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Sample records for fish diversion screen

  1. Washington Phase II Fish Diversion Screen Evaluations in the Yakima River Basin, 1998.

    Energy Technology Data Exchange (ETDEWEB)

    Blanton, S.L.; McMichael, Geoffrey A.; Neitzel, D.A.

    1999-12-01

    Pacific Northwest National Laboratory (PNNL) evaluated 19 Phase II screen sites in the Yakima River Basin as part of a multi-year study for the Bonneville Power Administration (BPA) on the effectiveness of fish screening devices. The sites were examined to determine if they were being effectively operated and maintained to provide fish a safe, efficient return to the Yakima River.

  2. Washington Phase II Fish Diversion Screen Evaluations in the Yakima River Basin, 2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Carter, J.; McMichael, G.; Chamness, M. (Pacific Northwest National Laboratory)

    2003-01-01

    In 2002, the Pacific Northwest National Laboratory evaluated 23 Phase II fish screen sites in the Yakima River Basin as part of a multi-year project for the Bonneville Power Administration on the effectiveness of fish screening devices. Pacific Northwest National Laboratory collected data to determine whether velocities in front of the screens and in the bypasses met National Marine Fisheries Service criteria to promote safe and timely fish passage and whether bypass outfall conditions allowed fish to safely return to the river. In addition, Pacific Northwest National Laboratory conducted underwater video surveys to evaluate the environmental and operational conditions of the screen sites with respect to fish passage. Based on evaluations in 2002, PNNL concluded that: (1) In general, water velocity conditions at the screen sites met fish passage criteria set by the National Marine Fisheries Service. (2) Conditions at most facilities would be expected to provide for safe juvenile fish passage. (3) Conditions at some facilities indicate that operation and/or maintenance should be modified to increase safe juvenile fish passage. (4) Automated cleaning brushes generally functioned properly; chains and other moving parts were typically well greased and operative. (5) Removal of sediment buildup and accumulated leafy and woody debris should be improved at some sites.

  3. Washington Phase II Fish Diversion Screen Evaluations in the Yakima and Touchet River Basins, 2005-2006 Annual Reports.

    Energy Technology Data Exchange (ETDEWEB)

    Chamness, Mickie; Abernethy, C.; Tunnicliffe, Cherylyn (PNNL)

    2006-02-01

    In 2005, Pacific Northwest National Laboratory (PNNL) researchers evaluated 25 Phase II fish screen sites in the Yakima and Touchet river basins. Pacific Northwest National Laboratory performs these evaluations for Bonneville Power Administration (BPA) to determine whether the fish screening devices meet National Marine Fisheries Service (NMFS) criteria to promote safe and timely fish passage. Evaluations consist of measuring velocities in front of the screens, using an underwater camera to look at the condition and environment in front of the screens, and noting the general condition and operation of the sites. Results of the evaluations in 2005 include the following: (1) Most approach velocities met the NMFS criterion of less than or equal to 0.4 fps. Less than 13% of all approach measurements exceeded the criterion, and these occurred at 10 of the sites. Flat-plate screens had more problems than drum screens with high approach velocities. (2) Bypass velocities generally were greater than sweep velocities, but sweep velocities often did not increase toward the bypass. The latter condition could slow migration of fish through the facility. (3) Screen and seal materials generally were in good condition. (4) Automated cleaning brushes generally functioned properly; chains and other moving parts were typically well-greased and operative. (5) Washington Department of Fish and Wildlife (WDFW) and U.S. Bureau of Reclamation (USBR) generally operate and maintain fish screen facilities in a way that provides safe passage for juvenile fish. (6) In some instances, irrigators responsible for specific maintenance at their sites (e.g., debris removal) are not performing their tasks in a way that provides optimum operation of the fish screen facility. New ways need to be found to encourage them to maintain their facilities properly. (7) We recommend placing datasheets providing up-to-date operating criteria and design flows in each sites logbox. The datasheet should include

  4. Evaluation of Low and High Frequency Sound for Enhancing Fish Screening Facilities to Protect Outmigrating Salmonids.

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Robert P.; Neitzel, Duane A.; Mavros, William V.

    1998-02-01

    The need to provide passage and protective screens at irrigation diversions has always been a necessary part of the Columbia River Basin Fish and Wildlife Program (NPPC 1984, 1987, 1994). From 1985 through 1990, fish protection facilities in large irrigation diversions throughout the Columbia Basin, especially in the Yakima Basin, were updated. After 1990, fish protection efforts turned to installation of new facilities on unscreened diversions and to repair and upgrade of older facilities. The screening program also includes funds to monitor and evaluate the facilities. The screen evaluations indicate they are an effective means for protecting juvenile fish larger than 40 mm in length. As state and federal agencies change screening criteria to protect smaller fish (e.g., bull trout fry), the physical barrier may not always be effective. Screen mesh small enough to protect fish may be vulnerable to frequent plugging. Gap tolerances on side and bottom seals may be difficult to install and maintain. Physical barrier screens can be enhanced with behavioral barriers that cause fish to avoid a hazard. Behavioral barriers may consist of sound generator, strobe lights, bubble curtains, or electrical barriers. State of Oregon House Bill 3112 states that "Standards and criteria shall address the overall level of protection necessary at a given water diversion and shall not favor one technology or technique over another." Additionally, it goes on to say, "Screening device means a fish screen or behavior barrier." Other Northwest states, in particular Washington, have taken a comprehensive program to install barriers at all unscreened diversions by 1999. Protecting all fish at all water withdrawals will probably require both physical and behavioral barriers. The purpose of this study is to evaluate the effectiveness of using an underwater sound-generator as a behavioral barrier for possible use at fish diversion facilities. This study did not include engineering and economic

  5. Preliminary documentation and assessment of fish diversity in sub ...

    African Journals Online (AJOL)

    Preliminary documentation and assessment of fish diversity in sub-Saharan ... upon their life histories and degree of association with estuarine environments. ... Estuarine fish communities in Africa are strongly influenced by the prevailing ...

  6. Synthetic Pattern of Fish Diversity in Alabama, USA

    Directory of Open Access Journals (Sweden)

    Chen, X.

    2006-12-01

    Full Text Available The state of Alabama has a rich fish fauna. Analyzing the current distributional patterns of fish diversity by synthesizing information and integrating different spatial and temporal scales is important for understanding the underlying mechanisms of diversity and making strategies for fish conservation. Basing the study on long-term intensive samples (9,244 collections of fish species at 3,716 field stations across Alabama from 1845 to 1994, I analyzed the general pattern of fish diversity in Alabama at the county level. The results indicate that more than half the area of Alabama has high fish diversity, including fish species endemic to the USA. Most of the counties with the highest fish diversity are in southwestern Alabama. Nonnative fish species occurred mainly in the southernmost counties, such as Mobile and Baldwin. Twelve counties have the rare species which has only one occurence location in each country, with Lauderdale County having the most (10 rare species; the counties with the rare species are generally distributed at the four corner areas of the state boundaries, particularly on the northern and southern boundaries. A high positive correlation exists between species diversity and endemic species, but there is no significant correlation between species diversity and diversification. Both Power-law and logarithmic relationships exist between class of species diversity and its frequency; counties with higher fish diversity tend to have low human-population densities, and are located at or nearby the Alluvial-deltaic Plain and Gulf Coast floodplain.

  7. Yakima River Basin Phase II Fish Screen Evaluations, 2002

    Energy Technology Data Exchange (ETDEWEB)

    Carter, Jessica A.; McMichael, Geoffrey A.; Chamness, Mickie A.

    2003-03-01

    In 2002, the Pacific Northwest National Laboratory evaluated 23 Phase II fish screen sites in the Yakima River Basin as part of a multi-year project for the Bonneville Power Administration on the effectiveness of fish screening devices. Pacific Northwest National Laboratory collected data to determine whether velocities in front of the screens and in the bypasses met National Marine Fisheries Service criteria to promote safe and timely fish passage and whether bypass outfall conditions allowed fish to safely return to the river. In addition, Pacific Northwest National Laboratory conducted underwater video surveys to evaluate the environmental and operational conditions of the screen sites with respect to fish passage. Based on evaluations in 2002, PNNL concluded that: (1) In general, water velocity conditions at the screen sites met fish passage criteria set by the National Marine Fisheries Service. (2) Conditions at most facilities would be expected to provide for safe juvenile fish passage. (3) Conditions at some facilities indicate that operation and/or maintenance should be modified to increase safe juvenile fish passage. (4) Automated cleaning brushes generally functioned properly; chains and other moving parts were typically well greased and operative. (5) Removal of sediment buildup and accumulated leafy and woody debris should be improved at some sites.

  8. Effects of Fishing and Regional Species Pool on the Functional Diversity of Fish Communities

    Science.gov (United States)

    Martins, Gustavo M.; Arenas, Francisco; Neto, Ana I.; Jenkins, Stuart R.

    2012-01-01

    The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities’ functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities’ functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning. PMID:22952950

  9. Effects of fishing and regional species pool on the functional diversity of fish communities.

    Science.gov (United States)

    Martins, Gustavo M; Arenas, Francisco; Neto, Ana I; Jenkins, Stuart R

    2012-01-01

    The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities' functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities' functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning.

  10. Composite fish diversity off southern California

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This map shows composite diversity averaged between 4 data sets: RecFIN recreational hook and line, SCCWRP trawls, NMFS benthic trawls, and kelp diver surveys....

  11. Impact of fishing and stocking practices on Coregonid diversity

    Science.gov (United States)

    Anneville, Orlane; Lasne, Emilien; Guillard, Jean; Eckmann, Reiner; Stockwell, Jason D.; Gillet, Christian; Yule, Daniel

    2015-01-01

    Fish species diversity can be lost through interacting stressors including habitat loss, stocking and overfishing. Although a multitude of stressors have played a role in the global decline of coregonid (Coregonus spp.) diversity, a number of contemporary studies have identified habitat loss stemming from eutrophication as the primary cause. Unfortunately, reconstructing the role of fishing and stocking practices can be difficult, because these records are incomplete or appear only in hard-to-access historic grey literature. Based on an illustrative set of historic and contemporary studies, we describe how fisheries management practices may have contributed to coregonid diversity loss in European and North American lakes. We provide case studies examining how fishing and stocking may reduce coregonid diversity through demographic decline and introgressive hybridization. In some lakes, fisheries management practices may have led to a loss of coregonid diversity well before issues with habitat degradation manifested. Our review suggests that fish conservation policies could beneficially consider the relative importance of all stressors, including management practices, as potential drivers of diversity loss.

  12. Maintenance of fish diversity on disturbed coral reefs

    Science.gov (United States)

    Wilson, S. K.; Dolman, A. M.; Cheal, A. J.; Emslie, M. J.; Pratchett, M. S.; Sweatman, H. P. A.

    2009-03-01

    Habitat perturbations play a major role in shaping community structure; however, the elements of disturbance-related habitat change that affect diversity are not always apparent. This study examined the effects of habitat disturbances on species richness of coral reef fish assemblages using annual surveys of habitat and 210 fish species from 10 reefs on the Great Barrier Reef (GBR). Over a period of 11 years, major disturbances, including localised outbreaks of crown-of-thorns sea star ( Acanthaster planci), severe storms or coral bleaching, resulted in coral decline of 46-96% in all the 10 reefs. Despite declines in coral cover, structural complexity of the reef framework was retained on five and species richness of coral reef fishes maintained on nine of the disturbed reefs. Extensive loss of coral resulted in localised declines of highly specialised coral-dependent species, but this loss of diversity was more than compensated for by increases in the number of species that feed on the epilithic algal matrix (EAM). A unimodal relationship between areal coral cover and species richness indicated species richness was greatest at approximately 20% coral cover declining by 3-4 species (6-8% of average richness) at higher and lower coral cover. Results revealed that declines in coral cover on reefs may have limited short-term impact on the diversity of coral reef fishes, though there may be fundamental changes in the community structure of fishes.

  13. Beyond the zebrafish: diverse fish species for modeling human disease

    Directory of Open Access Journals (Sweden)

    Manfred Schartl

    2014-02-01

    Full Text Available In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research.

  14. Functional diversity of fish in estuaries at a global extent

    Directory of Open Access Journals (Sweden)

    Rita P Vasconcelos

    2015-10-01

    Full Text Available Biodiversity is currently viewed as a framework encompassing multiple facets of the variety of life, including taxonomic and functional aspects. Species richness and composition of fish assemblages in estuaries is defined by global to local processes acting on community colonization. The present study further investigates how biodiversity of fish assemblages varies among estuaries globally, by simultaneously analysing taxonomic and functional richness and diversity of assemblages. A comprehensive worldwide database was compiled on the fish assemblage composition and environmental characteristics of estuaries. In addition, functional attributes of the fish species were characterized such as body size, habitat use and trophic ecology. We investigated the relationship between taxonomic and functional aspects of biodiversity, i.e. the match or mismatch between the two. We also explored how functional diversity of fish assemblages varied among estuaries globally and related to environmental features of estuaries, i.e. historic and contemporary, global and local constraints. The results are explored in the context of ecosystem functioning and resilience, and outcomes relevant to assist in prioritizing conservation efforts are highlighted.

  15. Diversity and stability of herbivorous fishes on coral reefs.

    Science.gov (United States)

    Thibaut, Loic M; Connolly, Sean R; Sweatman, Hugh P A

    2012-04-01

    Biodiversity may provide insurance against ecosystem collapse by stabilizing assemblages that perform particular ecological functions (the "portfolio effect"). However, the extent to which this occurs in nature and the importance of different mechanisms that generate portfolio effects remain controversial. On coral reefs, herbivory helps maintain coral dominated states, so volatility in levels of herbivory has important implications for reef ecosystems. Here, we used an extensive time series of abundances on 35 reefs of the Great Barrier Reef of Australia to quantify the strength of the portfolio effect for herbivorous fishes. Then, we disentangled the contributions of two mechanisms that underlie it (compensatory interactions and differential responses to environmental fluctuations ["response diversity"]) by fitting a community-dynamic model that explicitly includes terms for both mechanisms. We found that portfolio effects operate strongly in herbivorous fishes, as shown by nearly independent fluctuations in abundances over time. Moreover, we found strong evidence for high response diversity, with nearly independent responses to environmental fluctuations. In contrast, we found little evidence that the portfolio effect in this system was enhanced by compensatory ecological interactions. Our results show that portfolio effects are driven principally by response diversity for herbivorous fishes on coral reefs. We conclude that portfolio effects can be very strong in nature and that, for coral reefs in particular, response diversity may help maintain herbivory above the threshold levels that trigger regime shifts.

  16. Lake size and fish diversity in southern Brazil coastal lagoons

    Directory of Open Access Journals (Sweden)

    Lucia Ribeiro Rodrigues

    2015-10-01

    Full Text Available The coastal plain of Rio Grande do Sul, southern Brazil, presents a series of shallow lagoons with diverse size and morphology. The objective of this study is to determine whether the size of the lagoon is an effective factor for structuring fish diversity. In this regard, nine lagoons with distinct areas were sampled: three with an area up to 40 hectares, three with area between 40 and 80 hectares, and three with an area of over 80 hectares. Each lagoon was sampled once on the littoral and pelagic zones. At each point, fish were captured through a set of gill nets with different mesh sizes. Captured specimens were identified, quantified and evaluated for weight and length. A total of 24 fish species belonging to 10 families was obtained, with Characidae presenting the highest species richness. Cyanocharax alburnus was the only species that occurred in all lagoons. Cyphocharax voga, Astyanax eigenmmaniorum, Oligosarcus jenynsii and O. robustus were also frequent species, present in most of the sampled lagoons. Lycengraulis grossidens was captured in just two lagoons with increased conductivity. The community structure showed the highest species richness in lakes with an area over 40 ha, however the highest mean diversity values were observed in ponds up to 40 ha. Cluster Analysis yielded the formation of two groups: a group formed by just one lagoon and a second one cluster grouping all the other lagoons. This pattern may be associated with the presence of Lycengraulis grossidens as a dominant species in this lagoon clustered apart. The results indicate that lagoons with up to 40 ha present greater homogeneity on the species composition and higher average values of diversity; while intermediate ponds (between 40 and 80 ha have lower average diversity for the fish fauna due to increased heterogeneity in species abundance.

  17. Impact of fishing on size composition and diversity of demersal fish communities

    DEFF Research Database (Denmark)

    Bianchi, G.; Gislason, Henrik; Graham, K.;

    2000-01-01

    . but particularly in high-latitude regions, we observe a decreasing trend in the slope, reflecting changes in size composition toward a relative decline in larger fish. The results from tropical regions are less conclusive, partly owing to the difficulty in obtaining consistent data series, but probably also......By analysing data sets from different world regions we add evidence to documented changes in demersal fish community structure that may be related to fishing. Changes are analysed by community properties that might be expected to capture relevant overall changes - size spectra slopes and intercepts...... because the generally higher growth rates of the constituent species make the slope less sensitive to changes in fishing. No evidence was found of any decline in species richness, while changes in diversity (richness and evenness) were caused either by changes in patterns of dominance or by changes...

  18. Velocity Measurements at Six Fish Screening Facilities in the Yakima River Basin, Washington, Summer 1988 : Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Abernethy, C. Scott; Neitzel, Duane A.; Lusty, E. William

    1989-11-01

    The Bonneville Power Administration (BPA), the United States Bureau of Reclamation (USSR), and the Washington State Department of Ecology (WDOE) are funding the construction and evaluation of fish passage facilities and fish protection facilities at irrigation and hydroelectric diversions in the Yakima River Basin, Washington State. The program provides offsite enhancement to compensate for fish and wildlife losses caused by hydroelectric development throughout the Columbia River Basin, and addresses natural propagation of salmon to help mitigate the impact of irrigation in the Yakima River Basin. This report evaluates the flow characteristics of the screening facilities. Studies consisted of velocity measurements taken in front of the rotary drum screens and within the fish bypass systems during peak flows. Measurements of approach velocity and sweep velocity were emphasized in these studies; however, vertical velocity was also measured. 5 refs., 18 figs., 15 tabs.

  19. Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities.

    Science.gov (United States)

    Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernandez, Domingo; Mouillot, David

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules.

  20. Genomic diversity of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum.

    Science.gov (United States)

    Castillo, Daniel; Middelboe, Mathias

    2016-12-01

    Bacteriophages infecting the fish pathogen Flavobacterium psychrophilum can potentially be used to prevent and control outbreaks of this bacterium in salmonid aquaculture. However, the application of bacteriophages in disease control requires detailed knowledge on their genetic composition. To explore the diversity of F. pyschrophilum bacteriophages, we have analyzed the complete genome sequences of 17 phages isolated from two distant geographic areas (Denmark and Chile), including the previously characterized temperate bacteriophage 6H. Phage genome size ranged from 39 302 to 89 010 bp with a G+C content of 27%-32%. None of the bacteriophages isolated in Denmark contained genes associated with lysogeny, whereas the Chilean isolates were all putative temperate phages and similar to bacteriophage 6H. Comparative genome analysis showed that phages grouped in three different genetic clusters based on genetic composition and gene content, indicating a limited genetic diversity of F. psychrophilum-specific bacteriophages. However, amino acid sequence dissimilarity (25%) was found in putative structural proteins, which could be related to the host specificity determinants. This study represents the first analysis of genomic diversity and composition among bacteriophages infecting the fish pathogen F. psychrophilum and discusses the implications for the application of phages in disease control. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Analysis of fish diversion efficiency and survivorship in the fish return system at San Onofre Nuclear Generating Station

    OpenAIRE

    Love, Milton S.; Sandhu, Meenu; Stein, Jeffrey; Herbinson, Kevin T.; Moore, Robert H; Mullin, Michael; Stephens, John S.

    1989-01-01

    This study examined the efficiency of fish diversion and survivorship of diverted fishes in the San Onofre Nuclear Generating Station Fish Return System in 1984 and 1985. Generally, fishes were diverted back to the ocean with high frequency, particularly in 1984. Most species were diverted at rates of 80% or more. Over 90% of the most abundant species, Engraulis mordax, were diverted. The system worked particularly well for strong-swimming forms such as Paralobrax clothratus, Atherinopsis cal...

  2. Influence of approach velocity and mesh size on the entrainment and contact of a lowland river fish assemblage at a screened irrigation pump.

    Directory of Open Access Journals (Sweden)

    Craig A Boys

    Full Text Available Fish screens can help prevent the entrainment or injury of fish at irrigation diversions, but only when designed appropriately. Design criteria cannot simply be transferred between sites or pump systems and need to be developed using an evidence-based approach with the needs of local species in mind. Laboratory testing is typically used to quantify fish responses at intake screens, but often limits the number of species that can studied and creates artificial conditions not directly applicable to screens in the wild. In this study a field-based approach was used to assess the appropriateness of different screen design attributes for the protection of a lowland river fish assemblage at an experimental irrigation pump. Direct netting of entrained fish was used along with sonar technology to quantify the probability of screen contact for a Murray-Darling Basin (Australia fish species. Two approach velocities (0.1 and 0.5 m.sec(-1 and different sizes of woven mesh (5, 10 and 20 mm were evaluated. Smaller fish (<150 mm in the assemblage were significantly more susceptible to entrainment and screen contact, especially at higher approach velocities. Mesh size appeared to have little impact on screen contact and entrainment, suggesting that approach velocity rather than mesh size is likely to be the primary consideration when developing screens. Until the effects of screen contacts on injury and survival of these species are better understood, it is recommended that approach velocities not exceed 0.1 m.sec(-1 when the desire is to protect the largest range of species and size classes for lowland river fish assemblages in the Murray-Darling Basin. The field method tested proved to be a useful approach that could compliment laboratory studies to refine fish screen design and facilitate field validation.

  3. Patterns of Macroinvertebrate and Fish Diversity in Freshwater Sulphide Springs

    Directory of Open Access Journals (Sweden)

    Ryan Greenway

    2014-09-01

    Full Text Available Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates and cyprinodontiforms (among fishes appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.

  4. A Fisheries Evaluation of the Richland and Wapato Canal Fish Screening Facilities, Spring 1987 : Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Neitzel, Duane A.; Abernethy, C.Scott; Lusty, E.William; Wampler, Sally J.

    1988-02-01

    We evaluated the effectiveness of new fish screening facilities at the Richland and Wapato canals in south-central Washington State. The screen integrity tests at the Richland Screens indicated that 100% of fall chinook salmon fry (Oncorhynchus tshawytscha) released in front of the screens were prevented from entering the canal behind the screens. Our estimate is based on a 61% catch efficiency for control fish planted behind the screens. At the Wapato Canal, we estimated that between 3% and 4% of the test fish were either impinged on the screen surface and passed over the screens or passed through faulty screen seals. Our estimate is based over the screens or passed through faulty screen seals. Our estimate is based on a greater than 90% capture of control fish released in front of the screens. At the Wapato Screens, we estimated that 0.8% of steelhead smolts (Salmo gairdneri) and 1.4% of spring chinook salmon smolts released during low canal flow tests wee descaled. During full canal flow tests, 1.6% of the steelhead and 3.1% of the spring chinook salmon released were descaled. The fish return pipe at the Wapato Canal was tested: the estimate of descaled test fish wa not different from the estimate of descaled control fish. The time required for fish to exit from the Wapato Screen forebay varied with species and with canal flow. During low canal flows, 43.2% of steelhead and 61.6% of spring chinook salmon smolts released at the trash racks were captured in the fish return within 96 hr. 11 refs., 11 figs., 10 tabs.

  5. Marine fish diversity and habitat use along the western coast of the Black Sea

    OpenAIRE

    Viorel Dumitru Gavril

    2015-01-01

    Over the years the conditions of the Black Sea marine habitats have been modified due to anthropogenic impacts and climate change, and it is likely that the diversity of fish fauna changed as a result. This study provides new data regarding marine fish population diversity and habitat use along the western coast of the Black Sea. I recorded fish species and habitat data between 2011 and 2014 in two locations: Constanta, Romania and Shabla-Tyulenovo coast, Bulgaria, using fishing (only in R...

  6. Dioxin screening in fish product by pattern recognition of biomarkers.

    Science.gov (United States)

    Bassompierre, Marc; Tomasi, Giorgio; Munck, Lars; Bro, Rasmus; Engelsen, Søren Balling

    2007-04-01

    Two alternative, cost- and time-effective dioxin screening methods relying on two categories of potential lipid biomarkers were investigated. A dioxin range varying from 1.1 to 47.1 pg PCDD/F TEQ-WHO/g lipid using 64 fish meal samples was used for model calibration. The methods were based on multivariate models using either (1) fatty acid composition monitored by GC-FID or (2) fluorescence landscape signals analysed using the PARAFAC model and in both cases predicting dioxin content as pgPCDD/F TEQ-WHO/g lipid. In both cases, Partial Least Squares (PLS) regression was performed for predicting the dioxin content of a sample. The GC-FID data analyses was based on automatic peak alignment and integration, enabling extraction of the area of 140 peaks from the gas chromatograms, as opposed to the 31 fatty acids usually considered for fish oil characterisation. In addition to classic PLS employing the whole dataset for calibration, a two-step local PLS modeling approach was performed based upon an initial selection of k number of calibration samples providing the best match to the prediction sample using a so-called k Nearest Neighbors (kNN) approach, then followed by PLS calibration on these kNN selected samples for dioxin prediction. Fluorescence spectroscopy offers a promising non-invasive and ultra-rapid technique, with less than two minutes analysis time. However, fluorescence spectroscopy using the pattern recognition "kNN-PLS" yielded a correlation of 0.76 (r2) and a high root mean square error of prediction of 11.4 pg PCDD/F TEQ-WHO/g lipid. The predictions were improved when the PLS calibration was performed on all the sample with a root mean square error of prediction of 7.0 pg PCDD/F TEQ-WHO/g lipid. Unfortunately, these results failed to demonstrate the potential of fluorophore monitoring as a screening method. In contrast, the overall best screening performance was obtained with the fatty acid profile, when the kNN-PLS combination employed for pattern

  7. Determination of a Screening Metric for High Diversity DNA Libraries.

    Science.gov (United States)

    Guido, Nicholas J; Handerson, Steven; Joseph, Elaine M; Leake, Devin; Kung, Li A

    2016-01-01

    The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

  8. Supplement Analysis for the Watershed Management Program EIS (DOE/EIS-0265/SA-103) - Install Fish Screens to Protect ESA Listed Steelhead and Bull Trout in the Walla Walla Basin – Phase II

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Shannon C. [Bonneville Power Administration (BPA), Portland, OR (United States)

    2003-06-11

    Proposed Action: Install Fish Screens to Protect ESA Listed Steelhead and Bull Trout in the Walla Walla Basin – Phase II Minor Diversion Screen Installations. BPA is proposing to provide cost share for a program that will protect ESA-listed salmonid species in the Walla Walla River Basin through the installation of state and federally approved fish screen on over 300 water diversions in the Walla Walla River Basin. This program will involve a wide variety of projects including the installation of screens for both pump and gravity fed surface water diversions. This project will be implemented in conjunction with the Walla Walla County Conservation District, Columbia County Conservation District, Washington Department of Fish and Wildlife, Walla Walla Community College, Washington Department of Ecology, and local irrigators. ESA-listed steelhead and bull trout are presently at risk in the Walla Walla Basin as a result of a combination of factors that primarily involve insufficient flow, extensive habitat degradation, and mortality from surface water diversions. Unscreened or improperly screened diversions can damage fish scaling and induce stress, both of which can be lethal. They are also known to cause migration delays and increased predation; impinge fish against screen surfaces; or, in cases where screen mesh size is too large, allow juvenile fish to be drawn directly into functioning irrigation systems resulting in direct mortality. The goal of this project is to eliminate imminent mortality risks to ESA-listed fish arising from inadequate irrigation diversions in the Walla Walla Basin by upgrading screens to current state and federal juvenile fish screen standards.

  9. Local and regional rarity in a diverse tropical fish assemblage.

    Science.gov (United States)

    Hercos, A P; Sobansky, M; Queiroz, H L; Magurran, A E

    2013-01-22

    Because most species in an ecological assemblage are rare, much of the species richness we value is due to taxa with few individuals or a restricted distribution. It has been apparent since the time of ecological pioneers such as Bates and Darwin that tropical systems have disproportionately large numbers of rare species, yet the distribution and abundance patterns of these species remain largely unknown. Here, we examine the diversity of freshwater fish in a series of lakes in the Amazonian várzea, and relate relative abundance, both as numbers of individuals and as biomass, to the occurrence of species in space and time. We find a bimodal relationship of occurrence that distinguishes temporally and spatially persistent species from those that are infrequent in both space and time. Logistic regression reveals that information on occurrence helps distinguish those species that are rare in this locality but abundant elsewhere, from those that are rare throughout the region. These results form a link between different approaches used to evaluate commonness and rarity. In doing so, they provide a tool for identifying species of high conservation priority in poorly documented but species rich localities.

  10. Global functional diversity of freshwater fish is concentrated in the Neotropics while functional vulnerability is widespread.

    Science.gov (United States)

    Toussaint, A; Charpin, N; Brosse, S; Villéger, S

    2016-03-16

    Worldwide biodiversity assessments have mainly focused on species richness but little is known about the diversity of species roles, i.e. functional diversity, while this is a key facet to understanding the consequences of global changes on the ecosystem services to human societies. Here, we report the world pattern of functional diversity of freshwater fish using a database encompassing morphological characteristics of more than 9,000 species. The Neotropical realm hosts more than 75% of global functional diversity while other realms each host less than 25%. This discrepancy is mediated by high functional uniqueness in some diversified Neotropical fish orders. Surprisingly, functional diversity patterns were weakly related to functional vulnerability. In the Neotropics the loss of threatened species will cause a limited loss of functional diversity (functional diversity will reach 43% and 33%, respectively, conferring a high functional vulnerability to these realms. Conservation of the Neotropical fish diversity is a key target to maintain world fish functional diversity, but this should not hide the pressing need to conserve the vulnerable fish faunas of the rest of the world, in which functional diversity is to a large extent supported by threatened species.

  11. Breast cancer screening: cultural beliefs and diverse populations.

    Science.gov (United States)

    Simon, Cassandra E

    2006-02-01

    This article addresses the role of culture in breast cancer screening behavior among African American, American Indian/Alaskan Native, Asian American/Pacific Islander, and Hispanic/ Latina women. It reviews cultural beliefs, attitudes, and knowledge and their relative influence on women's decisions regarding health tests. The article explores how to build on these cultural values, simultaneously mediating their barrier effects. Building on cultural explanatory models of health behavior, suggestions for incorporating culture into early detection strategies for ethnically and racially diverse, underserved women are provided. In addition, the article offers four practice principles that can be used with all of the groups: inclusion and use of indigenous support; cross-application of approaches for diverse populations; honor and incorporation of culture; and attention to language, literacy, and cultural information.

  12. Species-specific mercury bioaccumulation in a diverse fish community.

    Science.gov (United States)

    Donald, David B; Wissel, Björn; Anas, M U Mohamed

    2015-12-01

    Mercury bioaccumulation models developed for fish provide insight into the sources and transfer of Hg within ecosystems. Mercury concentrations were assessed for 16 fish species of the western reach of Lake Diefenbaker, Saskatchewan, Canada. For top predators (northern pike, Esox Lucius; walleye, Sander vitreum), Hg concentrations were positively correlated to δ(15)N, and δ(15)N to fish age, suggesting that throughout life these fish fed on organisms with increasingly higher trophic values and Hg concentrations. However, fish mass and/or age were the principal parameters related to Hg concentrations for most species. For 9 common species combined, individual variation in Hg concentration was explained in declining order of importance by fish mass, trophic position (δ(15)N), and fish age. Delta (15)N value was not the leading variable related to Hg concentration for the assemblage, probably because of the longevity of lower--trophic-level species (3 species ≥ 20 yr), substantial overlap in Hg concentration and δ(15)N values for large-bodied fish up to 3000 g, and complex relationships between Hg concentration and δ(15)N among species. These results suggest that the quantity of food (and Hg) consumed each year and converted to fish mass, the quantity of Hg bioaccumulated over years and decades, and trophic position were significant determinants of Hg concentration in Lake Diefenbaker fish.

  13. Predictors of colorectal cancer screening in diverse primary care practices

    Directory of Open Access Journals (Sweden)

    Tabbarah Melissa

    2006-09-01

    Full Text Available Abstract Background To explain why rates of colorectal cancer (CRC screening including fecal occult blood testing (FOBT, flexible sigmoidoscopy (FS, colonoscopy (CS, and barium enema (BE, are low, this study assessed determinants of CRC screening from medical records. Methods Data were abstracted from patients aged ≥64 years selected from each clinician from 30 diverse primary care practices (n = 981. Measurements included the rates of annual FOBT, ever receiving FOBT, ever receiving FS/CS/BE under a combination variable, endoscopy/barium enema (EBE. Results Over five years, 8% had received annual FOBT, 53% had ever received FOBT and 22% had ever received EBE. Annual FOBT was negatively associated with female gender, odds ratio (OR = .23; 95% confidence interval = .12–.44 and positively associated with routinely receiving influenza vaccine, OR = 2.55 (1.45–4.47; and more office visits: 3 to Conclusion Overall CRC screening rates were low, but were related to the number of primary care office visits. FOBT was related to immunization status, suggesting the possible benefit of linking these preventive services.

  14. Fish diversity in southern California using trawl data from the National Marine Fisheries Service

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Shannon Index of diversity was calculated from National Marine Fisheries Service Groundfish Survey Program (NMFS GSP) fish trawl data. Data from 477 fishery...

  15. Study on Fishery Ecological Environment and Fish Species Diversity in Yantan Water Area

    Institute of Scientific and Technical Information of China (English)

    Yaoquan; HAN; Anyou; HE; Li; HUANG; Jun; SHI; Dapeng; WANG; Weijun; WU

    2015-01-01

    Through analysis on water quality,planktonic organism,fish resources,and fish species diversity in Yantan water area,this paper evaluated current situation of quality of fishery ecological environment in Yantan water area. The survey recorded all 52365 fishes and 1410. 2kg catches obtained by fishermen in half a year,and more than 98% catches are small fishes. The Shannon-Weiner diversity index of Yantan water area is 0. 162,Wilhm improvement index is 1. 814,DG- Findex is 0. 083,and the index of fish species diversity is far lower than other water areas. The average quantity per unit of phytoplankton is 1. 0134 million ind. / L,and the average quantity per unit of organisms is 1. 1151 mg / L. The average quantity per unit of zooplankton is 459. 6 ind. / L,and the average quantity per unit of organisms is 0. 6422 mg / L. Evaluation results indicate that water quality and planktonic organism in Yantan water area are basically normal,but fish resources are increasingly exhausted,fish resource composition is not reasonable,and fish species diversity is extremely low. From the perspective of biomanipulation,it is required to restore fishery ecological environment of reservoir area through restoring normal composition of aquatic organisms.

  16. Additive partitioning of coral reef fish diversity across hierarchical spatial scales throughout the Caribbean.

    Science.gov (United States)

    Francisco-Ramos, Vanessa; Arias-González, Jesús Ernesto

    2013-01-01

    There is an increasing need to examine regional patterns of diversity in coral-reef systems since their biodiversity is declining globally. In this sense, additive partitioning might be useful since it quantifies the contribution of alpha and beta to total diversity across different scales. We applied this approach using an unbalanced design across four hierarchical scales (80 sites, 22 subregions, six ecoregions, and the Caribbean basin). Reef-fish species were compiled from the Reef Environmental Education Foundation (REEF) database and distributions were confirmed with published data. Permutation tests were used to compare observed values to those expected by chance. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species), with the highest β-diversity at the site scale. [Formula: see text]-diversity was higher than expected by chance in all scenarios and at all studied scales. This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. Our results highlight the importance of ecoregions as a spatial scale to conserve local

  17. Additive partitioning of coral reef fish diversity across hierarchical spatial scales throughout the Caribbean.

    Directory of Open Access Journals (Sweden)

    Vanessa Francisco-Ramos

    Full Text Available There is an increasing need to examine regional patterns of diversity in coral-reef systems since their biodiversity is declining globally. In this sense, additive partitioning might be useful since it quantifies the contribution of alpha and beta to total diversity across different scales. We applied this approach using an unbalanced design across four hierarchical scales (80 sites, 22 subregions, six ecoregions, and the Caribbean basin. Reef-fish species were compiled from the Reef Environmental Education Foundation (REEF database and distributions were confirmed with published data. Permutation tests were used to compare observed values to those expected by chance. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species, with the highest β-diversity at the site scale. [Formula: see text]-diversity was higher than expected by chance in all scenarios and at all studied scales. This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. Our results highlight the importance of ecoregions as a spatial scale to

  18. Marine fish diversity and habitat use along the western coast of the Black Sea

    Directory of Open Access Journals (Sweden)

    Viorel Dumitru Gavril

    2015-11-01

    I identified 34 species of fish in the Shabla-Tyulenovo area and 39 species in the Constanta area, of which 19 species preferred sandy bottoms, 21 rocky bottoms, 16 rocky habitats with Cystoseira sp., 19 man-made structures and 9 were pelagic. For 7 species habitat preferences could not be determined as a result of capture only by fishing. In conclusion, the scuba visual transects along with fishing methods provide a relevant image to the current state of the fish diversity along the western coast of the Black Sea.

  19. Connecting ground water influxes with fish species diversity in an urbanized watershed

    Science.gov (United States)

    Steffy, L.Y.; McGinty, A.L.; Welty, C.; Kilham, S.S.

    2004-01-01

    Valley Creek watershed is a small stream system that feeds the Schuylkill River near Philadelphia, Pennsylvania. The watershed is highly urbanized, including over 17 percent impervious surface cover (ISC) by area. Imperviousness in a watershed has been linked to fish community structure and integrity. Generally, above 10 to 12 percent ISC there is marked decline in fish assemblages with fish being absent above 25 percent ISC. This study quantifies the importance of ground water in maintaining fish species diversity in subbasins with over 30 percent ISC. Valley Creek contains an atypical fish assemblage in that the majority of the fish are warm-water species, and the stream supports naturally reproducing brown trout, which were introduced and stocked from the early 1900s to 1985. Fish communities were quantified at 13 stations throughout the watershed, and Simpson's species diversity index was calculated. One hundred and nine springs were located, and their flow rates measured. A cross covariance analysis between Simpson's species diversity index and spring flow rates upstream of fish stations was performed to quantify the spatial correlation between these two variables. The correlation was found to be highest at lag distances up to about 400 m and drop off significantly beyond lag distances of about 800 m.

  20. Fish parasites in the Arctic deep-sea: Poor diversity in pelagic fish species vs. heavy parasite load in a demersal fish

    Science.gov (United States)

    Klimpel, Sven; Palm, Harry Wilhelm; Busch, Markus Wilhelm; Kellermanns, Esra; Rückert, Sonja

    2006-07-01

    A total of 219 deep-sea fishes belonging to five families were examined for the parasite fauna and stomach contents. The demersal fish Macrourus berglax, bathypelagic Bathylagus euryops, and mesopelagic Argentina silus, Borostomias antarcticus, Chauliodus sloani, and Lampanyctus macdonaldi were caught at 243-708 m trawling depth in the Greenland and the Irminger Sea in 2002. A total of 21 different parasite species, six Digenea, one Monogenea, two Cestoda, seven Nematoda, one Acanthocephala, and four Crustacea, were found. The parasite diversity in the meso- and bathypelagic environment was less diverse in comparison to the benthal. Macrourus berglax had the highest diversity (20 species), usually carrying 4-10 different parasite species (mean 7.1), whereas Bathylagus euryops harbored up to three and Argentina silus, Borostomias antarcticus, Chauliodus sloani and Lampanyctus macdonaldi each up to two species. Most Digenea, Cestoda, Nematoda, Acanthocephala, and Crustacea are known from a wide host range. Several of the encountered parasites occurred at a very low prevalence (<10%), indicating that the studied deep-sea fishes are most probably not instrumental to complete the parasite life cycles in the area of investigation. It is suggested that the lack of nutrients in the meso- and bathypelagial limits the abundance of potential first intermediate hosts of nematodes and cestodes, resulting in low infestation rates even of widely distributed, non-specific species. In contrast, the higher biomass in the benthic deep-sea environment increases the availability of potential intermediate hosts, such as molluscs for the digeneans, resulting in increased parasite diversity. Because many deep-sea fish have a generalistic feeding behavior, the observed different parasite diversity reflects a different depth range of the fish and not necessarily a specific fish feeding ecology.

  1. Chromosomal diversity in tropical reef fishes is related to body size and depth range.

    Science.gov (United States)

    Martinez, P A; Zurano, J P; Amado, T F; Penone, C; Betancur-R, R; Bidau, C J; Jacobina, U P

    2015-12-01

    Tropical reef fishes show contrasting patterns of karyotypic diversity. Some families have a high chromosomal conservatism while others show wide variation in karyotypic macrostructure. However, the influence of life-history traits on karyotypic diversity is largely unknown. Using phylogenetic comparative methods, we assessed the effects of larval and adult species traits on chromosomal diversity rates of 280 reef species in 24 families. We employed a novel approach to account for trait variation within families as well as phylogenetic uncertainties. We found a strong negative relationship between karyotypic diversity rates and body size and depth range. These results suggest that lineages with higher dispersal potential and gene flow possess lower karyotypic diversity. Taken together, these results provide evidence that biological traits might modulate the rate of karyotypic diversity in tropical reef fishes.

  2. Evidence of increased antibiotic resistance in phylogenetically-diverse Aeromonas isolates from semi-intensive fish ponds treated with antibiotics

    Directory of Open Access Journals (Sweden)

    Hemant J Patil

    2016-11-01

    Full Text Available The genus Aeromonas is ubiquitous in aquatic environments encompassing a broad range of fish and human pathogens. Aeromonas strains are known for their enhanced capacity to acquire and exchange antibiotic resistance genes and therefore, are frequently targeted as indicator bacteria for monitoring antimicrobial resistance in aquatic environments. This study evaluated temporal trends in Aeromonas diversity and antibiotic resistance in two adjacent semi-intensive aquaculture facilities to ascertain effects of antibiotic treatment on antimicrobial resistance. In the first facility, sulfadiazine-trimethoprim was added prophylactically upon fingerling stocking and water column-associated Aeromonas were monitored periodically over an eleven-month fish-fattening cycle to assess temporal dynamics in taxonomy and antibiotic resistance. In the second facility, Aeromonas were isolated from fish skin ulcers sampled over a three-year period and from pond water samples to assess associations between pathogenic strains to those in the water column. A total of 1200 Aeromonas spp. were isolated, initially screened for sulfadiazine resistance and further screened against five additional antibiotics. In both facilities, strong correlations were observed between sulfadiazine resistance and trimethoprim and tetracycline resistances, whereas correlations between sulfadiazine resistance and ceftriaxone, gentamycin and chloramphenicol resistances were low. Abundance of multi-drug resistant strains as well as sul1, tetA and intI1 gene-harboring strains was significantly higher in profiles sampled during the fish cycle than those isolated prior to stocking and these genes were extremely abundant in the pathogenic strains. Five phylogenetically-distinct Aeromonas clusters were revealed using partial rpoD gene sequence analysis. Interestingly, prior to fingerling stocking the diversity of water column strains was high, and representatives from all five clusters were

  3. Additive diversity partitioning of fish in a Caribbean coral reef undergoing shift transition.

    Directory of Open Access Journals (Sweden)

    Gilberto Acosta-González

    Full Text Available Shift transitions in dominance on coral reefs from hard coral cover to fleshy macroalgae are having negative effects on Caribbean coral reef communities. Data on spatiotemporal changes in biodiversity during these modifications are important for decision support for coral reef biodiversity protection. The main objective of this study is to detect the spatiotemporal patterns of coral reef fish diversity during this transition using additive diversity-partitioning analysis. We examined α, β and γ fish diversity from 2000 to 2010, during which time a shift transition occurred at Mahahual Reef, located in Quintana Roo, Mexico. Data on coral reef fish and benthic communities were obtained from 12 transects per geomorphological unit (GU in two GUs (reef slope and terrace over six years (2000, 2005, 2006, 2007, 2008, 2010. Spatial analysis within and between the GUs indicated that the γ-diversity was primarily related to higher β-diversity. Throughout the six study years, there were losses of α, β and γ-diversity associated spatially with the shallow (reef slope and deeper (reef terrace GUs and temporally with the transition in cover from mound corals to fleshy macroalgae and boulder corals. Despite a drastic reduction in the number of species over time, β-diversity continues to be the highest component of γ-diversity. The shift transition had a negative effect on α, β and γ-diversity, primarily by impacting rare species, leading a group of small and less vulnerable fish species to become common and an important group of rare species to become locally extinct. The maintenance of fish heterogeneity (β-diversity over time may imply the abetment of vulnerability in the face of local and global changes.

  4. Genetic diversity of geographically distinct Streptococcus dysgalactiae isolates from fish

    Directory of Open Access Journals (Sweden)

    M. Abdelsalam

    2015-03-01

    Full Text Available Streptococcus dysgalactiae is an emerging pathogen of fish. Clinically, infection is characterized by the development of necrotic lesions at the caudal peduncle of infected fishes. The pathogen has been recently isolated from different fish species in many countries. Twenty S. dysgalactiae isolates collected from Japan, Taiwan, Malaysia and Indonesia were molecularly characterized by biased sinusoidal field gel electrophoresis (BSFGE using SmaI enzyme, and tuf gene sequencing analysis. DNA sequencing of ten S. dysgalactiae revealed no genetic variation in the tuf amplicons, except for three strains. The restriction patterns of chromosomal DNA measured by BSFGE were differentiated into six distinct types and one subtype among collected strains. To our knowledge, this report gives the first snapshot of S. dysgalactiae isolates collected from different countries that are localized geographically and differed on a multinational level. This genetic unrelatedness among different isolates might suggest a high recombination rate and low genetic stability.

  5. The astonishing diversity of Ig classes and B cell repertoires in teleost fish

    Directory of Open Access Journals (Sweden)

    Simon eFillatreau

    2013-02-01

    Full Text Available With lympoid tissue anatomy different than mammals, and diverse adaptations to all aquatic environments, fish constitute a fascinating group of vertebrate to study the biology of B cell repertoires in a comparative perspective. Fish B lymphocytes express immunoglobulin (Ig on their surface and secrete antigen-specific antibodies in response to immune challenges. Three antibody classes have been identified in fish, namely IgM, IgD and IgT, while IgG, IgA and IgE are absent. IgM and IgD have been found in all fish species analyzed, and thus seem to be primordial antibody classes. IgM and IgD are normally co-expressed from the same mRNA through alternative splicing, as in mammals. Tetrameric IgM is the main antibody class found in serum. Some species of fish also have IgT, which seems to exist only in fish and is specialized in mucosal immunity. IgM/IgD and IgT are expressed by two different sub-populations of B cells. The tools available to investigate B cell responses at the cellular level in fish are limited, but the progress of fish genomics has started to unravel a rich diversity of IgH and IgL locus organization, which might be related to the succcession of genome remodellings that occured during fish evolution. Moreover, the development of deep sequencing techniques has allowed the investigation of the global features of the expressed fish B cell repertoires in zebrafish and rainbow trout, in steady state or after infection. This review provides a description of the organization of fish Ig loci, with a particular emphasis on their heterogeneity between species, and presents recent data on the structure of the expressed Ig repertoire in healthy and infected fish.

  6. Food-web patterns and diversity in tropical fish communities

    NARCIS (Netherlands)

    Amarasinghe, U.S.; Vijverberg, J.; Weliange, W.S.; Vos, M.

    2014-01-01

    The food webs for three Sri Lankan reservoirs, Minneriya (ancient and shallow), Udawalawe (young and shallow) and Victoria (young and deep), were compared. The species richness of the fish communities was highest in Minneriya (30 species), intermediate in Udawalawe (21 species) and lowest in Victori

  7. Food-web patterns and diversity in tropical fish communities

    NARCIS (Netherlands)

    Amarasinghe, U.S.; Vijverberg, J.; Weliange, W.S.; Vos, M.

    2014-01-01

    The food webs for three Sri Lankan reservoirs, Minneriya (ancient and shallow), Udawalawe (young and shallow) and Victoria (young and deep), were compared. The species richness of the fish communities was highest in Minneriya (30 species), intermediate in Udawalawe (21 species) and lowest in

  8. A UK guide to intake fish-screening regulations, policy and best practice with particular reference to hydroelectric power schemes

    Energy Technology Data Exchange (ETDEWEB)

    Turnpenny, A.W.H.; Struthers, G.; Hanson, P.

    1998-07-01

    A review of fish screening regulations in England, Wales, Scotland, and Northern Ireland is presented, and a summary of findings on screening legislation is given. The views of hydroelectric scheme developers, owners and operators are considered, and recommendations including the development of a risk assessment procedure are discussed. Fish screening technology, bypasses and other escape routes, and common fault in screen design and operation are examined, and guidance to Best Practice is given. (UK)

  9. Rodent neurotoxicity bioassays for screening contaminated Great Lakes fish

    Energy Technology Data Exchange (ETDEWEB)

    Beattie, M.K.; Hoffman, R. [Univ. of Minnesota, Duluth, MN (United States); Gerstenberger, S. [Univ. of Illinois, Urbana, IL (United States). Dept. of Veterinary Biosciences; Dellinger, J.A. [Medical Coll. of Wisconsin, Milwaukee, MI (United States). Dept. of Preventive Medicine

    1996-03-01

    Standard laboratory rat neurotoxicity protocols were used to study the consequences resulting from the consumption of walleye (Stizostedion vitreum), whitefish (Coregonus clupeaformis), and lake trout (Salvelinus namaycush) from Lake Superior (LS) and the consumption of carp (Cyprinus carpio) from Little Lake Butte des Morte (LLBM) near Oshkosh, Wisconsin, USA. Two 90-d subchronic studies are described, including a 45-d exposure to fish diets using male Sprague-Dawley hooded rats, and a 90-d exposure to fish diets using female rats of the same species. Behavioral alterations were tested using a battery of behavioral tests. In addition, pharmacologic challenges using apomorphine and D-amphetamine were administered to the rats to reveal latent neurotoxic effects. Cumulative fish consumption data were recorded daily, weight gain recorded weekly, and behavior data collected prior to exposure, and on days 7, 14, 55 {+-} 2, 85 {+-} 2. Motor activity data were collected on days 30 {+-} 2, 60 {+-} 2, and 90 {+-} 2 of the feeding protocols. Brain tissue from rodents fed these fish were subsequently analyzed for either mercury (Hg) or polychlorinated biphenyls (PCB). Mercury concentrations were increased in the brains of the walleye-fed rats, and PCB concentrations ranged from 0.5 nl/L to 10 nl/L in the brains of rats fed carp from LLBM, a Lake Michigan tributary. Adult male rats fed LLBM carp for 45 d exhibited the greatest behavior responses to the dopaminergic agonist apomorphine on the accelerating rotarod, although these differences were not significant. The 90-d exposure of LS walleye or Hg-spiked LS walleye resulted in behavior alterations on tactile startle response and second footsplay. D-Amphetamine challenge caused changes in tactile startle response, second footsplay, and accelerating rotarod performance after consuming walleye diets. Rats fed LLBM carp had altered behavioral responses to apomorphine on the accelerating rotarod.

  10. Plate-based diversity subset screening generation 2: an improved paradigm for high-throughput screening of large compound files.

    Science.gov (United States)

    Bell, Andrew S; Bradley, Joseph; Everett, Jeremy R; Loesel, Jens; McLoughlin, David; Mills, James; Peakman, Marie-Claire; Sharp, Robert E; Williams, Christine; Zhu, Hongyao

    2016-11-01

    High-throughput screening (HTS) is an effective method for lead and probe discovery that is widely used in industry and academia to identify novel chemical matter and to initiate the drug discovery process. However, HTS can be time consuming and costly and the use of subsets as an efficient alternative to screening entire compound collections has been investigated. Subsets may be selected on the basis of chemical diversity, molecular properties, biological activity diversity or biological target focus. Previously, we described a novel form of subset screening: plate-based diversity subset (PBDS) screening, in which the screening subset is constructed by plate selection (rather than individual compound cherry-picking), using algorithms that select for compound quality and chemical diversity on a plate basis. In this paper, we describe a second-generation approach to the construction of an updated subset: PBDS2, using both plate and individual compound selection, that has an improved coverage of the chemical space of the screening file, whilst only selecting the same number of plates for screening. We describe the validation of PBDS2 and its successful use in hit and lead discovery. PBDS2 screening became the default mode of singleton (one compound per well) HTS for lead discovery in Pfizer.

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

    Science.gov (United States)

    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.

  12. Detection of a diverse marine fish fauna using environmental DNA from seawater samples

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Kielgast, Jos; Iversen, Lars Lønsmann

    2012-01-01

    Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly...... for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from 1/2-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain....... Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied...

  13. Chlamydial infections of fish: diverse pathogens and emerging causes of disease in aquaculture species.

    Science.gov (United States)

    Stride, M C; Polkinghorne, A; Nowak, B F

    2014-05-14

    Chlamydial infections of fish are emerging as an important cause of disease in new and established aquaculture industries. To date, epitheliocystis, a skin and gill disease associated with infection by these obligate intracellular pathogens, has been described in over 90 fish species, including hosts from marine and fresh water environments. Aided by advances in molecular detection and typing, recent years have seen an explosion in the description of these epitheliocystis-related chlamydial pathogens of fish, significantly broadening our knowledge of the genetic diversity of the order Chlamydiales. Remarkably, in most cases, it seems that each new piscine host studied has revealed the presence of a phylogenetically unique and novel chlamydial pathogen, providing researchers with a fascinating opportunity to understand the origin, evolution and adaptation of their traditional terrestrial chlamydial relatives. Despite the advances in this area, much still needs to be learnt about the epidemiology of chlamydial infections in fish if these pathogens are to be controlled in farmed environments. The lack of in vitro methods for culturing of chlamydial pathogens of fish is a major hindrance to this field. This review provides an update on our current knowledge of the taxonomy and diversity of chlamydial pathogens of fish, discusses the impact of these infections on the health, and highlights further areas of research required to understand the biology and epidemiology of this important emerging group of fish pathogens of aquaculture species.

  14. PLASMA PROTEIN PROFILING AS A HIGH THROUGHPUT TOOL FOR CHEMICAL SCREENING USING A SMALL FISH MODEL

    Science.gov (United States)

    Hudson, R. Tod, Michael J. Hemmer, Kimberly A. Salinas, Sherry S. Wilkinson, James Watts, James T. Winstead, Peggy S. Harris, Amy Kirkpatrick and Calvin C. Walker. In press. Plasma Protein Profiling as a High Throughput Tool for Chemical Screening Using a Small Fish Model (Abstra...

  15. Assessing the functional diversity of herbivorous reef fishes using a compound-specific stable isotope approach

    KAUST Repository

    Tietbohl, Matthew

    2016-12-01

    Herbivorous coral reef fishes play an important role in helping to structure their environment directly by consuming algae and indirectly by promoting coral health and growth. These fishes are generally separated into three broad groups: browsers, grazers, and excavators/scrapers, with these groupings often thought to have a fixed general function and all fishes within a group thought to have similar ecological roles. This categorization assumes a high level of functional redundancy within herbivorous fishes. However, recent evidence questions the use of this broad classification scheme, and posits that there may actually be more resource partitioning within these functional groupings. Here, I use a compound-specific stable isotope approach (CSIA) to show there appears to be a greater diversity of functional roles than previously assumed within broad functional groups. The δ13C signatures from essential amino acids of reef end-members (coral, macroalgae, detritus, and phytoplankton) and fish muscle were analyzed to investigate differences in resource use between fishes. Most end-members displayed clear isotopic differences, and most fishes within functional groups were dissimilar in their isotopic signature, implying differences in the resources they target. No grazers closely resembled each other isotopically, implying a much lower level of functional redundancy within this group; scraping parrotfish were also distinct from excavating parrotfish and to a lesser degree distinct between scrapers. This study highlights the potential of CSIA to help distinguish fine-scale ecological differences within other groups of reef organisms as well. These results question the utility of lumping nominally herbivorous fishes into broad groups with assumed similar roles. Given the apparent functional differences between nominally herbivorous reef fishes, it is important for managers to incorporate the diversity of functional roles these fish play.

  16. Nearshore marine fish diversity in southern California using trawl information from the Southern California Coastal Water Research Project.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is a point file of mean fish diversity within 5 minute grid cells. The Shannon Index of diversity was calculated from Southern California Coastal Water Research...

  17. Diversity and distribution of fishes in tropical estuary Kuantan, Pahang, Malaysia.

    Science.gov (United States)

    Jalal, K C A; Kamaruzzaman, B Y; Arshad, A; Ara, R; Rahman, M F

    2012-06-15

    A study on diversity and distribution of fish communities and water qualities were carried out from January 2009 to December 2010 to cover monsoon and non-monsoon at Kuantan estuary, Pahang, Malaysia. A total of 19 species of primary marine fish belong to 12 families were recorded. Out of 311 individuals the fish fauna was dominated by Ariidae followed by Lutjanidae and Lactaridae. As such Ariidae contributes 50% of the fish caught in the study area and its diversity index (H') was 0.97. A The Ariidae family consist of four (4) species; Arius maculatus, Arius sumatranus, Arius tenuispinis and Arius thalassinus. The Ariidae family can be found in all stations as they are euryhaline (highly tolerant to salinity) and this fish family are known to be a hardy estuarine catfish. Among all species in family Ariidae, Arius thalassinus was the most dominant (23%) among all species. As such collected species showed highest species diversity (0.34) followed by Arius tenuispinis (0.25) compared to other species. Arius tenuispinis alone contributed 11.90% among the samples caught from all stations. The fishes were caught and recorded highest in September-December. Pseudorhombus quinque ocellatus, Nibea soldado, Sardinella fimbriata, Toxotes jaculatrix, Dasyatis ushiei, Setipinna taty were the least dominant in the Kuantan estuary with 9.33% of total abundance. Physico-temperatures, such as temperature (22.03-30 degrees C), Conductivity (10.342.43 mS cm(-1)), TDS (0.06-26.34 mg L(-1)), salinity (0.05-29.09 ppt), DO (6.37-8.38 mg L(-1)), pH (4.97-8.03), Chl a (0.01-1.33 microg L(-1)), nitrite (0.01-0.08 mg L(-1)), nitrate (0.60-0.88 mg L(-1)), phosphate (0.24-0.40 mg L(-1)). Nevertheless, the study envisages that the water quality and fish diversity are still conducive in the Kuantan estuary. The fish diversity of Pahang estuary was high monsoon compared to non-monsoons. The station 4 (LKIM fishing boat jetty and adjacent Hospital Kuantan) is the most polluted area due to the

  18. Diversity in Fish Auditory Systems: One of the Riddles of Sensory Biology

    Directory of Open Access Journals (Sweden)

    Friedrich eLadich

    2016-03-01

    Full Text Available An astonishing diversity of inner ears and accessory hearing structures (AHS that can enhance hearing has evolved in fishes. Inner ears mainly differ in the size of the otolith end organs, the shape and orientation of the sensory epithelia, and the orientation patterns of ciliary bundles of sensory hair cells. Despite our profound morphological knowledge of inner ear variation, two main questions remain widely unanswered. (i What selective forces and/or constraints led to the evolution of this inner ear diversity? (ii How is the morphological variability linked to hearing abilities? Improved hearing is mainly based on the ability of many fish species to transmit oscillations of swim bladder walls or other gas-filled bladders to the inner ears. Swim bladders may be linked to the inner ears via a chain of ossicles (in otophysans, anterior extensions (e.g. some cichlids, squirrelfishes, or the gas bladders may touch the inner ears directly (labyrinth fishes. Studies on catfishes and cichlids demonstrate that larger swim bladders and more pronounced linkages to the inner ears positively affect both auditory sensitivities and the detectable frequency range, but lack of a connection does not exclude hearing enhancement. This diversity of auditory structures and hearing abilities is one of the main riddles in fish bioacoustics research. Hearing enhancement might have evolved to facilitate intraspecific acoustic communication. A comparison of sound-producing species, however, indicates that acoustic communication is widespread in taxa lacking AHS. Eco-acoustical constraints are a more likely explanation for the diversity in fish hearing sensitivities. Low ambient noise levels may have facilitated the evolution of AHS, enabling fish to detect low-level abiotic noise and sounds from con- and heterospecifics, including predators and prey. Aquatic habitats differ in ambient noise regimes, and preliminary data indicate that hearing sensitivities of fishes

  19. Competition for shelter in a high-diversity system: structure use by large reef fishes

    Science.gov (United States)

    Kerry, J. T.; Bellwood, D. R.

    2016-03-01

    Competition among large reef fishes for shelter beneath tabular structures provides a rare opportunity to study competition in a species-rich environment. The system permits a detailed study of localised competition with major implications for coral reefs with respect to human impacts including climate change. Using underwater video cameras, this study examined competition among 30 species of large reef fishes (from nine families) for access to shelter provided by 26 tabular structures, which may be the highest reported diversity of vertebrates competing for a single resource. Mean concentrations of fishes under tabular structures were also among the highest biomass recorded on reefs (4.71 kg m-2). A generated dominance hierarchy for the occupation of shelter appeared to be primarily driven by the size of fishes. In contrast to previous studies, fishes higher in the hierarchy tended to exhibit the lowest levels of aggression. However, size difference between fishes was found to be strongly negatively correlated with the proportion of aggressive interactions ( R 2 = 0.971, P concerns about future shifts in the structure of large reef fish communities as corals are lost. This is particularly concerning given the critical functional roles played by certain species of large reef fishes that utilise tabular structure for shelter and which occupy the lower ranks of the dominance hierarchy.

  20. Changes in Diversity of Fish Fauna of the Chu River Basin (Central Asia

    Directory of Open Access Journals (Sweden)

    Eleonora Byrlykzhanovna Kozhabaeva

    2015-11-01

    Full Text Available The Chu River originates in the Central Tien Shan Mountains and dissipates into the Muyunkum desert. The first information about the fish of the river was received in the middle 19-th century. Several expeditions collected data during 20-th century. Results of our investigations last decade in comparison with previous data allow tracking changes in the fish fauna after growing human impact. In the main, our data concern of the Kazakhstan part of the river. About 34 species and subspecies were discovered here; about 19 species between them are native. Origin or taxonomy of some species are disputable. In the last publications of the XX-th century 38 fish species and subspecies were mentioned. Native fish species as Aral barbel Barbus brachycephalus and Bulatmai barbel Barbus capito, Chu sharpray Capoetobrama kuschakewitschii and alien Sea trout Salmo trutta, Sevan trout Salmo ischchan were not found last decade in the Kazakhstan part of the river. Distribution area of native Balkhash marinka Schizothorax argentatus and alien Balkhash perch Perca schrenkii were reduced. The most widespread and numerous fish species are native roach, carp, dace, gudgeon and alien stone moroco. Native fishes like pike, asp, Aral ide, striped bystranka, golden spiny loach, southern ninespine stickleback and others were found only in certain sites. Fish species composition for each investigated site was not stable during recent years. Significant variations in fish composition were observed between different water bodies of the basin too. It reflects diversity of human impacts and unsteady water regimen here.

  1. The Digital Fish Library: using MRI to digitize, database, and document the morphological diversity of fish.

    Directory of Open Access Journals (Sweden)

    Rachel M Berquist

    Full Text Available Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org, an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators.

  2. The Digital Fish Library: using MRI to digitize, database, and document the morphological diversity of fish.

    Science.gov (United States)

    Berquist, Rachel M; Gledhill, Kristen M; Peterson, Matthew W; Doan, Allyson H; Baxter, Gregory T; Yopak, Kara E; Kang, Ning; Walker, H J; Hastings, Philip A; Frank, Lawrence R

    2012-01-01

    Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D) digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org), an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI) scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators.

  3. Survey of estrogenic activity in fish feed by yeast estrogen-screen assay.

    Science.gov (United States)

    Matsumoto, Takeru; Kobayashi, Makito; Moriwaki, Toshihisa; Kawai, Shin'ichiro; Watabe, Shugo

    2004-10-01

    Fishes have been used as laboratory animal for research of estrogenic endocrine disrupters by many researchers. However, much less attention was paid to the possibility that compounds with estrogenic activity are present in fish diets. In order to examine this possibility, we measured the estrogenic activity in commercial fish feed by in vitro yeast estrogen-screen (YES) assay based on the binding ability of tested compounds to estrogen receptors. Estrogenic activity was detected in all the commercial fish feed examined (0.2-6.2 ng estradiol equivalent/g fish feed), some phytoestrogens (genistein, formononetin, equol and coumestrol; relative activity to estradiol, 8.6 x 10(-6)-1.1 x 10(-4) by giving a value of 1.0 to estradiol) and some androgens (testosterone, 11-ketotestosterone and 5 alpha-dihydrotestosterone; relative activity to estradiol, 3.0 x 10(-6)-1.2 x 10(-4)). Therefore, it is possible that these compounds could affect the results of in vivo estrogen assay, such as vitellogenin production in male fish, especially when fish are fed commercial feed.

  4. A review of Monogenean diversity in India: Pathogens of fish diseases

    Directory of Open Access Journals (Sweden)

    Anshu Chaudhary

    2013-09-01

    Full Text Available The monogeneans parasitizing skin, fins, gills of fishes and are pathogenic to cultivated fish and a few have caused epizootic events. This paper presents a catalogue of known species of the class monogenea from the freshwater fishes of five major river systems of India. Data is gathered from all the published records of monogenean species from India and also from NCBI database for molecular studies, including the fish data gathered from Fishbase. Approximately 50 families of freshwater fishes have been reported from five Indian major river systems, having 159 nominal genera. As far as freshwater monogeneans are concerned about, 14 families having 44 genera and 208 species have been reported. In all, the present study takes a broad look at monogenean diversity in the freshwater fishes of India. The available information indicates the rich diversity of these parasites in India for that an integrated approach is necessary which should start with morphological characterization followed by molecular characterization of monogenean parasites in all river system of India. So that subsequent comparison of monogenean fauna present in different river systems of India can be made.

  5. A review of Monogenean diversity in India:Pathogens of fish diseases

    Institute of Scientific and Technical Information of China (English)

    Anshu Chaudhary; Chandni Verma; Shobhna; Manu Varma; Hridaya Shanker Singh

    2013-01-01

    The monogeneans parasitizing skin, fins, gills of fishes and are pathogenic to cultivated fish and a few have caused epizootic events. This paper presents a catalogue of known species of the class monogenea from the freshwater fishes of five major river systems of India. Data is gathered from all the published records of monogenean species from India and also from NCBI database for molecular studies, including the fish data gathered from Fishbase. Approximately 50 families of freshwater fishes have been reported from five Indian major river systems, having 159 nominal genera. As far as freshwater monogeneans are concerned about, 14 families having 44 genera and 208 species have been reported. In all, the present study takes a broad look at monogenean diversity in the freshwater fishes of India. The available information indicates the rich diversity of these parasites in India for that an integrated approach is necessary which should start with morphological characterization followed by molecular characterization of monogenean parasites in all river system of India. So that subsequent comparison of monogenean fauna present in different river systems of India can be made.

  6. Functional diversity of fish communities in two tropical estuaries subjected to anthropogenic disturbance.

    Science.gov (United States)

    Dolbeth, M; Vendel, A L; Pessanha, A; Patrício, J

    2016-11-15

    The functional diversity of fish communities was studied along the salinity gradient of two estuaries in Northeast Brazil subjected to different anthropogenic pressures, to gain a better understanding of the response of fish communities to disturbance. We evaluated functional complementarity indices, redundancy and analysed functional composition through functional groups based on combinations of different traits. The fish communities in both estuaries share similar functions performed by few functional groups. The upstream areas had generally lower taxonomic, functional diversity and lower redundancy, suggesting greater vulnerability to impacts caused by human activities. Biomass was slightly more evenly distributed among functional groups in the less disturbed estuary, but total biomass and redundancy were lower in comparison to the urbanized estuary. The present findings lend strength to the notion that the less disturbed estuary may be more susceptible to anthropogenic impacts, underscoring the need for more effective conservation measures directed at this estuary.

  7. Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle

    Science.gov (United States)

    Johnson, J.A.; Tingay, R.E.; Culver, M.; Hailer, F.; Clarke, M.L.; Mindell, D.P.

    2009-01-01

    The critically endangered Madagascar fish-eagle (Haliaeetus vociferoides) is considered to be one of the rarest birds of prey globally and at significant risk of extinction. In the most recent census, only 222 adult individuals were recorded with an estimated total breeding population of no more than 100-120 pairs. Here, levels of Madagascar fish-eagle population genetic diversity based on 47 microsatellite loci were compared with its sister species, the African fish-eagle (Haliaeetus vocifer), and 16 of these loci were also characterized in the white-tailed eagle (Haliaeetus albicilla) and the bald eagle (Haliaeetus leucocephalus). Overall, extremely low genetic diversity was observed in the Madagascar fish-eagle compared to other surveyed Haliaeetus species. Determining whether this low diversity is the result of a recent bottleneck or a more historic event has important implications for their conservation. Using a Bayesian coalescent-based method, we show that Madagascar fish-eagles have maintained a small effective population size for hundreds to thousands of years and that its low level of neutral genetic diversity is not the result of a recent bottleneck. Therefore, efforts made to prevent Madagascar fish-eagle extinction should place high priority on maintenance of habitat requirements and reducing direct and indirect human persecution. Given the current rate of deforestation in Madagascar, we further recommend that the population be expanded to occupy a larger geographical distribution. This will help the population persist when exposed to stochastic factors (e.g. climate and disease) that may threaten a species consisting of only 200 adult individuals while inhabiting a rapidly changing landscape. ?? 2008 The Authors.

  8. Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle.

    Science.gov (United States)

    Johnson, Jeff A; Tingay, Ruth E; Culver, Melanie; Hailer, Frank; Clarke, Michèle L; Mindell, David P

    2009-01-01

    The critically endangered Madagascar fish-eagle (Haliaeetus vociferoides) is considered to be one of the rarest birds of prey globally and at significant risk of extinction. In the most recent census, only 222 adult individuals were recorded with an estimated total breeding population of no more than 100-120 pairs. Here, levels of Madagascar fish-eagle population genetic diversity based on 47 microsatellite loci were compared with its sister species, the African fish-eagle (Haliaeetus vocifer), and 16 of these loci were also characterized in the white-tailed eagle (Haliaeetus albicilla) and the bald eagle (Haliaeetus leucocephalus). Overall, extremely low genetic diversity was observed in the Madagascar fish-eagle compared to other surveyed Haliaeetus species. Determining whether this low diversity is the result of a recent bottleneck or a more historic event has important implications for their conservation. Using a Bayesian coalescent-based method, we show that Madagascar fish-eagles have maintained a small effective population size for hundreds to thousands of years and that its low level of neutral genetic diversity is not the result of a recent bottleneck. Therefore, efforts made to prevent Madagascar fish-eagle extinction should place high priority on maintenance of habitat requirements and reducing direct and indirect human persecution. Given the current rate of deforestation in Madagascar, we further recommend that the population be expanded to occupy a larger geographical distribution. This will help the population persist when exposed to stochastic factors (e.g. climate and disease) that may threaten a species consisting of only 200 adult individuals while inhabiting a rapidly changing landscape.

  9. Yakima and Touchet River Basins Phase II Fish Screen Evaluation, 2006-2007 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Chamness, Mickie; Tunnicliffe, Cherylyn [Pacific Northwest National Laboratory

    2007-03-01

    In 2006, Pacific Northwest National Laboratory (PNNL) researchers evaluated 27 Phase II fish screen sites in the Yakima and Touchet river basins. Pacific Northwest National Laboratory performs these evaluations for Bonneville Power Administration (BPA) to determine whether the fish screening devices meet those National Marine Fisheries (NMFS) criteria for juvenile fish screen design, that promote safe and timely passage of juvenile salmonids. The NMFS criteria against which the sites were evaluated are as follows: (1) a uniform flow distribution over the screen surface to minimize approach velocity; (2) approach velocities less than or equal to 0.4 ft/s protects the smallest salmonids from impingement; (3) sweep velocities that are greater than approach velocities to minimize delay of out-migrating juveniles and minimize sediment deposition near the screens; (4) a bypass flow greater than or equal to the maximum flow velocity vector resultant upstream of the screens to also minimize delay of out-migrating salmonids; (5) a gradual and efficient acceleration of flow from the upstream end of the site into the bypass entrance to minimize delay of out-migrating salmonids; and (6) screen submergence between 65% and 85% for drum screen sites. In addition, the silt and debris accumulation next to the screens should be kept to a minimum to prevent excessive wear on screens, seals and cleaning mechanisms. Evaluations consist of measuring velocities in front of the screens, using an underwater camera to assess the condition and environment in front of the screens, and noting the general condition and operation of the sites. Results of the evaluations in 2006 include the following: (1) Most approach velocities met the NMFS criterion of less than or equal to 0.4 ft/s. Of the sites evaluated, 31% exceeded the criterion at least once. Thirty-three percent of flat-plate screens had problems compared to 25% of drum screens. (2) Woody debris and gravel deposited during high river

  10. Global cooperation among diverse organizations to reduce illegal fishing in the Southern Ocean.

    Science.gov (United States)

    Osterblom, Henrik; Bodin, Orjan

    2012-08-01

    Illegal, unreported, and unregulated (IUU) fishing is prevalent globally and has detrimental effects on commercial fish stocks and nontarget species. Effective monitoring and enforcement aimed at reducing the level of IUU fishing in extensive, remote ocean fisheries requires international collaboration. Changes in trade and vessel activities further complicate enforcement. We used a web-based survey of governmental and nongovernmental organizations engaged in reducing IUU fishing in the Southern Ocean to collect information on interorganizational collaborations. We used social-network analyses to examine the nature of collaborations among the identified 117 organizations engaged in reducing IUU fishing. International collaboration improved the ability to control and manage harvest of commercially important toothfish (Dissostichus spp.) stocks and reduced bycatch of albatrosses (Diomedeidae) and petrels (Procellariidae) in longlines of IUU fishing vessels. The diverse group of surveyed organizations cooperated frequently, thereby making a wide range of resources available for improved detection of suspected IUU vessels and trade flows, cooperation aimed at prosecuting suspected offenders or developing new policy measures. Our results suggest the importance of a central agency for coordination and for maintaining commonly agreed-upon protocols for communication that facilities collaboration. Despite their differences, the surveyed organizations have developed common perceptions about key problems associated with IUU fishing. This has likely contributed to a sustained willingness to invest in collaborations. Our results show that successful international environmental governance can be accomplished through interorganizational collaborations. Such cooperation requires trust, continuous funding, and incentives for actors to participate.

  11. Community structure and diversity of demersal fish assemblages: the role of fishery

    Directory of Open Access Journals (Sweden)

    Mary Labropoulou

    2004-04-01

    Full Text Available Seasonal experimental trawl surveys were carried out in the Northern Aegean and Thracian seas (NE Mediterranean, Greece, from summer 1990 to autumn 1993, during which a total of 172 fish species were caught. In these areas, fishing pressure is very high, since approximately 50% of the Greek otter trawl fleet operates there, producing more than 57% of the total demersal landings. Different statistics were used to assess spatial structure, seasonal changes and diversity of the demersal fish assemblages on the continental shelf and upper slope. The following measures were applied to the species abundance matrix: species diversity, species richness, evenness and dominance. The analysis of 501 bottom trawls revealed that, in general, species diversity, richness and evenness decreased with water depth, with the highest values at depths 200 m. The effect of depth on the diversity patterns observed was always significant, while seasonal trends were similar with those described for the overall diversity characteristics in each area. Classification and ordination methods showed the existence of 4 groups associated with the continental shelf and upper slope in each area. Classification of the top ranking species at each group and area revealed that commercially important species were dominant in the shallowest zone (

  12. Diversity of Inner Ears in Fishes: Possible Contribution Towards Hearing Improvements and Evolutionary Considerations.

    Science.gov (United States)

    Schulz-Mirbach, Tanja; Ladich, Friedrich

    2016-01-01

    Fishes have evolved the largest diversity of inner ears among vertebrates. While G. Retzius introduced us to the diversity of the gross morphology of fish ears in the late nineteenth century, it was A. N. Popper who unraveled the large variety of the fine structure during the last four decades. Modifications of the basic inner ear structure-consisting of three semicircular canals and their sensory epithelia, the cristae and three otolithic end organs (utricle, saccule, lagena) including the maculae-mainly relate to the saccule and lagena and the respective sensory epithelia, the macula sacculi and macula lagenae. Despite the profound morphological knowledge of inner ears and the morphological variability, the functional significance of this diversity is still largely unknown. The aims of this review are therefore twofold. First it provides an update of the state of the art of inner ear diversity in bony fishes. Second it summarizes and discusses hypotheses on the evolution of this diversity as well as formulates open questions and promising approaches to tackle these issues.

  13. Diversity of CD2 subfamily receptors in cyprinid fishes.

    Science.gov (United States)

    Sameshima, Shiro; Nakao, Miki; Somamoto, Tomonori

    2012-01-01

    CD2 family receptor (CD2f) is evolutionarily conserved and is widely expressed by various types of leukocytes. To elucidate the phylogenetic diversity of the CD2f, we characterized CD2f in teleosts using ginbuna crucian carp and zebrafish. The identified CD2f isoforms of the ginbuna carp (caauCD2f) exhibited high sequence similarity to the mammalian CD2 subsets CD48, CD244, and CD319, but it was difficult to classify them into their respective mammalian CD2f based on sequence similarity, the presence of an immunoreceptor tyrosine-based switch motif (ITSM), and phylogenetic tree analysis. Although the four caauCD2f isoforms share an extracellular domain with quite high identity (83-94% identity at the nucleic acid level), they differ in the number of ITSM motifs in their cytoplasmic tail. RT-PCR and in situ hybridization analyses showed that the caauCD2f isoforms are expressed by different cell populations, suggesting that they, like mammalian CD2f, have diverse roles. Interestingly, immunoglobulin (Ig) domain-like sequences with high identity to caauCD2fs are clustered close together within 0.6 Mbp on zebrafish chromosomes 1 and 2 (at least 8 and 35 sequences, respectively), and many pairs of the Ig domains share more than 90% identity at the amino acid level. Therefore, the teleost CD2fs with considerably high identity have been probably generated from a common ancestral Ig-domain gene by a very recent gene duplication event. These findings suggest that the identified CD2f acquired functional diversification through successive duplications together with the acquisition of ITSM.

  14. Digenean species diversity in teleost fishes from the Gulf of Gabes, Tunisia (Western Mediterranean

    Directory of Open Access Journals (Sweden)

    Derbel H.

    2012-05-01

    Full Text Available This study is the first attempt to survey the diversity of fish digeneans in the Gulf of Gabes (southern coast of Tunisia. A total of 779 fishes belonging to 32 species were sampled. 53 species of Digenea belonging to 15 families were recorded. Among these species, 24 are reported for the first time from the coast of Tunisia. We report one new host record, Lecithochirium sp. from Sardinella aurita. The Hemiuridae is the dominant family. A host-parasite list is presented with the information on the prevalence, abundance and mean intensity of each species collected. The diversity of Digenea is compared with other localities in the Mediterranean Sea and the northern east of Tunisia. The Gulf of Gabes shows the lowest diversity linked to the anthropogenic activities and impact of exotic species. The use of Digenea as indicators of the state of the ecosystem is discussed.

  15. Applicability of ELISA to screen for dioxin-like PCBs in retail fish

    Energy Technology Data Exchange (ETDEWEB)

    Tsutsumi, T.; Amakura, Y.; Sasaki, K.; Maitani, T. [National Institute of Health Sciences, Tokyo (Japan); Okuyama, A.; Mizukami, H. [EnBioTec Laboratories Co., Ltd., Tokyo (Japan); Tanioka, Y.; Ueda, K.; Sakata, K. [Daiichi Fine Chemical Co., Ltd., Toyama (Japan)

    2004-09-15

    The group of dioxin-like PCBs, consisting of four non-ortho PCBs and eight mono-ortho PCBs, is classified among the dioxins. Humans are considerably exposed to dioxin through consumption of fish in Japan. The TEQ contribution of dioxin-like PCBs in fish is dominant, contributing about 70% of the total TEQ. Therefore, it is important to reveal TEQ levels of dioxin-like PCBs as well as PCDD/Fs in retail fish. HRGC/HRMS is currently the most widely used method to determine levels of dioxin-like PCBs. This method is very reliable and highly sensitive, but it is also timeconsuming and requires expensive equipment and highly trained analysts. One possible alternative method for screening dioxin-like PCBs is a bioassay, such as an ELISA. We recently developed an ELISA kit using a monoclonal antibody (MAb) specific to 2,3{sup '},4,4{sup '},5-pentachlorobiphenyl (PCB 118). PCB 118 is generally the most abundant isomer among dioxin-like PCBs in fish, although it has a relatively small contribution to the total TEQ derived from dioxin-like PCBs. Based on our HRGC/HRMS data, we found that the concentrations of PCB 118 correlated well to the TEQ levels of dioxin-like PCBs in retail fish (r>0.85, n = 181). Here, we examined the application of the ELISA kit in determining TEQ levels of dioxin-like PCBs in retail fish.

  16. Yakima and Touchet River Basins Phase II Fish Screen Evaluation, 2006-2007 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Chamness, Mickie; Tunnicliffe, Cherylyn [Pacific Northwest National Laboratory

    2007-03-01

    In 2006, Pacific Northwest National Laboratory (PNNL) researchers evaluated 27 Phase II fish screen sites in the Yakima and Touchet river basins. Pacific Northwest National Laboratory performs these evaluations for Bonneville Power Administration (BPA) to determine whether the fish screening devices meet those National Marine Fisheries (NMFS) criteria for juvenile fish screen design, that promote safe and timely passage of juvenile salmonids. The NMFS criteria against which the sites were evaluated are as follows: (1) a uniform flow distribution over the screen surface to minimize approach velocity; (2) approach velocities less than or equal to 0.4 ft/s protects the smallest salmonids from impingement; (3) sweep velocities that are greater than approach velocities to minimize delay of out-migrating juveniles and minimize sediment deposition near the screens; (4) a bypass flow greater than or equal to the maximum flow velocity vector resultant upstream of the screens to also minimize delay of out-migrating salmonids; (5) a gradual and efficient acceleration of flow from the upstream end of the site into the bypass entrance to minimize delay of out-migrating salmonids; and (6) screen submergence between 65% and 85% for drum screen sites. In addition, the silt and debris accumulation next to the screens should be kept to a minimum to prevent excessive wear on screens, seals and cleaning mechanisms. Evaluations consist of measuring velocities in front of the screens, using an underwater camera to assess the condition and environment in front of the screens, and noting the general condition and operation of the sites. Results of the evaluations in 2006 include the following: (1) Most approach velocities met the NMFS criterion of less than or equal to 0.4 ft/s. Of the sites evaluated, 31% exceeded the criterion at least once. Thirty-three percent of flat-plate screens had problems compared to 25% of drum screens. (2) Woody debris and gravel deposited during high river

  17. Composition and diversity of larval fish in the mangrove estuarine area of Marudu Bay, Sabah, Malaysia.

    Science.gov (United States)

    Rezagholinejad, Sadaf; Arshad, Aziz; Amin, S M Nurul; Ara, Roushon

    2016-07-01

    The composition of fish larvae and their diversity in different habitats are very important for fisheries management. Larval fishes were investigated in a mangrove estuary of Marudu Bay, Sabah, Malaysia from October 2012 to September 2013 at five different sites. Monthly samples of fish larvae were collected at five sampling sites by a plankton net with a mouth opening of 40.5 cm in diameter. In total, 3879 larval fish were caught in the investigated area. The mean density of ichthyoplankton at this area was 118 larvae/100 m(3). The fish larval assemblage comprised of 20 families whereas 13 families occurred at St1, 16 at St2, 16 at St3, 12 at St4 and 16 at St5. The top major families were Sillaginidae, Engraulidae, Mugilidae and Sparidae with Sillaginidae consisted 44% of total larval composition. St3 with 143 larvae/100 m(3) had the highest density amongst the stations which was due to higher abundance of Sillaginidae. Shannon-Wiener diversity index represented significant variation during monsoon and inter-monsoon seasons, peaking in the months December-January and May-June. However, Shannon-Wiener index, evenness and family richness showed significant differences among stations and months (p < 0.05).

  18. Diversity and Distribution of Freshwater Fishes in Aceh Water, Northern-Sumatra,Indonesia

    Directory of Open Access Journals (Sweden)

    M.N. Siti Azizah

    2009-01-01

    Full Text Available The objective of the present study was to evaluate the diversity of freshwater fish and its distribution and to establish an inventory of the freshwater fish fauna in Aceh water. Sampling was done in five regions of NAD at 17 sites. Explorative research was conducted from January to June 2008 by investigating rivers based on information by local residents. Sampling was carried out in both lotic and lentic ecosystems. A total of 711 fishes belonging to 114 species, 69 genera, 41 families and 12 orders. Five families were distributed widely and observed in all the five regions i.e., Anguillidae, Clariidae, Cyprinidae, Anabantidae and Channidae. Sixteen families were found in only a single site. The diversity index of fishes in Aceh water ranged from 1.31 to 3.41 with an average of 2.17 indicating moderate values. The highest diversity was found in Lembang River of Aceh Selatan, while regionally, the North and south regions were higher but not significantly different from the West region. Highest similarity was found between Simpang dam and Sibreh irrigation canal of Sibreh. The similarity index between West and North region were relatively higher compared to other regional comparisons.

  19. Nocturnality constrains morphological and functional diversity in the eyes of reef fishes

    Directory of Open Access Journals (Sweden)

    Schmitz Lars

    2011-11-01

    Full Text Available Abstract Background Ambient light levels are often considered to drive the evolution of eye form and function. Diel activity pattern is the main mechanism controlling the visual environment of teleost reef fish, with day-active (diurnal fish active in well-illuminated conditions, whereas night-active (nocturnal fish cope with dim light. Physiological optics predicts several specific evolutionary responses to dim-light vision that should be reflected in visual performance features of the eye. Results We analyzed a large comparative dataset on morphological traits of the eyes in 265 species of teleost reef fish in 43 different families. The eye morphology of nocturnal reef teleosts is characterized by a syndrome that indicates better light sensitivity, including large relative eye size, high optical ratio and large, rounded pupils. Improved dim-light image formation comes at the cost of reduced depth of focus and reduction of potential accommodative lens movement. Diurnal teleost reef fish, released from the stringent functional requirements of dim-light vision have much higher morphological and optical diversity than nocturnal species, with large ranges of optical ratio, depth of focus, and lens accommodation. Conclusions Physical characteristics of the environment are an important factor in the evolution and diversification of the vertebrate eye. Both teleost reef fish and terrestrial amniotes meet the functional requirements of dim-light vision with a similar evolutionary response of morphological and optical modifications. The trade-off between improved dim-light vision and reduced optical diversity may be a key factor in explaining the lower trophic diversity of nocturnal reef teleosts.

  20. Marine dock pilings foster diverse, native cryptobenthic fish assemblages across bioregions.

    Science.gov (United States)

    Brandl, Simon J; Casey, Jordan M; Knowlton, Nancy; Duffy, James Emmett

    2017-09-01

    Anthropogenic habitats are increasingly prevalent in coastal marine environments. Previous research on sessile epifauna suggests that artificial habitats act as a refuge for nonindigenous species, which results in highly homogenous communities across locations. However, vertebrate assemblages that live in association with artificial habitats are poorly understood. Here, we quantify the biodiversity of small, cryptic (henceforth "cryptobenthic") fishes from marine dock pilings across six locations over 35° of latitude from Maine to Panama. We also compare assemblages from dock pilings to natural habitats in the two southernmost locations (Panama and Belize). Our results suggest that the biodiversity patterns of cryptobenthic fishes from dock pilings follow a Latitudinal Diversity Gradient (LDG), with average local and regional diversity declining sharply with increasing latitude. Furthermore, a strong correlation between community composition and spatial distance suggests distinct regional assemblages of cryptobenthic fishes. Cryptobenthic fish assemblages from dock pilings in Belize and Panama were less diverse and had lower densities than nearby reef habitats. However, dock pilings harbored almost exclusively native species, including two species of conservation concern absent from nearby natural habitats. Our results suggest that, in contrast to sessile epifaunal assemblages on artificial substrates, artificial marine habitats can harbor diverse, regionally characteristic assemblages of vertebrates that follow macroecological patterns that are well documented for natural habitats. We therefore posit that, although dock pilings cannot function as a replacement for natural habitats, dock pilings may provide cost-effective means to preserve native vertebrate biodiversity, and provide a habitat that can be relatively easily monitored to track the status and trends of fish biodiversity in highly urbanized coastal marine environments.

  1. Diversity of trypanorhynch metacestodes in teleost fishes from coral reefs off eastern Australia and New Caledonia

    Directory of Open Access Journals (Sweden)

    Beveridge Ian

    2014-01-01

    Full Text Available Trypanorhynch metacestodes were examined from teleosts from coral reefs in eastern Australia and from New Caledonia. From over 12,000 fishes examined, 33 named species of trypanorhynchs were recovered as well as three species of tentacularioids which are described but not named. Host-parasite and parasite-host lists are provided, including more than 100 new host records. Lacistorhynchoid and tentacularioid taxa predominated with fewer otobothrioid and gymnorhynchoids. Five species, Callitetrarhynchus gracilis, Floriceps minacanthus, Pseudotobothrium dipsacum, Pseudolacistorhynchus heroniensis and Ps. shipleyi, were particularly common and exhibited low host specificity. Limited data suggested a higher diversity of larval trypanorhynchs in larger piscivorous fish families. Several fish families surveyed extensively (Blenniidae, Chaetodontidae, Gobiidae, Kyphosidae and Scaridae yielded no trypanorhynch larvae. The overall similarity between the fauna of the Great Barrier Reef and New Caledonia was 45%. Where available, information on the adult stages in elasmobranchs has been included.

  2. Fish diversity and assemblage structure in Ken River of Panna landscape, central India

    Directory of Open Access Journals (Sweden)

    J.A. Johnson

    2012-10-01

    Full Text Available Fish diversity and assemblage structure in relation to habitat variables were studied in 15 sites in Panna landscape, central India. The sampling was performed between February-April 2009. Fifty species of fishes belonging to 32 genera, 15 families and four orders were recorded from the study area. Cyprinids were the dominant assemblage members in all study streams (abundance ranges from 56.6-94.5 %. The cyprinid Devario aequipinnatus and the snakehead Channa gachua had highest local dominance (80% each in Panna landscape. High Shannon and Margalef’s diversity was recorded in Madla region of Ken River. Similarity cluster analysis explained the study sites along Ken River (Gahrighat, Magradabri and Madla had similar faunal assemblage. Canonical Correspondence Analysis (CCA was performed to study the species association with a set of environmental variables. The CCA revealed that cyprinid abundance was associated with stream order, deeper habitat, flow and water temperature.

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

    Science.gov (United States)

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

    2013-12-30

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

  4. Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics.

    Science.gov (United States)

    Artoni, Roberto Ferreira; Castro, Jonathan Pena; Jacobina, Uedson Pereira; Lima-Filho, Paulo Augusto; da Costa, Gideão Wagner Werneck Félix; Molina, Wagner Franco

    2015-01-01

    Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

  5. Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics

    Directory of Open Access Journals (Sweden)

    Roberto Ferreira Artoni

    2015-01-01

    Full Text Available Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

  6. Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

    Science.gov (United States)

    Hitt, Nathaniel P.; Chambers, Douglas B.

    2014-01-01

    Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

  7. Environmental drivers of fish functional diversity and composition in the Lower Colorado River Basin

    Science.gov (United States)

    Pool, T.K.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

    2010-01-01

    Freshwater conservation efforts require an understanding of how natural and anthropogenic factors shape the present-day biogeography of native and non-native species. This knowledge need is especially acute for imperiled native fishes in the highly modified Lower Colorado River Basin (LCRB), USA. In the present study we employed both a taxonomic and functional approach to explore how natural and human-related environmental drivers shape landscape-scale patterns of fish community composition in the LCRB. Our results showed that hydrologic alteration, watershed land use, and regional climate explained 30.3% and 44.7% of the total variation in fish community taxonomic and functional composition, respectively. Watersheds with greater dam densities and upstream storage capacity supported higher non-native functional diversity, suggesting that dams have provided additional "niche opportunities" for non-native equilibrium life-history strategists by introducing new reservoir habitat and modifying downstream flow and thermal regimes. By contrast, watersheds characterized by greater upstream land protection, lower dam densities, and higher variation in spring and summer precipitation supported fish communities with a strong complement of native species (opportunistic-periodic strategists). In conclusion, our study highlights the utility of a life-history approach to better understand the patterns and processes by which fish communities vary along environmental gradients.

  8. A regional perspective on the diversity and conservation of tropical Andean fishes.

    Science.gov (United States)

    Anderson, Elizabeth P; Maldonado-Ocampo, Javier A

    2011-02-01

    The tropical Andes harbor an extraordinarily varied concentration of species in a landscape under increasing pressure from human activities. Conservation of the region's native plants and animals has received considerable international attention, but the focus has been on terrestrial biota. The conservation of freshwater fauna, particularly the conservation of fishes, has not been emphasized. Tropical Andean fishes are among the most understudied vertebrates in the world. We estimate that between 400 and 600 fish species inhabit the diverse aquatic environments in the region. Nearly 40% of these species are endemic. Tropical Andean fishes are vulnerable to ongoing environmental changes related to deforestation, water withdrawals, water pollution, species introductions, and hydropower development. Additionally, their distributions and population dynamics may be affected by hydrologic alterations and warmer water temperatures associated with projected climate change. Presently, at least three species are considered extinct, some populations are endangered, and some species are likely to decline or disappear. The long-term persistence of tropical Andean fishes will depend on greater consideration of freshwater systems in regional conservation initiatives.

  9. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    Science.gov (United States)

    Strecker, Angela; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates

  10. Contrasting changes in taxonomic vs. functional diversity of tropical fish communities after habitat degradation.

    Science.gov (United States)

    Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernández, Domingo; Mouillot, David

    2010-09-01

    Human activities have strong impacts on ecosystem functioning through their effect on abiotic factors and on biodiversity. There is also growing evidence that species functional traits link changes in species composition and shifts in ecosystem processes. Hence, it appears to be of utmost importance to quantify modifications in the functional structure of species communities after human disturbance in addition to changes in taxonomic structure. Despite this fact, there is still little consensus on the actual impacts of human-mediated habitat alteration on the components of biodiversity, which include species functional traits. Therefore, we studied changes in taxonomic diversity (richness and evenness), in functional diversity, and in functional specialization of estuarine fish communities facing drastic environmental and habitat alterations. The Terminos Lagoon (Gulf of Mexico) is a tropical estuary of primary concern for its biodiversity, its habitats, and its resource supply, which have been severely impacted by human activities. Fish communities were sampled in four zones of the Terminos Lagoon 18 years apart (1980 and 1998). Two functions performed by fish (food acquisition and locomotion) were studied through the measurement of 16 functional traits. Functional diversity of fish communities was quantified using three independent components: richness, evenness, and divergence. Additionally, we measured the degree of functional specialization in fish communities. We used a null model to compare the functional and the taxonomic structure of fish communities between 1980 and 1998. Among the four largest zones studied, three did not show strong functional changes. In the northern part of the lagoon, we found an increase in fish richness but a significant decrease of functional divergence and functional specialization. We explain this result by a decline of specialized species (i.e., those with particular combinations of traits), while newly occurring species are

  11. Calibration of FISK, an invasiveness screening tool for nonnative freshwater fishes.

    Science.gov (United States)

    Copp, Gordon H; Vilizzi, Lorenzo; Mumford, John; Fenwick, Gemma V; Godard, Michael J; Gozlan, Rodolphe E

    2009-03-01

    Adapted from the weed risk assessment (WRA) of Pheloung, Williams, and Halloy, the fish invasiveness scoring kit (FISK) was proposed as a screening tool for freshwater fishes. This article describes improvements to FISK, in particular the incorporation of confidence (certainty/uncertainty) ranking of the assessors' responses, and reports on the calibration of the score system, specifically: determination of most appropriate score thresholds for classifying nonnative species into low-, medium-, and high-risk categories, assessment of the patterns of assessors' confidences in their responses in the FISK assessments. Using receiver operating characteristic (ROC) curves, FISK was demonstrated to distinguish accurately (and with statistical confidence) between potentially invasive and noninvasive species of nonnative fishes, with the statistically appropriate threshold score for high-risk species scores being >/=19. Within the group of species classed as high risk using this new threshold, a "higher risk" category could be visually identified, at present consisting of two species (topmouth gudgeon Pseudorasbora parva and gibel carp Carassius gibelio). FISK represents a useful and viable tool to aid decision- and policymakers in assessing and classifying freshwater fishes according to their potential invasiveness.

  12. Distribution, abundance, diversity and habitat associations of fishes across a bioregion experiencing rapid coastal development

    Science.gov (United States)

    McLean, Dianne L.; Langlois, Tim J.; Newman, Stephen J.; Holmes, Thomas H.; Birt, Matthew J.; Bornt, Katrina R.; Bond, Todd; Collins, Danielle L.; Evans, Scott N.; Travers, Michael J.; Wakefield, Corey B.; Babcock, Russ C.; Fisher, Rebecca

    2016-09-01

    Knowledge of the factors that influence spatial patterns in fish abundance, distribution and diversity are essential for informing fisheries and conservation management. The present study was conducted in the nearshore Pilbara bioregion of north-western Australia where the dynamic marine environment is characterised by large embayments, numerous islands and islets, coexisting with globally significant petrochemical and mineral industries. Within Western Australia, this nearshore bioregion has high biodiversity and is considered to play an essential role in the recruitment of species of commercial importance. To better inform future investigations into both ecological processes and planning scenarios for management, a rapid assessment of the distribution, abundance and associations with nearshore habitats of fishes across the region was conducted. Baited remote underwater stereo-video systems (stereo-BRUVs) were used to simultaneously sample the fish assemblage and habitat composition. Generalised additive mixed models (GAMMs) were used to determine whether the abundance of fishes were related to habitat and a range of environmental variables (visibility, depth, distance to 30 m and 200 m depth isobars, boat ramps and the nearest large embayment (Exmouth Gulf). A diverse fish assemblage comprising 343 species from 58 families was recorded. The abundance and distribution patterns of fishery-target species and of the five most common and abundant species and families were linked positively with areas of high relief, hard coral cover, reef and macroalgae and negatively with the distance to the nearest oceanic waters (200 m depth isobar). This study provides information that can contribute to future marine spatial planning scenarios for management of the Pilbara using a unique, analytical approach that has broad application in biogeography.

  13. Diversity among macroalgae-consuming fishes on coral reefs: a transcontinental comparison.

    Directory of Open Access Journals (Sweden)

    Adriana Vergés

    Full Text Available Despite high diversity and abundance of nominally herbivorous fishes on coral reefs, recent studies indicate that only a small subset of taxa are capable of removing dominant macroalgae once these become established. This limited functional redundancy highlights the potential vulnerability of coral reefs to disturbance and stresses the need to assess the functional role of individual species of herbivores. However, our knowledge of species-specific patterns in macroalgal consumption is limited geographically, and there is a need to determine the extent to which patterns observed in specific reefs can be generalised at larger spatial scales. In this study, video cameras were used to quantify rates of macroalgae consumption by fishes in two coral reefs located at a similar latitude in opposite sides of Australia: the Keppel Islands in the Great Barrier Reef (eastern coast and Ningaloo Reef (western coast. The community of nominally herbivorous fish was also characterised in both systems to determine whether potential differences in the species observed feeding on macroalgae were related to spatial dissimilarities in herbivore community composition. The total number of species observed biting on the dominant brown alga Sargassum myriocystum differed dramatically among the two systems, with 23 species feeding in Ningaloo, compared with just 8 in the Keppel Islands. Strong differences were also found in the species composition and total biomass of nominally herbivorous fish, which was an order of magnitude higher in Ningaloo. However, despite such marked differences in the diversity, biomass, and community composition of resident herbivorous fishes, Sargassum consumption was dominated by only four species in both systems, with Naso unicornis and Kyphosus vaigiensis consistently emerging as dominant feeders of macroalgae.

  14. Diversity among macroalgae-consuming fishes on coral reefs: a transcontinental comparison.

    Science.gov (United States)

    Vergés, Adriana; Bennett, Scott; Bellwood, David R

    2012-01-01

    Despite high diversity and abundance of nominally herbivorous fishes on coral reefs, recent studies indicate that only a small subset of taxa are capable of removing dominant macroalgae once these become established. This limited functional redundancy highlights the potential vulnerability of coral reefs to disturbance and stresses the need to assess the functional role of individual species of herbivores. However, our knowledge of species-specific patterns in macroalgal consumption is limited geographically, and there is a need to determine the extent to which patterns observed in specific reefs can be generalised at larger spatial scales. In this study, video cameras were used to quantify rates of macroalgae consumption by fishes in two coral reefs located at a similar latitude in opposite sides of Australia: the Keppel Islands in the Great Barrier Reef (eastern coast) and Ningaloo Reef (western coast). The community of nominally herbivorous fish was also characterised in both systems to determine whether potential differences in the species observed feeding on macroalgae were related to spatial dissimilarities in herbivore community composition. The total number of species observed biting on the dominant brown alga Sargassum myriocystum differed dramatically among the two systems, with 23 species feeding in Ningaloo, compared with just 8 in the Keppel Islands. Strong differences were also found in the species composition and total biomass of nominally herbivorous fish, which was an order of magnitude higher in Ningaloo. However, despite such marked differences in the diversity, biomass, and community composition of resident herbivorous fishes, Sargassum consumption was dominated by only four species in both systems, with Naso unicornis and Kyphosus vaigiensis consistently emerging as dominant feeders of macroalgae.

  15. Climate mediates hypoxic stress on fish diversity and nursery function at the land-sea interface.

    Science.gov (United States)

    Hughes, Brent B; Levey, Matthew D; Fountain, Monique C; Carlisle, Aaron B; Chavez, Francisco P; Gleason, Mary G

    2015-06-30

    Coastal ecosystems provide numerous important ecological services, including maintenance of biodiversity and nursery grounds for many fish species of ecological and economic importance. However, human population growth has led to increased pollution, ocean warming, hypoxia, and habitat alteration that threaten ecosystem services. In this study, we used long-term datasets of fish abundance, water quality, and climatic factors to assess the threat of hypoxia and the regulating effects of climate on fish diversity and nursery conditions in Elkhorn Slough, a highly eutrophic estuary in central California (United States), which also serves as a biodiversity hot spot and critical nursery grounds for offshore fisheries in a broader region. We found that hypoxic conditions had strong negative effects on extent of suitable fish habitat, fish species richness, and abundance of the two most common flatfish species, English sole (Parophrys vetulus) and speckled sanddab (Citharichthys stigmaeus). The estuary serves as an important nursery ground for English sole, making this species vulnerable to anthropogenic threats. We determined that estuarine hypoxia was associated with significant declines in English sole nursery habitat, with cascading effects on recruitment to the offshore adult population and fishery, indicating that human land use activities can indirectly affect offshore fisheries. Estuarine hypoxic conditions varied spatially and temporally and were alleviated by strengthening of El Niño conditions through indirect pathways, a consistent result in most estuaries across the northeast Pacific. These results demonstrate that changes to coastal land use and climate can fundamentally alter the diversity and functioning of coastal nurseries and their adjacent ocean ecosystems.

  16. Permian-Triassic Osteichthyes (bony fishes): diversity dynamics and body size evolution.

    Science.gov (United States)

    Romano, Carlo; Koot, Martha B; Kogan, Ilja; Brayard, Arnaud; Minikh, Alla V; Brinkmann, Winand; Bucher, Hugo; Kriwet, Jürgen

    2016-02-01

    The Permian and Triassic were key time intervals in the history of life on Earth. Both periods are marked by a series of biotic crises including the most catastrophic of such events, the end-Permian mass extinction, which eventually led to a major turnover from typical Palaeozoic faunas and floras to those that are emblematic for the Mesozoic and Cenozoic. Here we review patterns in Permian-Triassic bony fishes, a group whose evolutionary dynamics are understudied. Based on data from primary literature, we analyse changes in their taxonomic diversity and body size (as a proxy for trophic position) and explore their response to Permian-Triassic events. Diversity and body size are investigated separately for different groups of Osteichthyes (Dipnoi, Actinistia, 'Palaeopterygii', 'Subholostei', Holostei, Teleosteomorpha), within the marine and freshwater realms and on a global scale (total diversity) as well as across palaeolatitudinal belts. Diversity is also measured for different palaeogeographical provinces. Our results suggest a general trend from low osteichthyan diversity in the Permian to higher levels in the Triassic. Diversity dynamics in the Permian are marked by a decline in freshwater taxa during the Cisuralian. An extinction event during the end-Guadalupian crisis is not evident from our data, but 'palaeopterygians' experienced a significant body size increase across the Guadalupian-Lopingian boundary and these fishes upheld their position as large, top predators from the Late Permian to the Late Triassic. Elevated turnover rates are documented at the Permian-Triassic boundary, and two distinct diversification events are noted in the wake of this biotic crisis, a first one during the Early Triassic (dipnoans, actinistians, 'palaeopterygians', 'subholosteans') and a second one during the Middle Triassic ('subholosteans', neopterygians). The origination of new, small taxa predominantly among these groups during the Middle Triassic event caused a

  17. Zooplankton diversity and the predatory impact by larval and small juvenile fish at the Fisher Banks in the North Sea

    DEFF Research Database (Denmark)

    Nielsen, Torkel Gissel; Munk, Peter

    1998-01-01

    The biomass and diversity of the mesozooplankton and fish larvae community were investigated across a frontal zone in the central North Sea in the early summer, to investigate whether larval fish predation is a regulator of mesozooplankton production. Pronounced changes in the mesozooplankton com...

  18. Fish assemblages and diversity in three tributaries of the Irrawaddy River in China: changes, threats and conservation perspectives

    Directory of Open Access Journals (Sweden)

    Yang M.-L.

    2016-01-01

    Full Text Available Incompletely known fish assemblages and species diversity are substantial obstacles in fish conservation, particularly when their aquatic habitats are under threat due to rapid human-induced changes. Fish assemblages and diversity in three tributaries of the upper Irrawaddy River in China (the Dulong, Daying and Ruili rivers were examined based on field collections and literature resources. The newly compiled fish assemblage recorded 85 species (in 8 orders, 20 families and 51 genera distributed in the upper Irrawaddy. The fish compositions in the Daying (67 species, 44 genera, 19 families, 7 orders and Ruili rivers (65 species, 44 genera, 19 families, 8 orders were more similar to each other and more speciose than that in the Dulong River (14 species, 10 genera, 4 families, 3 orders. Two indices of taxonomic diversity (the average taxonomic distinctness (Δ+, and the variation in taxonomic distinctness (Λ+ were used to discriminate four collections spanning a ten-year period. A decrease in taxonomic diversity and an increase in unevenness of the fish assemblages were found in both the Daying River and Ruili rivers, which indicated that the impacts were accumulated gradually during this decade, when dams and the spread of non-native species were major threats. Comparatively speaking, the Dulong River is still in a near-natural state, and thus the fish community has experienced less disturbance. In situ conservation (nature reserves and tributary protection and ex situ conservation (artificial propagation and release should be combined and managed to promote fish conservation in the future.

  19. Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

    Science.gov (United States)

    Díaz-Pérez, Leopoldo; Rodríguez-Zaragoza, Fabián Alejandro; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María Del Carmen

    2016-01-01

    This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea.

  20. Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea

    Science.gov (United States)

    Díaz-Pérez, Leopoldo; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D.; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María del Carmen

    2016-01-01

    This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea. PMID:27579575

  1. Human-mediated loss of phylogenetic and functional diversity in coral reef fishes.

    Science.gov (United States)

    D'agata, Stéphanie; Mouillot, David; Kulbicki, Michel; Andréfouët, Serge; Bellwood, David R; Cinner, Joshua E; Cowman, Peter F; Kronen, Mecki; Pinca, Silvia; Vigliola, Laurent

    2014-03-03

    Beyond the loss of species richness, human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional diversity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional diversity of parrotfishes, at 25 and 15 inhabitants/km(2), respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7%, while phylogenetic and functional diversity dropped by 35.8% and 46.6%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems.

  2. Proximate and ultimate causes of signal diversity in the electric fish Gymnotus.

    Science.gov (United States)

    Crampton, W G R; Rodríguez-Cattáneo, A; Lovejoy, N R; Caputi, A A

    2013-07-01

    A complete understanding of animal signal evolution necessitates analyses of both the proximate (e.g. anatomical and physiological) mechanisms of signal generation and reception, and the ultimate (i.e. evolutionary) mechanisms underlying adaptation and diversification. Here we summarize the results of a synthetic study of electric diversity in the species-rich neotropical electric fish genus Gymnotus. Our study integrates two research directions. The first examines the proximate causes of diversity in the electric organ discharge (EOD) - which is the carrier of both the communication and electrolocation signal of electric fishes - via descriptions of the intrinsic properties of electrocytes, electrocyte innervation, electric organ anatomy and the neural coordination of the discharge (among other parameters). The second seeks to understand the ultimate causes of signal diversity - via a continent-wide survey of species diversity, species-level phylogenetic reconstructions and field-recorded head-to-tail EOD (ht-EOD) waveforms (a common procedure for characterizing the communication component of electric fish EODs). At the proximate level, a comparative morpho-functional survey of electric organ anatomy and the electromotive force pattern of the EOD for 11 species (representing most major clades) revealed four distinct groups of species, each corresponding to a discrete area of the phylogeny of the genus and to a distinct type of ht-EOD waveform. At the ultimate level, our analyses (which emphasize the ht-EOD) allowed us to conclude that selective forces from the abiotic environment have had minimal impact on the communication component of the EOD. In contrast, selective forces of a biotic nature - imposed by electroreceptive predators, reproductive interference from heterospecific congeners, and sexual selection - may be important sources of diversifying selection on Gymnotus signals.

  3. Far from superficial: microbial diversity associated with the skin and mucus of fish

    Science.gov (United States)

    Cipriano, Rocco C.; Dove, Alistair; Cipriano, R.C.; Bruckner, A.W.; Shchelkunov, I.S.

    2011-01-01

    During horizontal or water-borne infection involving an obligate pathogen (e.g. – Aeromonas salmonicida, cause of furunculosis), the pathogen interacted with and influenced the microbial diversity of the dermal mucus of fish. Prior to infection, the prevalent bacterial flora cultured from juvenile Atlantic salmon (Salmo salar) included Pseudomonas fluorescens, Comomonas terrigenia, Acinetobacter sp., Moraxella sp., Pseudomonas dimunita, Alcaligenes denitrificans, Pseudomonas pseudoalcaligenes, and Pseudomonas alcaligenes, Serratia liquefaciens, Aeromonas hydrophila, other motile Aeromonas spp., and Corynebacterium aquaticum. After A. salmonicida was initially detected in this population as an external mucus infection, Acinetobacter sp., Moraxella sp., C. terrigenia, P. fluorescens, and P. dimunita, Staphylococcus sp., and A. hydrophila, were also present in appreciable numbers. Within several weeks, however, the A. salmonicida infection amplified and composed 78% of the total flora in the mucus. Only P. dimunita (4%). P. fluorescens (2%), and C. terrigenia (1%) were cultured at that time and more than a third of these fish showed evidence of a systemic A. salmonicida infection within their kidneys. Eight weeks after oral oxytetracycline treatments, A. salmonicida was no longer isolated from the mucus or kidneys of any fish and glucose inert or other oxidative microbes (e.g., P. fluorescens, C. terrigenia, Acinetobacter sp., Moraxella sp.) were beginning to repopulate the external surface of the salmon in increasing frequency. Still present and composing fairly large percentages of the total flora were A. hydrophila, as well as Enterobacter sp., and P. putrefaciens. A normal microbial diversity was re-established as the fish recovered. In another investigation, reduced biological diversity was noted in the dermal mucus among smallmouth bass that were sampled from the Jackson River (Covington, VA). In these fish, A. hydrophila and P. putrefaciens were the two

  4. CEPF Western Ghats Special Series: Fishes of River Bharathapuzha, Kerala, India: diversity, distribution, threats and conservation

    Directory of Open Access Journals (Sweden)

    A. Bijukumar

    2013-11-01

    Full Text Available We present here a comprehensive account of the diversity, distribution, threats, and suggest conservation measures for the fishes of Bharathapuzha, the largest west flowing river in the southern Indian state of Kerala. A total of 117 species under 43 families and 81 genera were recorded from the river, of which 98 were primary freshwater and 19 were secondary freshwater and/or diadromous species. Six species of non-native fish were also recorded, of which three were exotic to the country and three were transplanted from the gangetic plains. Twenty-eight percent (S = 33 of species that occur in the Bharathapuzha are endemic to the Western Ghats, while three species (Balitora jalpalli, Mesonoemacheilus remadevii and Pseudolaguvia austrina are restricted in their distribution to the river system. A little more than one-tenth (11%; S = 13 of species that occur in the river are listed under various threatened categories on the IUCN Red List. As part of this study, we also extend the distribution range of Osteochilichthys longidorsalis to the Bharathapuzha River system, based on its collection from the Thoothapuzha tributary. Several anthropogenic stressors including deforestation and loss of riparian cover, dams and other impoundments, pollution, sand mining, non-native species and destructive fishing practices are threatening the rich ichthyofaunal diversity and endemism in the Bharathapuzha. There is hence an urgent need to develop and implement conservation plans, some of which are discussed.

  5. Richness and diversity of helminth communities in tropical freshwater fishes: Empirical evidence

    Science.gov (United States)

    Choudhury, A.; Dick, T.A.

    2000-01-01

    Aim: Published information on the richness and diversity of helminth parasite communities in tropical freshwater fishes is reviewed in response to expectations of species-rich parasite communities in tropical regions. Location: Areas covered include the tropics and some subtropical areas. In addition, the north temperate area of the nearctic zone is included for comparison. Methods: Data from 159 communities in 118 species of tropical freshwater fish, summarized from 46 published studies, were used for this review. Parasite community descriptors used in the analyses included component community richness and calculated mean species richness. Data from 130 communities in 47 species of nearctic north temperate freshwater fish were summarized from 31 studies and used for comparison. Results: The component helminth communities of many tropical freshwater fish are species-poor, and considerable proportions of fish from certain parts of the tropics, e.g. West African drainages, are uninfected or lightly infected. Mean helminth species richness was low and equaled or exceeded 2.0 in only 22 of 114 communities. No single group of helminths was identified as a dominant component of the fauna and species composition was variable among and within broader geographical areas. The richest enteric helminth assemblages were found in mochokid and clariid catfish with a mixed carnivorous diet, whereas algal feeders, herbivores and detritivores generally had species-poor gut helminth communities. Comparisons indicated that certain areas in the north temperate region had higher helminth species richness in fishes than areas in the tropics. Main conclusions: Expectations of high species richness in helminth communities of tropical freshwater fishes are not fulfilled by the data. Direct comparisons of infracommunities and component communities in host species across widely separated phylogenetic and geographical lines are inappropriate. Examination of latitudinal differences in richness

  6. Fish community diversity in the middle continental shelf of the East China Sea

    Institute of Scientific and Technical Information of China (English)

    SHAN Xiujuan; JIN Xianshi; ZHOU Zhipeng; DAI Fangqun

    2011-01-01

    The status of fishery stocks in the coastal waters of China is far from ideal,mainly due to climate change and the impacts of human activities (e.g.,pollution and overfishing).Thus,the restoration and protection of fishery resources have become critical and complex.The stability and balanced structure of the fish community is a basic foundation for the protection of fishery resources.Based on data collected from bottom trawls by the R/V Beidou in continental shelf of the East China Sea in November 2006 and February 2007,changes in the composition and diversity of fish species and functional groups were analyzed.The research area was divided into offshore waters and inshore waters by the two-way indicator species analysis (TWIA).The results showed that the dominant species were different between offshore waters and inshore waters and also varied with the survey time.The most abundant family was Sciaenidae and Teraponidae in November 2006,Sciaenidae,Engraulidae and Triglidae were most abundant in February 2007.The species belonged mainly to mobile piscivores (G6),benthivores/piscivores (G4),benthivores (G3) and planktivores (G1),and the dominant species in November 2006 were commercial species (e.g.Larimichthys polyactis and Trichiurus japonicus),but small-sized species were dominant in February 2007 (e.g.,Harpadon nehereus,Benthosema pterotum,Champsodon capensis,and Acropoma japonicum).The species diversity showed a similar trend as the functional group diversity.Stations with higher diversity were mainly distributed in inshore waters in February 2007,whereas higher diversity was found in offshore waters in November 2006.The highest biomass and species number were found in G6 group,followed by the G4,G5 and G1 groups.The distribution of the number of individuals of each functional group showed the opposite trend as that of the biomass distribution.In addition,the size spectra were mainly concentrated around 3-29 cm,and the individual number of fish species gradually

  7. Diversity screening for novel enzymes degrading synthetic polymers

    DEFF Research Database (Denmark)

    Lezyk, Mateusz Jakub

    The objective of this PhD study was to evaluate the feasibility of enzymatic degradation of synthetic polymers used as binder materials in marine coatings. Enzymatic modification of synthetic polymers like epoxy resin, polyurethanes and various acrylics is desirable in several industrial processes...... is reported. First, a collection of fungal strains was screened for the capability to degrade several compounds of synthetic origin. Strains with the ability to modify colloidal polyester polyurethane, as well as various commercial emulsions of acrylates were identified. Secondly, we have used metagenomic...... and the choice of proper substrates for identification of promising enzyme candidates. Several genes coding for enzymes with the capability to oxidize various natural and synthetic substrates were identified, expressed heterologously and characterized. Three multicopper oxidases (MCOs) were identified encoded...

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

    Science.gov (United States)

    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.

  9. Trematode diversity in freshwater fishes of the Globe II: 'New World'.

    Science.gov (United States)

    Choudhury, Anindo; Aguirre-Macedo, M Leopoldina; Curran, Stephen S; de Núñez, Margarita Ostrowski; Overstreet, Robin M; de León, Gerardo Pérez-Ponce; Santos, Cláudia Portes

    2016-03-01

    We provide a summary overview of the diversity of trematode parasites in freshwater fishes of the 'New World', i.e. the Americas, with emphasis on adult forms. The trematode fauna of three regions, South America, Middle America, and USA and Canada (North America north of Mexico), are considered separately. In total, 462 trematode species have been reported as adults from the Americas. The proportion of host species examined for parasites varies widely across the Americas, from a high of 45% in the Mexican region of Middle America to less than 5% in South America. North and South America share no adult species, and one exclusively freshwater genus, Creptotrema Travassos, Artigas & Pereira, 1928 in the Allocreadiidae Looss, 1902 is the most widely distributed. Metacercariae of strigeiforms maturing in fish-eating birds (e.g. species of the Diplostomidae Poirier, 1886) are common and widely distributed. The review also highlights the paucity of known life-cycles. The foreseeable future of diversity studies belongs to integrative approaches and the application of molecular ecological methods. While opportunistic sampling will remain important in describing and cataloguing the trematode fauna, a better understanding of trematode diversity and biology will also depend on strategic sampling throughout the Americas.

  10. The influence of Pacific Equatorial Water on fish diversity in the southern California Current System

    Science.gov (United States)

    McClatchie, Sam; Thompson, Andrew R.; Alin, Simone R.; Siedlecki, Samantha; Watson, William; Bograd, Steven J.

    2016-08-01

    The California Undercurrent transports Pacific Equatorial Water (PEW) into the Southern California Bight from the eastern tropical Pacific Ocean. PEW is characterized by higher temperatures and salinities, with lower pH, representing a source of potentially corrosive (aragonite,Ωfish diversity. We use hydrographic data to characterize the interannual and seasonal variability of estimated pH and aragonite saturation with depth. Although there is substantial variability in PEW presence as measured by spice on the 26.25-26.75 isopycnal layer, as well as in pH and aragonite saturation, we found fish diversity to be stable over the decades 1985-1996 and 1999-2011. We detected significant difference in species structure during the 1998 La Niña period, due to reduced species evenness. Species richness due to rare species was higher during the 1997/1998 El Niño compared to the La Niña but the effect on species structure was undetectable. Lack of difference in the species abundance structure in the decade before and after the 1997/1999 ENSO event showed that the assemblage reverted to its former structure following the ENSO perturbation, indicating resilience. While the interdecadal species structure remained stable, the long tail of the distributions shows that species richness increased between the decades consistent with intrusion of warm water with more diverse assemblages into the southern California region.

  11. Vertical distribution, diversity and assemblages of mesopelagic fishes in the western Mediterranean

    Science.gov (United States)

    Olivar, M. P.; Bernal, A.; Molí, B.; Peña, M.; Balbín, R.; Castellón, A.; Miquel, J.; Massutí, E.

    2012-04-01

    The mesopelagic fish community of the western Mediterranean was studied during two cruises carried out in December 2009 and July 2010 in the shelf and slope zones around the Balearic Islands. Much of what was previously known about this deep water group of fishes in the Mediterranean Sea came from studies performed using planktonic and small midwater nets. This study was the first attempt to use large pelagic trawls and small nets combined with information about the main sound scattering layers to analyse mesopelagic fish composition, diversity and species assemblages. This community is characterised by a relatively low diversity compared to other oceanic regions of the world, with Myctophiformes and Stomiiformes being the main contributors. Bathymetry and the level of the water column were the most important factors structuring the investigated fish assemblages, and similar vertical patterns were observed for the different species collected during the two study periods. A shelf assemblage composed of a few species of myctophids, with Notoscopelus elongatus being the main contributor, was distinguished. The slope assemblage included both Myctophiformes and Stomiiformes that showed differences in their day-night main location along the water column. In terms of species behaviour, two important groups were detected. The first was non-migrant or weakly migrant species, with the paradigmatic example being the gonostomatid Cyclothone braueri, which occurred at a depth of 400-600 m; this species is partly responsible for the permanent acoustic (38 kHz) response at this depth. The second group, near-surface migrants at night, was represented by most of the juvenile and adult myctophids, exemplified by Ceratoscopelus maderensis, with the exception of just a few of the largest size classes of some species, such as Lampanyctus crocodilus and N. elongatus that remain near the bottom.

  12. Diversity and composition of estuarine and lagoonal fish assemblages of Socotra Island, Yemen.

    Science.gov (United States)

    Lavergne, E; Zajonz, U; Krupp, F; Naseeb, F; Aideed, M S

    2016-05-01

    Estuarine and lagoonal surveys of Socotra Island and selected sites on the Hadhramout coast of Yemen were conducted with the objective of documenting and analysing fish diversity and assemblage structure. A total of 74 species in 35 families were recorded, among which 65 species in 32 families were from Socotra and 20 species in 17 families were from mainland Yemen. Twenty-one species represent new faunal records for Socotra. Including historic records re-examined in this study, the total fish species richness of estuaries and lagoons of Socotra Island reaches 76, which is relatively high compared to species inventories of well-researched coastal estuaries in southern Africa. Five species dominate the occurrence and abundance frequencies: Terapon jarbua, Hyporhamphus sindensis, Aphanius dispar, Ambassis gymnocephala and Chelon macrolepis. Rarefaction and extrapolation analyses suggest that the actual number of fish species inhabiting some of those estuaries might be higher than the one observed. Thus, additional sampling at specific sites should be conducted to record other less conspicuous species. Ordination and multivariate analyses identified four main distinct assemblage clusters. Two groups are geographically well structured and represent northern Socotra and mainland Yemen, respectively. The other two assemblage groups tend to be determined to a greater extent by the synchrony between physical (e.g. estuary opening periods) and biological (e.g. spawning and recruitment periods) variables than by geographical location. Finally, the single intertidal lagoon of Socotra represents by itself a specific fish assemblage. The high proportion of economically important fish species (38) recorded underscores the paramount importance of these coastal water bodies as nursery sites, and for sustaining vital provisioning ecosystem services.

  13. Detection of a diverse marine fish fauna using environmental DNA from seawater samples.

    Directory of Open Access Journals (Sweden)

    Philip Francis Thomsen

    Full Text Available Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly limited to commercial species, and restricted to particular areas with favourable conditions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA obtained directly from seawater samples to account for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from ½-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus. Additionally, we detect four bird species. Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied conventional methods. Our study demonstrates that even small samples of seawater contain eDNA from a wide range of local fish species. Finally, in order to examine the potential dispersal of eDNA in oceans, we performed an experiment addressing eDNA degradation in seawater, which shows that even small (100-bp eDNA fragments degrades beyond detectability within days. Although further studies are needed to validate the eDNA approach in varying environmental

  14. Spatial and temporal fish diversity patterns from Santa Catarina Island, Brazil

    Directory of Open Access Journals (Sweden)

    André Cattani

    2015-11-01

    Full Text Available The Santa Catarina Island has a mosaic of ecosystems, with great importance for the fishes. There is the presence of estuaries, lagoons, mangroves and sandy beaches in the same island. Thus, the objectives of this study were to evaluate the spatio and temporal fish diversity patterns in estuaries, lagoons and beach systems of Santa Catarina Island, Santa Catarina, Brazil. Fish data collected between 1983 to 2011 in the baía Norte, saco dos Limões, Itacorubi and Ratones mangroves, Conceição lagoon and Índio beach was analyzed. Fish were sampled with different gear techniques. In the North Bay and saco dos Limões individuals were caught by trawl, but in the mangroves and lagoon were used gillnets, cast nets and dip nets. In the Índio beach the fishes were collected using fyke nets. For each local, species accumulation curves were plotted to compare the observed pattern with modelled data, using first order Jackknife estimator. Species richness differences among locals and seasons were tested using PERMANOVA, followed by a canonical analysis of principal coordinates (CAP. To assess the taxonomic structures at each location, the average taxonomic distinctness (AvTD and the variation in taxonomic distinctness (VarTD were also used. Higher average species richness was found in the saco dos Limões (mean ± SE; 59.8 ± 2.5, followed by Índio Beach (55.7 ± 2.7, Conceição lagoon (52.3 ± 6.4, North bay (45.0 ± 2.5, mangrove Itacorubi (34.5 ± 3.2 and mangrove Ratones (30.8 ± 3.8. No significate differences for the taxonomic patterns were observed between seasons. Furthermore the hereby data suggest that the fish assemblages of the inner portion of the island of Santa Catarina are mainly formed by estuarine and marine fish, but differing in species richness among locals.

  15. Vertical zonation and functional diversity of fish assemblages revealed by ROV videos at oil platforms in The Gulf.

    Science.gov (United States)

    Torquato, F; Jensen, H M; Range, P; Bach, S S; Ben-Hamadou, R; Sigsgaard, E E; Thomsen, P F; Møller, P R; Riera, R

    2017-09-01

    An assessment of vertical distribution, diel migration, taxonomic and functional diversity of fishes was carried out at offshore platforms in The (Arabian-Iranian-Persian) Gulf. Video footage was recorded at the Al Shaheen oil field between 2007 and 2014 using a remotely operated vehicle (ROV). A total of 12 822 individual fishes, from 83 taxonomic groups were recorded around the platforms. All the species identified are considered native to The Gulf, although Cyclichthys orbicularis and Lutjanus indicus were recorded for the first time in Qatari waters. Several trends were uncovered in the vertical distribution of the fish community; most species were observed between 20 and 50 m depth and fish abundance decreased towards the bottom, with the highest abundances recorded in the upper layers, i.e. down to 40 m depth. Vertical variation in fish diversity, however, was generally not accompanied by differences in vertical movements. Carnivores and invertivores were the dominant trophic groups, being found at each depth range from surface to seabed. The functional indices showed no significant differences between water depths or diel cycles. The study demonstrates that oil platforms represent a hotspot of fish diversity and interesting sites for studying fish communities, abundance and behaviour. © 2017 The Fisheries Society of the British Isles.

  16. Diversity and distribution of fishes of Gaji River, Bauchi State, Nigeria

    Directory of Open Access Journals (Sweden)

    Ahmad J. Nayaya

    2012-08-01

    Full Text Available Fish sampling was conducted along the Gaji River with a view to assessing the Diversity andDistribution of the fishes. The river which is the major source of water for the diverse wild fauna in andaround the Yankari National Park, is located on Latitude 9o 45’ 16” and Longitude 10o 30’ 37” andcovers an area of about 2,244 km² (870 mi² and is home to several natural warm water springs, aswell as a wide variety of flora and fauna (Wikipedia 2011. A total of twenty sampling locations wereestablished on the river and throughout the period of the work, different fishing gears which includedcast nets, gill nets, entrance traps, hooks and line and in some cases seines were used. Furthermore,Mitochondrial DNA cytochrome b sequencing was employed to study the genetic diversity of Clariasgariepinus sampled from the study area due to its economic importance. Amplification of thecytochrome b (cyt b gene was done using the polymerase chain reaction (PCR. A portion of mtDNAcontaining the gene was amplified using primers L15267, 5’-AAT GAC TTG AAG AAC CAC CGT-3’ andH15891, 5’-GTT TGA TCC CGT TTC GTG TA-3’ described by Briolay et al (1998. A total of 13 specieswere identified from the 4,218 individuals collected, representing 12 families and 13 genera. Theirpercentage distribution showed that Oreochromis niloticus had the highest percentage occurrence ofabout 31% followed by Parachanna obscura with 27%. This was followed by Clarias gariepinus whichhad about 20% distribution of occurrence. On the distribution of the identified species in the varioussampling locations, Ruwan Bangiya had the highest occurrence of the different species with 11 out ofthe total 13 species found in this location. Ruwan Dinya, Ruwan Sarki and Ruwan Gajin Gwaza also hadrelatively high occurrence of the identified fish species. The lowest occurrence was found in RuwanDalamiri, Ruwan Kunkuru and Ruwan Kankwana. Ruwan Gada and Ruwan Kakkida had moderatedistribution of the

  17. Diversity and Universality of Endosymbiotic Rickettsia in the Fish Parasite Ichthyophthirius multifiliis.

    Science.gov (United States)

    Zaila, Kassandra E; Doak, Thomas G; Ellerbrock, Hannah; Tung, Che-Huang; Martins, Mauricio L; Kolbin, Daniel; Yao, Meng-Chao; Cassidy-Hanley, Donna M; Clark, Theodore G; Chang, Wei-Jen

    2017-01-01

    Although the presence of endosymbiotic rickettsial bacteria, specifically Candidatus Megaira, has been reported in diverse habitats and a wide range of eukaryotic hosts, it remains unclear how broadly Ca. Megaira are distributed in a single host species. In this study we seek to address whether Ca. Megaira are present in most, if not all isolates, of the parasitic ciliate Ichthyophthirius multifiliis. Conserved regions of bacterial 16S rRNA genes were either PCR amplified, or assembled from deep sequencing data, from 18 isolates/populations of I. multifiliis sampled worldwide (Brazil, Taiwan, and USA). We found that rickettsial rRNA sequences belonging to three out of four Ca. Megaira subclades could be consistently detected in all I. multifiliis samples. I. multifiliis collected from local fish farms tend to be inhabited by the same subclade of Ca. Megaira, whereas those derived from pet fish are often inhabited by more than one subclade of Ca. Megaira. Distributions of Ca. Megaira in I. multifiliis thus better reflect the travel history, but not the phylogeny, of I. multifiliis. In summary, our results suggest that I. multifiliis may be dependent on this endosymbiotic relationship, and the association between Ca. Megaira and I. multifiliis is more diverse than previously thought.

  18. Functional diversity of the lateral line system among populations of a native Australian freshwater fish.

    Science.gov (United States)

    Spiller, Lindsey; Grierson, Pauline F; Davies, Peter M; Hemmi, Jan; Collin, Shaun P; Kelley, Jennifer L

    2017-06-15

    Fishes use their mechanoreceptive lateral line system to sense nearby objects by detecting slight fluctuations in hydrodynamic motion within their immediate environment. Species of fish from different habitats often display specialisations of the lateral line system, in particular the distribution and abundance of neuromasts, but the lateral line can also exhibit considerable diversity within a species. Here, we provide the first investigation of the lateral line system of the Australian western rainbowfish (Melanotaenia australis), a species that occupies a diversity of freshwater habitats across semi-arid northwest Australia. We collected 155 individuals from eight populations and surveyed each habitat for environmental factors that may contribute to lateral line specialisation, including water flow, predation risk, habitat structure and prey availability. Scanning electron microscopy and fluorescent dye labelling were used to describe the lateral line system in M. australis, and to examine whether the abundance and arrangement of superficial neuromasts (SNs) varied within and among populations. We found that the SNs of M. australis were present in distinct body regions rather than lines. The abundance of SNs within each body region was highly variable, and also differed among populations and individuals. Variation in SN abundance among populations was best explained by habitat structure and the availability of invertebrate prey. Our finding that specific environmental factors explain among-population variation in a key sensory system suggests that the ability to acquire sensory information is specialised for the particular behavioural needs of the animal. © 2017. Published by The Company of Biologists Ltd.

  19. Diversity and Universality of Endosymbiotic Rickettsia in the Fish Parasite Ichthyophthirius multifiliis

    Science.gov (United States)

    Zaila, Kassandra E.; Doak, Thomas G.; Ellerbrock, Hannah; Tung, Che-Huang; Martins, Mauricio L.; Kolbin, Daniel; Yao, Meng-Chao; Cassidy-Hanley, Donna M.; Clark, Theodore G.; Chang, Wei-Jen

    2017-01-01

    Although the presence of endosymbiotic rickettsial bacteria, specifically Candidatus Megaira, has been reported in diverse habitats and a wide range of eukaryotic hosts, it remains unclear how broadly Ca. Megaira are distributed in a single host species. In this study we seek to address whether Ca. Megaira are present in most, if not all isolates, of the parasitic ciliate Ichthyophthirius multifiliis. Conserved regions of bacterial 16S rRNA genes were either PCR amplified, or assembled from deep sequencing data, from 18 isolates/populations of I. multifiliis sampled worldwide (Brazil, Taiwan, and USA). We found that rickettsial rRNA sequences belonging to three out of four Ca. Megaira subclades could be consistently detected in all I. multifiliis samples. I. multifiliis collected from local fish farms tend to be inhabited by the same subclade of Ca. Megaira, whereas those derived from pet fish are often inhabited by more than one subclade of Ca. Megaira. Distributions of Ca. Megaira in I. multifiliis thus better reflect the travel history, but not the phylogeny, of I. multifiliis. In summary, our results suggest that I. multifiliis may be dependent on this endosymbiotic relationship, and the association between Ca. Megaira and I. multifiliis is more diverse than previously thought. PMID:28232825

  20. Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes.

    Science.gov (United States)

    Valdez-Moreno, M; Ivanova, N V; Elías-Gutiérrez, M; Contreras-Balderas, S; Hebert, P D N

    2009-02-01

    The freshwater fish fauna of Mexico and Guatemala is exceptionally diverse with >600 species, many endemic. In this study, patterns of sequence divergence were analysed in representatives of this fauna using cytochrome c oxidase subunit 1 (COI) DNA barcodes for 61 species in 36 genera. The average divergence among conspecific individuals was 0.45%, while congeneric taxa showed 5.1% divergence. Three species of Poblana, each occupying a different crater lake in the arid regions of Central Mexico, have had a controversial taxonomic history but are usually regarded as endemics to a single lake. They possess identical COI barcodes, suggesting a very recent history of isolation. Representatives of the Cichlidae, a complex and poorly understood family, were well discriminated by barcodes. Many species of Characidae seem to be young, with low divergence values (clusters were apparent in the Bramocharax-Astyanax complex. The symbranchid, Opisthernon aenigmaticum, has been regarded as a single species ranging from Guatemala to Mexico, but it includes two deeply divergent barcode lineages, one a possible new endemic species. Aside from these special cases, the results confirm that DNA barcodes will be highly effective in discriminating freshwater fishes from Central America and that a comprehensive analysis will provide new important insights for understanding diversity of this fauna.

  1. Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru.

    Directory of Open Access Journals (Sweden)

    Maarten van Zonneveld

    Full Text Available For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1 Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2 Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3 Select promising accessions for different uses after screening; and 4 Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens. The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium. Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct

  2. Screening Genetic Resources of Capsicum Peppers in Their Primary Center of Diversity in Bolivia and Peru.

    Science.gov (United States)

    van Zonneveld, Maarten; Ramirez, Marleni; Williams, David E; Petz, Michael; Meckelmann, Sven; Avila, Teresa; Bejarano, Carlos; Ríos, Llermé; Peña, Karla; Jäger, Matthias; Libreros, Dimary; Amaya, Karen; Scheldeman, Xavier

    2015-01-01

    For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in

  3. Comparative phylogeography of Atlantic reef fishes indicates both origin and accumulation of diversity in the Caribbean

    Directory of Open Access Journals (Sweden)

    Robertson D Ross

    2008-05-01

    Full Text Available Abstract Background Two processes may contribute to the formation of global centers of biodiversity: elevated local speciation rates (the center of origin hypothesis, and greater accumulation of species formed elsewhere (the center of accumulation hypothesis. The relative importance of these processes has long intrigued marine biogeographers but rarely has been tested. Results To examine how origin and accumulation affected the Greater Caribbean center of diversity, we conducted a range-wide survey of mtDNA cytochrome b in the widespread Atlantic reef damselfish Chromis multilineata (N = 183 that included 10 locations in all four tropical Atlantic biogeographic provinces: the Greater Caribbean, Brazil, the mid-Atlantic ridge, and the tropical eastern Atlantic. We analyzed this data and re-evaluated published genetic data from other reef fish taxa (wrasses and parrotfishes to resolve the origin and dispersal of mtDNA lineages. Parsimony networks, mismatch distributions and phylogenetic analyses identify the Caribbean population of C. multilineata as the oldest, consistent with the center of origin model for the circum-Atlantic radiation of this species. However, some Caribbean haplotypes in this species were derived from Brazilian lineages, indicating that mtDNA diversity has not only originated but also accumulated in the Greater Caribbean. Data from the wrasses and parrotfishes indicate an origin in the Greater Caribbean in one case, Caribbean origin plus accumulation in another, and accumulation in the remaining two. Conclusion Our analyses indicate that the Greater Caribbean marine biodiversity hotspot did not arise through the action of a single mode of evolutionary change. Reef fish distributions at the boundaries between Caribbean and Brazilian provinces (the SE Caribbean and NE Brazil, respectively indicate that the microevolutionary patterns we detected in C. multilineata and other reef fishes translate into macroevolutionary processes

  4. COMPARING PREDATOR ABUNDANCE AND FISH DIVERSITY IN MPA SITES (KORNATI NP, CROATIA AND ADJACENT SITES EXPLOITED BY FISHERIES

    Directory of Open Access Journals (Sweden)

    Donat Petricioli

    2012-12-01

    Full Text Available Fishing activities and other anthropogenic influences have direct and indirect effects on fish community structure. One expectation may be that with increasing fishing pressure and decreasing size selectivity of fisheries all predator populations decline and consequently fish assemblages change. Comparisons of MPAs with unprotected areas are considered valid natural experiments to test hypotheses on how predation structures communities. Here we report on the use of a lure-assisted visual census in the Central Croatian Adriatic to assess and compare fish assemblages in MPA sites (Kornati NP with adjacent unprotected sites. We detected a significant protection effect on mesopredator abundance and overall fish diversity/richness and that protection status explained a significant portion of the fish assemblage variability, all independent of additional predictor variables, like habitat and depth. As we continue to expand the spatiotemporal scale and magnitude of the approach, we hope that it will eventually provide us with a long-term data series needed for testing many hypotheses in coastal ecology, including the effects of MPAs, coastal development, fishing and global climate change on the species interactions, abundance, diversity and assembly of animal species across multiple spatial scales.

  5. Vast assembly of vocal marine mammals from diverse species on fish spawning ground.

    Science.gov (United States)

    Wang, Delin; Garcia, Heriberto; Huang, Wei; Tran, Duong D; Jain, Ankita D; Yi, Dong Hoon; Gong, Zheng; Jech, J Michael; Godø, Olav Rune; Makris, Nicholas C; Ratilal, Purnima

    2016-03-17

    Observing marine mammal (MM) populations continuously in time and space over the immense ocean areas they inhabit is challenging but essential for gathering an unambiguous record of their distribution, as well as understanding their behaviour and interaction with prey species. Here we use passive ocean acoustic waveguide remote sensing (POAWRS) in an important North Atlantic feeding ground to instantaneously detect, localize and classify MM vocalizations from diverse species over an approximately 100,000 km(2) region. More than eight species of vocal MMs are found to spatially converge on fish spawning areas containing massive densely populated herring shoals at night-time and diffuse herring distributions during daytime. We find the vocal MMs divide the enormous fish prey field into species-specific foraging areas with varying degrees of spatial overlap, maintained for at least two weeks of the herring spawning period. The recorded vocalization rates are diel (24 h)-dependent for all MM species, with some significantly more vocal at night and others more vocal during the day. The four key baleen whale species of the region: fin, humpback, blue and minke have vocalization rate trends that are highly correlated to trends in fish shoaling density and to each other over the diel cycle. These results reveal the temporospatial dynamics of combined multi-species MM foraging activities in the vicinity of an extensive fish prey field that forms a massive ecological hotspot, and would be unattainable with conventional methodologies. Understanding MM behaviour and distributions is essential for management of marine ecosystems and for accessing anthropogenic impacts on these protected marine species.

  6. Spatial gradients in freshwater fish diversity, abundance and current pattern in the Himalayan region of Upper Ganges Basin, India

    Directory of Open Access Journals (Sweden)

    AJEY KUMAR PATHAK

    2014-10-01

    Full Text Available Pathak AK, Sarkar UK, Singh SP. 2014. Spatial gradients in freshwater fish diversity, abundance and current pattern in the Himalayan region of Upper Ganges Basin, India. Biodiversitas 15: 186-194.The present study describes the analysis and mapping of the different measurements of freshwater fish biodiversity of the Upper Ganges basin in the Himalayan region using spatial interpolation methods of Geographical Information System. The diversity, richness and abundance of fishes for each sampling location were determined and Kriging interpolation was applied on each fisheries measurement to predict and produce semivariogram. The semivariogarms produced were cross validated and reclassified. The reclassified maps for richness, abundance and diversity of fishes, occurrence of cold water threatened fish and abundance of important genera like Tor, Schziothorax and species were produced. The result of the Kriging produced good results and overall error in the estimation process was found significant. The cross validation of semovariograms also provided a better result with the observed data sets. Moreover, weighted overlay analysis of the reclassified raster maps of richness and abundance of fishes produced the classified raster map at different evaluation scale (0-10 qualitatively describing the gradient of species richness and abundance compositely. Similarly, the classified raster map at same evaluation scale qualitatively describing the gradient of species abundance and diversity compositely was produced and published. Further, basin wise analysis between Alaknanda/Pindar and Ganga1 sub basins showed 0.745 disparities at 0.745 distances in 2 dimensional spaces. The richness, diversity and abundance of threatened fishes among the different sampling locations were not significant (p = 0.9.

  7. Multiplex screening of persistent organic pollutants in fish using spectrally encoded microspheres.

    Science.gov (United States)

    Meimaridou, Anastasia; Kalachova, Kamila; Shelver, Weilin L; Franek, Milan; Pulkrabova, Jana; Haasnoot, Willem; Nielen, Michel W F

    2011-11-15

    Persistent organic pollutants (POPs) are environmental and food-related contaminants of global public health concern and known to be carcinogenic and endocrine disruptors. Their monitoring is essential, and an easy-to-use, rapid, and affordable multianalyte screening method with simplified sample preparation can be a valuable tool prior to instrumental analysis. For this purpose, a flow cytometric immunoassay (FCIA), based on a spectrally encoded microbeads technology, was developed for the multiplex detection of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (BDEs) in buffer and fish extracts. The sensitivities of the assays in the three-plex FCIA format were similar to the individual FCIAs for the marker compounds benzo[a]pyrene (BaP), 3,3',4,4'-tetrachlorobiphenyl (PCB77), and 2,2',4,4'-tetrabromodiphenyl ether (BDE47) in buffer with IC(50) values of 0.4, 20, and 2 μg L(-1), respectively. Apart from the three markers, we could detect at least 14 other POPs. Extracts of fish with different fat content, prepared with a simplified extraction and cleanup procedure, had an insignificant influence on the overall three-plex FCIA performance, with the exception of some impact on the PAHs detection. The performance of the three-plex FCIA, in combination with the simple extraction procedure, is adequate for regulatory control in accordance with the required limits.

  8. Validation of rapid dioxin screening by GC-FID in fish products

    Energy Technology Data Exchange (ETDEWEB)

    Bassompierre, M.; Munck, L.; Bro, R.; Tomasi, G.; Engelsen, S.B. [Royal Veterinary and Agricultural Univ., Copenhagen (Denmark). Food Technology, Institute of Food Science, Centre for Advanced Food Studies

    2004-09-15

    A novel, cost- and time-effective dioxin screening method was developed and validated for fish product. The method is based on multivariate covariance between fatty acid composition monitored by GC-FID and dioxin content as teq WHO pg/ g fat. A dioxin range varying from 1.1 to 47.1 pg TEQ-WHO/ g fat using 65 fish meal samples was accessible for model calibration. An optimal multivariate dioxin prediction model was developed based on automatic peak integration, thereby enabling extraction of the area of 140 peaks from the gas chromatogramms. Models were produced employing partial least squares regression (PLS) based upon the duplicate GC-FID run and 46 specific peaks, selected after variable selection from the 140 investigated. The best results were yielded by local pls modelling employing three latent variables based upon the 12 nearest neighbors. For each prediction sample, the neighbors, yielding the 12 smallest sum of squares of differences to the test sample using the 140 peaks, were extracted from the whole calibration set and a local model built using these 12 chromatograms and related dioxin content. Prediction performance was thereafter validated for 10 fully independent samples. The performance of this model, yielded a correlation of 0.85 (r{sup 2}) and a root mean square error of prediction of 2.3 pg PCDD/F TEQWHO/ g fat.

  9. 76 FR 20368 - Llano Seco Riparian Sanctuary Unit Restoration and Pumping Plant/Fish Screen Facility Protection...

    Science.gov (United States)

    2011-04-12

    ... Protection Project. FOR FURTHER INFORMATION CONTACT: Kelly Moroney, Refuge Manager, (530) 934-2801... Plant Protection Feasibility Study in August 2005 to identify alternatives that meet the PCGID-PID's pumping plant and fish screen protection objectives. In 2005, River Partners prepared a...

  10. Validation of an optical surface plasmon resonance biosensor assay for screening (fluoro)quinolones in egg, fish and poultry

    NARCIS (Netherlands)

    Huet, A.C.; Charlier, C.; Weigel, S.; Benrejeb Godefroy, S.; Delahaut, P.

    2009-01-01

    A surface plasmon resonance biosensor immunoassay has been developed for multi-residue determination of 13 (fluoro)quinolone antibiotics in poultry meat, eggs and fish. The following performance characteristics were determined according to the guidelines laid down for screening assay validation in E

  11. Validation of an optical surface plasmon resonance biosensor assay for screening (fluoro)quinolones in egg, fish and poultry

    NARCIS (Netherlands)

    Huet, A.C.; Charlier, C.; Weigel, S.; Benrejeb Godefroy, S.; Delahaut, P.

    2009-01-01

    A surface plasmon resonance biosensor immunoassay has been developed for multi-residue determination of 13 (fluoro)quinolone antibiotics in poultry meat, eggs and fish. The following performance characteristics were determined according to the guidelines laid down for screening assay validation in E

  12. Validation of an optical surface plasmon resonance biosensor assay for screening (fluoro)quinolones in egg, fish and poultry

    NARCIS (Netherlands)

    Huet, A.C.; Charlier, C.; Weigel, S.; Benrejeb Godefroy, S.; Delahaut, P.

    2009-01-01

    A surface plasmon resonance biosensor immunoassay has been developed for multi-residue determination of 13 (fluoro)quinolone antibiotics in poultry meat, eggs and fish. The following performance characteristics were determined according to the guidelines laid down for screening assay validation in

  13. Genetic diversity affects the strength of population regulation in a marine fish.

    Science.gov (United States)

    Johnson, D W; Freiwald, J; Bernardi, G

    2016-03-01

    Variation is an essential feature of biological populations, yet much of ecological theory treats individuals as though they are identical. This simplifying assumption is often justified by the perception that variation among individuals does not have significant effects on the dynamics of whole populations. However, this perception may be skewed by a historic focus on studying single populations. A true evaluation of the extent to which among-individual variation affects the dynamics of populations requires the study of multiple populations. In this study, we examined variation in the dynamics of populations of a live-bearing, marine fish (black surfperch; Embiotoca jacksoni). In collaboration with an organization of citizen scientists (Reef Check California), we were able to examine the dynamics of eight populations that were distributed throughout approximately 700 km of coastline, a distance that encompasses much of this species' range. We hypothesized that genetic variation within a local population would be related to the intensity of competition and to the strength of population regulation. To test this hypothesis, we examined whether genetic diversity (measured by the diversity of mitochondrial DNA haplotypes) was related to the strength of population regulation. Low-diversity populations experienced strong density dependence in population growth rates and population sizes were regulated much more tightly than they were in high-diversity populations. Mechanisms that contributed to this pattern include links between genetic diversity, habitat use, and spatial crowding. On average, low-diversity populations used less of the available habitat and exhibited greater spatial clustering (and more intense competition) for a given level of density (measured at the scale of the reef). Although the populations we studied also varied with respect to exogenous characteristics (habitat complexity, densities of predators, and interspecific competitors), none of these

  14. Evaluation of Juvenile Fish Bypass and Adult Fish Facilities at Water Diversions in the Umatilla River; 1992 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, Suzanne M.

    1993-03-01

    We report on our progress from October 1991 through September 1992 in evaluating juvenile fish bypass facilities at Three Mile Falls and Westland dams on the Umatilla River. We also report on our progress from October 1991 through June 1992 in evaluating adult fish passage in the lower Umatilla River and adult fish passage facilities at Three Mile Falls Dam. The study is a cooperative effort by the Oregon Department of Fish and Wildlife (ODFW) and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR). These are the study objectives addressed by ODFW and CTUIR: (1) Report A (ODFW): To evaluate the juvenile fish bypass facility in the West Extension Irrigation District Canal at Three Mile Falls Dam and document juvenile salmonid passage through the juvenile fish bypass facility and east-bank adult fish ladder. To measure velocity and develop trap designs at Westland Dam. (2) Report B (CTUIR): To examine the passage of adult salmonids at Three Mile Falls Dam. The study is part of a program to rehabilitate anadromous fish stocks in the Umatilla River Basin, including restoration of coho salmon (Oncorhynchus kisutch) and chinook salmon (Oncorhynchus tshawytscha), as well as enhancement of summer steelhead (Oncorhynchus mykiss).

  15. Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics.

    Science.gov (United States)

    Lau, Wan F; Withka, Jane M; Hepworth, David; Magee, Thomas V; Du, Yuhua J; Bakken, Gregory A; Miller, Michael D; Hendsch, Zachary S; Thanabal, Venkataraman; Kolodziej, Steve A; Xing, Li; Hu, Qiyue; Narasimhan, Lakshmi S; Love, Robert; Charlton, Maura E; Hughes, Samantha; van Hoorn, Willem P; Mills, James E

    2011-07-01

    Fragment Based Drug Discovery (FBDD) continues to advance as an efficient and alternative screening paradigm for the identification and optimization of novel chemical matter. To enable FBDD across a wide range of pharmaceutical targets, a fragment screening library is required to be chemically diverse and synthetically expandable to enable critical decision making for chemical follow-up and assessing new target druggability. In this manuscript, the Pfizer fragment library design strategy which utilized multiple and orthogonal metrics to incorporate structure, pharmacophore and pharmacological space diversity is described. Appropriate measures of molecular complexity were also employed to maximize the probability of detection of fragment hits using a variety of biophysical and biochemical screening methods. In addition, structural integrity, purity, solubility, fragment and analog availability as well as cost were important considerations in the selection process. Preliminary analysis of primary screening results for 13 targets using NMR Saturation Transfer Difference (STD) indicates the identification of uM-mM hits and the uniqueness of hits at weak binding affinities for these targets.

  16. Functional diversity of non-lethal effects, chemical camouflage, and variation in fish avoidance in colonizing beetles.

    Science.gov (United States)

    Resetarits, William J; Pintar, Matthew R

    2016-12-01

    Predators play an extremely important role in natural communities. In freshwater systems, fish can dominate sorting both at the colonization and post-colonization stage. Specifically, for many colonizing species, fish can have non-lethal, direct effects that exceed the lethal direct effects of predation. Functionally diverse fish species with a range of predatory capabilities have previously been observed to elicit functionally equivalent responses on oviposition in tree frogs. We tested this hypothesis of functional equivalence of non-lethal effects for four predatory fish species, using naturally colonizing populations of aquatic beetles. Among taxa other than mosquitoes, and with the exception of the chemically camouflaged pirate perch, Aphredoderus sayanus, we provide the first evidence of variation in colonization or oviposition responses to different fish species. Focusing on total abundance, Fundulus chrysotus, a gape-limited, surface-feeding fish, elicited unique responses among colonizing Hydrophilidae, with the exception of the smallest and most abundant taxa, Paracymus, while Dytiscidae responded similarly to all avoided fish. Neither family responded to A. sayanus. Analysis of species richness and multivariate characterization of the beetle assemblages for the four fish species and controls revealed additional variation among the three avoided species and confirmed that chemical camouflage in A. sayanus results in assemblages essentially identical to fishless controls. The origin of this variation in beetle responses to different fish is unknown, but may involve variation in cue sensitivity, different behavioral algorithms, or differential responses to species-specific fish cues. The identity of fish species occupying aquatic habitats is crucial to understanding community structure, as varying strengths of lethal and non-lethal effects, as well as their interaction, create complex landscapes of predator effects and challenge the notion of functional

  17. Application of neural networks to prediction of fish diversity and salmonid production in the Lake Ontario basin

    Science.gov (United States)

    McKenna, James E.

    2005-01-01

    Diversity and fish productivity are important measures of the health and status of aquatic systems. Being able to predict the values of these indices as a function of environmental variables would be valuable to management. Diversity and productivity have been related to environmental conditions by multiple linear regression and discriminant analysis, but such methods have several shortcomings. In an effort to predict fish species diversity and estimate salmonid production for streams in the eastern basin of Lake Ontario, I constructed neural networks and trained them on a data set containing abiotic information and either fish diversity or juvenile salmonid abundance. Twenty percent of the original data were retained as a test data set and used in the training. The ability to extend these neural networks to conditions throughout the streams was tested with data not involved in the network training. The resulting neural networks were able to predict the number of salmonids with more than 84% accuracy and diversity with more than 73% accuracy, which was far superior to the performance of multiple regression. The networks also identified the environmental variables with the greatest predictive power, namely, those describing water movement, stream size, and water chemistry. Thirteen input variables were used to predict diversity and 17 to predict salmonid abundance.

  18. Evaluation of Juvenile Fish Bypass and Adult Fish Passage Facilities at Water Diversions in the Umatilla River; 1993 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, Suzanne M.

    1994-03-01

    This report presents progress from October 1992 through September 1993 in evaluating juvenile fish bypass facilities at Three Mile Falls, Maxwell, Westland, and Feed Canal dams on the Umatilla River, and in evaluating adult fish passage in the lower Umatilla River. Also reported is an effort to evaluate delayed mortality and stress responses of juvenile salmonids resulting from trapping and transport at high temperatures. These studies are part of a program to rehabilitate anadromous fish stocks in the matilla River Basin, including restoration of coho salmon and chinook salmon, as well as enhancement of summer steelhead.

  19. Environmental Determinants Influencing Fish Community Structure and Diversity in Two Distinct Seasons among Wetlands of Northern Region (Ghana

    Directory of Open Access Journals (Sweden)

    Collins Ayine Nsor

    2016-01-01

    Full Text Available Fish community structure was assessed in six wetlands using cast nets, to correlate with environmental variables with diversity and distribution patterns, from 2010 to 2012. A total of 2,239 individuals belonging to 44 species and 1,938 individuals belonging to 40 species were sampled in the dry and wet seasons. Mochokid and Mormyrid families dominated fish community and constituted 14.8%, respectively, followed by Alestids (12.9% and Chlariids (11.1%. Rarer taxons were centropomids, channids, malapteruds, and oesteoglossids and represented 1.9%, respectively. Overall, CPUE per net did not vary significantly (Tukey HSD test, p=0.27 in the dry and wet seasons. Wuntori marsh consistently showed dominance in mean monthly CPUE per net (dry = 115±4.5; wet = 107±7.7 seasons, while Bunglung constructed wetland was the least recorded (dry = 56.5±6.2; wet = 58.3±4.1 seasons. Fish diversity and richness differed significantly (F=0.11, p=0.03 among seasons. Environmental disturbances were season-specific and did not differ significantly (F=0.16, df=14, p=0.97 among sites. A DCA ordination explained 69% variability in fish distribution patterns, while PCA showed that 81.8% of nitrate-nitrogen, phosphate, and grazing intensity on axis 1 and conductivity, temperature, and turbidity on axis 2 influenced fish community structure. Wetland conservation must be promoted to sustain fish abundance and overall ecosystem stability.

  20. Contribution of different mesohabitats to the maintenance of fish richness and diversity in the lower Preto River

    Directory of Open Access Journals (Sweden)

    Jaquelini Oliveira Zeni

    2015-07-01

    Full Text Available The presence of different mesohabitats in freshwater systems can support higher local and regional fish richness. Thus, their suppression by dam-building represents a real threat to aquatic biodiversity. Our aims were: (1 to survey the fish fauna in two different mesohabitats in lower Preto River: a riffle indirectly threatened by dam-building and a run with different physical structure; and (2 to analyze and compare the fish community structure in these different mesohabitats. Six samplings were made during one year in two reaches (R1 and R2. We conducted a ‘one way’ ANOSIM to assess the differences in fish community structure between R1 and R2. Fifty-three species were recorded, with the occurrence of Aphyocheirodon hemigrammus and Myleus tiete, two Brazilian threatened species. The highest richness was observed in R2. Nevertheless, diversity and evenness were significantly higher in R1. Rheophilic species were more common and restricted to R1 and species typical of lentic environments were predominant in R2. Fish community structure was different between R1 and R2 (R = 1, p = 0.02. Our results demonstrated that mesohabitats mosaic through rivers can contribute to the maintenance of a diverse fish assemblage.

  1. National Patterns of Philippine Reef Fish Diversity and Its Implications on the Current Municipal-Level Management

    Directory of Open Access Journals (Sweden)

    Jonathan A. Anticamara

    2015-06-01

    Full Text Available Recent national-level assessments of Philippine reef fish diversity have been mainly based on species richness surveys, but generally do not account for reef f ish abundance and biomass—metrics that better describe fish community assemblages. Given that the Philippines is considered a major biodiversity hotspot and is heavily reliant on coastal resources, there is a great need to quantify the current status of its reef fish diversity using standardized methods. Here, standardized Underwater Visual Census (UVC belt transect sampling methods were used to quantify current levels of reef fish species richness, relative abundance, and relative biomass throughout the Philippines. Results showed that most surveyed municipalities were still species-rich (22.2 ± 0.8 reef fish species per 100 m2, but appeared depleted in terms of reef f ish abundance and biomass. Partitioning analysis revealed significant differences in reef fish species richness patterns across municipalities, suggesting the presence of a few restricted-range and rare species per site. However, partitioning analysis accounting for relative abundance showed that reef fish diversity was generally homogenous across study sites, suggesting the dominance of a few highly-abundant species. SIMPER analysis revealed that Philippine reefs were generally dominated by small and medium-bodied species, rather than large-bodied species—the latter of which are especially vulnerable to fishing due to certain life history traits (e.g. , late age at maturity and slow growth rate and commercial exploitation. While current municipal-level management may be sufficient for restricted-range fish species, large-scale conservation efforts (i.e., in the form of collaborative marine reserve networks are needed for wide-range and large-bodied species that are not confined to politically-defined municipal boundaries. In addition, long-term and nationwide efforts to systematically monitor Philippine reef

  2. FISH DIVERSITY ALONG THE LONGITUDINAL GRADIENT IN A MAN–MADE LAKE OF WEST AFRICA, TAABO HYDROELECTRIC RESERVOIR, IVORY COAST

    Directory of Open Access Journals (Sweden)

    N. G. Aliko

    2010-04-01

    Full Text Available Fish assemblage patterns in Taabo Reservoir, a hydroelectric lake of Ivory Coast, were studied and related to the longitudinal gradient (river–dam gradient composed of riverine, transitional, and lacustrine zones. Data were collected at 5 stations and each one was sampled during 5 surveys. Fish community structure was analysed using alpha and beta diversity indices. In total, 53 fish species were obtained in the whole ecosystem. Total species richness recorded at each ecological zone was 42, 43 and 45 species respectively in the riverine, transitional and lacustrine zones. Alpha diversity did not differed significantly along the longitudinal gradient but reached the highest value (33 species in the transitional zone and the lowest (18 species occurred in both the riverine and lacustrine zones. Temporal variability of Alpha diversity according to the hydrological regime of the lake differed with the zone. Beta diversity showed that fish assemblages similarity was higher between the transitional and the riverine zones (βw = 0.43 and lower between the riverine and the lacustrine zones (βw = 0.79.

  3. Species composition and diversity of pelagic fishes based on a longline fishery catch in the North Pacific Ocean

    Institute of Scientific and Technical Information of China (English)

    ZHU Jiangfeng; DAI Xiaojie; CHEN Yong

    2011-01-01

    Evaluation of spatial-temporal variability of species composition and diversity in oceanic ecosystems is not easy because it is usually difficult to obtain sufficient data quantifying such variability.In this study, we examined pelagic species diversity indicators, species richness, Shannon-Wiener index of diversity and Hurlbert's species evenness, for fish assemblages from two areas (north and south) in the North Pacific Ocean (2°-12°N, 178°E-165°W) during May-July 2008. The assemblages were based on data collected by an onboard scientific observer during a commercial longline fishing trip. The species richness and Shannon-Wiener diversity index of fish assemblages in the northern area were slightly higher than those in the southern area, although these differences were not significant (t test,P>0.05). Non-parametric multidimensional scaling and analysis of similarities indicated that there were significant differences in fish assemblages between the two areas (P<0.01).

  4. Eimeria that infect fish are diverse and are related to, but distinct from, those that infect terrestrial vertebrates.

    Science.gov (United States)

    Molnár, Kálmán; Ostoros, Györgyi; Dunams-Morel, Detiger; Rosenthal, Benjamin M

    2012-12-01

    The Eimeria are ubiquitous parasites (Phylum: Apicomplexa; family: Coccidia) of the gut epithelium of vertebrates which complete their development in a single host species and whose sporocysts may be recognized by the presence of a Stieda body through which their sporozoites excyst. Their diversity and relationship to other kinds of coccidia have been successfully explored by molecular systematic studies based on the sequencing the 18S ribosomal DNA. To date, most attention has been paid to the diversity and evolutionary relationships of Eimeria spp. parasitizing terrestrial vertebrates, most especially those species infecting domesticated birds and mammals. Regrettably, no Eimeria have yet been considered from the Earth's first vertebrates: the fish. If Eimeria first evolved in fish, then extant piscine parasites should comprise a deeply branching assemblage at the base of well-constructed phylogenetic trees. Here, we sequenced portions of ribosomal DNA from several such isolates (from Eimeria anguillae, Eimeria daviesae, Eimeria percae, Eimeria variabilis, Eimeria rutili and Eimeria nemethi) and compared them to one another as well as to other available sequences from the parasites of fish and terrestrial vertebrates, in order to better understand their diversity and origins. By establishing that such piscine parasites comprise a deeply branching clade at the base of the Eimeriidae, these data substantiate the hypothesis that Eimeria may have originated in fish. Plainly, a great deal of coccidian diversity awaits future discovery and description.

  5. Findings from an Independent Evaluation of the AMNH's Online Seminars on Science Course: "The Diversity of Fishes"

    Science.gov (United States)

    Inverness Research, 2008

    2008-01-01

    Inverness Research studied the American Museum of Natural History (AMNH) Seminars on Science program for eight years, from its inception in 1998 to 2006. This paper presents teacher survey ratings for "The Diversity of Fishes", along with profiles of two teachers who took the course. Course takers report on the annual follow-up surveys…

  6. Fish Diversity and Abundance of Lake Tanganyika: Comparison between Protected Area (Mahale Mountains National Park and Unprotected Areas

    Directory of Open Access Journals (Sweden)

    Emmanuel A. Sweke

    2013-01-01

    Full Text Available High biodiversity is the most remarkable characteristic of Lake Tanganyika including vertebrates, invertebrates, and plants. A few protected areas have been created along the lake to protect its biodiversity. However, limited studies have been carried out to ascertain their effectiveness. The current study aimed at assessing and comparing fish diversity and abundance of Lake Tanganyika in a protected area (Mahale Mountains National Park (MMNP and unprotected areas surrounding it. The data were collected in the near shore zone at 5 m and 10 m depths using stationary visual census (SVC technique. The protected area recorded higher fish richness and abundance than unprotected areas (P<0.05. It was concluded that the protected area is effective in conserving the fish diversity and abundance of the lake. However, more studies should be carried out regularly to explore the efficacy of the protected area in conservation of aquatic biodiversity and abundance.

  7. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Risk assessment of non-native fishes in the Balkans Region using FISK, the invasiveness screening tool for non-native freshwater fishes

    Directory of Open Access Journals (Sweden)

    P. SIMONOVIC

    2013-06-01

    Full Text Available A high level of freshwater fish endemism in the Balkans Region emphasizes the need for non-native species risk assessments to inform management and control measures, with pre-screening tools, such as the Fish Invasiveness Screening Kit (FISK providing a useful first step. Applied to 43 non-native and translocated freshwater fishes in four Balkan countries, FISK reliably discriminated between invasive and non-invasive species, with a calibration threshold value of 9.5 distinguishing between species of medium and high risk sensu lato of becoming invasive. Twelve of the 43 species were assessed by scientists from two or more Balkan countries, and the remaining 31 species by a single assessor. Using the 9.5 threshold, three species were classed as low risk, 10 as medium risk, and 30 as high risk, with the latter category comprised of 26 moderately high risk, three high risk, and one very high risk species. Confidence levels in the assessments were relatively constant for all species, indicating concordance amongst assessors.

  9. Spatial Complexity, Resilience, and Policy Diversity: Fishing on Lake-rich Landscapes

    Directory of Open Access Journals (Sweden)

    Stephen R. Carpenter

    2004-06-01

    Full Text Available The dynamics of and policies governing spatially coupled social-ecological mosaics are considered for the case of fisheries in a lake district. A microeconomic model of households addresses agent decisions at three hierarchic levels: (1 selection of the lake district from among a larger set of alternative places to live or visit, (2 selection of a base location within the lake district, and (3 selection of a portfolio of ecosystem services to use. Ecosystem services are represented by dynamics of fish production subject to multiple stable domains and trophic cascades. Policy calculations show that optimal policies will be highly heterogeneous in space and fluid in time. The diversity of possible outcomes is illustrated by simulations for a hypothetical lake district based loosely on the Northern Highlands of the State of Wisconsin. Lake districts are frequently managed as if lakes were independent, similar, endogenously regulating systems. Our findings contradict that view. One-size-fits-all (OSFA policies erode ecological and social resilience. If regulations are too stringent, social resilience declines because of the potential rewards of overharvesting. If regulations are too lax, ecological resilience is diminished by overharvesting in some lakes. In either case, local collapses of fish populations evoke spatial shifts of angling effort that can lead to serial collapses in neighboring fisheries and degraded fisheries in most or all of the lakes. Under OSFA management, the natural resources of the entire landscape become more vulnerable to transformation because of changes in, e.g., human population, the demand for resources, or fish harvesting technology. Multiplicity of management regimes can increase the ecological resilience, social resilience, and inclusive value of a spatially heterogeneous social-ecological system. Because of the complex interactions of mobile people and multistable ecosystems, management regimes must also be flexible

  10. Screening for Viral Hemorrhagic Septicemia Virus in Marine Fish along the Norwegian Coastal Line

    DEFF Research Database (Denmark)

    Sandlund, Nina; Gjerset, Britt; Bergh, Øivind

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted...

  11. Body ram, not suction, is the primary axis of suction-feeding diversity in spiny-rayed fishes.

    Science.gov (United States)

    Longo, Sarah J; McGee, Matthew D; Oufiero, Christopher E; Waltzek, Thomas B; Wainwright, Peter C

    2016-01-01

    Suction-feeding fishes exhibit diverse prey-capture strategies that vary in their relative use of suction and predator approach (ram), which is often referred to as the ram-suction continuum. Previous research has found that ram varies more than suction distance among species, such that ram accounts for most differences in prey-capture behaviors. To determine whether these findings hold at broad evolutionary scales, we collected high-speed videos of 40 species of spiny-rayed fishes (Acanthomorpha) feeding on live prey. For each strike, we calculated the contributions of suction, body ram (swimming) and jaw ram (mouth movement relative to the body) to closing the distance between predator and prey. We confirm that the contribution of suction distance is limited even in this phylogenetically and ecologically broad sample of species, with the extreme suction area of prey-capture space conspicuously unoccupied. Instead of a continuum from suction to ram, we find that variation in body ram is the major factor underlying the diversity of prey-capture strategies among suction-feeding fishes. Independent measurement of the contribution of jaw ram revealed that it is an important component of diversity among spiny-rayed fishes, with a number of ecomorphologies relying heavily on jaw ram, including pivot feeding in syngnathiforms, extreme jaw protruders and benthic sit-and-wait ambush predators. A combination of morphological and behavioral innovations has allowed fish to invade the extreme jaw ram area of prey-capture space. We caution that while two-species comparisons may support a ram-suction trade-off, these patterns do not speak to broader patterns across spiny-rayed fishes.

  12. Prevalence and diversity of fish-borne zoonotic trematodes in tilapia (Oreochromis niloticus) culture in Guangdong, China

    DEFF Research Database (Denmark)

    Li, Kang; Murrell, Kenneth Darwin; Clausen, Jesper Hedegaard

    ), and Carassius auratus (4).The FZT species recovered were mainly Haplorchis taichui, and H. pumilio along with some unknown species whose identifications are still being determined. Subsequently a cross-sectional survey for the prevalence and diversity of FZT in tilapia culture systems was conducted in Guangdong...... Province during August-October 2011. A total of 389 tilapias sized 2.33-1450.00 g were collected from 30 farms, and examined for FZT metacercariae by the pepsin digestion method. Ten percent of the farms surveyed had fish with FZT infections. The overall FZT prevalence in fish was 1.5% and the infection...

  13. Fish collection of the Universidade Federal de Rondônia: its importance to the knowledge of Amazonian fish diversity

    Directory of Open Access Journals (Sweden)

    Willian Massaharu Ohara

    2015-08-01

    Full Text Available Biological collections preserve the biodiversity of a nation. The fish collection of the Universidade Federal de Rondônia, recently established, contains about 41% of freshwater fish species known to occur in Brazil, and 24% of South America. The biological material is distributed into 1,067 species, 21,963 lots and 149,192 specimens, gathered during five years of work. From this collection, 99% of the lots have georeferenced location, and 94% of the species were sampled in the Madeira River basin, the largest tributary in flow, drainage area and sediment discharge of the Amazonas River basin. Among the 1,008 species collected in the Madeira River basin, 80% were reviewed by Brazilian, North American and French experts, and represents the highest richness among tributaries of the Amazonas River and other rivers worldwide. Fish collection from the Madeira River basin deposited in the ichthyological collection of the Universidade Federal de Rondônia accounts for about 75% of the lots and specimens of fish from that basin available for study in collections worldwide.

  14. Hollow fiber cell fishing with high performance liquid chromatography for screening bioactive compounds from traditional Chinese medicines.

    Science.gov (United States)

    Xue, Xue; Li, Lihua; Chen, Xuan; Hu, Shuang; Bai, Xiaohong

    2013-03-08

    A novel hollow fiber cell fishing method with high performance liquid chromatography was proposed and used to screen, isolate, and analyze bioactive compounds from Traditional Chinese Medicines (TCMs). The active compounds that interact with the living cells acceptor inside the hollow fiber lumen were screened and isolated from the TCM extracts in phosphate buffer solution (pH 7.4). Subsequently, the active compounds bound to the cells were desorbed with methanol, and were analyzed using HPLC. HFCF with HPLC was introduced for the screening and analysis of lignans in Schisandra chinensis (Turcz) Baill and coumarins in Fructus Cnidii and Fructus Psoraleae. The surface properties of the hollow fibers filled with living cells were characterized. The nonspecific binding between the active centers of the hollow fibers and the bioactive compounds were investigated. The cell survival rates were determined before and after the screening. The repeatability of the method was tested. Some structures of the lignans and coumarins screened from TCMs were identified by the comparison to the retention times of the reference substances. HFCF-HPLC is a simple, fast, effective, and reliable method for the screening and analysis of bioactive compounds, and it can be extended to screen other bioactive compounds from TCMs.

  15. Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes

    Directory of Open Access Journals (Sweden)

    Alba Ardura

    2016-10-01

    Full Text Available Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant. A few species were cosmopolitan and others latitude-specific, as was expected. The latitudinal pattern of diversity did not exhibit a temperate-tropical cline; instead, it was likely correlated with environmental conditions with a decline in low-oxygen zones. Importantly, gaps and inconsistencies in reference DNA databases impeded accurate identification to the species level of 49% of the individuals. Fish sampled from tropical latitudes and some orders, such as Perciformes, Myctophiformes and Stomiiformes, were largely unidentified due to incomplete references. Some larvae were identified based on morphology and COI analysis for comparing time and costs employed from each methodology. These results suggest the need of reinforcing DNA barcoding reference datasets of Atlantic bathypelagic tropical fish that, as main prey of top predators, are crucial for ecosystem-based management of fisheries resources.

  16. Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes

    Science.gov (United States)

    Morote, Elvira; Kochzius, Marc; Garcia-Vazquez, Eva

    2016-01-01

    Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI) as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant. A few species were cosmopolitan and others latitude-specific, as was expected. The latitudinal pattern of diversity did not exhibit a temperate-tropical cline; instead, it was likely correlated with environmental conditions with a decline in low-oxygen zones. Importantly, gaps and inconsistencies in reference DNA databases impeded accurate identification to the species level of 49% of the individuals. Fish sampled from tropical latitudes and some orders, such as Perciformes, Myctophiformes and Stomiiformes, were largely unidentified due to incomplete references. Some larvae were identified based on morphology and COI analysis for comparing time and costs employed from each methodology. These results suggest the need of reinforcing DNA barcoding reference datasets of Atlantic bathypelagic tropical fish that, as main prey of top predators, are crucial for ecosystem-based management of fisheries resources. PMID:27761307

  17. Diversity of the skin microbiota of fishes: evidence for host species specificity.

    Science.gov (United States)

    Larsen, Andrea; Tao, Zhen; Bullard, Stephen A; Arias, Covadonga R

    2013-09-01

    Skin microbiota of Gulf of Mexico fishes were investigated by ribosomal internal spacer analysis (RISA) and 16S rRNA gene sequencing. A total of 102 fish specimens representing six species (Mugil cephalus, Lutjanus campechanus, Cynoscion nebulosus, Cynoscion arenarius, Micropogonias undulatus, and Lagodon rhomboides) were sampled at regular intervals throughout a year. The skin microbiota from each individual fish was analyzed by RISA and produced complex profiles with 23 bands on average. Similarities between RISA profiles ranged from 97.5% to 4.0%. At 70% similarity, 11 clusters were defined, each grouping individuals from the same fish species. Multidimensional scaling and analysis of similarity correlated the RISA-defined clusters with geographic locality, date, and fish species. Global R values indicated that fish species was the most indicative variable for group separation. Analysis of 16S rRNA gene sequences (from pooled samples of 10 individual fish for each fish species) showed that the Proteobacteria was the predominant phylum in skin microbiota, followed by the Firmicutes and the Actinobacteria. The distribution and abundance of bacterial sequences were different among all species analyzed. Aeribacillus was found in all fish species representing 19% of all clones sequenced, while some genera were fish species-specific (Neorickettsia in M. cephalus and Microbacterium in L. campechanus). Our data provide evidence for the existence of specific skin microbiota associated with particular fish species. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  18. Mapping spatial variation in demersal fish species diversity and composition in the North Sea: accounting for species- and size-related catchability in survey trawls

    NARCIS (Netherlands)

    Fraser, H.M.; Greenstreet, S.P.R.; Fryer, R.J.; Piet, G.J.

    2008-01-01

    The paper maps spatial patterns of groundfish species diversity. It considers how the catchability of different fish species in two different types of bottom trawls, the IBTS GOV and the 8-m beam trawl, influences the estimates of species diversity. Maps of groundfish species diversity derived from

  19. Security screening via computational imaging using frequency-diverse metasurface apertures

    Science.gov (United States)

    Smith, David R.; Reynolds, Matthew S.; Gollub, Jonah N.; Marks, Daniel L.; Imani, Mohammadreza F.; Yurduseven, Okan; Arnitz, Daniel; Pedross-Engel, Andreas; Sleasman, Timothy; Trofatter, Parker; Boyarsky, Michael; Rose, Alec; Odabasi, Hayrettin; Lipworth, Guy

    2017-05-01

    Computational imaging is a proven strategy for obtaining high-quality images with fast acquisition rates and simpler hardware. Metasurfaces provide exquisite control over electromagnetic fields, enabling the radiated field to be molded into unique patterns. The fusion of these two concepts can bring about revolutionary advances in the design of imaging systems for security screening. In the context of computational imaging, each field pattern serves as a single measurement of a scene; imaging a scene can then be interpreted as estimating the reflectivity distribution of a target from a set of measurements. As with any computational imaging system, the key challenge is to arrive at a minimal set of measurements from which a diffraction-limited image can be resolved. Here, we show that the information content of a frequency-diverse metasurface aperture can be maximized by design, and used to construct a complete millimeter-wave imaging system spanning a 2 m by 2 m area, consisting of 96 metasurfaces, capable of producing diffraction-limited images of human-scale targets. The metasurfacebased frequency-diverse system presented in this work represents an inexpensive, but tremendously flexible alternative to traditional hardware paradigms, offering the possibility of low-cost, real-time, and ubiquitous screening platforms.

  20. Fishing

    Institute of Scientific and Technical Information of China (English)

    姜群山

    2002-01-01

    @@ Last Saturday my cousin (表兄) came to my home. We were very happy to see each other. We decided that the next day we went to fish. We got up very early that day. When we left home,the moon could still be seen in the sky.

  1. [Advanced approaches to studying the population diversity of marine fishes: new opportunities for fisheries control and management].

    Science.gov (United States)

    Zelenina, D A; Martinson, Ia T; Ogden, R; Volkov, A A; Zelenina, I A; Carvalho, G R

    2011-12-01

    Recent conceptual and technological advances now enable fisheries geneticists to detect and monitor the dynamics and distribution of marine fish populations more effectively than ever before. Information on the extent of genetically-based divergence among populations, so-called "population diversity", is crucial in the quest to manage exploited living resources sustainably since it endows evolutionary potential in the face of environmental change. The generally limited dialogue between scientists, fisheries managers and policy makers, however, continues to constrain integration of population genetic data into tangible policy applications. Largely drawing on the approach and outputs from a European research project, FishPopTrace, we provide an example how the uncovering of marine fish population diversity enables players from genetics, forensics, management and the policy realm to generate a framework tackling key policy-led questions relating to illegal fishing and traceability. We focus on the use of single-nucleotide polymorphisms (SNPs) in European populations of cod, herring, hake and common sole, and explore how forensics together with a range of analytical approaches, and combined with improved communication of research results to stakeholders, can be used to secure sufficiently robust, tractable and targeted data for effective engagement between science and policy. The essentially binary nature of SNPs, together with generally elevated signals of population discrimination by SNPs under selection, allowed assignment of fish to populations from more areas and with higher certainty than previously possible, reaching standards suitable for use in a court of law. We argue that the use of such tools in enforcement and deterrence, together with the greater integration of population genetic principles and methods into fisheries management, provide tractable elements in the arsenal of tools to achieve sustainable exploitation and conservation of depleted marine fish

  2. Consensus Recommendations for Advancing Breast Cancer: Risk Identification and Screening in Ethnically Diverse Younger Women

    Directory of Open Access Journals (Sweden)

    Alexander Stojadinovic, Thomas A Summers, John Eberhardt, Albert Cerussi, Warren Grundfest, Charles M. Peterson, Michael Brazaitis, Elizabeth Krupinski, Harold Freeman

    2011-01-01

    Full Text Available A need exists for a breast cancer risk identification paradigm that utilizes relevant demographic, clinical, and other readily obtainable patient-specific data in order to provide individualized cancer risk assessment, direct screening efforts, and detect breast cancer at an early disease stage in historically underserved populations, such as younger women (under age 40 and minority populations, who represent a disproportionate number of military beneficiaries. Recognizing this unique need for military beneficiaries, a consensus panel was convened by the USA TATRC to review available evidence for individualized breast cancer risk assessment and screening in young (< 40, ethnically diverse women with an overall goal of improving care for military beneficiaries. In the process of review and discussion, it was determined to publish our findings as the panel believes that our recommendations have the potential to reduce health disparities in risk assessment, health promotion, disease prevention, and early cancer detection within and in other underserved populations outside of the military. This paper aims to provide clinicians with an overview of the clinical factors, evidence and recommendations that are being used to advance risk assessment and screening for breast cancer in the military.

  3. A role for partially protected areas on coral reefs: Maintaining fish diversity?

    KAUST Repository

    Tyler, Elizabeth

    2011-04-15

    1. Completely banning fishing from coral reefs is now accepted to have significant benefits for marine biodiversity and in many cases, fisheries. However, the benefits of regulating fishing on coral reefs, by restricting the methods used, or the total amount of fishing, are less well understood, even though such regulations are much more likely to be supported by fishermen. 2. This study assesses whether banning illegal, destructive fishing methods and reducing the numbers of fishermen visiting from outside an area benefits a coral reef fishery, despite unregulated fishing by local fishermen using non-destructive methods. 3. The abundance, biomass, mean length, and species richness of nine commercially important fish families are compared across ten independent patch reefs inside and outside the 470km2 Menai Bay Conservation Area in Zanzibar, Tanzania. 4. Even after taking into account the effect of differences in habitat and the distance between reefs, 61% (±19.7%) more fish species were found in regulated than unregulated reefs. Fish abundance, biomass, and length were not affected, suggesting that banning destructive fishing may improve biodiversity, but that further regulations may be required to improve fish stocks. © 2011 John Wiley and Sons, Ltd.

  4. Diversity and composition of demersal fishes along a depth gradient assessed by baited remote underwater stereo-video.

    Directory of Open Access Journals (Sweden)

    Vincent Zintzen

    Full Text Available BACKGROUND: Continental slopes are among the steepest environmental gradients on earth. However, they still lack finer quantification and characterisation of their faunal diversity patterns for many parts of the world. METHODOLOGY/PRINCIPAL FINDINGS: Changes in fish community structure and diversity along a depth gradient from 50 to 1200 m were studied from replicated stereo baited remote underwater video deployments within each of seven depth zones at three locations in north-eastern New Zealand. Strong, but gradual turnover in the identities of species and community structure was observed with increasing depth. Species richness peaked in shallow depths, followed by a decrease beyond 100 m to a stable average value from 700 to 1200 m. Evenness increased to 700 m depth, followed by a decrease to 1200 m. Average taxonomic distinctness △(+ response was unimodal with a peak at 300 m. The variation in taxonomic distinctness Λ(+ first decreased sharply from 50 to 300 m, then increased beyond 500 m depth, indicating that species from deep samples belonged to more distant taxonomic groups than those from shallow samples. Fishes with northern distributions progressively decreased in their proportional representation with depth whereas those with widespread distributions increased. CONCLUSIONS/SIGNIFICANCE: This study provides the first characterization of diversity patterns for bait-attracted fish species on continental slopes in New Zealand and is an imperative primary step towards development of explanatory and predictive ecological models, as well as being fundamental for the implementation of efficient management and conservation strategies for fishery resources.

  5. Support for a 'Center of Origin' in the Coral Triangle: cryptic diversity, recent speciation, and local endemism in a diverse lineage of reef fishes (Gobiidae: Eviota).

    Science.gov (United States)

    Tornabene, Luke; Valdez, Samantha; Erdmann, Mark; Pezold, Frank

    2015-01-01

    The Coral Triangle is widely regarded as the richest marine biodiversity hot-spot in the world. One factor that has been proposed to explain elevated species-richness within the Coral Triangle is a high rate of in situ speciation within the region itself. Dwarfgobies (Gobiidae: Eviota) are a diverse genus of diminutive cryptobenthic reef fishes with limited dispersal ability, and life histories and ecologies that increase potential for speciation. We use molecular phylogenetic and biogeographic data from two clades of Eviota species to examine patterns, processes and timing associated with species origination within the Coral Triangle. Sequence data from mitochondrial and nuclear DNA were used to generate molecular phylogenies and median-joining haplotype networks for the genus Eviota, with emphasis on the E. nigriventris and E. bifasciata complexes - two species groups with distributions centered in the Coral Triangle. The E. nigriventris and E. bifasciata complexes both contain multiple genetically distinct, geographically restricted color morphs indicative of recently-diverged species originating within the Coral Triangle. Relaxed molecular-clock dating estimates indicate that most speciation events occurred within the Pleistocene, and the geographic pattern of genetic breaks between species corresponds well with similar breaks in other marine fishes and sessile invertebrates. Regional isolation due to sea-level fluctuations may explain some speciation events in these species groups, yet other species formed with no evidence of physical isolation. The timing of diversification events and present day distributions of Eviota species within the Coral Triangle suggest that both allopatric speciation (driven by ephemeral and/or 'soft' physical barriers to gene flow) and sympatric speciation (driven by niche partitioning and assortative mating) may be driving diversification at local scales within the Coral Triangle. The presence of multiple young, highly

  6. Inventory of the freshwater fishes from a densely collected area in South America-a case study of the current knowledge of Neotropical fish diversity.

    Science.gov (United States)

    Bertaco, Vinicius A; Ferrer, Juliano; Carvalho, Fernando R; Malabarba, Luiz R

    2016-07-18

    We herein analyse the history of the description of the freshwater fish fauna from three drainages in one of the most densely collected areas of Brazil, and possibly of South America, the Rio Grande do Sul State, southern Brazil. An updated inventory of the freshwater fish species from rio Uruguay (partial) in Brazil, Laguna dos Patos (complete) and rio Tramandaí basins (complete) is presented. We found the number of new species described in these drainages increased nearly 56% since 1981, reaching a total of 422 species, but even now 10% of this number still corresponds to undescribed species. This rate of species description suggests that previous estimates of the Neotropical fish fauna are low, and we predict a final number of Neotropical fishes larger than the largest prediction estimate (8,000 species), after other regions of South and Central Americas become densely sampled. We discuss and attempt to demonstrate that species diversity knowledge is historically and strictly related to collecting efforts. We also demonstrate that the ecoregions in eastern South America with the highest density of species per area correspond to the areas more densely sampled in collections, and this may represent a bias in such kinds of analyses. This uneven sampling in Brazilian regions is apparently associated with the uneven distribution of Zoological research centers in different regions of the country. Small-sized species represents an important source of new species, along with little explored regions or little explored habitats, sometimes associated with restricted range species, and species complexes that need revisionary work. In contrast to other Neotropical regions, Atheriniformes are relatively diverse, sharing the fifth place in species richness with Gymnotiformes, and there is a remarkably high number of species of Rivulidae. Eight species are endemic to the rio Tramandaí drainage, 68 to the Laguna dos Patos system, and 78 to the rio Uruguay drainage. Almost 10

  7. Screening of organochlorine insecticides (DDT and heptachlor in dry fish available in Bangladesh

    Directory of Open Access Journals (Sweden)

    Md. Nurul Huda Bhuiyan

    2008-06-01

    Full Text Available The concentrations of organochlorine insecticides DDT and heptachlor were investigated to estimate the current status of insecticides used in dry fish. The most popular dry fish– ribbon fish (Chhuri, shrimp (Chingri and bombay duck (Loittya were selected for this study and these dry fishes were collected from different markets of Dhaka and Chittagong. The range of DDT used in all the samples was 3.038 ppb to 874.966 ppb. The range of DDT in ribbon fish 131.611 ppb to 149.430 ppb, in shrimp 3.038 ppb to 318.206 ppb and in bombay duck 61.918 ppb to 874.966 ppb was found. The range of heptachlor used in all the samples was 0.682 ppb to 5.464 ppb. The range of heptachlor in ribbon fish 1.710 ppb to 2.306 ppb, in shrimp 0.682 ppb to 3.806 ppb and in bombay duck 1.762 ppb to 5.464 ppb was found. The heptachlor was not found in ribbon fish (CTG-2, shrimp (DHK-2 and CTG-1 and bombay duck (DHK-1. The concentration of heptachlor in dry fish compare to DDT was found too much less.

  8. Screening for dioxin contamination in fish oil by PARAFAC and N-PLSR analysis of fluorescence landscapes

    DEFF Research Database (Denmark)

    Pedersen, Dorthe Kjær; Engelsen, Søren Balling

    2002-01-01

    A preliminary investigation of fish oils demonstrates that fluorescence excitation-emission landscapes evaluated by 3-way chemometric methods may be a candidate for an inexpensive screening method to indicate the level of contamination by dioxins and PCB’s which are normally analysed with expensive...... and time-consuming physicochemical separation techniques such as GC-MS. Fluorescence landscapes of 88 fish oils have been investigated and showed great variation due to species, season and treatment, depicting a variation in natural fluorescent components. The fluorescence landscapes were analysed...... by PARAFAC. Samples with similar fluorescence fingerprints were selected from a PARAFAC score plot and local significant prediction models with PARAFAC/MLR, N-PLSR and PLSR were established with correlation coefficients in the range from r=0.69 (n=10) to r=0.97 (n=75) for dioxin and r=0.92 (n=12) for PCB...

  9. Carbon sources supporting a diverse fish community in a tropical coastal ecosystem (Gazi Bay, Kenya)

    Science.gov (United States)

    Nyunja, J.; Ntiba, M.; Onyari, J.; Mavuti, K.; Soetaert, K.; Bouillon, S.

    2009-07-01

    Interlinked mangrove-seagrass ecosystems are characteristic features of many tropical coastal areas, where they act as feeding and nursery grounds for a variety of fishes and invertebrates. The autotrophic carbon sources supporting fisheries in Gazi bay (Kenya) were studied in three sites, two located in the tidal creeks flowing through extensive mangrove forests, another site located in the subtidal seagrass meadows, approximately 2.5 km away from the forest. Carbon and nitrogen stable isotope composition of 42 fish species, 2 crustacean species and a range of potential primary food sources (e.g., mangroves, seagrasses and epiphytes, macroalgae) were analysed. There was considerable overlap in the δ 13C signatures between fish (-16.1 ± 2.1‰), seagrasses (-15.1 ± 3.0‰), seagrass epiphytes (-13.6 ± 3.3‰), and macroalgae (-20.4 ± 3.1‰). Nevertheless, the signatures for most primary producers were sufficiently distinct to indicate that the dominant carbon sources for fish were mainly derived from the seagrass and their associated epiphytic community, and possibly macroalgae. Mangrove-derived organic matter contributes only marginally to the overall fish food web. Carbon supporting these fish communities was derived directly through grazing by herbivorous and some omnivorous fishes, or indirectly through the benthic food web. Fishes from the mangrove creeks had distinctly lower δ 13C signatures (-16.8 ± 2.0‰) compared to those collected in the adjacent seagrass beds (-14.7 ± 1.7‰). This indicated that these habitats were used as distinct sheltering and feeding zones for the fishes collected, with minimal degree of exchange within the fish communities despite their regular movement pattern.

  10. Genotypic diversity of anogenital human papillomavirus in women attending cervical cancer screening in Harare, Zimbabwe.

    Science.gov (United States)

    Dube Mandishora, Racheal S; Christiansen, Irene K; Chin'ombe, Nyasha; Duri, Kerina; Ngara, Bernard; Rounge, Trine B; Meisal, Roger; Ambur, Ole H; Palefsky, Joel M; Stray-Pedersen, Babill; Chirenje, Zvavahera M

    2017-09-01

    Although anogenital cancers have been on a gradual rise in developing countries in the past few decades, they have been understudied. The objective was to investigate genotypic diversity of anogenital HPV amongst women reporting for routine cervical cancer screening in Harare in Zimbabwe. A cross-sectional study that enrolled 144 women ≥18 years from a cervical cancer-screening clinic was performed. Each woman provided a self-collected cervico-vaginal swab (VS) and a clinician-collected anal swab (CCAS). HIV testing was offered and cervical cytology was performed. Both VS and CCAS samples were HPV genotyped, using amplicon sequencing of the L1 gene region with Illumina technology. Mean age of the women was 39.9 (range 18-83 years, SD ± 11.0). HPV prevalence was 72% (104/144) in VS and 48% (69/144) in CCAS. The most common genotypes detected in both VS and CCAS were HPV18, HPV52, and HPV16. Sixty two percent of the subjects had multiple genotypic HPV infections. The odds of being HPV-positive among HIV-infected women were higher than in HIV-negative women in both the vagina and the anus (CCAS OR = 4.8; CI 2.4-9.8, P < 0.001) and (VS OR = 2.9; CI 1.3-6.4, P = 0.005). High HPV prevalence and diverse genotypes were detected in both the vagina and anus. Anal oncogenic HPV infection was common. HPV 52 was one of the most common oncogenic genotypes in both the vagina and anus. HIV co-infection played a significant role in the prevalence of HPV. These data have implications for design of primary and secondary programs for prevention of anogenital cancer in Zimbabwe. © 2017 Wiley Periodicals, Inc.

  11. Ecological consequences of hydropower development in Central America: Impacts of small dams and water diversion on neotropical stream fish assemblages

    Science.gov (United States)

    Anderson, Elizabeth P.; Freeman, Mary C.; Pringle, C.M.

    2006-01-01

    Small dams for hydropower have caused widespread alteration of Central American rivers, yet much of recent development has gone undocumented by scientists and conservationists. We examined the ecological effects of a small hydropower plant (Dona Julia Hydroelectric Center) on two low-order streams (the Puerto Viejo River and Quebradon stream) draining a mountainous area of Costa Rica. Operation of the Dona Julia plant has dewatered these streams, reducing discharge to ~ 10% of average annual flow. This study compared fish assemblage composition and aquatic habitat upstream and downstream of diversion dams on two streams and along a ~ 4 km dewatered reach of the Puerto Viejo River in an attempt to evaluate current instream flow recommendations for regulated Costa Rican streams. Our results indicated that fish assemblages directly upstream and downstream of the dam on the third order Puerto Viejo River were dissimilar, suggesting that the small dam (fishes. Along the ~ 4 km dewatered reach of the Puerto Viejo River, species count increased with downstream distance from the dam. However, estimated species richness and overall fish abundance were not significantly correlated with downstream distance from the dam. Our results suggested that effects of stream dewatering may be most pronounced for a subset of species with more complex reproductive requirements, classified as equilibrium-type species based on their life-history. In the absence of changes to current operations, we expect that fish assemblages in the Puerto Viejo River will be increasingly dominated by opportunistic-type, colonizing fish species. Operations of many other small hydropower plants in Costa Rica and other parts of Central America mirror those of Doha Julia; the methods and results of this study may be applicable to some of those projects.

  12. Characterization and virulence potential of phenotypically diverse Aeromonas veronii isolates recovered from moribund freshwater ornamental fishes of Kerala, India.

    Science.gov (United States)

    Sreedharan, Krishnan; Philip, Rosamma; Singh, Isaac Sarojani Bright

    2013-01-01

    In the present study, we investigated the involvement of Aeromonas spp. in eliciting disease outbreaks in freshwater ornamental fishes across the state of Kerala, India. We investigated three incidences of disease, in which the moribund fishes exhibited clinical signs such as haemorrhagic septicemia (in gouramy, Trichogaster sp.), dropsy (in Oscar, Astronotus ocellatus) and tail rot/fin rot (in gold fish, Carassius carassius). Pure cultures (n = 20 from each fish; 60 in total) of Aeromonas spp. were recovered from the abdominal fluid as well as from internal organs of affected fishes, although they could not be identified to species level because of the variations in their phenotypic characters. The molecular fingerprinting of the isolates using Enterobacterial Repetitive Intergenic Consensus PCR proved the genetic diversity of the isolates from the three sites. The phylogenetic trees constructed using concatenated sequences (using 16S rRNA, gyrA, gyrB and rpoD genes) indicated that they were related to Aeromonas veronii. They exhibited marked cytotoxic and haemolytic activity, which were responsible for the pathogenic potential of the isolates. The isolates possessed multiple virulence genes such as enterotoxins (act and alt), haemolytic toxins (aerA and hlyA), genes involved in type III secretion system (ascV, aexT and ascF-ascG), glycerophospholipid-cholesterol acyltransferase (gcat) and a type IV pilus (tapA) gene, as determined by PCR. Virulence of representative isolates to goldfish was also tested, and we found LD(50) values of 10(4.07)-10(5.35) cfu/fish. Furthermore, the organisms could be recovered as pure cultures from the lesions as well as from the internal organs.

  13. Wireless Smartphone ECG Enables Large-Scale Screening in Diverse Populations.

    Science.gov (United States)

    Haberman, Zachary C; Jahn, Ryan T; Bose, Rupan; Tun, Han; Shinbane, Jerold S; Doshi, Rahul N; Chang, Philip M; Saxon, Leslie A

    2015-05-01

    The ubiquitous presence of internet-connected phones and tablets presents a new opportunity for cost-effective and efficient electrocardiogram (ECG) screening and on-demand diagnosis. Wireless, single-lead real-time ECG monitoring supported by iOS and android devices can be obtained quickly and on-demand. ECGs can be immediately downloaded and reviewed using any internet browser. We compared the standard 12-lead ECG to the smartphone ECG in healthy young adults, elite athletes, and cardiology clinic patients. Accuracy for determining baseline ECG intervals and rate and rhythm was assessed. In 381 participants, 30-second lead I ECG waveforms were obtained using an iPhone case or iPad. Standard 12-lead ECGs were acquired immediately after the smartphone tracing was obtained. De-identified ECGs were interpreted by automated algorithms and adjudicated by two board-certified electrophysiologists. Both smartphone and standard ECGs detected atrial rate and rhythm, AV block, and QRS delay with equal accuracy. Sensitivities ranged from 72% (QRS delay) to 94% (atrial fibrillation). Specificities were all above 94% for both modalities. Smartphone ECG accurately detects baseline intervals, atrial rate, and rhythm and enables screening in diverse populations. Efficient ECG analysis using automated discrimination and an enhanced smartphone application with notification capabilities are features that can be easily incorporated into the acquisition process. © 2015 Wiley Periodicals, Inc.

  14. Screening for viral hemorrhagic septicemia virus in marine fish along the Norwegian coastal line.

    Directory of Open Access Journals (Sweden)

    Nina Sandlund

    Full Text Available Viral hemorrhagic septicemia virus (VHSV infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted in 2009 to 2011. In total, VHSV was detected by rRT-PCR in twelve samples originating from Atlantic herring (Clupea harengus, haddock (Melanogrammus aeglefinus, whiting (Merlangius merlangus and silvery pout (Gadiculus argenteus. All fish tested positive in gills while four herring and one silvery pout also tested positive in internal organs. Successful virus isolation in cell culture was only obtained from one pooled Atlantic herring sample which shows that today's PCR methodology have a much higher sensitivity than cell culture for detection of VHSV. Sequencing revealed that the positive samples belonged to VHSV genotype Ib and phylogenetic analysis shows that the isolate from Atlantic herring and silvery pout are closely related. All positive fish were sampled in the same area in the northern county of Finnmark. This is the first detection of VHSV in Atlantic herring this far north, and to our knowledge the first detection of VHSV in silvery pout. However, low prevalence of VHSV genotype Ib in Atlantic herring and other wild marine fish are well known in other parts of Europe. Earlier there have been a few reports of disease outbreaks in farmed rainbow trout with VHSV of genotype Ib, and our results show that there is a possibility of transfer of VHSV from wild to farmed fish along the Norwegian coast line. The impact of VHSV on wild fish is not well documented.

  15. Chemoecological Screening Reveals High Bioactivity in Diverse Culturable Portuguese Marine Cyanobacteria

    Directory of Open Access Journals (Sweden)

    Vitor M. Vasconcelos

    2013-04-01

    Full Text Available Marine cyanobacteria, notably those from tropical regions, are a rich source of bioactive secondary metabolites. Tropical marine cyanobacteria often grow to high densities in the environment, allowing direct isolation of many secondary metabolites from field-collected material. However, in temperate environments culturing is usually required to produce enough biomass for investigations of their chemical constituents. In this work, we cultured a selection of novel and diverse cyanobacteria isolated from the Portuguese coast, and tested their organic extracts in a series of ecologically-relevant bioassays. The majority of the extracts showed activity in at least one of the bioassays, all of which were run in very small scale. Phylogenetically related isolates exhibited different activity profiles, highlighting the value of microdiversity for bioprospection studies. Furthermore, LC-MS analyses of selected active extracts suggested the presence of previously unidentified secondary metabolites. Overall, the screening strategy employed here, in which previously untapped cyanobacterial diversity was combined with multiple bioassays, proved to be a successful strategy and allowed the selection of several strains for further investigations based on their bioactivity profiles.

  16. Chemoecological screening reveals high bioactivity in diverse culturable Portuguese marine cyanobacteria.

    Science.gov (United States)

    Leão, Pedro N; Ramos, Vitor; Gonçalves, Patrício B; Viana, Flávia; Lage, Olga M; Gerwick, William H; Vasconcelos, Vitor M

    2013-04-22

    Marine cyanobacteria, notably those from tropical regions, are a rich source of bioactive secondary metabolites. Tropical marine cyanobacteria often grow to high densities in the environment, allowing direct isolation of many secondary metabolites from field-collected material. However, in temperate environments culturing is usually required to produce enough biomass for investigations of their chemical constituents. In this work, we cultured a selection of novel and diverse cyanobacteria isolated from the Portuguese coast, and tested their organic extracts in a series of ecologically-relevant bioassays. The majority of the extracts showed activity in at least one of the bioassays, all of which were run in very small scale. Phylogenetically related isolates exhibited different activity profiles, highlighting the value of microdiversity for bioprospection studies. Furthermore, LC-MS analyses of selected active extracts suggested the presence of previously unidentified secondary metabolites. Overall, the screening strategy employed here, in which previously untapped cyanobacterial diversity was combined with multiple bioassays, proved to be a successful strategy and allowed the selection of several strains for further investigations based on their bioactivity profiles.

  17. Receptor-Based Virtual Screening of EGFR Kinase Inhibitors from the NCI Diversity Database

    Directory of Open Access Journals (Sweden)

    Kiattawee Choowongkomon

    2010-06-01

    Full Text Available Epidermal growth factor receptor (EGFR abnormalities have been associated with several types of human cancer. The crystal structures of its tyrosine kinase domain (EGFR-TK complexed with small molecule inhibitors revealed the kinase inhibition modes, prompting us to search for novel anti-cancer drugs. A total of 1,990 compounds from the National Cancer Institute (NCI diversity set with nonredundant structures have been tested to inhibit cancer cell lines with unknown mechanism. Cancer inhibition through EGFR-TK is one of the mechanisms of these compounds. In this work, we performed receptor-based virtual screening against the NCI diversity database. Using two different docking algorithms, AutoDock and Gold, combined with subsequent post-docking analyses, we found eight candidate compounds with high scoring functions that all bind to the ATP-competitive site of the kinase. None of these compounds belongs to the main group of the currently known EGFR-TK inhibitors. Binding mode analyses revealed that the way these compounds complexed with EGFR-TK differs from quinazoline inhibitor binding and the interaction mainly involves hydrophobic interactions. Also, the common kinase-inhibitor (NH---N and CO---HC hydrogen bonds between the hinge region and the hit compounds are rarely observed. Our results suggest that these molecules could be developed as novel lead compounds in anti-cancer drug design.

  18. Investigation into the fungal diversity within different regions of the gastrointestinal tract of Panaque nigrolineatus, a wood-eating fish

    Directory of Open Access Journals (Sweden)

    Caroline L. Marden

    2017-09-01

    Full Text Available The Amazonian catfish, Panaque nigrolineatus have several physiological adaptions enabling the scraping and consumption of wood (xylivory, facilitating a detritivorous dietary strategy. Composed of lignocellulose, wood is a difficult substrate to degrade and as yet, it is unclear whether the fish obtains any direct nutritional benefits from wood ingestion and degradation. However, there are numerous systems that rely on microbial symbioses to provide energy and other nutritional benefits for host organisms via lignocellulose decomposition. While previous studies on the microbial community of P. nigrolineatus have focused upon the bacterial population, the role of fungi in lignocellulose degradation in the fish has not yet been examined. This study describes the detection of fungi within the fish gastrointestinal tract. Using next generation sequencing, the effects of diet on enteric fungal populations were examined in each gastrointestinal tract region. Fungal species were found to vary in different regions of the gastrointestinal tract as a function of diet. This study is the first to examine the fungal community in a xylivorous fish and results support the hypothesis that diet influences fungal distribution and diversity within the gastrointestinal tract of P. nigrolineatus.

  19. Diversity of Mesozoic semionotiform fishes and the origin of gars (Lepisosteidae)

    Science.gov (United States)

    Cavin, Lionel

    2010-12-01

    Gars (Lepisosteidae) are ray-finned fishes with controversial relationships to other actinopterygian lineages. When fossil taxa are considered, gars are grouped with Mesozoic macrosemiids and `semionotids' in the Semionotiformes, but the intra-relationships within this order are still elusive. Here, the evolutionary history of gars is reinvestigated using a set of well-preserved extinct semionotiform taxa in a phylogenetic analysis. Results indicate that the gar lineage roots in a clade of Late Jurassic-Cretaceous semionotiform fishes. The closest relatives to gars were plant-eating and detritivorous freshwater fishes. The occurrence of semionotiform remains in Early and early Late Cretaceous continental deposits worldwide possibly reflects an important radiation of this group, comparable to the present-day diversification of cypriniforms. Other Late Triassic to Early Cretaceous semionotiform taxa are gathered in a single clade with weakly supported internal nodes, pointing out the necessity to better understand the osteology of these fishes.

  20. Diversity of lampreys and fishes of the Upper Vistula River drainage, Poland: present state and future challenges

    Directory of Open Access Journals (Sweden)

    Michał Nowak

    2010-12-01

    Full Text Available There have been some 57 lamprey and fish species recorded in the Upper Vistula Riverdrainage (S-E Poland. Among these there are a number of species-complexes (Carassius auratus, Gobiogobio, Cobitis taenia with unresolved taxonomy. Identity of some others (Barbus waleckii, Romanogobioalbipinnatus, Cottus gobio is questionable and needs a review. Phylogenetic relationships of anotherones (Eudontomyzon mariae, Lampetra planeri, Lampetra fluviatilis is also under debate. Knowledgeabout the distribution of many species is very scarce and needs to be filled. In the current work webriefly summarise present state of the diversity and classification of lampreys and fishes of the UpperVistula drainage and point some urgent questions that have arose in recent years and are waiting fornew solutions.

  1. Diversity and ancestry of flatworms infecting blood of nontetrapod craniates "fishes".

    Science.gov (United States)

    Orélis-Ribeiro, Raphael; Arias, Cova R; Halanych, Kenneth M; Cribb, Thomas H; Bullard, Stephen A

    2014-01-01

    We herein review all published molecular studies (life history, taxonomy, and phylogeny) and summarize all GenBank sequences and primer sets for the "fish blood flukes". Further, by analysing new and all available sequence data for the partial D1-D2 domains of 28S from 83 blood fluke taxa, we explore the evolutionary expansion of flatworm parasitism in the blood of craniates. Based on this analysis, the blood flukes infecting marine bony fishes (Euteleostei) are monophyletic. The clade comprising the chondrichthyan blood fluke plus the marine euteleost blood flukes is the sister group to tetrapod blood flukes (spirorchiids and schistosomes). The innominate blood fluke cercariae from freshwater gastropods were monophyletic and sister to the clade comprising spirorchiids and schistosomes, but low nodal support indicated that they may represent a distinct blood fluke lineage with phylogenetic affinities also to fish blood flukes. Blood flukes that utilize gastropod intermediate hosts were monophyletic (unidentified gastropod cercariae+tetrapod blood flukes) and those utilizing bivalves and polychaetes were monophyletic (marine fish blood flukes). Low or no taxon sampling among blood flukes of basal fish lineages and primary division freshwater fish lineages are significant data gaps needing closure. We also note that no record of an infection exists in a hagfish (Myxiniformes), lamprey (Petromyzontiformes), or nontetrapod sarcopterygiian, i.e., coelacanth (Coelacanthimorpha) or lungfish (Dipnoi). The present phylogenetic analysis reiterated support for monophyly of Schistosomatidae and paraphyly of spirorchiids, with the blood flukes of freshwater turtles basal to those of marine turtles and schistosomes.

  2. COMPARISON OF AN IN VIVO FISH VTG ASSAY WITH YES AND E-SCREEN

    Science.gov (United States)

    This study compares the efficacy of two in vitro, estrogen-sensitive bioassays to rank the "relative estrogenicity" of five natural, pharmaceutical and xenoestrogens with a newly developed in vivo bioassay. The E-SCREEN (MCF-7 tumor cells) and YES (Yeast Estrogen Screen) assays w...

  3. Variation in fish mercury concentrations in streams of the Adirondack region, New York: A simplified screening approach using chemical metrics

    Science.gov (United States)

    Burns, Douglas A.; Riva-Murray, Karen

    2018-01-01

    Simple screening approaches for the neurotoxicant methylmercury (MeHg) in aquatic ecosystems may be helpful in risk assessments of natural resources. We explored the development of such an approach in the Adirondack Mountains of New York, USA, a region with high levels of MeHg bioaccumulation. Thirty-six perennial streams broadly representative of 1st and 2nd order streams in the region were sampled during summer low flow and analyzed for several solutes and for Hg concentrations in fish. Several landscape and chemical metrics that are typically strongly related to MeHg concentrations in aquatic biota were explored for strength of association with fish Hg concentrations. Data analyses were based on site mean length-normalized and standardized Hg concentrations (assumed to be dominantly MeHg) in whole juvenile and adult Brook Trout Salvelinus fontinalis, Creek Chub Semotilus atromaculatus, Blacknose Dace Rhinichthys atratulus, and Central Mudminnow Umbra limi, as well as on multi-species z-scores. Surprisingly, none of the landscape metrics was related significantly to regional variation in fish Hg concentrations or to z-scores across the study streams. In contrast, several chemical metrics including dissolved organic carbon (DOC) concentrations, sulfate concentrations (SO42−), pH, ultra-violet absorbance (UV254), and specific ultra-violet absorbance were significantly related to regional variation in fish Hg concentrations. A cluster analysis based on DOC, SO42−, and pH identified three distinct groups of streams: (1) high DOC, acidic streams, (2) moderate DOC, slightly acidic streams, and (3) low DOC circum-neutral streams with relatively high SO42−. Preliminary analysis indicated no significant difference in fish Hg z-scores between the moderate and high DOC groups, so these were combined for further analysis. The resulting two groups showed strong differences (p 6.9 mg/L, SO42− 0.31 cm−1 were tested as thresholds to identify Adirondack

  4. Coccidian parasites of fish encompass profound phylogenetic diversity and gave rise to each of the major parasitic groups in terrestrial vertebrates.

    Science.gov (United States)

    Rosenthal, Benjamin M; Dunams-Morel, Detiger; Ostoros, Gyorgyi; Molnár, Kálmán

    2016-06-01

    Fish are the oldest and most diverse group of vertebrates; it therefore stands to reason that fish may have been the original hosts for many types of extant vertebrate parasites. Here, we sought to determine whether coccidian parasites of fish are especially diverse. We therefore sampled such parasites from thirty-nine species of fish and tested phylogenetic hypotheses concerning their relationships, using 18S rDNA. We found compelling phylogenetic support for distinctions among at least four lineages of piscine parasites presently ascribed to the genus Goussia. Some, but not all parasites attributed to Eimeria were confirmed as such. Major taxonomic revisions are likely justified for these parasites of fish, which appear to have given rise to each of the major lineages of coccidian parasites that subsequently proliferated in terrestrial vertebrates, including those such as Toxoplasma gondii that form tissue cysts in intermediate hosts. Published by Elsevier B.V.

  5. Tuneable surface enhanced Raman spectroscopy hyphenated to chemically derivatized thin-layer chromatography plates for screening histamine in fish.

    Science.gov (United States)

    Xie, Zhengjun; Wang, Yang; Chen, Yisheng; Xu, Xueming; Jin, Zhengyu; Ding, Yunlian; Yang, Na; Wu, Fengfeng

    2017-09-01

    Reliable screening of histamine in fish was of urgent importance for food safety. This work presented a highly selective surface enhanced Raman spectroscopy (SERS) method mediated by thin-layer chromatography (TLC), which was tailored for identification and quantitation of histamine. Following separation and derivatization with fluram, plates were assayed with SERS, jointly using silver nanoparticle and NaCl. The latter dramatically suppressed the masking effect caused by excessive fluram throughout the plate, thus offering clear baseline and intensive Raman fingerprints specific to the analyte. Under optimized conditions, the usability of this method was validated by identifying the structural fingerprints of both targeted and unknown compounds in fish samples. Meanwhile, the quantitative results of this method agreed with those by an HPLC method officially suggested by EU for histamine determination. Showing remarkable cost-efficiency and user-friendliness, this facile TLC-SERS method was indeed screening-oriented and may be more attractive to controlling laboratories of limited resource. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions.

    Science.gov (United States)

    Hennersdorf, Philipp; Kleinertz, Sonja; Theisen, Stefan; Abdul-Aziz, Muslihudeen A; Mrotzek, Grit; Palm, Harry W; Saluz, Hans Peter

    2016-01-01

    In this study we analysed fecal bacterial communities and parasites of three important Indonesian fish species, Epinephelus fuscoguttatus, Epinephelus sexfasciatus and Atule mate. We then compared the biodiversity of bacterial communities and parasites of these three fish species collected in highly polluted Jakarta Bay with those collected in less polluted Indonesian areas of Cilacap (E. sexfasciatus, A. mate) and Thousand Islands (E. fuscoguttatus). In addition, E. fuscoguttatus from net cages in an open water mariculture facility was compared with free living E. fuscoguttatus from its surroundings. Both core and shared microbiomes were investigated. Our results reveal that, while the core microbiomes of all three fish species were composed of fairly the same classes of bacteria, the proportions of these bacterial classes strongly varied. The microbial composition of phylogenetically distant fish species, i.e. A. mate and E. sexfasciatus from Jakarta Bay and Cilacap were more closely related than the microbial composition of more phylogentically closer species, i.e. E. fuscoguttatus, E. sexfasciatus from Jakarta Bay, Cilacap and Thousand Islands. In addition, we detected a weak negative correlation between the load of selected bacterial pathogens, i.e. Vibrio sp. and Photobacterium sp. and the number of endoparasites. In the case of Flavobacterium sp. the opposite was observed, i.e. a weak positive correlation. Of the three recorded pathogenic bacterial genera, Vibrio sp. was commonly found in E. fuscoguttatus from mariculture, and lessly in the vicinity of the net cages and rarely in the fishes from the heavily polluted waters from Jakarta Bay. Flavobacterium sp. showed higher counts in mariculture fish and Photobacteria sp. was the most prominent in fish inside and close to the net cages.

  7. Patterns of change in the size spectra of numbers and diversity of the North Sea fish assemblage, as reflected in surveys and models

    DEFF Research Database (Denmark)

    Rice, J.; Gislason, Henrik

    1996-01-01

    . The diversity size spectrum was curvilinear, with diversity increasing among smaller sizes and decreasing linearly over larger sizes. The slope of the linear component of the spectrum varied with a multi-year pattern. but without an overall trend. The much greater stability of the diversity spectrum compared...... with the abundance spectrum suggests that the fish community structure has remained Fairly stable over the period, despite significant increases in harvesting on component populations. To explore the hypothesis that the regulation of the community structure arises from trophic interactions, the same community...... factor in the fish community structure in the North Sea. (C) 1996 International Council for the Exploration of the Sea....

  8. Ex vivo transfection of trout pronephros leukocytes, a model for cell culture screening of fish DNA vaccine candidates.

    Science.gov (United States)

    Ortega-Villaizan, M; Martinez-Lopez, A; Garcia-Valtanen, P; Chico, V; Perez, L; Coll, J M; Estepa, A

    2012-09-07

    DNA vaccination opened a new era in controlling and preventing viral diseases since DNA vaccines have shown to be very efficacious where some conventional vaccines have failed, as it occurs in the case of the vaccines against fish novirhabdoviruses. However, there is a big lack of in vitro model assays with immune-related cells for preliminary screening of in vivo DNA vaccine candidates. In an attempt to solve this problem, rainbow trout pronephros cells in early primary culture were transfected with two plasmid DNA constructions, one encoding the green fluorescent protein (GFP) and another encoding the viral haemorrhagic septicaemia virus (VHSV) glycoprotein G (G(VHSV)) - the only viral antigen which has conferred in vivo protection. After assessing the presence of GFP- and G(VHSV)-expressing cells, at transcription and protein levels, the immune response in transfected pronephros cells was evaluated. At 24h post-transfection, G(VHSV) up-regulated migm and tcr transcripts expression, suggesting activation of B and T cells, as well, a high up-regulation of tnfα gene was observed. Seventy-two hours post-transfection, we detected the up-regulation of mx and tnfα genes transcripts and Mx protein which correlated with the induction of an anti-VHSV state. All together we have gathered evidence for successful transfection of pronephros cells with pAE6G, which correlates with in vivo protection results, and is less time-consuming and more rapid than in vivo assays. Therefore, this outcome opens the possibility to use pronephros cells in early primary culture for preliminary screening fish DNA vaccines as well as to further investigate the function that these cells perform in fish immune response orchestration after DNA immunisation.

  9. Diversity and distribution of parasites from potentially cultured freshwater fish in Nakhon Si Thammarat

    Directory of Open Access Journals (Sweden)

    Supamattaya, K.

    2005-02-01

    Full Text Available Twenty-one species from 16 genera of potentially cultured freshwater fish were examined for external and internal parasites. Ten individuals of each fish species were sampled from various places in Nakhon Si Thammarat. Eight groups, 72 species were identified and the majority was external (52 spp.. The parasites found were ciliated protozoan (2 spp., myxozoan (2 spp., monogenean (44 spp., digenean (7 spp., cestode (6 spp., nematode (6 spp., acanthocephalan (2 spp. and crustacean (3 spp.. Monogenean was regarded as a major group of parasites with 44 species. Dactylogyrus (Monogenea had the highest number of species (12 spp., whereas Trichodina pediculus (Ciliophora was the most widely distributed species observed from at least 7 fish species (7 families. Most of the parasites (72 % found in this study were specific to their host species.

  10. Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity.

    Science.gov (United States)

    Reinen, Jelle; Postma, Geert; Tump, Cornelis; Bloemberg, Tom; Engel, Jasper; Vermeulen, Nico P E; Commandeur, Jan N M; Honing, Maarten

    2016-02-01

    In the present study, the validity of using a cocktail screening method in combination with a chemometrical data mining approach to evaluate metabolic activity and diversity of drug-metabolizing bacterial Cytochrome P450 (CYP) BM3 mutants was investigated. In addition, the concept of utilizing an in-house-developed library of CYP BM3 mutants as a unique biocatalytic synthetic tool to support medicinal chemistry was evaluated. Metabolic efficiency of the mutant library towards a selection of CYP model substrates, being amitriptyline (AMI), buspirone (BUS), coumarine (COU), dextromethorphan (DEX), diclofenac (DIC) and norethisterone (NET), was investigated. First, metabolic activity of a selection of CYP BM3 mutants was screened against AMI and BUS. Subsequently, for a single CYP BM3 mutant, the effect of co-administration of multiple drugs on the metabolic activity and diversity towards AMI and BUS was investigated. Finally, a cocktail of AMI, BUS, COU, DEX, DIC and NET was screened against the whole in-house CYP BM3 library. Different validated quantitative and qualitative (U)HPLC-MS/MS-based analytical methods were applied to screen for substrate depletion and targeted product formation, followed by a more in-depth screen for metabolic diversity. A chemometrical approach was used to mine all data to search for unique metabolic properties of the mutants and allow classification of the mutants. The latter would open the possibility of obtaining a more in-depth mechanistic understanding of the metabolites. The presented method is the first MS-based method to screen CYP BM3 mutant libraries for diversity in combination with a chemometrical approach to interpret results and visualize differences between the tested mutants.

  11. Evolution of microhabitat association and morphology in a diverse group of cryptobenthic coral reef fishes (Teleostei: Gobiidae: Eviota).

    Science.gov (United States)

    Tornabene, Luke; Ahmadia, Gabby N; Berumen, Michael L; Smith, Dave J; Jompa, Jamaluddin; Pezold, Frank

    2013-01-01

    Gobies (Teleostei: Gobiidae) are an extremely diverse and widely distributed group and are the second most species rich family of vertebrates. Ecological drivers are key to the evolutionary success of the Gobiidae. However, ecological and phylogenetic data are lacking for many diverse genera of gobies. Our study investigated the evolution of microhabitat association across the phylogeny of 18 species of dwarfgobies (genus Eviota), an abundant and diverse group of coral reef fishes. In addition, we also explore the evolution of pectoral fin-ray branching and sensory head pores to determine the relationship between morphological evolution and microhabitat shifts. Our results demonstrate that Eviota species switched multiple times from a facultative hard-coral association to inhabiting rubble or mixed sand/rubble habitat. We found no obvious relationship between microhabitat shifts and changes in pectoral fin-ray branching or reduction in sensory pores, with the latter character being highly homoplasious throughout the genus. The relative flexibility in coral-association in Eviota combined with the ability to move into non-coral habitats suggests a genetic capacity for ecological release in contrast to the strict obligate coral-dwelling relationship commonly observed in closely related coral gobies, thus promoting co-existence through fine scale niche partitioning. The variation in microhabitat association may facilitate opportunistic ecological speciation, and species persistence in the face of environmental change. This increased speciation opportunity, in concert with a high resilience to extinction, may explain the exceptionally high diversity seen in Eviota compared to related genera in the family.

  12. Greater Genetic Diversity in Spatially Restricted Coral Reef Fishes Suggests Secondary Contact among Differentiated Lineages

    Directory of Open Access Journals (Sweden)

    M. Julian Caley

    2011-09-01

    Full Text Available The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in populations on the margins of distributional ranges, making such species or populations more vulnerable to environmental perturbations. Using mtDNA and nuclear Inter Simple Sequence Repeat (ISSR data we investigated how the genetic diversity and structure of three con-generic species pairs of coral reef fishes (Pomacentridae was related to species’ range size and position of populations within these ranges. Estimates of genetic structure did not differ significantly among species, but mtDNA and nucDNA genetic diversities were up to 10 times greater in spatially restricted species compared to their widespread congeners. In two of the three species pairs, the distribution of genetic variation indicated secondary contact among differentiated lineages in the spatially restricted species. In contrast, the widespread species displayed a typical signature of population expansion suggesting recent genetic bottlenecks, possibly associated with the (re colonization of the Great Barrier Reef. These results indicate that historical processes, involving hybridization and founder effects, possibly associated with Pleistocene sea level fluctuations, have differentially influenced the widespread and spatially restricted coral reef damselfish species studied here.

  13. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution.

    Science.gov (United States)

    Zakon, Harold H; Lu, Ying; Zwickl, Derrick J; Hillis, David M

    2006-03-07

    We investigated whether the evolution of electric organs and electric signal diversity in two independently evolved lineages of electric fishes was accompanied by convergent changes on the molecular level. We found that a sodium channel gene (Na(v)1.4a) that is expressed in muscle in nonelectric fishes has lost its expression in muscle and is expressed instead in the evolutionarily novel electric organ in both lineages of electric fishes. This gene appears to be evolving under positive selection in both lineages, facilitated by its restricted expression in the electric organ. This view is reinforced by the lack of evidence for selection on this gene in one electric species in which expression of this gene is retained in muscle. Amino acid replacements occur convergently in domains that influence channel inactivation, a key trait for shaping electric communication signals. Some amino acid replacements occur at or adjacent to sites at which disease-causing mutations have been mapped in human sodium channel genes, emphasizing that these replacements occur in functionally important domains. Selection appears to have acted on the final step in channel inactivation, but complementarily on the inactivation "ball" in one lineage, and its receptor site in the other lineage. Thus, changes in the expression and sequence of the same gene are associated with the independent evolution of signal complexity.

  14. Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

    Science.gov (United States)

    Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

    2015-09-25

    In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

  15. The Diverse Uses Of Fish-Poison Plants In Northwest Guyana

    NARCIS (Netherlands)

    Andel, T.R. van

    2000-01-01

    Although prohibited by law, fish poison plants are still widely used by indigenous tribes in Guyana. The latest ethnobotanical collections date from the first half of the 20th century and, from recent anthropological studies, it cannot be deduced whether the same species are still used today. The pr

  16. The Diverse Uses Of Fish-Poison Plants In Northwest Guyana

    NARCIS (Netherlands)

    Andel, T.R. van

    2000-01-01

    Although prohibited by law, fish poison plants are still widely used by indigenous tribes in Guyana. The latest ethnobotanical collections date from the first half of the 20th century and, from recent anthropological studies, it cannot be deduced whether the same species are still used today. The

  17. Carbon sources supporting a diverse fish community in a tropical coastal ecosystem (Gazi Bay, Kenya)

    NARCIS (Netherlands)

    Nyunja, J.; Ntiba, M.; Onyari, J.; Mavuti, K.; Soetaert, K.E.R.; Bouillon, S.

    2009-01-01

    Interlinked mangrove–seagrass ecosystems are characteristic features of many tropical coastal areas, where they act as feeding and nursery grounds for a variety of fishes and invertebrates. The autotrophic carbon sources supporting fisheries in Gazi bay (Kenya) were studied in three sites, two locat

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

    Science.gov (United States)

    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.

  19. The Diverse Uses Of Fish-Poison Plants In Northwest Guyana

    NARCIS (Netherlands)

    Andel, T.R. van

    2000-01-01

    Although prohibited by law, fish poison plants are still widely used by indigenous tribes in Guyana. The latest ethnobotanical collections date from the first half of the 20th century and, from recent anthropological studies, it cannot be deduced whether the same species are still used today. The pr

  20. Detection of a diverse marine fish fauna using environmental DNA from seawater samples

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Kielgast, Jos; Iversen, Lars Lønsman;

    2012-01-01

    for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from 1/2-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain...

  1. Landscape Diversity as a Screening Tool to Assess Agroecosystems Sustainability; Preliminary Study in Central Italy

    Directory of Open Access Journals (Sweden)

    Francesco Visicchio

    2007-06-01

    Full Text Available Modernization of agricultural activities has strongly modified agricultural landscapes. Intensive agriculture, with the increased use of inorganic fertiliser and density of livestock, affects water quality discharging nutrients such as nitrogen and phosphorus in water bodies. Nutrients in rivers, subsequently, are excellent indicators to assess sustainability/ land-use intensity in agroecosystems. Landscape, however, is a dynamic system and is the product of interaction amongst the natural environment and human activities, including farming which is a main driving force. At present not much has been investigated on the predictive role of landscape on land-use intensity. Aim of this study is to determine if, in Italian agroecosystem, landscape complexity can be related to land-use intensity. Indexes of landscape complexity (i.e. edge density, number of patches, Shannon’s diversity index, Interspersion-Juxtaposition index derived by processing Corine Land Cover data (level IV, 1:25.000 of Lazio Region, were related with landuse intensity (values of compounds of nitrogen and phosphorus and other parameters found in rivers monitored in accordance to European Directives on Waste Water. Results demonstrate that some landscape indexes were related to some environment parameters. Consequently landscape complexity, with further investigation, could be an efficient screening tool, at large scale, to assess water quality and ultimately agroecosystems sustainability in the absence of monitoring stations.

  2. Understanding the Spatio-Temporal Response of Coral Reef Fish Communities to Natural Disturbances: Insights from Beta-Diversity Decomposition.

    Science.gov (United States)

    Lamy, Thomas; Legendre, Pierre; Chancerelle, Yannick; Siu, Gilles; Claudet, Joachim

    2015-01-01

    Understanding how communities respond to natural disturbances is fundamental to assess the mechanisms of ecosystem resistance and resilience. However, ecosystem responses to natural disturbances are rarely monitored both through space and time, while the factors promoting ecosystem stability act at various temporal and spatial scales. Hence, assessing both the spatial and temporal variations in species composition is important to comprehensively explore the effects of natural disturbances. Here, we suggest a framework to better scrutinize the mechanisms underlying community responses to disturbances through both time and space. Our analytical approach is based on beta diversity decomposition into two components, replacement and biomass difference. We illustrate this approach using a 9-year monitoring of coral reef fish communities off Moorea Island (French Polynesia), which encompassed two severe natural disturbances: a crown-of-thorns starfish outbreak and a hurricane. These disturbances triggered a fast logistic decline in coral cover, which suffered a 90% decrease on all reefs. However, we found that the coral reef fish composition remained largely stable through time and space whereas compensatory changes in biomass among species were responsible for most of the temporal fluctuations, as outlined by the overall high contribution of the replacement component to total beta diversity. This suggests that, despite the severity of the two disturbances, fish communities exhibited high resistance and the ability to reorganize their compositions to maintain the same level of total community biomass as before the disturbances. We further investigated the spatial congruence of this pattern and showed that temporal dynamics involved different species across sites; yet, herbivores controlling the proliferation of algae that compete with coral communities were consistently favored. These results suggest that compensatory changes in biomass among species and spatial

  3. Microelectrophoretic study of environmentally induced DNA damage in fish and its use for early toxicity screening of freshwater bodies.

    Science.gov (United States)

    Hussain, Bilal; Sultana, Tayyaba; Sultana, Salma; Al-Ghanim, K A; Masood, Shahreef; Ali, Muhammad; Mahboob, Shahid

    2017-03-01

    This study investigates the potential of the comet and micronucleus assays of fish DNA as a means of screening the toxicity of aquatic environments. Catla catla and Cirrhinus mrigala collected from the River Chenab in Pakistan were used as a case study for the application of comet and micronucleus techniques. Comet and micronucleus assays were used to compare DNA damage in C. catla and C. mrigala collected from polluted areas of the River Chenab and farmed fish. Atomic absorption spectrophotometry showed an acute level of toxicity from Cd, Cu, Mn, Zn, Pb, Cr, Sn, and Hg in river water. Comet assay showed significant (p river. Tail moment was observed as 10.06 ± 2.71, 3.11 ± 0.74, and 14.70 ± 1.89, while olive moment was 8.85 ± 1.84, 3.83 ± 0.76, and 7.11 ± 0.73, respectively. Highly significant (p < 0.01) damage was reported in C. mrigala as 37.29 ± 2.51, 34.96 ± 2.53, and 38.80 ± 2.42% DNA in comet tail, tail moment was 23.48 ± 3.90, 19.78 ± 4.26, and 14.30 ± 1.82, and olive moment was 16.22 ± 2.04, 13.83 ± 1.96, and10.99 ± 0.90. Significant (p < 0.05) differences were observed in genotoxicity between farmed and polluted area fish. Micronucleus assay showed a similar picture of significant difference in respect to single and double micronucleus induction: i.e., 23.20 ± 4.19 and 2.80 ± 1.07‰ in C. catla and 44.80 ± 3.73 and 06.20 ± 0.97‰, respectively, in C. mrigala. Nuclear abnormalities were found as 6.00 ± 0.84 and 09.60 ± 1.72/thousand cells, respectively, in both species. The results of this study suggest that these novel fish DNA damage assays can be used as an expedient toxicity screening for aquatic environments.

  4. Invasive species and habitat degradation in Iberian streams: an analysis of their role in freshwater fish diversity loss.

    Science.gov (United States)

    Hermoso, Virgilio; Clavero, Miguel; Blanco-Garrido, Francisco; Prenda, José

    2011-01-01

    Mediterranean endemic freshwater fish are among the most threatened biota in the world. Distinguishing the role of different extinction drivers and their potential interactions is crucial for achieving conservation goals. While some authors argue that invasive species are a main driver of native species declines, others see their proliferation as a co-occurring process to biodiversity loss driven by habitat degradation. It is difficult to discern between the two potential causes given that few invaded ecosystems are free from habitat degradation, and that both factors may interact in different ways. Here we analyze the relative importance of habitat degradation and invasive species in the decline of native fish assemblages in the Guadiana River basin (southwestern Iberian Peninsula) using an information theoretic approach to evaluate interaction pathways between invasive species and habitat degradation (structural equation modeling, SEM). We also tested the possible changes in the functional relationships between invasive and native species, measured as the per capita effect of invasive species, using ANCOVA. We found that the abundance of invasive species was the best single predictor of natives' decline and had the highest Akaike weight among the set of predictor variables examined. Habitat degradation neither played an active role nor influenced the per capita effect of invasive species on natives. Our analyses indicated that downstream reaches and areas close to reservoirs had the most invaded fish assemblages, independently of their habitat degradation status. The proliferation of invasive species poses a strong threat to the persistence of native assemblages in highly fluctuating environments. Therefore, conservation efforts to reduce native freshwater fish diversity loss in Mediterranean rivers should focus on mitigating the effect of invasive species and preventing future invasions.

  5. Fish diversity in southern California using scuba surveys in kelp forests.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Shannon Index of diversity was calculated from diver surveys on kelp beds in Southern California. Kelp diver visual census data was combined for two separate...

  6. Abundance and Diversity of Crypto- and Necto-Benthic Coastal Fish Are Higher in Marine Forests than in Structurally Less Complex Macroalgal Assemblages

    Science.gov (United States)

    Thiriet, Pierre D.; Cheminée, Adrien; Guidetti, Paolo; Bianchimani, Olivier; Basthard-Bogain, Solène; Cottalorda, Jean-Michel; Arceo, Hazel; Moranta, Joan; Lejeune, Pierre; Francour, Patrice; Mangialajo, Luisa

    2016-01-01

    In Mediterranean subtidal rocky reefs, Cystoseira spp. (Phaeophyceae) form dense canopies up to 1 m high. Such habitats, called ‘Cystoseira forests’, are regressing across the entire Mediterranean Sea due to multiple anthropogenic stressors, as are other large brown algae forests worldwide. Cystoseira forests are being replaced by structurally less complex habitats, but little information is available regarding the potential difference in the structure and composition of fish assemblages between these habitats. To fill this void, we compared necto-benthic (NB) and crypto-benthic (CB) fish assemblage structures between Cystoseira forests and two habitats usually replacing the forests (turf and barren), in two sampling regions (Corsica and Menorca). We sampled NB fish using Underwater Visual Census (UVC) and CB fish using Enclosed Anaesthetic Station Vacuuming (EASV), since UVC is known to underestimate the diversity and density of the ‘hard to spot’ CB fish. We found that both taxonomic diversity and total density of NB and CB fish were highest in Cystoseira forests and lowest in barrens, while turfs, that could be sampled only at Menorca, showed intermediate values. Conversely, total biomass of NB and CB fish did not differ between habitats because the larger average size of fish in barrens (and turfs) compensated for their lower densities. The NB families Labridae and Serranidae, and the CB families Blenniidae, Cliniidae, Gobiidae, Trypterigiidae and Scorpaenidae, were more abundant in forests. The NB taxa Diplodus spp. and Thalassoma pavo were more abundant in barrens. Our study highlights the importance of using EASV for sampling CB fish, and shows that Cystoseira forests support rich and diversified fish assemblages. This evidence suggests that the ongoing loss of Cystoseira forests may impair coastal fish assemblages and related goods and services to humans, and stresses the need to implement strategies for the successful conservation and/or recovery

  7. Multiplex Screening of Persistent Organic Pollutants in Fish Using Spectrally Encoded Microspheres

    NARCIS (Netherlands)

    Meimaridou, A.; Kalachova, K.; Shelver, W.L.; Franek, M.; Pulkrabova, J.; Haasnoot, W.; Nielen, M.W.F.

    2011-01-01

    Persistent organic pollutants (POPs) are environmental and food-related contaminants of global public health concern and known to be carcinogenic and endocrine disruptors. Their monitoring is essential, and an easy-to-use, rapid, and affordable multianalyte screening method with simplified sample

  8. Multiplex screening of persistent organic pollutants in fish using spectrally encoded microspheres

    Science.gov (United States)

    Persistent organic pollutants (POPs) are food contaminants of global public health concern and known to be carcinogenic and endocrine disruptors. Their monitoring is essential and an easy-to-use, rapid and affordable multi-analyte screening method with simplified sample preparation can be a valuable...

  9. Multiplex Screening of Persistent Organic Pollutants in Fish Using Spectrally Encoded Microspheres

    NARCIS (Netherlands)

    Meimaridou, A.; Kalachova, K.; Shelver, W.L.; Franek, M.; Pulkrabova, J.; Haasnoot, W.; Nielen, M.W.F.

    2011-01-01

    Persistent organic pollutants (POPs) are environmental and food-related contaminants of global public health concern and known to be carcinogenic and endocrine disruptors. Their monitoring is essential, and an easy-to-use, rapid, and affordable multianalyte screening method with simplified sample pr

  10. Anal Cancer Screening: Barriers and Facilitators Among Ethnically Diverse Gay, Bisexual, Transgender, and Other Men Who Have Sex With Men

    OpenAIRE

    Newman, Peter A; Roberts, Kathleen J.; Masongsong, Emmanuel; Wiley, D. J.

    2008-01-01

    Knowledge and beliefs about anal cancer screening among gay and other men who have sex with men remains unclear, despite data that suggests significant risk for intra-anal HPV-related cancers. Nevertheless, community-based screening activities may be most effective when stake-holder perspectives are addressed. We conducted four focus groups among 16 male and 3 female health care advocates experienced in working with diverse gay and other men who have sex with men in Los Angeles. Barriers to a...

  11. Carbon sources supporting a diverse fish community in a tropical coastal ecosystem (Gazi Bay, Kenya)

    OpenAIRE

    Nyunja, J; Ntiba, M; Onyari, J.; Mavuti, K.; Soetaert, K.; Bouillon, S.

    2009-01-01

    Interlinked mangrove-seagrass ecosystems are characteristic features of many tropical coastal areas, where they act as feeding and nursery grounds for a variety of fishes and invertebrates. The autotrophic carbon sources supporting fisheries in Gazi bay (Kenya) were studied in three sites, two located in the tidal creeks flowing through extensive mangrove forests, another site located in the subtidal seagrass meadows, approximately 2.5 km away from the forest. Carbon and nitrogen stable isoto...

  12. Influence of host diet and phylogeny on parasite sharing by fish in a diverse tropical floodplain.

    Science.gov (United States)

    Lima, L B; Bellay, S; Giacomini, H C; Isaac, A; Lima-Junior, D P

    2016-03-01

    The patterns of parasite sharing among hosts have important implications for ecosystem structure and functioning, and are influenced by several ecological and evolutionary factors associated with both hosts and parasites. Here we evaluated the influence of fish diet and phylogenetic relatedness on the pattern of infection by parasites with contrasting life history strategies in a freshwater ecosystem of key ecological importance in South America. The studied network of interactions included 52 fish species, which consumed 58 food types and were infected with 303 parasite taxa. Our results show that both diet and evolutionary history of hosts significantly explained parasite sharing; phylogenetically close fish species and/or species sharing food types tend to share more parasites. However, the effect of diet was observed only for endoparasites in contrast to ectoparasites. These results are consistent with the different life history strategies and selective pressures imposed on these groups: endoparasites are in general acquired via ingestion by their intermediate hosts, whereas ectoparasites actively seek and attach to the gills, body surface or nostrils of its sole host, thus not depending directly on its feeding habits.

  13. Decisional Stage Distribution for Colorectal Cancer Screening among Diverse, Low-Income Study Participants

    Science.gov (United States)

    Hester, C. M.; Born, W. K.; Yeh, H. W.; Young, K. L.; James, A. S.; Daley, C. M.; Greiner, K. A.

    2015-01-01

    Colorectal cancer (CRC) screening uptake among minorities and those with lower incomes is suboptimal. Behavioral interventions specifically tailored to these populations can increase screening rates and save lives. The Precaution Adoption Process Model (PAPM) allows assignment of a decisional stage for adoption of a behavior such as CRC screening.…

  14. Terrestrial actinomycetes from diverse locations of Uttarakhnad, India: Isolation and screening for their antibacterial activity.

    Directory of Open Access Journals (Sweden)

    Vijay Kumar

    2013-09-01

    Full Text Available Uttarakhand region is less explored, but possess a great biodiversity. This diversity can be explored for isolation and characterization of new actinomycetes strains for seeking antimicrobial molecules. It can therefore be predicted that novel bioactive metabolite producing actinomycetes can be discovered to combat multidrug resistant bacterial pathogens.Variations in the viable count of actinomycetes were accessed in different altitudes. Actinomycetes were isolated, indentified and screened for their antibacterial activity.The highest viable counts of actinomycetes were recorded in valleys followed by mid hills and high hills. A total of 512 actinomycetes were isolated which were found to belong the 14 different genera of actinomycetes. Mainly the genus Streptomyces was dominant in all the soil samples. Out of 512 isolates recovered, 23.44% exhibited antibacterial activity against one or more tested bacterial pathogens. Of these 56.67% showed activity against Gram-positive bacteria, 26.67% against Gram-negative bacteria while 16.67% showed broad spectrum activity. Isolate DV1S and GR9a-5 showed highest antibacterial properties against several multi-drug resistant bacterial pathogens and were identified using polyphasic approach. DV1S and GR9a-5 were found to be most closely related with S. massasporeus NBRC 12796(T and Nocardia nova JCM 6044(T respectively.The results of this study strongly support the idea that the viable count of actinomycetes varied greatly with altitude. The actinomycetes species isolated from valleys, mid hills and high hills possess significant capacity to produce compounds which are active against several drug resistant bacterial pathogens.

  15. Combination of genetics and spatial modelling highlights the sensitivity of cod (Gadus morhua) population diversity in the North Sea to distributions of fishing

    DEFF Research Database (Denmark)

    Heath, Michael R.; Culling, Mark A.; Crozier, Walter W.

    2014-01-01

    Conserving genetic diversity in animal populations is important for sustaining their ability to respond to environmental change. However, the “between-population” component of genetic diversity (biocomplexity) is threatened in many exploited populations, particularly marine fish, where harvest...... North Sea (Viking) unit by the more widespread (Dogger) unit, and its premature extinction under some spatial patterns of fishing. Fishery catch limits for cod are set at the scale of the whole North Sea without regard to such subpopulation dynamics. Our model offers a method to quantify adjustments...

  16. Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH)

    NARCIS (Netherlands)

    Leveau, J.H.J.; Gerards, S.; De Boer, W.; Van Veen, J.A.

    2004-01-01

    We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia

  17. A SIMPLE AND RAPID MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME OF FLIGHT MASS SPECTROMETRY METHOD TO SCREEN FISH PLASMA SAMPLES FOR ESTROGEN-RESPONSIVE BIOMARKERS

    Science.gov (United States)

    In this study, we describe and evaluate the performance of a simple and rapid mass spectral method for screening fish plasma for estrogen-responsive biomarkers using matrix assisted laster desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) couopled with a short...

  18. Evolution of microhabitat association and morphology in a diverse group of cryptobenthic coral reef fishes (Teleostei: Gobiidae: Eviota)

    KAUST Repository

    Tornabene, Luke

    2013-01-01

    Gobies (Teleostei: Gobiidae) are an extremely diverse and widely distributed group and are the second most species rich family of vertebrates. Ecological drivers are key to the evolutionary success of the Gobiidae. However, ecological and phylogenetic data are lacking for many diverse genera of gobies. Our study investigated the evolution of microhabitat association across the phylogeny of 18 species of dwarfgobies (genus Eviota), an abundant and diverse group of coral reef fishes. In addition, we also explore the evolution of pectoral fin-ray branching and sensory head pores to determine the relationship between morphological evolution and microhabitat shifts. Our results demonstrate that Eviota species switched multiple times from a facultative hard-coral association to inhabiting rubble or mixed sand/rubble habitat. We found no obvious relationship between microhabitat shifts and changes in pectoral fin-ray branching or reduction in sensory pores, with the latter character being highly homoplasious throughout the genus. The relative flexibility in coral-association in Eviota combined with the ability to move into non-coral habitats suggests a genetic capacity for ecological release in contrast to the strict obligate coral-dwelling relationship commonly observed in closely related coral gobies, thus promoting co-existence through fine scale niche partitioning. The variation in microhabitat association may facilitate opportunistic ecological speciation, and species persistence in the face of environmental change. This increased speciation opportunity, in concert with a high resilience to extinction, may explain the exceptionally high diversity seen in Eviota compared to related genera in the family. © 2012 Elsevier Inc.

  19. Diversity of bacteriocinogenic lactic acid bacteria isolated from Mediterranean fish viscera.

    Science.gov (United States)

    Migaw, Sarra; Ghrairi, Taoufik; Belguesmia, Yanath; Choiset, Yvan; Berjeaud, Jean-Marc; Chobert, Jean-Marc; Hani, Khaled; Haertlé, Thomas

    2014-04-01

    Nine lactic acid bacteria strains showing bacteriocin-like activity were isolated from various fresh fish viscera. The following species were identified based on 16S rDNA sequences: Enterococcus durans (7 isolates), Lactococcus lactis (1) and Enterococcus faecium (1). These strains were active against Listeria innocua and other LAB. Random amplified polymorphic DNA analyses showed four major patterns for the E. durans species. PCR analyses revealed a nisin gene in the genome of the Lc. lactis strain. Genes coding enterocins A, B and P were found in the genome of the E. faecium isolate. Enterocins A and B genes were also present in the genome of E. durans GM19. Hence, this is the first report describing E. durans strains producing enterocins A and B. Electrospray ionization mass spectrometry revealed that the purified bacteriocin produced by the E. durans GMT18 strain had an exact molecular mass of 6,316.89 Da. This bacteriocin was designated as durancin GMT18. Edman sequencing failed to proceed; suggesting that durancin GTM18 may contain terminal lanthionine residues. Overall, the results obtained revealed the presence of a variety of enterococci in Mediterranean fish viscera, as evidenced by their genetic profiles and abilities to produce different bacteriocins. These strains could be useful for food biopreservation or as probiotics.

  20. Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish

    Directory of Open Access Journals (Sweden)

    Isabel Santos Magalhaes

    2013-11-01

    Full Text Available Reduced male aggression towards different phenotypes generating negative frequency-dependent intrasexual selection has been suggested as a mechanism to facilitate the invasion and maintenance of novel phenotypes in a population. To date, the best empirical evidence for the phenomenon has been provided by laboratory studies on cichlid fish with different colour polymorphisms. Here we experimentally tested the hypothesis in a natural population of Lake Malawi cichlid fish, in which males build sand-castles (bowers to attract females during seasonal leks. We predicted that if bower shape plays an important role in male aggressive interactions, aggression among conspecific males should decrease when their bower shape is altered. Accordingly, we allocated randomly chosen bowers in a Nyassachromis cf. microcephalus lek into three treatments: control, manipulated to a different shape, and simulated manipulation. We then measured male behaviours and bower shape before and after these treatments. We found that once bower shape was altered, males were involved in significantly fewer aggressive interactions with conspecific males than before manipulation. Mating success was not affected. Our results support the idea that an extended phenotype, such as bower shape, can be important in maintaining polymorphic populations. Specifically, reduced male conspecific aggression towards males with different extended phenotypes (here, bower shapes may cause negative frequency-dependent selection, allowing the invasion and establishment of a new phenotype (bower builder. This could help our understanding of mechanisms of diversification within populations, and in particular, the overall diversification of bower shapes within Lake Malawi cichlids.

  1. Bacterial diversity in the intestine of young farmed puffer fish Takifugu rubripes

    Science.gov (United States)

    Li, Yanyu; Zhang, Tao; Zhang, Congyao; Zhu, Ying; Ding, Jianfeng; Ma, Yuexin

    2015-07-01

    The aim of the study was to examine the bacterial community associated with the intestinal mucus of young farmed puffer fish Takifugu rubripes. Polymerase chain reaction and partial 16S rDNA sequencing was performed on DNA from bacteria cultivated on Zobell 2216E medium. All the isolates were classified into two phyla—Proteobacteria and Firmicutes. Proteobacteria were the dominant, culturable intestinal microbiota (68.3%). At the genus level, Vibrio, Enterobacter, Bacillus, Pseudomonas, Exiguobacterium, Staphylococcus, Acinetobacter, Pseudoalteromonas and Shewanella were isolated from the intestine, with representatives of the genera Vibrio, Enterobacter and Bacillus accounting for 70.7% of the total. This is the first report of Enterobacter, Bacillus, Exiguobacterium and Staphylococcus as part of the intestinal bacterial microflora in T. rubripes. The profile of the culturable bacterial community differed between samples collected from the same tank at 2-month intervals, as indicated by Bray-Curtis and Sorensen indices, and the impact on the intestinal physiology and health of puffer fish requires further investigation.

  2. Trematodes of the Great Barrier Reef, Australia: emerging patterns of diversity and richness in coral reef fishes.

    Science.gov (United States)

    Cribb, Thomas H; Bott, Nathan J; Bray, Rodney A; McNamara, Marissa K A; Miller, Terrence L; Nolan, Mathew J; Cutmore, Scott C

    2014-10-15

    The Great Barrier Reef holds the richest array of marine life found anywhere in Australia, including a diverse and fascinating parasite fauna. Members of one group, the trematodes, occur as sexually mature adult worms in almost all Great Barrier Reef bony fish species. Although the first reports of these parasites were made 100 years ago, the fauna has been studied systematically for only the last 25 years. When the fauna was last reviewed in 1994 there were 94 species known from the Great Barrier Reef and it was predicted that there might be 2,270 in total. There are now 326 species reported for the region, suggesting that we are in a much improved position to make an accurate prediction of true trematode richness. Here we review the current state of knowledge of the fauna and the ways in which our understanding of this fascinating group is changing. Our best estimate of the true richness is now a range, 1,100-1,800 species. However there remains considerable scope for even these figures to be incorrect given that fewer than one-third of the fish species of the region have been examined for trematodes. Our goal is a comprehensive characterisation of this fauna, and we outline what work needs to be done to achieve this and discuss whether this goal is practically achievable or philosophically justifiable.

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

    Science.gov (United States)

    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

  4. Towards a full karyotype screening of interphase cells: 'FISH and chip' technology

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulli G.; Munne, Santiago; Lersch, Robert A.; Hsieh, H.-Ben; Smida, Jan; Chen, Xiao-Ning; Korenberg, Julie R.; Pedersen, Roger A.; Fung, Jingley

    2003-06-23

    Numerical chromosome aberrations are incompatible with normal human development. Our laboratories develop hybridization based screening tools that generate a maximum of cytogenetic information for each polar body or blastomere analyzed. The methods are developed considering that the abnormality might require preparation of case-specific probes and that only one or two cells will be available for diagnosis, most of which might be in the interphase stage. Further more, assay efficiencies have to be high, since there is typically not enough time to repeat an experiment or reconfirm a result prior to fertilization or embryo transfer. Structural alterations are delineated with break point-spanning probes. When screening for numerical abnormalities, we apply a Spectral Imaging-based approach to simultaneously score as many as ten different chromosome types in individual inter phase cells. Finally, DNA micro-arrays are under development to score all of the human chromosomes in a single experiment and to increase the resolution with which micro-deletions can be delineated.

  5. Comparative phylogeography of Atlantic reef fishes indicates both origin and accumulation of diversity in the Caribbean

    OpenAIRE

    Robertson D Ross; Rocha Claudia R; Rocha Luiz A; Bowen Brian W

    2008-01-01

    Abstract Background Two processes may contribute to the formation of global centers of biodiversity: elevated local speciation rates (the center of origin hypothesis), and greater accumulation of species formed elsewhere (the center of accumulation hypothesis). The relative importance of these processes has long intrigued marine biogeographers but rarely has been tested. Results To examine how origin and accumulation affected the Greater Caribbean center of diversity, we conducted a range-wid...

  6. Chromosomal diversity in three species of electric fish (Apteronotidae, Gymnotiformes) from the Amazon Basin.

    Science.gov (United States)

    Silva, Fernando Henrique Ramos; Pieczarka, Julio Cesar; Cardoso, Adauto Lima; da Silva, Patrícia Corrêa; de Oliveira, Jonas Alves; Nagamachi, Cleusa Yoshiko

    2014-10-01

    Cytogenetic studies were carried out on samples of Parapteronotus hasemani, Sternarchogiton preto and Sternarchorhamphus muelleri (Apteronotidae, Gymnotiformes) from the Amazon basin. The first two species exhibited both a 2n = 52 karyotype, but differed in their karyotypic formulae, distribution of constitutive heterochromatin, and chromosomal location of the NOR. The third species, Sternarchorhamphus muelleri, was found to have a 2n = 32 karyotype. In all three species the DAPI and chromomycin A3 staining results were consistent with the C-banding results and nucleolar organizer region (NOR) localization. The 18S rDNA probe confirmed that there was only one pair of ribosomal DNA cistron bearers per species. The telomeric probe did not reveal interstitial telomeric sequences (ITS). The karyotypic differences among these species can be used for taxonomic identification. These data will be useful in future studies of these fishes and help understanding the phylogenetic relationships and chromosomal evolution of the Apteronotidae.

  7. Integrated Taxonomy Reveals Hidden Diversity in Northern Australian Fishes: A New Species of Seamoth (Genus Pegasus.

    Directory of Open Access Journals (Sweden)

    Deborah Osterhage

    Full Text Available Fishes are one of the most intensively studied marine taxonomic groups yet cryptic species are still being discovered. An integrated taxonomic approach is used herein to delineate and describe a new cryptic seamoth (genus Pegasus from what was previously a wide-ranging species. Preliminary mitochondrial DNA barcoding indicated possible speciation in Pegasus volitans specimens collected in surveys of the Torres Strait and Great Barrier Reef off Queensland in Australia. Morphological and meristic investigations found key differences in a number of characters between P. volitans and the new species, P. tetrabelos. Further mt DNA barcoding of both the COI and the slower mutating 16S genes of additional specimens provided strong support for two separate species. Pegasus tetrabelos and P. volitans are sympatric in northern Australia and were frequently caught together in trawls at the same depths.

  8. Trematode diversity in freshwater fishes of the Globe I: 'Old World'.

    Science.gov (United States)

    Scholz, Tomáš; Besprozvannykh, Vladimir V; Boutorina, Tamara E; Choudhury, Anindo; Cribb, Thomas H; Ermolenko, Alexey V; Faltýnková, Anna; Shedko, Marina B; Shimazu, Takeshi; Smit, Nico J

    2016-03-01

    In this paper, we review, continent by continent, the trematode fauna of freshwater fishes of the 'Old World', a vast area consisting of the Palaearctic, Ethiopian, Oriental and Australasian zoogeographical regions. Knowledge of this fauna is highly uneven and clearly incomplete for almost all regions, sometimes dramatically so. Although the biggest problem remains the completion of the 'first pass' of alpha taxonomy, there are in addition great problems relating to biogeography and elucidation of life-cycles. For the latter, molecular data, i.e. matching DNA sequences of larval stages and corresponding adults, may represent a powerful tool that should be used in future studies. Another challenging problem represents the existence of cryptic species and, in particular, considerable decrease of experts in taxonomy and life-cycles of trematodes.

  9. Diversity of deep-sea fishes of the Easter Island Ecoregion

    Science.gov (United States)

    Easton, Erin E.; Sellanes, Javier; Gaymer, Carlos F.; Morales, Naiti; Gorny, Matthias; Berkenpas, Eric

    2017-03-01

    The Easter Island Ecoregion is in the center of the South Pacific gyre and experiences ultra-oligotrophic conditions that could make it highly susceptible to global change and anthropogenic activities, so it is imperative that these regions are characterized and studied so that conservation and sustainable management strategies can be developed. From the few studies from the region, we know that the coastal areas are relatively depauperate and have relatively high rates of endemism. Here, we present a brief report from the first video observations from this region of the deep-dwelling fishes from ROV exploration of benthic communities from 157 to 281 m and baited drop-camera videos from 150 to 1850 m. We observed a total of 55 fish species from the ROV and Drop-Cam surveys; nine could not be assigned family level or lower, 26 were observed in the ROV surveys, 29 were observed in the Drop-Cam surveys, nine were observed with both survey methods, at least six species are potentially new to science, and nine species were observed at deeper depths than previously reported. These new reports may be indicative of the unique oceanographic conditions in the area and the relative isolation of the communities that have provided opportunity for the evolution of new species and favorable conditions for range expansion. In contrast, these new reports may be indicative of the severe undersampling in the south Pacific at mesopelagic depths. The prevalence of potentially new species suggests that the region likely harbors a wealth of undiscovered biodiversity.

  10. Diversity of the bacterial community in Myanmar traditional salted fish yegyo ngapi.

    Science.gov (United States)

    Kobayashi, Takeshi; Taguchi, Chihiro; Kida, Kakeru; Matsuda, Hiroko; Terahara, Takeshi; Imada, Chiaki; Moe, Nant Kay Thwe; Thwe, Su Myo

    2016-10-01

    The distribution and characterization of bacteria including lactic acid bacteria (LAB) in the traditional and popular salted fish yegyo ngapi in Myanmar were studied to clarify the contribution of these bacteria to the curing and ripening of this product. Samples of yegyo ngapi purchased from a market in Yangon were used. Most of the isolates obtained using de Man, Rogosa and Sharpe medium containing 10 % NaCl were identified as coccoid LAB on the basis of their basic phenotypic characteristics. From the results of 16S rRNA gene sequencing and PCR-restriction fragment length polymorphism analysis of this gene, most of the isolates were identified as the halophilic LAB Tetragenococcus muriaticus. Analyses of the 16S rRNA gene based on the clone library using DNA extracted from salted fish products were also performed. The results of these molecular-analysis-based techniques showed that spore-forming and non-spore-forming anaerobic bacteria including the genera Clostridium and Halanaerobium in addition to T. muriaticus were also frequently found in bacterial communities. These findings suggest that the anaerobic condition during curing and ripening resulted in bacterial communities composed of strictly anaerobic bacteria and halophilic LAB, and that these bacteria might also contribute to the manufacturing processes of this product. In addition, DNA sequences similar to that of Clostridium botulinum were found in the clone library analysis. Therefore, despite no reports of botulism poisoning from the region where the samples were taken, closer surveillance should be carried out from the viewpoint of food safety.

  11. IMPACT OF JUTE RETTING ON NATIVE FISH DIVERSITY AND AQUATIC HEALTH OF ROADSIDE TRANSITORY WATER BODIES: AN ASSESSMENT IN EASTERN INDIA

    Directory of Open Access Journals (Sweden)

    Dipankar Ghosh

    2015-09-01

    Full Text Available Roadside transitory water bodies being manmade depressions have a great ecological and socio-economic importance from years. The effects of agricultural runoffs, jute retting, macro-phytes infestations and inadequate rainfall in changed climate often degrade transitory water bodies’ environment while the biodiversity have impacted severely because of population pressure, over exploitation and indiscriminate use of fine meshed fishing gears as a whole. Physico-chemical and biological analysis with fish species composition, relative abundance, diversity indices like species richness, evenness and Shannon-Wiener index were carried out for pre-, during and post-jute retting season and for year mean as a whole to assess impact of jute retting on the roadside transitory water body’s environmental health and indigenous fish diversity at Sahebnagar village in Nadia District, India. All the physico-chemical parameters barring biochemical oxygen demand and water transparency remained more or less same or marginally got little changed during those three seasons. As much as 19 native fish species with varied relative abundances and dominances were identified. Jute retting impacted lower native fish diversity indices like Shannon-Wiener index values (1.94 to 2.68 clearly indicated poor to moderate pollution status of the transitory water body in that area during monsoon in particular and throughout the year in general. So we opined there should be some control over the intense jute retting in the road side transitory water bodies for sustainable management of these manmade resources.

  12. Low-dose CT screening in an Asian population with diverse risk for lung cancer: A retrospective cohort study

    Energy Technology Data Exchange (ETDEWEB)

    Yi, Chin A. [Sungkyunkwan University School of Medicine, Department of Radiology and Center for Imaging Science, Seoul (Korea, Republic of); Lee, Kyung Soo [Sungkyunkwan University School of Medicine, Department of Radiology and Center for Imaging Science, Seoul (Korea, Republic of); Sungkyunkwan University School of Medicine, Department of Radiology, Samsung Medical Center, Seoul (Korea, Republic of); Shin, Myung-Hee; Cho, Yun Yung [Sungkyunkwan University School of Medicine, Department of Social and Preventive Medicine, Seoul (Korea, Republic of); Choi, Yoon-Ho [Sungkyunkwan University School of Medicine, Center for Health Promotion, Seoul (Korea, Republic of); Kwon, O. Jung [Sungkyunkwan University School of Medicine, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Seoul (Korea, Republic of); Shin, Kyung Eun [Sungkyunkwan University School of Medicine, Department of Radiology and Center for Imaging Science, Seoul (Korea, Republic of); Kyung Hee University Hospital, Department of Diagnostic Radiology, Seoul (Korea, Republic of)

    2015-08-15

    To evaluate the performance of low-dose CT (LDCT) screening for lung cancer (LCA) detection in an Asian population with diverse risks for LCA. LCA screening was performed in 12,427 symptomless Asian subjects using either LDCT (5,771) or chest radiography (CXR) (6,656) in a non-trial setting. Subjects were divided into high-risk and non-high-risk groups. Data were collected on the number of patients with screening-detected LCAs and their survival in order to compare outcomes between LDCT and CXR screening with the stratification of risks considering age, sex and smoking status. In the non-high-risk group, a significant difference was observed for the detection of lung cancer (adjusted OR, 5.07; 95 % CI, 2.72-9.45) and survival (adjusted HR of LCA survival between LDCT vs. CXR group, 0.08; 95 % CI, 0.01-0.62). No difference in detection or survival of LCA was noticed in the high-risk group. LCAs in the non-high-risk group were predominantly adenocarcinomas (96 %), and more likely to be part-solid or non-solid compared with those in the high-risk group (p = 0.023). In the non-high-risk group, LDCT helps detect more LCAs and offers better survival than CXR screening, due to better detection of part solid or non-solid lung adenocarcinomas. (orig.)

  13. Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae, from Mekong Basin

    Directory of Open Access Journals (Sweden)

    Surapon Yodsiri

    2017-01-01

    Full Text Available The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

  14. [Environmental heterogeneity and its relationship with diversity and abundance of the fish community in a coastal system of Gulf of Mexico].

    Science.gov (United States)

    Aguirre-León, Arturo; Pérez-Ponce, Hilda Elín; Díaz-Ruiz, Silvia

    2014-03-01

    The coastal lagoons of Veracruz, Gulf of Mexico, include a great variety of biological resources. These resources, especially fish communities, have been barely described and that require more ecological studies. With this aim, this investigation analyzed the spatial and temporal variation of diversity, abundance and assemblages of the fish community and its relationship with physical-chemical parameters of the Chica-Grande coastal system. For this, eight defined sites were monthly sampled for water characteristics and fish community composition (10min hauls of 1 500m2 a shrimp trawl net), between September 2005 and November 2006. The spatial-temporal variation of physical-chemical parameters, allowed the definition of two contrasting environments according to salinity, temperature, transparency, dissolved oxygen and depth gradients. A total of 1 947 fishes were collected for a total weight of 57.88kg. From these, 22 species, 20 genera and 14 families were identified; and four species were new records for the system. As it was detected for the physical-chemical conditions, the diversity of the fish community also showed a spatial gradient, with high values (H'=2.37, D=3.35, J'=0.82) in the brackish habitat, and low ones in freshwater environments. Fish abundance did not show such a marked gradient response, however, it was higher in the freshwater habitat. The highest diversity (H'=2.05) and species richness (D=2.99) was recorded during the North winds ("nortes") months (November-February), while density and biomass were higher (0.034 ind./m2, 1.42g/m2) during the rainy months (July-October). The Importance Value Index (IVI) defined six dominant species accounting for 77.8% of the fish abundance and 87.9% of total catch by weight. The Canonical Correspondence Analysis (CCA) showed that the fish-habitat relationship was explained by 68% of total variance for the two first axes, where salinity, transparency and temperature changes were the most important

  15. Coupling Numerical and Physical Modeling for Analysis of Flow in a Diversion Structure with Coanda-effect Screens

    Directory of Open Access Journals (Sweden)

    Julie Coonrod

    2011-07-01

    Full Text Available There is an increasing need to screen water in surface water collection systems to remove floating debris and small aquatic organisms to protect receiving water bodies. Recently, the Albuquerque Metropolitan Arroyo Flood Control Authority (AMAFCA, New Mexico, USA has actively introduced structural debris removal from storm-water facilities as a best management practice. In the South Diversion Channel Project, AMAFCA’s objective is to divert the flow at the upstream end of the existing concrete structure and remove debris from this flow using Coanda-effect screens before allowing it to re-enter the channel. Design limitations, such as access to the debris removal site, existing components of the concrete structure, topography of the site, and need for flow-regulating structures complicate the design. This paper shows how numerical modeling tools (Delft3D-FLOW model and physical modeling can be used in conjunction to observe flow patterns in a diversion structure and around Coanda-effect screens, estimate design parameters and thereby provide design recommendations.

  16. Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia.

    Science.gov (United States)

    Liu, Yiying; Rzeszutek, Elzbieta; van der Voort, Menno; Wu, Cheng-Hsuan; Thoen, Even; Skaar, Ida; Bulone, Vincent; Dorrestein, Pieter C; Raaijmakers, Jos M; de Bruijn, Irene

    2015-01-01

    Emerging fungal and oomycete pathogens are increasingly threatening animals and plants globally. Amongst oomycetes, Saprolegnia species adversely affect wild and cultivated populations of amphibians and fish, leading to substantial reductions in biodiversity and food productivity. With the ban of several chemical control measures, new sustainable methods are needed to mitigate Saprolegnia infections in aquaculture. Here, PhyloChip-based community analyses showed that the Pseudomonadales, particularly Pseudomonas species, represent one of the largest bacterial orders associated with salmon eggs from a commercial hatchery. Among the Pseudomonas species isolated from salmon eggs, significantly more biosurfactant producers were retrieved from healthy salmon eggs than from Saprolegnia-infected eggs. Subsequent in vivo activity bioassays showed that Pseudomonas isolate H6 significantly reduced salmon egg mortality caused by Saprolegnia diclina. Live colony mass spectrometry showed that strain H6 produces a viscosin-like lipopeptide surfactant. This biosurfactant inhibited growth of Saprolegnia in vitro, but no significant protection of salmon eggs against Saprolegniosis was observed. These results indicate that live inocula of aquatic Pseudomonas strains, instead of their bioactive compound, can provide new (micro)biological and sustainable means to mitigate oomycete diseases in aquaculture.

  17. Threshold effects of habitat fragmentation on fish diversity at landscapes scales.

    Science.gov (United States)

    Yeager, Lauren A; Keller, Danielle A; Burns, Taylor R; Pool, Alexia S; Fodrie, F Joel

    2016-08-01

    Habitat fragmentation involves habitat loss concomitant with changes in spatial configuration, confounding mechanistic drivers of biodiversity change associated with habitat disturbance. Studies attempting to isolate the effects of altered habitat configuration on associated communities have reported variable results. This variability may be explained in part by the fragmentation threshold hypothesis, which predicts that the effects of habitat configuration may only manifest at low levels of remnant habitat area. To separate the effects of habitat area and configuration on biodiversity, we surveyed fish communities in seagrass landscapes spanning a range of total seagrass area (2-74% cover within 16 000-m(2) landscapes) and spatial configurations (1-75 discrete patches). We also measured variation in fine-scale seagrass variables, which are known to affect faunal community composition and may covary with landscape-scale features. We found that species richness decreased and the community structure shifted with increasing patch number within the landscape, but only when seagrass area was low (fragmentation threshold hypothesis and we suggest that poor matrix quality and low dispersal ability for sensitive taxa in our system may explain why our results support the hypothesis, while previous empirical work has largely failed to match predictions. © 2016 by the Ecological Society of America.

  18. Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia.

    Directory of Open Access Journals (Sweden)

    Yiying Liu

    Full Text Available Emerging fungal and oomycete pathogens are increasingly threatening animals and plants globally. Amongst oomycetes, Saprolegnia species adversely affect wild and cultivated populations of amphibians and fish, leading to substantial reductions in biodiversity and food productivity. With the ban of several chemical control measures, new sustainable methods are needed to mitigate Saprolegnia infections in aquaculture. Here, PhyloChip-based community analyses showed that the Pseudomonadales, particularly Pseudomonas species, represent one of the largest bacterial orders associated with salmon eggs from a commercial hatchery. Among the Pseudomonas species isolated from salmon eggs, significantly more biosurfactant producers were retrieved from healthy salmon eggs than from Saprolegnia-infected eggs. Subsequent in vivo activity bioassays showed that Pseudomonas isolate H6 significantly reduced salmon egg mortality caused by Saprolegnia diclina. Live colony mass spectrometry showed that strain H6 produces a viscosin-like lipopeptide surfactant. This biosurfactant inhibited growth of Saprolegnia in vitro, but no significant protection of salmon eggs against Saprolegniosis was observed. These results indicate that live inocula of aquatic Pseudomonas strains, instead of their bioactive compound, can provide new (microbiological and sustainable means to mitigate oomycete diseases in aquaculture.

  19. Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes.

    Science.gov (United States)

    Colombo, M; Damerau, M; Hanel, R; Salzburger, W; Matschiner, M

    2015-02-01

    According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation. © 2014 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

  20. Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen.

    Directory of Open Access Journals (Sweden)

    Eric F Joyce

    Full Text Available The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate "pairing promoting genes" and candidate "anti-pairing genes," providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.

  1. Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO.

    Directory of Open Access Journals (Sweden)

    Uma D Vempati

    Full Text Available Huge amounts of high-throughput screening (HTS data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO. BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.

  2. Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).

    Science.gov (United States)

    Vempati, Uma D; Przydzial, Magdalena J; Chung, Caty; Abeyruwan, Saminda; Mir, Ahsan; Sakurai, Kunie; Visser, Ubbo; Lemmon, Vance P; Schürer, Stephan C

    2012-01-01

    Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.

  3. Diverse juvenile life-history behaviours contribute to the spawning stock of an anadromous fish population

    Science.gov (United States)

    Walsworth, Timothy E.; Schindler, Daniel E.; Griffiths, Jennifer R.; Zimmerman, Christian E.

    2015-01-01

    Habitat quality often varies substantially across space and time, producing a shifting mosaic of growth and mortality trade-offs across watersheds. Traditional studies of juvenile habitat use have emphasised the evolution of single optimal strategies that maximise recruitment to adulthood and eventual fitness. However, linking the distribution of individual behaviours that contribute to recruitment at the population level has been elusive, particularly for highly fecund aquatic organisms. We examined juvenile habitat use within a population of sockeye salmon (Oncorhynchus nerka) that spawn in a watershed consisting of two interconnected lakes and a marine lagoon. Otolith microchemical analysis revealed that the productive headwater lake accounted for about half of juvenile growth for those individuals surviving to spawn in a single river in the upper watershed. However, 47% of adults had achieved more than half of their juvenile growth in the downstream less productive lake, and 3% of individuals migrated to the estuarine environment during their first summer and returned to freshwater to overwinter before migrating back to sea. These results describe a diversity of viable habitat-use strategies by juvenile sockeye salmon that may buffer the population against poor conditions in any single rearing environment, reduce density-dependent mortality and have implications for the designation of critical habitat for conservation purposes. A network of accessible alternative habitats providing trade-offs in growth and survival may be important for long-term viability of populations.

  4. Assessing the recovery of functional diversity after sustained sediment screening at an aggregate dredging site in the North Sea

    Science.gov (United States)

    Barrio Froján, Christopher R. S.; Cooper, Keith M.; Bremner, Julie; Defew, Emma C.; Wan Hussin, Wan M. R.; Paterson, David M.

    2011-05-01

    The effects of dredging the seabed for aggregate on benthic functional diversity were assessed using a suite of suitable indices on a recovering macrofaunal assemblage. Recovery was assessed as the return of a dredged assemblage to a state found in neighbouring undisturbed (reference) sites. In situ sediment screening was permitted during dredging operations; a difference in the sedimentary profile of the seabed between dredged and undisturbed reference sites was also observed. At sites of relatively high and low dredging intensity the sediment appeared more homogenous than reference sites after the selective removal of the coarser component. Initial assessment of the macrofaunal assemblage using univariate analytical techniques suggested a recovery of functional diversity at the low dredging intensity site after two years (according to the Infaunal Trophic Index, Taxonomic Distinctness index and Rao's Quadratic Entropy coefficient). However, multivariate analyses of the same data and of all indices except Taxonomic Distinctness indicated that assemblages at both high and low dredging intensity sites remained statistically indistinguishable from each other yet markedly different to the assemblage present in the reference area during the four-year study. The study concluded that recovery of functional diversity to a level found in a neighbouring undredged habitat had not occurred at either dredged site five years after the cessation of dredging. It is thought that the damage by dredging to functional diversity and to the capacity of the macrofaunal assemblage to recover is immediate and not so dependent on dredging intensity. The cumulative and wider ranging effects of sediment screening cannot be ignored or dismissed as a contributing factor to the similarities observed. The wider significance of these findings on the regulation of dredging activities is discussed.

  5. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    Science.gov (United States)

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation.

  6. Acanthocephalan fish parasites (Rhadinorhynchidae Lühe, 1912) as potential biomarkers: Molecular-chemical screening by pyrolysis-field ionization mass spectrometry

    Science.gov (United States)

    Kleinertz, S.; Eckhardt, K.-U.; Theisen, S.; Palm, H. W.; Leinweber, P.

    2016-07-01

    The present study represents the first molecular-chemical screening by pyrolysis-field ionization mass spectrometry applied on fish parasites. A total of 71 fishes from Balinese fish markets, 36 Auxis rochei (Risso, 1810) and 35 A. thazard (Lacepède, 1800), were studied for their acanthocephalan parasites. This is the first record of Rhadinorhynchus zhukovi in Balinese waters, Indonesia, and we describe for the first time A. rochei and A. thazard as R. zhukovi hosts. Using this method, small scale variations within the chemical compounds of acanthocephalans could be detected. Using this methodology it will be possible to generate additional, pollutant specific information from aquatic habitats in future with the potential of a new bioindicator application for parasite/host origin and/or environmental pollution.

  7. Local and regional variability in fish community structure, richness and diversity of 56 Danish lakes with contrasting depth and trophic state

    DEFF Research Database (Denmark)

    Menezes, Rosemberg; Borchsenius, Finn; Svenning, J.-C.

    /profundal zones. Nevertheless, information about how the within-lake variability in fish abundance, richness and diversity changes in the littoral and pelagic areas along contrasting depth and trophic state is scarce. It is expected that eutrophic lakes present lower within lake habit heterogeneity than...... oligotrophic lakes due to high turbidity leading to loss of submerged macrophytes and thus habitat variability. Also the influence of piscivorous birds on the fish distribution in the littoral zone may differ between lake types leading to a more homogeneous distribution along the littoral area in eutrophic...

  8. Can parasites be indicators of free-living diversity? Relationships between species richness and the abundance of larval trematodes and of local benthos and fishes.

    Science.gov (United States)

    Hechinger, Ryan F; Lafferty, Kevin D; Huspeni, Todd C; Brooks, Andrew J; Kuris, Armand M

    2007-02-01

    Measuring biodiversity is difficult. This has led to efforts to seek taxa whose species richness correlates with the species richness of other taxa. Such indicator taxa could then reduce the time and cost of assessing the biodiversity of the more extensive community. The search for species richness correlations has yielded mixed results, however. This may be primarily because of the lack of functional relationships between the taxa studied. Trematode parasites are highly promising bioindicators. Diverse assemblages of larval trematode parasites are easily sampled in intermediate host snails. Through their life cycles these parasites are functionally coupled with the surrounding free-living diversity of vertebrate and invertebrate animals. It has been shown that larval trematodes in snails correlate positively with bird diversity and abundance. Here, we explore whether trematodes also correlate with standard measures of fishes, and large and small benthos, for 32 sites in three wetlands. We found associations between trematodes and benthic communities that were not consistent across wetlands. The associations were, however, consistently positive for large benthic species richness and density. Some of the contrasting associations between trematode and benthos may be explained by negative associations between large and small benthos. We found no associations with fish communities (probably because of the inadequacy of standard "snapshot" sampling methods for highly mobile fishes). The results support further exploration of trematodes as bioindicators of diversity and abundance of animal communities.

  9. Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: evidence for cryptic allopatric diversity.

    Science.gov (United States)

    García-Machado, Erik; Hernández, Damir; García-Debrás, Alfredo; Chevalier-Monteagudo, Pedro; Metcalfe, Cushla; Bernatchez, Louis; Casane, Didier

    2011-11-01

    Underground environments are increasingly recognized as reservoirs of faunal diversity. Extreme environmental conditions and limited dispersal ability of underground organisms have been acknowledged as important factors promoting divergence between species and conspecific populations. However, in many instances, there is no correlation between genetic divergence and morphological differentiation. Lucifuga Poey is a stygobiotic fish genus that lives in Cuban and Bahamian caves. In Cuba, it offers a unique opportunity to study the influence of habitat fragmentation on the genetic divergence of stygobiotic species and populations. The genus includes four species and one morphological variant that have contrasting geographical distributions. In this study, we first performed a molecular phylogenetic analysis of the Lucifuga Cuban species using mitochondrial and nuclear markers. The mitochondrial phylogeny revealed three deeply divergent clades that were supported by nuclear and morphological characters. Within two of these main clades, we identified five lineages that are candidate cryptic species and a taxonomical synonymy between Lucifuga subterranea and Lucifuga teresinarum. Secondly, phylogeographic analysis using a fragment of the cytochrome b gene was performed for Lucifuga dentata, the most widely distributed species. We found strong geographical organization of the haplotype clades at different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. At a larger temporal scale, these processes could also explain the diversification and the distribution of the different species.

  10. Coming out of the starting blocks: extended lag time rearranges genetic diversity in introduced marine fishes of Hawai'i.

    Science.gov (United States)

    Gaither, Michelle R; Toonen, Robert J; Bowen, Brian W

    2012-10-07

    Biological invasions with known histories are rare, especially in the sea, and empirical studies of the genetic consequences are even rarer. Fifty-five years ago, the state of Hawai'i began a remarkable, if unintentional, 'experiment' with the introduction of three reef fishes, Lutjanus fulvus, Cephalopholis argus and Lutjanus kasmira. All have since expanded from the initial introduction of 2204 to 3163 individuals; however, historical records show that initially L. fulvus remained scarce, C. argus had modest population expansion and L. kasmira experienced rapid population growth. The consequences of differential population growth rates are apparent in F-statistics: Hawaiian L. fulvus demonstrate strong and significant haplotype frequency shifts from the founder location (F(ST) = 0.449), C. argus shows low but significant differentiation (F(ST) = 0.066) and L. kasmira is nearly identical to the founder location (F(ST) = 0.008). All three species had higher mtDNA diversity in the introduced range, which can be explained by multiple sources for L. fulvus and L. kasmira, but not for C. argus. We conclude that lag time before population expansion, in conjunction with genetic drift, has defined the genetic architecture of these three species in the introduced range.

  11. Coming out of the starting blocks: extended lag time rearranges genetic diversity in introduced marine fishes of Hawai‘i

    Science.gov (United States)

    Gaither, Michelle R.; Toonen, Robert J.; Bowen, Brian W.

    2012-01-01

    Biological invasions with known histories are rare, especially in the sea, and empirical studies of the genetic consequences are even rarer. Fifty-five years ago, the state of Hawai‘i began a remarkable, if unintentional, ‘experiment’ with the introduction of three reef fishes, Lutjanus fulvus, Cephalopholis argus and Lutjanus kasmira. All have since expanded from the initial introduction of 2204 to 3163 individuals; however, historical records show that initially L. fulvus remained scarce, C. argus had modest population expansion and L. kasmira experienced rapid population growth. The consequences of differential population growth rates are apparent in F-statistics: Hawaiian L. fulvus demonstrate strong and significant haplotype frequency shifts from the founder location (FST = 0.449), C. argus shows low but significant differentiation (FST = 0.066) and L. kasmira is nearly identical to the founder location (FST = 0.008). All three species had higher mtDNA diversity in the introduced range, which can be explained by multiple sources for L. fulvus and L. kasmira, but not for C. argus. We conclude that lag time before population expansion, in conjunction with genetic drift, has defined the genetic architecture of these three species in the introduced range. PMID:22874747

  12. Diversity of trophic niches among herbivorous fishes on a Caribbean reef (Guadeloupe, Lesser Antilles), evidenced by stable isotope and gut content analyses

    Science.gov (United States)

    Dromard, Charlotte R.; Bouchon-Navaro, Yolande; Harmelin-Vivien, Mireille; Bouchon, Claude

    2015-01-01

    While herbivorous fishes have been widely studied due to the major ecological role they play on coral reefs, the description of their trophic niche remains challenging. In this study, we asked how 10 species of parrotfishes and surgeonfishes partition trophic resources on a Caribbean reef. The determination of trophic niches was conducted using gut and stomach content and stable isotope analyses (15N:14N and 13C:12C ratios). The contributions of food source to fish diet were calculated with concentration-dependent mixing models. Stomach content analyses distinguished two species of Acanthuridae from other fish species: Acanthurus coeruleus due to its high ingestion of fleshy macroalgae and Acanthurus chirurgus due to its high ingestion of calcified macroalgae. Acanthuridae and Sparisoma aurofrenatum presented similar diets in terms of assimilation of food resources with a high contribution of detritus and invertebrates to their diets. The diets of Sparisoma rubripinne and Sparisoma chrysopterum were more heterogeneous by comparison to the previous species. Scarus iseri, Scarus vetula, Scarus taeniopterus and Sparisoma viride appeared to share a similar trophic niche characterized by the contribution of live coral and fleshy macroalgae to their diet. The resource use among herbivorous fishes was partially related to the nutritional quality of food sources, but also to their physical structure and the capacity of fish to process them efficiently. These results showed that the ten species occupy distinct trophic niches, indicating a high functional diversity among the Caribbean herbivorous fishes.

  13. Screening a diverse soybean germplasm collection for reaction to purple seed stain caused by Cercospora kikuchii

    Science.gov (United States)

    Purple seed stain (PSS), caused by Cercospora kikuchii, is a prevalent soybean disease that causes latent seed infection, seed decay, purple seed discoloration, and overall quality deterioration. The objective of this research was to screen soybean accessions from the USDA germplasm collection for r...

  14. An in vivo zebrafish screen identifies organophosphate antidotes with diverse mechanisms of action.

    Science.gov (United States)

    Jin, Shan; Sarkar, Kumar S; Jin, Youngnam N; Liu, Yan; Kokel, David; Van Ham, Tjakko J; Roberts, Lee D; Gerszten, Robert E; Macrae, Calum A; Peterson, Randall T

    2013-01-01

    Organophosphates are a class of highly toxic chemicals that includes many pesticides and chemical weapons. Exposure to organophosphates, either through accidents or acts of terrorism, poses a significant risk to human health and safety. Existing antidotes, in use for over 50 years, have modest efficacy and undesirable toxicities. Therefore, discovering new organophosphate antidotes is a high priority. Early life stage zebrafish exposed to organophosphates exhibit several phenotypes that parallel the human response to organophosphates, including behavioral deficits, paralysis, and eventual death. Here, we have developed a high-throughput zebrafish screen in a 96-well plate format to find new antidotes that counteract organophosphate-induced lethality. In a pilot screen of 1200 known drugs, we identified 16 compounds that suppress organophosphate toxicity in zebrafish. Several in vitro assays coupled with liquid chromatography/tandem mass spectrometry-based metabolite profiling enabled determination of mechanisms of action for several of the antidotes, including reversible acetylcholinesterase inhibition, cholinergic receptor antagonism, and inhibition of bioactivation. Therefore, the in vivo screen is capable of discovering organophosphate antidotes that intervene in distinct pathways. These findings suggest that zebrafish screens might be a broadly applicable approach for discovering compounds that counteract the toxic effects of accidental or malicious poisonous exposures.

  15. Fish diversity in the Río de la Plata and adjacent waters: an overview of environmental influences on its spatial and temporal structure.

    Science.gov (United States)

    Jaureguizar, A J; Solari, A; Cortés, F; Milessi, A C; Militelli, M I; Camiolo, M D; Luz Clara, M; García, M

    2016-07-01

    The fish diversity and the main environmental factors affecting the spatial distribution of species, life history stages and community structure in the Río de la Plata (RdP) and adjacent waters are reviewed and analysed, with emphasis on the functional guild classification. The functional guild classification indicated that most species in the RdP were marine stragglers, zoobenthivores and oviparous species, although the biomass was dominated by estuarine species. Salinity had a stronger influence than temperature on the spatial pattern for all life stages, shallower and fresher waters are the preferred habitats of neonates and juveniles. During the breeding season (spring-summer), adults showed an intrusion into the inner part of RdP or to its adjacent nearshore waters from the offshore waters for spawning or mating, respectively. Variations in river discharge and wind patterns greatly affected the spatial extent of estuarine water, which ultimately influenced the domain of the main life-history stages (juveniles or adults) for both marine and estuarine fishes, as well as species and fish assemblage composition. The strong environmental gradient restricts some species and life-history stages to a particular section and defines three main fish assemblage areas. The composition of the fish assemblage is indicative of the recruitment of freshwater and marine species to the estuary in opposite ways, determined by the vertical stratification. Seasonal changes in the species composition were related to migration as a result of salinity and temperature variations and reproductive migrations to spawning and mating areas. This overview reveals that the RdP is under environmental variations that are likely to produce modifications to fish distribution and abundance that affect its fisheries. This context plus fish stock declines and changes in exploitation patterns could amplify the magnitude of the variations in the fisheries resources availability and affect the

  16. Discovery of structurally-diverse inhibitor scaffolds by high-throughput screening of a fragment library with dimethylarginine dimethylaminohydrolase.

    Science.gov (United States)

    Linsky, Thomas W; Fast, Walter

    2012-09-15

    Potent and selective inhibitors of the enzyme dimethylarginine dimethylaminohydrolase (DDAH) are useful as molecular probes to better understand cellular regulation of nitric oxide. Inhibitors are also potential therapeutic agents for treatment of pathological states associated with the inappropriate overproduction of nitric oxide, such as septic shock, selected types of cancer, and other conditions. Inhibitors with structures dissimilar to substrate may overcome limitations inherent to substrate analogs. Therefore, to identify structurally-diverse inhibitor scaffolds, high-throughput screening (HTS) of a 4000-member library of fragment-sized molecules was completed using the Pseudomonas aeruginosa DDAH and human DDAH-1 isoforms. Use of a substrate concentration equal to its K(M) value during the primary screen allowed for the detection of inhibitors with different modes of inhibition. A series of validation tests were designed and implemented in the identification of four inhibitors of human DDAH-1 that were unknown prior to the screen. Two inhibitors share a 4-halopyridine scaffold and act as quiescent affinity labels that selectively and covalently modify the active-site Cys residue. Two inhibitors are benzimidazole-like compounds that reversibly and competitively inhibit human DDAH-1 with Ligand Efficiency values ≥0.3 kcal/mol/heavy (non-hydrogen) atom, indicating their suitability for further development. Both inhibitor scaffolds have available sites to derivatize for further optimization. Therefore, use of this fragment-based HTS approach is demonstrated to successfully identify two novel scaffolds for development of DDAH-1 inhibitors.

  17. Evolution and biogeography of an emerging quasispecies: diversity patterns of the fish Viral Hemorrhagic Septicemia virus (VHSv).

    Science.gov (United States)

    Pierce, Lindsey R; Stepien, Carol A

    2012-05-01

    Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus that causes one of the most important finfish diseases, affecting over 70 marine and freshwater species. It was discovered in European cultured fish in 1938 and since has been described across the Northern Hemisphere. Four strains and several substrains have been hypothesized, whose phylogenetic relationships and evolutionary radiation are evaluated here in light of a quasispecies model, including an in-depth analysis of the novel and especially virulent new substrain (IVb) that first appeared in the North American Laurentian Great Lakes in 2003. We analyze the evolutionary patterns, genetic diversity, and biogeography of VHSv using all available RNA sequences from the glycoprotein (G), nucleoprotein (N), and non-virion (Nv) genes, with Maximum Likelihood and bayesian approaches. Results indicate that the G gene evolves at an estimated rate of μ=2.58×10(-4) nucleotide substitutions per site per year, the N gene at μ=4.26×10(-4), and Nv fastest at μ=1.25×10(-3). Phylogenetic trees from the three genes largely are congruent, distinguishing strains I-IV as reciprocally monophyletic with high bootstrap and posterior probability support. VHSv appears to have originated from a marine ancestor in the North Atlantic Ocean, diverging into two primary clades: strain IV in North America (the Northwestern Atlantic Ocean), and strains I-III in the Northeastern Atlantic region (Europe). Strain II may comprise the basal group of the latter clade and diverged in Baltic Sea estuarine waters; strains I and III appear to be sister groups (according to the G and Nv genes), with the former mostly in European freshwaters and the latter in North Sea marine/estuarine waters. Strain IV is differentiated into three monophyletic substrains, with IVa infecting Northeastern Pacific salmonids and many marine fishes (with 44 unique G gene haplotypes), IVb endemic to the freshwater Great Lakes (11 haplotypes), and a newly

  18. Diversity and characterization of antagonistic bacteria from tropical estuarine habitats of Cochin, India for fish health management.

    Science.gov (United States)

    Nair, Anusree V; Vijayan, K K; Chakraborty, Kajal; Leo Antony, M

    2012-07-01

    Mortalities due to pathogenic bacteria are a major problem in aquaculture, especially in larval rearing systems. Use of antibiotics to overcome this problem is not an option any more due to the increasing antibiotic resistance among pathogens. The present study aims to understand the diversity of bacteria with antagonistic properties in the tropical estuarine habitats of Cochin, located along the southwest coast of India, and to use them as an alternative to antibiotics in aquaculture. Among the 4,870 isolates screened, approximately 1 % showed significant antibacterial activity against six common aquaculture pathogens belonging to the genera Aeromonas and Vibrio. The antagonistic bacteria were identified as Bacillus (81 %) and Pseudomonas (19 %) using biochemical and 16S rRNA gene sequence homology. The isolates showing stable and higher levels of antibacterial activity were subjected to enzymatic expression profile, antibiotic resistance pattern and abiotic stress tolerance assays. As a result, five Pseudomonas spp. and four Bacillus spp., were identified as promising antagonistic isolates that could be exploited as probionts or microbial products (MP's), to control bacterial diseases in aquaculture rearing systems.

  19. Revisions of the Fish Invasiveness Screening Kit (FISK) for its application in warmer climatic zones, with particular reference to peninsular Florida.

    Science.gov (United States)

    Lawson, Larry L; Hill, Jeffrey E; Vilizzi, Lorenzo; Hardin, Scott; Copp, Gordon H

    2013-08-01

    The initial version (v1) of the Fish Invasiveness Scoring Kit (FISK) was adapted from the Weed Risk Assessment of Pheloung, Williams, and Halloy to assess the potential invasiveness of nonnative freshwater fishes in the United Kingdom. Published applications of FISK v1 have been primarily in temperate-zone countries (Belgium, Belarus, and Japan), so the specificity of this screening tool to that climatic zone was not noted until attempts were made to apply it in peninsular Florida. To remedy this shortcoming, the questions and guidance notes of FISK v1 were reviewed and revised to improve clarity and extend its applicability to broader climatic regions, resulting in changes to 36 of the 49 questions. In addition, upgrades were made to the software architecture of FISK to improve overall computational speed as well as graphical user interface flexibility and friendliness. We demonstrate the process of screening a fish species using FISK v2 in a realistic management scenario by assessing the Barcoo grunter Scortum barcoo (Terapontidae), a species whose management concerns are related to its potential use for aquaponics in Florida. The FISK v2 screening of Barcoo grunter placed the species into the lower range of medium risk (score = 5), suggesting it is a permissible species for use in Florida under current nonnative species regulations. Screening of the Barcoo grunter illustrates the usefulness of FISK v2 as a proactive tool serving to inform risk management decisions, but the low level of confidence associated with the assessment highlighted a dearth of critical information on this species.

  20. Diversity, molecular characterization and expression of T cell receptor γ in a teleost fish, the sea bass (Dicentrarchus labrax, L.

    Directory of Open Access Journals (Sweden)

    Francesco Buonocore

    Full Text Available Two lineages of T cells, expressing either the αβ T cell receptor (TR or the γδ TR, exist in Gnathostomes. The latter type of T cells account for 1-10 % of T cells in blood and up to 30 % in the small intestine. They may recognize unconventional antigens (phosphorylated microbial metabolites, lipid antigens without the need of major histocompatibility class I (MH1 or class II (MH2 presentation. In this work we have described cloning and structural characterization of TR -chain (TRG from the teleost Dicentrarchus labrax. Further, by means of quantitative PCR analysis, we analyzed TRG expression levels both in poly I:C stimulated leukocytes in vitro, and following infection with betanodavirus in vivo. Two full length cDNAs relative to TRG, with the highest peptide and nucleotide identity with Japanese flounder, were identified. A multiple alignment analysis showed the conservation of peptides fundamental for TRG biological functions, and of the FGXG motif in the FR4 region, typical of most TR and immunoglobulin light chains. A 3D structure consisting of two domains mainly folded as beta strands with a sandwich architecture for each domain was also reported. TRG CDR3 of 8-18 AA in length and diversity in the TRG rearrangements expressed in thymus and intestine for a given V/C combination were evidenced by junction length spectratyping. TRG mRNA expression levels were high in basal conditions both in thymus and intestine, while in kidney and gut leukocytes they were up-regulated after in vitro stimulation by poly I:C. Finally, in juveniles the TRG expression levels were up-regulated in the head kidney and down-regulated in intestine after in vivo infection with betanodavirus. Overall, in this study the involvement of TRG-bearing T cells during viral stimulation was described for the first time, leading to new insights for the identification of T cell subsets in fish.

  1. Diversity of monogenean parasites in belonid fishes off the Mediterranean Sea with redescription of Aspinatrium gallieniEuzet and Ktari, 1971 andAxine belonesAbildgaard, 1794

    Institute of Scientific and Technical Information of China (English)

    Manel Châari; Hela Derbel; Lassâd Neifar

    2016-01-01

    Objective:To provide informations on the diversity of Monogenea parasitizing belonid fishes from the Mediterranean Sea. Monogenean speciesAspinatrium gallieniEuzet and Ktari, 1971 (A. gallieni) and Axine belonesAbildgaard, 1794 (A. belones) from belonids Tylosurus acus imperialis Rafinesque, 1810 (T. a. imperialis) and Belone belone Lowe, 1839 (B. belone) off Tunisian coast were redescribed. Methods:During the sampling period between 2004 and 2009, a total of 624 belonid fish belonging to three species, 453 B. belone, 45 Belone svetovidoviCollette and Parin, 1970 and 126 T. a. imperialiswere investigated for monogenean parasites. Results: Five Polyopisthocotylean monogenean parasites species were founded infected belonid fishes from Tunisian coast. These are,Nudaciraxine imperium Châari, Derbel and Neifar, 2010,A. belones, Axinesp.,Axinoidessp. (Axinidae) andA. gallieni (Micrcotylidae). Among them, the most prevalent speciesA. gallieni from the inner gill cover and gill filaments of T. a. imperialisandA. belones from the gills of B. belone were redescribed.A. gallieni represented new host record for T. a. imperialis. A complete list of monogenean parasites found in belonid fishes from our study and those reported from the Mediterranean Sea was presented. Conclusions: This paper enhances the current knowledge of Monogenea infecting belonids off the Mediterranean Sea. It’s the first study on monogenean parasites of the overall belonid fishes off Tunisia.

  2. Diversity of monogenean parasites in belonid fishes off the Mediterranean Sea with redescription of Aspinatrium gallieni Euzet and Ktari, 1971 and Axine belones Abildgaard, 1794

    Directory of Open Access Journals (Sweden)

    Manel Châari

    2016-04-01

    Full Text Available Objective: To provide informations on the diversity of Monogenea parasitizing belonid fishes from the Mediterranean Sea. Monogenean species Aspinatrium gallieni Euzet and Ktari, 1971 (A. gallieni and Axine belones Abildgaard, 1794 (A. belones from belonids Tylosurus acus imperialis Rafinesque, 1810 (T. a. imperialis and Belone belone Lowe, 1839 (B. belone off Tunisian coast were redescribed. Methods: During the sampling period between 2004 and 2009, a total of 624 belonid fish belonging to three species, 453 B. belone, 45 Belone svetovidovi Collette and Parin, 1970 and 126 T. a. imperialis were investigated for monogenean parasites. Results: Five Polyopisthocotylean monogenean parasites species were founded infected belonid fishes from Tunisian coast. These are, Nudaciraxine imperium Châari, Derbel and Neifar, 2010, A. belones, Axine sp., Axinoides sp. (Axinidae and A. gallieni (Micrcotylidae. Among them, the most prevalent species A. gallieni from the inner gill cover and gill filaments of T. a. imperialis and A. belones from the gills of B. belone were redescribed. A. gallieni represented new host record for T. a. imperialis. A complete list of monogenean parasites found in belonid fishes from our study and those reported from the Mediterranean Sea was presented. Conclusions: This paper enhances the current knowledge of Monogenea infecting belonids off the Mediterranean Sea. It’s the first study on monogenean parasites of the overall belonid fishes off Tunisia.

  3. Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways.

    Directory of Open Access Journals (Sweden)

    Kai-Cheng Hsu

    Full Text Available Many virtual screening methods have been developed for identifying single-target inhibitors based on the strategy of "one-disease, one-target, one-drug". The hit rates of these methods are often low because they cannot capture the features that play key roles in the biological functions of the target protein. Furthermore, single-target inhibitors are often susceptible to drug resistance and are ineffective for complex diseases such as cancers. Therefore, a new strategy is required for enriching the hit rate and identifying multitarget inhibitors. To address these issues, we propose the pathway-based screening strategy (called PathSiMMap to derive binding mechanisms for increasing the hit rate and discovering multitarget inhibitors using site-moiety maps. This strategy simultaneously screens multiple target proteins in the same pathway; these proteins bind intermediates with common substructures. These proteins possess similar conserved binding environments (pathway anchors when the product of one protein is the substrate of the next protein in the pathway despite their low sequence identity and structure similarity. We successfully discovered two multitarget inhibitors with IC50 of <10 µM for shikimate dehydrogenase and shikimate kinase in the shikimate pathway of Helicobacter pylori. Furthermore, we found two selective inhibitors (IC50 of <10 µM for shikimate dehydrogenase using the specific anchors derived by our method. Our experimental results reveal that this strategy can enhance the hit rates and the pathway anchors are highly conserved and important for biological functions. We believe that our strategy provides a great value for elucidating protein binding mechanisms and discovering multitarget inhibitors.

  4. Coral-macroalgal phase shifts or reef resilience: links with diversity and functional roles of herbivorous fishes on the Great Barrier Reef

    Science.gov (United States)

    Cheal, A. J.; MacNeil, M. Aaron; Cripps, E.; Emslie, M. J.; Jonker, M.; Schaffelke, B.; Sweatman, H.

    2010-12-01

    Changes from coral to macroalgal dominance following disturbances to corals symbolize the global degradation of coral reefs. The development of effective conservation measures depends on understanding the causes of such phase shifts. The prevailing view that coral-macroalgal phase shifts commonly occur due to insufficient grazing by fishes is based on correlation with overfishing and inferences from models and small-scale experiments rather than on long-term quantitative field studies of fish communities at affected and resilient sites. Consequently, the specific characteristics of herbivorous fish communities that most promote reef resilience under natural conditions are not known, though this information is critical for identifying vulnerable ecosystems. In this study, 11 years of field surveys recorded the development of the most persistent coral-macroalgal phase shift (>7 years) yet observed on Australia’s Great Barrier Reef (GBR). This shift followed extensive coral mortality caused by thermal stress (coral bleaching) and damaging storms. Comparisons with two similar reefs that suffered similar disturbances but recovered relatively rapidly demonstrated that the phase shift occurred despite high abundances of one herbivore functional group (scraping/excavating parrotfishes: Labridae). However, the shift was strongly associated with low fish herbivore diversity and low abundances of algal browsers (predominantly Siganidae) and grazers/detritivores (Acanthuridae), suggesting that one or more of these factors underpin reef resilience and so deserve particular protection. Herbivorous fishes are not harvested on the GBR, and the phase shift was not enhanced by unusually high nutrient levels. This shows that unexploited populations of herbivorous fishes cannot ensure reef resilience even under benign conditions and suggests that reefs could lose resilience under relatively low fishing pressure. Predictions of more severe and widespread coral mortality due to global

  5. Complimentary analysis of metacommunity nestedness and diversity partitioning highlights the need for a holistic conservation strategy for highland lake fish assemblages

    Directory of Open Access Journals (Sweden)

    Jun Xu

    2015-01-01

    Full Text Available Metacommunity nestedness can be affected by both idiosyncratic species and species turnover, and diversity partitioning allows one to separate turnover and nested components within β-diversity. Thus, complimentary analysis of metacommunity nestedness and diversity partitioning allows for the identification of the underlying changes at both local and regional scales. We examined changes of fish assemblages in metacommunity nestedness and α-, β-, and γ-diversities resulting from the intense loss of native species and the invasion of nonnative species in Chinese highland lakes over the past 60 years. We found metacommunity nestedness rose markedly over time, following the loss of both β- and γ-diversity resulting from the loss of native species, and the increase of α diversity by the addition of nonnative species. This pattern is contradictory to the selective extinction leading to larger nestedness in natural ecosystems and indicates the human-induced negative effects on the metacommunity. However, β-diversity partitioning showed that the turnover component due to species replacement among lakes still contributes more than the nested component, suggesting the importance of avoiding setting conservation priorities based exclusively on metacommunity nestedness theory, but taking a more holistic metacommunity-approach to conservation instead.

  6. Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays.

    Science.gov (United States)

    Rantala, Juha K; Kwon, Sunjong; Korkola, James; Gray, Joe W

    2013-04-11

    Over the past decade, great strides have been made in identifying gene aberrations and deregulated pathways that are associated with specific disease states. These association studies guide experimental studies aimed at identifying the aberrant genes and networks that cause the disease states. This requires functional manipulation of these genes and networks in laboratory models of normal and diseased cells. One approach is to assess molecular and biological responses to high-throughput RNA interference (RNAi)-induced gene knockdown. These responses can be revealed by immunofluorescent staining for a molecular or cellular process of interest and quantified using fluorescence image analysis. These applications are typically performed in multiwell format, but are limited by high reagent costs and long plate processing times. These limitations can be mitigated by analyzing cells grown in cell spot microarray (CSMA) format. CSMAs are produced by growing cells on small (~200 mm diameter) spots with each spot carrying an siRNA with transfection reagent. The spacing between spots is only a few hundred micrometers, thus thousands of cell spots can be arranged on a single cell culture surface. These high-density cell cultures can be immunofluorescently stained with minimal reagent consumption and analyzed quickly using automated fluorescence microscopy platforms. This review covers basic aspects of imaging-based CSMA technology, describes a wide range of immunofluorescence assays that have already been implemented successfully for CSMA screening and suggests future directions for advanced RNAi screening experiments.

  7. Vitellogenin synthesis in primary cultures of fish liver cells as endpoint for in vitro screening of the (anti)estrogenic activity of chemical substances.

    Science.gov (United States)

    Navas, José M; Segner, Helmut

    2006-10-25

    Concern over possible adverse effects of endocrine-disrupting compounds on fish has caused the development of appropriate testing methods. In vitro screening assays may provide initial information on endocrine activities of a test compound and thereby may direct and optimize subsequent testing. Induction of vitellogenin (VTG) is used as a biomarker of exposure of fish to estrogen-active substances. Since VTG induction can be measured not only in vivo but also in fish hepatocytes in vitro, the use of VTG induction response in isolated fish liver cells has been suggested as in vitro screen for identifying estrogenic-active substances. The main advantages of the hepatocyte VTG assay are considered its ability to detect effects of estrogenic metabolites, since hepatocytes in vitro remain metabolically competent, and its ability to detect both estrogenic and anti-estrogenic effects. In this article, we critically review the current knowledge on the VTG response of cultured fish hepatocytes to (anti)estrogenic substances. In particular, we discuss the sensitivity, specificity, and variability of the VTG hepatocyte assay. In addition, we review the available data on culture factors influencing basal and induced VTG production, the response to natural and synthetic estrogens as well as to xenoestrogens, the detection of indirect estrogens, and the sources of assay variability. The VTG induction in cultured fish hepatocytes is clearly influenced by culture conditions (medium composition, temperature, etc.) and culture system (hepatocyte monolayers, aggregates, liver slices, etc.). The currently available database on estrogen-mediated VTG induction in cultured teleost hepatocytes is too small to support conclusive statements on whether there exist systematic differences of the VTG response between in vitro culture systems, VTG analytical methods or fish species. The VTG hepatocyte assay detects sensitively natural and synthetic estrogens, whereas the response to

  8. Fish species diversity and trophic level in the Jiulong Estuary%九龙江口鱼类多样性和营养级分析

    Institute of Scientific and Technical Information of China (English)

    杜建国; 刘正华; 余兴光; 许章程; 胡文佳; 陈彬; 马志远; 林金兰

    2012-01-01

    The community structure and species diversity of fishes in the Jiulong Estuary were evaluated based on two trawling surveys conducted in May and November, 2009. Totally 35 fish species were identified, belonging to two classes, 12 orders and 22 families. According to their habitats, three species are pelagic fish, seven near-demersal fish and 25 demersal; and 10 species are estuarine and 25 marine. Based on their temperature adaptions, 22 species are warm water fish, and the rest 13 are temperate warm water fish. According to their feeding habits, seven species are lower carnivorous fish and 28 middle carnivorous fish. Arius sinensis, Coilia mystus and Odontamblyopus rubicundus were dominant species in the samples of May, and A. sinensis, C. mystus and Johnius belengerii were dominant species in the samples of November. The weight densities were 471.53 and 143.97kg·km-2, and the individual densities were 40811 and 3804ind-km~2 in May and November, respectively. The Shannon-Wiener index, Pielou index, Margalef index and Trophic index of the fishes in the Jiulong Estuary were 1.20, 0.39, 3.11 and 3.55, respectively. Compare to the survey data conducted in the same periods in 1985, the fish community structure and species diversity changed largely, and the trophic index deceased significantly in the Jiulong Estuary. Overfishing, environmental pollution and habitat loss are suggested to be the main factors contributing to the decline of fish diversity in the Jiulong Estuary.%2009年5月和11月对九龙江口进行了两个航次的拖网渔业资源调查,探讨了该河口鱼类群落结构和物种多样性特征.结果表明,两次拖网调查共鉴定鱼类35种,隶属于2纲12目22科.其中中上层鱼类3种,近底层鱼类7种,底层鱼类25种;暖水种22种,暖温种13种;河口性鱼类10种,海洋性鱼类25种;低级肉食性鱼类7种,中级肉食性鱼类28种.中华海鲇Arius sinensis、凤鲚Coilia mystus

  9. Geological differentiation explains diversity and composition of fish communities in upland streams in the southern Amazon of Colombia

    NARCIS (Netherlands)

    Arbeláez, F.; Duivenvoorden, J.F.; Maldonado-Ocampo, J.A.

    2008-01-01

    Fish biomass, species richness and composition were compared between upland streams draining two contrasting geological units (Pebas and Tsa) in Colombian Amazonia. Because Pebas sediments reportedly show higher levels of base concentrations than Tsa sediments, we expected that the fish communities

  10. Detailed screening of the soil faunal diversity using a tiered DNA metabarcoding approach

    DEFF Research Database (Denmark)

    Groot, G.A. de; Geisen, S.; Costa, D.

    for automated identification of six different groups of soil fauna at high taxonomic detail, with a single integrated method. We adopted a tiered approach, in which a general eukaryotic marker is used to screen for the presence of different eukaryotic clades and a set of more specific markers is simultaneously...... analyzed to obtain high resolution data for six different groups: mites, collembola, enchytraeids, nematodes, earthworms and protists. New primer sets, as well as reference barcode datasets were established for several of them. Here, we show the results of two test runs based on 454 pyrosequencing...... results for DNA pools that contained different relative amounts of DNA of the six groups, we could show that for most markers the number of taxa of the targeted group recovered depended on the presence of DNA from non-targeted groups. In the second run we moved towards the analysis of actual soil (e...

  11. Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening.

    Science.gov (United States)

    Croucher, Nicholas J; Campo, Joseph J; Le, Timothy Q; Liang, Xiaowu; Bentley, Stephen D; Hanage, William P; Lipsitch, Marc

    2017-01-17

    Characterizing the immune response to pneumococcal proteins is critical in understanding this bacterium's epidemiology and vaccinology. Probing a custom-designed proteome microarray with sera from 35 healthy US adults revealed a continuous distribution of IgG affinities for 2,190 potential antigens from the species-wide pangenome. Reproducibly elevated IgG binding was elicited by 208 "antibody binding targets" (ABTs), which included 109 variants of the diverse pneumococcal surface proteins A and C (PspA and PspC) and zinc metalloprotease A and B (ZmpA and ZmpB) proteins. Functional analysis found ABTs were enriched in motifs for secretion and cell surface association, with extensive representation of cell wall synthesis machinery, adhesins, transporter solute-binding proteins, and degradative enzymes. ABTs were associated with stronger evidence for evolving under positive selection, although this varied between functional categories, as did rates of diversification through recombination. Particularly rapid variation was observed at some immunogenic accessory loci, including a phage protein and a phase-variable glycosyltransferase ubiquitous among the diverse set of genomic islands encoding the serine-rich PsrP glycoprotein. Nevertheless, many antigens were conserved in the core genome, and strains' antigenic profiles were generally stable. No strong evidence was found for any epistasis between antigens driving population dynamics, or redundancy between functionally similar accessory ABTs, or age stratification of antigen profiles. These results highlight the paradox of why substantial variation is observed in only a subset of epitopes. This result may indicate only some interactions between immunoglobulins and ABTs clear pneumococcal colonization or that acquired immunity to pneumococci is an accumulation of individually weak responses to ABTs evolving under different levels of functional constraint.

  12. Taxonomic distinctness of demersal fishes of the California current: moving beyond simple measures of diversity for marine ecosystem-based management.

    Directory of Open Access Journals (Sweden)

    Nick Tolimieri

    Full Text Available BACKGROUND: Large-scale patterns or trends in species diversity have long interested ecologists. The classic pattern is for diversity (e.g., species richness to decrease with increasing latitude. Taxonomic distinctness is a diversity measure based on the relatedness of the species within a sample. Here we examined patterns of taxonomic distinctness in relation to latitude (ca. 32-48 degrees N and depth (ca. 50-1220 m for demersal fishes on the continental shelf and slope of the US Pacific coast. METHODOLOGY/PRINCIPAL FINDINGS: Both average taxonomic distinctness (AvTD and variation in taxonomic distinctness (VarTD changed with latitude and depth. AvTD was highest at approximately 500 m and lowest at around 200 m bottom depth. Latitudinal trends in AvTD were somewhat weaker and were depth-specific. AvTD increased with latitude on the shelf (50-150 m but tended to decrease with latitude at deeper depths. Variation in taxonomic distinctness (VarTD was highest around 300 m. As with AvTD, latitudinal trends in VarTD were depth-specific. On the shelf (50-150 m, VarTD increased with latitude, while in deeper areas the patterns were more complex. Closer inspection of the data showed that the number and distribution of species within the class Chondrichthyes were the primary drivers of the overall patterns seen in AvTD and VarTD, while the relatedness and distribution of species in the order Scorpaeniformes appeared to cause the relatively low observed values of AvTD at around 200 m. CONCLUSIONS/SIGNIFICANCE: These trends contrast to some extent the patterns seen in earlier studies for species richness and evenness in demersal fishes along this coast and add to our understanding of diversity of the demersal fishes of the California Current.

  13. Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH).

    Science.gov (United States)

    Leveau, Johan H J; Gerards, Saskia; de Boer, Wietse; van Veen, Johannes A

    2004-09-01

    We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia coli of large-sized genomic DNA fragments of the mycophagous soil bacterium Collimonas fungivorans, and hybridized 768 library clones with the Collimonas-specific fluorescent probe CTE998-1015. Critical to the success of this approach (which we refer to as large-insert library FISH or LIL-FISH) was the ability to induce fosmid copy number, the exponential growth status of library clones in the FISH assay and the use of a simple pooling strategy to reduce the number of hybridizations. Twelve out of 768 E. coli clones were suspected to harbour and express Collimonas 16S rRNA genes based on their hybridization to CTE998-1015. This was confirmed by the finding that all 12 clones were also identified in an independent polymerase chain reaction-based screening of the same 768 clones using a primer set for the specific detection of Collimonas 16S ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by restriction analysis into two distinct contigs, confirming that C. fungivorans harbours at least two 16S rRNA genes. For one contig, representing 1-2% of the genome, the nucleotide sequence was determined, providing us with a narrow but informative view of Collimonas genome structure and content.

  14. Application of FISK, an invasiveness screening tool for non-native freshwater fishes, in the Murray-Darling Basin (southeastern Australia).

    Science.gov (United States)

    Vilizzi, Lorenzo; Copp, Gordon H

    2013-08-01

    The Fish Invasiveness Scoring Kit (FISK) is currently one of the most popular pre-screening tools for freshwater fishes. A recent upgrade has ensured its wider climatic relevance to countries with subtropical regions. This enhancement is of particular importance to Australia, which encompasses tropical, arid, and temperate zones, and where the introduction of non-native fish species poses a significant risk to biodiversity. In this study, 55 fish species previously evaluated in a U.K.-based calibration of FISK are reassessed for their potential invasiveness in the Murray-Darling Basin (MDB; southeastern Australia), the continent's largest catchment encompassing arid and temperate climates. Approximately half of the species were classed as "medium risk" and the other half as "high risk," and the ≥19 threshold previously identified from the calibration study was confirmed. The three highest scoring species (common carp Cyprinus carpio carpio, goldfish Carassius auratus, and eastern mosquitofish Gambusia holbrooki) were those already present and invasive in the area, whereas nearly half of the tropical and subtropical species had lower scores compared to U.K. assessments, possibly because of climate change predictions of drier conditions across the MDB. There were some discordances between FISK and two Australian-based assessment protocols, one of which is qualitative and the other represents a simplified version of FISK. Notably, the Australian origins of FISK should provide for an additional reason for further applications of the tool in other RA areas (i.e., drainage basins) of the continent, ultimately encouraging adoption as the country's reference screening tool for management and conservation purposes.

  15. Elucidating the diversity of aquatic microdochium and trichoderma species and their activity against the fish pathogen Saprolegnia diclina

    NARCIS (Netherlands)

    Liu, Yiying; Zachow, Christin; Raaijmakers, J.M.; Bruijn, De Irene

    2016-01-01

    Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security

  16. Elucidating the diversity of aquatic microdochium and trichoderma species and their activity against the fish pathogen Saprolegnia diclina

    NARCIS (Netherlands)

    Liu, Yiying; Zachow, Christin; Raaijmakers, J.M.; Bruijn, De Irene

    2016-01-01

    Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food

  17. Elucidating the diversity of aquatic Microdochium and Trichoderma species and their activity against the fish pathogen Saprolegnia diclina

    NARCIS (Netherlands)

    Liu, Yiying; Zachow, Christin; Raaijmakers, J.M.; De Bruijn, I.

    2016-01-01

    Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security.

  18. Multiresidue Screening of Veterinary Drugs in Meat, Milk, Egg, and Fish Using Liquid Chromatography Coupled with Ion Trap Time-of-Flight Mass Spectrometry.

    Science.gov (United States)

    Kang, JeongWoo; Park, Su-Jeong; Park, Hae-Chul; Hossain, Md Akil; Kim, Myeong-Ae; Son, Seong-Wan; Lim, Chae-Mi; Kim, Tae-Wan; Cho, Byung-Hoon

    2017-06-01

    New approaches to veterinary drug screening based on liquid chromatography-mass spectrometry (LC-MS/MS) and time-of-flight mass spectrometry (ToF/MS) are rapid and have high selectivity and sensitivity. In this study, we developed a multiresidue method for screening over 100 veterinary drug residues using ion trap (IT)-ToF/MS. The screened compounds comprised major drug classes used in veterinary practice, representing the following: amphenicols, anthelmintics, benzimidazoles, β-lactams, coccidiostats, ionophores, macrolides, non-steroidal anti-inflammatory drugs, quinolones, sulfonamides, tetracyclines, and tranquilizers. The method was developed based on chromatographic retention time, specific accurate mass, isotope distribution, and fragment data. Each compound was validated at three levels, and the mass accuracy, accuracy, and repeatability were calculated. All parameters showed acceptable values and conformed to the Commission Decision 2002/657/EC criteria. This screening method can simultaneously analyze over 100 veterinary drugs in meat, milk, eggs, and fish in a single analytical run.

  19. 太湖鱼类群落结构及多样性%Community structure and diversity of fish in Lake Taihu

    Institute of Scientific and Technical Information of China (English)

    毛志刚; 谷孝鸿; 曾庆飞; 周露洪; 王小林; 吴林坤; 曹萍; 孙明波

    2011-01-01

    In 2009-2010, bottom trawl surveys were conducted on the fish resources in Lake Taihu, aimed to understand the characteristics of fish community structure and diversity in the Lake. A total of 50 fish species were collected, belonging to 40 genera, 15 families, and 10 orders, among which, Cypriniformes had the largest species number, accounting for 68% of the total. The fish community was composed of three ecological guilds, and limnology species were most abundant (78% of the total abundance). The dominant species were of mini-type fish such as Coilia ectenes taihuensis, Hyporhamphus intermedius, and Salangichthys jordani. As compared with historical data, the fish species number in the Lake decreased, the composition of dominant species changed greater, and the mini-type fishes with body mass <30 g were absolutely dominant , with an obvious tendency of fish resources becoming smaller-scale. Due to overfishing and water pollution, the Margalef richness index D, Shannon diversity indices H'N and H'N, and Pielou evenness indices J'N and J'w in the Lake all decreased, being 1.54, 0.21, 0.46, 0.07, and 0. 14, respectively. To some extent, the differences in the fish species composition and biodiversity reflected the adaption characteristics of the fishes to the environmental variables such as nutrients and transparency in the Lake.%为了解太湖鱼类群落结构和多样性的分布特征,于2009-2010年利用拖网等网具对该水域的鱼类资源进行了调查.结果表明:本次调查共采获鱼类50种,隶属10目15科40属,其中鲤形目种类最多,占总数的68%;鱼类生态类型以湖泊定居性种类为主,群落优势种为湖鲚(Coilia ectenes taihuensis)、间下鱵(Hyporhamphus intermedius)和陈氏短吻银鱼(Salangichthys jordani)等小型鱼类;与历史资料相比,太湖鱼类的物种数量下降,优势种组成发生较大变化,鱼类群落中体质量<30 g的小型鱼类占绝对优势,渔业资源小型化趋势明显.由

  20. Wide-Scope Screening Method for Multiclass Veterinary Drug Residues in Fish, Shrimp, and Eel Using Liquid Chromatography-Quadrupole High-Resolution Mass Spectrometry.

    Science.gov (United States)

    Turnipseed, Sherri B; Storey, Joseph M; Lohne, Jack J; Andersen, Wendy C; Burger, Robert; Johnson, Aaron S; Madson, Mark R

    2017-01-13

    A screening method for veterinary drug residues in fish, shrimp, and eel using LC with a high-resolution MS instrument has been developed and validated. The method was optimized for over 70 test compounds representing a variety of veterinary drug classes. Tissues were extracted by vortex mixing with acetonitrile acidified with 2% acetic acid and 0.2% p-toluenesulfonic acid. A centrifuged portion of the extract was passed through a novel solid phase extraction cartridge designed to remove interfering matrix components from tissue extracts. The eluent was then evaporated and reconstituted for analysis. Data were collected with a quadrupole-Orbitrap high-resolution mass spectrometer using both nontargeted and targeted acquisition methods. Residues were detected on the basis of the exact mass of the precursor and a product ion along with isotope pattern and retention time matching. Semiquantitative data analysis compared MS(1) signal to a one-point extracted matrix standard at a target testing level. The test compounds were detected and identified in salmon, tilapia, catfish, shrimp, and eel extracts fortified at the target testing levels. Fish dosed with selected analytes and aquaculture samples previously found to contain residues were also analyzed. The screening method can be expanded to monitor for an additional >260 veterinary drugs on the basis of exact mass measurements and retention times.

  1. Preliminary screening of perfluorooctane sulfonate (PFOS) and other fluorochemicals in fish, birds and marine mammals from Greenland and the Faroe Islands

    Energy Technology Data Exchange (ETDEWEB)

    Bossi, Rossana [National Environmental Research Institute, Frederiksborgvej 399, 4000-Roskilde (Denmark)]. E-mail: rbo@dmu.dk; Riget, Frank F. [National Environmental Research Institute, Frederiksborgvej 399, 4000-Roskilde (Denmark); Dietz, Rune [National Environmental Research Institute, Frederiksborgvej 399, 4000-Roskilde (Denmark); Sonne, Christian [National Environmental Research Institute, Frederiksborgvej 399, 4000-Roskilde (Denmark); Fauser, Patrik [National Environmental Research Institute, Frederiksborgvej 399, 4000-Roskilde (Denmark); Dam, Maria [Food and Environmental Agency, Thorshavn, Faroe Islands (Denmark); Vorkamp, Katrin [National Environmental Research Institute, Frederiksborgvej 399, 4000-Roskilde (Denmark)

    2005-07-15

    Extensive screening analyses of perfluorooctane sulfonate (PFOS) and related perfluorinated compounds in biota samples from all over the world have identified PFOS as a global pollutant and have shown its bioaccumulation into higher trophic levels in the food chain. Perfluorinated compounds have been found in remote areas as the Arctic. In this study a preliminary screening of PFOS and related compounds has been performed in liver samples of fish, birds and marine mammals from Greenland and the Faroe Islands. PFOS was the predominant fluorochemical in the biota analyzed, followed by perfluorooctane sulfonamide (PFOSA). PFOS was found at concentrations above LOQ (10 ng/g wet weight) in 13 out of 16 samples from Greenland and in all samples from the Faroe Islands. The results from Greenland showed a biomagnification of PFOS along the marine food chain (shorthorn sculpinfish, birds and marine mammals from Greenland and the Faroe Islands.

  2. Evaluation of genetic diversity and population structure in a commercially important freshwater fish Prochilodus costatus (Characiformes, Prochilodontidae) using complex hypervariable repeats.

    Science.gov (United States)

    Barroca, T M; Santos, G B; Duarte, N V R; Kalapothakis, E

    2012-12-17

    We used complex hypervariable repeats to evaluate the genetic diversity and structure of Prochilodus costatus (Characiformes), an ecologically and economically important species endemic to the São Francisco River basin. Hydroelectric dams along the river have led to population fragmentation, which can limit gene flow. Restocking from hatcheries has been used to repopulate declining populations. To determine how fragmentation and hatchery supplementation affect P. costatus population structure, we studied populations from three sites up and downstream of the Gafanhoto Dam (Pará River, State of Minas Gerais). High levels of genetic diversity were found within populations (0.926 to 0.873); the three populations showed significant differentiation (F(ST) = 0.16), suggesting that populations from the three sites were affected by fragmentation of the river and by hatchery contributions. These results will be useful for developing a management and conservation plan for fish species in this area.

  3. Life-history diversity and its importance to population stability and persistence of a migratory fish: steelhead in two large North American watersheds.

    Science.gov (United States)

    Moore, Jonathan W; Yeakel, Justin D; Peard, Dean; Lough, Jeff; Beere, Mark

    2014-09-01

    Life-history strategies can buffer individuals and populations from environmental variability. For instance, it is possible that asynchronous dynamics among different life histories can stabilize populations through portfolio effects. Here, we examine life-history diversity and its importance to stability for an iconic migratory fish species. In particular, we examined steelhead (Oncorhynchus mykiss), an anadromous and iteroparous salmonid, in two large, relatively pristine, watersheds, the Skeena and Nass, in north-western British Columbia, Canada. We synthesized life-history information derived from scales collected from adult steelhead (N = 7227) in these watersheds across a decade. These migratory fishes expressed 36 different manifestations of the anadromous life-history strategy, with 16 different combinations of freshwater and marine ages, 7·6% of fish performing multiple spawning migrations, and up to a maximum of four spawning migrations per lifetime. Furthermore, in the Nass watershed, various life histories were differently prevalent through time - three different life histories were the most prevalent in a given year, and no life history ever represented more than 45% of the population. These asynchronous dynamics among life histories decreased the variability of numerical abundance and biomass of the aggregated population so that it was > 20% more stable than the stability of the weighted average of specific life histories: evidence of a substantial portfolio effect. Year of ocean entry was a key driver of dynamics; the median correlation coefficient of abundance of life histories that entered the ocean the same year was 2·5 times higher than the median pairwise coefficient of life histories that entered the ocean at different times. Simulations illustrated how different elements of life-history diversity contribute to stability and persistence of populations. This study provides evidence that life-history diversity can dampen fluctuations in

  4. IN VIVO SCREENING OF CHEMICAL MODIFICATIONS OF siRNAs FOR EFFECT ON THE INNATE IMMUNE RESPONSE IN FISH

    DEFF Research Database (Denmark)

    Lorenzen, Niels; Schyth, Brian Dall; Bramsen, J. B.;

    the antiviral activities of these duplexes. We conclude that the fish in vivo model is a potent tool for gaining insight into the overall triggering of antiviral reactions by siRNAs in vertebrates. The perspective is to learn how to avoid triggering of non-specific antiviral responses and still allow uptake...

  5. 78 FR 16705 - Llano Seco Riparian Sanctuary Unit Restoration and Pumping Plant/Fish Screen Facility Protection...

    Science.gov (United States)

    2013-03-18

    ... Street, Orland, CA 95963. Chico Branch Library, 1108 Sherman Avenue, Chico, CA 95926. CDFW Office, 629 Entler Ave, Suite 12, Chico, CA 95928. PCGID-PID Office, 258 South Butte Street, Willows, CA 95988... PCGID-PID consolidated three pumping plants into one new facility equipped with state-of-the-art fish...

  6. Diets and trophic-guild structure of a diverse fish assemblage in Chesapeake Bay, U.S.A.

    Science.gov (United States)

    Buchheister, A; Latour, R J

    2015-03-01

    Dietary habits and trophic-guild structure were examined in a fish assemblage (47 species) of the Chesapeake Bay estuary, U.S.A., using 10 years of data from >25 000 fish stomachs. The assemblage was comprised of 10 statistically significant trophic guilds that were principally differentiated by the relative amounts of Mysida, Bivalvia, Polychaeta, Teleostei and other Crustacea in the diets. These guilds were broadly aggregated into five trophic categories: piscivores, zooplanktivores, benthivores, crustacivores and miscellaneous consumers. Food web structure was largely dictated by gradients in habitat (benthic to pelagic) and prey size. Size classes within piscivorous species were more likely to be classified into different guilds, reflecting stronger dietary changes through ontogeny relative to benthivores and other guilds. Relative to predator species and predator size, the month of sampling had negligible effects on dietary differences within the assemblage. A majority of sampled fishes derived most of their nutrition from non-pelagic prey sources, suggesting a strong coupling of fish production to benthic and demersal food resources. Mysida (predominantly the opossum shrimp Neomysis americana) contributed substantially to the diets of over 25% of the sampled predator groups, indicating that this species is a critical, but underappreciated, node in the Chesapeake Bay food web.

  7. The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation

    Directory of Open Access Journals (Sweden)

    Yingxin Zhang

    2017-10-01

    Full Text Available Transposable elements (TEs in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4% of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like

  8. Diverse Screenings: Multicultural Videos.

    Science.gov (United States)

    Mitchell-Powell, Brenda

    1994-01-01

    The videos in this selected, annotated bibliography combine educational and entertainment elements. All 35 are suitable for classroom, library, and family use, but those designed specifically for educational use are designated. Subjects include minority issues in the United States and abroad and race hatred. (SLD)

  9. Prevalence, genetic diversity and antimicrobial resistance of Listeria monocytogenes isolated from fresh and smoked fish in Poland.

    Science.gov (United States)

    Wieczorek, Kinga; Osek, Jacek

    2017-06-01

    A total of 57 out of 301 (18.9%) fresh and smoked fish samples in Poland were positive for Listeria monocytotgenes. The bacteria were most frequently identified in fresh and smoked salmon (32.0% and 33.8% respectively) as well as in fresh cod (31.8%). Only three samples of smoked salmon were contaminated with the bacteria above 100 CFU/g. Four molecular serogroups were identified and the most prevalent, 1/2a-3a (40 isolates; 70.2%), was present in samples from both marine (33 strains; 71.7%) and freshwater fish (7 isolates; 63.6%). Similar duality of prevalence was observed only for L. monocytogenes of 1/2b-3b-7 serogroup (14 strains; 24.6%), which was identified in 11 (23.9%) marine and 3 (27.3%) freshwater fish. All isolates harboured 10 virulence-associated genes (inlA, inlB, inlC, inlJ, lmo2672, plcA, plcB, hlyA, actA, and mpl) and most of them (56; 98.2%) also possessed the flaA marker. Several strains displayed resistance to oxacillin (33; 57.9%), ceftriaxone (18; 31.6%), or clindamycin (5; 8.8%), and two isolates of serogroup 1/2a-3a showed multiresistance to all three. Genetic subtyping showed the presence of different pulsotypes belonging to six PFGE clusters. The obtained results provide useful information regarding fish contamination with L. monocytogenes which may have implications for public health.

  10. Fishing for Nature’s Hits: Establishment of the Zebrafish as a Model for Screening Antidiabetic Natural Products

    Directory of Open Access Journals (Sweden)

    Nadia Tabassum

    2015-01-01

    Full Text Available Diabetes mellitus affects millions of people worldwide and significantly impacts their quality of life. Moreover, life threatening diseases, such as myocardial infarction, blindness, and renal disorders, increase the morbidity rate associated with diabetes. Various natural products from medicinal plants have shown potential as antidiabetes agents in cell-based screening systems. However, many of these potential “hits” fail in mammalian tests, due to issues such as poor pharmacokinetics and/or toxic side effects. To address this problem, the zebrafish (Danio rerio model has been developed as a “bridge” to provide an experimentally convenient animal-based screening system to identify drug candidates that are active in vivo. In this review, we discuss the application of zebrafish to drug screening technologies for diabetes research. Specifically, the discovery of natural product-based antidiabetes compounds using zebrafish will be described. For example, it has recently been demonstrated that antidiabetic natural compounds can be identified in zebrafish using activity guided fractionation of crude plant extracts. Moreover, the development of fluorescent-tagged glucose bioprobes has allowed the screening of natural product-based modulators of glucose homeostasis in zebrafish. We hope that the discussion of these advances will illustrate the value and simplicity of establishing zebrafish-based assays for antidiabetic compounds in natural products-based laboratories.

  11. Screening fungicides for use in fish culture: Evaluation of the agar plug transfer, cellophane transfer, and agar dilution methods

    Science.gov (United States)

    Bailey, Tom A.

    1983-01-01

    The reliability, reproducibility, and usefulness of three screening methods -- the cellophane transfer, the agar plug transfer, and the agar dilution -- to screen aquatic fungicides were evaluated. Achlya flagellata and Saprolegnia hypogyna were exposed to 1, 10, and 100 mg/L of malachite green to test each method. The cellophane transfer and agar plug transfer techniques had similar reliability and reproducibility in rating fungicidal activity, and were both superior to the agar dilution technique. The agar plug transfer and agar dilution techniques adequately projected in vivo activity of malachite green, but the cellophane transfer technique overestimated its activity. Overall, the agar plug transfer technique most accurately rated the activity of malachite green and was the easiest test to perform. It therefore appears to be the method of choice for testing aquatic fungicides.

  12. Screening of lactic acid bacteria from gastrointestinal tracts of marine fish for their potential use as probiotics

    Directory of Open Access Journals (Sweden)

    Tipparat Hongpattarakere

    2008-04-01

    Full Text Available One hundred and sixty isolates of lactic acid bacteria (LAB with inhibitory activity against pathogenic Escherichia coli were isolated from gastrointestinal tracts of fish, shrimp and shellfish. One hundred and sixteen isolates were obtained from fish, twenty isolates from shrimp and twenty-four isolates from shellfish. Three strains were selected based on their bile and acid tolerances. All acid-tolerant strains showed inhibitory activity against human pathogens, including Staphylococcus aureus, Listeria monocytogenes, Salmonella sp. and Escherichia coli. However, the antibacterial activities were lost when the culture supernatants were neutralized to pH 6.5- 7.0 and treated with catalase, indicating that the inhibition may be contributed by acid and hydrogen-peroxide production of the strains. Nucleotide sequences of their 16s rDNA showed 98% (655/668 bp, 97% (691/712 bp and 98% (492/501 bp homology to Pediococcus pentosaceus LM2, Pediococcus pentosaceus SL4 and Enterococcus faecium SF, respectively.

  13. Fish pathogens near the Arctic Circle: molecular, morphological and ecological evidence for unexpected diversity of Diplostomum (Digenea: Diplostomidae) in Iceland.

    Science.gov (United States)

    Blasco-Costa, Isabel; Faltýnková, Anna; Georgieva, Simona; Skírnisson, Karl; Scholz, Tomáš; Kostadinova, Aneta

    2014-09-01

    Host-parasite systems at high latitudes are promising model systems for detecting and predicting the impact of accelerated environmental change. A major challenge is the lack of baselines for the diversity and distribution of parasites in Arctic wildlife, especially in the freshwater environment. Here we present the first known estimates of the species diversity and host associations of Diplostomum spp. in sub-Arctic freshwater ecosystems of the Palaearctic. Our analyses integrating different analytical approaches, phylogenies based on mitochondrial and nuclear DNA, estimates of genetic divergence, character-based barcoding, morphological examination, precise detection of microhabitat specialisation and host use, led to the discovery of one described and five putative new species that complete their life-cycles within a fairly narrow geographic area in Iceland. This increases the species richness of Diplostomum in Iceland by 200% and raises the number of molecularly characterised species from the Palaearctic to 17 species. Our results suggest that the diversity of Diplostomum spp. is underestimated globally in the high latitude ecosystems and call for a cautionary approach to pathogen identification in developing the much needed baselines of pathogen diversity that may help detect effects of climate change in the freshwater environment of the sub-Arctic.

  14. The Model of Zebra Fish and Its Application to the Screening of Angiogenesis Inhibitor%斑马鱼模型及其在血管生成抑制剂筛选中的应用

    Institute of Scientific and Technical Information of China (English)

    冯康虎; 方鹏飞; 张文贤; 韩立文

    2014-01-01

    Since there are high genetic similarities between zebra fish and human, the model organisms of ze-bra fish are widely used to many studies about human physiology and pathology as well as the screening of new drugs, the paper is discussing the model of zebra fish and its application to the screening of angiogenesis inhibitor.%斑马鱼基因与人类高度相似,其模式生物正广泛应用到人体生理和病理的多项研究以及新型药物的筛选中,就目前斑马鱼模型及其在血管生成抑制剂筛选中的应用状况进行阐述。

  15. Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina.

    Science.gov (United States)

    Liu, Yiying; Zachow, Christin; Raaijmakers, Jos M; de Bruijn, Irene

    2016-01-21

    Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security. Due to the prohibition of several chemical control agents, novel sustainable measures are required to control Saprolegnia infections in aquaculture. Previously, fungal community analysis by terminal restriction fragment length polymorphism (T-RFLP) revealed that the Ascomycota, specifically the genus Microdochium, was an abundant fungal phylum associated with salmon eggs from a commercial fish farm. Here, phylogenetic analyses showed that most fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride species. Phylogenetic and quantitative PCR analyses showed both a quantitative and qualitative difference in Trichoderma population between diseased and healthy salmon eggs, which was not the case for the Microdochium population. In vitro antagonistic activity of the fungi against Saprolegnia diclina was isolate-dependent; for most Trichoderma isolates, the typical mycoparasitic coiling around and/or formation of papilla-like structures on S. diclina hyphae were observed. These results suggest that among the fungal community associated with salmon eggs, Trichoderma species may play a role in Saprolegnia suppression in aquaculture.

  16. Correlation between host specificity and genetic diversity for the muscle-dwelling fish parasite Myxobolus pseudodispar: examples of myxozoan host-shift?

    Science.gov (United States)

    Forro, Barbara; Eszterbauer, Edit

    2016-06-02

    Myxobolus pseudodispar Gorbunova, 1936 (Myxozoa) is capable of infecting and developing mature myxospores in several cyprinid species. However, M. pseudodispar isolates from different fish show up to 5% differences in the SSU rDNA sequences. This is an unusually large intraspecific difference for myxozoans and only some of the muscle-dwelling myxozoan species possess such a high genetic variability. We intended to study the correlation between the host specificity and the phylogenetic relationship of the parasite isolates, and to find experimental proof for the putatively wide host range of M. pseudodispar with cross-infection experiments and phylogenetic analyses based on SSU rDNA. The experimental findings distinguished 'primary' and less-susceptible 'secondary' hosts. With some exceptions, M. pseudodispar isolates showed a tendency to cluster according to the fish host on the phylogenetic tree. Experimental and phylogenetic findings suggest the cryptic nature of the species. It is likely that host-shift occurred for M. pseudodispar and the parasite speciation in progress might explain the high genetic diversity among isolates which are morphologically indistinguishable.

  17. Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH.

    Science.gov (United States)

    Pandey, Neeti; Rajagopal, Raman

    2016-10-01

    Dialeurolonga malleswaramensis Sundararaj (Hemiptera: Aleyrodidae) is a phytophagous sap sucking insect. It infests Polyalthia longifolia, an important avenue tree of India, effective in alleviating noise pollution and having immense medicinal importance. Samples of this insect were collected from Polyalthia longifolia. The cytochrome c oxidase subunit I gene (mtCO1) helped in the molecular characterization of the insect. This study reports the bacterial diversity in D. malleswaramensis adults by high throughput 16S rDNA amplicon pyrosequencing. The major genera identified were Portiera and Arsenophonus. Other bacterial genera detected were uncultured alpha proteobacterium, Sphingopyxis and Methylobacterium. We also employed fluorescence in situ hybridization (FISH) in whole mount samples to confirm the presence of dominant endosymbionts Portiera and Arsenophonus to the bacteriocyte of D. malleswaramensis. This study concludes that combining techniques like 16S rDNA amplicon pyrosequencing and FISH reveal both dominant and rare bacteria. The data also predict the evolutionary position of this pest with respect to other whitefly species using a mitochondrial marker.

  18. Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes).

    Science.gov (United States)

    Poulsen, Jan Yde; Sado, Tetsuya; Hahn, Christoph; Byrkjedal, Ingvar; Moku, Masatoshi; Miya, Masaki

    2016-01-01

    The family Opisthoproctidae (barreleyes) constitutes one of the most peculiar looking and unknown deep-sea fish groups in terms of taxonomy and specialized adaptations. All the species in the family are united by the possession of tubular eyes, with one distinct lineage exhibiting also drastic shortening of the body. Two new species of the mesopelagic opisthoproctid mirrorbelly genus Monacoa are described based on pigmentation patterns of the "sole"-a unique vertebrate structure used in the reflection and control of bioluminescence in most short-bodied forms. Different pigmentation patterns of the soles, previously noted as intraspecific variations based on preserved specimens, are here shown species-specific and likely used for communication in addition to counter-illumination of down-welling sunlight. The genus Monacoa is resurrected from Opisthoproctus based on extensive morphological synaphomorphies pertaining to the anal fin and snout. Doubling the species diversity within sole-bearing opisthoproctids, including recognition of two genera, is unambiguously supported by mitogenomic DNA sequence data. Regular fixation with formalin and alcohol preservation is shown problematic concerning the retention of species-specific pigmentation patterns. Examination or photos of fresh material before formalin fixation is shown paramount for correct species recognition of sole-bearing opisthoproctids-a relatively unknown issue concerning species diversity in the deep-sea pelagic realm.

  19. Supplement Analysis for the Watershed Management Program EIS - Idaho Model Watershed Habitat Projects - L-9 Irrigation Diversion Modification

    Energy Technology Data Exchange (ETDEWEB)

    N/A

    2004-08-02

    The Bonneville Power Administration is proposing to fund a fish passage improvement project at the L-9 diversion on the Lemhi River in Lemhi County, Idaho with the Lemhi Soil and Water Conservation District. The project proposes to replace the existing rock push-up irrigation diversion dam with a single rock weir that will incorporate a geotextile membrane to create a permanent diversion. The new weir will be a v-shaped vortex weir with a six-foot wide notch for fish passage. In addition, a ramp flume will be constructed in the diversion canal between the headgate and existing fish screen to provide for water measurement. The new diversion will provide better water delivery/control and improved passage for adult and juvenile resident and anadromous fish.

  20. Screening of marine seaweeds for bioactive compound against fish pathogenic bacteria and active fraction analysed by gas chromatography– mass spectrometry

    Directory of Open Access Journals (Sweden)

    Rajasekar Thirunavukkarasu

    2014-05-01

    Full Text Available Objective: To isolate bioactive molecules from marine seaweeds and check the antimicrobial activity against the fish pathogenic bacteria. Methods: Fresh marine seaweeds Gracilaria edulis, Kappaphycus spicifera, Sargassum wightii (S. wightii were collected. Each seaweed was extracted with different solvents. In the study, test pathogens were collected from microbial type culture collection. Antibacterial activity was carried out by using disc diffusion method and minimum inhibition concentration (MIC was calculated. Best seaweed was analysed by fourier transform infrared spectroscopy. The cured extract was separated by thin layer chromatography (TLC. Fraction was collected from TLC to check the antimicrobial activity. Best fraction was analysed by gas chromatography mass spectrometer (GCMS. Results: Based on the disc diffusion method, S. wightii showed a better antimicrobial activity than other seaweed extracts. Based on the MIC, methanol extract of S. wightii showed lower MIC than other solvents. S. wightii were separated by TLC. In this TLC, plate showed a two fraction. These two fractions were separated in preparative TLC and checked for their antimicrobial activity. Fraction 2 showed best MIC value against the tested pathogen. Fraction 2 was analysed by GCMS. Based on the GCMS, fraction 2 contains n-hexadecanoic acid (59.44%. Conclusions: From this present study, it can be concluded that S. wightii was potential sources of bioactive compounds.

  1. 5S rDNA characterization in twelve Sciaenidae fish species (Teleostei, Perciformes: depicting gene diversity and molecular markers

    Directory of Open Access Journals (Sweden)

    Fernanda A. Alves-Costa

    2008-01-01

    Full Text Available In order to extend the genetic data on the Sciaenidae fish family, the present study had the purpose to characterize PCR-generated 5S rDNA repeats of twelve species of this group through PAGE (Polyacrylamide Gel Electrophoresis analysis. The results showed the occurrence of at least two different 5S rDNA size classes in all the species. Moreover, 5S rDNA repeats of one of the studied species - Isopisthus parvipinnis - were cloned and subjected to nucleotide sequencing and Southern blot membrane hybridization analyses, which permitted to confirm the existence of two major 5S rDNA classes. Phylogenetic analysis based on the nucleotide sequences of different 5S rDNA repeats of I. parvipinnis lead to their separation into two major clusters. These results may reflect the high dynamism that rules the evolution rate of 5S rDNA repeats. The obtained data suggest that 5S rDNA can be useful in genetic analyses to identify species-specific markers and determine relationships among species of the Sciaenidae group.

  2. Screening and identification of Staphylococcus from traditional fish products%专统鱼制品中优良葡萄球菌的筛选与鉴定

    Institute of Scientific and Technical Information of China (English)

    张琦琳; 林胜利; 聂小华

    2012-01-01

    从盐干鱼及糟腌鱼中分离纯化得到158株葡萄球菌,按照肉制品发酵剂筛选标准,获得3株优良葡萄球菌S8、S61和S92,其具有良好的生长特性及耐盐性。经梅里埃VITEK-2全自动微生物系统鉴定及16SrDNA序列分析.优良葡萄球茵S8、S61和S92分别为沃氏葡萄球茵(StaphylococcuswarIteri)、松鼠葡萄球菌(Staphylococcussciun)和木糖葡萄球菌(Staphylococcus xylosus)。%According to the standards of meat fermentation starter,three Staphylococcus strains (S8, S61 and S92) with excellent characteristics were isolated and screened from traditional fish products. And the results of BioMerieux VITEK-2 automation microbe system and 16S rDNA sequence analysis showed that they were Staphylococcus warner, Staphylococcus sciuri and Staphylococcus xylosus respectively.

  3. Past and present fish species recorded in the estuarine Lake Ichkeul ...

    African Journals Online (AJOL)

    Past and present fish species recorded in the estuarine Lake Ichkeul, northern Tunisia. ... appear to be the principal causes for the decline in fish abundance and diversity. Keywords: estuarine fish, freshwater fish, marine fish, salinity, seasonal ...

  4. Species composition and diversity of fish larvae in the Subtropical Convergence Zone of the Sargasso Sea from morphology and DNA barcoding

    DEFF Research Database (Denmark)

    Ayala, Daniel Jiro; Munk, Peter; Riemann, Lasse

    2016-01-01

    Specific regions of otherwise oligotrophic oceans seem to attract fish spawning and sustain significant abundances of fish larvae. The Sargasso Sea in the North Atlantic subtropical gyre is known as the spawning area of the Atlantic eels, but numerous other fish species also spawn in the area. In...

  5. Diversity, occurrence and socio-economic aspects of snappers and job fish (Family: Lutjanidae) fisheries from Gulf of Mannar region, south-east coast of India.

    Digital Repository Service at National Institute of Oceanography (India)

    Murugan, A.; Vinod, K.; Saravanan, K.R.; Anbalagan, T.; Saravanan, R.; Sanaye, S.V.; Mojjada, S.K.; Rajagopal, S.; Balasubramanian, T.

    -9. The fishermen of Gulf of Mannar use different fishing practices based on the traditional knowledge to harvest the reef associated fishes based on seasonal pattern. The exploited reef fishes in Gulf of Mannar region have a good market value in the domestic... market10, the fishermen use different gear types, which results in variable fishing pressure on the reef area. In most of the South-east Asian countries, the reef fishes are mainly caught by the traditional sectors11, however, the data on reef...

  6. Zoonoses associated with fish.

    Science.gov (United States)

    Boylan, Shane

    2011-09-01

    The taxonomic group that composes the fishes is the most diverse group of vertebrates worldwide. The challenges of unique physiologies, a foreign environment, and many unknowns attract a passionate group of biologists and veterinarians. Economically, fishes have become vital as food, bait, and companion animals. Fishermen and fish handlers (processing plants) represent the historical human population exposed to fish zoonoses, but growth in aquaculture and aquarium hobbyists have led to an increase in published fish-borne zoonotic cases starting in the late 1950s that bloomed in the 1980s. Human physicians, particularly dermatologists and infectious disease specialists, are now more aware of fish-borne zoonoses, but they can be assisted with diagnosis when informed patients give more detailed histories with fish/water exposure.

  7. A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Blair, Matthew W; Cortés, Andrés J; Penmetsa, R Varma; Farmer, Andrew; Carrasquilla-Garcia, Noelia; Cook, Doug R

    2013-02-01

    Single nucleotide polymorphism (SNP) detection has become a marker system of choice, because of the high abundance of source polymorphisms and the ease with which allele calls are automated. Various technologies exist for the evaluation of SNP loci and previously we validated two medium throughput technologies. In this study, our goal was to utilize a 768 feature, Illumina GoldenGate assay for common bean (Phaseolus vulgaris L.) developed from conserved legume gene sequences and to use the new technology for (1) the evaluation of parental polymorphisms in a mini-core set of common bean accessions and (2) the analysis of genetic diversity in the crop. A total of 736 SNPs were scored on 236 diverse common bean genotypes with the GoldenGate array. Missing data and heterozygosity levels were low and 94 % of the SNPs were scorable. With the evaluation of the parental polymorphism genotypes, we estimated the utility of the SNP markers in mapping for inter-genepool and intra-genepool populations, the latter being of lower polymorphism than the former. When we performed the diversity analysis with the diverse genotypes, we found Illumina GoldenGate SNPs to provide equivalent evaluations as previous gene-based SNP markers, but less fine-distinctions than with previous microsatellite marker analysis. We did find, however, that the gene-based SNPs in the GoldenGate array had some utility in race structure analysis despite the low polymorphism. Furthermore the SNPs detected high heterozygosity in wild accessions which was probably a reflection of ascertainment bias. The Illumina SNPs were shown to be effective in distinguishing between the genepools, and therefore were most useful in saturation of inter-genepool genetic maps. The implications of these results for breeding in common bean are discussed as well as the advantages and disadvantages of the GoldenGate system for SNP detection.

  8. Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity

    Directory of Open Access Journals (Sweden)

    Carla Sousa-Santos

    2016-02-01

    Full Text Available Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern. Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences. Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins. Discussion. Targeting multiple co-distributed species of primary

  9. Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity.

    Science.gov (United States)

    Sousa-Santos, Carla; Robalo, Joana I; Pereira, Ana M; Branco, Paulo; Santos, José Maria; Ferreira, Maria Teresa; Sousa, Mónica; Doadrio, Ignacio

    2016-01-01

    Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern. Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins) in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences. Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary) seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins. Discussion. Targeting multiple co-distributed species of primary freshwater fish allowed

  10. Long-term monitoring dataset of fish assemblages impinged at nuclear power plants in northern Taiwan.

    Science.gov (United States)

    Chen, Hungyen; Liao, Yun-Chih; Chen, Ching-Yi; Tsai, Jeng-I; Chen, Lee-Sea; Shao, Kwang-Tsao

    2015-12-08

    The long-term species diversity patterns in marine fish communities are garnering increasing attention from ecologists and conservation biologists. However, current databases on quantitative abundance information lack consistent long-term time series, which are particularly important in exploring the possible underlying mechanism of community changes and evaluating the effectiveness of biodiversity conservation measures. Here we describe an impinged fish assemblage dataset containing 1, 283, 707 individuals from 439 taxa. Once a month over 19 years (1987-1990 and 2000-2014), we systematically collected the fish killed by impingement upon cooling water intake screens at two nuclear power plants on the northern coast of Taiwan. Because impingement surveys have low sampling errors and can be carried out over many years, they serve as an ideal sampling tool for monitoring how fish diversity and community structure vary over an extended period of time.

  11. Fishing effects in northeast Atlantic shelf seas : patterns in fishing effort, diversity and community structure. III. International trawling effort in the North Sea : an analysis of spatial and temporal trends

    DEFF Research Database (Denmark)

    Jennings, S.; Alsväg, J.; Cotter, A.J.R.;

    1999-01-01

    of beam trawling effort increases from north to south. Plots of annual fishing effort by ICES statistical rectangle (211 boxes of 0.5 degrees latitude x 1 degrees longitude) indicate that the majority of fishing effort in the North Sea are concentrated in a very few rectangles. Thus mean annual total...

  12. A direct pre-screen for marine bacteria producing compounds inhibiting quorum sensing reveals diverse planktonic bacteria that are bioactive.

    Science.gov (United States)

    Linthorne, Jamie S; Chang, Barbara J; Flematti, Gavin R; Ghisalberti, Emilio L; Sutton, David C

    2015-02-01

    A promising new strategy in antibacterial research is inhibition of the bacterial communication system termed quorum sensing. In this study, a novel and rapid pre-screening method was developed to detect the production of chemical inhibitors of this system (quorum-quenching compounds) by bacteria isolated from marine and estuarine waters. This method involves direct screening of mixed populations on an agar plate, facilitating specific isolation of bioactive colonies. The assay showed that between 4 and 46 % of culturable bacteria from various samples were bioactive, and of the 95 selectively isolated bacteria, 93.7 % inhibited Vibrio harveyi bioluminescence without inhibiting growth, indicating potential production of quorum-quenching compounds. Of the active isolates, 21 % showed further activity against quorum-sensing-regulated pigment production by Serratia marcescens. The majority of bioactive isolates were identified by 16S ribosomal DNA (rDNA) amplification and sequencing as belonging to the genera Vibrio and Pseudoalteromonas. Extracts of two strongly bioactive Pseudoalteromonas isolates (K1 and B2) were quantitatively assessed for inhibition of growth and quorum-sensing-regulated processes in V. harveyi, S. marcescens and Chromobacterium violaceum. Extracts of the isolates reduced V. harveyi bioluminescence by as much as 98 % and C. violaceum pigment production by 36 % at concentrations which had no adverse effect on growth. The activity found in the extracts indicated that the isolates may produce quorum-quenching compounds. This study further supports the suggestion that quorum quenching may be a common attribute among culturable planktonic marine and estuarine bacteria.

  13. The taxonomic diversity of fish community in the coastal waters of Xiamen%厦门海域鱼类群落分类学多样性的研究

    Institute of Scientific and Technical Information of China (English)

    黄良敏; 谢仰杰; 李军; 张雅芝; 王家樵

    2013-01-01

    根据厦门海域鱼类种类组成历史资料和调查资料,系统整理了厦门海域的鱼类总名录和现有名录,并应用分类学等级多样性指数和分类差异变异指数分析了厦门海域鱼类群落分类学多样性的时空变化.结果表明:厦门海域有记录鱼类共649种;现有鱼类有331种,隶属2纲22目90科181属,其中软骨鱼纲共5目9科9属15种,辐鳍鱼纲共17目81科172属316种.厦门海域鱼类总名录的等级多样性指数△+和分类差异变异指数(A)+分别为79.267和220.96;现有鱼类群落分类多样性指数△+和分类差异指数(A)+分别为77.504和245.34.分类多样性指数△+在冬、春季较高,秋季次之,而夏季最低;而分类差异指数(A)+夏季较高,秋季次之,冬春季较低.秋季和冬季鱼类组成的相似度最高,其次为夏季,最后为春季.与历史总名录相比,厦门海域的现有鱼类群落分类学范围较小,生态幅变窄,群落稳定性较差.%Based on literature and survey data of fish composition collected by bottom trawl investigation from 2006 to 2007 in Xiamen coastal waters, the fish fauna was set up, fish community and the taxonomic diversity and distinctness by using taxonomic diversity △+ and taxonomic distinctness △+ were analyzed. The results show that: there were 649 species of fishes recorded in Xiamen coastal waters. 331 species of fishes were available at present, belonging to 2 classes, 22 orders, 90 families and 181 genera, as for the Chondrichthyes fishes were composed of 5 orders, 9 families, 9 genera and 15 species, while the Actinopterygii fishes were composed of 17 orders, 81 families, 172 genera and 316 species. The taxonomic diversity △+ and taxonomic distinctness △+ of the fish community master list in Xiamen coastal waters were 79. 267 and 220. 96, 77. 504 and 245. 34 at present, respectively. The taxonomic diversity △+ in winter and spring was higher than summer and autumn, and it was lowest in summer

  14. Mycobacterium avium restriction fragment lenght polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains

    Directory of Open Access Journals (Sweden)

    Patrícia Carvalho de Sequeira

    2005-11-01

    Full Text Available Simple double repetitive element polymerase chain reaction (MaDRE-PCR and Pvu II-IS1245 restriction fragment length polymorphism (RFLP typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 Aids inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

  15. Breast Density Awareness and Knowledge, and Intentions for Breast Cancer Screening in a Diverse Sample of Women Age Eligible for Mammography.

    Science.gov (United States)

    Santiago-Rivas, Marimer; Benjamin, Shayna; Andrews, Janna Z; Jandorf, Lina

    2017-08-14

    The objectives of this study were to assess breast density knowledge and breast density awareness, and to identify information associated with intention to complete routine and supplemental screening for breast cancer in a diverse sample of women age eligible for mammography. We quantitatively (self-report) assessed breast density awareness and knowledge (N = 264) in black (47.7%), Latina (35.2%), and white (17%) women recruited online and in the community. Most participants reported having heard about breast density (69.2%); less than one third knew their own breast density status (30.4%). Knowing their own breast density, believing that women should be notified of their breast density in their mammogram report, and feeling informed if being provided this information are associated with likelihood of completing mammogram. Intending mammogram completion and knowledge regarding the impact of breast density on mammogram accuracy are associated with likelihood of completing supplemental ultrasound tests of the breast. These findings help inform practitioners and policy makers about information and communication factors that influence breast cancer screening concerns and decisions. Knowing this information should prepare practitioners to better identify women who may have not been exposed to breast density messages.

  16. Fish production and diversity in the Paleocene-Eocene Thermal Maximum—Increased production but no novel faunas during a "Future Earth" analog

    Science.gov (United States)

    Tomczik, D. W.; Norris, R. D.; Gaskell, D. E.

    2014-12-01

    A partial analog for future global change is the Paleocene-Eocene Thermal Maximum—a transient episode of warming, acidification, and biogeographic change at ~55.5 Ma. The PETM is known to have triggered extinction in some deep sea biotas, extensive biogeographic range shifts, and the common occurrence of 'excursion biotas'—non-analog occurrences of species that are typically rare in the open ocean before or after the PETM. Here we report on the impact of the PETM on fish production and biodiversity. Our data include the mass accumulation rate of fish teeth and denticles as well as an analysis of tooth morphotypes for three PETM sites: ODP 1220 and 1209 in the Pacific, and ODP 1260 in the equatorial Atlantic. Tooth morphotypes hardly change through the PETM and consist of abundant midwater species (angler fish and flashlight fish) in addition to sharks and epipelagic fish. There is no evidence for a non-analog 'excursion biota' during the PETM, suggesting that fish experienced fewer geographic range shifts than the calcareous and organic-walled plankton where excursion biotas are commonplace. Fish mass accumulation rates are also relatively stable before and after the PETM although all sites show a transient rise in fish production at the onset of the PETM or within the later part of the "PETM Core". These results broadly match published estimates of PETM export production from biogenic barium fluxes. Our findings run counter to "Future Earth" models that use climate forecasts for the next century to predict the impact of global change on fish stocks. These models suggest that future warming and ocean stratification will decrease most tropical and subtropical ocean fish production, accentuate fish production in the boundary currents and generally shift production toward higher latitudes. A resolution of "Future Earth" models and PETM data may reflect the different timescales of observation and stages of ecological response to severe global change.

  17. Fish Allergy

    Science.gov (United States)

    ... Old Feeding Your 1- to 2-Year-Old Fish Allergy KidsHealth > For Parents > Fish Allergy Print A ... From Home en español Alergia al pescado About Fish Allergy A fish allergy is not exactly the ...

  18. Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens.

    Directory of Open Access Journals (Sweden)

    Laura Audrey Hug

    2013-11-01

    Full Text Available Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed for bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated in the global halogen cycle. Reductive dehalogenase sequence diversity is informative for the dechlorination potential of the site or enrichment culture. A suite of degenerate PCR primers targeting a comprehensive curated set of reductive dehalogenase genes was designed and applied to twelve DNA samples extracted from contaminated and pristine sites, as well as six enrichment cultures capable of reducing chlorinated compounds to non-toxic end-products. The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and the reductive dehalogenase complement of each sample determined. The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted for: one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% of the sequenced reductive dehalogenase genes were broadly distributed, being identified in four or more samples, and often in previously sequenced genomes as well. In contrast, 17% of the sequenced reductive dehalogenases were unique, present in only a single sample and bearing less than 90% pairwise amino acid identity to any previously identified proteins. Many of the broadly distributed reductive dehalogenases are uncharacterized in terms of their substrate specificity, making these intriguing targets for further biochemical experimentation. Finally, comparison of samples from a contaminated site and an enrichment culture derived from the same site eight years prior allowed examination of the effect of the enrichment process.

  19. Identification of common genetic modifiers of neurodegenerative diseases from an integrative analysis of diverse genetic screens in model organisms

    Directory of Open Access Journals (Sweden)

    Chen Xi

    2012-02-01

    Full Text Available Abstract Background An array of experimental models have been developed in the small model organisms C. elegans, S. cerevisiae and D. melanogaster for the study of various neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and expanded polyglutamine diseases as exemplified by Huntington's disease (HD and related ataxias. Genetic approaches to determine the nature of regulators of the disease phenotypes have ranged from small scale to essentially whole genome screens. The published data covers distinct models in all three organisms and one important question is the extent to which shared genetic factors can be uncovered that affect several or all disease models. Surprisingly it has appeared that there may be relatively little overlap and that many of the regulators may be organism or disease-specific. There is, however, a need for a fully integrated analysis of the available genetic data based on careful comparison of orthologues across the species to determine the real extent of overlap. Results We carried out an integrated analysis using C. elegans as the baseline model organism since this is the most widely studied in this context. Combination of data from 28 published studies using small to large scale screens in all three small model organisms gave a total of 950 identifications of genetic regulators. Of these 624 were separate genes with orthologues in C. elegans. In addition, 34 of these genes, which all had human orthologues, were found to overlap across studies. Of the common genetic regulators some such as chaperones, ubiquitin-related enzymes (including the E3 ligase CHIP which directly links the two pathways and histone deacetylases were involved in expected pathways whereas others such as the peroxisomal acyl CoA-oxidase suggest novel targets for neurodegenerative disease therapy Conclusions We identified a significant number of overlapping regulators of neurodegenerative disease models. Since the diseases

  20. Diversity of Pharmacological Properties in Chinese and European Medicinal Plants: Cytotoxicity, Antiviral and Antitrypanosomal Screening of 82 Herbal Drugs

    Directory of Open Access Journals (Sweden)

    Thomas Efferth

    2011-09-01

    Full Text Available In an extensive screening, the antiviral, antitrypanosomal and anticancer properties of extracts from 82 plants used in traditional Chinese medicine and European phytomedicine were determined. Several promising plants that were highly effective against hepatitis B virus (HBV, bovine viral diarrhoea virus (BVDV—a flavivirus used here as a surrogate in vitro model of hepatitis C virus, trypanosomes (Trypanosoma brucei brucei and several cancer cell lines were identified. Six aqueous extracts from Celosia cristata, Ophioglossum vulgatum, Houttuynia cordata, Selaginella tamariscina, Alpinia galanga and Alpinia oxyphylla showed significant antiviral effects against BVDV without toxic effects on host embryonic bovine trachea (EBTr cells, while Evodia lepta, Hedyotis diffusa and Glycyrrhiza spp. demonstrated promising activities against the HBV without toxic effects on host human hepatoblastoma cells transfected with HBV-DNA (HepG2 2.2.15 cells. Seven organic extracts from Alpinia oxyphylla, Coptis chinensis, Kadsura longipedunculata, Arctium lappa, Panax ginseng, Panax notoginseng and Saposhnikovia divaricata inhibited T. b. brucei. Moreover, among fifteen water extracts that combined high antiproliferative activity (IC50 0.5–20 µg/mL and low acute in vitro toxicity (0–10% reduction in cell viability at IC50, Coptis chinensis presented the best beneficial characteristics. In conclusion, traditional herbal medicine from Europe and China still has a potential for new therapeutic targets and therapeutic applications.

  1. A methodological approach to screen diverse cheese-related bacteria for their ability to produce aroma compounds.

    Science.gov (United States)

    Pogačić, Tomislav; Maillard, Marie-Bernadette; Leclerc, Aurélie; Hervé, Christophe; Chuat, Victoria; Yee, Alyson L; Valence, Florence; Thierry, Anne

    2015-04-01

    Microorganisms play an important role in the development of cheese flavor. The aim of this study was to develop an approach to facilitate screening of various cheese-related bacteria for their ability to produce aroma compounds. We combined i) curd-based slurry medium incubated under conditions mimicking cheese manufacturing and ripening, ii) powerful method of extraction of volatiles, headspace trap, coupled to gas chromatography-mass spectrometry (HS-trap-GC-MS), and iii) metabolomics-based method of data processing using the XCMS package of R software and multivariate analysis. This approach was applied to eleven species: five lactic acid bacteria (Leuconostoc lactis, Lactobacillus sakei, Lactobacillus paracasei, Lactobacillus fermentum, and Lactobacillus helveticus), four actinobacteria (Brachybacterium articum, Brachybacterium tyrofermentans, Brevibacterium aurantiacum, and Microbacterium gubbeenense), Propionibacterium freudenreichii, and Hafnia alvei. All the strains grew, with maximal populations ranging from 7.4 to 9.2 log (CFU/mL). In total, 52 volatile aroma compounds were identified, of which 49 varied significantly in abundance between bacteria. Principal component analysis of volatile profiles differentiated species by their ability to produce ethyl esters (associated with Brachybacteria), sulfur compounds and branched-chain alcohols (H. alvei), branched-chain acids (H. alvei, P. freudenreichii and L. paracasei), diacetyl and related carbonyl compounds (M. gubbeenense and L. paracasei), among others.

  2. 硬骨鱼类免疫球蛋白分类及多样性产生机制研究进展%Research Advances in Immunoglobulin Classification and Diversity Mechanism in Fish

    Institute of Scientific and Technical Information of China (English)

    宿斌; 王荻; 刘红柏

    2013-01-01

    The immunoglobulin is first found in fish in vivo, and becomes the important candidates for understanding of the origin, and evolution of the immunoglobulin. The immunoglobulins IgM and IgD arefirst discovered in fish, and as technology and research advances, IgZ, IgT, and Ig M-Z have been found in the zebra fish (Danio rerio), rainbow trout (Oncorhynchus mykiss) and common carp (Cyprinus carpio). Like marnmalian immunoglobulin, the fish immunoglobulins are varied interspecies, and intraspeoies in biolpgical functions such as morphology and structure, genetic type. In order to further understanding of immuneoglobiilins in fishes and their immune response mechanism, this article is intended to review class-ification, mechanism and diversity of immune globulin in fish.%鱼类是最先出现免疫球蛋白的低等脊椎动物,对研究免疫球蛋白的起源、进化具有重要的意义.IgM和IgD是最先被人类发现和认识的鱼类免疫球蛋白,随着科技进步和研究深入,陆续在斑马鱼(Danio rerio)、虹鳟(Oncorhynchus mykiss)及鲤鱼(Cyprinus carpio)中发现了IgZ、IgT、IgM-Z等.与哺乳动物的免疫球蛋白一样,不同种鱼,甚至同种鱼不同个体间,免疫球蛋白的形态结构、基因类型、生物学功能等均有差异.为了进一步认识鱼类免疫球蛋白及其免疫应答的机制,本文综述了鱼类免疫球蛋白的分类和多样性机制等.

  3. Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.

    Science.gov (United States)

    López-López, Olalla; Knapik, Kamila; Cerdán, Maria-Esperanza; González-Siso, María-Isabel

    2015-01-01

    A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species "Candidatus Caldiarchaeum subterraneum." Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8.

  4. Metagenomics of an alkaline hot spring in Galicia (Spain: microbial diversity analysis and screening for novel lipolytic enzymes

    Directory of Open Access Journals (Sweden)

    Olalla eLópez-López

    2015-11-01

    Full Text Available A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH=8.2 located in Ourense (Spain. Metagenomic sequencing of the fosmid library allowed the assembly of 9,722 contigs ranging in size from 500 to 56,677 bp and spanning approximately 18 Mbp. 23,207 ORFs (Open Reading Frames were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The 6 most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species Candidatus Caldiarchaeum subterraneum. Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases and lipases, was also revealed in the metagenomic library.Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 minutes at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5-8.

  5. Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes

    Science.gov (United States)

    López-López, Olalla; Knapik, Kamila; Cerdán, Maria-Esperanza; González-Siso, María-Isabel

    2015-01-01

    A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species “Candidatus Caldiarchaeum subterraneum.” Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8. PMID:26635759

  6. Las Vegas Wash Monitoring and Characterization Study: Ecotoxicologic Screening Assessment of Selected Contaminants of Potential Concern in Sediment, Whole Fish, Bird Eggs, and Water, 2005-2006

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Las Vegas Wash is the sole drainage from the Las Vegas Valley watershed to Lake Mead. The four flow components in the Las Vegas Wash are tertiary treated...

  7. Las Vegas Wash Monitoring and Characterization Study: Ecotoxicologic Screening Assessment of Selected Contaminants of Potential Concern in Sediment, Whole Fish, Bird Eggs, and Water, 2007-2008

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Since 1998, the Las Vegas Wash Coordination Committee has implemented long-term management strategies for the Las Vegas Wash (Wash). A series of projects was...

  8. Diversidad morfológica del sistema de conductos excretores de los peces teleósteos Morphological diversity of the excretory duct system of teleostean fishes

    Directory of Open Access Journals (Sweden)

    Abraham Kobelkowsky

    2007-06-01

    Full Text Available Mediante el análisis anatómico de 70 especies de teleósteos, pertenecientes a 62 géneros, 39 familias y 20 órdenes, se reconoce la diversidad morfológica de los conductos excretores y de la vejiga urinaria. Se define como un patrón morfológico general de los teleósteos la fusión de ambos conductos arquinéfricos en el conducto urinario común y, en los machos, la unión del conducto urinario común con el conducto espermático común, formándose el conducto urogenital. Se reconoce una relación inversa de la longitud de los conductos arquinéfricos y la longitud de los riñones. Se describe la diversidad de situaciones morfológicas del trayecto y fusiones de los conductos excretores. Se reconoce la diversidad de formas de vejiga urinaria. Resalta la “inversión” de la posición de los conductos urinarios y urogenitales en los Pleuronectiformes. Se sugiere el origen de la vejiga urinaria a partir del conducto urinario común. Se manifiesta en algunas especies el dimorfismo sexual en la forma de las papilas urinaria y urogenital.By means of an anatomical analysis from 70 species of teleostean fishes, belonging to 62 genera, and 39 families, and 20 orders, the morphological diversity of the urinary Duch system is described. A general morphological teleostean pattern is defined as the fusion of both archinephric ducts in the common urinay duct, and the fusion in malesof the common urinary duct with the common spermatic duct in the urogenital duct. A relation between the length of thekidney and of the archinephric ducts is recongnized. The trajectory of the urinary ducts is described, with the “reversal”of the orientation of the urinary and urogenital ducts in Pleuronectiformes being noteworthy. The origin of the urinary bladder from the common urinary duct is suggested.

  9. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

    Directory of Open Access Journals (Sweden)

    Hong Jin

    Full Text Available The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ~50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

  10. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

    Science.gov (United States)

    Jin, Hong; Stojnic, Robert; Adryan, Boris; Ozdemir, Anil; Stathopoulos, Angelike; Frasch, Manfred

    2013-01-01

    The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP) from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ~50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

  11. Aquatic macroinvertebrate sampling at Fish Spring National Wildlife Refuge : Diverse needs for migratory, wintering and breeding waterfowl, wading birds, shorebirds and other priority species

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This preliminary proposal is targeted to better understanding of how prescribed water management, including depth and duration, influence water quality, food...

  12. Variation in fish community structure, richness, and diversity in 56 Danish lakes with contrasting depth, size, and trophic state: does the method matter?

    DEFF Research Database (Denmark)

    Menezes, Rosemberg; Borchsenius, Finn; Svenning, J.-C.

    2013-01-01

    The distribution of freshwater fish is influenced by food availability, habitat heterogeneity, competition, predation, trophic state, and presence/absence of macrophytes. This poses a challenge to monitoring, and researchers have been struggling to develop accurate sampling methods for obtaining...... community, as all methods miss some important species that other methods capture. However, electrofishing seems to be a fast alternative to gillnets for monitoring fish species richness and composition in littoral habitats of Danish lakes....

  13. The hypothalamic-pituitary-thyroid (HPT) axis in fish and its role in fish development and reproduction.

    Science.gov (United States)

    Blanton, Michael L; Specker, Jennifer L

    2007-01-01

    Bony fishes represent the largest vertebrate class and are a very diverse animal group. This chapter provides a thorough review of the available scientific literature on the thyroid system in these important vertebrate animals. The molecular components of the hypothalamic-pituitary-thyroid (HPT) axis in this group correspond closely to those of mammals. The thyroid tissue in the fishes is organized as diffuse follicles, with a few exceptions, rather than as an encapsulated gland as is found in most other vertebrate species. The features of this diffuse tissue in fishes are reviewed with an emphasis on feedback relationships within the HPT axis, the molecular biology of the thyroid system in fishes, and comparisons versus the thyroid systems of other vertebrate taxa. A review of the role of thyroid hormone in fish development and reproduction is included. Available information about the HPT axis in fishes is quite detailed for some species and rather limited or absent in others. This review focuses on species that have been intensively studied for their value as laboratory models in assays to investigate disruption in normal function of the thyroid system. In addition, in vitro and in vivo assay methods for screening chemicals for their potential to interfere with the thyroid system are reviewed. It is concluded that there are currently no in vitro or in vivo assays in fish species that are sufficiently developed to warrant recommendation for use to efficiently screen chemicals for thyroid disruption. Methods are available that can be used to measure thyroid hormones, although our ability to interpret the causes and implications of potential alterations in T4 or T3 levels in fishes is nonetheless limited without further research.

  14. Species richness and diversity of the parasites of two predatory fish species - perch (Perca fluviatilis Linnaeus, 1758) and zander (Sander lucioperca Linnaeus, 1758) from the Pomeranian Bay.

    Science.gov (United States)

    Bielat, Iwona; Legierko, Monika; Sobecka, Ewa

    2015-01-01

    Pomeranian Bay as an ecotone is a transition zone between two different biocenoses, which is characterized by an increase in biodiversity and species density. Therefore, Pomeranian Bay is a destination of finding and reproductive migrations of fish from the rivers entered the area. The aim of the study was to compare parasitic fauna of two predatory fish species from the Pomeranian Bay, collected from the same fishing grounds at the same period. A total of 126 fish studied (53 perches and 73 zanders) were collected in the summer 2013. Parasitological examinations included: skin, fins, gills, vitreous humour and lens of the eye, mouth cavity, body cavity and internal organs. Apart from the prevalence and intensity of infection (mean, range) the parasite communities of both fish species were compared. European perch and zander were infected with parasites from five different taxonomic units. The most numerous parasites were Diplostomum spp. in European perch and Bucephalus polymorphus in zander. The prevalence of infection of European perch ranged from 5.7% (Diphyllobothrium latum) to 22.3% (Diplostomum spp.) and for zander from 1.4% (Ancyrocephalus paradoxus, Hysterothylacium aduncum) to 12.3% (Bucephalus polymorphus). Different composition of the parasitic fauna is likely due to the different biology of both fish species.

  15. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Directory of Open Access Journals (Sweden)

    Borja Milá

    Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

  16. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Science.gov (United States)

    Milá, Borja; Tavares, Erika S; Muñoz Saldaña, Alberto; Karubian, Jordan; Smith, Thomas B; Baker, Allan J

    2012-01-01

    The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys

  17. Deep Fish.

    Science.gov (United States)

    Ishaq, Omer; Sadanandan, Sajith Kecheril; Wählby, Carolina

    2017-01-01

    Zebrafish ( Danio rerio) is an important vertebrate model organism in biomedical research, especially suitable for morphological screening due to its transparent body during early development. Deep learning has emerged as a dominant paradigm for data analysis and found a number of applications in computer vision and image analysis. Here we demonstrate the potential of a deep learning approach for accurate high-throughput classification of whole-body zebrafish deformations in multifish microwell plates. Deep learning uses the raw image data as an input, without the need of expert knowledge for feature design or optimization of the segmentation parameters. We trained the deep learning classifier on as few as 84 images (before data augmentation) and achieved a classification accuracy of 92.8% on an unseen test data set that is comparable to the previous state of the art (95%) based on user-specified segmentation and deformation metrics. Ablation studies by digitally removing whole fish or parts of the fish from the images revealed that the classifier learned discriminative features from the image foreground, and we observed that the deformations of the head region, rather than the visually apparent bent tail, were more important for good classification performance.

  18. Virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors.

    Science.gov (United States)

    Li, Chenglong; Xu, Lan; Wolan, Dennis W; Wilson, Ian A; Olson, Arthur J

    2004-12-30

    AICAR transformylase (5-aminoimidazole-4-carboxamide ribonucleotide transformylase) is a folate-dependent activity of the bifunctional protein ATIC (AICAR transformylase and IMP cyclohydrolase) and is responsible for catalyzing the penultimate step of the de novo purine biosynthetic pathway. As such, AICAR transformylase has been proposed as a potential target for antineoplastic drug design. Virtual screening of the human AICAR transformylase active site by use of AutoDock against the NCI diversity set, a library of compounds with nonredundant pharmacophore profiles, has revealed 44 potential inhibitor candidates. In vitro inhibition assay of 16 soluble compounds from this list revealed that eight compounds with novel scaffolds, relative to the general folate template, had micromolar inhibition. Subsequent extension of docking trials on compounds with similar scaffolds from the entire NCI-3D database has unveiled 11 additional inhibitors that were confirmed by the in vitro inhibition assay. In particular, one compound, NSC30171, had nanomolar inhibition (K(i) = 154 nM, IC(50) = 600 nM) against AICAR transformylase. These 19 inhibitors serve as novel templates/scaffolds for development of more potent and specific non-folate-based AICAR transformylase inhibitors.

  19. Application of endocrine disruptor screening program fish short-term reproduction assay: Reproduction and endocrine function in fathead minnow (Pimephales promelas) and killifish (Fundulus heteroclitus) exposed to Bermuda pond sediment.

    Science.gov (United States)

    Fort, Douglas J; Mathis, Michael; Fort, Chelsea E; Fort, Hayley M; Bacon, Jamie P

    2015-06-01

    A modified tier 1 Endocrine Disruptor Screening Program (EDSP) 21-d fish short-term reproduction assay (FSTRA) was used to evaluate the effects of sediment exposure from freshwater and brackish ponds in Bermuda on reproductive fecundity and endocrine function in fathead minnow (Pimephales promelas) and killifish (Fundulus heteroclitus). Reproductively active male and female fish were exposed to control sediment and sediment from 2 freshwater ponds (fathead minnow) and 2 marine ponds (killifish) contaminated with polyaromatic hydrocarbons and metals via flow-through exposure for 21 d. Reproductive fecundity was monitored daily. At termination, the status of the reproductive endocrine system was assessed by the gonadosomatic index, gonadal histology, plasma steroids (estrogen [E2], testosterone [T], and 11-ketotestosterone [11-KT]), steroidogenic enzymes (aromatase and combined 3β/17β -hydroxysteroid dehydrogenase [3β/17β-HSD]), and plasma vitellogenin (VTG). Decreased reproductive fecundity, lower male body weight, and altered endocrinological measures of reproductive status were observed in both species. Higher plasma T levels in female minnows and 11-KT levels in both male and female minnows and female killifish exposed to freshwater and brackish sediments, respectively. Decreased female E2 and VTG levels and gonadal cytochrome P19 (aromatase) activity were also found in sediment exposed females from both species. No effect on female 3β/17β-HSD activity was found in either species. The FSTRA provided a robust model capable of modification to evaluate reproductive effects of sediment exposure in fish.

  20. In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important

    DEFF Research Database (Denmark)

    Schyth, Brian Dall; Bramsen, Jesper Bertram; Pakula, Malgorzata Maria;

    2012-01-01

    but often only examining the expression of specific immunologically relevant genes in selected cell populations typically blood cells from treated animals or humans. Assays using a relevant physiological state in biological models as read-out are not common. Here we use a fish model where the innate......, increase the antiviral effect of siRNAs. The applied fish model represents a potent tool for conducting fast but statistically and scientifically relevant evaluations of chemically optimized siRNAs with respect to non-specific antiviral effects in vivo....

  1. Analysis on screen results of cervical cancer for 2 739 women in fishing village and countryside%渔农村妇女2739人宫颈癌筛选结果的分析

    Institute of Scientific and Technical Information of China (English)

    周悠燕

    2011-01-01

    Objective To analysis the screen results of cervical cancer and improve prevention for women with cervical cancer in fishing village and countryside. Method Analyze the information on cervical cancer for 2739 women in fishing village and countryside. Analyze the relation between age, marriage, education level, medical insurance, economic conditions and positive screen result of cervical cancer. Result 51 of 2739 women show positive results. Women with older age, lower education level and poorer economic conditions tend to have a higher rate of positive result. Conclusion Enhancing health education for women with cervical cancer in fishing village and countryside can improve the early detection, early diagnosis and early treatment of cervical cancer.%目的 分析渔农村妇女宫颈癌筛选的结果,提出对策.方法 对渔农村妇女 2 739 人的宫颈癌筛选资料进行分析,了解渔农村妇女年龄、婚姻状况、文化程度、医疗保险及经济状况与宫颈癌筛选阳性之间关系.结果 2 739 人中,宫颈癌筛选阳性检出 51 人,年龄越大阳性检出率越高,文化程度越低、经济状况越差阳性检出率越高.结论 加强渔农村妇女保健及健康教育工作,促使宫颈癌早发现、早诊断、早治疗.

  2. Fish Hearing.

    Science.gov (United States)

    Blaxter, J. H. S.

    1980-01-01

    Provides related information about hearing in fish, including the sensory stimulus of sound in the underwater environment, mechanoreceptors in fish, pressure perception and the swimbladder, specializations in sound conduction peculiar to certain fish families. Includes numerous figures. (CS)

  3. Fish Allergy

    Science.gov (United States)

    ... in a clear and consistent manner, so that consumers with food allergies and their caregivers can be informed as ... the menu, cross-contact with fish is possible. Ethnic ... fish. Avoid foods like fish sticks and anchovies. Some individuals with ...

  4. Hood River Production Program : Hood River Fish Habitat Protection, Restoration, and Monitoring Plan.

    Energy Technology Data Exchange (ETDEWEB)

    Coccoli, Holly; Lambert, Michael

    2000-02-01

    Effective habitat protection and rehabilitation are essential to the long-term recovery of anadromous fish populations in the Hood River subbasin. This Habitat Protection, Restoration, and Monitoring Plan was prepared to advance the goals of the Hood River Production Program (HRRP) which include restoring self-sustaining runs of spring chinook salmon and winter and summer steelhead. The HRPP is a fish supplementation and monitoring and evaluation program initiated in 1991 and funded by the Bonneville Power Administration (BPA) as part of the Northwest Power Planning Council Fish and Wildlife Program. The HRPP is a joint effort of the Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO) and Oregon Department of Fish and Wildlife (ODFW). Using recent watershed assessment and federal watershed analysis reports, this Plan reviews the historic and current condition of riparian, instream and upland habitats; natural watershed processes; anadromous and resident fish populations; identifies limiting factors, and indicates those subbasin areas that need protection or are likely to respond to restoration. Primary habitat restoration needs were identified as (1) improved fish screening and upstream adult passage at water diversions; (2) improved spawning gravel availability, instream habitat structure and diversity; and (3) improved water quality and riparian conditions. While several early action projects have been initiated in the Hood River subbasin since the mid 1990s, this Plan outlines additional projects and strategies needed to protect existing high quality habitat, correct known fish survival problems, and improve the habitat capacity for natural production to meet HRPP goals.

  5. cDNA expression library screening and identification of two novel antigens, ubiquitin and receptor for activated C kinase (RACK) homologue, of the fish parasite Trypanosoma carassii

    NARCIS (Netherlands)

    Ruszczyk, A.; Joerink, M.; Guldenaar, C.; Hermsen, G.J.; Savelkoul, H.F.J.; Wiegertjes, G.F.

    2008-01-01

    Trypanosoma carassii is a kinetoplastid parasite infecting cyprinid fish with a high prevalence in nature. Antibodies have been shown to play a protective role in the immune response against this parasite in common carp, Cyprinus carpio. To identify immunogenic and putative protective T. carassii an

  6. Coccidian parasites of fish encompass profound phylogenetic diversity and gave rise to each of the major parasitic groups in terrestrial vertebrates

    Science.gov (United States)

    Coccidian paraasites are ubiquitous single-celled protists that cause enteric disease in all manner of vertebrate hosts. These include infections of wildlife, livestock, and people, resulting in a variety of disease outcomes. The diversity and relationships among these diverse parasites is best kn...

  7. Sequence and Expression Analysis of Interferon Regulatory Factor 10 (IRF10 in Three Diverse Teleost Fish Reveals Its Role in Antiviral Defense.

    Directory of Open Access Journals (Sweden)

    Qiaoqing Xu

    Full Text Available Interferon regulatory factor (IRF 10 was first found in birds and is present in the genome of other tetrapods (but not humans and mice, as well as in teleost fish. The functional role of IRF10 in vertebrate immunity is relatively unknown compared to IRF1-9. The target of this research was to clone and characterize the IRF10 genes in three economically important fish species that will facilitate future evaluation of this molecule in fish innate and adaptive immunity.In the present study, a single IRF10 gene was cloned in grass carp Ctenopharyngodon idella and Asian swamp eel Monopterus albus, and two, named IRF10a and IRF10b, in rainbow trout Oncorhynchus mykiss. The fish IRF10 molecules share highest identities to other vertebrate IRF10s, and have a well conserved DNA binding domain, IRF-associated domain, and an 8 exon/7 intron structure with conserved intron phase. The presence of an upstream ATG or open reading frame (ORF in the 5'-untranslated region of different fish IRF10 cDNA sequences suggests potential regulation at the translational level, and this has been verified by in vitro transcription/translation experiments of the trout IRF10a cDNA, but would still need to be validated in fish cells.Both trout IRF10 paralogues are highly expressed in thymus, blood and spleen but are relatively low in head kidney and caudal kidney. Trout IRF10b expression is significantly higher than IRF10a in integumentary tissues i.e. gills, scales, skin, intestine, adipose fin and tail fins, suggesting that IRF10b may be more important in mucosal immunity. The expression of both trout IRF10 paralogues is up-regulated by recombinant IFN-γ. The expression of the IRF10 genes is highly induced by Poly I:C in vitro and in vivo, and by viral infection, but is less responsive to peptidoglycan and bacterial infection, suggesting an important role of fish IRF10 in antiviral defense.

  8. A small-fish model for behavioral-toxicological screening of new antimalarial drugs: a comparison between erythro- and threo-mefloquine

    OpenAIRE

    Maaswinkel, Hans; Zhu, Liqun; Weng, Wei

    2015-01-01

    Background New antimalarial drugs need to be developed because over time resistance against the existing drugs develops. Furthermore, some of the drugs have severe side effects. Here we describe a behavioral small-fish model for early detection of neurotoxic effects of new drugs. As case example we compare the effects of two mefloquine diastereomers on the behavior of goldfish using an automated 3D tracking system. Findings In a preliminary experiment, the overall toxic effects in terms of mo...

  9. The fish egg microbiome

    NARCIS (Netherlands)

    Liu, Y.

    2016-01-01

    Y. Liu Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp. The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia Emerging oomycete pat

  10. The fish egg microbiome

    NARCIS (Netherlands)

    Liu, Y.

    2016-01-01

    Y. Liu Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp. The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia Emerging oomycete

  11. Fish allergy and fish allergens

    DEFF Research Database (Denmark)

    Kuehn, A; Hilger, Christiane; Ollert, Markus

    2016-01-01

    but patients with this phenotype constitute an important sub-group among fish-allergic individuals. 2. Newly identified fish allergens, enolases, aldolases, and fish gelatin, are of high relevance as the majority of the fish-allergic individuals seem to develop specific IgE against these proteins. The present...

  12. Bioassay-directed identification of novel antiandrogenic compounds in bile of fish exposed to wastewater effluents.

    Science.gov (United States)

    Rostkowski, Pawel; Horwood, Julia; Shears, Janice A; Lange, Anke; Oladapo, Francis O; Besselink, Harrie T; Tyler, Charles R; Hill, Elizabeth M

    2011-12-15

    The widespread occurrence of feminized male fish downstream of some UK Wastewater Treatment Works (WwTWs) has been associated with exposure to estrogenic and potentially antiandrogenic (AA) contaminants in the effluents. In this study, profiling of AA contaminants in WwTW effluents and fish was conducted using HPLC in combination with in vitro androgen receptor transcription screens. Analysis of extracts of wastewater effluents revealed complex profiles of AA activity comprising 21-53 HPLC fractions. Structures of bioavailable antiandrogens were identified by exposing rainbow trout to a WwTW effluent and profiling the bile for AA activity using yeast (anti-YAS) and mammalian-based (AR-CALUX) androgen receptor transcription screens. The predominant fractions with AA activity in both androgen receptor screens contained the germicides chlorophene and triclosan, and together these contaminants accounted for 51% of the total anti-YAS activity in the fish bile. Other AA compounds identified in bile included chloroxylenol, dichlorophene, resin acids, napthols, oxybenzone, 4-nonylphenol, and bisphenol A. Pure standards of these compounds were active in the androgen receptor screens at potencies relative to flutamide of between 0.1 and 13.0. Thus, we have identified, for the first time, a diverse range of AA chemicals in WwTWs that are bioavailable to fish and which need to be assessed for their risk to the reproductive health of these organisms and other aquatic biota.

  13. Non-chromatographic screening procedure for arsenic speciation analysis in fish-based baby foods by using electrothermal atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Garcia, Ignacio; Briceno, Marisol [Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, E-30071 Murcia (Spain); Hernandez-Cordoba, Manuel, E-mail: hcordoba@um.es [Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, E-30071 Murcia (Spain)

    2011-08-05

    Highlights: {yields} Arsenic in fish-based food samples can be determined without the need of a dissolution stage. {yields} Speciation of the main forms of arsenic in fish-based baby foods does not require chromatography. {yields} The behavior of arsenic compounds in ETAAS strongly depends on the chemical modifier used. - Abstract: A procedure for the speciation analysis of arsenic in fish-based baby foods is presented. Inorganic arsenic, methylarsonic acid (MA), dimethylarsinic acid (DMA) and arsenobetaine (AB) were determined by electrothermal atomic absorption spectrometry (ETAAS) using suspensions prepared in a 0.01 mol L{sup -1} tetramethylammonium hydroxide (TMAH) solution. Speciation is based on the use of three different chemically modified ETAAS atomizers to obtain the analytical signals. Using a palladium salt as the chemical modifier, the signal corresponding to the total arsenic concentration is obtained. When palladium is replaced by Ce(IV), the signal is solely due to inorganic arsenic (III and V) + MA. If no signal is obtained in this latter case, it is possible to distinguish between DMA and AB using a zirconium coated atomizer. The signal obtained in this way is due solely to DMA, and the concentration of AB can be obtained by the difference with the total arsenic content. Determinations by ETAAS require the use of the standard additions method. The limits of detection for the determination of AB, DMA and inorganic arsenic (+MA) are 15, 25 and 50 ng g{sup -1} expressed as arsenic, respectively. These detection limits are good enough for the procedure to be appropriate for the rapid determination of these compounds, avoiding extraction processes and/or chromatographic separations. Data for commercial samples, as well as for four standard reference materials, are given.

  14. Fluorescence in situ hybridization (FISH screening for the 22q11.2 deletion in patients with clinical features of velocardiofacial syndrome but without cardiac anomalies

    Directory of Open Access Journals (Sweden)

    Paula Sandrin-Garcia

    2007-01-01

    Full Text Available The velocardiofacial syndrome (VCFS, a condition associated with 22q11.2 deletions, is characterized by a typical facies, palatal anomalies, learning disabilities, behavioral disturbances and cardiac defects. We investigated the frequency of these chromosomal deletions in 16 individuals with VCFS features who presented no cardiac anomalies, one of the main characteristics of VCFS. Fluorescent in situ hybridization (FISH with the N25 (D22S75; 22q11.2 probe revealed deletions in ten individuals (62%. Therefore, even in the absence of cardiac anomalies testing for the 22q11.2 microdeletions in individuals showing other clinical features of this syndrome is recommended.

  15. Community structure and coral status across reef fishing intensity gradients in Palk Bay reef, southeast coast of India.

    Digital Repository Service at National Institute of Oceanography (India)

    Manikandan, B.; Ravindran, J.; Shrinivaasu, S.; Marimuthu, N.; Paramasivam, K.

    the neighbouring reefs, it becomes important to maintain a no fishing zones of reef fish in the neighbourhood of reef fishing hotspots. In addition, long term data on diversity, quantity, age, size structure and sex of the reef fishes exploited...

  16. Analysis of taxonomic diversity of fish community in Yangtze River estuary%长江口鱼类群落分类学多样性变动的分析

    Institute of Scientific and Technical Information of China (English)

    沈新强; 史赟荣; 晁敏; 全为民; 黄厚见; 吴庆元

    2013-01-01

    为研究长江口鱼类群落分类学多样性值(平均分类差异指数△+与分类变异差异指数∧+)的长期变动,根据1985~1986年、2004年及2010~2011年3个时期共12个航次长江口鱼类调查资料,分别计算了反映鱼类群落不同物种亲缘关系△+和亲缘关系均匀性∧+值.结果显示,2004年4个航次及2010~2011年3个航次鱼类△+均位于长江口鱼类群落总名录△+95%置信区间以下,与1985~1986年相比,2004年及2010~2011年各航次平均△+均较低;∧+的分布格局则与△+有所不同,主要表现为12个航次的∧+均在95%置信区间内.长江口鱼类群落△+的降低跟过度捕捞、环境污染、生境破坏等有关,其下降也反映出群落种类组成在形态亲缘关系上更加接近.%For studying the long-term changes in taxonomic diversity (average taxonomic distinctness and variations in taxonomic distinctness) of fish community in Yangtze River estuary,fish species recorded at three periods (1985~1986,2004,2010~2011) were used to estimate the△+ and ∧ + for respective survey.The results showed that △+ in 2004 and 2010~2011 (except the spring survey) fell below the 95% probability limits for △+ of all fish species from Yangtze River estuary.Moreover,the decreasing trends in △+ were also observed.However,patterns of variation in ∧ + was different from △+,as all ∧+ distributed in the 95% probability limits for ∧ + of all fish species.Declines in △+ of Yangtze River estuary may be a result of overfishing,pollution and habitat destruction,as shown in closer relationships among fish species,implying for increased niche similarity between species and potential loss of stability or resilience of the community.

  17. Diversity and Community Structure of the Fishes in the Headstream Region of the Dongjiang River%东江源头区域鱼类物种多样性及群落组成的特征

    Institute of Scientific and Technical Information of China (English)

    邓凤云; 张春光; 赵亚辉; 周岐海; 张洁

    2013-01-01

    Opsariichthys bidens (9.93%) and Acrossocheilus parallens (9.36%). Temporal and spatial variations were also conducted fish community similarity analyses. The evaluation of fish diversity in the study area was made based on the combined information of G-F index, Shannon-Wiener index, Pielou' s evenness index, Margalef species richness index and Simpson index. Fish community structure in headstream region was dominated by omnivore, sedentary, mid & superstratum and benthic species, which is similar with that of the lower reach. However, the similarity index of fishes between headstream and lower reach was only 0. 39. The major adverse impacts on the fish biodiversity in the headstream included dam construction, water pollution, sand excavation, excessive catching and harmful fishing gear.

  18. 汀江中上游鱼类多样性及其影响因子%Factors Affecting Diversity of Fish Species in Mid-and Upper-streams of Tingjiang River

    Institute of Scientific and Technical Information of China (English)

    何美峰

    2016-01-01

    基于2012-2013年的2、5、7、10对汀江中上游河流水域的6个江段的调查数据,探讨鱼类多样性的时空差异以及鱼类组成与环境因子间的关联。共采集鱼类71种,隶属4目15科54属,其中福建省保护动物1种、福建省特有种4种;优势种有宽鳍鱲 Zacco platypus 、黄颡鱼 Pseudobagrus fulvidraco 、银 Gnathopogon argentatus 3种;常见种有马口鱼 Opsariichthys bidens 等12种。鱼类多样性指数(香农指数)在站位间和季节间差异均显著。根据典范对应分析(CCA)对鱼类群落与环境因子间关联进行了分析,结果显示:水温和人类活动是决定鱼类群落分布的主导因子,总氮、溶解氧、高锰酸盐指数、底质、堤岸稳定性、植被多样性和河道变化在决定鱼类群落分布上也有一定作用。人类活动的加剧不仅改变了汀江中上游物种组成(即洄游性、敏感性地方物种减少,而外来物种、广布耐受性鱼类增多),也降低了该河流鱼类的物种多样性。%Correlations among the habitat conditions,diversity of fish species,and human activities were studied using the data collected from 6 locations on the mid-and upper-streams of Tingjiang River in February,May,July, and October from 2012 to 2013. The results showed that the 71 fishes caught belonged to 4 orders,15 families,and 54 genera.They included the provincial protected species,such as Mastacembelus armatus ,the endemic species, Pseudogastromyzon fasciatus ,Pseudogastromyzon cheni ,Crossostoma stigmata and Crossostoma fascicauda ,and the dominant species,Zacco platypus ,Pseudobagrus fulvidraco ,and Gnathopogon argentatus ,along with 12 commonly found species.Based onthe one-way ANOVA,the Shannon-Wiener indices on samples collected from the 6 locations varied significantly.The indices for fish caught at Xinqiao were higher than other localities,with significant seasonal variations.The canonical correspondence

  19. The Effectiveness of Screening with Interferon-Gamma Release Assays in a University Health Care Setting with a Diverse Global Population

    Science.gov (United States)

    Birch, Samantha J.; Golbeck, Amanda L.

    2015-01-01

    Objective: This analysis examined the effectiveness of utilizing interferon-gamma release assay (IGRA) technology in a TB (TB) screening program at a university. Participants: Participants were 2299 students at a Montana university who had presented to the university health center for TB screening during 2012 and 2013. Methods: A retrospective…

  20. Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data

    Science.gov (United States)

    Meirelles, Pedro M.; Amado-Filho, Gilberto M.; Pereira-Filho, Guilherme H.; Pinheiro, Hudson T.; de Moura, Rodrigo L.; Joyeux, Jean-Christophe; Mazzei, Eric F.; Bastos, Alex C.; Edwards, Robert A.; Dinsdale, Elizabeth; Paranhos, Rodolfo; Santos, Eidy O.; Iida, Tetsuya; Gotoh, Kazuyoshi; Nakamura, Shota; Sawabe, Tomoo; Rezende, Carlos E.; Gadelha, Luiz M. R.; Francini-Filho, Ronaldo B.; Thompson, Cristiane; Thompson, Fabiano L.

    2015-01-01

    Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions. PMID:26090804

  1. Baseline Assessment of Mesophotic Reefs of the Vitoria-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.

    Directory of Open Access Journals (Sweden)

    Pedro M Meirelles

    Full Text Available Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame. A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90% than the CCA reefs (~40% and rhodolith beds (~10%. Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon. VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

  2. Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.

    Science.gov (United States)

    Meirelles, Pedro M; Amado-Filho, Gilberto M; Pereira-Filho, Guilherme H; Pinheiro, Hudson T; de Moura, Rodrigo L; Joyeux, Jean-Christophe; Mazzei, Eric F; Bastos, Alex C; Edwards, Robert A; Dinsdale, Elizabeth; Paranhos, Rodolfo; Santos, Eidy O; Iida, Tetsuya; Gotoh, Kazuyoshi; Nakamura, Shota; Sawabe, Tomoo; Rezende, Carlos E; Gadelha, Luiz M R; Francini-Filho, Ronaldo B; Thompson, Cristiane; Thompson, Fabiano L

    2015-01-01

    Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

  3. Antarctic Fishes.

    Science.gov (United States)

    Eastman, Joseph T.; DeVries, Arthur L.

    1986-01-01

    Explains the adaptations to Antarctic waters that Notothenioidei, a group of advanced bony fishes, have exhibited. Discusses the fishes' mechanisms of production of antifreeze properties and their capacities for neutral buoyancy in water. (ML)

  4. Fish Dishes.

    Science.gov (United States)

    Derby, Marie

    2003-01-01

    Describes an art project that was inspired by Greek pottery, specifically dishes shaped as fish. Explains that fourth-grade students drew a fish shape that was later used to create their clay version of the fish. Discusses how the students examined the pottery to make decisions about color and design. (CMK)

  5. Screening of marine seaweeds for bioactive compound against fish pathogenic bacteria and active fraction analysed by gas chromatography-mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Rajasekar Thirunavukkarasu; Priyadharshini Pandiyan; Kumaran Subaramaniyan; Deivasigamani Balaraman; Sakthivel Manikkam; Balamurugan Sadaiyappan; George Edward Gnana Jothi

    2014-01-01

    Objective:To isolate bioactive molecules from marine seaweeds and check the antimicrobial activity against the fish pathogenic bacteria. Methods: Fresh marine seaweeds Gracilaria edulis, Kappaphycus spicifera, Sargassum wightii (S. wightii) were collected. Each seaweed was extracted with different solvents. In the study, test pathogens were collected from microbial type culture collection. Antibacterial activity was carried out by using disc diffusion method and minimum inhibition concentration (MIC) was calculated. Best seaweed was analysed by fourier transform infrared spectroscopy. The cured extract was separated by thin layer chromatography (TLC). Fraction was collected from TLC to check the antimicrobial activity. Best fraction was analysed by gas chromatography mass spectrometer (GCMS). Results: Based on the disc diffusion method, S. wightii showed a better antimicrobial activity than other seaweed extracts. Based on the MIC, methanol extract of S. wightii showed lower MIC than other solvents. S. wightii were separated by TLC. In this TLC, plate showed a two fraction. These two fractions were separated in preparative TLC and checked for their antimicrobial activity. Fraction 2 showed best MIC value against the tested pathogen. Fraction 2 was analysed by GCMS. Based on the GCMS, fraction 2 contains n-hexadecanoic acid (59.44%). Conclusions:From this present study, it can be concluded that S. wightii was potential sources of bioactive compounds.

  6. A targeted/non-targeted screening method for perfluoroalkyl carboxylic acids and sulfonates in whole fish using quadrupole time-of-flight mass spectrometry and MS(e).

    Science.gov (United States)

    Crimmins, Bernard S; Xia, Xiaoyan; Hopke, Philip K; Holsen, Thomas M

    2014-02-01

    A new method for measuring perfluoroalkyl contaminants (PFCs) in biological matrices has been developed. An ultra-high pressure liquid chromatograph equipped with a quadrupole time-of-flight mass spectrometer (UPLC-QToF) was optimized using a continuous precursor/product ion monitoring mode. Unlike traditional targeted studies that isolate precursor/product ion pairs, the current method alternates between two ionization energy channels to continuously capture standard electrospray ionization (low energy) and collision induced dissociation (high energy) spectra. The result is the indiscriminant acquisition of paired low and high energy spectra for all constituents eluting from the chromatographic system. This technique was evaluated for the routine analysis of perfluoroalkyl species. Using this technique, linear perfluoroalkyl carboxylic acids (C4 to C14) and perfluoroalkyl sulfonates (C4, C6, C8 and C10) exhibited a linear range spanning over three orders of magnitude and were detectable at levels less than 1 pg on column with a root mean squared signal to noise ratio of 5 to 20. Lake trout (Salvelinus namaycush) and National Institutes of Standards and Technology Standard Reference Material 1946 were used to evaluate matrix effects and the accuracy of this method when applied to a whole fish extract. The current method was also evaluated as a diagnostic tool to identify unknown PFCs using experimental fragmentation patterns, mass defect filtering and Kendrick plots.

  7. 鳜亚科鱼类资源多样性的研究进展%Research Progress on Resources Diversity of Sinipercinae Fishes

    Institute of Scientific and Technical Information of China (English)

    冉辉; 姚俊杰; 杨兴; 禹真; 牟洪民

    2012-01-01

    In recent decades. Owing to the decrease of water flow and various degrees of pollution of inland natural waters, together with the fisheries overfishing in rivers and lakes, the wildlife resources of Sinipercinae are seriously threatened, the species and numbers of Sinipercinae are in decline. In this paper the research status of species diversity, taxonomy and genetic diversity of Sinipercinae were reviewed.%近数十年来,随着内陆天然水域流量下降和水质受到不同程度的污染,加上江湖渔业的过度捕捞,使鳜类的野生资源受到严重威胁,其种类和数量逐渐减少.对近年来鳜类资源的物种多样性、分类地位和遗传多样性等方面的研究现状进行了综述.

  8. Evaluating invasion risk for freshwater fishes in South Africa

    Directory of Open Access Journals (Sweden)

    Sean M. Marr

    2017-03-01

    Full Text Available Background: South Africa, as a signatory of the Convention on Biological Diversity, has an obligation to identify, prioritise and manage invasive species and their introduction pathways. However, this requires knowledge of the introduction pathways, factors influencing establishment success, invasive potential, current distributions and ecological impacts. Objectives: To evaluate the Fish Invasiveness Screening Kit (FISK to predict the invasion risk posed by fish species proposed for introduction into South Africa. Method: FISK assessments were compiled for species whose invasion status in South Africa was known. A Receiver operating characteristic (ROC analysis was conducted to calibrate the FISK for South Africa. The calibrated FISK was used to evaluate the risk that three species recently proposed for importation for aquaculture could become invasive in South Africa. Results: A FISK score of 14 was identified as the threshold to delineate between species that could become invasive in South Africa and those that are unlikely to become invasive. Of the three species evaluated, Silurus glanis had a high risk of becoming invasive in South Africa, Lates calcarifer was likely to be invasive and Oncorhynchus tshawytscha was unlikely to be invasive in South Africa. Conclusion: FISK was demonstrated to be a useful risk assessment tool to evaluate the invasion risk posed by species proposed for use in aquaculture. For the large number of fish imported for the pet trade, a rapid screening assessment to flag potentially high risk species was recommended prior to a full FISK assessment for flagged species.

  9. The roles of marginal lagoons in the maintenance of genetic diversity in the Brazilian migratory fishes Prochilodus argenteus and P. costatus

    Directory of Open Access Journals (Sweden)

    Bruno F. Melo

    2013-09-01

    Full Text Available The rio São Francisco basin contains many endemic species, such as Prochilodus argenteus and P. costatus, which have great commercial importance. However, information about the main recruitment sites and genetic studies containing extensive sampling of these species are scarce. To investigate the roles of the marginal lagoons in the maintenance of genetic variability and in the population structure, we analyzed six microsatellite loci in nine sampling groups of P. argenteusand five sampling groups of P. costatus. Our results showed high levels of genetic variability and low values of genetic differentiation for P. argenteus (FST =0.008, P< 0.05 and for P. costatus(FST =0.031, P < 0.05. In addition, high values of gene flow combined with a small genetic distance suggest the presence of a single population for each species in the middle rio São Francisco basin. Moreover, putative migration routes involving marginal lagoons during the reproductive season could be detected, confirming the importance of these nurseries in the lifecycle of these species. Our results also indicate the necessity of adequate management of the fish resources and the conservation of the floodplains in the rio São Francisco basin.

  10. Application of a yeast estrogen screen in non-biomarker species Varicorhinus barbatulus fish with two estrogen receptor subtypes to assess xenoestrogens.

    Science.gov (United States)

    Fu, Keng-Yen; Chen, Chung-Yuan; Chang, Whei-Meih

    2007-06-01

    Xenoestrogens can interfere with normal estrogen signaling by competitively binding to the estrogen receptor (ER) and activating transcription of target genes. In this study, we cloned the estrogen receptor alpha (vbERalpha) and beta 2 (vbERbeta2) genes from liver of the indigenous Taiwanese cyprinid fish Varicorhinus barbatulus and tested the direct impact of several xenoestrogens on these ERs. Transcriptional activity of xenoestrogens was measured by the enzymatic activity of estrogen responsive element (ERE)-containing beta-galactosidase in a yeast reporter system. The xenoestrogens tested were phenol derivatives, DDT-related substances, phthalic acid esters, and polychlorinated biphenyls, with 17beta-estradiol (E2) as a subjective standard. The phenol derivatives [4-nonylphenol (4-NP), 4-t-octylphenol (4-t-OP) and bisphenol A (BPA)] exhibited significant dose-dependent responses in both ligand potency and ligand efficiency. Consistent with yeast assays using human or rainbow trout ERs, we observed a general subtype preference in that vbERalpha displayed higher relative potencies and efficiencies than vbERbeta2, although our assays induced a stronger response for xenoestrogens than did human or trout ERs. Whereas 4-NP and 4-t-OP have similar EC50 values relative to E2 for both ER subtypes, the strong estrogenic response of BPA markedly differentiates vbERalpha from vbERbeta2, suggesting possible species-specific BPA sensitivity. We report that the ameliorative yeast tool is readily applicable for indigenous wildlife studies of the bio-toxic influence of xenoestrogens with wildlife-specific estrogen receptors.

  11. Screening complex effluents for estrogenic activity with the T47D-KBluc cell bioassay: assay optimization and comparison with in vivo responses in fish.

    Science.gov (United States)

    Wehmas, Leah C; Cavallin, Jenna E; Durhan, Elizabeth J; Kahl, Michael D; Martinovic, Dalma; Mayasich, Joe; Tuominen, Tim; Villeneuve, Daniel L; Ankley, Gerald T

    2011-02-01

    Wastewater treatment plant (WWTP) effluents can contain estrogenic chemicals, which potentially disrupt fish reproduction and development. The current study focused on the use of an estrogen-responsive in vitro cell bioassay (T47D-KBluc), to quantify total estrogenicity of WWTP effluents. We tested a novel sample preparation method for the T47D-KBluc assay, using powdered media prepared with direct effluent. Results of the T47D-KBluc assay were compared with the induction of estrogen receptor-regulated gene transcription in male fathead minnows (Pimephales promelas) exposed to the same effluents. Effluent samples for the paired studies were collected over the course of three months. According to the T47D-KBluc assay, the effluent estrogenicity ranged from 1.13 to 2.00 ng 17β-estradiol (E2) equivalents/L. Corresponding in vivo studies exposing male fathead minnows to 0, 10, 50, and 100% effluent dilutions demonstrated that exposure to 100% effluent significantly increased hepatic vitellogenin (VTG) and estrogen receptor α subunit transcripts relative to controls. The induction was also significant in males exposed to 250 ng E2/L or 100 ng E2/L. The in vitro and in vivo results support the conclusion that the effluent contains significant estrogenic activity, but there was a discrepancy between in vitro- and in vivo-based E2 equivalent estimates. Our results suggest that the direct effluent preparation method for the T47D-KBluc assay is a reasonable approach to estimate the estrogenicity of wastewater effluent.

  12. Analytical method for fast screening and confirmation of multi-class veterinary drug residues in fish and shrimp by LC-MS/MS.

    Science.gov (United States)

    Kim, Junghyun; Suh, Joon Hyuk; Cho, Hyun-Deok; Kang, Wonjae; Choi, Yong Seok; Han, Sang Beom

    2016-01-01

    A multi-class, multi-residue analytical method based on LC-MS/MS detection was developed for the screening and confirmation of 28 veterinary drug and metabolite residues in flatfish, shrimp and eel. The chosen veterinary drugs are prohibited or unauthorised compounds in Korea, which were categorised into various chemical classes including nitroimidazoles, benzimidazoles, sulfones, quinolones, macrolides, phenothiazines, pyrethroids and others. To achieve fast and simultaneous extraction of various analytes, a simple and generic liquid extraction procedure using EDTA-ammonium acetate buffer and acetonitrile, without further clean-up steps, was applied to sample preparation. The final extracts were analysed by ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The method was validated for each compound in each matrix at three different concentrations (5, 10 and 20 ng g(-1)) in accordance with Codex guidelines (CAC/GL 71-2009). For most compounds, the recoveries were in the range of 60-110%, and precision, expressed as the relative standard deviation (RSD), was in the range of 5-15%. The detection capabilities (CCβs) were below or equal to 5 ng g(-1), which indicates that the developed method is sufficient to detect illegal fishery products containing the target compounds above the residue limit (10 ng g(-1)) of the new regulatory system (Positive List System - PLS).

  13. Arapahoe NWR diversion reconstruction : Preliminary

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a preliminary plan for a diversion reconstruction for Hubbard #2. Oklahoma #1, Dryer, Hill and Crowder sites on the Arapahoe National Wildlife Refuge.

  14. Fish Ontology framework for taxonomy-based fish recognition

    Science.gov (United States)

    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

  15. Comparison of diverse nanomaterial bioactivity profiles based on high-throughput screening (HTS) in ToxCast™ (FutureToxII)

    Science.gov (United States)

    Most nanomaterials (NMs) in commerce lack hazard data. Efficient NM testing requires suitable toxicity tests for prioritization of NMs to be tested. The EPA’s ToxCast program is screening NM bioactivities and ranking NMs by their bioactivities to inform targeted testing planning....

  16. Comparison of diverse nanomaterial bioactivity profiles based on high-throughput screening (HTS) in ToxCast™ (FutureToxII)

    Science.gov (United States)

    Most nanomaterials (NMs) in commerce lack hazard data. Efficient NM testing requires suitable toxicity tests for prioritization of NMs to be tested. The EPA’s ToxCast program is screening NM bioactivities and ranking NMs by their bioactivities to inform targeted testing planning....

  17. Fish health and fish quality

    DEFF Research Database (Denmark)

    Ingerslev, Hans-Christian

    Aquaculture is an expanding worldwide industry producing an increasing amount of fish every year. The quality of the fish meat is dependent upon many biological and non-biological factors. Infectious diseases are known to cause bleedings and damage of the muscle tissue that may lead to scarring...... are poorly described in fish. The present work in this thesis focused on: 1) examination of potential changes in the quality regarding texture of the muscle tissue in rainbow trout (Oncorhynchus mykiss) after previous infection with the bacterial pathogens Yersinia ruckeri and Vibrio anguillarum; 2...... of these studies showed that previous infections by Yersinia ruckeri and Vibrio anguillarum gave rise to subsequent changes regarding textural quality parameters in fresh fish meat, while no differences were seen for cold-smoked meat from the same fish. The texture in previous infected fish was less flaky and less...

  18. Epigenomics in marine fishes.

    Science.gov (United States)

    Metzger, David C H; Schulte, Patricia M

    2016-12-01

    Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Fish parasites

    DEFF Research Database (Denmark)

    This book contains 22 chapters on some of the most important parasitic diseases in wild and farmed fish. International experts give updated reviews and provide solutions to the problems......This book contains 22 chapters on some of the most important parasitic diseases in wild and farmed fish. International experts give updated reviews and provide solutions to the problems...

  20. Screening genetically diverse pear species for in vitro CaCl2, MgSO4 and KH2PO4 requirements

    Science.gov (United States)

    Conservation of important plant germplasm is often difficult due to the specific growth requirements of genetically diverse species. This also applies to in vitro culture collections where a wide range of plants may have suboptimal growth or remain recalcitrant to growth on standard media. A series ...

  1. Beyond the point of no return? A comparison of genetic diversity in captive and wild populations of two nearly extinct species of Goodeid fish reveals that one is inbred in the wild.

    Science.gov (United States)

    Bailey, N W; Macías Garcia, C; Ritchie, M G

    2007-06-01

    The relative importance of genetic and non-genetic factors in extinction liability has been extensively debated. Here, we examine the levels of genetic variability at 13 (seven informative) loci in wild and captive populations of two endangered species of Mexican Goodeid fish, Ameca splendens and Zoogoneticus tequila. Allelic diversity was higher in the wild populations, and F(IS) lower. Values of theta (=4Nemu) were estimated using a coalescent approach. These implied that the effective population size of all captive populations of A. splendens were smaller than that of the wild population; qualitatively similar results were obtained using an analytical method based on within-population gene identity disequilibrium. However, the wild population of Z. tequila did not show a significantly greater estimate of theta. We used the Beaumont approach to infer population declines, and found that both species showed clear evidence of a decline in effective population size, although this was stronger and probably occurred over a longer period of time in Z. tequila than in A. splendens. The decline in Z. tequila probably occurred before captive populations were established. We discuss implications for the conservation of critically endangered populations.

  2. One Fish, Two Fish, Redfish, You Fish!

    Science.gov (United States)

    White, Katherine; Timmons, Maryellen; Medders, Paul

    2011-01-01

    The recreational fishing activity presented in this article provides a hands-on, problem-based experience for students; it unites biology, math, economics, environmental policy, and population dynamics concepts. In addition, the activity allows students to shape environmental policy in a realistic setting and evaluate their peers' work. By…

  3. Variabilidad espacial y temporal de la abundancia y diversidad de la comunidad de peces en la costa de Campeche, México Spatial and temporal variability of fish community abundance and diversity off the coast of Campeche, Mexico

    Directory of Open Access Journals (Sweden)

    Luis Amado Ayala-Pérez

    2012-03-01

    Full Text Available La comunidad de peces en el sur del golfo de México es abundante y diversa y sus componentes se encuentran afectados por la captura incidental de la pesquería del camarón siete barbas. El presente trabajo describe y analiza los patrones de variación espacial y temporal de la abundancia y diversidad de la comunidad de peces, identificando las especies con dominio ecológico. Los muestreos se realizaron mensualmente entre febrero 2006 y enero 2007 en 37 sitios localizados desde la desembocadura del sistema Grijalva-Usumacinta hasta la desembocadura del sistema Chumpam-Balchacah al interior de la Laguna de Términos, en el estado de Campeche al sur del golfo de México. Se realizaron 444 arrastres experimentales con una red de prueba camaronera y se capturaron 26.386 peces con un peso conjunto de 407,1 kg. Se identificaron 94 especies agrupadas en 65 géneros y 38 familias. La abundancia y diversidad de la comunidad de peces se analizó en escalas espacial y temporal en términos de densidad (ind m-2, biomasa (g m-2, peso promedio (g ind-1, índice de diversidad (H'n, riqueza de especies (DMg e índice de equidad (J'. En cuanto a abundancia se distinguieron los altos valores registrados en agosto y septiembre, en sitios cercanos a las desembocaduras de los sistemas Grijalva-Usumacinta y Palizada-Del Este. La especie más importante en términos de abundancia fue el bagre Cathorops melanopus. Los intervalos de variación de los índices de diversidad en escala espacial fueron: H'n = 0,5-2,8 bits; Dmg = 2,6-5,3 sp. ind-1 y J'= 0,1-0,8 bits. En escala temporal los intervalos fueron H'n = 1,8-2,6 bits; Dmg = 5,1-6,7 sp. ind-1 y J'= 0,4-0,6 bits. Se identificaron nueve especies dominantes con 16.840 individuos y un peso conjunto de 278,5 kg, equivalente al 63,8% de la captura total.The fish community of the southern Gulf of Mexico is abundant and diverse, and its components are affected by the bycatch of the seabob shrimp fishery. The spatial and

  4. Marine sponge Craniella austrialiensis-associated bacterial diversity revelation based on 16S rDNA library and biologically active Actinomycetes screening, phylogenetic analysis.

    Science.gov (United States)

    Li, Z-Y; Liu, Y

    2006-10-01

    The aim of this study was to investigate the bacterial diversity associated with the sponge Craniella australiensis using a molecular strategy and isolating Actinomycetes with antimicrobial potentials. The bacterial diversity associated with South China Sea sponge C. austrialiensis was assessed using a 16S rDNA clone library alongside restriction fragment length polymorphism and phylogenetic analysis. It was found that the C. austrialiensis-associated bacterial community consisted of alpha, beta and gamma-Proteobacteria, Firmicutes, Bacteroidetes as well as Actinobacterium. Actinomycetes were isolated successfully using seawater medium with sponge extracts. According to the BLAST and phylogenetic analysis based on about 600-bp 16S rDNA sequences, 11 of the representative 23 isolates closely matched the Streptomyces sp. while the remaining 12 matched the Actinomycetales. Twenty Actinomycetes have antimicrobial potentials, of which 15 are found to possess broad-spectrum antimicrobial potentials. The sponge C. austrialiensis-associated bacterial community is very abundant including Proteobacteria, Firmicutes, Bacteroidetes and Actinobacterium while Actinomycetes is not predominant. Artificial seawater medium with sponge extracts is suitable for Actinomycetes isolation. Most of the isolated C. austrialiensis-associated Actinomycetes have a broad spectrum of antimicrobial activity. This study revealed the diversity of the bacterial community and the isolated Actinomycetes with antimicrobial potentials associated with sponge C. australiensis.

  5. Illegal Fishing: The Case of Mozambique

    OpenAIRE

    2001-01-01

    The fisheries sector plays an important role in the economy of Mozambique, contributing to 40-50 per cent of the country’s foreign exchange earnings. The extensive coast supporting diverse fisheries makes Mozambique a sensitive place for illegal, unreported and unregulated (IUU) fishing. This paper discuss the relation between IUU fishing and the surveillance capacity, the length of the coastal zone, the commercial value of the resources and the national fishing capacity of ...

  6. Fighting fish

    Science.gov (United States)

    Duchi, E.; Guerrini, V.; Rinaldi, S.; Schaeffer, G.

    2017-01-01

    We introduce new combinatorial structures, called fighting fish, that generalize directed convex polyominoes by allowing them to branch out of the plane into independent substructures. On the one hand the combinatorial structure of fighting fish appears to be particularly rich: we show that their generating function with respect to the perimeter and number of tails is algebraic, and we conjecture a mysterious multivariate equidistribution property with the left ternary trees introduced by Del Lungo et al On the other hand, fighting fish provide a simple and natural model of random branching surfaces which displays original features: in particular, we show that the average area of a uniform random fighting fish with perimeter 2n is of order n 5/4: to the best of our knowledge this behaviour is non-standard and suggests that we have identified a new universality class of random structures. Dedicated to Tony Guttmann on the occasion of his 70th birthday.

  7. Fishes and humankind III. Editorial.

    Directory of Open Access Journals (Sweden)

    Andrew K. G. Jones

    1999-12-01

    Full Text Available The publication of this group of three papers form part of the 1987 meeting of the International Council for Archaeozoologists Fish Remains Working Group which took place at the University of York, U. K. The papers illustrate an increased awareness of the significance of ichthyological research to archaeology and cover three areas of research: taphonomy; fishing artefacts; and fish remains recovered from an excavation. Jones sheds some light on the relative robustness of the bewildering array of elements in a fish skeleton by recording damage to a skeleton when it is trampled. His paper suggests an index of robustness which might be used to assess the degree of fragmentation in archaeological assemblages. Kemp reports on the excavation of a small medieval building located adjacent to medieval fish ponds created by Cistercian monks in North Yorkshire, England. In addition to the structural evidence, an impressive assemblage of weights, presumably net weights, found on or near the site is published. Perhaps most significant is a large lead weight which may have been used to weight catches of fish from the ponds. Fish remains recovered from two excavations at the quayside at Newcastle-upon-Tyne, England are discussed by Nicholson. Around 6000 identified bones form the basis for the study, the majority of which were identified as Gadid (cod family or herring. While the main food fishes typify fish bone assemblages from most post-Roman urban archaeological sites, the identification of small fishes such as sandeels, smelt, gobies and buttefish may indicate the utilisation of fish not nowadays considered as food at all. Given the diversity of species (30 individual species identified it is suggested that the remains from the main bone-producing organic horizons, dated to the late twelfth to thirteenth centuries, may include discard from a nearby fishmarket.

  8. Fish benefits from offshore wind farm development

    DEFF Research Database (Denmark)

    Leonhard, Simon B.; Stenberg, Claus; Støttrup, Josianne

    2013-01-01

    The studies up until 2006 showed few effects on the fish fauna that could be attributed to the establishment and operation of the wind farms. Fish abundance and diversity were not higher inside the wind farms than in the areas outside the wind farms. One obvious reason for this could be that the ...

  9. Efficient PCR-Based Amplification of Diverse Alcohol Dehydrogenase Genes from Metagenomes for Improving Biocatalysis: Screening of Gene-Specific Amplicons from Metagenomes

    Science.gov (United States)

    Kariya, Satomi; Kurokawa, Junji

    2014-01-01

    Screening of gene-specific amplicons from metagenomes (S-GAM) has tremendous biotechnological potential. We used this approach to isolate alcohol dehydrogenase (adh) genes from metagenomes based on the Leifsonia species adh gene (lsadh), the enzyme product of which can produce various chiral alcohols. A primer combination was synthesized by reference to homologs of lsadh, and PCR was used to amplify nearly full-length adh genes from metagenomic DNAs. All adh preparations were fused with lsadh at the terminal region and used to construct Escherichia coli plasmid libraries. Of the approximately 2,000 colonies obtained, 1,200 clones were identified as adh positive (∼60%). Finally, 40 adh genes, Hladh-001 to Hladh-040 (for homologous Leifsonia adh), were identified from 223 clones with high efficiency, which were randomly sequenced from the 1,200 clones. The Hladh genes obtained via this approach encoded a wide variety of amino acid sequences (8 to 99%). After screening, the enzymes obtained (HLADH-012 and HLADH-021) were confirmed to be superior to LSADH in some respects for the production of anti-Prelog chiral alcohols. PMID:25085492

  10. Diverse small molecule inhibitors of human apurinic/apyrimidinic endonuclease APE1 identified from a screen of a large public collection.

    Directory of Open Access Journals (Sweden)

    Dorjbal Dorjsuren

    Full Text Available The major human apurinic/apyrimidinic endonuclease APE1 plays a pivotal role in the repair of base damage via participation in the DNA base excision repair (BER pathway. Increased activity of APE1, often observed in tumor cells, is thought to contribute to resistance to various anticancer drugs, whereas down-regulation of APE1 sensitizes cells to DNA damaging agents. Thus, inhibiting APE1 repair endonuclease function in cancer cells is considered a promising strategy to overcome therapeutic agent resistance. Despite ongoing efforts, inhibitors of APE1 with adequate drug-like properties have yet to be discovered. Using a kinetic fluorescence assay, we conducted a fully-automated high-throughput screen (HTS of the NIH Molecular Libraries Small Molecule Repository (MLSMR, as well as additional public collections, with each compound tested as a 7-concentration series in a 4 µL reaction volume. Actives identified from the screen were subjected to a panel of confirmatory and counterscreen tests. Several active molecules were identified that inhibited APE1 in two independent assay formats and exhibited potentiation of the genotoxic effect of methyl methanesulfonate with a concomitant increase in AP sites, a hallmark of intracellular APE1 inhibition; a number of these chemotypes could be good starting points for further medicinal chemistry optimization. To our knowledge, this represents the largest-scale HTS to identify inhibitors of APE1, and provides a key first step in the development of novel agents targeting BER for cancer treatment.

  11. Diverse small molecule inhibitors of human apurinic/apyrimidinic endonuclease APE1 identified from a screen of a large public collection.

    Science.gov (United States)

    Dorjsuren, Dorjbal; Kim, Daemyung; Vyjayanti, Vaddadi N; Maloney, David J; Jadhav, Ajit; Wilson, David M; Simeonov, Anton

    2012-01-01

    The major human apurinic/apyrimidinic endonuclease APE1 plays a pivotal role in the repair of base damage via participation in the DNA base excision repair (BER) pathway. Increased activity of APE1, often observed in tumor cells, is thought to contribute to resistance to various anticancer drugs, whereas down-regulation of APE1 sensitizes cells to DNA damaging agents. Thus, inhibiting APE1 repair endonuclease function in cancer cells is considered a promising strategy to overcome therapeutic agent resistance. Despite ongoing efforts, inhibitors of APE1 with adequate drug-like properties have yet to be discovered. Using a kinetic fluorescence assay, we conducted a fully-automated high-throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR), as well as additional public collections, with each compound tested as a 7-concentration series in a 4 µL reaction volume. Actives identified from the screen were subjected to a panel of confirmatory and counterscreen tests. Several active molecules were identified that inhibited APE1 in two independent assay formats and exhibited potentiation of the genotoxic effect of methyl methanesulfonate with a concomitant increase in AP sites, a hallmark of intracellular APE1 inhibition; a number of these chemotypes could be good starting points for further medicinal chemistry optimization. To our knowledge, this represents the largest-scale HTS to identify inhibitors of APE1, and provides a key first step in the development of novel agents targeting BER for cancer treatment.

  12. Hydrodynamics of fossil fishes.

    Science.gov (United States)

    Fletcher, Thomas; Altringham, John; Peakall, Jeffrey; Wignall, Paul; Dorrell, Robert

    2014-08-07

    From their earliest origins, fishes have developed a suite of adaptations for locomotion in water, which determine performance and ultimately fitness. Even without data from behaviour, soft tissue and extant relatives, it is possible to infer a wealth of palaeobiological and palaeoecological information. As in extant species, aspects of gross morphology such as streamlining, fin position and tail type are optimized even in the earliest fishes, indicating similar life strategies have been present throughout their evolutionary history. As hydrodynamical studies become more sophisticated, increasingly complex fluid movement can be modelled, including vortex formation and boundary layer control. Drag-reducing riblets ornamenting the scales of fast-moving sharks have been subjected to particularly intense research, but this has not been extended to extinct forms. Riblets are a convergent adaptation seen in many Palaeozoic fishes, and probably served a similar hydrodynamic purpose. Conversely, structures which appear to increase skin friction may act as turbulisors, reducing overall drag while serving a protective function. Here, we examine the diverse adaptions that contribute to drag reduction in modern fishes and review the few attempts to elucidate the hydrodynamics of extinct forms.

  13. Diversity and phylogenetic analysis of endosymbiotic bacteria from field caught Bemisia tabaci from different locations of North India based on 16S rDNA library screening.

    Science.gov (United States)

    Singh, Shalini Thakur; Priya, Natarajan Gayatri; Kumar, Jitendra; Rana, Vipin Singh; Ellango, R; Joshi, Adita; Priyadarshini, Garima; Asokan, R; Rajagopal, Raman

    2012-03-01

    Bemisia tabaci is the major vector pest of agricultural crops all over the world. In this study we report the different bacterial endosymbionts associated with B. tabaci sampled from 14 different locations in North India. Using 16S rDNA clone library sequences we were able to identify Portiera, the primary endosymbiont of B. tabaci, and other secondary endosymbionts like Cardinium, Wolbachia, Rickettsia and Arsenophonus. Along with these we also detected Bacillus, Enterobacter, Paracoccus and Acinetobacter. These secondary endosymbionts were not uniformly distributed in all the locations. Phylogenetic analysis of 16S rDNA sequences of Cardinium, Wolbachia, Rickettsia and Arsenophonus showed that each of these bacteria form a separate cluster when compared to their respective counterparts from other parts of the world. MtCO1 gene based phylogenetic analysis showed the presence of Asia I and Asia II genetic groups of B. tabaci in N. India. The multiple correspondence analyses showed no correlation between the host genetic group and the endosymbiont diversity. These results suggest that the bacterial endosymbiont diversity of B. tabaci is much larger and complex than previously perceived and probably N. Indian strains of the bacterial symbionts could have evolved from some other ancestor.

  14. Virginia ESI: FISH (Fish Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for marine, estuarine, anadromous, and brackishwater fish species in Virginia. Vector polygons in this data...

  15. Hawaii ESI: FISH (Fish Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for reef, marine, estuarine, and native stream fish species in coastal Hawaii. Vector polygons in this data...

  16. Alabama ESI: FISH (Fish Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for marine, estuarine, and freshwater fish species in Alabama. Vector polygons in this data set represent...

  17. Louisiana ESI: FISH (Fish Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for freshwater (inland) fish species in coastal Louisiana. Vector polygons represent water-bodies and other...

  18. Speciation in fishes.

    Science.gov (United States)

    Bernardi, Giacomo

    2013-11-01

    The field of speciation has seen much renewed interest in the past few years, with theoretical and empirical advances that have moved it from a descriptive field to a predictive and testable one. The goal of this review is to provide a general background on research on speciation as it pertains to fishes. Three major components to the question are first discussed: the spatial, ecological and sexual factors that influence speciation mechanisms. We then move to the latest developments in the field of speciation genomics. Affordable and rapidly available, massively parallel sequencing data allow speciation studies to converge into a single comprehensive line of investigation, where the focus has shifted to the search for speciation genes and genomic islands of speciation. We argue that fish present a very diverse array of scenarios, making them an ideal model to study speciation processes.

  19. Screening of cytoplasmic DNA diversity between and within Lupinus mutabilis Sweet and Lupinus albus sensu lato by restriction fragment length polymorphism (RFLP).

    Science.gov (United States)

    Olczak, T; Rurek, M; Jańska, H; Augustyniak, H; Sawicka-Sienkiewicz, E J

    2001-01-01

    Seven populations and five mutant lines of the Andean lupin and four species from the section Albus were screened for their mitochondrial and chloroplast polymorphisms. For this purpose the RFLP method with EcoRI as a restriction enzyme was used. Lupinus luteus, Lupinus albus and Phaseolus vulgaris organellar clones as well as amplified fragments were used as probes. We found that mitochondrial probes were more suitable than chloroplast probes for identification of inter- and intra-specific variations within the examined material. Most mitochondrial probes differentiate the two species investigated. A high level of mitochondrial polymorphism was observed among the populations of L. mutabilis in contrast to monomorphism among the species in the section Albus. A limited polymorphism was detected between the mutant lines of L. mutabilis. We conclude from this study that the mitochondrial RFLP analysis is a valuable tool for identification of variability among Andean lupin populations.

  20. Optimal waist-to-height ratio values for cardiometabolic risk screening in an ethnically diverse sample of South African urban and rural school boys and girls.

    Directory of Open Access Journals (Sweden)

    Tandi E Matsha

    Full Text Available BACKGROUND: The proposed waist-to-height ratio (WHtR cut-off of 0.5 is less optimal for cardiometabolic risk screening in children in many settings. The purpose of this study was to determine the optimal WHtR for children from South Africa, and investigate variations by gender, ethnicity and residence in the achieved value. METHODS: Metabolic syndrome (MetS components were measured in 1272 randomly selected learners, aged 10-16 years, comprising of 446 black Africans, 696 mixed-ancestry and 130 Caucasians. The Youden's index and the closest-top-left (CTL point approaches were used to derive WHtR cut-offs for diagnosing any two MetS components, excluding the waist circumference. RESULTS: The two approaches yielded similar cut-off in girls, 0.465 (sensitivity 50.0, specificity 69.5, but two different values in boys, 0.455 (42.9, 88.4 and 0.425 (60.3, 67.7 based on the Youden's index and the CTL point, respectively. Furthermore, WHtR cut-off values derived differed substantially amongst the regions and ethnic groups investigated, whereby the highest cut-off was observed in semi-rural and white children, respectively, Youden's index0.505 (31.6, 87.1 and CTL point 0.475 (44.4, 75.9. CONCLUSION: The WHtR cut-off of 0.5 is less accurate for screening cardiovascular risk in South African children. The optimal value in this setting is likely gender and ethnicity-specific and sensitive to urbanization.

  1. CRCHD Launches National Colorectal Cancer Outreach and Screening Initiative

    Science.gov (United States)

    The NCI CRCHD launches National Screen to Save Colorectal Cancer Outreach and Screening Initiative which aims to increase colorectal cancer screening rates among racially and ethnically diverse and rural communities.

  2. Prevalence and seasonality of parasites of fish in Agulu Lake ...

    African Journals Online (AJOL)

    Owner

    2014-01-15

    Jan 15, 2014 ... parasites of fish in a natural, freshwater, tropical lake, southeast Nigeria. A total of 1191 fish ... Fish interacts with the various levels of food chain and influence the ..... clear indication of a high species diversity characteristic ..... University of George, College of Agricultural and Environmental. Sciences.

  3. 山口红树林区稚幼鱼多样性及其对渔业资源的补充作用%Juvenile Fish Diversity in Shankou Mangrove Reserve and Their Recruitment to the Fishery Resources

    Institute of Scientific and Technical Information of China (English)

    刘超; 胡文佳; 陈明茹; 杨圣云

    2013-01-01

    species in the creek were Ambassis gymnocephalus and C. punctatus in spring;L. brevirostris in autumn;M. ophuyseni and Tridentiger trigono-cephalus in winter;and Acentrogobius caninus in summer. Species biodiversity indices of the juvenile fish were calculated. The species richness D,Shannon diversity index H' and evenness index / were 1. 83,1. 5 and 0. 53 at the mudflat and 1. 63,1. 46,0. 58 at the creek respectively. Compared with other mangrove areas, the biodiversity indices of juvenile fish were lower in Shankou mangrove are-a. By analyzing habitat shifting of Engraulidae.Clupeidae and Mugilidae.it could be concluded that Shankou mangrove provided nursery area and shelters for the juvenile fish, which played an important role of recruitment to local fishery resources.

  4. Accuracy of Whole-Body DWI for Metastases Screening in a Diverse Group of Malignancies: Comparison With Conventional Cross-Sectional Imaging and Nuclear Scintigraphy.

    Science.gov (United States)

    Paruthikunnan, Samir Mustaffa; Kadavigere, Rajagopal; Karegowda, Lakshmikanth Halegubbi

    2017-09-01

    The purpose of this study is to assess the role of whole-body (WB) DWI as a screening modality for the detection of metastases and to compare it to conventional cross-sectional imaging modalities or nuclear scintigraphy in a population with various histopathologic malignancies. WB DWI and conventional imaging (CT, MRI, or scintigraphy) were performed for patients with known malignancies for metastatic workup, and these patients were followed up for a period of 1 year. Two radiologists assessed WB DW images separately, and conventional images were assessed by the senior radiologist. The metastatic lesions were classified into four regions: liver, lung, skeletal system, and lymph nodes. The reference standard was considered on the basis of histopathologic confirmation or clinical follow-up of the metastatic lesions. WB DWI was slightly inferior to conventional imaging modalities for the detection of hepatic metastases (sensitivity, 86.6% vs 93.3%; specificity, 91.6% vs 95.8%; and accuracy, 89.7% vs 94.8%) and skeletal metastases (sensitivity, 81.8% vs 89.4%; specificity, 86.4% vs 94.3%; and accuracy, 85.2% vs 93.0%); however, the differences were not statistically significant (p = 0.625 for hepatic metastases and p = 0.0953 for skeletal metastases, McNemar test). WB DWI was statistically significantly inferior to conventional imaging for the detection of lymph node metastases (sensitivity, 74.0% vs 81.5%; specificity, 87.9% vs 90.1%; accuracy, 81.4% vs 86.0%; p = 0.0389). WB DWI was statistically significantly inferior to conventional imaging for the detection of pulmonary metastases (sensitivity, 33.3% vs 100.0%; specificity, 90.9% vs 100.0%; accuracy, 60.8% vs 100.0%; p = 0.045). WB DWI can be used for screening hepatic and skeletal metastases, but its reliability as the sole imaging sequence for the detection of lymph nodal and pulmonary metastases is poor and, at present, it cannot replace conventional imaging modalities.

  5. Ecomorphology as a predictor of fish diet: a case study on the North Sea benthic fish community

    NARCIS (Netherlands)

    Diderich, W.P.

    2006-01-01

    A methodological approach based on fish ecomorphology was chosen to predict potential fish diet. This study tests a method used in earlier research on a marine ecosystem containing phylogenetically diverse organisms: the North Sea. Fish feeding morphology imposes constraints on feeding options. A bo

  6. Fishing Access Areas

    Data.gov (United States)

    Vermont Center for Geographic Information — The Vermont Fish & Wildlife Department maintains developed fishing access areas. These sites provide public access to waters in Vermont for shore fishing...

  7. "Gone fishing": modeling diversity in work ethics

    NARCIS (Netherlands)

    Freyberg-Inan, A.; Koçer, R.G.

    2012-01-01

    In his "Anecdote Concerning the Lowering of Productivity", written in 1963, the West-German writer Heinrich Böll humorously contrasts the mindset of an enterprising capitalist, bent on the maximization of profit, with that of a person we might call a profit "satisficer," a maximizer of leisure or ha

  8. Screening, diversity and partial sequence comparison of vegetative insecticidal protein (vip3A) genes in the local isolates of Bacillus thuringiensis Berliner.

    Science.gov (United States)

    Asokan, R; Swamy, H M Mahadeva; Arora, D K

    2012-04-01

    Characterization, direct sequencing of the PCR amplicon and phylogenetic relationship was done to discover a novel Vip protein genes of the Bt isolates, to improve the prospects for insect control, more Vip proteins should be sought out and researched to predict their insecticidal activity. Characterization was based on direct sequencing of PCR amplicon using primers specific to vip3A gene was presented here. 12 out of 18 isolates screened were positive for vip gene-specific primers. Homology search for the partial sequences using BLAST showed that 11 isolates had high similarity to vip3Aa gene and only one fragment with vip3Ae gene (25-100% at nucleotide and amino acid level). Phylogenetic analysis showed that the gene sequences were responsible for geographic separation for divergence within vip genes, consistent with the evaluation of distinct bacterial population. Despite the geographical distances, strains harbouring vip genes have originated from common ancestors may significantly contribute to control resistant insect pests. Some strains have evolved to be quite distinct and others remain as members of closely related groups. The reported method is a powerful tool to find novel Vip3A proteins from large-scale Bt strains which is effective in terms of time and cost. Further the Vip proteins produced by different strains of B. thuringiensis are unique in terms of the sequence divergence and hence may also differ in their insecticidal activities.

  9. Screen time behaviors may interact with obesity genes, independent of physical activity, to influence adolescent BMI in an ethnically-diverse cohort

    Science.gov (United States)

    Graff, M; North, KE; Richardson, AS; Young, K M; Mohlke, KL; Lange, LA; Lange, EM; Harris, KM; Gordon-Larsen, P

    2013-01-01

    Background There has been little investigation of gene-by-environment interactions related to sedentary behavior, a risk factor for obesity defined as leisure screen time (ST; i.e., TV, video, and computer games). Objective To test the hypothesis that limiting ST use attenuates the genetic predisposition to increased BMI, independent of physical activity. Design Using 7,642 wave II participants of the National Longitudinal Study of Adolescent Health, (Add Health; mean=16.4 years, 52.6% female), we assessed the interaction of ST (h/wk) and 41 established obesity SNPs with age- and sex-specific BMI Z scores in 4,788 European-(EA),1,612 African- (AA), and 1,242 Hispanic-American(HA)adolescents. Results Nominally significant SNP*ST interaction were found for FLJ35779 in EA, GNPDA2 in AA, and none in HA (EA: beta[SE]=0.016[0.007]), AA: beta[SE]=0.016[0.011]) per 7 h/wk ST and 1 risk allele in relation to BMI Z-score. Conclusions While for two established BMI loci, we find evidence that high levels of ST exacerbate the influence of obesity susceptibility variants on body mass, overall we do not find strong evidence for interactions between the majority of established obesity loci. However, future studies with larger sample sizes, or that may build on our current study and the growing published literature, are clearly warranted. PMID:24039247

  10. Screening of Strains with Degradation Activity for Biogenic Amines in Fish Sauce%鱼露中生物胺降解菌的筛选及其特性

    Institute of Scientific and Technical Information of China (English)

    杨利昆; 付湘晋; 胡叶碧; 周其中; 李滨

    2012-01-01

    In the present study,strains with degradation activity for biogenic amines were screened from naturally fermented fish sauce,and the effects of fermentation time and temperature on the content of biogenic amines were investigated.A total of 10 strains were obtained from natural fish sauce subjected to fermentation for 3 months.After 72 hours of fermentation at 30 ℃,the degradation rate of histamine was in the range of 17.3%-62.2%,and the degradation rate of tyramine was in the range of 12.4%-57.3%.The strain M8 with the highest activity was identified as Kodamaea ohmeri yeast through 26S rDNA sequence and online sequence alignment.Meanwhile,the strain revealed the strongest degradation activity for biogenic amines at 30 ℃.During fermentation,the content of biogenic amines revealed a decrease on the first day and an increase on the second day as well as the highest level on the third day,and then exhibited a decrease trend until the end of fermentation.After 9 days of fermentation at 30 ℃,the contents of histamine and tyramine were reduced to 30.4% and 20.8% of the initial levels,respectively.The strain M8 Kodamaea ohmeri yeast could reveal the best degradation activity for biogenic amines in the presence of 25% salt.Under the optimal conditions,histamine and tyramine were reduced to 35.6% and 27.6%,respectively.%从天然发酵鱼露中筛选具有生物胺降解活性的微生物,并研究发酵时间和发酵温度对其降解生物胺的影响。以天然发酵3个月的鱼露为分离材料,对鱼露中的生物胺降解菌进行分离纯化,获得10株具有生物胺降解活性的微生物。分离到的10株菌株在30℃发酵72h组胺降解率在17.3%~62.2%,酪胺降解率在12.4%~57.3%。其中M8菌株生物胺降解活性最高,经26S rDNA测序及在线序列比对,M8菌株鉴定为奥默柯达酵母。奥默柯达酵母M8在30℃条件下降解生物胺活性最强;其降解生物胺的时间变化规律为发酵第1

  11. Tropical fishes dominate temperate reef fish communities within western Japan.

    Science.gov (United States)

    Nakamura, Yohei; Feary, David A; Kanda, Masaru; Yamaoka, Kosaku

    2013-01-01

    Climate change is resulting in rapid poleward shifts in the geographical distribution of tropical and subtropical fish species. We can expect that such range shifts are likely to be limited by species-specific resource requirements, with temperate rocky reefs potentially lacking a range of settlement substrates or specific dietary components important in structuring the settlement and success of tropical and subtropical fish species. We examined the importance of resource use in structuring the distribution patterns of range shifting tropical and subtropical fishes, comparing this with resident temperate fish species within western Japan (Tosa Bay); the abundance, diversity, size class, functional structure and latitudinal range of reef fishes utilizing both coral reef and adjacent rocky reef habitat were quantified over a 2 year period (2008-2010). This region has undergone rapid poleward expansion of reef-building corals in response to increasing coastal water temperatures, and forms one of the global hotspots for rapid coastal changes. Despite the temperate latitude surveyed (33°N, 133°E) the fish assemblage was both numerically, and in terms of richness, dominated by tropical fishes. Such tropical faunal dominance was apparent within both coral, and rocky reef habitats. The size structure of the assemblage suggested that a relatively large number of tropical species are overwintering within both coral and rocky habitats, with a subset of these species being potentially reproductively active. The relatively high abundance and richness of tropical species with obligate associations with live coral resources (i.e., obligate corallivores) shows that this region holds the most well developed temperate-located tropical fish fauna globally. We argue that future tropicalisation of the fish fauna in western Japan, associated with increasing coral habitat development and reported increasing shifts in coastal water temperatures, may have considerable positive economic

  12. Tropical fishes dominate temperate reef fish communities within western Japan.

    Directory of Open Access Journals (Sweden)

    Yohei Nakamura

    Full Text Available Climate change is resulting in rapid poleward shifts in the geographical distribution of tropical and subtropical fish species. We can expect that such range shifts are likely to be limited by species-specific resource requirements, with temperate rocky reefs potentially lacking a range of settlement substrates or specific dietary components important in structuring the settlement and success of tropical and subtropical fish species. We examined the importance of resource use in structuring the distribution patterns of range shifting tropical and subtropical fishes, comparing this with resident temperate fish species within western Japan (Tosa Bay; the abundance, diversity, size class, functional structure and latitudinal range of reef fishes utilizing both coral reef and adjacent rocky reef habitat were quantified over a 2 year period (2008-2010. This region has undergone rapid poleward expansion of reef-building corals in response to increasing coastal water temperatures, and forms one of the global hotspots for rapid coastal changes. Despite the temperate latitude surveyed (33°N, 133°E the fish assemblage was both numerically, and in terms of richness, dominated by tropical fishes. Such tropical faunal dominance was apparent within both coral, and rocky reef habitats. The size structure of the assemblage suggested that a relatively large number of tropical species are overwintering within both coral and rocky habitats, with a subset of these species being potentially reproductively active. The relatively high abundance and richness of tropical species with obligate associations with live coral resources (i.e., obligate corallivores shows that this region holds the most well developed temperate-located tropical fish fauna globally. We argue that future tropicalisation of the fish fauna in western Japan, associated with increasing coral habitat development and reported increasing shifts in coastal water temperatures, may have considerable

  13. DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae

    Directory of Open Access Journals (Sweden)

    Peter Huemer

    2014-04-01

    Full Text Available We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae, based on data from 44 European species (including 4 subspecies. Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c oxidase 1 gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924 and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum crypticum sp. n. from northern Italy, Switzerland and Greece. The new species and the hitherto intermixed closest relative C. amaurella are described in detail and adults and genitalia of both species are illustrated and a lectotype of C. amaurella is designated; a diagnostic comparison of the closely related C. iranicum Huemer, 1989, is added.

  14. DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae).

    Science.gov (United States)

    Huemer, Peter; Karsholt, Ole; Mutanen, Marko

    2014-01-01

    We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924) and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum crypticum sp. n. from northern Italy, Switzerland and Greece. The new species and the hitherto intermixed closest relative C. amaurella are described in detail and adults and genitalia of both species are illustrated and a lectotype of C. amaurella is designated; a diagnostic comparison of the closely related C. iranicum Huemer, 1989, is added.

  15. Vision Screening

    Science.gov (United States)

    ... of Prematurity Strabismus Stye (defined) Vision Screening Vision Screening Recommendations Loading... Most Common Searches Adult Strabismus Amblyopia Cataract Conjunctivitis Corneal Abrasions Dilating Eye ...

  16. Do bacteria, not fish, produce 'fish kairomone'?

    NARCIS (Netherlands)

    Ringelberg, J.; Van Gool, E.

    1998-01-01

    Fish-associated chemicals enhance phototactic downward swimming in Daphnia. If perch were treated with the antibiotic ampicillin, this enhancement was significantly decreased. Therefore, not fish, but bacteria associated with fish, seem to produce this kairomone. [KEYWORDS: Diel vertical migration;

  17. Screening for Iron Overload: Lessons from the HEmochromatosis and IRon Overload Screening (HEIRS Study

    Directory of Open Access Journals (Sweden)

    Paul C Adams

    2009-01-01

    Full Text Available BACKGROUND: The HEmochromatosis and IRon Overload Screening (HEIRS Study provided data on a racially, ethnically and geographically diverse cohort of participants in North America screened from primary care populations.

  18. 基于Rag1基因序列变异的鲤形目鱼类系统发育重建:采样策略对生命之树的影响%Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling

    Institute of Scientific and Technical Information of China (English)

    Richard L. MAYDEN; Phillip M. HARRIS; Junbing LI; Xuzhen WANG; Kenji SAITOH; Shunping HE; Huanzhang LIU; Yiyu CHEN; Mutsumi NISHIDA; Masaki MIYA; Kevin L. TANG; Robert M. WOOD; Wei-Jen CHEN; Mary K. AGNEW; Kevin W. CONWAY; Lei YANG; Andrew M. SIMONS; Henry L. BART

    2008-01-01

    The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future climatic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent molecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential

  19. The interleukins of fish.

    Science.gov (United States)

    Secombes, C J; Wang, T; Bird, S

    2011-12-01

    Interleukins are a subgroup of cytokines, molecules involved in the intercellular regulation of the immune system. The term interleukin was first coined in 1979 to refer to molecules that signal between different leucocyte types, although not exclusively restricted to leucocyte communication. Whilst it is now known that interleukins are produced by a wide variety of cell types, nevertheless many are synthesised by CD4(+) T helper cells, macrophages/monocytes and endothelial cells. The nomenclature is relatively straightforward, with interleukin 1 the first discovered and interleukin 2 the second, etc. However, whilst 35 interleukins are currently described in mammals, several are in fact terms referring to subfamilies of more molecules, as with the IL-1 family where 11 members (IL-1F1-IL-1F11) are present, and the IL-17 family where 6 members (IL-17A-IL-17F) are present. So the total is much higher and splice variants and allelic variation increase this diversity further. This review will focus on what is known about interleukins in fish, and will refer to the major subfamilies rather than try to work through 35 descriptions in a row. It is clear that many direct homologues of molecules known in mammals are present in fish, but that not all are present and some novel interleukins exist that may have arisen from fish specific gene duplication events. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Comparison of LC/MS and SFC/MS for screening of a large and diverse library of pharmaceutically relevant compounds.

    Science.gov (United States)

    Pinkston, J David; Wen, Dong; Morand, Kenneth L; Tirey, Debra A; Stanton, David T

    2006-11-01

    The search for greater speed of analysis has fueled many innovations in high-performance liquid chromatography (HPLC), such as the use of higher pressures and smaller stationary-phase particles, and the development of monolithic columns. Alternatively, one might alter the chromatographic mobile phase. The low viscosity and high diffusivity of the mobile phase in supercritical fluid chromatography (SFC) allows higher flow rates and lower pressure drops than is possible in traditional HPLC. In addition, SFC requires less organic, or aqueous-organic, solvent than LC (important in preparative-scale chromatography) and provides an alternative, normal-phase retention mechanism. But fluids that are commonly used as the main mobile-phase component in SFC, such as CO2, are relatively nonpolar. As a result, SFC is commonly believed to only be applicable to nonpolar and relatively low-polarity compounds. Here we build upon recent work with SFC of polar and ionic compounds and peptides, and we compare the LC/MS and SFC/MS of a diverse library of druglike compounds. A total of 75.0% of the library compounds were eluted and detected by SFC/MS, while 79.4% were eluted and detected by LC/MS. Some samples provided strong peaks that appeared to be related to the purported compound contained in the sample. When these were added to the "hits", the numbers rose to 86.7 and 89.9%, respectively. A total of 3.7% of the samples were observed by SFC/MS, but not by LC/MS, and 8.1% of the samples were observed by LC/MS, but not by SFC/MS. The only compound class that appeared to be consistently detected in LC/MS, but not in SFC/MS under our conditions, consisted of compounds containing a phosphate, a phosphonate, or a bisphosphonate. The SFC/MS method was at least as durable, reliable, and user-friendly as the LC/MS method. The APCI source required less cleaning during the SFC/MS separations than it did during LC/MS.

  1. The Fishing Cat

    Institute of Scientific and Technical Information of China (English)

    孙雅飞; 乐伟国

    2008-01-01

    @@ 一、故事内容 A cat goes fishing every day. He wants to eat fish, but he can't catch any fish. One day, he goes to the river as usual. Suddenly, a fish comes out. He catches the fish and putsthe fish in the basket. He's very happy, but he forgest to put the lid on the basket.

  2. Gradientes de diversidade nas comunidades de peixes da bacia do rio Iguatemi, Mato Grosso do Sul, Brasil Diversity gradients in fish communities of Iguatemi river basin, Mato Grosso do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Yzel Rondon Súarez

    2006-06-01

    Full Text Available Com o objetivo de verificar a importância da variação longitudinal, sazonal e a influência das características físicas e químicas da água sobre a diversidade de espécies de peixes realizamos amostragens trimestrais, entre Novembro/1999 e Agosto/2000, em três pontos amostrais no rio Jogui e oito pontos amostrais no rio Iguatemi-MS. A variação longitudinal foi mais importante que a variação sazonal na determinação da riqueza e número de indivíduos no rio Jogui, no entanto, a equitabilidade não apresentou diferença significativa sazonal ou longitudinal. No rio Jogui 78,3% da variação na riqueza de espécies, 81,6% no número de indivíduos e 41,1% na equitabilidade foram explicadas pelas características físicas e químicas da água. No rio Iguatemi nós não detectamos diferenças estatisticamente significativas longitudinais ou sazonais nos descritores analisados das comunidades nem influência significativa dos fatores ambientais.In order to verify the importance of longitudinal and seasonal variations and the effect of physical and chemical water characteristics to fish species diversity we accomplished three-month samplings, between November/1999 and August/2000, in three selected points in the Jogui River and eight points in the Iguatemi River-MS. The longitudinal variation was more important than seasonal variation in determining richness and number of individuals in the Jogui River, however, evenness did not present statistically significant differences either longitudinal or seasonal. In the Jogui River 78.3% of species richness, 81.6% of number of individuals and 41.1% of evenness variation was explained by the water chemical and physical characteristics. In the Iguatemi River we did not detect longitudinal or seasonal statistically significant differences in the analyzed community descriptors nor significant influence of environmental factors.

  3. Marine Fish Hybridization

    KAUST Repository

    He, Song

    2017-04-01

    Natural hybridization is reproduction (without artificial influence) between two or more species/populations which are distinguishable from each other by heritable characters. Natural hybridizations among marine fishes were highly underappreciated due to limited research effort; it seems that this phenomenon occurs more often than is commonly recognized. As hybridization plays an important role in biodiversity processes in the marine environment, detecting hybridization events and investigating hybridization is important to understand and protect biodiversity. The first chapter sets the framework for this disseration study. The Cohesion Species Concept was selected as the working definition of a species for this study as it can handle marine fish hybridization events. The concept does not require restrictive species boundaries. A general history and background of natural hybridization in marine fishes is reviewed during in chapter as well. Four marine fish hybridization cases were examed and documented in Chapters 2 to 5. In each case study, at least one diagnostic nuclear marker, screened from among ~14 candidate markers, was found to discriminate the putative hybridizing parent species. To further investigate genetic evidence to support the hybrid status for each hybrid offspring in each case, haploweb analysis on diagnostic markers (nuclear and/or mitochondrial) and the DAPC/PCA analysis on microsatellite data were used. By combining the genetic evidences, morphological traits, and ecological observations together, the potential reasons that triggered each hybridization events and the potential genetic/ecology effects could be discussed. In the last chapter, sequences from 82 pairs of hybridizing parents species (for which COI barcoding sequences were available either on GenBank or in our lab) were collected. By comparing the COI fragment p-distance between each hybridizing parent species, some general questions about marine fish hybridization were discussed: Is

  4. Supplement Analysis for the Watershed Management Program Final EIS (DOE EIS /SA-156) - Upper Salmon River Anadromous Fish Passage Improvement Projects

    Energy Technology Data Exchange (ETDEWEB)

    Keller, Carl J. [Bonneville Power Administration (BPA), Portland, OR (United States)

    2004-07-13

    BPA proposes to fund IDFG to plan and complete construction of fish passage improvements and water conservation activities that are contained within IDFG’s Statement of Work (SOW) for the period 7/1/04 to 6/30/05. The funding request contained in their SOW is part of an ongoing IDFG effort to fund anadromous fish passage projects that fall outside the scope of the Mitchell Act. The proposed SOW activities fall within the following four categories: Phase I-Planning and Design (gather data, perform investigations, and exchange information; perform surveys and assessments to be compliant; survey project sites and perform engineering designs; perform contract and project management); Phase II-Construction and Implementation (procure materials and supplies, prepare contracts and solicit bids, plant native seedlings, complete capital improvements); Phase III-Operation and Maintenance (maintain office operations); and Phase IV- Monitoring and Evaluation (monitor and evaluate post-project effects, reporting). The SOW culminates with proposed construction of 18 capital improvement projects (Table 1 attached). The types of capital improvements include: screening gravity water diversions; consolidating and/or eliminating ditches; evaluating and screening pump diversions; evaluating and implementing water conservation activities; constructing screens along migration routes and rearing areas for hatchery and wild salmon; improving upstream and downstream passage for anadromous fish; and maximize benefits to aquatic habitat. Because each of the proposed projects in the SOW is still in the planning stages, the specifics of each still need to be completed.

  5. Fish gelatin.

    Science.gov (United States)

    Boran, Gokhan; Regenstein, Joe M

    2010-01-01

    Gelatin is a multifunctional ingredient used in foods, pharmaceuticals, cosmetics, and photographic films as a gelling agent, stabilizer, thickener, emulsifier, and film former. As a thermoreversible hydrocolloid with a narrower gap between its melting and gelling temperatures, both of which are below human body temperature, gelatin provides unique advantages over carbohydrate-based gelling agents. Gelatin is mostly produced from pig skin, and cattle hides and bones. Some alternative raw materials have recently gained attention from both researchers and the industry not just because they overcome religious concerns shared by Jews and Muslims but also because they provide, in some cases, technological advantages over mammalian gelatins. Fish skins from a number of fish species are among the other sources that have been comprehensively studied as sources for gelatin production. Fish skins have a significant potential for the production of high-quality gelatin with different melting and gelling temperatures over a much wider range than mammalian gelatins, yet still have a sufficiently high gel strength and viscosity. Gelatin quality is industrially determined by gel strength, viscosity, melting or gelling temperatures, the water content, and microbiological safety. For gelatin manufacturers, yield from a particular raw material is also important. Recent experimental studies have shown that these quality parameters vary greatly depending on the biochemical characteristics of the raw materials, the manufacturing processes applied, and the experimental settings used for quality control tests. In this review, the gelatin quality achieved from different fish species is reviewed along with the experimental procedures used to determine gelatin quality. In addition, the chemical structure of collagen and gelatin, the collagen-gelatin conversion, the gelation process, and the gelatin market are discussed.

  6. Fish hemoglobins

    Directory of Open Access Journals (Sweden)

    P.C. de Souza

    2007-06-01

    Full Text Available Vertebrate hemoglobin, contained in erythrocytes, is a globular protein with a quaternary structure composed of 4 globin chains (2 alpha and 2 beta and a prosthetic group named heme bound to each one. Having myoglobin as an ancestor, hemoglobin acquired the capacity to respond to chemical stimuli that modulate its function according to tissue requirements for oxygen. Fish are generally submitted to spatial and temporal O2 variations and have developed anatomical, physiological and biochemical strategies to adapt to the changing environmental gas availability. Structurally, most fish hemoglobins are tetrameric; however, those from some species such as lamprey and hagfish dissociate, being monomeric when oxygenated and oligomeric when deoxygenated. Fish blood frequently possesses several hemoglobins; the primary origin of this finding lies in the polymorphism that occurs in the globin loci, an aspect that may occasionally confer advantages to its carriers or even be a harmless evolutionary remnant. On the other hand, the functional properties exhibit different behaviors, ranging from a total absence of responses to allosteric regulation to drastic ones, such as the Root effect.

  7. Salmonids surveys, number of juvenile fish, fork length, and species diversity conducted in the Little Campbell Creek watershed, Alaska from 2010-11-01 to 2011-03-01 (NCEI Accession 0148761)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Over the past few years biologists and other researchers have encountered noticeable fish die-offs, mostly of young salmonid, in various stretches of Little Campbell...

  8. Biodiversity enhances reef fish biomass and resistance to climate change.

    Science.gov (United States)

    Duffy, J Emmett; Lefcheck, Jonathan S; Stuart-Smith, Rick D; Navarrete, Sergio A; Edgar, Graham J

    2016-05-31

    Fishes are the most diverse group of vertebrates, play key functional roles in aquatic ecosystems, and provide protein for a billion people, especially in the developing world. Those functions are compromised by mounting pressures on marine biodiversity and ecosystems. Because of its economic and food value, fish biomass production provides an unusually direct link from biodiversity to critical ecosystem services. We used the Reef Life Survey's global database of 4,556 standardized fish surveys to test the importance of biodiversity to fish production relative to 25 environmental drivers. Temperature, biodiversity, and human influence together explained 47% of the global variation in reef fish biomass among sites. Fish species richness and functional diversity were among the strongest predictors of fish biomass, particularly for the large-bodied species and carnivores preferred by fishers, and these biodiversity effects were robust to potentially confounding influences of sample abundance, scale, and environmental correlations. Warmer temperatures increased biomass directly, presumably by raising metabolism, and indirectly by increasing diversity, whereas temperature variability reduced biomass. Importantly, diversity and climate interact, with biomass of diverse communities less affected by rising and variable temperatures than species-poor communities. Biodiversity thus buffers global fish biomass from climate change, and conservation of marine biodiversity can stabilize fish production in a changing ocean.

  9. Review of Arapaho NWR Diversion Reconstruction

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A summary of the issues and suggestions for each structure for the Diversion Reconstruction Project at the Arapaho National Wildlife Refuge after inspection by Water...

  10. Arapahoe NWR diversion reconstruction : As-Builts

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a as-built plan for diversion reconstruction for Hubbard #2, Oklahoma #1, Dryer, Hill and Crowder sites on the Arapahoe National Wildlife Refuge.

  11. Page 1 Tropical Freshwater Biology, 7 (1998) 37-51 37 FISH ...

    African Journals Online (AJOL)

    KEY WORDS: fish diversity - distribution - abundance - River Jamieson -. Nigeria. ... The river flows all year round with the highest level and discharge during .... Mormyridae O 50 6 40 .... Studies On the fish community of River Ase, Bendel.

  12. Malheur NWR: Initial Survey Instructions for Fish Assemblage and Carp Presence/Absence

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — An understanding of the diversity of fishes, their location and abundance in refuge ecosystems is a vital foundation for protecting and restoring the aquatic health...

  13. 76 FR 57717 - Endangered and Threatened Species; Take of Anadromous Fish

    Science.gov (United States)

    2011-09-16

    ... different geographic populations and identify potential salmonid sources for introduction into the San... sturgeon (Acipenser medirostris) for scientific research purposes. NRSI will collect fish entrainment data... of the study are: to determine correlation of fish entrainment with river diversion flows,...

  14. Effects of cage fish culture on water quality and selected biological ...

    African Journals Online (AJOL)

    Effects of cage fish culture on water quality and selected biological ... varied spatially and temporally but were generally within safe ranges for freshwater habitats. ... and depressed zooplankton diversity at WC suggested impacts from the fish ...

  15. Distribution of the three major species of fish in the Hartbeespoort ...

    African Journals Online (AJOL)

    1985-08-05

    Aug 5, 1985 ... ... of fish in the. Hartbeespoort Dam in relation to some environmental .... The factors considered most likely to influence fish distribution were ..... and species diversity of benthic invertebrates decreases with increasing depth ...

  16. Isolation and Identification of a New Tetrodotoxin-Producing Bacterial Species, Raoultella terrigena, from Hong Kong Marine Puffer Fish Takifugu niphobles

    Directory of Open Access Journals (Sweden)

    Fred Wang-Fat Lee

    2011-11-01

    Full Text Available Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01 was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX. Based on the Microbial Identification (MIDI and 16S-23S rDNA internal transcribed spacer (ITS phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF. Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.

  17. Isolation and identification of a new tetrodotoxin-producing bacterial species, Raoultella terrigena, from Hong Kong marine puffer fish Takifugu niphobles.

    Science.gov (United States)

    Yu, Vincent Chung-Him; Yu, Peter Hoi-Fu; Ho, Kin-Chung; Lee, Fred Wang-Fat

    2011-01-01

    Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01) was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX). Based on the Microbial Identification (MIDI) and 16S-23S rDNA internal transcribed spacer (ITS) phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF). Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.

  18. Whole genome data for omics-based research on the self-fertilizing fish Kryptolebias marmoratus.

    Science.gov (United States)

    Rhee, Jae-Sung; Lee, Jae-Seong

    2014-08-30

    Genome resources have advantages for understanding diverse areas such as biological patterns and functioning of organisms. Omics platforms are useful approaches for the study of organs and organisms. These approaches can be powerful screening tools for whole genome, proteome, and metabolome profiling, and can be used to understand molecular changes in response to internal and external stimuli. This methodology has been applied successfully in freshwater model fish such as the zebrafish Danio rerio and the Japanese medaka Oryzias latipes in research areas such as basic physiology, developmental biology, genetics, and environmental biology. However, information is still scarce about model fish that inhabit brackish water or seawater. To develop the self-fertilizing killifish Kryptolebias marmoratus as a potential model species with unique characteristics and research merits, we obtained genomic information about K. marmoratus. We address ways to use these data for genome-based molecular mechanistic studies. We review the current state of genome information on K. marmoratus to initiate omics approaches. We evaluate the potential applications of integrated omics platforms for future studies in environmental science, developmental biology, and biomedical research. We conclude that information about the K. marmoratus genome will provide a better understanding of the molecular functions of genes, proteins, and metabolites that are involved in the biological functions of this species. Omics platforms, particularly combined technologies that make effective use of bioinformatics, will provide powerful tools for hypothesis-driven investigations and discovery-driven discussions on diverse aspects of this species and on fish and vertebrates in general.

  19. Chemical avoidance responses of fishes.

    Science.gov (United States)

    Tierney, Keith B

    2016-05-01

    The hydrosphere is a repository for all of our waste and mistakes, be they sewage, garbage, process-affected waters, runoff, and gases. For fish living in environments receiving undesirable inputs, moving away seems an obvious way to avoid harm. While this should occur, there are numerous examples where it will not. The inability to avoid harmful environments may lead to sensory impairments that in turn limit the ability to avoid other dangers or locate benefits. For avoidance to occur, the danger must first be perceived, which may not happen if the fish is 'blinded' in some capacity. Second, the danger must be recognized for what it is, which may also not happen if the fish is cognitively confused or impaired. Third, it is possible that the fish may not be able to leave the area, or worse, learns to prefer a toxic environment. Concerning generating regulations around avoidance, there are two possibilities: that an avoidance threshold be used to set guidelines for effluent release with the intention of driving fishes away; the second is to set a contaminant concentration that would not affect the avoidance or attraction responses to other cues. With the complexities of the modern world in which we release diverse pollutants, from light to municipal effluents full of 1000s of chemicals, to the diversity present in ecosystems, it is impossible to have avoidance data on every stimulus-species combination. Nevertheless, we may be able to use existing avoidance response data to predict the likelihood of avoidance of untested stimuli. Where we cannot, this review includes a framework that can be used to direct new research. This review is intended to collate existing avoidance response data, provide a framework for making decisions in the absence of data, and suggest studies that would facilitate the prediction of risk to fish health in environments receiving intentional and unintentional human-based chemical inputs.

  20. Fish Tales

    Energy Technology Data Exchange (ETDEWEB)

    McLerran, L.

    2010-07-06

    This talk is about fishing and the friendships that have resulted in its pursuit. It is also about theoretical physics, and the relationship of imagination and fantasy to the establishment of ideas about nature. Fishermen, like theoretical physicists, are well known for their inventive imaginations. Perhaps neither are as clever as sailors, who conceived of the mermaid. If one doubts the power of this fantasy, one should remember the ghosts of the many sailors who drowned pursuing these young nymphs. An extraordinary painting by J. Waterhouse is shown as Fig. 1. The enchantment of a mermaid must reflect an extraordinary excess of imagination on the part of the sailor, perhaps together with an impractical turn of mind. A consummated relationship with a mermaid is after all, by its very nature a fantasy incapable of realization. To a theoretical physicist, she is symbolic of many ideas we develop. There are many truths known to fisherman in which one might also find parallels to the goals of scientists: (1) A fish is the only animal that keeps growing after its death; (2) Nothing makes a fish bigger than almost being caught; (3) ''...of all the liars among mankind, the fisherman is the most trustworthy.'' (William Sherwood Fox, in Silken Lines and Silver Hooks); and (4) Men and fish are alike. They both get into trouble when they open their mouths. These quotes may be interpreted as reflecting skepticism regarding the honesty of fisherman, and probably do not reflect adequate admiration for a creative imagination. Is it fair to criticize a person for believing a falsehood that he or she sincerely believes to be true? The fisherman simultaneously invents the lie, and believes in it himself. The parallel with theoretical physics is perhaps only approximate, although we physicists may invent stories that we come to believe, on some rare occasions our ideas actually correspond to a more or less true descriptions of nature. These minor philosophical

  1. Fish Immunoglobulins

    Science.gov (United States)

    Mashoof, Sara; Criscitiello, Michael F.

    2016-01-01

    The B cell receptor and secreted antibody are at the nexus of humoral adaptive immunity. In this review, we summarize what is known of the immunoglobulin genes of jawed cartilaginous and bony fishes. We focus on what has been learned from genomic or cDNA sequence data, but where appropriate draw upon protein, immunization, affinity and structural studies. Work from major aquatic model organisms and less studied comparative species are both included to define what is the rule for an immunoglobulin isotype or taxonomic group and what exemplifies an exception. PMID:27879632

  2. Depression Screening

    Science.gov (United States)

    ... Centers Diseases + Condition Centers Mental Health Medical Library Depression Screening (PHQ-9) - Instructions The following questions are ... this tool, there is also text-only version . Depression Screening - Manual Instructions The following questions are a ...

  3. Impact of entrainment and impingement on fish populations in the Hudson River Estuary. Volume II. Impingement impact analyses, evaluations of alternative screening devices, and critiques of utility testimony relating to density-dependent growth, the age-composition of the striped bass spawning stock, and the LMS real-time life cycle model

    Energy Technology Data Exchange (ETDEWEB)

    Barnthouse, L. W.; Van Winkle, W.; Golumbek, J.; Cada, G. F.; Goodyear, C. P.; Christensen, S. W.; Cannon, J. B.; Lee, D. W.

    1982-04-01

    This volume includes a series of four exhibits relating to impacts of impingement on fish populations, together with a collection of critical evaluations of testimony prepared for the utilities by their consultants. The first exhibit is a quantitative evaluation of four sources of bias (collection efficiency, reimpingement, impingement on inoperative screens, and impingement survival) affecting estimates of the number of fish killed at Hudson River power plants. The two following exhibits contain, respectively, a detailed assessment of the impact of impingement on the Hudson River white perch population and estimates of conditional impingement mortality rates for seven Hudson River fish populations. The fourth exhibit is an evaluation of the engineering feasibility and potential biological effectiveness of several types of modified intake structures proposed as alternatives to cooling towers for reducing impingement impacts. The remainder of Volume II consists of critical evaluations of the utilities' empirical evidence for the existence of density-dependent growth in young-of-the-year striped bass and white perch, of their estimate of the age-composition of the striped bass spawning stock in the Hudson River, and of their use of the Lawler, Matusky, and Skelly (LMS) Real-Time Life Cycle Model to estimate the impact of entrainment and impingement on the Hudson River striped bass population.

  4. Multiplex-FISH (M-FISH): technique, developments and applications.

    Science.gov (United States)

    Kearney, L

    2006-01-01

    Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.

  5. Cancer Screening

    Directory of Open Access Journals (Sweden)

    Krishna Prasad

    2004-10-01

    Full Text Available Cancer screening is a means to detect cancer early with the goal of decreasing morbidity and mortality. At present, there is a reasonable consensus regarding screening for breast, cervical and colorectal cances and the role of screening is under trial in case of cancers of the lung,  ovaries and prostate. On the other hand, good screening tests are not available for some of the commonest cancers in India like the oral, pharyngeal, esophageal and stomach cancers.

  6. Cancer Screening

    OpenAIRE

    Krishna Prasad

    2004-01-01

    Cancer screening is a means to detect cancer early with the goal of decreasing morbidity and mortality. At present, there is a reasonable consensus regarding screening for breast, cervical and colorectal cances and the role of screening is under trial in case of cancers of the lung,  ovaries and prostate. On the other hand, good screening tests are not available for some of the commonest cancers in India like the oral, pharyngeal, esophageal and stomach cancers.

  7. 50 CFR 80.4 - Diversion of license fees.

    Science.gov (United States)

    2010-10-01

    ... (CONTINUED) FINANCIAL ASSISTANCE-WILDLIFE SPORT FISH RESTORATION PROGRAM ADMINISTRATIVE REQUIREMENTS, PITTMAN-ROBERTSON WILDLIFE RESTORATION AND DINGELL-JOHNSON SPORT FISH RESTORATION ACTS § 80.4 Diversion of license... charges imposed by the State to hunt or fish for sport or recreation. (2) Sale, lease, rental, or other...

  8. Fishing activities

    Science.gov (United States)

    Oberle, Ferdinand; Puig, Pere; Martin, Jacobo; Micallef, Aaron; Krastel, Sebastian; Savini, Alessandra

    2018-01-01

    Unlike the major anthropogenic changes that terrestrial and coastal habitats underwent during the last centuries such as deforestation, river engineering, agricultural practices or urbanism, those occurring underwater are veiled from our eyes and have continued nearly unnoticed. Only recent advances in remote sensing and deep marine sampling technologies have revealed the extent and magnitude of the anthropogenic impacts to the seafloor. In particular, bottom trawling, a fishing technique consisting of dragging a net and fishing gear over the seafloor to capture bottom-dwelling living resources has gained attention among the scientific community, policy makers and the general public due to its destructive effects on the seabed. Trawling gear produces acute impacts on biota and the physical substratum of the seafloor by disrupting the sediment column structure, overturning boulders, resuspending sediments and imprinting deep scars on muddy bottoms. Also, the repetitive passage of trawling gear over the same areas creates long-lasting, cumulative impacts that modify the cohesiveness and texture of sediments. It can be asserted nowadays that due to its recurrence, mobility and wide geographical extent, industrial trawling has become a major force driving seafloor change and affecting not only its physical integrity on short spatial scales but also imprinting measurable modifications to the geomorphology of entire continental margins.

  9. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

    Science.gov (United States)

    Perryman, Alexander L; Santiago, Daniel N; Forli, Stefano; Martins, Diogo Santos; Olson, Arthur J

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  10. ARTIFICIAL FISH PROPAGATION IN KANEV RESERVOIR

    Directory of Open Access Journals (Sweden)

    O. B. Gurbik

    2014-11-01

    Full Text Available Based on the analysis of the dynamics of structural parameters of fish fauna of the Kanev reservoir, we determined the major measures for artificial fish propagation (stocking, which would allow increasing their commercial stocks and maintain biological diversity. It was found that main biological factors, which defined the conditions of existence of fish at different stages of their life cycle in the Kanev reservoir was as a whole favorable for providing sufficient efficiency of measures for stocking it with juveniles of commercially and environmentally valuable fishes. With current state of fish fauna and possibilities of fish hatcheries, the priority in the part of artificial maintenance of fish populations should be given to pike-perch, wels, and tench. An increase of amounts of commercial catches should be based first of all on full-scale stocking with silver and bighead carps, the created stock of which will be available for effective exploitation at a regime, which is protective for native fish fauna. The current bioproductive potential allows increasing the indices of the stock of commercially valuable species up to 120 kg/ha that is twice more than the actual indices for 2012-2013. Key words: fish fauna, artificial propagation, commercial stock, Kanev reservoir.

  11. Double screening

    Energy Technology Data Exchange (ETDEWEB)

    Gratia, Pierre [Department of Physics, University of Chicago,South Ellis Avenue, Chicago, IL 60637 (United States); Hu, Wayne [Department of Astronomy and Astrophysics, University of Chicago,South Ellis Avenue, Chicago, IL 60637 (United States); Enrico Fermi Institute and Kavli Institute for Cosmological Physics, University of Chicago,South Ellis Avenue, Chicago, IL 60637 (United States); Joyce, Austin [Enrico Fermi Institute and Kavli Institute for Cosmological Physics, University of Chicago,South Ellis Avenue, Chicago, IL 60637 (United States); Ribeiro, Raquel H. [School of Physics and Astronomy, Queen Mary University of London,Mile End Road, London, E1 4NS (United Kingdom)

    2016-06-15

    Attempts to modify gravity in the infrared typically require a screening mechanism to ensure consistency with local tests of gravity. These screening mechanisms fit into three broad classes; we investigate theories which are capable of exhibiting more than one type of screening. Specifically, we focus on a simple model which exhibits both Vainshtein and kinetic screening. We point out that due to the two characteristic length scales in the problem, the type of screening that dominates depends on the mass of the sourcing object, allowing for different phenomenology at different scales. We consider embedding this double screening phenomenology in a broader cosmological scenario and show that the simplest examples that exhibit double screening are radiatively stable.

  12. Hierarchical spatial structure of stream fish colonization and extinction

    Science.gov (United States)

    Hitt, N.P.; Roberts, J.H.

    2012-01-01

    Spatial variation in extinction and colonization is expected to influence community composition over time. In stream fish communities, local species richness (alpha diversity) and species turnover (beta diversity) are thought to be regulated by high extinction rates in headwater streams and high colonization rates in downstream areas. We evaluated the spatiotemporal structure of fish communities in streams originally surveyed by Burton and Odum 1945 (Ecology 26: 182-194) in Virginia, USA and explored the effects of species traits on extinction and colonization dynamics. We documented dramatic changes in fish community structure at both the site and stream scales. Of the 34 fish species observed, 20 (59%) were present in both time periods, but 11 (32%) colonized the study area and three (9%) were extirpated over time. Within streams, alpha diversity increased in two of three streams but beta diversity decreased dramatically in all streams due to fish community homogenization caused by colonization of common species and extirpation of rare species. Among streams, however, fish communities differentiated over time. Regression trees indicated that reproductive life-history traits such as spawning mound construction, associations with mound-building species, and high fecundity were important predictors of species persistence or colonization. Conversely, native fishes not associated with mound-building exhibited the highest rates of extirpation from streams. Our results demonstrate that stream fish colonization and extinction dynamics exhibit hierarchical spatial structure and suggest that mound-building fishes serve as keystone species for colonization of headwater streams.

  13. Fishing amplifies forage fish population collapses.

    Science.gov (United States)

    Essington, Timothy E; Moriarty, Pamela E; Froehlich, Halley E; Hodgson, Emma E; Koehn, Laura E; Oken, Kiva L; Siple, Margaret C; Stawitz, Christine C

    2015-05-26

    Forage fish support the largest fisheries in the world but also play key roles in marine food webs by transferring energy from plankton to upper trophic-level predators, such as large fish, seabirds, and marine mammals. Fishing can, thereby, have far reaching consequences on marine food webs unless safeguards are in place to avoid depleting forage fish to dangerously low levels, where dependent predators are most vulnerable. However, disentangling the contributions of fishing vs. natural processes on population dynamics has been difficult because of the sensitivity of these stocks to environmental conditions. Here, we overcome this difficulty by collating population time series for forage fish populations that account for nearly two-thirds of global catch of forage fish to identify the fingerprint of fisheries on their population dynamics. Forage fish population collapses shared a set of common and unique characteristics: high fishing pressure for several years before collapse, a sharp drop in natural population productivity, and a lagged response to reduce fishing pressure. Lagged response to natural productivity declines can sharply amplify the magnitude of naturally occurring population fluctuations. Finally, we show that the magnitude and frequency of collapses are greater than expected from natural productivity characteristics and therefore, likely attributed to fishing. The durations of collapses, however, were not different from those expected based on natural productivity shifts. A risk-based management scheme that reduces fishing when populations become scarce would protect forage fish and their predators from collapse with little effect on long-term average catches.

  14. DNA barcoding for species assignment: the case of Mediterranean marine fishes.

    Directory of Open Access Journals (Sweden)

    Monica Landi

    Full Text Available BACKGROUND: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. METHODOLOGY/PRINCIPAL FINDINGS: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1 a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2 the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS and 72% (GenBank of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%, most of them of high commercial relevance, suggesting possible cryptic species. CONCLUSION/SIGNIFICANCE: We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA

  15. Walla Walla River Fish Passage Operations Program, 2004-2005 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Bronson, James P. (Confederated Tribes of the Umatilla Indian Reservation, Department of Natural Resources, Pendleton, OR); Duke, Bill B. (Oregon Department of Fish and Wildlife, Pendleton, OR)

    2006-02-01

    In the late 1990s, the Confederated Tribes of the Umatilla Indian Reservation, Oregon Department of Fish and Wildlife, and Washington Department of Fish and Wildlife, along with many other agencies, began implementing fisheries restoration activities in the Walla Walla Basin. An integral part of these efforts is to alleviate the inadequate fish migration conditions in the basin. The migration concerns are being addressed by removing diversion structures, constructing fish passage facilities, implementing minimum instream flow requirements, and providing trap and haul efforts when needed. The objective of the Walla Walla River Fish Passage Operations Project is to increase the survival of migrating adult and juvenile salmonids in the Walla Walla River basin. The project is responsible for coordinating operation and maintenance of ladders, screen sites, bypasses, trap facilities, and transportation equipment. In addition, the project provides technical input on passage criteria and passage and trapping facility design and operation. Operation of the various passage facilities and passage criteria guidelines are outlined in an annual operations plan that the project develops. During the 2004-2005 project year, there were 590 adult summer steelhead, 31 summer steelhead kelts (Oncorhynchus mykiss), 70 adult bull trout (Salvelinus confluentus); 80 adult and 1 jack spring Chinook (O. tshawytscha) enumerated at the Nursery Bridge Dam fishway video counting window between December 13, 2004, and June 16, 2005. Summer steelhead and spring chinook were observed moving upstream while bull trout were observed moving both upstream and downstream of the facility. In addition, the old ladder trap was operated by ODFW in order to enumerate fish passage. Of the total, 143 adult summer steelhead and 15 summer steelhead kelts were enumerated at the west ladder at Nursery Bridge Dam during the video efforts between February 4 and May 23, 2005. Operation of the Little Walla Walla River

  16. Sport Fishing Regulations

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The regulations for sport fishing on St. Vincent National Wildlife Refuge are outlined in this document. Fishing is only permitted from sunrise to sunset, and only...

  17. Fish Springs pond snail

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Communication scenario between the branch of Listing and Recovery, Fish and Wildlife Enhancement, and Fish Springs National Wildlife Refuge (NWR), in regards to the...

  18. Fish tapeworm infection

    Science.gov (United States)

    Fish tapeworm infection is an intestinal infection with the tapeworm parasite found in fish. ... The fish tapeworm ( Diphyllobothrium latum ) is the largest parasite that infects humans. Humans become infected when they eat raw ...

  19. Got a Sick Fish?

    Science.gov (United States)

    ... Welfare Veterinary Careers Public Health Got a sick fish? Fish with disease can show a variety of signs. If you notice your pet fish having any unusual disease signs, contact your veterinarian ...

  20. Colon cancer screening

    Science.gov (United States)

    Screening for colon cancer; Colonoscopy - screening; Sigmoidoscopy - screening; Virtual colonoscopy - screening; Fecal immunochemical test; Stool DNA test; sDNA test; Colorectal cancer - screening; Rectal ...

  1. DETERMINATION OF HISTAMINE IN FISH USING ELISA TECHNIQUE

    NARCIS (Netherlands)

    KRUGER, C; SEWING, U; STENGEL, G; KEMA, [No Value; WESTERMANN, J; MANZ, B

    1995-01-01

    The analysis of histamine in fish and fish products via competitive ELISA is described. The advantages of this method are easy sample preparation and handling, screening capabilities, and low costs. Automation enables the performance of the assay with higher series of samples. The Histamine-ELISA is

  2. Fish mycobacteriosis (Tuberculosis)

    Science.gov (United States)

    Parisot, T.J.; Wood, J.W.

    1959-01-01

    The etiologic agent for the bacterial disease, "fish tuberculosis" (more correctly "mycobacteriosis"), was first observed in carp in 189& from a pond in France. Subsequently similar agents have been isolated from or observed in fish in fresh water, salt water, and brackish water, in fish in aquaria, hatcheries, and natural habitat~ (wild populations of fish). The disease has been recognized as an important infection among hatchery reared salmonid fishes on the West Coast of the United States, and in aquarium fishes such as the neon tetra, the Siamese fighting fish, and in salt water fish held in zoological displays.

  3. No Fishing Now,More Fish Later

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Fishing ban for ecological purposes starts on the Pearl River Since April1,a two-month ban on fishing has been imposed on the Pearl River valley in south China.It is the first fishing ban in this area with the purpose of preserving biodiversity in China’s third longest

  4. Microbiological spoilage of fish and fish products

    DEFF Research Database (Denmark)

    Gram, Lone; Huss, Hans Henrik

    1996-01-01

    Spoilage of fresh and lightly preserved fish products is caused by microbial action. This paper reviews the current knowledge in terms of the microbiology of fish and fish products with particular emphasis on identification of specific spoilage bacteria and the qualitative and quantitative...

  5. Use Of Poachers’ Catches For Studying Fish Fauna In The Water Bodies Of The Transcarpathian Region (Ukraine

    Directory of Open Access Journals (Sweden)

    Didenko Alexander

    2014-10-01

    Full Text Available We compared techniques used by poachers to capture fishes in the streams and stagnant water bodies of the Tisa River basin in Ukraine, which included: gill nets, lift nets, screen nets, electrofishing devices, spears, concussion, and beach seine. In total, 38 species were observed in poachers’ catches, among which the most abundant were nase (Chondrostoma nasus, Carpathian barbel (Barbus carpathicus, chub (Squalius cephalus, crucian carp (Carassius gibelio, and minnow (Phoxinus phoxinus. The highest diversity of species was observed in gill nets (25 species in rivers and 10 in stagnant waters, lift nets (20 species in rivers and eight in stagnant waters, and electrofishing (19 species. Poachers’ catches can provide information on fish species’ compositions and relative abundance in montane rivers; but there are biases associated with each technique.

  6. Fish Springs National Wildlife Refuge aquatic invertebrate survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The primary objective of the 1993 study was to investigate the premise that macroinvertebrate species diversity and abundance increases significantly following a...

  7. Biofilm responses to marine fish farm wastes

    Energy Technology Data Exchange (ETDEWEB)

    Sanz-Lazaro, Carlos, E-mail: carsanz@um.es [Departamento de Ecologia e Hidrologia, Facultad de Biologia, Universidad de Murcia, 30100 Murcia (Spain); Navarrete-Mier, Francisco; Marin, Arnaldo [Departamento de Ecologia e Hidrologia, Facultad de Biologia, Universidad de Murcia, 30100 Murcia (Spain)

    2011-03-15

    The changes in the biofilm community due to organic matter enrichment, eutrophication and metal contamination derived from fish farming were studied. The biofilm biomass, polysaccharide content, trophic niche and element accumulation were quantified along an environmental gradient of fish farm wastes in two seasons. Biofilm structure and trophic diversity was influenced by seasonality as well as by the fish farm waste load. Fish farming enhanced the accumulation of organic carbon, nutrients, selenium and metals by the biofilm community. The accumulation pattern of these elements was similar regardless of the structure and trophic niche of the community. This suggests that the biofilm communities can be considered a reliable tool for assessing dissolved aquaculture wastes. Due to the ubiquity of biofilms and its wide range of consumers, its role as a sink of dissolved wastes may have important implications for the transfer of aquaculture wastes to higher trophic levels in coastal systems. - Research highlights: > Biofilms can act as a trophic pathway of fish farm dissolved wastes. > Biofilms are reliable tools for monitoring fish farm dissolved wastes. > The influence of the fish farm dissolved wastes can be detected 120-350 m from farm. - Under the influence of fish farming biofilm accumulates organic carbon, nutrients, selenium and metals, regardless of the structure and trophic niche of the community.

  8. Plastic fish

    CERN Multimedia

    Antonella Del Rosso

    2015-01-01

    In terms of weight, the plastic pollution in the world’s oceans is estimated to be around 300,000 tonnes. This plastic comes from both land-based and ocean-based sources. A lecture at CERN by chemist Wolfgang Trettnak addressed this issue and highlighted the role of art in raising people’s awareness.   Artwork by Wolfgang Trettnak. Packaging materials, consumer goods (shoes, kids’ toys, etc.), leftovers from fishing and aquaculture activities… our oceans and beaches are full of plastic litter. Most of the debris from beaches is plastic bottles. “PET bottles have high durability and stability,” explains Wolfgang Trettnak, a chemist by education and artist from Austria, who gave a lecture on this topic organised by the Staff Association at CERN on 26 May. “PET degrades very slowly and the estimated lifetime of a bottle is 450 years.” In addition to the beach litter accumulated from human use, rivers bring several ki...

  9. Fluorescence in situ hybridization (FISH using non-commercial probes in the diagnosis of clinically suspected microdeletion syndromes

    Directory of Open Access Journals (Sweden)

    Ashutosh Halder

    2013-01-01

    Interpretation & conclusion: We conclude that FISH should not be the method of choice for clinically suspected microdeletion syndromes. We propose to follow strict clinical criteria for FISH testing or preferably to follow better methods (genotype first approach. Whole genome screening may be used as first line of test and FISH may be used for confirmation of screening result, screening of family members and prenatal diagnosis.

  10. A checklist of the fish fauna of Greenland waters

    DEFF Research Database (Denmark)

    Møller, Peter R.; Nielsen, Jørgen G.; Knudsen, Steen W.

    2010-01-01

    Although the Greenland fish fauna has been studied for more than 200 years, new species continue to be discovered. We here take the opportunity of the International Polar Year 2007-08 (IPY) to present an updated check-list of the fishes of Greenland and discuss whether the growing diversity can...

  11. Microscopic recognition and identification of fish meal in compound feeds

    NARCIS (Netherlands)

    Raamsdonk, van L.W.D.; Prins, Theo; Rhee, van de N.; Vliege, J.J.M.; Pinckaers, V.G.Z.

    2017-01-01

    Fish meal is an accepted ingredient in compound feed. Unauthorised application is primarily enforced by visual inspection, i.e., microscopy. In order to document the visually available diversity, fragments of bones and scales of 17 teleost fish species belonging to seven different orders were

  12. Screening CO

    NARCIS (Netherlands)

    Ramírez, A.; Hagedoorn, S.; Kramers, L.; Wildenborg, T.; Hendriks, C.

    2010-01-01

    This paper describes the development and application of a methodology to screen and rank Dutch reservoirs suitable for long-term large scale CO2 storage. The screening focuses on off- and on-shore individual aquifers, gas and oil fields. In total 176 storage reservoirs have been taken int

  13. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    – The work can encourage policy makers, diversity and HR managers to question their own practices and assumptions leading to more theoretical informed diversity management practices. Originality/value – The theoretical connections between identity and diversity literature have so far not been reviewed...... systematically. The work foregrounds how important it is for diversity scholars to consider identity underpinnings of diversity research to help further develop the field within and beyond the three streams the authors discuss.......The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...

  14. Three Kinds of Fish

    DEFF Research Database (Denmark)

    Høst, Jeppe Engset

    2012-01-01

    There are three kinds of fish. Fish you were given, fish you bought and fish you lease. This might sound a bit odd, but it is nevertheless the basis for the activities of Danish commercial fishers since the introduction of transferable fishing concessions (TFCs) in 2007. In the current 2012 reform...... of market based systems are wild speculation, concentration and monopolization of fishing access and subsequent leasing with fishing communities and new entrants very likely being worse off (see for example the chapter “From fishing rights to financial derivatives” is this volume or Olson 2011; Sumaila 2010...... will examine five Danish fishing operations and discuss how they have reacted in different ways to the newly introduced system of transferable fishing concessions. By introducing TFCs as a solution to fleet overcapacity, the EU Commission will also be introducing a system where buying, selling and leasing...

  15. Composição e diversidade da ictiofauna em riachos do Cerrado, bacia do ribeirão Ouvidor, alto rio Paraná, Goiás, Brasil Fish diversity and composition in Cerrado streams, Ribeirão Ouvidor basin, upper Paraná River basin, Goiás, Brazil

    Directory of Open Access Journals (Sweden)

    Nicelly B. Araújo

    2007-12-01

    Full Text Available Este estudo tem como objetivo descrever ecologicamente a ictiofauna quanto à riqueza, abundância, diversidade de Shannon-Wiener, uniformidade, relação riqueza/abundância e constância. As amostragens da ictiofauna foram realizadas bimestralmente de agosto de 2004 a junho de 2005 num trecho de 50 m de comprimento em nove afluentes e na calha principal do ribeirão Ouvidor, bacia do Alto Paraná. A coleta dos peixes foi realizada utilizando-se a pesca elétrica. Foram coletados 4049 indivíduos distribuídos em 35 espécies, seis ordens e 14 famílias. As espécies mais abundantes na bacia foram Astyanax cf. fasciatus Cuvier, 1819 (762 indivíduos, Poecilia reticulata Peters, 1859 (725 e Astyanax altiparanae Garutti & Britski, 2000 (650. A correlação encontrada entre a largura da calha e a riqueza sugere que riachos largos apresentam maior riqueza que estes estreitos. Apenas a diversidade de Shannon-Wiener variou significativamente entre os riachos amostrados. Astyanax cf. fasciatus e Rhamdia quelen Quoy & Gaimard, 1824 estiveram presentes em todos os trechos considerados, enquanto que a maior quantidade de espécies constantes foi encontrada no riacho Santo Antônio.This study aims to describe the fish assemblage using ecological descriptors (richness, abundance, diversity of Shannon-Wiener, uniformity, relation richness/abundance and constancy. Fish sampling were carried out every two month from August 2004 to June 2005 in a stretch of 50 m long in nine tributaries and in the main channel of the Ribeirão Ouvidor. Four thousand forty-nine fish were collected using electric fishing equipment. These individuals are distributed in 35 species, six Orders and fourteen families. The most abundant species were Astyanax cf. fasciatus Cuvier, 1819 (762 individuals, Poecilia reticulata Peters, 1859 (725 and Astyanax altiparanae Garutti & Britski, 2000 (650. The correlation between the channel width and the richness suggests that width streams has

  16. Anticonvulsant effects of structurally diverse GABA(B) positive allosteric modulators in the DBA/2J audiogenic seizure test: Comparison to baclofen and utility as a pharmacodynamic screening model.

    Science.gov (United States)

    Brown, Jordan W; Moeller, Achim; Schmidt, Martin; Turner, Sean C; Nimmrich, Volker; Ma, Junli; Rueter, Lynne E; van der Kam, Elizabeth; Zhang, Min

    2016-02-01

    The GABA(B) receptor has been indicated as a promising target for multiple CNS-related disorders. Baclofen, a prototypical orthosteric agonist, is used clinically for the treatment of spastic movement disorders, but is associated with unwanted side-effects, such as sedation and motor impairment. Positive allosteric modulators (PAM), which bind to a topographically-distinct site apart from the orthosteric binding pocket, may provide an improved side-effect profile while maintaining baclofen-like efficacy. GABA, the major inhibitory neurotransmitter in the CNS, plays an important role in the etiology and treatment of seizure disorders. Baclofen is known to produce anticonvulsant effects in the DBA/2J mouse audiogenic seizure test (AGS), suggesting it may be a suitable assay for assessing pharmacodynamic effects. Little is known about the effects of GABA(B) PAMs, however. The studies presented here sought to investigate the AGS test as a pharmacodynamic (PD) screening model for GABA(B) PAMs by comparing the profile of structurally diverse PAMs to baclofen. GS39783, rac-BHFF, CMPPE, A-1295120 (N-(3-(4-(4-chloro-3-fluorobenzyl)-6-methoxy-3,5-dioxo-4,5-dihydro-1,2,4-triazin-2(3H)-yl)phenyl)acetamide), and A-1474713 (N-(3-(4-(4-chlorobenzyl)-3,5-dioxo-4,5-dihydro-1,2,4-triazin-2(3H)-yl)phenyl)acetamide) all produced robust, dose-dependent anticonvulsant effects; a similar profile was observed with baclofen. Pre-treatment with the GABA(B) antagonist SCH50911 completely blocked the anticonvulsant effects of baclofen and CMPPE in the AGS test, indicating such effects are likely mediated by the GABA(B) receptor. In addition to the standard anticonvulsant endpoint of the AGS test, video tracking software was employed to assess potential drug-induced motor side-effects during the acclimation period of the test. This analysis was sensitive to detecting drug-induced changes in total distance traveled, which was used to establish a therapeutic index (TI = hypoactivity

  17. Why are freshwater fish so threatened?

    Science.gov (United States)

    Closs, Gerard P.; Angermeier, Paul; Darwall, William R.T.; Balcombe, Stephen R.

    2015-01-01

    The huge diversity of freshwater fishes is concentrated into an area of habitat that covers only about 1% of the Earth's surface, and much of this limited area has already been extensively impacted and intensively managed to meet human needs (Dudgeon et al., 2006). As outlined in Chapter 1, the number and proportions of threatened species tend to rise wherever fish diversity coincides with dense human populations, intensive resource use and development pressure. Of particular concern is the substantial proportion of the global diversity of freshwater fishes concentrated within the Mekong and Amazon Basins and west-central Africa (Berra, 2001; Abell et al., 2008; Dudgeon, 2011; Chapter 1) with extensive exploitation of water resources planned to accelerate in future years (Dudgeon, 2011; Chapter 1). If current trends continue, and the social, political and economic models that have been used to develop industrialised regions of the world over the past two centuries prevail, then the future of a significant proportion of global diversity of freshwater fish species is clearly uncertain.

  18. SHORT COMMUNICATION Rapid Visual Assessment of Fish ...

    African Journals Online (AJOL)

    Abstract— Rapid visual censuses were conducted of fish on eight coral reefs in the .... species diversity (Table 2). Overall,. 19 families ..... a predator-dominated environment, but further .... Bell, J.D. & Galzin, R. (1984) Influence of. Live Coral ...

  19. The role of prolactin in fish reproduction.

    Science.gov (United States)

    Whittington, Camilla M; Wilson, Anthony B

    2013-09-15

    Prolactin (PRL) has one of the broadest ranges of functions of any vertebrate hormone, and plays a critical role in regulating aspects of reproduction in widely divergent lineages. However, while PRL structure, mode of action and functions have been well-characterised in mammals, studies of other vertebrate lineages remain incomplete. As the most diverse group of vertebrates, fish offer a particularly valuable model system for the study of the evolution of reproductive endocrine function. Here, we review the current state of knowledge on the role of prolactin in fish reproduction, which extends to migration, reproductive development and cycling, brood care behaviour, pregnancy, and nutrient provisioning to young. We also highlight significant gaps in knowledge and advocate a specific bidirectional research methodology including both observational and manipulative experiments. Focusing research efforts towards the thorough characterisation of a restricted number of reproductively diverse fish models will help to provide the foundation necessary for a more explicitly evolutionary analysis of PRL function.

  20. Forage fish, their fisheries, and their predators: who drives whom?

    DEFF Research Database (Denmark)

    Engelhard, Georg H.; Peck, Myron A.; Rindorf, Anna;

    2014-01-01

    The North Sea has a diverse forage fish assemblage, including herring, targeted for human consumption; sandeel, sprat, and Norway pout, exploited by industrial fisheries; and some sardine and anchovy, supporting small-scale fisheries. All show large abundance fluctuations, impacting on fisheries...... exist, as in the North Sea. Sandeel appears to be the most important prey forage fish. Seabirds are most dependent on forage fish, due to specialized diet and distributional constraints (breeding colonies). Other than fisheries, key predators of forage fish are a few piscivorous fish species including...... saithe, whiting, mackerel, and horse-mackerel, exploited in turn by fisheries; seabirds and seals have a more modest impact. Size-based foodwebmodelling suggests that reducing fishing mortality may not necessarily lead to larger stocks of piscivorous fish, especially if their early life stages compete...