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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Impact of Polymicrobial Infection on Fitness of Streptococcus gordonii In Vivo

Pathogenic microbial ecosystems are often polymicrobial, and interbacterial interactions drive emergent properties of these communities. In the oral cavity, Streptococcus gordonii is a foundational species in the development of plaque biofilms, which can contribute to periodontal disease and, after gaining access to the bloodstream, target remote sites such as heart valves. Here, we used a transposon sequencing (Tn-Seq) library of S. gordonii to identify genes that influence fitness in a murine abscess model, both as a monoinfection and as a coinfection with an oral partner species, Porphyromonas gingivalis. In the context of a monoinfection, conditionally essential genes were widely distributed among functional pathways. Coinfection with P. gingivalis almost completely changed the nature of in vivo gene essentiality. Community-dependent essential (CoDE) genes under the coinfection condition were primarily related to DNA replication, transcription, and translation, indicating that robust growth and replication are required to survive with P. gingivalis in vivo. Interestingly, a group of genes in an operon encoding streptococcal receptor polysaccharide (RPS) were associated with decreased fitness of S. gordonii in a coinfection with P. gingivalis. Individual deletion of two of these genes (SGO_2020 and SGO_2024) resulted in the loss of RPS production by S. gordonii and increased susceptibility to killing by neutrophils. P. gingivalis protected the RPS mutants by inhibiting neutrophil recruitment, degranulation, and neutrophil extracellular trap (NET) formation. These results provide insight into genes and functions that are important for S. gordonii survival in vivo and the nature of polymicrobial synergy with P. gingivalis. Furthermore, we show that RPS-mediated immune protection in S. gordonii is dispensable and detrimental in the presence of a synergistic partner species that can interfere with neutrophil killing mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli

There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (Tet R ) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of Tet R E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of Tet R E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized Tet R E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the Tet R strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗
DOE OSTI2020

Rossi-alpha Uncertainty Quantification by Analytic, Bootstrap, and Sample Methods to Inform Fitting Best Practices

The prompt neutron period (the negative reciprocal of the prompt neutron decay constant) can be estimated using the Rossi-alpha technique that is predicated on fitting Rossi alpha histograms and of interest in nuclear criticality safety and nonproliferation. The histograms are traditionally fit with a one-exponential model; however, recent work has proposed a two-exponential model to account for reflector induced phenomenon. Until recently, the uncertainty quantification for either model was inadequate (inaccurate and demanded large measurement times). Measurement uncertainty quantification by sample and analytic methods was developed and validated in Ref. The purpose of this transaction is to (i) validate a new bootstrap method by comparing bin-by-bin error bar estimates and (ii) demonstrate how to choose bin widths and reset times to optimize precision and accuracy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Hybrid time–frequency domain dual-probe coherent anti-Stokes Raman scattering for simultaneous temperature and pressure measurements in compressible flows via spectral fitting

We demonstrate a hybrid time–frequency spectroscopic method for simultaneous temperature/pressure measurements in nonreacting compressible flows with known gas composition. Hybrid femtosecond–picosecond, pure-rotational coherent anti-Stokes Raman scattering (CARS), with two independent, time-delayed probe pulses, is deployed for single-laser-shot measurements of temperature and pressure profiles along an ∼ <#comment/> 5 -mm line. The theory of dual-probe CARS is presented, along with a discussion of the iterative fitting of experimental spectra. Temperature is obtained from spectra acquired with an early, near-collision-free probe time delay ( τ <#comment/> 1 = 0 p s ) and pressure from spectra obtained at probe delays of τ <#comment/> 2 = 150 − <#comment/> 1000 p s , where collisions significantly impact the spectral profile. Unique solutions for temperature and pressure are obtained by iteratively fitting the two spectra to account for small collisional effects observed for the near zero probe delay spectrum. A dual-probe pure-rotational CARS system, in a 1D line-imaging configuration, is developed to demonstrate effectively the simultaneous temperature and pressure profiles recorded along the axial centerline of a highly underexpanded jet. The underexpanded air jet permits evaluation of this hybrid time–frequency domain approach for temperature and pressure measurements across a wide range of low-temperature–low-pressure conditions of interest in supersonic ground-test facilities. Single-laser-shot measurement precisions in both quantities and pressure measurement accuracy are systematically evaluated in the quiet zone upstream of the Mach disk. Precise thermometry approaching 1%−2% is observed in regions of high CARS signal-to-noise ratios. Pressure measurements are optimized at probe time delays where the ratio of the late probe delay to the Raman lifetime exceeds four ( τ <#comment/> 2 / τ <#comment/> R > <#comment/> 4 ). The impact of low-temperature Raman linewidths on CARS pressure measurements is evaluated, and comparisons of CARS pressures obtained with our recent low-temperature pure-rotational Raman linewidth data and extrapolated high-temperature Q -branch linewidths are presented. Considering all measurements with τ <#comment/> 2 / τ <#comment/> R ≥ <#comment/> 4.0 , measured pressures were on average 7.9% of the computed isentropic values with average shot-to-shot deviations representing a combination of instrument noise and fluid fluctuations of 5.0%.

Retter, Jonathan E.↗
DOE OSTI2023

Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Abstract The Escherichia coli genome‐scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision–recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene‐protein‐reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high‐throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

AK112: Full Waveform Inversion Tomography of Alaska Improves Waveform Fits While Imaging Crustal, Mantle, and Slab Structure

We report a full waveform inversion tomography model of Alaska and the surrounding regions, inferring radially anisotropic shear and isotropic compressional wavespeeds by fitting complete waveforms from 120 regional earthquakes. Our multiscale approach inverted time–frequency phase misfits (maximum period of 100 s), starting with a minimum period of 40 s and ending at 20 s in 7 stages and 112 total iterations. The model (AK112) was evaluated by computing the misfits for 36 independent validation events. We find that misfit reductions were large and equal (∼55%) for both the inversion and validation data sets, providing confidence in the model. AK112 also provides much better waveform fits compared to other reported models for the region, including an isotropic version of itself, highlighting the importance of anisotropy. The model resolves known crustal, upper mantle, and slab structure to depths of 100 km with new detail: sedimentary basins in the Alaskan Shelf, Cook Inlet, and Colville basins, among others; discontinuous lithospheric structure across major terrane boundaries; and subducting slab geometry and back‐arc volcanic sources. In addition to tectonic interpretations, the model enables full waveform simulations for long‐period earthquake ground motions and source characterization (e.g., moment tensor and finite‐fault inversion).

Rodgers, Arthur [Lawrence Livermore National Labor↗
DOE OSTI2022

University of Missouri Research Reactor (MURR) Design Demonstration Element End Fitting Structural Rigidity Analysis

The primary objective of this work is to assess the extent to which the stiffness (measured by means of maximum displacement) of the end fittings in the DDE contributes to the stiffness of the entire element, and how it compares to the equivalent stiffness of the end fittings in the LEU element. Structural analysis of both the LEU element and the DDE were performed using COMSOL 5.3a finite element software. Supporting combs are used on the leading and trailing edges of fuel plates for both the LEU element and the DDE. Therefore, simulations with and without combs are performed as two bounding boundary conditions on the leading edge of the fuel plates. Three types of loads are analyzed in this work: the hydraulic load due to the channel flow disparity-induced pressure differential, the thermal load due to the thermal expansion of the fuel plates, and a point load equal in magnitude to the LEU element’s weight.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Fitting $\overline{\nu}$ for minor Pu isotopes

After successful fitting of prompt $\overline{\nu}$ for 235 U, 238 U, and 239 Pu(n,f) using CGMF, we will move on to the minor plutonium isotopes. Minor isotopes pose a greater challenge both because there is less data available and we do not, by default, have parametrizations in CGMF already. To mitigate these challenges— and provide consistency within CGMF—we will take a stepped approach to the optimization. Continuing from the 239 Pu work, we will then fit 241 Pu(n,f) $\overline{\nu}$, where there is also a number of experimental measurements, keeping consistency between the parameters that are included in the calculation for 239 Pu and 241 Pu. With these parametrizations settled, we can consistently optimize 240 Pu(n,f) $\overline{\nu}$. Following that step, we will move on to 242 Pu(n,f) (and increasing neutron number) and 238 Pu(n,f) (and decreasing neutron number). By including the fissioning systems in this manner, we should be able to minimize the unknown parameters in CGMF. We will possibly also be able to develop systematics for the CGMF input parameters along the Pu isotopic chain. This work can serve as a guide to broadening the reactions available in CGMF. In this short report, we first give an example of how we have updated CGMF to include 240 Pu(n,f) and 242 Pu(n,f), keeping consistency with the current 239 Pu and 241 Pu calculations, but without rigorous optimization (Sec. 2). Then, we will shown in Section 3 what experimental data exist for the various isotopes to provide some insight into why 241 Pu and 239 Pu are used as anchor points.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2023

Fitting $\overline{ν}$ for Minor Pu Isotopes

After successful fitting of prompt ν for 235 U, 238 U, and 239 Pu(n,f) using CGMF, we have moved on to the minor plutonium isotopes. Minor isotopes pose a greater challenge both because there is less data available and we do not, by default, have parametrizations in CGMF already. Initially, we had planned to mitigate these challenges—and provide consistency within CGMF—by taking a stepped approach to the optimization. Continuing from the 239 Pu work, we would then fit 241Pu(n,f) $\overline{ν}$, where there is also a number of experimental measurements, keeping consistency between the parameters that are included in the calculation for 239 Pu and 241 Pu. With these parametrizations settled, we could consistently optimize 240 Pu(n,f) $\overline{ν}$. Following that step, we would move on to 242 Pu(n,f) (and increasing neutron number) and 238 Pu(n,f) (and decreasing neutron number). By including the fissioning systems in this manner, we should be able to minimize the unknown parameters in CGMF. We were also able to develop systematics for the CGMF input parameters along the Pu isotopic chain. However, after studies in the beginning of FY23, where we found reasonable agreement between CGMF and experimental prompt neutron multiplicities for 238−242 Pu, using a compound mass dependent parametrization from, and from discussions with I. Stetcu and P. Talou, we instead performed the evaluation of all five isotopes simultaneously. For all parameters in CGMF, they are either the same for each compound nucleus, or have a dependence on the compound mass. The details of these updates are given in. This report builds upon those details. In this short report, we first give an example of how we have updated CGMF to include 240 Pu(n,f) and 242 Pu(n,f), keeping consistency with the current 239 Pu and 241 Pu calculations, but without rigorous optimization (Sec. 2). Then, we will show in Section 3 what experimental data exist for the various isotopes to provide some insight into why 241 Pu and 239 Pu are used as anchor points. The evaluation is detailed in Section 4, and the comparison between CGMF calculations using the evaluated parameters and other prompt observables besides average neutron multiplicity are discussed in Section 2.2. Finally, we present conclusions and future work in Section 5.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2024

The Gene Fitness Atlas: A Roadmap for Predicting Evolution

We developed a novel, high-throughput microfluidic device design containing “interaction zones” where progeny cell lines compete against each other allowing for accurate analysis of bacterial cell fitness. The goal of the project was to use the device for two applications: 1) gene knockout screening and 2) antibiotic resistance screening. The microfluidic platform was fabricated using photolithography and soft lithography in polydimethylsiloxane (PDMS). E.coli Keio mutants and fluorescent wildtype parent were chosen for the study. Cells were grown overnight and their loading into the devices and seeding in mother machines was optimized. For mutant screening, the least fit mutant and wildtype parent were cultured individually and then added to the microfluidic device. The mother machines which were seeded with mutant and wildtype were imaged through time lapse microscopy and the growth of cells was observed. For antibiotic screening, wildtype E.coli cells which were grown overnight were added to the device and washed with media containing the antibiotic ampicillin. The growth pattern in presence and absence of ampicillin was observed through time lapse microscopy. It was observed that over a period of four hours, both the mutant and the wildtype divided in the mother machine and pushed daughter cells out into the interaction zone. In case of the antibiotic screening experiment, the fluorescent wildtype divided both in the absence and presence of sublethal concentration of ampicillin. This study is a proof of concept demonstration of high- throughput single cell analysis of cells using a novel microfluidics device.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Light Output Fitting Software

Light output response of scintillators is crucial to the utilization of organic scintillators as effective tools in radiation detection and measurement. While the response is a continuous distribution, the light output corresponding to the maximum energy deposition is crucial in effectively understanding and simulating a detector. There are a variety of fits derived in literature that will vary for every detector material. The Light Output Response Fitter, or LORF Program is a python script designed to easily and quickly compute and plot fits for a variety of scintillator light output models. It includes a stopping power library constructed from SRIM including Organic Glass, EJ309, EJ301, Stilbene, EJ276, and their deuterated counterparts by default, with the ability for the user to add custom stopping power libraries. The user is also capable of importing the python package and utilizing its in-built functions as appropriate. Uses for this capability include plotting and computing a model with known parameters.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

The Dependence of the Type Ia Supernova Host Bias on Observation or Fitting Technique

More luminous Type Ia supernovae prefer less massive hosts and regions of higher star formation. This correlation is inverted during width–color–luminosity light-curve standardization resulting in step-like biases of distance measurements with respect to host properties. Using the PMAS/PPak Integral-field Supernovahosts COmpilation (PISCO) supernova host sample and Sloan Digital Sky Survey, Galaxy Evolution Explorer, and Two Micron All Sky Survey photometry, we compare host stellar mass and specific star-formation rate (sSFR) from different observation methods, including local versus global, and fitting techniques to measure their impact on the host step biases. Mass-step measurements for all our mass samples are consistent within a 1σ significance from –0.03 ± 0.02 mag to –0.04 ± 0.02 mag. Including or excluding UV information had no effect on measured mass-step size or location. sSFR step sizes are more significant than mass-step measurements and varied from 0.05 ± 0.03 mag (Hα) and 0.06 ± 0.02 mag (UV) for a 51 host sample. The sSFR step location is influenced by the mass sample used to normalize star formation and by sSFR tracer choice. The step size is reduced to 0.04 ± 0.03 mag when using all available 73 hosts with Hα measurements. This 73 PISCO host subsample overall lacked a clear step signal, but here we are searching for whether different choices of mass or sSFR estimation can create a step signal. We find no evidence that different observation or fitting techniques choices can create a distance measurement step in either mass or sSFR.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1967

Portable fixture facilitates pressure testing of instrumentation fittings

Portable fixture facilitates pressure testing to detect possible leaks in instrumentation fittings mounted on tank bulkheads. It uses a vacuum cup which seals a pressure regulator adapter around one side of the fitting to be pressure tested. Leakage is detected with a gas sniffer.

Olson, G. A.↗
NASA NTRS1967

Computer program performs rectangular fitting stress analysis

Computer program simulates specific bulkhead fittings by subjecting the desired geometry configuration to a membrane force, an external force, an external moment, an external tank pressure, or any combination of the above. This program generates a general model of bulkhead fittings for the Saturn booster.

Bertrand, A. R.↗
NASA NTRS1972

An elastic analysis of stresses in a uniaxially loaded sheet containing an interference-fit bolt

The stresses in a sheet with an interference-fit bolt have been calculated for two sheet-bolt interface conditions: a frictionless interface and a fixed (no-slip) interface. The stress distributions were calculated for various combinations of sheet and bolt moduli. The results show that for repeated loading the local stress range is significantly smaller if an interference bolt is used instead of a loosely fitting one. This reduction in local stress range is more pronounced when the ratio of bolt modulus to sheet modulus is large. The analysis also indicates that currently used standard values of interference cause yielding in the sheet.

Crews, J. H., Jr.↗