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At least 1,387 records · Page 77

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs

RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring phage–host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics

Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage–host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.

Bacterial Pathogenesis↗

[Activities of System Studies and Simulation, Inc.]

Contents include the following: 1. Launch Vehicle Interface Work Performed: a. S3 provided to KSC the new launch inclination targets needed for the April '04 launch date. 2. Prelaunch operations work performed: a. S3 updated the staffing plan for MSFC on-console personnel\during the Final Countdown prior to launch. 3. Software Assessment Work Performed: a. S3 evaluated and recommended approval for Program Control Board (PCB) proposed change 649 for ground software changes, as well as change 650 and 650A for Stored Program Commands. 4. Education and Public Outreach Work Performed: a. S3 continues to coordinate the effort for the design and fabrication of scale models of the GP-3 for use at the launch site, education forums, and management/technical briefings. S3 also prepared a Change Request for additional funds needed for fabrication of additional scale models. S3 drafted the planned uses of these models, including the possibility of participation in the Boston, MA showings of the traveling Einstein Exhibit. 5. Program Management Support Work Performed: a. S3 prepared the input for and closed three MSFC Centerwide Action Item Tracking Systems (CAITS) actions during this period.

Source record↗

Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents

SARS-CoV-2 3CL protease (Main protease) and human cathepsin L are proteases that play unique roles in the infection of human cells by SARS-CoV-2, the causative agent of COVID-19. Both proteases recognize leucine and other hydrophobic amino acids at the P 2 position of a peptidomimetic inhibitor. At the P 1 position, cathepsin L accepts many amino acid side chains, with a partial preference for phenylalanine, while 3CL-PR protease has a stringent specificity for glutamine or glutamine analogues. We have designed, synthesized, and evaluated peptidomimetic aldehyde dual-target (dual-acting) inhibitors using two peptide scaffolds based on those of two Pfizer 3CL-PR inhibitors, Nirmatrelvir, and PF-835321. Our inhibitors contain glutamine isosteres at the P 1 position, including 2-pyridon-3-yl-alanine, 3-pyridinyl-alanine, and 1,3-oxazo-4-yl-alanine groups. Inhibition constants for these new inhibitors ranged from K i = 0.6–18 nM (cathepsin L) and K i = 2.6–124 nM (3CL-PR), for which inhibitors with the 2-pyridon-3-yl-alanal substituent were the most potent for 3CL-PR. The anti-CoV-2 activity of these inhibitors ranged from EC 50 = 0.47–15 μM. X-ray structures of the peptidomimetic aldehyde inhibitors of 3CL-PR with similar scaffolds all demonstrated the formation of thiohemiacetals with Cys 145 , and hydrogen-bonding interactions with the heteroatoms of the pyridon-3-yl-alanyl group, as well as the nitrogen of the N-terminal indole and its appended carbonyl group at the P 3 position. The absence of these hydrogen bonds for the inhibitors containing the 3-pyridinyl-alanyl and 1,3-oxazo-4-yl-alanyl groups was reflected in the less potent inhibition of the inhibitors with 3CL-PR. In summary, our studies demonstrate the value of a second generation of cysteine protease inhibitors that comprise a single agent that acts on both human cathepsin L and SARS-CoV-2 3CL protease. Such dual-target inhibitors will provide anti-COVID-19 drugs that remain active despite the development of resistance due to mutation of the viral protease. Such dual-target inhibitors are more likely to remain useful therapeutics despite the emergence of inactivating mutations in the viral protease because the human cathepsin L will not develop resistance. This particular dual-target approach is innovative since one of the targets is viral (3CL-PR) required for viral protein maturation and the other is human (hCatL) which enables viral infection.

60 APPLIED LIFE SCIENCES↗

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

The pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to expand. Papain-like protease (PLpro) is one of two SARS-CoV-2 proteases potentially targetable with antivirals. PLpro is an attractive target because it plays an essential role in cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex, and disruption of host responses. We report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the SARS-CoV-2 enzyme. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. This collection of structures details inhibitors recognition and interactions providing fundamental molecular and mechanistic insight into PLpro. All compounds inhibit the peptidase activity of PLpro in vitro, some block SARS-CoV-2 replication in cell culture assays. These findings will accelerate structure-based drug design efforts targeting PLpro to identify high-affinity inhibitors of clinical value.

59 BASIC BIOLOGICAL SCIENCES↗

A Bilevel Voltage Regulation Operation for Distribution Systems With Self-Operated Microgrids

The emerging of microgrids in distribution systems has significantly enhanced the resilience of power grids. However, the operators of a distribution system and microgrids therein can be different and have accessibility to different devices. To model the operation of such a grid, this work proposes a bilevel formulation and probes into the voltage regulation operation, considering the interaction between different systems. The proposed bilevel formulation considers the cooperation of active energy resources (AER), transformer tap-changers, and capacitor banks that are controlled by different operators. To facilitate the solution time of the target bilevel optimization, the lower-level problems with different objectives are modeled using deep neural networks (DNNs) which are then converted into a set of constraints. Hence, the bilevel problem can be reformed to a single-level problem. Lastly, the proposed solution procedures are validated using a customized joint system constructed by the IEEE 123-bus system and a real distribution system in Iowa. According to the numerical validation results, the solution time of the proposed nonlinear activation function based DNN model is 69 times faster than other methods in solving voltage regulation with a bilevel structure.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Spallation Neutron Source Second Target Station Construction Project: Biological Assessment

The Endangered Species Act of 1973 (16 U.S.C. 153 et seq.), as amended (ESA or Act) in section 7(a)(1) directs Federal agencies to conserve and recover listed species and use their authorities in the furtherance of the purposes of the Act by carrying out programs for the conservation of endangered and threatened species so that listing is no longer necessary (50 CFR §402). Furthermore, the Act in section 7(a)(2) directs Federal agencies to consult (referred to as section 7 consultation) with the U.S. Fish and Wildlife Service (USFWS) when their activities “may affect” a listed species or designated critical habitat. This biological assessment (BA) analyzes the potential effects of the proposed Spallation Neutron Source Second Target Station STS construction project on the U. S. Department of Energy Oak Ridge Reservation (ORR) on Federal listed threatened, endangered, proposed, and under consideration for Federal listing bat species, pursuant to section 7(a)(2) of the ESA.

54 ENVIRONMENTAL SCIENCES↗

Neutron production and dosimetry with D(D,n) 3 He, 12 C(D,n) 13 N and 7 Li(p,n) 7 Be reactions at the Sandia Ion Beam Laboratory

Neutrons are produced at the Sandia Ion Beam Laboratory (IBL) using a beam of 280 keV D 2 + ions onto an erbium deuteride target. At test locations in the forward direction these neutrons have energies of about 2.9 MeV and a maximum flux on the flange of the test chamber of about 10 10 n/cm 2 /hour. Dosimetry is done by counting associated charged particles and by nickel foil activation dosimetry. Neutrons with higher energies, up to 6 MeV are produced using higher energy deuterium, up to 3 MeV, from the Pelletron ion accelerator at the IBL on a deuteride target. This report provides detailed information on the methods used for the production and dosimetry of neutrons by the D(D,n) 3 He nuclear reaction at the IBL. Neutron production by the 7 Li(p,n) 7 Be reaction with a proton beam from the Pelletron on a lithium target, such as LiF is also discussed. This produces neutrons with lower energy, in the range from about 0.1 to 1.3 MeV. Neutron production by the 12 C(D,n) 13 N reaction is also discussed. The purpose of this report is to provide information needed to test the effects of neutron irradiation on semiconductor materials and devices at the Sandia IBL.

36 MATERIALS SCIENCE↗

CENC PSN VOID FY20 Report

Maritime trade accounts for approximately 80 percent of international commerce. The high volume of vessels traversing domestic and international ports makes port areas prime targets for terrorism as well as illegal trafficking of drugs and arms (conventional or nuclear). Port security is therefore a worldwide concern affecting global economies, freedom of movement, and national security. However, extensive port monitoring is inherently complex and time consuming — making it truly viable only via an automated framework that can detect potential illicit activity and alert authorities in a timely manner. The development of image processing algorithms for this purpose requires access to large, labeled datasets that cover the breadth of targets of interest as well as the environments that they are observed within. Curated and labeled datasets of this nature are of enormous value to Sandia's Defense Nuclear Nonproliferation and National Security Program portfolios, as well as to Sandia's machine learning/automatic target recognition (ML/ATR) algorithm development and R&D communities. The goal of this project is to create a commercial satellite imagery dataset of labeled maritime vessels in port areas to support the development of ML/ATR algorithms for port security nonproliferation purposes. This dataset — Port Security Nonproliferation Vessel Overhead Imagery Dataset (PSN VOID) — has the potential to support a variety of other ancillary missions, such as maritime domain awareness, domestic and international security, drug interdiction, and weapons trafficking.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Analysis of 26S Proteasome Activity across Arabidopsis Tissues

Plants utilize the ubiquitin proteasome system (UPS) to orchestrate numerous essential cellular processes, including the rapid responses required to cope with abiotic and biotic stresses. The 26S proteasome serves as the central catalytic component of the UPS that allows for the proteolytic degradation of ubiquitin-conjugated proteins in a highly specific manner. Despite the increasing number of studies employing cell-free degradation assays to dissect the pathways and target substrates of the UPS, the precise extraction methods of highly potent tissues remain unexplored. Here, we utilize a fluorogenic reporting assay using two extraction methods to survey proteasomal activity in different Arabidopsis thaliana tissues. This study provides new insights into the enrichment of activity and varied presence of proteasomes in specific plant tissues.

26S proteasome↗

Towards Net Zero: Modeling Approach to the Right-Sized Facilities

As the concentration of greenhouse gases (GHGs) in the atmosphere increases, the concerns about carbon emissions are growing. Several net-zero initiatives are taking place around the globe to achieve a balance between the GHGs put into the atmosphere and those taken out. While most efforts present a sectorized approach, this paper describes the importance of integrating information across different sectors for effective modeling of carbon emissions and holistic reduction opportunity analysis. Using the Idaho National Laboratory (INL) campus as a test case, this work provides a web-based tool for INL stakeholders to use when engaging in strategic planning to achieve carbon emissions reduction. This net-zero engineering support tool (NEST) uses historical data as foundational information for applying the modeling framework. Prediction of CO 2 emissions throughout project completion integrates various approaches and schedules aimed at energy conservation, fleet decarbonization, and other GHG reduction activities. Using NEST, stakeholders can visualize carbon emissions, electricity consumption, and costs for decision making when planning the pathway for reaching carbon net zero. The INL’s initiative to transition into an EV fleet was used to demonstrate the developed framework and the advantages of using NEST. It was shown that electrifying different fossil-fueled campus vehicles before 2030 with aggressive replacement schedules require high annual capital expenditure (CAPEX), which may not be available. The tool allows decision makers to test different replacement schedules and prioritize those that yield CAPEX below a certain threshold while meeting target milestones. While the demonstration focused on vehicle electrification, the developed framework lays the foundation for further quantitative analysis of other GHG reduction activities.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Towards the Verification of Human-Robot Teams

Human-Agent collaboration is increasingly important. Not only do high-profile activities such as NASA missions to Mars intend to employ such teams, but our everyday activities involving interaction with computational devices falls into this category. In many of these scenarios, we are expected to trust that the agents will do what we expect and that the agents and humans will work together as expected. But how can we be sure? In this paper, we bring together previous work on the verification of multi-agent systems with work on the modelling of human-agent teamwork. Specifically, we target human-robot teamwork. This paper provides an outline of the way we are using formal verification techniques in order to analyse such collaborative activities. A particular application is the analysis of human-robot teams intended for use in future space exploration.

Fisher, Michael↗

Nonclassical autophagy activation pathways are essential for production of infectious Influenza A virus in vitro

Autophagy is a critical mechanism deployed by eukaryotic cells in response to stress, including viral infection, to boost the innate antimicrobial responses. However, an increasing number of pathogens hijack the autophagic machinery to facilitate their own replication. Influenza A virus (IAV), responsible for several global pandemics, has an intricate dependence on autophagy for successful replication in mammalian cells. To elucidate key chokepoints in the host stress responses facilitating IAV replication, we constructed a meta-transcriptome of IAV and host gene expression dynamics during early (1–3 hpi), mid (4–6 hpi), and late (8–12 hpi) stages of the viral replication cycle at two multiplicities of infection (MOI): 1 and 5. We supplemented the global transcriptome study with phosphoproteomic analysis of stress-activated protein kinase (SAPK/JNK) signaling in lung carcinoma (predominantly used as an in vitro model of IAV replication) and normal human bronchial epithelial cells. We report significant differences in the activation profiles of autophagy regulating genes upon IAV infection at the two MOI as well as divergent dependence on ULK1 signaling within the normal and cancer cells. Regardless of the cell model, JNK-Thr187 signaling was crucial for the production of infectious viral particles.

59 BASIC BIOLOGICAL SCIENCES↗

Crosstalk Suppression in Individually Addressed Two-Qubit Gates in a Trapped-Ion Quantum Computer

Crosstalk between target and neighboring spectator qubits due to spillover of control signals represents a major error source limiting the fidelity of two-qubit entangling gates in quantum computers. We show that in our laser-driven trapped-ion system coherent crosstalk error can be modeled as residual $X\hat{σ}_{\phi}$ interaction and can be actively canceled by single-qubit echoing pulses. We propose and demonstrate a crosstalk suppression scheme that eliminates all first-order crosstalk utilizing only local control of target qubits, as opposed to an existing scheme which requires control over all neighboring qubits. We report a two-qubit Bell state fidelity of 99.52(6)% with the echoing pulses applied after collective gates and 99.37(5)% with the echoing pulses applied to each gate in a five-ion chain. Finally, this scheme is widely applicable to other platforms with analogous interaction Hamiltonians.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ARPA-E PNDIODES "PN Junctions by Ion Implantation" Project (Final Report)

Electricity accounts for nearly 40% of the energy generated in the United States, of which 65% is lost to electrical system inefficiency before reaching end-use sectors. Power electronics will play a growing role in this distribution and end-use, with up to 80% of electricity estimated to pass through power electronics from generation to consumption by 2030. This gives technical improvements in power electronics enormous potential to drive efficiency gains throughout the U.S. economy. Current Si-based power architectures including MOSFETs and IGBTs are limited by high losses, low switching frequency, and poor high-temperature performance. Given the material properties of GaN, devices can exhibit a given turn-on resistance and breakdown voltage with a minute fraction of the area of a Si device—all with higher switching speeds. While n-type doping of III-nitrides has reached a high level of maturity and integration into commercialized products, p-type doping presents distinct challenges that requires continued research. The success of the next generation of GaN-based power devices depends in large part on the ability to form selective-area p-type regions, which can be accomplished by ion implantation of the prevailing acceptor dopant, Mg. This approach is relatively inexpensive and is a fab-ready processing step for creation of current-generation power electronic devices including BJTs, IGBTs, and diode rectifiers. However, ion implantation induces lattice damage and creates point defects within the material, which negatively impacts dopant activation annealing. These forms of damage may be removed by high-temperature annealing, however short annealing time and higher pressures are required to prevent decomposition of the material. We approach this challenge through an innovative combination of approaches toward obtaining high-conductivity p-type GaN. By the novel employment of a gyrotron, a microwave source that can be shaped into a highly localized beam to dissipate very high power in a semiconductor target, a wafer of GaN can be annealed in short (<2 s) ‘pulses’ at temperatures of 1450 °C (2640 °F) to achieve p-type activation without appreciable surface degradation. The p-type activation of Mg-implanted GaN can be further aided by co-implantation with N, believed to enhance the removal of point defects that compensate the acceptors dopant. Elevation to such high temperatures for even a short time induces degradation of GaN-to overcome, we have implemented additional measures to retain high-quality crystalline GaN while removing implant damage and activating Mg dopant. A bilayer cap of AlN is deposited by a combination of chemical and physical vapor deposition to protect the GaN surface. To prevent decomposition of GaN loss of N during annealing, a custom vessel—to contain pressurized N while allowing injection of microwave energy—is employed. By detailed study of the interaction of various measures that are implemented to protect the sample surface (GaN), activate the implanted dopants, and mitigate damage of the lattice heating damage during annealing, we are able to achieve p-type GaN and observe recovery of the crystal and removal of substantial density of defects created during the implantation process.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Results from InSight Robotic Arm Activities

The InSight lander carried an Instrument Deployment System (IDS) that included an Instrument Deployment Arm (IDA), scoop, five finger “claw” grapple, forearm-mounted Instrument Deployment Camera (IDC) requiring arm motion to image a target, and landermounted Instrument Context Camera (ICC), designed to image the workspace, and to place the instruments onto the surface. As originally proposed, the IDS included a previously built arm and flight spare black and white cameras and had no science objectives or requirements, or expectation to be used after instrument deployment (90 sols). During project development the detectors were upgraded to color, and it was recognized that the arm could be used to carry out a wide variety of activities that would enable both geology and physical properties investigations. During surface operations for two martian years, the IDA was used during major campaigns to image the surface around the lander, to deploy the instruments, to assist the mole in penetrating beneath the surface, to bury a portion of the seismometer tether, to clean dust from the solar arrays to increase power, and to conduct a surface geology investigation including soil mechanics and physical properties experiments. No other surface mission has engaged in such a sustained and varied campaign of arm and scoop activities directed at such a diverse suite of objectives. Images close to the surface and continuous meteorology measurements provided important constraints on the threshold friction wind speed needed to initiate aeolian saltation and surface creep. The IDA was used extensively for almost 22 months to assist the mole in penetrating into the subsurface. Soil was scraped into piles and dumped onto the seismometer tether six times in an attempt to bury the tether and ∼ 30% was entrained in the wind and dispersed downwind 1-2 m, darkening the surface. Seven solar array cleaning experiments were conducted by dumping scoops of soil from 35 cm above the lander deck during periods of high wind that dispersed the sand onto the panels that kicked dust off of the panels into suspension in the atmosphere, thereby increasing the power by ∼15% during this period. Final IDA activities included an indentation experiment that used the IDA scoop to push on the ground to measure the plastic deformation of the soil that complemented soil mechanics measurements from scoop interactions with the surface, and two experiments in which SEIS measured the tilt from the arm pressing on the ground to derive near surface elastic properties.

Mars↗

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Hagen, Live↗

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗