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DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗

DOE OSTI2022

Observed Covariations in Boundary Layer and Cumulus Cloud Layer Processes

In this paper we examine variations in boundary-layer processes spanning the shallow to deep cumulus transition. This is accomplished by differentiating boundary layer properties on the basis of convective outcomes, ranging from shallow to deep, as observed at the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site in Oklahoma, USA. Doppler lidar, radar, and radiosonde data are combined to determine statistical differences in boundary layer and cloud layer properties using a large sample (236) of days with a range of convective outcomes: shallow, congestus, and deep convection. In these analyses, the radar characterizes diurnal cloud depth, the lidar quantifies updraft and downdraft properties in the subcloud layer, and daily radiosonde data provides the convective inhibition (CIN). Combined, these data are used to test the hypothesis that deep convection occurs when the strength of the boundary layer turbulence (i.e., TKE) exceeds the strength of the energy barrier (i.e., CIN) at the top of the CBL. Results show that days with deep convective clouds have significantly lower vertical velocity variance and weaker updrafts within the subcloud layer. However, CIN values are also found to be significantly lower on deep convective days, allowing for these weaker updrafts to penetrate the energy barrier and reach the level of free convection (LFC). In contrast, shallow convective outcomes occur when the updrafts are strong in an absolute sense, but are weak when compared to the strength of the energy barrier. These findings support the use of the CIN/TKE framework in parameterizing convection in coarse resolution models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Profiling the molecular destruction rates of temperature and humidity as well as the turbulent kinetic energy dissipation in the convective boundary layer

A simultaneous deployment of Doppler, temperature, and water-vapor lidars is able to provide profiles of molecular destruction rates and turbulent kinetic energy (TKE) dissipation in the convective boundary layer (CBL). Horizontal wind profiles and profiles of vertical wind, temperature, and moisture fluctuations are combined, and transversal temporal autocovariance functions (ACFs) are determined for deriving the dissipation and molecular destruction rates. These are fundamental loss terms in the TKE as well as the potential temperature and mixing ratio variance equations. These ACFs are fitted to their theoretical shapes and coefficients in the inertial subrange. Error bars are estimated by a propagation of noise errors. Sophisticated analyses of the ACFs are performed in order to choose the correct range of lags of the fits for fitting their theoretical shapes in the inertial subrange as well as for minimizing systematic errors due to temporal and spatial averaging and micro- and mesoscale circulations. We demonstrate that we achieve very consistent results of the derived profiles of turbulent variables regardless of whether 1 or 10 s time resolutions are used. We also show that the temporal and spatial length scales of the fluctuations in vertical wind, moisture, and potential temperature are similar with a spatial integral scale of ≈160 m at least in the mixed layer (ML). The profiles of the molecular destruction rates show a maximum in the interfacial layer (IL) and reach values of ϵ m ≃ 7 x 10 -4 g 2 kg −2 s −1 for mixing ratio and ϵ θ ≃ 1.6 x 10 -3 K 2 s −1 for potential temperature. In contrast, the maximum of the TKE dissipation is reached in the ML and amounts to ≃ 10 -2 m 2 s −3 . We also demonstrate that the vertical wind ACF coefficient k w ∝ $\overline{w'^{2}}$ and the TKE dissipation ϵ ∝ ($\overline{w'^{2}}$) 3/2 . For the molecular destruction rates, we show that ϵ m ∝ $\overline{m'^{2}}$ ($\overline{w'^{2}}$) 1/2 and ϵ θ ∝ $\overline{θ'^{2}}$ ($\overline{w'^{2}}$) 1/2 . These equations can be used for parameterizations of ϵ, ϵ m , and ϵ θ . All noise error bars are derived by error propagation and are small enough to compare the results with previous observations and large-eddy simulations. The results agree well with previous observations but show more detailed structures in the IL. Consequently, the synergy resulting from this new combination of active remote sensors enables the profiling of turbulent variables such as integral scales, variances, TKE dissipation, and the molecular destruction rates as well as deriving relationships between them. The results can be used for the parameterization of turbulent variables, TKE budget analyses, and the verification of large-eddy simulations.

dissipation rate↗

DOE OSTI2026

Machine learning of factors for improving oyster hatchery production

Oyster aquaculture and restoration in the Chesapeake Bay are vital, yet hatcheries frequently struggle with inconsistent larval growth and sudden mass mortality events. Unpredictable disruptions in larval production cause large economic losses, represent a perceived risk to growers, and impede industry expansion. To better understand associations between production yield and its potential predictors, we applied machine learning (random forest, and neural network) and statistical (generalized additive model) models to a comprehensive dataset of environmental, water quality, and operational parameters from a Maryland oyster hatchery, aiming to identify key yield predictors and develop a robust forecasting tool. We used recursive Boruta algorithm for variable selection, pinpointing critical predictors, and employed cross-validation to fine-tune model settings. Shapley value analysis offered crucial insights into model interpretations, highlighting week number, Normalized Difference Vegetation Index, salinity, turbidity, and fecundity as primary drivers of yield variability. For low-yield cases, salinity-related variables were particularly important. Our findings provide an early warning system for potential production downturns, empowering hatchery operators to make data-driven decisions for optimizing water conditions, feeding schedules, and broodstock management. By boosting predictability and efficiency, this research directly supports economic stability of the oyster industry and ecological health of the Chesapeake Bay.

Vishwakarma, Srishti [Oak Ridge National Laborator↗

DOE OSTI2021

Utah FORGE Well 78B-32 Daily Drilling Reports and Logs

This data set includes the daily drilling reports and Pason data for well 78B-32 and Schlumberger logs acquired after drilling completion. This well was drilled between June 27th and July 31st of 2021. Also included is raw and processed data for a variety of well data metrics including temperature, porosity, density, and sonic data. This data was taken at the Utah FORGE site as part of the Utah FORGE project.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

Utah FORGE: Well 16B(78)-32 Logs from Schlumberger Technologies

This dataset is a collection of well logs provided by Schlumberger Technologies from the Utah FORGE well 16B(78)-32 drilling project. Information here includes critical borehole information collected by an ultrasonic borehole imager (UBI) and a fullbore formation microimager (FMI). Well 16B(78)-32 serves as the production well for reservoir creation, fluid circulation, and demonstration of heat extraction for the FORGE project. It has been drilled as a doublet approximately 300 feet parallel to and above the injection well 16A(78)-32. The total depth measured 10,947 feet and the vertical depth measured 8,357 feet.

11.5 inch intermediate casing logs↗