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DOE OSTI2017

Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough

ABSTRACT Due in large part to their ability to facilitate the diffusion of a diverse range of solutes across the outer membrane (OM) of Gram-negative bacteria, the porins represent one of the most prominent and important bacterial membrane protein superfamilies. Notably, for the Gram-negative bacterium Desulfovibrio vulgaris Hildenborough, a model organism for studies of sulfate-reducing bacteria, no genes for porins have been identified or proposed in its annotated genome. Results from initial biochemical studies suggested that the product of the DVU0799 gene, which is one of the most abundant proteins of the D. vulgaris Hildenborough OM and purified as a homotrimeric complex, was a strong porin candidate. To investigate this possibility, this protein was further characterized biochemically and biophysically. Structural analyses via electron microscopy of negatively stained protein identified trimeric particles with stain-filled depressions and structural modeling suggested a β-barrel structure for the monomer, motifs common among the known porins. Functional studies were performed in which crude OM preparations or purified DVU0799 was reconstituted into proteoliposomes and the proteoliposomes were examined for permeability against a series of test solutes. The results obtained establish DVU0799 to be a pore-forming protein with permeability properties similar to those observed for classical bacterial porins, such as those of Escherichia coli . Taken together, these findings identify this highly abundant OM protein to be the major porin of D. vulgaris Hildenborough. Classification of DVU0799 in this model organism expands the database of functionally characterized porins and may also extend the range over which sequence analysis strategies can be used to identify porins in other bacterial genomes. IMPORTANCE Porins are membrane proteins that form transmembrane pores for the passive transport of small molecules across the outer membranes of Gram-negative bacteria. The present study identified and characterized the major porin of the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, observing its preference for anionic sugars over neutral ones. Its predicted architecture appears to be novel for a classical porin, as its core β-barrel structure is of a type typically found in solute-specific channels. Broader use of the methods employed here, such as assays for channel permeability and electron microscopy of purified samples, is expected to help expand the database of confirmed porin sequences and improve the range over which sequence analysis-based strategies can be used to identify porins in other Gram-negative bacteria. Functional characterization of these critical gatekeeping proteins from divergent Desulfovibrio species should offer an improved understanding of the physiological features that determine their habitat range and supporting activities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Complete genomes of Mucilaginibacter sabulilitoris SNA2 and Mucilaginibacter sp. cycad4: microbes with the potential for plant growth promotion

Mucilaginibacter species have been isolated from various environments, often in association with plants. Here, we report the complete genomes of Mucilaginibacter sabulilitoris SNA2 and Mucilaginibacter sp. cycad4. The former is the first available for that species, and based on 16S sequence analysis, the latter strain is likely a new species.

Mucilaginibacter↗

DOE OSTI2021

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A new mud shrimp of the genus Pugnatrypaea from outer continental shelf waters of the northern Gulf of Mexico, commonly associated with hydrocarbon seeps (Crustacea: Decapoda: Callianassidae)

A new species of callianassid mud shrimp is described from outer continental shelf waters of the northwestern Gulf of Mexico, where it appears to commonly live in close association with sediments on or near natural hydrocarbon seeps. Recent genus-level taxonomic revisions of the Callianassidae, based on gene sequence analyses and comparative morphological studies, included specimens representing this new species, assigning it with strong support to the genus Pugnatrypaea Poore et al., 2019. The other known species of this genus are also typically found in offshore waters of continental shelves, but are all restricted in distribution to the Indo-West Pacific and are known from relatively few specimens. Collections of this new Gulf of Mexico representative of the genus are all from slightly deeper waters than for other known congeners, and commonly occur near hydrocarbon seeps, on some occasions being directly associated with sulfidic substrates that include waxy crude oil globules.

Zoology↗

DOE OSTI2018

High-throughput binding affinity calculations at extreme scales

Background Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High-throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. Results We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. Conclusions As such, HTBAC advances the state of the art of binding affinity calculations and protocols. HTBAC provides the platform to enable scientists to study a wide range of cancer drugs and candidate ligands in order to support personalized clinical decision making based on genome sequencing and drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Key findings and remaining questions in the areas of core-concrete interaction and debris coolability

The reactor accidents at Fukushima-Dai-ichi have rekindled interest in late phase severe accident behavior involving reactor pressure vessel breach and discharge of molten core melt into the containment. Two technical issues of interest in this area include core-concrete interaction and the extent to which the core debris may be quenched and rendered coolable by top flooding. The OECD-sponsored Melt Coolability and Concrete Interaction (MCCI) programs at Argonne National Laboratory included the conduct of large scale reactor material experiments and associated analysis with the objectives of resolving the ex-vessel debris coolability issue, and to address remaining uncertainties related to long-term two-dimensional molten core-concrete interactions under both wet and dry cavity conditions. These tests provided a broad database to support accident management planning, as well as the development and validation of models and codes that can be used to extrapolate the experiment results to plant conditions. This paper provides a high level overview of the key experiment results obtained during the program. Finally, a discussion is also provided that describes technical gaps that remain in this area, several of which have arisen based on the sequence of events and operator actions during Fukushima.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

Inferring transmission heterogeneity using virus genealogies: estimation and targeted prevention

Spread of HIV typically involves uneven transmission patterns where some individuals spread to a large number of individuals while others to only a few or none. Such transmission heterogeneity can impact how fast and how much an epidemic spreads. Further, more efficient interventions may be achieved by taking such transmission heterogeneity into account. To address these issues, we developed two phylogenetic methods based on virus sequence data: 1) to generally detect if significant transmission heterogeneity is present, and 2) to pinpoint where in a phylogeny high-level spread is occurring. We derive inference procedures to estimate model parameters, including the amount of transmission heterogeneity, in a sampled epidemic. We show that it is possible to detect transmission heterogeneity under a wide range of simulated situations, including incomplete sampling, varying levels of heterogeneity, and including within-host genetic diversity. When evaluating real HIV-1 data from different epidemic scenarios, we found a lower level of transmission heterogeneity in slowly spreading situations and a higher level of heterogeneity in data that included a rapid outbreak, while R0 and Sackin’s index (overall tree shape statistic) were similar in the two scenarios, suggesting that our new method is able to detect transmission heterogeneity in real data. We then show by simulations that targeted prevention, where we pinpoint high-level spread using a coalescence measurement, is efficient when sequence data are collected in an ongoing surveillance system. Such phylogeny-guided prevention is efficient under both single-step contact tracing as well as iterative contact tracing as compared to random intervention.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Genome Variations Associated with Viral Susceptibility and Calcification in Emiliania huxleyi

Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Soil organic matter, tree communities, and fungal communities across mycorrhizal gradients in the Eastern United States

We collected these data to investigate how mycorrhizal associations are related to soil C and N across four sites in the eastern U.S. broadleaf forest biome, which capture broad variability in climate and tree species. Our sites represented each of the four ecoregions in the eastern United States temperate forest—warm continental (New Hampshire), hot continental (Wisconsin), Prairie (Illinios), and subtropical (Georgia). This breadth naturally provided tree species diversity and allowed us to also investigate how soil C and N are related to canopy tree and EcM fungal community composition. Specifically, we analyzed the effects of mycorrhizal association, canopy tree family, and EcM fungal taxa on the proportion of C and N associated with soil minerals (MAOM) and bulk soil C:N. These are plot level data from forests in New Hampshire, Georgia, Wisconsin, and Illinois. The plots are 10 m in radius and vary across gradients of ectomycorrhizal tree basal area. Within each plot, data include the basal area of all trees >2 cm in diameter identified to species, the abundance of different fungal taxa based on ITS sequences, and the %C, %N, C:N of bulk soil and of soil density fractions (free light, occluded light, and particulate) as well as the proportion of soil C and N within each fraction. The soil data (both organic matter and fungal communities) are from the top 10 cm of the mineral soil. This also includes a meta-analysis of leaf litter k and C:N values for the tree species present in the forests.The "Tree_BA_ALL.csv" files include the basal area of all trees >2 cm in diameter at breast height within our 10 cm radii plots. The "Soil_Data_Final.csv" file contains the soil carbon and nitrogen in bulk and density fractions (concentrations as well as proportion for free light fraction (fLF), occluded light fraction (oLF), and heavy or dense fraction (HF), oxalate extractable iron and aluminum concentrations, as well as the geographic coordinates of each plot's location. The "FungiNonRelative.csv" file contains the abundances of fungal taxa identified via ITS sequencing for each plot (with the exception of 4 plots from GA where there was not enough quality DNA to extract).The "R_ReadyK.csv" and "R_Ready_CN.csv" files contain leaf litter decomposition constant (k) and C:N values from the literature for the tree species found at our sites.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Air Dispersion Modeling of Radioactive Releases During Proposed 236Z Rubble Pile Removal Activities

This report is part of the planning process for the removal of the 236Z rubble remaining as of January 1, 2018, at the Plutonium Finishing Plant (PFP) on the Hanford Site. This report documents an analysis considering standard techniques for the removal of demolition rubble. It does not document any decisions about the removal approaches. This document is intended to guide the establishment of a boundary for the application of an air monitoring regime. Atmospheric dispersion modeling using estimated release rates has been conducted to provide information on the location and levels of radioactive contamination that may be expected as the result of rubble removal activities. Hourly meteorological data collected over a 6-year period (2004–2009) were used to examine the effects of wind speed, direction, and stability on projected concentrations of contaminants in air and deposited on nearby surfaces. The source terms modeled in this report were based on the residual transuranic contamination levels that are anticipated to remain in the 236Z rubble following building demolition. The potential airborne concentrations were established using the five-factor formula from DOE-HDBK-3010 (DOE 1994) considering material-at-risk, damage ratio, airborne release fraction, respirable fraction, and leak path factor. Radioactive contamination emissions were calculated by release mechanism and rubble pile area for on-shift and off-shift activities. The emissions from the applicable sources were combined to provide emissions estimates for each day from each cleanup area. The U.S. Environmental Protection Agency’s (EPA’s) AERMOD computer code was used to estimate atmospheric dispersion and deposition of the released radioactive materials in the immediate vicinity of the planned rubble removal activities Both airborne and surface concentrations were modeled with AERMOD. Hourly derived air concentrations (DAC) were modeled for an array of receptors covering the rubble pile site and surrounding area. Peak (95th and 99th percentile) values of time-integrated air concentrations at these receptor points are derived from these hourly values, with modeling results reported as total incremental air concentrations in DAC-hours occurring over the selected time period. Total accumulated deposition amounts were also evaluated with AERMOD using the same array of receptors, with results reported as disintegrations per minute (dpm) per 100 cm2. Each rubble pile was considered in terms of its size, location, and estimated contamination levels. The modeling was based on the assumed sequence of the rubble removal activities. The results in this report are based on cleanup schedules and methods proposed by CHPRC. As of January 1, 2018, there are broadly three large rubble piles (west, footprint, and east) remaining of the 236Z Building process cell. It is assumed that the overall cleanup will require either 1) 30 days over a 6-week period, or 2) 60 days over a 12-week period. Work was assumed to be performed during 10-hour day shifts. The analysis shows that some releases of radioactive material are to be anticipated during the cleanup of the 236Z rubble piles. The modeling results presented here are closely tied to the details of how the rubble removal is to be conducted. The results indicate that for the rubble removal, the radiological exposures from the planned activities are predicted to be well below the designated limits for air and soil exposures. The cleanup of the 236Z main process cell rubble is expected to release some alpha-emitting radionuclides. However, results based on 6 years of hourly climatological data, two representative cleanup periods, realistic mitigating actions, and a bounding source term indicate that concentrations at the fence line of the PFP facilities should remain well below 12 DAC-hours/week. The results presented in this report are a reevaluation of a subset of the results presented in PNNL-20173 Rev. 4.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Functional Biomimetic Polymers with Antimicrobial Activity

At PNNL, we have developed a completely new class of synthetic biomimetic sequence-defined polymers based on triazine chemistry, which we call TZPs. PNNL's new polymers offer the opportunity to achieve similar functions to natural macromolecules; specifically we designed and synthesized a diversity of test molecules for antimicrobial activity. Antimicrobial activity against a variety of wild type and drug resistant pathogens was found.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response

Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis , and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis -acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Non-LTE Stellar Population Synthesis of Globular Clusters Using Synthetic Integrated Light Spectra. I. Constructing the IL Spectra

We present an investigation of the globular cluster population synthesis method of McWilliam and Bernstein, focusing on the impact of non-LTE (NLTE) modeling effects and color–magnitude diagram (CMD) discretization. Johnson–Cousins–Bessel U – B, B−V, V−I, and J−K colors are produced for 96 synthetic integrated light (IL) spectra with two different discretization prescriptions and three degrees of NLTE treatment. These color values are used to compare NLTE- and LTE-derived population ages. Relative contributions of different spectral types to the IL spectra for different wavebands are measured. IL NLTE spectra are shown to be more luminous in the UV and optical than LTE spectra, but show stronger absorption features in the IR. The main features showing discrepancies between NLTE and LTE IL spectra may be attributed to light metals, primarily Fe i, Ca i, and Ti i, as well as TiO molecular bands. Main-sequence stars are shown to have negligible NLTE effects at IR wavelengths compared to more evolved stars. Photometric color values are shown to vary at the millimagnitude level as a function of CMD discretization. Finer CMD sampling for the upper main sequence and turnoff, base of the red giant branch, and the horizontal branch minimizes this variation. Differences in ages derived from LTE and NLTE IL spectra are found to range from 0.55 to 2.54 Gyr, comparable to the uncertainty in GC ages derived from color indices with observational uncertainties of 0.01 mag, the limiting precision of the Harris catalog.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

The SDSS-Gaia View of the Color–Magnitude Relation for Blue Horizontal-branch Stars

We present an updated sample of blue horizontal-branch (BHB) stars selected from the photometric and spectroscopic data from Sloan Digital Sky Survey and its associated project Sloan Extension for Galactic Understanding and Exploration (SEGUE). With these data, we selected candidates for A-type stars in the color–color space and then a mixture modeling technique was implemented in order to distinguish between BHB and main-sequence/blue-straggler stars based on their surface gravity values (log g) estimated by the SEGUE Stellar Parameter Pipeline. Our robust approach allows us to attribute individual probabilities of each star truly being in the BHB stage. Hence, our method is advantageous in comparison to previous SEGUE BHB selections that adopted simple log g cuts. We also revisit the color–magnitude relation for these stars and propose two calibrations, based on updated distances for Galactic globular clusters, to estimate absolute magnitudes with (g – r) 0 and (u – r) 0 colors.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1964

Stellar evolution. ii. the hydrogen-burning phase of a star of 7.0 solar masses <sternentwicklung. ii. die wasserstoff- brennende phase eines sterns von 7.0 sonnenmassen<

With the computer program by Hofmeister, Kippenhahn, Weigert (1964, from now on referred to as ''I") the evolution of a population I star of 7.0 solar masses has been followed. The results presented here are based on a sequence of 119 models, the first of which represents the homogeneous main sequence state and has a convective core containing 26% of the mass. The following models describe the phase of depletion of hydrogen in the core, which is shrinking in mass until the convection around the centre disappears. After this the gradual development of a hydrogen burning shell source is shown. The models show the evolution into the red giant region, while the helium core is contracting until helium burning starts at the centre and a new convective core is built up. The luminousity is increased about 1 magnitude compared with the main sequence state. At the same time the outer convective region grows in mass and covers at the maximum 71% of the total mass of the star. During the evolution to the red giant state, the evolutionary track crosses the region of the cepheids. Some aspects of the corresponding models are discussed.

STELLAR EVOLUTION↗

NASA NTRS1972

Some new techniques for processing remotely obtained images by self-generated spectral masks.

An extension of a new technique that makes possible parallel, simultaneous processing of remotely obtained images is presented. The technique holds out promise for automatic onboard classification of data. The central feature involves the generation of binary masks, directly from the image, based on object reflectance data, that group objects into equivalence classes. These masks, called equivalence class masks, can be used in various logical combinations to isolate classes of objects with a priori known reflectance or radiance signatures. Experimental verification of the technique is furnished for simple scenes. A computational scheme, based on a sequence of integrated irradiance measurements on the image, that makes it possible to identify objects within an equivalence class is suggested.

Stark, H.↗

NASA NTRS1973

Model experiments to evaluate vortex dissipation devices proposed for installation on or near aircraft runways

The effectiveness of various vortex dissipation devices proposed for installation on or near aircraft runways is evaluated on basis of results of experiments conducted with a 0.03-scale model of a Boeing 747 transport aircraft in conjunction with a simulated runway. The test variables included type of vortex dissipation device, mode of operation of the powered devices, and altitude, lift coefficient and speed of the generating aircraft. A total of fifteen devices was investigated. The evaluation is based on time sequence photographs taken in the vertical and horizontal planes during each run.

Kohl, R. E.↗

NASA NTRS1974

Recursive estimation of prior probabilities using the mixture approach

The problem of estimating the prior probabilities q sub k of a mixture of known density functions f sub k(X), based on a sequence of N statistically independent observations is considered. It is shown that for very mild restrictions on f sub k(X), the maximum likelihood estimate of Q is asymptotically efficient. A recursive algorithm for estimating Q is proposed, analyzed, and optimized. For the M = 2 case, it is possible for the recursive algorithm to achieve the same performance with the maximum likelihood one. For M 2, slightly inferior performance is the price for having a recursive algorithm. However, the loss is computable and tolerable.

Kazakos, D.↗