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At least 253 records · Page 14

Heterologous Gene Expression of N -Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N -terminus of Modular Polyketide Synthase

Streptomyces genomes have a high G + C content and typically use an ATG or GTG codon to initiate protein synthesis. Although gene-finding tools perform well in low GC genomes, it is known that the accuracy in predicting a translational start site (TSS) is much less for high GC genomes. LipPks1 is a Streptomyces-derived, well-characterized modular polyketide synthase (PKS). Here, using this enzyme as a model, we experimentally investigated the effects of alternative TSSs using a heterologous host, Streptomyces venezuelae. One of the TSSs employed boosted the protein level by 59-fold and the product yield by 23-fold compared to the originally annotated start codon. Interestingly, a structural model of the PKS indicated the presence of a structural motif in the N-terminus, which may explain the observed different protein levels together with a proline and arginine-rich sequence that may inhibit translational initiation. Lastly, this structure was also found in six other modular PKSs that utilize noncarboxylated starter substrates, which may guide the selection of optimal TSSs in conjunction with start-codon prediction software.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer-Grafted Nanoparticles as All-in-One Nanoplatforms

Polymer-grafted nanoparticles (PGNPs) represent a versatile class of hybrid nanomaterials, in which nanoparticle cores and tethered polymer coronas are integrated into structurally programmable building blocks. Rapid advances in nanoparticle surface functionalization and surface-initiated polymerization have enabled increasingly precise control over the nanoparticle core composition and brush architecture, greatly expanding the accessible structural and functional landscape of PGNPs. This review summarizes recent progress in the modular design and structural regulation of PGNPs, with an emphasis on nanoparticle platforms and associated surface functionalization strategies, polymer brush synthesis and architectural control, and the structure−property relationships that govern PGNP behavior. Emerging applications are further highlighted, including additive manufacturing, self-healing materials, membrane-based gas separations, and battery-related systems, where PGNPs provide unique opportunities to couple nanoscale interfacial design with macroscopic performance. Finally, future opportunities are discussed for extending PGNP concepts to increasingly complex, multifunctional, and application-oriented hybrid materials.

functional nanocomposites↗

Thermal-Fluid and Thermal-Structural Response of the T-Tube Modular Divertor to Spatiotemporally Varying Heat Loads

Tungsten (W) is the leading candidate for divertor target plates because of its high melting point (>3000°C), thermal conductivity, and ultimate tensile stress. While W and its alloys are the only solid materials that can survive the high heat fluxes incident on the divertor, W’s low-ductility high ductile-to-brittle transition temperature of ~600°C and relatively low recrystallization temperature (RT) of ~1300°C pose structural (among other) challenges. The objective of this work is to estimate the thermal-fluid and thermal-structural performance of the helium (He)-cooled T-tube divertor, which was originally developed by the Advanced Reactor Innovation and Evaluation Study (ARIES) using numerical simulations. Here, predictions of temperature distributions across the plasma-facing structural component and surface pressures from computational fluid dynamics simulations are used to determine stress distributions using commercial structural finite element modeling software over a range of fusion-relevant conditions. The maximum allowable incident heat fluxes are determined based on the temperature limits imposed by the ITER elastic Structural Design Criteria for In-vessel Components (SDC-IC) and the maximum RT over a range of He mass flow rates and presented in the form of performance design charts. Our recent work found that thermal- structural criteria accounting for the low ductility of W in a finger-type modular divertor constrain the maximum incident heat fluxes to values well below the ITER specifications, and those based on considering only the RT demonstrate that integrated thermal-fluid and elastic structural performance evaluation are required for accurate assessment of divertor performance. This novel analysis of the T-tube considers how nonuniform and transient incident heat fluxes affect its thermal-fluid and thermal-structural performance, as well as the effect of volumetric heating, which can be as great as 27% of the power incident on the divertor surface. The W tile of the T-tube, with its relatively large plasma-facing area of ~15 cm 2 , will likely experience significant spatial variations in incident heat flux. This work therefore assesses whether steady-state incident heat flux profiles with a peak of 10 MW/m 2 and maximum heat flux gradients of 200 MW/m 2 per m exceed the structural limits imposed by the ITER elastic SDC-IC and the maximum RT over a range of fusion-relevant conditions. The effect of transient heat fluxes typical of plasma detachment and reattachment from the target plate due, for example, to gas injection are also evaluated

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Inflatable structures for a lunar base habitat

Design and construction of a structure on the moon requires addressing a host of issues not encountered on earth. A modular quilted inflatable structure consisting of thin membranes of composite material integrated with supporting columns and arches is proposed. An initial linear analysis of the proposed structure is briefly reviewed. The actual response of an inflatable membrane is nonlinear and, hence, a nonlinear numerical analysis for the stresses and displacements was undertaken. Initial results clearly indicate that an inflatable structure is a feasible concept and is ideally suited for a lunar structure.

Nowak, Paul S.↗

An analysis of an inflatable module for planetary surfaces

Design and construction of a structure on planetary surfaces requires addressing a host of issues not encountered on earth. A modular quilted inflatable structure consisting of thin membranes of composite material integrated with supporting columns and arches is proposed. An initial linear analysis of the structure is briefly reviewed. The actual response of an inflatable membrane is nonlinear and, hence, a nonlinear numerical analysis of the stresses and displacements was undertaken. Results based on the loadings on a lunar structure clearly indicate that an inflatable structure is a feasible concept and is ideally suited for a planetary surface structure.

Nowak, Paul S.↗

Paralogous Radiations of PIN Proteins with Multiple Origins of Noncanonical PIN Structure

The plant hormone auxin is a conserved regulator of development which has been implicated in the generation of morphological novelty. PIN-FORMED1 (PIN) auxin efflux carriers are central to auxin function by regulating its distribution. PIN family members have divergent structures and cellular localizations, but the origin and evolutionary significance of this variation is unresolved. To characterize PIN family evolution, we have undertaken phylogenetic and structural analyses with a massive increase in taxon sampling over previous studies. Our phylogeny shows that following the divergence of the bryophyte and lycophyte lineages, two deep duplication events gave rise to three distinct lineages of PIN proteins in euphyllophytes. Subsequent independent radiations within each of these lineages were taxonomically asymmetric, giving rise to at least 21 clades of PIN proteins, of which 15 are revealed here for the first time. Although most PIN protein clades share a conserved canonical structure with a modular central loop domain, a small number of noncanonical clades dispersed across the phylogeny have highly divergent protein structure. We propose that PIN proteins underwent sub- and neofunctionalization with substantial modification to protein structure throughout plant evolution. Our results have important implications for plant evolution as they suggest that structurally divergent PIN proteins that arose in paralogous radiations contributed to the convergent evolution of organ systems in different land plant lineages.

59 BASIC BIOLOGICAL SCIENCES↗

Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites

Poly-N-acetyl-lactosamine (poly-LacNAc) structures are composed of repeating [-Galβ(1,4)-GlcNAcβ(1,3)-]n glycan extensions. They are found on both N- and O-glycoproteins and glycolipids and play an important role in development, immune function, and human disease. The majority of mammalian poly-LacNAc is synthesized by the alternating iterative action of β1,3-N-acetylglucosaminyltransferase 2 (B3GNT2) and β1,4-galactosyltransferases. B3GNT2 is in the largest mammalian glycosyltransferase family, GT31, but little is known about the structure, substrate recognition, or catalysis by family members. Here we report the structures of human B3GNT2 in complex with UDP:Mg 2+ and in complex with both UDP:Mg 2+ and a glycan acceptor, lacto-N-neotetraose. The B3GNT2 structure conserves the GT-A fold and the DxD motif that coordinates a Mg 2+ ion for binding the UDP-GlcNAc sugar donor. The acceptor complex shows interactions with only the terminal Galβ(1,4)-GlcNAcβ(1,3)- disaccharide unit, which likely explains the specificity for both N- and O-glycan acceptors. Modeling of the UDP-GlcNAc donor supports a direct displacement inverting catalytic mechanism. Comparative structural analysis indicates that nucleotide sugar donors for GT-A fold glycosyltransferases bind in similar positions and conformations without conserving interacting residues, even for enzymes that use the same donor substrate. In contrast, the B3GNT2 acceptor binding site is consistent with prior models suggesting that the evolution of acceptor specificity involves loops inserted into the stable GT-A fold. These observations support the hypothesis that GT-A fold glycosyltransferases employ coevolving donor, acceptor, and catalytic subsite modules as templates to achieve the complex diversity of glycan linkages in biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experiences with a preliminary NICE/SPAR structural analysis system

Development of a new structural analysis system based on the original SPAR finite element code and the NICE system is described. The system is denoted NICE/SPAR. NICE was designed at Lockheed Palo Alto Research Laboratory and contains data management utilities, a command language interpreter, and a command language definition for integrating engineering computational modules. SPAR is a system of programs used for finite element structural analysis developed for NASA by Engineering Information Systems, Inc. It includes many complementary structural analysis and utility functions which communicate through a common database. The work on NICE/SPAR was motivated by requirements for a highly modular and flexible structural analysis system to use as a tool in carrying out research in computational methods and exploring new computer hardware. Analysis examples are presented which demonstrate the benefits gained from a combination of the NICE command language with the SPAR computational modules.

Lotts, C. G.↗

Introduction to the computational structural mechanics testbed

The Computational Structural Mechanics (CSM) testbed software system based on the SPAR finite element code and the NICE system is described. This software is denoted NICE/SPAR. NICE was developed at Lockheed Palo Alto Research Laboratory and contains data management utilities, a command language interpreter, and a command language definition for integrating engineering computational modules. SPAR is a system of programs used for finite element structural analysis developed for NASA by Lockheed and Engineering Information Systems, Inc. It includes many complementary structural analysis, thermal analysis, utility functions which communicate through a common database. The work on NICE/SPAR was motivated by requirements for a highly modular and flexible structural analysis system to use as a tool in carrying out research in computational methods and exploring computer hardware. Analysis examples are presented which demonstrate the benefits gained from a combination of the NICE command language with a SPAR computational modules.

Lotts, C. G.↗

SIRU development. Volume 1: System development

A complete description of the development and initial evaluation of the Strapdown Inertial Reference Unit (SIRU) system is reported. System development documents the system mechanization with the analytic formulation for fault detection and isolation processing structure; the hardware redundancy design and the individual modularity features; the computational structure and facilities; and the initial subsystem evaluation results.

Gilmore, J. P.↗

Regulatory interplay between TFIID’s conformational transitions and its modular interaction with core promoter DNA

Recent structural and biochemical studies of human TFIID have significantly increased our understanding of the mechanisms underlying the recruitment of TFIID to promoter DNA and its role in transcription initiation. Structural studies using cryoEM revealed that modular interactions underlie TFIID’s ability to bind simultaneously multiple promoter motifs and to define a DNA state that will facilitate transcription initiation. Here we propose a general model of promoter binding by TFIID, where co-activators, activators, and histone modifications promote and/or stabilize a conformational state of TFIID that results in core promoter engagement. Within this high affinity conformation, we propose that TFIID’s extensive interaction with promoter DNA leads to topological changes in the DNA that facilitate the eventual loading of RNAP II. While more work is required to dissect the individual contributions of activators and repressors to TFIID’s DNA binding, the recent cryoEM studies provide a physical framework to guide future structural, biophysical, and biochemical experiments.

59 BASIC BIOLOGICAL SCIENCES↗

An across-the-bay flight support structure designed specifically for the Spartan program

The preliminary design of an across-the-bay Flight Support Structure optimized to the specific requirements of the Spartan program has been completed. Although approximately 15 percent heavier than the initial goal, preliminary analysis indicate very low stress levels and significant reduction in weight should be possible in the final design. This structure is capable of supporting two Spartan 200-class spacecraft or attached payloads of equivalent total weight. The inherent structural efficiency of monocoque type construction is utilized. The minimization of fabrication and assembly costs and provision for simple and versatile payload interfacing where given significant considerations. Modularity of this structure allows it to be readily adapted for use as the primary structure of an Aries-class Spartan free-flyer utilizing the Orbit trunning latch mechanisms, thus eliminating the need for a flight support structure.

Rast, J. J.↗

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

ABSTRACT Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ- d -Glu-A 2 pm (A 2 pm is diaminopimelic acid) cysteine amidase (or dl -endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l -Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. IMPORTANCE Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.

Xu, Qingping↗

Modular hybrid modeling to increase efficiency, explore structural uncertainty, and allow multidimensional complexity scaling in land surface models

Land surface models (LSMs) are indispensable tools for predicting hydrologic extremes, as well as a particularly uncertain component of Earth system models that has stubbornly resisted the convergence in projections over several successive generations of model intercomparisons. This uncertainty in LSMs is poorly quantified and poorly attributed to specific processes, which has hampered efforts to focus research in reducing uncertainty. This has resulted from sparse sampling of the possible uncertainty space—which is high-dimensional and has contributions from parametric, structural, initial, and boundary condition uncertainties—as an artifact of CMIP-type ensembles of opportunity and limitations inherent in observational benchmarks. A new approach is needed to understand and reduce this uncertainty, based around individual LSMs that can represent the breadth of assumptions represented in current CMIP-type efforts, while at the same time exploring that uncertainty in a systematic way, confronting multiple types of observations, and where justified, replacing process representations with ML-driven emulators. We propose an approach of modular hybrid modeling to address these challenges.

58 GEOSCIENCES↗

Class 1 Permit Modification Notification Addition of Structures within Technical Area 54, Area G, Pad 11, Dome 375 Los Alamos National Laboratory Hazardous Waste Facility Permit, July 2012

The purpose of this letter is to notify the New Mexico Environment Department-Hazardous Waste Bureau (NMED-HWB) of a Class 1 Permit Modification to the Los Alamos National Laboratory (LANL) Hazardous Waste Facility Permit issued to the Department of Energy (DOE) and Los Alamos National Security, LLC (LANS) in November 2010. The modification adds structures to the container storage unit at Technical Area (TA) 54 Area G, Pad 11. Permit Section 3.1(3) requires that changes to the location of a structure that does not manage hazardous waste shall be changed within the Permit as a Class 1 modification without prior approval in accordance with Code of Federal Regulations, Title 40 (40 CFR), {section}270.42(a)(1). Structures have been added within Dome 375 located at TA-54, Area G, Pad 11 that will be used in support of waste management operations within Dome 375 and the modular panel containment structure located within Dome 375, but will not be used as waste management structures. The Class 1 Permit Modification revises Figure 36 in Attachment N, Figures; and Figure G.12-1 in Attachment G.12, Technical Area 54, Area G, Pad 11 Outdoor Container Storage Unit Closure Plan. Descriptions of the structures have also been added to Section A.4.2.9 in Attachment A, TA - Unit Descriptions; and Section 2.0 in Attachment G.12, Technical Area 54, Area G, Pad 11 Outdoor Container Storage Unit Closure Plan. Full description of the permit modification and the necessary changes are included in Enclosure 1. The modification has been prepared in accordance with 40 CFR {section}270.42(a)(l). This package includes this letter and an enclosure containing a description of the permit modification, text edits of the Permit sections, and the revised figures (collectively LA-UR-12-22808). Accordingly, a signed certification page is also enclosed. Three hard copies and one electronic copy of this submittal will be delivered to the NMED-HWB.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Modeling and simulation of earthquake soil structure interaction excited by inclined seismic waves

Presented is an application of wave potential formulation (WPF) together with domain reduction method (DRM) to modeling earthquake soil structure interaction (ESSI) behavior in horizontally layered ground under inclined incident seismic waves. Wave potential formulation is used to develop a spatially varying, inclined seismic wave field from incident Primary (P) and Secondary (S) waves that propagate through layered ground. Developed seismic wave field is then used to develop effective forces for Domain Reduction Method that are then used for analyzing ESSI response of a soil structure system. Developed methodology, called WPF-DRM, is verified using analytic solution for a free field response of layered ground subjected to inclined incident waves. Developed WPF-DRM methodology is illustrated through analysis of an ESSI response of a deeply embedded structure, a small modular reactor (SMR) subjected to incident S wave polarized in vertical plane (SV) with variation in inclinations and frequencies. Presented example highlights the influences of incident wave inclination and frequency on ESSI response of analyzed SMR.

58 GEOSCIENCES↗

Mars habitat

The objective of this study is to develop a conceptual design for a permanently manned, self-sustaining Martian facility, to accommodate a crew of 20 people. The goal is to incorporate the major functions required for long term habitation in the isolation of a barren planet into a thriving ecosystem. These functions include living, working, service, and medical facilities as well as a green house. The main design task was to focus on the internal layout while investigating the appropriate structure, materials, and construction techniques. The general concept was to create a comfortable, safe living environment for the crew members for a stay of six to twelve months on Mars. Two different concepts were investigated, a modular assembly reusable structure (MARS) designated Lavapolis, and a prefabricated space frame structure called Hexamars. Both models take into account factors such as future expansion, radiation shielding, and ease of assembly.

Ayers, Dale↗

Development of a low-aspect ratio fin for flight research experiments

A second-generation flight test fixture, developed at NASA Dryden Flight Research Center, offers a generic testbed for aerodynamic and fluid mechanics research. The new fixture, a low-aspect ratio vertical fin shape mounted on the centerline of an F-15B aircraft lower fuselage, is designed for flight research at Mach numbers up to 2.0. The new fixture is a composite structure with a modular configuration and removable components for functional flexibility. This report describes the multidisciplinary design and analysis approach used to develop the fixture. The approach integrates conservative assumptions with simple analysis techniques to minimize the time and cost associated with its development. Presented are the principal disciplines required for this effort, which include aerodynamics, structures, stability, and operational considerations. In addition, preliminary results from the first phase of flight testing are presented. Acceptable directional stability and flow quality are documented and show agreement with predictions. Future envelope expansion activities will minimize current limitations so that the fixture can be used for a wide variety of high-speed aerodynamic and fluid mechanics research experiments.

Richwine, David M.↗