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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Voltage Regulation Performance Evaluation of Distributed Energy Resource Management via Advanced Hardware-in-the-Loop Simulation

This paper evaluates the performance of coordinated control across advanced distribution management systems (ADMS), distributed energy resources (DERs), and distributed energy resource management systems (DERMS) using an advanced hardware-in-the-loop (HIL) platform. This platform provides a realistic laboratory testing environment, including accurate dynamic modeling of a real-world distribution system from a utility partner, real controllers (ADMS and DERMS), physical power hardware (DERs), and standard communications protocols. One grid service—voltage regulation—is evaluated to show the performance of the coordinated grid automation system. The testing results demonstrate that the coordinated DERMS and ADMS system can effectively regulate system voltages within target operation limits using DERs. The realistic laboratory HIL testing results give utilities confidence in adopting the grid automation systems to manage DERs to achieve system-level control and operation objectives (e.g., voltage regulation). This helps utilities mitigate potential risks (e.g., instability) prior to field deployment.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Kölliker's Organ Functions as a Developmental Hub in Mouse Cochlea Regulating Spiral Limbus and Tectorial Membrane Development

Kölliker's organ is a transient developmental structure in the mouse cochlea that undergoes significant remodeling postnatally. Utilizing an epithelial-specific conditional deletion mouse model of Prdm16 (marker and regulator of Kölliker's organ), we show that Prdm16 is required for interdental cell development, and thereby the development of the limbal domain of the tectorial membrane and its medial anchorage to the spiral limbus. Additionally, we show that Kölliker's organ is involved in normal tectorial membrane collagen fibril development and maturation. Interestingly, mesenchymal cells of the spiral limbus underneath Prdm16 -deficient Kölliker's organ failed to produce interstitial matrix proteins, resulting in a hypoplastic and truncated spiral limbus, indicating a non-cell autonomous role of Prdm16 in regulating spiral mesenchymal matrix development. Single-cell RNA sequencing identified differentially expressed genes in Prdm16 -deficient Kölliker's organ suggesting a role for connective tissue growth factor (CTGF) downstream Prdm16 in epithelial-mesenchymal signaling involved in spiral limbus matrix deposition. Prdm16 -deficient mice showed a hearing deficit, as indicated by elevated auditory brainstem response thresholds at most frequencies, consistent with the cochlear structural defects. Both sexes were studied. This work establishes Prdm16 as a deafness gene in mice through its role in regulating Kölliker's organ development. Such understanding recognizes Kölliker's organ as a developmental hub regulating multiple surrounding cochlear structures.

Zhang, Hongji↗
DOE OSTI2022

State Indicators for Advancing Demand Flexibility and Energy Efficiency in Buildings - Part I [Slides]

This slide deck report identifies objectives and key indicators for state activities that advance demand flexibility in buildings — legislation, utility regulatory proceedings, executive orders and programs. It also illustrates progress to date and identifies trends, gaps, and opportunities. Part I of the report focuses on (1) demand response and (2) energy efficiency targeted to reduce peak demand or integrate with demand response. This section covers building energy codes, appliance and equipment standards, resource standards, utility planning, utility programs, advanced metering infrastructure and meter data, rate design, state programs, state energy planning, and related state policies and regulations. Part II of the report addresses traditional energy efficiency indicators, including utility and state programs, codes, and standards that support annual energy savings. See the additional links for an infographic, library of cited state documents on demand flexibility, and presentation to the NASEO-NARUC Grid-Interactive Efficient Buildings Working Group.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Assessing the Optimality of LinDist3Flow for Optimal Tap Selection of Step Voltage Regulators in Unbalanced Distribution Networks

The adoption of distributed energy resources such as photovoltaics (PVs) has increased dramatically during the previous decade. The increased penetration of PVs into distribution networks (DNs) can cause voltage fluctuations that have to be mitigated. One of the key utility assets employed to this end are step-voltage regulators (SVRs). It is desirable to include tap selection of SVRs in optimal power flow (OPF) routines, a task that turns out to be challenging because the resultant OPF problem is nonconvex with added complexities stemming from accurate SVR modeling. While several convex relaxations based on semi-definite programming (SDP) have been presented in the literature for optimal tap selection, SDP based schemes do not scale well and are challenging to implement in large-scale planning or operational frameworks. This paper deals with the optimal tap selection (OPTS) problem for wye-connected SVRs using linear approximations of power flow equations. Specifically, the LinDist3Flow model is adopted and the effective SVR ratio is assumed to be continuous- enabling the formulation of a problem called LinDist3Flow-OPTS, which amounts to a linear program. The scalability and optimality gap of LinDist3Flow-OPTS are evaluated with respect to existing SDP-based and nonlinear programming techniques for optimal tap selection in three standard feeders, namely, the IEEE 13-bus, 123-bus, and 8500-node DNs. For all DNs considered, LinDist3Flow-OPTS achieves an optimality gap of approximately 1% or less while significantly lowering the computational burden.

linear approximations↗
DOE OSTI2022

Assessing the Optimality of LinDist3Flow for Optimal Tap Selection of Step Voltage Regulators in Unbalanced Distribution Networks: Preprint

The adoption of distributed energy resources such as photovoltaics (PVs) has increased dramatically during the previous decade. The increased penetration of PVs into distribution networks (DNs) can cause voltage fluctuations that have to be mitigated. One of the key utility assets employed to this end are step-voltage regulators (SVRs). It is desirable to include tap selection of SVRs in optimal power flow (OPF) routines, a task that turns out to be challenging because the resultant OPF problem is nonconvex with added complexities stemming from accurate SVR modeling. While several convex relaxations based on semi-definite programming (SDP) have been presented in the literature for optimal tap selection, SDP based schemes do not scale well and are challenging to implement in large-scale planning or operational frameworks. This paper deals with the optimal tap selection (OPTS) problem for wye-connected SVRs using linear approximations of power flow equations. Specifically, the LinDist3Flow model is adopted and the effective SVR ratio is assumed to be continuous–enabling the formulation of a problem called LinDist3Flow-OPTS, which amounts to a linear program. The scalability and optimality gap of LinDist3Flow-OPTS are evaluated with respect to existing SDP-based and nonlinear programming techniques for optimal tap selection in three standard feeders, namely, the IEEE 13-bus, 123-bus, and 8500-node DNs. For all DNs considered, LinDist3Flow-OPTS achieves an optimality gap of approximately 1% or less while significantly lowering the computational burden.

linear approximations↗
DOE OSTI2013

The Value of Energy Storage for Grid Applications

This analysis evaluates several operational benefits of electricity storage, including load-leveling, spinning contingency reserves, and regulation reserves. Storage devices were simulated in a utility system in the western United States, and the operational costs of generation was compared to the same system without the added storage. This operational value of storage was estimated for devices of various sizes, providing different services, and with several sensitivities to fuel price and other factors. Overall, the results followed previous analyses that demonstrate relatively low value for load-leveling but greater value for provision of reserve services. The value was estimated by taking the difference in operational costs between cases with and without energy storage and represents the operational cost savings from deploying storage by a traditional vertically integrated utility. The analysis also estimated the potential revenues derived from a merchant storage plant in a restructured market, based on marginal system prices. Due to suppression of on-/off-peak price differentials and incomplete capture of system benefits (such as the cost of power plant starts), the revenue obtained by storage in a market setting appears to be substantially less than the net benefit provided to the system. This demonstrates some of the additional challenges for storage deployed in restructured energy markets.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Assessment of Commercial Building Lighting as a Frequency Regulation Resource

This paper evaluates the potential for automated lighting control as a resource for frequency regulation of the electric grid system in the context of current energy policies, economic incentives, and technological trends. The growing prevalence of renewable energy has increased the need for ancillary services to maintain grid frequency and stability. While demand side resources like heating, ventilating, and air-conditioning systems, as well as water treatment plants are already evaluated as regulation service providers, the potential application to electrical lighting systems has largely been ignored. Yet, aggregations of lighting systems that are retrofitted with intelligent controls could conceivably contribute to frequency regulation services with little impact on user comfort. To further explore the feasibility of lighting potential, this paper explores (1) how lighting control systems are limited by visual comfort perception and acceptability, (2) how such limitations impact the performance of the lighting system as an frequency regulation resource, and (3) how the market potential of lighting systems as demand side resources compares in different regional transmission organizations. Finally, the impact of developing technologies on the application of lighting systems for frequency regulation is discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Experimental Validation of a 40kW, 480V Point-to-Point DC Interlinks for Controller-Agnostic, Interoperable Networked Microgrids

This paper presents the experimental validation of point-to-point dc-interlinks for interconnecting two solar-based, laboratory-scale AC microgrids. DC interlinks provide a solution to numerous technical and operational challenges encountered in networked microgrids, including precise power flow control, stable and fast synchronization, enhanced stability, and improved voltage and frequency regulation. By decoupling microgrids through power converters, dc-interlinks enable power exchange among microgrids that can be owned by different entities (such as communities, utilities, or universities) and managed by diverse microgrid controller vendors. This characteristic makes this dc-interlinks a promising solution for networking real-world microgrids. The presented point-to-point dc interlink utilizes two four-quadrant converters: a 40kW 3-phase ac/dc regulating the dc-link voltage to 800V, and a 3-phase dc/ac controlling power flow. These converters, connected via a 20-foot dc cable, interconnect two ac microgrids operating at 480V, each featuring energy storage, photovoltaic generation, and load emulation. Experimental validation employs commercially available off-the-shelf (COTS) converters and real-world data from solar-powered microgrids in Adjuntas, Puerto Rico. To the authors’ knowledge, this work provides the first at-scale experimental validation of dc-interlinks for networked ac microgrids using COTS inverters, demonstrating their practicality and effectiveness in addressing real-world operational challenges.

Ferrari Maglia, Max [ORNL]↗
DOE OSTI2022

De novo transcriptome sequencing of Capsicum frutescens . L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU ‐9

Abstract Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth–promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress‐treated plants grown in a microorganism‐controlled environment. Our previous reports have selected Bacillus atrophaeus WU‐9 as PGPR significantly alleviating pepper ( Capsicum frutescens . L) salt stress. In this work, the RNA‐seq analysis of salt stress‐treated and untreated plants, grown with and without WU‐9 in a microorganism‐controlled environment, was used to reveal the plant salt stress alleviating mechanisms of WU‐9. Twelve sequencing libraries, prepared by treating with WU‐9 and salt (150 mM NaCl for 36 h), were constructed by RNA‐Seq technique. Non‐inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene‐activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU‐9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress‐responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens . L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR.

Wang, Wenfei↗
DOE OSTI2013

Identification and In-vivo Characterization of a Novel OhrR Transcriptional Regulator in Burkholderia xenovorans LB400

Transcriptional regulators (TRs) are an important and versatile group of proteins, yet very little progress has been achieved towards the discovery and annotation of their biological functions. We have characterized a previously unknown organic hydroperoxide resistance regulator from Burkholderia xenovoransLB400, Bxe_B2842, which is homologous to E. coli’s OhrR. Bxe_B2842 regulates the expression of an organic hydroperoxide resistance protein (OsmC). We utilized frontal affinity chromatography coupled with mass spectrometry (FAC-MS) and electrophoretic mobility gel shift assays (EMSA) to identify and characterize the possible effectors of the regulation by Bxe_B2842. Without an effector, Bxe_B2842 binds a DNA operator sequence (DOS) upstream of osmC. FAC-MS results suggest that 2-aminophenol binds to the protein and is potentially an effector molecule. EMSA analysis shows that 2-aminophenol also attenuates the Bxe_B2842’s affinity for its DOS. EMSA analysis also shows that organic peroxides attenuate Bxe_B2842/DOS affinity, suggesting that binding of the TR to its DOS is regulated by the two-cysteine mechanism, common to TRs in this family. Bxe_B2842 is the first OhrR TR to have both oxidative and effector-binding mechanisms of regulation. Our paper reveals further mechanistic diversity TR mediated gene regulation and provides insights into methods for function discovery of TRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Accuracy of automated measurement and verification (M&V) techniques for energy savings in commercial buildings

Trustworthy savings calculations are critical to convincing investors in energy efficiency projects of the benefit and cost-effectiveness of such investments and their ability to replace or defer supply-side capital investments. However, today’s methods for measurement and verification (M&V) of energy savings constitute a significant portion of the total costs of efficiency projects. They also require time-consuming manual data acquisition and often do not deliver results until years after the program period has ended. The rising availability of “smart” meters, combined with new analytical approaches to quantifying savings, has opened the door to conducting M&V more quickly and at lower cost, with comparable or improved accuracy. These meter- and software-based approaches, increasingly referred to as “M&V 2.0”, are the subject of surging industry interest, particularly in the context of utility energy efficiency programs. Program administrators, evaluators, and regulators are asking how M&V 2.0 compares with more traditional methods, how proprietary software can be transparently performance tested, how these techniques can be integrated into the next generation of whole-building focused efficiency programs. This paper expands recent analyses of public-domain whole-building M&V methods, focusing on more novel M&V2.0 modeling approaches that are used in commercial technologies, as well as approaches that are documented in the literature, and/or developed by the academic building research community. We present a testing procedure and metrics to assess the performance of whole-building M&V methods. We then illustrate the test procedure by evaluating the accuracy of ten baseline energy use models, against measured data from a large dataset of 537 buildings. The results of this study show that the already available advanced interval data baseline models hold great promise for scaling the adoption of building measured savings calculations using Advanced Metering Infrastructure (AMI) data. Median coefficient of variation of the root mean squared error (CV(RMSE)) was less than 25% for every model tested when twelve months of training data were used. With even six months of training data, median CV(RMSE) for daily energy total was under 25% for all models tested. Finally, these findings can be used to build confidence in model robustness, and the readiness of these approaches for industry uptake and adoption

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Leveraging Pre-Built Catalogs and Object-Level Scheduling to Eliminate I/O Bottlenecks in HPC Environments

Modern High-Performance Computing (HPC) environments face mounting challenges due to the shift from large to small file datasets, along with an increasing number of users and parallelized applications. As HPC systems rely on Parallel File Systems (PFS), such as Lustre for data processing, performance bottlenecks stemming from Object Storage Target (OST) contention have become a significant concern. Existing solutions, such as LADS with its object-level scheduling approach, fall short in large-scale HPC environments due to their inability to effectively address metadata I/O bottlenecks and the growing number of I/O processes. This study highlights the pressing need for a comprehensive solution that tackles both OST contention and metadata I/O challenges in diverse HPC workloads. To address these challenges, we propose SwiftLoad, an object-level I/O scheduling framework that leverages a metadata catalog to enhance the performance and efficiency of parallel HPC utilities. The adoption of the metadata catalog mitigates the metadata I/O bottlenecks that commonly occur in HPC utilities, a challenge that is particularly pronounced in object-level I/O scheduling. SwiftLoad addresses OST contention and the uneven distribution of I/O processes across different OSTs through mathematical modeling and incorporates a Loader Configuration Module to regulate the number of I/O processes. Evaluated with two representative utilities—data deduplication profiling and data augmentation—SwiftLoad achieved performance improvements of up to 5.63x and 11.0x, respectively, on a production supercomputer.

HPC↗
DOE OSTI2018

A Review of Classical Swine Fever Virus and Routes of Introduction into the United States and the Potential for Virus Establishment

Classical swine fever (CSF) is caused by CSF virus (CSFV) which can be the source of substantial morbidity and mortality events in affected swine. The disease can take one of several forms (acute, chronic, or prenatal) and depending on the virulence of the inoculating strain may result in a lethal infection irrespective of the form acquired. Because of the disease-free status of the United States and the high cost of a viral incursion, a summary of US vulnerabilities for viral introduction and persistence is provided. The legal importation of live animals as well as animal products, byproducts, and animal feed serve as a potential route of viral introduction. Current import regulations are described as are mitigation strategies that are commonly utilized to prevent pathogens, including CSFV, from entering the US. The illegal movement of suids and their products as well as an event of bioterrorism are both feasible routes of viral introduction but are difficult to restrict or regulate. Ultimately, recommendations are made for data that would be useful in the event of a viral incursion. Population and density mapping for feral swine across the United States would be valuable in the event of a viral introduction or spillover; density data could further contribute to understanding the risk of infection in domestic swine. Additionally, ecological and behavioral studies, including those that evaluate the effects of anthropogenic food sources that support feral swine densities far above the carrying capacity would provide invaluable insight to our understanding of how human interventions affect feral swine populations. Further analyses to determine the sampling strategies necessary to detect low levels of antibody prevalence in feral swine would also be valuable.

Veterinary Sciences↗
DOE OSTI2014

Isoproterenol effects evaluated in heart slices of human and rat in comparison to rat heart in vivo

Human response to isoproterenol induced cardiac injury was evaluated by gene and protein pathway changes in human heart slices, and compared to rat heart slices and rat heart in vivo. Isoproterenol (10 and 100 μM) altered human and rat heart slice markers of oxidative stress (ATP and GSH) at 24 h. In this in vivo rat study (0.5 mg/kg), serum troponin concentrations increased with lesion severity, minimal to mild necrosis at 24 and 48 h. In the rat and the human heart, isoproterenol altered pathways for apoptosis/necrosis, stress/energy, inflammation, and remodeling/fibrosis. The rat and human heart slices were in an apoptotic phase, while the in vivo rat heart exhibited necrosis histologically and further progression of tissue remodeling. In human heart slices genes for several heat shock 70 kD members were altered, indicative of stress to mitigate apoptosis. The stress response included alterations in energy utilization, fatty acid processing, and the up-regulation of inducible nitric oxide synthase, a marker of increased oxidative stress in both species. Inflammation markers linked with remodeling included IL-1α, Il-1β, IL-6 and TNFα in both species. Tissue remodeling changes in both species included increases in the TIMP proteins, inhibitors of matrix degradation, the gene/protein of IL-4 linked with cardiac fibrosis, and the gene Ccl7 a chemokine that induces collagen synthesis, and Reg3b a growth factor for cardiac repair. This study demonstrates that the initial human heart slice response to isoproterenol cardiac injury results in apoptosis, stress/energy status, inflammation and tissue remodeling at concentrations similar to that in rat heart slices. - Highlights: • Human response to isoproterenol induced cardiac injury evaluated in heart slices. • Isoproterenol altered apoptosis, energy, inflammation and remodeling pathways. • Human model verified by comparison to rat heart slices and rat heart in vivo. • Human and rat respond to isoproterenol at similar concentrations in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Sequential programmable self-assembly: Role of cooperative interactions

Here, we propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenient platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Glycyl-tRNA synthetase (GlyRS) is the enzyme that covalently links glycine to cognate tRNA for translation. It is of great interest because of its nonconserved quaternary structures, unique species-specific aminoacylation properties, and noncanonical functions in neurological diseases, but none of these is fully understood. We report two crystal structures of human GlyRS variants, in the free form and in complex with tRNA Gly respectively, and reveal new aspects of the glycylation mechanism. We discover that insertion 3 differs considerably in conformation in catalysis and that it acts like a "switch" and fully opens to allow tRNA to bind in a cross-subunit fashion. The flexibility of the protein is supported by molecular dynamics simulation, as well as enzymatic activity assays. The biophysical and biochemical studies suggest that human GlyRS may utilize its flexibility for both the traditional function (regulate tRNA binding) and alternative functions (roles in diseases).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Grid Integration of Small-Scale Photovoltaic Systems in Secondary Distribution Network—A Review

The relative share of renewable energy, specifically the solar photovoltaic (PV), is increasing exponentially in the world electric energy sector. This is a cumulative result of reduction in the cost of solar panels, improvement in the panel efficiency, and advancement in the associated power electronics. Among different types of PV plants, installation of small-scale rooftop PV is growing rapidly due to direct end-user benefits and lucrative governmental incentives. There are various standards developed in regards to grid integration of PVs and other distributed generations (DGs). Different power converter topologies are developed to interface the PV panel with the utility grid. To keep up with the stringent regulations imposed by the standards, various control strategies and grid synchronization methods have been developed. This review article amalgamates and summarizes all of the aforementioned aspects of a grid-integrated PV system including various standards, power stage architectures, grid synchronization methods, operation under extreme events, and control methodologies, pertaining to small-scale PV plants. This article will help freshman researchers to gain some familiarity with the topic and introduce them to some of the key issues encountered in this field.

14 SOLAR ENERGY↗
DOE OSTI2023

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗