Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “FISH”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus )

Abstract Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus . We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus . Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter‐ and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.

Benestan, Laura M.↗
DOE OSTI2023

Utility of parentage‐based tagging for monitoring Coho salmon ( Oncorhynchus kisutch ) in the interior Columbia River basin

Abstract By the 1980s, after decades of declining numbers in the mid‐1900s, Coho salmon ( Oncorhynchus kisutch ) were considered extirpated from the interior Columbia River. In the mid‐1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage‐based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples. Analyses of baseline collections revealed that genetic structure followed a temporal pattern based on 3‐year broodlines rather than geographic location or stocking history. Across hatchery programs, similar levels of genetic diversity was present. The PBT baseline provided multiple direct applications such as identification of origin for Coho salmon collected in a mixed stock at Priest Rapids Dam and the detection of the proportion and distribution of hatchery‐origin fish on the spawning grounds in the Methow River basin. The PBT baseline for Coho salmon is freely available for use and can be downloaded from FishGen.net .

Horn, Rebekah L.↗
DOE OSTI2023

Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline

Abstract Genetic stock identification (GSI) is an important fisheries management tool to identify the origin of fish harvested in mixed stock fisheries. Periodic updates of genetic baselines can improve performance via the addition of unsampled or under‐sampled populations and the inclusion of more informative markers. We used a combination of baselines to evaluate how population representation, marker number, and marker type affected the performance and accuracy of genetic stock assignments (self‐assignment, bias, and holdout group tests) for steelhead ( Oncorhynchus mykiss ) in the Snake River basin. First, we compared the performance of an existing genetic baseline with a newly developed one which had a reduced number of individuals from more populations using the same set of markers. Self‐assignment rates were significantly higher ( p < 0.001; +5.4%) for the older, larger baseline, bias did not differ significantly between the two, but there was a significant improvement in performance for the new baseline in holdout results ( p < 0.001; mean increase of 25.0%). Second, we compared the performance of the new baseline with increased numbers of genetic markers (~2x increase of single‐nucleotide polymorphisms; SNPs) for the same set of baseline individuals. In this comparison, results produced significantly higher rates of self‐assignment ( p < 0.001; +9.7%) but neither bias nor leave‐one‐out were significantly affected. Third, we compared 334 SNPs versus opportunistically discovered microhaplotypes from the same amplicons for the new baseline, and showed the latter produced significantly higher rates of self‐assignment ( p < 0.01; +2.6%), similar bias, but slightly lower holdout performance (−0.1%). Combined, we show the performance of genetic baselines can be improved via representative and efficient sampling, that increased marker number consistently improved performance over the original baseline, and that opportunistic discovery of microhaplotypes can lead to small improvements in GSI performance.

Hargrove, John S.↗
DOE OSTI2024

Visual and genetic stock identification of a test fishery to forecast Columbia River spring Chinook salmon stocks 2 weeks into the future

Abstract Modern fisheries management strives to balance opposing goals of protection for weak stocks and opportunity for harvesting healthy stocks. Test fisheries can aid management of anadromous fishes if they can forecast the strength and timing of an annual run with adequate time to allow fisheries planning. Integration of genetic stock identification (GSI) can further maximize utility of test fisheries by resolving run forecasts into weak‐ and healthy‐stock subcomponents. Using 5 years (2017–2022) of test fishery data, our study evaluated accuracy, resolution, and lead time of predictions for stock‐specific run timing and abundance of Columbia River spring Chinook salmon ( Oncorhynchus tshawytscha ). We determined if this test fishery (1) could use visual stock identification (VSI) to forecast at the coarse stock resolution (i.e., classification of “lower” vs. “upriver” stocks) upon which current management is based and (2) could be enhanced with GSI to forecast at higher stock resolution. VSI accurately identified coarse stocks (83.3% GSI concordance), and estimated a proxy for abundance (catch per unit effort, CPUE) of the upriver stock in the test fishery that was correlated ( R 2 = 0.90) with spring Chinook salmon abundance at Bonneville dam (Rkm 235). Salmon travel rates (~8.6 Rkm/day) provided predictions with 2‐week lead time prior to dam passage. Importantly, GSI resolved this predictive ability as finely as the hatchery broodstock level. Lower river stock CPUE in the test fishery was correlated with abundance at Willamette Falls (Rkm 196, R 2 = 0.62), but could not be as finely resolved as achieved for upriver stocks. We described steps to combine VSI and GSI to provide timely in‐season information and with prediction accuracy of ~12.4 mean absolute percentage error and high stock resolution to help plan Columbia River mainstem fisheries.

Hess, Jon E.↗
DOE OSTI2016

Influences of ocean conditions and feeding ecology on the survival of juvenile Chinook Salmon ( Oncorhynchus tshawytscha )

Abstract Recruitment variability in many fish populations is postulated to be influenced by climatic and oceanographic variability. However, a mechanistic understanding of the influence of specific variables on recruitment is generally lacking. Feeding ecology is one possible mechanism that more directly links ocean conditions and recruitment. We test this mechanism using juvenile Chinook Salmon ( Oncorhynchus tshawytscha ) collected off the west coast of Vancouver Island, British Columbia, Canada, in 2000–2009. Stable isotopes of carbon ( δ 13 C), an indicator of temperature or primary productivity, and nitrogen ( δ 15 N), an indicator of trophic position, were taken from muscle tissues of genetically stock‐identified salmon. We also collated large‐scale climate indices (e.g., Pacific Decadal Oscillation, North Pacific Gyre Oscillation), local climate variables (e.g., sea surface temperature) and copepod community composition across these years. We used a Bayesian network to determine how ocean conditions influenced feeding ecology, and subsequent survival rates. We found that smolt survival of Chinook Salmon is predicted by their δ 13 C value, but not their δ 15 N. In turn, large‐scale climate variability determined the δ 13 C values of salmon, thus linking climate to survival through feeding ecology, likely through qualities propagated from the base of the food chain.

Hertz, E.↗
DOE OSTI2014

Analysis of Daily Peaking and Run-of-River Operations with Flow Variability Metrics, Considering Subdaily to Seasonal Time Scales

Environmental flows are an important consideration in licensing hydropower projects because operational flow releases can result in adverse conditions to downstream ecological communities. Flow variability assessments have typically focused on pre- and post-dam conditions using metrics based on daily-averaged flow values. This study used subdaily and daily flow data to assess environmental flow response to changes in hydropower operations from daily-peaking to run-of-river. An analysis tool was developed to quantify subdaily to seasonal flow variability metrics and was applied to four hydropower projects that underwent operational changes based on regulatory requirements. Results indicate that the distribution of flows is significantly different between daily-peaking and run-of- river operations and that daily-peaking operations are flashier than run-of-river operations; these differences are seen using hourly-averaged flow datasets and are less pronounced or not noticeable using daily-averaged flow datasets. Of all variability metrics analyzed, hydrograph rise and fall rates were the most sensitive to using daily versus subdaily flow data. This outcome has implications for the development of flow-ecology relationships that quantify effects of rate of change on processes such as fish stranding and displacement, along with habitat stability. The quantification of flow variability statistics should be done using subdaily datasets and metric to accurately represent the nature of hydropower operations , especially for facilities that utilize daily-peaking operations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Prey composition and ontogenetic shift in coastal populations of longnose gar Lepisosteus osseus

Longnose gar Lepisosteus osseus were collected from May 2012 to July 2013 in the Charleston Harbor and Winyah Bay estuaries ( SC , U.S.A.). This study examined trends in stomach fullness, described major prey components and their importance in the diet of L. osseus , compared stomach content‐based trophic level estimates with the stable‐isotope‐based proxy: δ 15 N and tested for the occurrence of an ontogenetic diet shift using stomach content analysis and stable C and N isotopes ( δ 13 C and δ 15 N ). Dominant prey families were Clupeidae, Sciaenidae, Penaeidae, Fundulidae and Mugilidae, with the highest consumption rates in autumn. Trophic levels calculated using stomach contents did not correspond to δ 15 N ( P > 0·05). Stomach contents and stable‐isotope signatures indicate ontogenetic prey composition shifts from low trophic level benthic prey (fundulids) to higher trophic level pelagic prey (clupeids) as the fish grow between 400 and 600 mm in standard length. Due to their biomass, abundance and top predator status, L. osseus play a significant ecological role in the estuarine community composition, although this effect has often been overlooked by past researchers and should be considered in future estuarine community studies.

Smylie, M.↗
DOE OSTI2019

Otoliths of sub-adult Lake Sturgeon Acipenser fulvescens contain aragonite and vaterite calcium carbonate polymorphs

In this paper we quantified the percent CaCO 3 polymorph composition in otoliths of larval and juvenile Lake Sturgeon Acipenser fulvescens via X-ray microdiffraction. Sagittal otoliths of sub-adults were primarily composed of aragonite (> 90%) while the lapilli otoliths were 100% vaterite. This is the first time the presence of aragonite in otoliths has been reported in an acipenseriform and is surprising given that the ability to form aragonite otoliths was not thought to have evolved until the separation of teleost and holostean species from other Actinopterygian fishes (e.g., sturgeon, paddlefish, gar).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effect of water velocity and temperature on energy use, behaviour and mortality of pallid sturgeon Scaphirhynchus albus larvae

Abstract Natural reproduction of pallid sturgeon Scaphirhynchus albus has been limited for decades and a recruitment bottleneck is hypothesized to occur during the larval stage of development. In this study, we evaluated the effects of water velocity and temperature on the swimming activity, energy use, settling behaviour and mortality of endogenously feeding larvae. The swimming activity of drifting sturgeon larvae ( i.e. , fish exhibiting negative rheotaxis) increased at low water velocity. In subsequent experiments, we observed greater energy depletion and resultant mortality of larvae in no‐flow environments (0 cm s −1 ) compared to tanks with water velocity ranging from 3.5 to 8.3 cm s −1 . The growth rate of drifting larvae was positively related to water temperature (18.7–23.3°C), but reduced growth rate at low water temperature (18.7°C) resulted in protracted development that extended average drift duration by ~4 days compared to larvae reared at 23.3°C. This study provides evidence that cooler summer water temperatures, characteristic of present‐day conditions in the upper Missouri River, can reduce larval development and extend both the drift duration and distance requirements of S. albus . Moreover, if dispersed into low velocity environments, such as in reservoir headwaters, larvae may experience increased mortality owing to a mismatch between early life stage drift requirements and habitat conditions in the river. Manipulation of water releases to increase seasonal water temperature below dams may aid survival of S. albus larvae by shortening the time and distance spent drifting.

Mrnak, Joseph T.↗
DOE OSTI2021

Age and growth of early‐life‐stage Atlantic tarpon ( Megalops atlanticus) from the northcentral Gulf of Mexico

Abstract Age and growth of early‐life‐stage Atlantic tarpon Megalops atlanticus collected from Mississippi coastal waters in the northcentral Gulf of Mexico (GOM) are described using otolith microstructure analysis. Tarpon leptocephali ( n = 95, 16.0—27.8 mm standard length, L S ) collected from June throughOctober 2013—2018, ranged in age from 22 to 43 days (mean = 30.9 ± 0.5 days). Leptocephalus somatic growth rates ranged 0.46—1.24 mm day −1 (mean = 0.76 ± 0.02 mm day −1 ), and leptocephalus otolith growth rates ranged 1.78—3.97 μm day −1 (mean = 2.58 ± 0.04 μm day −1 ). Growth rates were inversely correlated to leptocephalus age, indicating the shrinkage phase associated with leptocephalus metamorphosis. Juvenile tarpon ( n = 358, 50—359 mm fork length, L F ) were collected from August through December 2007—2018. Juveniles exhibited a positive allometric relationship (adjusted R 2 = 0.99, P < 0.001) between length and mass. The age of 100 juveniles (71—277 mm L F ) ranged from 76 to 174 days. Juvenile growth rate was estimated as 1.56 ± 0.11 mm day −1 . Significant ( P < 0.001) linear relationships were found between juvenile age and otolith metrics, including otolith mass ( R 2 = 0.81) and radius ( R 2 = 0.68). Evaluation of the backcalculated hatch dates suggests that specimens in the collection hatched from late May through mid‐September with slight peaks during July and August. A Rao's Spacing Test of Uniformity indicates the presence of significant lunar periodicity in leptocephalus hatch dates ( n = 95, U = 250.1, P < 0.05), with 50% of the leptocephali hatched within 5 days (before or after) of the full moon. This study fills critical gaps in the scientific knowledge of tarpon and provides estimates of early‐life‐history metrics for an iconic game fish at the northernmost extent of its GOM range.

Graham, Patrick M.↗
DOE OSTI2022

Survival, growth and tag retention of juvenile European eel ( Anguilla anguilla L.) with implanted 12 mm passive integrated transponder tags and acoustic tags

To evaluate the efficiency of tagging juvenile European eels with implanted 12 mm passive integrated transponder (PIT) tags or Eel/Lamprey acoustic transmitters (ELATs), the authors studied tag retention, survival and growth of eels (7–25 g). Experimental eels were obtained from an eel farm, tagged and then released in a series of shallow dug-out ponds with a surface area of c. 200 m 2 . Tagged and control eels were distributed evenly, with 50 tagged and 50 control eels in each of four ponds, giving a total of 200 tagged and 200 control eels mixed. After 76 days, the ponds were drained, and eels were sampled and measured. A total of 344 eels (86%) were recaptured, indicating high survival. Tag retention was 99% as only one of the recaptured PIT-tagged eels had lost the tag and none of the ELAT tagged. The results demonstrated that tagging juvenile eels >16 cm with these small tags is indeed feasible. The growth of tagged and control fish was differentiated but generally low in length and negative in mass but did not differ between the three groups.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Riparian vegetation shade restoration and loss effects on recent and future stream temperatures

River temperatures are expected to increase this century harming species requiring cold-water habitat unless restoration activities protect or improve habitat availability. Local shading by riparian vegetation can cool water temperatures, but uncertainty exists over the scaling of this local effect to larger spatial extents. Here, we evaluate this issue using a regional spatial stream network temperature model with covariates representing shade effects to predict mean August stream temperatures across 78,195 km of tributaries flowing into the Columbia River in the northwestern United States. We evaluate nine scenarios predicting stream temperatures for three riparian shade conditions (current, restored, and no riparian vegetation) within three different climate periods (2000s, 2040s, and 2080s). Results suggest riparian shade restoration (2000s climate) could decrease mean August stream temperatures by 0.62°C across the study network. Under the same restored shade conditions, temperature predictions for tributaries at their confluence with the Columbia River range from 0.02 to 2.08°C cooler than under current shade conditions. The climate warming effect predicted for the 2040s and 2080s, however, is greater than the cooling effect from restoring riparian shade. Streams less than 10-m bankfull width cooled more frequently with riparian shade restoration. In Oregon, the proportion of fish habitat for salmon and trout rearing and migration that meet temperature numeric water quality criteria could be increased by 20% under restored shade conditions although net habitat declines may still occur in the future. We conclude riparian vegetation restoration could partially mitigate future warming and help maintain cold-water habitats that function as thermal refuges if implemented strategically.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Technical Note: Synchrotron-based high-energy x-ray phase sensitive microtomography for biomedical research

Purpose: Propagation-based phase-contrast CT (PPCT) utilizes highly sensitive phase-contrast technology applied to x-ray microtomography. Performing phase retrieval on the acquired angular projections can enhance image contrast and enable quantitative imaging. In this work, the authors demonstrate the validity and advantages of a novel technique for high-resolution PPCT by using the generalized phase-attenuation duality (PAD) method of phase retrieval. Methods: A high-resolution angular projection data set of a fish head specimen was acquired with a monochromatic 60-keV x-ray beam. In one approach, the projection data were directly used for tomographic reconstruction. In two other approaches, the projection data were preprocessed by phase retrieval based on either the linearized PAD method or the generalized PAD method. The reconstructed images from all three approaches were then compared in terms of tissue contrast-to-noise ratio and spatial resolution. Results: The authors’ experimental results demonstrated the validity of the PPCT technique based on the generalized PAD-based method. In addition, the results show that the authors’ technique is superior to the direct PPCT technique as well as the linearized PAD-based PPCT technique in terms of their relative capabilities for tissue discrimination and characterization. Conclusions: This novel PPCT technique demonstrates great potential for biomedical imaging, especially for applications that require high spatial resolution and limited radiation exposure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Use of Integrated Instrumentation to Detect and Classify Targets in Shallow Water

The detection and classification of targets in shallow water environments (e.g., depth < 20 m) is of increasing interest, both in security applications and more general environmental studies. Here, we report the ability of a cabled integrated instrumentation system to detect and classify targets in a shallow (15 m deep), narrow (150 m wide) channel influenced by moderate tidal currents (peak currents < 2 m/s). The instrumentation system incorporates a passive acoustic array, multibeam sonar, acoustic camera, stereo-optical camera, and acoustic Doppler current profiler. The system effectiveness is benchmarked using autonomous “cooperative” targets (e.g., drifters with known position and acoustic characteristics), divers, and opportunistic observations of fish and marine mammals. By fusing data streams from multiple sensors, detection and classification rates are improved, particularly for smaller targets. Approaches to data management (data rates exceed 80 MB/s), real-time classification, and de-noising of acoustic imagery are also discussed.

16 TIDAL AND WAVE POWER↗
DOE OSTI2016

Global marine pollutants inhibit P-glycoprotein: Environmental levels, inhibitory effects, and cocrystal structure

The world’s oceans are a global reservoir of persistent organic pollutants to which humans and other animals are exposed. Although it is well known that these pollutants are potentially hazardous to human and environmental health, their impacts remain incompletely understood. We examined how persistent organic pollutants interact with the drug efflux transporter P-glycoprotein (P-gp), an evolutionarily conserved defense protein that is essential for protection against environmental toxicants. We identified specific congeners of organochlorine pesticides, polychlorinated biphenyls, and polybrominated diphenyl ethers that inhibit mouse and human P-gp, and determined their environmental levels in yellowfin tuna from the Gulf of Mexico. In addition, we solved the cocrystal structure of P-gp bound to one of these inhibitory pollutants, PBDE (polybrominated diphenyl ether)–100, providing the first view of pollutant binding to a drug transporter. The results demonstrate the potential for specific binding and inhibition of mammalian P-gp by ubiquitous congeners of persistent organic pollutants present in fish and other foods, and argue for further consideration of transporter inhibition in the assessment of the risk of exposure to these chemicals.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Rhodoxanthin synthase from honeysuckle; a membrane diiron enzyme catalyzes the multistep conversation of β-carotene to rhodoxanthin

Rhodoxanthin is a vibrant red carotenoid found across the plant kingdom and in certain birds and fish. It is a member of the atypical retro class of carotenoids, which contain an additional double bond and a concerted shift of the conjugated double bonds relative to the more widely occurring carotenoid pigments, and whose biosynthetic origins have long remained elusive. In this work, we identify LHRS ( Lonicera hydroxylase rhodoxanthin synthase), a variant β-carotene hydroxylase (BCH)–type integral membrane diiron enzyme that mediates the conversion of β-carotene into rhodoxanthin. We identify residues that are critical to rhodoxanthin formation by LHRS. Substitution of only three residues converts a typical BCH into a multifunctional enzyme that mediates a multistep pathway from β-carotene to rhodoxanthin via a series of distinct oxidation steps in which the product of each step becomes the substrate for the next catalytic cycle. We introduce a biosynthetic pathway from β-carotene to rhodoxanthin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An interpretable model of pre-mRNA splicing for animal and plant genes

Pre-mRNA splicing is a fundamental step in gene expression, conserved across eukaryotes, in which the spliceosome recognizes motifs at the 3' and 5' splice sites (SSs), excises introns, and ligates exons. SS recognition and pairing is often influenced by protein splicing factors (SFs) that bind to splicing regulatory elements (SREs). Here, we describe SMsplice, a fully interpretable model of pre-mRNA splicing that combines models of core SS motifs, SREs, and exonic and intronic length preferences. We learn models that predict SS locations with 83 to 86% accuracy in fish, insects, and plants and about 70% in mammals. Learned SRE motifs include both known SF binding motifs and unfamiliar motifs, and both motif classes are supported by genetic analyses. Our comparisons across species highlight similarities between non-mammals, increased reliance on intronic SREs in plant splicing, and a greater reliance on SREs in mammalian splicing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Human perturbations to mercury in global rivers

Mercury compounds are potent neurotoxins that pose threats to human health, primarily through fish consumption. Rivers, critical for drinking water and food supply, have seen rapid increases in mercury concentrations and export to coastal margins since the Industrial Revolution (~1850). However, patterns of these changes remain understudied, limiting assessments of environmental policies. Here, we develop a global model to simulate preindustrial riverine total mercury and assess human perturbations by comparing it to present-day conditions. We find that global rivers transported ~390 megagrams annually of mercury to the oceans in the preindustrial era, with spatial variability. Human activities have elevated riverine mercury budgets by two to three times in the present day. Establishing a baseline riverine mercury level, our findings reveal rapid responses of riverine mercury to human perturbations and could be used to inform targets for global riverine mercury restoration. Total riverine mercury concentrations could also be used as indicators to comprehensively understand the effectiveness of mercury pollution governance.

Science & Technology - Other Topics↗