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At least 1,315 records · Page 73

All sources NASA NTRS DOE OSTI

DOE OSTI2019

Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB

Methylmercury (MeHg) is a potent bioaccumulative neurotoxin that is produced by certain anaerobic bacteria and archaea. Mercury (Hg) methylation has been linked to the gene pair hgcAB , which encodes a membrane-associated corrinoid protein and a ferredoxin. Although microbial Hg methylation has been characterized in vivo , the cellular biochemistry and the specific roles of the gene products HgcA and HgcB in Hg methylation are not well understood. Here, we report the kinetics of Hg methylation in cell lysates of Desulfovibrio desulfuricans ND132 at nanomolar Hg concentrations. The enzymatic Hg methylation mediated by HgcAB is highly oxygen sensitive, irreversible, and follows Michaelis-Menten kinetics, with an apparent K m of 3.2 nM and V max of 19.7 mol · min -1 · mg -1 total protein for the substrate Hg(II). Although the abundance of HgcAB in the cell lysates is extremely low, Hg(II) was quantitatively converted to MeHg at subnanomolar substrate concentrations. Interestingly, increasing thiol/Hg(II) ratios did not impact Hg methylation rates, which suggests that HgcAB-mediated Hg methylation effectively competes with cellular thiols for Hg(II), consistent with the low apparent K m . Supplementation of 5-methyltetrahydrofolate or pyruvate did not enhance MeHg production, while both ATP and a nonhydrolyzable ATP analog decreased Hg methylation rates in cell lysates under the experimental conditions. These studies provide insights into the biomolecular processes associated with Hg methylation in anaerobic bacteria. The concentration of Hg in the biosphere has increased dramatically over the last century as a result of industrial activities. The microbial conversion of inorganic Hg to MeHg is a global public health concern due to bioaccumulation and biomagnification of MeHg in food webs. Exposure to neurotoxic MeHg through the consumption of fish represents a significant risk to human health and can result in neuropathies and developmental disorders. Anaerobic microbial communities in sediments and periphyton biofilms have been identified as sources of MeHg in aquatic systems, but the associated biomolecular mechanisms are not fully understood. In the present study, we investigate the biochemical mechanisms and kinetics of MeHg formation by HgcAB in sulfate-reducing bacteria. These findings advance our understanding of microbial MeHg production and may help inform strategies to limit the formation of MeHg in the environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Increased mortality in mice following immunoprophylaxis therapy with high dosage of nicotinamide in Burkholderia persistent infections

Bacterial persistence, known as non-inherited antibacterial resistance, is a contributing factor to the establishment of long-lasting chronic bacterial infections. In this study, we examined the ability of nicotinamide (NA) to potentiate different classes of antibiotics against Burkholderia thailandensis persister cells. Here we demonstrate that addition of NA in in vitro models of B. thailandensis infection resulted in a significant depletion of the persister population in response to various classes of antibiotics. We applied microfluidic bioreactors with a continuous media flow to study the effect of supplementation with a NA gradient on the recovery of B. thailandensis persister populations. A co-culture of human neutrophils pre-activated with 50 µM NA and B. thailandensis resulted in the most efficient reduction in the persister population. Applying single cell RNA FISH analysis and quantitative PCR, we found that NA inhibited gene expression of the stringent response regulator relA , implicated in the regulation of the persister metabolic state. In conclusion, we also demonstrate that a therapeutic dose of NA (250mg/kg), previously applied as immunoprophylaxis against antibiotic-resistant bacterial species, produced adverse effects in an in vivo murine infection model of the highly pathogenic Burkholderia pseudomallei , indicating that therapeutic dose and metabolite effects have to be carefully evaluated and tailored for every case of potential clinical application.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Formation and Properties of New Types of Metal–Dielectric Nanostructures for Creating Optical Metamaterials

“Herein, we consider the technologies of obtaining composite structures that can exhibit the properties of metamaterials, namely layered metal–dielectric (metal–polymer) structures and fish-net metal-polymeric structures. The dielectric and resonance properties of the synthesized structures are studied both theoretically and experimentally, and the excitation features of new types of quasi-non-diffraction plasmon-polaritons generated in them are established. Original methods and tools for characterizing the optical properties of the created composite structures (in particular, a differential polarization interferometer, a method and a device for detecting a negative refractive index) are proposed. Based on the developed and created metamaterials, a number of new devices are proposed and implemented, in particular, new configurations of flat lenses (so-called superlenses) of the near and far fields in the spectral range from ultraviolet to infrared radiation”.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Has primary production declined in the Salish Sea?

Declining primary production has been proposed as an explanation for the declines in coho (Oncorhynchus kisutch) and Chinook (Oncorhynchus tshawytscha) salmon in the Salish Sea since the 1970s. Marine sediments maintain a continuous record of conditions in the overlying water. We used stable isotopes of organic carbon and nitrogen measured in 21 sediment cores to determine the contributions and fluxes of marine-derived and terrigenous organic matter over time. The flux of marine-derived organic matter shows no trend for at least the last 100 years. An apparent increase in the marine flux in recent years is due to remineralization of organic matter as it passes through surface sediments. In contrast, the flux of terrigenous organic matter has increased over the last century in the Strait of Georgia, while in Puget Sound, terrigenous flux peaked in the mid-20th century. Total primary production has neither increased nor decreased in the Salish Sea over the last century. Consequently, a decline in primary production cannot explain recent declines in fish populations.

58 GEOSCIENCES↗

DOE OSTI2014

Feeding habits and trophic level of the Panama grunt Pomadasys panamensis, an important bycatch species from the shrimp trawl fishery in the Gulf of California

The Panama grunt is an abundant and commercially important species in the SE Gulf of California, but the research undertaken on this species is scarce despite its ecological and economic importance. We studied the feeding habits of Panama grunt through stomach content analyses as a first step towards understanding the biology of this species in the study area. Our results show that the Panama grunt is a benthic predator throughout its life cycle and feeds mainly on infaunal crustaceans. Diet differences were not found according to size, diet or season. Shannon diversity index results indicate that Panama grunt have a limited trophic niche breadth with a diet dominated by a limited number of taxa. The estimated trophic level of this species is 3.59. Overall, the Panama grunt is a carnivorous fish occupying the intermediate levels of the trophic pyramid.

demersal↗

DOE OSTI2022

Assessment of Spoilage Microbiota of Rainbow Trout (Oncorhynchus mykiss) during Storage by 16S rDNA Sequencing

Due to the high contents of protein and fat in rainbow trout, it is highly susceptible to spoilage, which limits the storage and transportation processes. Exploring the spoilage microbial community during rainbow trout storage is essential to develop an effective preservation method. Here, the changes in the total bacterial colony and total volatile base nitrogen (TVB-N) during the storage of rainbow trout were investigated. Storage at 0 °C can effectively slow down the spoilage process with bacterial counts and TVB-N contents decreased from 8.7 log CFU/g and 18.7 mg/100 g obtained at 4 °C to 5.6 log CFU/g and 14.5 mg/100 g, respectively. 16S rDNA high-throughput sequencing results showed that the diversity of microbial genera decreased during storage. Acinetobacter, Pseudomonas, and Shewanells gradually became the dominant spoilage genera with contents of 59.9%, 18.6%, and 1.7%, respectively, in the late stage of storage. The spoilage abilities of bacteria belonging to the Pseudomonas and Shewanells genera were analyzed. Shewanella sp. S5-52 showed the highest level of TVB-N content (100.6 mg/100 g) in sterile fish juice, indicating that it had a strong spoilage ability. This study confirmed the dominant spoilage bacterial genera and evaluated the spoilage abilities of isolated strains during the storage of rainbow trout, which laid the foundation for further investigation of the spoilage mechanism of rainbow trout and other aquatic products.

Du, Guangqing↗

DOE OSTI2012

Aquatic Acoustic Metrics Interface

Fishes and marine mammals may suffer a range of potential effects from exposure to intense underwater sound generated by anthropogenic activities such as pile driving, shipping, sonars, and underwater blasting. Several underwater sound recording (USR) devices have been built to acquire samples of the underwater sound generated by anthropogenic activities. Software becomes indispensable for processing and analyzing the audio files recorded by these USRs. The new Aquatic Acoustic Metrics Interface Utility Software (AAMI) is specifically designed for analysis of underwater sound recordings to provide data in metrics that facilitate evaluation of the potential impacts of the sound on aquatic animals. In addition to the basic functions, such as loading and editing audio files recorded by USRs and batch processing of sound files, the software utilizes recording system calibration data to compute important parameters in physical units. The software also facilitates comparison of the noise sound sample metrics with biological measures such as audiograms of the sensitivity of aquatic animals to the sound, integrating various components into a single analytical frame.

Source record↗

DOE OSTI2016

A 3D approximate maximum likelihood localization solver

A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with acoustic transmitters and vocalizing marine mammals to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives and support Marine Renewable Energy. 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.

Source record↗

DOE OSTI2024

Wetlands Geoprocessor (v 1.0)

Wetlands have often been described as the “Earth’s kidneys” because wetlands have the ability filter pollutants and purify water. Based upon wetland storage capacity, average daily flow, and inflow nutrient loading this model estimates potential load reductions of nitrate and orthophosphate) from a constructed surface flow wetland (CW). The model relies upon equations, coefficients, and models provided by Cheng et al. 2020 and Cheng & Basu 2017. Nitrogen (N) and phosphorus are important nutrients to ecosystems, but high concentrations can lead to water quality issues. Major sources of these nutrients come from agricultural areas where fertilizer is applied in large quantitates and/or animal waste is present. Excess nitrate and phosphorus may result in overgrowth of algae, which can decrease the dissolved oxygen in water, thereby harming and killing fish and other aquatic species. This model evaluates water purification results and estimates cost to install a surface flow constructed wetlands.

Davis, Cleve↗

DOE OSTI2018

pnnl/ZebrafishBMD

ZebrafishBMD: A software tool to perform benchmark dose calculations using toxicity screening data of high-throughput zebrafish assays. High-content imaging of larval zebrafish behavior can be used as a screening approach to rapidly evaluate the relative potential for chemicals to cause toxicity. However, most statistical methods applied to these data transform movement values to incidence-based “hits” and calculate lowest effect levels (LELs), which loses individual fish resolution of behavior and defies hazard ranking due to reliance on applied dose levels. We developed a parallelizable workflow to calculate benchmark dose (BMD) values from dynamic, high-content zebrafish behavior data that scales for high throughput chemical screening. To capture the zebrafish movement response from light to dark stimulus, we summarized time-dependent data using both area under the curve and the immediate change at the transition point into two novel metrics that characterized abnormal behavior as a function of chemical concentration. The BMD workflow was applied to calculate BMD10 values of 1,060 ToxCast chemicals for 24 zebrafish endpoints, including behavior, mortality and morphology. ZebrafishBMD implements the BMD workflow and provides Matlab scripts to read the data (stored in a specific structure) from a .mat file, to calculate the behavioral endpoint values from movement versus time data, to construct concentrationresponse curves, to perform curve-fitting, and to calculate BMD10 values.

Thomas, Dennis↗

DOE OSTI2024

Ecological Benchmark for Chemicals

The Ecological Benchmark Tool dataset serves as a comprehensive repository of benchmarks designed to assess ecological risks at contaminated sites. This tool facilitates the evaluation of various environmental media and contaminants, supporting regulatory compliance and ecological protection. Benchmarks are available for air, biota, sediment, soil, and surface water. The dataset also provides species-specific benchmarks for fish, plants, birds, mammals, and invertebrates. Users can select benchmark sources, media, individual chemicals, and retrieve results in tabular or spreadsheet formats for analysis. Benchmarks are derived from authoritative sources, including government agencies, scientific councils, and academic publications. The dataset supports ecological risk assessments, regulatory decision-making, and environmental planning, with tools for benchmarking against chemical thresholds, sensitive species protection, and habitat impact evaluations. This structured approach ensures a robust evaluation of ecological risks tailored to site-specific and regulatory needs.

Stewart, Debra [Oak Ridge National Laboratory (ORN↗

DOE OSTI2024

Ecological Benchmark for Radionuclides

The Ecological Benchmark Tool for radionuclides dataset serves as a comprehensive repository of benchmarks designed to assess ecological risks at contaminated sites. This tool facilitates the evaluation of various environmental media and contaminants, supporting regulatory compliance and ecological protection. Benchmarks are available for sediment, soil, and surface water. The dataset also provides species-specific benchmarks for fish, plants, birds, mammals, and invertebrates. Users can select benchmark sources, media, individual radionuclides, and retrieve results in tabular or spreadsheet formats for analysis. Benchmarks are derived from authoritative sources, including government agencies, scientific councils, and academic publications. The dataset supports ecological risk assessments, regulatory decision-making, and environmental planning, with tools for benchmarking against radiological thresholds, sensitive species protection, and habitat impact evaluations. This structured approach ensures a robust evaluation of ecological risks tailored to site-specific and regulatory needs.

Stewart, Debra [Oak Ridge National Laboratory (ORN↗

DOE OSTI2021

Chromosome 8 gain is associated with high-grade transformation in MPNST

One of the most common malignancies affecting adults with Neurofibromatosis type 1 (NF1) is the malignant peripheral nerve sheath tumor (MPNST), an aggressive and often fatal sarcoma which most often arises from within benign plexiform neurofibromas. Despite advances in our understanding of the pathobiology of MPNST, there are few effective therapeutic options, and no investigational agents have proven successful in clinical trials. To further understand the genomic heterogeneity of MPNST, and to generate a preclinical platform that encompasses this heterogeneity, we developed a collection of NF1-MPNST patient derived xenografts (PDX). These PDX were compared to the primary tumors from which they were derived using copy number analysis, whole exome and RNA sequencing. We identified chromosome 8 gain as a recurrent genomic event in MPNST and validated its occurrence by FISH in the PDX and parental tumors, in a validation cohort, and by single cell sequencing in the PDX. Finally, we show that chromosome 8 gain is associated with inferior overall survival in soft tissue sarcomas. Taken together, these data suggest that chromosome 8 gain is a critical event in MPNST pathogenesis, and may account for the aggressive nature and poor outcomes in this sarcoma subtype.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Late Holocene fire and vegetation reconstruction from the western Klamath Mountains, California, USA: A multi-disciplinary approach for examining potential human land-use impacts

The influence of Native American land-use practices on vegetation composition and structure has long been a subject of significant debate. This is particularly true in portions of the western United States where tribal hunter-gatherers did not use agriculture to meet subsistence and other cultural needs. Climate has been viewed as the dominant determinant of vegetation structure and composition change over time, but ethnographic and anthropological evidence suggests that Native American land-use practices (particularly through the use of fire) had significant landscape effects on vegetation. However, it is difficult to distinguish climatically driven vegetation change from human-caused vegetation change using traditional paleoecological methods. To address this problem, we use a multidisciplinary methodology that incorporates paleoecology with local ethnographic and archaeological information at two lake sites in northwestern California. We show that anthropogenic impacts can be distinguished at our Fish Lake site during the cool and wet ‘Little Ice Age’, when we have evidence for open-forest or shade-intolerant vegetation, fostered for subsistence and cultural purposes, rather than the closed-forest or shade-tolerant vegetation expected due to the climatic shift. We also see a strong anthropogenic influence on modern vegetation at both sites following European settlement, decline in tribal use, and subsequent fire exclusion. These results demonstrate that Native American influences on vegetation structure and composition can be distinguished using methods that take into account both physical and cultural aspects of the landscape. Furthermore, they also begin to determine the scale at which western forests were influenced by Native American land-use practices and how modern forests of northwestern California are not solely products of climate alone.

58 GEOSCIENCES↗

DOE OSTI2014

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

Background: There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. Results: This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. Conclusions: In this paper, we presented a highly scalable and efficient genome assembly software, SWAPAssembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Juvenile salmonid migratory behavior at the mouth of the Columbia River and within the plume

A total of 8,159 acoustic-tagged salmonid smolts were detected at the mouth of the Columbia River. Of the fish detected at the mouth, 14% of yearling Chinook salmon, 9% of steelhead, and 22% of subyearling Chinook salmon were detected on a sparse array deployed in the Columbia River plume. Chinook salmon smolts decreased travel rate as they left the river and entered the plume, while steelhead increased travel rate. Chinook salmon also spent more time in the transitional area between the river mouth and plume as compared to steelhead. In early spring, yearling Chinook salmon and steelhead predominately migrated past the plume array towards the edge of the shelf and to the south. Later in the season, yearling Chinook salmon and steelhead smolts tended to migrate out of the river mouth in a northerly direction. Subyearling Chinook salmon migrated predominately past the portion of the plume array to the north of the river mouth.

salmon, migratory behavior, JSATS, Columbia River,↗

DOE OSTI2013

Performance assessment of bi-directional knotless tissue-closure devices in juvenile Chinook salmon surgically implanted with acoustic transmitters

Acoustic transmitters used in survival and telemetry studies are often surgically implanted in fish. While this is a well-established method, it has the potential to affect health, behavior, and survival, thus affecting study results. Much research has been done to try to minimize the harmful effects caused by the transmitter and tagging process. In 2009, we first investigated the use of a bi-directional knotless (barbed) suture material in juvenile Chinook salmon (Oncorhynchus tshawytscha). We found that it resulted in higher tag retention than the simple interrupted suture pattern; however, the occurrence of ulceration and redness increased. The objective of this study was to refine the suturing patterns of the bi-directional knotless suture and retest suture performance in juvenile Chinook salmon. We tested the bi-directional suture using 3 different suture patterns and two needle types: 6-Point (12-mm needle circumference), Wide “N” (12-mm needle circumference), Wide “N” Knot 12 (12-mm needle circumference), and Wide “N” Knot 18 (18-mm needle circumference).

bio-effect↗

DOE OSTI2016

Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation

Background A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern. Results Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection. Conclusion These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods.

Evolutionary Biology↗