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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

EcoFAB 3.0: a sterile system for studying sorghum that replicates previous field and greenhouse observations

Introduction Studying plant-microbe interactions is one of the key elements in understanding the path to sustainable agricultural practices. These interactions play a crucial role in ensuring survival of healthy plants, soil and microbial communities. Many platforms have been developed over the years to isolate these highly complex interactions however, these are designed for small model plants. This creates a need for complementary devices for larger plants, such as sorghum. Methods This work introduces a novel platform, EcoFAB 3.0, which is designed to enable studying bioenergy plants such as sorghum for up to 4 weeks in a controlled sterile environment. Several other advantages of this platform such as dark root chambers and user-friendly assembly are also discussed in this work. Results and discussion EcoFAB 3.0 was found to replicate previous greenhouse and field observations when comparing an engineered sorghum line overproducing 4-hydroxybenzoic acid (4-HBA) and wildtype (variety BTx430). Consistent with greenhouse and field observations, it was found that the engineered line of sorghum grown in EcoFAB 3.0 had a higher 4-HBA content and a lower dry biomass.

Gupta, Kshitiz↗
DOE OSTI2023

The Interaction between the DOCK7 Protein and the E2 Protein of Classical Swine Fever Virus Is Not Involved with Viral Replication or Pathogenicity

The classical swine fever virus (CSFV) particle consists of three glycoproteins, all of which have been shown to be important proteins involved in many virus functions, including interaction with several host proteins. One of these proteins, E2, has been shown to be directly involved with adsorption to the host cell and important for virus virulence. Using the yeast two-hybrid system, we have previously shown that CSFV E2 specifically interacts with the (DOCK7) dedicator of cytokinesis, a scaffolding protein. In this report, the interaction between E2 and DOCK7 was evaluated. To confirm the yeast two-hybrid results and to determine that DOCK7 interacts in swine cells with E2, we performed co-immunoprecipitation and proximity ligation assay (PLA). After demonstrating the protein interaction in swine cells, E2 amino acid residues Y65, V283, and T149 were determined to be critical for interaction with Dock7 by using a random mutated library of E2 and a reverse yeast two-hybrid approach. That disruption of these three residues with mutations Y65F, V283D, and T149A abrogated the Dock7-E2 protein interaction. These mutations were then introduced into a recombinant CSFV, E2DOCK7v, by a reverse genomics approach using the highly virulent CSFV Brescia isolate as a backbone. E2DOCKv was shown to have similar growth kinetics in swine primary macrophages and SK6 cell cultures to the parental Brescia strain. Similarly, E2DOCK7v demonstrated a similar level of virulence to the parental Brescia when inoculated in domestic pigs. Animals intranasally inoculated with 10 5 TCID 50 developed a lethal form of clinical disease with virological and hematological kinetics changes indistinguishable from that produced by the parental strain. Therefore, interaction between CSFV E2 and host DOCK7 is not critically involved in the process of virus replication and disease production.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Replication Package for "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifier

This replication package is a case study on automated deductive verification for Rust for practical programs. It is a companion artifact to a corresponding usability study on verification titled "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifiers". It seeks to answer the question "Can Rust developers today use Rust verifiers to verify their code?". To answer this question, the study contrasts the verification experience of two mature Rust verifiers, Creusot and Prusti, by using the tools to develop a verified implementation of union-find in Rust. The union-find implementation is based on real-world code as used in the popular egg E-graph library. The artifact consists of two different verified libraries, one using Creusot and one using Prusti. The libraries have similar Rust interfaces and high-level proofs but differ in their details: Creusot and Prusti have different annotation languages and support different proof styles. Each implementation can be verified with its respective tool and compiles as a traditional Rust development.

Sarracino, John↗
NASA NTRS1977

A passive chevron replicator

Instrument design provides replicate function between device storage area and guardrail detector in order that nondestructive read-out of memory can be achieved. Use of guardrail detectors in magnetic domain (bubble) circuits is proposed method of increasing detector signal output by increasing detector size without dedicating an excessive amount of device chip area to detector portion.

Oeffinger, T. R.↗
NASA NTRS1982

A theory for the origin of a self-replicating chemical system. II - Computer simulation of the autogen

In order to better understand the feasibility and limitations of the autogen (White 1980), a computer simulation based on the fluctuating clay environment was used to test whether autocatalytic growth would occur under various conditions. The results suggest that overall accuracies of replication and translation in the range of 90% and 10%, and protoenzyme turnover numbers of 10-120 monomers/protoenzyme/day are adequate for exponential growth. Nucleation of the components of the autogen from random background oligomers would be extremely rapid if oligomers lengths 2-6 were adequately functional, whereas oligomer lengths much greater than 10 are prohibited. The autogen would most likely nucleate and grow to dominance either rapidly (10-100 cycles of roughly 1 day each) or not at all.

White, D. H.↗
NASA NTRS1982

Population control of self-replicating systems

The literature concerning fibonacci sequence and the mathematics of self replication are reviewed. One option allows each primary to generate n-replicas, one in each sequential time frame after its own generation with no restrictions on the number of ancestors per replica. The state vector of the replicas in an efficient manner is determined. Option-B has a fixed number of replicas per primary and no restrictions on the number of ancestors for a replica. Any element fij represents the number of elements of type-j in time frame k+1 generated from type-i in time frame k. Option-D is a diagonal matrix whose eigenvalues are precisely those of f.

Mccord, R. L.↗
NASA NTRS1985

Electroform replication of grazing incidence X-ray optics

Work to produce mirrors via electroform replication is reported. Work on small (6 cm by 9 cm) cylindrical pieces and on 40 cm long by 12 cm wide Wolter shaped mirrors is summarized. It is shown that electroforming is a viable technique for producing relatively inexpensive grazing incidence X-ray optics, as long as modest resolution (1 min of arc) and size (12 cm diameter by 40 cm long) are specified.

Ulmer, M. P.↗
NASA NTRS1986

Molecular replication

The object of our research program is to understand how polynucleotide replication originated on the primitive Earth. This is a central issue in studies of the origins of life, since a process similar to modern DNA and RNA synthesis is likely to have formed the basis for the most primitive system of genetic information transfer. The major conclusion of studies so far is that a preformed polynucleotide template under many different experimental conditions will facilitate the synthesis of a new oligonucleotide with a sequence complementary to that of the template. It has been shown, for example, that poly(C) facilitates the synthesis of long oligo(G)s and that the short template CCGCC facilities the synthesis of its complement GGCGG. Very recently we have shown that template-directed synthesis is not limited to the standard oligonucleotide substrates. Nucleic acid-like molecules with a pyrophosphate group replacing the phosphate of the standard nucleic acid backbone are readily synthesized from deoxynucleotide 3'-5'-diphosphates on appropriate templates.

Orgel, L. E.↗
NASA NTRS1986

Performance analysis of replication ALOHA for fading mobile communications channels

This paper describes an ALOHA random access protocol for fading communications channels. A two-state Markov model is used for the channel error process to account for the channel fading memory. The ALOHA protocol is modified to send multiple contiguous copies of a message at each transmission attempt. Both pure and slotted ALOHA channels are considered. The analysis is applicable to fading environments where the channel memory is short compared to the propagation delay. It is shown that smaller delay may be achieved using replications and, in noisy conditions, can also improve throughput.

Yan, Tsun-Yee↗
NASA NTRS1988

An experiment in software reliability: Additional analyses using data from automated replications

A study undertaken to collect software error data of laboratory quality for use in the development of credible methods for predicting the reliability of software used in life-critical applications is summarized. The software error data reported were acquired through automated repetitive run testing of three independent implementations of a launch interceptor condition module of a radar tracking problem. The results are based on 100 test applications to accumulate a sufficient sample size for error rate estimation. The data collected is used to confirm the results of two Boeing studies reported in NASA-CR-165836 Software Reliability: Repetitive Run Experimentation and Modeling, and NASA-CR-172378 Software Reliability: Additional Investigations into Modeling With Replicated Experiments, respectively. That is, the results confirm the log-linear pattern of software error rates and reject the hypothesis of equal error rates per individual fault. This rejection casts doubt on the assumption that the program's failure rate is a constant multiple of the number of residual bugs; an assumption which underlies some of the current models of software reliability. data raises new questions concerning the phenomenon of interacting faults.

Dunham, Janet R.↗