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

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At least 1,603 records · Page 89
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Natural variation in the C‐repeat binding factor cold response pathway correlates with local adaptation of Arabidopsis ecotypes

Summary The natural range of Arabidopsis thaliana (Arabidopsis) encompasses geographical regions that have greatly differing local climates, including harshness of winter temperatures. A question thus raised is whether differences in freezing tolerance might contribute to local adaptation in Arabidopsis. Consistent with this possibility is that Arabidopsis accessions differ in freezing tolerance and that those collected from colder northern latitudes are generally more tolerant to freezing than those collected from warmer southern latitudes. Moreover, recent studies with Arabidopsis genotypes collected from sites in Sweden ( SW ) and Italy ( IT ) have established that the two accessions are locally adapted, that the SW ecotype is more tolerant of freezing than the IT ecotype, and that genetic differences between the two ecotypes that condition local adaptation and freezing tolerance map to a region that includes the C‐repeat binding factor ( CBF ) locus. The CBF locus includes three genes – CBF 1 , CBF 2 and CBF 3 – that are induced by low temperature and encode transcription factors that regulate a group of more than 100 genes, the CBF regulon, which impart freezing tolerance. Here we show that cold induction of most CBF regulon genes is lower in IT plants compared with SW plants, and that this is due to the IT CBF 2 gene encoding a non‐functional CBF 2 protein. The non‐functional IT CBF 2 protein also contributes to the lower freezing tolerance of the IT plants compared with the SW plants. Taken together, studies on the SW and IT ecotypes provide evidence that natural variation in the CBF pathway has contributed to adaptive evolution in these Arabidopsis populations.

Gehan, Malia A.↗
DOE OSTI2021

Data-Driven Forgetting and Discount Factors for Vehicle Speed Forecasting in Ecological Adaptive Cruise Control

Abstract This paper investigates temporal correlations in human driving behavior using real-world driving to improve speed forecasting accuracy. These correlations can point to a measurement weighting function with two parameters: a forgetting factor for past speed measurements that the vehicle itself drove with, and a discount factor for the speeds of vehicles ahead based on information from vehicle-to-vehicle communication. The developed weighting approach is applied to a vehicle speed predictor using polynomial regression, a prediction method well-known in the literature. The performance of the developed approach is then assessed in both real-world and simulated traffic scenarios for accuracy and robustness. The new weighting method is applied to an ecological adaptive cruise control system, and its influence is analyzed on the prediction accuracy and the performance of the ecological adaptive cruise control in an electric vehicle powertrain model. The results show that the new prediction method improves energy saving from the eco-driving by up to 4.7% compared to a baseline least-square-based polynomial regression. This is a 10% improvement over the constant speed/acceleration model, a conventional speed predictor.

Automation & Control Systems↗
DOE OSTI2016

Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach

A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies.

42 ENGINEERING↗
DOE OSTI2015

SU-C-304-06: Determination of Intermediate Correction Factors for Three Dosimeters in Small Composite Photon Fields Used in Robotic Radiosurgery

Purpose: To calculate using Monte-Carlo the intermediate and total correction factors (CFs) for two microchambers and a plastic scintillator for composite fields delivered by the CyberKnife system. Methods: A linac model was created in BEAMnrc by matching percentage depth dose (PDD) curves and output factors (OFs) measured using an A16 microchamber with Monte Carlo calculations performed in egs-chamber to explicitly model detector response. Intermediate CFs were determined for the A16 and A26 microchambers and the W1 plastic scintillator in fourteen different composite fields inside a solid water phantom. Seven of these fields used a 5 mm diameter collimator; the remaining fields employed a 7.5 mm collimator but were otherwise identical to the first seven. Intermediate CFs are reported relative to the respective CF for a 60 mm collimator (800 mm source to detector distance and 100 mm depth in water). Results: For microchambers in composite fields, the intermediate CFs that account for detector density and volume were the largest contributors to total CFs. The total CFs for the A26 were larger than those for the A16, especially for the 5 mm cone (1.227±0.003 to 1.144±0.004 versus 1.142±0.003 to 1.099±0.004), due to the A26’s larger active volume (0.015 cc) relative to the A16 (0.007 cc), despite the A26 using similar wall and electrode material. The W1 total and intermediate CFs are closer to unity, due to its smaller active volume and near water-equivalent composition, however, 3–4% detector volume corrections are required for 5 mm collimator fields. In fields using the 7.5 mm collimator, the correction is nearly eliminated for the W1 except for a non-isocentric field. Conclusion: Large and variable CFs are required for microchambers in small composite fields primarily due to density and volume effects. Corrections are reduced but not eliminated for a plastic scintillator in the same fields.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-98: An Analysis of TG-51 Electron Beam Calibration Correction Factor Uncertainty

Purpose: To analyze the uncertainty of the TG-51 electron beam calibration correction factors for farmer type ion chambers currently used by institutions visited by IROC Houston. Methods: TG-51 calibration data were collected from 181 institutions visited by IROC Houston physicists for 1174 and 197 distinct electron beams from modern Varian and Elekta accelerators, respectively. Data collected and analyzed included ion chamber make and model, nominal energy, N{sub D,w}, I{sub 50}, R{sub 50}, k’R{sub 50}, d{sub ref}, P{sub gr} and pdd(d{sub ref}). k’R{sub 50} data for parallel plate chambers were excluded from the analysis. Results: Unlike photon beams, electron nominal energy is a poor indicator of the actual energy as evidenced by the range of R{sub 50} values for each electron beam energy (6–22MeV). The large range in R{sub 50} values resulted k’R{sub 50} values with a small standard deviation but large range between maximum value used and minimum value (0.001–0.029) used for a specific Varian nominal energy. Varian data showed more variability in k’R{sub 50} values than the Elekta data (0.001–0.014). Using the observed range of R{sub 50} values, the maximum spread in k’R{sub 50} values was determined by IROC Houston and compared to the spread of k’R{sub 50} values used in the community. For Elekta linacs the spreads were equivalent, but for Varian energies of 6 to 16MeV, the community spread was 2 to 6 times larger. Community P{sub gr} values had a much larger range of values for 6 and 9 MeV values than predicted. The range in Varian pdd(d{sub ref} ) used by the community for low energies was large, (1.4–4.9 percent), when it should have been very close to unity. Exradin, PTW Roos and PTW farmer chambers N{sub D,w} values showed the largest spread, ≥11 percent. Conclusion: While the vast majority of electron beam calibration correction factors used are accurate, there is a surprising spread in some of the values used.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2015

SU-E-T-577: Obliquity Factor and Surface Dose in Proton Beam Therapy

Purpose: The advantage of lower skin dose in proton beam may be diminished creating radiation related sequalae usually seen with photon and electron beams. This study evaluates the surface dose as a complex function of beam parameters but more importantly the effect of beam angle. Methods: Surface dose in proton beam depends on the beam energy, source to surface distance, the air gap between snout and surface, field size, material thickness in front of surface, atomic number of the medium, beam angle and type of nozzle (ie double scattering, (DS), uniform scanning (US) or pencil beam scanning (PBS). Obliquity factor (OF) is defined as ratio of surface dose in 0° to beam angle Θ. Measurements were made in water phantom at various beam angles using very small microdiamond that has shown favorable beam characteristics for high, medium and low proton energy. Depth dose measurements were performed in the central axis of the beam in each respective gantry angle. Results: It is observed that surface dose is energy dependent but more predominantly on the SOBP. It is found that as SSD increases, surface dose decreases. In general, SSD, and air gap has limited impact in clinical proton range. High energy has higher surface dose and so the beam angle. The OF rises with beam angle. Compared to OF of 1.0 at 0° beam angle, the value is 1.5, 1.6, 1,7 for small, medium and large range respectively for 60 degree angle. Conclusion: It is advised that just like range and SOBP, surface dose should be clearly understood and a method to reduce the surface dose should be employed. Obliquity factor is a critical parameter that should be accounted in proton beam therapy and a perpendicular beam should be used to reduce surface dose.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2016

SU-F-J-108: TMR Correction Factor Based Online Adaptive Radiotherapy for Stereotactic Radiosurgery (SRS) of L-Spine Tumors Using Cone Beam CT

Purpose: To investigate the feasibility of using TMR ratio correction factors for a fast online adaptive plan to compensate for anatomical changes in stereotactic radiosurgery (SRS) of L-spine tumors. Methods: Three coplanar treatment plans were made for 11 patients: Uniform (9 IMRT beams equally distributed around the patient); Posterior (IMRT with 9 posterior beams every 20 degree) and VMAT (2 360° arcs). For each patient, the external body and bowel gas were contoured on the planning CT and pre-treatment CBCT. After registering CBCT and the planning CT by aligning to the tumor, the CBCT contours were transferred to the planning CT. To estimate the actual delivered dose while considering patient’s anatomy of the treatment day, a hybrid CT was created by overriding densities in planning CT using the differences between CT and CBCT external and bowel gas contours. Correction factors (CF) were calculated using the effective depth information obtained from the planning system using the hybrid CT: CF = TMR (delivery)/TMR (planning). The adaptive plan was generated by multiplying the planned Monitor Units with the CFs. Results: The mean absolute difference (MAD) in V16Gy of the target between planned and estimated delivery with and without TMR correction was 0.8 ± 0.7% vs. 2.4 ± 1.3% for Uniform and 1.0 ± 0.9% vs. 2.6 ± 1.3% for VMAT plans(p<0.05), respectively. For V12Gy of cauda-equina with and without TMR correction, MAD was 0.24 ± 0.19% vs. 1.2 ± 1.02% for Uniform and 0.23 ± 0.20% vs. 0.78 ± 0.79% for VMAT plans(p<0.05), respectively. The differences between adaptive and original plans were not significant for posterior plans. Conclusion: The online adaptive strategy using TMR ratios and pre-treatment CBCT information was feasible strategy to compensate for anatomical changes for the patients treated for L-spine tumors, particularly for equally spaced IMRT and VMAT plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-TeP1-03: Beam Quality Correction Factors for Linear Accelerator with and Without Flattening Filter

Purpose: The impact of removing the flattening filter on absolute dosimetry based on IAEA’s TPR-398 and AAPM’s TG-51 was investigated in this study using Monte Carlo simulations. Methods: The EGSnrc software package was used for all Monte Carlo simulations performed in this work. Five different ionization chambers and nine linear accelerator heads have been modeled according to technical drawings. To generate a flattening filter free radiation field the flattening filter was replaced by a 2 mm thick aluminum layer. Dose calculation in a water phantom were performed to calculate the beam quality correction factor k{sub Q} as a function of the beam quality specifiers %dd(10){sub x}, TPR{sub 20,10} and mean photon and electron energies at the point of measurement in photon fields with (WFF) and without flattening filter (FFF). Results: The beam quality correction factor as a function of %dd(10){sub x} differs systematically between FFF and WFF beams for all investigated ionization chambers. The largest difference of 1.8% was observed for the largest investigated Farmer-type ionization chamber with a sensitive volume of 0.69 cm{sup 3}. For ionization chambers with a smaller nominal sensitive volume (0.015 – 0.3 cm{sup 3}) the deviation was less than 0.4% between WFF and FFF beams for %dd(10){sub x} > 62%. The specifier TPR{sub 20,10} revealed only a good correlation between WFF and FFF beams (< 0.3%) for low energies. Conclusion: The results confirm that %dd(10){sub x} is a suitable beam quality specifier for FFF beams with an acceptable bias. The deviation depends on the volume of the ionization chamber. Using %dd(10){sub x} to predict k{sub Q} for a large volume chamber in a FFF photon field may lead to not acceptable errors according to the results of this study. This bias may be caused by the volume effect due to the inhomogeneous photon fields of FFF linear accelerators.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-TeP3-02: Determination of Geometry-Specific Backscatter Factors for Radiobiology Studies

Purpose: Radiation biology research relies on an accurate radiation dose delivered to the biological target. Large field irradiations in a cabinet irradiator may use the AAPM TG-61 protocol. This relies on an air-kerma measurement and conversion to absorbed dose to water (Dw) on the surface of a water phantom using provided backscatter factors. Cell or small animal studies differ significantly from this reference geometry. This study aims to determine the impact of the lack of full scatter conditions in four representative geometries that may be used in radiobiology studies. Methods: MCNP6 was used to model the Dw on the surface of a full scatter phantom in a validated orthovoltage x-ray reference beam. Dw in a cylindrical mouse, 100 mm Petri dish, 6-well and 96-well cell culture dishes was simulated and compared to this full scatter geometry. A reference dose rate was measured using the TG-61 protocol in a cabinet irradiator. This nominal dose rate was used to irradiate TLDs in each phantom to a given dose. Doses were obtained based on TLDs calibrated in a NIST-traceable beam. Results: Compared to the full scattering conditions, the simulated dose to water in the representative geometries were found to be underestimated by 12-26%. The discrepancy was smallest with the cylindrical mouse geometry, which most closely approximates adequate lateral- and backscatter. TLDs irradiated in the mouse and petri dish phantoms using the TG-61 determined dose rate showed similarly lower values of Dw. When corrected for this discrepancy, they agreed with the predicted Dw within 5%. Conclusion: Using the TG-61 in-air protocol and given backscatter factors to determine a reference dose rate in a biological irradiator may not be appropriate given the difference in scattering conditions between irradiation and calibration. Without accounting for this, the dose rate is overestimated and is dependent on irradiation geometry.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-H-207A-01: Development of Conversion Factors to Account for Different CTDI Phantom Setups On a Wide-Beam CT Scanner

Purpose: A fundamental measure performed during an annual physics CT evaluation confirms that system displayed CTDIvol nearly matches the independently measured value in phantom. For wide-beam (z-direction) CT scanners, AAPM Report 111 defined an ideal measurement method; however, the method often lacks practicality. The purpose of this preliminary study is to develop a set of conversion factors for a wide-beam CT scanner, relating the CTDIvol measured with a conventional setup (single CTDI phantom) versus the AAPM Report 111 approach (three abutting CTDI phantoms). Methods: For both the body CTDI and head CTDI, two acquisition setups were used: A) conventional single phantom and B) triple phantom. Of primary concern were the larger nominal beam widths for which a standard CTDI phantom setup would not provide adequate scatter conditions. Nominal beam width (160 or 120 mm) and kVp (100, 120, 140) were modulated based on the underlying clinical protocol. Exposure measurements were taken using a CT pencil ion chamber in the center and 12 o’clock position, and CTDIvol was calculated with ‘nT’ limited to 100 mm. A conversion factor (CF) was calculated as the ratio of CTDIvol measured in setup B versus setup A. Results: For body CTDI, the CF ranged from 1.04 up to 1.10, indicating a 4–10% difference between usage of one and three phantoms. For a nominal beam width of 160 mm, the CF did vary with selected kVp. For head CTDI at nominal beam widths of 120 and 160 mm, the CF was 1.00 and 1.05, respectively, independent of the kVp used (100, 120, and 140). Conclusions: A clear understanding of the manufacturer method of estimating the displayed CTDIvol is important when interpreting annual test results, as the acquisition setup may lead to an error of up to 10%. With appropriately defined CF, single phantom use is feasible.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

TH-AB-BRA-03: Backscatter Dose Factors Re-Evaluated for Inhomogeneities in the Presence of a 1.5 T Magnetic Field Using the GPUMCD Monte Carlo Algorithm

Purpose: To quantify the backscatter dose factors near the interfaces for clinically relevant high atomic number materials using GPUMCD for the Elekta MRI Linac. Methods: Backscatter dose factors (BSDF) were calculated as the ratio of the dose with and without the presence of the heterogeneity. The BSDF’s were calculated either in the absence or presence of an orthogonal 1.5 T magnetic field. Doses were scored in small voxels of side 1 mm in a water phantom with dimensions of 20×20×20 cm using GPUMCD (Elekta). The minimum uncertainty in dose calculations was kept to 0.5%. A slab of thickness 2 cm, representing the inhomogeneity, was placed inside the phantom with variable position from the surface of the phantom. The slab was filled with either bone, aluminum, titanium, stainless steel, or dental amalgam. The phantom was irradiated using particles sampled from a histogram which represented the true MRI Linac spectrum. Results: With the application of the 1.5 T magnetic field (B-On), all of the BSDF’s were reduced by at least 8% compared to the no magnetic field (B-Off) cases. For the B-Off case, the BSDF decreases exponentially with the upstream distance away from the interface. With B-On, the BSDF decreases exponentially for titanium, SS, and amalgam. However, it remains constant for Aluminum. In the case of bone, the BSDF increases up to a distance of 4 mm away from the interface in the presence of the magnetic field. Conclusion: The BSDF does not depend upon the thickness of the homogeneous material above the inhomogeneity for either the B-Off or B-On cases. For all the materials investigated, the BSDF is lower at the interface for the B-On case. The exponential fall-off of the BSDF away from the interface is not valid for all the materials when the magnetic field is turned ON. Funding support for this research was provided by Elekta.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. Furthermore, these comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The military gear microbiome: risk factors surrounding the warfighter

ABSTRACT Combat extremity wounds are highly susceptible to contamination from surrounding environmental material. This bioburden could be partially transferred from materials in immediate proximity to the wound, including fragments of the uniform and gear. However, the assessment of the microbial bioburden present on military gear during operational conditions of deployment or training is relatively unexplored. Opportunistic pathogens that can survive on gear represent risk factors for infection following injury, especially following combat blasts, where fibers and other materials are embedded in wounded tissue. We utilized 16S rRNA sequencing to assess the microbiome composition of different military gear types (boot, trouser, coat, and canteen) from two operational environments (training in Hawai’i and deployed in Indonesia) across time (days 0 and 14). We found that microbiome diversity, stability, and composition were dependent on gear type, training location, and sampling timepoint. At day 14, species diversity was significantly higher in Hawai’i samples compared to Indonesia samples for boot, coat, and trouser swabs. In addition, we observed the presence of potential microbial risk factors, as opportunistic pathogenic species, such as Acinetobacter , Pseudomonas, and Staphylococcus , were found to be present in all sample types and in both study sites. These study outcomes will be used to guide the design of antimicrobial materials and uniforms and for infection control efforts following combat blasts and other injuries, thereby improving treatment guidance during military training and deployment. IMPORTANCE Combat extremity wounds are vulnerable to contamination from environments of proximity to the warfighter, leading to potential detrimental outcomes such as infection and delayed wound healing. Therefore, microbial surveillance of such environments is necessary to aid the advancement of military safety and preparedness through clinical diagnostics, treatment protocols, and uniform material design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Hybridization capture sequencing for Vibrio spp. and associated virulence factors

ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

Microbiology↗
DOE OSTI2022

The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune

Wood-decaying fungi of the class Agaricomycetes (phylum Basidiomycota) are saprotrophs that break down lignocellulose and play an important role in nutrient recycling. They secrete a wide range of extracellular plant cell wall degrading enzymes that break down cellulose, hemicellulose, and lignin, the main building blocks of plant biomass. Although the production of these enzymes is regulated mainly at the transcriptional level, no activating regulators have been identified in any wood-decaying fungus in the class Agaricomycetes. We studied the regulation of cellulase expression in the wood-decaying fungus Schizophyllum commune. Comparative genomics and transcriptomics on two wild isolates revealed a Zn 2 Cys 6 -type transcription factor gene (roc1) that was highly upregulated during growth on cellulose, compared to glucose. It is only conserved in the class Agaricomycetes. A roc1 knockout strain showed an inability to grow on medium with cellulose as sole carbon source, and growth on cellobiose and xylan (other components of wood) was inhibited. Growth on non-wood-related carbon sources was not inhibited. Cellulase gene expression and enzyme activity were reduced in the Δroc1 strain. ChIP-Seq identified 1474 binding sites of the Roc1 transcription factor. Promoters of genes involved in lignocellulose degradation were enriched with these binding sites, especially those of LPMO (lytic polysaccharide monooxygenase) CAZymes, indicating that Roc1 directly regulates these genes. A conserved motif was identified as the binding site of Roc1, which was confirmed by a functional promoter analysis. Together, Roc1 is a key regulator of cellulose degradation and the first identified in wood-decaying fungi in the phylum Basidiomycota.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Physiological roles of an Acinetobacter -specific σ factor

ABSTRACT The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF “SigAb”; however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE-like ECFs. We combine promoter mutagenesis, motif scanning, and chromatin immunoprecipitation-sequencing (ChIP-seq) to define the direct SigAb regulon, which consists of genes encoding SigAb itself, the stringent response mediator, RelA, and the uncharacterized small RNA, “SabS.” However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper-induced SigAb-dependent transcription. Furthermore, we found that two uncharacterized genes in the sigAb operon, “ aabA ” and “ aabB ,” have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb , aabA , and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii . IMPORTANCE Acinetobacter baumannii is a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding how A. baumannii senses and responds to stress may uncover novel routes to treat infections. Here, we examine how the Acinetobacter -specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically relevant contexts.

Bacon, Emily E. (ORCID:0000000180907689)↗
DOE OSTI2015

POLARCALC: A program for calculating the linear-polarization factor using an area detector

A graphical interface program has been developed to determine the linear-polarization factor of a monochromatic X-ray beam when analyzing scattering from an amorphous object. An area coordinate detector is used in measurements. The change in intensity over the azimuthal angle at a constant diffraction angle is interpolated by a theoretical cosine dependence, which contains the polarization factor.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Calculation of the Geometric Factor in a New Experiment Aimed at Studying Radiative Neutron Decay

A new experiment aimed at studying radiative neutron decay is proposed. The respective experimental procedure reduces to measuring the time spectra of triple coincidences of the emitted photon, beta electron, and recoil proton along with the spectrum of double coincidences of ordinary decay products. By means of this procedure, we were able to measure for the first time the branching ratio for radiative neutron decay, BR = (3.2 ± 1.6) × 10{sup −3} (at a confidence level of C.L. = 99.7%, the photon energy being in excess of 35 keV) in 2005 at our old setup. The average value of this branching ratio was greater by a factor of 1.5 than its theoretical counterpart calculated on the basis of the Standard Model. However, we cannot state that we have seen a deviation fromthe StandardModel prediction since the experimental error was quite large in that experiment. The present study is devoted to implementing, by means of the popular Geant4 code package, a computer analog of the respective experiment at a new facility. Our calculations reveal that the resulting geometri©factor values make it possible to a accumulate, in a live experiment, a data sample sufficient for measuring the above branching ratio to a precision of a few percent.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗