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DOE OSTI2023

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii ) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae . Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

Conversion↗

DOE OSTI2018

FRMAC Laboratory Analysis RadResponder Gap Analysis and Web Portal Enhancements

The Federal Radiological Monitoring and Assessment Center (FRMAC) relies on accurate and defensible analytical laboratory data to support its mission. FRMAC Laboratory Analysis personnel are responsible for (1) receiving samples, (2) managing samples, and (3) providing data quality assurance. Currently, the RadResponder software application does not meet all these needs. With some modifications, RadResponder could meet the needs for sample receiving functions, but it does not meet the needs of sample management and data quality assurance functions. The FRMAC Laboratory Analysis team has discussed and reviewed the following options moving forward: Option 1: Make minor revisions to RadResponder to improve sample receiving capability, purchase and configure a commercial laboratory information management system (LIMS) to perform sample management and data quality assurance, and build an interface between RadResponder and the commercial-off-the-shelf LIMS. Option 2: Make major revisions to RadResponder for all FRMAC Laboratory Analysis functions to support required sample management and data quality assurance activities. Option 3: Create a custom-built LIMS system to interface with RadResponder. Note: All three options will require the development of a Laboratory Analysis web portal and will require funding for ongoing maintenance and training. The FRMAC Laboratory Analysis team highly recommends Option 1 as the best and most efficient path forward. Commercial-off-the-shelf LIMS products have been proven successful in the laboratory community for decades. Option 1 leverages these proven technologies and takes advantage of RadResponder's current strengths.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2021

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2011

Three-dimensional anisotropic adaptive filtering of projection data for noise reduction in cone beam CT

Purpose: The combination of quickly rotating C-arm gantry with digital flat panel has enabled the acquisition of three-dimensional data (3D) in the interventional suite. However, image quality is still somewhat limited since the hardware has not been optimized for CT imaging. Adaptive anisotropic filtering has the ability to improve image quality by reducing the noise level and therewith the radiation dose without introducing noticeable blurring. By applying the filtering prior to 3D reconstruction, noise-induced streak artifacts are reduced as compared to processing in the image domain. Methods: 3D anisotropic adaptive filtering was used to process an ensemble of 2D x-ray views acquired along a circular trajectory around an object. After arranging the input data into a 3D space (2D projections + angle), the orientation of structures was estimated using a set of differently oriented filters. The resulting tensor representation of local orientation was utilized to control the anisotropic filtering. Low-pass filtering is applied only along structures to maintain high spatial frequency components perpendicular to these. The evaluation of the proposed algorithm includes numerical simulations, phantom experiments, and in-vivo data which were acquired using an AXIOM Artis dTA C-arm system (Siemens AG, Healthcare Sector, Forchheim, Germany). Spatial resolution and noise levels were compared with and without adaptive filtering. A human observer study was carried out to evaluate low-contrast detectability. Results: The adaptive anisotropic filtering algorithm was found to significantly improve low-contrast detectability by reducing the noise level by half (reduction of the standard deviation in certain areas from 74 to 30 HU). Virtually no degradation of high contrast spatial resolution was observed in the modulation transfer function (MTF) analysis. Although the algorithm is computationally intensive, hardware acceleration using Nvidia's CUDA Interface provided an 8.9-fold speed-up of the processing (from 1336 to 150 s). Conclusions: Adaptive anisotropic filtering has the potential to substantially improve image quality and/or reduce the radiation dose required for obtaining 3D image data using cone beam CT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2014

Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis

Background: Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure. Results: To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase. Conclusions: Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Using Lomb–Scargle Analysis to Derive Empirical Orthogonal Functions from Gappy Meteorological Data

The Lomb–Scargle discrete Fourier transform (LSDFT) is a well-known technique for analyzing time series. In this study, a solution for empirical orthogonal functions (EOFs) based on irregularly sampled data is derived from the LSDFT. It is demonstrated that this particular algorithm has no hard limit on its accuracy and yields results comparable to those of complex Hilbert EOF analysis. Two LSDFT algorithms are compared in terms of their performance in evaluating EOFs for precipitation observations from the Tropical Rainfall Measuring Mission satellite. Both are shown to be able to capture the pattern of the diurnal cycle of rainfall over the complex topography and diverse land cover of South America, and both also show other consistent features in the 0–12-day frequency band.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Flocking of the Motsch–Tadmor Model with a Cut-Off Interaction Function

In this paper, we study the flocking behavior of the Motsch–Tadmor model with a cut-off interaction function. Our analysis shows that connectedness is important for flocking of this kind of model. Fortunately, we get a sufficient condition imposed only on the model parameters and initial data to guarantee the connectedness of the neighbor graph associated with the system. Then we present a theoretical analysis for flocking, and show that the system achieves consensus at an exponential rate.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2012

Influence of Radiofrequency Ablation of Lung Cancer on Pulmonary Function

Purpose: The purpose of this study was to evaluate altered pulmonary function retrospectively after RFA. Methods: This retrospective study comprised 41 ablation sessions for 39 patients (22 men and 17 women; mean age, 64.8 years). Vital capacity (VC) and forced expiratory volume in 1 s (FEV{sub 1}) at 1 and 3 months after RFA were compared with the baseline (i.e., values before RFA). To evaluate the factors that influenced impaired pulmonary function, univariate analysis was performed by using multiple variables. If two or more variables were indicated as statistically significant by univariate analysis, these variables were subjected to multivariate analysis to identify independent factors. Results: The mean VC and FEV{sub 1} before RFA and 1 and 3 months after RFA were 3.04 and 2.24 l, 2.79 and 2.11 l, and 2.85 and 2.13 l, respectively. The values at 1 and 3 months were significantly lower than the baseline. Severe pleuritis after RFA was identified as the independent factor influencing impaired VC at 1 month (P = 0.003). For impaired FEV{sub 1} at 1 month, only severe pleuritis (P = 0.01) was statistically significant by univariate analysis. At 3 months, severe pleuritis (VC, P = 0.019; FEV{sub 1}, P = 0.003) and an ablated parenchymal volume {>=}20 cm{sup 3} (VC, P = 0.047; FEV{sub 1}, P = 0.038) were independent factors for impaired VC and FEV{sub 1}. Conclusions: Pulmonary function decreased after RFA. RFA-induced severe pleuritis and ablation of a large volume of marginal parenchyma were associated with impaired pulmonary function.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2011

CONSTRAINTS ON THE SYNCHROTRON SHOCK MODEL FOR THE FERMI GRB 090820A OBSERVED BY GAMMA-RAY BURST MONITOR

Discerning the radiative dissipation mechanism for prompt emission in gamma-ray bursts (GRBs) requires detailed spectroscopic modeling that straddles the {nu}F{sub {nu}} peak in the 100 keV-1 MeV range. Historically, empirical fits such as the popular Band function have been employed with considerable success in interpreting the observations. While extrapolations of the Band parameters can provide some physical insight into the emission mechanisms responsible for GRBs, these inferences do not provide a unique way of discerning between models. By fitting physical models directly, this degeneracy can be broken, eliminating the need for empirical functions; our analysis here offers a first step in this direction. One of the oldest, and leading, theoretical ideas for the production of the prompt signal is the synchrotron shock model. Here we explore the applicability of this model to a bright Fermi gamma-ray burst monitor (GBM) burst with a simple temporal structure, GRB 090820A. Our investigation implements, for the first time, thermal and non-thermal synchrotron emissivities in the RMFIT forward-folding spectral analysis software often used in GBM burst studies. We find that these synchrotron emissivities, together with a blackbody shape, provide at least as good a match to the data as the Band GRB spectral fitting function. This success is achieved in both time-integrated and time-resolved spectral fits.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Analysis of Magnetization as a Function of Temperature for CoMn{sub 1−x}Fe{sub x}Ge

Our experimental measurements for the magnetization M as a function of temperature are analyzed for the multilayer structure of CoMn{sub 1−x}Fe{sub x}Ge for x = 0.085 and x = 0.12 at constant magnetic fields of 3, 5, and 7 T. For this analysis, a power-law formula is used below the transition temperature T{sub C} for these compositions and the values of the critical exponent β for the magnetization M (order parameter) are determined. Our analysis indicates that a first order transition at lower concentrations (x = 0.085) changes toward a second order at higher concentrations (x = 0.12) at constant magnetic fields (3, 5, and 7 T) for the multilayer CoMn{sub 1−x}Fe{sub x}Ge, as observed experimentally.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Hidden Chloroplast Functions Revealed Through Deep Genomic Analysis

Photosynthesis is a highly complex and orchestrated process that is tuned to plant development and the environment. This project has focused on the gene regulatory mechanisms underlying the elaboration of the photosynthetic apparatus. Particular emphasis has been placed on the regulation of genes encoded in the chloroplast compartment, where photosynthesis takes place. These genes specify both major core proteins of the photosynthetic complexes, as well as proteins that have structural or regulatory properties. The project initially identified structures and sequences in the mRNAs encoding these proteins, that allowed them to be properly regulated during plant development, as well as regulatory proteins that interact with these sequences and structures. It was shown that much of the regulation of chloroplast genes was exerted at the RNA level, rather than at the level of gene transcription. Then, insights were obtained into the enzyme functions that are required to express these RNAs correctly. A series of ribonucleases was studied, with each one having particular specificities and roles in RNA maturation and decay. In the latter part of the project, new genomics tools were employed to study gene regulation in a data-intensive and exploratory manner. Through this work, a new class of “non-coding” and mainly antisense RNAs was identified in chloroplasts, and some of these appear to in fact encode novel proteins that may have unstudied roles in photosynthesis. Overall, the project has taken a trajectory from gene-by-gene analysis to a holistic study of chloroplast coding capacity, including opening the door to identifying new chloroplast-encoded photosynthetic functions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Microfluidic electrochemical cell for in situ structural characterization of amorphous thin-film catalysts using high-energy X-ray scattering

Porous, high-surface-area electrode architectures are described that allow structural characterization of interfacial amorphous thin films with high spatial resolution under device-relevant functional electrochemical conditions using high-energy X-ray (>50 keV) scattering and pair distribution function (PDF) analysis. Porous electrodes were fabricated from glass-capillary array membranes coated with conformal transparent conductive oxide layers, consisting of either a 40 nm–50 nm crystalline indium tin oxide or a 100 nm–150 nm-thick amorphous indium zinc oxide deposited by atomic layer deposition. These porous electrodes solve the problem of insufficient interaction volumes for catalyst thin films in two-dimensional working electrode designs and provide sufficiently low scattering backgrounds to enable high-resolution signal collection from interfacial thin-film catalysts. For example, PDF measurements were readily obtained with 0.2 Å spatial resolution for amorphous cobalt oxide films with thicknesses down to 60 nm when deposited on a porous electrode with 40 µm-diameter pores. This level of resolution resolves the cobaltate domain size and structure, the presence of defect sites assigned to the domain edges, and the changes in fine structure upon redox state change that are relevant to quantitative structure–function modeling. The results suggest the opportunity to leverage the porous, electrode architectures for PDF analysis of nanometre-scale surface-supported molecular catalysts. In addition, a compact 3D-printed electrochemical cell in a three-electrode configuration is described which is designed to allow for simultaneous X-ray transmission and electrolyte flow through the porous working electrode.

36 MATERIALS SCIENCE↗

DOE OSTI2014

CD8{sup +}CD25{sup +} T cells reduce atherosclerosis in apoE(−/−) mice

Highlights: •The role of a sub-population of CD8{sup +} T cells with suppressor functions was investigated in atherosclerosis. •CD8{sup +}CD25{sup +} T cells from adult apoE(−/−) mice had phenotype characteristics of T suppressor cells. •These CD8{sup +}CD25{sup +} T cells reduced CD4{sup +} T cell proliferation and CD8{sup +} cytotoxic activity in vitro. •Adoptive transfer of CD8{sup +}CD25{sup +} T cells significantly reduced atherosclerosis. •CD8{sup +}CD25{sup +} T cells have a suppressive function in atherosclerosis. -- Abstract: Background: It is increasingly evident that CD8{sup +} T cells are involved in atherosclerosis but the specific subtypes have yet to be defined. CD8{sup +}CD25{sup +} T cells exert suppressive effects on immune signaling and modulate experimental autoimmune disorders but their role in atherosclerosis remains to be determined. The phenotype and functional role of CD8{sup +}CD25{sup +} T cells in experimental atherosclerosis were investigated in this study. Methods and results: CD8{sup +}CD25{sup +} T cells were observed in atherosclerotic plaques of apoE(−/−) mice fed hypercholesterolemic diet. Characterization by flow cytometric analysis and functional evaluation using a CFSE-based proliferation assays revealed a suppressive phenotype and function of splenic CD8{sup +}CD25{sup +} T cells from apoE(−/−) mice. Depletion of CD8{sup +}CD25{sup +} from total CD8{sup +} T cells rendered higher cytolytic activity of the remaining CD8{sup +}CD25{sup −} T cells. Adoptive transfer of CD8{sup +}CD25{sup +} T cells into apoE(−/−) mice suppressed the proliferation of splenic CD4{sup +} T cells and significantly reduced atherosclerosis in recipient mice. Conclusions: Our study has identified an athero-protective role for CD8{sup +}CD25{sup +} T cells in experimental atherosclerosis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[ a ]pyrene Biodegradation in Sediments by Microbial Electrochemistry

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[ a ]pyrene (B a P) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c -type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased B a P bioavailability and increased degradation rates. In conclusion, tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of B a P enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2010

Diffraction in time in tunneling phenomena

This paper reviews exact analytical results on diffraction in time for tunneling of a particle through an arbitrary potential of finite range. It emphasizes the essential role played by the formalism of resonant states to derive the analytical solution to the time-dependent Schroedinger equation as an initial value problem and in the analysis of the corresponding transient behavior.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2014

Structural analysis of highly porous γ-Al{sub 2}O{sub 3}

Two highly porous γ-aluminas, a commercial catalyst obtained from the calcination of boehmite and a highly mesoporous product obtained from amorphous aluminum (oxy)hydroxide via a sol–gel-based process were investigated by {sup 27}Al nuclear magnetic resonance (NMR), transmission electron microscopy (TEM), and atomic pair distribution function (PDF) analysis of synchrotron powder diffraction data. NMR data showed for both materials a distribution of tetrahedrally and octahedrally coordinated Al at a 0.30:0.70 ratio, which is typical for γ-aluminas. TEM studies revealed that rod-shaped particles with about 5 nm in thickness are the building blocks of the porous structure in both materials. These particles often extend to a length of 50 nm in the commercial catalyst and are considerably shorter in the sol–gel-based material, which has a higher surface area. Refinement of PDFs revealed the presence of a ∼1 nm scale local structure and the validity of a tetragonal average structure for both materials. This tetragonal average structure contains a substantial fraction of non-spinel octahedral Al atoms. It is argued that the presence of local structure is a general feature of γ-alumina, independent of precursor and synthesis conditions. The concentration of “non-spinel” Al atoms seems to correlate with surface properties, and increases with increasing pore size/surface area. This should have implications to the catalytic properties of porous γ-alumina. - Graphical abstract: Boehmite-derived and sol–gel synthesized porous γ-Al{sub 2}O{sub 3} possess identical structural properties, featuring a nm scale local structure and a tetragonal average structure. - Highlights: • Porous γ-Al{sub 2}O{sub 3} generally possesses a nm-scale local structure. • The tetragonal average structure contains a substantial fraction of “non-spinel” Al atoms. • The concentration of “non-spinel” Al atoms correlates with surface properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Solving disorder in (3D) real space: a comparative study of the three-dimensional difference pair distribution function and atomic resolution holography reconstructions

The quantitative analysis of local ordering principles in disordered crystalline systems has gained much attention over the past few years, as it is often considered crucial for optimizing material functionality. This development has been driven by significant advancements in computational and experimental methods, which have led to the establishment and widespread use of various analytical techniques. In this study, we perform model calculations to compare the effectiveness of atomic resolution holography and three-dimensional difference pair distribution function analysis (3D-ΔPDF). Using Cu 3 Au as a model system, we demonstrate an approach to derive local order parameters quantitatively and show that both techniques are well suited to quantifying chemical short-range order correlations and local bond-distance variations. By evaluating the strengths and limitations of both techniques, we advocate for their combined use to solve complex short-range order problems accurately.

3D-ΔPDF↗