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NASA NTRS1989

Antigen presentation by non-immune B-cell hybridoma clones: presentation of synthetic antigenic sites reveals clones that exhibit no specificity and clones that present only one epitope

Recently, we reported the preparation and antigen-presenting properties of hybridoma B-cell clones obtained after fusing non-secreting, non-antigen presenting Balb/c 653-myeloma cells with non-immune SJL spleen cells. It was found that antigen presentation at the clonal level can be specific or non-specific, depending on the particular B-cell clone. In the present work, one specific and one general presenter B-cell clones were tested for their epitope presentation ability to SJL T-cells that were specific to lysozyme or myoglobin. B-cell clone A1G12, a general presenter which presented both lysozyme and myoglobin to their respective T-cell lines, was found to present all five myoglobin epitopes while clone A1L16, a lysozyme specific presenter presented only one of the three epitopes of lysozyme. The latter reveals a hitherto unknown submolecular specificity (to a given epitope within a protein) for antigen presenting cells at the clonal level. Therefore, the specificity of T-cell recognition does not only derive from the T-cell but may also be dependent on the epitope specificity of the antigen-presenting B-cell.

Hybridomas/immunology↗

NASA NTRSDate not supplied

A Multiphysics Study to Improve Specific Energy of Primary Batteries for Low Temperature Operation for Deep Space Missions

Several lander missions on the outer planets such as Europa, Enceladus, and Titan require electrical power to operate scientific and communication equipment. The traditional power generation methods, such as a photovoltaic array, are not feasible as their efficiency drops significantly at these vast distances. The novel radioisotope power systems are not practical today based on current lander designs and the effectiveness of these systems. To perform in situ science on distant planets, a high specific energy battery (>700 Wh/kg) needs to operate for about 480 hours under cold temperatures (-40C or 0C) [1]. While a primary battery such as Li-CFx can provide high specific energy at room temperature, its specific capacity decreases significantly at low temperatures. One of the causes for this drop is low ion and electrical conductivity, and slower reaction kinetics. Slower transport and facile kinetics lead to an increase in the battery’s resistance and higher voltage drops during the cell operation, thus reducing specific capacity. Both the transport and kinetics show a strong dependence on temperature. Thus, a small temperature rise can lead to an increase in the reaction rate and ion conductivity; since the temperature, cell resistance, and specific capacity are interdependent. A conventional battery model accounts for ohmic, thermodynamic, and, electrochemical, and chemical decomposition heating. The ohmic heating can be controlled by designing a resistive microstructure and varying the ratios of the active materials [2]. The kinetics can be improved by increasing the surface area, reducing the particle size, or adding a catalyst. These parameters are often optimized to achieve high specific energy at room temperatures. A similar optimization study is not available at low temperatures and for a primary (high specific energy) battery. For this presentation, we will explore the effect of geometrical, microstructural, and material properties on optimal specific capacity at low temperatures through multiphysics simulations. The ion transport resistance depends on the porosity and the tortuosity of an electrode and the separator.

M. Mehta↗

DOE OSTI2019

Evalulation of the Specification for Safety-Related Steel Structures for Nuclear Facilities, ANSI/AISC N690-18, for Application to Nuclear Power Plants

This report describes the assessment of the recently published ANSI/AISC N690-18, Specification for Safety-Related Steel Structures for Nuclear Facilities. This work was performed for the U.S. Nuclear Regulatory Commission for potential endorsement of N690-18 for use in the design of nuclear power plants. Currently the NRC endorses the use of an earlier version: N690-1994 (R2004), and thus, a technical review of the updated N690 Specification, which contains significant changes, is warranted. The N690-18 Specification reflects advances and improvements in steel design gained from experience, analytical studies, and experimental data over the years. The N690-18 specification also contains a new Appendix N9 that addresses the design of safety-related steel-plate composite (SC) walls which are a relatively new type of structural member for which previously there has not been any U.S. code or standard that governs its design. The technical review of N690-18 was performed in order to assess the adequacy of the provisions for use by the NRC in updating its regulatory guidance for nuclear power plants. The research developed the technical basis for acceptance of the new specification and also identified areas where additional staff guidance is needed for the design of safety-related steel structures at nuclear power plants. The results of the research have determined that the N690-18 specification is a significant enhancement from the N690-1994 (R2004) edition. The new specification contains substantial upgrades in the design of structural steel and includes new provisions for design of SC wall sections, which can benefit the nuclear power industry as well as the NRC review process. All of the improvements, if endorsed by the NRC with certain regulatory positions, will allow clearer and more consistent regulatory guidance, and will avoid the need for justification by licensees and related reviews each time certain methods or approaches are used.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Is the exquisite specificity of lymphocytes generated by thymic selection or due to evolution?

We have previously argued that the antigen receptors of T and B lymphocytes evolved to be sufficiently specific to avoid massive deletion of clonotypes by negative selection. Their optimal ‘specificity’ level, i.e., probability of binding any particular epitope, was shown to be inversely related to the number of self-antigens that the cells have to be tolerant to. Experiments have demonstrated that T lymphocytes also become more specific during negative selection in the thymus, because cells expressing the most crossreactive receptors have the highest likelihood of binding a self-antigen, and hence to be tolerized (i.e., deleted, anergized, or diverted into a regulatory T cell phenotype). Thus, there are two —not mutually exclusive— explanations for the exquisite specificity of T cells, one involving evolution and the other thymic selection. To better understand the impact of both, we extend a previously developed mathematical model by allowing for T cells with very different binding probabilities in the pre-selection repertoire. We confirm that negative selection tends to tolerize the most crossreactive clonotypes. As a result, the average level of specificity in the functional post-selection repertoire depends on the number of self-antigens, even if there is no evolutionary optimization of binding probabilities. However, the evolutionary optimal range of binding probabilities in the pre-selection repertoire also depends on the number of self-antigens. Species with more self antigens need more specific pre-selection repertoires to avoid excessive loss of T cells during thymic selection, and hence mount protective immune responses. We conclude that both evolution and negative selection are responsible for the high level of specificity of lymphocytes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism

Position-specific 13 C/ 12 C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids. Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The 13 C/ 12 C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ 13 C values relative to a working standard. This methodology constrains position-specific δ 13 C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ 13 C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7–5‰ for each carbon position. Position-specific δ 13 C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO 2 , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline. Here this study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Nephron segment-specific gene expression using AAV vectors

AAV9 vector provides efficient gene transfer in all segments of the renal nephron, with minimum expression in non-renal cells, when administered retrogradely via the ureter. It is important to restrict the transgene expression to the desired cell type within the kidney, so that the physiological endpoints represent the function of the transgene expressed in that specific cell type within kidney. We hypothesized that segment-specific gene expression within the kidney can be accomplished using the highly efficient AAV9 vectors carrying the promoters of genes that are expressed exclusively in the desired segment of the nephron in combination with administration by retrograde infusion into the kidney via the ureter. We constructed AAV vectors carrying eGFP under the control of: kidney-specific cadherin (KSPC) gene promoter for expression in the entire nephron; Na{sup +}/glucose co-transporter (SGLT2) gene promoter for expression in the S1 and S2 segments of the proximal tubule; sodium, potassium, 2 chloride co-transporter (NKCC2) gene promoter for expression in the thick ascending limb of Henle's loop (TALH); E-cadherin (ECAD) gene promoter for expression in the collecting duct (CD); and cytomegalovirus (CMV) early promoter that provides expression in most of the mammalian cells, as control. We tested the specificity of the promoter constructs in vitro for cell type-specific expression in mouse kidney cells in primary culture, followed by retrograde infusion of the AAV vectors via the ureter in the mouse. Our data show that AAV9 vector, in combination with the segment-specific promoters administered by retrograde infusion via the ureter, provides renal nephron segment-specific gene expression.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Administration of plasmacytoid dendritic cell-stimulative lactic acid bacteria enhances antigen-specific immune responses

Lactic acid bacteria (LAB) have been reported to have beneficial effects on protective immunity against viruses and pathogenic bacteria by activating innate immune cells such as dendritic cells (DC) or macrophages. However, little is known about whether LAB contributes to antigen-specific immune responses. Because plasmacytoid DC (pDC) links innate and acquired immunity, here we investigated whether the pDC-stimulative LAB, Lactococcus lactis strain Plasma (LC-Plasma), influences antigen-specific immune responses. In in vitro co-culture experiments, LC-Plasma enhanced the expression of MHC class I and II, and CD80 and CD86 on both pDC and conventional DC, and this enhancement was abolished by treatment with a Toll-like receptor 9 antagonist. A subsequent in vitro study showed that LC-Plasma increased antigen-specific T cell responses via DC activation. In mice, oral administration of LC-Plasma in combination with intraperitoneal antigen administration enhanced the percentage of antigen-specific CD8{sup +} T cells and the amount of antigen-specific IgG. Furthermore, continuous intake of LC-Plasma increased T helper 1 responses, which contribute to antigen-specific cellular and humoral immune responses. Taken together, these results reveal that the oral intake of pDC-stimulative LAB enhances antigen-specific immune responses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Visualization of specific collagen-producing cells by Col1-GFP transgenic mice revealed novel type I collagen-producing cells other than fibroblasts in systemic organs/tissues

Highlights: • A new reporter mouse was generated to label type I collagen-producing cells. • Type I collagen-producing cells were specifically labeled in this reporter mouse. • Podocytes and Leydig cells showed the ability to produce type I collagen. Type I collagen is one of the most abundant proteins in mammals and plays important roles in maintaining the integrity of many tissues. Although fibroblasts are the main source of type I collagen, other cells also produce it; however, these cells are not well-defined owing to the lack of a specific marker. A transgenic (Tg) mouse line has been generated in which type I collagen-producing cells are labeled with enhanced green fluorescent protein (EGFP), which enables the monitoring of these cells without requiring an additional cell marker. This Tg mouse line has since been widely used to study type I collagen-producing cells and fibrosis; one study revealed that podocytes, which were not previously considered to produce type I collagen, expressed EGFP. This raises a question regarding the specificity of EGFP expression in this Tg mouse line. To exclude the possibility of non-specific EGFP expression in the existing Tg mouse line and specifically monitor type I collagen-producing cells, we generated a new Tg mouse line and histologically confirmed the specificity of EGFP expression throughout the body. Moreover, we explored type I collagen-producing cells other than fibroblasts and revealed for the first time that Leydig cells have the ability to produce type I collagen. Because of its highly specific and physiologically accurate expression, our new Tg mouse line will help to accurately elucidate not only type I collagen-producing cells in normal tissues but also the potential cells in fibrotic tissues, providing new insights into the pathology of fibrosis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Identification of candidate host-specificity genes in Exserohilum turcicum using comparative genomics and transcriptomics

Abstract Exserohilum turcicum causes northern corn leaf blight and sorghum leaf blight. While the same species cause disease in both crops, the strains are host-specific. Here, we report the sequence and de novo annotated assemblies of one sorghum- and one maize-specific E. turcicum strain. The strains were sequenced using the PacBio Sequel II system. The total genome length for both assemblies was between 44 and 45 Mb with N50 of ∼2.5 Mb. Ninety-eight percent of the Benchmarking Universal Single-Copy Orthologs (BUSCO) for both assemblies had complete status. The estimated number of genes was 11,762 and 12,029 in the sorghum- and maize-specific isolates, respectively. Funannotate, EffectorP, SignalP, and transcriptome data were used to create functional annotation of each genome. The whole-genome comparison identified ten large-scale inversions and three translocations between the maize- and sorghum-specific strains, along with homologous genes and gene duplications. RNA was sequenced from the maize- and sorghum-specific isolate 10 days post-inoculation in maize and sorghum and from axenic cultures. Gene expression data from planta and axenic growth experiments were compared for each strain. Candidate host-specificity genes were identified by combining results from whole-genome comparison, synteny analysis, gene annotations, and transcriptome data. Overall, this study identified several candidate host-specificity genes that provide insights into E. turcicum interaction with its hosts.

Krone, Mara J. (ORCID:0000000159006624)↗

DOE OSTI2021

The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold

Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVR A1 , AVR A7 , AVR A9 , AVR A13 , and allelic AVR A10 /AVR A22 , which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVR A6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVR A1 , AVR A7 , AVR A10 /AVR A22 , and AVR A13 , suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVR A1 and AVR A6 as well as allelic AVR A10 and AVR A22 is largely determined by the receptors’ C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVR A10 and five specific AVR A22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVR A effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Domain Specific Language Support for Exascale

A multi-institutional project known as D-TEC (short for “Domain- specific Technology for Exascale Computing”) set out to explore technologies to support the construction of Domain Specific Languages (DSLs) to map application programs to exascale architectures. DSLs employ automated code transformation to shift the burden of delivering portable performance from application programmers to compilers. Two chief properties contribute: DSLs permit expression at a high level of abstraction so that a programmer’s intent is clear to a compiler and DSL implementations encapsulate human domain-specific optimization knowledge so that a compiler can be smart enough to achieve good results on specific hardware. Domain specificity is what makes these properties possible in a programming language. If leveraging domain specificity is the key to keep exascale software tractable, a corollary is that many different DSLs will be needed to encompass the full range of exascale computing applications; moreover, a single application may well need to use several different DSLs in conjunction. As a result, developing a general toolkit for building domain-specific languages was a key goal for the D-TEC project. Different aspects of the D-TEC research portfolio were the focus of work at each of the partner institutions in the multi-institutional project. D-TEC research and development work at Rice University focused on on three principal topics: understanding how to automate the tuning of code for complex architectures, research and development of the Rosebud DSL engine, and compiler technology to support complex execution platforms. This report provides a summary of the research and development work on the D-TEC project at Rice University.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Evaluation of the Specification for Safety-Related Steel Structures for Nuclear Facilities, ANSI/AISC N690-18, for Application to Nuclear Power Plants

42 ENGINEERING↗

NASA NTRS1983

The SIFT Code Specification

The specification of Software Implemented Fault Tolerance (SIFT) consists of two parts, the specifications of the SIFT models and the specifications of the SIFT PASCAL program which actually implements the SIFT system. The code specifications are the last of a hierarchy of models describing the operation of the SIFT system and are related to the SIFT models as well as the PASCAL program. These Specifications serve to link the SIFT models to the running program. The specifications are very large and detailed and closely follow the form and organization of the PASCAL code. In addition to describing each of the components of the SIFT code, the code specifications describe the assumptions of the upper SIFT models which are required to actually prove that the code will work as specified. These constraints are imposed primarily on the schedule tables.

Source record↗

NASA NTRS1991

Automatic derivation of formal software specifications from informal descriptions

SPECIFIER, an interactive system which derives formal specifications of data types and programs from their informal descriptions, is described. The process of deriving formal specifications is viewed as a problem-solving process. The system uses common problem-solving techniques such as schemas, analogy, and difference-based reasoning to derive formal specifications. If an informal description is a commonly occurring operation for which the system has a schema, then the formal specification is derived by instantiating the schema. If there is no such schema, SPECIFIER tries to find a previously solved problem which is analogous to the current problem. If the problem found is directly analogous to the current problem, it applies an analogy mapping to obtain a formal specification. On the other hand, if the analogy found is only approximate, it solves the directly analogous part of the problem by analogy and performs difference-based reasoning using the remaining (unmatched) parts to transform the formal specification obtained by analogy to a formal specification for the entire original problem.

Miriyala, Kanth↗

NASA NTRS1993

ARIES: Acquisition of Requirements and Incremental Evolution of Specifications

This paper describes a requirements/specification environment specifically designed for large-scale software systems. This environment is called ARIES (Acquisition of Requirements and Incremental Evolution of Specifications). ARIES provides assistance to requirements analysts for developing operational specifications of systems. This development begins with the acquisition of informal system requirements. The requirements are then formalized and gradually elaborated (transformed) into formal and complete specifications. ARIES provides guidance to the user in validating formal requirements by translating them into natural language representations and graphical diagrams. ARIES also provides ways of analyzing the specification to ensure that it is correct, e.g., testing the specification against a running simulation of the system to be built. Another important ARIES feature, especially when developing large systems, is the sharing and reuse of requirements knowledge. This leads to much less duplication of effort. ARIES combines all of its features in a single environment that makes the process of capturing a formal specification quicker and easier.

Roberts, Nancy A.↗

NASA NTRS1993

Towards the formal specification of the requirements and design of a processor interface unit: HOL listings

This technical report contains the HOL listings of the specification of the design and major portions of the requirements for a commercially developed processor interface unit (or PIU). The PIU is an interface chip performing memory interface, bus interface, and additional support services for a commercial microprocessor within a fault-tolerant computer system. This system, the Fault-Tolerant Embedded Processor (FTEP), is targeted towards applications in avionics and space requiring extremely high levels of mission reliability, extended maintenance-free operation, or both. This report contains the actual HOL listings of the PIU specification as it currently exists. Section two of this report contains general-purpose HOL theories that support the PIU specification. These theories include definitions for the hardware components used in the PIU, our implementation of bit words, and our implementation of temporal logic. Section three contains the HOL listings for the PIU design specification. Aside from the PIU internal bus (I-Bus), this specification is complete. Section four contains the HOL listings for a major portion of the PIU requirements specification. Specifically, it contains most of the definition for the PIU behavior associated with memory accesses initiated by the local processor.

Fura, David A.↗

NASA NTRS2009

System and method for deriving a process-based specification

A system and method for deriving a process-based specification for a system is disclosed. The process-based specification is mathematically inferred from a trace-based specification. The trace-based specification is derived from a non-empty set of traces or natural language scenarios. The process-based specification is mathematically equivalent to the trace-based specification. Code is generated, if applicable, from the process-based specification. A process, or phases of a process, using the features disclosed can be reversed and repeated to allow for an interactive development and modification of legacy systems. The process is applicable to any class of system, including, but not limited to, biological and physical systems, electrical and electro-mechanical systems in addition to software, hardware and hybrid hardware-software systems.

Hinchey, Michael Gerard↗

DOE OSTI2017

Development of a highly specific HER2 monoclonal antibody for immunohistochemistry using protein microarray chips

HER2 is an orphan receptor tyrosine kinase of the EGFR families and is considered to be a key tumor driver gene [1]. Breast cancer and gastric cancer with HER2 amplification can be effectively treated by its neutralizing antibody, Herceptin. In clinic, Immunohistochemistry (IHC) was used as the primary screening method to diagnose HER2 amplification [2]. However, recent evidence suggested that the frequently used rabbit HER2 antibody 4B5 cross reacted with another family member HER4 [3]. IHC staining with 4B5 also indicated that there was strong non-specific cytoplasmic and nuclear signals in normal gastric mucosal cells and some gastric cancer samples. Using a protein lysate array which covers 85% of the human proteome, we have confirmed that the 4B5 bound to HER4 and a nuclear protein ZSCAN18 besides HER2. The non-specific binding accounts for the unexpected cytoplasmic and nuclear staining of 4B5 of normal gastric epithelium. Finally, we have developed a novel mouse HER2 monoclonal antibody UMAB36 with similar sensitivity to 4B5 but only reacted to HER2 across the 17,000 proteins on the protein chip. In 129 breast cancer and 158 gastric cancer samples, UMAB36 showed 100% sensitivity and specificity comparing to the HER2 FISH reference results with no unspecific staining in the gastric mucosa layer. Therefore, UMAB36 could provide as an alternative highly specific IHC reagent for testing HER2 amplification in gastric cancer populations. - Highlights: • HER2 antibody 4B5 cross-interacts with HER4 and ZSCAN18, which would interfere with the accuracy of IHC diagnosis of HER2. • A HER2 antibody UMAB36 has been developed with high sensitivity and specificity and can be utilized in HER2 diagnosis. • Protein lysate array is a novel strategy to screen for highly specific antibody.

60 APPLIED LIFE SCIENCES↗