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DOE OSTI2026

DISARM: Target Electronic Device Informed Mitigation of Software Runtime Side-Channel Vulnerabilities

Program runtime/timing attacks exploit variations in a program’s execution times to extract sensitive information from the program (e.g. encryption keys, sensitive variable data, intellectual property). State-of-the-art solutions to runtime side-channel attacks attempt to balance the execution time of the sensitive code for different control flow paths to eliminate the timing leakage. However, during the mitigation process, most techniques do not consider the underlying hardware/device on which the target program is supposed to run on. This can lead to over-fixing (unnecessary extra operations), under-fixing (not solving the imbalance properly), and even failures. Here, we propose DISARM, a joint hardware-software methodology (unlike any existing solution) for mitigating runtime side-channel vulnerabilities that utilizes timing values from real embedded devices to generate targeted software fixes. We implement DISARM to support C/C++/Java source codes and validate it across 22 standard benchmarks. DISARM outperforms state-of-the-art solutions such as PENDULUM and DifFuzzaR in terms of execution time overhead, code size overhead, and correctness on five different embedded/edge devices.

Timing/runtime side-channel↗

DOE OSTI2024

Research and Development to Reduce Impurity Production and Transport of the Impurities to the Target in Linear Plasma Devices Using Helicon Plasma Sources

Linear plasma devices used to test plasma facing materials (PFMs) and components for fusion reactors are often suffering under the production of intrinsic impurities from the plasma source system. Most linear plasma devices use internal electrodes (hollow cathodes, reflex arc, or cascading arc), which typically are the source of the main impurities. The next-generation plasma generators use radio frequency (RF) plasma sources like helicons to avoid internal electrodes. However, high power operation of helicons has proven to result in impurity production due to the high rectified sheath voltages created. Depending on the plasma parameters and magnetic configuration, these impurities can be transported to the target and deposited there to unacceptable high levels. Here, in this contribution, the experimental results from Proto-MPEX are summarized, and the conclusions of the impurity source physics are given. Methods to reduce the impurity production, the impurity transport, and the net deposition on the target are presented. These methods to reduce the impurity production include Faraday screens to reduce the sheath voltage drop, high-Z refractory coatings to reduce the erosion yield, and wall conditioning methods. Methods to reduce the impurity transport include changes in the magnetic configuration as well as electron heating to change axial and radial temperature profiles. Preliminary results on the effectiveness of some of these methods are presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

SIRT1 targeted by miR ‐211‐5p regulated proliferation and apoptosis of Dex‐treated growth plate chondrocytes via mediating SOX2

Abstract Dexamethasone (Dex) is reported to cause bone growth retardation in children, which is associated with the increased apoptosis and decreased proliferation of growth plate chondrocytes. Sirtuin 1 (SIRT1) plays an important role in chondrocyte function and homeostasis. Thus, we further explored the regulatory mechanism of SIRT1 in Dex‐induced growth plate chondrocyte dysfunction. SIRT1 expression was detected in Dex‐treated growth plate chondrocytes using RT‐qPCR and western blot assay. The modulation of SIRT1 on SOX2 expression was evaluated. Besides, we identified that SIRT1 was targeted by miR‐211‐5p using TargetScan and RNA pull‐down assay. A loss‐of‐function assay was performed to evaluate the effects of miR‐211‐5p on Dex‐induced growth plate chondrocyte dysfunction in vitro and in vivo. We found that SIRT1 was downregulated in Dex‐treated growth plate chondrocytes. The expression of SOX2 was upregulated by overexpression SIRT1. Meanwhile, downregulation of SOX2 weakened the positive function of SIRT1 overexpression on Dex‐induced growth plate chondrocytes dysfunction. Subsequently, we confirmed that SIRT1 was targeted by miR‐211‐5p. MiR‐211‐5p inhibitor increased the expression levels of SIRT1 and SOX2, and restored the Dex‐treated growth plate chondrocyte function. Animal assays further demonstrated that the effects of miR‐211‐5p on the growth plate chondrogenesis. In conclusion, our data suggest that SIRT1 exerts a protective effect on growth plate chondrocyte under Dex stimulation. MiR‐211‐5p/SIRT1/SOX2 axis regulates the process of Dex‐inhibited growth plate chondrogenesis.

Cheng, Deliang↗

DOE OSTI2023

Rutin is a potent senomorphic agent to target senescent cells and can improve chemotherapeutic efficacy

Aging is a major risk factor for most chronic disorders, for which cellular senescence is one of the central hallmarks. Senescent cells develop the pro-inflammatory senescence-associated secretory phenotype (SASP), which significantly contributes to organismal aging and age-related disorders. Development of senotherapeutics, an emerging class of therapeutic agents to target senescent cells, allows to effectively delay aging and alleviate chronic pathologies. Here we report preliminary outputs from screening of a natural medicinal agent (NMA) library for senotherapeutic candidates and validated several agents with prominent potential as senomorphics. Rutin, a phytochemical constituent found in a number of plants, showed remarkable capacity in targeting senescent cells by dampening expression of the full spectrum SASP. Further analysis indicated that rutin restrains the acute stress-associated phenotype (ASAP) by specifically interfering with the interactions of ATM with HIF1α, a master regulator of cellular and systemic homeostasis activated during senescence, and of ATM with TRAF6, part of a key signaling axis supporting the ASAP development toward the SASP. Conditioned media produced by senescent stromal cells enhanced the malignant phenotypes of prostate cancer cells, including in vitro proliferation, migration, invasion, and more importantly, chemoresistance, while rutin remarkably downregulated these gain-of-functions. Although classic chemotherapy reduced tumor progression, the treatment outcome was substantially improved upon combination of a chemotherapeutic agent with rutin. Our study provides a proof of concept for rutin as an emerging natural senomorphic agent, and presents an effective therapeutic avenue for alleviating age-related pathologies including cancer.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Structure and epitope of a neutralizing monoclonal antibody that targets the stem helix of β coronaviruses

Monoclonal antibodies that retain neutralizing activity against multiple coronavirus (CoV) lineages and variants of concern (VoC) must be developed to protect against future pandemics. These broadly neutralizing MAbs (BNMAbs) may be used as therapeutics and/or to assist in the rational design of vaccines that induce BNMAbs. 1249A8 is a BNMAb that targets the stem helix (SH) region of CoV spike (S) protein and neutralizes Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) original strain, delta, and omicron VoC, Severe Acute Respiratory Syndrome CoV (SARS-CoV), and Middle East Respiratory Syndrome CoV (MERS-CoV). To understand its mechanism of action, the crystal structure of 1249A8 bound to a MERS-CoV SH peptide was determined at 2.1 Å resolution. BNMAb 1249A8 mimics the SARS-CoV-2 S loop residues 743–749, which interacts with the N-terminal end of the SH helix in the S post-fusion conformation. The conformation of 1249A8-bound SH is distinct from the SH conformation observed in the post-fusion SARS-CoV-2 S structure, suggesting 1249A8 disrupts the secondary structure and refolding events required for CoV post-fusion S to initiate membrane fusion and ultimately infection. This study provides novel insights into the neutralization mechanisms of SH-targeting CoV BNMAbs that may inform vaccine development and the design of optimal BNMAb therapeutics.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Targeting KDM4 for treating PAX3-FOXO1–driven alveolar rhabdomyosarcoma

Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3–Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1 + RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1–governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1 + RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1–related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.

Cell Biology↗

DOE OSTI2023

Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity

Novel therapeutic monoclonal antibodies (MAbs) must accommodate comprehensive breadth of activity against diverse sarbecoviruses and high neutralization potency to overcome emerging variants. Here, in this study, we report the crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD) in complex with MAb WRAIR-2063, a moderate-potency neutralizing antibody with exceptional sarbecovirus breadth, that targets the highly conserved cryptic class V epitope. This epitope overlaps substantially with the spike protein N-terminal domain (NTD) -interacting region and is exposed only when the spike is in the open conformation, with one or more RBDs accessible. WRAIR-2063 binds the RBD of SARS-CoV-2 WA-1, all variants of concern (VoCs), and clade 1 to 4 sarbecoviruses with high affinity, demonstrating the conservation of this epitope and potential resiliency against variation. We compare structural features of additional class V antibodies with their reported neutralization capacity to further explore the utility of the class V epitope as a pan-sarbecovirus vaccine and therapeutic target.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Targeted Adaptive Design

Modern advanced manufacturing and advanced materials design often require searches of relatively high-dimensional process control parameter spaces for settings that result in optimal structure, property, and performance parameters. The mapping from the former to the latter must be determined from noisy experiments or from expensive simulations. Here, we abstract this problem to a mathematical framework in which an unknown function from a control space to a design space must be ascertained by means of expensive noisy measurements, which locate control settings generating desired design features within specified tolerances, with quantified uncertainty. We describe targeted adaptive design (TAD), a new algorithm that performs this sampling task efficiently. TAD creates a Gaussian process surrogate model of the unknown mapping at each iterative stage, proposing a new batch of control settings to sample experimentally and optimizing the updated expected log-predictive probability density of the target design. TAD either stops upon locating a solution with uncertainties that fit inside the tolerance box or uses a measure of expected future information to determine that the search space has been exhausted with no solution. TAD thus embodies the exploration-exploitation tension in a manner that recalls, but is essentially different from, Bayesian optimization and optimal experimental design.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Measurements of neutrino oscillation parameters from the T2K experiment using $$3.6\times 10^{21}$$ protons on target

Abstract The T2K experiment presents new measurements of neutrino oscillation parameters using $$19.7(16.3)\times 10^{20}$$ 19.7 ( 16.3 ) × 10 20 protons on target (POT) in (anti-)neutrino mode at the far detector (FD). Compared to the previous analysis, an additional $$4.7\times 10^{20}$$ 4.7 × 10 20 POT neutrino data was collected at the FD. Significant improvements were made to the analysis methodology, with the near-detector analysis introducing new selections and using more than double the data. Additionally, this is the first T2K oscillation analysis to use NA61/SHINE data on a replica of the T2K target to tune the neutrino flux model, and the neutrino interaction model was improved to include new nuclear effects and calculations. Frequentist and Bayesian analyses are presented, including results on $$\sin ^2\theta _{13}$$ sin 2 θ 13 and the impact of priors on the $$\delta _{\textrm{CP}}$$ δ CP measurement. Both analyses prefer the normal mass ordering and upper octant of $$\sin ^2\theta _{23}$$ sin 2 θ 23 with a nearly maximally CP-violating phase. Assuming the normal ordering and using the constraint on $$\sin ^2\theta _{13}$$ sin 2 θ 13 from reactors, $$\sin ^2\theta _{23}=0.561^{+0.021}_{-0.032}$$ sin 2 θ 23 = 0 . 561 - 0.032 + 0.021 using Feldman–Cousins corrected intervals, and $$\varDelta {}m^2_{32}=2.494_{-0.058}^{+0.041}\times 10^{-3}~\text {eV}^2$$ Δ m 32 2 = 2 . 494 - 0.058 + 0.041 × 10 - 3 eV 2 using constant $$\varDelta \chi ^{2}$$ Δ χ 2 intervals. The CP-violating phase is constrained to $$\delta _{\textrm{CP}}=-1.97_{-0.70}^{+0.97}$$ δ CP = - 1 . 97 - 0.70 + 0.97 using Feldman–Cousins corrected intervals, and $$\delta _{\textrm{CP}}=0,\pi $$ δ CP = 0 , π is excluded at more than 90% confidence level. A Jarlskog invariant of zero is excluded at more than $$2\sigma $$ 2 σ credible level using a flat prior in $$\delta _{\textrm{CP}},$$ δ CP , and just below $$2\sigma $$ 2 σ using a flat prior in $$\sin \delta _{\textrm{CP}}.$$ sin δ CP . When the external constraint on $$\sin ^2\theta _{13}$$ sin 2 θ 13 is removed, $$\sin ^2\theta _{13}=28.0^{+2.8}_{-6.5}\times 10^{-3},$$ sin 2 θ 13 = 28 . 0 - 6.5 + 2.8 × 10 - 3 , in agreement with measurements from reactor experiments. These results are consistent with previous T2K analyses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Preserving Contextual Awareness during Selection of Moving Targets in Animated Stream Visualizations

In many types of dynamic interactive visualizations, it is often desired to interact with moving objects. Stopping moving objects can make selection easier, but pausing animated content can disrupt perception and understanding of the visualization. To address such problems, we explore selection techniques that only pause a subset of all moving targets in the visualization. We present various designs for controlling pause regions based on cursor trajectory or cursor position. We then report a dual-task experiment that evaluates how different techniques affect both target selection performance and contextual awareness of the visualization. Our findings indicate that all pause techniques significantly improved selection performance as compared to the baseline method without pause, but the results also show that pausing the entire visualization can interfere with contextual awareness. However, the problem with reduced contextual awareness was not observed with our new techniques that only pause a limited region of the visualization. Thus, our research provides evidence that region-limited pause techniques can retain the advantages of selection in dynamic visualizations without imposing a negative effect on contextual awareness.

Ragan, Eric↗

DOE OSTI2022

Identification of therapeutic targets in a murine model of severe exertional heat stroke

Exertional heat stroke (EHS) is a potentially lethal condition resulting from high core body temperatures (T C ) in combination with a systemic inflammatory response syndrome (SIRS) with varying degrees of severity across victims, and limited understanding of the underlying mechanism(s). We established a mouse model of severe EHS to identify mechanisms of hyperthermia/inflammation that may be responsible for organ damage. Mice were forced to run on a motorized wheel in a 37.5°C chamber until loss of consciousness and were either removed immediately (exertional heat injury or EHI; T CMax = 42.4 ± 0.2°C) or remained in the chamber an additional 20 min (EHS; T CMax = 42.5 ± 0.4°C). Exercise control mice (ExC) experienced identical procedures to EHS at 25°C. At 3 h post-EHS, there was evidence for an immune/inflammatory response as elevated blood chemokine [interferon γ-induced protein 10 (IP-10), keratinocytes-derived chemokine (KC), macrophage inflammatory proteins (MIP-1α), MIP-1β, MIP-2] and cytokine [granulocyte colony-stimulating factor (G-CSF), interleukins (IL-10), IL-6] levels peaked and were highest in EHS mice compared with EHI and ExC mice. Immunoblotting of organs susceptible to EHS damage indicated that several kinases were sensitive to stress associated with heat/inflammation and exercise; specifically, phosphorylation of liver c-Jun NH 2 -terminal kinase (JNK) at threonine 183/tyrosine 185 immediately (0 h) postheating related to heat illness severity. We have established a mouse EHS model, and JNK [or its downstream target(s)] could underlie EHS symptomatology, allowing the identification of molecular pathways or countermeasure targets to mitigate heat illness severity, enable complete recovery, and decrease overall EHS-related fatalities.

Physiology↗

DOE OSTI2022

Study on Closely Related Citrus CMMs based on Chemometrics and Prediction of Components-Targets-Diseases Network by Ingenuity Pathway Analysis

As the representatives of closely related Chinese medicinal materials (CMMs) originated from Rutaceae family, Aurantii fructus immaturus (AFI), Aurantii fructus (AF), Citri reticulatae pericarpium viride (CRPV), and Citri reticulatae pericarpium (CRP) have better functions in regulating qi and promoting gastrointestinal motility. However, differences in the quality of closely related Citrus CMMs have not yet been revealed until now. Herein, this study focused on the systematic differentiation and in-depth understanding of closely related Citrus CMMs by a strategy integrating chemometrics and network pharmacology. Determined by ultra performance liquid chromatography, the content of nine flavonoids showed obvious fluctuations in the decoction pieces from different species (Citrus aurantium Linnaeus and Citrus reticulate Blanco) with decreasing levels in the samples of ripe fruits. Decoction pieces from the different species and ripening stages were well distinguished by orthogonal projection to latent structure-discriminate analysis (OPLS-DA) and cluster analysis. As a result, four active components including narirutin, naringenin, hesperidin, and 3,5,6,7,8,3′,4′-heptemthoxyflavone were filtered out by variable importance for the projection (VIP) value (VIP > 1.0), which were regarded as chemotaxonomic markers. Furthermore, a components-targets-diseases network was constructed via ingenuity pathway analysis (IPA), and the correlations were predicted between four chemotaxonomic markers, 223 targets, and three diseases including colitis, breast cancer, and colorectal cancer. The obtained results will be of great significance for identifying closely related Citrus CMMs and conduce to improving the resource utilization of CMMs.

Mu, Qixuan↗

DOE OSTI2021

Building Efficiency Targeting Tool for Energy Retrofits (BETTER) Web Application (BETTER Web App) v1.0

The Building Efficiency Targeting Tool for Energy Retrofits (BETTER) V.1.0 web application identifies cost-saving energy and emissions reductions in buildings and portfolios, without site visits or complex modeling. With minimal data entry, BETTER benchmarks a building's or portfolio's energy use against peers; quantifies energy, cost, and greenhouse gas (GHG) reduction potential; and recommends energy efficiency measures for individual buildings or portfolios, targeting specific energy savings levels. The source code of BETTER's modular, cross-platform analytical engine has previously been disclosed (2019-001) and is available on GitHub and can be adopted, redeveloped, and redistributed freely under an open-source license, allowing users to incorporate BETTER's analytical capabilities into their own software platforms and tools. The BETTER V.1.0 web application, developed with the Django web-framework and the Model-View-Controller (MVC) architecture being disclosed here, provides a graphical user interface (GUI) for any user to view the software tutorials, download and upload a data entry template, configure and run the BETTER analyses, and view the final analytical reports.

Szum, Carolyn↗

DOE OSTI2022

Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment

Abstract Purpose: Leukemia inhibitory factor (LIF) is a multifunctional cytokine with numerous reported roles in cancer and is thought to drive tumor development and progression. Characterization of LIF and clinical-stage LIF inhibitors would increase our understanding of LIF as a therapeutic target. Experimental Design: We first tested the association of LIF expression with transcript signatures representing multiple processes regulating tumor development and progression. Next, we developed MSC-1, a high-affinity therapeutic antibody that potently inhibits LIF signaling and tested it in immune competent animal models of cancer. Results: LIF was associated with signatures of tumor-associated macrophages (TAM) across 7,769 tumor samples spanning 22 solid tumor indications. In human tumors, LIF receptor was highly expressed within the macrophage compartment and LIF treatment drove macrophages to acquire immunosuppressive capacity. MSC-1 potently inhibited LIF signaling by binding an epitope that overlaps with the gp130 receptor binding site on LIF. MSC-1 showed monotherapy efficacy in vivo and drove TAMs to acquire antitumor and proinflammatory function in syngeneic colon cancer mouse models. Combining MSC-1 with anti-PD1 leads to strong antitumor response and a long-term tumor-free survival in a significant proportion of treated mice. Conclusions: Overall, our findings highlight LIF as a therapeutic target for cancer immunotherapy.

Oncology↗

DOE OSTI2022

Targeting a proteolytic neoepitope on CUB domain containing protein 1 ( CDCP1 ) for RAS -driven cancers

Extracellular proteolysis is frequently dysregulated in disease and can generate proteoforms with unique neoepitopes not found in healthy tissue. Here, we demonstrate that Abs that selectively recognize a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) could enable more effective and safer treatments for solid tumors. CDCP1 is highly overexpressed in RAS-driven cancers, and its ectodomain is cleaved by extracellular proteases. Biochemical, biophysical, and structural characterization revealed that the 2 cleaved fragments of CDCP1 remain tightly associated with minimal proteolysis-induced conformational change. Using differential phage display, we generated recombinant Abs that are exquisitely selective to cleaved CDCP1 with no detectable binding to the uncleaved form. These Abs potently targeted cleaved CDCP1-expressing cancer cells as an Ab-drug conjugate, an Ab-radionuclide conjugate, and a bispecific T cell engager. In a syngeneic pancreatic tumor model, these cleaved-specific Abs showed tumor-specific localization and antitumor activity with superior safety profiles compared with a pan-CDCP1 approach. Targeting proteolytic neoepitopes could provide an orthogonal "AND" gate for improving the therapeutic index.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Development of 225Ac-doped biocompatible nanoparticles for targeted alpha therapy

Abstract Targeted alpha therapy (TAT) relies on chemical affinity or active targeting using radioimmunoconjugates as strategies to deliver α-emitting radionuclides to cancerous tissue. These strategies can be affected by transmetalation of the parent radionuclide by competing ions in vivo and the bond-breaking recoil energy of decay daughters. The retention of α-emitting radionuclides and the dose delivered to cancer cells are influenced by these processes. Encapsulating α-emitting radionuclides within nanoparticles can help overcome many of these challenges. Poly(lactic- co -glycolic acid) (PLGA) nanoparticles are a biodegradable and biocompatible delivery platform that has been used for drug delivery. In this study, PLGA nanoparticles are utilized for encapsulation and retention of actinium-225 ([ 225 Ac]Ac 3+ ). Encapsulation of [ 225 Ac]Ac 3+ within PLGA nanoparticles (Z ave = 155.3 nm) was achieved by adapting a double-emulsion solvent evaporation method. The encapsulation efficiency was affected by both the solvent conditions and the chelation of [ 225 Ac]Ac 3+ . Chelation of [ 225 Ac]Ac 3+ to a lipophilic 2,9-bis-lactam-1,10-phenanthroline ligand ([ 225 Ac]AcBLPhen) significantly decreased its release (< 2%) and that of its decay daughters (< 50%) from PLGA nanoparticles. PLGA nanoparticles encapsulating [ 225 Ac]AcBLPhen significantly increased the delivery of [ 225 Ac]Ac 3+ to murine (E0771) and human (MCF-7 and MDA-MB-231) breast cancer cells with a concomitant increase in cell death over free [ 225 Ac]Ac 3+ in solution. These results demonstrate that PLGA nanoparticles have potential as radionuclide delivery platforms for TAT to advance precision radiotherapy for cancer. In addition, this technology offers an alternative use for ligands with poor aqueous solubility, low stability, or low affinity, allowing them to be repurposed for TAT by encapsulation within PLGA nanoparticles. Graphical Abstract

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Targeting hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase for lignin modification in Brachypodium distachyon

Abstract Background Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is a central enzyme of the so-called “esters” pathway to monolignols. As originally envisioned, HCT functions twice in this pathway, to form coumaroyl shikimate and then, in the “reverse” direction, to convert caffeoyl shikimate to caffeoyl CoA. The discovery of a caffeoyl shikimate esterase (CSE) that forms caffeic acid directly from caffeoyl shikimate calls into question the need for the reverse HCT reaction in lignin biosynthesis. Loss of function of HCT gives severe growth phenotypes in several dicot plants, but less so in some monocots, questioning whether this enzyme, and therefore the shikimate shunt, plays the same role in both monocots and dicots. The model grass Brachypodium distachyon has two HCT genes, but lacks a classical CSE gene. This study was therefore conducted to evaluate the utility of HCT as a target for lignin modification in a species with an “incomplete” shikimate shunt. Results The kinetic properties of recombinant B. distachyon HCTs were compared with those from Arabidopsis thaliana , Medicago truncatula , and Panicum virgatum (switchgrass) for both the forward and reverse reactions. Along with two M. truncatula HCTs, B. distachyon HCT2 had the least kinetically unfavorable reverse HCT reaction, and this enzyme is induced when HCT1 is down-regulated. Down regulation of B. distachyon HCT1, or co-down-regulation of HCT1 and HCT2, by RNA interference led to reduced lignin levels, with only modest changes in lignin composition and molecular weight. Conclusions Down-regulation of HCT1, or co-down-regulation of both HCT genes, in B. distachyon results in less extensive changes in lignin content/composition and cell wall structure than observed following HCT down-regulation in dicots, with little negative impact on biomass yield. Nevertheless, HCT down-regulation leads to significant improvements in biomass saccharification efficiency, making this gene a preferred target for biotechnological improvement of grasses for bioprocessing.

09 BIOMASS FUELS↗

DOE OSTI2020

A pipeline for targeted metagenomics of environmental bacteria

Background:Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has the potential to enrich taxonomically well-defined clades for genomic analyses. Methods:Cells hybridized with a taxon-specific FISH probe are enriched based on their fluorescence signal via flow cytometric cell sorting. A recently developed FISH procedure, the hybridization chain reaction (HCR)-FISH, provides the high signal intensities required for flow cytometric sorting while maintaining the integrity of the cellular DNA for subsequent genome sequencing. Sorted cells are subjected to shotgun sequencing, resulting in targeted metagenomes of low diversity. Results: Pure cultures of different taxonomic groups were used to (1) adapt and optimize the HCR-FISH protocol and (2) assess the effects of various cell fixation methods on both the signal intensity for cell sorting and the quality of subsequent genome amplification and sequencing. Best results were obtained for ethanol-fixed cells in terms of both HCR-FISH signal intensity and genome assembly quality. Our newly developed pipeline was successfully applied to a marine plankton sample from the North Sea yielding good quality metagenome assembled genomes from a yet uncultivated flavobacterial clade. Conclusions: With the developed pipeline, targeted metagenomes at various taxonomic levels can be efficiently retrieved from environmental samples. The resulting metagenome assembled genomes allow for the description of yet uncharacterized microbial clades.

59 BASIC BIOLOGICAL SCIENCES↗