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At least 73 records · Page 4

Inferring Properties of Ancient Cyanobacteria from Biogeochemical Activity and Genomes of Siderophilic Cyanobacteria

Interrelationships between life and the planetary system could have simultaneously left landmarks in genomes of microbes and physicochemical signatures in the lithosphere. Verifying the links between genomic features in living organisms and the mineralized signatures generated by these organisms will help to reveal traces of life on Earth and beyond. Among contemporary environments, iron-depositing hot springs (IDHS) may represent one of the most appropriate natural models [1] for insights into ancient life since organisms may have originated on Earth and probably Mars in association with hydrothermal activity [2,3]. IDHS also seem to be appropriate models for studying certain biogeochemical processes that could have taken place in the late Archean and,-or early Paleoproterozoic eras [4, 5]. It has been suggested that inorganic polyphosphate (PPi), in chains of tens to hundreds of phosphate residues linked by high-energy bonds, is environmentally ubiquitous and abundant [6]. Cyanobacteria (CB) react to increased heavy metal concentrations and UV by enhanced generation of PPi bodies (PPB) [7], which are believed to be signatures of life [8]. However, the role of PPi in oxygenic prokaryotes for the suppression of oxidative stress induced by high Fe is poorly studied. Here we present preliminary results of a new mechanism of Fe mineralization in oxygenic prokaryotes, the effect of Fe on the generation of PPi bodies in CB, as well as preliminary analysis of the diversity and phylogeny of proteins involved in the prevention of oxidative stress in phototrophs inhabiting IDHS.

McKay, David S.↗

Fluid/electrolyte and endocrine changes in space flight

The primary effects of space flight that influence the endocrine system and fluid and electrolyte regulation are the reduction of hydrostatic gradients, reduction in use and gravitational loading of bone and muscle, and stress. Each of these sets into motion a series of responses that culminates in alteration of some homeostatic set points for the environment of space. Set point alterations are believed to include decreases in venous pressure; red blood cell mass; total body water; plasma volume; and serum sodium, chloride, potassium, and osmolality. Serum calcium and phosphate increase. Hormones such as erythropoietin, atrial natriuretic peptide, aldosterone, cortisol, antidiuretic hormone, and growth hormone are involved in the dynamic processes that bring about the new set points. The inappropriateness of microgravity set points for 1-G conditions contributes to astronaut postflight responses.

Huntoon, Carolyn Leach↗

The influence of altered gravity on carbohydrate metabolism in excised wheat leaves

We developed a system to study the influence of altered gravity on carbohydrate metabolism in excised wheat leaves by means of clinorotation. The use of excised leaves in our clinostat studies offered a number of advantages over the use of whole plants, most important of which were minimization of exogenous mechanical stress and a greater amount of carbohydrate accumulation during the time of treatment. We found that horizontal clinorotation of excised wheat leaves resulted in significant reductions in the accumulation of fructose, sucrose, starch and fructan relative to control, vertically clinorotated leaves. Photosynthesis, dark respiration and the extractable activities of ADP glucose pyrophosphorylase (EC 2.7.7.27), sucrose phosphate synthase (EC 2.4.4.14), sucrose sucrose fructosyltransferase (EC 2.4.1.99), and fructan hydrolase (EC 3.2.1.80) were unchanged due to altered gravity treatment.

NASA Center KSC↗

A Real-Time Degradation Estimation Approach for Batteries in PV and Battery Hybrid Plant Operation

Conventional cyclic degradation assessment for batteries is often limited in its ability to provide real-time degradation information during operation, because the estimation of degradation is commonly performed after a specific evaluation period. Modified methods can provide real-time evaluation but at the cost of high computation complexity. This paper proposes a novel estimation method that addresses these limitations. It efficiently determines the incremental degradation of any two consecutive state-of-charge (SOC) samples during battery operation, thus enabling real-time estimation. To validate the proposed method, measurement data from lithium-ion phosphate (LFP) battery testing was adopted, and the results were compared with the conventional model and the measured capacity. The results demonstrate accuracy over the evaluation period in terms of cumulative degradation, and a reduced computation cost compared with other methods. This approach has benefits in various applications, especially in cases where batteries experience irregular charging and discharging stress cycles such as PV and battery hybrid plants.

Wang, Shumeng↗

Sac1 links phosphoinositide turnover to cryptococcal virulence

Cryptococcus neoformans is an environmentally acquired fungal pathogen that causes over 140,000 deaths per year. Cryptococcal infection occurs when infectious particles are deposited into the lung, where they encounter host phagocytic cells. C. neoformans may be engulfed by these phagocytes, an important step of infection that leads to outcomes ranging from termination of infection to cryptococcal dissemination. To study this critical process, we screened approximately 4,700 cryptococcal gene deletion mutants for altered uptake, using primary mouse and human phagocytic cells. Among the hits of these two screens, we identified 93 mutants with perturbed uptake in both systems, as well as others with differences in uptake by only one cell type. We further screened the hits for changes in thickness of the capsule, a protective polysaccharide layer around the cell which is an important cryptococcal virulence factor. The combination of our three screens yielded 45 mutants, including one lacking the phosphatidylinositol-4-phosphate phosphatase Sac1. In this work, we implicate Sac1 in both host cell uptake and capsule production. We found that sac1 mutants exhibit lipid trafficking defects, reductions in secretory system function, and changes in capsule size and composition. Many of these changes occur specifically in tissue culture media, highlighting the role of Sac1 phosphatase activity in responding to the stress of host-like conditions. Overall, these findings show how genome-scale screening can identify cellular factors that contribute to our understanding of cryptococcal biology and demonstrate the role of Sac1 in determining fungal virulence.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis of Nd3+:glass, solar-pumped, high-powr laser systems

The operating characteristics of Nd(3+):glass lasers energized by a solar concentrator were analyzed for the hosts YAG, silicate glass, and phosphate glass. The modeling is based on the slab zigzag laser geometry and assumes that chemical hardening methods for glass are successful in increasing glass hardness by a factor of 4. On this basis, it was found that a realistic 1-MW solar-pumped laser might be constructed from phosphate glass 4 sq m in area and 2 mm thick. If YAG were the host medium, a 1-MW solar-pumped laser need only be 0.5 sq m in area and 0.5 cm thick, which is already possible. In addition, Nd(3+) doped glass fibers were found to be excellent solar-pumped laser candidates. The small diameter of fibers eliminates thermal stress problems, and if their diameter is kept small (10 microns), they propagate a Gaussian single mode which can be expanded and transmitted long distances in space. Fiber lasers could then be used for communications in space or could be bundled and the individual beams summed or phase-matched for high-power operation.

Zapata, L. E.↗

Data for A Role for Differential Rubisco Activase Isoform Expression in C4 Bioenergy Grasses at High Temperature

Rubisco activase (Rca) facilitates the release of sugar-phosphate inhibitors at Rubisco catalytic sites during CO2 fixation. Most plant species express two Rca isoforms, the larger Rca-α and the shorter Rca-β, either by alternative splicing from a single gene or expression from separate genes. The mechanism of Rubisco activation by Rca isoforms has been intensively studied in C3 plants. However, the functional role of Rca in C4 plants where Rubisco and Rca are located in a much higher [CO2] compartment is less clear. In this study, we selected four C4 bioenergy grasses and the model C4 grass setaria ( Setaria viridis ) to investigate the role of Rca in C4 photosynthesis. All five C4 grass species contained two Rca genes, one encoding Rca-α and the other Rca-β, which were positioned closely together in the genomes. A variety of abiotic stress-related motifs were identified in the Rca-α promoter of each grass, and while the Rca-β gene was constantly highly expressed at ambient temperature, Rca-α isoforms were expressed only at high temperature but never surpassed 30% of Rca-β content. The pattern of Rca-α induction on transition to high temperature and reduction on return to ambient temperature was the same in all five C4 grasses. In sorghum ( Sorghum bicolor ), sugarcane ( Saccharum officinarum ), and setaria, the induction rate of Rca-α was similar to the recovery rate of photosynthesis and Rubisco activation at high temperature. This association between Rca-α isoform expression and maintenance of Rubisco activation at high temperature suggests that Rca-α has a functional thermo-protective role in carbon fixation in C4 grasses by sustaining Rubisco activation at high temperature.

Genomics↗

Study of the thermal degradation mechanism of a composite propellant

The current experimental program was designed to systematically investigate the role of the oxidizer in the thermal degradation process of composite propellants. The scanning electron microscope (SEM) was used to examine the failure sites in thermally degraded propellant samples. The formulation variables tested were oxidizer purity, oxidizer particle size, and oxidizer to binder bonding agent. The binder, a saturated hydrocarbon, was kept constant throughout the experiments. The oxidizers were: AP, chlorate-doped AP, arsenate-doped AP, and phosphate-doped AP. The oxidizer particle size distribution was 60% of the large fraction and 40% of the small fraction. The bonding agent, when present, was used at the 0.15% level. The data showed that both the oxidizer purity and particle size had an important affect on the thermal degradation process. The affect of the oxidizer particle size was more noticeable at the higher temperature and stress levels. An examination of the failure site, by SEM, of propellants subject to these latter conditions indicated that the fracturing of the large oxidizer particles led to the propellant cracking.

Schmidt, W. G.↗

Study of the Genes and Mechanism Involved in the Radioadaptive Response

The radioadaptive response is a phenomenon where exposure to a prior low dose of radiation reduces the level of damage induced by a subsequent high radiation dose. The molecular mechanism behind this is still not well understood. Learning more about the radioadaptive response is critical for long duration spaceflight since astronauts are exposed to low levels of cosmic radiation. The micronucleus assay was used to measure the level of damage caused by radiation. Although cells which were not washed with phosphate buffered saline (PBS) after a low priming dose of 5cGy did not show adaptation to the challenge dose, washing the cells with PBS and giving the cells fresh media after the low dose did allow radioadaptation to occur. This is consistent with the results of a previous publication by another research group. In the present study, genes involved in DNA damage signaling and the oxidative stress response were studied using RT PCR techniques in order to look at changes in expression level after the low dose with or without washing. Our preliminary results indicate that upregulation of oxidative stress response genes ANGPTL7, NCF2, TTN, and SRXN1 may be involved in the radioadaptive response. The low dose of radiation alone was found to activate the oxidative stress response genes GPR156 and MTL5, whereas, washing the cells alone caused relatively robust upregulation of the oxidative stress response genes DUSP1 and PTGS2. Washing after the priming dose showed some changes in the expression level of several DNA damage signaling genes. In addition, we studied whether washing the cells after the priming dose has an effect on the level of nitric oxide in both the media and cells, since nitric oxide levels are known to increase in the media of the cells after a high dose of radiation only if the cells were already exposed to a low priming dose. Based on this preliminary study, we propose that washing the cells after priming exposure actually eliminates some factor secreted by the cells that inhibits radioadaptation leading to the upregulation of some genes which initiates the response.

Dasgupta, Pushan R.↗

Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide

RtcB enzymes comprise a widely distributed family of manganese- and GTP-dependent RNA repair enzymes that join 2',3'-cyclic phosphate ends to 5'-OH ends via RtcB-(histidinyl-N)–GMP, RNA 3'-phosphate, and RNA 3 'pp 5 'G intermediates. RtcB can ligate either 5'-OH RNA or 5'-OH DNA strands in vitro. The nucleic acid contacts of RtcB are uncharted. In this work, we report a 2.7 Å crystal structure of Pyrococcus horikoshii RtcB in complex with a 6-mer 5'-OH DNA oligonucleotide HO A 1 pT 2 pG 3 pT 4 pC 5 pC 6 , which reveals enzymic contacts of Asn202 to the terminal 5'-OH nucleophile; Arg238 to the A1pT2 and T2pG3 phosphates; Arg190 and Gln194 to the T 2 pG 3 phosphate; and an Arg190 π-cation interaction with the G 3 nucleobase. The structural insights affirm functional studies of E. coli RtcB that implicated the conserved counterpart of Arg238 in engagement of the 5'-OH strand for ligation. The essential active site Cys98 that coordinates two manganese ions is oxidized to cysteine sulfonic acid in our structure, raising the prospect that RtcB activity might be sensitive to modulation during oxidative stress.

59 BASIC BIOLOGICAL SCIENCES↗

Secondary metabolism in simulated microgravity

We have studied microbial secondary metabolism in a simulated microgravity (SMG) environment provided by NASA rotating-wall bioreactors (RWBs). These reactors were designed to simulate some aspects of actual microgravity that occur in space. Growth and product formation were observed in SMG in all cases studied, i.e., Bacillus brevis produced gramicidin S (GS), Streptomyces clavuligerus made beta-lactam antibiotics, Streptomyces hygroscopicus produced rapamycin, and Escherichia coli produced microcin B17 (MccB17). Of these processes, only GS production was unaffected by SMG; production of the other three products was inhibited. This was determined by comparison with performance in an RWB positioned in a different mode to provide a normal gravity (NG) environment. Carbon source repression by glycerol of the GS process, as observed in shaken flasks, was not observed in the RWBs, whether operated in the SMG or NG mode. The same phenomenon occurred in the case of MccB17 production, with respect to glucose repression. Thus, the negative effects of carbon source on GS and beta-lactam formation are presumably dependent on shear, turbulence, and/or vessel geometry, but not on gravity. Stimulatory effects of phosphate and the precursor L-lysine on beta-lactam antibiotic production, as observed in flasks, also occurred in SMG. An almost complete shift in the localization of produced MccB17 from cells to extracellular medium was observed when E. coli was grown in the RWB under SMG or NG. If a plastic bead was placed in the RWB, accumulation became cellular, as it is in shaken flasks, indicating that sheer stress favors a cellular location. In the case of rapamycin, the same type of shift was observed, but it was less dramatic, i.e., growth in the RWB under SMG shifted the distribution of produced rapamycin from 2/3 cellular:1/3 extracellular to 1/3 cellular:2/3 extracellular. Stress has been shown to induce or promote secondary metabolism in a number of other microbial systems. RWBs provide a low stress SMG environment, which, however, supports only poor production of MccB17, as compared to production in shaken flasks. We wondered whether the poor production in RWBs under SMG is due to the low level of stress, and whether increasing stress in the RWBs would raise the amount of MccB17 formed. We found that increasing shear stress by adding a single Teflon bead to the RWB improved MccB17 production. Although shear stress seems to have a marked positive effect on MccB17 production in SMG, addition of various concentrations of ethanol to RWBs (or to shaken flasks) failed to increase MccB17 production. Ethanol stress merely decreased production and, at higher concentrations, inhibited growth. Interestingly, cells growing in the RWB were much more resistant to the growth- and production-inhibitory effects of ethanol than cells growing in shaken flasks. With respect to S. hygroscopicus, addition of Teflon beads to the RWB reversed the inhibition of growth, but rapamycin production was still markedly inhibited, and the distribution did not revert back to a preferential cellular site.

NASA Discipline Cell Biology↗

Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes

Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

Petrologic and In Situ Geochemical Constraints on Diogenite Genesis

Diogenites, members of the howardite, eucrite and diogenite (HED) clan, are orthopyroxenite, harzburgite and dunite meteorites [1-3]. Most are breccias, but remnant textures indicate they were originally coarse-grained rocks, with grain sizes of order of cm. Their petrography and compositions support an origin as crustal cumulates from a differentiated asteroid. Astronomical observations, and surface mineralogy and composition of Vesta determined by the Dawn spacecraft suggest that asteroid (4) Vesta is the parent object for HED meteorites [4-6]. The origin of diogenites is an unsettled issue. It is difficult to fit their bulk compositional characteristics into global magma ocean models that successfully describe the compositions of basaltic and cumulate eucrites [7]. Compositional analyses of acid-leached bulk samples have led to the hypothesis that many diogenites were formed late by interaction of their parent melts with a eucritic crust [8]. Those observations may alternatively be explained by subsolidus equilibration of trace elements between orthopyroxene and minor/ accessory phases in the rocks such as plagioclase and phosphate [7]. These competing hypotheses can be tested through in situ measurements of trace and minor elements in orthopyroxene. Our new petrologic observations and in situ minor and trace element data for a suite of diogenites are used to discuss the petrologic evolution of diogenites. Our preliminary data on two diogenites are consistent with the hypothesis that subsolidus element mobilization processes caused unusual trace element signatures seen in some diogenites [7]. We cannot stress strongly enough, however, that the sample set is too small and that additional data are required before definitive conclusions can be made.

Mittlefehldt, David W.↗

Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage

Reactive Intermediate Deaminase (Rid) protein superfamily includes eight families among which the RidA is conserved in all domains of life. RidA proteins accelerate the deamination of the reactive 2-aminoacrylate (2AA), an enamine produced by some pyridoxal phosphate (PLP)-dependent enzymes. 2AA accumulation inhibits target enzymes with a detrimental impact on fitness. As a consequence of whole genome duplication, teleost fish have two ridA paralogs, while other extant vertebrates contain a single-copy gene. We investigated the biochemical properties of the products of two paralogs, identified in Salmo salar. Ss RidA-1 and Ss RidA-2 complemented the growth defect of a Salmonella enterica ridA mutant, an in vivo model of 2AA stress. In vitro, both proteins hydrolyzed 2-imino acids (IA) to keto-acids and ammonia. Ss RidA-1 was active on IA derived from nonpolar amino acids and poorly active or inactive on IA derived from other amino acids tested. In contrast, SsRidA-2 had a generally low catalytic efficiency, but showed a relatively higher activity with IA derived from L-Glu and aromatic amino acids. The crystal structures of Ss RidA-1 and Ss RidA-2 provided hints of the remarkably different conformational stability and substrate specificity. Overall, Ss RidA-1 is similar to the mammalian orthologs whereas SsRidA-2 displays unique properties likely generated by functional specialization of a duplicated ancestral gene.

59 BASIC BIOLOGICAL SCIENCES↗

Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils

Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. Here, to illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5N T . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.

59 BASIC BIOLOGICAL SCIENCES↗

A study to investigate the chemical stability of gallium phosphate oxide/gallium arsenide phosphide

The elemental composition with depth into the oxide films was examined using secondary ion mass spectrometry. Results indicate that the layers are arsenic-deficient through the bulk of the oxide and arsenic-rich near both the oxide surface and the oxide-semiconductor interface region. Phosphorus is incorporated into the oxide in an approximately uniform manner. The MIS capacitor structures exhibited deep-depletion characteristics and hysteresis indicative of electron trapping at the oxide-semiconductor interface. Post-oxidation annealing of the films in argon or nitrogen generally results in slightly increased dielectric leakage currents and decreased C-V hysteresis effects, and is associated with arsenic loss at the oxide surface. The results of bias-temperature stress experiments indicate that the major instability effects are due to changes in the electron trapping behavior. No changes were observed in the elemental profiles following electrical stressing, indicating that the grown films are chemically stable under device operating conditions.

Kuhlman, G. J.↗

A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency

Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied. We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency. In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency. Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗

Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

ABSTRACTSulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Trotter, Valentine V↗