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At least 451 records · Page 25

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DOE OSTI2020

Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects of 56 Fe, 16 O, and 28 Si irradiation on the induction of murine hepatocellular carcinoma

One of the health risks posed to astronauts during deep space flights is exposure to high charge, high-energy (HZE) ions (Z > 13), which can lead to the induction of hepatocellular carcinoma (HCC). However, little is known on the molecular mechanisms of HZE irradiation-induced HCC. We performed comparative RNA-Seq transcriptomic analyses to assess the carcinogenic effects of 600 MeV/n 56 Fe (0.2 Gy), 1 GeV/n 16 O (0.2 Gy), and 350 MeV/n 28 Si (0.2 Gy) ions in a mouse model for irradiation-induced HCC. C3H/HeNCrl mice were subjected to total body irradiation to simulate space environment HZE-irradiation, and liver tissues were extracted at five different time points post-irradiation to investigate the time-dependent carcinogenic response at the transcriptomic level. Our data demonstrated a clear difference in the biological effects of these HZE ions, particularly immunological, such as Acute Phase Response Signaling, B Cell Receptor Signaling, IL-8 Signaling, and ROS Production in Macrophages. Also seen in this study were novel unannotated transcripts that were significantly affected by HZE. To investigate the biological functions of these novel transcripts, we used a machine learning technique known as self-organizing maps (SOMs) to characterize the transcriptome expression profiles of 60 samples (45 HZE-irradiated, 15 non-irradiated control) from liver tissues. A handful of localized modules in the maps emerged as groups of co-regulated and co-expressed transcripts. The functional context of these modules was discovered using overrepresentation analysis. We found that these spots typically contained enriched populations of transcripts related to specific immunological molecular processes (e.g., Acute Phase Response Signaling, B Cell Receptor Signaling, IL-3 Signaling), and RNA Transcription/Expression. A large number of transcripts were found differentially expressed post-HZE irradiation. These results provide valuable information for uncovering the differences in molecular mechanisms underlying HZE specific induced HCC carcinogenesis. Additionally, a handful of novel differentially expressed unannotated transcripts were discovered for each HZE ion. Taken together, these findings may provide a better understanding of biological mechanisms underlying risks for HCC after HZE irradiation and may also have important implications for the discovery of potential countermeasures against and identification of biomarkers for HZE-induced HCC.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2005

Medial vestibular connections with the hypocretin (orexin) system

The mammalian medial vestibular nucleus (MVe) receives input from all vestibular endorgans and provides extensive projections to the central nervous system. Recent studies have demonstrated projections from the MVe to the circadian rhythm system. In addition, there are known projections from the MVe to regions considered to be involved in sleep and arousal. In this study, afferent and efferent subcortical connectivity of the medial vestibular nucleus of the golden hamster (Mesocricetus auratus) was evaluated using cholera toxin subunit-B (retrograde), Phaseolus vulgaris leucoagglutinin (anterograde), and pseudorabies virus (transneuronal retrograde) tract-tracing techniques. The results demonstrate MVe connections with regions mediating visuomotor and postural control, as previously observed in other mammals. The data also identify extensive projections from the MVe to regions mediating arousal and sleep-related functions, most of which receive immunohistochemically identified projections from the lateral hypothalamic hypocretin (orexin) neurons. These include the locus coeruleus, dorsal and pedunculopontine tegmental nuclei, dorsal raphe, and lateral preoptic area. The MVe itself receives a projection from hypocretin cells. CTB tracing demonstrated reciprocal connections between the MVe and most brain areas receiving MVe efferents. Virus tracing confirmed and extended the MVe afferent connections identified with CTB and additionally demonstrated transneuronal connectivity with the suprachiasmatic nucleus and the medial habenular nucleus. These anatomical data indicate that the vestibular system has access to a broad array of neural functions not typically associated with visuomotor, balance, or equilibrium, and that the MVe is likely to receive information from many of the same regions to which it projects.

Non-NASA Center↗

DOE OSTI2020

Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform

Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Multiscale simulation of spatially correlated microstructure via a latent space representation

When deformation gradients act on the scale of the microstructure of a part due to geometry and loading, spatial correlations and finite-size effects in simulation cells cannot be neglected. We propose a multiscale method that accounts for these effects using a variational autoencoder to encode the structure–property map of the stochastic volume elements making up the statistical description of the part. In this paradigm the autoencoder can be used to directly encode the microstructure or, alternatively, its latent space can be sampled to provide likely realizations. Furthermore, we demonstrate the method on three examples using the common additively manufactured material AlSi10Mg in: (a) a comparison with direct numerical simulation of the part microstructure, (b) a push forward of microstructural uncertainty to performance quantities of interest, and (c) a simulation of functional gradation of a part with stochastic microstructure.

Elastoplasticity↗

DOE OSTI2020

Tracking elemental changes in an ischemic stroke model with X-ray fluorescence imaging

Stroke is a leading cause of long-term disability in adults and a leading cause of death in developed nations. The cascade of cellular events and signalling that occur after cerebral ischemia are complex, however, analyzing global element markers of metabolic state affords the means to monitor stroke severity, status of injury, and recovery. These markers provide a multi-parameter method for assessing changes through the post-stroke time course. We employ synchrotron-based elemental mapping to follow elemental changes in the brain at 1 h, 1-, 2-, and 3-days, and at 1-, 2-, 3-, and 4-weeks post-stroke in a photothrombotic stroke model in mice. Our analysis reveals a highly consistent metabolic penumbra that can be readily identified based on the level of dysregulated potassium and other key elements. Maps of elemental distributions are also useful to demarcate events in the cellular response to the inflammatory cascade, including ion dysregulation, recruitment of cells to the lesion, and glial scar formation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Interface-driven magnetic anisotropy in relaxed La 0.7 Sr 0.3 CrO 3 /La 0.7 Sr 0.3 MnO 3 heterostructures on MgO

We investigate the structural and magnetic properties of La 0.7 Sr 0.3 CrO 3 /La 0.7 Sr 0.3 MnO 3 (LSMO) heterostructures grown on (001)-oriented MgO by molecular beam epitaxy. Due to the large film-substrate lattice mismatch, strain relaxation is found to occur within the first 2–3 unit cells (uc) of the film as evidenced by reflection high energy electron diffraction and high-resolution synchrotron x-ray reciprocal space mapping. Furthermore, we find that the presence of the LSCO spacer and capping layers leads to ferromagnetism in ultra-thin LSMO layers with thicknesses of the order of 2 uc with the magnetic easy axis oriented in the film plane. Net magnetic moments of 1.4 and 2.4 μ B /Mn are measured for (2 uc LSCO/2 uc LSMO) and (2 uc LSCO/4 uc LSMO) superlattices, respectively, by superconducting quantum interference device magnetometry. The effective magnetic anisotropy of the relaxed (2 uc LSCO/4 uc LSMO) heterostructure is found to be an order of magnitude higher than bulk LSMO highlighting the critical role of interfacial interactions in tuning magnetic anisotropy at complex oxide interfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2009

Development of a GCR Event-based Risk Model

A goal at NASA is to develop event-based systems biology models of space radiation risks that will replace the current dose-based empirical models. Complex and varied biochemical signaling processes transmit the initial DNA and oxidative damage from space radiation into cellular and tissue responses. Mis-repaired damage or aberrant signals can lead to genomic instability, persistent oxidative stress or inflammation, which are causative of cancer and CNS risks. Protective signaling through adaptive responses or cell repopulation is also possible. We are developing a computational simulation approach to galactic cosmic ray (GCR) effects that is based on biological events rather than average quantities such as dose, fluence, or dose equivalent. The goal of the GCR Event-based Risk Model (GERMcode) is to provide a simulation tool to describe and integrate physical and biological events into stochastic models of space radiation risks. We used the quantum multiple scattering model of heavy ion fragmentation (QMSFRG) and well known energy loss processes to develop a stochastic Monte-Carlo based model of GCR transport in spacecraft shielding and tissue. We validated the accuracy of the model by comparing to physical data from the NASA Space Radiation Laboratory (NSRL). Our simulation approach allows us to time-tag each GCR proton or heavy ion interaction in tissue including correlated secondary ions often of high multiplicity. Conventional space radiation risk assessment employs average quantities, and assumes linearity and additivity of responses over the complete range of GCR charge and energies. To investigate possible deviations from these assumptions, we studied several biological response pathway models of varying induction and relaxation times including the ATM, TGF -Smad, and WNT signaling pathways. We then considered small volumes of interacting cells and the time-dependent biophysical events that the GCR would produce within these tissue volumes to estimate how GCR event rates mapped to biological signaling induction and relaxation times. We considered several hypotheses related to signaling and cancer risk, and then performed simulations for conditions where aberrant or adaptive signaling would occur on long-duration space mission. Our results do not support the conventional assumptions of dose, linearity and additivity. A discussion on how event-based systems biology models, which focus on biological signaling as the mechanism to propagate damage or adaptation, can be further developed for cancer and CNS space radiation risk projections is given.

Cucinotta, Francis A.↗

DOE OSTI2024

CO2 response screen in grass Brachypodium reveals the key role of a MAP kinase in CO2-triggered stomatal closure

Abstract Plants respond to increased CO2 concentrations through stomatal closure, which can contribute to increased water use efficiency. Grasses display faster stomatal responses than eudicots due to dumbbell-shaped guard cells flanked by subsidiary cells working in opposition. However, forward genetic screening for stomatal CO2 signal transduction mutants in grasses has yet to be reported. The grass model Brachypodium distachyon is closely related to agronomically important cereal crops, sharing largely collinear genomes. To gain insights into CO2 control mechanisms of stomatal movements in grasses, we developed an unbiased forward genetic screen with an EMS-mutagenized B. distachyon M5 generation population using infrared imaging to identify plants with altered leaf temperatures at elevated CO2. Among isolated mutants, a “chill1” mutant exhibited cooler leaf temperatures than wild-type Bd21-3 parent control plants after exposure to increased CO2. chill1 plants showed strongly impaired high CO2-induced stomatal closure despite retaining a robust abscisic acid-induced stomatal closing response. Through bulked segregant whole-genome sequencing analyses followed by analyses of further backcrossed F4 generation plants and generation and characterization of sodium azide and CRISPR-cas9 mutants, chill1 was mapped to a protein kinase, Mitogen-Activated Protein Kinase 5 (BdMPK5). The chill1 mutation impaired BdMPK5 protein-mediated CO2/HCO3− sensing together with the High Temperature 1 (HT1) Raf-like kinase in vitro. Furthermore, AlphaFold2-directed structural modeling predicted that the identified BdMPK5-D90N chill1 mutant residue is located at the interface of BdMPK5 with the BdHT1 Raf-like kinase. BdMPK5 is a key signaling component that mediates CO2-induced stomatal movements and is proposed to function as a component of the primary CO2 sensor in grasses.

Lopez, Bryn N. K. (ORCID:0009000937288216)↗

DOE OSTI2023

exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers

Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A Comprehensive Stress Drop Map From Trench to Depth in the Northern Chilean Subduction Zone

We compute stress drops for earthquakes in Northern Chile recorded between 2007 and 2021. By applying two analysis techniques, (a) the spectral ratio (SR) method and (b) the spectral decomposition (SDC) method, a stress drop map for the subduction zone consisting of 51,510 stress drop values is produced. We build an extended set of empirical Green’s functions (EGF) for the SR method by systematic template matching. Outputs are used to compare with results from the SDC approach, where we apply cell-wise obtained global EGF's to compensate for the structural heterogeneity of the subduction zone. We find a good consistency of results of the two methods. The increased spatial coverage and quantity of stress drop estimates from the SDC method facilitate a consistent stress drop mapping of the different seismotectonic domains. Albeit only small differences of median stress drop, strike-perpendicular depth sections clearly reveal systematic variations, with earthquakes at different seismotectonic locations exhibiting distinct values. In particular, interface seismicity is characterized by the lowest observed median value, whereas upper plate earthquakes show noticeably higher stress drop values. Intermediate depth earthquakes show comparatively high average stress drop and a rather strong depth-dependent increase of median stress drop. Additionally, we observe spatio-temporal variability of stress drops related to the occurrence of the two megathrust earthquakes in the study region. The presented study is the first coherent large scale 3D stress drop mapping of the Northern Chilean subduction zone. It provides an important component for further detailed analysis of the physics of earthquake ruptures.

58 GEOSCIENCES↗

DOE OSTI2025

Hemicellulose Modulates Nanoscale Lignin Architecture in Synthetic Plant Cell Walls

Cellulose, hemicellulose, and lignin─the most abundant biopolymers on Earth─compose the structural matrix of plant biomass, providing renewable resources critical to bioenergy and sustainable materials. Despite their importance, the nanoscale mechanochemical processes underlying lignocellulose assembly during plant secondary cell wall formation remain poorly understood, hindering advancements in biomass conversion technologies. Here, in this study, we synthesize a biomimetic model system comprising cellulose–hemicellulose nanofibrils (CHN) to examine guaiacyl lignin polymerization in a physiologically relevant context. Using advanced nanocharacterization─scattering-type scanning near-field optical microscopy (s-SNOM) with infrared nanospectroscopy coupled to solid-state nuclear magnetic resonance (NMR)─we reveal that hemicellulose presence considerably modulates lignin deposition and alters its interunit bond distribution. Specifically, hemicellulose-rich environments dramatically reduce lignin deposition by approximately 50% and yield highly condensed lignin structures characterized by severely reduced β–O–4′ linkages (<2%) and suppressed β–β′ linkages. Conversely, cellulose-alone scaffolds support notably higher β–O–4′ content (∼10%), resulting in a more uniform nanoscale lignin coating. Our work helps explain how accessible hemicellulose sites, both sterically and chemically, direct radical coupling during lignification, fundamentally reshaping lignin’s nanoscale architecture. These findings deepen our mechanistic understanding of plant cell wall biosynthesis and inform strategies aimed at enhancing biomass deconstruction efficiency for sustainable bioenergy applications.

NMR↗

DOE OSTI2025

Topological phase diagram of generalized Su-Schrieffer-Heeger models with interactions

We investigate interacting Su-Schrieffer-Heeger (SSH) chains with two- and three-site unit cells using density matrix renormalization group (DMRG) simulations. By selecting appropriate filling fractions and sweeping across interaction strength 𝐽 𝑧 and dimerization 𝛿, we map out their phase diagrams and identify transition lines via entanglement entropy and magnetization measurements. In the two-site model, we observe the emergence of an interaction-induced antiferromagnetic intermediate phase between the topologically trivial and nontrivial regimes, as well as a critical region at negative 𝐽 𝑧 with suppressed magnetization and finite-size scaling of entanglement entropy. In contrast, the three-site model lacks an intermediate phase and exhibits asymmetric edge localization and antiferromagnetic ordering in both positive and negative 𝐽 𝑧 regimes. We further examine the response of edge states to Ising perturbations. In the two-site model, zero-energy edge modes are topologically protected and remain robust up to a finite interaction strength. However, in the three-site model, where the edge states reside at finite energy, this protection breaks down. Despite this, the edge-localized nature of these states survives in the form of polarized modes whose spatial profiles reflect the noninteracting limit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Self-driving thin film laboratory: autonomous epitaxial atomic-layer synthesis via real-time computer vision analysis of electron diffraction

Emerging materials science platforms with the ability to make autonomous decisions on the fly are fundamentally changing the outlook and protocols for materials optimization and discovery. Because AI-driven self-navigating schemes can effectively reduce the total number of iterations needed to arrive at the "answer" (i.e. the best stochiometric composition for a desired physical property, optimum materials processing parameters, etc.) by significant margins, they have the potential to revolutionize materials and chemical manufacturing processes at large in research laboratory settings as well as in industrial plants. Here, we demonstrate a successful implementation of real-time closed-loop autonomous navigation of a multi-dimensional materials synthesis parameter space for fabricating phase-pure epitaxial films of a metastable phase of a functional oxide in a combinatorial pulsed laser deposition chamber. Sequential epitaxial growth iterations in search of the optimized recipe to stabilize the desired crystal phase were performed using frame-by-frame quantitative computer vision analysis of reflection high-energy electron diffraction (RHEED) images of the unit-cell level film being deposited. The autonomous scheme regularly resulted in > 30-fold reduction in the number of required experiments compared to a comprehensive mapping of the parameter space. The real-time workflow developed here can be readily extended to a variety of thin film synthesis platforms opening the door for self-driving atomic-level materials design as well as autonomous optimization of semiconductor manufacturing.

36 MATERIALS SCIENCE↗

NASA NTRS1977

Measurements of magnetic fluxes and field strengths in the photospheric network

Digital pictures of an active-region network cell are presented in five quantities measured simultaneously: continuum intensity, line-center intensity, equivalent width, magnetogram signal, and magnetic-field strength. These maps are derived from computer analysis of circularly polarized line profiles of Fe I 5250.2-A; spectral and spatial resolution are 1/40 A and 1.5 arcsec, respectively. Measured Zeeman splittings show the existence of strong magnetic fields (1000-1800 G) at nearly all points with a magnetogram signal exceeding 125 G. The mean and rms deviation of the field strengths change by less than 20% over a factor-of-four range of fluxes. From the significant disparity between measured fluxes and field strengths, it is concluded that large flux patches (up to 4 arcsec across) consist of closely-packed unresolved filaments. The smallest filaments must be less than 0.7 arcsec in diameter. The dark component of the photospheric network, which appears to contain sizable transverse fields, is also observed.

Tarbell, T. D.↗

NASA NTRS1982

Impact of Demographic Siting Criteria and Environmental Suitability on Land Availability for Nuclear Reactor Siting

The effect of population and certain environmental characteristics on the availability of land for siting nuclear power plants was assessed. The study area, consisting of the 48 contiguous states, was divided into 5 kilometer (km) square grid cells yielding a total of 600,000 cells. Through the use of a modern geographic information system, it was possible to provide a detailed analysis of a quite large area. Numerous maps and statistical tables were produced, the detail of which were limited only by available data. Evaluation issues included population density, restricted lands, seismic hardening, site preparation, water availability, and cost factors.

Hansen, K. L.↗

NASA NTRS2004

NASA Tech Briefs, August 2004

Topics covered include: Data Relay Board with Protocol for High-Speed, Free-Space Optical Communications; Software and Algorithms for Biomedical Image Data Processing and Visualization; Rapid Chemometric Filtering of Spectral Data; Prioritizing Scientific Data for Transmission; Determining Sizes of Particles in a Flow from DPIV Data; Faster Processing for Inverting GPS Occultation Data; FPGA-Based, Self-Checking, Fault-Tolerant Computers; Ultralow-Power Digital Correlator for Microwave Polarimetry; Grounding Headphones for Protection Against ESD; Lightweight Stacks of Direct Methanol Fuel Cells; Highly Efficient Vector-Inversion Pulse Generators; Estimating Basic Preliminary Design Performances of Aerospace Vehicles; Framework for Development of Object-Oriented Software; Analyzing Spacecraft Telecommunication Systems; Collaborative Planning of Robotic Exploration; Tools for Administration of a UNIX-Based Network; Preparing and Analyzing Iced Airfoils; Evaluating Performance of Components; Fuels Containing Methane of Natural Gas in Solution; Direct Electrolytic Deposition of Mats of MnxOy Nanowires; Bubble Eliminator Based on Centrifugal Flow; Inflatable Emergency Atmospheric-Entry Vehicles; Lightweight Deployable Mirrors with Tensegrity Supports; Centrifugal Adsorption Cartridge System; Ultrasonic Apparatus for Pulverizing Brittle Material; Transplanting Retinal Cells using Bucky Paper for Support; Using an Ultrasonic Instrument to Size Extravascular Bubbles; Coronagraphic Notch Filter for Raman Spectroscopy; On-the-Fly Mapping for Calibrating Directional Antennas; Working Fluids for Increasing Capacities of Heat Pipes; Computationally-Efficient Minimum-Time Aircraft Routes in the Presence of Winds; Liquid-Metal-Fed Pulsed Plasma Thrusters; Personal Radiation Protection System; and Attitude Control for a Solar-Sail Spacecraft.

Source record↗

NASA NTRS1998

MAP kinase pathways in the yeast Saccharomyces cerevisiae

A cascade of three protein kinases known as a mitogen-activated protein kinase (MAPK) cascade is commonly found as part of the signaling pathways in eukaryotic cells. Almost two decades of genetic and biochemical experimentation plus the recently completed DNA sequence of the Saccharomyces cerevisiae genome have revealed just five functionally distinct MAPK cascades in this yeast. Sexual conjugation, cell growth, and adaptation to stress, for example, all require MAPK-mediated cellular responses. A primary function of these cascades appears to be the regulation of gene expression in response to extracellular signals or as part of specific developmental processes. In addition, the MAPK cascades often appear to regulate the cell cycle and vice versa. Despite the success of the gene hunter era in revealing these pathways, there are still many significant gaps in our knowledge of the molecular mechanisms for activation of these cascades and how the cascades regulate cell function. For example, comparison of different yeast signaling pathways reveals a surprising variety of different types of upstream signaling proteins that function to activate a MAPK cascade, yet how the upstream proteins actually activate the cascade remains unclear. We also know that the yeast MAPK pathways regulate each other and interact with other signaling pathways to produce a coordinated pattern of gene expression, but the molecular mechanisms of this cross talk are poorly understood. This review is therefore an attempt to present the current knowledge of MAPK pathways in yeast and some directions for future research in this area.

Non-NASA Center↗

DOE OSTI2021

Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei

Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.

60 APPLIED LIFE SCIENCES↗