically, oedema of the skin and multifocal petechial haemorrhaging were observed towards the end of the trials. Abnormal fish behaviour consisting of “flashing” and excessive mucous production was noted from 15 dpc onwards. Fish with severe PSD lesions also displayed inappetence and associated emaciation. Rodlet cells were observed in 41% of the fresh skin scrapes analysed from the second trial. Histologically epidermal oedema was observed in 31% of the naive fish showing gross pathology, with additional 12% displaying epidermal hyperplasia, mostly observed at the end of the challenge. Other concomitant features of the PSD lesions in challenged fish were epithelial erosion and sloughing, and occasionally mild or focal inflammation. No consistent pathology of internal organs was observed. The parasites Ichthyophthirius multifiliis and Ichthyobodo necator were observed in skin samples of a proportion of naïve challenged fish and in Trojans but not in control fish. The presence of these and other known fish pathogens in the skin of PSD-fish was confirmed by high-throughput sequencing analysis. In summary, we have demonstrated that PSD is a transmissible condition. However, even though a number of known fish pathogens were identified in the skin tissues of PSD-fish, the actual causative infectious agent(s) remain(s) unknown. PMID:27391648

Biological Entanglement-Like Effect After Communication of Fish Prior to X-Ray Exposure.

PubMed

Mothersill, Carmel; Smith, Richard; Wang, Jiaxi; Rusin, Andrej; Fernandez-Palomo, Cris; Fazzari, Jennifer; Seymour, Colin

2018-01-01

The phenomenon by which irradiated organisms including cells in vitro communicate with unirradiated neighbors is well established in biology as the radiation-induced bystander effect (RIBE). Generally, the purpose of this communication is thought to be protective and adaptive, reflecting a highly conserved evolutionary mechanism enabling rapid adjustment to stressors in the environment. Stressors known to induce the effect were recently shown to include chemicals and even pathological agents. The mechanism is unknown but our group has evidence that physical signals such as biophotons acting on cellular photoreceptors may be implicated. This raises the question of whether quantum biological processes may occur as have been demonstrated in plant photosynthesis. To test this hypothesis, we decided to see whether any form of entanglement was operational in the system. Fish from 2 completely separate locations were allowed to meet for 2 hours either before or after which fish from 1 location only (group A fish) were irradiated. The results confirm RIBE signal production in both skin and gill of fish, meeting both before and after irradiation of group A fish. The proteomic analysis revealed that direct irradiation resulted in pro-tumorigenic proteomic responses in rainbow trout. However, communication from these irradiated fish, both before and after they had been exposed to a 0.5 Gy X-ray dose, resulted in largely beneficial proteomic responses in completely nonirradiated trout. The results suggest that some form of anticipation of a stressor may occur leading to a preconditioning effect or temporally displaced awareness after the fish become entangled.

Soundscapes and the sense of hearing of fishes.

PubMed

Fay, Richard

2009-03-01

Underwater soundscapes have probably played an important role in the adaptation of ears and auditory systems of fishes throughout evolutionary time, and for all species. These sounds probably contain important information about the environment and about most objects and events that confront the receiving fish so that appropriate behavior is possible. For example, the sounds from reefs appear to be used by at least some fishes for their orientation and migration. These sorts of environmental sounds should be considered much like "acoustic daylight," that continuously bathes all environments and contain information that all organisms can potentially use to form a sort of image of the environment. At present, however, we are generally ignorant of the nature of ambient sound fields impinging on fishes, and the adaptive value of processing these fields to resolve the multiple sources of sound. Our field has focused almost exclusively on the adaptive value of processing species-specific communication sounds, and has not considered the informational value of ambient "noise." Since all fishes can detect and process acoustic particle motion, including the directional characteristics of this motion, underwater sound fields are potentially more complex and information-rich than terrestrial acoustic environments. The capacities of one fish species (goldfish) to receive and make use of such sound source information have been demonstrated (sound source segregation and auditory scene analysis), and it is suggested that all vertebrate species have this capacity. A call is made to better understand underwater soundscapes, and the associated behaviors they determine in fishes. © 2009 ISZS, Blackwell Publishing and IOZ/CAS.

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes

PubMed Central

Li, Tongtong; Long, Meng; Li, Huan; Gatesoupe, François-Joël; Zhang, Xujie; Zhang, Qianqian; Feng, Dongyue; Li, Aihua

2017-01-01

Gut microbiota play key roles in host nutrition and metabolism. However, little is known about the relationship between host genetics, gut microbiota and metabolic profiles. Here, we used high-throughput sequencing and gas chromatography/mass spectrometry approaches to characterize the microbiota composition and the metabolite profiles in the gut of five cyprinid fish species with three different feeding habits raised under identical husbandry conditions. Our results showed that host species and feeding habits significantly affect not only gut microbiota composition but also metabolite profiles (ANOSIM, p ≤ 0.05). Mantel test demonstrated that host phylogeny, gut microbiota, and metabolite profiles were significantly related to each other (p ≤ 0.05). Additionally, the carps with the same feeding habits had more similarity in gut microbiota composition and metabolite profiles. Various metabolites were correlated positively with bacterial taxa involved in food degradation. Our results shed new light on the microbiome and metabolite profiles in the gut content of cyprinid fishes, and highlighted the correlations between host genotype, fish gut microbiome and putative functions, and gut metabolite profiles. PMID:28367147

Quantitative analysis of species specificity of two anti-parvalbumin antibodies for detecting southern hemisphere fish species demonstrating strong phylogenetic association.

PubMed

Liang, Ji; Tan, Chui Choo; Taylor, Steve L; Baumert, Joseph L; Lopata, Andreas L; Lee, N Alice

2017-12-15

This study aimed to develop a novel approach to determine the correlation between the parvalbumin (PAV) contents and their corresponding immunoreactivity (detectability) in southern hemisphere fish species. The immuno-detected PAV contents of the test fish species were estimated by a quantitative SDS-PAGE. A quantitative Enzyme-Linked ImmunoSorbent Assay (ELISA) was formatted to assess relative immunoreactivity of PAV. Sixteen species (forty-three percent) displayed a positive correlation with the anti-cod PAV polyclonal antibody, but no correlation with the anti-carp PAV monoclonal antibody. There was a strong phylogenetic association of the PAV immunoreactivity. Species from the order of Perciformes showed strong binding with both antibodies; whereas species from Salmoniformes, Ophidiiformes, Scombriformes, Scorpaeniformes, and Tetraodontiformes showed weak or no binding. This approach showed for the first time a statistical correlation between the PAV content and the immunoreactivity and allowed to rank the relative species/order specificity of the two antibodies for the southern hemisphere fish PAV. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bifurcation and Control in a Singular Phytoplankton-Zooplankton-Fish Model with Nonlinear Fish Harvesting and Taxation

NASA Astrophysics Data System (ADS)

Meng, Xin-You; Wu, Yu-Qian

In this paper, a delayed differential algebraic phytoplankton-zooplankton-fish model with taxation and nonlinear fish harvesting is proposed. In the absence of time delay, the existence of singularity induced bifurcation is discussed by regarding economic interest as bifurcation parameter. A state feedback controller is designed to eliminate singularity induced bifurcation. Based on Liu’s criterion, Hopf bifurcation occurs at the interior equilibrium when taxation is taken as bifurcation parameter and is more than its corresponding critical value. In the presence of time delay, by analyzing the associated characteristic transcendental equation, the interior equilibrium loses local stability when time delay crosses its critical value. What’s more, the direction of Hopf bifurcation and stability of the bifurcating periodic solutions are investigated based on normal form theory and center manifold theorem, and nonlinear state feedback controller is designed to eliminate Hopf bifurcation. Furthermore, Pontryagin’s maximum principle has been used to obtain optimal tax policy to maximize the benefit as well as the conservation of the ecosystem. Finally, some numerical simulations are given to demonstrate our theoretical analysis.

Broadband and polarization reflectors in the lookdown, Selene vomer

PubMed Central

Zhao, Shulei; Brady, Parrish Clawson; Gao, Meng; Etheredge, Robert Ian; Kattawar, George W.; Cummings, Molly E.

2015-01-01

Predator evasion in the open ocean is difficult because there are no objects to hide behind. The silvery surface of fish plays an important role in open water camouflage. Various models have been proposed to account for the broadband reflectance by the fish skin that involve one-dimensional variations in the arrangement of guanine crystal reflectors, yet the three-dimensional organization of these guanine platelets have not been well characterized. Here, we report the three-dimensional organization and the optical properties of integumentary guanine platelets in a silvery marine fish, the lookdown (Selene vomer). Our structural analysis and computational modelling show that stacks of guanine platelets with random yaw angles in the fish skin produce broadband reflectance via colour mixing. Optical axes of the guanine platelets and the collagen layer are aligned closely and provide bulk birefringence properties that influence the polarization reflectance by the skin. These data demonstrate how the lookdown preserves or alters polarization states at different incident polarization angles. These optical properties resulted from the organization of these guanine platelets and the collagen layer may have implications for open ocean camouflage in varying light fields. PMID:25673301

Intraguild Predation Dynamics in a Lake Ecosystem Based on a Coupled Hydrodynamic-Ecological Model: The Example of Lake Kinneret (Israel)

PubMed Central

Makler-Pick, Vardit; Hipsey, Matthew R.; Zohary, Tamar; Carmel, Yohay; Gal, Gideon

2017-01-01

The food web of Lake Kinneret contains intraguild predation (IGP). Predatory invertebrates and planktivorous fish both feed on herbivorous zooplankton, while the planktivorous fish also feed on the predatory invertebrates. In this study, a complex mechanistic hydrodynamic-ecological model, coupled to a bioenergetics-based fish population model (DYCD-FISH), was employed with the aim of revealing IGP dynamics. The results indicate that the predation pressure of predatory zooplankton on herbivorous zooplankton varies widely, depending on the season. At the time of its annual peak, it is 10–20 times higher than the fish predation pressure. When the number of fish was significantly higher, as occurs in the lake after atypical meteorological years, the effect was a shift from a bottom-up controlled ecosystem, to the top-down control of planktivorous fish and a significant reduction of predatory and herbivorous zooplankton biomass. Yet, seasonally, the decrease in predatory-zooplankton biomass was followed by a decrease in their predation pressure on herbivorous zooplankton, leading to an increase of herbivorous zooplankton biomass to an extent similar to the base level. The analysis demonstrates the emergence of non-equilibrium IGP dynamics due to intra-annual and inter-annual changes in the physico-chemical characteristics of the lake, and suggests that IGP dynamics should be considered in food web models in order to more accurately capture mass transfer and trophic interactions. PMID:28353646

Quantification of viable bacterial starter cultures of Virgibacillus sp. and Tetragenococcus halophilus in fish sauce fermentation by real-time quantitative PCR.

PubMed

Udomsil, Natteewan; Chen, Shu; Rodtong, Sureelak; Yongsawatdigul, Jirawat

2016-08-01

Real-time quantitative polymerase chain reaction (qPCR) methods were developed for the quantification of Virgibacillus sp. SK37 and Tetragenococcus halophilus MS33, which were added as starter cultures in fish sauce fermentation. The PCR assays were coupled with propidium monoazide (PMA) treatment of samples to selectively quantify viable cells and integrated with exogenous recombinant Escherichia coli cells to control variabilities in analysis procedures. The qPCR methods showed species-specificity for both Virgibacillus halodenitrificans and T. halophilus as evaluated using 6 reference strains and 28 strains of bacteria isolated from fish sauce fermentation. The qPCR efficiencies were 101.1% for V. halodenitrificans and 90.2% for T. halophilus. The quantification limits of the assays were 10(3) CFU/mL and 10(2) CFU/mL in fish sauce samples with linear correlations over 4 Logs for V. halodenitrificans and T. halophilus, respectively. The matrix effect was not observed when evaluated using fish sauce samples fermented for 1-6 months. The developed PMA-qPCR methods were successfully applied to monitor changes of Virgibacillus sp. SK37 and T. halophilus MS33 in a mackerel fish sauce fermentation model where culture-dependent techniques failed to quantify the starter cultures. The results demonstrated the usability of the methods as practical tools for monitoring the starter cultures in fish sauce fermentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

A rare case of a three way complex variant positive Philadelphia translocation involving chromosome (9;11;22)(q34;p15;q11) in chronic myeloid leukemia: A case report

PubMed Central

Asif, Muhammad; Hussain, Abrar; Rasool, Mahmood

2016-01-01

The t(9;22)(q34;q11) translocation is present in 90–95% of patients with chronic myeloid leukemia (CML). Variant complex translocations have been observed in 5–8% of CML patients, in which a third chromosome other than (9;22) is involved. Imatinib mesylate is the first line breakpoint cluster region-Abelson gene (BCR/ABL)-targeted oral therapy for CML, and may produce a complete response in 70–80% of CML patients in the chronic phase. In the present study, a bone marrow sample was used for conventional cytogenetic analysis, and the fluorescence in situ hybridization (FISH) test was used for BCR/ABL gene detection. A hematological analysis was also performed to determine the white blood cell (WBC) count, red blood cell count, hemoglobin levels, packed and mean cell volumes, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration and platelet values of the patient. The hematological analysis of the patient indicated the increased WBC of 186.5×103 cells/µl, and decreased hemoglobin levels of 11.1 g/dl. The FISH test revealed that 67% cells demonstrated BCR/ABL gene translocation. The patient was treated with 400 mg imatinib mesylate daily, and was monitored at various intervals over a 6-month period. The present study reports the rare case of a patient that demonstrates a three-way Philadelphia chromosome-positive translocation involving 46XY,t(9;11;22)(q34;p15;q11)[10], alongside CML in the chronic phase. The translocation was analyzed using cytogenetic and FISH tests. PMID:27602125

Cytology specimens offer an effective alternative to formalin-fixed tissue as demonstrated by novel automated detection for ALK break-apart FISH testing and immunohistochemistry in lung adenocarcinoma.

PubMed

Rosenblum, Frida; Hutchinson, Lloyd M; Garver, Joann; Woda, Bruce; Cosar, Ediz; Kurian, Elizabeth M

2014-11-01

Minimally invasive sampling by cytology or core needle biopsy often provides an initial diagnosis for treatment in patients with lung nodules. From these limited specimens, multiple molecular studies are frequently requested. Current guidelines from the US Food and Drug Administration recommend using formalin-fixed paraffin-embedded tissue sections for the detection of anaplastic lymphoma kinase (ALK) gene rearrangement by fluorescence in situ hybridization (FISH). The authors compared alcohol-fixed and formalin-fixed cytology specimens using a novel automated detection for ALK rearrangements by FISH and immunohistochemistry (IHC). ALK FISH testing was performed on 129 lung adenocarcinomas from 71 cytology cases and 58 biopsy/resection specimens using Papanicolaou staining with integrated cytomorphology. IHC with the ALK D5F3 antibody was performed on cases with residual material (88 of 129 cases). The mean age of the patients was 66 years; there were 62 women and 67 men. ALK gene rearrangement was present in 4% of cytology specimens (3 of 71 specimens) and 7% of surgical specimens (4 of 58 specimens). FISH in 13 cases was technically unsuccessful. Of the 7 FISH-positive cases, only 2 cytology cases (4%) and 2 surgical cases (6%) were found to be positive with the ALK antibody, demonstrating 80% concordance. The one case found to be negative for ALK by IHC demonstrated a variant rearrangement of the ALK 2p23 gene locus by FISH. The results of the current study validate the usefulness of alcohol-fixed and/or formalin-fixed cytology specimens for ALK rearrangement by a novel automated FISH method. IHC using the D5F3 antibody for ALK is specific in this limited cohort. The authors also demonstrated that alcohol-fixed cytology specimens can be used for ALK rearrangement by automated FISH, alone or in conjunction with IHC. © 2014 American Cancer Society.

How Are Fishing Patterns and Fishing Communities Responding to Climate Change? A Test Case from the Northwest Atlantic

NASA Astrophysics Data System (ADS)

Young, T.; Fuller, E.; Coleman, K.; Provost, M.; Pinsky, M. L.; St Martin, K.

2016-02-01

We know climate is changing and fish are moving in response to those changes. But we understand less about how harvesters are responding to these changes in fish distribution and the ramifications of those changes for fishing communities. Ecological and evolutionary theory suggests that organisms must move, adapt, or die in response to environmental changes, and a related frame may be relevant for human harvesters in the face of climate change. Furthermore, research suggests that there may be a portfolio effect: a wider diversity of catch may buffer harvesters from some effects of climate change. To get at these questions, we explored changes in fishing patterns among commercial fishing communities in the northeast US from 1997-2014 using NOAA-collected logbook data. We found that communities using more mobile gear (large trawl vessels) demonstrated a greater range of latitudinal shift than communities using any other gear. Latitudinal shift was also inversely related to species diversity of catch and port latitude in those communities: southern communities that caught few species shifted dramatically northward, and northern communities that caught many species did not demonstrate marked latitudinal shifts. Those communities that demonstrated larger latitudinal shifts also demonstrated smaller changes in catch composition than their more stationary counterparts. We also found that vessels are indeed leaving many, but not all, fisheries in this region. These results suggest that harvesters are moving, adapting, and leaving fisheries, and that there does appear to be a portfolio effect, with catch diversity mediating some of these responses. While these changes in fishing patterns cannot all be directly attributed to climate change per se, marine fishes in this region are shifting north rapidly, as is expected under climate change. This study provides a valuable test case for exploring the potential ramifications of climate change on coastal socio-ecological systems.

Prey selection by two benthic fish species in a Mato Grosso stream, Rio de Janeiro, Brazil.

PubMed

Rezende, Carla Ferreira; Mazzoni, Rosana; Caramaschi, Erica Pellegrini; Rodrigues, Daniela; Moraes, Maíra

2011-12-01

Key to understand predator choice is the relationship between predator and prey abundance. There are few studies related to prey selection and availability. Such an approach is still current, because the ability to predict aspects of the diet in response to changes in prey availability is one of the major problems of trophic ecology. The general objective of this study was to evaluate prey selection by two species (Characidium cf. vidali and Pimelodella lateristriga) of the Mato Grosso stream, in Saquarema, Rio de Janeiro, Brazil. Benthos and fishes were collected in June, July and September of 2006 and January and February of 2007. Fish were collected with electric fishing techniques and benthos with a surber net. Densities of benthic organisms were expressed as the number of individuals per/m2. After sampling, the invertebrates were fixed in 90% ethanol, and, in the laboratory, were identified to the lowest taxonomical level. Approximately, seventy individuals from each species were selected randomly in each month. Fishes were fixed in 10% formalin in the field and transferred to 70 degrees GL ethanol in the laboratory. Fishes had their stomachs removed for subsequent analysis. Fish diet was described according to the numeric frequency method. The Manly Electivity Index was applied in order to verify prey selection. The most abundant families in both benthos and diet of both fish species were the same, indicating that these species consume mainly most abundant prey in the environment. We concluded that prey selection occurs even for preys that had small abundance in the environment. However, it is the availability of the macroinvertebrate resources that determines the major composition of items in diet of fish, demonstrating that the abundance is the factor that most influences the choice of prey.

Multiple biomarker responses in Prochilodus lineatus subjected to short-term in situ exposure to streams from agricultural areas in Southern Brazil.

PubMed

Vieira, Carlos Eduardo Delfino; Costa, Patrícia Gomes; Lunardelli, Bruna; de Oliveira, Luciana Fernandes; Cabrera, Liziara da Costa; Risso, Wagner Ezequiel; Primel, Ednei Gilberto; Meletti, Paulo César; Fillmann, Gilberto; Martinez, Claudia Bueno dos Reis

2016-01-15

In order to assess the quality of streams susceptible to contamination by pesticides we apply biochemical and genotoxic biomarkers in the Neotropical fish Prochilodus lineatus submitted to in situ tests. Fish were caged, for 96 h, in two streams located in areas with intensive use of pesticides, the Apertados (AP) and the Jacutinga (JC), and in a small stream (Godoy stream — GD) found inside a forest fragment adjacent to a State Park. Biochemical parameters, such as biotransformation enzymes 7-ethoxyresorufin-O-deethylase (EROD) and glutathione-S-transferase (GST), non-protein thiols (NPSH), lipoperoxidation (LPO), protein carbonylation (PCO) and acetylcholinesterase (AChE) were evaluated in various fish organs, as well as genotoxic biomarkers (damage to DNA and occurrence of micronuclei and erythrocyte nuclear abnormalities). Samples of water and sediment were collected for analysis of metals (Cu, Cr, Pb, Ni, Mn, Cd and Zn), organochloride pesticides, and triazine and glyphosate herbicides. We observed an increase in liver GST activity in fish at AP and gill GST activity in fish at JC. An increase in liver LPO was also observed in fish exposed to AP and JC. The same animals also exhibited increased DNA damage and erythrocyte nuclear abnormalities (ENAs) compared to the fish kept in GD. A number of compounds showed concentrations higher than the permitted levels, in particular, dichlorodiphenyltrichloroethane (DDT), its metabolites dichlorodiphenyldichloroethylene (DDE) and dichlorodiphenyldichloroethane (DDD), hexachlorocyclohexanes (HCH), heptachloride, diclofluanid and aldrins. These pesticides were detected at higher concentrations in water and sediment samples from AP, followed by JC and GD. The Integrated Biomarker Response Index (IBR) indicated that AP and JC (AP: 21.7 > JC: 18.5 > GD: 12.6) have the worst environmental quality. Integrated biomarker analysis revealed that the alterations observed related well with the levels of environmental contaminants, demonstrating the effectiveness of this biomonitoring approach.

Modification of the plasma complement protein profile by exogenous estrogens is indicative of a compromised immune competence in marine medaka (Oryzias melastigma).

PubMed

Dong, Miao; Seemann, Frauke; Humble, Joseph L; Liang, Yimin; Peterson, Drew R; Ye, Rui; Ren, Honglin; Kim, Hui-Su; Lee, Jae-Seong; Au, Doris W T; Lam, Yun Wah

2017-11-01

Growing evidence suggests that the immune system of teleost is vulnerable to xenoestrogens, which are ubiquitous in the marine environment. This study detected and identified the major circulatory immune proteins deregulated by 17α-ethinylestradiol (EE2), which may be linked to fish susceptibility to pathogens in the marine medaka, Oryzias melastigma. Fish immune competence was determined using a host resistance assay to pathogenic bacteria Edwardsiella tarda. Females were consistently more susceptible to infection-induced mortality than males. Exposure to EE2 could narrow the sex gap of mortality by increasing infection-induced death in male fish. Proteomic analysis revealed that the major plasma immune proteins of adult fish were highly sexually dimorphic. EE2 induced pronounced sex-specific changes in the plasma proteome, with the male plasma composition clearly becoming "feminised". Male plasma was found to contain a higher level of fibrinogens, WAP63 and ependymin-2-like protein, which are involved in coagulation, inflammation and regeneration. For the first time, we demonstrated that expression of C1q subunit B (C1Q), an initiating factor of the classical complement pathway, was higher in males and was suppressed in both sexes in response to EE2 and bacterial challenge. Moreover, cleavage and post-translational modification of C3, the central component of the complement system, could be altered by EE2 treatment in males (C3dg down; C3g up). Multiple regression analysis indicated that C1Q is possibly an indicator of fish survival, which warrants further confirmation. The findings support the potential application of plasma immune proteins for prognosis/diagnosis of fish immune competence. Moreover, this study provides the first biochemical basis of the sex-differences in fish immunity and how these differences might be modified by xenoestrogens. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic diversity based on SSR analysis of the cultured snakehead fish, Channa argus, (Channidae) in China.

PubMed

Zhu, S-R; Li, J-L; Xie, N; Zhu, L-M; Wang, Q; Yue, G-H

2014-02-13

The snakehead fish Channa argus is an important food fish in China. We identified six microsatellite loci for C. argus. These six microsatellite loci and four other microsatellite markers were used to analyze genetic diversity in four cultured populations of C. argus (SD, JX, HN, and ZJ) and determine their relationships. A total of 154 alleles were detected at the 10 microsatellite loci. The average expected and observed heterozygosities varied from 0.70-0.84 and 0.69-0.83, respectively, and polymorphism information content ranged between 0.66 and 0.82 in the four populations, indicating high genetic diversity. Population JX deviated from mutation-drift equilibrium and may have experienced a recent bottleneck. Analysis of pairwise genetic differentiation revealed FST values that ranged from 0.028 to 0.100, which indicates a moderate level of genetic differentiation. The largest distances were observed between populations HN and SD, whereas the smallest distances were obtained between populations HN and JX. Genetic clustering analysis demonstrated that the ZJ and HN populations probably share the same origin. This information about the genetic diversity within each of the four populations, and their genetic relationships will be useful for future genetic improvement of C. argus through selective breeding.

Semi-automated scoring of triple-probe FISH in human sperm using confocal microscopy.

PubMed

Branch, Francesca; Nguyen, GiaLinh; Porter, Nicholas; Young, Heather A; Martenies, Sheena E; McCray, Nathan; Deloid, Glen; Popratiloff, Anastas; Perry, Melissa J

2017-09-01

Structural and numerical sperm chromosomal aberrations result from abnormal meiosis and are directly linked to infertility. Any live births that arise from aneuploid conceptuses can result in syndromes such as Kleinfelter, Turners, XYY and Edwards. Multi-probe fluorescence in situ hybridization (FISH) is commonly used to study sperm aneuploidy, however manual FISH scoring in sperm samples is labor-intensive and introduces errors. Automated scoring methods are continuously evolving. One challenging aspect for optimizing automated sperm FISH scoring has been the overlap in excitation and emission of the fluorescent probes used to enumerate the chromosomes of interest. Our objective was to demonstrate the feasibility of combining confocal microscopy and spectral imaging with high-throughput methods for accurately measuring sperm aneuploidy. Our approach used confocal microscopy to analyze numerical chromosomal abnormalities in human sperm using enhanced slide preparation and rigorous semi-automated scoring methods. FISH for chromosomes X, Y, and 18 was conducted to determine sex chromosome disomy in sperm nuclei. Application of online spectral linear unmixing was used for effective separation of four fluorochromes while decreasing data acquisition time. Semi-automated image processing, segmentation, classification, and scoring were performed on 10 slides using custom image processing and analysis software and results were compared with manual methods. No significant differences in disomy frequencies were seen between the semi automated and manual methods. Samples treated with pepsin were observed to have reduced background autofluorescence and more uniform distribution of cells. These results demonstrate that semi-automated methods using spectral imaging on a confocal platform are a feasible approach for analyzing numerical chromosomal aberrations in sperm, and are comparable to manual methods. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Selective uptake and biological consequences of environmentally relevant antidepressant pharmaceutical exposures on male fathead minnows

USGS Publications Warehouse

Schultz, M.M.; Painter, M.M.; Bartell, S.E.; Logue, A.; Furlong, E.T.; Werner, S.L.; Schoenfuss, H.L.

2011-01-01

Antidepressant pharmaceuticals have been reported in wastewater effluent at the nanogram to low microgram-per-liter range, and include bupropion (BUP), fluoxetine (FLX), sertraline (SER), and venlafaxine (VEN). To assess the effects of antidepressants on reproductive anatomy, physiology, and behavior, adult male fathead minnows (Pimephales promelas) were exposed for 21 days either to a single concentration of the antidepressants FLX, SER, VEN, or BUP, or to an antidepressant mixture. The data demonstrated that exposure to VEN (305. ng/L and 1104. ng/L) and SER (5.2. ng/L) resulted in mortality. Anatomical alterations were noted within the testes of fish exposed to SER and FLX, both modulators of the neurotransmitter serotonin. Additionally, FLX at 28. ng/L induced vitellogenin in male fish-a common endpoint for estrogenic endocrine disruption. Significant alterations in male secondary sex characteristics were noted with single exposures. Effects of single compound exposures neither carried over, nor became additive in the antidepressant mixtures, and reproductive behavior was not affected. Analysis of brain tissues from the exposed fish suggested increased uptake of FLX, SER and BUP and minimal uptake of VEN when compared to exposure water concentrations. Furthermore, the only metabolite detected consistently in the brain tissues was norfluoxetine. Similar trends of uptake by brain tissue were observed when fish were exposed to antidepressant mixtures. The present study demonstrates that anatomy and physiology, but not reproductive behavior, can be disrupted by exposure to environmental concentrations of some antidepressants. The observation that antidepressant uptake into fish tissues is selective may have consequences on assessing the mode-of-action and effects of these compounds in future studies. ?? 2011 Elsevier B.V.

Kernel analysis of partial least squares (PLS) regression models.

PubMed

Shinzawa, Hideyuki; Ritthiruangdej, Pitiporn; Ozaki, Yukihiro

2011-05-01

An analytical technique based on kernel matrix representation is demonstrated to provide further chemically meaningful insight into partial least squares (PLS) regression models. The kernel matrix condenses essential information about scores derived from PLS or principal component analysis (PCA). Thus, it becomes possible to establish the proper interpretation of the scores. A PLS model for the total nitrogen (TN) content in multiple Thai fish sauces is built with a set of near-infrared (NIR) transmittance spectra of the fish sauce samples. The kernel analysis of the scores effectively reveals that the variation of the spectral feature induced by the change in protein content is substantially associated with the total water content and the protein hydration. Kernel analysis is also carried out on a set of time-dependent infrared (IR) spectra representing transient evaporation of ethanol from a binary mixture solution of ethanol and oleic acid. A PLS model to predict the elapsed time is built with the IR spectra and the kernel matrix is derived from the scores. The detailed analysis of the kernel matrix provides penetrating insight into the interaction between the ethanol and the oleic acid.

Exploring Spatiotemporal Trends in Commercial Fishing Effort of an Abalone Fishing Zone: A GIS-Based Hotspot Model

PubMed Central

Jalali, M. Ali; Ierodiaconou, Daniel; Gorfine, Harry; Monk, Jacquomo; Rattray, Alex

2015-01-01

Assessing patterns of fisheries activity at a scale related to resource exploitation has received particular attention in recent times. However, acquiring data about the distribution and spatiotemporal allocation of catch and fishing effort in small scale benthic fisheries remains challenging. Here, we used GIS-based spatio-statistical models to investigate the footprint of commercial diving events on blacklip abalone (Haliotis rubra) stocks along the south-west coast of Victoria, Australia from 2008 to 2011. Using abalone catch data matched with GPS location we found catch per unit of fishing effort (CPUE) was not uniformly spatially and temporally distributed across the study area. Spatial autocorrelation and hotspot analysis revealed significant spatiotemporal clusters of CPUE (with distance thresholds of 100’s of meters) among years, indicating the presence of CPUE hotspots focused on specific reefs. Cumulative hotspot maps indicated that certain reef complexes were consistently targeted across years but with varying intensity, however often a relatively small proportion of the full reef extent was targeted. Integrating CPUE with remotely-sensed light detection and ranging (LiDAR) derived bathymetry data using generalized additive mixed model corroborated that fishing pressure primarily coincided with shallow, rugose and complex components of reef structures. This study demonstrates that a geospatial approach is efficient in detecting patterns and trends in commercial fishing effort and its association with seafloor characteristics. PMID:25992800

Immunopathogenesis of fish allergy: identification of fish-allergic adults by skin test and radioallergosorbent test.

PubMed

Helbling, A; McCants, M L; Musmand, J J; Schwartz, H J; Lehrer, S B

1996-07-01

As the consumption of fish increases in the United States, the importance of allergic reactions to fish has become clear. Since most previous studies on fish allergy have focused on children reacting mainly to codfish, there is a need to investigate allergic reactions to other fish in adults. To identify fish-allergic adults, and to assess cross-reactivity among different species of fish by RAST inhibition. Thirty-nine individuals who reported fish allergy were selected for study; 32 (82%) were atopic as defined by two or more positive skin tests to common inhalant allergens and a history of allergic reactions and 33 (85%) experienced allergic symptoms within 30 minutes after ingesting fish. The most frequently reported symptoms were hives (69%), itching (69%), and wheezing/chest tightness (54%). Study subjects were skin tested with fish extracts and their sera assayed for IgE antibodies to different fish species. Thirty-six (92%) of the subjects tested had a positive skin test to at least one of 17 fish extracts tested; 9/35 (26%) reacted to all 17 extracts. Of the atopic (two or more positive skin tests to common inhalant allergens plus a personal and/or family history of allergy) and nonatopic fish-tolerant controls, 20/26 (77%) reacted by skin test to one or more fish extracts tested; the most prevalent positive reaction was to anchovy (73%). A significant correlation (P < .01) was observed between skin test reactivity of fish-allergic subjects to most fish extracts and fish RAST reactions. Radioallergosorbent inhibition testing demonstrated significant cross-reactivity among pollack, salmon, trout, and tuna; and between mackerel and anchovy. These results suggest that fish-allergic subjects may be clinically sensitive to more than one species of fish. Skin test reactivity to fish by itself is not an adequate criterion for the confirmation of clinically relevant fish allergy; consequently, fish-allergic subjects with positive skin tests to several fish species should exercise caution when eating fish until tolerance can be demonstrated by double-blind, placebo-controlled food challenge, at the patient's earliest convenience.

The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors.

PubMed

Pratte, Zoe A; Besson, Marc; Hollman, Rebecca D; Stewart, Frank J

2018-05-01

Teleost fish represent the most diverse of the vertebrate groups and play important roles in food webs, as ecosystem engineers, and as vectors for microorganisms. However, the microbial ecology of fishes remains underexplored for most host taxa and for certain niches on the fish body. This is particularly true for the gills, the key sites of respiration and waste exchange in fishes. Here we provide a comprehensive analysis of the gill microbiome. We focus on ecologically diverse taxa from coral reefs around Moorea, sampling the gills and intestines of adults and juveniles representing 15 families. The gill microbiome composition differed significantly from that of the gut for both adults and juveniles, with fish-associated niches having lower alpha diversity values and higher beta diversity values than those for seawater, sediment, and alga-associated microbiomes. Of ∼45,000 operational taxonomic units (OTUs) detected across all samples, 11% and 13% were detected only in the gill and the intestine, respectively. OTUs most enriched in the gill included members of the gammaproteobacterial genus Shewanella and the family Endozoicimonaceae In adult fish, both gill and intestinal microbiomes varied significantly among host species grouped by diet category. Gill and intestinal microbiomes from the same individual were more similar to one another than to gill and intestinal microbiomes from different individuals. These results demonstrate that distinct body sites are jointly influenced by host-specific organizing factors operating at the level of the host individual. The results also identify taxonomic signatures unique to the gill and the intestine, confirming fish-associated niches as distinct reservoirs of marine microbial diversity. IMPORTANCE Fish breathe and excrete waste through their gills. The gills are also potential sites of pathogen invasion and colonization by other microbes. However, we know little about the microbial communities that live on the gill and the factors shaping their diversity. Focusing on ecologically distinct types of coral reef fish, we provide a comprehensive analysis of the fish gill microbiome. By comparison to microbiomes of the gut and the surrounding environment, we identify microbes unique to the gill niche. These microbes may be targets for further studies to determine the contribution of the microbiome to waste exchange or host immunity. We also show that despite exhibiting a unique taxonomic signature, the gill microbiome is influenced by factors that also influence the gut microbiome. These factors include the specific identity of the host individual. These results suggest basic principles describing how association with fishes structures the composition of microbial communities. Copyright © 2018 American Society for Microbiology.

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet

PubMed Central

2011-01-01

Background Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax). Results We report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies. Conclusions Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies. PMID:22017880

Isolation and identification of a lethal rhabdovirus from farmed rice field eels Monopterus albus.

PubMed

Ou, Tong; Zhu, Ruo-Lin; Chen, Zhong-Yuan; Zhang, Qi-Ya

2013-11-06

We provide the first description of a virus responsible for a systemic hemorrhagic disease causing high mortality in farmed rice field eels Monopterus albus in China. Typical signs exhibited by the diseased fish were extensive hemorrhages in the skin and viscera and some neurological signs, such as loss of equilibrium and disorganized swimming. Histopathological examination revealed various degrees of necrosis within the spleen and liver. Virus isolation was attempted from visceral tissues of diseased fish by inoculation on 6 fish cell lines. Typical cytopathic effects (CPE) were produced in bluegill fry (BF2) cells, so this cell line was chosen for further isolation and propagation of the virus. Electron microscopy observation showed that the negative stained viral particles had the characteristic bullet shape of rhabdoviruses and an estimated size of 60 × 120 nm. We therefore tentatively refer to this virus as Monopterus albus rhabdovirus (MoARV). Molecular characterization of MoARV, including sequence analysis of the nucleoprotein (N), phosphoprotein (P), and glycoprotein (G) genes, revealed 94.5 to 97.3% amino acid similarity to that of Siniperca chuatsi rhabdovirus. Phylogenetic analysis based on the amino acid sequences of N and G proteins indicated that MoARV should be a member of the genus Vesiculovirus. Koch's postulates were fulfilled by infecting healthy rice field eels with MoARV, which produced an acute infection. RT-PCR analysis demonstrated that MoARV RNA could be detected in both naturally and experimentally infected fish. The data suggest that MoARV was the causative pathogen of the disease.

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes.

PubMed

Thomsen, Philip Francis; Møller, Peter Rask; Sigsgaard, Eva Egelyng; Knudsen, Steen Wilhelm; Jørgensen, Ole Ankjær; Willerslev, Eske

2016-01-01

Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188-918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity-especially in polar ecosystems.

DEVELOPMENT OF STANDARDIZED LARGE RIVER BIOASSESSMENT PROTOCOLS (LR-BP) FOR FISH ASSEMBLAGES

EPA Science Inventory

We conducted research comparing several methods currently in use for the bioassessment and monitoring of fish and benthic macroinvertebrate assemblages for large rivers. Fish data demonstrate that electrofishing 1000 m of shoreline is sufficient for bioassessments on boatable ri...

Comprehensive Analysis of ETS Family Members in Melanoma by Fluorescence In Situ Hybridization Reveals Recurrent ETV1 Amplification

PubMed Central

Mehra, Rohit; Dhanasekaran, Saravana M; Palanisamy, Nallasivam; Vats, Pankaj; Cao, Xuhong; Kim, Jung H; Kim, David SL; Johnson, Timothy; Fullen, Douglas R; Chinnaiyan, Arul M

2013-01-01

E26 transformation-specific (ETS) transcription factors are known to be involved in gene aberrations in various malignancies including prostate cancer; however, their role in melanoma oncogenesis has yet to be fully explored. We have completed a comprehensive fluorescence in situ hybridization (FISH)-based screen for all 27 members of the ETS transcription factor family on two melanoma tissue microarrays, representing 223 melanomas, 10 nevi, and 5 normal skin tissues. None of the melanoma cases demonstrated ETS fusions; however, 6 of 114 (5.3%) melanomas were amplified for ETV1 using a break-apart FISH probe. For the six positive cases, locus-controlled FISH probes revealed that two of six cases were amplified for the ETV1 region, whereas four cases showed copy gains of the entire chromosome 7. The remaining 26 ETS family members showed no chromosomal aberrations by FISH. Quantitative polymerase chain reaction showed an average 3.4-fold (P value = .00218) increased expression of ETV1 in melanomas, including the FISH ETV1-amplified cases, when compared to other malignancies (prostate, breast, and bladder carcinomas). These data suggest that a subset of melanomas overexpresses ETV1 and amplification of ETV1 may be one mechanism for achieving high gene expression. PMID:23908683

Effect of industrial processing on the IgE reactivity of three commonly consumed Mo-roccan fish species in Fez region.

PubMed

Mejrhit, N; Azdad, O; Aarab, L

2018-03-02

Objectives. The aim of this work was to study the effect of industrial processing on the allergenicity of three commonly consumed Moroccan fish species in Fez region (sardine, common pandora, and shrimp). Methods. This work was conducted by a sera-bank obtained from 1248 patients recruited from Fez Hospitals. Their sera were analyzed for specific IgE binding to raw fish extracts. Among them, 60 patients with higher specific IgE levels were selected, and used to estimate the binding variation of IgE to these products under several processing (frying, cooking, canning, marinade, and fermentation) using ELISA analysis. Results. ELISA results demonstrated that all the studied processing cause a reduction in the immunoreactivity of human IgE to fish products, with a high action with marinade and fermentation compared to other processing. This alteration was also observed with rabbit IgG in all processed products, showing that the maximum reduction was marked in fermented sardine with 64.5%, in cooked common pandora with 58%, and in fermented shrimp with 69.2%. Conclusion. In conclusion, our study has shown that the allergenicity of the three studied fish could be reduced by different industrial processes with different degrees.

A review of the global relationship among freshwater fish, autotrophic activity, and regional climate

USGS Publications Warehouse

Deines, Andrew M.; Bunnell, David B.; Rogers, Mark W.; Beard, T. Douglas; Taylor, William W.

2015-01-01

The relationship between autotrophic activity and freshwater fish populations is an important consideration for ecologists describing trophic structure in aquatic communities, fisheries managers tasked with increasing sustainable fisheries development, and fish farmers seeking to maximize production. Previous studies of the empirical relationships of autotrophic activity and freshwater fish yield have found positive relationships but were limited by small sample sizes, small geographic scopes, and the inability to compare patterns among many types of measurement techniques. Individual studies and reviews have also lacked consistent consideration of regional climate factors which may inform relationships between fisheries and autotrophic activity. We compiled data from over 700 freshwater systems worldwide and used meta-analysis and linear models to develop a comprehensive global synthesis between multiple metrics of autotrophic activity, fisheries, and climate indicators. Our results demonstrate that multiple metrics of fish (i.e., catch per unit effort, yield, and production) increase with autotrophic activity across a variety of fisheries. At the global scale additional variation in this positive relationship can be ascribed to regional climate differences (i.e., temperature and precipitation) across systems. Our results provide a method and proof-of-concept for assessing inland fisheries production at the global scale, where current estimates are highly uncertain, and may therefore inform the continued sustainable use of global inland fishery resources.

FISH Finder: a high-throughput tool for analyzing FISH images

PubMed Central

Shirley, James W.; Ty, Sereyvathana; Takebayashi, Shin-ichiro; Liu, Xiuwen; Gilbert, David M.

2011-01-01

Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes. Availability: FISH Finder is a standalone MATLAB application and platform independent software. The program is freely available from: http://code.google.com/p/fishfinder/downloads/list Contact: gilbert@bio.fsu.edu PMID:21310746

Comparative myology of the unicornfishes, Naso (Acanthuridae, Percomorpha), with implications for phylogenetic analysis.

PubMed

Borden, W Calvin

1999-02-01

Striated muscles of 15 species of unicornfishes (Naso, Acanthuridae) are described in detail. Of 93 muscles dissected, only five demonstrate intrageneric variation, providing only ten characters suitable for phylogenetic analysis. Thus, myology appears to be highly conservative at the species level and has been so for approximately 50-55 million years in this particular group of fishes. Furthermore, myology is static relative to osteology in Naso and at any taxonomic rank within fishes, implying osteology provides a larger but not necessarily more valuable data source for systematic studies. Although important for their epistomological value, these descriptions provide a basis for further studies ranging from functional, comparative, and systematic analyses, ultimately with the potential to address questions of historical ecology (i.e., speciation, adaptation, coevolution) within Naso. J. Morphol. 239:191-224, 1999. © 1999 Wiley-Liss, Inc. Copyright © 1999 Wiley-Liss, Inc.

Studying fish near ocean energy devices using underwater video

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matzner, Shari; Hull, Ryan E.; Harker-Klimes, Genevra EL

The effects of energy devices on fish populations are not well-understood, and studying the interactions of fish with tidal and instream turbines is challenging. To address this problem, we have evaluated algorithms to automatically detect fish in underwater video and propose a semi-automated method for ocean and river energy device ecological monitoring. The key contributions of this work are the demonstration of a background subtraction algorithm (ViBE) that detected 87% of human-identified fish events and is suitable for use in a real-time system to reduce data volume, and the demonstration of a statistical model to classify detections as fish ormore » not fish that achieved a correct classification rate of 85% overall and 92% for detections larger than 5 pixels. Specific recommendations for underwater video acquisition to better facilitate automated processing are given. The recommendations will help energy developers put effective monitoring systems in place, and could lead to a standard approach that simplifies the monitoring effort and advances the scientific understanding of the ecological impacts of ocean and river energy devices.« less

Over-the-counter fish oil use in a county hospital: Medication use evaluation and efficacy analysis

PubMed Central

Tatachar, Amulya; Pio, Margaret; Yeung, Denise; Moss, Elizabeth; Chow, Diem; Boatright, Steven; Quinones, Marissa; Mathew, Annie; Hulstein, Jeffrey; Adams-Huet, Beverley; Ahmad, Zahid

2016-01-01

BACKGROUND Little is known about the use and effectiveness of over-the-counter (OTC) fish oil supplements for triglyceride (TG) lowering. OBJECTIVES To (1) perform a medication-use evaluation (MUE) and (2) assess the efficacy of OTC fish oil. METHODS Retrospective, observational cohort study using electronic medical records and the pharmacy database from Parkland Health and Hospital System in Dallas, Texas. Parkland is a tax-supported county institution that provides patients with single-brand OTC fish oil. Two separate analyses were conducted. Six hundred seventeen patients (prescribed fish oil between July 1, 2012, and August 31, 2012) were included in the MUE analysis and 235 patients (109 fish oil, 72 fenofibrate, and 54 gemfibrozil, prescribed between January 1, 2012, and July 31, 2013) were included in the efficacy analysis. The main outcome measure for the MUE was fish oil prescribing habits including dosages and patient adherence, as defined by medication possession ratio. The main outcome measure for the efficacy analysis was change in lipids measured using the last value before fish oil treatment and the first value after fish oil treatment. RESULTS MUE: 617 patients received prescriptions for OTC fish oil. Sixty-four percent were prescribed a total daily dose of 2000 mg. Only 25% of patients were adherent. Efficacy analysis: despite being prescribed suboptimal doses, fish oil reduced TGs by 29% (95% confidence interval, 34.3–22.7). Compared with fish oil therapy, fibrate therapy resulted in a greater TG reduction: 48.5% (55.1–41.0) with fenofibrate and 49.8% (57.6–40.5) with gemfibrozil (P < 0001, both medications compared with fish oil). CONCLUSIONS Health care providers prescribe suboptimal doses of fish oil, and adherence is poor. Even at low doses (2 g/d), though, fish oil lowers TGs by 29%. PMID:26073390

Contour matching for a fish recognition and migration-monitoring system

NASA Astrophysics Data System (ADS)

Lee, Dah-Jye; Schoenberger, Robert B.; Shiozawa, Dennis; Xu, Xiaoqian; Zhan, Pengcheng

2004-12-01

Fish migration is being monitored year round to provide valuable information for the study of behavioral responses of fish to environmental variations. However, currently all monitoring is done by human observers. An automatic fish recognition and migration monitoring system is more efficient and can provide more accurate data. Such a system includes automatic fish image acquisition, contour extraction, fish categorization, and data storage. Shape is a very important characteristic and shape analysis and shape matching are studied for fish recognition. Previous work focused on finding critical landmark points on fish shape using curvature function analysis. Fish recognition based on landmark points has shown satisfying results. However, the main difficulty of this approach is that landmark points sometimes cannot be located very accurately. Whole shape matching is used for fish recognition in this paper. Several shape descriptors, such as Fourier descriptors, polygon approximation and line segments, are tested. A power cepstrum technique has been developed in order to improve the categorization speed using contours represented in tangent space with normalized length. Design and integration including image acquisition, contour extraction and fish categorization are discussed in this paper. Fish categorization results based on shape analysis and shape matching are also included.

Chromosomal microarray analysis as the first-tier test for the identification of pathogenic copy number variants in chromosome 9 pericentric regions and its challenge.

PubMed

Wang, Jia-Chi; Boyar, Fatih Z

2016-01-01

Chromosomal microarray analysis (CMA) has been recommended and practiced routinely in the large reference laboratories of U.S.A. as the first-tier test for the postnatal evaluation of individuals with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. Using CMA as a diagnostic tool and without a routine setting of fluorescence in situ hybridization with labeled bacterial artificial chromosome probes (BAC-FISH) in the large reference laboratories becomes a challenge in the characterization of chromosome 9 pericentric region. This region has a very complex genomic structure and contains a variety of heterochromatic and euchromatic polymorphic variants. These variants were usually studied by G-banding, C-banding and BAC-FISH analysis. Chromosomal microarray analysis (CMA) was not recommended since it may lead to false positive results. Here, we presented a cohort of four cases, in which high-resolution CMA was used as the first-tier test or simultaneously with G-banding analysis on the proband to identify pathogenic copy number variants (CNVs) in the whole genome. CMA revealed large pathogenic CNVs from chromosome 9 in 3 cases which also revealed different G-banding patterns between the two chromosome 9 homologues. Although we demonstrated that high-resolution CMA played an important role in the identification of pathogenic copy number variants in chromosome 9 pericentric regions, the lack of BAC-FISH analysis or other useful tools renders significant challenges in the characterization of chromosome 9 pericentric regions. None; it is not a clinical trial, and the cases were retrospectively collected and analyzed.

Impact of treated wastewater reuse and floods on water quality and fish health within a water reservoir in an arid climate.

PubMed

Zaibel, Inbal; Zilberg, Dina; Groisman, Ludmila; Arnon, Shai

2016-07-15

Treated wastewater (TWW) reuse for agricultural irrigation is a well-established approach to coping with water shortages in semi-arid and arid environments. Recently, additional uses of TWW have emerged, including streamflow augmentation and aquatic ecosystem restoration. The purpose of the current study was to evaluate the water quality and fish health, in an artificial reservoir located in an arid climate (the Yeruham Reservoir, Israel), which regularly receives TWW and sporadic winter floods. The temporal distribution of water levels, nutrients and organic micropollutants (OMPs) were measured during the years 2013-2014. OMPs were also measured in sediment and fish tissues. Finally, the status of fish health was evaluated by histopathology. Water levels and quality were mainly influenced by seasonal processes such as floods and evaporation, and not by the discharge of TWW. Out of 16 tested OMPs, estrone, carbamazepine, diclofenac and bezafibrate were found in the reservoir water, but mostly at concentrations below the predicted no-effect concentration (PNEC) for fish. Concentrations of PCBs and dioxins in fish muscle and liver were much lower than the EU maximal permitted concentrations, and similar to concentrations that were found in food fish in Israel and Europe. In the histopathological analysis, there were no evident tissue abnormalities, and low to moderate infection levels of fish parasites were recorded. The results from the Yeruham Reservoir demonstrated a unique model for the mixture effect between TWW reuse and natural floods to support a unique stable and thriving ecosystem in a water reservoir located in an arid region. This type of reservoir can be widely used for recreation, education, and the social and economic development of a rural environment, such as has occurred in the Yeruham region. Copyright © 2016 Elsevier B.V. All rights reserved.

Ecosystem and human health assessment in relation to aquatic environment pollution by heavy metals: case study of the Murmansk region, northwest of the Kola Peninsula, Russia

NASA Astrophysics Data System (ADS)

Moiseenko, T. I.; Morgunov, B. A.; Gashkina, N. A.; Megorskiy, V. V.; Pesiakova, A. A.

2018-06-01

Throughout the Euro-Arctic region of Russia (Murmansk region), there is a substantial increase of metal concentrations in water, which are related to local discharges from the metallurgical and mining industry, transboundary pollution, as well as indirect leaching of elements by acid precipitation. This study collates data to investigate the relationship between surface water contamination by metals, and fish and human health. Fish are used as a biological indicator to show the impact of water pollution by metals on the ecosystem’s health. The etiology of fish and human diseases are related to the water pollution and accumulation of metals in organisms. High concentrations of Ni and Cd in water drives an accumulation of these elements in organs and tissues of fish, especially in kidneys. The relation between the accumulation of Ni in kidneys and the development of fish nephrocalcinosis and fibroelastosis was established. Statistical analysis demonstrated that human populations in cities close in proximity to smelters show the highest incidence of disease. The results of histological, clinical, and post-mortem examination of patients shows the highest content of toxic metals, especially Cd, in livers and kidneys. Our complex investigation of a set of disorders observed in fish and human populations indicates that there is a high probability that the negative impact on human health is caused by prolonged water contamination by heavy metals. As a novel finding, this paper shows that based on the similarity of pathological processes and bioaccumulation of metals in fish and humans, examining the content of heavy metals in fish can be used to confirm etiology and evaluate the potential risk to human health by pollution of surface waters.

The effects of elevated temperature and ocean acidification on the metabolic pathways of notothenioid fish

PubMed Central

Enzor, Laura A.; Hunter, Evan M.

2017-01-01

Abstract The adaptations used by notothenioid fish to combat extreme cold may have left these fish poorly poised to deal with a changing environment. As such, the expected environmental perturbations brought on by global climate change have the potential to significantly affect the energetic demands and subsequent cellular processes necessary for survival. Despite recent lines of evidence demonstrating that notothenioid fish retain the ability to acclimate to elevated temperatures, the underlying mechanisms responsible for temperature acclimation in these fish remain largely unknown. Furthermore, little information exists on the capacity of Antarctic fish to respond to changes in multiple environmental variables. We have examined the effects of increased temperature and pCO2 on the rate of oxygen consumption in three notothenioid species, Trematomus bernacchii, Pagothenia borchgrevinki, and Trematomus newnesi. We combined these measurements with analysis of changes in aerobic and anaerobic capacity, lipid reserves, fish condition, and growth rates to gain insight into the metabolic cost associated with acclimation to this dual stress. Our findings indicated that temperature is the major driver of the metabolic responses observed in these fish and that increased pCO2 plays a small, contributing role to the energetic costs of the acclimation response. All three species displayed varying levels of energetic compensation in response to the combination of elevated temperature and pCO2. While P. borchgrevinki showed nearly complete compensation of whole animal oxygen consumption rates and aerobic capacity, T. newnesi and T. bernacchii displayed only partial compensation in these metrics, suggesting that at least some notothenioids may require physiological trade-offs to fully offset the energetic costs of long-term acclimation to climate change related stressors. PMID:28852515

The effects of elevated temperature and ocean acidification on the metabolic pathways of notothenioid fish.

PubMed

Enzor, Laura A; Hunter, Evan M; Place, Sean P

2017-01-01

The adaptations used by notothenioid fish to combat extreme cold may have left these fish poorly poised to deal with a changing environment. As such, the expected environmental perturbations brought on by global climate change have the potential to significantly affect the energetic demands and subsequent cellular processes necessary for survival. Despite recent lines of evidence demonstrating that notothenioid fish retain the ability to acclimate to elevated temperatures, the underlying mechanisms responsible for temperature acclimation in these fish remain largely unknown. Furthermore, little information exists on the capacity of Antarctic fish to respond to changes in multiple environmental variables. We have examined the effects of increased temperature and p CO 2 on the rate of oxygen consumption in three notothenioid species, Trematomus bernacchii , Pagothenia borchgrevinki , and Trematomus newnesi . We combined these measurements with analysis of changes in aerobic and anaerobic capacity, lipid reserves, fish condition, and growth rates to gain insight into the metabolic cost associated with acclimation to this dual stress. Our findings indicated that temperature is the major driver of the metabolic responses observed in these fish and that increased p CO 2 plays a small, contributing role to the energetic costs of the acclimation response. All three species displayed varying levels of energetic compensation in response to the combination of elevated temperature and p CO 2 . While P. borchgrevinki showed nearly complete compensation of whole animal oxygen consumption rates and aerobic capacity, T. newnesi and T. bernacchii displayed only partial compensation in these metrics, suggesting that at least some notothenioids may require physiological trade-offs to fully offset the energetic costs of long-term acclimation to climate change related stressors.

In vivo regulation of colonic cell proliferation, differentiation, apoptosis, and P27Kip1 by dietary fish oil and butyrate in rats.

PubMed

Hong, Mee Young; Turner, Nancy D; Murphy, Mary E; Carroll, Raymond J; Chapkin, Robert S; Lupton, Joanne R

2015-11-01

We have shown that dietary fish oil is protective against experimentally induced colon cancer, and the protective effect is enhanced by coadministration of pectin. However, the underlying mechanisms have not been fully elucidated. We hypothesized that fish oil with butyrate, a pectin fermentation product, protects against colon cancer initiation by decreasing cell proliferation and increasing differentiation and apoptosis through a p27(Kip1)-mediated mechanism. Rats were provided diets of corn or fish oil, with/without butyrate, and terminated 12, 24, or 48 hours after azoxymethane (AOM) injection. Proliferation (Ki-67), differentiation (Dolichos Biflorus Agglutinin), apoptosis (TUNEL), and p27(Kip1) (cell-cycle mediator) were measured in the same cell within crypts in order to examine the coordination of cell cycle as a function of diet. DNA damage (N(7)-methylguanine) was determined by quantitative IHC analysis. Dietary fish oil decreased DNA damage by 19% (P = 0.001) and proliferation by 50% (P = 0.003) and increased differentiation by 56% (P = 0.039) compared with corn oil. When combined with butyrate, fish oil enhanced apoptosis 24 hours after AOM injection compared with a corn oil/butyrate diet (P = 0.039). There was an inverse relationship between crypt height and apoptosis in the fish oil/butyrate group (r = -0.53, P = 0.040). The corn oil/butyrate group showed a positive correlation between p27(Kip1) expression and proliferation (r = 0.61, P = 0.035). These results indicate the in vivo effect of butyrate on apoptosis and proliferation is dependent on dietary lipid source. These results demonstrate the presence of an early coordinated colonocyte response by which fish oil and butyrate protects against colon tumorigenesis. ©2015 American Association for Cancer Research.

Management and Feasibility Analysis of Smoked Fish Business in Ambon

NASA Astrophysics Data System (ADS)

Nanlohy, Hellen; Apituley, Yolanda M. T. N.; Tapotubun, Alfonsina M.; Reiuwpassa, Frederik; Matrutty, Theodora E. A. A.

2017-10-01

This research aims to examine management and feasibility aspects of smoked fish business in Ambon. By using survey, this research focused on smoked fish business in Negeri Hative Kecil and Silale, known as dried fish producer villages.Primary and secondary data collected by using interview, observation, and recording. Analysis methods used are qualitative descriptive analysis and business feasibility analysis covers NPV, Payback Period (PP), and Break Even Point (BEP). The result shows that most of the smoked fish businessmen do not apply the proper management in their business. Two to three people do all the works (from production to marketing) without a clear job description. Feasibility analysis for smoked fish business in Negeri Hative Kecil shows that NPV is 21.501.053,- PP is 58 days, and Benefit Cost Ratio (B/C) is 1,06. BEP Production is 1,455 kg, and BEP Price is IDR 19,941, while the feasibility analysis for smoked fish business in Desa Silale shows that NPV is 30.745.837,-, PP is 24 days and Benefit Cost Ratio (B/C) is 1,41. BEP Production is 988 kg, and BEP Price is IDR 7,966. Based on the result, the two smoked fish business in Ambon is feasible to be developed. However, good management with clear job description should be applied to improve the business.

Cognition Enhancing Activity of Sulforaphane Against Scopolamine Induced Cognitive Impairment in Zebra Fish (Danio rerio).

PubMed

Rajesh, Venugopalan; Ilanthalir, Sakthivel

2016-10-01

Several epidemiological studies have shown that consumption of large quantities of vegetables especially cruciferous vegetables (Broccoli and Brussels sprouts) can protect against chronic diseases. Sulforaphane, an isothiocynate found in cruciferous vegetables has been demonstrated to have neuroprotective effects in several experimental paradigms. This study was undertaken to examine the effect of sulforaphane on cognitive impairment in zebra fish model using a novel method of fear conditioning. Initially, the normal behaviour of zebra fishes was studied in light-dark tank for 10 min daily for 10 days. Fishes were then divided into seven groups of twelve in each. Group I served as normal, group II served as fear conditioned control, group III and group IV were sulforaphane (25 µM/L) and piracetam (200 mg/L) treated respectively. Group V served as scopolamine (400 µM/L) induced memory impairment fishes. Group VI and VII were sulforaphane (25 µM/L) and piracetam (200 mg/L) treated scopolamine induced memory impairment groups respectively. In normal behavioural analysis, fishes preferred to stay in dark compartment. The average number of entries into the dark and time spent in dark were significantly more. Fishes in group II to VII were individually subjected to fear conditioning passive avoidance task and evaluated for learned task memory. It was observed that the average number of entries into dark and time spent in dark were significantly decreased. After exposure to respective treatment fishes in group III to VII were subjected to cognitive evaluation. There was no significant difference in cognition of group III and IV fishes exposed to sulforaphane and piracetam alone respectively. Fishes exposed to scopolamine showed a significant cognitive impairment. Sulforaphane exposure prior to scopolamine significantly retained the memory of learned task. These findings suggest that sulforaphane might be a promising therapeutic agent for cognitive enhancement in Alzheimer's disease.

A hepatic metabolomics-based diagnostic approach to assess lethal toxicity of dithiocarbamate fungicide polycarbamate in three marine fish species.

PubMed

Hano, Takeshi; Ohkubo, Nobuyuki; Mochida, Kazuhiko

2017-04-01

The present study was performed to evaluate the toxic effect of the dithiocarbamate fungicide polycarbamate (PC) on the hepatic metabolic profiles of three marine fish species, red sea bream (Pagrus major), spotted halibut (Verasper variegatus), and marbled flounder (Pleuronectes yokohamae). First, juvenile fish were exposed to graded concentrations of PC for 96h; the 96-h LC 50 values obtained were 22-29, 239-553, and 301-364µgL -1 for red sea bream, spotted halibut, and marbled flounder, respectively, indicating that red sea bream possessed higher sensitivity to PC than the two benthic species. Second, the fish were exposed to lethal-equivalent concentration (H group) or sub-lethal (one-tenth of the H group concentrations; L group) for 24 and 96h and gas-chromatography based metabolomics approach was employed to explore the crucial biomarker metabolite associated with lethal toxicity. Of the 53 metabolites identified, only reduced glutathione (GSH) was consistently elevated in the H group for the three fish species at 96h. The calculated cut-off value of GSH (mM) based on receiver operating curve analysis between H group and the other treatment groups (control, solvent control, and L group) was obtained at 0.56mM, which allowed to distinguish between the groups with high confidence for the three fish species. These results are the first to demonstrate the potential of using GSH as a possible biomarker metabolite and its usefulness of threshold cut-off value for diagnosing life-threatening health conditions of fish. Copyright © 2016 Elsevier Inc. All rights reserved.

The Relevance of External Quality Assessment for Molecular Testing for ALK Positive Non-Small Cell Lung Cancer: Results from Two Pilot Rounds Show Room for Optimization

PubMed Central

Tembuyser, Lien; Tack, Véronique; Zwaenepoel, Karen; Pauwels, Patrick; Miller, Keith; Bubendorf, Lukas; Kerr, Keith; Schuuring, Ed; Thunnissen, Erik; Dequeker, Elisabeth M. C.

2014-01-01

Background and Purpose Molecular profiling should be performed on all advanced non-small cell lung cancer with non-squamous histology to allow treatment selection. Currently, this should include EGFR mutation testing and testing for ALK rearrangements. ROS1 is another emerging target. ALK rearrangement status is a critical biomarker to predict response to tyrosine kinase inhibitors such as crizotinib. To promote high quality testing in non-small cell lung cancer, the European Society of Pathology has introduced an external quality assessment scheme. This article summarizes the results of the first two pilot rounds organized in 2012–2013. Materials and Methods Tissue microarray slides consisting of cell-lines and resection specimens were distributed with the request for routine ALK testing using IHC or FISH. Participation in ALK FISH testing included the interpretation of four digital FISH images. Results Data from 173 different laboratories was obtained. Results demonstrate decreased error rates in the second round for both ALK FISH and ALK IHC, although the error rates were still high and the need for external quality assessment in laboratories performing ALK testing is evident. Error rates obtained by FISH were lower than by IHC. The lowest error rates were observed for the interpretation of digital FISH images. Conclusion There was a large variety in FISH enumeration practices. Based on the results from this study, recommendations for the methodology, analysis, interpretation and result reporting were issued. External quality assessment is a crucial element to improve the quality of molecular testing. PMID:25386659

Platelet Arachidonic Acid Deficiency May Contribute to Abnormal Platelet Function During Parenteral Fish Oil Monotherapy in a Piglet Model.

PubMed

Turner, Justine M; Field, Catherine J; Goruk, Sue; Wizzard, Pamela; Dicken, Bryan J; Bruce, Aisha; Wales, Paul W

2016-05-01

Fish oil monotherapy has been an advance for treating intestinal failure-associated liver disease (IFALD). However, such patients are at risk of bleeding complications from liver disease and because fish oil can inhibit thrombosis. We have previously reported abnormal platelet function in neonatal piglets given fish oil monotherapy during parenteral nutrition (PN). The purpose of this study was to determine if abnormal fatty acid composition of the platelets could explain the prior observed antiplatelet effect. Neonatal piglets were assigned to 2 treatments: PN with fish oil monotherapy (FO; n = 4) or PN with soy oil (SO; n = 5). On day 14, plasma was collected and platelets isolated by centrifuging. The fatty acid content in plasma and platelet plug were measured using gas liquid chromatography and compared with controls (CON; n = 5). The arachidonic acid (AA) content in the FO group was on average half that of the SO group, in both the platelets (FO, 3.5% vs SO, 7.6%; P = .021; CON, 4.5%-11%) and the plasma (FO, 3.8% vs SO, 9.2%; P = .002; CON, 6.1%-9.5%). No bleeding complications were observed for any piglets during PN treatment. Using platelet mapping, we have previously shown that neonatal piglets given fish oil monotherapy have abnormal platelet function in the AA pathway. This report demonstrates that such an abnormality can be explained by platelet AA deficiency. Platelet mapping and platelet fatty acid analysis should be undertaken in human infants treated with fish oil monotherapy during PN. © 2015 American Society for Parenteral and Enteral Nutrition.

Dietary Lactobacillus acidophilus modulated skin mucus protein profile, immune and appetite genes expression in gold fish (Carassius auratus gibelio).

PubMed

Hosseini, Marjan; Kolangi Miandare, Hamed; Shabani, Ali; Hoseinifar, Seyed Hossein; Yarahmadi, Peyman

2016-12-01

The objective of the present study was to investigate the effect of dietary Lactobacillus acidophilus on skin mucus protein pattern, immune and appetite related genes expression as well as growth performance in gold fish (Carassius auratus gibelio). Three hundred healthy gold fish (2.5 ± 0.05) juveniles were randomly distributed in 12 glass aquariums (400-L; 25 fish per aquaria) and fed experimental diets contain different levels of L. acidophilus (0, 1.5 × 10 8 , 3 × 10 8 and 6 × 10 8 ) for 8 weeks. SDS-PAGE analysis of skin mucus protein profile at the end of the feeding trial revealed differences in protein profile of probiotic fed fish and control group; even three new bands were observed in L. acidophilus treated groups. Furthermore, fish fed 6 × 10 8  CFU g -1 supplemented diet showed up-regulation of both TNF-1α and TNF-2α gene expression (P < 0.05). Evaluation of appetite related gene expression showed down-regulation of ghrelin in probiotic fed fish compared those of control treatment (P < 0.05). However, administration of different levels of L. acidophilus had no significant effects on growth performance (P > 0.05). These results demonstrated that while no beneficial effects on growth performance, dietary L. acidophilus affects immune and appetite related genes expression as well as skin mucus protein profile. Copyright © 2016 Elsevier Ltd. All rights reserved.

The relevance of external quality assessment for molecular testing for ALK positive non-small cell lung cancer: results from two pilot rounds show room for optimization.

PubMed

Tembuyser, Lien; Tack, Véronique; Zwaenepoel, Karen; Pauwels, Patrick; Miller, Keith; Bubendorf, Lukas; Kerr, Keith; Schuuring, Ed; Thunnissen, Erik; Dequeker, Elisabeth M C

2014-01-01

Molecular profiling should be performed on all advanced non-small cell lung cancer with non-squamous histology to allow treatment selection. Currently, this should include EGFR mutation testing and testing for ALK rearrangements. ROS1 is another emerging target. ALK rearrangement status is a critical biomarker to predict response to tyrosine kinase inhibitors such as crizotinib. To promote high quality testing in non-small cell lung cancer, the European Society of Pathology has introduced an external quality assessment scheme. This article summarizes the results of the first two pilot rounds organized in 2012-2013. Tissue microarray slides consisting of cell-lines and resection specimens were distributed with the request for routine ALK testing using IHC or FISH. Participation in ALK FISH testing included the interpretation of four digital FISH images. Data from 173 different laboratories was obtained. Results demonstrate decreased error rates in the second round for both ALK FISH and ALK IHC, although the error rates were still high and the need for external quality assessment in laboratories performing ALK testing is evident. Error rates obtained by FISH were lower than by IHC. The lowest error rates were observed for the interpretation of digital FISH images. There was a large variety in FISH enumeration practices. Based on the results from this study, recommendations for the methodology, analysis, interpretation and result reporting were issued. External quality assessment is a crucial element to improve the quality of molecular testing.

96 h LC50, behavioural alterations and histopathological effects due to wastewater toxicity in a freshwater fish Channa punctatus.

PubMed

Kaur, Rajbir; Dua, Anish

2015-04-01

The aim of the study was to evaluate the toxic impact of wastewater from sites 1 and 2 of Tung Dhab drain in the state of Punjab, India, on fish behaviour, morphology and gill histopathological biomarkers in comparison to control group. Static non-renewal tests were conducted for 96 h to determine LC50 of the wastewater for both sites using five concentrations (6.25-100%). Fish were regularly noticed for any deviation in behaviour and external morphology. Physico-chemical analysis of wastewater was done using standard methods recommended by APHA/AWWA/WEF (2005). Chronic toxicity tests were conducted for 15 and 30 days with sublethal concentrations of wastewater (50-90% of LC50) and gill histopathology was assessed. Wastewater near a paper mill was more toxic as observed from LC50 values of 72.45%. There was evident deterioration of water quality as the recorded values of some parameters were higher than the standard discharge limits. The test fish exhibited increased air gulping and surfacing, erratic movements initially and decreased opercular movements as the exposure period increased. Morphological observations include increased body colouration, mucus secretion, scale loss and haemorrhages on the skin and lower lip. Alterations in the gill histology such as complete lamellar fusion, epithelial lifting and intraepithelial oedema, haemorrhages, lamellar necrosis and aneurysm were noted in the test fish. Results demonstrate that the fish exposed to wastewater from both sites showed significantly greater change in gill organ index (IG) as compared to control fish for 15 and 30 days.

New approach for fish breeding by chemical mutagenesis: establishment of TILLING method in fugu (Takifugu rubripes) with ENU mutagenesis.

PubMed

Kuroyanagi, Miwa; Katayama, Takashi; Imai, Tadashi; Yamamoto, Yoshihisa; Chisada, Shin-ichi; Yoshiura, Yasutoshi; Ushijima, Tomokazu; Matsushita, Tomonao; Fujita, Masashi; Nozawa, Aoi; Suzuki, Yuzuru; Kikuchi, Kiyoshi; Okamoto, Hiroyuki

2013-11-13

In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. Presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivation of a gene. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetics strategy that combines random chemical mutagenesis with high-throughput discovery technologies for screening the induced mutations in target genes. Although the chemical mutagenesis has been used widely in a variety of model species and also genetic breeding of microorganisms and crops, the application of the mutagenesis in fish breeding has been only rarely reported. In this study, we developed the TILLING method in fugu with ENU mutagenesis and high-resolution melting (HRM) analysis to detect base pair changes in target sequences. Fugu males were treated 3 times at weekly intervals with various ENU concentrations, and then the collected sperm after the treatment was used to fertilize normal female for generating the mutagenized population (F1). The fertilization and the hatching ratios were similar to those of the control and did not reveal a dose dependency of ENU. Genomic DNA from the harvested F1 offspring was used for the HRM analysis. To obtain a fish exhibiting a useful phenotype (e.g. high meat production and rapid growth), fugu myostatin (Mstn) gene was examined as a target gene, because it has been clarified that the mstn deficient medaka exhibited double-muscle phenotype in common with MSTN knockout mice and bovine MSTN mutant. As a result, ten types of ENU-induced mutations were identified including a nonsense mutation in the investigated region with HRM analysis. In addition, the average mutation frequency in fugu Mstn gene was 1 mutant per 297 kb, which is similar to values calculated for zebrafish and medaka TILLING libraries. These results demonstrate that the TILLING method in fugu was established. We anticipate that this TILLING approach can be used to generate a wide range of mutant alleles, and be applicable to many farmed fish that can be chemically mutagenized.

Exceptional fossil preservation demonstrates a new mode of axial skeleton elongation in early ray-finned fishes.

PubMed

Maxwell, Erin E; Furrer, Heinz; Sánchez-Villagra, Marcelo R

2013-01-01

Elongate body plans have evolved independently multiple times in vertebrates, and involve either an increase in the number or in the length of the vertebrae. Here, we describe a new mechanism of body elongation in saurichthyids, an extinct group of elongate early ray-finned fishes. The rare preservation of soft tissue in a specimen of Saurichthys curionii from the Middle Triassic (Ladinian) of Switzerland provides significant new information on the relationship between the musculature and the skeleton. This new fossil material shows that elongation in these fishes results from doubling the number of neural arch-like elements per myomeric segment. This unique way of generating an elongate body plan demonstrates the evolutionary lability of the vertebral column in non-teleostean fishes. The shape and arrangement of preserved myosepta suggest that S. curionii was not a highly flexible fish, in spite of the increase in the number of neural arch-like elements.

Marine Biogeochemistry Under The Influence of Fish And Fisheries: An Ecosystem Modeling Study

NASA Astrophysics Data System (ADS)

Disa, Deniz; Akoglu, Ekin; Salihoglu, Baris

2017-04-01

The ocean and the marine ecosystems are important controllers of the global carbon cycle. They play a pivotal role in capturing atmospheric carbon into the ocean body, transforming it into organic carbon through photosynthesis and transporting it to the depths of the ocean. Fish, which has a significant role in the marine food webs, is thought to have a considerable impact on carbon export. More specifically, fish has a control on plankton dynamics as a predator, it provides nutrient to the ecosystem by its metabolic activities and it has the ability of moving actively and transporting materials. Fishing is also expected to impact carbon cycle because it directly changes the fish biomasses. However, how fish impacts the biogeochemistry of marine ecosystems is not studied extensively. The aim of this study is to analyze the impact of fish and fisheries on marine biogeochemical processes by setting up an end-to-end model, which simulates lower and higher tropic levels of marine ecosystems simultaneously. For this purpose, a one dimensional biogeochemical model simulating lower tropic level dynamics (e.g. carbon export, nutrient cycles) and an food web model simulating fisheries exploitation and higher tropic level dynamics were online and two-way coupled. Representing the marine ecosystem from one end to the other, the coupled model served as a tool for the analysis of fishing impacts on marine biogeochemical dynamics. Results obtained after incorporation of higher trophic level model changed the plankton compositions and enhanced detritus pools and increased carbon export. Additionally, our model showed that active movement of fish contributed to transport of carbon from surface to the deeper parts of the ocean. Moreover, results after applying different fishing intensities indicated that changes in fisheries exploitation levels directly influence the marine nutrient cycles and hence, the carbon export. Depending on the target and the intensity of fisheries, considerable changes in the biogeochemical responses observed. In conclusion, unlike the models that do not represent the fish explicitly, we demonstrate how marine biogeochemical processes are impacted by the activity of fish assemblages and fisheries exploitation.

Pubertal effects of 17α-methyltestosterone on GH-IGF-related genes of the hypothalamic-pituitary-liver-gonadal axis and other biological parameters in male, female and sex-reversed Nile tilapia.

PubMed

Phumyu, Nonglak; Boonanuntanasarn, Surintorn; Jangprai, Araya; Yoshizaki, Goro; Na-Nakorn, Uthairat

2012-06-01

The influence of 17α-methyltestosterone (MT) on growth responses, biological parameters and the expression of genes involved in the GH-IGF pathway of the hypothalamic-pituitary-liver-gonadal axis were investigated in female, male, and sex-reversed Nile tilapia to evaluate the relationship between sex and MT-induced changes in these parameters. Female fish had a lower growth rate than male and sex-reversed fish, and MT increased growth performance and duodenal villi in females. Most but not all biological parameters of sex-reversed fish were similar to those of male fish. Male fish had higher red blood cell counts and hemoglobin levels than female and sex-reversed fish, suggesting that these hematological indices reflect a higher metabolic rate in male fish. Greater blood triglyceride levels indicated the vitellogenin process in female fish. MT increased the alternative complement activity in female fish (P<0.05). Sex and MT had no significant effects on the hypothalamic mRNAs of GHRH and PACAP. Although not statistically significant, females tended to have higher GH mRNA levels than male and sex-reversed fish. Additionally, MT tended to decrease and increase GH mRNA levels in female and male fish, respectively. There were significant differences among sexes in the expression of GHR, and IGF mRNAs at the peripheral level in the liver and gonads. Females had lower hepatic GHRs and higher ovarian GHRs than male and sex-reversed fish. While the mRNA levels of IGF-1 were lower in the ovary, the levels of IGF-2 were higher compared with those in testes. A significant correlation between GHRs and IGFs was demonstrated in the liver and gonad (except for IGF-1). Multiple regression analysis showed a significant relationship between GH mRNA and both GHRs and IGFs in the liver and gonad. MT exerted androgenic and, to some extent, estrogenic effects on several physiological parameters and GH-IGF action. Copyright © 2012 Elsevier Inc. All rights reserved.

Forecasting fish biomasses, densities, productions, and bioaccumulation potentials of mid-atlantic wadeable streams.

PubMed

Barber, M Craig; Rashleigh, Brenda; Cyterski, Michael J

2016-01-01

Regional fishery conditions of Mid-Atlantic wadeable streams in the eastern United States are estimated using the Bioaccumulation and Aquatic System Simulator (BASS) bioaccumulation and fish community model and data collected by the US Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP). Average annual biomasses and population densities and annual productions are estimated for 352 randomly selected streams. Realized bioaccumulation factors (BAF) and biomagnification factors (BMF), which are dependent on these forecasted biomasses, population densities, and productions, are also estimated by assuming constant water exposures to methylmercury and tetra-, penta-, hexa-, and hepta-chlorinated biphenyls. Using observed biomasses, observed densities, and estimated annual productions of total fish from 3 regions assumed to support healthy fisheries as benchmarks (eastern Tennessee and Catskill Mountain trout streams and Ozark Mountains smallmouth bass streams), 58% of the region's wadeable streams are estimated to be in marginal or poor condition (i.e., not healthy). Using simulated BAFs and EMAP Hg fish concentrations, we also estimate that approximately 24% of the game fish and subsistence fishing species that are found in streams having detectable Hg concentrations would exceed an acceptable human consumption criterion of 0.185 μg/g wet wt. Importantly, such streams have been estimated to represent 78.2% to 84.4% of the Mid-Atlantic's wadeable stream lengths. Our results demonstrate how a dynamic simulation model can support regional assessment and trends analysis for fisheries. © 2015 SETAC.

Spatial and temporal variation at major histocompatibility complex class IIB genes in the endangered Blakiston's fish owl.

PubMed

Kohyama, Tetsuo I; Omote, Keita; Nishida, Chizuko; Takenaka, Takeshi; Saito, Keisuke; Fujimoto, Satoshi; Masuda, Ryuichi

2015-01-01

Quantifying intraspecific genetic variation in functionally important genes, such as those of the major histocompatibility complex (MHC), is important in the establishment of conservation plans for endangered species. The MHC genes play a crucial role in the vertebrate immune system and generally show high levels of diversity, which is likely due to pathogen-driven balancing selection. The endangered Blakiston's fish owl (Bubo blakistoni) has suffered marked population declines on Hokkaido Island, Japan, during the past several decades due to human-induced habitat loss and fragmentation. We investigated the spatial and temporal patterns of genetic diversity in MHC class IIβ genes in Blakiston's fish owl, using massively parallel pyrosequencing. We found that the Blakiston's fish owl genome contains at least eight MHC class IIβ loci, indicating recent gene duplications. An analysis of sequence polymorphism provided evidence that balancing selection acted in the past. The level of MHC variation, however, was low in the current fish owl populations in Hokkaido: only 19 alleles were identified from 174 individuals. We detected considerable spatial differences in MHC diversity among the geographically isolated populations. We also detected a decline of MHC diversity in some local populations during the past decades. Our study demonstrated that the current spatial patterns of MHC variation in Blakiston's fish owl populations have been shaped by loss of variation due to the decline and fragmentation of populations, and that the short-term effects of genetic drift have counteracted the long-term effects of balancing selection.

RP-HPLC method using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate incorporated with normalization technique in principal component analysis to differentiate the bovine, porcine and fish gelatins.

PubMed

Azilawati, M I; Hashim, D M; Jamilah, B; Amin, I

2015-04-01

The amino acid compositions of bovine, porcine and fish gelatin were determined by amino acid analysis using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate as derivatization reagent. Sixteen amino acids were identified with similar spectral chromatograms. Data pre-treatment via centering and transformation of data by normalization were performed to provide data that are more suitable for analysis and easier to be interpreted. Principal component analysis (PCA) transformed the original data matrix into a number of principal components (PCs). Three principal components (PCs) described 96.5% of the total variance, and 2 PCs (91%) explained the highest variances. The PCA model demonstrated the relationships among amino acids in the correlation loadings plot to the group of gelatins in the scores plot. Fish gelatin was correlated to threonine, serine and methionine on the positive side of PC1; bovine gelatin was correlated to the non-polar side chains amino acids that were proline, hydroxyproline, leucine, isoleucine and valine on the negative side of PC1 and porcine gelatin was correlated to the polar side chains amino acids that were aspartate, glutamic acid, lysine and tyrosine on the negative side of PC2. Verification on the database using 12 samples from commercial products gelatin-based had confirmed the grouping patterns and the variables correlations. Therefore, this quantitative method is very useful as a screening method to determine gelatin from various sources. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of low level 226Ra analysis for live fish using gamma-ray spectrometry

NASA Astrophysics Data System (ADS)

Chandani, Z.; Prestwich, W. V.; Byun, S. H.

2017-06-01

A low level 226Ra analysis method for live fish was developed using a 4π NaI(Tl) gamma-ray spectrometer. In order to find out the best algorithm for accomplishing the lowest detection limit, the gamma-ray spectrum from a 226Ra point was collected and nine different methods were attempted for spectral analysis. The lowest detection limit of 0.99 Bq for an hour counting occurred when the spectrum was integrated in the energy region of 50-2520 keV. To extend 226Ra analysis to live fish, a Monte Carlo simulation model with a cylindrical fish in a water container was built using the MCNP code. From simulation results, the spatial distribution of the efficiency and the efficiency correction factor for the live fish model were determined. The MCNP model will be able to be conveniently modified when a different fish or container geometry is employed as fish grow up in real experiments.

Sequence and functional characterization of hypoxia-inducible factors, HIF1α, HIF2αa, and HIF3α, from the estuarine fish, Fundulus heteroclitus

PubMed Central

Townley, Ian K.; Karchner, Sibel I.; Skripnikova, Elena; Wiese, Thomas E.; Hahn, Mark E.

2017-01-01

The hypoxia-inducible factor (HIF) family of transcription factors plays central roles in the development, physiology, pathology, and environmental adaptation of animals. Because many aquatic habitats are characterized by episodes of low dissolved oxygen, fish represent ideal models to study the roles of HIF in the response to aquatic hypoxia. The estuarine fish Fundulus heteroclitus is found in habitats prone to hypoxia. It responds to low oxygen via behavioral, physiological, and molecular changes, and one member of the HIF family, HIF2α, has been previously described. Herein, cDNA sequencing, phylogenetic analyses, and genomic approaches were used to determine other members of the HIFα family from F. heteroclitus and their relationships to HIFα subunits from other vertebrates. In vitro and cellular approaches demonstrated that full-length forms of HIF1α, HIF2α, and HIF3α independently formed complexes with the β-subunit, aryl hydrocarbon receptor nuclear translocator, to bind to hypoxia response elements and activate reporter gene expression. Quantitative PCR showed that HIFα mRNA abundance varied among organs of normoxic fish in an isoform-specific fashion. Analysis of the F. heteroclitus genome revealed a locus encoding a second HIF2α—HIF2αb—a predicted protein lacking oxygen sensing and transactivation domains. Finally, sequence analyses demonstrated polymorphism in the coding sequence of each F. heteroclitus HIFα subunit, suggesting that genetic variation in these transcription factors may play a role in the variation in hypoxia responses among individuals or populations. PMID:28039194

Sequence and functional characterization of hypoxia-inducible factors, HIF1α, HIF2αa, and HIF3α, from the estuarine fish, Fundulus heteroclitus.

PubMed

Townley, Ian K; Karchner, Sibel I; Skripnikova, Elena; Wiese, Thomas E; Hahn, Mark E; Rees, Bernard B

2017-03-01

The hypoxia-inducible factor (HIF) family of transcription factors plays central roles in the development, physiology, pathology, and environmental adaptation of animals. Because many aquatic habitats are characterized by episodes of low dissolved oxygen, fish represent ideal models to study the roles of HIF in the response to aquatic hypoxia. The estuarine fish Fundulus heteroclitus is found in habitats prone to hypoxia. It responds to low oxygen via behavioral, physiological, and molecular changes, and one member of the HIF family, HIF2α, has been previously described. Herein, cDNA sequencing, phylogenetic analyses, and genomic approaches were used to determine other members of the HIFα family from F. heteroclitus and their relationships to HIFα subunits from other vertebrates. In vitro and cellular approaches demonstrated that full-length forms of HIF1α, HIF2α, and HIF3α independently formed complexes with the β-subunit, aryl hydrocarbon receptor nuclear translocator, to bind to hypoxia response elements and activate reporter gene expression. Quantitative PCR showed that HIFα mRNA abundance varied among organs of normoxic fish in an isoform-specific fashion. Analysis of the F. heteroclitus genome revealed a locus encoding a second HIF2α-HIF2αb-a predicted protein lacking oxygen sensing and transactivation domains. Finally, sequence analyses demonstrated polymorphism in the coding sequence of each F. heteroclitus HIFα subunit, suggesting that genetic variation in these transcription factors may play a role in the variation in hypoxia responses among individuals or populations. Copyright © 2017 the American Physiological Society.

miRNA detection at single-cell resolution using microfluidic LNA flow-FISH

DOE PAGES

Wu, Meiye; Piccini, Matthew Ernest; Koh, Chung -Yan; ...

2014-08-20

Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155more » and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. Here, we also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.« less

Analyzing notochord segmentation and intervertebral disc formation using the twhh:gfp transgenic zebrafish model.

PubMed

Haga, Yutaka; Dominique, Vincent J; Du, Shao Jun

2009-10-01

To characterize the process of vertebral segmentation and disc formation in living animals, we analyzed tiggy-winkle hedgehog (twhh):green fluorescent protein (gfp) and sonic hedgehog (shh):gfp transgenic zebrafish models that display notochord-specific GFP expression. We found that they showed distinct patterns of expression in the intervertebral discs of late stage fish larvae and adult zebrafish. A segmented pattern of GFP expression was detected in the intervertebral disc of twhh:gfp transgenic fish. In contrast, little GFP expression was found in the intervertebral disc of shh:gfp transgenic fish. Treating twhh:gfp transgenic zebrafish larvae with exogenous retinoic acid (RA), a teratogenic factor on normal development, resulted in disruption of notochord segmentation and formation of oversized vertebrae. Histological analysis revealed that the oversized vertebrae are likely due to vertebral fusion. These studies demonstrate that the twhh:gfp transgenic zebrafish is a useful model for studying vertebral segmentation and disc formation, and moreover, that RA signaling may play a role in this process.

Genetic analysis of five sedentary fish species in middle Laranjinha River (upper Paraná River basin): A case study.

PubMed

Frantine-Silva, W; Ferreira, D G; Nascimento, R H C; Fracasso, J F; Conte, J E; Ramos, F P; Carvalho, S; Galindo, B A

2015-12-29

Most studies of diversity and genetic structure in neotropical fish have focused on commercial species from large rivers or their reservoirs. However, smaller tributaries have been identified as an important alternative migratory route, with independent pools of genetic diversity. In this context, the present study aimed to evaluate genetic diversity and structure in five neotropical fish species from a region of Laranjinha River in the upper Paraná River basin. PCR-RAPD (random amplified polymorphic DNA) markers were used to characterize around 40 individuals of each species distributed upstream and downstream of Corredeira Dam that interrupts the river. The descriptive index of genetic diversity (P = 30.5-82%; HE 0.122-0.312) showed that the populations have acceptable levels of genetic diversity. The values for Nei's genetic distance (DN min 0.0110 and max 0.0306) as well as the genetic structure index and the analysis of molecular variance (AMOVA, ϕST min 0.0132 and max 0.0385) demonstrated low, but significant levels of genetic structure. Bayesian analysis of assignment found two k clusters, including several individuals with mixed ancestry for all populations from the five species analyzed. These findings along with historical data on rainfall and the low dimensions of the dam studied here support the hypothesis that periodic floods enable the transit of individuals between different localities mitigating the differentiation process between populations.

Morphological variation of siscowet lake trout in Lake Superior

USGS Publications Warehouse

Bronte, C.R.; Moore, S.A.

2007-01-01

Historically, Lake Superior has contained many morphologically distinct forms of the lake trout Salvelinus namaycush that have occupied specific depths and locations and spawned at specific times of the year. Today, as was probably the case historically, the siscowet morphotype is the most abundant. Recent interest in harvesting siscowets to extract oil containing omega-3 fatty acids will require additional knowledge of the biology and stock structure of these lightly exploited populations. The objective of this study was to determine whether shape differences exist among siscowet populations across Lake Superior and whether these shape differences can be used to infer stock structure. Morphometric analysis (truss protocol) was used to differentiate among siscowets sampled from 23 locations in Lake Superior. We analyzed 31 distance measurements among 14 anatomical landmarks taken from digital images of fish recorded in the field. Cluster analysis of size-corrected data separated fish into three geographic groups: The Isle Royale, eastern (Michigan), and western regions (Michigan). Finer scales of stock structure were also suggested. Discriminant function analysis demonstrated that head measurements contributed to most of the observed variation. Cross-validation classification rates indicated that 67–71% of individual fish were correctly classified to their region of capture. This is the first study to present shape differences associated with location within a lake trout morphotype in Lake Superior.

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

PubMed

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

2013-03-01

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

Broadband and polarization reflectors in the lookdown, Selene vomer.

PubMed

Zhao, Shulei; Brady, Parrish Clawson; Gao, Meng; Etheredge, Robert Ian; Kattawar, George W; Cummings, Molly E

2015-03-06

Predator evasion in the open ocean is difficult because there are no objects to hide behind. The silvery surface of fish plays an important role in open water camouflage. Various models have been proposed to account for the broadband reflectance by the fish skin that involve one-dimensional variations in the arrangement of guanine crystal reflectors, yet the three-dimensional organization of these guanine platelets have not been well characterized. Here, we report the three-dimensional organization and the optical properties of integumentary guanine platelets in a silvery marine fish, the lookdown (Selene vomer). Our structural analysis and computational modelling show that stacks of guanine platelets with random yaw angles in the fish skin produce broadband reflectance via colour mixing. Optical axes of the guanine platelets and the collagen layer are aligned closely and provide bulk birefringence properties that influence the polarization reflectance by the skin. These data demonstrate how the lookdown preserves or alters polarization states at different incident polarization angles. These optical properties resulted from the organization of these guanine platelets and the collagen layer may have implications for open ocean camouflage in varying light fields. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

[Adaptive specific features of energy metabolism in fish ontogenesis].

PubMed

Ozerniuk, N D

2011-01-01

A review of data on the pattern of change of the intensity of oxygen consumption during early ontogenesis of different fish species (rainbow trout, loach, zebrafish, carp, and grass carp) is provided. It has a similar pattern: this index increases in the period of embryonic and larval development and, after passing of larvae to an active feeding, it begins to gradually decline. This dynamics is determined by specific features of an increase in the rate of oxygen uptake and body weight in the course of early stages of fish ontogenesis. For determining optimal temperature conditions of development, a method of total (for a definite stage of development) oxygen uptake was suggested, which makes it possible to determine minimal energy expenditures necessary for the process of a particular stage of embryogenesis to take place. Analysis of temperature dependence of kinetic properties of enzymes with reference to the Michaelis constant (Km) for lactate dehydrogenase demonstrated that minimal Km, corresponding to maximal enzyme-substrate affinity, for embryos of different fish species differs in correspondence with differences in temperature conditions of development of these species in nature. For embryos of one species developing at changing temperature conditions (salmonids), this index changes in accordance with a temperature drift in nature.

[The level of available methionine and the biological value of fish protein].

PubMed

Lipka, Z; Ganowiak, Z

1992-01-01

Food value of fish protein in fish canning was evaluated biologically and chemically (by available methionine). High-temperature sterilization (126 degrees) proved the least adequate for it causes the greatest loss in the protein food value. The chemical method by available methionine showing close correlation with biological techniques (NPU and PER rates) is thought demonstrative and convenient for technological control in fish processing industry.

Boys Go Fishing, Girls Work at Home: Gender Roles, Poverty and Unequal School Access among Semi-Nomadic Fishing Communities in South Western Madagascar

ERIC Educational Resources Information Center

Nascimento Moreira, Catarina; Rabenevanana, Man Wai; Picard, David

2017-01-01

Drawing from data gathered in South Western Madagascar in 2011, the work explores the combination of poverty and traditional gender roles as a critical factor in determining unequal school access among young people from semi-nomadic fishing communities. It demonstrates that from the age of early puberty, most boys go fishing with their fathers and…

Fishing for gaps in science: a bibliographic analysis of Brazilian freshwater ichthyology from 1986 to 2005.

PubMed

Azevedo, P G; Mesquita, F O; Young, R J

2010-06-01

To investigate Brazilian freshwater ichthyology, from 1986 to 2005, a bibliometric analysis was conducted using abstracts downloaded from The Web of Science database searching for the keywords 'fish', 'pisces', 'teleostei' and the address field having the word 'Brazil'. The results of this study showed that Brazilian freshwater ichthyology publications have been increasing during the study period. This process is a consequence of a series of investments that the Brazilian Government has made. Furthermore, data analyses identified scientific areas where there was a lack of scientific knowledge (e.g. studies of species threatened with extinction and certain hydrologic basins). Research institutions from the north-east and northern region of Brazil had the lowest participation in scientific productivity, which was a reflection of their regions poorer economic situation. This study showed that scientific productivity in Brazilian ichthyology was a direct reflection of state investment in research. Furthermore, data in this study follow expected statistical probabilities, for example, fishes from the most diverse families were the most studied. Thus, the study shows that great progress has been made by Brazilian ichthyologists in the last 20 years; however, due to the mega diversity of fishes in Brazil, much remains to be done if many species are to become known to science and to be saved from extinction. This it seems will depend on continued and further investment by Brazilian Government funding agencies, as Brazilian ichthyologists have demonstrated their capacity to generate high quality information about their study species.

Cloning metallothionein gene in Zacco platypus and its potential as an exposure biomarker against cadmium.

PubMed

Lee, Sangwoo; Kim, Cheolmin; Kim, Jungkon; Kim, Woo-Keun; Shin, Hyun Suk; Lim, Eun-Suk; Lee, Jin Wuk; Kim, Sunmi; Kim, Ki-Tae; Lee, Sung-Kyu; Choi, Cheol Young; Choi, Kyungho

2015-07-01

Zacco platypus, pale chub, is an indigenous freshwater fish of East Asia including Korea and has many useful characteristics as indicator species for water pollution. While utility of Z. platypus as an experimental species has been recognized, genetic-level information is very limited and warrants extensive research. Metallothionein (MT) is widely used and well-known biomarker for heavy metal exposure in many experimental species. In the present study, we cloned MT in Z. platypus and evaluated its utility as a biomarker for metal exposure. For this purpose, we sequenced complete complementary DNA (cDNA) of MT in Z. platypus and carried out phylogenetic analysis with its sequences. The transcription-level responses of MT gene following the exposure to CdCl2 were also assessed to validate the utility of this gene as an exposure biomarker. Analysis of cDNA sequence of MT gene demonstrated high conformity with those of other fish. MT messenger RNA (mRNA) expression and enzymatic MT content significantly increased following CdCl2 exposure in a concentration-dependent manner. The level of CdCl2 that resulted in significant MT changes in Z. platypus was within the range that was reported from other fish. The MT gene of Z. platypus sequenced in the present study can be used as a useful biomarker for heavy metal exposure in the aquatic environment of Korea and other countries where this freshwater fish species represents the ecosystem.

Effect of fish skin mucus on the soluble proteome of Vibrio salmonicida analysed by 2-D gel electrophoresis and tandem mass spectrometry.

PubMed

Raeder, Inger Lin Uttakleiv; Paulsen, Steinar M; Smalås, Arne O; Willassen, Nils Peder

2007-01-01

Vibrio salmonicida is the causative agent of cold-water vibriosis in farmed marine fish species. Adherence of pathogenic bacteria to mucosal surfaces is considered to be the first steps in the infective processes, and proteins involved are regarded as virulence factors. The global protein expression profile of V. salmonicida, grown with and without the presence of fish skin mucus in the synthetic media, was compared. Increased levels of proteins involved in motility, oxidative stress responses, and general stress responses were demonstrated as an effect of growth in the presence of mucus compared to non-mucus containing media. Enhanced levels of the flagellar proteins FlaC, FlaD and FlaE indicate increased motility capacity, while enhanced levels of the heat shock protein DnaK and the chaperonin GroEL indicate a general stress response. In addition, we observed that peroxidases, TPx.Grx and AhpC, involved in the oxidative stress responses, were induced by mucus proteins. The addition of mucus to the culture medium did not significantly alter the growth rate of V. salmonicida. An analysis of mucus proteins suggests that the mucus layer harbours a protein species that potentially possesses catalytic activity against DNA, and a protein with iron chelating activity. This study represents the first V. salmonicida proteomic analysis, and provides specific insight into the proteins necessary for the bacteria to challenge the skin mucus barrier of the fish.

Assessment of biological effects of pollutants in a hyper eutrophic tropical water body, Lake Beira, Sri Lanka using multiple biomarker responses of resident fish, Nile tilapia (Oreochromis niloticus).

PubMed

Pathiratne, Asoka; Pathiratne, K A S; De Seram, P K C

2010-08-01

Biomarkers measured at the molecular and cellular level in fish have been proposed as sensitive "early warning" tools for biological effect measurements in environmental quality assessments. Lake Beira is a hypertrophic urban water body with a complex mixture of pollutants including polycyclic aromatic hydrocarbons (PAHs) and Microcystins. In this study, a suite of biomarker responses viz. biliary fluorescent aromatic compounds (FACs), hepatic ethoxyresorufin O-deethylase (EROD) and glutathione S-transferase (GST), brain and muscle cholinesterases (ChE), serum sorbitol dehydrogenase (SDH), and liver histology of Oreochromis niloticus, the dominant fish inhabiting this tropical Lake were evaluated to assess the pollution exposure and biological effects. Some fish sampled in the dry periods demonstrated prominent structural abnormalities in the liver and concomitant increase in serum SDH and reduction in hepatic GST activities in comparison to the control fish and the fish sampled in the rainy periods. The resident fish with apparently normal liver demonstrated induction of hepatic EROD and GST activities and increase in biliary FACs irrespective of the sampling period indicating bioavailability of PAHs. Muscle ChE activities of the resident fish were depressed significantly indicating exposure to anticholinesterase substances. The results revealed that fish populations residing in this Lake is under threat due to the pollution stress. Hepatic abnormalities in the fish may be mainly associated with the pollution stress due to recurrent exposure to PAHs and toxigenic Microcystis blooms in the Lake.

Immediate systemic allergic reaction in an infant to fish allergen ingested through breast milk

PubMed Central

Arima, Takayasu; Campos-Alberto, Eduardo; Funakoshi, Hiraku; Inoue, Yuzaburo; Tomiita, Minako; Kohno, Yoichi

2016-01-01

This is a rare case report of systemic allergic reaction to fish allergen ingested through breast milk. Mother ate raw fish more than 3 times a week. Her consumption of fish was associated with urticaria and wheeze in an infant via breast-feeding. Fish-specific IgE antibodies were detected by skin prick test but not by in vitro IgE test. This case demonstrates that fish protein ingested by mother can cause an immediate systemic allergic reaction in offspring through breast-feeding. Although fish intake is generally recommended for prevention of allergy, one should be aware that frequent intake of fish by a lactating mother may sensitize the baby and induce an allergic reaction through breast-feeding. PMID:27803887

Relative impacts of the fragmentation and spatial structure of habitats on freshwater fish distributions: application on French watersheds (Invited)

NASA Astrophysics Data System (ADS)

Le Pichon, C.; Belliard, J.; Talès, E.; Gorges, G.; Clément, F.

2009-12-01

Most of the rivers of the Ile de France region, intimately linked with the megalopolis of Paris, are severely altered and freshwater fishes are exposed to habitat alteration, reduced connectivity and pollution. Several species thus present fragmented distributions and decreasing densities. In this context, the European Water Framework Directive (2000) has goals of hydrosystems rehabilitation and no further damage. In particular, the preservation and restoration of ecological connectivity of river networks is a key element for fish populations. These goals require the identification of natural and anthropological factors which influence the spatial distribution of species. We have proposed a riverscape approach, based on landscape ecology concepts, combined with a set of spatial analysis methods to assess the multiscale relationships between the spatial pattern of fish habitats and processes depending on fish movements. In particular, we used this approach to test the relative roles of spatial arrangement of fish habitats and the presence of physical barriers in explaining fish spatial distributions in a small rural watershed (106 km2). We performed a spatially continuous analysis of fish-habitat relationships. Fish habitats and physical barriers were mapped along the river network (33 km) with a GPS and imported into a GIS. In parallel, a longitudinal electrofishing survey of the distribution and abundance of fishes was made using a point abundance sampling scheme. Longitudinal arrangement of fish habitats were evaluated using spatial analysis methods: patch/distance metrics and moving window analysis. Explanatory models were developed to test the relative contribution of local environmental variables and spatial context in explaining fish presence. We have recorded about 100 physical barriers, on average one every 330 meters; most artificial barriers were road pipe culverts, falls associated with ponds and sluice gates. Contrasted fish communities and densities were observed in the different areas of the watershed, related to various land use (riparian forest or agriculture). The first results of fish-habitat association analysis on a 5 km stream are that longitudinal distribution of fish species was mainly impacted by falls associated with ponds. The impact was both due to the barrier effect and to the modification of aquatic habitats. Abundance distribution of Salmo trutta and Cottus gobio was particularly affected. Spatially continuous analysis of fish-habitat relationships allowed us to identify the relative impacts of habitat alteration and presence of physical barriers to fish movements. These techniques could help prioritize preservation and restoration policies in human-impacted watersheds, in particular, identifying the key physical barriers to remove.

Depth-related trends in morphological and functional diversity of demersal fish assemblages in the western Mediterranean Sea

NASA Astrophysics Data System (ADS)

Farré, Marc; Tuset, Víctor M.; Cartes, Joan E.; Massutí, Enric; Lombarte, Antoni

2016-09-01

The morphological and functional traits of fishes are key factors defining the ecological and biological habits of species within ecosystems. However, little is known about how the depth gradient affects these factors. In the present study, several demersal fish assemblages from the Balearic Islands (western Mediterranean Sea) along a wide depth range (40-2200 m) were morphologically, functionally and ecologically described. The morphological characterization of communities was performed using geometric morphometric methods, while the functional structures were obtained by the functional categorization of species and the application of principal coordinates analysis (PCoA). The results revealed that morphospaces presented less richness of body forms as depth increases, although they showed a progressive spreading of species toward the periphery, with a proliferation of more extreme body traits, demonstrating lower morphological redundancy. In addition, a trend toward the elongation of body shape was also observed with depth. Moreover, functional diversity increased with bathymetry up to 1400 m, where it sharply decreased downwards. This decrease was parallel to a progressive fall of H‧ (ecological diversity) up to 2200 m. Functional redundancy progressively decreased until the deepest assemblage (more constantly in the deeper levels), which was almost exclusively dominated by benthopelagic wandering species feeding on suprabenthos. Redundancy analysis (RDA) demonstrated that both morphological and functional spaces showed high variation along the bathymetric range. Mantel test indicated that the majority of species presented similar spatial distribution within the morphospace and functional space, although in the functional space the more abundant species were always located at the periphery. These results demonstrate that the assessment of the morpho-functional variation between marine communities helps to understand the processes that affect the structure and functioning of communities, such as resource partitioning, trophic interactions, or interspecific relationships within ecosystem such as coexistence and dominance.

Sound extinction by fish schools: forward scattering theory and data analysis.

PubMed

Raveau, M; Feuillade, C

2015-02-01

A model used previously to study collective back scattering from fish schools [Feuillade et al., J. Acoust. Soc. Am. 99(1), 196-208 (1996)], is used to analyze the forward scattering properties of these objects. There is an essential physical difference between back and forward scattering from fish schools. Strong frequency dependent interference effects, which affect the back scattered field amplitude, are absent in the forward scattering case. This is critically important for data analysis. There is interest in using back scattering and transmission data from fish schools to study their size, the species and abundance of fish, and fish behavior. Transmission data can be processed to determine the extinction of the field by a school. The extinction of sound depends on the forward scattering characteristics of the school, and data inversion to provide information about the fish should be based upon a forward scattering paradigm. Results are presented of an analysis of transmission data obtained in September 1995 during an experiment performed in the Gulf of Lion in the Mediterranean Sea [Diachok, J. Acoust. Soc. Am. 105(4), 2107-2128 (1999)]. The analysis shows that using forward scattering leads to significantly larger estimates of fish abundance than previous analysis based upon back scattering approaches.

Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea Fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)

PubMed Central

Dunlap, Paul V.; Ast, Jennifer C.

2005-01-01

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040T, and the type strain of Photobacterium iliopiscarium, ATCC 51760T. Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040T. These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes. PMID:15691950

Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae).

PubMed

Dunlap, Paul V; Ast, Jennifer C

2005-02-01

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040(T), and the type strain of Photobacterium iliopiscarium, ATCC 51760(T). Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040(T). These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.

Comparison of fish and macroinvertebrates as bioindicators of Neotropical streams.

PubMed

Ruaro, Renata; Gubiani, Éder André; Cunico, Almir Manoel; Moretto, Yara; Piana, Pitágoras Augusto

2016-01-01

The biomonitoring of aquatic ecosystems in developing countries faces several limitations, especially related to gathering resources. The present study aimed at comparing the responses of fish and benthic macroinvertebrates to environmental change, to identify which group best indicates the differences between reference and impacted streams in southern Brazil. We determined reference and impacted sites based on physical and chemical variables of the water. For the analysis and comparison of biological responses, we calculated 22 metrics and submitted them to a discriminant analysis. We selected from this analysis only six metrics, which showed that the two studied assemblages respond differently to environmental change. A larger number of metrics were selected for macroinvertebrates than for fish in the separate analysis. The metrics selected for macroinvertebrates in the pooled analysis (i.e., fish and macroinvertebrates together) were different from those selected in the separate analysis for macroinvertebrates alone. However, the metrics selected for fish in the pooled analysis were the same selected in the separate analysis for fish alone. The macroinvertebrate assemblage was more effective for distinguishing reference from impacted sites. We suggest the use of macroinvertebrates as bioindicators of Neotropical streams, especially in situations in which time and money are short.

Bioavailability of pollutants sets risk of exposure to biota and human population in reservoirs from Iguaçu River (Southern Brazil).

PubMed

Yamamoto, F Y; Pereira, M V M; Lottermann, E; Santos, G S; Stremel, T R O; Doria, H B; Gusso-Choueri, P; Campos, S X; Ortolani-Machado, C F; Cestari, M M; Neto, F Filipak; Azevedo, J C R; Ribeiro, C A Oliveira

2016-09-01

The Iguaçu River, located at the Southern part of Brazil, has a great socioeconomic and environmental importance due to its high endemic fish fauna and its potential to generate hydroelectric power. However, Iguaçu River suffers intense discharge of pollutants in the origin of the river. In a previous report, the local environmental agency described water quality to improve along the river course. However, no study with integrated evaluation of chemical analysis and biological responses has been reported so far for the Iguaçu River. In the current study, three different Brazilian fish species (Astyanax bifasciatus, Chrenicicla iguassuensis, and Geophagus brasiliensis) were captured in the five cascading reservoirs of Iguaçu River for a multi-biomarker study. Chemical analysis in water, sediment, and muscle indicated high levels of bioavailable metals in all reservoirs. Polycyclic aromatic hydrocarbons (PAHs) were detected in the bile of the three fish species. Integration of the data through a FA/PCA analysis demonstrated the poorest environmental quality of the reservoir farthest from river's source, which is the opposite of what has been reported by the environmental agency. The presence of hazardous chemicals in the five reservoirs of Iguaçu River, their bioaccumulation in the muscle of fish, and the biological responses showed the impacts of human activities to this area and did not confirm a gradient of pollution between the five reservoirs, from the source toward Iguaçu River's mouth. Therefore, diffuse source of pollutants present along the river course are increasing the risk of exposure to biota and human populations.

Using mitochondrial and ribosomal DNA sequences to test the taxonomic validity of Clinostomum complanatum Rudolphi, 1814 in fish-eating birds and freshwater fishes in Mexico, with the description of a new species.

PubMed

Sereno-Uribe, Ana L; Pinacho-Pinacho, Carlos D; García-Varela, Martín; de León, Gerardo Pérez-Ponce

2013-08-01

The taxonomic history and species composition of the genus Clinostomum has been unstable. Two species, Clinostomum complanatum Rudolphi, 1814 and Clinostomum marginatum Rudolphi, 1819, have been particularly problematic and its validity has been disputed for nearly 200 years. In this paper, we have made use of an integrative taxonomy approach, and we used, in first instance, DNA sequences of two genes (cox1 and ITS) to test the validity of C. complanatum, a species apparently widely distributed in Mexico and to link the metacercariae and adult forms of the recognized species of Clinostomum. Combining molecular data with morphology, host association, and geographical distribution, we searched for the potential existence of undescribed species. A new species of Clinostomum is described based on adults found in the mouthy cavity of three species of fish-eating birds as well as in metacercariae found in freshwater and estuarine fishes. A few morphological characteristics distinguish the new species from other congeners even though reciprocal monophyly in a phylogenetic tree based on maximum-likelihood and Bayesian analysis, genetic divergence, and a multivariate analysis of variance and a principal component analysis of 18 morphometric traits for adults and metacercariae demonstrates the validity of the new species. Based on our results, it seems that C. complanatum is not currently distributed in Mexico, although this requires further verification with a more thoroughful sampling in other areas of the country, but it is plausible to support the hypothesis that C. marginatum is the American form, as previously suggested by other authors.

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

PubMed Central

Thomsen, Philip Francis; Møller, Peter Rask; Sigsgaard, Eva Egelyng; Knudsen, Steen Wilhelm; Jørgensen, Ole Ankjær; Willerslev, Eske

2016-01-01

Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188–918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems. PMID:27851757

Fish assemblages

USGS Publications Warehouse

McGarvey, Daniel J.; Falke, Jeffrey A.; Li, Hiram W.; Li, Judith; Hauer, F. Richard; Lamberti, G.A.

2017-01-01

Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

An effective and robust method for tracking multiple fish in video image based on fish head detection.

PubMed

Qian, Zhi-Ming; Wang, Shuo Hong; Cheng, Xi En; Chen, Yan Qiu

2016-06-23

Fish tracking is an important step for video based analysis of fish behavior. Due to severe body deformation and mutual occlusion of multiple swimming fish, accurate and robust fish tracking from video image sequence is a highly challenging problem. The current tracking methods based on motion information are not accurate and robust enough to track the waving body and handle occlusion. In order to better overcome these problems, we propose a multiple fish tracking method based on fish head detection. The shape and gray scale characteristics of the fish image are employed to locate the fish head position. For each detected fish head, we utilize the gray distribution of the head region to estimate the fish head direction. Both the position and direction information from fish detection are then combined to build a cost function of fish swimming. Based on the cost function, global optimization method can be applied to associate the target between consecutive frames. Results show that our method can accurately detect the position and direction information of fish head, and has a good tracking performance for dozens of fish. The proposed method can successfully obtain the motion trajectories for dozens of fish so as to provide more precise data to accommodate systematic analysis of fish behavior.

Fish oil supplementation and insulin sensitivity: a systematic review and meta-analysis.

PubMed

Gao, Huanqing; Geng, Tingting; Huang, Tao; Zhao, Qinghua

2017-07-03

Fish oil supplementation has been shown to be associated with a lower risk of metabolic syndrome and benefit a wide range of chronic diseases, such as cardiovascular disease, type 2 diabetes and several types of cancers. However, the evidence of fish oil supplementation on glucose metabolism and insulin sensitivity is still controversial. This meta-analysis summarized the exist evidence of the relationship between fish oil supplementation and insulin sensitivity and aimed to evaluate whether fish oil supplementation could improve insulin sensitivity. We searched the Cochrane Library, PubMed, Embase database for the relevant studies update to Dec 2016. Two researchers screened the literature independently by the selection and exclusion criteria. Studies were pooled using random effect models to estimate a pooled SMD and corresponding 95% CI. This meta-analysis was performed by Stata 13.1 software. A total of 17 studies with 672 participants were included in this meta-analysis study after screening from 498 published articles found after the initial search. In a pooled analysis, fish oil supplementation had no effects on insulin sensitivity compared with the placebo (SMD 0.17, 95%CI -0.15 to 0.48, p = 0.292). In subgroup analysis, fish oil supplementation could benefit insulin sensitivity among people who were experiencing at least one symptom of metabolic disorders (SMD 0.53, 95% CI 0.17 to 0.88, p < 0.001). Similarly, there were no significant differences between subgroups of methods of insulin sensitivity, doses of omega-3 polyunsaturated fatty acids (n-3 PUFA) of fish oil supplementation or duration of the intervention. The sensitivity analysis indicated that the results were robust. Short-term fish oil supplementation is associated with increasing the insulin sensitivity among those people with metabolic disorders.

An Energy Harvesting Underwater Acoustic Transmitter for Aquatic Animals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Huidong; Tian, Chuan; Lu, Jun

This paper presents a self-powered underwater acoustic transmitter using a piezoelectric beam to harvest the mechanical energy from fish swimming. This transmitter does not require a battery and is demonstrated in live fish. It transmits an acoustic waveform as the implanted fish swims. It enables long-term monitoring of aquatic animals.

How many fish in a tank? Constructing an automated fish counting system by using PTV analysis

NASA Astrophysics Data System (ADS)

Abe, S.; Takagi, T.; Takehara, K.; Kimura, N.; Hiraishi, T.; Komeyama, K.; Torisawa, S.; Asaumi, S.

2017-02-01

Because escape from a net cage and mortality are constant problems in fish farming, health control and management of facilities are important in aquaculture. In particular, the development of an accurate fish counting system has been strongly desired for the Pacific Bluefin tuna farming industry owing to the high market value of these fish. The current fish counting method, which involves human counting, results in poor accuracy; moreover, the method is cumbersome because the aquaculture net cage is so large that fish can only be counted when they move to another net cage. Therefore, we have developed an automated fish counting system by applying particle tracking velocimetry (PTV) analysis to a shoal of swimming fish inside a net cage. In essence, we treated the swimming fish as tracer particles and estimated the number of fish by analyzing the corresponding motion vectors. The proposed fish counting system comprises two main components: image processing and motion analysis, where the image-processing component abstracts the foreground and the motion analysis component traces the individual's motion. In this study, we developed a Region Extraction and Centroid Computation (RECC) method and a Kalman filter and Chi-square (KC) test for the two main components. To evaluate the efficiency of our method, we constructed a closed system, placed an underwater video camera with a spherical curved lens at the bottom of the tank, and recorded a 360° view of a swimming school of Japanese rice fish (Oryzias latipes). Our study showed that almost all fish could be abstracted by the RECC method and the motion vectors could be calculated by the KC test. The recognition rate was approximately 90% when more than 180 individuals were observed within the frame of the video camera. These results suggest that the presented method has potential application as a fish counting system for industrial aquaculture.

Predicting invasiveness of species in trade: Climate match, trophic guild and fecundity influence establishment and impact of non-native freshwater fishes

USGS Publications Warehouse

Howeth, Jennifer G.; Gantz, Crysta A.; Angermeier, Paul; Frimpong, Emmanuel A.; Hoff, Michael H.; Keller, Reuben P.; Mandrak, Nicholas E.; Marchetti, Michael P.; Olden, Julian D.; Romagosa, Christina M.; Lodge, David M.

2016-01-01

AimImpacts of non-native species have motivated development of risk assessment tools for identifying introduced species likely to become invasive. Here, we develop trait-based models for the establishment and impact stages of freshwater fish invasion, and use them to screen non-native species common in international trade. We also determine which species in the aquarium, biological supply, live bait, live food and water garden trades are likely to become invasive. Results are compared to historical patterns of non-native fish establishment to assess the relative importance over time of pathways in causing invasions.LocationLaurentian Great Lakes region.MethodsTrait-based classification trees for the establishment and impact stages of invasion were developed from data on freshwater fish species that established or failed to establish in the Great Lakes. Fishes in trade were determined from import data from Canadian and United States regulatory agencies, assigned to specific trades and screened through the developed models.ResultsClimate match between a species’ native range and the Great Lakes region predicted establishment success with 75–81% accuracy. Trophic guild and fecundity predicted potential harmful impacts of established non-native fishes with 75–83% accuracy. Screening outcomes suggest the water garden trade poses the greatest risk of introducing new invasive species, followed by the live food and aquarium trades. Analysis of historical patterns of introduction pathways demonstrates the increasing importance of these trades relative to other pathways. Comparisons among trades reveal that model predictions parallel historical patterns; all fishes previously introduced from the water garden trade have established. The live bait, biological supply, aquarium and live food trades have also contributed established non-native fishes.Main conclusionsOur models predict invasion risk of potential fish invaders to the Great Lakes region and could help managers prioritize efforts among species and pathways to minimize such risk. Similar approaches could be applied to other taxonomic groups and geographic regions.

In vitro differentiation of fertile sperm from cryopreserved spermatogonia of the endangered endemic cyprinid honmoroko (Gnathopogon caerulescens)

NASA Astrophysics Data System (ADS)

Higaki, Shogo; Shimada, Manami; Kawamoto, Kazuaki; Todo, Takaaki; Kawasaki, Toshihiro; Tooyama, Ikuo; Fujioka, Yasuhiro; Sakai, Noriyoshi; Takada, Tatsuyuki

2017-02-01

Many endemic fish species are threatened with extinction. Conservation strategies and the restoration of endemic fish after extinction must therefore be investigated. Although sperm cryopreservation is indispensable for the conservation of endangered fishes, the limited number of mature fish and limited availability (volume and period) of sperm from small endemic fish hinders the optimization and practical use of this material. In this report, we demonstrate the in vitro differentiation of fertile sperm from cryopreserved spermatogonia of juveniles of the endangered small cyprinid honmoroko (Gnathopogon caerulescens), which is endemic to Lake Biwa in Japan. The entire process of spermatogenesis was recapitulated in vitro using cryopreserved spermatogonia of non-spawning adult and juvenile fish. The differentiation of sperm from spermatogonia was captured as a time-lapse video and confirmed by 5-ethynyl-2‧-deoxyuridine (EdU) incorporation into sperm. Fertility was demonstrated by artificial insemination. These results suggest that the combination of cryopreservation of spermatogonia and in vitro sperm differentiation will provide a new and promising strategy for the preservation of paternal genetic materials.

Accumulation of contaminants in fish from wastewater treatment wetlands

USGS Publications Warehouse

Barber, L.B.; Keefe, S.H.; Antweiler, Ronald C.; Taylor, Howard E.; Wass, R.D.

2006-01-01

Increasing demands on water resources in arid environments make reclamation and reuse of municipal wastewater an important component of the water budget. Treatment wetlands can be an integral part of the water-reuse cycle providing both water-quality enhancement and habitat functions. When used for habitat, the bioaccumulation potential of contaminants in the wastewater is a critical consideration. Water and fish samples collected from the Tres Rios Demonstration Constructed Wetlands near Phoenix, Arizona, which uses secondary-treated wastewater to maintain an aquatic ecosystem in a desert environment, were analyzed for hydrophobic organic compounds (HOC) and trace elements. Semipermeable membrane devices (SPMD) were deployed to investigate uptake of HOC. The wetlands effectively removed HOC, and concentrations of herbicides, pesticides, and organic wastewater contaminants decreased 40-99% between inlet and outlet. Analysis of Tilapia mossambica and Gambusia affinis indicated accumulation of HOC, including p,p???-DDE and trans-nonachlor. The SPMD accumulated the HOC detected in the fish tissue as well as additional compounds. Trace-element concentrations in whole-fish tissue were highly variable, but were similar between the two species. Concentrations of HOC and trace elements varied in different fish tissue compartments, and concentrations in Tilapia liver tissue were greater than those in the whole organism or filet tissue. Bioconcentration factors for the trace elements ranged from 5 to 58 000 and for the HOC ranged from 530 to 150 000. ?? 2006 American Chemical Society.

Reduction of the pectoral spine and girdle in domesticated Channel catfish is likely caused by changes in selection pressure.

PubMed

Fine, Michael L; Lahiri, Shweta; Sullivan, Amanda D H; Mayo, Mark; Newton, Scott H; Sismour, Edward N

2014-07-01

Locked pectoral spines of the Channel Catfish Ictalurus punctatus more than double the fish's width and complicate ingestion by gape-limited predators. The spine mates with the pectoral girdle, a robust structure that anchors the spine. This study demonstrates that both spine and girdle exhibit negative allometric growth and that pectoral spines and girdles are lighter in domesticated than in wild Channel Catfish. This finding could be explained by changes in selection pressure for spine growth during domestication or by an epigenetic effect in which exposure to predators in wild fish stimulates pectoral growth. We tested the epigenetic hypothesis by exposing domesticated Channel Catfish fingerlings to Largemouth Bass Micropterus salmoides predators for 13 weeks. Spines and girdles grow isometrically in the fingerlings, and regression analysis indicates no difference in proportional pectoral growth between control and predator-exposed fish. Therefore a change in selection pressure likely accounts for smaller pectoral growth in domesticated Channel Catfish. Decreasing spine growth in older fish suggests anti-predator functions are most important in smaller fish. Additionally, growth of the appendicular and axial skeleton is controlled differentially, and mechanical properties of the spine and not just its length are an important component of this defensive adaptation. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Delimiting Evolutionarily Significant Units of the Fish, Piaractus brachypomus (Characiformes: Serrasalmidae), from the Orinoco and Amazon River Basins with Insight on Routes of Historical Connectivity.

PubMed

Escobar, Maria Doris; Andrade-López, Juana; Farias, Izeni P; Hrbek, Tomas

2015-01-01

The freshwater fish Piaractus brachypomus is an economically important for human consumption both in commercial fisheries and aquaculture in all South American countries where it occurs. In recent years the species has decreased in abundance due to heavy fishing pressure. The species occurs in the Amazon and Orinoco basins, but lack of meristic differences between fishes from the 2 basins, and extensive migration associated with reproduction, have resulted in P. brachypomus being considered a single panmictic species. Analysis of 7 nuclear microsatellites, mitochondrial DNA sequences (D-loop and COI), and body shape variables demonstrated that each river basin is populated by a distinct evolutionarily significant unit (ESU); the 2 groups had an average COI divergence of 3.5% and differed in body depth and relative head length. Historical connection between the 2 basins most probably occurred via the Rupununi portal rather than via the Casiquiare canal. The 2 ESUs will require independent fishery management, and translocation of fisheries stocks between basins should be avoided to prevent loss of local adaptations or extinction associated with outbreeding depression. Introductions of fishes from the Orinoco basin into the Putumayo River basin, an Amazon basin drainage, and evidence of hybridization between the 2 ESUs have already been detected. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Regulation of branchial V-H(+)-ATPase, Na(+)/K(+)-ATPase and NHE2 in response to acid and base infusions in the Pacific spiny dogfish (Squalus acanthias).

PubMed

Tresguerres, Martin; Katoh, Fumi; Fenton, Heather; Jasinska, Edyta; Goss, Greg G

2005-01-01

To study the mechanisms of branchial acid-base regulation, Pacific spiny dogfish were infused intravenously for 24 h with either HCl (495+/- 79 micromol kg(-1) h(-1)) or NaHCO(3) (981+/-235 micromol kg(-1) h(-1)). Infusion of HCl produced a transient reduction in blood pH. Despite continued infusion of acid, pH returned to normal by 12 h. Infusion of NaHCO(3) resulted in a new steady-state acid-base status at approximately 0.3 pH units higher than the controls. Immunostained serial sections of gill revealed the presence of separate vacuolar proton ATPase (V-H(+)-ATPase)-rich or sodium-potassium ATPase (Na(+)/K(+)-ATPase)-rich cells in all fish examined. A minority of the cells also labeled positive for both transporters. Gill cell membranes prepared from NaHCO(3)-infused fish showed significant increases in both V-H(+)-ATPase abundance (300+/-81%) and activity. In addition, we found that V-H(+)-ATPase subcellular localization was mainly cytoplasmic in control and HCl-infused fish, while NaHCO(3)-infused fish demonstrated a distinctly basolateral staining pattern. Western analysis in gill membranes from HCl-infused fish also revealed increased abundance of Na(+)/H(+) exchanger 2 (213+/-5%) and Na(+)/K(+)-ATPase (315+/-88%) compared to the control.

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.« less

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

DOE PAGES

Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

2016-04-18

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.« less

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

PubMed

Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

2016-01-01

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.

A genetically distinct hybrid zone occurs for two globally invasive mosquito fish species with striking phenotypic resemblance.

PubMed

Wilk, Rebecca J; Horth, Lisa

2016-12-01

Hybrid zones allow for the investigation of incipient speciation and related evolutionary processes of selection, gene flow, and migration. Interspecific dynamics, like competition, can impact the size, shape, and directional movement of species in hybrid zones. Hybrid zones contribute to a paradox for the biological species concept because interbreeding between species occurs while parental forms remain distinct. A long-standing zone of intergradation or introgression exists for eastern and western mosquito fish ( Gambusia holbrooki and G. affinis ) around Mobile Bay, AL. The region has been studied episodically, over decades, making it perfect for addressing temporal dynamics and for providing a deeper understanding of the genetics of these periodically reclassified fishes (as species or subspecies). We used six microsatellite markers to assess the current population structure and gene flow patterns across 19 populations of mosquito fish and then compared our results with historical data. Genetic evidence demonstrates that the current hybrid zone is located in a similar geographic region as the historical one, even after three decades. Hybrid fish, however, demonstrate relatively low heterozygosity and are genetically distinct from western and eastern mosquito fish populations. Fin ray counts, sometimes used to distinguish the two species from one another, demonstrate more eastern ( G. holbrooki) phenotype fish within the molecular genetic hybrid zone today. Mosquito fish are globally invasive, often found on the leading edge of flooded waters that they colonize, so the impact of hurricanes in the wake of climate change was also evaluated. An increase in the frequency and intensity of hurricanes in the hybrid region has occurred, and this point warrants further attention since hurricanes are known to move these aggressive, invasive species into novel territory. This work contributes to our classical understanding of hybrid zone temporal dynamics, refines our understanding of mosquito fish genetics in their native range, evaluates important genotype-phenotype relationships, and identifies a potential new impact of climate change.

Genetic adaptation to captivity can occur in a single generation

PubMed Central

Christie, Mark R.; Marine, Melanie L.; French, Rod A.; Blouin, Michael S.

2012-01-01

Captive breeding programs are widely used for the conservation and restoration of threatened and endangered species. Nevertheless, captive-born individuals frequently have reduced fitness when reintroduced into the wild. The mechanism for these fitness declines has remained elusive, but hypotheses include environmental effects of captive rearing, inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to captivity). We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild. PMID:22184236

Rapid prenatal diagnosis of chromosomal aneuploidies by fluorescence in situ hybridization: clinical experience with 4,500 specimens.

PubMed Central

Ward, B E; Gersen, S L; Carelli, M P; McGuire, N M; Dackowski, W R; Weinstein, M; Sandlin, C; Warren, R; Klinger, K W

1993-01-01

Detection of chromosome aneuploidies in uncultured amniocytes is possible using fluorescence in situ hybridization (FISH). We herein describe the results of the first clinical program which utilized FISH for the rapid detection of chromosome aneuploidies in uncultured amniocytes. FISH was performed on physician request, as an adjunct to cytogenetics in 4,500 patients. Region-specific DNA probes to chromosomes 13, 18, 21, X, and Y were used to determine ploidy by analysis of signal number in hybridized nuclei. A sample was considered to be euploid when all autosomal probes generated two hybridization signals and when a normal sex chromosome pattern was observed in greater than or equal to 80% of hybridized nuclei. A sample was considered to be aneuploid when greater than or equal to 70% of hybridized nuclei displayed the same abnormal hybridization pattern for a specific probe. Of the attempted analyses, 90.2% met these criteria and were reported as informative to referring physicians within 2 d of receipt. Based on these reporting parameters, the overall detection rate for aneuploidies was 73.3% (107/146), with an accuracy of informative results for aneuploidies of 93.9% (107/114). Compared to cytogenetics, the accuracy of all informative FISH results, euploid and aneuploid, was 99.8%, and the specificity was 99.9%. In those pregnancies where fetal abnormalities had been observed by ultrasound, referring physicians requested FISH plus cytogenetics at a significantly higher rate than they requested cytogenetics alone. The current prenatal FISH protocol is not designed to detect all chromosome abnormalities and should only be utilized as an adjunctive test to cytogenetics. This experience demonstrates that FISH can provide a rapid and accurate clinical method for prenatal identification of chromosome aneuploidies. PMID:8488836

Scombroid poisoning. A report of seven cases involving the Western Australian salmon, Arripis truttaceus.

PubMed

Smart, D R

To present the clinical findings of scombroid poisoning due to ingestion of the Western Australian salmon, Arripis truttaceus, occurring in two separate outbreaks involving seven patients. Both outbreaks occurred in March and the fish had been caught in South Australian waters. Onset of symptoms in all patients occurred within half an hour of ingestion of the affected fish. The clinical syndrome included erythema and urticaria of the skin, facial flushing and sweating, palpitations, hot flushes of the body, headache, nausea, vomiting and dizziness. The fish implicated in one outbreak was noted to have a peppery taste. The diagnosis of scombroid poisoning was confirmed by the presence of the clinical syndrome, and by demonstration of high histamine levels in the cooked fish. Two patients had minor symptoms which had resolved before seeking medical advice. Another two patients had mild symptoms which disappeared after two hours of observation and required no specific treatment. Three patients had evidence of major toxicity which was successfully treated with parenterally administered promethazine. One of the three patients with major toxicity required overnight admission and repeated doses of promethazine to eradicate her symptoms. No patient had symptoms for longer than 12 hours. Scombroid poisoning is caused by ingestion of fish which has accumulated scombrotoxin during spoilage. The toxin is heat stable and has been identified as histamine. The clinical presentation closely resembles an acute allergic reaction. This similarity in symptoms may result in the diagnosis of scombroid poisoning being missed by clinicians. Patients with the symptom complex may be incorrectly informed that they are allergic to the fish species. Diagnosis is clinical and can be confirmed by analysis of the histamine content of the fish. Treatment is with antihistamines, however major toxicity may require the same aggressive management as acute anaphylaxis.

Kinetic analysis of the swimming behavior of the goldfish, Carassius auratus, exposed to nickel: Hypoactivity induced by sublethal concentrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ellgaard, E.G.; Ashley, S.E.; Langford, A.E.

1995-12-01

The discharge of nickel into aquatic environments from numerous industries poses a threat to fish populations because of its toxcity. Although little is known, however, about the precise mechanism of its toxicity in freshwater fish, it produces some of the symptoms associated with heavy-metal poisoning in general; it accumulates in fish tissues and results in alterations in gill structure, including hypertrophy of respiratory and mucous cells, separation of the epithelial layer from the pillar cell system, cauterization and sloughing, and necrosis of the epithelium. The destruction of the gill lamellae decreases the ventilation rate and if severe, as after acutemore » exposure, may cause blood hypoxia and death. The effects of short-term exposure of fish to sublethal concentrations of nickel and not as well defined. The kinetic method of Ellgaard et al., which uses locomotor activity to assess the general health of fish, is ideally suited to examine whether sublethal concentrations of nickel adversely affect fish. In previous studies, the measured changes in locomotor activity observed when fish are exposed to pollutants correlate with more specific changes, e.g., physiological, biochemical, histological or neurosensory changes, which occur under the same conditions. Thus, the kinetic method also meets the criterial for pollution early warning systems as discussed by Cairns and van der Schale. This method has previously been used to demonstrate that short-term exposure to sublethal concentrations of the heavy metals cadmium, chromium, and zinc and copper are detrimental to the health of bluegills. The present study examines the effects of short-term exposures of sublethal concentrations of nickel on the locomotor activity of the goldfish, Carassius auratus. 11 refs., 1 fig., 2 tabs.« less

Assessing food web dynamics and relative importance of organic matter sources for fish species in two Portuguese estuaries: a stable isotope approach.

PubMed

França, Susana; Vasconcelos, Rita P; Tanner, Susanne; Máguas, Cristina; Costa, Maria José; Cabral, Henrique N

2011-10-01

Stable carbon and nitrogen isotopes (δ¹³C, δ¹⁵N) were used to analyse food web dynamics of two of the main estuaries of the Portuguese coast: Tejo and Mira. The ultimate sources of organic matter supporting production of some of the most abundant and commercially important fish species were determined; and seasonal, inter- and intra- estuarine differences in the trophic relations among producers and consumers were identified. Stable isotope analysis was performed in different producers, primary consumers (main prey items for fish) and fish species (Solea solea, Solea senegalensis, Pomatoschistus microps, Dicentrarchus labrax, Liza ramada, Diplodus vulgaris and Atherina presbyter) of two areas in each estuary, in July and October 2009. Model calculations showed that the main prey for the fish species in the Tejo estuary used mostly salt marsh-derived organic matter as nutritional sources, with no marked differences between the sampled months. Trophic levels of fish species from the same estuary differed at multiple scales: inter-species, seasonally and spatially (both between and within estuaries). Significant differences in isotopic composition of fish species were more pronounced spatially (between the two sampled areas in the estuary) than seasonally (between sampled months). Trophic relationships in both estuaries demonstrated that organic matter is transferred to higher trophic positions mainly through benthic pathways. This shows the flexibility of these species to share resources and to exploit temporary peaks in prey populations. The present results showed that extensive disturbance in intertidal habitats from both estuaries may potentially change the balance of organic matter in the base of these complex food webs. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Simplified Digestion Protocol for the Analysis of Hg in Fish by Cold Vapor Atomic Absorption Spectroscopy

ERIC Educational Resources Information Center

Kristian, Kathleen E.; Friedbauer, Scott; Kabashi, Donika; Ferencz, Kristen M.; Barajas, Jennifer C.; O'Brien, Kelly

2015-01-01

Analysis of mercury in fish is an interesting problem with the potential to motivate students in chemistry laboratory courses. The recommended method for mercury analysis in fish is cold vapor atomic absorption spectroscopy (CVAAS), which requires homogeneous analyte solutions, typically prepared by acid digestion. Previously published digestion…

Novel venous thromboembolic disease (VTED) prophylaxis for total knee arthroplasty—aspirin and fish oil

PubMed Central

Sodhi, Nipun; Patel, Yatindra H.; Sultan, Assem A.; Khlopas, Anton; Chughtai, Morad; Kolisek, Frank R.; Williams, Nick; Mont, Michael A.

2017-01-01

Background Despite the demonstrated success of multiple anticoagulation therapies for post-operative prophylaxis of thromboembolic disease in lower extremity arthroplasties, each modality comes with a unique set of limitations. Thus, the ideal anticoagulation medication which provides adequate therapy with minimal cost, complications, or added patient work is yet to be defined. One promising novel thrombophylactic supplement is fish oil, as many preliminary clinical trials have demonstrated a protective effect of fish oil against thrombosis in multiple clinical settings. In addition, others have demonstrated synergistic effect when combined with aspirin. However, there are paucity of studies that compared combined aspirin and fish oil therapy for venous thromboembolism prophylaxis with other pharmacological agents, especially in the field of orthopaedics. Therefore, this study evaluated: (I) risk of post-operative deep vein thrombosis (DVT) and pulmonary embolism (PE), and (II) bleeding complications; among patients who had primary total knee arthroplasty (TKA) and received one of the following regimens: (i) 325 mg aspirin and mechanical pulsatile stocking; (ii) rivaroxaban; or (iii) 325 mg aspirin and 1,000 mg fish oil. Methods This was a 6-year prospective study analyzing the postoperative thromboembolic prophylaxis received by patients who underwent primary TKA. Patients who had a previous history of thromboembolic disease were excluded from the study due to an increased risk of recurrent clot formation. A total of 850 patients were enrolled. A total of 300 patients enrolled between October 2011 and June 2013 received 325 mg aspirin and mechanical pulsatile stocking, while 250 patients enrolled between June 2013 and December 2014 received rivaroxaban. A total of 300 patients enrolled between January 2015 and July 2017 received 325 mg aspirin and 1,000 mg fish oil. Major venous thromboembolic events (VTEs) and bleeding complications within the first 90 days post-operatively were recorded in each cohort. The odds ratios (ORs) and 95% confidence intervals (CIs), for thromboembolic and bleeding events were calculated and compared between the aspirin and fish oil cohort vs. aspirin and pulsatile stocking cohort, and aspirin and fish oil cohort vs. rivaroxaban cohort. A P value of <0.05 was used to determine statistical significance. Results A total of 25 DVT events were recorded including 1 of 300 (0.33%) in the aspirin and fish oil cohort, 22 of 300 (7.33%) in the aspirin and pulsatile stocking cohort and 2 of 250 (0.8%) in the rivaroxaban cohort. When comparing ORs, patients who received aspirin and fish oil demonstrated significantly lower risk for thromboembolic events when compared to the aspirin and pulsatile stocking group (OR: 0.045; 95% CI: 0.0061–0.3394; P<0.05). When compared to the rivaroxaban cohort the ORs did not differ significantly (OR: 0.416; 95% CI: 0.0376–4.6223; P>0.05). In addition, no PE events were recorded in any of the cohorts. When compared to rivaroxaban, the fish oil and aspirin cohort demonstrated significantly lower incidence of bleeding episodes (1 of 300, 0.33% vs. 30 of 250 patients, 12%; OR: 0.0278; 95% CI: 0.0038–0.2051; P<0.05). No bleeding events were recorded in the aspirin and pulsatile stocking cohort. Conclusions This study demonstrated the potentially synergistic anti-thromboembolic effect of aspirin and fish oil in the prevention of post-operative venous thromboembolism in primary TKA patients. Based on the results from this study, the authors conclude that the combination of aspirin and fish oil maybe an excellent thromboprophylactic modality for patients to use after TKA. These results warrant further, larger prospective studies analyzing the use of fish oil supplements in VTE prophylaxis. PMID:29299477

Novel venous thromboembolic disease (VTED) prophylaxis for total knee arthroplasty-aspirin and fish oil.

PubMed

Bonutti, Peter M; Sodhi, Nipun; Patel, Yatindra H; Sultan, Assem A; Khlopas, Anton; Chughtai, Morad; Kolisek, Frank R; Williams, Nick; Mont, Michael A

2017-12-01

Despite the demonstrated success of multiple anticoagulation therapies for post-operative prophylaxis of thromboembolic disease in lower extremity arthroplasties, each modality comes with a unique set of limitations. Thus, the ideal anticoagulation medication which provides adequate therapy with minimal cost, complications, or added patient work is yet to be defined. One promising novel thrombophylactic supplement is fish oil, as many preliminary clinical trials have demonstrated a protective effect of fish oil against thrombosis in multiple clinical settings. In addition, others have demonstrated synergistic effect when combined with aspirin. However, there are paucity of studies that compared combined aspirin and fish oil therapy for venous thromboembolism prophylaxis with other pharmacological agents, especially in the field of orthopaedics. Therefore, this study evaluated: (I) risk of post-operative deep vein thrombosis (DVT) and pulmonary embolism (PE), and (II) bleeding complications; among patients who had primary total knee arthroplasty (TKA) and received one of the following regimens: (i) 325 mg aspirin and mechanical pulsatile stocking; (ii) rivaroxaban; or (iii) 325 mg aspirin and 1,000 mg fish oil. This was a 6-year prospective study analyzing the postoperative thromboembolic prophylaxis received by patients who underwent primary TKA. Patients who had a previous history of thromboembolic disease were excluded from the study due to an increased risk of recurrent clot formation. A total of 850 patients were enrolled. A total of 300 patients enrolled between October 2011 and June 2013 received 325 mg aspirin and mechanical pulsatile stocking, while 250 patients enrolled between June 2013 and December 2014 received rivaroxaban. A total of 300 patients enrolled between January 2015 and July 2017 received 325 mg aspirin and 1,000 mg fish oil. Major venous thromboembolic events (VTEs) and bleeding complications within the first 90 days post-operatively were recorded in each cohort. The odds ratios (ORs) and 95% confidence intervals (CIs), for thromboembolic and bleeding events were calculated and compared between the aspirin and fish oil cohort vs. aspirin and pulsatile stocking cohort, and aspirin and fish oil cohort vs. rivaroxaban cohort. A P value of <0.05 was used to determine statistical significance. A total of 25 DVT events were recorded including 1 of 300 (0.33%) in the aspirin and fish oil cohort, 22 of 300 (7.33%) in the aspirin and pulsatile stocking cohort and 2 of 250 (0.8%) in the rivaroxaban cohort. When comparing ORs, patients who received aspirin and fish oil demonstrated significantly lower risk for thromboembolic events when compared to the aspirin and pulsatile stocking group (OR: 0.045; 95% CI: 0.0061-0.3394; P<0.05). When compared to the rivaroxaban cohort the ORs did not differ significantly (OR: 0.416; 95% CI: 0.0376-4.6223; P>0.05). In addition, no PE events were recorded in any of the cohorts. When compared to rivaroxaban, the fish oil and aspirin cohort demonstrated significantly lower incidence of bleeding episodes (1 of 300, 0.33% vs . 30 of 250 patients, 12%; OR: 0.0278; 95% CI: 0.0038-0.2051; P<0.05). No bleeding events were recorded in the aspirin and pulsatile stocking cohort. This study demonstrated the potentially synergistic anti-thromboembolic effect of aspirin and fish oil in the prevention of post-operative venous thromboembolism in primary TKA patients. Based on the results from this study, the authors conclude that the combination of aspirin and fish oil maybe an excellent thromboprophylactic modality for patients to use after TKA. These results warrant further, larger prospective studies analyzing the use of fish oil supplements in VTE prophylaxis.

Constitutional Mosaic Trisomy 13 in Two Germ Cell Layers is Different from Patau Syndrome? A Case Report.

PubMed

Kunwar, Fulesh; Pandya, Vidhi; Bakshi, Sonal R

2016-03-01

The heterogeneous phenotype of known syndromes is a clinical challenge, and harmonized description using globally accepted ontology is desirable. This report attempts phenotypic analysis in a patient of constitutional mosaic trisomy 13 in mesoderm and ectoderm to make globally comparable clinical description. Phenotypic features (minor/major abnormalities) were recorded and matched with the Human Phenotype Ontology terms that were used to query web-based tool Phenomizer. We report here a case of 24-year-old girl born to non consanguineous parents with history of one abortion. Her phenotypic evaluation included short columella, low-set ears, seizures, enlarged naris, bifid tongue, infra-orbital fold, smooth philtrum, microtia, microcephaly, carious teeth, downslanted palpebral fissures, proportionate short stature, high palate, thin upper lip vermilion, small for gestational age, broad fingertip, broad hallux, mandibular prognathia and dental malocclusion. Karyotype and interphase FISH (Fluorescence in situ hybridization) was done in blood cells. Interphase FISH was also performed on buccal epithelial cells. Cytogenetic analysis demonstrated trisomy 13 mosaicism in 25% cells i.e. 47, XX,+13(9)/46,XX(27). The interphase FISH in blood cells showed trisomy 13 in 15%, whereas in buccal mucosa cells showed nearly 6%. Mosaic aneuploidy in constitutional karyotype can be responsible for variation in clinical and morphological presentation of patient with genetic disorder.

Global Trophic Position Comparison of Two Dominant Mesopelagic Fish Families (Myctophidae, Stomiidae) Using Amino Acid Nitrogen Isotopic Analyses

PubMed Central

Choy, C. Anela; Davison, Peter C.; Drazen, Jeffrey C.; Flynn, Adrian; Gier, Elizabeth J.; Hoffman, Joel C.; McClain-Counts, Jennifer P.; Miller, Todd W.; Popp, Brian N.; Ross, Steve W.; Sutton, Tracey T.

2012-01-01

The δ15N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ15N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ15N values. Regional differences in the δ15N values of phenylalanine confirmed that bulk tissue δ15N values reflect region-specific water mass biogeochemistry controlling δ15N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ∼2.9) largely align with expectations from stomach content studies (TP ∼3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ∼3.2) were lower than TPs derived from stomach content studies (TP∼4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure. PMID:23209656

Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses

USGS Publications Warehouse

Choy, C. Anela; Davison, Peter C.; Drazen, Jeffrey C.; Flynn, Adrian; Gier, Elizabeth J.; Hoffman, Joel C.; McClain-Counts, Jennifer P.; Miller, Todd W.; Popp, Brian N.; Ross, Steve W.; Sutton, Tracey T.

2012-01-01

The δ15N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ15N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ15N values. Regional differences in the δ15N values of phenylalanine confirmed that bulk tissue δ15N values reflect region-specific water mass biogeochemistry controlling δ15N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ~2.9) largely align with expectations from stomach content studies (TP ~3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ~3.2) were lower than TPs derived from stomach content studies (TP~4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

Paradoxical anaerobism in desert pupfish.

PubMed

Heuton, Matt; Ayala, Luis; Burg, Chris; Dayton, Kyle; McKenna, Ken; Morante, Aldo; Puentedura, Georgina; Urbina, Natasha; Hillyard, Stanley; Steinberg, Spencer; van Breukelen, Frank

2015-12-01

In order to estimate metabolic demands of desert pupfish for conservation purposes, we measured oxygen consumption in fish acclimated to the ecologically relevant temperatures of 28 or 33°C. For these experiments, we used fish derived from a refuge population of Devils Hole pupfish (Cyprinodon diabolis). Measurement of routine oxygen consumption (V̇O2,routine) revealed some 33°C-acclimated fish (10% of 295 assayed fish) periodically exhibited periods of no measurable oxygen consumption despite available ambient oxygen tensions that were above the critical PO2. We call this phenomenon paradoxical anaerobism. The longest observed continuous bout with no oxygen consumption was 149 min, although typical bouts were much shorter. Fish maintained normal posture and ventilation rate (>230 ventilations per minute) during paradoxical anaerobism. Fish rarely demonstrated a compensatory increase in oxygen use following a period of paradoxical anaerobism. In contrast, only one out of 262 sampled fish acclimated at 28°C spontaneously demonstrated paradoxical anaerobism. Muscle lactate concentration was not elevated during periods of paradoxical anaerobism. However, the amount of ethanol released by the 33°C-acclimated fish was 7.3 times greater than that released by the 28°C acclimation group, suggesting ethanol may be used as an alternative end product of anaerobic metabolism. Exposure to exogenous ethanol, in concentrations as low as 0.1%, produced periods of paradoxical anaerobism even in 28°C-acclimated fish. © 2015. Published by The Company of Biologists Ltd.

The effect of fish meal replacement by soyabean products on fish growth: a meta-analysis.

PubMed

Sales, James

2009-12-01

Meta-analysis was applied to quantify the effect of replacement of fish meal by soyabean products in diets on fish growth. Measurement of growth in different units among studies required the use of a standardised effect size (Hedges' d). From a total of ninety-nine studies concentrating on fish meal replacement by defatted soyabean meal, 53 % were eliminated due to, among others, absence of a fish meal control diet (n 18), or no statistical differences or measurement of dispersion (n 6) indicated. Replacement of 4 to 40 % fish meal by soyabean meal (inclusion levels of 71-366 g/kg) resulted in a mean effect size of - 0.1142 (95 % CI - 0.4665, 0.2382) obtained in forty-eight comparisons evaluated with seventeen different fish species. However, at higher fish meal replacement levels the 95 % CI calculated for combined effect sizes did not overlap with zero. With soya protein concentrate replacing 25 to 100 % of fish meal in diets for seven fish species, methionine supplementation (mean - 2.4373 (95 % CI - 3.9004, - 0.9742); n 10) did not have a substantial influence on the magnitude of cumulative effect sizes relative to no supplementation (mean - 2.7306 (95 % CI - 3.7991, - 1.6620); n 16). Information on other soyabean products (full-fat soyabeans, soya flour) used as protein sources in fish diets was found as too limited for analysis and definite conclusions. The present study contributes by putting a numerical value to the magnitude of growth differences in fish when replacing dietary fish meal by soyabean products.

Effects of dams in river networks on fish assemblages in non-impoundment sections of rivers in Michigan and Wisconsin, USA

USGS Publications Warehouse

Stewart, Jana S.; Lizhu Wang,; Infante, Dana M.; Lyons, John D.; Arthur Cooper,

2011-01-01

Regional assessment of cumulative impacts of dams on riverine fish assemblages provides resource managers essential information for dam operation, potential dam removal, river health assessment and overall ecosystem management. Such an assessment is challenging because characteristics of fish assemblages are not only affected by dams, but also influenced by natural variation and human-induced modification (in addition to dams) in thermal and flow regimes, physicochemical habitats and biological assemblages. This study evaluated the impacts of dams on river fish assemblages in the non-impoundment sections of rivers in the states of Michigan and Wisconsin using multiple fish assemblage indicators and multiple approaches to distinguish the influences of dams from those of other natural and human-induced factors. We found that environmental factors that influence fish assemblages in addition to dams should be incorporated when evaluating regional effects of dams on fish assemblages. Without considering such co-influential factors, the evaluation is inadequate and potentially misleading. The role of dams alone in determining fish assemblages at a regional spatial scale is relatively small (explained less than 20% of variance) compared with the other environmental factors, such as river size, flow and thermal regimes and land uses jointly. However, our results do demonstrate that downstream and upstream dams can substantially modify fish assemblages in the non-impoundment sections of rivers. After excluding river size and land-use influences, our results clearly demonstrate that dams have significant impacts on fish biotic-integrity and habitat-and-social-preference indicators. The influences of the upstream dams, downstream dams, distance to dams, and dam density differ among the fish indicators, which have different implications for maintaining river biotic integrity, protecting biodiversity and managing fisheries.

Effects of dams in river networks on fish assemblages in non-impoundment sections of rivers in Michigan and Wisconsin, USA

USGS Publications Warehouse

Wang, L.; Infante, D.; Lyons, J.; Stewart, J.; Cooper, A.

2011-01-01

Regional assessment of cumulative impacts of dams on riverine fish assemblages provides resource managers essential information for dam operation, potential dam removal, river health assessment and overall ecosystem management. Such an assessment is challenging because characteristics of fish assemblages are not only affected by dams, but also influenced by natural variation and human-induced modification (in addition to dams) in thermal and flow regimes, physicochemical habitats and biological assemblages. This study evaluated the impacts of dams on river fish assemblages in the non-impoundment sections of rivers in the states of Michigan and Wisconsin using multiple fish assemblage indicators and multiple approaches to distinguish the influences of dams from those of other natural and human-induced factors. We found that environmental factors that influence fish assemblages in addition to dams should be incorporated when evaluating regional effects of dams on fish assemblages. Without considering such co-influential factors, the evaluation is inadequate and potentially misleading. The role of dams alone in determining fish assemblages at a regional spatial scale is relatively small (explained less than 20% of variance) compared with the other environmental factors, such as river size, flow and thermal regimes and land uses jointly. However, our results do demonstrate that downstream and upstream dams can substantially modify fish assemblages in the non-impoundment sections of rivers. After excluding river size and land-use influences, our results clearly demonstrate that dams have significant impacts on fish biotic-integrity and habitat-and-social-preference indicators. The influences of the upstream dams, downstream dams, distance to dams, and dam density differ among the fish indicators, which have different implications for maintaining river biotic integrity, protecting biodiversity and managing fisheries. ?? 2010 John Wiley & Sons, Ltd.

Narrowing the position of the Treacher Collins syndrome locus to a small interval between three new microsatellite markers at 5q32-33. 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, M.J.; Dixon, J.; Houseal, T.

Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate. The TCOF1 locus has been localized to chromosome 5q32-33.2. In the present study the authors have used the combined techniques of genetic linkage analysis and fluorescence in situ hybridization (FISH) to more accurately define the TCOF1 critical region. Cosmids IG90 and SPARC, which map to distal 5q, encompass two and one hypervariable microsatellite markers, respectively. The heterozygosity values of these three markers range from .72 to .81. Twenty-two unrelated TCOF1 families have been analyzed for linkage tomore » these markers. There is strong evidence demonstrating linkage to all three markers, the strongest support for positive linkage being provided by haplotyping those markers at the locus encompassed by the cosmid IG90 (Z[sub max]= 19.65; 0 = .010). FISH to metaphase chromosomes and interphase nuclei established that IG90 lies centromeric to SPARC. This information combined with the data generated by genetic linkage analysis demonstrated that the TCOF1 locus is closely flanked proximally by IG90 and distally by SPARC. 30 refs., 2 figs., 4 tabs.« less

Immunostimulants in fish diets

USGS Publications Warehouse

Gannam, A.L.; Schrock, R.M.

1999-01-01

Various immunostimulants and their methods of application in fish culture are examined in this review. Important variables such as life stage and innate disease resistance of the fish; immunostimulant used, its structure and mode of action; and the fish's environment are discussed. Conflicting results have been published about the efficacy of immunostimulants in fish diets. Some researchers have had positive responses demonstrated as increased fish survival, others have not. Generally, immunostimulants enhance individual components of the non-specific immune response but that does not always translate into increased fish survival. In addition, immunostimulants fed at too high a dose or for too long can be immunosuppressive. [Article copies available for a fee from The Haworth Document Delivery Service: 1-800-342-9678. E-mail address: getinfo@haworthpressinc.com ].

Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments.

PubMed

Yuan, Zihao; Liu, Shikai; Zhou, Tao; Tian, Changxu; Bao, Lisui; Dunham, Rex; Liu, Zhanjiang

2018-02-13

Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases.

Identifying nutrient reference sites in nutrient-enriched regions-Using algal, invertebrate, and fish-community measures to identify stressor-breakpoint thresholds in Indiana rivers and streams, 2005-9

USGS Publications Warehouse

Caskey, Brian J.; Bunch, Aubrey R.; Shoda, Megan E.; Frey, Jeffrey W.; Selvaratnam, Shivi; Miltner, Robert J.

2013-01-01

Excess nutrients in aquatic ecosystems can lead to shifts in species composition, reduced dissolved oxygen concentrations, fish kills, and toxic algal blooms. In this study, nutrients, periphyton chlorophyll a (CHLa), and invertebrate- and fishcommunity data collected during 2005-9 were analyzed from 318 sites on Indiana rivers and streams. The objective of this study was to determine which invertebrate and fish-taxa attributes best reflect the conditions of streams in Indiana along a gradient of nutrient concentrations by (1) determining statistically and ecologically significant relations among the stressor (total nitrogen, total phosphorus, and periphyton CHLa) and response (invertebrate and fish community) variables; and (2) determining the levels at which invertebrate- and fish-community measures change in response to nutrients or periphyton CHLa. For water samples at the headwater sites, total nitrogen (TN) concentrations ranged from 0.343 to 21.6 milligrams per liter (mg/L) (median 2.12 mg/L), total phosphorus (TP) concentrations ranged from 0.050 to 1.44 mg/L (median 0.093 mg/L), and periphyton CHLa ranged from 0.947 to 629 mg/L (median 69.7 mg/L). At the wadable sites, TN concentrations ranged from 0.340 to 10.0 mg/L (median 2.31 mg/L), TP concentrations ranged from 0.050 to 1.24 mg/L (median 0.110 mg/L), and periphyton CHLa ranged from 0.383 to 719 mg/L (median 44.7 mg/L). Recursive partitioning identified statistically significant low and high breakpoint thresholds on invertebrate and fish measures, which demonstrated the ecological response in enriched conditions. The combined community (invertebrate and fish) mean low and high TN breakpoint thresholds were 1.03 and 2.61 mg/L, respectively. The mean low and high breakpoint thresholds for TP were 0.083 and 0.144 mg/L, respectively. The mean low and high breakpoint thresholds for periphyton CHLa were 20.9 and 98.6 milligrams per square meter (mg/m2), respectively. Additive quantile regression analysis found similar thresholds (TN of 0.656 mg/L, mean TP of 0.118 mg/L, and periphyton CHLa of 27.2 mg/m2) for some stressor variables as determined by the breakpoint analysis. The TN and TP concentrations in this study showed a nutrient gradient that spanned three orders of magnitude. Sites were divided into Low, Medium, and High nutrient groups based on the 10th and 75th percentiles. The invertebrate and fish communities were similar along the nutrient gradient, using an analysis of similarity, demonstrating there was not a species trophic gradient. Within all nutrient groups, invertebrate and fish communities were dominated by nutrient tolerant taxa (algivores, herbivores, and omnivores) that included invertebrates, such as Cheumatopsyche sp., Physella sp., and fish such as Stonerollers (Campostoma spp.) and Bluntnose Minnow (Pimephales notatus). To determine if low nutrient concentrations at some sites were caused by algal uptake and not oligotrophic conditions, sites with low nutrient concentrations (less than 10th percentile for TN or TP) were examined based on the Low (less than or equal to the 10th percentile) and High (greater than the 75th percentile) periphyton CHLa concentrations. Within low nutrient sites, the invertebrate and fish communities were statistically different between Low and High periphyton CHLa categories. The majority of variance between the Low and High periphyton CHLa categories was caused by Cheumatopsyche sp. (caddisfly), Physella sp. (pulmonate snail), and Caenis latipennis (a mayfly) in the invertebrate community; and caused by Stonerollers, Western Blacknose Dace (Rhinichthys atratulus meleagris), and Creek Chub (Semotilus atromaculatus) in the fish community. The dominance of tolerant herbivore and omnivore taxa in the High periphyton CHLa group indicates that low nutrient concentrations are a result of nutrient uptake and increased algal growth. This study highlights the importance of assessing multiple lines of evidence when attempting to identify the trophic condition of a site.

Actuation of a robotic fish caudal fin for low reaction torque

NASA Astrophysics Data System (ADS)

Yun, Dongwon; Kim, Kyung-Soo; Kim, Soohyun; Kyung, Jinho; Lee, Sunghee

2011-07-01

In this paper, a novel caudal fin for actuating a robotic fish is presented. The proposed caudal fin waves in a vertical direction with a specific spatial shape, which is determined by a so-called shape factor. For a specific shape factor, a traveling wave with a vertical phase difference is formed on a caudal fin during fin motion. It will be shown by the analysis that the maximum reaction torque at the joint of a caudal fin varies depending on the shape factors. Compared with a conventional plate type caudal fin, the proposed fin with a shape factor of 2π can eliminate the reaction torque perfectly, while keeping the propulsion force unchanged. The benefits of the proposed fin will be demonstrated by experiments.

Isolated contact urticaria caused by immunoglobulin E-mediated fish allergy.

PubMed

Onesimo, Roberta; Giorgio, Valentina; Pill, Stefania; Monaco, Serena; Sopo, Stefano Miceli

2012-01-01

Fish is a common cause of food allergy. The reactions usually occur after its ingestion. In most immunoglobulin E-mediated reactions, the allergens are gastroresistant and heat-stable proteins of low molecularweight (parvalbumin). On the other hand, isolated contact urticaria following the handling of raw fish but without symptoms after its ingestion was found among cooks and professional fish handlers. In these cases, the fish allergens are gastrosensitive and thermolabile, as demonstrated by the decrease in the diameter of the wheal in the skin-prick test using cooked fish. To the best of our knowledge isolated fish contact urticaria in children has not been previously reported. We analyze the features of three pediatric cases of contact urticaria from cod (one of them was sensitized to parvalbumin), with tolerance after ingestion of this fish on oral food challenge.

A novel variant of aquaporin 3 is expressed in killifish (Fundulus heteroclitus) intestine

PubMed Central

Jung, Dawoon; Adamo, Meredith A.; Lehman, Rebecca M.; Barnaby, Roxanna; Jackson, Craig E.; Jackson, Brian P.; Shaw, Joseph R.; Stanton, Bruce A.

2015-01-01

Killifish (Fundulus heteroclitus) are euryhaline teleosts that are widely used in environmental and toxicological studies, and they are tolerant to arsenic, in part due to very low assimilation of arsenic from the environment. The mechanism of arsenic uptake by the intestine, a major route of arsenic uptake in humans is unknown. Thus, the goal of this study was to determine if aquaglyceroporins (AQP), which transport water and other small molecules including arsenite across cell membranes, are expressed in the killifish intestine, and whether AQP expression is affected by osmotic stress. Through RT-PCR and sequence analysis of PCR amplicons, we demonstrated that the intestine expresses kfAQP3a and kfAQP3b, two previously identified variants, and also identified a novel variant of killifish AQP3 (kfAQP3c) in the intestine. The variants likely represent alternate splice forms. A BLAST search of the F. heteroclitus reference genome revealed that the AQP3 gene resides on a single locus, while an alignment of the AQP3 sequence among 384 individuals from eight population ranging from Rhode Island to North Carolina revealed that its coding sequence was remarkably conserved with no fixed polymorphism residing in the region that distinguishes these variants. We further demonstrate that the novel variant transports arsenite into HEK293T cells. Whereas kfAQP3a, which does not transport arsenite, was expressed in both freshwater (FW) and saltwater (SW) acclimated fish, kfAQP3b, an arsenic transporter, was expressed only in FW acclimated fish, and kfAQP3c was expressed only in SW acclimated fish. Thus, we have identified a novel, putative splice variant of kfAQP3, kfAQP3c, which transports arsenic and is expressed only in SW acclimated fish. PMID:25766383

Sequence conservation on the Y chromosome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, L.H.; Yang-Feng, L.; Lau, C.

The Y chromosome is present in all mammals and is considered to be essential to sex determination. Despite intense genomic research, only a few genes have been identified and mapped to this chromosome in humans. Several of them, such as SRY and ZFY, have been demonstrated to be conserved and Y-located in other mammals. In order to address the issue of sequence conservation on the Y chromosome, we performed fluorescence in situ hybridization (FISH) with DNA from a human Y cosmid library as a probe to study the Y chromosomes from other mammalian species. Total DNA from 3,000-4,500 cosmid poolsmore » were labeled with biotinylated-dUTP and hybridized to metaphase chromosomes. For human and primate preparations, human cot1 DNA was included in the hybridization mixture to suppress the hybridization from repeat sequences. FISH signals were detected on the Y chromosomes of human, gorilla, orangutan and baboon (Old World monkey) and were absent on those of squirrel monkey (New World monkey), Indian munjac, wood lemming, Chinese hamster, rat and mouse. Since sequence analysis suggested that specific genes, e.g. SRY and ZFY, are conserved between these two groups, the lack of detectable hybridization in the latter group implies either that conservation of the human Y sequences is limited to the Y chromosomes of the great apes and Old World monkeys, or that the size of the syntenic segment is too small to be detected under the resolution of FISH, or that homologeous sequences have undergone considerable divergence. Further studies with reduced hybridization stringency are currently being conducted. Our results provide some clues as to Y-sequence conservation across species and demonstrate the limitations of FISH across species with total DNA sequences from a particular chromosome.« less

Selective uptake and biological consequences of environmentally relevant antidepressant pharmaceutical exposures on male fathead minnows

USGS Publications Warehouse

Schultz, Melissa M.; Painter, Meghan M.; Bartell, Stephen E.; Logue, Amanda; Furlong, Edward T.; Werner, Stephen L.; Schoenfuss, Heiko L.

2011-01-01

Antidepressant pharmaceuticals have been reported in wastewater effluent at the nanogram to low microgram-per-liter range, and include bupropion (BUP), fluoxetine (FLX), sertraline (SER), and venlafaxine (VEN). To assess the effects of antidepressants on reproductive anatomy, physiology, and behavior, adult male fathead minnows (Pimeplwles promelas) were exposed for 21 days either to a single concentration of the antidepressants FLX, SER, VEN, or BUP, or to an antidepressant mixture. The data demonstrated that exposure to VEN (305 ng/L and 1104 ng/L) and SER (5.2 ng/L) resulted in mortality. Anatomical alterations were noted within the testes of fish exposed to SER and FLX, both modulators of the neurotransmitter serotonin. Additionally, FLX at 28 ng/L induced vitellogenin in male fish—a common endpoint for estrogenic endocrine disruption. Significant alterations in male secondary sex characteristics were noted with single exposures. Effects of single compound exposures neither carried over, nor became additive in the antidepressant mixtures, and reproductive behavior was not affected. Analysis of brain tissues from the exposed fish suggested increased uptake of FLX, SER and BUP and minimal uptake of VEN when compared to exposure water concentrations. Furthermore, the only metabolite detected consistently in the brain tissues was norfluoxetine. Similar trends of uptake by brain tissue were observed when fish were exposed to antidepressant mixtures. The present study demonstrates that anatomy and physiology, but not reproductive behavior, can be disrupted by exposure to environmental concentrations of some antidepressants. The observation that antidepressant uptake into fish tissues is selective may have consequences on assessing the mode-of-action and effects of these compounds in future studies.

Indicators of AEI applied to the Delaware Estuary.

PubMed

Barnthouse, Lawrence W; Heimbuch, Douglas G; Anthony, Vaughn C; Hilborn, Ray W; Myers, Ransom A

2002-05-18

We evaluated the impacts of entrainment and impingement at the Salem Generating Station on fish populations and communities in the Delaware Estuary. In the absence of an agreed-upon regulatory definition of "adverse environmental impact" (AEI), we developed three independent benchmarks of AEI based on observed or predicted changes that could threaten the sustainability of a population or the integrity of a community. Our benchmarks of AEI included: (1) disruption of the balanced indigenous community of fish in the vicinity of Salem (the "BIC" analysis); (2) a continued downward trend in the abundance of one or more susceptible fish species (the "Trends" analysis); and (3) occurrence of entrainment/impingement mortality sufficient, in combination with fishing mortality, to jeopardize the future sustainability of one or more populations (the "Stock Jeopardy" analysis). The BIC analysis utilized nearly 30 years of species presence/absence data collected in the immediate vicinity of Salem. The Trends analysis examined three independent data sets that document trends in the abundance of juvenile fish throughout the estuary over the past 20 years. The Stock Jeopardy analysis used two different assessment models to quantify potential long-term impacts of entrainment and impingement on susceptible fish populations. For one of these models, the compensatory capacities of the modeled species were quantified through meta-analysis of spawner-recruit data available for several hundred fish stocks. All three analyses indicated that the fish populations and communities of the Delaware Estuary are healthy and show no evidence of an adverse impact due to Salem. Although the specific models and analyses used at Salem are not applicable to every facility, we believe that a weight of evidence approach that evaluates multiple benchmarks of AEI using both retrospective and predictive methods is the best approach for assessing entrainment and impingement impacts at existing facilities.

The utility of fluorescence in situ hybridization for diagnosis and surveillance of bladder urothelial carcinoma.

PubMed

Huang, Jian Wen; Mu, Jia Gui; Li, Yun Wei; Gan, Xiu Guo; Song, Lu Jie; Gu, Bao Jun; Fu, Qiang; Xu, Yue Min; An, Rui Hua

2014-11-30

To evaluate the clinical value of fluorescence in situ hybridization (FISH) for diagnosis and surveillance of bladder urothelial carcinoma (BUC). Between November 2010 and December 2013, patients suspected of having BUC were examined using urine cytology and FISH assay. Based on histopathological examination results, FISH results were com­pared with urine cytology. In addition, patients with a history of non-muscle invasive BUC were also examined using urine cytology and FISH assay at the first time of visit and then monitored with cystoscopy during follow-up period. A total of 162 patients included in this study and 12 patients were excluded due to uninformative FISH assays. The remaining 150 patients consisted of 108 patients suspected for BUC and 42 patients with a history of non-muscle invasive BUC. The sensitivities of FISH analysis and urine cytology were 72.8% and 27.2%, respectively, and the difference was statistically significant (P <.05). Difference between specificity of urine cytology (100%) and FISH assay (85%) was not statistically significant (P >.05). At the first visit, of 42 patients, one patient had positive cystoscopy, and FISH assay was positive in 26 of 41 patients with negative cystoscopy. During the follow-up period (mean, 29.5 months), 18 of 26 patients developed recurrence, and recurrence occurred in only one of 15 patients with negative FISH analysis. Our results suggest that FISH analysis can be used as a non-invasive diagnostic tool for patients suspect­ed of having new BUC. In addition, FISH analysis may provide important prognostic information to better define the individual risk for BUC recurrence.& nbsp;

Toward a Molecular Cytogenetic Map for Cultivated Sunflower (Helianthus annuus L.) by Landed BAC/BIBAC Clones

PubMed Central

Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

2013-01-01

Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (∼100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC- fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)−derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources. PMID:23316437

The Big Fish Down Under: Examining Moderators of the "Big-Fish-Little-Pond" Effect for Australia's High Achievers

ERIC Educational Resources Information Center

Seaton, Marjorie; Marsh, Herbert W.; Yeung, Alexander Seeshing; Craven, Rhonda

2011-01-01

Big-fish-little-pond effect (BFLPE) research has demonstrated that academic self-concept is negatively affected by attending high-ability schools. This article examines data from large, representative samples of 15-year-olds from each Australian state, based on the three Program for International Student Assessment (PISA) databases that focus on…

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei.

PubMed

Müller, Patrick; Rößler, Jens; Schwarz-Finsterle, Jutta; Schmitt, Eberhard; Hausmann, Michael

2016-07-01

Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes) or TINA-DNA (Twisted Intercalating Nucleic Acids). Gene targets can be specifically labelled with at least about 20 probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3d-nanostructure and even the viability of the cell target. The method is demonstrated with the detection of Her2/neu and GRB7 genes, which are indicators in breast cancer diagnosis and therapy. Copyright © 2016. Published by Elsevier Inc.

Comparison of Diagnostic Yield of a FISH Panel Against Conventional Cytogenetic Studies for Hematological Malignancies: A South Indian Referral Laboratory Analysis Of 201 Cases

PubMed Central

Ashok, Vishal; Ranganathan, Ramya; Chander, Smitha; Damodar, Sharat; Bhat, Sunil; KS, Nataraj; A, Satish Kumar; Jadav, Sachin Suresh; Rajashekaraiah, Mahesh; TS, Sundareshan

2017-01-01

Objectives: Genetic markers are crucial fort diagnostic and prognostic investigation of hematological malignancies (HM). The conventional cytogenetic study (CCS) has been the gold standard for more than five decades. However, FISH (Fluorescence in Situ Hybridization) testing has become a popular modality owing to its targeted approach and the ability to detect abnormalities in non-mitotic cells. We here aimed to compare the diagnostic yields of a FISH panel against CCS in HMs. Methods: Samples of bone marrow and peripheral blood for a total of 201 HMs were tested for specific gene rearrangements using multi-target FISH and the results were compared with those from CCS. Results: Exhibited a greater diagnostic yield with a positive result in 39.8% of the cases, as compared to 17.9% of cases detected by CCS. Cases of chronic lymphocytic leukaemia (CLL) benefited the most by FISH testing, which identified chromosomal aberrations beyond the capacity of CCS. FISH was least beneficial in myelodysplastic syndrome (MDS) where the highest concordance with CCS was exhibited. Acute lymphocytic leukaemia (ALL) demonstrated greater benefit with CCS. In addition, we found the following abnormalities to be most prevalent in HMs by FISH panel testing: RUNX1 (21q22) amplification in ALL, deletion of D13S319/LAMP1 (13q14) in CLL, CKS1B (1q21) amplification in multiple myeloma and deletion of EGR1/RPS14 (5q31/5q32) in MDS, consistent with the literature. Conclusions: In conclusion, FISH was found to be advantageous in only a subset of HMs and cannot completely replace CCS. Utilization of the two modalities in conjunction or independently should depend on the indicated HM for an optimal approach to detecting chromosomal aberrations. PMID:29286619

Variable responses of fish assemblages, habitat, and stability to natural-channel-design restoration in Catskill Mountain streams

USGS Publications Warehouse

Baldigo, Barry P.; Ernst, Anne G.; Warren, Dana R.; Miller, Sarah J.

2010-01-01

Natural-channel-design (NCD) restorations were recently implemented within large segments of five first- and second-order streams in the Catskill Mountains of New York in an attempt to increase channel stability, reduce bed and bank erosion, and sustain water quality. In conjunction with these efforts, 54 fish and habitat surveys were done from 1999 to 2007 at six restored reaches and five stable control reaches to evaluate the effects of NCD restoration on fish assemblages, habitat, and bank stability. A before–after–control–impact study design and two-factor analysis of variance were used to quantify the net changes in habitat and fish population and community indices at treatment reaches relative to those at unaltered control reaches. The density and biomass of fish communities were often dominated by one or two small prey species and no or few predator species before restoration and by one or more trout (Salmonidae) species after restoration. Significant increases in community richness (30%), diversity (40%), species or biomass equitability (32%), and total biomass (up to 52%) in at least four of the six restored reaches demonstrate that NCD restorations can improve the health and sustainability of fish communities in geomorphically unstable Catskill Mountain streams over the short to marginally long term. Bank stability, stream habitat, and trout habitat suitability indices (HSIs) generally improved significantly at the restored reaches, but key habitat features and trout HSIs did not change or decreased at two of them. Fish communities and trout populations at these two reaches were not positively affected by NCD restorations. Though NCD restorations often had a positive effect on habitat and fish communities, our results show that the initial habitat conditions limit the relative improvements than can be achieved, habitat quality and stability do not necessarily respond in unison, and biotic and abiotic responses cannot always be generalized.

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessing changes in the toxicity of effluents from intensive marine fish farms over time by using a battery of bioassays.

PubMed

Carballeira, Carlos; Cebro, Alesandra; Villares, Rubén; Carballeira, Alejo

2018-05-01

Although intensive marine fish farming is often assumed to be eco-friendly, the associated activity can lead to chronic exposure of marine organisms to potentially toxic discharges. Moreover, despite the increasing popularity of integrated multi-trophic aquaculture (IMTA), studies of the effects of fish farm effluents are almost non-existent. In the present study, the changes in the toxic potential of effluents from five land-based marine fish farms in NW Spain subjected for different lengths of time to a biodegradation procedure (for 0, 48, 120, and 240 h) were assessed in a battery of bioassays including organisms from different trophic levels (Vibrio fischeri, Isochrysis galbana, and Paracentrotus lividus). The results of the bioassays at the different times were then considered together with farm water flow in the Potential Ecotoxic Effects Probe (PEEP) index. Despite the high volumes of effluents discharged, the generally low toxicity of the effluents hinders assessment of potentially toxic effects. However, dose-response curves and statistical analysis demonstrated the existence of toxic effects during the first five days of the biodegradation procedure, especially immediately after sampling. The proposed modification of the PEEP index better reflects the changes in toxicity over time. Graphical abstract ᅟ.

Constituent bioconcentration in rainbow trout exposed to a complex chemical mixture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linder, G.; Bergman, H.L.; Meyer, J.S.

1984-09-01

Classically, aquatic contaminant fate models predicting a chemical's bioconcentration factor (BCF) are based upon single-compound derived models, yet such BCF predictions may deviate from observed BCFs when physicochemical interactions or biological responses to complex chemical mixture exposures are not adequately considered in the predictive model. Rainbow trout were exposed to oil-shale retort waters. Such a study was designed to model the potential biological effects precluded by exposure to complex chemical mixtures such as solid waste leachates, agricultural runoff, and industrial process waste waters. Chromatographic analysis of aqueous and nonaqueous liquid-liquid reservoir components yielded differences in mixed extraction solvent HPLC profilesmore » of whole fish exposed for 1 and 3 weeks to the highest dilution of the complex chemical mixture when compared to their corresponding control, yet subsequent whole fish extractions at 6, 9, 12, and 15 weeks into exposure demonstrated no qualitative differences between control and exposed fish. Liver extractions and deproteinized bile samples from exposed fish were qualitatively different than their corresponding controls. These findings support the projected NOEC of 0.0045% dilution, even though the differences in bioconcentration profiles suggest hazard assessment strategies may be useful in evaluating environmental fate processes associated with complex chemical mixtures. 12 references, 4 figures, 2 tables.« less

Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies

NASA Astrophysics Data System (ADS)

Wu, Nan; Song, Yu-Long; Wang, Bei; Zhang, Xiang-Yang; Zhang, Xu-Jie; Wang, Ya-Li; Cheng, Ying-Yin; Chen, Dan-Dan; Xia, Xiao-Qin; Lu, Yi-Shan; Zhang, Yong-An

2016-11-01

The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.

Exploring polycythaemia vera with fluorescence in situ hybridization: additional cryptic 9p is the most frequent abnormality detected.

PubMed

Najfeld, Vesna; Montella, Lya; Scalise, Angela; Fruchtman, Steven

2002-11-01

Between 1986 and 2001, 220 patients with polycythaemia vera (PV) were studied using conventional cytogenetics. Of 204 evaluable patients, 52 (25.4%) had clonal abnormalities. The recurrent chromosomal rearrangements were those of chromosome 9 (21.1%), del(20q) (19.2%), trisomy 8 (19.2%), rearrangements of 13q (13.4%), abnormalities of 1q (11.5%), and of chromosomes 5 and 7 (9.6%). Subsequent analysis of 32 patients, performed at follow-up of up to 14.8 years, revealed new clonal abnormalities in five patients and the disappearance of an abnormal clone in four. Eleven patients remained normal up to 11.5 years and seven patients maintained an abnormality for over 10 years. Fifty-three patients were studied retrospectively using interphase fluorescence in situ hybridization (I-FISH), utilizing probes for centromere enumeration of chromosomes 8 and 9, and for 13q14 and 20q12 loci. Conventional cytogenetics demonstrated clonal chromosome abnormalities in 23% of these 53 patients. The addition of I-FISH increased the detection of abnormalities to 29% and permitted clarification of chromosome 9 rearrangements in an additional 5.6% of patients. FISH uncovered rearrangements of chromosome 9 in 53% of patients with an abnormal FISH pattern, which represented the most frequent genomic alteration in this series.

Identification and evaluation of cyp1a transcript expression in fish as molecular biomarker for petroleum contamination in tropical fresh water ecosystems.

PubMed

dos Anjos, Nislanha Ana; Schulze, Tobias; Brack, Werner; Val, Adalberto Luis; Schirmer, Kristin; Scholz, Stefan

2011-05-01

In order to monitor potential contamination deriving from exploration and transport of oil in the Urucu region (Brazil), there is a need to establish suitable biomarkers for native Amazonian fish. Therefore, the transcript expression of various potentially sensitive genes (ahr2(1), cyp1a, hmox1, hsp70, maft, mt, nfe212, gstp1 and nqo1) in fish exposed to water soluble fractions of oil (WSF) was compared. The analysis was first performed in an established laboratory model, the zebrafish embryo. The cyp1a gene proved to be the most sensitive and robust marker for oil contamination and, hence, was selected to study the effect of oil-derived contaminants in the Amazonian cichlid Astronotus ocellatus. Induction of cyp1a transcript expression was observed for ≥0.0061% (v/v) WSFs. In liver samples of fish, collected from different lakes in the Urucu oil mining area, no elevated expression of cyp1a transcripts was observed. The data demonstrate the high sensitivity of cyp1a as indicator of oil exposure; further studies should be considered to test its usefulness at known contaminated sites and to evaluate influential factors by, e.g. mesocosm experiments. Copyright © 2011 Elsevier B.V. All rights reserved.

Deciphering Interactions in Moving Animal Groups

PubMed Central

Gautrais, Jacques; Ginelli, Francesco; Fournier, Richard; Blanco, Stéphane; Soria, Marc; Chaté, Hugues; Theraulaz, Guy

2012-01-01

Collective motion phenomena in large groups of social organisms have long fascinated the observer, especially in cases, such as bird flocks or fish schools, where large-scale highly coordinated actions emerge in the absence of obvious leaders. However, the mechanisms involved in this self-organized behavior are still poorly understood, because the individual-level interactions underlying them remain elusive. Here, we demonstrate the power of a bottom-up methodology to build models for animal group motion from data gathered at the individual scale. Using video tracks of fish shoal in a tank, we show how a careful, incremental analysis at the local scale allows for the determination of the stimulus/response function governing an individual's moving decisions. We find in particular that both positional and orientational effects are present, act upon the fish turning speed, and depend on the swimming speed, yielding a novel schooling model whose parameters are all estimated from data. Our approach also leads to identify a density-dependent effect that results in a behavioral change for the largest groups considered. This suggests that, in confined environment, the behavioral state of fish and their reaction patterns change with group size. We debate the applicability, beyond the particular case studied here, of this novel framework for deciphering interactions in moving animal groups. PMID:23028277

Deciphering interactions in moving animal groups.

PubMed

Gautrais, Jacques; Ginelli, Francesco; Fournier, Richard; Blanco, Stéphane; Soria, Marc; Chaté, Hugues; Theraulaz, Guy

2012-01-01

Collective motion phenomena in large groups of social organisms have long fascinated the observer, especially in cases, such as bird flocks or fish schools, where large-scale highly coordinated actions emerge in the absence of obvious leaders. However, the mechanisms involved in this self-organized behavior are still poorly understood, because the individual-level interactions underlying them remain elusive. Here, we demonstrate the power of a bottom-up methodology to build models for animal group motion from data gathered at the individual scale. Using video tracks of fish shoal in a tank, we show how a careful, incremental analysis at the local scale allows for the determination of the stimulus/response function governing an individual's moving decisions. We find in particular that both positional and orientational effects are present, act upon the fish turning speed, and depend on the swimming speed, yielding a novel schooling model whose parameters are all estimated from data. Our approach also leads to identify a density-dependent effect that results in a behavioral change for the largest groups considered. This suggests that, in confined environment, the behavioral state of fish and their reaction patterns change with group size. We debate the applicability, beyond the particular case studied here, of this novel framework for deciphering interactions in moving animal groups.

Serum disposition of bovine lactoferrin after oral and anal administration and its proteolytic cleavage by gastric transit in rainbow trout (Oncorhynchus mykiss W.).

PubMed

Cecchini, Stefano; Caputo, Anna R

2009-01-01

Several studies have shown an immunomodulatory effect of orally administered bovine lactoferrin (LF) in fish, but the process of digestion was not characterized. In the present study, we investigated the fate of bovine LF after oral and anal administration, and studied the appearance of intact LF in the bloodstream and its proteolytic attack during the gastric transit in rainbow trout (Oncorhynchus mykiss) held at 9 degrees C and 18 degrees C. Data obtained showed the presence of intact bovine LF in the bloodstream only after anal administration in fish held at 18 degrees C and the presence of several peptides derived from bovine LF in the gastric content. Immunoblotting analysis showed that only a part of bovine LF-derived peptides reacted with the applied anti-bovine LF antibody. The concentration of intact bovine LF, after 30 min of administration, in the gastric content of fish reared at 18 degrees C, being extremely low, if any, led us to suspect that the immunoregulatory effect of dietary bovine LF shown in fish by several authors is not due to the intact form but to bioactive fragments, originated by the proteolytic attack during the gastric transit, as demonstrated in higher vertebrates.

Constitutive expression of thymidylate synthase from LCDV-C induces a transformed phenotype in fish cells.

PubMed

Zhao, Zhe; Shi, Yan; Ke, Fei; Wei, Sun; Gui, Jianfang; Zhang, Qiya

2008-03-01

Thymidylate synthase (TS), an essential enzyme in DNA synthesis and repair, plays a key role in the events of cell cycle regulation and tumor formation. Here, an investigation was presented about subcellular location and biological function of viral TS from lymphocystis disease virus from China (LCDV-C) in fish cells. Fluorescence microscopy revealed that LCDV-C TS was predominantly localized in the cytoplasm in fish cells. Cell cycle analysis demonstrated that LCDV-C TS promoted cell cycle progression into S and G2/M phase in the constitutive expressed cells. As a result, the cells have a faster growth rate compared with the control cells as revealed by cell growth curves. For foci assay, the TS-expressed cells gave rise to foci 4-5 weeks after incubation. Microscopic examination of the TS-induced foci revealed multilayered growth and crisscross morphology characteristic of transformed cells. Moreover, LCDV-C TS predisposed the transfected cells to acquire an anchorage-independent phenotype and could grow in 0.3% soft agar. So the data reveal LCDV-C TS is sufficient to induce a transformed phenotype in fish cells in vitro and exhibits its potential ability in cell transformation. To our knowledge, it is the first report on viral TS sequences associated with transforming activity.

Analysis of the nicotinamide phosphoribosyltransferase family provides insight into vertebrate adaptation to different oxygen levels during the water-to-land transition.

PubMed

Fang, Chengchi; Guan, Lihong; Zhong, Zaixuan; Gan, Xiaoni; He, Shunping

2015-08-01

One of the most important events in vertebrate evolutionary history is the water-to-land transition, during which some morphological and physiological changes occurred in concert with the loss of specific genes in tetrapods. However, the molecular mechanisms underlying this transition have not been well explored. To explore vertebrate adaptation to different oxygen levels during the water-to-land transition, we performed comprehensive bioinformatics and experimental analysis aiming to investigate the NAMPT family in vertebrates. NAMPT, a rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, is critical for cell survival in a hypoxic environment, and a high level of NAMPT significantly augments oxidative stress in normoxic environments. Phylogenetic analysis showed that NAMPT duplicates arose from a second round whole-genome duplication event. NAMPTA existed in all classes of vertebrates, whereas NAMPTB was only found in fishes and not tetrapods. Asymmetric evolutionary rates and purifying selection were the main evolutionary forces involved. Although functional analysis identified several functionally divergent sites during NAMPT family evolution, in vitro experimental data demonstrated that NAMPTA and NAMPTB were functionally conserved for NAMPT enzymatic function in the NAD+ salvage pathway. In situ hybridization revealed broad NAMPTA and NAMPTB expression patterns, implying regulatory functions over a wide range of developmental processes. The morpholino-mediated knockdown data demonstrated that NAMPTA was more essential than NAMPTB for vertebrate embryo development. We propose that the retention of NAMPTB in water-breathing fishes and its loss in air-breathing tetrapods resulted from vertebrate adaptation to different oxygen levels during the water-to-land transition. © 2015 FEBS.

Markov chain model for demersal fish catch analysis in Indonesia

NASA Astrophysics Data System (ADS)

Firdaniza; Gusriani, N.

2018-03-01

As an archipelagic country, Indonesia has considerable potential fishery resources. One of the fish resources that has high economic value is demersal fish. Demersal fish is a fish with a habitat in the muddy seabed. Demersal fish scattered throughout the Indonesian seas. Demersal fish production in each Indonesia’s Fisheries Management Area (FMA) varies each year. In this paper we have discussed the Markov chain model for demersal fish yield analysis throughout all Indonesia’s Fisheries Management Area. Data of demersal fish catch in every FMA in 2005-2014 was obtained from Directorate of Capture Fisheries. From this data a transition probability matrix is determined by the number of transitions from the catch that lie below the median or above the median. The Markov chain model of demersal fish catch data was an ergodic Markov chain model, so that the limiting probability of the Markov chain model can be determined. The predictive value of demersal fishing yields was obtained by calculating the combination of limiting probability with average catch results below the median and above the median. The results showed that for 2018 and long-term demersal fishing results in most of FMA were below the median value.

75 FR 81586 - Western Pacific Fishery Management Council; Public Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-28

... spatial closure impacts on the fishing community 2. Guam Fisheries Act 3. Indigenous Fishing Rights 4.... Impact of land-based pollution in fish from Saipan Lagoon 3. Saipan Lagoon net fishing data analysis 4...

Hibernation in an antarctic fish: on ice for winter.

PubMed

Campbell, Hamish A; Fraser, Keiron P P; Bishop, Charles M; Peck, Lloyd S; Egginton, Stuart

2008-03-05

Active metabolic suppression in anticipation of winter conditions has been demonstrated in species of mammals, birds, reptiles and amphibians, but not fish. This is because the reduction in metabolic rate in fish is directly proportional to the decrease in water temperature and they appear to be incapable of further suppressing their metabolic rate independently of temperature. However, the Antarctic fish (Notothenia coriiceps) is unusual because it undergoes winter metabolic suppression irrespective of water temperature. We assessed the seasonal ecological strategy by monitoring swimming activity, growth, feeding and heart rate (f(H)) in N. coriiceps as they free-ranged within sub-zero waters. The metabolic rate of wild fish was extrapolated from f(H )recordings, from oxygen consumption calibrations established in the laboratory prior to fish release. Throughout the summer months N. coriiceps spent a considerable proportion of its time foraging, resulting in a growth rate (G(w)) of 0.18 +/- 0.2% day(-1). In contrast, during winter much of the time was spent sedentary within a refuge and fish showed a net loss in G(w) (-0.05 +/- 0.05% day(-1)). Whilst inactive during winter, N. coriiceps displayed a very low f(H), reduced sensory and motor capabilities, and standard metabolic rate was one third lower than in summer. In a similar manner to other hibernating species, dormancy was interrupted with periodic arousals. These arousals, which lasted a few hours, occurred every 4-12 days. During arousal activity, f(H) and metabolism increased to summer levels. This endogenous suppression and activation of metabolic processes, independent of body temperature, demonstrates that N. coriiceps were effectively 'putting themselves on ice' during winter months until food resources improved. This study demonstrates that at least some fish species can enter a dormant state similar to hibernation that is not temperature driven and presumably provides seasonal energetic benefits.

RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis).

PubMed

Aballai, Víctor; Aedo, Jorge E; Maldonado, Jonathan; Bastias-Molina, Macarena; Silva, Herman; Meneses, Claudio; Boltaña, Sebastian; Reyes, Ariel; Molina, Alfredo; Valdés, Juan Antonio

2017-12-01

Stress is a primary contributing factor of fish disease and mortality in aquaculture. We have previously reported that the red cusk-eel (Genypterus chilensis), an important farmed marine fish, demonstrates a handling-stress response that results in increased juvenile mortality, which is mainly associated with skeletal muscle atrophy and liver steatosis. To better understand the systemic effects of stress on red cusk-eel immune-related gene expression, the present study assessed the transcriptomic head-kidney response to handling-stress. The RNA sequencing generated a total of 61,655,525 paired-end reads from control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,840 transcripts and created a reference transcriptome with a N50 of 1426bp. Reads mapped onto the assembled reference transcriptome resulted in the identification of 569 up-regulated and 513 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of the biological processes, like response to stress, response to biotic stimulus, and immune response. Conversely, a significant down-regulation of biological processes is associated with metabolic processes. These results were validated by RT-qPCR analysis for nine candidate genes involved in the immune response. The present data demonstrated that short term stress promotes the immune innate response in the marine teleost G. chilensis. This study is an important step towards understanding the immune adaptive response to stress in non-model teleost species. Copyright © 2017 Elsevier Inc. All rights reserved.

Constellation of phase singularities in a speckle-like pattern for optical vortex metrology applied to biological kinematic analysis.

PubMed

Wang, Wei; Qiao, Yu; Ishijima, Reika; Yokozeki, Tomoaki; Honda, Daigo; Matsuda, Akihiro; Hanson, Steen G; Takeda, Mitsuo

2008-09-01

A novel technique for biological kinematic analysis is proposed that makes use of the pseudophase singularities in a complex signal generated from a speckle-like pattern. In addition to the information about the locations and the anisotropic core structures of the pseudophase singularities, we also detect the spatial structures of a cluster of phase singularities, which serves as a unique constellation characterizing the mutual position relation between the individual pseudophase singularities. Experimental results of in vivo measurements for a swimming fish along with its kinematic analysis are presented, which demonstrate the validity of the proposed technique.

[THE TECHNOLOGY "CELL BLOCK" IN CYTOLOGICAL PRACTICE].

PubMed

Volchenko, N N; Borisova, O V; Baranova, I B

2015-08-01

The article presents summary information concerning application of "cell block" technology in cytological practice. The possibilities of implementation of various modern techniques (immune cytochemnical analysis. FISH, CISH, polymerase chain reaction) with application of "cell block" method are demonstrated. The original results of study of "cell block" technology made with gelatin, AgarCyto and Shadon Cyoblock set are presented. The diagnostic effectiveness of "cell block" technology and common cytological smear and also immune cytochemical analysis on samples of "cell block" technology and fluid cytology were compared. Actually application of "cell block" technology is necessary for ensuring preservation of cell elements for subsequent immune cytochemical and molecular genetic analysis.

Karyotype analysis in large sample cases from Shenyang Women's and Children's hospital: a study of 16,294 male infertility patients.

PubMed

Gao, M; Pang, H; Zhao, Y-H; Hua, J; Tong, D; Zhao, H; Liu, Y; Zhao, Y; Zhang, M; Yan, X-J; Chen, H; Ma, H-P; Jin, T-Y; Dong, S-L

2017-05-01

To explore that it is necessary to routinely detect chromosomes in infertile patients, we investigated peripheral blood lymphocyte karyotype in 16,294 male infertile patients in the north-east of China and analysed the incidence and type of chromosomal anomaly and polymorphism. G-banding karyotype analysis of peripheral blood lymphocytes was performed in 16,294 cases. Semen analysis was performed three times in all the men. PCR and FISH confirmed the presence of the SRY gene. The rate of chromosomal anomaly in the 16,294 male infertile patients was 4.15% (677/16,294). The rates of chromosomal anomaly were 0.24% in normal semen group, 12.6% in light oligoasthenospermia group, 4.7% in moderate-to-severe oligoasthenospermia group and 9.59% in azoospermia group. There are two male infertile patients with 45,X chromosome karyotype. One X male patient had confirmed the presence of the SRY gene and FISH analysis demonstrated its location on the p arm of chromosome 13. The other X male patient had not found SRY gene in its whole-genome DNA. Meanwhile, sperm motility is slightly oligo-asthenozoospermic at the age of 35-39 and nearly azoospermic at the age of 40-45. As the rates of chromosomal anomaly are 0.24% and 12.6% even in normal semen group and light oligoasthenospermia group, the rates of chromosomal polymorphism are 5.36% and 25.51% in normal semen group and light oligoasthenospermia group, respectively; it is necessary to explore peripheral blood lymphocyte karyotype in all infertile couples. We mentioned that Y, 1, 2, 9 and 12 chromosomes were quite important about male infertility. These findings demonstrate that autosomal retention of SRY can be submicroscopic and emphasise the importance of PCR and FISH in the genetic workup of the monosomic X male. At the same time, it suggested that male infertility might be related to meiotic disturbances with spermatogenetic arrest in Y-autosome translocations, which could result in infertility by reduction of sperm production. Last but not least, ageing is one of the factors that could reduce sperm motility and quality. © 2016 Blackwell Verlag GmbH.

Isolation and characterisation of mRNA encoding the salmon- and chicken-II type gonadotrophin-releasing hormones in the teleost fish Rutilus rutilus (Cyprinidae).

PubMed

Penlington, M C; Williams, M A; Sumpter, J P; Rand-Weaver, M; Hoole, D; Arme, C

1997-12-01

The complementary DNAs (cDNA) encoding the [Trp7,Leu8]-gonadotrophin-releasing hormone (salmon-type GnRH; sGnRH:GeneBank accession no. u60667) and the [His5,Trp7,Tyr8]-GnRH (chicken-II-type GnRH; cGnRH-II: GeneBank accession no. u60668) precursor in the roach (Rutilus rutilus) were isolated and sequenced following reverse transcription and rapid amplification of cDNA ends (RACE). The sGnRH and cGnRH-II precursor cDNAs consisted of 439 and 628 bp, and included open reading frames of 282 and 255 bp respectively. The structures of the encoded peptides were the same as GnRHs previously identified in other vertebrates. The sGnRH and cGnRH-II precursor cDNAs, including the non-coding regions, had 88.6 and 79.9% identity respectively, to those identified in goldfish (Carassius auratus). However, significant similarity was not observed between the non-coding regions of the GnRH cDNAs of Cyprinidae and other fish. The presumed third exon, encoding partial sGnRH associated peptide (GAP) of roach, demonstrated significant nucleotide and amino acid similarity with the appropriate regions in the goldfish, but not with other species, and this may indicate functional differences of GAP between different families of fish. cGnRH-II precursor cDNAs from roach had relatively high nucleotide similarity across this GnRH variant. Cladistic analysis classified the sGnRH and cGnRH-II precursor cDNAs into three and two groups respectively. However, the divergence between nucleotide sequences within the sGnRH variant was greater than those encoding the cGnRH-II precursors. Consistent with the consensus developed from previous studies, Northern blot analysis demonstrated that expression of sGnRH and cGnRH-II was restricted to the olfactory bulbs and midbrain of roach respectively. This work forms the basis for further study on the mechanisms by which the tapeworm, Ligula intestinalis, interacts with the pituitary-gonadal axis of its fish host.

Trophic characteristics of a mangrove fish community in Southwest Thailand: Important mangrove contribution and intraspecies feeding variability

NASA Astrophysics Data System (ADS)

Zagars, Matiss; Ikejima, Kou; Kasai, Akihide; Arai, Nobuaki; Tongnunui, Prasert

2013-03-01

Mangrove production has been found to make a major contribution to the nutrition of a fish community in the Sikao Creek mangrove estuary, Southwest Thailand. Gut content analysis and carbon and nitrogen stable isotope analysis were used to assess fish feeding behavior and trophic reliance on different primary producers (mangrove leaves, phytoplankton, microphytobenthos) focusing on 19 dominant fish species, and 4 potential fish food items. Cluster analysis identified 5 trophic groups and the IsoSource model indicated the importance of primary food sources in trophically supporting different fish species. Most analyzed fish species had carbon isotopic signatures that were more depleted than those reported in previous studies, and the IsoSource model indicated that mangrove leaves were an important primary food source. This may be a specific characteristic of our study site, which is not well connected to other productive coastal habitats that provide alternative primary food sources. Thus we suggest that food chains in trophically isolated mangrove estuaries of southwest Thailand are more dependent on mangrove tree production. We also assessed the relationship of individuality in fish feeding habits and variability of δ13C values and showed that several mangrove fish species have significant intraspecies variability in feeding habits, possibly due to high intraspecific competition.

Fish consumption in a sample of people in Bandar Abbas, Iran: application of the theory of planned behavior.

PubMed

Aghamolaei, Teamur; Sadat Tavafian, Sedigheh; Madani, Abdoulhossain

2012-09-01

This study aimed to apply the conceptual framework of the theory of planned behavior (TPB) to explain fish consumption in a sample of people who lived in Bandar Abbass, Iran. We investigated the role of three traditional constructs of TPB that included attitude, social norms, and perceived behavioral control in an effort to characterize the intention to consume fish as well as the behavioral trends that characterize fish consumption. Data were derived from a cross-sectional sample of 321 subjects. Alpha coefficient correlation and linear regression analysis were applied to test the relationships between constructs. The predictors of fish consumption frequency were also evaluated. Multiple regression analysis revealed that attitude, subjective norms, and perceived behavioral control significantly predicted intention to eat fish (R2 = 0.54, F = 128.4, P < 0.001). Multiple regression analysis for the intention to eat fish and perceived behavioral control revealed that both factors significantly predicted fish consumption frequency (R2 = 0.58, F = 223.1, P < 0.001). The results indicated that the models fit well with the data. Attitude, subjective norms, and perceived behavioral control all had significant positive impacts on behavioral intention. Moreover, both intention and perceived behavioral control could be used to predict the frequency of fish consumption.

Tetrapod-type [Asp1] angiotensin is present in a holostean fish, Amia calva.

PubMed

Takei, Y; Itahara, Y; Butler, D G; Watanabe, T X; Oudit, G Y

1998-05-01

The renin-angiotensin system has been identified in various vertebrates, from elasmobranchs to mammals. Tetrapod (amphibians to mammals) angiotensin (ANG) has Asp at the N-terminus, but Asp is replaced by Asn in elasmobranch and teleost fish. ANG I has been isolated from incubates of plasma and kidney extracts of the bowfin Amia calva, a holostean fish, using the eel vasopressor activity as an assay system; its sequence was found to be H-Asp-Arg-Val-Tyr-Val-His-Pro-Phe-Asn-Leu-OH after sequence analysis, mass spectrometry, and comparison with the synthetic peptide. This sequence is identical to bullfrog ANG I. [Asn1] ANG I was not detected. Thus the bowfin is the first fish species which contains only [Asp1] ANG I. The bowfin ANG I and II were no more vasopressor than eel peptides in the bowfin, indicating that bowfin ANG II receptors do not distinguish between [Asp1] and [Asn1] peptides. In the rat, bowfin ANG I and rat [Ile5, His9] ANG I have equipressor activities when examined in different animals, but the vasopressor activity of bowfin ANG I decreased following rat ANG I in the same animals, although the activity of rat ANG I was unaffected after bowfin ANG I. The present study directly demonstrates the presence of the renin-angiotensin system in a holostean fish and showed that its ANG II receptors have not yet fully coevolved with the homologous [Asp1] peptide.

Estimated dietary intake and risk assessment of polychlorinated dibenzo-p-dioxins and dibenzofurans and dioxin-like polychlorinated biphenyls from fish consumption in the Korean general population.

PubMed

Shin, Eun-su; Kim, Jongchul; Choi, Sung-Deuk; Kang, Young-Woon; Chang, Yoon-Seok

2016-03-01

We analyzed 17 polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), and 12 dioxin-like polychlorinated biphenyls (DL-PCBs) in samples from various fish species available at food markets in nine Korean cities. The estimated dietary intake of these chemicals was calculated from the raw concentrations of PCDD/Fs and DL-PCBs in each sample and from the food consumption of the Korean general population, and a comparison was made with the provisional tolerable monthly intake (PTMI). The average daily dietary exposure and the 95th percentile of intake of PCDD/Fs and DL-PCBs were 0.21 and 0.49 pg WHO05-toxic equivalents (TEQ) kg(-1) body weight d(-1) representing 5.27% and 12.26%, respectively, of the Korean tolerable daily intake (TDI). We applied the monthly fish consumption limits to the evaluation of improved risk assessment and concluded that unlimited consumption of most fish species does not contribute to the elevated cancer risk. This investigation was the first such large-scale study in Korea, and incorporated 37 species, including a species of whale, and 480 samples. The major aims of this study were to demonstrate the health risks associated with fish intake and to ensure food safety through total analysis of PCDD/Fs and DL-PCBs using gas chromatography/high-resolution mass spectrometry (GC-HRMS). Copyright © 2015 Elsevier Ltd. All rights reserved.

An Analysis of Fish Communities on Structured Habitat in the Northwestern Gulf of Mexico: Potential Impacts of "Rigs-to-Reefs" Programs and a Comparison with Natural Banks

NASA Astrophysics Data System (ADS)

Wetz, J. J.; Ajemian, M. J.; Streich, M.; Stunz, G. W.

2016-02-01

Artificial habitat in the northwestern Gulf of Mexico is predominantly comprised of both active and reefed oil and gas platforms. In the last few decades, Texas alone has converted over 140 decommissioned oil and gas platforms into permitted artificial reefs. Despite the predominance of this habitat type, the associated fish communities remain poorly studied and few comparisons with natural habitat have been done. Using remotely operated vehicles in 2012 and 2013, we documented fish assemblages surrounding 15 artificial structures and several natural banks located on the Texas shelf. Artificial sites were variable in depth (30-84 m), number of structures, and vertical relief. Both structure type and relief influenced species richness and community structure at these sites. However, bottom depth was most influential with a shift in community composition and high diversity observed at approximately 60 m depth. In this same region, drowned coralgal reefs (the South Texas Banks) provide natural hard substrate with relief up to 20 m. Comparisons between these natural habitats and artificial reefs with similar depths and relief clearly demonstrate fish community differences, perhaps indicating differences in habitat function. To attain species-specific management goals, reefing programs should carefully consider the ambient environmental conditions (i.e., depth) and proximity of natural habitats, as these will most certainly affect the fish assemblage and characteristics of exploited fisheries species.

Transgenic labeling of higher order neuronal circuits linked to phospholipase C-β2-expressing taste bud cells in medaka fish.

PubMed

Ieki, Takashi; Okada, Shinji; Aihara, Yoshiko; Ohmoto, Makoto; Abe, Keiko; Yasuoka, Akihito; Misaka, Takumi

2013-06-01

The sense of taste plays a pivotal role in the food-selecting behaviors of vertebrates. We have shown that the fish ortholog of the phospholipase C gene (plc-β2) is expressed in a subpopulation of taste bud cells that transmit taste stimuli to the central nervous system to evoke favorable and aversive behaviors. We generated transgenic medaka expressing wheat germ agglutinin (WGA) under the control of a regulatory region of the medaka plc-β2 gene to analyze the neuronal circuit connected to these sensory cells. Immunohistochemical analysis of the transgenic fish 12 days post fertilization revealed that the WGA protein was transferred to cranial sensory ganglia and several nuclei in the hindbrain. WGA signals were also detected in the secondary gustatory nucleus in the hindbrain of 3-month-old transgenic fish. WGA signals were observed in several diencephalic and telencephalic regions in 9-month-old transgenic fish. The age-dependent increase in the labeled brain regions strongly suggests that labeling occurred at taste bud cells and progressively extended to cranial nerves and neurons in the central nervous system. These data are the first to demonstrate the tracing of higher order gustatory neuronal circuitry that is associated with a specific subpopulation of taste bud cells. These results provide insight into the basic neuronal architecture of gustatory information processing that is common among vertebrates. Copyright © 2012 Wiley Periodicals, Inc.

Studying the effects of genistein on gene expression of fish embryos as an alternative testing approach for endocrine disruption.

PubMed

Schiller, Viktoria; Wichmann, Arne; Kriehuber, Ralf; Muth-Köhne, Elke; Giesy, John P; Hecker, Markus; Fenske, Martina

2013-01-01

Assessment of endocrine disruption currently relies on testing strategies involving adult vertebrates. In order to minimize the use of animal tests according to the 3Rs principle of replacement, reduction and refinement, we propose a transcriptomics and fish embryo based approach as an alternative to identify and analyze an estrogenic activity of environmental chemicals. For this purpose, the suitability of 48 h and 7 days post-fertilization zebrafish and medaka embryos to test for estrogenic disruption was evaluated. The embryos were exposed to the phytoestrogen genistein and subsequently analyzed by microarrays and quantitative real-time PCR. The functional analysis showed that the genes affected related to multiple metabolic and signaling pathways in the early fish embryo, which reflect the known components of genistein's mode of actions, like apoptosis, estrogenic response, hox gene expression and steroid hormone synthesis. Moreover, the transcriptomic data also suggested a thyroidal mode of action and disruption of the nervous system development. The parallel testing of two fish species provided complementary data on the effects of genistein at gene expression level and facilitated the separation of common from species-dependent effects. Overall, the study demonstrated that combining fish embryo testing with transcriptomics can deliver abundant information about the mechanistic effects of endocrine disrupting chemicals, rendering this strategy a promising alternative approach to test for endocrine disruption in a whole organism in-vitro scale system. Copyright © 2012 Elsevier Inc. All rights reserved.

Predation and landscape characteristics independently affect reef fish community organization.

PubMed

Stier, Adrian C; Hanson, Katharine M; Holbrook, Sally J; Schmitt, Russell J; Brooks, Andrew J

2014-05-01

Trophic island biogeography theory predicts that the effects of predators on prey diversity are context dependent in heterogeneous landscapes. Specifically, models predict that the positive effect of habitat area on prey diversity should decline in the presence of predators, and that predators should modify the partitioning of alpha and beta diversity across patchy landscapes. However, experimental tests of the predicted context dependency in top-down control remain limited. Using a factorial field experiment we quantify the effects of a focal predatory fish species (grouper) and habitat characteristics (patch size, fragmentation) on the partitioning of diversity and assembly of coral reef fish communities. We found independent effects of groupers and patch characteristics on prey communities. Groupers reduced prey abundance by 50% and gamma diversity by 45%, with a disproportionate removal of rare species relative to common species (64% and 36% reduction, respectively; an oddity effect). Further, there was a 77% reduction in beta diversity. Null model analysis demonstrated that groupers increased the importance of stochastic community assembly relative to patches without groupers. With regard to patch size, larger patches contained more fishes, but a doubling of patch size led to a modest (36%) increase in prey abundance. Patch size had no effect on prey diversity; however, fragmented patches had 50% higher species richness and modified species composition relative to unfragmented patches. Our findings suggest two different pathways (i.e., habitat or predator shifts) by which natural and/or anthropogenic processes can drive variation in fish biodiversity and community assembly.

From sanddabs to blue whales: the pervasiveness of domoic acid.

PubMed

Lefebvre, Kathi A; Bargu, Sibel; Kieckhefer, Tom; Silver, Mary W

2002-07-01

Domoic acid (DA) is a potent food web transferred algal toxin that has caused dramatic mortality events involving sea birds and sea lions. Although no confirmed DA toxicity events have been reported in whales, here we present data demonstrating that humpback and blue whales are exposed to the toxin and consume DA contaminated prey. Whale fecal samples were found to contain DA at levels ranging from 10 to 207microg DA g(-1) feces via HPLC-UV methods. SEM analysis of whale feces containing DA, collected from krill-feeding whales, revealed the presence of diatom frustules identified as Pseudo-nitzschia australis, a known DA producer. Humpback whales were observed feeding on anchovies and sardines that contained DA at levels ranging from 75 to 444microg DA g(-1) viscera. DA contamination of whale feces and fish occurred only during blooms of toxic Pseudo-nitzschia. Additionally, several novel fish species collected during a toxic diatom bloom were tested for DA. Fish as diverse as benthic sanddabs and pelagic albacore were found to contain the neurotoxin, suggesting that DA permeates benthic as well as pelagic communities.

Pathways of Barotrauma in Juvenile Salmonids Exposed to Simulated Hydroturbine Passage: Boyle’s Law vs. Henry’s Law

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Richard S.; Pflugrath, Brett D.; Colotelo, Alison HA

2012-06-01

On their seaward migration, juvenile salmonids commonly pass hydroelectric dams. Fish passing by the turbine blade may experience rapid decompression, the severity of which can be highly variable and may result in a number of barotraumas. The mechanisms of these injuries can be due to expansion of existing bubbles or gases coming out of solution; governed by Boyle’s Law and Henry’s Law, respectively. This paper combines re-analysis of published data with new experiments to gain a better understanding of the mechanisms of injury and mortality for fish experiencing rapid decompression associated with hydroturbine passage. From these data it appears thatmore » the majority of decompression related injuries are due to the expansion of existing bubbles in the fish, particularly the expansion and rupture of the swim bladder. This information is particularly useful for fisheries managers and turbine manufacturers, demonstrating that reducing the rate of swim bladder ruptures by reducing the frequency of occurrence and severity of rapid decompression during hydroturbine passage could reduce the rates of injury and mortality for hydroturbine passed juvenile salmonids.« less

Post-depositional behaviour of mercury and arsenic in submarine mine tailings deposited in Buyat Bay, North Sulawesi, Indonesia.

PubMed

Shepherd, Thomas; Rumengan, Inneke; Sahami, Ali

2018-06-01

The post-depositional geochemical behaviour of mercury and arsenic in submarine mine tailings from the Mesel Gold Mine in Buyat Bay, North Sulawesi, Indonesia was assessed by in situ sampling of tailings porewaters using dialysis arrays and seawater and fish monitoring. Under steady-state conditions one year after cessation of tailings discharge, the calculated arsenic efflux incrementally added 0.8 μg/L of arsenic to the overlying seawater. The mercury efflux across the tailings-seawater interface was negligible. The arsenic and mercury concentration in seawater bottom samples monitored biannually during a 9-year post-closure program were 1.54 μg/L and <0.05 μg/L, respectively. Analysis of 650 fish tissue samples, from the post-closure monitoring had mean mercury and arsenic concentrations consistently below the FAO/WHO CODEX, and Australian and New Zealand National Food Standards, respectively. The results of the porewater, seawater and fish tissue demonstrate that the arsenic and mercury-bearing bearing compounds in the tailings are geochemically stable. Copyright © 2018 Elsevier Ltd. All rights reserved.

Phase shifts and the role of herbivory in the resilience of coral reefs

NASA Astrophysics Data System (ADS)

Ledlie, M. H.; Graham, N. A. J.; Bythell, J. C.; Wilson, S. K.; Jennings, S.; Polunin, N. V. C.; Hardcastle, J.

2007-09-01

Cousin Island marine reserve (Seychelles) has been an effectively protected no-take marine protected area (MPA) since 1968 and was shown in 1994 to support a healthy herbivorous fish assemblage. In 1998 Cousin Island reefs suffered extensive coral mortality following a coral bleaching event, and a phase shift from coral to algal dominance ensued. By 2005 mean coral cover was <1%, structural complexity had fallen and there had been a substantial increase in macroalgal cover, up to 40% in some areas. No clear trends were apparent in the overall numerical abundance and biomass of herbivorous fishes between 1994 and 2005, although smaller individuals became relatively scarce, most likely due to the loss of reef structure. Analysis of the feeding habits of six abundant and representative herbivorous fish species around Cousin Island in 2006 demonstrated that epilithic algae were the preferred food resource of all species and that macroalgae were avoided. Given the current dominance of macroalgae and the apparent absence of macroalgal consumers, it is suggested that the increasing abundance of macroalgae is reducing the probability of the system reverting to a coral dominated state.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Copeland, Timothy; Putnam, Scott

The goal of Idaho Steelhead Monitoring and Evaluation Studies is to collect monitoring data to evaluate wild and natural steelhead populations in the Clearwater and Salmon river drainages. During 2007, intensive population data were collected in Fish Creek (Lochsa River tributary) and Rapid River (Little Salmon River tributary); extensive data were collected in other selected spawning tributaries. Weirs were operated in Fish Creek and Rapid River to estimate adult escapement and to collect samples for age determination and genetic analysis. Snorkel surveys were conducted in Fish Creek, Rapid River, and Boulder Creek (Little Salmon River tributary) to estimate parr density.more » Screw traps were operated in Fish Creek, Rapid River, Secesh River, and Big Creek to estimate juvenile emigrant abundance, to tag fish for survival estimation, and to collect samples for age determination and genetic analysis. The estimated wild adult steelhead escapement in Fish Creek was 81 fish and in Rapid River was 32 fish. We estimate that juvenile emigration was 24,127 fish from Fish Creek; 5,632 fish from Rapid River; and 43,674 fish from Big Creek. The Secesh trap was pulled for an extended period due to wildfires, so we did not estimate emigrant abundance for that location. In cooperation with Idaho Supplementation Studies, trap tenders PIT tagged 25,618 steelhead juveniles at 18 screw trap sites in the Clearwater and Salmon river drainages. To estimate age composition, 143 adult steelhead and 5,082 juvenile steelhead scale samples were collected. At the time of this report, 114 adult and 1,642 juvenile samples have been aged. Project personnel collected genetic samples from 122 adults and 839 juveniles. We sent 678 genetic samples to the IDFG Eagle Fish Genetics Laboratory for analysis. Water temperature was recorded at 37 locations in the Clearwater and Salmon river drainages.« less

Fish Ontology framework for taxonomy-based fish recognition

PubMed Central

Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

2017-01-01

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

Consumption of particulate wastes derived from cage fish farming by aggregated wild fish. An experimental approach.

PubMed

Ballester-Moltó, M; Sanchez-Jerez, P; Aguado-Giménez, F

2017-09-01

Particulate wastes derived from cage fish farming are a trophic resource used by wild fish. This study assesses waste consumption by wild fish and the impact on the final balance of wastes. Consumption was determined according to the difference between the particulate matter exiting the cages and that reaching 5 m away at three different depths, in the presence and absence of wild fish. Wild fish around the experimental cages were counted during feeding and non-feeding periods. A weighted abundance of 1057 fish 1000 m -3 consumed 17.75% of the particulate wastes exiting the cages, on average. Consumption was higher below the cages, where waste outflow was greater. However, waste removal by wild fish was noteworthy along the shallow and deep sides of the cages. Wild fish diminished the net particulate wastes by about 14%, transforming them into more easily dispersible and less harmful wastes. This study demonstrates the mitigating potential of wild fish in reducing environmental impact. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and Characterization of Prostate Cancer Stem Cells

DTIC Science & Technology

2011-08-01

and ability to induce prostate tubule formation in vivo. FISH analysis of prostaspheres derived from patient specimens containing the TMPRSS-ERG...hybridization (FISH)[6]. Analysis of prostate tumor surgical cohorts have found 36-78% of prostate cancers possess the TMPRSS-ERG fusion[6]. We wondered...suggest that cancer stem/early progenitor cells can be expanded in our cultures. 6 To test the feasibility of this approach, FISH analysis was

Analysis of EPA and DHA in the viscera of marine fish using gas chromatography.

PubMed

Zhang, De-Yong; Xu, Xiao-Lu; Shen, Xiu-Ying; Mei, Yu; Xu, Hui-Ying

2016-03-01

The viscera of 10 kinds of marine fishes were collected for fish oil extraction and detection of DHA and EPA, two most important polyunsaturated fatty acids. The fish oil extraction ratio for the evaluated fishes varied from 0.95% to 10.18% (wt%). Pseudosciaena crocea presented the highest fish oil yield, followed by Mustelus manazo, Hippoglossus and Sciaenopsocellatus. A gas chromatography method was then established for analysis of EPA/DHA. The EPA concentration (in methyl ester form) in the fish oil varied from 1.39 to 10.65(mg/g). Epinephelus awoara presented the highest EPA concentration (p<0.05), followed by Epinephelussp, Sciaenopsocellatus and Hippoglossus. The DHA concentration (in methyl ester form) in the fish oil varied from 0.58 to 37.02 (mg/g). Epinephelus awoara presented the highest DHA concentration (p<0.05), followed by Sciaenopsocellatus, Pseudosciaena crocea and Hippoglossus. No strict positive correlation between the EPA/DHA concentration and the sea depth where the fish live was observed. The fishes living in middle depth presented highest EPA/DHA concentration.

Modeling the effect of varying swim speeds on fish passage through velocity barriers

USGS Publications Warehouse

Castro-Santos, T.

2006-01-01

The distance fish can swim through zones of high-velocity flow is an important factor limiting the distribution and conservation of riverine and diadromous fishes. Often, these barriers are characterized by nonuniform flow conditions, and it is likely that fish will swim at varying speeds to traverse them. Existing models used to predict passage success, however, typically include the unrealistic assumption that fish swim at a constant speed regardless of the speed of flow. This paper demonstrates how the maximum distance of ascent through velocity barriers can be estimated from the swim speed-fatigue time relationship, allowing for variation in both swim speed and water velocity.

Analysis of occupational injuries in the sea fishing industry according to the type of fishery and the fishing activity.

PubMed

Chauvin, Christine; Le Bouar, Gilbert; Lardjane, Salim

2017-01-01

Sea fishing is one of the most dangerous occupations. Numerous studies have already sought to evaluate the risk level of this occupation through the analysis of the frequency and seriousness of occupational injuries. The purpose of the present study is to analyse these accidents in terms of two main characteristics of the vessels involved: the fishery type (high seas, offshore, coastal, or inshore fishery) and the fishing activity (use of passive or active gears). Injury rates were calculated for the Brittany region and for the year 2012. A second analysis was carried out on 8,286 reported injuries that occurred in France from 2002 to 2012, while vessels were in the process of fishing. This first analysis shows that the incidence rate is very high (103 per 1,000 full-time equivalent fishermen) and that it depends more on the fishery type than on the fishing activity; the highest rates concern the offshore and the coastal fleets. Results of the second analysis show that the nature of accidents depends more on the fishing activity than on the type of fishery. These findings lead to a discussion of the causes of the highest incidence rate values and the causes of the observed variations. The discussion also involves the methodological difficulties related to the incidence rate calculations.

The association of metal ion exposure with alpha-synuclein-like immunoreactivity in the central nervous system of fish, Catostomus commersoni.

PubMed

Boudreau, Heather S; Krol, Karmen M; Eibl, Joseph K; Williams, Linda D; Rossiter, John P; Palace, Vincent P; Ross, Gregory M

2009-05-17

Alpha-synuclein protein aggregates are a major component of Lewy bodies, the intracytoplasmic inclusions found in dopaminergic neurons that are a defining characteristic of Parkinson's disease. Other "synucleopathies" include dementia with Lewy bodies and multisystem atrophy. In vitro, the formation of these deposits can be induced by a number of substances, including metal ions. Fish provide a useful model to study the long-term biological effects of metal ion exposure, but to date no studies have been reported concerning such exposures with respect to alpha-synuclein aggregation. Mature white sucker fish (Catostomus commersoni; aged 5-8 years) were sampled from two sites within the Red Lake area of Northwestern Ontario, a region highly contaminated by metal ions due to mining activity. Individual fish were characterized with respect to liver metal ion uptake and metallothionein levels. Central nervous system (CNS) tissues of fish from test sites representing high and low metal ion contamination were examined immunohistochemically using a polyclonal antibody recognising alpha-synuclein protein. We demonstrate here that the CNS of fish exposed to elevated metal ion environments had increased alpha-synuclein-like immunoreactive aggregates, potentially reflecting metal ion exposure leading to CNS toxicity. These findings demonstrate that fish may be an important new model for studying environmental risk factors and the pathology associated with Parkinson's disease.

Effects of temperature on disease progression and swimming stamina in Ichthyophonus-infected rainbow trout, Oncorhynchus mykiss (Walbaum).

PubMed

Kocan, R; Hershberger, P; Sanders, G; Winton, J

2009-10-01

Rainbow trout, Oncorhynchus mykiss, were infected with Ichthyophonus sp. and held at 10 degrees C, 15 degrees C and 20 degrees C for 28 days to monitor mortality and disease progression. Infected fish demonstrated more rapid onset of disease, higher parasite load, more severe host tissue reaction and reduced mean-day-to-death at higher temperature. In a second experiment, Ichthyophonus-infected fish were reared at 15 degrees C for 16 weeks then subjected to forced swimming at 10 degrees C, 15 degrees C and 20 degrees C. Stamina improved significantly with increased temperature in uninfected fish; however, this was not observed for infected fish. The difference in performance between infected and uninfected fish became significant at 15 degrees C (P = 0.02) and highly significant at 20 degrees C (P = 0.005). These results have implications for changes in the ecology of fish diseases in the face of global warming and demonstrate the effects of higher temperature on the progression and severity of ichthyophoniasis as well as on swimming stamina, a critical fitness trait of salmonids. This study helps explain field observations showing the recent emergence of clinical ichthyophoniasis in Yukon River Chinook salmon later in their spawning migration when water temperatures were high, as well as the apparent failure of a substantial percentage of infected fish to successfully reach their natal spawning areas.

Effects of temperature on disease progression and swimming stamina in Ichthyophonus-infected rainbow trout, Oncorhynchus mykiss (Walbaum)

USGS Publications Warehouse

Kocan, R.; Hershberger, P.; Sanders, G.; Winton, J.

2009-01-01

Rainbow trout, Oncorhynchus mykiss, were infected with Ichthyophonus sp. and held at 10 ??C, 15 ??C and 20 ??C for 28 days to monitor mortality and disease progression. Infected fish demonstrated more rapid onset of disease, higher parasite load, more severe host tissue reaction and reduced mean-day-to-death at higher temperature. In a second experiment, Ichthyophonus-infected fish were reared at 15 ??C for 16 weeks then subjected to forced swimming at 10 ??C, 15 ??C and 20 ??C. Stamina improved significantly with increased temperature in uninfected fish; however, this was not observed for infected fish. The difference in performance between infected and uninfected fish became significant at 15 ??C (P = 0.02) and highly significant at 20 ??C (P = 0.005). These results have implications for changes in the ecology of fish diseases in the face of global warming and demonstrate the effects of higher temperature on the progression and severity of ichthyophoniasis as well as on swimming stamina, a critical fitness trait of salmonids. This study helps explain field observations showing the recent emergence of clinical ichthyophoniasis in Yukon River Chinook salmon later in their spawning migration when water temperatures were high, as well as the apparent failure of a substantial percentage of infected fish to successfully reach their natal spawning areas. ?? 2009 Blackwell Publishing Ltd.

Effect of ploidy on scale-cover pattern in linear ornamental (koi) common carp Cyprinus carpio.

PubMed

Gomelsky, B; Schneider, K J; Glennon, R P; Plouffe, D A

2012-09-01

The effect of ploidy on scale-cover pattern in linear ornamental (koi) common carp Cyprinus carpio was investigated. To obtain diploid and triploid linear fish, eggs taken from a leather C. carpio female (genotype ssNn) and sperm taken from a scaled C. carpio male (genotype SSnn) were used for the production of control (no shock) and heat-shocked progeny. In heat-shocked progeny, the 2 min heat shock (40° C) was applied 6 min after insemination. Diploid linear fish (genotype SsNn) demonstrated a scale-cover pattern typical for this category with one even row of scales along lateral line and few scales located near operculum and at bases of fins. The majority (97%) of triploid linear fish (genotype SssNnn) exhibited non-typical scale patterns which were characterized by the appearance of additional scales on the body. The extent of additional scales in triploid linear fish was variable; some fish had large scales, which covered almost the entire body. Apparently, the observed difference in scale-cover pattern between triploid and diploid linear fish was caused by different phenotypic expression of gene N/n. Due to incomplete dominance of allele N, triploids Nnn demonstrate less profound reduction of scale cover compared with diploids Nn. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

STS-54 MS3 Helms uses DSO 802 & Physics of Toys fish toy on OV-105's middeck

NASA Image and Video Library

1993-01-15

STS054-S-019 (15 Jan 1993) --- Helms with a fish toy on the middeck demonstrates some of the physics of toys to students watching on television. Four schools were chosen to ask questions of the astronauts during the lengthy program. Helms fielded questions from students at Shaver Elementary School in Portland, Oregon. The fish was used to demonstrate Newton's third law of motion and the conservation of angular momentum. The entire collection of toys will be videotaped for an educational program to be distributed to schools in the fall of this year. The scene was recorded at 17:50:08:27 GMT, Jan. 15, 1993.

Scombrotoxic fish poisoning in Britain: features of over 250 suspected incidents from 1976 to 1986.

PubMed Central

Bartholomew, B. A.; Berry, P. R.; Rodhouse, J. C.; Gilbert, R. J.; Murray, C. K.

1987-01-01

Between 1976 and 1986, 258 incidents of suspected scombrotoxic fish poisoning were reported in Britain. Histamine analysis was carried out on 240 fish samples from these incidents, and 101 were found to contain greater than 5 mg histamine/100 g fish. The symptoms most consistently reported were rash, diarrhoea, flushing and headache. In recent years there has been a decrease in the number of confirmed scombrotoxic outbreaks and a trend towards more sporadic incidents. Of fish samples with greater than 20 mg histamine/100 g, 94% were from incidents in which scombrotoxic symptoms were characteristic, but where fish had 5-20 mg/100 g only 38% of incidents were clinically distinctive. Guidelines are presented based on the interpretation of quantitative histamine analysis of fish samples from scombrotoxic poisoning incidents. PMID:3428380

Effects of dietary vitamin B6 supplementation on fillet fatty acid composition and fatty acid metabolism of rainbow trout fed vegetable oil based diets.

PubMed

Senadheera, Shyamalie D; Turchini, Giovanni M; Thanuthong, Thanongsak; Francis, David S

2012-03-07

Fish oil replacement in aquaculture feeds results in major modifications to the fatty acid makeup of cultured fish. Therefore, in vivo fatty acid biosynthesis has been a topic of considerable research interest. Evidence suggests that pyridoxine (vitamin B(6)) plays a role in fatty acid metabolism, and in particular, the biosynthesis of LC-PUFA has been demonstrated in mammals. However, there is little information on the effects of dietary pyridoxine availability in fish fed diets lacking LC-PUFA. This study demonstrates a relationship between dietary pyridoxine supplementation and fatty acid metabolism in rainbow trout. In particular, the dietary pyridoxine level was shown to modulate and positively stimulate the activity of the fatty acid elongase and Δ-6 and Δ-5 desaturase enzymes, deduced by the whole-body fatty acid balance method. This activity was insufficient to compensate for a diet lacking in LC-PUFA but does highlight potential strategies to maximize this activity in cultured fish, especially when fish oil is replaced with vegetable oils.

Endogenous orienting in the archer fish.

PubMed

Saban, William; Sekely, Liora; Klein, Raymond M; Gabay, Shai

2017-07-18

The literature has long emphasized the neocortex's role in volitional processes. In this work, we examined endogenous orienting in an evolutionarily older species, the archer fish, which lacks neocortex-like cells. We used Posner's classic endogenous cuing task, in which a centrally presented, spatially informative cue is followed by a target. The fish responded to the target by shooting a stream of water at it. Interestingly, the fish demonstrated a human-like "volitional" facilitation effect: their reaction times to targets that appeared on the side indicated by the precue were faster than their reaction times to targets on the opposite side. The fish also exhibited inhibition of return, an aftermath of orienting that commonly emerges only in reflexive orienting tasks in human participants. We believe that this pattern demonstrates the acquisition of an arbitrary connection between spatial orienting and a nonspatial feature of a centrally presented stimulus in nonprimate species. In the literature on human attention, orienting in response to such contingencies has been strongly associated with volitional control. We discuss the implications of these results for the evolution of orienting, and for the study of volitional processes in all species, including humans.

A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

USGS Publications Warehouse

Adams, Noah S.; Hatton, Tyson W.

2012-01-01

Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the spillway before passing the dam. In comparison, greater than 0.20 of the Chinook salmon passed within the powerhouse areas. Less milling behavior was observed for all species for fish that first approached the spillway. Compared to the powerhouse areas, a higher proportion of fish, regardless of species, passed the spillway areas and fewer transitioned to adjoining areas in the powerhouse. In addition to quantifying what had been previously speculated about the behavior of fish in the forebay of McNary Dam, the Markov chain analysis refined our understanding of how fish behavior and passage can be influenced by changes to the operations and structure of McNary Dam. For example, the addition of TSWs to the spillway area clearly influenced the passage of fish. Previous results have been reported showing that TSWs increased the number of fish passing through non-turbine routes and the fish-track videos indicated, in general, how fish behaved before passing through the TSWs. However, the analysis presented in this report allowed us to better understand how fish moved across the face of the dam before passing the TSWs and provided a way to quantify the effect of TSW location. Installation of the TSWs in bays 22 and 20 clearly increased passage proportions through the southern one-third of the spillway area for all species, most significantly for steelhead. When the TSWs were moved to bays 19 and 20 in 2008, overall passage through the southern one-third of the spillway remained higher than 2006, but decreased from what was observed in 2007. Shifting the TSWs to the north decreased the proportion of fish passing through the TSWs and increased the number of fish that moved to adjoining areas before passing the dam. Perhaps the most interesting new information to come out of the two-step Markov chain analysis relates to how the performance of the TSWs was influenced by their proximity to the powerhouse. During 2007, the highest proportion of fish passing through TSW22 was for fish that transitioned from the powerhouse area. In contrast, a relatively low proportion of fish passed through TSW20 after coming from the powerhouse area. Instead, the proportion of fish that passed TSW20 after coming from the northern part of the spillway was twice as high as the proportion of fish that passed through TSW20 after coming from the powerhouse. During 2008, the TSW in bay 22 was moved to bay 19, leaving the TSW in bay 20 as the one closest to the powerhouse. As was the case when a TSW was located in bay 22; the proportion of fish passing TSW20 after coming from the powerhouse was greater than the proportion of fish passing through TSW20 after coming from the northern part of the spillway. Passage proportions for fish passing through TSW19, the farthest north of the two TSWs during 2008, was higher for fish that came from the northern part of the spillway compared to the proportion of fish that passed through TSW19 after coming from the powerhouse. The Markov chain analysis provided a mathematical way to characterize fish behavior in the forebay of McNary Dam and helped refine our understanding of how fish movements were influenced by operational and structural changes at McNary Dam. The Markov chain analysis also could be used to examine how future structural and operational changes proposed for McNary Dam might influence the passage of juvenile salmonids.

Managing for desired experiences and site preferences: the case of fee-fishing anglers.

PubMed

Schuett, Michael A; Pierskalla, Chad D

2007-02-01

Fee-fishing involves paying a fee for the privilege of fishing a body of water where fish populations are enhanced by stocking fish. Past literature on this activity has focused more on the operation of the enterprise and management of the fish than the people and site characteristics. The objectives of the study were to profile anglers and describe their site/management preferences. This study utilized an on-site interview and mail-back questionnaire at fee-fishing establishments in West Virginia (n = 212). Factor analysis of desired recreation experiences yielded five factors: Experience nature & adventure, Stress release & relaxation, Trophy fishing, Escape, and Family time. Cluster analysis showed that these anglers can be segmented into two distinct clusters, differing by sociodemographic characteristics, fishing behavior, and site/management preferences. The findings from this study provide baseline data to aid public resource managers and fee-fishing business owners in determining how to provide satisfying outdoor experiences and deliver desired services on-site. Future research will be needed from additional fee-fishing sites to obtain more detail about this outdoor recreation cohort and be able to generalize to a larger population of participants.

Managing for Desired Experiences and Site Preferences: The Case of Fee-Fishing Anglers

NASA Astrophysics Data System (ADS)

Schuett, Michael A.; Pierskalla, Chad D.

2007-02-01

Fee-fishing involves paying a fee for the privilege of fishing a body of water where fish populations are enhanced by stocking fish. Past literature on this activity has focused more on the operation of the enterprise and management of the fish than the people and site characteristics. The objectives of the study were to profile anglers and describe their site/management preferences. This study utilized an on-site interview and mail-back questionnaire at fee-fishing establishments in West Virginia ( n = 212). Factor analysis of desired recreation experiences yielded five factors: Experience nature & adventure, Stress release & relaxation, Trophy fishing, Escape, and Family time. Cluster analysis showed that these anglers can be segmented into two distinct clusters, differing by sociodemographic characteristics, fishing behavior, and site/management preferences. The findings from this study provide baseline data to aid public resource managers and fee-fishing business owners in determining how to provide satisfying outdoor experiences and deliver desired services on-site. Future research will be needed from additional fee-fishing sites to obtain more detail about this outdoor recreation cohort and be able to generalize to a larger population of participants.

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

PubMed Central

2010-01-01

Background Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish. Results RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution. Conclusion This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history of immunogenetics from fish to mammals. PMID:20707909

Helminth parasites of native Hawaiian freshwater fishes: an example of extreme ecological isolation.

PubMed

Font, W F; Tate, D C

1994-10-01

The Hawaiian Islands harbor a depauperate native freshwater fish fauna comprised of 4 endemic gobies (Gobiidae) and 1 endemic sleeper (Eleotridae). We hypothesized that the natural helminth parasite community of these stream fishes would be depauperate because of colonizing constraints. In the absence of exotic fishes, native fishes in streams of Hanakapi'ai and Nu'alolo valleys harbored no adult helminth parasites. In Hakalau Stream on Hawai'i and Wainiha River on Kaua'i, we found introduced swordtails and guppies (Poeciliidae); here, the native gobioid fishes shared species of helminths with poeciliids. They were the nematode Camallanus cotti, the Asian tapeworm Bothriocephalus acheilognathi, and the leech Myzobdella lugubris. Such parasitological data should be incorporated into management plans for the conservation of native Hawaiian stream fishes as these parasites have been previously demonstrated to cause disease.

Fish collagen is an important panallergen in the Japanese population.

PubMed

Kobayashi, Y; Akiyama, H; Huge, J; Kubota, H; Chikazawa, S; Satoh, T; Miyake, T; Uhara, H; Okuyama, R; Nakagawara, R; Aihara, M; Hamada-Sato, N

2016-05-01

Collagen was identified as a fish allergen in early 2000s. Although its allergenic potential has been suggested to be low, risks associated with collagen as a fish allergen have not been evaluated to a greater extent. In this study, we aimed to clarify the importance of collagen as a fish allergen. Our results showed that 50% of Japanese patients with fish allergy had immunoglobulin E (IgE) against mackerel collagen, whereas 44% had IgE against mackerel parvalbumin. IgE inhibition assay revealed high cross-reactivity of mackerel collagen to 22 fish species (inhibition rates: 87-98%). Furthermore, a recently developed allergy test demonstrated that collagen triggered IgE cross-linking on mast cells. These data indicate that fish collagen is an important and very common panallergen in fish consumed in Japan. The high rate of individuals' collagen allergy may be attributable to the traditional Japanese custom of raw fish consumption. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The oxidation of drugs by fishes

USGS Publications Warehouse

Buhler, Donald R.; Rasmusson, Mary E.

1968-01-01

1. Fish liver microsomal systems have been found to catalyze the hydroxylation of aniline and acetanilide, the N-demethylation of aminopyrine and the O-dealkylation of phenacetin.2. These systems are similar to the corresponding mammalian enzymes and they may be considered to be mixed function oxidase since they require NADPH and oxygen. An absolute requirement for oxygen, however, was difficult to demonstrate for the hepatic phenacetin cleavage system from fish.3. Microsomal drug metabolizing systems from fish have temperature optima which are considerably lower than those of corresponding mammalian systems

Replicating vaccines

USDA-ARS?s Scientific Manuscript database

Early work on fish immunology and disease resistance demonstrated fish (like animals and humans) that survived infection were typically resistant to re-infection with the same pathogen. The concepts of resistance upon reinfection lead to the research and development of replicating (live) vaccines in...

An index of biological integrity for northern Mid-Atlantic Slope drainages

USGS Publications Warehouse

Daniels, R.A.; Riva-Murray, K.; Halliwell, D.B.; Vana-Miller, D. L.; Bilger, Michael D.

2002-01-01

An index of biological integrity (IBI) was developed for streams in the Hudson, Delaware, and Susquehanna River drainages in the northeastern United States based on fish assemblage data from the Mohawk River drainage of New York. The original IBI, developed for streams in the U.S. Midwest, was modified to reflect the assemblage composition and structure present in Mid-Atlantic Slope drainages. We replaced several of the Midwestern IBI metrics and criteria scores because fishes common to the Midwest are absent from or poorly represented in the Northeast and because stream fish assemblages in the Northeast are less rich than those in the Midwest. For all replacement metrics we followed the ecology-based rationale used in the development of each of the metrics of the Midwestern IBI so that the basic theoretical underpinnings of the IBI remained unchanged. The validity of this modified IBI is demonstrated by examining the quality of streams in the Hudson, Delaware, and lower Susquehanna River basins. The relationships between the IBI and other indicators of environmental quality are examined using data on assemblages of fish and benthic macroinvertebrates and on chemical and physical stream characteristics obtained during 1993-2000 by the U.S. Geological Survey's National Water Quality Assessment Program in these three river basins. A principal components analysis (PCA) of chemical and physical variables from 27 sites resulted in an environmental quality gradient as the primary PCA axis (eigenvalue, 0.41 ). Principal components analysis site scores were significantly correlated with such benthic macroinvertebrate metrics as the percentage of Ephemeroptera, Plecoptera, and Trichoptera taxa (Spearman R = -0.66, P < 0.001). Index of biological integrity scores for sites in these three river basins were significantly correlated with this environmental quality gradient (Spearman R = -0.78, P = 0.0001). The northern Mid-Atlantic Slope IBI appears to be sensitive to environmental degradation in all three of the river basins addressed in this study. Adjustment of metric scoring criteria may be warranted, depending on composition of fish species in streams in the study area and on the relative effort used in the collection of fish assemblage data.

Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs.

PubMed

Tornabene, Luke; Van Tassell, James L; Robertson, D Ross; Baldwin, Carole C

2016-08-01

Mesophotic and deeper reefs of the tropics are poorly known and underexplored ecosystems worldwide. Collectively referred to as the 'twilight zone', depths below ~30-50 m are home to many species of reef fishes that are absent from shallower depths, including many undescribed and endemic species. We currently lack even a basic understanding of the diversity and evolutionary origins of fishes on tropical mesophotic reefs. Recent submersible collections in the Caribbean have provided new specimens that are enabling phylogenetic reconstructions that incorporate deep-reef representatives of tropical fish genera. Here, we investigate evolutionary depth transitions in the family Gobiidae (gobies), the most diverse group of tropical marine fishes. Using divergence-time estimation coupled with stochastic character mapping to infer the timing of shallow-to-deep habitat transitions in gobies, we demonstrate at least four transitions from shallow to mesophotic depths. Habitat transitions occurred in two broad time periods (Miocene, Pliocene-Pleistocene), and may have been linked to the availability of underutilized niches, as well as the evolution of morphological/behavioural adaptations for life on deep reefs. Further, our analysis shows that at least three evolutionary lineages that invaded deep habitats subsequently underwent speciation, reflecting another unique mode of radiation within the Gobiidae. Lastly, we synthesize depth distributions for 95 species of Caribbean gobies, which reveal major bathymetric faunal breaks at the boundary between euphotic and mesophotic reefs. Ultimately, our study is the first rigorous investigation into the origin of Caribbean deep-reef fishes and provides a framework for future studies that utilize rare, deep-reef specimens. © 2016 John Wiley & Sons Ltd.

Ocean acidification alters the otoliths of a pantropical fish species with implications for sensory function.

PubMed

Bignami, Sean; Enochs, Ian C; Manzello, Derek P; Sponaugle, Su; Cowen, Robert K

2013-04-30

Ocean acidification affects a wide diversity of marine organisms and is of particular concern for vulnerable larval stages critical to population replenishment and connectivity. Whereas it is well known that ocean acidification will negatively affect a range of calcareous taxa, the study of fishes is more limited in both depth of understanding and diversity of study species. We used new 3D microcomputed tomography to conduct in situ analysis of the impact of ocean acidification on otolith (ear stone) size and density of larval cobia (Rachycentron canadum), a large, economically important, pantropical fish species that shares many life history traits with a diversity of high-value, tropical pelagic fishes. We show that 2,100 μatm partial pressure of carbon dioxide (pCO2) significantly increased not only otolith size (up to 49% greater volume and 58% greater relative mass) but also otolith density (6% higher). Estimated relative mass in 800 μatm pCO2 treatments was 14% greater, and there was a similar but nonsignificant trend for otolith size. Using a modeling approach, we demonstrate that these changes could affect auditory sensitivity including a ∼50% increase in hearing range at 2,100 μatm pCO2, which may alter the perception of auditory information by larval cobia in a high-CO2 ocean. Our results indicate that ocean acidification has a graded effect on cobia otoliths, with the potential to substantially influence the dispersal, survival, and recruitment of a pelagic fish species. These results have important implications for population maintenance/replenishment, connectivity, and conservation efforts for other valuable fish stocks that are already being deleteriously impacted by overfishing.

Spatially-Resolved Influence of Temperature and Salinity on Stock and Recruitment Variability of Commercially Important Fishes in the North Sea

PubMed Central

Akimova, Anna; Núñez-Riboni, Ismael; Kempf, Alexander; Taylor, Marc H.

2016-01-01

Understanding of the processes affecting recruitment of commercially important fish species is one of the major challenges in fisheries science. Towards this aim, we investigated the relation between North Sea hydrography (temperature and salinity) and fish stock variables (recruitment, spawning stock biomass and pre-recruitment survival index) for 9 commercially important fishes using spatially-resolved cross-correlation analysis. We used high-resolution (0.2° × 0.2°) hydrographic data fields matching the maximal temporal extent of the fish population assessments (1948–2013). Our approach allowed for the identification of regions in the North Sea where environmental variables seem to be more influential on the fish stocks, as well as the regions of a lesser or nil influence. Our results confirmed previously demonstrated negative correlations between temperature and recruitment of cod and plaice and identified regions of the strongest correlations (German Bight for plaice and north-western North Sea for cod). We also revealed a positive correlation between herring spawning stock biomass and temperature in the Orkney-Shetland area, as well as a negative correlation between sole pre-recruitment survival index and temperature in the German Bight. A strong positive correlation between sprat stock variables and salinity in the central North Sea was also found. To our knowledge the results concerning correlations between North Sea hydrography and stocks’ dynamics of herring, sole and sprat are novel. The new information about spatial distribution of the correlation provides an additional help to identify mechanisms underlying these correlations. As an illustration of the utility of these results for fishery management, an example is provided that incorporates the identified environmental covariates in stock-recruitment models. PMID:27584155

Ocean acidification alters the otoliths of a pantropical fish species with implications for sensory function

PubMed Central

Bignami, Sean; Enochs, Ian C.; Manzello, Derek P.; Sponaugle, Su; Cowen, Robert K.

2013-01-01

Ocean acidification affects a wide diversity of marine organisms and is of particular concern for vulnerable larval stages critical to population replenishment and connectivity. Whereas it is well known that ocean acidification will negatively affect a range of calcareous taxa, the study of fishes is more limited in both depth of understanding and diversity of study species. We used new 3D microcomputed tomography to conduct in situ analysis of the impact of ocean acidification on otolith (ear stone) size and density of larval cobia (Rachycentron canadum), a large, economically important, pantropical fish species that shares many life history traits with a diversity of high-value, tropical pelagic fishes. We show that 2,100 μatm partial pressure of carbon dioxide (pCO2) significantly increased not only otolith size (up to 49% greater volume and 58% greater relative mass) but also otolith density (6% higher). Estimated relative mass in 800 μatm pCO2 treatments was 14% greater, and there was a similar but nonsignificant trend for otolith size. Using a modeling approach, we demonstrate that these changes could affect auditory sensitivity including a ∼50% increase in hearing range at 2,100 μatm pCO2, which may alter the perception of auditory information by larval cobia in a high-CO2 ocean. Our results indicate that ocean acidification has a graded effect on cobia otoliths, with the potential to substantially influence the dispersal, survival, and recruitment of a pelagic fish species. These results have important implications for population maintenance/replenishment, connectivity, and conservation efforts for other valuable fish stocks that are already being deleteriously impacted by overfishing. PMID:23589887

STS-54 MS3 Helms uses DSO 802 and Physics of Toys fish toy on OV-105's middeck

NASA Technical Reports Server (NTRS)

1993-01-01

STS-54 Mission Specialist 3 (MS3) Susan J. Helms with a fish toy on the middeck of the Earth-orbiting Endeavour, Orbiter Vehicle (OV) 105, demonstrates some of the physics of toys to students watching on television (TV). The demonstration was part of Application Specific Preprogrammed Experiment Culture System Physics of Toys (ASPEC) and Detailed Supplementary Objective (DSO) 802, Educational activities. Through telephone and TV downlinks, Helms fielded questions from students at Shaver Elementary School in Portland, Oregon. The fish was used to demonstrate Newton's third law of motion and the conservation of angular momentum. The entire collection of toys will be videotaped for an educational program to be distributed to schools in the fall of this year. Helms wears an Oregon Trail t-shirt. This scene was downlinked at 17:50:08:27 GMT.

Of travertine and time: otolith chemistry and microstructure detect provenance and demography of endangered humpback chub in Grand Canyon, USA

USGS Publications Warehouse

Limburg, Karin E.; Hayden, Todd A.; Pine, William E.; Yard, Michael D.; Kozdon, Reinhard; Valley, John W.

2013-01-01

We developed a geochemical atlas of the Colorado River in Grand Canyon and in its tributary, the Little Colorado River, and used it to identify provenance and habitat use by Federally Endangered humpback chub, Gila cypha. Carbon stable isotope ratios (δ13C) discriminate best between the two rivers, but fine scale analysis in otoliths requires rare, expensive instrumentation. We therefore correlated other tracers (SrSr, Ba, and Se in ratio to Ca) to δ13C that are easier to quantify in otoliths with other microchemical techniques. Although the Little Colorado River’s water chemistry varies with major storm events, at base flow or near base flow (conditions occurring 84% of the time in our study) its chemistry differs sufficiently from the mainstem to discriminate one from the other. Additionally, when fish egress from the natal Little Colorado River to the mainstem, they encounter cold water which causes the otolith daily growth increments to decrease in size markedly. Combining otolith growth increment analysis and microchemistry permitted estimation of size and age at first egress; size at first birthday was also estimated. Emigrants < 1 year old averaged 51.2 ± 4.4 (SE) days and 35.5 ± 3.6 mm at egress; older fish that had recruited to the population averaged 100 ± 7.8 days old and 51.0 ± 2.2 mm at egress, suggesting that larger, older emigrants recruit better. Back-calculated size at age 1 was unimodal and large (78.2 ± 3.3 mm) in Little Colorado caught fish but was bimodally distributed in Colorado mainstem caught fish (49.9 ± 3.6 and 79 ± 4.9 mm) suggesting that humpback chub can also rear in the mainstem. The study demonstrates the coupled usage of the two rivers by this fish and highlights the need to consider both rivers when making management decisions for humpback chub recovery.

Of Travertine and Time: Otolith Chemistry and Microstructure Detect Provenance and Demography of Endangered Humpback Chub in Grand Canyon, USA

PubMed Central

Limburg, Karin E.; Hayden, Todd A.; Pine, William E.; Yard, Michael D.; Kozdon, Reinhard; Valley, John W.

2013-01-01

We developed a geochemical atlas of the Colorado River in Grand Canyon and in its tributary, the Little Colorado River, and used it to identify provenance and habitat use by Federally Endangered humpback chub, Gila cypha.  Carbon stable isotope ratios (δ13C) discriminate best between the two rivers, but fine scale analysis in otoliths requires rare, expensive instrumentation. We therefore correlated other tracers (SrSr, Ba, and Se in ratio to Ca) to δ13C that are easier to quantify in otoliths with other microchemical techniques. Although the Little Colorado River’s water chemistry varies with major storm events, at base flow or near base flow (conditions occurring 84% of the time in our study) its chemistry differs sufficiently from the mainstem to discriminate one from the other. Additionally, when fish egress from the natal Little Colorado River to the mainstem, they encounter cold water which causes the otolith daily growth increments to decrease in size markedly. Combining otolith growth increment analysis and microchemistry permitted estimation of size and age at first egress; size at first birthday was also estimated. Emigrants < 1 year old averaged 51.2 ± 4.4 (SE) days and 35.5 ± 3.6 mm at egress; older fish that had recruited to the population averaged 100 ± 7.8 days old and 51.0 ± 2.2 mm at egress, suggesting that larger, older emigrants recruit better. Back-calculated size at age 1 was unimodal and large (78.2 ± 3.3 mm) in Little Colorado caught fish but was bimodally distributed in Colorado mainstem caught fish (49.9 ± 3.6 and 79 ± 4.9 mm) suggesting that humpback chub can also rear in the mainstem. The study demonstrates the coupled usage of the two rivers by this fish and highlights the need to consider both rivers when making management decisions for humpback chub recovery. PMID:24358346

FISH analysis for diagnostic evaluation of challenging melanocytic lesions.

PubMed

Zimmermann, A K; Hirschmann, A; Pfeiffer, D; Paredes, B E; Diebold, J

2010-09-01

The differential diagnosis of malignant melanomas and atypical melanocytic nevi is still a diagnostic challenge. The currently accepted morphologic criteria show substantial interobserver variability, likewise immunohistochemical studies are often not able to discriminate these lesions reliably. Techniques that support diagnostic accuracy are of the greatest importance considering the growing incidence of malignant melanomas and their increase in younger patients. In this study we analyzed the feasibility of fluorescence in situ hybridization (FISH) analysis for the discrimination of malignant and benign melanocytic tumors. A panel of DNA probes was used to detect chromosomal aberrations of chromosomes 6 and 11. On a series of 5 clearly malignant and benign melanocytic tumors we confirmed the applicability of the test. Then we focused on examination of ambiguous melanocytic lesions, where atypical cells are often difficult to relocalize in the 4',6-Diamidino-2-phenylindol (DAPI)-fluorescence stain. FISH analyses were conducted on destained H&E-stained slides. By comparison of the DAPI-image with photos taken from the H&E stain, unambiguous assignment of the FISH results to the conspicuous groups of cells was possible. The results of FISH analysis were consistent with the conventional diagnosis in 11 of 14 small ambiguous lesions. Of the remaining 3 cases, 2 showed FISH-results close to the cut-off level. Comparison of FISH results on thin and thick sections revealed that the cut-off values have to be adapted for 2 microm destained sections. In conclusion, FISH analysis is a useful and applicable tool for assessment of even smallest melanocytic neoplasms, although there will remain unclear cases that cannot be solved even after additional FISH evaluation.

Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha).

PubMed

Ford, Michael J; Murdoch, Andrew; Hughes, Michael

2015-03-01

We used parentage analysis based on microsatellite genotypes to measure rates of homing and straying of Chinook salmon (Oncorhynchus tshawytscha) among five major spawning tributaries within the Wenatchee River, Washington. On the basis of analysis of 2248 natural-origin and 11594 hatchery-origin fish, we estimated that the rate of homing to natal tributaries by natural-origin fish ranged from 0% to 99% depending on the tributary. Hatchery-origin fish released in one of the five tributaries homed to that tributary at a far lower rate than the natural-origin fish (71% compared to 96%). For hatchery-released fish, stray rates based on parentage analysis were consistent with rates estimated using physical tag recoveries. Stray rates among major spawning tributaries were generally higher than stray rates of tagged fish to areas outside of the Wenatchee River watershed. Within the Wenatchee watershed, rates of straying by natural-origin fish were significantly affected by spawning tributary and by parental origin: progeny of naturally spawning hatchery-produced fish strayed at significantly higher rates than progeny whose parents were themselves of natural origin. Notably, none of the 170 offspring that were products of mating by two natural-origin fish strayed from their natal tributary. Indirect estimates of gene flow based on FST statistics were correlated with but higher than the estimates from the parentage data. Tributary-specific estimates of effective population size were also correlated with the number of spawners in each tributary. Published [2015]. This article is a U.S. Government work and is in the public domain in the USA.

Biochemical effects of commercial feedstuffs on the fry of climbing perch (Anabas testudineus) and its impact on Swiss albino mice as an animal model.

PubMed

Munshi, Mita; Tumu, Khairun Nafiz; Hasan, Md Nazmul; Amin, Md Ziaul

2018-01-01

This study assesses the biochemical effects of commercially available fish feedstuffs on the fry of climbing perch ( Anabas testudineus ). Subsequently, its impact on experimental animal, Swiss albino mice, is also examined. In order to access the impact of commercial fish feed and feed consumption fish on the experimental animal, the proximate, biochemical and histopathological analyses were done using standard methods. The proximate composition as well as the concentrations of Pb, Ni, Mn, As, Zn, and Cd in the fish feed, different parts of the A. testudineus fish and different parts of the A. testudineus fish-treated experimental mice liver, were all determined using Energy Dispersive X-ray Fluorescence (EDXRF) Spectrometry. The highest levels of Cr, Pb and As were observed in the liver of Swiss albino mice treated with FFT2 and FFBB2 and their concentrations were 0.156, 0.491, 0.172 μg/g and 0.166, 0.771, 0.157 μg/g respectively. No significant changes of protein, fat, crude fiber, moisture and ash contents were observed after proximate composition analysis of fish feeds, A. testudineus and A. testudineus treated experimental mice. Significant amounts of heavy metals (Cr, Mn, Zn Cu, Ni) were found in fish feed, different parts of A. testudineus fish and in the experimental mice. However, remarkably high amounts were observed in the A. testudineus fish's head and bone with body parts. Biochemical analysis of blood samples of A. testudineus fish treated experimental mice indicated that the cholesterol, TG, LDL and glucose levels were significantly higher. Yet no significant alteration in the HDL level was observed when compared to the control. In histopathological analysis, a remarkable degeneration was observed in the liver and kidney of A. testudineus treated mice. It can therefore be concluded that although A. testudineus has nutritional benefits the quality of this fish may be compromised as a consequence of contamination through various anthropogenic activities. This analysis suggests the commercial fish feed producers must take special caution to reduce the toxic metals in various fish feed products and make it nutritionally rich and safe for fish to eat. Finally, it needs to be safe for human consumption as well.

Analysis of Trends in Fish Assemblages in Narragansett Bay, RI/MA

EPA Science Inventory

Estuarine fish are highly valued resources that are affected by several factors, including climate, landscape, pollution, and fishing pressure. Here, we examine patterns of variability in estuarine fish assemblages in Narragansett Bay, an estuary located in Rhode Island and Mass...

An inverse problem for a mathematical model of aquaponic agriculture

NASA Astrophysics Data System (ADS)

Bobak, Carly; Kunze, Herb

2017-01-01

Aquaponic agriculture is a sustainable ecosystem that relies on a symbiotic relationship between fish and macrophytes. While the practice has been growing in popularity, relatively little mathematical models exist which aim to study the system processes. In this paper, we present a system of ODEs which aims to mathematically model the population and concetrations dynamics present in an aquaponic environment. Values of the parameters in the system are estimated from the literature so that simulated results can be presented to illustrate the nature of the solutions to the system. As well, a brief sensitivity analysis is performed in order to identify redundant parameters and highlight those which may need more reliable estimates. Specifically, an inverse problem with manufactured data for fish and plants is presented to demonstrate the ability of the collage theorem to recover parameter estimates.

A demonstration of the instream flow incremental methodology, Shenandoah River

USGS Publications Warehouse

Zappia, Humbert; Hayes, Donald C.

1998-01-01

Current and projected demands on the water resources of the Shenandoah River have increased concerns for the potential effect of these demands on the natural integrity of the Shenandoah River system. The Instream Flow Incremental Method (IFIM) process attempts to integrate concepts of water-supply planning, analytical hydraulic engineering models, and empirically derived habitat versus flow functions to address water-use and instream-flow issues and questions concerning life-stage specific effects on selected species and the general well being of aquatic biological populations.The demonstration project also sets the stage for the identification and compilation of the major instream-flow issues in the Shenandoah River Basin, development of the required multidisciplinary technical team to conduct more detailed studies, and development of basin specific habitat and flow requirements for fish species, species assemblages, and various water uses in the Shenandoah River Basin. This report presents the results of an IFIM demonstration project, conducted on the main stem Shenandoah River in Virginia, during 1996 and 1997, using the Physical Habitat Simulation System (PHABSIM) model.Output from PHABSIM is used to address the general flow requirements for water supply and recreation and habitat for selected life stages of several fish species. The model output is only a small part of the information necessary for effective decision making and management of river resources. The information by itself is usually insufficient for formulation of recommendations regarding instream-flow requirements. Additional information, for example, can be obtained by analysis of habitat time-series data, habitat duration data, and habitat bottlenecks. Alternative-flow analysis and habitat-duration curves are presented.

Risk factors for Clonorchis sinensis infection transmission in humans in northern Vietnam: A descriptive and social network analysis study.

PubMed

Vinh, Hoang Quang; Phimpraphai, Waraphon; Tangkawattana, Sirikachorn; Smith, John F; Kaewkes, Sasithorn; Dung, Do Trung; Duong, Tran Thanh; Sripa, Banchob

2017-04-01

Clonorchis sinensis is major fish-borne trematode, endemic in North Vietnam. Risk factors described so far include individual eating behaviors and environmental factors. Here, additional to conventional risk factors, we report on socially influenced liver fluke transmission in endemic communities. A cross-sectional study on risk factors and fish sharing networks was conducted in 4 villages of Gia Thinh Commune, Ninh Binh Province. A total of 510 residents in 272 households were recruited for risk factor analysis while 220 households, 28 fishermen and 10 fish-sellers were enrolled for social network study. Fecal examination for C. sinensis eggs was performed. Average C. sinensis infection rate at Gia Thinh commune was 16.5% (range 2% to 34.4%). Higher infection rates were significantly associated with males, lower educational levels, eating raw fish, and location of the villages. Social network analysis (SNA) showed a strong positive correlation between ego network size (number of households in fish sharing network) and quantity of raw fish consumed (r=0.603, P<0.05). The infection rate in people who ate raw-fish caught from a nearby river was significantly higher than those who consumed fish taken from farmed ponds (P<0.05). The amount of raw-fish meal consumed per resident/year was significantly higher in villages that had a strong network of sharing raw-fish food (P<0.001). This study reports for the first time on fish-food sharing among neighbors, proximity to water bodies, frequency of eating raw fish from natural water bodies and low education were key risk factors in C. sinensis infection transmission in northern Vietnam. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Risk factors for Clonorchis sinensis infection transmission in humans in northern Vietnam: A descriptive and social network analysis study

PubMed Central

Vinh, Hoang Quang; Phimpraphai, Waraphon; Tangkawattana, Sirikachorn; Smith, John F.; Kaewkes, Sasithorn; Dung, Do Trung; Duong, Tran Thanh; Sripa, Banchob

2016-01-01

Clonorchis sinensis is major fish-borne trematode, endemic in North Vietnam. Risk factors described so far include individual eating behaviors and environmental factors. Here, additional to conventional risk factors, we report on socially influenced liver fluke transmission in endemic communities. A cross-sectional study on risk factors and fish sharing networks was conducted in 4 villages of Gia Thinh Commune, Ninh Binh Province. A total of 510 residents in 272 households were recruited for risk factor analysis while 220 households, 28 fishermen and 10 fish-sellers were enrolled for social network study. Fecal examination for C. sinensis eggs was performed. Average C. sinensis infection rate at Gia Thinh commune was 16.5% (range 2% to 34.4%). Higher infection rates were significantly associated with males, lower educational levels, eating raw fish, and location of the villages. Social network analysis (SNA) showed a strong positive correlation between ego network size (number of households in fish sharing network) and quantity of raw fish consumed (r=0.603, P< 0.05). The infection rate in people who ate raw-fish caught from a nearby river was significantly higher than those who consumed fish taken from farmed ponds (P<0.05). The amount of raw-fish meal consumed per resident/year was significantly higher in villages that had a strong network of sharing raw-fish food (P<0.001). This study reports for the first time on fish-food sharing among neighbors, proximity to water bodies, frequency of eating raw fish from natural water bodies and low education were key risk factors in C. sinensis infection transmission in northern Vietnam. PMID:27939296

Fluorescent in situ hybridization (FISH) on corneal impression cytology specimens (CICS): study of epithelial cell survival after keratoplasty.

PubMed

Catanese, Muriel; Popovici, Cornel; Proust, Hélène; Hoffart, Louis; Matonti, Frédéric; Cochereau, Isabelle; Conrath, John; Gabison, Eric E

2011-02-22

To assess corneal epithelial cell survival after keratoplasty. Corneal impression cytology (CIC) was performed on sex-mismatched corneal transplants. Fluorescent in situ hybridization (FISH) with sex chromosome-specific probes was performed to identify epithelial cell mosaicism and therefore allocate the donor or recipient origin of the cells. Twenty-four samples of corneal epithelial cells derived from 21 transplanted patients were analyzed. All patients received post-operative treatment using dexamethasone eye drops, with progressive tapering over 18 months, and nine patients also received 2% cyclosporine eye drops. Out of the 24 samples reaching quality criteria, sex mosaicism was found in 13, demonstrating the presence of donor-derived cells at the center of the graft for at least 211 days post keratoplasty. Kaplan-Meier analysis established a median survival of donor corneal epithelial cells of 385 days. Although not statistically significant, the disappearance of donor cells seemed to be delayed and the average number of persistent cells appeared to be greater when 2% cyclosporine was used topically as an additional immunosuppressive therapy. The combination of corneal impressions and FISH analysis is a valuable tool with negligible side effects to investigate the presence of epithelial cell mosaicism in sex-mismatched donor transplants. Epithelial cells survived at the center of the graft with a median survival of more than one year, suggesting slower epithelial turnover than previously described.

Determining the arsenic, cadmium, lead, copper and chromium contents by atomic absorption spectrometry in Pangasius fillets from Vietnam.

PubMed

Molognoni, Luciano; Vitali, Luciano; Ploêncio, Leandro As; Santos, Jacson N; Daguer, Heitor

2016-07-01

Pangasius is a fish produced on a large scale in Vietnam and exported to many countries. Since river contamination from human activities can affect the safety of this food, fish consumption can cause exposure to potentially toxic elements for humans. The aim of this study, therefore, was to assess arsenic, cadmium, lead, copper and chromium contents by atomic absorption spectrometry in Pangasius fillet produced in the provinces of Dong Thap and Can Tho (Vietnam) and exported to Brazil. The limits of detection were: arsenic 0.5443 µg kg(-1) , cadmium 0.0040 mg kg(-1) , chromium 0.0004 mg kg(-1) , copper 0.0037 mg kg(-1) and lead 0.0284 mg kg(-1) . Analysis of 20 samples showed results below the limit of detection for arsenic, chromium and lead, while copper average concentration was 0.0234 mg kg(-1) . Cadmium average concentration was 0.0547 mg kg(-1) , with no significant difference between the two regions studied. The samples of Pangasius had no detectable concentrations of arsenic, chromium, copper and lead, and do not represent a hazard to public health. However, cadmium analysis revealed non-compliant samples, demonstrating the importance of monitoring the quality of imported Pangasius fish. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf

Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failedmore » to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.« less

Constitutional Mosaic Trisomy 13 in Two Germ Cell Layers is Different from Patau Syndrome? A Case Report

PubMed Central

Kunwar, Fulesh; Pandya, Vidhi

2016-01-01

The heterogeneous phenotype of known syndromes is a clinical challenge, and harmonized description using globally accepted ontology is desirable. This report attempts phenotypic analysis in a patient of constitutional mosaic trisomy 13 in mesoderm and ectoderm to make globally comparable clinical description. Phenotypic features (minor/major abnormalities) were recorded and matched with the Human Phenotype Ontology terms that were used to query web-based tool Phenomizer. We report here a case of 24-year-old girl born to non consanguineous parents with history of one abortion. Her phenotypic evaluation included short columella, low-set ears, seizures, enlarged naris, bifid tongue, infra-orbital fold, smooth philtrum, microtia, microcephaly, carious teeth, downslanted palpebral fissures, proportionate short stature, high palate, thin upper lip vermilion, small for gestational age, broad fingertip, broad hallux, mandibular prognathia and dental malocclusion. Karyotype and interphase FISH (Fluorescence in situ hybridization) was done in blood cells. Interphase FISH was also performed on buccal epithelial cells. Cytogenetic analysis demonstrated trisomy 13 mosaicism in 25% cells i.e. 47, XX,+13(9)/46,XX(27). The interphase FISH in blood cells showed trisomy 13 in 15%, whereas in buccal mucosa cells showed nearly 6%. Mosaic aneuploidy in constitutional karyotype can be responsible for variation in clinical and morphological presentation of patient with genetic disorder. PMID:27134897

Benthic food webs support the production of sympatric flatfish ...

EPA Pesticide Factsheets

Identifying nursery habitats is of paramount importance to define proper management and conservation strategies for flatfish species. Flatfish nursery studies usually report upon habitat occupation, but few attempted to quantify the importance of those habitats to larvae development. The reliance of two sympatric flatfish species larvae, the European flounder Platichthys flesus and the common sole Solea solea, on the estuarine food web (benthic vs. pelagic) was determined through carbon and nitrogen stable isotope analysis. The organic matter sources supporting the production of P. flesus and S. solea larvae biomass originates chiefly in the benthic food web. However, these species have significantly different ä13C and ä15N values which suggests that they prey on organisms that use a different mixture of sources or assimilate different components from similar OM pools (or both). Fisheries production is a highly-valued ecosystem service of coastal habitats globally. Developing ecological production functions to relate nursery habitat to this ecosystem service, however, has proved challenging owing to lack of techniques to effectively relate habitat use with the early life stages of fish. In this study, we demonstrate how stable isotopes can be used to evaluate nursery habitat-fish production linkages using stable isotope analysis of an estuarine food web. In particular, we show how to quantify the reliance of two commercially-important fish species to various h

Limnological study with reference to fish culture of Bothali (Mendha) reservoir, district - Gadchiroli (India).

PubMed

Tijare, Rajendra V

2012-04-01

Limnological study with reference to fish culture was carried out at Bothali (Mendha) reservoir, district Gadchiroli, India. Water samples from different sampling locations were collected and processed for physico-chemical analysis. The physico-chemical analysis revealed that the reservoir is favourable for fish culture as the phosphate content in water is moderate in amount. This reservoir can produce a good yield of fishes. Though the reservoir is presently exploited and is under pisciculture, a better treatment of the reservoir such as prevention of entry of organic matter, reduction of phosphate ion concentration to certain extent is necessary to obtain a maximum fish yield.

Differential susceptibility in steelhead trout populations to an emergent MD strain of infectious hematopoietic necrosis virus

USGS Publications Warehouse

Breyta, R.; Jones, Amelia; Kurath, Gael

2014-01-01

A significant emergence of trout-adapted MD subgroup infectious hematopoietic necrosis virus (IHNV) began in the coastal region of Washington State, USA, in 2007. This emergence event lasted until 2011 and caused both asymptomatic adult fish infection and symptomatic epidemic disease and mortality in juvenile fish. Incidence of virus during this emergence demonstrated a heterogeneous distribution among rivers of the coastal region, leaving fish populations of some rivers apparently untouched while others suffered significant and recurrent infection and mortality (Breyta et. al. 2013; Dis Aquat Org 104:179-195). In this study, we examined the possible contribution of variations in susceptibility of fish populations, age-related resistance, and virus virulence to the observed landscape heterogeneity. We found that the most significant variable was host susceptibility: by controlled experimental challenge studies steelhead trout populations with no history of IHNV infection were 1 to 3 orders of magnitude more sensitive than a fish population with a long history of IHNV infection. In addition, 2 fish populations from the same river, which descended relatively recently from a common ancestral population, demonstrated 1 to 2 orders of magnitude difference in susceptibility. Fish age-related development of resistance was most evident in the more susceptible of 2 related fish populations. Finally, the strain of virus involved in the 2007 coastal Washington emergence had high virulence but was within the range of other known M group viruses tested. These results suggest that one major driver of landscape heterogeneity in the 2007 coastal Washington IHNV emergence was variation in fish population susceptibility and that this trait may have a heritable component.

Ozone-Induced Vascular Contractility and Pulmonary Injury Are Differentially Impacted by Diets Enriched With Coconut Oil, Fish Oil, and Olive Oil.

PubMed

Snow, Samantha J; Cheng, Wan-Yun; Henriquez, Andres; Hodge, Myles; Bass, Virgina; Nelson, Gail M; Carswell, Gleta; Richards, Judy E; Schladweiler, Mette C; Ledbetter, Allen D; Chorley, Brian; Gowdy, Kymberly M; Tong, Haiyan; Kodavanti, Urmila P

2018-05-01

Fish, olive, and coconut oil dietary supplementation have several cardioprotective benefits, but it is not established if they protect against air pollution-induced adverse effects. We hypothesized that these dietary supplements would attenuate ozone-induced systemic and pulmonary effects. Male Wistar Kyoto rats were fed either a normal diet, or a diet supplemented with fish, olive, or coconut oil for 8 weeks. Animals were then exposed to air or ozone (0.8 ppm), 4 h/day for 2 days. Ozone exposure increased phenylephrine-induced aortic vasocontraction, which was completely abolished in rats fed the fish oil diet. Despite this cardioprotective effect, the fish oil diet increased baseline levels of bronchoalveolar lavage fluid (BALF) markers of lung injury and inflammation. Ozone-induced pulmonary injury/inflammation were comparable in rats on normal, coconut oil, and olive oil diets with altered expression of markers in animals fed the fish oil diet. Fish oil, regardless of exposure, led to enlarged, foamy macrophages in the BALF that coincided with decreased pulmonary mRNA expression of cholesterol transporters, cholesterol receptors, and nuclear receptors. Serum microRNA profile was assessed and demonstrated marked depletion of a variety of microRNAs in animals fed the fish oil diet, several of which were of splenic origin. No ozone-specific changes were noted. Collectively, these data indicate that although fish oil offered vascular protection from ozone exposure, it increased pulmonary injury/inflammation and impaired lipid transport mechanisms resulting in foamy macrophage accumulation, demonstrating the need to be cognizant of potential off-target pulmonary effects that might offset the overall benefit of this vasoprotective supplement.

Dacomitinib (PF-00299804), a second-generation irreversible pan-erbB receptor tyrosine kinase inhibitor, demonstrates remarkable activity against HER2-amplified uterine serous endometrial cancer in vitro.

PubMed

Zhu, Liancheng; Lopez, Salvatore; Bellone, Stefania; Black, Jonathan; Cocco, Emiliano; Zigras, Tiffany; Predolini, Federica; Bonazzoli, Elena; Bussi, Beatrice; Stuhmer, Zachary; Schwab, Carlton L; English, Diana P; Ratner, Elena; Silasi, Dan-Arin; Azodi, Masoud; Schwartz, Peter E; Rutherford, Thomas J; Santin, Alessandro D

2015-07-01

Uterine serous carcinoma (USC) is an aggressive subtype of endometrial cancer that carries an extremely poor prognosis. Up to 35 % of USC may overexpress the epidermal growth factor receptor-2 (HER2/neu) at strong (i.e., 3+) level by immunohistochemistry (IHC) or harbor HER2/neu gene amplification by fluorescence in situ hybridization (FISH). In this study, we assessed the sensitivity of a panel of USC cell lines with and without HER2/neu gene amplification to dacomitinib (PF-00299804), an irreversible pan-human epidermal growth factor receptor tyrosine kinase inhibitor. Eight primary cell lines (i.e., four harboring HER2/neu gene amplification by FISH and four FISH- cell lines), all demonstrating similar in vitro growth rates, were evaluated in viability/proliferation assays. The effect of dacomitinib on cell growth, cell cycle distribution, and signaling was determined using flow cytometry-based assays. Dacomitinib caused a significantly stronger growth inhibition in HER2/neu FISH+ USC cell lines when compared to FISH- USC (dacomitinib half maximal inhibitory concentration (IC50) mean ± SEM = 0.02803 ± 0.003355 μM in FISH+ versus 1.498 ± 0.2209 μM in FISH- tumors, P < 0.0001). Dacomitinib growth inhibition was associated with a significant and dose-dependent decline in phosphorylated HER2/neu and S6 transcription factor and a dose-dependent and time-dependent cell cycle arrest in G0/G1 in FISH+ USC. Dacomitinib is remarkably effective against chemotherapy-resistant HER2/neu gene-amplified USC. Clinical studies with dacomitinib in HER2/neu FISH+ USC patients resistant to standard salvage chemotherapy are warranted.

Fish intake and risk of heart failure: A meta-analysis of five prospective cohort studies

PubMed Central

HOU, LI-NA; LI, FEI; ZHOU, YOU; NIE, SHI-HUAI; SU, LIANG; CHEN, PING-AN; TAN, WAN-LONG; XU, DING-LI

2012-01-01

The findings on the association between fish intake and the risk of heart failure (HF) have been inconsistent. The purpose of this study was to clarify this potential association. We searched for relevant studies in the PubMed database through January 2012 and manually reviewed references. Five independent prospective cohort studies involving 5,273 cases and 144,917 participants were included. The summary relative risk estimates (SRRE) based on the highest compared with the lowest category of fish consumption were estimated by variance-based meta-analysis. In addition, we performed sensitivity and dose-response analyses to examine the association. Overall, an absence of an association between fish intake and HF was observed (SRRE=1.00; 95% CI, 0.81–1.24). However, fried fish intake positively associated with HF (SRRE=1.40; 95% CI, 1.22–1.61). In addition, dose-response analysis of fried fish suggested that each increment of six fried fish per month corresponded to a 37% increase of HF rate (RR=1.37; 95% CI, 1.20–1.56). In conclusion, our findings suggest that there is no significant association between fish intake and risk of HF, with the exception of a possible positive correlation with individuals comsuming fried fish, based on a limited number of studies. Future studies are required to confirm these findings. PMID:23181122

Identification and Characterization of Genomic Amplifications in Ovarian Serous Carcinoma

DTIC Science & Technology

2009-07-01

oncogenes, Rsf1 and Notch3, which were up-regulated in both genomic DNA and transcript levels in ovarian cancer. In a large- scale FISH analysis, Rsf1...associated with worse disease outcome, suggesting that Rsf1 could be potentially used as a prognostic marker in the future (Appendix #1). For the...over- expressed in a recurrent carcinoma. Although the follow-up study in a larger- scale sample size did not demonstrate clear amplification in NAC1

Synchronization and collective swimming patterns in fish (Hemigrammus bleheri).

PubMed

Ashraf, I; Godoy-Diana, R; Halloy, J; Collignon, B; Thiria, B

2016-10-01

In this work, we address the case of red nose tetra fish Hemigrammus bleheri swimming in groups in a uniform flow, giving special attention to the basic interactions and cooperative swimming of a single pair of fish. We first bring evidence of synchronization of the two fish, where the swimming modes are dominated by 'out-phase' and 'in-phase' configurations. We show that the transition to this synchronization state is correlated with the swimming speed (i.e. the flow rate), and thus with the magnitude of the hydrodynamic pressure generated by the fish body during each swimming cycle. From a careful spatio-temporal analysis corresponding to those synchronized modes, we characterize the distances between the two individuals in a pair in the basic schooling pattern. We test the conclusions of the analysis of fish pairs with a second set of experiments using groups of three fish. By identifying the typical spatial configurations, we explain how the nearest neighbour interactions constitute the building blocks of collective fish swimming. © 2016 The Author(s).

Synchronization and collective swimming patterns in fish (Hemigrammus bleheri)

PubMed Central

Ashraf, I.; Collignon, B.

2016-01-01

In this work, we address the case of red nose tetra fish Hemigrammus bleheri swimming in groups in a uniform flow, giving special attention to the basic interactions and cooperative swimming of a single pair of fish. We first bring evidence of synchronization of the two fish, where the swimming modes are dominated by ‘out-phase’ and ‘in-phase’ configurations. We show that the transition to this synchronization state is correlated with the swimming speed (i.e. the flow rate), and thus with the magnitude of the hydrodynamic pressure generated by the fish body during each swimming cycle. From a careful spatio-temporal analysis corresponding to those synchronized modes, we characterize the distances between the two individuals in a pair in the basic schooling pattern. We test the conclusions of the analysis of fish pairs with a second set of experiments using groups of three fish. By identifying the typical spatial configurations, we explain how the nearest neighbour interactions constitute the building blocks of collective fish swimming. PMID:27798281

Assessing contamination of smoked sprats (Sprattus sprattus) with polycyclic aromatic hydrocarbons (PAHs) and changes in its level during storage in various types of packaging.

PubMed

Kuźmicz, Kamila; Ciemniak, Artur

2018-01-02

The analysis of material used in this study demonstrated that the amount of polycyclic aromatic hydrocarbons (PAHs) in smoked sprats varies from the level below the lowest detection limit in muscles up to 9.99 µg kg -1 of benzo[a]pyrene (BaP) in fish skin. Such a high level of PAHs in skin was reported only in one of six batches of sprats, while mean BaP level was at 1.69 µg kg -1 . Regardless such a high BaP level in skin, its concentration in muscles did not exceed the maximum acceptable level. The study objective was to assess to what extent packaging materials adsorb PAH compounds from food. Changes in the PAH levels were monitored in fish during their storage in packages made of various materials. The storage time was from 0 to 168 hours. The obtained results varied considerably, therefore their scatter did not allow to confirm unequivocally the preliminary hypothesis about the reduction of PAHs due to their migration to packaging material. However, analysis of the packaging used in this study demonstrated a significant increase in the level of total 16 PAHs. When high-density polyethylene (HDPE) packaging was analysed, a six-fold increase in the total 16 PAHs was observed comparing to the blank sample.

Medaka as a model for studying environmentally induced epigenetic transgenerational inheritance of phenotypes

PubMed Central

2016-01-01

Abstract Ability of environmental stressors to induce transgenerational diseases has been experimentally demonstrated in plants, worms, fish, and mammals, indicating that exposures affect not only human health but also fish and ecosystem health. Small aquarium fish have been reliable model to study genetic and epigenetic basis of development and disease. Additionally, fish can also provide better, economic opportunity to study transgenerational inheritance of adverse health and epigenetic mechanisms. Molecular mechanisms underlying germ cell development in fish are comparable to those in mammals and humans. This review will provide a short overview of long-term effects of environmental chemical contaminant exposure in various models, associated epigenetic mechanisms, and a perspective on fish as model to study environmentally induced transgenerational inheritance of altered phenotypes. PMID:29492282

Molecular Cloning, Functional Characterization, and Evolutionary Analysis of Vitamin D Receptors Isolated from Basal Vertebrates

PubMed Central

Kollitz, Erin M.; Zhang, Guozhu; Hawkins, Mary Beth; Whitfield, G. Kerr; Reif, David M.; Kullman, Seth W.

2015-01-01

The vertebrate genome is a result of two rapid and successive rounds of whole genome duplication, referred to as 1R and 2R. Furthermore, teleost fish have undergone a third whole genome duplication (3R) specific to their lineage, resulting in the retention of multiple gene paralogs. The more recent 3R event in teleosts provides a unique opportunity to gain insight into how genes evolve through specific evolutionary processes. In this study we compare molecular activities of vitamin D receptors (VDR) from basal species that diverged at key points in vertebrate evolution in order to infer derived and ancestral VDR functions of teleost paralogs. Species include the sea lamprey (Petromyzon marinus), a 1R jawless fish; the little skate (Leucoraja erinacea), a cartilaginous fish that diverged after the 2R event; and the Senegal bichir (Polypterus senegalus), a primitive 2R ray-finned fish. Saturation binding assays and gel mobility shift assays demonstrate high affinity ligand binding and classic DNA binding characteristics of VDR has been conserved across vertebrate evolution. Concentration response curves in transient transfection assays reveal EC50 values in the low nanomolar range, however maximum transactivational efficacy varies significantly between receptor orthologs. Protein-protein interactions were investigated using co-transfection, mammalian 2-hybrid assays, and mutations of coregulator activation domains. We then combined these results with our previous study of VDR paralogs from 3R teleosts into a bioinformatics analysis. Our results suggest that 1, 25D3 acts as a partial agonist in basal species. Furthermore, our bioinformatics analysis suggests that functional differences between VDR orthologs and paralogs are influenced by differential protein interactions with essential coregulator proteins. We speculate that we may be observing a change in the pharmacodynamics relationship between VDR and 1, 25D3 throughout vertebrate evolution that may have been driven by changes in protein-protein interactions between VDR and essential coregulators. PMID:25855982

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.

Application of truss analysis for the quantification of changes in fish condition

USGS Publications Warehouse

Fitzgerald, Dean G.; Nanson, Jeffrey W.; Todd, Thomas N.; Davis, Bruce M.

2002-01-01

Conservation of skeletal structure and unique body ratios in fishes facilitated the development of truss analysis as a taxonomic tool to separate physically-similar species. The methodology is predicated on the measurement of across-body distances from a sequential series of connected polygons. Changes in body shape or condition among members of the same species can be quantified with the same technique, and we conducted a feeding experiment using yellow perch (Perca flavescens) to examine the utility of this approach. Ration size was used as a surrogate for fish condition, with fish receiving either a high (3.0% body wt/d) or a low ration (0.5%). Sequentially over our 11-week experiment, replicate ration groups of fish were removed and photographed while control fish were repeatedly weighed and measured. Standard indices of condition (total lipids, weight-length ratios, Fulton's condition) were compared to truss measurements determined from digitized pictures of fish. Condition indices showed similarity between rations while truss measures from the caudal region were important for quantifying changing body shape. These findings identify truss analysis as having use beyond traditional applications. It can potentially be used as a cheap, accurate, and precise descriptor of fish condition in the lab as shown here, and we hypothesize that it would be applicable in field studies.

Numerical prediction of the energy efficiency of the three-dimensional fish school using the discretized Adomian decomposition method

NASA Astrophysics Data System (ADS)

Lin, Yinwei

2018-06-01

A three-dimensional modeling of fish school performed by a modified Adomian decomposition method (ADM) discretized by the finite difference method is proposed. To our knowledge, few studies of the fish school are documented due to expensive cost of numerical computing and tedious three-dimensional data analysis. Here, we propose a simple model replied on the Adomian decomposition method to estimate the efficiency of energy saving of the flow motion of the fish school. First, the analytic solutions of Navier-Stokes equations are used for numerical validation. The influences of the distance between the side-by-side two fishes are studied on the energy efficiency of the fish school. In addition, the complete error analysis for this method is presented.

Detection and genetic analysis of aquabirnaviruses in subclinically infected aquarium fish.

PubMed

Shin, Sang Phil; Gomez, Dennis Kaw; Kim, Ji Hyung; Choresca, Casiano Hermorpia; Han, Jee Eun; Jun, Jin Woo; Park, Se Chang

2011-03-01

Aquabirnaviruses (ABVs) cause serious diseases in a variety of fish species used worldwide in aquaculture and have been isolated from a variety of healthy fish and shellfish species. The type species of ABV is Infectious pancreatic necrosis virus (IPNV), which is the causative agent of a highly contagious disease in juvenile salmonid fish. Marine birnaviruses (MABVs) have been isolated from various marine fish and shellfish. In Korea, ABV infection has been identified in several fish and shellfish. The current study presents sequence data from nested polymerase chain reaction products of 3 ABV strains obtained from different species of asymptomatic aquarium fish collected from a private commercial aquarium in Korea. Phylogenetic analysis of these strains, based on the partial nucleotide sequence of the VP2/NS junction, placed them within the genogroup VII (95-99% bootstrap confidence), which also contains MABV. The subclinically infected fish may be a source of MABV infection for other susceptible fish species inside the aquarium and potentially represent a serious challenge for the management of MABV infections. Additionally, the presence of MABV in these subclinically infected aquarium fish imported from other countries indicates that there is a need for the establishment of appropriate quarantine practices.

Risks and benefits of fish consumption for childbearing women.

PubMed

Del Gobbo, Liana C; Archbold, Josephine A; Vanderlinden, Loren D; Eckley, Chris S; Diamond, Miriam L; Robson, Matthew

2010-01-01

Pregnant women's fish consumption provides both benefits and risks to the developing fetus. Docosahexaenoic acid (DHA) from fish may enhance fetal neurodevelopment, while methylmercury (MeHg) can have detrimental effects. Dietitians would benefit from information on the frequency with which fish species may be consumed to increase DHA intake among Canadian women of childbearing age, and on minimizing the risks from MeHg, especially for those who consume fish frequently. Eighteen fish species were selected for DHA and mercury analysis from retail markets in the Toronto area. Consumption scenarios using analytical results for these fish species indicate that women of childbearing age can consume nine of 18 fish species every day (14 servings a week) or often (up to four servings a week) and remain below toxicological benchmarks for mercury. Moreover, women can also attain the recommended DHA level by consuming six of those nine fish: four 75-g servings of smelt, porgie, or bluefish a week, or two 75-g servings of milkfish, silver pomfret, or tilapia a day. Our analysis indicates that the DHA level recommended for childbearing women can be attained through fish consumption alone, without the need for supplementation and without posing a risk to the woman (or the fetus) from mercury.

Analysis and Evaluation of Parameters Determining Maximum Efficiency of Fish Protection

NASA Astrophysics Data System (ADS)

Khetsuriani, E. D.; Kostyukov, V. P.; Khetsuriani, T. E.

2017-11-01

The article is concerned with experimental research findings. The efficiency of fish fry protection from entering water inlets is the main criterion of any fish protection facility or device. The research was aimed to determine an adequate mathematical model E = f(PCT, Vp, α), where PCT, Vp and α are controlled factors influencing the process of fish fry protection. The result of the processing of experimental data was an adequate regression model. We determined the maximum of fish protection Emax=94,21 and the minimum of optimization function Emin=44,41. As a result of the statistical processing of experimental data we obtained adequate dependences for determining an optimal rotational speed of tip and fish protection efficiency. The analysis of fish protection efficiency dependence E% = f(PCT, Vp, α) allowed the authors to recommend the following optimized operating modes for it: the maximum fish protection efficiency is achieved at the process pressure PCT=3 atm, stream velocity Vp=0,42 m/s and nozzle inclination angle α=47°49’. The stream velocity Vp has the most critical influence on fish protection efficiency. The maximum efficiency of fish protection is obtained at the tip rotational speed of 70.92 rpm.

Transmission routes maintaining a viral pathogen of steelhead trout within a complex multi-host assemblage

USGS Publications Warehouse

Breyta, Rachel; Brito, Ilana L.; Ferguson, Paige; Kurath, Gael; Naish, Kerry A.; Purcell, Maureen; Wargo, Andrew R.; LaDeau, Shannon L.

2017-01-01

This is the first comprehensive region wide, spatially explicit epidemiologic analysis of surveillance data of the aquatic viral pathogen infectious hematopoietic necrosis virus (IHNV) infecting native salmonid fish. The pathogen has been documented in the freshwater ecosystem of the Pacific Northwest of North America since the 1950s, and the current report describes the disease ecology of IHNV during 2000–2012. Prevalence of IHNV infection in monitored salmonid host cohorts ranged from 8% to 30%, with the highest levels observed in juvenile steelhead trout. The spatial distribution of all IHNV-infected cohorts was concentrated in two sub-regions of the study area, where historic burden of the viral disease has been high. During the study period, prevalence levels fluctuated with a temporal peak in 2002. Virologic and genetic surveillance data were analyzed for evidence of three separate but not mutually exclusive transmission routes hypothesized to be maintaining IHNV in the freshwater ecosystem. Transmission between year classes of juvenile fish at individual sites (route 1) was supported at varying levels of certainty in 10%–55% of candidate cases, transmission between neighboring juvenile cohorts (route 2) was supported in 31%–78% of candidate cases, and transmission from adult fish returning to the same site as an infected juvenile cohort was supported in 26%–74% of candidate cases. The results of this study indicate that multiple specific transmission routes are acting to maintain IHNV in juvenile fish, providing concrete evidence that can be used to improve resource management. Furthermore, these results demonstrate that more sophisticated analysis of available spatio-temporal and genetic data is likely to yield greater insight in future studies.

CompCytogen of two of the smallest Amazonian fishes: Fluviphylax simplex Costa, 1996 and Fluviphylax zonatus Costa, 1996 (Cyprinodontiformes, Poeciliidae).

PubMed

Souza, E R; Ribeiro, L B; Feldberg, E; Hrbek, I P Farias T; Gross, M C

2011-01-01

The genus Fluviphylax Whitley, 1965is comprized of five valid species (Fluviphylax pygmaeus Myers et Carvalho, 1955, Fluviphylax zonatus, Fluviphylax simplex, Fluviphylax obscurus Costa, 1996,and Fluviphylax palikur Costa et Le Bail, 1999), which are endemic to the Amazon region. These fishes are the smallest known South American vertebrates and among the smallest know vertebrates on Earth. All species but the type Fluviphylax pygmaeus have been described in late 1990's, and much remains unknown about the biology, taxonomy and systematics of this group of fishes. The aims of the present study were to establish the diploid and haploid number of Fluviphylax zonatus and Fluviphylax simplex, and to find species-specific markers for the discrimination of taxa. The diploid number for both species was 48 chromosomes, with no sex chromosome heteromorphism. Fluviphylax zonatus exhibited the karyotypic formula 4m+8sm+22st+14a and FN=82, and Fluviphylax simplex exhibited 4m+16sm+18st+10a and FN=86. The determination of the total mean length of the chromosomes and their grouping into five size classes demonstrated different chromosome composition of the two species. This difference was further supported by the distribution of constitutive heterochromatin. The meiotic analysis revealed 24 bivalents in both species, but Fluviphylax zonatus exhibited chromosomes with late pairing of the telomeric portions in the pachytene. These data reveal that cytogenetic characterization is useful and important for the discrimination of these species. Our study further indicates that this method could be employed in the analysis of other species of small fishes that are difficult to distinguish using traditional morphological traits or are morphologically cryptic.

mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis).

PubMed

Aedo, Jorge E; Maldonado, Jonathan; Aballai, Víctor; Estrada, Juan M; Bastias-Molina, Macarena; Meneses, Claudio; Gallardo-Escarate, Cristian; Silva, Herman; Molina, Alfredo; Valdés, Juan A

2015-12-01

Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cortisol, each species presents specificities in the cell response and stress tolerance. Therefore, culturing new species requires a detailed knowledge of these specific responses. The red cusk-eel (Genypterus chilensis) is a new economically important marine species for the Chilean aquaculture industry. However, there is no information on the stress- and cortisol-induced mechanisms that decrease skeletal muscle growth in this teleost. Using Illumina RNA-seq technology, skeletal muscle sequence reads for G. chilensis were generated under control and handling stress conditions. Reads were mapped onto a reference transcriptome, resulting in the in silico identification of 785 up-regulated and 167 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of catabolic genes associated with skeletal muscle atrophy. These results were validated by RT-qPCR analysis for ten candidates genes involved in ubiquitin-mediated proteolysis, autophagy and skeletal muscle growth. Additionally, using a primary culture of fish skeletal muscle cells, the effect of cortisol was evaluated in relation to red cusk-eel skeletal muscle atrophy. The present data demonstrated that handling stress promotes skeletal muscle atrophy in the marine teleost G. chilensis through the expression of components of the ubiquitin-proteasome and autophagy-lysosome systems. Furthermore, cortisol was a powerful inductor of skeletal muscle atrophy in fish myotubes. This study is an important step towards understanding the atrophy system in non-model teleost species and provides novel insights on the cellular and molecular mechanisms that control skeletal muscle growth in early vertebrates.

Induction of cytochromes P450 1A1 and 1B1 in human lung adenocarcinoma CL5 cells by frying-meat emission particulate.

PubMed

Wang, H-W; Chen, T-L; Yang, P-C; Ma, Y-C; Yu, C-C; Ueng, T-H

2002-05-01

The effect of airborne frying-meat emission particulate (FMEP) on cytochrome P450 (P450)-dependent monooxygenase was determined using human lung adenocarcinoma cell line CL5 treated with organic extract of FMEP prepared from beef, fish or pork. Treatment with fish FMEP extract caused greater increases of intracellular peroxide production and glutathione content than did beef and pork FMEP extracts. Treatment with 200 microg/ml beef, fish or pork FMEP extract for 6 h increased benzo[a]pyrene hydroxylase, 7-ethoxyresorufin and methoxyresorufin O-dealkylases activities in S9. Immunoblot analysis of S9 proteins from control cells and cells treated with FMEP extracts revealed that the airborne particulates increased proteins immunorelated to CYP1A1 and CYP1B1. Northern blot analysis of total cellular RNA from controls and cells treated with FMEP extracts showed that the cooking by-products increased the levels of CYP1A1 and CYP1B1 mRNA. Treatment with 1 microM dibenzo[a,h]anthracene for 6 h increased monooxygenase activities, CYP1A1 and CYP1B1 protein and mRNA levels in CL5 cells. Beef FMEP extract and dibenzo[a,h]anthracene also induced CYP1A1 and CYP1B1 in human lung carcinoma NCI-H322 cells. The present finding demonstrates that airborne particulates generated during the frying of beef, fish and pork can induce carcinogen-metabolizing CYP1A1 and CYP1B1 in the human lung-derived cell line CL5.

Differentiation between microcystin contaminated and uncontaminated fish by determination of unconjugated MCs using an ELISA anti-Adda test based on receiver-operating characteristic curves threshold values: application to Tinca tinca from natural ponds.

PubMed

Moreno, Isabel María; Herrador, M Ángeles; Atencio, Loyda; Puerto, María; González, A Gustavo; Cameán, Ana María

2011-02-01

The aim of this study was to evaluate whether the enzyme-linked immunosorbent assay (ELISA) anti-Adda technique could be used to monitor free microcystins (MCs) in biological samples from fish naturally exposed to toxic cyanobacteria by using receiver operating characteristic (ROC) curve software to establish an optimal cut-off value for MCs. The cut-off value determined by ROC curve analysis in tench (Tinca tinca) exposed to MCs under laboratory conditions by ROC curve analysis was 5.90-μg MCs/kg tissue dry weight (d.w.) with a sensitivity of 93.3%. This value was applied in fish samples from natural ponds (Extremadura, Spain) in order to asses its potential MCs bioaccumulation by classifying samples as either true positive (TP), false positive (FP), true negative (TN), or false negative (FN). In this work, it has been demonstrated that toxic cyanobacteria, mainly Microcystis aeruginosa, Aphanizomenon issatchenkoi, and Anabaena spiroides, were present in two of these ponds, Barruecos de Abajo (BDown) and Barruecos de Arriba (BUp). The MCs levels were detected in waters from both ponds with an anti-MC-LR ELISA immunoassay and were of similar values (between 3.8-6.5-μg MC-LR equivalent/L in BDown pond and 4.8-6.0-μg MC-LR equivalent/L in BUp). The MCs cut-off values were applied in livers from fish collected from these two ponds using the ELISA anti-Adda technique. A total of 83% of samples from BDown pond and only 42% from BUp were TP with values of free MCs higher than 8.8-μg MCs/kg tissue (d.w.). Copyright © 2009 Wiley Periodicals, Inc.

Deletion patterns of the STS gene and flanking sequences in Israeli X-linked ichthyosis patients and carriers: analysis by polymerase chain reaction and fluorescence in situ hybridization techniques.

PubMed

Aviram-Goldring, A; Goldman, B; Netanelov-Shapira, I; Chen-Shtoyerman, R; Zvulunov, A; Tal, O; Ilan, T; Peleg, L

2000-03-01

Deletion of the entire steroid sulfatase (STS) gene is the most common molecular defect in X-linked ichthyosis (XLI) patients. Usually, additional flanking sequences are also missing. The aim of this study was to estimate the extent of deletions in an ethnically heterogeneous population of Israeli XLI patients. Multiplex polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) techniques were applied in the analysis of blood samples of 24 patients and amniotic cells of seven affected fetuses from 22 unrelated families. In 19 families, a large deletion of the 2-3 megabase was found. It included the whole STS gene and spanned adjacent areas up- and downstream between the loci DXS 1139 and DXS 1132. Two unrelated families of Iraqi ancestry had a partial deletion of the gene and its centromeric adjacent sequence. In another family, the telomeric end of the extragenic segment was only partially missing. Application of FISH on metaphase blood cells and interphase amniotic cells confirmed the diagnosis of XLI in all patients, except the three with partial intragenic deletion. In those cases, the remaining fraction of the gene was sufficient to provide a false negative result. Diagnosis of carriers and prenatal diagnosis in uncultured cells was applicable only by FISH. Our study revealed a remarkable heterogeneity in the deletion pattern among Israeli patients with XLI. This heterogeneity could not be attributed to specific ethnic groups because of the small size of the study group. More studies involving patients of various ancestries should be carried out. In addition, this study demonstrated the usefulness of the FISH technique in the prenatal diagnosis of fetuses with suspected XLI.

Transcriptome Profiling of the Abdominal Skin of Larimichthys crocea in Light Stress

NASA Astrophysics Data System (ADS)

Han, Zhaofang; Lv, Changhuan; Xiao, Shijun; Ye, Kun; Zhang, Dongling; Tsai, Huai Jen; Wang, Zhiyong

2018-04-01

Large yellow croaker ( Larimichthys crocea), one of the most important marine fish species in China, can change its abdominal skin color when it is shifted from light to dark or from dark to light, providing us an opportunity of investigating the molecular responding mechanism of teleost in light stress. The gene expression profile of fish under light stress is rarely documented. In this research, the transcriptome profiles of the abdominal skin of L. crocea exposed to light or dark for 0 h, 0.5 h and 2 h were produced by next-generation sequencing (NGS). The cluster results demonstrated that stress period, rather than light intensity ( e.g., light or dark), is the major influencing factor. Differently expressed genes (DEGs) were identified between 0 h and 0.5 h groups, between 0 h and 2 h groups, between 0.5 h light and 0.5 h dark, and between 2 h light and 2 h dark, respectively. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation revealed that the genes relating to immunity, energy metabolism, and cytoskeletal protein binding were significantly enriched. The detailed analysis of transcriptome profiles also revealed regular gene expression trends, indicating that the elaborate gene regulation networks underlined the molecular responses of the fish to light stress. This transcriptome analysis suggested that systematic and complicated regulatory cascades were functionally activated in response to external stress, and coloration change caused by light stress was mainly attributed to the change in the density of chromatophores for L. crocea. This study also provided valuable information for skin coloration or light stress research on other marine fish species.

Transcriptomic analysis of spleen infected with infectious salmon anemia virus reveals distinct pattern of viral replication on resistant and susceptible Atlantic salmon (Salmo salar).

PubMed

Dettleff, Phillip; Moen, Thomas; Santi, Nina; Martinez, Victor

2017-02-01

The infectious salmon anemia virus (ISAv) produces a systemic infection in salmonids, causing large losses in salmon production. However, little is known regarding the mechanisms exerting disease resistance. In this paper, we perform an RNA-seq analysis in Atlantic salmon challenged with ISAv (using individuals coming from families that were highly susceptible or highly resistant to ISAv infection). We evaluated the differential expression of both host and ISAv genes in a target organ for the virus, i.e. the spleen. The results showed differential expression of host genes related to response to stress, immune response and protein folding (genes such as; atf3, mhc, mx1-3, cd276, cd2, cocs1, c7, il10, il10rb, il13ra2, ubl-1, ifng, ifngr1, hivep2, sigle14 and sigle5). An increased protein processing activity was found in susceptible fish, which generates a subsequent unfolded protein response. We observed extreme differences in the expression of viral segments between susceptible and resistant groups, demonstrating the capacity of resistant fish to overcome the virus replication, generating a very low viral load. This phenomenon and survival of this higher resistant fish seem to be related to differences in immune and translational process, as well as to the increase of HIV-EP2 (hivep2) transcript in resistant fish, although the causal mechanism is yet to be discovered. This study provides valuable information about disease resistance mechanisms in Atlantic salmon from a host-pathogen interaction point of view. Copyright © 2017 Elsevier Ltd. All rights reserved.

A survey of fish viruses isolated from wild marine fishes from the coastal waters of southern Korea.

PubMed

Kim, Wi-Sik; Choi, Shin-Young; Kim, Do-Hyung; Oh, Myung-Joo

2013-11-01

A survey was conducted to investigate viral infection in 253 wild marine fishes harvested in the southern coastal area of Korea from 2010 to 2012. The fish that were captured by local anglers were randomly bought and sampled for virus examination. The samples were tested for presence of virus by virus isolation with FHM, FSP, and BF-2 cells and molecular methods (polymerase chain reaction and sequencing). Of the 253 fish sampled, 9 fish were infected with virus. Aquabirnaviruses (ABVs), Viral hemorrhagic septicemia virus (VHSV), and Red seabream iridovirus (RSIV) were detected in 7, 1, and 1 fish, respectively. Molecular phylogenies demonstrated the detected viruses (ABV, VHSV, and RSIV) were more closely related to viruses reported of the same type from Korea and Japan than from other countries, suggesting these viruses may be indigenous to Korean and Japanese coastal waters.

[Helminthic fauna of commercial fishes from the Saya-de-Malya bank (Indian Ocean)].

PubMed

Parukhin, A M

1988-01-01

The data on infestation of 8 species of commercial fishes from Saya-de-Malya bank (the Indian Ocean) are presented. 43 helminth species were identified: 10 Monogenea species, 18 trematode, 7 cestode and 8 nematode species. The mature worms are observed to be related to a certain host, whereas the nematode and cestode larvae have wide specificity. High infestation degree by Anisakis larvae is found in fishes, especially in Carangidae. At the bank area fishes are found to be free from Acanthocephala while those Acanthocephala are found in fishes from other areas of the Indian Ocean which may be attributed to the specific diet at the Saya-de-Malya bank. On the whole the helminth fauna of fishes examined at the Saya-de-Malya bank does not demonstrate the endemic pattern. The most specific helminth species were found in some fish species.

Quantitative proteomics in teleost fish: insights and challenges for neuroendocrine and neurotoxicology research.

PubMed

Martyniuk, Christopher J; Popesku, Jason T; Chown, Brittany; Denslow, Nancy D; Trudeau, Vance L

2012-05-01

Neuroendocrine systems integrate both extrinsic and intrinsic signals to regulate virtually all aspects of an animal's physiology. In aquatic toxicology, studies have shown that pollutants are capable of disrupting the neuroendocrine system of teleost fish, and many chemicals found in the environment can also have a neurotoxic mode of action. Omics approaches are now used to better understand cell signaling cascades underlying fish neurophysiology and the control of pituitary hormone release, in addition to identifying adverse effects of pollutants in the teleostean central nervous system. For example, both high throughput genomics and proteomic investigations of molecular signaling cascades for both neurotransmitter and nuclear receptor agonists/antagonists have been reported. This review highlights recent studies that have utilized quantitative proteomics methods such as 2D differential in-gel electrophoresis (DIGE) and isobaric tagging for relative and absolute quantitation (iTRAQ) in neuroendocrine regions and uses these examples to demonstrate the challenges of using proteomics in neuroendocrinology and neurotoxicology research. To begin to characterize the teleost neuroproteome, we functionally annotated 623 unique proteins found in the fish hypothalamus and telencephalon. These proteins have roles in biological processes that include synaptic transmission, ATP production, receptor activity, cell structure and integrity, and stress responses. The biological processes most represented by proteins detected in the teleost neuroendocrine brain included transport (8.4%), metabolic process (5.5%), and glycolysis (4.8%). We provide an example of using sub-network enrichment analysis (SNEA) to identify protein networks in the fish hypothalamus in response to dopamine receptor signaling. Dopamine signaling altered the abundance of proteins that are binding partners of microfilaments, integrins, and intermediate filaments, consistent with data suggesting dopaminergic regulation of neuronal stability and structure. Lastly, for fish neuroendocrine studies using both high-throughput genomics and proteomics, we compare gene and protein relationships in the hypothalamus and demonstrate that correlation is often poor for single time point experiments. These studies highlight the need for additional time course analyses to better understand gene-protein relationships and adverse outcome pathways. This is important if both transcriptomics and proteomics are to be used together to investigate neuroendocrine signaling pathways or as bio-monitoring tools in ecotoxicology. Copyright © 2011 Elsevier Inc. All rights reserved.

Behavioral and Single-Neuron Sensitivity to Millisecond Variations in Temporally Patterned Communication Signals

PubMed Central

Baker, Christa A.; Ma, Lisa; Casareale, Chelsea R.

2016-01-01

In many sensory pathways, central neurons serve as temporal filters for timing patterns in communication signals. However, how a population of neurons with diverse temporal filtering properties codes for natural variation in communication signals is unknown. Here we addressed this question in the weakly electric fish Brienomyrus brachyistius, which varies the time intervals between successive electric organ discharges to communicate. These fish produce an individually stereotyped signal called a scallop, which consists of a distinctive temporal pattern of ∼8–12 electric pulses. We manipulated the temporal structure of natural scallops during behavioral playback and in vivo electrophysiology experiments to probe the temporal sensitivity of scallop encoding and recognition. We found that presenting time-reversed, randomized, or jittered scallops increased behavioral response thresholds, demonstrating that fish's electric signaling behavior was sensitive to the precise temporal structure of scallops. Next, using in vivo intracellular recordings and discriminant function analysis, we found that the responses of interval-selective midbrain neurons were also sensitive to the precise temporal structure of scallops. Subthreshold changes in membrane potential recorded from single neurons discriminated natural scallops from time-reversed, randomized, and jittered sequences. Pooling the responses of multiple neurons improved the discriminability of natural sequences from temporally manipulated sequences. Finally, we found that single-neuron responses were sensitive to interindividual variation in scallop sequences, raising the question of whether fish may analyze scallop structure to gain information about the sender. Collectively, these results demonstrate that a population of interval-selective neurons can encode behaviorally relevant temporal patterns with millisecond precision. SIGNIFICANCE STATEMENT The timing patterns of action potentials, or spikes, play important roles in representing information in the nervous system. However, how these temporal patterns are recognized by downstream neurons is not well understood. Here we use the electrosensory system of mormyrid weakly electric fish to investigate how a population of neurons with diverse temporal filtering properties encodes behaviorally relevant input timing patterns, and how this relates to behavioral sensitivity. We show that fish are behaviorally sensitive to millisecond variations in natural, temporally patterned communication signals, and that the responses of individual midbrain neurons are also sensitive to variation in these patterns. In fact, the output of single neurons contains enough information to discriminate stereotyped communication signals produced by different individuals. PMID:27559179

Behavioral and Single-Neuron Sensitivity to Millisecond Variations in Temporally Patterned Communication Signals.

PubMed

Baker, Christa A; Ma, Lisa; Casareale, Chelsea R; Carlson, Bruce A

2016-08-24

In many sensory pathways, central neurons serve as temporal filters for timing patterns in communication signals. However, how a population of neurons with diverse temporal filtering properties codes for natural variation in communication signals is unknown. Here we addressed this question in the weakly electric fish Brienomyrus brachyistius, which varies the time intervals between successive electric organ discharges to communicate. These fish produce an individually stereotyped signal called a scallop, which consists of a distinctive temporal pattern of ∼8-12 electric pulses. We manipulated the temporal structure of natural scallops during behavioral playback and in vivo electrophysiology experiments to probe the temporal sensitivity of scallop encoding and recognition. We found that presenting time-reversed, randomized, or jittered scallops increased behavioral response thresholds, demonstrating that fish's electric signaling behavior was sensitive to the precise temporal structure of scallops. Next, using in vivo intracellular recordings and discriminant function analysis, we found that the responses of interval-selective midbrain neurons were also sensitive to the precise temporal structure of scallops. Subthreshold changes in membrane potential recorded from single neurons discriminated natural scallops from time-reversed, randomized, and jittered sequences. Pooling the responses of multiple neurons improved the discriminability of natural sequences from temporally manipulated sequences. Finally, we found that single-neuron responses were sensitive to interindividual variation in scallop sequences, raising the question of whether fish may analyze scallop structure to gain information about the sender. Collectively, these results demonstrate that a population of interval-selective neurons can encode behaviorally relevant temporal patterns with millisecond precision. The timing patterns of action potentials, or spikes, play important roles in representing information in the nervous system. However, how these temporal patterns are recognized by downstream neurons is not well understood. Here we use the electrosensory system of mormyrid weakly electric fish to investigate how a population of neurons with diverse temporal filtering properties encodes behaviorally relevant input timing patterns, and how this relates to behavioral sensitivity. We show that fish are behaviorally sensitive to millisecond variations in natural, temporally patterned communication signals, and that the responses of individual midbrain neurons are also sensitive to variation in these patterns. In fact, the output of single neurons contains enough information to discriminate stereotyped communication signals produced by different individuals. Copyright © 2016 the authors 0270-6474/16/368985-16$15.00/0.

San Francisco Estuary Striped Bass Migration History Determined by Electron-microprobe Analysis of Otolith Sr/Ca Ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ostrach, D J; Phillis, C C; Weber, P K

2004-09-17

Habitat use has been shown to be an important factor in the bioaccumulation of contaminants in striped bass. This study examines migration in striped bass as part of a larger study investigating bioaccumulation and maternal transfer of xenobiotics to progeny in the San Francisco Estuary system. Habitat use, residence time and spawning migration over the life of females (n = 23) was studied. Female striped bass were collected between Knights Landing and Colusa on the Sacramento River during the spawning runs of 1999 and 2001. Otoliths were removed, processed and aged via otolith microstructure. Subsequently, otoliths were analyzed for strontium/calciummore » (Sr/Ca) ratio using an electron-microprobe to measure salinity exposure and to distinguish freshwater, estuary, and marine habitat use. Salinity exposure during the last year before capture was examined more closely for comparison of habitat use by the maternal parent to contaminant burden transferred to progeny. Results were selectively confirmed by ion microprobe analyses for habitat use. The Sr/Ca data demonstrate a wide range of migratory patterns. Age of initial ocean entry differs among individuals before returning to freshwater, presumably to spawn. Some fish reside in freshwater year-round, while others return to more saline habitats and make periodic migrations to freshwater. Frequency of habitat shifts and residence times differs among fish, as well as over the lifetime of individual fish. While at least one fish spent its final year in freshwater, the majority of spawning fish spent their final year in elevated salinity. However, not all fish migrated to freshwater to spawn in the previous year. Results from this investigation concerning migration history in striped bass can be combined with contaminant and histological developmental analyses to better understand the bioaccumulation of contaminants and the subsequent effects they and habitat use have on fish populations in the San Francisco Estuary system.« less

Effectiveness of Quantitative Real Time PCR in Long-Term Follow-up of Chronic Myeloid Leukemia Patients.

PubMed

Savasoglu, Kaan; Payzin, Kadriye Bahriye; Ozdemirkiran, Fusun; Berber, Belgin

2015-08-01

To determine the use of the Quantitative Real Time PCR (RQ-PCR) assay follow-up with Chronic Myeloid Leukemia (CML) patients. Cross-sectional observational. Izmir Ataturk Education and Research Hospital, Izmir, Turkey, from 2009 to 2013. Cytogenetic, FISH, RQ-PCR test results from 177 CMLpatients' materials selected between 2009 - 2013 years was set up for comparison analysis. Statistical analysis was performed to compare between FISH, karyotype and RQ-PCR results of the patients. Karyotyping and FISH specificity and sensitivity rates determined by ROC analysis compared with RQ-PCR results. Chi-square test was used to compare test failure rates. Sensitivity and specificity values were determined for karyotyping 17.6 - 98% (p=0.118, p > 0.05) and for FISH 22.5 - 96% (p=0.064, p > 0.05) respectively. FISH sensitivity was slightly higher than karyotyping but there was calculated a strong correlation between them (p < 0.001). RQ-PCR test failure rate did not correlate with other two tests (p > 0.05); however, karyotyping and FISH test failure rate was statistically significant (p < 0.001). Besides, the situation needed for karyotype analysis, RQ-PCR assay can be used alone in the follow-up of CMLdisease.

Inhibition of return in the archer fish.

PubMed

Gabay, Shai; Leibovich, Tali; Ben-Simon, Avi; Henik, Avishai; Segev, Ronen

2013-01-01

Inhibition of return is the inhibitory tagging of recently attended locations or objects. It was previously suggested that inhibition of return is a foraging facilitator in visual search. Inhibition of return was first discovered in humans and was demonstrated also in monkeys, yet it has never been demonstrated in non-primates. Here we report the presence of inhibition of return in the archer fish, which shoots down prey on overhanging vegetation, using squirts of water spouted from its mouth. Moreover, we find similar attentional effects for fish as for human participants. Our results show that the generation of inhibition of return does not require a fully developed cortex and strengthen the view that inhibition of return functions as a foraging facilitator.

Measuring drug absorption improves interpretation of behavioral responses in a larval zebrafish locomotor assay for predicting seizure liability.

PubMed

Cassar, Steven; Breidenbach, Laura; Olson, Amanda; Huang, Xin; Britton, Heather; Woody, Clarissa; Sancheti, Pankajkumar; Stolarik, DeAnne; Wicke, Karsten; Hempel, Katja; LeRoy, Bruce

2017-11-01

Unanticipated effects on the central nervous system are a concern during new drug development. A larval zebrafish locomotor assay can reveal seizure liability of experimental molecules before testing in mammals. Relative absorption of compounds by larvae is lacking in prior reports of such assays; having those data may be valuable for interpreting seizure liability assay performance. Twenty-eight reference drugs were tested at multiple dose levels in fish water and analyzed by a blinded investigator. Responses of larval zebrafish were quantified during a 30min dosing period. Predictive metrics were calculated by comparing fish activity to mammalian seizure liability for each drug. Drug level analysis was performed to calculate concentrations in dose solutions and larvae. Fifteen drug candidates with neuronal targets, some having preclinical convulsion findings in mammals, were tested similarly. The assay has good predictive value of established mammalian responses for reference drugs. Analysis of drug absorption by larval fish revealed a positive correlation between hyperactive behavior and pro-convulsive drug absorption. False negative results were associated with significantly lower compound absorption compared to true negative, or true positive results. The predictive value for preclinical toxicology findings was inferior to that suggested by reference drugs. Disproportionately low exposures in larvae giving false negative results demonstrate that drug exposure analysis can help interpret results. Due to the rigorous testing commonly performed in preclinical toxicology, predicting convulsions in those studies may be more difficult than predicting effects from marketed drugs. Copyright © 2017 Elsevier Inc. All rights reserved.

Toxicity assessment on haemotology, biochemical and histopathological alterations of silver nanoparticles-exposed freshwater fish Labeo rohita

NASA Astrophysics Data System (ADS)

Rajkumar, K. S.; Kanipandian, N.; Thirumurugan, R.

2016-01-01

The increasing use of nano based-products induces the potential hazards from their manufacture, transportation, waste disposal and management processes. In this report, we emphasized the acute toxicity of silver nanoparticles (AgNPs) using freshwater fish Labeo rohita as an aquatic animal model. The AgNPs were synthesized using chemical reduction method and the formation of AgNPs was monitored by UV-Visible spectroscopy analysis. The functional groups, crystaline nature and morphological characterizations were carried out by fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and high resolution transmission electron microscopy (HRTEM) analysis. UV-Vis range was observed at 420 nm and XRD pattern showed that the particles are crystalline nature. HRTEM analysis revealed that the morphology of particles was spherical and size ranges between 50 and 100 nm. This investigation was extended to determine the potential acute toxicity, L. rohita was treated orally with the lethal concentration (LC50) of AgNPs. The antioxidative responses were studied in the three major tissues such as gill, liver and muscle of L. rohita. The results of this investigation showed that increasing the concentration of AgNPs led to bioaccumulation of AgNPs in the major tissues. The haematological parameters showed significant alterations in the treated fish. The histological changes caused by chemically synthesized AgNPs demonstrated the damages in the tissues, primary lamella and blood vessels of L. rohita. The histological study also displayed the formation of vacuolation in liver and muscle when compared with untreated tissues (control) of L. rohita.

Utilization of fish bone as adsorbent of Fe3+ ion by controllable removal of its carbonaceous component

NASA Astrophysics Data System (ADS)

Nurhadi, M.; Kusumawardani, R.; Widiyowati, I. I.; Wirhanuddin; Nur, H.

2018-05-01

The performance of fish bone to adsorb Fe3+ ion in solution was studied. Powdered fish bone and carbonized fish bone were used as adsorbent. All absorbents were characterized by X-ray diffraction (XRD), IR spectroscopy, nitrogen adsorption, scanning electron microscopy (SEM) and TG analysis. Powdered fish bone and carbonized fish bone were effective as adsorbent for removing Fe3+ ion in solution. The metal adsorptions of Fe3+ ion were 94 and 98% for powdered fish bone and fish bone which carbonized at 400 and 500 °C.

Multiscale analysis of river networks using the R package linbin

USGS Publications Warehouse

Welty, Ethan Z.; Torgersen, Christian E.; Brenkman, Samuel J.; Duda, Jeffrey J.; Armstrong, Jonathan B.

2015-01-01

Analytical tools are needed in riverine science and management to bridge the gap between GIS and statistical packages that were not designed for the directional and dendritic structure of streams. We introduce linbin, an R package developed for the analysis of riverscapes at multiple scales. With this software, riverine data on aquatic habitat and species distribution can be scaled and plotted automatically with respect to their position in the stream network or—in the case of temporal data—their position in time. The linbin package aggregates data into bins of different sizes as specified by the user. We provide case studies illustrating the use of the software for (1) exploring patterns at different scales by aggregating variables at a range of bin sizes, (2) comparing repeat observations by aggregating surveys into bins of common coverage, and (3) tailoring analysis to data with custom bin designs. Furthermore, we demonstrate the utility of linbin for summarizing patterns throughout an entire stream network, and we analyze the diel and seasonal movements of tagged fish past a stationary receiver to illustrate how linbin can be used with temporal data. In short, linbin enables more rapid analysis of complex data sets by fisheries managers and stream ecologists and can reveal underlying spatial and temporal patterns of fish distribution and habitat throughout a riverscape.

Improved Quantum Artificial Fish Algorithm Application to Distributed Network Considering Distributed Generation.

PubMed

Du, Tingsong; Hu, Yang; Ke, Xianting

2015-01-01

An improved quantum artificial fish swarm algorithm (IQAFSA) for solving distributed network programming considering distributed generation is proposed in this work. The IQAFSA based on quantum computing which has exponential acceleration for heuristic algorithm uses quantum bits to code artificial fish and quantum revolving gate, preying behavior, and following behavior and variation of quantum artificial fish to update the artificial fish for searching for optimal value. Then, we apply the proposed new algorithm, the quantum artificial fish swarm algorithm (QAFSA), the basic artificial fish swarm algorithm (BAFSA), and the global edition artificial fish swarm algorithm (GAFSA) to the simulation experiments for some typical test functions, respectively. The simulation results demonstrate that the proposed algorithm can escape from the local extremum effectively and has higher convergence speed and better accuracy. Finally, applying IQAFSA to distributed network problems and the simulation results for 33-bus radial distribution network system show that IQAFSA can get the minimum power loss after comparing with BAFSA, GAFSA, and QAFSA.

Spatial extent and dynamics of dam impacts on tropical island freshwater fish assemblages

USGS Publications Warehouse

Cooney, Patrick B.; Kwak, Thomas J.

2013-01-01

Habitat connectivity is vital to the persistence of migratory fishes. Native tropical island stream fish assemblages composed of diadromous species require intact corridors between ocean and riverine habitats. High dams block fish migration, but low-head artificial barriers are more widespread and are rarely assessed for impacts. Among all 46 drainages in Puerto Rico, we identified and surveyed 335 artificial barriers that hinder fish migration to 74.5% of the upstream habitat. We also surveyed occupancy of native diadromous fishes (Anguillidae, Eleotridae, Gobiidae, and Mugilidae) in 118 river reaches. Occupancy models demonstrated that barriers 2 meters (m) high restricted nongoby fish migration and extirpated those fish upstream of 4-m barriers. Gobies are adapted to climbing and are restricted by 12-m barriers and extirpated upstream of 32-m barriers. Our findings quantitatively illustrate the extensive impact of low-head structures on island stream fauna and provide guidance for natural resource management, habitat restoration, and water development strategies.

Improved Quantum Artificial Fish Algorithm Application to Distributed Network Considering Distributed Generation

PubMed Central

Hu, Yang; Ke, Xianting

2015-01-01

An improved quantum artificial fish swarm algorithm (IQAFSA) for solving distributed network programming considering distributed generation is proposed in this work. The IQAFSA based on quantum computing which has exponential acceleration for heuristic algorithm uses quantum bits to code artificial fish and quantum revolving gate, preying behavior, and following behavior and variation of quantum artificial fish to update the artificial fish for searching for optimal value. Then, we apply the proposed new algorithm, the quantum artificial fish swarm algorithm (QAFSA), the basic artificial fish swarm algorithm (BAFSA), and the global edition artificial fish swarm algorithm (GAFSA) to the simulation experiments for some typical test functions, respectively. The simulation results demonstrate that the proposed algorithm can escape from the local extremum effectively and has higher convergence speed and better accuracy. Finally, applying IQAFSA to distributed network problems and the simulation results for 33-bus radial distribution network system show that IQAFSA can get the minimum power loss after comparing with BAFSA, GAFSA, and QAFSA. PMID:26447713

Evaluation of the damage in fish spermatozoa cryopreservation

NASA Astrophysics Data System (ADS)

Li, Jun; Liu, Qinghua; Zhang, Shicui

2006-12-01

Cryodamages occur during sperm cryopreservation. Cryopreservation of fish sperm usually results in marked decrease in sperm quality, such as swelling or disruption of the plasma membrane, mitochondrial dysfunction, diminished sperm motility, impaired velocity, shorter motility period, denaturation, and release of some enzymes from spermatozoa. In this paper, damages in morphology, physiology, biochemistry and metabolism, and genetic integrity of fish semen after cryopreservation are discussed. New approaches in assessment of fish thawed sperm quality such as computer assisted sperm analysis, flow cytometic analysis combined with fluorescent probes and single cell gel electrophoresis are also briefly reviewed.

Relationships between mercury concentration and food selectivity of many kinds of fishes in Minamata Bay

NASA Astrophysics Data System (ADS)

Mori, K.; Kanaya, G.

2016-02-01

Serious injuries occurred in residents who consumed fish and shellfishes in Minamata Bay polluted by high-concentration methyl-mercury in the 1950s. Pollution has fallen to a safe level because of the pollution prevention project (dredging etc.) carried out from 1977 to 1990. From 2010 we have been researching the bioaccumulation of mercury in several fishes in Minamata Bay and surrounding areas. We selected several sampling points that showed different environmental conditions, species composition and food web patterns. For the determination of feeding types of 60 species fishes (600 samples) sampled by gill net, we measured mercury levels of each sample and directly checked food items in gut, and distinguished carnivore, omnivore, herbivore and detritivore. At this time, we introduced a stable isotope analysis for checking the food history and feeding habits of dominant fish. In about 300 individuals of 30 species of dominant fish selected from the 600 samples, we measured the stable nitrogen and carbon isotope ratios (δ15N, δ13C) of each sample. Checking the food items in gut of fishes, more than 80% of fishes were carnivorous, and showed different selectivity of food items, such as fish, crustacean and so on. From the results of stable isotope ratios, benthic fish tended to show a higher ratio of δ13C. Usually benthic microalgae evidenced a higher ratio of δ13C than planktonic microalgae, and the ratio conservative through the food chain. In general, δ15N increases through the food chain with +3 to +4 ‰ enrichment per trophic step. In these data, carnivorous fishes of benthic and pelagic type showed medium and high ratios of δ15N. From comparing the stable isotope ratio to the mercury concentration of fishes, all of the high-mercury fishes belonged to benthic and carnivorous types. We consider the joint method of food web analysis and stable isotope analysis to be useful for understanding the mechanism of mercury bioaccumulation through the food web

Identification of three duplicated Spin genes in medaka (Oryzias latipes).

PubMed

Wang, Xiao-Lei; Mei, Jie; Sun, Min; Hong, Yun-Han; Gui, Jian-Fang

2005-05-09

Gene and genomic duplications are very important and frequent events in fish evolution, and the divergence of duplicated genes in sequences and functions is a focus of research on gene evolution. Here, we report the identification and characterization of three duplicated Spindlin (Spin) genes from medaka (Oryzias latipes): OlSpinA, OlSpinB, and OlSpinC. Molecular cloning, genomic DNA Blast analysis and phylogenetic relationship analysis demonstrated that the three duplicated OlSpin genes should belong to gene duplication. Furthermore, Western blot analysis revealed significant expression differences of the three OlSpins among different tissues and during embryogenesis in medaka, and suggested that sequence and functional divergence might have occurred in evolution among them.

Prevalence of cymothoid isopods (Crustacea, Isopoda) and proximate analysis of parasites and their host fishes, Southeastern India.

PubMed

Rajaram, Rajendran; Rakesh Kumar, Kulanthasamy; Vinothkumar, Shanmugam; Metillo, Ephrime B

2018-06-01

Cymothoid isopods (Crustacea, Isopoda) are considered as potential threat to the health of different fish species. In order to evaluate the prevalence and proximate analysis of Cymothoid isopods and its host, an investigation was carried out fish species belonging to families Hemiramphidae and Belonidae in the Palk Bay region, Southeastern India. A total of 1265 individuals of teleost fish belonging to family Hemiramphidae species, Hemiramphus far (462), H. archipelagicus (78), and H. lutkie (277) and another family Belonidae species, Tylosurus crocodilus (448), were examined for cymothoid ectoparasitic infestation. Prevalence in H. far was the highest (39%) for the cymothoid Mothocys plagulophora , while T. crocodilus was most infested (13%) with Mothocys renardi, H. far and H. lutkie were not infested by M. renardi while T. crocodilus was not infested by M. plagulophora. Proximate analysis showed reduced level of protein in parasite infested fish compared with non-infested individuals. However, carbohydrate and lipid concentrations were lower in infested fish than non-infested individuals. Proximate analysis values in the two parasites of Mothocys species were similar, and these values were comparable to those unaffected fish species indicating that parasites were well nourished. The proximate analysis of isopod parasite M. plagulophora showed 21.6 ± 7.7, 1.26 ± 0.05, 5.49 ± 1.06% of protein, carbohydrate and lipid respectively, and in M. renardi, 21.09 ± 6.6, 1.32 ± 0.12, 5.83 ± 0.72% of protein, carbohydrate and lipid respectively. Cadmium levels were similar between affected and non-affected fish individuals and among species. The Pb levels were comparable among all T. crocodilus individuals, but the levels of Cd not showed much variation between affected and unaffected individuals in all four fish species.

PCC-FISH in skin fibroblasts for local dose assessment: biodosimetric analysis of a victim of the Georgian radiological accident.

PubMed

Pouget, J-P; Laurent, C; Delbos, M; Benderitter, M; Clairand, I; Trompier, F; Stéphanazzi, J; Carsin, H; Lambert, F; Voisin, P; Gourmelon, P

2004-10-01

We propose a new method of biodosimetry that could be applied in cases of localized irradiation. The approach is based on excess chromosome segments determination by the PCC-FISH technique in fibroblasts isolated from skin biopsy. Typically, 0 to 10 Gy ex vivo gamma-irradiated human skin biopsies were dissociated and fibroblasts were isolated and grown for several days. Cells next underwent PCC-FISH painting of whole chromosome 4, and the number of excess chromosome segments per metaphase was determined. An ex vivo reference curve correlating the number of excess chromosome segments per metaphase to the radiation dose was established and used to assess the dose delivered to the skin of one of the victims of the radiological accident that occurred at Lia in Georgia in December 2001. Specifically, the victim suffering from moist desquamation underwent skin excision in Hospital Percy (France). Measurement of excess chromosome segments per metaphase was done in fibroblasts isolated and grown from removed wounded skin and subsequent conversion to radiation doses was performed. The radiation dose map obtained was shown to be in accordance with clinical data and physical dosimetry as well as with conventional biodosimetry. These results demonstrated that PCC-FISH painting applied to skin fibroblasts may be a suitable technique for dose estimation. To assess its worth, this approach needs to be extended to future accidents involving localized radiation exposure.

A non-lethal method to estimate CYP1A expression in laboratory and wild Atlantic salmon (Salmo salar)

USGS Publications Warehouse

Rees, C.B.; McCormick, S.D.; Li, W.

2005-01-01

Expression of cytochrome P4501A (CYP1A) has been used as a biomarker for possible exposure to contaminants such as PCBs and dioxins in teleost fish. Using a quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) and a non-lethal gill biopsy, we estimated levels of CYP1A mRNA expression in Atlantic salmon (Salmo salar). Groups of ten Atlantic salmon juveniles (48–76 g) received an intraperitoneal injection of 50 μg g− 1 β-naphthoflavone (BNF) or vehicle. Their gill tissues were repeatedly sampled by non-lethal biopsies on day 0, 1, 2 and 7. Control fish expressed basal levels of CYP1A over the duration of sampling. BNF-treated salmon demonstrated similar levels of CYP1A to control fish at day 0 and higher levels over the course of each additional sampling point. Gill biopsies from wild salmon sampled from Millers River (South Royalston, Worcester County, MA, USA), known to contain PCBs, showed significantly higher CYP1A levels over an uncontaminated reference stream, Fourmile Brook (Northfield, Franklin County, MA, USA). We conclude that gill biopsies coupled with Q-RT-PCR analysis is a valuable tool in environmental assessment of wild Atlantic salmon populations and has the potential to be applied to other populations of fish as well.

A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos).

PubMed

Avila, Felipe; Baily, Malorie P; Perelman, Polina; Das, Pranab J; Pontius, Joan; Chowdhary, Renuka; Owens, Elaine; Johnson, Warren E; Merriwether, David A; Raudsepp, Terje

2014-01-01

Genome analysis of the alpaca (Lama pacos, LPA) has progressed slowly compared to other domestic species. Here, we report the development of the first comprehensive whole-genome integrated cytogenetic map for the alpaca using fluorescence in situ hybridization (FISH) and CHORI-246 BAC library clones. The map is comprised of 230 linearly ordered markers distributed among all 36 alpaca autosomes and the sex chromosomes. For the first time, markers were assigned to LPA14, 21, 22, 28, and 36. Additionally, 86 genes from 15 alpaca chromosomes were mapped in the dromedary camel (Camelus dromedarius, CDR), demonstrating exceptional synteny and linkage conservation between the 2 camelid genomes. Cytogenetic mapping of 191 protein-coding genes improved and refined the known Zoo-FISH homologies between camelids and humans: we discovered new homologous synteny blocks (HSBs) corresponding to HSA1-LPA/CDR11, HSA4-LPA/CDR31 and HSA7-LPA/CDR36, and revised the location of breakpoints for others. Overall, gene mapping was in good agreement with the Zoo-FISH and revealed remarkable evolutionary conservation of gene order within many human-camelid HSBs. Most importantly, 91 FISH-mapped markers effectively integrated the alpaca whole-genome sequence and the radiation hybrid maps with physical chromosomes, thus facilitating the improvement of the sequence assembly and the discovery of genes of biological importance. © 2015 S. Karger AG, Basel.

Development of molecular techniques for detection of lymphocystis disease virus in different marine fish species.

PubMed

Cano, I; Ferro, P; Alonso, M C; Bergmann, S M; Römer-Oberdörfer, A; Garcia-Rosado, E; Castro, D; Borrego, J J

2007-01-01

The development and evaluation of a protocol based on polymerase chain reaction (PCR) and nucleic acid hybridization techniques for the specific detection of lymphocystis disease virus (LCDV) in several marine fish species. The pair of primers for PCR, OBL3 and OBL4, was designed based on published nucleotide sequence (LCDV-1) and amplifies a fragment within the major capsid protein. The sensitivity was evaluated using DNA from purified viral particles, as well as from cells inoculated with several viral concentrations. The PCR combined with slot blot was the most sensitive methodology, detecting 2.5 ng of viral DNA. Using this methodology LCDV was detected at 5 days postinoculation from SAF-1 cells initially inoculated with 10(-5) TCID(50) ml(-1). The combination of PCR with membrane hybridization has also been proved to be adequate to detect LCDV from apparently healthy carriers by means of caudal fin sample analysis. This asymptomatic infection was also demonstrated by classical virological methods (cell culture and immunoblot). The protocol described in this study allows the specific detection of LCDV, both in cell cultures and in fin homogenates from asymptomatic fish. The detection of asymptomatic carriers by a rapid molecular method using caudal fin sampling, which does not imply animal killing, could be an important tool to control epizootics caused by LCDV, as fish could be analysed before their introduction and/or mobilization in farm facilities.

Assessment of diclofenac LC50 reference values in juvenile and embryonic stages of the zebrafish (Danio rerio).

PubMed

Praskova, E; Voslarova, E; Siroka, Z; Plhalova, L; Macova, S; Marsalek, P; Pistekova, V; Svobodova, Z

2011-01-01

The aim of the study was to compare the acute toxicity of diclofenac to juvenile and embryonic stages of the zebrafish (Danio rerio). Acute toxicity tests were performed on the aquarium fish Danio rerio, which is one of the model organisms most commonly used in toxicity testing. The tests were performed using a semi-static method according to OECD guideline No. 203 (Fish, acute toxicity test). Embryo toxicity tests were performed in zebrafish embryos (Danio rerio) in compliance with OECD No. 212 methodology (Fish, short-term toxicity test on embryo and sac-fry stages). The results were subjected to a probit analysis using the EKO-TOX 5.2 programme to determine 96hLC50 and 144hLC50 (median lethal concentration, 50% mortality after a 96 h or 144 h interval, respectively) values of diclofenac. The statistical significance of the difference between LC50 values in juvenile and embryonic stages of Danio rerio was tested using the Mann-Whitney non-parametric test implemented in the Unistat 5.1 programme. The LC50 mean value of diclofenac was 166.6 +/- 9.8 mg/L in juvenile Danio rerio, and 6.11 +/- 2.48 mg/L in embryonic stages of Danio rerio. The study demonstrated a statistically higher sensitivity to diclofenac (P < 0.05) in embryonic stages compared to the juvenile fish.

Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

PubMed

Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

2014-02-01

While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

A hedonic price analysis of the outfitter market for trout fishing in the Rocky Mountain West

Treesearch

Heidi M. Pitts; Jennifer A. Thacher; Patricia A. Champ; Robert P. Berrens

2012-01-01

Trout is the most popular sport fish in Montana, Wyoming, Colorado, and New Mexico where fishing outfitters bring revenues to many rural economies. This article uses the hedonic pricing method on a monopolistically competitive outfitter market in those four states to examine angler values for trout fishing characteristics. A total of 1,685 fishing trip observations...

A Method for Measuring Fishing Effort by Small-Scale Fish Aggregating Device (FAD) Fishers from the Commonwealth of Dominica

ERIC Educational Resources Information Center

Alvard, Michael; McGaffey, Ethan; Carlson, David

2015-01-01

We used global positioning system (GPS) technology and tracking analysis to measure fishing effort by marine, small-scale, fish aggregating device (FAD) fishers of the Commonwealth of Dominica. FADs are human-made structures designed to float on the surface of the water and attract fish. They are also prone to common pool resource problems. To…

Comparative Analysis of State Fish Consumption Advisories Targeting Sensitive Populations

PubMed Central

Scherer, Alison C.; Tsuchiya, Ami; Younglove, Lisa R.; Burbacher, Thomas M.; Faustman, Elaine M.

2008-01-01

Objective Fish consumption advisories are issued to warn the public of possible toxicological threats from consuming certain fish species. Although developing fetuses and children are particularly susceptible to toxicants in fish, fish also contain valuable nutrients. Hence, formulating advice for sensitive populations poses challenges. We conducted a comparative analysis of advisory Web sites issued by states to assess health messages that sensitive populations might access. Data sources We evaluated state advisories accessed via the National Listing of Fish Advisories issued by the U.S. Environmental Protection Agency. Data extraction We created criteria to evaluate advisory attributes such as risk and benefit message clarity. Data synthesis All 48 state advisories issued at the time of this analysis targeted children, 90% (43) targeted pregnant women, and 58% (28) targeted women of childbearing age. Only six advisories addressed single contaminants, while the remainder based advice on 2–12 contaminants. Results revealed that advisories associated a dozen contaminants with specific adverse health effects. Beneficial health effects of any kind were specifically associated only with omega-3 fatty acids found in fish. Conclusions These findings highlight the complexity of assessing and communicating information about multiple contaminant exposure from fish consumption. Communication regarding potential health benefits conferred by specific fish nutrients was minimal and focused primarily on omega-3 fatty acids. This overview suggests some lessons learned and highlights a lack of both clarity and consistency in providing the breadth of information that sensitive populations such as pregnant women need to make public health decisions about fish consumption during pregnancy. PMID:19079708

Is there an association between flow diverter fish mouthing and delayed-type hypersensitivity to metals?-a case-control study.

PubMed

Kocer, Naci; Mondel, Prabath Kumar; Yamac, Elif; Kavak, Ayse; Kizilkilic, Osman; Islak, Civan

2017-11-01

Flow diverters are increasingly used in the treatment of complex and giant intracranial aneurysms. However, they are associated with complications like late aneurysmal rupture. Additionally, flow diverters show focal structural decrease in luminal diameter without any intimal hyperplasia. This resembles a "fish mouth" when viewed en face. In this pilot study, we tested the hypothesis of a possible association between flow diverter fish-mouthing and delayed-type hypersensitivity to its metal constituents. We retrospectively reviewed patient records from our center between May 2010 and November 2015. A total of nine patients had flow diverter fish mouthing. A control group of 25 patients was selected. All study participants underwent prospective patch test to detect hypersensitivity to flow diverter metal constituents. Analysis was performed using logistic regression analysis and Wilcoxon sign rank sum test. Univariate and multivariate analyses were performed to test variables to predict flow diverter fish mouthing. The association between flow diverter fish mouthing and positive patch test was not statistically significant. In multivariate analysis, history of allergy and maximum aneurysm size category was associated with flow diverter fish mouthing. This was further confirmed on Wilcoxon sign rank sum test. The study showed statistically significant association between flow diverter fish mouthing and history of contact allergy and a small aneurysmal size. Further large-scale studies are needed to detect a statistically significant association between flow diverter fish mouthing and patch test. We recommend early and more frequent follow-up imaging in patients with contact allergy to detect flow diverter fish mouthing and its subsequent evolution.

Business Profile of Boat Lift Net and Stationary Lift Net Fishing Gear in Morodemak Waters Central Java

NASA Astrophysics Data System (ADS)

Hapsari, Trisnani D.; Jayanto, Bogi B.; Fitri, Aristi D. P.; Triarso, I.

2018-02-01

Lift net is one of the fishing gears that is used widely in the Morodemak coastal fishing port (PPP) for catching pelagic fish. The yield of fish captured by these fishing gear has high economic value, such as fish belt (Trichiurus sp), squids (Loligo sp) and anchovies (Stelophorus sp). The aims of this research were to determine the technical aspects of boat lift net and stationary lift net fishing gear in Morodemak Waters Demak Regency; to find out the financial aspect of those fishing gears and to analyze the financial feasibility by counting PP, NPV, IRR, and B/C ratio criteria. This research used case study method with descriptive analysis. The sampling method was purposive sampling with 22 fishermen as respondents. The result of the research showed that the average of boat lift net acceptance was Rp 388,580,000. The financial analysis of fisheries boat lift net with the result of NPV Rp 836,149,272, PP 2.44 years, IRR value 54%, and B/C ratio 1.73. The average of stationary lift net acceptance was Rp 27,750,000. The financial analysis lift net with the result of NPV Rp 37,937,601; PP 1.96 years, IRR value 86%, and B/C ratio 1.32. This research had a positive NPV value, B/C ratio >1, and IRR > discount rate (12 %). This study concluded that the fishery business of boat lift net and stationary lift net in Morodemak coastal fishing port (PPP) was worth running.

A pleiotropic interaction between vision loss and hypermelanism in Astyanax mexicanus cave x surface hybrids.

PubMed

Gross, Joshua B; Powers, Amanda K; Davis, Erin M; Kaplan, Shane A

2016-06-30

Cave-dwelling animals evolve various traits as a consequence of life in darkness. Constructive traits (e.g., enhanced non-visual sensory systems) presumably arise under strong selective pressures. The mechanism(s) driving regression of features, however, are not well understood. Quantitative trait locus (QTL) analyses in Astyanax mexicanus Pachón cave x surface hybrids revealed phenotypic effects associated with vision and pigmentation loss. Vision QTL were uniformly associated with reductions in the homozygous cave condition, however pigmentation QTL demonstrated mixed phenotypic effects. This implied pigmentation might be lost through both selective and neutral forces. Alternatively, in this report, we examined if a pleiotropic interaction may exist between vision and pigmentation since vision loss has been shown to result in darker skin in other fish and amphibian model systems. We discovered that certain members of Pachón x surface pedigrees are significantly darker than surface-dwelling fish. All of these "hypermelanic" individuals demonstrated severe visual system malformations suggesting they may be blind. A vision-mediated behavioral assay revealed that these fish, in stark contrast to surface fish, behaved the same as blind cavefish. Further, hypermelanic melanophores were larger and more dendritic in morphology compared to surface fish melanophores. However, hypermelanic melanophores responded normally to melanin-concentrating hormone suggesting darkening stemmed from vision loss, rather than a defect in pigment cell function. Finally, a number of genomic regions were coordinately associated with both reduced vision and increased pigmentation. This work suggests hypermelanism in hybrid Astyanax results from blindness. This finding provides an alternative explanation for phenotypic effect studies of pigmentation QTL as stemming (at least in part) from environmental, rather than exclusively genetic, interactions between two regressive phenotypes. Further, this analysis reveals persistence of background adaptation in Astyanax. As the eye was lost in cave-dwelling forms, enhanced pigmentation resulted. Given the extreme cave environment, which is often devoid of nutrition, enhanced pigmentation may impose an energetic cost. Such an energetic cost would be selected against, as a means of energy conservation. Thus, the pleiotropic interaction between vision loss and pigmentation may reveal an additional selective pressure favoring the loss of pigmentation in cave-dwelling animals.

THE EFFECTS OF DIETARY β-GUANIDINOPROPIONIC ACID ON GROWTH AND MUSCLE FIBER DEVELOPMENT IN JUVENILE RED PORGY, PAGRUS PAGRUS

PubMed Central

White, Dalon P.; Baumgarner, Bradley L.; Watanabe, Wade O.; Alam, Md Shah; Kinsey, Stephen T.

2018-01-01

β-guandinopropionic acid (β-GPA) has been used in mammalian models to reduce intracellular phosphocreatine (PCr) concentration, which in turn lowers the energetic state of cells. This leads to changes in signaling pathways that attempt to re-establish energetic homeostasis. Changes in those pathways elicit effects similar to those of exercise such as changes in body and muscle growth, metabolism, endurance and health. Generally, exercise effects are beneficial to fish health and aquaculture, but inducing exercise in fishes can be impractical. Therefore, this study evaluated the potential use of supplemental β-GPA to induce exercise-like effects in a rapidly growing juvenile teleost, the red porgy (Pagrus pagrus). We demonstrate for the first time that β-GPA can be transported into teleost muscle fibers and is phosphorylated, and that this perturbs the intracellular energetic state of the cells, although to a lesser degree than typically seen in mammals. β-GPA did not affect whole animal growth, nor did it influence skeletal muscle fiber size or myonuclear recruitment. There was, however, an increase in mitochondrial volume within myofibers in treated fish. GC/MS metabolomic analysis revealed shifts in amino acid composition of the musculature, putatively reflecting increases in connective tissue and decreases in protein synthesis that are associated with β-GPA treatment. These results suggest that β-GPA modestly affects fish muscle in a manner similar to that observed in mammals, and that β-GPA may have application to aquaculture by providing a more practical means of generating some of the beneficial effects of exercise in fishes. PMID:29175483

[BIODIVERSITY OF ACANTHOCEPHALANS (ACANTHOCEPHALA) IN FRESHWATER FISHES OF ASIATIC SUB-ARCTIC REGION].

PubMed

Atrashkevich, G I; Mikhailova, E I; Orlovskaya, O M; Pospekhov, V V

2016-01-01

The analysis of taxonomical and ecological diversity of acanthocephalans in fishes of Asiatic sub-Arctic region freshwaters, summarizing changes in modern views on species composition, life cycles, and ecology of background groups of these parasites is given. A priority role of studies provided by O. N. Bauer and his scientific school in organization and development of these aspects of acanthocephalology is demonstrated. Special attention is paid to the assessment of acanthocephalan biodiversity of the genus Neoechinorhynchus, the background group of freshwater fish parasites of the Asiatic sub-Arctic region, and an original key for their species is given. The distribution of acanthocephalans of the genus Acanthocephalus in northeastern Asia is analyzed and prospective study of this parasite group, evolutionary associated with freshwater isopods of the genus Asellus as intermediate hosts, is outlined. The absence of documented evidences on intermediate hosts of other background parasites of freshwater fishes in the region, acanthocephalans of the genus Metechinorhynchus, is revealed. It is assumed that subsequent taxonomic revisions based both on morphological and molecular genetic studies are necessary for the reliable revealing of species composition in each genus of the background acanthocephalans from freshwater fishes of Northern Asia. Theoretical significance of the study of acanthocephalan life cycles and revealing their natural intermediate hosts for the reliable estimation of structural and functional organization of their host-parasite systems in different parts of the range is substantiated and the possibility of the distribution of taxonomic conclusions in new territories is analyzed. A brief annotated taxonomical list of freshwater acanthocephalans of the Asiatic sub-Arctic region is given.

Effect of histidine on sorafenib-induced vascular damage: Analysis using novel medaka fish model.

PubMed

Shinagawa-Kobayashi, Yoko; Kamimura, Kenya; Goto, Ryo; Ogawa, Kohei; Inoue, Ryosuke; Yokoo, Takeshi; Sakai, Norihiro; Nagoya, Takuro; Sakamaki, Akira; Abe, Satoshi; Sugitani, Soichi; Yanagi, Masahiko; Fujisawa, Koichi; Nozawa, Yoshizu; Koyama, Naoto; Nishina, Hiroshi; Furutani-Seiki, Makoto; Sakaida, Isao; Terai, Shuji

2018-02-05

Sorafenib (SFN) is an anti-angiogenic chemotherapeutic that prolongs survival of patients with hepatocellular carcinoma (HCC); its side effects, including vascular damages such as hand-foot syndrome (HFS), are a major cause of therapy discontinuation. We previously reported that maintenance of peripheral blood flow by intake of dried bonito broth (DBB) significantly prevented HFS and prolonged the administration period. The amino acids contained in DBB probably contribute to its effects, but the mechanism has not been clarified. We hypothesized that histidine, the largest component among the amino acids contained in DBB, has effects on SFN-induced vascular damage, and evaluated this possibility using a novel medaka fish model. The fli::GFP transgenic medaka fish model has a fluorescently visible systemic vasculature. We fed the fish with SFN with and without histidine to compare blood flow and vascular structure among the differently fed models. The vascular cross-sectional area of each fish was measured to determine vascular diameter changes. Our results demonstrated that SFN-fed medaka developed a narrower vascular diameter. In addition, this narrowing was counteracted by addition of histidine to the medaka diet. We observed no positive effect of histidine on regeneration of cut vessels or on cell growth of endothelial cells and HCC cell lines. We proved the efficacy of the medaka model to assess vascular changes after administration of specific chemicals. And our results suggest that SFN causes vascular damage by narrowing peripheral vessel diameter, and that histidine effectively counteracts these changes to maintain blood flow. Copyright © 2018 Elsevier Inc. All rights reserved.

Inter-annual cascade effect on marine food web: A benthic pathway lagging nutrient supply to pelagic fish stock

PubMed Central

Fernandes, Lohengrin Dias de Almeida; Fagundes Netto, Eduardo Barros; Coutinho, Ricardo

2017-01-01

Currently, spatial and temporal changes in nutrients availability, marine planktonic, and fish communities are best described on a shorter than inter-annual (seasonal) scale, primarily because the simultaneous year-to-year variations in physical, chemical, and biological parameters are very complex. The limited availability of time series datasets furnishing simultaneous evaluations of temperature, nutrients, plankton, and fish have limited our ability to describe and to predict variability related to short-term process, as species-specific phenology and environmental seasonality. In the present study, we combine a computational time series analysis on a 15-year (1995–2009) weekly-sampled time series (high-resolution long-term time series, 780 weeks) with an Autoregressive Distributed Lag Model to track non-seasonal changes in 10 potentially related parameters: sea surface temperature, nutrient concentrations (NO2, NO3, NH4 and PO4), phytoplankton biomass (as in situ chlorophyll a biomass), meroplankton (barnacle and mussel larvae), and fish abundance (Mugil liza and Caranx latus). Our data demonstrate for the first time that highly intense and frequent upwelling years initiate a huge energy flux that is not fully transmitted through classical size-structured food web by bottom-up stimulus but through additional ontogenetic steps. A delayed inter-annual sequential effect from phytoplankton up to top predators as carnivorous fishes is expected if most of energy is trapped into benthic filter feeding organisms and their larval forms. These sequential events can explain major changes in ecosystem food web that were not predicted in previous short-term models. PMID:28886162

Use of Tetragenococcus halophilus as a starter culture for flavor improvement in fish sauce fermentation.

PubMed

Udomsil, Natteewan; Rodtong, Sureelak; Choi, Yeung Joon; Hua, Yanglin; Yongsawatdigul, Jirawat

2011-08-10

The potential of Tetragenococcus halophilus as a starter culture for flavor improvement in fish sauce fermentation was elucidated. Four strains of T. halophilus isolated from fish sauce mashes were inoculated to anchovy mixed with 25% NaCl with an approximate cell count of 10(6) CFU/mL. The α-amino content of 6-month-old fish sauce samples inoculated with T. halophilus was 780-784 mM. The addition of T. halophilus MRC10-1-3 and T. halophilus MCD10-5-10 resulted in a reduction of histamine (P < 0.05). Fish sauce inoculated with T. halophilus showed high contents of total amino acids with predominantly high glutamic acid. Major volatile compounds in fish sauce were 2-methylpropanal, 2-methylbutanal, 3-methylbutanal, and benzaldehyde. T. halophilus-inoculated fish sauce samples demonstrated the ability to reduce dimethyl disulfide, a compound contributing to a fecal note. The use of T. halophilus for fish sauce fermentation improves amino acid profiles and volatile compounds as well as reduces biogenic amine content of a fish sauce product.

Genetic heterogeneity in HER2 testing may influence therapy eligibility.

PubMed

Bernasconi, Barbara; Chiaravalli, Anna Maria; Finzi, Giovanna; Milani, Katia; Tibiletti, Maria Grazia

2012-05-01

Prospective studies have demonstrated that approximately 20% of HER2 testing may be inaccurate. When carefully validated testing is conducted, available data do not clearly demonstrate the superiority of either IHC or fluorescence in situ hybridization (FISH) as a predictor of benefit from anti-HER2 therapy. In addition, the interpretation of the findings of HER2 tests according to international guidelines is not uniform. The American Society of Clinical Oncology (ASCO) and the College of American Pathologists (CAP) recently published practice guidelines for a definition of HER2 amplification heterogeneity that can give rise to discrepant results between IHC and FISH assays for HER2. In this article, we compare the HER2 status of 291 non consecutive breast cancers. The status is determined by both IHC and FISH approaches, using a specific FISH strategy to investigate genetic heterogeneity. Our data demonstrate that HER2 amplified cells may be found as diffuse, clustered in a specific area or section, intermingled with non-amplified cells or confined to metastatic nodules. The correct evaluation of ratio value in the presence of genetic heterogeneity and of polysomy contributes to the accurate assessment of HER2 status and potentially affects the selection of appropriate anti-HER2 therapy. By taking into account the presence of different genetic cell populations, the immunotherapy eligibility criteria for HER2 FISH scoring proposed in the CAP (2009) and SIGU guidelines identify an additional subset of cases for trastuzumab or lapatinib therapy compared to the ASCO/CAP (2007) guidelines.

Sensory complementation and antipredator behavioural compensation in acid-impacted juvenile Atlantic salmon.

PubMed

Elvidge, C K; Macnaughton, C J; Brown, G E

2013-05-01

Prey incorporate multiple forms of publicly available information on predation risk into threat-sensitive antipredator behaviours. Changes in information availability have previously been demonstrated to elicit transient alterations in behavioural patterns, while the effects of long-term deprivation of particular forms of information remain largely unexplored. Damage-released chemical alarm cues from the epidermis of fishes are rendered non-functional under weakly acidic conditions (pH < 6.6), depriving fish of an important source of information on predation risk in acidified waterbodies. We addressed the effects of long-term deprivation on the antipredator responses to different combinations of chemical and visual threat cues via in situ observations of wild, free-swimming 0(+) Atlantic salmon (Salmo salar) fry in four neutral and four weakly acidic nursery streams. In addition, a cross-population transplant experiment and natural interannual variation in acidity enabled the examination of provenance and environment as causes of the observed differences in response. Fish living under weakly acidic conditions demonstrate significantly greater or hypersensitive antipredator responses to visual cues compared to fish under neutral conditions. Under neutral conditions, fish demonstrate complementary (additive or synergistic) effects of paired visual and chemical cues consistent with threat-sensitive responses. Cross-population transplants and interannual comparisons of responses strongly support the conclusion that differences in antipredator responses between neutral and weakly acidic streams result from the loss of chemical information on predation risk, as opposed to population-derived differences in behaviours.

DEVELOPMENT OF STANDARDIZED LARGE RIVER BIOASSESSMENT PROTOCOLS (LR-BP) FOR BENTHIC MACROINVERTEBRATE ASSEMBLAGES

EPA Science Inventory

We conducted research comparing several methods currently in use for the bioassessment and monitoring of fish and benthic macroinvertebrate assemblages of large rivers. Fish data demonstrate that electrofishing 1000 m of shoreline is sufficient for bioassessments on boatable riv...

Neoplastic and nonneoplastic liver lesions induced by dimethylinitrosamine in Japanese Medaka fish

EPA Science Inventory

Small fish models are becoming commonplace in the laboratory, and have been used for decades in chemical toxicity and carcinogenicity testing. However, extrapolation of findings from aquatic models to humans is still a concern in risk assessment. Demonstration of common morpholog...

Paleobiology: A Tooth for a Tooth.

PubMed

Johanson, Zerina

2017-02-06

Many vertebrates replace teeth through shedding of the functional tooth. New analyses of a fossil fish demonstrate that shedding involved tooth resorption, a primitive feature in bony fishes, but absent in sharks and their relatives. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Evaluation of Fish Passage at Whitewater Parks Using 2D and 3D Hydraulic Modeling

NASA Astrophysics Data System (ADS)

Hardee, T.; Nelson, P. A.; Kondratieff, M.; Bledsoe, B. P.

2016-12-01

In-stream whitewater parks (WWPs) are increasingly popular recreational amenities that typically create waves by constricting flow through a chute to increase velocities and form a hydraulic jump. However, the hydraulic conditions these structures create can limit longitudinal habitat connectivity and potentially inhibit upstream fish migration, especially of native fishes. An improved understanding of the fundamental hydraulic processes and potential environmental effects of whitewater parks is needed to inform management decisions about Recreational In-Channel Diversions (RICDs). Here, we use hydraulic models to compute a continuous and spatially explicit description of velocity and depth along potential fish swimming paths in the flow field, and the ensemble of potential paths are compared to fish swimming performance data to predict fish passage via logistic regression analysis. While 3d models have been shown to accurately predict trout movement through WWP structures, 2d methods can provide a more cost-effective and manager-friendly approach to assessing the effects of similar hydraulic structures on fish passage when 3d analysis in not feasible. Here, we use 2d models to examine the hydraulics in several WWP structures on the North Fork of the St. Vrain River at Lyons, Colorado, and we compare these model results to fish passage predictions from a 3d model. Our analysis establishes a foundation for a practical, transferable and physically-rigorous 2d modeling approach for mechanistically evaluating the effects of hydraulic structures on fish passage.

Comparative study between quantitative digital image analysis and fluorescence in situ hybridization of breast cancer equivocal human epidermal growth factor receptors 2 score 2(+) cases.

PubMed

Ayad, Essam; Mansy, Mina; Elwi, Dalal; Salem, Mostafa; Salama, Mohamed; Kayser, Klaus

2015-01-01

Optimization of workflow for breast cancer samples with equivocal human epidermal growth factor receptors 2 (HER2)/neu score 2(+) results in routine practice, remains to be a central focus of the on-going efforts to assess HER2 status. According to the College of American Pathologists/American Society of Clinical Oncology guidelines equivocal HER2/neu score 2(+) cases are subject for further testing, usually by fluorescence in situ hybridization (FISH) investigations. It still remains on open question, whether quantitative digital image analysis of HER2 immunohistochemistry (IHC) stained slides can assist in further refining the HER2 score 2(+). To assess utility of quantitative digital analysis of IHC stained slides and compare its performance to FISH in cases of breast cancer with equivocal HER2 score 2(+). Fifteen specimens (previously diagnosed as breast cancer and was evaluated as HER 2(-) score 2(+)) represented the study population. Contemporary new cuts were prepared for re-evaluation of HER2 immunohistochemical studies and FISH examination. All the cases were digitally scanned by iScan (Produced by BioImagene [Now Roche-Ventana]). The IHC signals of HER2 were measured using an automated image analyzing system (MECES, www.Diagnomx.eu/meces). Finally, a comparative study was done between the results of the FISH and the quantitative analysis of the virtual slides. Three out of the 15 cases with equivocal HER2 score 2(+), turned out to be positive (3(+)) by quantitative digital analysis, and 12 were found to be negative in FISH too. Two of these three positive cases proved to be positive with FISH, and only one was negative. Quantitative digital analysis is highly sensitive and relatively specific when compared to FISH in detecting HER2/neu overexpression. Therefore, it represents a potential reliable substitute for FISH in breast cancer cases, which desire further refinement of equivocal IHC results.

Endogenous orienting in the archer fish

PubMed Central

Sekely, Liora; Klein, Raymond M.; Gabay, Shai

2017-01-01

The literature has long emphasized the neocortex’s role in volitional processes. In this work, we examined endogenous orienting in an evolutionarily older species, the archer fish, which lacks neocortex-like cells. We used Posner’s classic endogenous cuing task, in which a centrally presented, spatially informative cue is followed by a target. The fish responded to the target by shooting a stream of water at it. Interestingly, the fish demonstrated a human-like “volitional” facilitation effect: their reaction times to targets that appeared on the side indicated by the precue were faster than their reaction times to targets on the opposite side. The fish also exhibited inhibition of return, an aftermath of orienting that commonly emerges only in reflexive orienting tasks in human participants. We believe that this pattern demonstrates the acquisition of an arbitrary connection between spatial orienting and a nonspatial feature of a centrally presented stimulus in nonprimate species. In the literature on human attention, orienting in response to such contingencies has been strongly associated with volitional control. We discuss the implications of these results for the evolution of orienting, and for the study of volitional processes in all species, including humans. PMID:28673997

Behavioural and biochemical investigations of the influence of altered gravity on the CNS of aquatic vertebrates during ontogeny

NASA Astrophysics Data System (ADS)

Slenzka, K.; Appel, R.; Hilbig, R.; Kappel, Th.; Vetter, S.; Freischütz, B.; Rahmann, H.

1994-08-01

Quantitative data are presented on the influences of hyper-gravity (3+/-1g) and of simulated weightlessness (~0g) during early ontogeny of cichild fish (Oreochromis mossambicus) and clawed toad (Xenopus laevis, Daudin) demonstrating changes in the swimming behaviour and the brain energy and plasma membrane metabolism. After return to 1g conditions, hyper-g reared fish and toads express the well known ``loop-swimming'' behaviour. By means of a computer based video analyzing system different types of swimming movements and velocities were quantitatively determined. Analyses of the brain energy and plasma-membrane metabolism of hyper-g fish larvae demonstrated an increase in energy availability (glucose 6Pi dehydrogenase, G-6P-DH), a decrease of cellular energy transformation (creatine kinase activity, CK) but no changes in energy consumptive processes (e.g. ATPases) and cytochrome oxidase activity (Cyt.-Ox). In contrast hypo-g fish larvae showed a slight increase in brain CK activity. In addition, unlike 1g controls, hyper-g fish larvae showed pronounced variations in the composition (=polarity) of sialoglycosphingolipids (=gangliosides), typical constituents of the nerve cell membranes, and a slight increase in the activity of sialidase, the enzyme responsible for ganglioside degradation.

Total Fat, n-3 Fatty Acids and Vitamin D3 in Selected Fish Species Sampled Under USDA’s National Food and Nutrient Analysis Program (NFNAP)

USDA-ARS?s Scientific Manuscript database

As part of the USDA’s National Food and Nutrient Analysis Program (NFNAP), new analytical data were determined for the 20 most frequently consumed raw fish identified for FDA’s voluntary nutrition labeling. Samples of 21 fish species were purchased from 12 supermarkets nationwide according to a sta...

Fishing-vessel fuel-conservation project. Final report, 25 June 1986-31 December 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1987-01-01

The Sea Grant Extension Program (SGEP) is the University of California's statewide education link with the commercial-fishing industry. SGEP's seven county-based marine advisors and three statewide specialists use applied research, demonstrations, workshops, publications, mass media, and individual consultations to help the industry put research-based information to work. SGEP has worked with the fishing industry for fifteen years. Two major ongoing long-term problems of the fishing industry have been chronically low-income levels and full- or over-exploitation of fish stocks. These problems were especially severe during the first half of the 1980s. With most fish resources fully utilized, one of the onlymore » means of improving the situation is improved economic efficiency, especially through fuel conservation. Fuel costs represent a large portion of most fishermen's variable costs.« less

Antimicrobial Peptides from Fish

PubMed Central

Masso-Silva, Jorge A.; Diamond, Gill

2014-01-01

Antimicrobial peptides (AMPs) are found widely distributed through Nature, and participate in the innate host defense of each species. Fish are a great source of these peptides, as they express all of the major classes of AMPs, including defensins, cathelicidins, hepcidins, histone-derived peptides, and a fish-specific class of the cecropin family, called piscidins. As with other species, the fish peptides exhibit broad-spectrum antimicrobial activity, killing both fish and human pathogens. They are also immunomodulatory, and their genes are highly responsive to microbes and innate immuno-stimulatory molecules. Recent research has demonstrated that some of the unique properties of fish peptides, including their ability to act even in very high salt concentrations, make them good potential targets for development as therapeutic antimicrobials. Further, the stimulation of their gene expression by exogenous factors could be useful in preventing pathogenic microbes in aquaculture. PMID:24594555

ALK rearrangement in a large series of consecutive non-small cell lung cancers: comparison between a new immunohistochemical approach and fluorescence in situ hybridization for the screening of patients eligible for crizotinib treatment.

PubMed

Alì, Greta; Proietti, Agnese; Pelliccioni, Serena; Niccoli, Cristina; Lupi, Cristiana; Sensi, Elisa; Giannini, Riccardo; Borrelli, Nicla; Menghi, Maura; Chella, Antonio; Ribechini, Alessandro; Cappuzzo, Federico; Melfi, Franca; Lucchi, Marco; Mussi, Alfredo; Fontanini, Gabriella

2014-11-01

Echinoderm microtubule associated proteinlike 4-anaplastic lymphoma receptor tyrosine kinase (EML4-ALK) translocation has been described in a subset of patients with non-small cell lung cancer (NSCLC) and has been shown to have oncogenic activity. Fluorescence in situ hybridization (FISH) is used to detect ALK-positive NSCLC, but it is expensive, time-consuming, and difficult for routine application. To evaluate the potential role of immunohistochemistry (IHC) as a screening tool to identify candidate cases for FISH analysis and for ALK inhibitor therapy in NSCLC. We performed FISH and IHC for ALK and mutational analysis for epidermal growth factor receptor (EGFR) and KRAS in 523 NSCLC specimens. We conducted IHC analysis with the monoclonal antibody D5F3 (Ventana Medical Systems, Tucson, Arizona) and a highly sensitive detection system. We also performed a MassARRAY-based analysis (Sequenom, San Diego, California) in a small subset of 11 samples to detect EML4-ALK rearrangement. Of the 523 NSCLC specimens, 20 (3.8%) were positive for ALK rearrangement by FISH analysis. EGFR and KRAS mutations were identified in 70 (13.4%) and 124 (23.7%) of the 523 tumor samples, respectively. ALK rearrangement and EGFR and KRAS mutations were mutually exclusive. Of 523 tumor samples analyzed, 18 (3.4%) were ALK(+) by IHC, 18 samples (3.4%) had concordant IHC and FISH results, and 2 ALK(+) cases (0.3%) by FISH failed to show ALK protein expression. In the 2 discrepant cases, we did not detect any mass peaks for the EML4-ALK variants by MassARRAY. Our results show that IHC may be a useful technique for selecting NSCLC cases to undergo ALK FISH analysis.

Inability to demonstrate fish-to-fish transmission of Ichthyophonus from laboratory infected Pacific herring Clupea pallasii to naïve conspecifics

USGS Publications Warehouse

Gregg, J.L.; Grady, C.A.; Friedman, C.S.; Hershberger, P.K.

2012-01-01

The parasite Ichthyophonus is enzootic in many marine fish populations of the northern Atlantic and Pacific Oceans. Forage fishes are a likely source of infection for higher trophic level predators; however, the processes that maintain Ichthyophonus in forage fish populations (primarily clupeids) are not well understood. Lack of an identified intermediate host has led to the convenient hypothesis that the parasite can be maintained within populations of schooling fishes by waterborne fish-to-fish transmission. To test this hypothesis we established Ichthyophonus infections in Age-1 and young-of-the-year (YOY) Pacific herring Clupea pallasii (Valenciennes) via intraperitoneal (IP) injection and cohabitated these donors with naïve conspecifics (sentinels) in the laboratory. IP injections established infection in 75 to 84% of donor herring, and this exposure led to clinical disease and mortality in the YOY cohort. However, after cohabitation for 113 d no infections were detected in naïve sentinels. These data do not preclude the possibility of fish-to-fish transmission, but they do suggest that other transmission processes are necessary to maintain Ichthyophonus in wild Pacific herring populations.

Design and testing of small scale fish meat bone separator useful for fish processing.

PubMed

Ali Muhammed, M; Manjunatha, N; Murthy, K Venkatesh; Bhaskar, N

2015-06-01

The present study relates to the food processing machinery and, more specifically machine for producing boneless comminuted meat from raw fish fillet. This machine is of belt and drum type meat bone separator designed for small scale fish processing in a continuous mode. The basic principal involved in this machine is compression force. The electric geared motor consists of 1HP and the conveyor belt has a linear velocity of 19 to 22 m min(-1), which was sufficient to debone the fish effectively. During the meat bone separation trials an efficiency up to 75 % on dressed fish weight basis was observed and with a capacity to separate 70 kg h(-1) of meat from fish at the machine speed of 25 rpm. During the trials, it was demonstrated that there was no significant change in the proximate composition of comminuted fish meat when compared to unprocessed fish meat. This design has a greater emphasis on hygiene, provision for cleaning-in-place (CIP) and gives cost effective need and reliability for small scale industries to produce fish meat in turn used for their value added products.

Why fish oil fails: a comprehensive 21st century lipids-based physiologic analysis.

PubMed

Peskin, B S

2014-01-01

The medical community suffered three significant fish oil failures/setbacks in 2013. Claims that fish oil's EPA/DHA would stop the progression of heart disease were crushed when The Risk and Prevention Study Collaborative Group (Italy) released a conclusive negative finding regarding fish oil for those patients with high risk factors but no previous myocardial infarction. Fish oil failed in all measures of CVD prevention-both primary and secondary. Another major 2013 setback occurred when fish oil's DHA was shown to significantly increase prostate cancer in men, in particular, high-grade prostate cancer, in the Selenium and Vitamin E Cancer Prevention Trial (SELECT) analysis by Brasky et al. Another monumental failure occurred in 2013 whereby fish oil's EPA/DHA failed to improve macular degeneration. In 2010, fish oil's EPA/DHA failed to help Alzheimer's victims, even those with low DHA levels. These are by no means isolated failures. The promise of fish oil and its so-called active ingredients EPA / DHA fails time and time again in clinical trials. This lipids-based physiologic review will explain precisely why there should have never been expectation for success. This review will focus on underpublicized lipid science with a focus on physiology.

Why Fish Oil Fails: A Comprehensive 21st Century Lipids-Based Physiologic Analysis

PubMed Central

Peskin, B. S.

2014-01-01

The medical community suffered three significant fish oil failures/setbacks in 2013. Claims that fish oil's EPA/DHA would stop the progression of heart disease were crushed when The Risk and Prevention Study Collaborative Group (Italy) released a conclusive negative finding regarding fish oil for those patients with high risk factors but no previous myocardial infarction. Fish oil failed in all measures of CVD prevention—both primary and secondary. Another major 2013 setback occurred when fish oil's DHA was shown to significantly increase prostate cancer in men, in particular, high-grade prostate cancer, in the Selenium and Vitamin E Cancer Prevention Trial (SELECT) analysis by Brasky et al. Another monumental failure occurred in 2013 whereby fish oil's EPA/DHA failed to improve macular degeneration. In 2010, fish oil's EPA/DHA failed to help Alzheimer's victims, even those with low DHA levels. These are by no means isolated failures. The promise of fish oil and its so-called active ingredients EPA / DHA fails time and time again in clinical trials. This lipids-based physiologic review will explain precisely why there should have never been expectation for success. This review will focus on underpublicized lipid science with a focus on physiology. PMID:24551453

Analyzing the association between fish consumption and osteoporosis in a sample of Chinese men.

PubMed

Li, Xia; Lei, Tao; Tang, Zihui; Dong, Jingcheng

2017-04-19

The main purpose of this study was to estimate the associations between frequency of fish food consumption and osteoporosis (OP) in general Chinese men. We conducted a large-scale, community-based, cross-sectional study to investigate the associations by using self-report questionnaire to access frequency of fish food intake. A total of 1092 men were available for data analysis in this study. Multiple regression models controlling for confounding factors to include frequency of fish food consumption variable were performed to investigate the relationships for OP. Positive correlations between frequency of fish food consumption and T score were reported (β = 0.084, P value = 0.025). Multiple regression analysis indicated that the frequency of fish food consumption was significantly associated with OP (P < 0.05 for model 1 and model 2). The men with high frequency of fish food consumption had a lower prevalence of OP. The findings indicated that frequency of fish food consumption was independently and significantly associated with OP. The prevalence of OP was less frequent in Chinese men preferring fish food habits. ClinicalTrials.gov Identifier: NCT02451397 retrospectively registered 28 May 2015.

Morphometric comparisons of plant-mimetic juvenile fish associated with plant debris observed in the coastal subtropical waters around Kuchierabu-jima Island, southern Japan

PubMed Central

2016-01-01

The general morphological shape of plant-resembling fish and plant parts were compared using a geometric morphometrics approach. Three plant-mimetic fish species, Lobotes surinamensis (Lobotidae), Platax orbicularis (Ephippidae) and Canthidermis maculata (Balistidae), were compared during their early developmental stages with accompanying plant debris (i.e., leaves of several taxa) in the coastal subtropical waters around Kuchierabu-jima Island, closely facing the Kuroshio Current. The degree of similarity shared between the plant parts and co-occurring fish species was quantified, however fish remained morphologically distinct from their plant models. Such similarities were corroborated by analysis of covariance and linear discriminant analysis, in which relative body areas of fish were strongly related to plant models. Our results strengthen the paradigm that morphological clues can lead to ecological evidence to allow predictions of behavioural and habitat choice by mimetic fish, according to the degree of similarity shared with their respective models. The resemblance to plant parts detected in the three fish species may provide fitness advantages via convergent evolutionary effects. PMID:27547571

Structural and functional characterizations of activin type 2B receptor (acvr2b) ortholog from the marine fish, gilthead sea bream, Sparus aurata: evidence for gene duplication of acvr2b in fish.

PubMed

Funkenstein, Bruria; Krol, Ekaterina; Esterin, Elena; Kim, Yong-Soo

2012-12-01

Myostatin (MSTN), a negative regulator of muscle growth and a member of the transforming growth factor-β superfamily, can bind the two activin type 2 receptors (ACVR2). It has been previously shown that WT mice injected with ACVR2B extracellular domain (ACVR2B-ECD) had higher muscle mass. Likewise, fish larvae immersed in Pichia pastoris culture supernatant, containing goldfish Acvr2b-ECD, showed enhanced larval growth. However, it is not clear whether fish Mstn1 and Mstn2 signal through the same receptor and whether fish express more than one acvr2b gene. In the current study, three cDNAs encoding acvr2b (saacvr2b-1, saacvr2b-2a, and saacvr2b-2b) were cloned from gilthead sea bream. All three contain the short extracellular binding domain, a short transmembrane region, and a conserved catalytic domain of serine/threonine protein kinase. Bioinformatics analysis provided evidence for the existence of two acvr2b genes (acvr2b-1 and acvr2b-2) in several other fish species as well, probably as a result of gene or genome duplication. The two isoforms differ in their amino acid sequences. The direct inhibitory effect of Acvr2b-ECD on Mstn activity was tested in vitro. The saAcvr2b-1-ECD was expressed in the yeast P. pastoris. Evidence is provided for N-glycosylation of Acvr2b-1-ECD. The affinity-purified Acvr2b-1-ECD inhibited recombinant mouse/rat/human mature MSTN activity when determined in vitro using the CAGA-luciferase assay in A204 cells. A lower inhibitory activity was obtained when unprocessed purified, furin-digested, and activated saMstn1 was used. Results of this study demonstrate for the first time the existence of two acvr2b genes in fish. In addition, the study shows that bioactive fish Acvr2b-ECD can be produced from P. pastoris.

Health Status of Sand Flathead (Platycephalus bassensis), Inhabiting an Industrialised and Urbanised Embayment, Port Phillip Bay, Victoria as Measured by Biomarkers of Exposure and Effects

PubMed Central

Baker, Jarrad K.; Long, Sara M.; Hassell, Kathryn L.; Pettigrove, Vincent J.

2016-01-01

Port Phillip Bay, Australia, is a large semi-closed bay with over four million people living in its catchment basin. The Bay receives waters from the Yarra River which drains the city of Melbourne, as well as receiving the discharges of sewage treatment plants and petrochemical and agricultural chemicals. A 1999 study demonstrated that fish inhabiting Port Phillip Bay showed signs of effects related to pollutant exposure despite pollution management practices having been implemented for over a decade. To assess the current health status of the fish inhabiting the Bay, a follow up survey was conducted in 2015. A suite of biomarkers of exposure and effects were measured to determine the health status of Port Phillip Bay sand flathead (Platycephalus bassensis), namely ethoxyresorufin-O-deethylase (EROD) activity, polycyclic aromatic hydrocarbons (PAH) biliary metabolites, carboxylesterase activity (CbE) and DNA damage (8-oxo-dG). The reduction in EROD activity in the present study suggests a decline in the presence of EROD activity-inducing chemicals within the Bay since the 1990s. Fish collected in the most industrialised/urbanised sites did not display higher PAH metabolite levels than those in less developed areas of the Bay. Ratios of PAH biliary metabolite types were used to indicate PAH contaminant origin. Ratios indicated fish collected at Corio Bay and Hobsons Bay were subjected to increased low molecular weight hydrocarbons of petrogenic origin, likely attributed to the close proximity of these sites to oil refineries, compared to PAH biliary metabolites in fish from Geelong Arm and Mordialloc. Quantification of DNA damage indicated a localised effect of exposure to pollutants, with a 10-fold higher DNA damage level in fish sampled from the industrial site of Corio Bay relative to the less developed site of Sorrento. Overall, integration of biomarkers by multivariate analysis indicated that the health of fish collected in industrialised areas was compromised, with biologically significant biomarkers of effects (LSI, CF and DNA damage) discriminating between individuals collected in industrialised areas from observations made in fish collected in less developed areas of the Bay. PMID:27711198

Downstream fish passage guide walls: A hydraulic scale model analysis

USGS Publications Warehouse

Mulligan, Kevin; Towler, Brett; Haro, Alexander J.; Ahlfeld, David P.

2018-01-01

Partial-depth guide walls are used to improve passage efficiency and reduce the delay of out-migrating anadromous fish species by guiding fish to a bypass route (i.e. weir, pipe, sluice gate) that circumvents the turbine intakes, where survival is usually lower. Evaluation and monitoring studies, however, indicate a high propensity for some fish to pass underneath, rather than along, the guide walls, compromising their effectiveness. In the present study we evaluated a range of guide wall structures to identify where/if the flow field shifts from sweeping (i.e. flow direction primarily along the wall and towards the bypass) to downward-dominant. Many migratory fish species, particularly juveniles, are known to drift with the flow and/or exhibit rheotactic behaviour during their migration. When these behaviours are present, fish follow the path of the flow field. Hence, maintaining a strong sweeping velocity in relation to the downward velocity along a guide wall is essential to successful fish guidance. Nine experiments were conducted to measure the three-dimensional velocity components upstream of a scale model guide wall set at a wide range of depths and angles to flow. Results demonstrated how each guide wall configuration affected the three-dimensional velocity components, and hence the downward and sweeping velocity, along the full length of the guide wall. In general, the velocities produced in the scale model were sweeping dominant near the water surface and either downward dominant or close to the transitional depth near the bottom of the guide wall. The primary exception to this shift from sweeping do downward flow was for the minimum guide wall angle tested in this study (15°). At 15° the flow pattern was fully sweeping dominant for every cross-section, indicating that a guide wall with a relatively small angle may be more likely to produce conditions favorable to efficient guidance. A critical next step is to evaluate the behaviour of migratory fish as they approach and swim along a guide wall in a controlled laboratory environment.

Health Status of Sand Flathead (Platycephalus bassensis), Inhabiting an Industrialised and Urbanised Embayment, Port Phillip Bay, Victoria as Measured by Biomarkers of Exposure and Effects.

PubMed

Baker, Jarrad K; Long, Sara M; Hassell, Kathryn L; Pettigrove, Vincent J; Gagnon, Marthe M

2016-01-01

Port Phillip Bay, Australia, is a large semi-closed bay with over four million people living in its catchment basin. The Bay receives waters from the Yarra River which drains the city of Melbourne, as well as receiving the discharges of sewage treatment plants and petrochemical and agricultural chemicals. A 1999 study demonstrated that fish inhabiting Port Phillip Bay showed signs of effects related to pollutant exposure despite pollution management practices having been implemented for over a decade. To assess the current health status of the fish inhabiting the Bay, a follow up survey was conducted in 2015. A suite of biomarkers of exposure and effects were measured to determine the health status of Port Phillip Bay sand flathead (Platycephalus bassensis), namely ethoxyresorufin-O-deethylase (EROD) activity, polycyclic aromatic hydrocarbons (PAH) biliary metabolites, carboxylesterase activity (CbE) and DNA damage (8-oxo-dG). The reduction in EROD activity in the present study suggests a decline in the presence of EROD activity-inducing chemicals within the Bay since the 1990s. Fish collected in the most industrialised/urbanised sites did not display higher PAH metabolite levels than those in less developed areas of the Bay. Ratios of PAH biliary metabolite types were used to indicate PAH contaminant origin. Ratios indicated fish collected at Corio Bay and Hobsons Bay were subjected to increased low molecular weight hydrocarbons of petrogenic origin, likely attributed to the close proximity of these sites to oil refineries, compared to PAH biliary metabolites in fish from Geelong Arm and Mordialloc. Quantification of DNA damage indicated a localised effect of exposure to pollutants, with a 10-fold higher DNA damage level in fish sampled from the industrial site of Corio Bay relative to the less developed site of Sorrento. Overall, integration of biomarkers by multivariate analysis indicated that the health of fish collected in industrialised areas was compromised, with biologically significant biomarkers of effects (LSI, CF and DNA damage) discriminating between individuals collected in industrialised areas from observations made in fish collected in less developed areas of the Bay.

Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar)

PubMed Central

Leaver, Michael J; Villeneuve, Laure AN; Obach, Alex; Jensen, Linda; Bron, James E; Tocher, Douglas R; Taggart, John B

2008-01-01

Background There is an increasing drive to replace fish oil (FO) in finfish aquaculture diets with vegetable oils (VO), driven by the short supply of FO derived from wild fish stocks. However, little is known of the consequences for fish health after such substitution. The effect of dietary VO on hepatic gene expression, lipid composition and growth was determined in Atlantic salmon (Salmo salar), using a combination of cDNA microarray, lipid, and biochemical analysis. FO was replaced with VO, added to diets as rapeseed (RO), soybean (SO) or linseed (LO) oils. Results Dietary VO had no major effect on growth of the fish, but increased the whole fish protein contents and tended to decrease whole fish lipid content, thus increasing the protein:lipid ratio. Expression levels of genes of the highly unsaturated fatty acid (HUFA) and cholesterol biosynthetic pathways were increased in all vegetable oil diets as was SREBP2, a master transcriptional regulator of these pathways. Other genes whose expression was increased by feeding VO included those of NADPH generation, lipid transport, peroxisomal fatty acid oxidation, a marker of intracellular lipid accumulation, and protein and RNA processing. Consistent with these results, HUFA biosynthesis, hepatic β-oxidation activity and enzymic NADPH production were changed by VO, and there was a trend for increased hepatic lipid in LO and SO diets. Tissue cholesterol levels in VO fed fish were the same as animals fed FO, whereas fatty acid composition of the tissues largely reflected those of the diets and was marked by enrichment of 18 carbon fatty acids and reductions in 20 and 22 carbon HUFA. Conclusion This combined gene expression, compositional and metabolic study demonstrates that major lipid metabolic effects occur after replacing FO with VO in salmon diets. These effects are most likely mediated by SREBP2, which responds to reductions in dietary cholesterol. These changes are sufficient to maintain whole body cholesterol levels but not HUFA levels. PMID:18577222

Late ovarian relapse of TEL/AML1 positive ALL confirming that TEL deletion is a secondary event in leukemogenesis.

PubMed

Ly-Sunnaram, Beatrice; Henry, Catherine; Gandemer, Virginie; Mee, Franseza Le; Burtin, Florence; Blayau, Martine; Cayuela, Jean-Michel; Oster, Magalie; Clech, Philippe; Rambeau, Marc; Marie, Celine; Pampin, Cecilia; Edan, Christine; Gall, Edouard Le; Goasguen, Jean E

2005-09-01

We describe here a late extramedullary ovarian relapse in an 18-year-old female who was diagnosed with hypotetraploid cell acute lymphoblastic leukaemia (cALL) at the age of 6. At both occurrences of the disease cells were analyzed by morphology, immunophenotyping, cytogenetics and molecular methods. TEL/AML1 was detected by RT-PCR and FISH analysis in both events. We demonstrated, using detection of IGH/TCR rearrangements and TEL/AML1 breakpoints sequencing that the cells were clonally related. Moreover, interphasic FISH using TEL and AML1 probes showed the loss of a second TEL at the time of relapse. This observation confirms that TEL/AML1 alone is not sufficient to trigger ALL and that TEL deletion is a secondary event in leukemogenesis. To our knowledge, it is the first complete description of extramedullary ALL relapse combining all methodologies.

In vivo microsampling to capture the elusive exposome

NASA Astrophysics Data System (ADS)

Bessonneau, Vincent; Ings, Jennifer; McMaster, Mark; Smith, Richard; Bragg, Leslie; Servos, Mark; Pawliszyn, Janusz

2017-03-01

Loss and/or degradation of small molecules during sampling, sample transportation and storage can adversely impact biological interpretation of metabolomics data. In this study, we performed in vivo sampling using solid-phase microextraction (SPME) in combination with non-targeted liquid chromatography and high-resolution tandem mass spectrometry (LC-MS/MS) to capture the fish tissue exposome using molecular networking analysis, and the results were contrasted with molecular differences obtained with ex vivo SPME sampling. Based on 494 MS/MS spectra comparisons, we demonstrated that in vivo SPME sampling provided better extraction and stabilization of highly reactive molecules, such as 1-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoleoyl-glycero-3-phosphocholine, from fish tissue samples. This sampling approach, that minimizes sample handling and preparation, offers the opportunity to perform longitudinal monitoring of the exposome in biological systems and improve the reliability of exposure-measurement in exposome-wide association studies.

Habitat, not resource availability, limits consumer production in lake ecosystems

USGS Publications Warehouse

Craig, Nicola; Jones, Stuart E.; Weidel, Brian C.; Solomon, Christopher T.

2015-01-01

Food web productivity in lakes can be limited by dissolved organic carbon (DOC), which reduces fish production by limiting the abundance of their zoobenthic prey. We demonstrate that in a set of 10 small, north temperate lakes spanning a wide DOC gradient, these negative effects of high DOC concentrations on zoobenthos production are driven primarily by availability of warm, well-oxygenated habitat, rather than by light limitation of benthic primary production as previously proposed. There was no significant effect of benthic primary production on zoobenthos production after controlling for oxygen, even though stable isotope analysis indicated that zoobenthos do use this resource. Mean whole-lake zoobenthos production was lower in high-DOC lakes with reduced availability of oxygenated habitat, as was fish biomass. These insights improve understanding of lake food webs and inform management in the face of spatial variability and ongoing temporal change in lake DOC concentrations.

In vivo microsampling to capture the elusive exposome

PubMed Central

Bessonneau, Vincent; Ings, Jennifer; McMaster, Mark; Smith, Richard; Bragg, Leslie; Servos, Mark; Pawliszyn, Janusz

2017-01-01

Loss and/or degradation of small molecules during sampling, sample transportation and storage can adversely impact biological interpretation of metabolomics data. In this study, we performed in vivo sampling using solid-phase microextraction (SPME) in combination with non-targeted liquid chromatography and high-resolution tandem mass spectrometry (LC-MS/MS) to capture the fish tissue exposome using molecular networking analysis, and the results were contrasted with molecular differences obtained with ex vivo SPME sampling. Based on 494 MS/MS spectra comparisons, we demonstrated that in vivo SPME sampling provided better extraction and stabilization of highly reactive molecules, such as 1-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoleoyl-glycero-3-phosphocholine, from fish tissue samples. This sampling approach, that minimizes sample handling and preparation, offers the opportunity to perform longitudinal monitoring of the exposome in biological systems and improve the reliability of exposure-measurement in exposome-wide association studies. PMID:28266605

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

PubMed Central

Sudhagar, Arun; El-Matbouli, Mansour

2018-01-01

In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology. PMID:29342931

Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

PubMed Central

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-01-01

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

Environmental Resources Analysis System, A Prototype DSS

USGS Publications Warehouse

Flug, M.; Campbell, S.G.; Bizier, P.; DeBarry, P.

2003-01-01

Since the 1960's, an increase in the public's environmental ethics, federal species preservation, water quality protection, and interest in free flowing rivers have evolved to the current concern for stewardship and conservation of natural resources. This heightened environmental awareness creates an appetite for data, models, information management, and systematic analysis of multiple scientific disciplines. A good example of this information and analysis need resides in the Green and Yampa Rivers, tributary to the Upper Colorado River. These rivers are home to endangered native fish species including the pikeminnow and razorback sucker. Two dams, Fontenelle and Flaming Gorge, impound the Green River headwaters. The respective reservoirs store water supplies as well as generate hydropower. Conversely, the Yampa River is considered unregulated and encompasses most of Dinosaur National Monument. Recreation is highly regarded on both rivers including fishing, whitewater rafting, and aesthetic values. Vast areas of irrigated agriculture, forestry, and mineral extraction also surround these rivers. To address this information need, we developed a prototype Environmental Resources Analysis System (ERAS) spreadsheet-based decision support system (DSS). ERAS provides access to historic data sets, scientific information, statistical analysis, model outputs, and comparative methods all in a familiar and user-friendly format. This research project demonstrates a simplified decision support system for use by a diverse mix of resource managers, special interest groups, and individuals concerned about the sustainability of the Green and Yampa River ecosystem.

Replacement of soybean oil by fish oil increases cytosolic lipases activities in liver and adipose tissue from rats fed a high-carbohydrate diets.

PubMed

Rodrigues, Angélica Heringer; Moreira, Carolina Campos Lima; Neves, Maria José; Botion, Leida Maria; Chaves, Valéria Ernestânia

2018-06-01

Several studies have demonstrated that fish oil consumption improves metabolic syndrome and comorbidities, as insulin resistance, nonalcoholic fatty liver disease, dyslipidaemia and hypertension induced by high-fat diet ingestion. Previously, we demonstrated that administration of a fructose-rich diet to rats induces liver lipid accumulation, accompanied by a decrease in liver cytosolic lipases activities. In this study, the effect of replacement of soybean oil by fish oil in a high-fructose diet (FRUC, 60% fructose) for 8 weeks on lipid metabolism in liver and epididymal adipose tissue from rats was investigated. The interaction between fish oil and FRUC diet increased glucose tolerance and decreased serum levels of triacylglycerol (TAG), VLDL-TAG secretion and lipid droplet volume of hepatocytes. In addition, the fish oil supplementation increased the liver cytosolic lipases activities, independently of the type of carbohydrate ingested. Our results firmly establish the physiological regulation of liver cytosolic lipases to maintain lipid homeostasis in hepatocytes. In epididymal adipose tissue, the replacement of soybean oil by fish oil in FRUC diet did not change the tissue weight and lipoprotein lipase activity; however, there was increased basal and insulin-stimulated de novo lipogenesis and glucose uptake. Increased cytosolic lipases activities were observed, despite the decreased basal and isoproterenol-stimulated glycerol release to the incubation medium. These findings suggest that fish oil increases the glycerokinase activity and glycerol phosphorylation from endogenous TAG hydrolysis. Our findings are the first to show that the fish oil ingestion increases cytosolic lipases activities in liver and adipose tissue from rats treated with high-carbohydrate diets. Copyright © 2018. Published by Elsevier Inc.

Allergenicity of bony and cartilaginous fish - molecular and immunological properties.

PubMed

Stephen, J N; Sharp, M F; Ruethers, T; Taki, A; Campbell, D E; Lopata, A L

2017-03-01

Allergy to bony fish is common and probably increasing world-wide. The major heat-stable pan-fish allergen, parvalbumin (PV), has been identified and characterized for numerous fish species. In contrast, there are very few reports of allergic reactions to cartilaginous fish despite widespread consumption. The molecular basis for this seemingly low clinical cross-reactivity between these two fish groups has not been elucidated. PV consists of two distinct protein lineages, α and β. The α-lineage of this protein is predominant in muscle tissue of cartilaginous fish (Chondrichthyes), while β-PV is abundant in muscle tissue of bony fish (Osteichthyes). The low incidence of allergic reactions to ingested rays and sharks is likely due to the lack of molecular similarity, resulting in reduced immunological cross-reactivity between the two PV lineages. Structurally and physiologically, both protein lineages are very similar; however, the amino acid homology is very low with 47-54%. Furthermore, PV from ancient fish species such as the coelacanth demonstrates 62% sequence homology to leopard shark α-PV and 70% to carp β-PV. This indicates the extent of conservation of the PV isoforms lineages across millennia. This review highlights prevalence data on fish allergy and sensitization to fish, and details the molecular diversity of the two protein lineages of the major fish allergen PV among different fish groups, emphasizing the immunological and clinical differences in allergenicity. © 2017 John Wiley & Sons Ltd.

Fish Oil Supplementation and Fatty Acid Synthase Expression in the Prostate: A Randomized Controlled Trial. Addendum

DTIC Science & Technology

2011-07-01

controls, Menendez et al demonstrated that addition of omega-3 fatty acids (-3 FA), docosahexanoic acid ( DHA ), alpha- linolenic acid , and -6 FA, γ...AD_________________ Award Number: W81XWH-04-1-0296 TITLE: Fish Oil Supplementation and Fatty Acid ...COVERED 1 March 2010 – 30 June 2011 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Fish Oil Supplementation and Fatty Acid Synthase Expression in the

Innovative techniques for analyzing the three-dimensional behavioral results from acoustically tagged fish

NASA Astrophysics Data System (ADS)

Steig, Tracey W.; Timko, Mark A.

2005-04-01

Acoustic tags were used to monitor the swimming patterns of downstream migrating salmon smolts approaching various dams on the Columbia River, USA. Downstream migrating yearling chinook (Oncorhynchus tshawytscha), steelhead (Oncorhynchus mykiss), sockeye (Oncorhynchus nerka), and sub-yearling chinook smolts were surgically implanted with acoustic tags. Fish were tracked in three-dimensions as they approached and passed into the turbine intakes, spillways, and surface bypass channel entrances at the dams during the 2004 spring and summer outmigrations. A number of advances in the analysis techniques and software have been made over the past few years. Some of these improvements include the development of various fish density algorithms, stream trace modeling analysis, and advances of three-dimensional animation programs. Three-dimensional tracks of fish approaching the turbine intakes, spillways, and surface bypass channel entrances will be presented. Concentrations of fish passage will be presented as three-dimensional fish densities superimposed over dam structures. Stream trace modeling animation will be presented showing predicted fish passage routes.

Array-based comparative genomic hybridization analysis reveals recurrent chromosomal alterations and prognostic parameters in primary cutaneous large B-cell lymphoma.

PubMed

Dijkman, Remco; Tensen, Cornelis P; Jordanova, Ekaterina S; Knijnenburg, Jeroen; Hoefnagel, Juliette J; Mulder, Aat A; Rosenberg, Carla; Raap, Anton K; Willemze, Rein; Szuhai, Károly; Vermeer, Maarten H

2006-01-10

To evaluate the clinical relevance of genomic aberrations in primary cutaneous large B-cell lymphoma (PCLBCL). Skin biopsy samples of 31 patients with a PCLBCL classified as either primary cutaneous follicle center lymphoma (PCFCL; n = 19) or PCLBCL, leg type (n = 12), according to the WHO-European Organisation for Research and Treatment of Cancer (EORTC) classification, were investigated using array-based comparative genomic hybridization, fluorescence in situ hybridization (FISH), and examination of promoter hypermethylation. The most recurrent alterations in PCFCL were high-level DNA amplifications at 2p16.1 (63%) and deletion of chromosome 14q32.33 (68%). FISH analysis confirmed c-REL amplification in patients with gains at 2p16.1. In PCLBCL, leg type, most prominent aberrations were a high-level DNA amplification of 18q21.31-q21.33 (67%), including the BCL-2 and MALT1 genes as confirmed by FISH, and deletions of a small region within 9p21.3 containing the CDKN2A, CDKN2B, and NSG-x genes. Homozygous deletion of 9p21.3 was detected in five of 12 patients with PCLBCL, leg type, but in zero of 19 patients with PCFCL. Complete methylation of the promoter region of the CDKN2A gene was demonstrated in one PCLBCL, leg type, patient with hemizygous deletion, in one patient without deletion, but in zero of 19 patients with PCFCL. Seven of seven PCLBCL, leg type, patients with deletion of 9p21.3 and/or complete methylation of CDKN2A died as a result of their lymphoma. Our results demonstrate prominent differences in chromosomal alterations between PCFCL and PCLBCL, leg type, that support their classification as separate entities within the WHO-EORTC scheme. Inactivation of CDKN2A by either deletion or methylation of its promoter could be an important prognostic parameter for the group of PCLBCL, leg type.

Intestinal coccidiosis of anadromous and landlocked alewives, Alosa pseudoharengus, caused by Goussia ameliae n. sp. and G. alosii n. sp. (Apicomplexa: Eimeriidae)

PubMed Central

Lovy, Jan; Friend, Sarah E.

2015-01-01

Anadromous alewives, Alosa pseudoharengus, have experienced significant population level declines caused by factors including habitat destruction. Alewives occur in two different life histories, anadromous and landlocked forms. The landlocked alewife evolved from ancestral anadromous populations, resulting in an exclusively freshwater and phenotypically unique form. The occurrence of parasites in a host is linked to the environment, making alewives an ideal model to compare parasitology within a single species with contrasting life histories. Currently, little information exists on the presence and impacts of parasites in these fish populations; the present study sets out to better understand coccidiosis in the threatened anadromous populations and to understand how coccidian parasites compare in both life history forms. The intestinal coccidian, Goussia ameliae n. sp., was described infecting the pyloric cecum of 76% and 86% of young-of-the-year and adult anadromous alewives, respectively, from the Maurice River, New Jersey, USA. The coccidian was found in landlocked alewife populations with a prevalence of 92% and 34% in YOY and adult fish, respectively. An analysis of the small subunit 18S ribosomal RNA gene of G. ameliae from both life history forms demonstrated that the coccidian had 100% sequence identity, confirming the same parasite species in both forms. Though genetic analysis demonstrated G. ameliae to be identical, some differences were observed in sporulation and morphology of the parasite within the two populations. The sporocysts in anadromous populations were shorter and wider, and sporulation timing differed from that of landlocked fish. These differences may either be attributed to differences in the host type or to the sporulation environment. Lastly, alewives from landlocked populations were frequently co-infected with a second coccidian species in the posterior intestine, which occurred at a lower prevalence. This species, G. alosii n. sp., was described based on morphological characters of the sporulated oocysts in fresh parasitological preparations. PMID:25853050

Fish consumption and risk of gastrointestinal cancers: A meta-analysis of cohort studies

PubMed Central

Yu, Xiao-Feng; Zou, Jian; Dong, Jie

2014-01-01

AIM: To assess quantitatively the relationship between fish intake and the incidence of gastrointestinal cancers in a meta-analysis of cohort studies. METHODS: We searched MEDLINE, Embase, Science Citation Index Expanded, and the bibliographies of retrieved articles. Prospective cohort studies were included if they reported relative risks (RRs) and corresponding 95% confidence intervals (CIs) of various cancers with respect to fish intake. When RRs were not available in the published article, they were computed from the exposure distributions. Two investigators extracted the data independently and discrepancies were resolved by discussion with a third investigator. We performed random-effect meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with a 20-g/d increment of fish consumption. RESULTS: Forty-two studies, comprising 27 independent cohorts, met our inclusion criteria. The studies included 2325040 participants and 24115 incident cases of gastrointestinal cancer, with an average follow-up of 13.6 years. Compared with individuals who did not eat, or seldom ate, fish, the pooled RR of gastrointestinal cancers was 0.93 (95%CI: 0.88-0.98) for regular fish consumers, 0.94 (0.89-0.99) for low to moderate fish consumers, and 0.91 (0.84-0.97) for high fish consumers. Overall, a 20-g increase in fish consumption per day was associated with a 2% reduced risk of gastrointestinal cancers (RR = 0.98; 95%CI: 0.96-1.01). In subgroup analyses, we noted that fish consumption was associated with reduced risk of colorectal (RR = 0.93; 95%CI: 0.87-0.99; P < 0.01), esophageal (RR = 0.91; 95%CI: 0.83-0.99; P < 0.05) and hepatocellular cancers (RR = 0.71; 95%CI: 0.48-0.95; P < 0.01). CONCLUSION: This meta-analysis suggested that fish consumption may reduce total gastrointestinal cancer incidence. Inverse relationships were also detected between fish consumption and specific types of cancers. PMID:25386090

Chemical analysis of fish bile extracts for monitoring endocrine disrupting chemical exposure in water: Bisphenol A, alkylphenols, and norethindrone.

PubMed

Wu, Minghong; Pan, Chenyuan; Yang, Ming; Xu, Bentuo; Lei, Xiangjie; Ma, Jing; Cai, Ling; Chen, Jingsi

2016-01-01

The present study determined concentrations of estrogenic bisphenol A (BPA), nonylphenol, octylphenol (4-tert-octylphenol), butylphenol (4-tert-butylphenol), and progestogenic norethindrone by liquid chromatography-tandem mass spectrometry in bile extracts from field fish from the Xin'an River and market fish in Shanghai, China. Compared with the field fish, endocrine disrupting chemical (EDC) concentrations in market fish bile were at relatively high levels with high detectable rates. The average concentrations of BPA, nonylphenol, 4-tert-octylphenol, 4-tert-butylphenol, and norethindrone in field fish bile were 30.1 µg/L, 203 µg/L, 4.69 µg/L, 7.84 µg/L, and 0.514 µg/L, respectively; in market fish bile they were 240 µg/L, 528 µg/L, 76.5 µg/L, 12.8 µg/L, and 5.26 µg/L, respectively; and in the surface water of Xin'an River they were 38.8 ng/L, 7.91 ng/L, 1.98 ng/L, 2.66 ng/L, and 0.116 ng/L, respectively. The average of total estrogenic activity of river water was 3.32 ng/L estradiol equivalents. High bioconcentration factors (BCFs) were discovered for all 5 EDCs (≧998-fold) in field fish bile. Furthermore, the authors analyzed the BCF value of BPA in fish bile after 30-d exposure to environmentally relevant concentrations of BPA in the laboratory, and the analysis revealed that BCF in fish bile (BCF(Fish bile)) changed in an inverse concentration-dependent manner based on the log10-transformed BPA concentration in water. Strikingly, the data from the field study were well fitted within this trend. The data together suggested that analysis of fish bile extracts could be an efficient method for assessing waterborne EDCs exposure for aquatic biota. © 2015 SETAC.

Fish consumption and risk of gastrointestinal cancers: a meta-analysis of cohort studies.

PubMed

Yu, Xiao-Feng; Zou, Jian; Dong, Jie

2014-11-07

To assess quantitatively the relationship between fish intake and the incidence of gastrointestinal cancers in a meta-analysis of cohort studies. We searched MEDLINE, Embase, Science Citation Index Expanded, and the bibliographies of retrieved articles. Prospective cohort studies were included if they reported relative risks (RRs) and corresponding 95% confidence intervals (CIs) of various cancers with respect to fish intake. When RRs were not available in the published article, they were computed from the exposure distributions. Two investigators extracted the data independently and discrepancies were resolved by discussion with a third investigator. We performed random-effect meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with a 20-g/d increment of fish consumption. Forty-two studies, comprising 27 independent cohorts, met our inclusion criteria. The studies included 2325040 participants and 24115 incident cases of gastrointestinal cancer, with an average follow-up of 13.6 years. Compared with individuals who did not eat, or seldom ate, fish, the pooled RR of gastrointestinal cancers was 0.93 (95%CI: 0.88-0.98) for regular fish consumers, 0.94 (0.89-0.99) for low to moderate fish consumers, and 0.91 (0.84-0.97) for high fish consumers. Overall, a 20-g increase in fish consumption per day was associated with a 2% reduced risk of gastrointestinal cancers (RR = 0.98; 95%CI: 0.96-1.01). In subgroup analyses, we noted that fish consumption was associated with reduced risk of colorectal (RR = 0.93; 95%CI: 0.87-0.99; P < 0.01), esophageal (RR = 0.91; 95%CI: 0.83-0.99; P < 0.05) and hepatocellular cancers (RR = 0.71; 95%CI: 0.48-0.95; P < 0.01). This meta-analysis suggested that fish consumption may reduce total gastrointestinal cancer incidence. Inverse relationships were also detected between fish consumption and specific types of cancers.

Molecular markers reveal spatially segregated cryptic species in a critically endangered fish, the common skate (Dipturus batis).

PubMed

Griffiths, Andrew M; Sims, David W; Cotterell, Stephen P; El Nagar, Aliya; Ellis, Jim R; Lynghammar, Arve; McHugh, Matthew; Neat, Francis C; Pade, Nicolas G; Queiroz, Nuno; Serra-Pereira, Bárbara; Rapp, Toby; Wearmouth, Victoria J; Genner, Martin J

2010-05-22

Many sharks and skates are particularly vulnerable to overfishing because of their large size, slow growth, late maturity and low fecundity. In Europe dramatic population declines have taken place in common skate (Dipturus batis L.), one of the largest demersal fish in regional shelf seas, leading to extirpations from substantial parts of its former range. Here we report the discovery of cryptic species in common skate collected from the northeast Atlantic continental shelf. Data from nuclear microsatellite markers indicated two clearly distinct clades and phylogenetic analysis of mitochondrial DNA sequences demonstrated monophyly of each one of them. Capture locations showed evidence of strong spatial segregation, with one taxon occurring mainly in waters off the southern British Isles and around Rockall, while the other was restricted to more northerly shelf waters. These apparently cryptic species showed overlapping substrate and depth preferences, but distributional limits were closely related to temperature gradients, potentially indicating thermal limits to their distributions. This discovery of hidden diversity within a large, critically endangered marine vertebrate demonstrates how marine biodiversity can be underestimated, even in such a relatively well-studied and heavily exploited region.

Molecular markers reveal spatially segregated cryptic species in a critically endangered fish, the common skate (Dipturus batis)

PubMed Central

Griffiths, Andrew M.; Sims, David W.; Cotterell, Stephen P.; El Nagar, Aliya; Ellis, Jim R.; Lynghammar, Arve; McHugh, Matthew; Neat, Francis C.; Pade, Nicolas G.; Queiroz, Nuno; Serra-Pereira, Bárbara; Rapp, Toby; Wearmouth, Victoria J.; Genner, Martin J.

2010-01-01

Many sharks and skates are particularly vulnerable to overfishing because of their large size, slow growth, late maturity and low fecundity. In Europe dramatic population declines have taken place in common skate (Dipturus batis L.), one of the largest demersal fish in regional shelf seas, leading to extirpations from substantial parts of its former range. Here we report the discovery of cryptic species in common skate collected from the northeast Atlantic continental shelf. Data from nuclear microsatellite markers indicated two clearly distinct clades and phylogenetic analysis of mitochondrial DNA sequences demonstrated monophyly of each one of them. Capture locations showed evidence of strong spatial segregation, with one taxon occurring mainly in waters off the southern British Isles and around Rockall, while the other was restricted to more northerly shelf waters. These apparently cryptic species showed overlapping substrate and depth preferences, but distributional limits were closely related to temperature gradients, potentially indicating thermal limits to their distributions. This discovery of hidden diversity within a large, critically endangered marine vertebrate demonstrates how marine biodiversity can be underestimated, even in such a relatively well-studied and heavily exploited region. PMID:20106849

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Expression, purification, crystallization and preliminary X-ray diffraction analysis of nurse shark β2-microglobulin.

PubMed

Lu, Shuangshuang; Yao, Shugang; Chen, Rong; Zhang, Nianzhi; Chen, Jianmin; Gao, Feng; Xia, Chun

2012-04-01

β(2)-Microglobulin (β(2)m) is an essential subunit of the major histocompatibility complex (MHC) class I molecule that helps to stabilize the structure of peptide-MHC I (pMHC I). It is also one of the typical immunoglobulin superfamily (IgSF) molecules in the adaptive immune system (AIS). Sharks belong to the cartilaginous fish, which are the oldest jawed vertebrate ancestors with an AIS to exist in the world. Thus, the study of cartilaginous fish β(2)m would help in understanding the evolution of IgSF molecules. In order to demonstrate this, β(2)m from a cartilaginous fish, nurse shark (Ginglymostoma cirratum), was expressed, refolded, purified and crystallized. Diffraction data were collected to a resolution of 2.3 Å. The crystal belonged to space group P3(2)21, with unit-cell parameters a = b = 88.230, c = 67.146 Å. The crystal structure contained two molecules in the asymmetric unit. The results will provide structural information for study of the evolution of β(2)m and IgSF in the AIS. © 2012 International Union of Crystallography. All rights reserved.

Pressurized liquid extraction and microwave-assisted extraction in the determination of organochlorine pesticides in fish muscle samples.

PubMed

Barriada-Pereira, Mercedes; Iglesias-García, Iván; González-Castro, María J; Muniategui-Lorenzo, Soledad; López-Mahía, Purificación; Prada-Rodríguez, Darío

2008-01-01

This paper describes a comparative study of 2 extraction methods, pressurized liquid extraction (PLE) and microwave-assisted extraction (MAE), for the determination of organochlorine pesticides (OCPs) in fish muscle samples. In both cases, samples were extracted with hexane-acetone (50 + 50), and the extracts were purified by solid-phase extraction using a carbon cartridge as the adsorbent. Pesticides were eluted with hexane-ethyl acetate (80 + 20) and determined by gas chromatography with electron-capture detection. Both methods demonstrated good linearity over the range studied (0.005-0.100 microg/mL). Detection limits ranged from 0.029 to 0.295 mg/kg for PLE and from 0.003 to 0.054 mg/kg for MAE. For most of the pesticides, analytical recoveries with both methods were between 80 and 120%, and the relative standard deviations were < 10%. The proposed methods were shown to be powerful techniques for the extraction of OCPs from fish muscle samples. Although good recovery rates were obtained with both extraction methods, MAE provided advantages with regard to sample handling, cost, analysis time, and solvent consumption. Acceptable validation parameters were obtained although MAE was shown to be more sensitive than PLE.

A unique epidermal mucus lectin identified from catfish (Silurus asotus): first evidence of intelectin in fish skin slime.

PubMed

Tsutsui, Shigeyuki; Komatsu, Yukie; Sugiura, Takaya; Araki, Kyosuke; Nakamura, Osamu

2011-11-01

The present study reports a new type of skin mucus lectin found in catfish Silurus asotus. The lectin exhibited calcium-dependent mannose-binding activity. When mannose eluate from chromatography with mannose-conjugated agarose was analysed by SDS-PAGE, the lectin appeared as a single 35-kDa band. Gel filtration showed that the lectin forms monomers and dimers. A 1216-bp cDNA sequence obtained by RACE-PCR from the skin encoded a 308 amino acid secretory protein with homology to mammalian and fish intelectins. RT-PCR demonstrated that the lectin gene was expressed in the gill, kidney and skin. Subsequent sequencing revealed the presence of an isoform in the gills. Antiserum detected the intelectin protein in club cells in the skin and gill, renal tubules and blood plasma. Although intelectin gene expression was not induced by in vivo bacterial stimulation, the intelectin showed agglutination activity against the pathogenic bacterium Aeromonas salmonicida, suggesting that the lectin plays an important role in self-defence against bacteria in the skin surface of the catfish. These findings represent one of the few examples of characterization and functional analysis of a fish intelectin protein.

Invasive aquarium fish transform ecosystem nutrient dynamics

PubMed Central

Capps, Krista A.; Flecker, Alexander S.

2013-01-01

Trade of ornamental aquatic species is a multi-billion dollar industry responsible for the introduction of myriad fishes into novel ecosystems. Although aquarium invaders have the potential to alter ecosystem function, regulation of the trade is minimal and little is known about the ecosystem-level consequences of invasion for all but a small number of aquarium species. Here, we demonstrate how ecological stoichiometry can be used as a framework to identify aquarium invaders with the potential to modify ecosystem processes. We show that explosive growth of an introduced population of stoichiometrically unique, phosphorus (P)-rich catfish in a river in southern Mexico significantly transformed stream nutrient dynamics by altering nutrient storage and remineralization rates. Notably, changes varied between elements; the P-rich fish acted as net sinks of P and net remineralizers of nitrogen. Results from this study suggest species-specific stoichiometry may be insightful for understanding how invasive species modify nutrient dynamics when their population densities and elemental composition differ substantially from native organisms. Risk analysis for potential aquarium imports should consider species traits such as body stoichiometry, which may increase the likelihood that an invasion will alter the structure and function of ecosystems. PMID:23966642

The Independent Technical Analysis Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duberstein, Corey A.; Ham, Kenneth D.; Dauble, Dennis D.

2007-04-13

The Bonneville Power Administration (BPA) contracted with the Pacific Northwest National Laboratory (PNNL) to provide technical analytical support for system-wide fish passage information (BPA Project No. 2006-010-00). The goal of this project was to produce rigorous technical analysis products using independent analysts and anonymous peer reviewers. In the past, regional parties have interacted with a single entity, the Fish Passage Center to access the data, analyses, and coordination related to fish passage. This project provided an independent technical source for non-routine fish passage analyses while allowing routine support functions to be performed by other well-qualified entities.

Trophic structure of a coastal fish community determined with diet and stable isotope analyses.

PubMed

Malek, A J; Collie, J S; Taylor, D L

2016-09-01

A combination of dietary guild analysis and nitrogen (δ(15) N) and carbon (δ(13) C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ(15) N and δ(13) C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles. © 2016 The Fisheries Society of the British Isles.

Incorporating spatial context into the analysis of salmonid habitat relations: Chapter 18

USGS Publications Warehouse

Torgersen, Christian E.; Baxter, Colden V.; Ebersole, J.L.; Gresswell, Bob; Church, Michael; Biron, Pascale M.; Roy, Andre G.

2012-01-01

In this response to the chapter by Lapointe (this volume), we discuss the question of why it is so difficult to predict salmonid-habitat relations in gravel-bed rivers and streams. We acknowledge that this cannot be an exhaustive treatment of the subject and, thus, identify what we believe are several key issues that demonstrate the necessity of incorporating spatial context into the analysis of fish-habitat data. Our emphasis is on spatial context (i.e., scale and location), but it is important to note that the same principles may be applied with some modification to temporal context, which is beyond the scope of this chapter.

Fish consumption and CHD mortality: an updated meta-analysis of seventeen cohort studies.

PubMed

Zheng, Jusheng; Huang, Tao; Yu, Yinghua; Hu, Xiaojie; Yang, Bin; Li, Duo

2012-04-01

Results of studies on fish consumption and CHD mortality are inconsistent. The present updated meta-analysis was conducted to investigate the up-to-date pooling effects. A random-effects model was used to pool the risk estimates. Generalized least-squares regression and restricted cubic splines were used to assess the possible dose-response relationship. Subgroup analyses were conducted to examine the sources of heterogeneity. PubMed and ISI Web of Science databases up to September 2010 were searched and secondary referencing qualified for inclusion in the study. Seventeen cohorts with 315,812 participants and average follow-up period of 15·9 years were identified. Compared with the lowest fish intake (<1 serving/month or 1-3 servings/month), the pooled relative risk (RR) of fish intake on CHD mortality was 0·84 (95% CI 0·75, 0·95) for low fish intake (1 serving/week), 0·79 (95% CI 0·67, 0·92) for moderate fish intake (2-4 servings/week) and 0·83 (95% CI 0·68, 1·01) for high fish intake (>5 servings/week). The dose-response analysis indicated that every 15 g/d increment of fish intake decreased the risk of CHD mortality by 6% (RR = 0·94; 95% CI 0·90, 0·98). The method of dietary assessment, gender and energy adjustment affected the results remarkably. Our results indicate that either low (1 serving/week) or moderate fish consumption (2-4 servings/week) has a significantly beneficial effect on the prevention of CHD mortality. High fish consumption (>5 servings/week) possesses only a marginally protective effect on CHD mortality, possibly due to the limited studies included in this group.

Transcriptomic analyses of tributyltin-induced sexual dimorphisms in rare minnow (Gobiocypris rarus) brains.

PubMed

Zhang, Ji-Liang; Liu, Min; Zhang, Chun-Nuan; Li, Er-Chao; Fan, Ming-Zhen; Huang, Mao-Xian

2018-07-30

The brain of fish displays sexual dimorphisms and exhibits remarkable sexual plasticity throughout their life span. Although reproductive toxicity of tributyltin (TBT) in fish is well documented in fish, it remains unknown whether TBT interrupts sexual dimorphisms of fish brains. In this work, brain transcriptomic profiles of rare minnow (Gobiocypris rarus) was characterized and sex-biased genes were identified using RNA sequencing. Functional annotation and enrichment analysis were performed to reveal differences of gene products and pathways between the brains of male and female fish. Furthermore, transcriptomic responses of male and female brains to TBT at 10 ng/L were also investigated to understand effects of TBT on brain sexual dimorphisms. Only 345 male-biased and 273 female-biased genes were found in the brains. However, significant female-biased pathways of circadian rhythm and phototransduction were identified in the brains by enrichment analysis. Interestingly, following TBT exposure in the female fish, the circadian rhythm pathway was significantly disrupted based on enrichment analysis, while in the male fish, the phototransduction pathway was significantly disrupted. In the female fish, expression of genes (Per, Cry, Rev-Erb α, Ror, Dec and CK1δ/ε) in the circadian rhythm pathway was down-regulated after TBT exposure; while in the male fish, expression of genes (Rec, GNAT1_2, GNGT1, Rh/opsin, PDE and Arr) in the phototransduction pathway was up-regulated after TBT exposure. Overall, our results not only provide key data on the molecular basis of brain sexual dimorphisms in fish, but also offer valuable resources for investigating molecular mechanisms by which environmental chemicals might influence brain sexual plasticity. Copyright © 2018 Elsevier Inc. All rights reserved.

Determining the trophic guilds of fishes and macroinvertebrates in a seagrass food web

USGS Publications Warehouse

Luczkovich, J.J.; Ward, G.P.; Johnson, J.C.; Christian, R.R.; Baird, D.; Neckles, H.; Rizzo, W.M.

2002-01-01

We established trophic guilds of macroinvertebrate and fish taxa using correspondence analysis and a hierarchical clustering strategy for a seagrass food web in winter in the northeastern Gulf of Mexico. To create the diet matrix, we characterized the trophic linkages of macroinvertebrate and fish taxa present in Halodule wrightii seagrass habitat areas within the St. Marks National Wildlife Refuge (Florida) using binary data, combining dietary links obtained from relevant literature for macroinvertebrates with stomach analysis of common fishes collected during January and February of 1994. Heirarchical average-linkage cluster analysis of the 73 taxa of fishes and macroinvertebrates in the diet matrix yielded 14 clusters with diet similarity ??? 0.60. We then used correspondence analysis with three factors to jointly plot the coordinates of the consumers (identified by cluster membership) and of the 33 food sources. Correspondence analysis served as a visualization tool for assigning each taxon to one of eight trophic guilds: herbivores, detritivores, suspension feeders, omnivores, molluscivores, meiobenthos consumers, macrobenthos consumers, and piscivores. These trophic groups, cross-classified with major taxonomic groups, were further used to develop consumer compartments in a network analysis model of carbon flow in this seagrass ecosystem. The method presented here should greatly improve the development of future network models of food webs by providing an objective procedure for aggregating trophic groups.

Chromosomal analysis of blastocyst derived from monopronucleated ICSI zygotes: approach by double trophectoderm biopsy.

PubMed

Mateo, Silvia; Vidal, Francesca; Coll, Lluc; Veiga, Anna; Boada, Montserrat

2017-09-01

This study aims to increase the knowledge about monopronucleated ICSI-derived blastocysts, analyzing trophectoderm biopsies by aCGH and FISH to evaluate their chromosome constitution. Fifteen monopronucleated ICSI-derived blastocysts were studied. Double trophectoderm biopsy was performed and analyzed by FISH and aCGH. The blastocysts were classified according to chromosome constitution. Disagreements between the two techniques were assessed. Results obtained after FISH and aCGH analyses showed the following: 20% (3/15) and 60% (9/15) diploid females, respectively; 26.7% (4/15) and 26.7% (4/15) diploid males, respectively; and 53.3% (8/15) and 13.3% (2/15) mosaics, respectively. No mosaic male embryos were found using FISH or aCGH. There were disagreements in 40% (6/15) of the cases due to the higher detection of mosaicism by FISH compared to aCGH. The combination of FISH and aCGH has been shown to be a suitable approach to increase the knowledge about monopronucleated ICSI-derived embryos. FISH analysis of blastocysts derived from monopronucleated ICSI zygotes enabled us to conclude that aCGH underestimates haploidy. Some diploid embryos diagnosed by aCGH are in fact mosaic. In cases where these embryos would be used for reproductive purposes, extra analysis of parental genome origin is recommended.

Poultry and fish intake and risk of esophageal cancer: A meta-analysis of observational studies.

PubMed

Jiang, Gengxi; Li, Bailing; Liao, Xiaohong; Zhong, Chongjun

2016-03-01

Mixed results regarding the association between white meat (including poultry and fish) intake and the risk of esophageal cancer (EC) have been reported. We performed a meta-analysis to provide a quantitative assessment of this association. Relevant studies were identified in MEDLINE until December 31, 2012. Summary relative risks (SRRs) with 95% confidence intervals (CIs) were pooled with a random-effects model. A total of 20 articles, including 3990 cases with EC, were included in this meta-analysis. Compared to individuals with the lowest level of fish intake, individuals with the highest fish intake were found to have reduced risk of EC (SRRs = 0.69; 95% CIs: 0.57-0.85), while poultry intake was not associated with EC (SRRs = 0.83; 95% CIs: 0.62-1.12). Total fish consumption is associated with reduced esophageal squamous cell carcinoma (ESCC) risk, while poultry consumption was not associated with ESCC risk. Additionally, neither poultry nor fish consumption was associated with esophageal adenocarcinoma risk. Our results suggest that fish consumption may have a potential role in EC prevention, while poultry intake has no effect. However, because the majority of data was from case-control studies, further well-designed prospective studies are warranted. © 2013 Wiley Publishing Asia Pty Ltd.

Black liquor and the hangover effect: fish assemblage recovery dynamics following a pulse disturbance

PubMed Central

Piller, Kyle R; Geheber, Aaron D

2015-01-01

Anthropogenic perturbations impact aquatic systems causing wide-ranging responses, from assemblage restructuring to assemblage recovery. Previous studies indicate the duration and intensity of disturbances play a role in the dynamics of assemblage recovery. In August 2011, the Pearl River, United States, was subjected to a weak black liquor spill from a paper mill which resulted in substantial loss of fish in a large stretch of the main channel. We quantified resilience and recovery of fish assemblage structure in the impacted area following the event. We compared downstream (impacted) assemblages to upstream (unimpacted) assemblages to determine initial impacts on structure. Additionally, we incorporated historic fish collections (1988–2011) to examine impacts on assemblage structure across broad temporal scales. Based on NMDS, upstream and downstream sites generally showed similar assemblage structure across sample periods with the exception of the 2 months postdischarge, where upstream and downstream sites visually differed. Multivariate analysis of variance (PERMANOVA) indicated significant seasonal variation among samples, but found no significant interaction between impacted and unimpacted assemblages following the discharge event. However, multivariate dispersion (MVDISP) showed greater variance among assemblage structure following the discharge event. These results suggest that 2 months following the disturbance represent a time period of stochasticity in regard to assemblage structure dynamics, and this was followed by rapid recovery. We term this dynamic the “hangover effect” as it represents the time frame from the cessation of the perturbation to the assemblage's return to predisturbance conditions. The availability and proximity of tributaries and upstream refugia, which were not affected by the disturbance, as well as the rapid recovery of abiotic parameters likely played a substantial role in assemblage recovery. This study not only demonstrates rapid recovery in an aquatic system, but further demonstrates the value of continuous, long-term, data collections which enhance our understanding of assemblage dynamics. PMID:26120432

Mechanosensation is evolutionarily tuned to locomotor mechanics

PubMed Central

Aiello, Brett R.; Westneat, Mark W.; Hale, Melina E.

2017-01-01

The biomechanics of animal limbs has evolved to meet the functional demands for movement associated with different behaviors and environments. Effective movement relies not only on limb mechanics but also on appropriate mechanosensory feedback. By comparing sensory ability and mechanics within a phylogenetic framework, we show that peripheral mechanosensation has evolved with limb biomechanics, evolutionarily tuning the neuromechanical system to its functional demands. We examined sensory physiology and mechanics of the pectoral fins, forelimb homologs, in the fish family Labridae. Labrid fishes exhibit extraordinary morphological and behavioral diversity and use pectoral fin-based propulsion with fins ranging in shape from high aspect ratio (AR) wing-like fins to low AR paddle-like fins. Phylogenetic character analysis demonstrates that high AR fins evolved independently multiple times in this group. Four pairs of species were examined; each included a plesiomorphic low AR and a high AR species. Within each species pair, the high AR species demonstrated significantly stiffer fin rays in comparison with the low AR species. Afferent sensory nerve activity was recorded during fin ray bending. In all cases, afferents of stiffer fins were more sensitive at lower displacement amplitudes, demonstrating mechanosensory tuning to fin mechanics and a consistent pattern of correlated evolution. We suggest that these data provide a clear example of parallel evolution in a complex neuromechanical system, with a strong link between multiple phenotypic characters: pectoral fin shape, swimming behavior, fin ray stiffness, and mechanosensory sensitivity. PMID:28396411

CLOSED-LOOP STRIPPING ANALYSIS (CLSA) OF SYNTHETIC MUSK COMPOUNDS FROM FISH TISSUES WITH MEASUREMENT BY GAS CHROMATOGRAPHY-MASS SPECTROMETRY WITH SELECTED-ION MONITORING

EPA Science Inventory

Synthetic musk compounds have been found in surface water, fish tissues, and human breast milk. Current techniques for separating these compounds from fish tissues require tedious sample clean-upprocedures A simple method for the deterrnination of these compounds in fish tissues ...

Socio-Economics of Lake Victoria's Fisheries: An Analysis of the Shifting Roles and Status of Women Fish Traders

ERIC Educational Resources Information Center

Craig, Heather

2007-01-01

Fishing industries around the world are currently undergoing a process of industrialization and commercialization. A similar story is unfolding in many fishing communities: large-scale industrial fishers who possess enormous capital and advanced technologies are threatening the lives of small-scale fisherfolk. The fishing industry in Lake Victoria…

The stress hormone cortisol: a (co)regulator of biofilm formation in Flavobacterum columnare?

USDA-ARS?s Scientific Manuscript database

Previously, we demonstrated a direct effect of cortisol on Flavobacterium columnare, a notorious fish pathogenic bacterium, engendering a new perspective to bacteria-host communication in aquaculture. As stressed fish harbour increased cortisol levels in the skin and gill mucus, highly virulent F. c...

Cortisol responsiveness to stress in channel catfish influences susceptibility to Edwardsiella ictaluri

USDA-ARS?s Scientific Manuscript database

Stress is unavoidable in aquaculture and hence strains of fish that are resilient and adaptable to stress need to be developed. Past studies have demonstrated that fish subjected to handling stress or poor water quality had reduced ability to resist pathogens. Cortisol is the primary stress hormone...

Plasma cortisol stress response in channel catfish, Ictalurus punctatus influences susceptibility to Edwardeseilla ictaluri

USDA-ARS?s Scientific Manuscript database

Cortisol is a primary stress hormone in fish as its plasma variations correlate with the occurrence of various stressful situations. Past studies have demonstrated that fish subjected to handling stress or poor water quality had a reduced ability to resist pathogens. Channel catfish fingerlings th...

Effects of Impulsive Pile-Driving Exposure on Fishes.

PubMed

Casper, Brandon M; Carlson, Thomas J; Halvorsen, Michele B; Popper, Arthur N

2016-01-01

Six species of fishes were tested under aquatic far-field, plane-wave acoustic conditions to answer several key questions regarding the effects of exposure to impulsive pile driving. The issues addressed included which sound levels lead to the onset of barotrauma injuries, how these levels differ between fishes with different types of swim bladders, the recovery from barotrauma injuries, and the potential effects exposure might have on the auditory system. The results demonstrate that the current interim criteria for pile-driving sound exposures are 20 dB or more below the actual sound levels that result in the onset of physiological effects on fishes.

Irradiation of fish fillets: Relation of vapor phase reactions to storage quality

USGS Publications Warehouse

Spinelli, J.; Dollar, A.M.; Wedemeyer, G.A.; Gallagher, E.C.

1969-01-01

Fish fillets irradiated under air, nitrogen, oxygen, or carbon dioxide atmospheres developed rancidlike flavors when they were stored at refrigerated temperatures. Packing and irradiating under vacuum or helium prevented development of off-flavors during storage.Significant quantities of nitrate and oxidizing substances were formed when oxygen, nitrogen, or air were present in the vapor or liquid phases contained in a Pyrex glass model system exposed to ionizing radiation supplied by a 60Co source. It was demonstrated that the delayed flavor changes that occur in stored fish fillets result from the reaction of vapor phase radiolysis products and the fish tissue substrates.

Do invasive corals alter coral reef processes? An empirical approach evaluating reef fish trophic interactions.

PubMed

Miranda, Ricardo J; Nunes, José de Anchieta C C; Mariano-Neto, Eduardo; Sippo, James Z; Barros, Francisco

2018-07-01

Understanding how invasive species affect key ecological interactions and ecosystem processes is imperative for the management of invasions. We evaluated the effects of invasive corals (Tubastraea spp.) on fish trophic interactions in an Atlantic coral reef. Remote underwater video cameras were used to examine fish foraging activity (bite rates and food preferences) on invasive cover levels. Using a model selection approach, we found that fish feeding rates declined with increased invasive cover. For Roving Herbivores (RH) and Sessile Invertivores (SI), an abrupt reduction of fish feeding rates corresponded with higher invasive cover, while feeding rates of Territorial Herbivores (TH) and Mobile Invertivores (MI) decreased linearly with cover increase. Additionally, some fish trophic groups, such as RH, SI and Omnivores (OM), had lower densities in reef sections with high invasive cover. These findings demonstrate that invasive corals negatively impact fish-benthic interactions, and could potentially alter existing trophic relationships in reef ecosystems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Spatio-temporal dynamics of a fish spawning aggregation and its fishery in the Gulf of California

PubMed Central

Erisman, Brad; Aburto-Oropeza, Octavio; Gonzalez-Abraham, Charlotte; Mascareñas-Osorio, Ismael; Moreno-Báez, Marcia; Hastings, Philip A.

2012-01-01

We engaged in cooperative research with fishers and stakeholders to characterize the fine-scale, spatio-temporal characteristics of spawning behavior in an aggregating marine fish (Cynoscion othonopterus: Sciaenidae) and coincident activities of its commercial fishery in the Upper Gulf of California. Approximately 1.5–1.8 million fish are harvested annually from spawning aggregations of C. othonopterus during 21–25 days of fishing and within an area of 1,149 km2 of a biosphere reserve. Spawning and fishing are synchronized on a semi-lunar cycle, with peaks in both occurring 5 to 2 days before the new and full moon, and fishing intensity and catch are highest at the spawning grounds within a no-take reserve. Results of this study demonstrate the benefits of combining GPS data loggers, fisheries data, biological surveys, and cooperative research with fishers to produce spatio-temporally explicit information relevant to the science and management of fish spawning aggregations and the spatial planning of marine reserves. PMID:22359736

Near-resonance scattering from arrays of artificial fish swimbladders.

PubMed

Nero, R W; Feuillade, C; Thompson, C H; Love, R H

2007-01-01

The air-filled swimbladders of fish resonate like damped air bubbles, and are very efficient acoustic scatterers at low to mid frequencies (typically <20 kHz). Scattering experiments were performed on an artificial "fish school" constructed from polyethylene bubbles. A mathematical model, developed to describe near-resonance backscattering from schooling fish [J. Acoust. Soc. Am. 99, 196-208 (1996)], was used to analyze the physical behavior for three different arrays of these bubbles. The measurements gave excellent agreement with the model, showing that coupled-resonance and interference effects cause the frequency response of tightly packed arrays, with spacing corresponding to the order of a body length for fish, to differ significantly from those of more dispersed arrays. As the array spacing is increased to the equivalent of several body lengths, these effects rapidly diminish. The results of this comparison demonstrate that, at low to mid frequencies, coupled resonance and interference effects are likely in schooling fish, and need to be considered in applications of underwater acoustic methods to the study of fish populations.

Influence of clove oil and eugenol on muscle contraction of silkworm (Bombyx mori).

PubMed

Kheawfu, Kantaporn; Pikulkaew, Surachai; Hamamoto, Hiroshi; Sekimizu, Kazuhisa; Okonogi, Siriporn

2017-05-30

Clove oil is used in fish anesthesia and expected to have a mechanism via glutamic receptor. The present study explores the activities of clove oil and its major compound, eugenol, in comparison with L-glutamic acid on glutamic receptor of silkworm muscle and fish anesthesia. It was found that clove oil and eugenol had similar effects to L-glutamic acid on inhibition of silkworm muscle contraction after treated with D-glutamic acid and kainic acid. Anesthetic activity of the test samples was investigated in goldfish. The results demonstrated that L-glutamic acid at 20 and 40 mM could induce the fish to stage 3 of anesthesia that the fish exhibited total loss of equilibrium and muscle tone, whereas clove oil and eugenol at 60 ppm could induce the fish to stage 4 of anesthesia that the reflex activity of the fish was lost. These results suggest that clove oil and eugenol have similar functional activities and mechanism to L-glutamic acid on muscle contraction and fish anesthesia.

Combined effects of fishing and oil spills on marine fish: Role of stock demographic structure for offspring overlap with oil.

PubMed

Stige, Leif Chr; Ottersen, Geir; Yaragina, Natalia A; Vikebø, Frode B; Stenseth, Nils Chr; Langangen, Øystein

2018-04-01

It has been proposed that the multiple pressures of fishing and petroleum activities impact fish stocks in synergy, as fishing-induced demographic changes in a stock may lead to increased sensitivity to detrimental effects of acute oil spills. High fishing pressure may erode the demographic structure of fish stocks, lead to less diverse spawning strategies, and more concentrated distributions of offspring in space and time. Hence an oil spill may potentially hit a larger fraction of a year-class of offspring. Such a link between demographic structure and egg distribution was recently demonstrated for the Northeast Arctic stock of Atlantic cod for years 1959-1993. We here estimate that this variation translates into a two-fold variation in the maximal proportion of cod eggs potentially exposed to a large oil spill. With this information it is possible to quantitatively account for demographic structure in prospective studies of population effects of possible oil spills. Copyright © 2018 Elsevier Ltd. All rights reserved.

Facial Recognition in a Group-Living Cichlid Fish.

PubMed

Kohda, Masanori; Jordan, Lyndon Alexander; Hotta, Takashi; Kosaka, Naoya; Karino, Kenji; Tanaka, Hirokazu; Taniyama, Masami; Takeyama, Tomohiro

2015-01-01

The theoretical underpinnings of the mechanisms of sociality, e.g. territoriality, hierarchy, and reciprocity, are based on assumptions of individual recognition. While behavioural evidence suggests individual recognition is widespread, the cues that animals use to recognise individuals are established in only a handful of systems. Here, we use digital models to demonstrate that facial features are the visual cue used for individual recognition in the social fish Neolamprologus pulcher. Focal fish were exposed to digital images showing four different combinations of familiar and unfamiliar face and body colorations. Focal fish attended to digital models with unfamiliar faces longer and from a further distance to the model than to models with familiar faces. These results strongly suggest that fish can distinguish individuals accurately using facial colour patterns. Our observations also suggest that fish are able to rapidly (≤ 0.5 sec) discriminate between familiar and unfamiliar individuals, a speed of recognition comparable to primates including humans.

Design and demonstration of a fish robot actuated by a SMA-driven actuation system

NASA Astrophysics Data System (ADS)

Le, Chan H.; Nguyen, Quang S.; Park, Hoon C.

2010-04-01

This paper presents a concept of a fish robot actuated by an SMA-based actuator. The bending-type actuator system is composed of a 0.1mm diameter SMA wire and a 0.5mm thick glass/epoxy strip. The SMA wire is installed to the bent composite strip. The actuator can produce about 200gf of blocking force and 3.5mm displacement at the center of the glass/epoxy strip. The bending motion of the actuator is converted into the tail-beat motion of a fish robot through a linkage system. The fish robot is evaluated by measuring the tail-beat angle, swimming speed and thrust produced by the fish robot. The tail-beat angle is about 20° and the maximum swimming speed is about 1.6cm/s. The measured thrust is about 0.4gf when the fish robot is operated at 0.9Hz.

Conservation of Toll-like receptor signaling pathways in teleost fish

USGS Publications Warehouse

Purcell, M.K.; Smith, K.D.; Aderem, A.; Hood, L.; Winton, J.R.; Roach, J.C.

2006-01-01

In mammals, toll-like receptors (TLR) recognize ligands, including pathogen-associated molecular patterns (PAMPs), and respond with ligand-specific induction of genes. In this study, we establish evolutionary conservation in teleost fish of key components of the TLR-signaling pathway that act as switches for differential gene induction, including MYD88, TIRAP, TRIF, TRAF6, IRF3, and IRF7. We further explore this conservation with a molecular phylogenetic analysis of MYD88. To the extent that current genomic analysis can establish, each vertebrate has one ortholog to each of these genes. For molecular tree construction and phylogeny inference, we demonstrate a methodology for including genes with only partial primary sequences without disrupting the topology provided by the high-confidence full-length sequences. Conservation of the TLR-signaling molecules suggests that the basic program of gene regulation by the TLR-signaling pathway is conserved across vertebrates. To test this hypothesis, leukocytes from a model fish, rainbow trout (Oncorhynchus mykiss), were stimulated with known mammalian TLR agonists including: diacylated and triacylated forms of lipoprotein, flagellin, two forms of LPS, synthetic double-stranded RNA, and two imidazoquinoline compounds (loxoribine and R848). Trout leukocytes responded in vitro to a number of these agonists with distinct patterns of cytokine expression that correspond to mammalian responses. Our results support the key prediction from our phylogenetic analyses that strong selective pressure of pathogenic microbes has preserved both TLR recognition and signaling functions during vertebrate evolution.

Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management

PubMed Central

McKechnie, Iain; Yang, Dongya Y.

2018-01-01

Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory. PMID:29438388

Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators.

PubMed

Chiao, Chuan-Chin; Wickiser, J Kenneth; Allen, Justine J; Genter, Brock; Hanlon, Roger T

2011-05-31

Camouflage is a widespread phenomenon throughout nature and an important antipredator tactic in natural selection. Many visual predators have keen color perception, and thus camouflage patterns should provide some degree of color matching in addition to other visual factors such as pattern, contrast, and texture. Quantifying camouflage effectiveness in the eyes of the predator is a challenge from the perspectives of both biology and optical imaging technology. Here we take advantage of hyperspectral imaging (HSI), which records full-spectrum light data, to simultaneously visualize color match and pattern match in the spectral and the spatial domains, respectively. Cuttlefish can dynamically camouflage themselves on any natural substrate and, despite their colorblindness, produce body patterns that appear to have high-fidelity color matches to the substrate when viewed directly by humans or with RGB images. Live camouflaged cuttlefish on natural backgrounds were imaged using HSI, and subsequent spectral analysis revealed that most reflectance spectra of individual cuttlefish and substrates were similar, rendering the color match possible. Modeling color vision of potential di- and trichromatic fish predators of cuttlefish corroborated the spectral match analysis and demonstrated that camouflaged cuttlefish show good color match as well as pattern match in the eyes of fish predators. These findings (i) indicate the strong potential of HSI technology to enhance studies of biological coloration and (ii) provide supporting evidence that cuttlefish can produce color-coordinated camouflage on natural substrates despite lacking color vision.

Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis

PubMed Central

2009-01-01

Background The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck (Anas platyrhynchos), an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu. Results We provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey. Conclusion Our results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots"). Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies. PMID:19656363

Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management.

PubMed

Rodrigues, Antonia T; McKechnie, Iain; Yang, Dongya Y

2018-01-01

Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.

Estimating the impact of oyster restoration scenarios on transient fish production

USGS Publications Warehouse

McCoy, Elizabeth; Borrett, Stuart R.; LaPeyre, Megan K.; Peterson, Bradley J.

2017-01-01

Oyster reef restoration projects are increasing in number both to enhance oyster density and to retain valuable ecosystem services provided by oyster reefs. Although some oyster restoration projects have demonstrated success by increasing density and biomass of transient fish, it still remains a challenge to quantify the effects of oyster restoration on transient fish communities. We developed a bioenergetics model to assess the impact of selected oyster reef restoration scenarios on associated transient fish species. We used the model to analyze the impact of changes in (1) oyster population carrying capacity; (2) oyster population growth rate; and (3) diet preference of transient fish on oyster reef development and associated transient fish species. Our model results indicate that resident fish biomass is directly affected by oyster restoration and oyster biomass, and oyster restoration can have cascading impacts on transient fish biomass. Furthermore, the results highlight the importance of a favorable oyster population growth rate during early restoration years, as it can lead to rapid increases in mean oyster biomass and biomass of transient fish species. The model also revealed that a transient fish's diet solely dependent on oyster reef-derived prey could limit the biomass of transient fish species, emphasizing the importance of habitat connectivity in estuarine areas to enhance transient fish species biomass. Simple bioenergetics models can be developed to understand the dynamics of a system and make qualitative predictions of management and restoration scenarios.

Demonstration of toxicity to fish and to mammalian cells by Pfiesteria species: Comparison of assay methods and strains

PubMed Central

Burkholder, JoAnn M.; Gordon, Andrew S.; Moeller, Peter D.; Law, J. Mac; Coyne, Kathryn J.; Lewitus, Alan J.; Ramsdell, John S.; Marshall, Harold G.; Deamer, Nora J.; Cary, S. Craig; Kempton, Jason W.; Morton, Steven L.; Rublee, Parke A.

2005-01-01

Toxicity and its detection in the dinoflagellate fish predators Pfiesteria piscicida and Pfiesteria shumwayae depend on the strain and the use of reliable assays. Two assays, standardized fish bioassays (SFBs) with juvenile fish and fish microassays (FMAs) with larval fish, were compared for their utility to detect toxic Pfiesteria. The comparison included strains with confirmed toxicity, negative controls (noninducible Pfiesteria strains and a related nontoxic cryptoperidiniopsoid dinoflagellate), and P. shumwayae strain CCMP2089, which previously had been reported as nontoxic. SFBs, standardized by using toxic Pfiesteria (coupled with tests confirming Pfiesteria toxin) and conditions conducive to toxicity expression, reliably detected actively toxic Pfiesteria, but FMAs did not. Pfiesteria toxin was found in fish- and algae-fed clonal Pfiesteria cultures, including CCMP2089, but not in controls. In contrast, noninducible Pfiesteria and cryptoperidiniopsoids caused no juvenile fish mortality in SFBs even at high densities, and low larval fish mortality by physical attack in FMAs. Filtrate from toxic strains of Pfiesteria spp. in bacteria-free media was cytotoxic. Toxicity was enhanced by bacteria and other prey, especially live fish. Purified Pfiesteria toxin extract adversely affected mammalian cells as well as fish, and it caused fish death at environmentally relevant cell densities. These data show the importance of testing multiple strains when assessing the potential for toxicity at the genus or species level, using appropriate culturing techniques and assays. PMID:15728353

Influence of Melatonin on the Immune System of Fish: A Review

PubMed Central

Esteban, M. Ángeles; Cuesta, Alberto; Chaves-Pozo, Elena; Meseguer, José

2013-01-01

Endocrine-immune system interactions have been widely demonstrated in mammals, whereas in fish, these relationships remain unclear. Of the organs that constitute the endocrine system, the pineal gland and its secretory product melatonin act in the synchronization of daily and seasonal rhythms in most vertebrates, including fish. Seasonal differences in immunocompetence and disease prevalence have been well documented in humans. Seasonality also strongly influences the life history of fish by controlling the timing of physiological events, such as reproduction, food intake, locomotor activity, and growth performance. Apart from its synchronizing capabilities, the role of melatonin in physiological processes in fish is not thoroughly understood. The purpose of this review is to summarize current studies on the effects of melatonin on the fish immune system. These studies suggest that melatonin represents an important component of fish endocrine-immune system interactions. The elucidation of the defense mechanisms of fish will facilitate the development of health management tools to support the growing finfish aquaculture industry as well as address questions concerning the origins and evolution of the immune system in vertebrates. PMID:23579958

Accumulation by fish of contaminants released from dredged sediments

USGS Publications Warehouse

Seelye, James G.; Hesselberg, Robert J.; Mac, Michael J.

1982-01-01

Inasmuch as the process of dredging and disposing of dredged materials causes a resuspension of these materials and an increase in bioavailability of associated contaminants, we conducted a series of experiments to examine the potential accumulation by fish of contaminants from suspended sediments. In the first experiment we compared accumulation of contaminants by yellow perch of hatchery and lake origin and found that after 10 days of exposure to nonaerated sediments, fish of hatchery origin accumulated PCBs and Fe, while fish of lake origin accumulated As, Cr, Fe, and Na. Two additional exposures were conducted to evaluate the effects of aerating the sediments prior to measuring bioavailability of associated contaminants. Fish of hatchery origin exposed to nonaerated sediments for 10 days accumulated PCBs and Hg, while fish of hatchery origin exposed to aerated sediments for 10 days accumulated PCBs, DDE, Zn, Fe, Cs, and Se. These results demonstrated not only the potential for uptake of contaminants by fish as a result of dredging but also the potential utility of fish bioassays in evaluating proposed dredging operations.

Influence of melatonin on the immune system of fish: a review.

PubMed

Esteban, M Ángeles; Cuesta, Alberto; Chaves-Pozo, Elena; Meseguer, José

2013-04-11

Endocrine-immune system interactions have been widely demonstrated in mammals, whereas in fish, these relationships remain unclear. Of the organs that constitute the endocrine system, the pineal gland and its secretory product melatonin act in the synchronization of daily and seasonal rhythms in most vertebrates, including fish. Seasonal differences in immunocompetence and disease prevalence have been well documented in humans. Seasonality also strongly influences the life history of fish by controlling the timing of physiological events, such as reproduction, food intake, locomotor activity, and growth performance. Apart from its synchronizing capabilities, the role of melatonin in physiological processes in fish is not thoroughly understood. The purpose of this review is to summarize current studies on the effects of melatonin on the fish immune system. These studies suggest that melatonin represents an important component of fish endocrine-immune system interactions. The elucidation of the defense mechanisms of fish will facilitate the development of health management tools to support the growing finfish aquaculture industry as well as address questions concerning the origins and evolution of the immune system in vertebrates.

Global trade in ornamental fish from an Australian perspective: the case for revised import risk analysis and management strategies.

PubMed

Whittington, R J; Chong, R

2007-09-14

Over 1 billion ornamental fish comprising more than 4000 freshwater and 1400 marine species are traded internationally each year, with 8-10 million imported into Australia alone. Compared to other commodities, the pathogens and disease translocation risks associated with this pattern of trade have been poorly documented. The aim of this study was to conduct an appraisal of the effectiveness of risk analysis and quarantine controls as they are applied according to the Sanitary and Phytosanitary (SPS) agreement in Australia. Ornamental fish originate from about 100 countries and hazards are mostly unknown; since 2000 there have been 16-fold fewer scientific publications on ornamental fish disease compared to farmed fish disease, and 470 fewer compared to disease in terrestrial species (cattle). The import quarantine policies of a range of countries were reviewed and classified as stringent or non-stringent based on the levels of pre-border and border controls. Australia has a stringent policy which includes pre-border health certification and a mandatory quarantine period at border of 1-3 weeks in registered quarantine premises supervised by government quarantine staff. Despite these measures there have been many disease incursions as well as establishment of significant exotic viral, bacterial, fungal, protozoal and metazoan pathogens from ornamental fish in farmed native Australian fish and free-living introduced species. Recent examples include Megalocytivirus and Aeromonas salmonicida atypical strain. In 2006, there were 22 species of alien ornamental fish with established breeding populations in waterways in Australia and freshwater plants and molluscs have also been introduced, proving a direct transmission pathway for establishment of pathogens in native fish species. Australia's stringent quarantine policies for imported ornamental fish are based on import risk analysis under the SPS agreement but have not provided an acceptable level of protection (ALOP) consistent with government objectives to prevent introduction of pests and diseases, promote development of future aquaculture industries or maintain biodiversity. It is concluded that the risk analysis process described by the Office International des Epizooties under the SPS agreement cannot be used in a meaningful way for current patterns of ornamental fish trade. Transboundary disease incursions will continue and exotic pathogens will become established in new regions as a result of the ornamental fish trade, and this will be an international phenomenon. Ornamental fish represent a special case in live animal trade where OIE guidelines for risk analysis need to be revised. Alternatively, for countries such as Australia with implied very high ALOP, the number of species traded and the number of sources permitted need to be dramatically reduced to facilitate hazard identification, risk assessment and import quarantine controls.