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Results for “sequence determinants”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1998

Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA

Bovine seminal ribonuclease (RNase) binds, melts, and (in the case of RNA) catalyzes the hydrolysis of double-stranded nucleic acid 30-fold better under physiological conditions than its pancreatic homologue, the well-known RNase A. Reported here are site-directed mutagenesis experiments that identify the sequence determinants of this enhanced catalytic activity. These experiments have been guided in part by experimental reconstructions of ancestral RNases from extinct organisms that were intermediates in the evolution of the RNase superfamily. It is shown that the enhanced interactions between bovine seminal RNase and double-stranded nucleic acid do not arise from the increased number of basic residues carried by the seminal enzyme. Rather, a combination of a dimeric structure and the introduction of two glycine residues at positions 38 and 111 on the periphery of the active site confers the full catalytic activity of bovine seminal RNase against duplex RNA. A structural model is presented to explain these data, the use of evolutionary reconstructions to guide protein engineering experiments is discussed, and a new variant of RNase A, A(Q28L K31C S32C D38G E111G), which contains all of the elements identified in these experiments as being important for duplex activity, is prepared. This is the most powerful catalyst within this subfamily yet observed, some 46-fold more active against duplex RNA than RNase A.

Non-NASA Center↗
DOE OSTI2021

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)

Abstract Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize ( Zea mays ) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 ( anther ear 2 ), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure-based design of nanobodies that inhibit seeding of Alzheimer’s patient–extracted tau fibrils

Despite much effort, antibody therapies for Alzheimer’s disease (AD) have shown limited efficacy. Challenges to the rational design of effective antibodies include the difficulty of achieving specific affinity to critical targets, poor expression, and antibody aggregation caused by buried charges and unstructured loops. To overcome these challenges, we grafted previously determined sequences of fibril-capping amyloid inhibitors onto a camel heavy chain antibody scaffold. These sequences were designed to cap fibrils of tau, known to form the neurofibrillary tangles of AD, thereby preventing fibril elongation. The nanobodies grafted with capping inhibitors blocked tau aggregation in biosensor cells seeded with postmortem brain extracts from AD and progressive supranuclear palsy (PSP) patients. The tau capping nanobody inhibitors also blocked seeding by recombinant tau oligomers. Another challenge to the design of effective antibodies is their poor blood–brain barrier (BBB) penetration. In this study, we also designed a bispecific nanobody composed of a nanobody that targets a receptor on the BBB and a tau capping nanobody inhibitor, conjoined by a flexible linker. We provide evidence that the bispecific nanobody improved BBB penetration over the tau capping inhibitor alone after intravenous administration in mice. Our results suggest that the design of synthetic antibodies that target sequences that drive protein aggregation may be a promising approach to inhibit the prion-like seeding of tau and other proteins involved in AD and related proteinopathies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy

Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.

Science & Technology - Other Topics↗
DOE OSTI2025

Cooperative On-Ramp Merging with Time-Varying Vehicle-to-Vehicle Communication Delay Compensation via a Model-Free Approach

Cooperative merging strategies enabled by vehicle-to-vehicle (V2V) communication have shown promise in addressing congestion, fuel inefficiency, and collision risks. However, their performance can be severely degraded by time-varying and uncertain communication delays-an issue often overlooked in existing research, which primarily focuses on merging sequence determination and trajectory planning. Furthermore, practical considerations such as heterogeneous vehicle dynamics, varying road conditions, and real-time implementation complexities are frequently neglected. This paper presents a model-free, online planning framework for cooperative on-ramp merging of connected and automated vehicles (CAVs), explicitly accounting for time-varying V2V communication delays. Without relying on detailed vehicle dynamics, the proposed method introduces a data-driven delay compensation scheme. A co-simulation platform integrating high-fidelity vehicle dynamics, traffic simulation (SUMO), and V2V communication within MATLAB/Simulink is developed to evaluate the proposed method. Simulation results demonstrate that unaddressed V2V communication delays significantly impair merging performance. In contrast, the proposed framework enhances intervehicle distance tracking and maintains low CO2 emissions and fuel consumption, under communication delay across different communication frequencies. In conclusion, its lightweight design also facilitates real-time implementation, making it well-suited for deployment in practical CAV systems.

Accounting↗
NASA NTRS1990

Autoplan: A self-processing network model for an extended blocks world planning environment

Self-processing network models (neural/connectionist models, marker passing/message passing networks, etc.) are currently undergoing intense investigation for a variety of information processing applications. These models are potentially very powerful in that they support a large amount of explicit parallel processing, and they cleanly integrate high level and low level information processing. However they are currently limited by a lack of understanding of how to apply them effectively in many application areas. The formulation of self-processing network methods for dynamic, reactive planning is studied. The long-term goal is to formulate robust, computationally effective information processing methods for the distributed control of semiautonomous exploration systems, e.g., the Mars Rover. The current research effort is focusing on hierarchical plan generation, execution and revision through local operations in an extended blocks world environment. This scenario involves many challenging features that would be encountered in a real planning and control environment: multiple simultaneous goals, parallel as well as sequential action execution, action sequencing determined not only by goals and their interactions but also by limited resources (e.g., three tasks, two acting agents), need to interpret unanticipated events and react appropriately through replanning, etc.

Dautrechy, C. Lynne↗
NASA NTRS1991

Photosynthetic reaction center complexes from heliobacteria

The goal of this project is to understand the early evolutionary development of photosynthesis by examining the properties of reaction centers isolated from certain contemporary organisms that appear to contain the simplest photosynthetic reaction centers. The major focus of this project is the family of newly discovered strictly anaerobic photosynthetic organisms known as Heliobacteria. These organisms are the only known photosynthetic organisms that are grouped with the gram-positive phylum of bacteria. The properties of these reaction centers suggest that they might be the decendants of an ancestor that also gave rise to Photosystem 1 found in oxygen-evolving photosynthetic organisms. Photoactive reaction center-core antenna complexes have been isolated from the photosynthetic bacteria Heliobacillus mobilis and Heliobacterium gestii. The absorption and fluorescence properties of membranes and reaction centers are almost identical, suggesting that a single pigment-protein complex serves as both antenna and reaction center. Experiments in progress include sequence determination of the 48,000 Mr reaction center protein, and evolutionary comparisons with other reaction center proteins.

Trost, J. T.↗
NASA NTRS1974

Apollo 17 petrology and experimental determination of differentiation sequences in model moon compositions

Experimental studies of model moon compositions are discussed, taking into account questions related to the differentiation of the outer layer of the moon. Phase relations for a series of proposed lunar compositions have been determined and a petrographic and electron microprobe study was conducted on four Apollo 17 samples. Two of the samples consist of high-titanium mare basalts, one includes crushed anorthosite and gabbro, and another contains blue-gray breccia.

Hodges, F. N.↗
NASA NTRS1981

Determination of load sequence effects on the degradation and failure of composite materials

A theoretical model was established to predict the fatigue behavior of composite materials, with emphasis placed on predictions of the degradation of residual strength and residual stiffness during fatigue cycling. The model parameters were evaluated from three test series including static strength fatigue life and residual strength tests. The tests were applied to two graphite/epoxy laminates. Load sequence effects were emphasized for both laminates and the predicted results agreed quite well with subsequent verification tests. Dynamic as well as static stiffness reduction data were collected by use of a PDP11-03 computer, which performed quite satisfactorily and permitted the recording of a substantial amount of dynamic stiffness reduction data.

Yang, J. N.↗
NASA NTRS1996

Calcium-Dependent Protein Kinase Genes in Corn Roots

Two cDNAs encoding Ca-2(+) - Dependent Protein Kinases (CDPKs), Corn Root Protein Kinase 1 and 2 (CRPK 1, CRPK 2) were isolated from the root tip library of corn (Zea mays L., cv. Merit) and their nucleotide sequences were determined. Deduced amino acid sequences of both the clones have features characteristic of plant CDPKS, including all 11 conserved serine/threonine kinase subdomains, a junction domain and a calmodulin-like domain with four Ca-2(+), -binding sites. Northern analysis revealed that CRPKI mRNA is preferentially expressed in roots, especially in the root tip; whereas, the expression of CRPK2 mRNA was very low in all the tissues tested. In situ hybridization experiments revealed that CRPKI mRNA is highly expressed in the root apex, as compared to other parts of the root. Partially purified CDPK from the root tip phosphorylates syntide-2, a common peptide substrate for plant CDPKs, and the phosphorylation was stimulated 7-fold by the addition of Ca-2(+). Our results show that two CDPK isoforms are expressed in corn roots and they may be involved in the Ca-2(+)-dependent signal transduction process.

Takezawa, D.↗
NASA NTRS1999

Sequence information signal processor

An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

Peterson, John C.↗
NASA NTRS1972

Manned space flight nuclear system safety. Volume 3: Reactor system preliminary nuclear safety analysis. Part 2: Accident Model Document (AMD)

The Accident Model Document is one of three documents of the Preliminary Safety Analysis Report (PSAR) - Reactor System as applied to a Space Base Program. Potential terrestrial nuclear hazards involving the zirconium hydride reactor-Brayton power module are identified for all phases of the Space Base program. The accidents/events that give rise to the hazards are defined and abort sequence trees are developed to determine the sequence of events leading to the hazard and the associated probabilities of occurence. Source terms are calculated to determine the magnitude of the hazards. The above data is used in the mission accident analysis to determine the most probable and significant accidents/events in each mission phase. The only significant hazards during the prelaunch and launch ascent phases of the mission are those which arise form criticality accidents. Fission product inventories during this time period were found to be very low due to very limited low power acceptance testing.

Source record↗
DOE OSTI2023

Potential for constraining sequence stratigraphy and cycle stratigraphy with U-Pb dating of carbonates

Studies of sequence stratigraphy and cycle stratigraphy in carbonate formations increasingly improve our understanding of depositional systems and basinal to global correlations. However, there is still a scarcity of dated sequences to determine the time length of sequences and cycles. Furthermore, the durations of sequences and cycles provide tests of the processes that produce them. Poor age resolution mostly stems from the lack of recognizable volcanic ash deposits in many sections. Through continuing advances in analytical techniques and approaches to sampling, the current state of Usingle bondPb dating of carbonate sedimentary rocks provides opportunities to fill in age gaps. The approach should build on well-constrained 3-dimensional stratigraphic architectures and diagenetic stratigraphies.

58 GEOSCIENCES↗
DOE OSTI2020

Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior

Phase separation of intrinsically disordered proteins (IDPs) commonly underlies the formation of membraneless organelles, which compartmentalize molecules intracellularly in the absence of a lipid membrane. Identifying the protein sequence features responsible for IDP phase separation is critical for understanding physiological roles and pathological consequences of biomolecular condensation, as well as for harnessing phase separation for applications in bioinspired materials design. To expand our knowledge of sequence determinants of IDP phase separation, we characterized variants of the intrinsically disordered RGG domain from LAF-1, a model protein involved in phase separation and a key component of P granules. Based on a predictive coarse-grained IDP model, we identified a region of the RGG domain that has high contact probability and is highly conserved between species; deletion of this region significantly disrupts phase separation in vitro and in vivo. We determined the effects of charge patterning on phase behavior through sequence shuffling. We designed sequences with significantly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mixed charged residues, to increase charge segregation. This result indicates the natural sequence is under negative selection to moderate this mode of interaction. We measured the contributions of tyrosine and arginine residues to phase separation experimentally through mutagenesis studies and computationally through direct interrogation of different modes of interaction using all-atom simulations. Finally, we show that despite these sequence perturbations, the RGG-derived condensates remain liquid-like. Together, these studies advance our fundamental understanding of key biophysical principles and sequence features important to phase separation.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Applicability of the Delplot method for the determination of catalytic reaction sequences: Hydrodeoxygenation of $\gamma$-valerolactone on Ni 2 P/MCM-41

Contact-time measurements based on sites are used to investigate the reaction sequence of the hydrodeoxygenation of γ-valerolactone (GVL) on Ni 2 P/MCM-41. Here the study is carried out at 300 °C and 0.5 MPa with site times of 0.29–6.1 s. A reaction network is proposed in which pentanoic acid and 2-methyltetrahydrofuran (2-MTHF) are formed in parallel initially and pentanal, butane and pentane are formed subsequently. A first-rank Delplot analysis (selectivity) gives a good fit, but higher-rank Delplots do not. The lack of applicability is explained by the magnitude of the rate constants, in which the rate constant for one of the later steps (the consumption of pentanal) is substantially larger than those for the preceding steps. For this reason, pentanal demonstrated the characteristics of a primary product and consequently affected the discrimination of higher rank products. A simulation of a model sequence with assumed rate constants confirms the reason why the Delplot method does not work for this reaction. Since the rate constants cannot be determined a priori to be of close magnitude, the Delplot method cannot be generally used to ascertain reaction sequences.

42 ENGINEERING↗