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At least 1,189 records · Page 66
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation

Abstract Knowing how switchgrass ( Panicum virgatum L . ) responds and adapts to phosphorus (P)‐limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P‐stress on genome transcription and whole‐plant metabolism, physiology and development in switchgrass. P‐limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P‐stress, and decreased root diameter with increased density and length of root hairs at severe P‐stress. RNA‐seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P‐stress in roots and/or shoots compared to P‐replete plants, with many stress‐induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P‐acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P‐stress in shoots and roots, although this trend reversed under severe P‐stress, especially in shoots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mechanism of Protein Transport on the Twin Arginine Translocation Pathway

This project was awarded in September 2018 and ran for one year. The overarching goals of this multi-award project was to understand the mechanism and energetics of the Tat protein transport system responsible to the transport of proteins into the chloroplast thylakoid lumen. This pathway is responsible for the delivery of a number of proteins required for chloroplast biogenesis and homeostasis, including subunits of the photosynthetic oxygen-evolving complex and of the three large protein complexes of the photosynthetic electron transport chain. The manner through which proteins are transported on this pathway is highly unusual, and through the research supported by his set of DOE grants are leading to a mechanism of action that is previously unknown for protein trafficking. During the course of this short project we have continued to uncover evidence that the Tat pathway allows proteins to cross membranes through lipid-lined toroidal pores. The experiments undertaken during this project have been continued during the subsequent on-going DOE award period.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

[The growth movements of moss protonemata under clinostatic and microgravity conditions]

Populations of dark-grown protonemata of moss Ceratodon purpureus wt-4 (Germany) and wt-U (Ukraine) were rotated on clinostat or flown in space (experiment "Protonema" aboard Bion-11, December 24, 1996-January 7, 1997) to determine the effects of altered gravity on orientation of protonemata growing filaments. Protonemata had been cultivated 8 days in vertical stationary position at dark to be transported to microgravity or placed in clinostat for the period of 14 days. In the ground control, protonemata demonstrated the negatively gravitropic growth (straight upwards in a bundle of compact filaments). The horizontal or circular rotation in clinostat and exposure to microgravity made filaments grow every each way within the substrate plane but with an apparent trend to rightward curling resulting in "spiral galaxies".

NASA Discipline Plant Biology↗
DOE OSTI2025

Enhanced Laser-Induced Graphene Microfluidic Integrated Sensors (LIGMIS) for On-Site Biomedical and Environmental Monitoring

The convergence of microfluidic and electrochemical biosensor technologies offers significant potential for rapid, in-field diagnostics in biomedical and environmental applications. Traditional systems face challenges in cost, scalability, and operational complexity, especially in remote settings. Addressing these issues, laser-induced graphene microfluidic integrated sensors (LIGMIS) are presented as an innovative platform that integrates microfluidics and electrochemical sensors both comprised of laser-induced graphene. This study advances the LIGMIS concept by resolving issues of uneven fluid transport, increased hydrophobicity during storage, and sensor biofunctionalization challenges. Key innovations include Y-shaped reservoirs for consistent fluid flow, hydrophilic polyethyleneimine coatings to maintain wettability, and separable microfluidic and electrochemical components enabling isolated electrode nanoparticle metallization and biofunctionalization. Multiplexed electrochemical detection of the neonicotinoid imidacloprid and nitrate ions in environmental water samples yields detection limits of 707 nm and 10 -5.4 m with wide sensing ranges of 5–100 µm and 10 -5 –10 -1 m, respectively. Similarly, uric acid and calcium ions are detected in saliva, demonstrating detection limits of 217 nm and 10 -5.3 m with sensing ranges of 10–50 µm, and 10 -5 –10 -2.5 m, respectively. Overall, this biosensing demonstrates the capability of the LIGMIS platform for multiplexed detection in biologically complex solutions, with applications in environmental water quality monitoring and oral cancer screening.

environmental monitoring↗
DOE OSTI2022

Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis

Abstract Little is known at the transcriptional level about microbial eukaryotic adaptations to short-term salinity change. Arctic microalgae are exposed to low salinity due to sea-ice melt and higher salinity with brine channel formation during freeze-up. Here, we investigate the transcriptional response of an ice-associated microalgae over salinities from 45 to 8. Our results show a bracketed response of differential gene expression when the cultures were exposed to progressively decreasing salinity. Key genes associated with salinity changes were involved in specific metabolic pathways, transcription factors and regulators, protein kinases, carbohydrate active enzymes, and inorganic ion transporters. The pelagophyte seemed to use a strategy involving overexpression of Na + -H + antiporters and Na + -Pi symporters as salinity decreases, but the K + channel complex at higher salinities. Specific adaptation to cold saline arctic conditions was seen with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Separation of isoprene from biologically-derived gas streams

Renewable organic precursors, including olefinic compounds such as isoprene, have attracted interest from the polymer and pharmaceutical industries. Biologically-derived processes can generate these target compounds; however, their gaseous product streams are complex mixtures of condensable organic vapors (COVs), water vapor, carbon dioxide (CO 2 ), and/or nitrogen (N 2 ). Because COVs, CO 2 and water vapor are known to alter polymer membranes, mixed gas separations data at ambient and elevated temperatures are limited. Here, this study focused on two classes of polymer membranes, glassy [polyetherimide (Ultem®)] and a rubbery [polydimethylsiloxane (PDMS)] with results indicating that isoprene separation is possible in humidified gas environment (2–4 vol% water). Gas permeabilities of these membranes did not noticeably change in the presence of humidity; however, the selectivity of these membranes was significantly lower compared to their performance under dry conditions. The role of water vapor in gas transport was derived from the energy of activation of permeation (E p ) for PDMS and Ultem® from 30–80°C in humidified mixed gas streams. For both polymers, E p data shows a slight decrease in selectivity with the other gases (hydrogen, N 2 , CO 2 , and methane) at elevated temperatures in the presence of water vapor. Thus, these COVs separations are feasible with polymer membranes in the presence of humidified gas streams, even in the case of glassy and rubbery membranes in series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations

Abstract Mutations within the mtrR gene are commonly found amongst multidrug resistant clinical isolates of Neisseria gonorrhoeae, which has been labelled a superbug by the Centers for Disease Control and Prevention. These mutations appear to contribute to antibiotic resistance by interfering with the ability of MtrR to bind to and repress expression of its target genes, which include the mtrCDE multidrug efflux transporter genes and the rpoH oxidative stress response sigma factor gene. However, the DNA-recognition mechanism of MtrR and the consensus sequence within these operators to which MtrR binds has remained unknown. In this work, we report the crystal structures of MtrR bound to the mtrCDE and rpoH operators, which reveal a conserved, but degenerate, DNA consensus binding site 5′-MCRTRCRN4YGYAYGK-3′. We complement our structural data with a comprehensive mutational analysis of key MtrR-DNA contacts to reveal their importance for MtrR-DNA binding both in vitro and in vivo. Furthermore, we model and generate common clinical mutations of MtrR to provide plausible biochemical explanations for the contribution of these mutations to multidrug resistance in N. gonorrhoeae. Collectively, our findings unveil key biological mechanisms underlying the global stress responses of N. gonorrhoeae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Taxonomic Re-Evaluation and Genomic Comparison of Novel Extracellular Electron Uptake-Capable Rhodovulum visakhapatnamense and Rhodovulum sulfidophilum Isolates

Rhodovulum spp. are anoxygenic phototrophic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). A total of 15 strains of Rhodovulum sulfidophilum were isolated from a marine estuary to observe these metabolisms in marine phototrophs. One representative strain, Rhodovulum sulfidophilum strain AB26, can perform phototrophic iron oxidation (photoferrotrophy) and couples carbon dioxide fixation to pEEU. Here, we reclassify two R. sulfidophilum isolates, strainAB26 and strain AB19, as Rhodovulum visakhapatnamense using taxonomic re-evaluation based on 16S and pufM phylogenetic analyses. The strain AB26 genome consists of 4,380,746 base-pairs, including two plasmids, and encodes 4296 predicted protein-coding genes. Strain AB26 contains 22 histidine kinases, 20 response regulators, and dedicates ~16% of its genome to transport. Transcriptomic data under aerobic, photoheterotrophy, photoautotrophy, and pEEU reveals how gene expression varies between metabolisms in a novel R. visakhapatnamense strain. Genome comparison led by transcriptomic data under pEEU reveals potential pEEU-relevant genes both unique to R. visakhapatnamense strains and shared within the R. sulfidophilum genomes. With these data we identify potential pEEU-important transcripts and how speciation may affect molecular mechanisms of pEEU in Rhodovulum species from the same environment.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

Overview of Mars Science Laboratory (MSL) Environmental Program

This viewgraph presentation is an overview of the Mars Science Laboratory (MSL) program. The engineering objectives of the program are to create a Mobile Science Laboratory capable of one Mars Year surface operational lifetime (670 Martian sols = 687 Earth days). It will be able to land and operation over wide range of latitudes, altitudes and seasons It must have controlled propulsive landing and demonstrate improved landing precision via guided entry The general science objectives are to perform science that will focus on Mars habitability, perform next generation analytical laboratory science investigations, perform remote sensing/contact investigations and carry a suite of environmental monitoring instruments. Specific scientific objectives of the MSL are: (1) Characterization of geological features, contributing to deciphering geological history and the processes that have modified rocks and regolith, including the role of water. (2) Determination of the mineralogy and chemical composition (including an inventory of elements such as C, H, N, O, P, S, etc. known to be building blocks for life) of surface and near-surface materials. (3) Determination of energy sources that could be used to sustain biological processes. (4) Characterization of organic compounds and potential biomarkers in representative regolith, rocks, and ices. (5) Determination the stable isotopic and noble gas composition of the present-day bulk atmosphere. (6) Identification potential bio-signatures (chemical, textural, isotopic) in rocks and regolith. (7) Characterization of the broad spectrum of surface radiation, including galactic cosmic radiation, solar proton events, and secondary neutrons. (8) Characterization of the local environment, including basic meteorology, the state and cycling of water and C02, and the near-surface distribution of hydrogen. Several views of the planned MSL and the rover are shown. The MSL environmental program is to: (1) Ensure the flight hardware design is capable of surviving all the environments throughout its mission life time, including ground, transportation, launch, cruise, entry decent and landing (EDL) and surface operation environments. (2) Verify environmental testing and analysis have adequately validated the flight hardware's ability to withstand all natural, self-induced, and mission-activity-induced environments. The planned tests to ascertain the capability of the MSL to perform as desired are reviewed.

spacecraft↗
NASA NTRS2023

Robotic and Crewed Mars Missions Increasing the Demand for Planetary Protection Technology Needs

Planetary protection (PP) policy seeks to avoid harmful contamination by limiting biological and relevant organic contamination from spacecraft as well as preventing adverse changes to Earth’s biosphere when extraterrestial samples are brought back to Earth. The PP policy at NASA was updated in 2021 (NPR 8715.24) and 2022 (NASA-STD-8719.27) to enable missions by expanding the decades old prescriptive requirements to allow for an option of adopting performance-based requirements that are objectivesdriven, risk-informed and case-assured. In parallel, the final PP knowledge gap workshop was completed representing the international consensus on the key areas to be considered in developing crew PP policy. These knowledge gaps focused on key technology development areas in 1) microbial and human health monitoring, 2) technical and operations needed for contamination control and 3) natural transport of contamination on Mars. As robotic missions start to implement performance-based approaches and research and technology efforts commence to inform crew policy the demand for data quality driven verification and validation in relevant space environments. Examples of the types of testing that is envisioned includes test as you fly validation and verification of decontamination systems in a relevant on-orbit and Mars environment, developing lethality curves of terrestrial organisms to further our understanding of the biocidal impacts of Mars and the space environment, and particle transport model validation and verification. Thus, the PP discipline has identified the need for groundbased space environments to perform preliminary testing as validation and verification of flight systems and to advance the technology readiness level prior to further testing on-orbit or lunar environments to prepare for Mars.

J. Nick Benardini↗
DOE OSTI2024

Bioavailability of molybdenite to support nitrogen fixation on early Earth by an anoxygenic phototroph

Biological nitrogen fixation, which converts atmospheric dinitrogen to ammonia, is catalyzed mostly by Mo-nitrogenase and is a primary contributor to bioavailable nitrogen on early Earth. Mo-nitrogenase is believed to have evolved during the Archean, despite the extremely low concentration of dissolved Mo. However, it remains unclear whether Mo minerals could serve as a source of Mo to support the prevalence of Mo-nitrogenase on early Earth. Here, in this study, we investigated the bioavailability of molybdenite by incubating it with a metabolically ancient anoxygenic phototroph (Rhodopseudomonas palustris) under anoxic conditions. In the laboratory, R. palustris utilized molybdenum from molybdenite as a cofactor for nitrogen fixation. This bacterium extracted Mo from molybdenite by secreting molybdophores rhodopetrobactin A and B and by expressing Mo transport proteins. Surface-sensitive techniques demonstrated significant changes in surface chemistry of molybdenite after its interaction with cells. These findings provide novel explanations for the prevalence of Mo-nitrogenase on early Earth, with significant implications for nitrogen fixation in modern Mo-deficient environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Microbial Influence on Radionuclide Transport through the Culebra

The potential release of radionuclides into the Culebra dolomite formation is modeled extensively in the Waste Isolation Pilot Plant’s Performance Assessment (WIPP PA) calculations. Uranium is of chief concern in these modeled scenarios, as it shows the greatest release. Because of this, a series of experiments was undertaken to determine if microbial activity in the Culebra formation could transform uranium, either directly or indirectly, to a state that could be immobilized.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1992

Microtubules as key cytoskeletal elements in cellular transport and shape changes: their expected responses to space environments

Application of reference standard reagents to alternatively depolymerize or stabilize microtubules in a cell that undergoes very regular cytoskeleton-dependent shape changes provides a model system in which some expected components of the environments of spacecraft and space can be tested on Earth for their effects on the cytoskeleton. The fertilized eggs of Ilyanassa obsoleta undergo polar lobe formation by repeated, dramatic, constriction and relaxation of a microfilamentous band localized in the cortical cytoplasm and activated by microtubules.

NASA Discipline Number 93-10↗
DOE OSTI2021

Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides

Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB–TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme

The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Transporters and ascorbate–glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes

Salix matsudana Koidz is a low cadmium (Cd)-accumulating willow, whereas its cultivated variety, Salix matsudana var. matsudana f. umbraculifera Rehd., is a high Cd-accumulating and tolerant willow (HCW). The physiological and molecular mechanisms underlying differential Cd accumulation and tolerance in the two Salix species are poorly understood. In this study, we confirmed that the differential Cd translocation capacity from roots to the shoots leads to the differential Cd accumulation in their aboveground parts between these two willow genotypes. Cadmium accumulation happens preferentially in the transport pathway, and Cd is mainly located in the vacuolar, cell wall and intercellular space in HCW bark by cadmium location analysis at tissue and subcellular levels. Comparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ATP-binding cassette transporters, K + transporters/channels, yellow stripe-like proteins, zinc-regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW; meanwhile, ascorbate–glutathione metabolic pathways play essential roles in Cd detoxification and higher tolerance of the Cd-accumulator HCW. These results lay the foundation for further understanding the molecular mechanisms of Cd accumulation in woody plants and provide new insights into molecular-assisted-screening woody plant varieties for phytoremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Range wide genetic differentiation in the bull kelp Nereocystis luetkeana with a seascape genetic focus on the Salish Sea

Introduction: In temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe N. luetkeana genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades. Methods: We utilized microsatellite markers to study N. luetkeana genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models. Results: At the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island’s outer coast and Juan de Fuca Strait; Washington’s inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region. Discussion: The levels of allelic, private allele richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in the Prince of Wales Island-Haida Gwaii region and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.

59 BASIC BIOLOGICAL SCIENCES↗