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DOE OSTI2016

A LuxR homolog in a cottonwood tree endophyte that activates gene expression in response to a plant signal or specific peptides

Homologs of the LuxR acyl-homoserine lactone (AHL) quorum-sensing signal receptor are prevalent in Proteobacteria isolated from roots of the Eastern cottonwood tree, Populus deltoides . Many of these isolates possess an orphan LuxR homolog, closely related to OryR from the rice pathogen Xanthomonas oryzae . OryR does not respond to AHL signals but, instead, responds to an unknown plant compound. We discovered an OryR homolog, PipR, in the cottonwood endophyte Pseudomonas sp. strain GM79. The genes adjacent to pipR encode a predicted ATP-binding cassette (ABC) peptide transporter and peptidases. We purified the putative peptidases, PipA and AapA, and confirmed their predicted activities. A transcriptional pipA-gfp reporter was responsive to PipR in the presence of plant leaf macerates, but it was not influenced by AHLs, similar to findings with OryR. We found that PipR also responded to protein hydrolysates to activate pipA-gfp expression. Among many peptides tested, the tripeptide Ser-His-Ser showed inducer activity but at relatively high concentrations. An ABC peptide transporter mutant failed to respond to leaf macerates, peptone, or Ser-His-Ser, while peptidase mutants expressed higher-than-wild-type levels of pipA-gfp in response to any of these signals. Our studies are consistent with a model where active transport of a peptidelike signal is required for the signal to interact with PipR, which then activates peptidase gene expression. As a result, the identification of a peptide ligand for PipR sets the stage to identify plant-derived signals for the OryR family of orphan LuxR proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Parameter Estimation for Decoding Sensor Signals

This paper introduces a parameter estimation approach for decoding digital sensor signals in a cyber-physical system. For unknown or not fully characterized digital sensor data, it can be difficult to decipher a desired signal from background or noise. In a cyber-physical system with networked sensors, we can leverage knowledge of the physical system to inform the decoding of the digital signals. This work in progress is a case study on deciphering commercial vehicle on-board sensor networks that communicate through the Controller Area Network (CAN). By understanding the stock vehicle sensor network, a vehicle can be extended into a scalable research platform with minimal instrumentation. Our challenge was to localize desired sensor signals encoded in network traffic that included other sensor data, control messages, as well as encoding and security overhead. Due to the vehicle’s unknown sensor network, our approach developed methods to efficiently analyze and identify key signals despite the large state-space for potential signal embeddings.

Nice, Matthew↗

DOE OSTI2021

NEMA-Phase Compliant Traffic Signal Controller Module in SUMO

The controller modules in SUMO use a stage-based control structure. A phase is defined as a stage of all allowed movements at a time instance. However, traffic signal controllers used in North America widely use National Electrical Manufacturers Association (NEMA) phase definition. A NEMA phase is defined by a certain flow movement at an intersection. At one time, more than one NEMA phase could happen together as long as they do not conflict with each other. We can visualize the NEMA phases and timings in Ring-and-Barrier structured NEMA diagrams. For one controller, only one phase from a ring can be activated at a time. Phases from different rings could be activated together as long as they are not from the different sides of a barrier. When a controller is operated in fixed-time control mode, we can model the NEMA phase timing as a corresponding stage-based control timing without any issues. When introducing actuation into the signal control, a Ring-and-Barrier structured traffic signal controller can be more flexible than stage-based controller by allowing different possible phase combinations. We made two efforts in modeling Ring-and-Barrier structured controllers in SUMO. One is to translate a NEMA phases timing into SUMO-readable phases and timings as an additional file for SUMO. This translation worked well for fixed-time control. To model actuated control and coordinated actuated control, we augmented the SUMO source code by adding a Ring-and-Barrier structured controller module. This module could implement traffic signal timing from controllers using NEMA phases. We also augmented TraCI to be able to set new NEMA phase timings during simulations. We examined the Ring-and-Barrier structured traffic signal controller module by both visually observing the simulation animations and the simulation records. The developed control module can model the generalized Ring-and-Barrier structured traffic signal timing that is used in North America. SEE: https://github.com/eclipse/sumo/blob/main/src/microsim/traffic_lights/NEMAController.cpp

Wang, Qichao↗

DOE OSTI2015

Computational expressions for signals in frequency-modulation spectroscopy

In this study, general expressions for the signals in frequency-modulation spectroscopy (FMS) appear in the literature but are often reduced to simple analytical equations following the assumption of a weak modulation index. This is little help to the experimentalist who wants to predict signals for modulation depths of the order of unity or greater, where strong FMS signals reside. Here, we develop general formulas for FMS signals in the case of an absorber with a Voigt line shape and then link these expressions to an example and existing numerical code for the line shape. The resulting computational recipe is easy to implement and exercised here to show where the larger FMS signals are found over the coordinates of modulation index and modulation frequency. One can also estimate from provided curves the in-phase FMS signal over a wide range of modulation parameters at either the Lorentzian-broadening or Doppler-broadening limit, or anywhere in between by interpolation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2013

Assigning Quantitative Function to Post-Translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output

Cell signaling systems transmit information by post-translationally modifying signaling proteins, often via phosphorylation. While thousands of sites of phosphorylation have been identified in proteomic studies, the vast majority of sites have no known function. Assigning functional roles to the catalog of uncharacterized phosphorylation sites is a key research challenge. Here we present a general approach to address this challenge and apply it to a prototypical signaling pathway, the pheromone response pathway in Saccharomyces cerevisiae. The pheromone pathway includes a mitogen activated protein kinase (MAPK) cascade activated by a G-protein coupled receptor (GPCR). We used mass spectrometry-based proteomics to identify sites whose phosphorylation changed when the system was active, and evolutionary conservation to assign priority to a list of candidate MAPK regulatory sites. We made targeted alterations in those sites, and measured the effects of the mutations on pheromone pathway output in single cells. Our work identified six new sites that quantitatively tuned system output. We developed simple computational models to find system architectures that recapitulated the quantitative phenotypes of the mutants. Our results identify a number of regulated phosphorylation events that contribute to adjust the input-output relationship of this model eukaryotic signaling system. We believe this combined approach constitutes a general means not only to reveal modification sites required to turn a pathway on and off, but also those required for more subtle quantitative effects that tune pathway output. Our results further suggest that relatively small quantitative influences from individual regulatory phosphorylation events endow signaling systems with plasticity that evolution may exploit to quantitatively tailor signaling outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Along-Trajectory Acoustic Signal Variations Observed During the Hypersonic Re-Entry of the OSIRIS-REx Sample Return Capsule

The re-entry of the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) sample return capsule (SRC) on 24 September 2023 presented a rare opportunity to study atmospheric entry dynamics through a dense network of ground-based infrasound sensors. As the first interplanetary capsule to re-enter over the United States since Stardust in 2006, this event allowed for unprecedented observations of infrasound signals generated during hypersonic descent. We deployed 39 single-sensor stations across Nevada and Utah, strategically distributed to capture signals from distinct trajectory points. Infrasound data were analyzed to examine how signal amplitude and period vary with altitude and propagation path for a nonablating hypersonic object with well-defined physical and aerodynamic properties. Raytracing simulations incorporated atmospheric specifications from the ground-2-space model to estimate source altitudes for observed signals. Results confirmed ballistic arrivals at all stations, with source altitudes ranging from 44 to 62 km along the trajectory. Signal period and amplitude exhibited strong dependence on source altitude, with higher altitudes corresponding to lower amplitudes, longer periods, and reduced high-frequency content. Regression analysis demonstrated strong correlations between signal characteristics and both altitude and propagation geometry. Our results suggest, when attenuation is considered, the amplitude is primarily determined by the source, with the propagation path playing a secondary role over the distances examined. These findings emphasize the utility of controlled SRC re-entries for advancing our understanding of natural meteoroid dynamics, refining atmospheric entry models, and improving methodologies for planetary defense. The OSIRIS-REx SRC campaign represents the most comprehensive infrasound study of a hypersonic re-entry to date, showcasing the potential of coordinated geophysical observational networks for high-energy atmospheric phenomena, including space debris re-entries.

58 GEOSCIENCES↗

DOE OSTI2013

NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals

The microenvironment of cells controls their phenotype, and thereby the architecture of the emerging multicellular structure or tissue. We have reported more than a dozen microenvironmental factors whose signaling must be integrated in order to effect an organized, functional tissue morphology. However, the factors that prevent integration of signaling pathways that merge form and function are still largely unknown. We have identified nuclear factor kappa B (NFkB) as a transcriptional regulator that disrupts important microenvironmental cues necessary for tissue organization. We compared the gene expression of organized and disorganized epithelial cells of the HMT-3522 breast cancer progression series: the non-malignant S1 cells that form polarized spheres (‘acini’), the malignant T4-2 cells that form large tumor-like clusters, and the ‘phenotypically reverted’ T4-2 cells that polarize as a result of correction of the microenvironmental signaling. We identified 180 genes that display an increased expression in disorganized compared to polarized structures. Network, GSEA and transcription factor binding site analyses suggested that NFkB is a common activator for the 180 genes. NFkB was found to be activated in disorganized breast cancer cells, and inhibition of microenvironmental signaling via EGFR, beta1 integrin, MMPs, or their downstream signals suppressed its activation. The postulated role of NFkB was experimentally verified: Blocking the NFkB pathway with a specific chemical inhibitor or shRNA induced polarization and inhibited invasion of breast cancer cells in 3D cultures. These results may explain why NFkB holds promise as a target for therapeutic intervention: Its inhibition can reverse the oncogenic signaling involved in breast cancer progression and integrate the essential microenvironmental control of tissue architecture.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

CHIRP-Like Signals: Estimation, Detection and Processing A Sequential Model-Based Approach

Chirp signals have evolved primarily from radar/sonar signal processing applications specifically attempting to estimate the location of a target in surveillance/tracking volume. The chirp, which is essentially a sinusoidal signal whose phase changes instantaneously at each time sample, has an interesting property in that its correlation approximates an impulse function. It is well-known that a matched-filter detector in radar/sonar estimates the target range by cross-correlating a replicant of the transmitted chirp with the measurement data reflected from the target back to the radar/sonar receiver yielding a maximum peak corresponding to the echo time and therefore enabling the desired range estimate. In this application, we perform the same operation as a radar or sonar system, that is, we transmit a “chirp-like pulse” into the target medium and attempt to first detect its presence and second estimate its location or range. Our problem is complicated by the presence of disturbance signals from surrounding broadcast stations as well as extraneous sources of interference in our frequency bands and of course the ever present random noise from instrumentation. First, we discuss the chirp signal itself and illustrate its inherent properties and then develop a model-based processing scheme enabling both the detection and estimation of the signal from noisy measurement data.

42 ENGINEERING↗

DOE OSTI2018

Signal Transduction Pathways of Chloroplast Quality Control

Chloroplasts (photosynthetic organelles) of higher plants contain about 3000 proteins, but fewer than 5% of these proteins are encoded by genes in the chloroplast. The rest are encoded by genes in the nucleus, which is a separate organelle within the plant cell. To avoid the accumulation of dangerous reactive oxygen species that are the inherent by-product of photosynthesis, gene expression of these spatially separated genomes is regulated by two-way signaling. Thus, while plastid differentiation and development are largely controlled by the nucleus and the proteins encoded within, developmentally arrested or damaged plastids can regulate expression of nuclear genes via retrograde signaling pathways. During the early years of this DOE-funded study, we performed a number of genetic screens to identify genes and protein involved in these signals. Based on the genes that we identified, we found that chloroplast gene expression and the chlorophyll (the major light-harvesting pigment that gives plant tissue its characteristic green color) biosynthetic pathway can act as the source of both positive and stress-related retrograde signals. We also found a new protein called GUN1, that plays a crucial role in retrograde signaling. Although the exact molecular mechanism of GUN1 remains a mystery, our work showed that it likely acts in the chloroplast to coordinate chloroplast gene expression with nuclear gene expression and to ensure that seedlings can quickly green after germination. Using that work as a foundation, we have recently uncovered a new type of retrograde signal that leads to the selective removal of damaged chloroplasts from the cell. We have only begun the characterization of this pathway, but our initial studies have suggested that this may be an extremely important mechanism that allows plants to adapt to stressful conditions. Together this will aid in the understanding of the developmental control of photosynthesis, the chloroplast assembly/disassembly pathways, and how plants adapt to stressful conditions. Ultimately, we hope this work will allow us to begin to engineer these crucial pathways into agriculturally important or bioenergy rich crops. This will be crucial to our quest for an abundant food supply and cheap, dependable sources of energy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Multichannel Deconvolution of Vibrational Shock Signals: An Inverse Filtering Approach

When transporting critical systems of national security interest, out-of-the ordinary, impulsive events that can potentially be undetected and affect overall system performance are of great concern. Impulsive events that can occur are essentially pulse-like, transient signals of short duration that evolve from various phenomena. Here the event can be created by either the dropping of a test object, the system, subjecting it to a compact high-energy blow or being struck unintentionally during transit resulting in potential damage. The intensity and location of the strike can cause an inoperability condition that is unacceptable in a national security environment. Therefore, it is essential to detect, classify and localize damage of any test object subjected to an impulsive-event. This effort was targeted to evaluate the vibrational response of test objects that are subjected to “transport” shocks and roadway vibrations during shipping and handling. Any potential damage that could be inflicted during transportation must not only be detected, but also be evaluated to determine the operational readiness of a test object before and after transport. This event is a critical task that must be addressed as part of the Lawrence Livermore National Laboratory (LLNL) national security mission. The estimation of excitation signals from noisy data is termed the deconvolution problem in the signal processing literature. The deconvolution problem is based on recovering the input excitation signal from a system characterized by its impulse response sequence. Using this model of the system, an “inverse” representation or filter is developed to remove the system from the measured data and recover the input. Deconvolution techniques have existed for a long-time; however, transient deconvolution presents a few uncommon problems, since the signal has a finite-length time duration resulting in a limited amount of data containing information about the excitation process. The transient is wideband in the frequency domain relative to any measurement sensor implying that the smaller bandwidth sensor system “filters” the excitation eliminating some of its essential information for recovery. This fact, coupled with the filtering effect of the test object itself makes this excitation recovery (deconvolution) problem a challenge for signal processing.

42 ENGINEERING↗

DOE OSTI2023

Signal Decomposition for Intrusion Detection in Reliability Assessment in Cyber Resilience (Summary Report)

The complexity of assuring cyber resilience for physical process interactions in connected systems such as energy grids increases dramatically as the coupling between processes becomes more direct and responsive. An example of this growing complexity is provided by Integrated Energy Systems (IES), in which various processes such as nuclear heat generation and commodity production are being directly coupled for increased responsiveness to highly variable signals such as market pricing or electricity demand. As such, the potential attack surface of the coupled processes is larger than the two processes independently. Securing these complex systems requires two-fold monitoring: cybersecure monitoring for potential malicious incursion, and physics monitoring for system tampering. Physics monitoring includes analyzing the behavior of the signals within the system for anomalous behavior. This analysis has been shown to be insufficient if approached by only data-driven machine learning and artificial intelligence (MLAI) techniques or only low-level model comparison. Previous efforts at Purdue University suggested combining high-fidelity models with MLAI algorithms as a basis for a software tool for detecting anomalies in physical processes. This work built on that suggestion, developing an advanced library for signal decomposition and analysis using both MLAI and high-fidelity physics algorithms for greatly improved anomaly detection, especially false data injection. This software can be used as part of a secure imbedded intelligence (SEI) system designed under Consequence-driven Cyber-informed Engineering (CCE) for complex coupled systems. This library established a foundation for online and posteriori analysis of digital signals for the purpose of detecting potential malicious tampering in digital signals representing physical processes. Demonstrations carried out throughout the development highlight the effective use of characterization algorithms to detect signal perturbations, particularly triangle attack-style perturbations, in three wide-ranging applications: seismic monitoring, nuclear thermal hydraulics system simulation, and custom manufacturing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Signal Processing in SBND with Calibrated and Validated Electronics and Field Responses

SBND is a liquid argon time projection chamber in Fermilab’s Short-Baseline Neutrino Program, located 110 m from the neutrino source and operating in a high-rate environment with unprecedented statistics. Charged particles from neutrino interactions ionize the argon, and the resulting electrons drift to the anode wires, inducing current signals recorded as raw waveforms. These waveforms are a convolution of deposited charge with the electronics and TPC field responses, making accurate signal processing essential for recovering the true charge distribution. Signal processing forms the starting point for SBND reconstruction, directly impacting hit finding, charge calibration, clustering, and the reconstruction of tracks and showers, and therefore playing a key role in energy reconstruction and particle identification. In this poster, we present an overview of the SBND signal processing chain, including noise removal, channel-by-channel electronics correction, signal identification, and deconvolution using measured electronics and TPC field responses. We demonstrate that the two kernel functions—electronics and field responses—achieve high precision when compared to data, ensuring that the SBND signal processing chain provides a robust and accurate foundation for event reconstruction and precision physics measurements.

Singh, Prabhjot [Louisiana State U.] (ORCID:000000↗

DOE OSTI2021

Targeting Drugs Against Fibroblast Growth Factor(s)-Induced Cell Signaling

Background:: The fibroblast growth factor (FGF) family is comprised of 23 highly regulatedmonomeric proteins that regulate a plethora of developmental and pathophysiological processes,including tissue repair, wound healing, angiogenesis, and embryonic development. Binding ofFGF to fibroblast growth factor receptor (FGFR), a tyrosine kinase receptor, is facilitated by a glycosaminoglycan,heparin. Activated FGFRs phosphorylate the tyrosine kinase residues that mediateinduction of downstream signaling pathways, such as RAS-MAPK, PI3K-AKT, PLCγ, andSTAT. Dysregulation of the FGF/FGFR signaling occurs frequently in cancer due to gene amplification,FGF activating mutations, chromosomal rearrangements, integration, and oncogenic fusions.Aberrant FGFR signaling also affects organogenesis, embryonic development, tissue homeostasis,and has been associated with cell proliferation, angiogenesis, cancer, and other pathophysiologicalchanges. Objective:: This comprehensive review will discuss the biology, chemistry, and functions of FGFs,and its current applications toward wound healing, diabetes, repair and regeneration of tissues, andfatty liver diseases. In addition, specific aberrations in FGFR signaling and drugs that target FGFRand aid in mitigating various disorders, such as cancer, are also discussed in detail. Conclusion:: Inhibitors of FGFR signaling are promising drugs in the treatment of several types ofcancers. The clinical benefits of FGF/FGFR targeting therapies are impeded due to the activationof other RTK signaling mechanisms or due to the mutations that abolish the drug inhibitory activityon FGFR. Thus, the development of drugs with a different mechanism of action for FGF/FGFRtargeting therapies is the recent focus of several preclinical and clinical studies.

Pharmacology & Pharmacy↗

DOE OSTI2018

Microenvironmental Signals and Biochemical Information Processing: Cooperative Determinants of Intratumoral Plasticity and Heterogeneity

Intra-tumor cellular heterogeneity is a major challenge in cancer therapy. Tumors are composed of multiple phenotypic subpopulations that vary in their ability to initiate metastatic tumors and in their sensitivity to chemotherapy. In many cases, cells can transition between these subpopulations, not by genetic mutation, but instead through reversible changes in signal transduction or gene expression programs. This plasticity begins at the level of the microenvironment where local autocrine and paracrine signals, exosomes, tumor–stroma interactions, and extracellular matrix (ECM) composition create a signaling landscape that varies over space and time. The integration of this complex array of signals engages signaling pathways that control gene expression. The resulting modulation of gene expression programs causes individual cells to sample a wide array of phenotypic states that support tumor growth, dissemination, and therapeutic resistance. In this review, we discuss how information flows dynamically within the microenvironmental landscape to inform cell state decisions and to create intra-tumoral heterogeneity. We address the role of plasticity in the acquisition of transient and prolonged drug resistant states and discuss how targeted pharmacological modification of the signaling landscape may be able to constrain phenotypic plasticity, leading to improved treatment responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗

DOE OSTI2017

Sunyaev–Zel’Dovich Signal from Quasar Hosts: Implications for Detection of Quasar Feedback

Several analytic and numerical studies have indicated that the interstellar medium of a quasar host galaxy heated by feedback can contribute to a substantial secondary signal in the cosmic microwave background (CMB) through the thermal Sunyaev–Zel’dovich (SZ) effect. Recently, many groups have tried to detect this signal by cross-correlating CMB maps with quasar catalogs. Using a self-similar model for the gas in the intra-cluster medium and a realistic halo occupation distribution (HOD) prescription for quasars, we estimate the level of SZ signal from gravitational heating of quasar hosts. The bias in the host halo signal estimation due to an unconstrained high mass HOD tail and yet unknown redshift dependence of the quasar HOD restricts us from drawing any robust conclusions at low redshift ( z < 1.5) from our analysis. However, at higher redshifts ( z > 2.5), we find an excess signal in recent observations than what is predicted from our model. The excess signal could be potentially generated from additional heating due to quasar feedback.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1966

Instrument automatically selects peak acceleration signal from several accelerometers

Solid state circuit selects the highest of several ac accelerometer signals and gates this signal to an output amplifier, preserving all the frequency information in the peak signal. If the amplitudes of the accelerometer signals change with time, the circuit will continually switch to the highest signal, rejecting the smaller signals.

Chapman, C. P.↗

NASA NTRS1973

Signal-to-noise ratio determination circuit

A signal-to-noise ratio (SNR) determination of an input is described, having signal components within a given frequency range and noise components, without actual measurement of the noise components. Bandpass limiter having a constant signal plus noise output level is connected to the output of the first filter, the signal-to-noise ratio of the input to the bandpass limiter being linearly related to the dbm level of signal components at the output. Calibration is connected to the bandpass limiter and is responsive to the signal components at the output to derive the SNR of the input to the determination circuit. The SNR determination circuit is disclosed for use in a diversity receiver having a plurality of input channels.

Deerkoski, L. F.↗