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Results for “mapping shift function”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Evolution of ʟ–DOPA 4,5–dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales

The evolution of ʟ-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that ʟ-DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation event has not been confirmed and the DODA gene lineage exhibits numerous gene duplication events, whose evolutionary significance is unclear. To address this, we functionally characterised 23 distinct DODA proteins for ʟ-DOPA 4,5-dioxygenase activity, from four betalain-pigmented and five anthocyanin-pigmented species, representing key evolutionary transitions across Caryophyllales. By mapping these functional data to an updated DODA phylogeny, we then explored the evolution of ʟ-DOPA 4,5-dioxygenase activity. We find that low ʟ-DOPA 4,5-dioxygenase activity is distributed across the DODA gene lineage. In this context, repeated gene duplication events within the DODA gene lineage give rise to polyphyletic occurrences of elevated ʟ-DOPA 4,5-dioxygenase activity, accompanied by convergent shifts in key functional residues and distinct genomic patterns of micro-synteny. In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated ʟ-DOPA 4,5-dioxygenase activity is consistent with recurrent specialisation to betalain synthesis in Caryophyllales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Non-geometric fluxes, quasi-Hopf twist deformations, and nonassociative quantum mechanics

We analyse the symmetries underlying nonassociative deformations of geometry in non-geometric R-flux compactifications which arise via T-duality from closed strings with constant geometric fluxes. Starting from the non-abelian Lie algebra of translations and Bopp shifts in phase space, together with a suitable cochain twist, we construct the quasi-Hopf algebra of symmetries that deforms the algebra of functions and the exterior differential calculus in the phase space description of nonassociative R-space. In this setting, nonassociativity is characterised by the associator 3-cocycle which controls non-coassociativity of the quasi-Hopf algebra. We use abelian 2-cocycle twists to construct maps between the dynamical nonassociative star product and a family of associative star products parametrized by constant momentum surfaces in phase space. We define a suitable integration on these nonassociative spaces and find that the usual cyclicity of associative noncommutative deformations is replaced by weaker notions of 2-cyclicity and 3-cyclicity. Using this star product quantization on phase space together with 3-cyclicity, we formulate a consistent version of nonassociative quantum mechanics, in which we calculate the expectation values of area and volume operators, and find coarse-graining of the string background due to the R-flux.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”

Microbes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection. While the majority of viruses and their associated impacts remain poorly characterized, a number of mechanisms by which viruses alter microbial cells and ecosystems have already been revealed. Here I outline how a comprehensive host-resolved mapping of viral sequence space will enable a thorough characterization of virus-encoded mechanisms for microbial manipulation. With soon-to-be millions of virus genomes obtained from metagenomes, one of the major challenges resides in the development of methods for high-throughput and high-resolution virus-host pairing, before multi-omics approaches can be leveraged to fully decipher virus-host dynamics in nature. Beyond novel fundamental biological knowledge, these studies will likely provide new molecular tools enabling a precise engineering of microbial cells and communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Size dependent lattice pseudosymmetry for frustrated decahedral nanoparticles

Geometric frustration—where geometry prevents simultaneous satisfaction of local interactions—generates pseudosymmetry and emergent behaviors across physical and biological systems. At the nanoscale, pseudosymmetric features in crystalline materials manifest as local strain and distortion, but how they depend on particle size and control structural stability remains unclear. Here, we report the first study of a size-dependent crossover in pseudosymmetry in multi-twinned gold nanoparticles (NPs), combining four-dimensional scanning transmission electron microscopy with nanoscale strain mapping grounded in continuum solid mechanics. Analysis of more than 20 decahedral NPs (20–55 nm) reveals pronounced heterogeneity in multiple modes of in-plane strain and displacement field in small NPs as five tetrahedral grains close the geometric gap, without extended defects. With increasing particle size, strain fields homogenize across grains and local phases shift from predominantly low-symmetry body-centered tetragonal motifs at small sizes to face-centered cubic character approaching the bulk limit. We identify a crossover particle size of ~35 nm, well below bulk, correlating with a transition from modified-Wulff shapes to pentagonal bipyramids, consistent with finite element predictions. This quantitative framework for mapping size-dependent strain and pseudosymmetry enables precise design and control of functional crystalline solids and phase transformation for catalysis, photonics, electronics, and energy storage.

Lin, Oliver [University of Illinois at Urbana-Cham↗
DOE OSTI2015

Synchronization, non-linear dynamics and low-frequency fluctuations: Analogy between spontaneous brain activity and networked single-transistor chaotic oscillators

In this paper, the topographical relationship between functional connectivity (intended as inter-regional synchronization), spectral and non-linear dynamical properties across cortical areas of the healthy human brain is considered. Based upon functional MRI acquisitions of spontaneous activity during wakeful idleness, node degree maps are determined by thresholding the temporal correlation coefficient among all voxel pairs. In addition, for individual voxel time-series, the relative amplitude of low-frequency fluctuations and the correlation dimension (D{sub 2}), determined with respect to Fourier amplitude and value distribution matched surrogate data, are measured. Across cortical areas, high node degree is associated with a shift towards lower frequency activity and, compared to surrogate data, clearer saturation to a lower correlation dimension, suggesting presence of non-linear structure. An attempt to recapitulate this relationship in a network of single-transistor oscillators is made, based on a diffusive ring (n = 90) with added long-distance links defining four extended hub regions. Similarly to the brain data, it is found that oscillators in the hub regions generate signals with larger low-frequency cycle amplitude fluctuations and clearer saturation to a lower correlation dimension compared to surrogates. The effect emerges more markedly close to criticality. The homology observed between the two systems despite profound differences in scale, coupling mechanism and dynamics appears noteworthy. These experimental results motivate further investigation into the heterogeneity of cortical non-linear dynamics in relation to connectivity and underline the ability for small networks of single-transistor oscillators to recreate collective phenomena arising in much more complex biological systems, potentially representing a future platform for modelling disease-related changes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

The sloan digital sky survey reverberation mapping project: velocity shifts of quasar emission lines

Quasar emission lines are often shifted from the systemic velocity due to various dynamical and radiative processes in the line-emitting region. The level of these velocity shifts depends both on the line species and on quasar properties. We study velocity shifts for the line peaks (not the centroids) of various narrow and broad quasar emission lines relative to systemic using a sample of 849 quasars from the Sloan Digital Sky Survey Reverberation Mapping (SDSS-RM) project. The coadded (from 32 epochs) spectra of individual quasars have sufficient signal-to-noise ratio (S/N) to measure stellar absorption lines to provide reliable systemic velocity estimates, as well as weak narrow emission lines. The large dynamic range in quasar luminosity (∼2 dex) of the sample allowed us to explore potential luminosity dependence of the velocity shifts. We derive average line peak velocity shifts as a function of quasar luminosity for different lines, and quantify their intrinsic scatter. We further quantify how well the peak velocity can be measured as a function of continuum S/N, and demonstrate that there is no systematic bias in the velocity measurements when S/N is degraded to as low as ∼3 per SDSS pixel (∼69 km s{sup −1}). Based on the observed line shifts, we provide empirical guidelines on redshift estimation from [O ii] λ3727, [O iii] λ5007, [Ne v] λ3426, Mg ii, C iii], He ii λ1640, broad Hβ, C iv, and Si iv, which are calibrated to provide unbiased systemic redshifts in the mean, but with increasing intrinsic uncertainties of 46, 56, 119, 205, 233, 242, 400, 415, and 477 km s{sup −1}, in addition to the measurement uncertainties. These results demonstrate the infeasibility of measuring quasar redshifts to better than ∼200 km s{sup −1} with only broad lines.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Herschel observations of the W3 GMC (II): Clues to the formation of clusters of high-mass stars

The W3 giant molecular cloud is a prime target for investigating the formation of high-mass stars and clusters. This second study of W3 within the HOBYS Key Program provides a comparative analysis of subfields within W3 to further constrain the processes leading to the observed structures and stellar population. Probability density functions (PDFs) and cumulative mass distributions (CMDs) were created from dust column density maps, quantified as extinction A{sub V}. The shape of the PDF, typically represented with a lognormal function at low A{sub V} “breaking” to a power-law tail at high A{sub V}, is influenced by various processes including turbulence and self-gravity. The breaks can also be identified, often more readily, in the CMDs. The PDF break from lognormal (A{sub V}(SF) ≈ 6–10 mag) appears to shift to higher A{sub V} by stellar feedback, so that high-mass star-forming regions tend to have higher PDF breaks. A second break at A{sub V}>50 mag traces structures formed or influenced by a dynamic process. Because such a process has been suggested to drive high-mass star formation in W3, this second break might then identify regions with potential for hosting high-mass stars/clusters. Stellar feedback appears to be a major mechanism driving the local evolution and state of regions within W3. A high initial star formation efficiency in a dense medium could result in a self-enhancing process, leading to more compression and favorable star formation conditions (e.g., colliding flows), a richer stellar content, and massive stars. This scenario would be compatible with the “convergent constructive feedback” model introduced in our previous Herschel study.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Mycobacterium tuberculosis (MTB) displays the remarkable ability to transition in and out of dormancy, a hallmark of the pathogen’s capacity to evade the immune system and exploit susceptible individuals. Uncovering the gene regulatory programs that underlie the phenotypic shifts in MTB during disease latency and reactivation has posed a challenge. We develop an experimental system to precisely control dissolved oxygen levels in MTB cultures in order to capture the transcriptional events that unfold as MTB transitions into and out of hypoxia-induced dormancy. Using a comprehensive genome-wide transcription factor binding map and insights from network topology analysis, we identify regulatory circuits that deterministically drive sequential transitions across six transcriptionally and functionally distinct states encompassing more than three-fifths of the MTB genome. The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multiple Mechanisms Mapped in Aryl Alkyl Ether Cleavage via Aqueous Electrocatalytic Hydrogenation over Skeletal Nickel

We present here detailed mechanistic studies of electrocatalytic hydrogenation (ECH) in aqueous solution over skeletal nickel cathodes to probe the various paths of reductive catalytic C–O bond cleavage among functionalized aryl ethers relevant to energy science. Heterogeneous catalytic hydrogenolysis of aryl ethers is important both in hydrodeoxygenation of fossil fuels and in upgrading of lignin from biomass. The presence or absence of simple functionalities such as carbonyl, hydroxyl, methyl, or methoxyl groups is known to cause dramatic shifts in reactivity and cleavage selectivity between sp3 C–O and sp2 C–O bonds. Specifically, reported hydrogenolysis studies with Ni and other catalysts have hinted at different cleavage mechanisms for the C–O ether bonds in α-keto and α-hydroxy β-O-4 type aryl ether linkages of lignin. Our new rate, selectivity, and isotopic labeling results from ECH reactions confirm that these aryl ethers undergo C–O cleavage via distinct paths. For the simple 2-phenoxy-1-phenylethane or its alcohol congener, 2-phenoxy-1-phenylethanol, the benzylic site is activated via Ni C–H insertion, followed by beta elimination of the phenoxide leaving group. But in the case of the ketone, 2-phenoxyacetophenone, the polarized carbonyl π system apparently binds directly with the electron rich Ni cathode surface without breaking the aromaticity of the neighboring phenyl ring, leading to rapid cleavage. Substituent steric and electronic perturbations across a broad range of β-O-4 type ethers create a hierarchy of cleavage rates that supports these mechanistic ideas while offering guidance to allow rational design of the catalytic method. Furthermore, on the basis of the new insights, the usage of cosolvent acetone is shown to enable control of product selectivity.

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

Distinctive mapping of strain and quantum size effects using depth-resolved photoluminescence in ZnO nanoneedles

In order to locate the spatially resolved influence of the strain, carrier localization, and quantum size effect (QSE) in tapered ZnO nanoneedles (NNs), the photoluminescence (PL) was measured as a function of the incident laser angle θ from 0{sup ∘} (normal to a surface) to 85{sup ∘}. With increasing θ, the excitation point is spatially restricted along the axis of the NNs and varies from the ZnO buffer/sapphire interface to the tips of the NNs. In this way, we identified a strain-induced blue-shift of 25.3 meV at the ZnO buffer/sapphire interface, which corresponds to a tensile strain of 0.319%. The influence of strain and the concomitant indications of carrier localization decreased as the excitation point moved to a higher location along the NNs with increasing θ whereas the QSE revealed an abrupt blue-shift near the tips of the NNs. Furthermore, time-resolved PL measurement as a function of the excitation angle was used to distinguish the strain effect from the QSE. We observed two spatially competing tendencies: (1) the decay times are influenced by the increase in the interfacial strain and (2) the decay times are influenced by the decrease in the diameter-dependent QSE near the tips of the tapered ZnO NNs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

Secondary structure of rat and human amylin across force fields

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Redshift Measurement and Spectral Classification for eBoss Galaxies with the Redmonster Software

“Cosmological redshift surveys” are experiments conducted with astronomical telescopes, imagers, and spectrographs, which map the three-dimensional structure of the universe on the largest scales. These maps are delineated by the positions of galaxies, quasars, and intergalactic hydrogen clouds. When interpreted in the context of Einstein’s theory of gravity, these maps can be used to infer the nature of the contents of the universe, including the mysterious “dark energy” that is driving the expansion of the universe to accelerate. While the directional positions of galaxies and other objects can be measured directly in images of the sky, the third dimension of their position (i.e., their distance from the Earth and the Milky Way Galaxy) must be measured by spectrographs that distribute their light as a function of frequency, enabling a measurement of their cosmological Doppler shift (or “redshift”), which serves as an observable proxy for distance. The largest cosmological redshift surveys, such as the “eBOSS” experiment of the fourth Sloan Digital Sky Survey, collect spectroscopic data for hundreds of thousands to millions of galaxies. Future experiments such as the Dark Energy Spectroscopic Instrument will in turn collect tens of millions of spectra. To be feasible, redshift measurement methods in datasets of this scale must be made with automated software. This paper describes the algorithms, astrophysical templates, and implementation of a new redshift measurement software package that is optimized to run on large numbers of spectra with relatively low signal-to-noise ratio, typical of the most ambitious current and future cosmological redshift surveys. The software is demonstrated on spectroscopic data from the eBOSS survey, with performance that meets the scientific requirements of that experiment. The software is implemented in a general framework that will allow application to spectra from the DESI project in the future.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies. Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a significant impact on the structure and function of soil microbial communities, including shifts in expression of specific metabolic pathways, such as those leading toward production of osmoprotectant compounds. This study demonstrates the application of an untargeted multi-omics approach to decipher details of the soil microbial community’s metaphenotypic response to environmental perturbations and should be applicable to studies of other complex microbial systems as well.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Transition of Site Programs and Implementation of Decommissioning Agent Oversight - 18653

San Onofre Nuclear Generating Station (SONGS), acting as the Decommissioning Agent (DA), retained its NRC License and contracted a Decommissioning General Contractor (DGC) to manage plant programs and execute the Demolition and Dismantlement (D and D) of the site. To support this effort, over twenty-one programs transitioned to the DGC, including Occupational Health and Safety, Radiation Protection, Maintenance, and Engineering. In addition, SONGS effected a cultural shift from an operating station performing work to one of overseeing it. The framework and road map for this kind of D and D model is new to the industry. This presentation shares the SONGS' experience and lessons learned associated with this transition. SONGS and the DGC entered an Agreement that established the contractual requirements and responsibilities of the parties, the Scope of Work, and the mechanisms to ensure effective transition of DA programs. As a part of defining the Scope of Work, the contract established functional areas and divisions of responsibilities divided into the roles of Governance, Oversight, Support, and Performance (GOSP). SONGS, as the site licensee, retained the Oversight Role, with exception of those areas that, as the licensee, would be considered 'non-transferrable'. Examples of those programs were Quality Assurance, Regulatory Affairs and the Employee Concerns Program. While the Company retained responsibility for those programs the DGC developed their own 'parallel' programs that the Company provided Oversight for. In 2017, SONGS completed program transition within one-year following the notice-to-proceed. The overall strategy was driven by three high-level principles: - Allow the DGC the most unfettered execution of the Scope of Work with limited interference and maximum self-governance. With the overriding principle that transitioned programs have a direct link to a basis in regulation or law. - Identify safety and compliance risks, and then bridge the transition of programs from the SONGS to the DGC such that identified risks are minimized and/or mitigated. - Allow the SONGS organization to transition from a Performance role to a primarily Oversight role as the DA. Working collaboratively with the DGC, programs were strategically grouped and sequenced for turnover. Central to the success of transition was fostering a collaborative environment with the DGC, facilitating knowledge transfer, applying schedule rigor, and keeping the team horizontally and vertically aligned to management expectations. SONGS achieved this alignment by embedding the formal process with management expectations for review and acceptance of proposed programs. SONGS' transitioned core programs to a general contractor and transition from a 'perform' organization to an 'oversight' organization. Lessons learned from this experience may benefit other nuclear generating station owners currently evaluating options for site D and D. (author)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

Clocked atom delivery to a photonic crystal waveguide

Experiments and numerical simulations are described that develop quantitative understanding of atomic motion near the surfaces of nanoscopic photonic crystal waveguides (PCWs). Ultracold atoms are delivered from a moving optical lattice into the PCW. Synchronous with the moving lattice, transmission spectra for a guided-mode probe field are recorded as functions of lattice transport time and frequency detuning of the probe beam. By way of measurements such as these, we have been able to validate quantitatively our numerical simulations, which are based upon detailed understanding of atomic trajectories that pass around and through nanoscopic regions of the PCW under the influence of optical and surface forces. The resolution for mapping atomic motion is roughly 50 nm in space and 100 ns in time. By introducing auxiliary guided-mode (GM) fields that provide spatially varying AC Stark shifts, we have, to some degree, begun to control atomic trajectories, such as to enhance the flux into the central vacuum gap of the PCW at predetermined times and with known AC Stark shifts. In conclusion, applications of these capabilities include enabling high fractional filling of optical trap sites within PCWs, calibration of optical fields within PCWs, and utilization of the time-dependent, optically dense atomic medium for novel nonlinear optical experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2017

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.

36 MATERIALS SCIENCE↗
DOE OSTI2012

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells

The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein–DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Pathways to Carbon Liberation: A Systems Approach to Understanding Carbon Transformations and Losses from Thawing Permafrost

Our objective in this project was to discover how microbial communities mediate the fate of carbon in thawing permafrost under climate change. We proposed a systems approach integrating (a) molecular microbial and viral ecology, (b) molecular organic chemistry and stable and radiocarbon isotopes, and (c) state-of-the-art modeling, along a chronosequence of permafrost thaw in subarctic Sweden. The fate of carbon (C) in thawing permafrost is an outstanding challenge of modern biogeochemistry and climate change. Permafrost C pools are large (~1700 PgC), and C dynamics of thawing permafrost complex: old C decomposes as it is liberated from thawing permafrost as CO 2 or CH 4 , with a significant fraction cycling through lake sediments, even as new C accumulates due to thaw-initiated ecological succession. Our work is allowing better prediction of the net effect of these processes. Microbes mediate C dynamics in thawing permafrost, but a mechanistic understanding of how to scale microbial population dynamics, genomic potential, and expression to ecosystem-scale processes has been missing. A key question was: What is the interplay of microbial communities and organic matter chemical structure in the decomposition/preservation of organic C across a thaw gradient? And intriguingly, what (if any) is the role of phage (viruses that infect prokaryotic cells) in mediating these processes? Viruses appear to play a large role in driving oceanic function, but these phenomena are virtually unstudied in terrestrial systems. This endeavor linking microbial and viral dynamics, organic geochemistry and trace gas production will improve models of C cycling in permafrost systems, and clarify the fate of C under future climates. Technical Approach – We conducted a study at Stordalen Mire, Sweden, along a permafrost thaw chronosequence encompassing permafrost palsas and their initial collapse stage, thawing bog sites (dominated by Sphagnum moss), fully-thawed and inundated fen sites (dominated by Eriophorum spp or Carex spp.), and lakes. Our project used cutting edge technologies in both biogeochemistry and molecular microbial ecology to advance systems biology research on microbial carbon cycling through: (a) systems-level mapping of chemical states and ages of organic matter (via FT-ICR-MS and 14 C analysis) along thaw gradients to associated microbial communities, biochemical potentials, and activities (via meta-genomics, -transcriptomics, –proteomics, and viral genomics), and to CO 2 and CH 4 fluxes; (b) experimental incubations using Quantum Dot Probing, to test key hypotheses, arising from (a), about particular microbially-driven biochemical degradation pathways; (c) bioinformatics designed to simultaneously enhance the DOE Knowledgebase, and (d) integrated ecosystem C-cycle modeling testable by soil organic chemical and microbial data. Results from this project spanned 4 categories: (i) integrative across disciplines, and disciplinarily-focused in (ii) microbiology, (iii) biogeochemistry, and (iv) modeling. In integrated understanding of the system, we answered the questions posed above, mapping resident microbes to carbon transformations to reveal a carbon-processing shift with permafrost thaw, and discovering abundant, diverse and habitat-specific viruses that appear to be impacting carbon cycling, while also relating microbial communities to modeled processes. In microbiology-specific papers, we dug into viromes, microbial community networks, and informatic methods, while also introducing a new permafrost-associated phylum and its ecogenomic context. Relevance to DOE FOA - With a focus on discovering how microbial communities mediate the fate of old and new carbon in permafrost systems with climate change, our work directly responds to the call for “–omics driven basic research on the contribution of... microbial communities to C cycling processes in terrestrial ecosystems.” We bridge all three of the focal areas of the call, including (i) “Systems biology studies”, and development of –omics approaches (ii) “to investigate microbial community functional processes”, and (iii) “for imaging and analysis of microbially-mediated carbon cycling.”

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗