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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites

Abstract Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Efficient gene activation in plants by the MoonTag programmable transcriptional activator

Abstract CRISPR/Cas-based transcriptional activators have been developed to induce gene expression in eukaryotic and prokaryotic organisms. The main advantages of CRISPR/Cas-based systems is that they can achieve high levels of transcriptional activation and are very easy to program via pairing between the guide RNA and the DNA target strand. SunTag is a second-generation system that activates transcription by recruiting multiple copies of an activation domain (AD) to its target promoters. SunTag is a strong activator; however, in some species it is difficult to stably express. To overcome this problem, we designed MoonTag, a new activator that works on the same basic principle as SunTag, but whose components are better tolerated when stably expressed in transgenic plants. We demonstrate that MoonTag is capable of inducing high levels of transcription in all plants tested. In Setaria, MoonTag is capable of inducing high levels of transcription of reporter genes as well as of endogenous genes. More important, MoonTag components are expressed in transgenic plants to high levels without any deleterious effects. MoonTag is also able to efficiently activate genes in eudicotyledonous species such as Arabidopsis and tomato. Finally, we show that MoonTag activation is functional across a range of temperatures, which is promising for potential field applications.

42 ENGINEERING↗
DOE OSTI2019

Hierarchical Majoranas in a programmable nanowire network

We propose a hierarchical architecture for building “logical” Majorana zero modes using “physical” Majorana zero modes at the Y-junctions of a hexagonal network of semiconductor nanowires. Each Y-junction contains three “physical” Majoranas, which hybridize when placed in close proximity, yielding a single effective Majorana mode near zero energy. The hybridization of effective Majorana modes on neighboring Y-junctions is controlled by applied gate voltages on the links of the honeycomb network. This gives rise to a tunable tight-binding model of effective Majorana modes. We show that selecting the gate voltages that generate a Kekule vortex pattern in the set of hybridization amplitudes yields an emergent “logical” Majorana zero mode bound to the vortex core. The position of a logical Majorana can be tuned adiabatically, without moving any of the “physical” Majoranas or closing any energy gaps, by programming the values of the gate voltages to change as functions of time. Furthermore, a nanowire network supporting multiple such “logical” Majorana zero modes provides a physical platform for performing adiabatic non-Abelian braiding operations in a fully controllable manner.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Programmable self-assembly of diamond polymorphs from chromatic patchy particles

In this paper, we present a method of controlling polymorphism in self-assembly and apply it to the long-standing problem of assembly of a colloidal diamond. The latter is often viewed as the “holy grail” of the self-assembly field, due to the challenge that it presents as well as thanks to its potential as a step towards manufacturing of photonic band-gap materials. In our approach, we use a “chromatic” version of traditional building blocks, the so-called patchy particle. Namely, the individual patches that belong to the same particle in our model are distinguishable (“colored”) and their pairwise interactions are color dependent, which could be implemented with the help of DNA fictionalization. We propose a design procedure and verify it with the help of Brownian dynamics simulations. Not only are we able to “program” the self-assembly of a high-quality cubic diamond lattice, but a small modification of the coloring scheme also allows us to “reprogram” the system to assemble into the alternative polymorph, a hexagonal diamond.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Programmable bias field observed in graded ferromagnetic semiconductor films with broken symmetry

We report on the observation of a field-induced magnetic bias effect in a Ga 0.94 Mn 0.06 As 1-y P y thin film with digitally graded phosphorus content. Although phosphorus concentration in the sample is changed in steps from y approximate to 0.03 to y approximate to 0.28, the magnetometry and magnetotransport data display a coherent magnetic response typical for single-layer in-plane magnetized films with cubic and weak [110] uniaxial anisotropy. Unexpectedly, low-temperature planar Hall resistance loops exhibit remarkable asymmetry tunable by application of strong in-plane initial magnetic field H Ini . We discuss this unusual memory effect, resembling the magnetization asymmetry in the exchange biased magnetic bilayers, in terms of a unidirectional bias field H b induced by H Ini . We show that such bias field defines the delayed or accelerated nucleation of domains with chiral domain walls performing the magnetization reversal.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution

Abstract Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research. Hence, the use of efficient methods to share, reproduce, and collaborate on code as well as document research is fundamental. GitHub is an online, cloud‐based service that can help researchers track, organize, discuss, share, and collaborate on software and other materials related to research production, including data, code for analyses, and protocols. Despite these benefits, the use of GitHub in ecology and evolution is not widespread. To help researchers in ecology and evolution adopt useful features from GitHub to improve their research workflows, we review 12 practical ways to use the platform. We outline features ranging from low to high technical difficulty, including storing code, managing projects, coding collaboratively, conducting peer review, writing a manuscript, and using automated and continuous integration to streamline analyses. Given that members of a research team may have different technical skills and responsibilities, we describe how the optimal use of GitHub features may vary among members of a research collaboration. As more ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries of collaborative, transparent, and open research.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗