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At least 55 records · Page 3

Targeted DNA insertion in plants

Conventional methods of DNA sequence insertion into plants, using Agrobacterium -mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.

Dong, Oliver Xiaoou↗

Energy metric prediction for double insertion mutants via the RoseNet deep learning framework

Studying the structural and functional implications of protein mutations is an important task in computational biology and bioinformatics. We leverage our previously proposed RoseNet neural network architecture to predict energy metrics of proteins with double amino acid insertions or deletions (InDels). We train models on previously generated benchmark datasets containing the exhaustive double InDel mutations for three proteins, as well as an additional three proteins for which ∼145k random mutants, each with two InDels, have been generated. We expand on our previous work by evaluating three additional proteins and analyzing domain features that impact the prediction capabilities of RoseNet. These features include InDels into secondary structures and the solvent accessible surface area (SASA) scores of the residues. We uncover further evidence to support that RoseNet has a higher proficiency of generalizing to unseen residue combinations than unseen insertion positions. We also observe that RoseNet produces higher-quality predictions when inserting into a β-sheet over an α-helix. Additionally, when the insertions fall in an area of high SASA, RoseNet often displays better performance than inserting into areas of low SASA.

59 BASIC BIOLOGICAL SCIENCES↗

Thermophilic site-specific recombination system for rapid insertion of heterologous DNA into the Clostridium thermocellum chromosome

Clostridium thermocellum is an anaerobic thermophile capable of producing ethanol and other commodity chemicals from lignocellulosic biomass. The insertion of heterologous DNA into the C. thermocellum chromosome is currently achieved via a time-consuming homologous recombination process, where a single stable insertion can take 2–4 weeks or more to construct. In this work, we developed a thermostable version of the Serine recombinase Assisted Genome Engineering (tSAGE) approach for gene insertion in C. thermocellum utilizing a site-specific recombinase from Geobacillus sp. Y412MC61, enabling quick and easy insertion of DNA into the chromosome for accelerated genetic tool screening and heterologous gene expression. Using tSAGE, chromosomal insertion of plasmid DNA occurred at a maximum transformation efficiency of 5 × 10 3 CFU/µg, which is comparable to the transformation efficiency of a replicating control plasmid in C. thermocellum. Using tSAGE, we chromosomally integrated and characterized 17 reporter genes, 15 homologous and 31 heterologous constitutive promoters of varying strengths, 4 inducible promoters, and 5 riboswitches in C. thermocellum. We also determined that a 6–7 nucleotide gap between the ribosome binding site (RBS) and the start codon is optimal for high expression by employing a library of superfolder green fluorescent protein expression constructs driven by our strongest tested promoter (P clo1313_1194 ) with different distances between the RBS and start codon. The tools developed here will aid in accelerating C. thermocellum strain engineering for producing sustainable fuels and chemicals directly from plant biomass.

Biofuels↗

Influence of Surface Treatment on the Interfacial and Mechanical Performance of Metal-Insert Overmolded Composites

Structural composites with metal inserts are gaining increasing interest enabling light weight design for energy efficiency, provide insulation, corrosion protection without compromising mechanical integrity. Such over molded metal-polymer composites show strong potential in many automotive and aerospace component parts, e.g. car bumper, chassis, door, brackets, fasteners, etc. Despite several advantages, metal-polymer dissimilar interface remains a weak spot in structural design, requiring further investigation to improve interfacial interlocking. The current work focuses on enhancing the metal-polymer adhesion between stainless steel inserts and polymer matrices (e.g. acrylonitrile butadiene styrene resin (ABS), and polyamide 66 (PA66) through surface treatment via chemical etching and mechanical roughening. In the chemical etching process, metal substrates were treated with aqua regia solution for different time intervals to evaluate surface roughness measured by water contact angle and morphology analysis. For mechanical roughening approach, metal inserts were subjected to blasting for surface abrasion. Treated samples were also functionalized with aminosilane coupling agent which showed successful grafting on the surface measured by water contact angle. Metal inserts with micro level surface roughness through etching exhibited significant 21% improvement in adhesion strength compared to untreated inserts; however, the effect of silane treatment on the interfacial strength was found to be highly matrix dependent.

Saha, Subhabrata [ORNL] (ORCID:000000033966064X)↗

Turbomachinery shaft insert

An insert is presented for a hollow rotatable shaft on the end of which an impeller is mounted, the insert having a first cylindrical portion receivable within the end of the shaft. The insert includes a radially extending portion adjacent the end of the shaft having an annular wall including radially inner and outer surfaces for engaging tightly similar surfaces in a recess formed in the impeller to provide inner and outer pilot surfaces. The insert also includes a tubular extension which is received within a bore in the impeller, the tubular extension having spaced longitudinally extending slits for permitting the extension together with radially extending hook-like tongues thereon to be received within radial slots in the bore of the impeller to lock the impeller to the insert.

Vonpragenau, George L.↗

Tool Removes Coil-Spring Thread Inserts

Tool removes coil-spring thread inserts from threaded holes. Threads into hole, pries insert loose, grips insert, then pulls insert to thread it out of hole. Effects essentially reverse of insertion process to ease removal and avoid further damage to threaded inner surface of hole.

Collins, Gerald J., Jr.↗

Screw-Thread Inserts As Temporary Flow Restrictors

Coil-spring screw-thread inserts found useful as temporary flow restrictors. Inserts placed in holes through which flow restricted, effectively reducing cross sections available for flow. Friction alone holds inserts against moderate upstream pressures. Use of coil-spring thread inserts as flow restrictors conceived as inexpensive solution to problem of adjusting flow of oxygen through orifices in faceplate into hydrogen/oxygen combustion chamber. Installation and removal of threaded inserts gentle enough not to deform orifice tubes.

Trimarchi, Paul↗

Insert Concepts for the Material Science Research Rack (MSRR-1) of the Material Science Research Facility (MSRF) on the International Space Station (ISS)

The Material Science Research Rack I (MSRR-1) of the Material Science Research Facility (MSRF) contains an Experiment Module (EM) being developed collaboratively by NASA and the European Space Agency (ESA). This NASA/ESA EM will accommodate several different removable and replaceable Module Inserts (MIs) which are installed on orbit NASA's planned inserts include the Quench Module Insert (QMI) and the Diffusion Module Insert (DMI). The QMI is a high-gradient Bridgman-type vacuum furnace with quench capabilities used for experiments on directional solidification of metal alloys. The DMI is a vacuum Bridgman-Stockbarger-type furnace for experiments on Fickian and Soret diffusion in liquids. This paper discusses specific design features and performance capabilities of each insert. The paper also presents current prototype QMI hardware analysis and testing activities and selected results.

Crouch, Myscha↗

Systems and Methods for Structurally Interrelating Components Using Inserts Made from Metallic Glass-Based Materials

Systems and methods in accordance with embodiments of the invention operate to structurally interrelate two components using inserts made from metallic glass-based materials. In one embodiment, a method of structurally interrelating two components includes: forming an insert from a metallic glass-based composition; where the formed insert includes a metallic glass-based material; affixing the insert to a first component; and structurally interrelating the second component to the first component using the insert.

Hofmann, Douglas C.↗

Reactor fuel pellets with thermally-conductive inserts, and related reactor fuel pellet arrangements

Fuel pellets and fuel pellet arrangements include thermally-conductive inserts within a fuel. The inserts have at least one portion of a thermally-conductive material, such as radially-extending fins. The inserts are configured to dissipate heat during use of the fuel pellets, while minimizing the amount of the total volume of the fuel pellet that is occupied by non-fissile material. The inclusion of heat-dissipating inserts enables the fuel pellets to exhibit improved thermal performance over the lifetime of the fuel, including a relatively low peak temperature and relatively low integrated average temperatures, while the minimal volume of the inserts avoids significantly decreasing the percent of enrichment achievable.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Σ3(111) Grain Boundaries Accelerate Hydrogen Insertion into Palladium Nanostructures

Grain boundaries (GBs) are frequently implicated as key defect structures facilitating metal hydride formation, yet their specific role remains poorly understood due to their structural complexity. Here, we investigate hydrogen insertion in Pd nanostructures enriched with well-defined Σ3(111) GBs (Pd GB ) synthesized via electrolysis-driven nanoparticle assembly. In situ synchrotron X-ray diffraction reveals that Pd GB exhibits dramatically accelerated hydriding and dehydriding kinetics compared with ligand-free and ligand-capped Pd nanoparticles with similar crystallite sizes. Strain mapping using environmental transmission electron microscopy shows that strain is highly localized at GBs and intensifies upon hydrogen exposure, indicating preferential hydrogen insertion along GB sites. Density functional theory calculations provide mechanistic insight supporting these findings, showing that hydrogen insertion near Σ3(111) GBs is energetically more favorable and that tensile strain lowers insertion barriers. Furthermore, these results provide atomic-level insights into the role of GBs in hydride formation and suggest new design strategies for GB-engineered Pd-based functional materials.

Anions↗

CFD Simulations of Molten Salts Within Plasma-Facing Components with Twisted Tape Inserts Under One-Sided–Heated Conditions

For liquid immersion blankets (LIBs), the heat removal within different plasma-facing components (PFCs) requires substantial heat removal capabilities that could benefit from the usage of heat transfer enhancements. Of consideration are twisted tape insert heat transfer enhancements that are ribbon-like metal pieces inserted within cooling channels that increase fluid mixing, resulting in higher heat transfer and pressure drop. Unlike traditional applications, PFCs such as divertor coolant tubes experience a significantly higher heat flux on one side versus the other or entirely one-sided heating. These conditions are not well studied for molten salts where the higher Prandtl numbers characteristic of the fluids are significantly higher than water, gases, and liquid metals. As an effort to study this knowledge gap, large eddy simulations were done with Prandtl numbers representative of FLiBe at proposed operating conditions. In this study, the effects of applying a surface heat flux to one side of a tube versus the entire tube with a twisted tape insert were investigated for the heat transfer coefficient and effects on the temperature profile. The findings of the study suggest that for Prandtl number fluids above unity, the Nusselt number was largely unaffected by the change in boundary condition. Both boundary conditions showed good agreement with the Manglik and Bergles Nusselt number correlation for tight-fitting twisted tapes. Finally, the outcomes of this study will be useful for future design studies of LIBs to provide fundamental guidance implementing twisted tape inserts and their performance in one-sided–heated conditions.

molten salts↗

Improving Longitudinal Impedance of Inductive Inserts

In this article, we discuss methods for improving the longitudinal impedance of inductive inserts used for space charge compensation in the proton storage ring (PSR) at Los Alamos Neutron Science Center (LANSCE) Facility. The PSR relies on inductive inserts to counteract the capacitive impedance produced by the space charge of the proton beam, which can otherwise lead to beam debunching. Existing inductive inserts, which utilize Toshiba M4C21A ferrite, have been effective but require heating to reduce resistive components that can cause instabilities at higher frequencies. This article explores the potential of alternative ferrite materials, specifically National Magnetics C2050, to enhance the performance of these inserts by reducing the need for heating and minimizing resistive impedance. Through both analytical modeling and CST Particle Studio simulations, it is demonstrated that optimized ferrite materials and geometries can significantly improve space charge compensation while mitigating instability risks, ultimately enhancing the performance of the PSR.

43 PARTICLE ACCELERATORS↗

High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes

Abstract Background Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency. Results We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T 1 generation of any crop transformed via Agrobacterium . We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes. Conclusion This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.

59 BASIC BIOLOGICAL SCIENCES↗

Departure Approval Request Compliance Effects on Overhead Stream Insertion

Integrated Arrival-Departure-Surface (IADS) air traffic management relies on information sharing and integration between automation systems for efficiency, predictability, and throughput improvements throughout the National Airspace System (NAS). The NASA Airspace Technology Demonstration 2 (ATD-2) project supports this effort by integrating SWIM (System Wide Information Management) information and evaluating and refining potential TFDM (Terminal Flight Data Manager) functionality in a surface traffic management system fielded at Charlotte-Douglas International Airport (CLT). Among the IADS areas under study during ATD-2 is the use of electronically negotiated departure times for efficiently inserting flights into overhead traffic streams. Stream-insertion accuracy is important for reducing excessive vectoring that negatively impacts the NAS by increasing controller workload along with aircraft fuel burn and emissions. Departure-time approval requests (APREQs) provide center-approved departure times to allow for smooth stream insertion. In this presentation, TBFM (Time-Based Flow Management) and ATD-2 flight summary data are used to empirically show that APREQ compliance leads to improved stream insertion.

Overhead-Stream Insertion↗

Single‐Crystal to Single‐Crystal Transformations: Stepwise CO 2 Insertions into Bridging Hydrides of [(NHC)CuH] 2 Complexes

Abstract Mechanistic studies of substrate insertion into dimeric [(NHC)CuH] 2 (NHC=N‐heterocyclic carbene) complexes with two bridging hydrides have been shown to require dimer dissociation to generate transient, highly reactive (NHC)Cu−H monomers in solution. Using single‐crystal to single‐crystal (SC‐SC) transformations, we discovered a new pathway of stepwise insertion of CO 2 into [(NHC)CuH] 2 without complete dissociation of the dimer. The first CO 2 insertion into dimeric [(IPr*OMe)CuH] 2 (IPr*OMe=N,N′‐bis(2,6‐bis(diphenylmethyl)‐4‐methoxy‐phenyl)imidazole‐2‐ylidene) produced a dicopper formate hydride [(IPr*OMe)Cu] 2 (μ‐1,3‐O 2 CH)(μ‐H). A second CO 2 insertion produced a dicopper bis(formate), [(IPr*OMe)Cu] 2 (μ‐1,3‐O 2 CH)(μ‐1,1‐O 2 CH), containing two different bonding modes of the bridging formate. These dicopper formate complexes are inaccessible from solution reactions since the dicopper core cleanly ruptures to monomeric complexes when dissolved in a solvent.

Patrick, Evan A.↗

Single‐Crystal to Single‐Crystal Transformations: Stepwise CO 2 Insertions into Bridging Hydrides of [(NHC)CuH] 2 Complexes

Abstract Mechanistic studies of substrate insertion into dimeric [(NHC)CuH] 2 (NHC=N‐heterocyclic carbene) complexes with two bridging hydrides have been shown to require dimer dissociation to generate transient, highly reactive (NHC)Cu−H monomers in solution. Using single‐crystal to single‐crystal (SC‐SC) transformations, we discovered a new pathway of stepwise insertion of CO 2 into [(NHC)CuH] 2 without complete dissociation of the dimer. The first CO 2 insertion into dimeric [(IPr*OMe)CuH] 2 (IPr*OMe=N,N′‐bis(2,6‐bis(diphenylmethyl)‐4‐methoxy‐phenyl)imidazole‐2‐ylidene) produced a dicopper formate hydride [(IPr*OMe)Cu] 2 (μ‐1,3‐O 2 CH)(μ‐H). A second CO 2 insertion produced a dicopper bis(formate), [(IPr*OMe)Cu] 2 (μ‐1,3‐O 2 CH)(μ‐1,1‐O 2 CH), containing two different bonding modes of the bridging formate. These dicopper formate complexes are inaccessible from solution reactions since the dicopper core cleanly ruptures to monomeric complexes when dissolved in a solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Construct design for precise DNA insertion in plants

Precise insertion of DNA sequences at targeted locations in plant genomes is pivotal for synthetic biology, genetics, and crop improvement. Construct design plays a critical role in achieving precise insertions, yet practical guidance remains limited. This review provides an in-depth overview of construct design principles and targeted DNA insertion (knock-in) strategies in plants. We assess the strengths, limitations, and construct requirements of current knock-in methods for specific applications, including short, large, and multifragment insertions. Additionally, we explore the potential of adopting advanced nonplant technologies to enhance knock-in efficiency and precision in plants. This review provides a valuable resource for facilitating the effective application of knock-in technologies to genetically improve crops with minimal off-target effects.

DNA construct↗