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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 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Predicting future coexistence in a North American ant community

Global climate change will remodel ecological communities worldwide. However, as a consequence of biotic interactions, communities may respond to climate change in idiosyncratic ways. This makes predictive models that incorporate biotic interactions necessary. We show how such models can be constructed based on empirical studies in combination with predictions or assumptions regarding the abiotic consequences of climate change. Specifically, we consider a well-studied ant community in North America. First, we use historical data to parameterize a basic model for species coexistence. Using this model, we determine the importance of various factors, including thermal niches, food discovery rates, and food removal rates, to historical species coexistence. We then extend the model to predict how the community will restructure in response to several climate-related changes, such as increased temperature, shifts in species phenology, and altered resource availability. Interestingly, our mechanistic model suggests that increased temperature and shifts in species phenology can have contrasting effects. Nevertheless, for almost all scenarios considered, we find that the most subordinate ant species suffers most as a result of climate change. More generally, our analysis shows that community composition can respond to climate warming in nonintuitive ways. For example, in the context of a community, it is not necessarily the most heatsensitive species that are most at risk. Our results demonstrate how models that account for niche partitioning and interspecific trade-offs among species can be used to predict the likely idiosyncratic responses of local communities to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

The RHIC polarized source upgrade

The RHIC polarized H{sup −} ion source is being upgraded to higher intensity and polarization for use in the RHIC polarization physics program at enhanced luminosity RHIC operation. The higher beam intensity will allow reduction of the longitudinal transverse beam emittance at injection to AGS to reduce polarization losses in AGS. There is also a planned RHIC luminosity upgrade by using the electron beam lens to compensate the beam-beam interaction at collision points. This upgrade is also essential for future BNL plans for a high-luminosity electron-proton (ion) Collider eRHIC. The basic limitations on the high-intensity H{sup −} ion beam production in charge-exchange collisions of the neutral atomic hydrogen beam in the Na-vapor jet ionizer cell were experimentally studied.

43 PARTICLE ACCELERATORS↗
DOE OSTI2015

Biological responses to engineered nanomaterials: Needs for the next decade

In this study, the interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Crystal Structure of VapBC-1 from Nontypeable Haemophilus influenzae and the Effect of PIN Domain Mutations on Survival during Infection

Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC ( v irulence- a ssociated p rotein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study reported here, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli , and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi Δ vapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Pseudospin-lattice coupling in the spin-orbit Mott insulator Sr 2 IrO 4

Spin-orbit entangled magnetic dipoles, often referred to as pseudospins, provide a new avenue to explore novel magnetism inconceivable in the weak spin-orbit coupling limit, but the nature of their low-energy interactions remains to be understood. In this paper, we present a comprehensive study of the static magnetism and low-energy pseudospin dynamics in the archetypal spin-orbit Mott insulator Sr 2 IrO 4 . We find that in order to understand even basic magnetization measurements, a formerly overlooked in-plane anisotropy is fundamental. In addition to magnetometry, we use neutron diffraction, inelastic neutron scattering, and resonant elastic and inelastic x-ray scattering to identify and quantify the interactions that determine the global symmetry of the system and govern the linear responses of pseudospins to external magnetic fields and their low-energy dynamics. We find that a pseudospin-only Hamiltonian is insufficient for an accurate description of the magnetism in Sr 2 IrO 4 and that pseudospin-lattice coupling is essential. In conclusion, this finding should be generally applicable to other pseudospin systems with sizable orbital moments sensitive to anisotropic crystalline environment

36 MATERIALS SCIENCE↗
DOE OSTI2017

Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

In this study we use mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein–ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water-mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy-driven or entropy-driven. Our findings highlight a possible asymmetry in protein–ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are present in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13 C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13 C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis

Interactions between species are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC–MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans, including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. Lastly, this finding is based on N. equitans’s consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans. Combining LC–MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins

Bacteria encode homooligomeric single-stranded (ss) DNA-binding proteins (SSBs) that coat and protect ssDNA intermediates formed during genome maintenance reactions. The prototypical Escherichia coli SSB tetramer can bind ssDNA using multiple modes that differ by the number of bases bound per tetramer and the magnitude of the binding cooperativity. Our understanding of the mechanisms underlying cooperative ssDNA binding by SSBs has been hampered by the limited amount of structural information available for interfaces that link adjacent SSB proteins on ssDNA. Here in this paper we present a crystal structure of Bacillus subtilis SsbA bound to ssDNA. The structure resolves SsbA tetramers joined together by a ssDNA “bridge” and identifies an interface, termed the “bridge interface,” that links adjacent SSB tetramers through an evolutionarily conserved surface near the ssDNA-binding site. E. coli SSB variants with altered bridge interface residues bind ssDNA with reduced cooperativity and with an altered distribution of DNA binding modes. These variants are also more readily displaced from ssDNA by RecA than wild-type SSB. In spite of these biochemical differences, each variant is able to complement deletion of the ssb gene in E. coli. Together our data suggest a model in which the bridge interface contributes to cooperative ssDNA binding and SSB function but that destabilization of the bridge interface is tolerated in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Community structure of arbuscular mycorrhizal fungi associated with Robinia pseudoacacia in uncontaminated and heavy metal contaminated soils

The significance of arbuscular mycorrhizal fungi (AMF) in soil remediation has been widely recognized because of their ability to promote plant growth and increase phytoremediation efficiency in heavy metal (HM) polluted soils by improving plant nutrient absorption and by influencing the fate of the metals in the plant and soil. However, the symbiotic functions of AMF in remediation of polluted soils depend on plant–fungus–soil combinations and are greatly influenced by environmental conditions. To better understand the adaptation of plants and the related mycorrhizae to extreme environmental conditions, AMF colonization, spore density and community structure were analyzed in roots or rhizosphere soils of Robinia pseudoacacia. Mycorrhization was compared between uncontaminated soil and heavy metal contaminated soil from a lead–zinc mining region of northwest China. Samples were analyzed by restriction fragment length polymorphism (RFLP) screening with AMF-specific primers (NS31 and AM1), and sequencing of rRNA small subunit (SSU). The phylogenetic analysis revealed 28 AMF group types, including six AMF families: Glomeraceae, Claroideoglomeraceae, Diversisporaceae, Acaulosporaceae, Pacisporaceae, and Gigasporaceae. Of all AMF group types, six (21%) were detected based on spore samples alone, four (14%) based on root samples alone, and five (18%) based on samples from root, soil and spore. Glo9 (Rhizophagus intraradices), Glo17 (Funneliformis mosseae) and Acau3 (Acaulospora sp.) were the three most abundant AMF group types in the current study. Soil Pb and Zn concentrations, pH, organic matter content, and phosphorus levels all showed significant correlations with the AMF species compositions in root and soil samples. Overall, the uncontaminated sites had higher species diversity than sites with heavy metal contamination. This study highlights the effects of different soil chemical parameters on AMF colonization, spore density and community structure in contaminated and uncontaminated sites. The tolerant AMF species isolated and identified from this study have potential for application in phytoremediation of heavy metal contaminated areas.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity

A benzoate CoA ligase (BadA), isolated from the bacterium Rhodopseudomonas palustris, catalyzes the conversion of benzoate to benzoyl CoA on the catabolic pathway of aromatic carboxylic acids. Herein, apparent Michaelis constants k cat app and K M app were determined for an expanded array of 31 substrates chosen to systematically probe the active site architecture of the enzyme and provide a baseline for expansion of wild-type substrate specificity. Acyl CoA products were observed for 25 of the 31 substrates; in general, BadA converted ortho-substituted substrates better than the corresponding meta and para regioisomers, and the turnover number was more affected by steric rather than electronic effects. The kinetic data are interpreted in relation to six crystal structures of BadA in complex with several substrates and a benzoyl-AMP reaction intermediate. In contrast to other known natural substrate-bound benzoate ligase structures, all substrate-bound BadA structures adopted the thiolation conformation instead of the adenylation conformation. We also observed all the aryl carboxylates to be uniquely oriented within the active site, relative to other structures. Together, the kinetics and structural data suggested a mechanism that involves substrate binding in the thiolation conformation, followed by substrate rotation to an active orientation upon the transition to the adenylation conformation. On the basis of this hypothesis and the structural data, sterically demanding active site residues were mutated, and the substrate specificity was expanded substantially versus that of BadA. Novel activities were seen for substrates with larger substituents, including phenyl acetate. Additionally, the mutant Lys427Ala identified this nonconserved residue as essential for the thiolation step of BadA, but not adenylation. Furthermore, these variously acylated CoAs can serve as novel substrates of acyl CoA-dependent acyltransferases in coupled enzyme assays to produce analogues of bioactive natural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Evidence from FTIR Difference Spectroscopy That a Substrate H 2 O Molecule for O 2 Formation in Photosystem II Is Provided by the Ca Ion of the Catalytic Mn 4 CaO 5 Cluster

The O 2 -producing Mn 4 CaO 5 catalyst in photosystem II oxidizes two water molecules (substrate) to produce one O 2 molecule. Considerable evidence supports the identification of one of the two substrate waters as the Mn 4 CaO 5 cluster’s oxo bridge known as O 5 . The identity of the second substrate water molecule is less clear. In one set of models, the second substrate is the Mn-bound water molecule known as W2. In another set of models, the second substrate is the Ca 2+ -bound water molecule known as W3. In all of these models, a deprotonated form of the second substrate moves to a position next to O5 during the catalytic step immediately prior to O–O bond formation. Here, FTIR difference spectroscopy was employed to identify the vibrational modes of hydrogen-bonded water molecules that are altered by the substitution of Sr 2+ for Ca 2+ . Our data show that the substitution substantially altered the vibrational modes of only a single water molecule: the water molecule whose D-O–D bending mode is eliminated during the catalytic step immediately prior to O–O bond formation. These data are most consistent with the identification of the Ca 2+ -bound W3 as the second substrate involved in O–O bond formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Pushing the Limits of Delta Bonding in Metal–Chromium Complexes with Redox Changes and Metal Swapping

Into the metalloligand Cr[N(o-(NCH 2 P( i Pr) 2 )C 6 H 4 ) 3 ] (1, CrL) was inserted a second chromium atom to generate the dichromium complex Cr 2 L (2), which is a homobimetallic analogue of the known MCrL complexes, where M is manganese (3) or iron (4). The cationic and anionic counterparts, [MCrL] + and [MCrL] - , respectively, were targeted, and each MCr pair was isolated in at least one other redox state. The solid-state structures of the [MCrL] +,0,– redox members are basically the same, with ultrashort metal–metal bonds between 1.96 and 1.74 Å. The formal shortness ratios (r) of these interactions are between 0.84 and 0.74 and are interpreted as triple to quintuple metal–metal bonds with the aid of theory. The trio of (d–d) 10 species [Cr 2 L] - ( 2 red), MnCrL (3), and [FeCrL] + (4 ox ) are S = 0 diamagnets. On the basis of M—Cr bond distances and theoretical calculations, the strength of the metal–metal bond across the (d–d) 10 series increases in the order Fe < Mn < Cr. The methylene protons in the ligand are shifted downfield in the 1H NMR spectra, and the diamagnetic anisotropy of the metal–metal bond was calculated as -3500 × 10 –36 , -3900 × 10 –36 , and -5800 × 10 –36 m 3 molecule –1 for 2 red , 3, and 4 ox respectively. The magnitude of diamagnetic anisotropy is, thus, affected more by bond polarity than by bond order. A comparative vis–NIR study of quintuply bonded 2 red and 3 revealed a large red shift in the δ 4 → δ 3 δ * transition energy upon swapping from the (Cr 2 ) 2+ to the (MnCr) 3+ core. Complex 2 red was further investigated by resonance Raman spectroscopy, and a band at 434 cm –1 was assigned as the Cr—Cr bond vibration. Lastly, 4 ox exhibited a Mössbauer doublet with an isomer shift of 0.18 mm/s that suggests a primarily Fe-based oxidation to Fe(I).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Tension-dependent free energies of nucleosome unwrapping

Here, nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗