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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

The confluences of ideas leading to, and the flow of ideas emerging from, individual-based modeling of riverine fishes

In this review article, we trace the history of events leading to the development of individual-based models (IBMs) to represent aquatic organisms in rivers and streams. As a metaphor, we present this history as a series of confluences between individual scientists (tributaries) sharing ideas. We describe contributions of these models to science and management. One iconic feature of river IBMs is the linkage between flow and the physical habitat experienced by individual animals, and the first model that focused on this linkage is briefly described. We continue by reviewing the contributions of riverine IBMs to eight broad areas of scientific inquiry. The first four areas include research to understand the effects of flow regimes on fish populations, species interactions (e.g., size-mediated competition and predation), fish movement and habitat selection, and contaminant and water quality impacts on populations. Next, we review research using IBMs to guide conservation biology of imperiled taxa through population viability analysis, including research to understand river fragmentation by dams and reconnection, to understand genetic outcomes for riverine metapopulations, and to anticipate the future effects of temperature and climate change. This rich body of literature has contributed to both theoretical insights (e.g., about animal behavior and life history) and applied insights (e.g., population-level effects of flow regimes, temperature, and the effects of hydropower and other industries that share rivers with aquatic biota). Lastly, we finish by exploring promising branches that lie ahead in the braided, downstream channel that represents future river modeling research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

How do measured PBDE and HCBD levels in river fish compare to the European Environmental Quality Standards?

This study evaluates the current situation regarding PBDE and HBCD levels in different river fish species. We collected published data in the last five years in different countries around the world. These levels of pollution were compared with Environmental Quality Standards (EQS) for biota established by the European Directive in the field of water policy. Although HBCD situation is not critical, with only some values exceeding the limit about 5 times, the PBDE levels clearly exceeded the established EQS, with 25% of fish samples exceeding up to ten thousand times. Although it is expected that levels of pollution by PBDEs will decrease over the next years due to the ban in their use, it is not expected that this decrease will reach the EQS values by the end of 2021, as demanded by the European Directive. Hence, it is necessary to implement new strategies in order to minimize the impact of PBDEs on the environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Synthesis of nitrogen and sulfur co-doped yolk-shell porous carbon microspheres and their application for Pb(II) detection in fish serum

Highlights: • N, S-YSPCMS was obtained via simple silica templating and pyrolysis method. • N, S-YSPCMS shows spherical morphology, porous structure and high N, S contents. • N, S-YSPCMS based electrochemical sensor shows good performance in Pb(II) analysis. • N, S-YSPCMS based sensor is feasible in detection of Pb(II) in fish serum. - Abstract: Nitrogen (N) and sulfur (S) co-doped carbonaceous material has shown remarkably improved performance in electrocatalysis, supercapacitor, and so on. While, the application of N, S co-doped carbon in electrochemical sensor was less investigated. Herein, N, S co-doped yolk-shell porous carbon microspheres (N, S-YSPCMSs) were synthesized by silica templating strategy and high-temperature pyrolysis method. The as-prepared N, S-YSPCMSs exhibited spherical morphologies, porous structures and high N, S-doping contents. Owing to the synergetic effect of the well-dispersed N, S-dopants, good conductivity of carbon skeleton, high surface area and pore volume of the microspheres, the N, S-YSPCMSs prepared at 900 °C showed good electrochemical performance for Pb(II) and with a linear range of 4–160 μg L{sup −1}, the limit of detection is 0.49 μg L{sup −1} (S/N = 3). The electrochemical sensor was consequently applied in detecting Pb(II) in fish serum samples with satisfying recoveries, indicating the N, S-YSPCMSs-900 are promising electrode components for electroanalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteo-bacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5'-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15 NH$+\atop{4}$ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living’ population, and are not dependent on methane or ANME activity. We investigated the possibility of N 2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. 15 N 2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, 15 N 2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced 15 N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. In conclusion, with this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Maternal consumption of fish oil programs reduced adiposity in broiler chicks

We report that maternal intake of eicosapentaenoic acid (EPA; 20:5 n-3) and docosahexaenoic acid (22:6 n-3) has been associated with reduced adiposity in children, suggesting the possibility to program adipose development through dietary fatty acids before birth. This study determined if enriching the maternal diet in fish oil, the primary source of EPA and DHA, affected adipose development in offspring. Broiler chickens were used because they are obesity-prone, and because fatty acids provided to the embryo can be manipulated through the hen diet. Hens were fed diets supplemented (2.8% wt:wt) with corn oil (CO; n-6) or fish oil (FO; n-3) for 28 d. Chicks from both maternal diet groups were fed the same diet after hatch. Maternal FO consumption enriched chick adipose tissue in EPA and DHA and reduced adiposity by promoting more, but smaller, adipocytes. This adipocyte profile was paralleled by lower expression of the adipogenic regulator PPARG and its co-activator PPARGC1B, and elevated expression of LPL. Proteomics identified 95 differentially abundant proteins between FO and CO adipose tissue, including components of glucose metabolism, lipid droplet trafficking, and cytoskeletal organization. Lastly, these results demonstrate that the maternal dietary fatty acid profile programs offspring adipose development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses

Aneuploidy has been reported to occur at remarkably high levels in normal somatic tissues using Fluorescence In Situ Hybridization (FISH). Recently, these reports were contradicted by single-cell low-coverage whole genome sequencing (scL-WGS) analyses, which showed aneuploidy frequencies at least an order of magnitude lower. To explain these seemingly contradictory findings, we used both techniques to analyze artificially generated mock aneuploid cells and cells with natural random aneuploidy. Our data indicate that while FISH tended to over-report aneuploidies, a modified 2-probe approach can accurately detect low levels of aneuploidy. Further, scL-WGS tends to underestimate aneuploidy levels, especially in a polyploid background.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. We then applied this workflow to a sample of yet uncultured multicellular magnetotactic bacteria. In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes at single cell resolution.

Schaible, George↗
DOE OSTI2014

A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Biogeographic classification of streams using fish community– and trait–environment relationships

Abstract Aim Present a hybrid biogeographic and environmentally constrained clustering approach to classify ~853,000 stream reaches in the eastern United States. Examine the frequency of stream typologies in the landscape relative to anthropogenic stressors to identify potential stream conservation needs. Location Eastern United States. Methods Fish communities at 956 least‐disturbed sampling reaches were characterized using taxonomic and functional composition of native species. Environmental variables summarized within stream reaches included stream discharge, channel gradient, hydrologic regime, summer water temperature and boundaries of freshwater ecoregions. Multivariate regression trees were used to relate environmental variables to fish communities while simultaneously developing taxa‐ and trait‐specific biogeographic classifications. We then overlaid stream classifications with indices of anthropogenic disturbances to evaluate rarity and risk of complete loss of natural representation of stream types. Results Taxonomically based classes represented a combination of ecoregional boundaries and environmental gradients, whereas temperature gradients were most important in differentiating functional composition. An optimal taxonomy‐based classification contained 13 classes and explained 26.4% of community variation, and the optimal trait‐based classification contained 6 classes, explaining 25.2% of community variation. Overlaying class maps with an anthropogenic disturbance index revealed substantial variation in the severity of degradation among classes relative to their abundance in the landscape, especially rare classes (i.e., large rivers and cold headwater systems). Main conclusions We demonstrate the value of integrating local, regional and historical biogeographic factors with taxonomic and functional characteristics of freshwater biota to classify ecosystems based on mechanistic biota–environment relationships. This approach is important to addressing the challenge of developing stream classifications that reconcile the environmental drivers of community trait composition with the constraints of biogeographic regionality at large spatial scales. Furthermore, the spatially explicit and high‐resolution maps disseminated here can uniquely inform management decisions regarding anthropogenic threats to the biodiverse freshwaters of the eastern United States.

Troia, Matthew J.↗
DOE OSTI2025

Feed the fish: A review of aquaculture feeders and their strategic implementation

Automatic feeders are revolutionizing aquaculture by enabling precise and controlled feeding regimens that optimize growth, reduce feed waste, and enhance the overall efficiency of farming operations. Demand feeders provide some similar benefits but with feeding tailored to fish appetites and, in some cases, feed dispersal without electricity. This review explores the evolution, technological advancements, and applications of these feeders with a survey of recent research. It looks at common feeder designs and compares the pros and cons of five automatic feeder configurations in commercial use today. The article contrasts feeders and feed sizes for farmed species in different life stages and facilities, from hatcheries to ponds and offshore cages. It discusses the importance of species-tailored feeding strategies as well as impacts on fish behavior and health, nutrient delivery, and environmental sustainability. Incorporating sensors and on-site computing enables optimization in feeding algorithms that feeders then implement precisely and reliably. The review compiles results from multiple studies comparing growth rate, weight, and feed conversion ratio (FCR) outcomes from automatic feeders and demand feeders versus traditional hand-feeding regimens. The integration of feeders with real-time monitoring and data analytics is also discussed, highlighting future directions for research and adoption across the industry.

42 ENGINEERING↗
DOE OSTI2023

Marine energy converters: Potential acoustic effects on fishes and aquatic invertebrates

The potential effects of underwater anthropogenic sound and substrate vibration from offshore renewable energy development on the behavior, fitness, and health of aquatic animals is a continuing concern with increased deployments and installation of these devices. Initial focus of related studies concerned offshore wind. However, over the past decade, marine energy devices, such as a tidal turbines and wave energy converters, have begun to emerge as additional, scalable renewable energy sources. Because marine energy converters (MECs) are not as well-known as other anthropogenic sources of potential disturbance, their general function and what is known about the sounds and substrate vibrations that they produce are introduced. Furthermore, while most previous studies focused on MECs and marine mammals, this paper considers the potential of MECs to cause acoustic disturbances affecting nearshore and tidal fishes and invertebrates. In particular, the focus is on particle motion and substrate vibration from MECs because these effects are the most likely to be detected by these animals. Finally, an analysis of major data gaps in understanding the acoustics of MECs and their potential impacts on fishes and aquatic invertebrates and recommendations for research needed over the next several years to improve understanding of these potential impacts are provided.

16 TIDAL AND WAVE POWER↗
DOE OSTI2019

Mortality and injury assessment for three species of fish exposed to simulated turbine blade strike

Injury and mortality of fish during downstream passage through hydropower turbines is among the leading direct impacts of hydropower. Understanding the relationships among various strike variables and injury and mortality rates are necessary for improvements in turbine design. We subjected three species of fish to simulated blade strike in laboratory studies with different blade thicknesses, impact velocities, and body orientations to develop relationships between these variables and probability of injury and mortality. Midbody strikes resulted in higher mortality than head strikes, and tail strikes produced the least mortality. Lateral strikes caused more mortality than dorsal and ventral strikes, and higher strike velocities and thinner blades contributed to increased mortality. Several injury types were significantly associated with increased mortality, including injuries to the operculum, gills, viscera, heart, liver, swim bladder, muscle, and bone fractures. Here, the results from this study will be used to define biologically based design criteria that can be used by turbine designers to improve designs (e.g., increased leading-edge thickness and slower turbine speeds) to minimize the probability and impact of blade strike.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Survival, healing, and swim performance of juvenile migratory sea lamprey ( Petromyzon marinus ) implanted with a new acoustic microtransmitter designed for small eel-like fishes

Background: Little is known about the transformer stage of the parasitic lampreys, a brief but critical period that encompasses juvenile out-migration from rivers to lakes or oceans to begin parasitic feeding. Information about this life stage could have significant conservation implications for both imperiled and invasive lampreys. We investigated tag retention, survival, wound healing, and swim performance of newly transformed sea lamprey (Petromyzon marinus) implanted with a new micro-acoustic transmitter, the eel–lamprey acoustic transmitter (ELAT), in a controlled laboratory environment. Results: The 61-day survival of our tagged subjects was 71%, within the range reported in similar studies of juvenile lampreys. However, survival was significantly lower in the tagged animals (vs control), with no effect statistically attributable to measures of animal length, mass, condition, or population of origin (Great Lakes vs. Atlantic drainage). Mortality in tagged fish was concentrated in the first four days post-surgery, suggesting injury from the surgical process. An unusually long recovery time from anesthesia may have contributed to the increased mortality. In a simple burst swim assay, tagged animals swam significantly slower (– 22.5%) than untagged animals, but were not significantly different in endurance swim tests. A composite wound healing score at day four was a significant predictor of maximum burst swim speed at day 20, and wound condition was related to animal mass, but not length, at the time of tagging. Conclusions: Impairments to survival and swim performance of juvenile sea lamprey implanted with the ELAT transmitter were within currently reported ranges for telemetry studies with small, difficult to observe fishes. Our results could be improved with more refined anesthesia and surgical techniques. The ability to track migratory movements of imperiled and pest populations of parasitic lampreys will improve our ability to estimate vital rates that underlie recruitment to the adult population (growth, survival) and to investigate the environmental factors that regulate the timing and rates of movement, in wild populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application

Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and conservation. We used Pacific lamprey ( Entosphenus tridentatus ) as a case study to highlight the utility of this model. We applied a global sensitivity analysis to explore the importance of individual life stage parameters to overall population size, and to better understand the implications of existing gaps in knowledge. We also provided example analyses of selected management scenarios (dam passage, fish translocations, and hatchery additions) influencing Pacific lamprey in fresh water. These applications illustrate how the model can be applied to inform conservation efforts. This tool will provide new capabilities for users to explore their own questions about lamprey biology and conservation. Simulations can hone hypotheses and predictions, which can then be empirically tested in the real world.

Gomes, Dylan G. E. (ORCID:0000000226423728)↗
DOE OSTI2023

The Association of Radiation Exposure with Stable Chromosome Aberrations in Atomic Bomb Survivors Based on DS02R1 Dosimetry and FISH Methods

The frequency of stable chromosome aberrations (sCA) in lymphocytes is a recognized radiation biological dosimeter. Its analysis can provide insights into factors that affect individual susceptibility as well as into the adequacy of radiation dose estimates used in studies of atomic bomb survivors. We analyzed the relationship between atomic bomb radiation exposure using the most recent DS02R1 dose estimates and the frequency of sCA as determined by FISH in 1,868 atomic bomb survivors. We investigated factors that may affect the background sCA rate and the shape and magnitude of the dose response. As in previous analyses of sCA in atomic bomb survivors that were based on Giemsa staining methods and used older DS86 dose estimates, the relationship between radiation dose and sCA rate was significant (P < 0.0001) with a linear-quadratic relationship at lower doses that did not persist at higher doses. As before, age at the time of the bombing and type of radiation shielding were significant dose-effect modifiers (P < 0.0001), but in contrast the difference in dose response by city was not so pronounced (P = 0.026) with a city effect not evident at doses below 1.25Gy. Background sCA rate increased with age at the time of examination (P < 0.0001), but neither sex, city, nor smoking was significantly associated with background rate. Based on FISH methods and recent dosimetry, the relationship between radiation dose and sCA frequency is largely consistent with previous findings, although the lesser importance of city as an effect modifier may reflect better dosimetry as well as more reproducible scoring of sCA. The persisting difference in sCA dose response by shielding category points to remaining problems with the accuracy or precision of radiation dose estimates in some A-bomb survivors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Deep Learning for Fish Identification from Sonar Data: CRADA 481 [Abstract only]

To help solve the challenges of hydropower energy production related to the potential for eel injury and mortality from passage through hydropower turbines, we will develop a deep learning method for identifying migrating eels from imaging sonar. This project continues with a prior project conducted by the Pacific Northwest National Laboratory (PNNL) and the Electric Power Research Institute (EPRI) in FY2018-2019. The proposed method employs Convolution Neural Network (CNN), a powerful deep learning method for image classification, to distinguish between images of eels and non-eel moving objects. We propose to collect more laboratory data and add more existing field data to train a powerful deep learning model. In addition to eels and sticks as classified in previous studies, we will add images containing several non-eel fish species and macrophyte mats to the training data. A multi-class classification model will be developed to distinguish these objects. Object detection algorithm will be explored and developed to locate and identify multiple objects in each sonar frame. Motion analysis will be performed to track the movement of objects in sonar video clips. We will also improve the data conversion algorithm so that it can read in both DIDSON and ARIS (both are imaging sonars developed by Sound Metrics Corp) data files and convert them to images with comparably high resolution, regardless of the varying detection ranges in different environments. The developed algorithms will be packaged as a software with a graphic user interface. The software will be evaluated by external collaborators in the field. The developed framework can be generalized for automatic monitoring of fish passage and migration using other imaging sonars like ARIS and will benefit the design and operation of ecologically friendly hydroelectric projects. The developed wavelet and CNN model configuration parameters can potentially be transferred to lamprey detection in similar riverine environments.

13 HYDRO ENERGY↗
DOE OSTI2022

Enhancing Lifetime and Reducing Costs for Fish Diversion Netting Structures (Abstract)

This effort will focus on technology transfer and commercialization of antifouling coatings with an enthusiastic and engaged industrial team. Environmental requirements and operational demands call for a nontoxic coating/paint to prevent fouling on fish passage guidance netting at hydropower facilities. For example, one netting customer estimated the capital cost for compliance at $\$12$ million to $\$15$ million. This project will build partnerships between PNNL and private companies to optimize, demonstrate, mature, and commercialize a novel PNNL-developed technology that addresses this critical coating need of the hydropower industry. This effort will support modification of existing coatings for application to flexible netting structures. Industrial partners include commercial coating development specialist (Lorama), hydrophobic material manufacturer and paint developer (Dry Surface Technologies), aquatic applications specialists (Prometheus Innovations and River Connectivity Systems), and hydropower netting producer (Pacific Netting Products). Engagement with the U.S. Army Corps of Engineers (USACE) and Bureau of Reclamation (BOR), two hydropower operators, throughout the project will provide expertise and field test sites that will provide crucial proof of real-world performance data (additional details provided in Teaming section). Taylor Shellfish Farms will provide organisms and fouling expertise as well as a perspective of potential broader impacts for the blue economy. Sample netting will demonstrate performance in a range of environments for key hydropower applications. PNNL will work with industrial partners to overcome commercialization barriers as well as resolving any manufacturing or regulatory issues. This Phase 1 effort is focused on technology optimization for application to fish passage guidance netting and technology validation as verified by independent testing (through USACE, BOR, Taylor Shellfish and Prometheus Innovations). Through this effort, SLIC will be demonstrated for netting applications at technology readiness level (TRL) 5. The field test data will allow optimization of SLIC formulation and performance which is key to enabling technology transfer of a mature proven technology to industry and production of a viable commercial product specifically focused for hydropower needs.

13 HYDRO ENERGY↗
DOE OSTI2023

Advanced Compact Generation Module with Fish Safe Runner Technology

Hydropower is an important contributor of stable, load-leveling renewable energy to our national grid. Increasingly, the development of new hydropower facilities or the retrofit of existing ones hinges not only on minimizing costs but also environmental impact. In this report, the analysis and testing of a modular and scalable low-head hydropower generation design using Natel Energy’s Restoration Hydro Turbine is described. This design leverages many established industry approaches for compactness and efficiency while simultaneously allowing for safe downstream fish passage through the turbines themselves. This unique approach reduces overall hydropower facility costs and enables a simpler inclusive method of project design and operation. To assess this design, mechanical and fluid computational analyses were used to study and optimize key parameters. Passage tests of important migratory species (salmonids, American eel) were conducted through representative turbines. The unique propeller geometry of the fish-safe Restoration Hydro Turbine was subjected to detailed design and testing using advanced manufacturing composite techniques. Comprehensive module cost models were developed and assessed alongside hydraulic efficiency. The results of this project show promising and economical applications for downstream passage offish through Restoration Hydro Turbine modules.

13 HYDRO ENERGY↗