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At least 577 records · Page 32

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DOE OSTI2015

Species interactions differ in their genetic robustness

Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species' interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S. enterica . The type of interaction between species was set by modulating the initial metabolites present in the environment. We found that the community was most robust to genetic perturbations when the organisms were cooperating. Species ratios were more stable in the cooperative community, and community biomass had equal variance in the two contexts. Additionally, the number of mutations that have a substantial effect is lower when the species cooperate than when they are competing. In contrast, when mutations were added to the S. enterica network the system was more robust when the bacteria were competing. These results highlight the utility of connecting metabolic mechanisms and studies of ecological stability. Cooperation and conflict alter the connection between genetic changes and properties that emerge at higher levels of biological organization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Automating methods for estimating metabolite volatility

The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called volcalc that uses chemoinformatic tools to automate these volatility estimates for all metabolites in an extensive and continuously updated pathway database: the Kyoto Encyclopedia of Genes and Genomes (KEGG) that connects metabolites, organisms, and reactions. We first benchmark the automated pipeline against a manually curated data set and show that the same category of volatility (e.g., nonvolatile, low, moderate, high) is predicted for 93% of compounds. We then demonstrate how volcalc might be used to generate and test hypotheses about the role of volatility in biological systems and organisms. Specifically, we estimate that 3.4 and 26.6% of compounds in KEGG have high volatility depending on the environment (soil vs. clean atmosphere, respectively) and that a core set of volatiles is shared among all domains of life (30%) with the largest proportion of kingdom-specific volatiles identified in bacteria. With volcalc , we lay a foundation for uncovering the role of the volatilome using an approach that is easily integrated with other bioinformatic pipelines and can be continually refined to consider additional dimensions to volatility. The volcalc package is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae

The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments.

Isokpehi, Raphael D. (ORCID:0000000268770840)↗

DOE OSTI2022

Performance of Graphene/Polydimethylsiloxane Surfaces against S. aureus and P. aeruginosa Single- and Dual-Species Biofilms

The increasing incidence of implant-associated infections has prompted the development of effective strategies to prevent biofilm formation on these devices. In this work, pristine graphene nanoplatelet/polydimethylsiloxane (GNP/PDMS) surfaces containing different GNP loadings (1, 2, 3, 4, and 5 wt%) were produced and evaluated on their ability to mitigate biofilm development. After GNP loading optimization, the most promising surface was tested against single- and dual-species biofilms of Staphylococcus aureus and Pseudomonas aeruginosa. The antibiofilm activity of GNP/PDMS surfaces was determined by the quantification of total, viable, culturable, and viable but nonculturable (VBNC) cells, as well as by confocal laser scanning microscopy (CLSM). Results showed that 5 wt% GNP loading reduced the number of total (57%), viable (69%), culturable (55%), and VBNC cells (85%) of S. aureus biofilms compared to PDMS. A decrease of 25% in total cells and about 52% in viable, culturable, and VBNC cells was observed for P. aeruginosa biofilms. Dual-species biofilms demonstrated higher resistance to the antimicrobial activity of GNP surfaces, with lower biofilm cell reductions (of up to 29% when compared to single-species biofilms). Still, the effectiveness of these surfaces in suppressing single- and dual-species biofilm formation was confirmed by CLSM analysis, where a decrease in biofilm biovolume (83% for S. aureus biofilms and 42% for P. aeruginosa and dual-species biofilms) and thickness (on average 72%) was obtained. Overall, these results showed that pristine GNPs dispersed into the PDMS matrix were able to inhibit biofilm growth, being a starting point for the fabrication of novel surface coatings based on functionalized GNP/PDMS composites.

Oliveira, Isabel M.↗

DOE OSTI2018

Defense Strategies for Asymmetric Networked Systems with Discrete Components

We consider infrastructures consisting of a network of systems, each composed of discrete components. The network provides the vital connectivity between the systems and hence plays a critical, asymmetric role in the infrastructure operations. The individual components of the systems can be attacked by cyber and physical means and can be appropriately reinforced to withstand these attacks. We formulate the problem of ensuring the infrastructure performance as a game between an attacker and a provider, who choose the numbers of the components of the systems and network to attack and reinforce, respectively. The costs and benefits of attacks and reinforcements are characterized using the sum-form, product-form and composite utility functions, each composed of a survival probability term and a component cost term. We present a two-level characterization of the correlations within the infrastructure: (i) the aggregate failure correlation function specifies the infrastructure failure probability given the failure of an individual system or network, and (ii) the survival probabilities of the systems and network satisfy first-order differential conditions that capture the component-level correlations using multiplier functions. We derive Nash equilibrium conditions that provide expressions for individual system survival probabilities and also the expected infrastructure capacity specified by the total number of operational components. We apply these results to derive and analyze defense strategies for distributed cloud computing infrastructures using cyber-physical models.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates

Bacterial-fungal interactions (BFIs) play an integral role in shaping microbial community composition, biogeochemical functions, spatial dynamics, and microbial dispersal. Mycelial networks created by filamentous fungi or other filamentous microorganisms (e.g., Oomycetes) act as 'fungal highways' that can be utilized by bacteria for transport throughout heterogeneous environments, greatly facilitating their mobility and granting them access to regions that may be challenging or impossible to reach on their own (e.g., due to air pockets within the soil). Several devices and experimental protocols have been created to study these fungal highways, including fungal highway columns. The fungal highway column designed by our group can be used for a variety of in situ or in vitro applications, as well as with diverse environmental and host-associated sample types. Herein, we describe the methods for performing experiments with these columns, including designing, printing, sterilizing, and preparing the devices. The options for analyzing data obtained from the use of these devices are also discussed here, and troubleshooting advice regarding potential pitfalls associated with experiments using fungal highway columns is offered. These devices can be used to gain a more comprehensive understanding of the diversity, mechanisms, and dynamics of fungal highway BFIs to provide valuable insights into the structural and functional dynamics within complex environments (e.g., soils) and across diverse habitats in which bacteria and fungi co-exist.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Data from: Harvesting biofuel grasslands has mixed effects on natural enemy communities and no effects on biocontrol services

1.Perennial bioenergy systems, such as switchgrass and restored prairies, are alternatives to commonly used annual monocultures such as maize. Perennial systems require lower chemical input, provide greater ecosystem services such as carbon storage, greenhouse gas mitigation, and support greater biodiversity of beneficial insects. However, biomass harvest will be necessary in managing these perennial systems for bioenergy production, and it is unclear how repeated harvesting might affect ecosystem services. 2.In this study, we examined how repeated production-scale harvesting of diverse perennial grasslands influences vegetation structure, natural enemy communities (arthropod predators and parasitoids), and natural biocontrol services in two states (Wisconsin and Michigan, USA) over multiple years. 3.We found that repeated biomass harvest reduced litter biomass and increased bare ground cover. Some natural enemy groups, such as ground-dwelling arthropods, decreased in abundance with harvest whereas others, such as foliar-dwelling arthropods increased in abundance. The disparity in responses is likely due to how different taxonomic groups utilize vegetation and differences in dispersal abilities. 4.At the community level, biomass harvest altered community composition, increased total arthropod abundance, and decreased evenness but did not influence species richness, diversity, or biocontrol services. Harvest effects varied with time, diminishing in strength both within the season (for total abundance and evenness), across seasons (for evenness), or were consistent throughout the duration of the study (for community composition). Greater functional redundancy and compensatory responses of the different taxonomic groups may have buffered against the potentially negative effects of harvest on biocontrol services. 5.Synthesis and applications. Our results show that in the short-term, repeated harvesting of perennial grasslands (when insect activity is low) consistently altered vegetation structure but had mixed effects on natural enemy communities and no discernable effects on biocontrol services. However, the long-term effects of repeated harvesting on vegetation structure, natural enemies, and other arthropod-derived ecosystem services such as pollination and decomposition remain largely unknown.

09 BIOMASS FUELS↗

DOE OSTI2016

A family of photoswitchable NMDA receptors

NMDA receptors, which regulate synaptic strength and are implicated in learning and memory, consist of several subtypes with distinct subunit compositions and functional properties. To enable spatiotemporally defined, rapid and reproducible manipulation of function of specific subtypes, we engineered a set of photoswitchable GluN subunits ('LiGluNs'). Photo-agonism of GluN2A or GluN2B elicits an excitatory drive to hippocampal neurons that can be shaped in time to mimic synaptic activation. Photo-agonism of GluN2A at single dendritic spines evokes spine-specific calcium elevation and expansion, the morphological correlate of LTP. Photo-antagonism of GluN2A alone, or in combination with photo-antagonism of GluN1a, reversibly blocks excitatory synaptic currents, prevents the induction of long-term potentiation and prevents spine expansion. In addition, photo-antagonism in vivo disrupts synaptic pruning of developing retino-tectal projections in larval zebrafish. By providing precise and rapidly reversible optical control of NMDA receptor subtypes, LiGluNs should help unravel the contribution of specific NMDA receptors to synaptic transmission, integration and plasticity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Composition, Reactivity and Regulation of Extracellular Metal-Reducing Structures (Bacterial Nanowires) Produced by Dissimilatory Metal - Reducing Bacteria

This is the final technical report for the project. There were two objectives in the proposal. The first was to describe the composition and function of electrically conductive appendages, known as bacterial nanowires, which resemble pili but are longer and are electrically conductive. They were first identified on the dissimilatory metal-reducing bacteria (DMRB), Shewanella and Geobacter. Specifically, this project investigated the role of these structures in: (i) the reductive transformation of iron oxides as solid phase electron acceptors; (ii) the use of as uranium as a dissolved electron acceptor to form nanocrystalline particles of uraninite upon reduction. The Beveridge group investigated these processes using advanced cryo-transmission electron microscopy (cryoTEM) to visualize the points of connection between the distal ends of nanowires and the effect they have on solid phase Fe minerals. At the same time, immuno-electron microscopy was applied in an attempt to identify where metal reductases and cytochromes are located on the cell surface, or in the nanowires. The second objective was to define the surface physicochemistry of Shewanella spp. in an attempt to decipher how weak bonding (electrostatics and hydrophobicity) affects the adherence of the bacteria to Fe oxides. This bonding could be dictated by the chemistry of lipopolysaccharide (LPS), or the presence/absence of capsular polysaccharide.

58 GEOSCIENCES↗

DOE OSTI2012

2012 PLANT CELL WALLS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, AUGUST 4-10, 2012

The sub-theme of this year’s meeting, ‘Cell Wall Research in a Post-Genome World’, will be a consideration of the dramatic technological changes that have occurred in the three years since the previous cell wall Gordon Conference in the area of DNA sequencing. New technologies are providing additional perspectives of plant cell wall biology across a rapidly growing number of species, highlighting a myriad of architectures, compositions, and functions in both "conventional" and specialized cell walls. This meeting will focus on addressing the knowledge gaps and technical challenges raised by such diversity, as well as our need to understand the underlying processes for critical applications such as crop improvement and bioenergy resource development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Al and Zn Impurity Diffusion in Binary and Ternary Magnesium Solid-Solutions

Magnesium alloys are considered for implementation into structural components where energy-efficiency and light-weighting are important. Two of the most common alloying elements in magnesium alloys are Aluminum and Zinc. The present work examines impurity diffusion coefficients of Al and Zn in Mg(Zn) and Mg(Al) binary solid solutions, respectively. Experimental investigation is carried out with ternary diffusion couples with polycrystalline alloys. Concentration profiles were measured by electron microprobe micro-analysis and the impurity diffusion coefficients were determined by the Hall Method. Results of Al and Zn impurity diffusion in Mg solid solutions are reported, and examined as a function of composition of Mg solid solution.

aluminum↗

DOE OSTI2017

Compositions and methods for hydrocarbon functionalization

Embodiments of the present disclosure provide for methods of hydrocarbon functionalization, methods and systems for converting a hydrocarbon into a compound including at least one group ((e.g., hydroxyl group) (e.g., methane to methanol)), functionalized hydrocarbons, and the like.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Microbiomes Have the Power to Help or Hinder Your Health

They are everywhere: countless microorganisms that inhabit our world—even in your skin, mouth, gut and other parts of your body. Called microbiomes, these communities play a fundamental role in our ecosystem and our bodies, influencing everything from climate to human health. And scientists at PNNL are studying microbiomes to better understand how they influence our daily lives. Scientist Janet Jansson studies complex microbiomes in soil and the human intestine to understand changes in the composition or function of microbes. In the soil, these microbes are associated with carbon cycling and degrading pollutants, as well as plant health. In the intestine, they are responsible for digestion of our food and protection from pathogens. When they go awry, they can be associated with numerous inflammatory bowel diseases, such as Crohn’s. Understanding the factors underlying these microbiome changes will ultimately help researchers develop solutions to problems encountered within our world and our bodies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Method and apparatus for fabricating ceramic and metal components via additive manufacturing with uniform layered radiation drying

A freeform extrusion fabrication process for producing three-dimensional ceramic, metal and functionally gradient composite objects, including the steps of filling a plurality of paste sources with a respective plurality of aqueous paste compositions, operationally connecting respective syringes containing respective aqueous paste compositions to a mixing chamber, moving a first aqueous paste composition from a first respective paste source into the mixing chamber, moving a second aqueous paste composition from a second respective paste source into the mixing chamber, mixing the first and second aqueous paste compositions to define a first admixture having a first admixture composition, extruding the first admixture onto a surface to define an extruded layer having a first admixture composition, surrounding the sides of the extruded layer with an oil bath, radiatively drying the extruded layer.

Leu, Ming C.↗

DOE OSTI2019

Compositions and methods for hydrocarbon functionalization

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Multiple-objective Reinforcement Learning for Inverse Design and Identification

Inverse chemical design using generative deep learning (DL) models is an emerging tool, which has early success in generating molecular structures with desired properties. We enhance this tool by developing heuristics for curriculum-learning based multiple-objective (20+ objectives) reinforcement learning, and apply it to the context of chemical identi?cation. We develop a generative DL framework that utilizes constraints pertaining to the unknown molecule’s mass and functional group composition, and show that multiple-objective RL-based generative DL models can correctly identify unknown molecules with a 80% success rate, compared to the baseline approach of 0%. Lastly, the heuristics developed are not limited to just chemistry research challenges; we anticipate any problem that utilizes reinforcement learning with multiple-objectives will bene?t from it.

Artificial Intelligence, Data Science, deep learni↗

DOE OSTI2015

Photoluminescence in solid solutions and thin films of tungstates CaWO{sub 4}-CdWO{sub 4}

In this study, we present two types of studies on the luminescence properties under UV and X-ray excitations of solid solutions Ca{sub 1-x}Cd{sub x}WO{sub 4} and of thin layers of CaWO{sub 4} and CdWO{sub 4}. These tungstate based solid solutions are susceptible to be integrated into new radiation sensors, in order to be used in different fields of applications such as reactor measurements, safeguards, homeland security, nuclear nondestructive assays, LINAC emission radiation measurement. However these complex materials were rarely investigated in the literature. One first objective of our studies was to establish correlations between luminescence efficiency, chemical substitution and the degree of crystallization resulting from elaboration conditions. A second objective will be to determine the efficiency of luminescence properties of thin layers of these materials. In the present work, we focus our attention on the role of chemical substitution on photon emissions under UV and X-ray irradiations. The luminescence spectra of Ca{sub 1-x}Cd{sub x}WO{sub 4} polycrystalline materials have been investigated at room temperature as a function of composition (0≤x≤1). In addition, we present a preliminary study of the luminescence of CaWO{sub 4} and CdWO{sub 4} thin layers: oscillations observed in the case of X-ray excitations in the luminescence spectra are discussed. (authors)

36 MATERIALS SCIENCE↗