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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.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Suite of Constitutive Promoters for Tuning Gene Expression in Plants

The need for convenient tools to express transgenes over a large dynamic range is pervasive throughout plant synthetic biology; however, current efforts are largely limited by the heavy reliance on a small set of strong promoters, precluding more nuanced and refined engineering endeavors in planta . To address this technical gap, we characterize a suite of constitutive promoters that span a wide range of transcriptional levels and develop a GoldenGate-based plasmid toolkit named PCONS, optimized for versatile cloning and rapid testing of transgene expression at varying strengths. We demonstrate how easy access to a stepwise gradient of expression levels can be used for optimizing synthetic transcriptional systems and the production of small molecules in planta . We also systematically investigate the potential of using PCONS as an internal standard in plant biology experimental design, establishing the best practices for signal normalization in experiments. Although our library has primarily been developed for optimizing expression in N. benthamiana , we demonstrate the translatability of our promoters across distantly related species using a multiplexed reporter assay with barcoded transcripts. In conclusion, our findings showcase the advantages of the PCONS library as an invaluable toolkit for plant synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Drought and plant litter chemistry alter microbial gene expression and metabolite production

Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. In grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct taxonomic and functional profiles. The most discernable physiological signatures of drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across precipitation treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade off between microbial drought stress tolerance, resource acquisition and growth traits in plant litter microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Understanding SYCL Portability for Pseudorandom Number Generation: a Case Study with Gene-Expression Connectivity Mapping

Towards the goal of improving functional and performance portability of SYCL, we study a bioinformatics application that has been accelerated with CUDA and fast pseudorandom number generation on a GPU. We describe the experience of migrating pseudorandom number generation from CUDA to SYCL, evaluate the performance of pseudorandom number generators using the CUDA random number generation library, suggest the support of the XORWOW pseudorandom number generator in the oneAPI math kernel library (oneMKL) interface for performance portability, and identify the performance gap using the MKL interface in SYCL that supports pseudorandom number generation with third-party libraries. We hope that the results are valuable for the development of the SYCL ecosystem.

Jin, Zheming↗
DOE OSTI2022

Astragaloside IV improved antioxidative stress capacity and related gene expression of the Keap1‐Nrf2 pathway in grass carp ( Ctenopharyngodon idella ) hepatocytes under heat stress

Abstract This study aims to investigate the protective effects of astragaloside IV (AS‐IV) on the hepatocytes of grass carp ( Ctenopharyngodon idella ) on heat stress. Cultured cells were treated with AS‐IV (0, 50, 100 and 200 μg/ml) at 28°C for 24 h and then exposed to heat stress by increasing the culturing temperature (32 ± 0.5°C) for 6 h. The increased temperatures significantly reduced cell viability and superoxide dismutase (SOD) activity, and increased malondialdehyde (MDA) levels in the 0 μg/ml AS‐IV treatment group at 32°C, but the grass carp hepatocytes treated with 100 and 200 μg/ml AS‐IV had significantly increased cell viability and SOD activity and decreased MDA levels. The mRNA levels of keap1a , keap1b , nrf2 , gsh‐px , cat , cu‐zn sod , mgst1 and il‐6 were significantly lower in the 0 μg/ml AS‐IV treatment group at 32°C, while those of keap1a , nrf2 , gsh‐px , cat , cu‐zn sod , gstp1 , ho‐1 and il‐6 were significantly higher in cells treated with 100 or 200 μg/ml AS‐IV. Our findings indicate that AS‐IV could enhance the antioxidative stress capacity of grass carp hepatocytes under heat stress, and its mechanism may be associated with the activation of the Keap1‐Nrf2 pathway. Thus, these results provide new insights into how to alleviate heat stress in grass carp.

Liu, Hua↗
DOE OSTI2023

Ammonia-Oxidizing Bacteria Maintain Abundance but Lower amoA -Gene Expression during Cold Temperature Nitrification Failure in a Full-Scale Municipal Wastewater Treatment Plant

The diverse microbial community of activated sludge used in biological treatment systems exhibits dynamic seasonal shifts in community composition and activity. Many wastewater treatment plants in temperate/continental climates experience seasonal cold temperature nitrification failure. “Seasonal nitrification failure” is the discharge of elevated concentrations of ammonia (greater than 4 mg/liter) with treated wastewater during the winter (influent wastewater temperatures below 13°C).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Gene Expression in Dunaliella salina Bardawil +/- Iron

Dunaliella salina Bardawil (also known as Dunaliella bardawil) is an extremophilic, unicellular green alga from the Chlorophyte lineage. D. salina is found in hypersaline environments where it can tolerate extremes of heat, light, pH, and up to saturating concentrations of salt. The D. salina Bardawil isolate (UTEX LB 2538) was found in a salt pond near the Bardawil Lagoon on the Sinai peninsula in 1976. This isolate of D. salina is the richest natural source of beta-carotene, a highly valuable commercial product. This accession includes an RNA-Seq analysis of D. salina Bardawil cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Gene Expression in Dunaliella tertiolecta +/- Iron

Dunaliella tertiolecta is an extremophilic, green alga from the Chlorophyte lineage. It is found in coastal marine environments around the world. D. tertiolecta can tolerate extremes of heat, light, pH, and salinity. D. tertiolecta is under development for the production biofuels and other bioproducts because it can produce large quantities of neutral lipids, and it can be grown in open raceway ponds using only the inputs of seawater and sunlight. This isolate of D. tertiolecta (UTEX LB 999) was found in Oslofjord, Norway in 1938. This accession includes an RNA-Seq analysis of D. tertiolecta cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Odor exposure during imprinting periods increases odorant-specific sensitivity and receptor gene expression in coho salmon ( Oncorhynchus kisutch )

ABSTRACT Pacific salmon are well known for their homing migrations; juvenile salmon learn odors associated with their natal streams prior to seaward migration, and then use these retained odor memories to guide them back from oceanic feeding grounds to their river of origin to spawn several years later. This memory formation, termed olfactory imprinting, involves (at least in part) sensitization of the peripheral olfactory epithelium to specific odorants. We hypothesized that this change in peripheral sensitivity is due to exposure-dependent increases in the expression of odorant receptor (OR) proteins that are activated by specific odorants experienced during imprinting. To test this hypothesis, we exposed juvenile coho salmon, Oncorhynchus kisutch, to the basic amino acid odorant l-arginine during the parr–smolt transformation (PST), when imprinting occurs, and assessed sensitivity of the olfactory epithelium to this and other odorants. We then identified the coho salmon ortholog of a basic amino acid odorant receptor (BAAR) and determined the mRNA expression levels of this receptor and other transcripts representing different classes of OR families. Exposure to l-arginine during the PST resulted in increased sensitivity to that odorant and a specific increase in BAAR mRNA expression in the olfactory epithelium relative to other ORs. These results suggest that specific increases in ORs activated during imprinting may be an important component of home stream memory formation and this phenomenon may ultimately be useful as a marker of successful imprinting to assess management strategies and hatchery practices that may influence straying in salmon.

Dittman, Andrew H. (ORCID:000000016482359X)↗
DOE OSTI2021

SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung

Extensive fibrin deposition in the lungs and altered levels of circulating blood coagulation proteins in COVID-19 patients imply local derangement of pathways that limit fibrin formation and/or promote its clearance. We examined transcriptional profiles of bronchoalveolar lavage fluid (BALF) samples to identify molecular mechanisms underlying these coagulopathies. mRNA levels for regulators of the kallikrein–kinin (C1-inhibitor), coagulation (thrombomodulin, endothelial protein C receptor), and fibrinolytic (urokinase and urokinase receptor) pathways were significantly reduced in COVID-19 patients. While transcripts for several coagulation proteins were increased, those encoding tissue factor, the protein that initiates coagulation and whose expression is frequently increased in inflammatory disorders, were not increased in BALF from COVID-19 patients. Our analysis implicates enhanced propagation of coagulation and decreased fibrinolysis as drivers of the coagulopathy in the lungs of COVID-19 patients.

59 BASIC BIOLOGICAL SCIENCES↗