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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Two-stage dynamic deregulation of metabolism improves process robustness & scalability in engineered E. coli.

Here, we report that two-stage dynamic control improves bioprocess robustness as a result of the dynamic deregulation of central metabolism. Dynamic control is implemented during stationary phase using combinations of CRISPR interference and controlled proteolysis to reduce levels of central metabolic enzymes. Reducing the levels of key enzymes alters metabolite pools resulting in deregulation of the metabolic network. Deregulated networks are less sensitive to environmental conditions improving process robustness. Process robustness in turn leads to predictable scalability, minimizing the need for traditional process optimization. We validate process robustness and scalability of strains and bioprocesses synthesizing the important industrial chemicals alanine, citramalate and xylitol. Predictive high throughput approaches that translate to larger scales are critical for metabolic engineering programs to truly take advantage of the rapidly increasing throughput and decreasing costs of synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantitative Separation of Unknown Organic–Metal Complexes by Liquid Chromatography–Inductively Coupled Plasma-Mass Spectrometry

Dissolved organic matter (DOM) is widely recognized to control the solubility and reactivity of trace metals in the environment. However, the mechanisms that govern metal-DOM complexation remain elusive, primarily due to the analytical challenge of fractionating and quantifying metal–organic species within the complex mixture of organic compounds that comprise DOM. Here, we describe a quantitative method for fractionation and element-specific detection of organic–metal complexes using liquid chromatography with online inductively coupled plasma mass spectrometry (LC–ICP-MS). The method implements a post-column compensation gradient to stabilize ICP–MS elemental response across the LC solvent gradient, thereby overcoming a major barrier to achieving quantitative accuracy with LC–ICP-MS. With external calibration and internal standard correction, the method yields concentrations of organic–metal complexes that were consistently within 6% of their true values, regardless of the complex’s elution time. We used the method to evaluate the effects of four stationary phases (C18, phenyl, amide, and pentafluoroylphenyl propyl) on the recovery and separation of environmentally relevant trace metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, and Pb) in Suwannee River Fulvic Acid and Suwannee River Natural Organic Matter. The C18, amide, and phenyl phases generally yielded optimal metal recoveries (>75% for all metals except Pb), with the phenyl phase separating polar species to a greater extent than C18 or amide. We also fractionated organic-bound Fe, Cu, and Ni in oxidized and reduced soils, revealing divergent metal-DOM speciation across soil redox environments. Finally, by enabling quantitative fractionation of DOM-bound metals, our method offers a means for advancing a mechanistic understanding of metal–organic complexation throughout the environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Quantifying Phospholipids in Organic Samples Using a Hydrophilic Interaction Liquid Chromatography–Inductively Coupled Plasma High-Resolution Mass Spectrometry (HILIC-ICP-HRMS) Method

Here, in this study, a novel method using hydrophilic interaction liquid chromatography (HILIC) coupled with inductively coupled plasma high-resolution mass spectrometry (ICP-HRMS) was introduced for the quantification of phospholipids in oil samples. The method employed a bridged ethyl hybrid (BEH) stationary phase HILIC column with a tetrahydrofuran (THF)/water mobile phase, enhancing the solubility and detection of phospholipids. During the study, a gradient/matrix effect on ICP-HRMS sensitivity was observed and successfully compensated for experimentally, ensuring reliable quantification results. This approach has proven effective for a wide range of different oil samples including vegetable oils, animal fats, and phospholipid supplements. Notably, this method allowed the direct quantification of phospholipids in oil samples, bypassing the need for prior sample preparation methods, such as solid phase extraction (SPE), thereby streamlining the analytical process. The precision, accuracy, and reduced need for extensive sample preparation offered by this method mark a significant advancement in lipids analysis. Its robustness and broad applicability have substantial implications for industries such as food and renewable energy production, where both efficient and accurate lipid identification and quantification are crucial.

09 BIOMASS FUELS↗
DOE OSTI2025

Intrinsic Kinetics of Polyethylene Terephthalate Pyrolysis via Micropyrolysis and Multivariate Chromatographic Analysis

This study provides an in-depth investigation of the primary decomposition of polyethylene terephthalate (PET) via pyrolysis, employing an experimental-analytic workflow that integrates design of experiments (DoE), micropyrolysis coupled with comprehensive two-dimensional gas chromatography (GC×GC), and multivariate data analysis to verify intrinsic kinetic conditions and elucidate evolving product distributions for mapping key reaction pathways. Peaks that could not be identified using commercial spectral libraries were assigned using Mass Frontier simulations, enabling the identification of divinyl terephthalate, ethyl vinyl terephthalate, and 2-(benzoyloxy)ethyl vinyl terephthalate. A polar×polar (non-orthogonal) column set tailored for the detection of carboxylic acids enhanced the quantification of benzoic acid, 4-vinylbenzoic acid, 4-ethylbenzoic acid, and methylbenzoic acid by up to 6-fold relative to an orthogonal column combination (non-polar×mid-polar). Moreover, pyrolysis variables were systematically evaluated using a Box- Behnken design (BBD), encompassing pyrolysis temperature (500−600 °C), sample weight (50−150 μg), and carrier gas flow rate (100−300 mL min −1 ). Among these, pyrolysis temperature was the only statistically significant factor influencing product yields, ranging from 58.78 to 84.26 wt %. In contrast, neither the sample weight nor the carrier gas flow rate had a significant effect on product yields within the evaluated experimental space. At 600 °C, the major pyrolysis products were benzoic acid (up to 20.20 ± 1.46 wt %) and CO 2 (up to 21.28 ± 1.46 wt %), which can be produced through decarboxylation reactions. These findings underscore the critical importance of selecting appropriate analytical columns for the accurate quantification of heteroatomcontaining products such as carboxylic acids, which may otherwise be underestimated or undetected due to their reactivity with the stationary phase of non-polar and mid-polar columns, as well as other GC components. They also highlight the importance of selecting pyrolysis conditions for investigating the primary decomposition of PET under an isothermal kinetically limited regime.

aromatic compounds↗
DOE OSTI2020

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. In this work, we observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Additionally, mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

β-Barrel proteins tether the outer membrane in many Gram-negative bacteria

Gram-negative bacteria have a cell envelope that comprises an outer membrane (OM), a peptidoglycan (PG) layer and an inner membrane (IM). The OM and PG are load-bearing, selectively permeable structures that are stabilized by cooperative interactions between IM and OM proteins. In Escherichia coli , Braun’s lipoprotein (Lpp) forms the only covalent tether between the OM and PG and is crucial for cell envelope stability; however, most other Gram-negative bacteria lack Lpp so it has been assumed that alternative mechanisms of OM stabilization are present. In this work we used a glycoproteomic analysis of PG to show that β-barrel OM proteins are covalently attached to PG in several Gram-negative species, including Coxiella burnetii, Agrobacterium tumefaciens and Legionella pneumophila . In C. burnetii , we found that four different types of covalent attachments occur between OM proteins and PG, with tethering of the β-barrel OM protein BbpA becoming most abundant in the stationary phase and tethering of the lipoprotein LimB similar throughout the cell cycle. Using a genetic approach, we demonstrate that the cell cycle-dependent tethering of BbpA is partly dependent on a developmentally regulated L,D-transpeptidase (Ldt). We use our findings to propose a model of Gram-negative cell envelope stabilization that includes cell cycle control and an expanded role for Ldts in covalently attaching surface proteins to PG.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Computational modeling of charge hopping dynamics along a disordered one-dimensional wire with energy gradients in quantum environments

This computational study investigates the effects of energy gradients on charge hopping dynamics along a one-dimensional chain of discrete sites coupled to quantum bath, which is modeled at the level of Pauli master equation (PME). This study also assesses the performance of different approximations for the hopping rates. Three different methods for solving the PME, a fourth order Runge–Kutta method, numerical diagonalization of the rate matrix followed by analytic propagation, and kinetic Monte Carlo simulation method, are tested and confirmed to produce virtually identical values of time dependent mean square displacement, diffusion constant, and mobility. Five different rate expressions, exact numerical evaluation of Fermi’s Golden Rule (FGR) rate, stationary phase interpolation (SPI) approximation, semiclassical approximation, classical Marcus rate, and Miller–Abrahams rate, are tested to help understand the effects of approximations in representing quantum environments in the presence of energy gradients. The results based on direct numerical evaluation of FGR rate exhibit transition from diffusive to non-diffusive behavior with the increase in the gradient and show that the charge transport in the quantum bath is more sensitive to the magnitude of the gradient and the disorder than in the classical bath. Among all the four approximations for the hopping rates, the SPI approximation is confirmed to work best overall. A comparison of two different methods to calculate the mobility identifies drift motion of the population distribution as the major source of non-diffusive behavior and provides more reliable information on the contribution of quantum bath.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Validation of IMEP on Alcator C-Mod and JET-ILW ELMy H-mode plasmas

Abstract The recently developed integrated model based on engineering parameters (IMEP) (Luda et al 2020 Nucl. Fusion 61 126048; Luda et al 2021 Nucl. Fusion 60 036023), so far validated on ASDEX Upgrade, has been tested on a database of 3 Alcator C-Mod and 55 JET-ILW ELMy (type I) H-mode stationary phases. The empirical pedestal transport model included in IMEP, consisting now of imposing a fixed value of R < ∇ T e > / T e , t o p = − 82.5 , allows an accurate prediction of the pedestal top temperature (when the pedestal top density is fixed to the experimental measurements) across these three machines with different sizes, when the pedestal is peeling–ballooning (PB) limited. Cases far from the ideal PB boundary, corresponding to high edge Spitzer resistivity, are instead strongly overpredicted by IMEP. A comparison between the predictions of Europed and IMEP for a subset of JET-ILW cases shows that IMEP can more accurately reproduce the experimental pedestal width. This allows IMEP to better capture profile effects on the pedestal stability, and therefore to correctly describe the negative effect of fueling on the pedestal pressure for PB limited cases. A strong correlation between the separatrix density and the fueling rate has been identified for a subset of JET-ILW cases, when taking into account different divertor configurations. Overall, these promising results encourage further developments of integrated models to obtain reliable predictions of pedestal and global confinement using only engineering parameters for present and future machines.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Instantaneous difference frequency locking observed during toroidicity-induced Alfvén eigenmode coupling in the DIII-D tokamak

In magnetic confinement fusion, toroidicity-induced Alfvén eigenmodes (TAEs) are well-studied, weakly stable solutions of the linearized ideal magnetohydrodynamic equations. Driven unstable by suprathermal populations of energetic particles, TAE pose a key vulnerability to the confinement of high-energy alpha particles generated by fusion reactions. Hence, it is paramount to understand TAE dynamics if a working reactor is to be realized. In this work, we detect and characterize signatures of nonstationary nonlinear coupling between TAE using a novel, time-resolved bispectral analysis; results are supported by analytic signal of band-passed data. Crucially, a stationary phase relationship between two TAE and a nascent low frequency fluctuation is observed precisely when the triple product of magnetic fluctuation amplitudes is enhanced. Local mode number and frequency spectrum, gleaned from beam-emission spectroscopy, corroborates simultaneous satisfaction of nonlinear matching conditions, and provides a tool to identify theorized pathways of energy transfer, e.g. TAE parametric instability.

bispectral analysis↗
DOE OSTI2021

An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids

Abstract Assessing central carbon metabolism in plants can be challenging due to the dynamic range in pool sizes, with low levels of important phosphorylated sugars relative to more abundant sugars and organic acids. Here, we report a sensitive liquid chromatography–mass spectrometry method for analysing central metabolites on a hybrid column, where both anion-exchange and hydrophilic interaction chromatography (HILIC) ligands are embedded in the stationary phase. The liquid chromatography method was developed for enhanced selectivity of 27 central metabolites in a single run with sensitivity at femtomole levels observed for most phosphorylated sugars. The method resolved phosphorylated hexose, pentose, and triose isomers that are otherwise challenging. Compared with a standard HILIC approach, these metabolites had improved peak areas using our approach due to ion enhancement or low ion suppression in the biological sample matrix. The approach was applied to investigate metabolism in high lipid-producing tobacco leaves that exhibited increased levels of acetyl-CoA, a precursor for oil biosynthesis. The application of the method to isotopologue detection and quantification was considered through evaluating 13C-labeled seeds from Camelina sativa. The method provides a means to analyse intermediates more comprehensively in central metabolism of plant tissues.

Plant Sciences↗
DOE OSTI2022

Lefschetz thimble quantum Monte Carlo for spin systems

Monte Carlo simulations are useful tools for modeling quantum systems, but in some cases they suffer from a sign problem, leading to an exponential slow down in their convergence to a value. While solving the sign problem is generically NP hard, many techniques exist for mitigating the sign problem in specific cases; in particular, the technique of deforming the Monte Carlo simulation's plane of integration onto Lefschetz thimbles (complex hypersurfaces of stationary phase) has seen significant success in the context of quantum field theories. We extend this methodology to spin systems by utilizing spin coherent state path integrals to reexpress the spin system's partition function in terms of continuous variables. Using some toy systems, we demonstrate its effectiveness at lessening the sign problem in this setting, despite the fact that the initial mapping to spin coherent states introduces its own sign problem. The standard formulation of the spin coherent path integral is known to make use of uncontrolled approximations; despite this, for large spins they are typically considered to yield accurate results, so it is somewhat surprising that our results show significant systematic errors. Furthermore, possibly of independent interest, our use of Lefschetz thimbles to overcome the intrinsic sign problem in spin coherent state path integral Monte Carlo enables a novel numerical demonstration of a breakdown in the spin coherent path integral.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Toward quantum tunneling from excited states: Recovering imaginary-time instantons from a real-time analysis

We revisit the path integral description of quantum tunneling and its generalization to excited states. For clarity, we focus on the simple toy model of a point particle in a double-well potential, for which we perform all steps explicitly. Instead of performing the familiar Wick rotation from physical to imaginary time—which is inconsistent with the requisite boundary conditions when treating tunneling from excited states—we regularize the path integral by adding an infinitesimal complex contribution to the Hamiltonian, while keeping time strictly real. We find that this gives rise to a complex stationary-phase solution, in agreement with recent insights from Picard-Lefshetz theory. We then show that there exists a class of analytic solutions for the corresponding equations of motion, which can be made to match the appropriate boundary conditions in the physically relevant limits of a vanishing regulator and an infinite physical time. We provide a detailed discussion of this nontrivial limit. We find that, for systems without an explicit time-dependence, our approach reproduces the picture of an instantonlike solution defined on a finite Euclidean-time interval. Lastly, we discuss the generalization of our approach to broader classes of systems, for which it serves as a reliable framework for high-precision calculations. Published by the American Physical Society 2025

Steingasser, Thomas (ORCID:0000000217262117)↗
DOE OSTI2022

Simple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental composition

Even subtle modifications in growth conditions elicit acclimation responses affecting the molecular and elemental makeup of organisms, both in the laboratory and in natural habitats. Here, we systematically explored the effect of temperature, pH, nutrient availability, culture density, and access to CO 2 and O 2 in laboratory-grown algal cultures on growth rate, the ionome, and the ability to accumulate Fe. We found algal cells accumulate Fe in alkaline conditions, even more so when excess Fe is present, coinciding with a reduced growth rate. Using a combination of Fe-specific dyes, X-ray fluorescence microscopy, and NanoSIMS, we show that the alkaline-accumulated Fe was intracellularly sequestered into acidocalcisomes, which are localized towards the periphery of the cells. At high photon flux densities, Zn and Ca specifically over-accumulate, while Zn alone accumulates at low temperatures. The impact of aeration was probed by reducing shaking speeds and changing vessel fill levels; the former increased the Cu quota of cultures, the latter resulted in a reduction in P, Ca, and Mn at low fill levels. Trace element quotas were also affected in the stationary phase, where specifically Fe, Cu, and Zn accumulate. Cu accumulation here depends inversely on the Fe concentration of the medium. Individual laboratory strains accumulate Ca, P, and Cu to different levels. All together, we identified a set of specific changes to growth rate, elemental composition, and the capacity to store Fe in response to subtle differences in culturing conditions of Chlamydomonas, affecting experimental reproducibility. Accordingly, we recommend that these variables be recorded and reported as associated metadata.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A distinct subpopulation of membrane vesicles in Pseudomonas putida is enriched in enzymes for lignin catabolism

Bacterial membrane vesicles (MVs) mediate diverse microbial processes and are emerging as powerful biomedical tools, but MV population heterogeneity remains an open question. Here, we separate, enumerate, and characterize two MV populations from the soil bacterium Pseudomonas putida during growth with or without lignin-derived carbon, a major carbon source from plant cells in the rhizosphere. Small MVs (MV-S, diameter ~100 nm) were produced from all cultures, whereas large MVs (MV-L, diameter ~300 nm) were observed during the late stationary phase of lignin cultivations. MV-S contained selectively packaged proteins with diverse physiological functions, whereas the MV-L proteome was smaller and largely enriched in outer membrane proteins. Interestingly, enzymes known to mediate the catabolism of lignin-derived aromatic compounds were enriched in MV-S. Overall, this study highlights the need for careful consideration of MV populations in microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. Comparative proteomics analysis combined with inorganic polyphosphate and guanosine tetra/pentaphosphate assays of the ΔprmA mutant in Escherichia coli revealed that bL11 methylation is important for stringent response signaling. In the stationary phase, we found that the ΔprmA mutant has impaired guanosine tetra/pentaphosphate production. This leads to a reduction in inorganic polyphosphate levels, accumulation of RNA and ribosomal proteins, and an abnormal polysome profile. Overall, our investigation demonstrates that the evolutionarily conserved bL11 methylation is important for stringent response signaling and ribosomal activity regulation and turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED

ABSTRACT Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans . In order to gain insight into how the cells sense and respond to the availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that the depletion of HdrED in vivo results in a higher abundance of transcripts for methyltransferases ( mtaC2, mtaB3, mtaC3 ), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate the methylotrophic methanogenesis regulator MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M, and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability. IMPORTANCE Methanosarcina is an emerging model archaeon and synthetic biology platform for the production of renewable energy and sustainable chemicals to reduce dependence on petroleum. Research into metabolic networks and gene regulation in this organism and other methanogens will inform genome-scale metabolic modeling and microbial function prediction in uncultured or non-model anaerobes and archaea. This study suggests methanogens use unknown mechanisms to efficiently couple methanogenesis to gene regulation via CoM-S-S-CoB and ATP availability.

Buan, Nicole R. (ORCID:000000027560973X)↗
DOE OSTI2023

RNAseq analysis of Cellvibrio japonicus during starch utilization differentiates between genes encoding carbohydrate active enzymes controlled by substrate detection or growth rate

ABSTRACT Bacterial utilization of starch is increasingly of interest as the importance and contributions of animal gut microbiomes become more defined. Consequently, identifying and characterizing the bacterial enzymes responsible for the degradation, transport, and metabolism of starch will enable developments in pharmaceutical, biotechnological, and culinary industries searching for novel prebiotics, carrier molecules, and low glycemic index sweeteners. The current challenge is that bacteria proficient at starch utilization often have hundreds of carbohydrate active enzymes, and it is unclear which are essential for starch utilization using only homology-based bioinformatics or computational methods. Complementary experimental data are also needed, especially to understand the regulation of bacterial starch utilization. We have completed an RNAseq analysis of the Gram-negative bacterium Cellvibrio japonicus and found that it has sophisticated regulation that includes substrate sensing and growth rate components for genes that encode starch-degrading enzymes. Among the 22 genes predicted to encode starch-active enzymes, C. japonicus has 10 alpha-amylases, 4 alpha-glucosidases, 2 pullulnases, and 2 cyclomaltodextrin glucanotransferases, 15 of which were up-regulated during exponential growth on starch and 8 up-regulated in stationary phase. Growth analyses with an enzyme secretion deficient mutant of C. japonicus suggested that secreted amylases are essential for this bacterium to degrade starch. Our approach of coupling a physiological growth assay with transcriptomic data provides a platform to identify targets for further genetic or biochemical analysis that can be broadly applied to other starch-utilizing bacteria. IMPORTANCE Understanding the bacterial metabolism of starch is important as this polysaccharide is a ubiquitous ingredient in foods, supplements, and medicines, all of which influence gut microbiome composition and health. Our RNAseq and growth data set provides a valuable resource to those who want to better understand the regulation of starch utilization in Gram-negative bacteria. These data are also useful as they provide an example of how to approach studying a starch-utilizing bacterium that has many putative amylases by coupling transcriptomic data with growth assays to overcome the potential challenges of functional redundancy. The RNAseq data can also be used as a part of larger meta-analyses to compare how C. japonicus regulates carbohydrate active enzymes, or how this bacterium compares to gut microbiome constituents in terms of starch utilization potential.

59 BASIC BIOLOGICAL SCIENCES↗