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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Early-type eclipsing binaries with intermediate orbital periods

We analyze 221 eclipsing binaries (EBs) in the Large Magellanic Cloud with B-type main-sequence (MS) primaries (M{sub 1} ≈ 4–14 M{sub ⊙}) and orbital periods P = 20–50 days that were photometrically monitored by the Optical Gravitational Lensing Experiment. We utilize our three-stage automated pipeline to (1) classify all 221 EBs, (2) fit physical models to the light curves of 130 detached well-defined EBs from which unique parameters can be determined, and (3) recover the intrinsic binary statistics by correcting for selection effects. We uncover two statistically significant trends with age. First, younger EBs tend to reside in dustier environments with larger photometric extinctions, an empirical relation that can be implemented when modeling stellar populations. Second, younger EBs generally have large eccentricities. This demonstrates that massive binaries at moderate orbital periods are born with a Maxwellian “thermal” orbital velocity distribution, which indicates they formed via dynamical interactions. In addition, the age-eccentricity anticorrelation provides a direct constraint for tidal evolution in highly eccentric binaries containing hot MS stars with radiative envelopes. The intrinsic fraction of B-type MS stars with stellar companions q = M{sub 2}/M{sub 1} > 0.2 and orbital periods P = 20–50 days is (7 ± 2)%. We find early-type binaries at P = 20–50 days are weighted significantly toward small mass ratios q ≈ 0.2–0.3, which is different than the results from previous observations of closer binaries with P < 20 days. This indicates that early-type binaries at slightly wider orbital separations have experienced substantially less competitive accretion and coevolution during their formation in the circumbinary disk.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Management, Analysis, and Visualization of Experimental and Observational Data – The Convergence of Data and Computing

Scientific user facilities—particle accelerators, telescopes, colliders, supercomputers, light sources, sequencing facilities, and more—operated by the U.S. Department of Energy (DOE) Office of Science (SC) generate ever increasing volumes of data at unprecedented rates from experiments, observations, and simulations. At the same time there is a growing community of experimentalists that require real-time data analysis feedback, to enable them to steer their complex experimental instruments to optimized scientific outcomes and new discoveries. Recent efforts in DOE-SC have focused on articulating the data-centric challenges and opportunities facing these science communities. Key challenges include difficulties coping with data size, rate, and complexity in the context of both real-time and post-experiment data analysis and interpretation. Solutions will require algorithmic and mathematical advances, as well as hardware and software infrastructures that adequately support data-intensive scientific workloads. This paper presents the summary findings of a workshop held by DOE-SC in September 2015, convened to identify the major challenges and the research that is needed to meet those challenges.

Bethel, E. Wes↗
DOE OSTI2020

Association between algal productivity and phycosphere composition in an outdoor Chlorella sorokiniana reactor based on multiple longitudinal analyses

Summary Microalgae as a biofuel source are of great interest. Bacterial phycosphere inhabitants of algal cultures are hypothesized to contribute to productivity. In this study, the bacterial composition of the Chlorella sorokiniana phycosphere was determined over several production cycles in different growing seasons by 16S rRNA gene sequencing and identification. The diversity of the phycosphere increased with time during each individual reactor run, based on Faith’s phylogenetic diversity metric versus days post‐inoculation ( R = 0.66, P < 0.001). During summer months, Vampirovibrio chlorellavorus , an obligate predatory bacterium, was prevalent. Bacterial sequences assigned to the Rhizobiales, Betaproteobacteriales and Chitinophagales were positively associated with algal biomass productivity. Applications of the general biocide, benzalkonium chloride, to a subset of experiments intended to abate V. chlorellavorus appeared to temporarily suppress phycosphere bacterial growth, however, there was no relationship between those bacterial taxa suppressed by benzalkonium chloride and their association with algal productivity, based on multinomial model correlations. Algal health was approximated using a model‐based metric, or the ‘Health Index’ that indicated a robust, positive relationship between C. sorokiniana fitness and presence of members belonging to the Burholderiaceae and Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium clade. Bacterial community composition was linked to the efficiency of microalgal biomass production and algal health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Two-Level Adaptive Algebraic Multigrid for a Sequence of Problems with Slowly Varying Random Coefficients [Adaptive Algebraic Multigrid for Sequence of Problems with Slowly Varying Random Coefficients]

Our paper proposes an adaptive strategy for reusing a previously constructed coarse space by algebraic multigrid to construct a two-level solver for a problem with nearby characteristics. Furthermore, a main target application is the solution of the linear problems that appear throughout a sequence of Markov chain Monte Carlo simulations of subsurface flow with uncertain permeability field. We demonstrate the efficacy of the method with extensive set of numerical experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Management, Analysis, and Visualization of Experimental and Observational Data -- The Convergence of Data and Computing

Scientific user facilities---particle accelerators, telescopes, colliders, supercomputers, light sources, sequencing facilities, and more---operated by the U.S. Department of Energy (DOE) Office of Science (SC) generate ever increasing volumes of data at unprecedented rates from experiments, observations, and simulations. At the same time there is a growing community of experimentalists that require real-time data analysis feedback, to enable them to steer their complex experimental instruments to optimized scientific outcomes and new discoveries. Recent efforts in DOE-SC have focused on articulating the data-centric challenges and opportunities facing these science communities. Key challenges include difficulties coping with data size, rate, and complexity in the context of both real-time and post-experiment data analysis and interpretation. Solutions will require algorithmic and mathematical advances, as well as hardware and software infrastructures that adequately support data-intensive scientific workloads. This paper presents the summary findings of a workshop held by DOE-SC in September 2015, convened to identify the major challenges and the research that is needed to meet those challenges.

Bethel, E. Wes↗
DOE OSTI2015

Solitons and protein folding: An In Silico experiment

Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Transition Core Planning and Safety Analyses in Support of LEU Fuel Conversion of the University of Missouri Research Reactor (MURR)

The University of Missouri Research Reactor (MURR®) is one of six U.S. High Performance Research Reactors (USHPRR), including one critical facility, that is working with the National Nuclear Security Administration (NNSA) Office of Material Management and Minimization (M3) Reactor Conversion Program to convert from highly enriched uranium (HEU) to low-enriched uranium (LEU) fuel. The M3 Reactor Conversion USHPRR Project objectives include the development of LEU fuel element designs that will ensure safe reactor operations and to maintain the existing experimental performance of each facility. The work is being conducted through many inter-related activities being completed by four Project Pillars: Fuel Qualification (FQ), Fuel Fabrication (FF), Reactor Conversion (RC), and Cross Cutting (CC). A new type of LEU fuel based on an alloy of uranium-10 wt% molybdenum (U-10Mo) is expected to allow the conversion of those USHPRR, like MURR, requiring higher density fuels. The very-high-density LEU U-10Mo monolithic fuel is currently undergoing irradiation testing and post-irradiation examination under a planned and documented fuel qualification effort. The FQ Pillar will document fuel property and fuel performance data and qualify the fuel for use in these reactors. The FF Pillar is fabricating fuel for ongoing and future irradiation tests, as well as conducting fabrication demonstrations to validate or update preliminary fabrication assumptions. The FF Pillar is also working to develop and install commercial manufacturing capacity with the U-10Mo monolithic fuel to produce prototypic fuel. Working with the RC Pillar at Argonne, MURR has progressed through a preliminary fuel element design using preliminary data for the proposed monolithic alloy of U-10Mo. Analyses were completed in previous work that found for typical equilibrium operations with the preliminary LEU fuel element design, in conjunction with a power uprate to 12 MW and appropriate changes to the MURR Limiting safety system settings (LSSS), MURR will have adequate margins to safety for steady-state operations and postulated transient accidents and will have experimental performance in key locations that meets or exceeds current operations with HEU fuel. The purpose of this work is to develop a sequence of transition cycles that will enable MURR to transition from operation with the reactor core loaded with fresh LEU fuel elements only to typical equilibrium operations with mixed-burnup cores following conversion while meeting operational requirements on safety and experimental performance. It is expected that the use of fresh LEU fuel at conversion and subsequent low burnup of the LEU fuel elements that will initially be available for use following conversion will result in critical control blade positions that will substantially change the axial power distribution in the core and the neutron flux available in key experimental locations relative to equilibrium LEU operations. Given the constraints of MURR safety margins, operational practices, and production and research, a novel method has been developed to identify a transition sequence that minimizes the time MURR operates atypically compared to the current prototypic cycles using HEU fuel. The proposed transition sequence moves quickly to the same sort of equilibrium cycles for the LEU fuel that have already been evaluated in documented preliminary safety analyses. Although shifting the neutron flux peak to the lower half of the core during initial cycles with LEU at 12 MW reduces the experiment performance in some key locations relative to current HEU operations at 10 MW, all LEU cores provide an average performance that meets or exceeds that of HEU. An LEU cycle is reached that meets or exceeds the level of experimental performance predicted for current HEU and equilibrium LEU operations in more than 450 key locations identified by a reactor specialist at MURR by the 23rd cycle following conversion and that afterwards will enable MURR to consistently meet its experimental performance requirements. The proposed transition sequence only requires the fabrication of 34 fresh LEU elements in the first year of operation and does not exceed the anticipated availability of fresh elements that can be produced by the fuel fabricator. By the third year after conversion, 22 fresh LEU elements will be required each year, which is the same as expected for equilibrium LEU operations and the same as current operations with HEU fuel. The proposed transition sequence thus combines a relatively short time period before equilibrium burnup is achieved, a temporary increase of fuel elements needed annually relative to typical operations that are within the production capabilities of the fuel fabricator, and demonstrates comparable experimental performance of the LEU cores relative to current HEU operations. Further measures may be taken to reduce any initial experimental performance penalty even further, where possible, by repositioning certain experiments to leverage the increased performance in the lower axial experimental positions in the initial cycles following conversion or leaving the experiments in the irradiation facilities longer in order to achieve the required neutron fluence. This analysis may require refinement depending on the experimental facilities in use at the time of conversion. Nonetheless, the results presented here, including the experimental performance, core burnup, and critical control blade positions throughout the transition cycles, show that the proposed transition cycle fuel management patterns are consistent with what is expected and desired for MURR operation with LEU U-10Mo fuel. Detailed core power distributions from the neutronics models were also used to evaluate safety margins during steady-state operations for the selected transition cycles and the equilibrium LEU core. It is shown that there are adequate safety margins for both steady-state operations and postulated accident scenarios. For the steady-state operations with the preliminary LEU fuel element design the analysis predicts at least 2.49 MW margin to the onset of flow instability at the LSSS power of 15 MW. Considering the LSSS power is 125% of full license power, the margin to OFI is sufficient. In addition, the critical heat flux ratio at LSSS power is well above the requirement of CHFR > 2.0 from NUREG-1537 for all considered cases. For postulated transient accidents, the minimum margin to the fuel temperature safety limit is at least 109 °C. In summary, the proposed sequence of core loadings for MURR operations following conversion to LEU fuel and a power uprate to 12 MW provides sufficient safety margins for both steady-state operations and postulated transient accidents during a proposed sequence of transition cycles to equilibrium operations. Analysis has shown that there are some local experimental performance penalties during the initial cycles. Although there are local shifts in the experimental performance, on average all LEU cores at 12 MW have equal or higher performance than HEU at 10 MW. Temporary adjustments are being planned that will produce suitable experimental performance during these cycles. The results indicate that for the equilibrium LEU core the experimental performance exceeds that of current HEU operations in all key locations while also demonstrating sufficient safety margins.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2015

Modeling dynamic stall on wind turbine blades under rotationally augmented flow fields

It is well known that airfoils under unsteady flow conditions with a periodically varying angle of attack exhibit aerodynamic characteristics different from those under steady flow conditions, a phenomenon commonly known as dynamic stall. It is also well known that the steady aerodynamic characteristics of airfoils in the inboard region of a rotating blade differ from those under steady two-dimensional (2D) flow conditions, a phenomenon commonly known as rotational augmentation. This paper presents an investigation of these two phenomena together in the inboard parts of wind turbine blades. This analysis is carried out using data from three sources: (1) the National Renewable Energy Laboratory’s Unsteady Aerodynamics Experiment Phase VI experimental data, including constant as well as continuously pitching blade conditions during axial operation, (2) data from unsteady Delayed Detached Eddy Simulations (DDES) carried out using the Technical University of Denmark’s in-house flow solver Ellipsys3D, and (3) data from a simplified model based on the blade element momentum method with a dynamic stall subroutine that uses rotationally augmented steady-state polars obtained from steady Phase VI experimental sequences, instead of the traditional 2D nonrotating data. The aim of this work is twofold. First, the blade loads estimated by the DDES simulations are compared to three select cases of the N sequence experimental data, which serves as a validation of the DDES method. Results show reasonable agreement between the two data in two out of three cases studied. Second, the dynamic time series of the lift and the moment polars obtained from the experiments are compared to those from the dynamic stall subroutine that uses the rotationally augmented steady polars. This allowed the differences between the stall phenomenon on the inboard parts of harmonically pitching blades on a rotating wind turbine and the classic dynamic stall representation in 2D flow to be investigated. Results from the dynamic stall subroutine indicated a good qualitative agreement between the model and the experimental data in many cases, which suggests that the current 2D dynamic stall model as used in BEM-based aeroelastic codes may provide a reasonably accurate representation of three-dimensional rotor aerodynamics when used in combination with a robust rotational augmentation model.

17 WIND ENERGY↗
DOE OSTI2018

Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments

Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N 2 O) to the atmosphere. While ammonium (NH 4 + ) pool size decreased, nitrate (NO 3 - ) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N 2 O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH 4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N 2 O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases – A hydrological scenario expected to become more important in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Interfacial characteristics of P91 steel - Inconel 740H bimetallic structure fabricated using wire-arc additive manufacturing

Although bimetallic structures can offer unique solutions to engineering problems with varying functionality, joining two dissimilar alloys using additive manufacturing involves challenges such as cracking and segregation. In this work, bimetallic structures of Inconel 740H superalloy and P91 steel are processed using wire-arc additive manufacturing (WAAM) for the first time. P91 steel is directly deposited over 740H with a cooling time of 20 minutes in between the two depositions. During microstructure characterization, a large gradient zone with coarse grains spanning for ~2200 μm is observed. Moreover, the microhardness of the gradient zone is the least in comparison with the P91 and 740H deposits. No deleterious phase formation is found; however, intergranular cracks are observed along the gradient zone. In order to deduce the reason for cracking, non-equilibrium solidification simulations are performed for the mixed compositions of P91 and 740H in the gradient zone. Here, the reasons for crack formation in the gradient zone are the sudden change in the volumetric coefficient of thermal expansion due to the formation of MC carbides as well as the development of local strains from the thermal residual stresses. Therefore, altering the deposition sequence and introducing gradient layers with mixed composition between the P91 and 740H deposits will be beneficial in achieving defect-free builds. Through the integration of experiments and simulation, this work gains valuable insights into the processability of dissimilar alloy manufacturing using the WAAM technique.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2022

Correlated Hofstadter spectrum and flavour phase diagram in magic-angle twisted bilayer graphene

In magic-angle twisted bilayer graphene, the moiré superlattice potential gives rise to narrow electronic bands that support a multitude of many-body quantum phases. Further richness arises in the presence of a perpendicular magnetic field, where the interplay between moiré and magnetic length scales leads to fractal Hofstadter subbands. In this strongly correlated Hofstadter platform, multiple experiments have identified gapped topological and correlated states, but little is known about the phase transitions between them in the intervening compressible regimes. Here we simultaneously unveil sequences of broken-symmetry Chern insulators and resolve sharp phase transitions between competing states with different topological quantum numbers and different occupations of the spin-valley flavour. Our measurements determine the energy spectrum of interacting Hofstadter subbands in magic-angle twisted bilayer graphene and map out the phase diagram of flavour occupancy. In addition, we observe full lifting of the degeneracy of the zeroth Landau levels together with level crossings, indicating moiré valley splitting. We propose a unified flavour polarization mechanism to understand the intricate interplay of topology, interactions and symmetry breaking as a function of density and applied magnetic field in this system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Light rare earth element depletion during Deepwater Horizon blowout methanotrophy

Rare earth elements have generally not been thought to have a biological role. However, recent work has demonstrated that the light REEs (LREEs: La, Ce, Pr, and Nd) are essential for at least some methanotrophs, being co-factors in the XoxF type of methanol dehydrogenase (MDH). We show here that dissolved LREEs were significantly removed in a submerged plume of methane-rich water during the Deepwater Horizon (DWH) well blowout. Furthermore, incubation experiments conducted with naturally methane-enriched waters from hydrocarbon seeps in the vicinity of the DWH wellhead also showed LREE removal concurrent with methane consumption. Metagenomic sequencing of incubation samples revealed that LREE-containing MDHs were present. Our field and laboratory observations provide further insight into the biochemical pathways of methanotrophy during the DWH blowout. Additionally, our results are the first observations of direct biological alteration of REE distributions in oceanic systems. In view of the ubiquity of LREE-containing MDHs in oceanic systems, our results suggest that biological uptake of LREEs is an overlooked aspect of the oceanic geochemistry of this group of elements previously thought to be biologically inactive and an unresolved factor in the flux of methane, a potent greenhouse gas, from the ocean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Observation of Low-Lying Isomeric States in 136 Cs: A New Avenue for Dark Matter and Solar Neutrino Detection in Xenon Detectors

We report on new measurements establishing the existence of low-lying isomeric states in 136 Cs using γ rays produced in 136 Xe(p,n) 136 Cs reactions. Here, two states with O(100) ns lifetimes are placed in the decay sequence of the 136 Cs levels that are populated in charged-current interactions of solar neutrinos and fermionic dark matter with 136 Xe. Xenon-based experiments can therefore exploit a delayed-coincidence tag of these interactions, greatly suppressing backgrounds to enable spectroscopic studies of solar neutrinos and dark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Harmonic Analysis of Common-mode Reduction Modulation for Three-level Inverter

This paper presents harmonic analysis of common-mode reduction (CMR) modulation for three-level voltage source inverters. The analytical model to calculate the harmonics of CMR modulation with arbitrary PWM sequence is developed. The impact of alternative PWM sequences of CMR modulation on harmonics is investigated. New three-state and four-state PWM sequences of CMR are proposed which spread the energy centered in the carrier frequency in the conventional CMR, and thus reduce the voltage peaks in frequency domain. Experiments are conducted on a three-level neutral point clamped inverter. Experiment results verify the developed analytical model and harmonic analysis.

Chen, Ruirui↗
DOE OSTI2025

Warming is Associated With More Encoded Antimicrobial Resistance Genes and Transcriptions Within Five Drug Classes in Soil Bacteria: A Case Study and Synthesis

ABSTRACT The effect of warming on anti‐microbial resistance (AMR) genes in the environment has critical implications for public health but is little studied. We collected published soil bacterial genomes from the BV‐BRC database and tested the correlation between reported optimal growth temperature and the number of encoded AMR genes. Furthermore, we tested the relationship between temperature and AMR gene transcription in a natural ecosystem by analysing soil transcriptomes from a warming manipulation experiment in an Alaskan boreal forest. We hypothesised that there is a positive relationship between warming and AMR prevalence in gene content in bacterial genomes and transcriptomic sequences, and that this effect would vary by drug class. Regarding the bacterial genomes, we found a positive relationship between the fraction of encoded AMR genes and the reported optimal temperature of soil bacteria. The drug classes tetracycline and lincosamide/macrolide/streptogramin had the strongest positive relationship with reported optimal temperature. For the case study in a natural ecosystem, we found 61 significantly upregulated AMR gene‐associated transcripts spanning eight drug classes in warmed plots. In the Alaskan soil samples, we found that warming elicited the strongest positive effect on transcripts targeting lincosamide/streptogramin, beta‐lactam and phenicol/quinolone antibiotics. Overall, higher temperatures were linked to AMR gene prevalence.

Hacopian, Melanie T. [Department of Ecology and Ev↗
DOE OSTI2017

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

Background: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to defne diferences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Methods: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specifc KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Efective DB to predict bacterial type III secreted proteins. The efect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures. Results: Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were afliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing efect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade. Conclusions: This is the frst report of bacterial type III secretion system genes being associated with high methane emissions in ruminants, and identifes these secretions systems as potential new targets for methane mitigation research. The effects of S. dextrinosolvens on the growth of rumen methanogens in co-cultures indicate that bacteriamethanogen interactions are important modulators of methane production in ruminant animals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Final Report for Award DE-FG02-09ER64721

The original goal of this award was to develop a proteoglycan “chip” containing suitable oligosaccharides that could be used as substrates for glycosyltransferases involved in synthesis or proteoglycans in higher plant cell walls. We had previously developed a suite of cloned enzymes that could be used to cleave most of the relevant glycosidic linkages in plant cell walls. The next step, supported by the previous award and this award, was to produce a series of transgenic plants in which synthetic proteins were introduced that contained each of the known sequence motifs that induce prolyl hydroxylation, and subsequent glycosylation. This work was completed and published in Estevez et al (2006). We then engaged on a series of experiments to define the properties of the prolyl hydroxylases that convert certain prolyl resides to hydroxyproline for subsequent glycosylation. This proved to be a challenging goal that required recruitment of an international team of complementary skills and several additional years or research. However, the effort was successful and has been published in Science recenty (Velasquez et al., 2011). In the course of this project, the postdoc supported by the award (Jose Estevez) was asked to provide technical assistance to a colleague at Stanford because of his expertise in marine polysaccharides. This led to the important discovery that marine algae have compounds that could be classified as lignin (Martone et al., 2009). Publications supported by the award Estévez, J.M., Kieliszewski, M.J., Khitrov, N., Somerville, C. (2006) Characterization of synthetic hydroxyproline-rich proteoglycans with AGP- and extensin-motifs in Arabidopsis. Plant Physiol., 142,458-470 Martone, P.T., Estevez, J.M., Lu, F., Ruel, K., Ralph, J., Denny, M.W., Somerville, C.R. (2009) Discovery of lignin in seaweed reveals convergent evolution of cell-wall architecture. Curr. Biol., 19, 169-175 Velasquez, S.M., M. Ricardi, M.M., Dorosz, J.G., Fernandez, P.V., Nadra, A.D., Pol-Fachin, L., Egelund, J., Gille, S., Harholt, J., Ciancia, M., Verli, H., Pauly, M., Bacic, A., Olsen, C.E., r Ulvskov, P., Petersen, B.L., Somerville, C., Iusem, N.D. & Estevez, J.M. (2011) O-glycosylated cell wall proteins are essential in root hair growth. Science 332,1401-1403

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp . PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis ( Spirulina ). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

59 BASIC BIOLOGICAL SCIENCES↗