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At least 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor

Hearing is a fundamental sense of many animals, including all mammals, birds, some reptiles, amphibians, fish, and arthropods. The auditory organs of these animals are extremely diverse in anatomy after hundreds of millions of years of evolution, yet all are made up of cellular tissue and are morphologically part of the bodies of animals. Here, we show that hearing in the orb-weaving spider Larinioides sclopetarius is not constrained by the organism’s body but is extended through outsourcing hearing to its extended phenotype, the proteinaceous, self-manufactured orb web. We find that the wispy, wheel-shaped orb web acts as a hyperacute acoustic antenna to capture the sound-induced air particle movements that approach the maximum physical efficiency better than the acoustic responsivity of all previously known eardrums. By sensing the motion of web threads, the spider remotely detects and localizes the source of an incoming airborne acoustic wave, such as those emitted by approaching prey or predators. By outsourcing its acoustic sensors to its web, the spider is released from body size constraints and permits the araneid spider to increase its sound-sensitive surface area enormously, up to 10,000 times greater than the spider itself. The spider also enables the flexibility to functionally adjust and regularly regenerate its external "eardrum" according to its needs. The outsourcing and supersizing of auditory function in spiders provides unique features for studying extended and regenerative sensing and designing novel acoustic flow detectors for precise fluid dynamic measurement and manipulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation

Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM—often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)—are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1–9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862–866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. Finally, the morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats

On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. But, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont. We propose an evolutionary model wherein the appearance of the most active enzyme isoform, glutaminase C (GAC), which is expressed in many cancers, was a late retrotransposition event that occurred in fishes from the Chondrichthyes class. The ankyrin (ANK) repeats in the glutaminases were acquired early in their evolution. In order to obtain information on ANK folding, we solved two high-resolution structures of the ANK repeat-containing C termini of both kidney-type glutaminase (KGA) and GLS2 isoforms (glutaminase B and liver-type glutaminase). We also found that the glutaminase ANK repeats form unique intramolecular contacts through two highly conserved motifs; curiously, this arrangement occludes a region usually involved in ANK-mediated protein-protein interactions. We also solved the crystal structure of full-length KGA and present a small-angle X-ray scattering model for full-length GLS2. These structures explain these proteins' compromised ability to assemble into catalytically active supra-tetrameric filaments, as previously shown for GAC. Collectively, these results provide information about glutaminases that may aid in the design of isoform-specific glutaminase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Numerical investigation of inertial sphere impaction on a cylinder in subcritical flow

We investigated the accuracy of a Lagrangian scheme for simulating both the motion and wall impaction of neutrally buoyant inertial spheres (8.85 ≤ St ≤ 18.04) moving in the subcritical regime (Re = 10,972 and 22,366) of flows past a circular cylinder. The accuracy of the eddy-resolving simulations of the flow field was verified based on available data at nearly comparable flow conditions. The accuracy of the eddy-resolving simulations of the flow field was verified based on available data at nearly comparable flow conditions. The accuracy of the particle tracking scheme was verified with respect to corresponding experimental data in a laboratory flume. Particle dispersion en route to the circular cylinder is mostly driven by the flow disturbance from the particle injector tube. The trends in collision rates are largely explained by the rate of particle entertainment into the boundary layer around the cylinder and the inertial condition of the spheres in this proximity region—both of which can be better assessed by post-processing of the numerical outcomes. Here, the primary incentive to undertake this work was the need for validating a particle-based method for quantifying the hydraulic stressors leading to bodily damage of fish passing flows influenced by hydraulic infrastructure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Survival and Traits of Reconditioned Kelt Steelhead Oncorhynchus mykiss in the Yakima River, Washington

Abstract We evaluated the traits and survival to release of reconditioned kelt steelhead Oncorhynchus mykiss in the Yakima River (Washington State, USA). From 2001 to 2011, we captured a total of 9,738 downstream-migrating kelts at an irrigation diversion facility, an average about 27% of each annual wild steelhead return. Captured kelts were reared for 4.5–10 months in an artificial environment, treated for diseases and parasites, and fed both krill and pellets. Surviving reconditioned fish were released into the Yakima River during the peak of the upstream migration of prespawn steelhead. Reconditioned steelhead kelts were predominantly (>92%) female. Annual survival to release ranged from 20% to 62% and averaged 38% over the course of the study, the surviving reconditioned kelts showing increases in FL, weight, and Fulton's K condition factor compared with their preconditioning status. Kelts in good condition and those with bright coloration at the time of collection were more likely to survive than those of poorer status at collection. Postrelease timing of upstream migration by reconditioned kelts was spread over several months and correlated well with the run timing of prespawn migrants upstream. The empirical results we observed demonstrate the potential for kelt reconditioning to provide recovery benefits for repeat spawning imperiled wild populations in highly developed river systems. Received July 17, 2012; accepted March 15, 2013

Hatch, Douglas R.↗
DOE OSTI2014

Assessment of Subyearling Chinook Salmon Survival through the Federal Hydropower Projects in the Main-Stem Columbia River

High survival through hydropower projects is an essential element in the recovery of salmonid populations in the Columbia River. It is also a regulatory requirement under the 2008 Federal Columbia River Power System (FCRPS) Biological Opinion (BiOp) established under the Endangered Species Act. It requires dam passage survival to be ≥0.96 and ≥0.93 for spring and summer outmigrating juvenile salmonids, respectively, and estimated with a standard error ≤ 0.015. An innovative virtual/paired-release design was used to estimate dam passage survival, defined as survival from the face of a dam to the tailrace mixing zone. A coordinated four-dam study was conducted during the 2012 summer outmigration using 14,026 run-of-river subyearling Chinook salmon surgically implanted with acoustic micro-transmitter (AMT) tags released at 9 different locations, and monitored on 14 different detection arrays. Each of the four estimates of dam passage survival exceeded BiOp requirements with values ranging from 0.9414 to 0.9747 and standard errors, 0.0031 to 0.0114. Two consecutive years of survival estimates must meet BiOp standards in order for a hydropower project to be in compliance with recovery requirements for a fish stock.

Skalski, J. R.↗
DOE OSTI2014

Physiological Stress Responses to Prolonged Exposure to MS-222 and Surgical Implantation in Juvenile Chinook Salmon

While many studies have investigated the effects of transmitters on fish condition, behavior, and survival, to our knowledge, no studies have taken into account anesthetic exposure time in addition to tag and surgery effects. We investigated stress responses to prolonged MS-222 exposure after stage 4 induction in surgically implanted juvenile Chinook salmon (Oncorhynchus tshawytscha). Survival, tag loss, plasma cortisol concentration, and blood Na + , K + , Ca 2+ , and pH were measured immediately following anesthetic exposure and surgical implantation and 1, 7, and 14 days post-treatment. Despite the prolonged anesthetic exposure, 3-15 minutes post Stage 4 induction, there were no mortalities or tag loss in any treatment. MS-222 was effective at delaying immediate cortisol release during surgical implantation; however, osmotic disturbances resulted, which were more pronounced in longer anesthetic time exposures. From day 1 to day 14, Na + , Ca 2+ , and pH significantly decreased, while cortisol significantly increased. The cortisol increase was exacerbated by surgical implantation. There was a significant interaction between MS-222 time exposure and observation day for Na + , Ca 2+ , K + , and pH; variations were seen in the longer time exposures, although not consistently. In conclusion, stress response patterns suggest stress associated with surgical implantation is amplified with increased exposure to MS-222.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Estimating Cohort Survival through Tributaries for Salmonid Populations with Variable Ages at Migration

Abstract Survival of juvenile anadromous Pacific salmonids from their earliest age of seaward movement (“out-migration”) through the tributaries that connect their rearing grounds to larger-order rivers (“cohort survival”) is an important yet often unmonitored factor in the complex life history of these species. Populations with variable age at out-migration (e.g., steelhead Oncorhynchus mykiss) or multiple juvenile rearing strategies (e.g., Chinook Salmon O. tshawytscha) raise particular challenges in survival monitoring. A multiple-state release–recapture model is presented to estimate cohort survival for salmonid species with variable age at out-migration and demonstrated in two case studies. Annual releases of fish tagged with passive integrated transponder (PIT) tags from the same brood year (cohort) and their detections by instream PIT-tag detection arrays in tributaries and at hydroelectric dams are used to estimate survival through tributaries and the age composition of juvenile migrants reaching downstream sites. The 2010 cohort of Chinook Salmon from the Chiwawa River in Washington State had estimated survival of 0.59 to the middle Wenatchee River array in Tumwater Dam Reservoir (river distance of 30 km) and 0.12 to McNary Dam (364 km) on the Columbia River. The age composition shifted from 60.1% subyearlings at the Wenatchee River array to 100% yearlings at McNary Dam, reflecting the use of the Wenatchee River as a nonnatal rearing area, whereas McNary Dam is in the migratory corridor. The 2010 cohort of steelhead from the Twisp River in Washington State had estimated survival from the yearling stage of 0.30 to Rocky Reach Dam (146 km from the Twisp River mouth) on the Columbia River and 0.17 to McNary Dam (439 km). The low survival to the Columbia River resulted from both mortality and adoption of a resident life history and reflects the diverse population structure in the Twisp River. Received February 4, 2015; accepted June 11, 2015

Buchanan, Rebecca A.↗
DOE OSTI2015

Stock Differences in Growth, Smolting, and Early Male Maturation in Hatchery Spring Chinook Salmon: a Common-Garden Experiment

Abstract Hatchery spring Chinook Salmon Oncorhynchus tshawytscha from Parkdale Hatchery on the Hood River, Oregon, and Carson National Fish Hatchery (CNFH) on the Wind River, Washington, were reared under a common-garden experimental regime at CNFH over three consecutive brood years (2008–2010) to assess the effects of stock on smoltification and early male maturation. Rearing groups were monitored for size, percent solid (a surrogate for whole-body lipid), gill Na+,K+-ATPase activity, and rate of precocious maturation in males (i.e., age-2 minijack rate). Despite rearing of the stocks under identical conditions, the out-of-basin Hood River stock was significantly smaller throughout the study and at release as smolts, had lower whole-body lipid at release, and had lower gill Na+,K+-ATPase activity at release than the Carson stock; furthermore, the Hood River stock exhibited much higher mean minijack rates than the Carson stock (45% versus 23% of males). Using logistic regression, we demonstrated that the threshold size for initiation of early male maturation was significantly lower for the Hood River stock than for the Carson stock, suggesting a genetic basis for this life history difference. The present study highlights the importance of understanding how specific genotypes may respond differently to the unique environmental conditions in a given hatchery environment. These differences may in turn influence physiological and life history pathways that affect smolt-to-adult return rates and the demography of returning adults.

Spangenberg, Dina K.↗
DOE OSTI2016

No Evidence of Increased Survival or Decreased Straying from Acclimating Subyearling Fall Chinook Salmon to Release Locations in the Umatilla River of Oregon

Abstract Smolt-to-adult survival (SAS) and straying of subyearling fall Chinook Salmon Oncorhynchus tshawytscha that were acclimated in waters of their release site before river release was compared with those of fish that were transported to the river and released directly into the river. Results showed that there were no differences in average SAS, which was 0.08% for both acclimated and direct-release groups, or straying, which averaged 33.8% and 35.3% for direct and acclimated release groups, respectively. We conclude that an acclimation period may not improve these metrics in subyearling-released salmon. Received June 19, 2015; accepted October 31, 2015

Clarke, Lance R.↗
DOE OSTI2016

Mapping Lake Sturgeon Spawning Habitat in the Upper Tennessee River using Side-Scan Sonar

Abstract The Lake Sturgeon Acipenser fulvescens is a fish species that was once dispersed widely throughout the Mississippi River drainage but was largely extirpated from the southern portions of its range by overfishing and habitat degradation. There is an ongoing restoration effort to reestablish the Lake Sturgeon to rivers of the southeastern United States. Reintroduced juvenile Lake Sturgeon now occupy several reservoirs separated from each other by hydroelectric dams along the upper Tennessee River. To complete their life history, Lake Sturgeon will migrate upriver from reservoir habitats to more lotic habitats and spawn over coarse rocky substrate, even in the tailwaters of impassable dams. Using low-cost, consumer-grade, side-scan sonar and a GIS, we mapped the substrate of four tailwaters that may be future spawning locations for Lake Sturgeon. We used video imagery collected from random locations within the mapped areas to validate our digitization of sonar imagery. We calculated the area of four substrate classes displayed in the maps to evaluate that aspect of the suitability of each of the tailwaters for Lake Sturgeon spawning. The revised maps showed that the best spawning substrate (unembedded, coarse, rocky substrate, 6–25 cm in diameter) comprised 17.0–30.5% of the total area mapped at each tailwater, while the least suitable substrate class (fine sediment, <0.2 cm in diameter) comprised 6.2–30.7% of the mapped areas. Our results suggest that any future spawning events by Lake Sturgeon below each of these dams are likely to encounter some suitable spawning substrate patches, while management opportunities exist to supplement tailwater areas with suitable spawning substrate. Received March 11, 2016; accepted May 30, 2016 Published online August 31, 2016

Walker, Daniel J.↗
DOE OSTI2016

Stock-Specific Size and Migration of Juvenile Coho Salmon in British Columbia and Southeast Alaska Waters

Abstract The variation at 17 microsatellites was analyzed for 5,270 juvenile Coho Salmon Oncorhynchus kisutch obtained from coastal British Columbia and Gulf of Alaska surveys during 1998–2012. A 270-population baseline was used to determine the individual identifications of the fish sampled, with individuals being identified to 22 stocks of origin. Columbia River and Washington juveniles were consistently larger than those from British Columbia and Alaska. During June, the larger individuals within a stock were observed in more northerly locations. There was a relationship between the timing of northward migration and juvenile body size, with larger individuals migrating earlier than smaller individuals from the same stocks. Stock composition was more diverse in the northern sampling regions than in those in southern British Columbia. There was only a modest change in stock composition between fall and winter samples in both the Strait of Georgia and west coast of Vancouver Island sampling regions, indicating that juvenile migration had largely been completed by the fall. There was a wide divergence among stocks in juvenile size and dispersion among sampling locations. Received December 9, 2015; accepted February 9, 2016

Beacham, Terry D.↗
DOE OSTI2017

The effects of sampling location and turbulence on discharge estimates in short converging turbine intakes

Standards provide recommendations for best practices when installing current meters to measure fluid flow in closed conduits. A central guideline requires the velocity distribution to be regular and the flow steady. Because of the nature of the short converging intakes typical of low-head hydroturbines, these assumptions may be invalid if current meters are intended to be used to estimate discharge. Usual concerns are (1) the effects of the number of devices, (2) the sampling location and (3) the high turbulence caused by blockage from submersible traveling screens usually deployed for safe downstream fish passage. These three effects were examined in the present study by using 3D simulated flow fields in both steady-state and transient modes. In the process of describing an application at an existing hydroturbine intake at Ice Harbor Dam, the present work outlined the methods involved, which combined computational fluid dynamics, laboratory measurements in physical models of the hydroturbine, and current meter performance evaluations in experimental settings. The main conclusions in this specific application were that a steady-state flow field sufficed to determine the adequate number of meters and their location, and that both the transverse velocity and turbulence intensity had a small impact on estimate errors. However, while it may not be possible to extrapolate these findings to other field conditions and measuring devices, the study laid out a path to conduct similar assessments in other applications.

computational fluid dynamics (CFD)↗
DOE OSTI2019

Lattice arrangement of myosin filaments correlates with fiber type in rat skeletal muscle

The thick (myosin-containing) filaments of vertebrate skeletal muscle are arranged in a hexagonal lattice, interleaved with an array of thin (actin-containing) filaments with which they interact to produce contraction. X-ray diffraction and EM have shown that there are two types of thick filament lattice. In the simple lattice, all filaments have the same orientation about their long axis, while in the superlattice, nearest neighbors have rotations differing by 0° or 60°. Tetrapods (amphibians, reptiles, birds, and mammals) typically have only a superlattice, while the simple lattice is confined to fish. We have performed x-ray diffraction and electron microscopy of the soleus (SOL) and extensor digitorum longus (EDL) muscles of the rat and found that while the EDL has a superlattice as expected, the SOL has a simple lattice. The EDL and SOL of the rat are unusual in being essentially pure fast and slow muscles, respectively. The mixed fiber content of most tetrapod muscles and/or lattice disorder may explain why the simple lattice has not been apparent in these vertebrates before. This is supported by only weak simple lattice diffraction in the x-ray pattern of mouse SOL, which has a greater mix of fiber types than rat SOL. We conclude that the simple lattice might be common in tetrapods. The correlation between fiber type and filament lattice arrangement suggests that the lattice arrangement may contribute to the functional properties of a muscle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Finny Merchandise: The Atlantic Cod (Gadus morhua) Trade in Gold Rush–Era San Francisco, California

During California’s Gold Rush of 1849–1855, thousands of miners rushed to San Francisco, Sacramento, and elsewhere throughout northern California, creating a significant demand for food. In this work, we investigate the role of Atlantic cod (Gadus morhua) and Pacific cod (G. macrocephalus) during the Gold Rush era using historical records, ancient DNA, and vertebral morphology in the cod assemblage recovered from Thompson’s Cove (CA-SFR-186H), a Gold Rush–era site in San Francisco. From the 18 cod bones recovered from Thompson’s Cove, our analysis of five specimens for ancient DNA indicates that Atlantic cod were imported during the 1850s, likely as a (largely) deboned, dried and salted product from the East Coast of the United States. Curiously, while locally available in very deep waters off the California coast, Pacific cod were minimally fished during the 1850s and became abundantly available in the 1860s after an Alaska-based fishery developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

VERY LARGE ARRAY DETECTION OF THE 36 GHz ZEEMAN EFFECT IN DR21W REVISITED

We report on the observation of the 36 GHz methanol maser line in the star-forming region DR21W to accurately measure the Zeeman effect. The Zeeman signature reported by Fish et al. became suspicious after an instrumental effect was discovered in the early days of the commissioning of the Very Large Array Wide-band Digital Architecture correlator. We conclude that the previously reported magnetic field strength of 58 mG (1.7 Hz mG{sup -1}/z) is instrumental in nature and thus incorrect. With the improved performance of the array, we now deduce a 3{sigma} limit of -4.7 to +0.4 mG (1.7 Hz mG{sup -1}/z) for the line-of-sight component of the magnetic field strength in DR21W.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

MAGNETIZED ACCRETION AND DEAD ZONES IN PROTOSTELLAR DISKS

The edges of magnetically dead zones in protostellar disks have been proposed as locations where density bumps may arise, trapping planetesimals and helping form planets. Magneto-rotational turbulence in magnetically active zones provides both accretion of gas on the star and transport of mass to the dead zone. We investigate the location of the magnetically active regions in a protostellar disk around a solar-type star, varying the disk temperature, surface density profile, and dust-to-gas ratio. We also consider stellar masses between 0.4 and 2 M{sub Sun }, with corresponding adjustments in the disk mass and temperature. The dead zone's size and shape are found using the Elsasser number criterion with conductivities including the contributions from ions, electrons, and charged fractal dust aggregates. The charged species' abundances are found using the approach proposed by Okuzumi. The dead zone is in most cases defined by the ambipolar diffusion. In our maps, the dead zone takes a variety of shapes, including a fish tail pointing away from the star and islands located on and off the midplane. The corresponding accretion rates vary with radius, indicating locations where the surface density will increase over time, and others where it will decrease. We show that density bumps do not readily grow near the dead zone's outer edge, independently of the disk parameters and the dust properties. Instead, the accretion rate peaks at the radius where the gas-phase metals freeze out. This could lead to clearing a valley in the surface density, and to a trap for pebbles located just outside the metal freezeout line.

79 ASTRONOMY AND ASTROPHYSICS↗