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The purpose of this analysis is to generate TPM or FPKM values for CRO_V2 transcripts (Franke et al. 2019) in different tissue types of C. roseus utilizing the tissue-specific RNA-seq analysis previously performed by Góngora-Castillo et al. 2012.
We study the time variability (over ≤7.3 yr) of ultra fast outflows (UFOs) detected in a sample of 64 C IV broad absorption line (BAL) quasars (with 80 distinct BAL components) monitored using the Southern African Large Telescope. By comparing the properties of the quasar in our sample with those of a control sample of non-BAL quasars, we show that the distributions of black hole mass are different and the bolometric luminosities and optical photometric variations of UFO BAL quasars are slightly smaller compared to that of non-BAL quasars. The detection fraction of C IV equivalent width (W) variability (∼95 per cent), the fractional variability amplitude $\left(\frac{\Delta W}{W}\right)$ and the fraction of ‘highly variable’ BAL (i.e. $\big|$$\frac{\Delta W}{W}$$\big|$ > 0.67) components (∼33 per cent) are higher in our sample compared to the general BAL population. The scatter in $\frac{\Delta W}{W}$ and the fraction of ‘highly variable’ BALs increase with the time-scale probed. The $\frac{\Delta W}{W}$ distribution is asymmetric at large time scales. We attribute this to the BAL strengthening time-scales being shorter than the weakening time-scales. The BAL variability amplitude correlates strongly with the BAL properties compared to the quasar properties. BALs with low W, high-velocity, shallow profiles, and low-velocity width tend to show more variability. When multiple BAL components are present, a correlated variability is seen between low- and high-velocity components with the latter showing a larger amplitude variations. We find an anticorrelation between the fractional variations in the continuum flux and W. While this suggests photoionization induced variability, the scatter in continuum flux is much smaller than that of W.
Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13 C-metabolic flux analysis ( 13 C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13 C labeling data were used with 13 C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.
Bio-oil is among the most economical approaches for advanced biofuel production. However, bio-oil faces several challenges including high acidity and viscosity, poor storage, and thermal stability. This study focuses on the upgradation of lignocellulosic (corn stover and yellow pine) bio-oil derived phenolic oil (PO), produced by the autothermal fast pyrolysis, through acid-catalyzed esterification reaction. Our strategy exploits a little recognized chemistry: the Fischer esterification of PO and carboxylic acids into carboxylic acid phenyl esters (CAPE) using Dean Stark distillation. Analyses by the Folin–Ciocalteu method, Karl Fischer titration, gas chromatography flame ionization detector, and the molecular weight determination by gel permeation chromatography suggest the conversion of 50 wt% added phenolics to their corresponding CAPE. The Fourier transform infrared spectroscopy analysis confirmed the formation of new C=O and two C–O stretching bands and decrease in the intensity of phenolic-OH bands in the CAPE. The 13 C NMR analysis supports the formation of CAPE together with some unreacted precursors. A base-catalyzed ester hydrolysis experiment and mass balance calculation show an excellent agreement (within 5% range) of the equivalent weight between the produced ester and the phenyl hexanoate. Brookfield analysis indicates that CAPE has 330-fold lower viscosity than starting PO. Heating values of CAPE were higher than PO, from which they were derived (42.2 and 43.6%, respectively, for PO from pyrolysis of corn stover and yellow pine), while moisture content decreased by 98.3 and 98.7%, respectively. The CAPE, which is a phenolic analogue of methyl esters used in biodiesel, has improved stability compared to PO from which it was derived.
This dataset complements the publication Mapping Linear Viscoelasticity for Design and Tactile Intuition (Corman & Ewoldt, 2019). It contains rigorous shear rheometry measurements for six commercial silicone putties, including creep recovery, SAOS, LAOS, and stress relaxation. Additional, unpublished data was generated as part of a graduate rheology course taught by Randy Ewoldt at University of Illinois Urbana-Champaign. Together, these datasets provide a comprehensive example of linear viscoelasticity of a commercial material. The collection is intended both as a pedagogical resource for developing physical intuition in linear viscoelasticity and as a reference dataset for data interpretation, model fitting, and comparative rheological analysis.
The microalga Chlorella sorokiniana has attracted much attention for lipid production and wastewater treatment. It can perform photosynthesis and organic carbon utilization concurrently. To understand its phototrophic metabolism, a biomass compositional analysis, a 13 C metabolic flux analysis, and metabolite pool size analyses were performed. Under dark condition, the oxidative pentose phosphate pathway (OPP) was the major route for glucose catabolism (88% carbon flux) and a cyclic OPP–glycolytic route for glucose catabolism was formed. Under light condition, fluxes in the glucose catabolism, tricarboxylic acid (TCA) cycle, and anaplerotic reaction (CO 2 fixation via phosphoenolpyruvate carboxylase) were all suppressed. Meanwhile, the RuBisCO reaction became active and the ratio of its carbon fixation to glucose carbon utilization was determined as 7:100. Moreover, light condition significantly reduced the pool sizes of sugar phosphate metabolites (such as E4P, F6P, and S7P) and promoted biomass synthesis (which reached 0.155 h –1 ). In addition, light condition increased glucose consumption rates, leading to higher ATP and NADPH production and a higher protein content (43% vs. 30%) in the biomass during the exponential growth phase.
This engineering calculation and analysis report documents the as-run nuclear-heating term, source-term, and radiation damage (measured in displacements per atom [dpa]) accumulation for the Electric Power Research Institute zirconium growth experiment's C capsule (EPRI-ZG-C). These data have been calculated using MCNP 6.1 and SCALE 6.2.3. These data can be used for: the shipping of the EPRI-ZG-C capsule, the acceptance of the capsule at the Materials and Fuels Complex, and programmatic scientific needs.
Accelerator mass spectrometry (AMS) is the method of choice for quantitation of low amounts of 14 C-labeled biomolecules. Despite exquisite sensitivity, an important limitation of AMS is its inability to provide structural information about the analyte. This limitation is not critical when the labeled compounds are well-characterized prior to AMS analysis. However, analyte identity is important in other experiments where, for example, a compound is metabolized and the structures of its metabolites are not known. We previously described a moving wire interface that enables direct AMS measurement of liquid sample in the form of discrete drops or HPLC eluent without the need for individual fraction collection, termed liquid sample-AMS (LS-AMS). Here, we now report the coupling of LS-AMS with a molecular mass spectrometer, providing parallel accelerator and molecular mass spectrometry (PAMMS) detection of analytes separated by liquid chromatography. The repeatability of the method was examined by performing repeated injections of 14 C-labeled tryptophan, and relative standard deviations of the 14 C peak areas were ≤10.57% after applying a normalization factor based on a standard. Five 14 C-labeled amino acids were separated and detected to provide simultaneous quantitative AMS and structural MS data, and AMS results were compared with solid sample-AMS (SS-AMS) data using Bland-Altman plots. To demonstrate the utility of the workflow, yeast cells were grown in a medium with 14 C-labeled tryptophan. The cell extracts were analyzed by PAMMS, and 14 C was detected in tryptophan and its metabolite kynurenine.
To date, 14 C tracer studies using accelerator mass spectrometry (AMS) have not yet resolved lipid-soluble analytes into individual lipoprotein density subclasses. The objective of this work was to develop a reliable method for lipoprotein separation and quantitative recovery for biokinetic modeling purposes. The novel method developed provides the means for use of small volumes (10–200 µL) of frozen plasma as a starting material for continuous isopycnic lipoprotein separation within a carbon- and pH-stable analyte matrix, which, following post-separation fraction clean up, created samples suitable for highly accurate 14 C/ 12 C isotope ratio determinations by AMS. Manual aspiration achieved 99.2 ± 0.41% recovery of [5- 14 CH 3 ]-(2R, 4'R, 8'R)-α-tocopherol contained within 25 µL plasma recovered in triacylglycerol rich lipoproteins (TRL = Chylomicrons + VLDL), LDL, HDL, and infranatant (INF) from each of 10 different sampling times for one male and one female subject, n = 20 total samples. Small sample volumes of previously frozen plasma and high analyte recoveries make this an attractive method for AMS studies using newer, smaller footprint AMS equipment to develop genuine tracer analyses of lipophilic nutrients or compounds in all human age ranges.
Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.
The next-to-next-to-leading-order (NNLO) perturbative QCD (pQCD) predictions for both the decay width and the transition form factor in the η c → γ γ process, based on nonrelativistic QCD (NRQCD), deviate from precise experimental measurements. These significant discrepancies have cast doubt on the applicability of NRQCD to charmonium processes. In this paper, we analyze the η c → γ γ process by applying the principle of maximum conformality (PMC), a systematic method for eliminating renormalization scheme-and-scale ambiguities. The PMC renormalization scales are determined by absorbing the nonconformal β -terms that govern the behavior of the QCD running coupling via the renormalization group equation. We obtain the PMC scale Q ⋆ = 4.49 m c for the η c → γ γ decay width. Even after using the PMC method, the convergence of the pQCD series is still poor, which indicates the importance of uncalculated next-to-next-to-next-to-leading-order and higher-order terms. The resulting value for Γ η c → γ γ is in agreement with the Particle Data Group’s reported value of Γ η c → γ γ = 5.1 ± 0.4 keV within the bounds of uncertainties. Moreover, the transition form factor obtained using the PMC is also in good agreement with precise experimental measurements. The application of the PMC suggests a potential resolution to η c → γ γ puzzle and supports the applicability of NRQCD to charmonium processes. Published by the American Physical Society 2025
We perform a study of the χ c 1 ( 3872 ) line shape using the data samples of e + e − → γ χ c 1 ( 3872 ) , χ c 1 ( 3872 ) → D 0 D ¯ 0 π 0 , and π + π − J / ψ collected with the BESIII detector. The effects of the coupled channels and the off-shell D * 0 are included in the parametrization of the line shape. The line shape mass parameter is obtained to be M X = ( 3871.63 ± 0.1 3 − 0.05 + 0.06 ) MeV . Two poles are found on the first and second Riemann sheets corresponding to the D * 0 D ¯ 0 branch cut. The pole location on the first sheet is much closer to the D * 0 D ¯ 0 threshold than the other, and is determined to be 7.04 ± 0.1 5 − 0.08 + 0.07 MeV above the D 0 D ¯ 0 π 0 threshold with an imaginary part − 0.19 ± 0.0 8 − 0.19 + 0.14 MeV . Published by the American Physical Society 2024
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EIC is planning to construct a new building on the outer ring berm at 10 o’clock which will provide RF power to cryogenically-cooled beam line components in the electron and hadron storage rings. The distance of the building from the RHIC Tunnel and the amount of soil shielding required are the focus of this report. Siting the building closer to the RHIC Tunnel is desirable from an RF operations viewpoint since the waveguide runs and RF power losses will be minimized, but this may require the use of higher density shield materials, e.g., concrete, in addition to soil shielding. The radiological source terms are the prompt radiation hazards from the Hadron Storage Ring (HSR) and Electron Storage Ring (ESR) beam losses in the 10 o’clock sector and the lateral dose rates propagated through the shields. See Figure 1 below.
A dibaryon which is an object with baryon number B = 2 has been studied for a long time. Dyson and Xuong classified non-strangeness dibaryon states based on SU(6) symmetries in 1960?s. In the framework, the deuteron is classified as one of the sextet states of dibaryons. Although dibaryon have been an interesting subject of research for a long time, most of the experimental studies up to the early 2000?s were unsuccessful. The CELCIUS/WASA collaboration reported this state via the double-pionic fusion reaction (?= ! 3c0c0) in 2009. Thereafter, the WASA-at-COSY collaboration revealed properties of the isoscaler resonance state via the ?= ! 3c0c0 reaction in 2011. The dibaryon resonance state with isospin ? = 0 and spin ( = 3 thought to be a ?03 which was predicted by Dyson and Xuong at 2.35 GeV?22 with a configuration of ??. The reported mass and width of that state were 2?37 GeV?22 and 0?07 GeV?22, espectively. The mass was ?0?08 GeV?22 smaller than that of 2?, the width was narrower than that of single ?. This surprising result made dibaryon study come back into the limelight. ?12 is one of the dibaryon states classified by Dyson and Xuong with isospin ? = 1, spin ( = 2. This state can be regarded as an s-wave #? resonance. ?12 is an interesting state from the point of view of the possibilities of existence as an internal structure of ?03 and contribution to many-body effects in nuclei. Though there were some experimental clues and theoretical studies of this state, it was unclear whether the obtained experimental results represented a real resonance or not due to the difficulty of separation from kinematical effects. Very recently, the FOREST group at Tohoku University reported a photoproduced isovector dibaryon state at mass of 2.14 GeV?22 in the 3c0 invariant mass spectra of the W3 ! 3c0c0 reaction. The most probable ?% configuration was 2¸ although they didn?t exclude the possibility of ?% = 1¸ or 3?. They separated the dibaryon production process from conventional pion production process for the first time using angular distribution of deuteron. We investigated the W3 ! 3c¸c? reaction for study of a possible #? dibaryon state using a deuterium target at the Research Center for Electron Photon Science, Tohoku University, Japan. In the experiment, ?3 ? 1012 tagged photon beam at energies ranging from 0.8 to 1.1 GeV was impinged to the liquid deuterium target (?520 mg?cm2) and the charged particles in the final state: deuteron, c¸, and c?, were detected by a magnetic spectrometer with a large solid angle named NKS2. NKS2 had capabilities of reconstructing momentum of charged particles, multi-track analysis, and ??c separation. We performed two different analyses named 2-track analysis and 3-track analysis. The 2-track (3-track) analysis was for events in which two (three) particles of 3c¸c? in the final state, including deuteron, were detected by NKS2. In the 3-track and 2-track analysis, ?2000? ?15000 events were identified as the W3 ! 3c¸c? reaction events, respectively. The 2-track analysis with higher statistics was mainly used to derive the cross sections, and the 3-track analysis was used to check the consistency of the 2-track analysis. In this thesis, we have shown the total cross section, the differential cross sections of the W3 ! 3c¸c? reaction in the region of jC j ¡ 0?15 GeV2. This is the world?s first measurement of this reaction in this energy region. Dibaryon resonance structures were observed below the #? threshold in the differential cross section of the invariant mass of 3c?. The mass and width of the structure were consistent with these of ?12 measured by the W3 ! 3c0c0 reaction. The mechanism of the production process was discussed based on the angular distribution of emitted deuteron.
The purpose of this document is to perform a single-failure analysis through the use of a Failure Modes and Effects Analysis (FMEA) for the Safety Related components of the MARVEL Instrumentation and Control (I&C) System. The intent is that this document will meet the requirements for a single-failure analysis described in IEEE-379, “IEEE Standard for Application of the Single-Failure Criterion to Nuclear Power Generating Station Safety Systems”, to verify that this design does indeed meet the single failure criterion. Principles of IEEE-352, “IEEE Guide for General Principles of Reliability Analysis of Nuclear Power Generating Station Safety Systems” are followed to ensure the analysis is consistent with industry standards.
Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2 H and 13 C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli . The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellummthan in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae , the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.
Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO 2 has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an efficient microbial platform for production of shinorine, a UV light absorbing compound with anti-aging properties. First, we methodically selected an appropriate host for shinorine production by analyzing central carbon flux distribution data from prior studies alongside predictions from genome-scale metabolic models (GEMs). We enhanced shinorine productivity through CRISPRi-mediated downregulation and utilized shotgun proteomics to pinpoint potential competing pathways. Simultaneously, we improved the shinorine biosynthetic pathway by refining its design, optimizing promoter usage, and altering the strength of ribosome binding sites. Finally, we conducted amino acid feeding experiments under various conditions to identify the key limiting factors in shinorine production. The study combines meta-analysis of 13 C-metabolic flux analysis, GEMs, synthetic biology, CRISPRi-mediated gene downregulation, and omics analysis to improve shinorine production, demonstrating the potential of Pseudomonas putida KT2440 as platform for shinorine production.