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At least 163 records · Page 9

Data for "Viral-mediated Delivery of Morphogenic Regulators Enables Leaf Transformation in Sorghum bicolor (L.)"

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom ( Bbm ), Wuschel2 ( Wus2 ), Wuschel-like homeobox protein 2a ( Wox2a ) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

gene editing↗

Effect of nonlinear instability on gravity-wave momentum transport

This paper investigates the nonlinear instability of internal gravity waves and the effects of their nonlinear interaction on momentum flux, using simple theoretical and numerical models. From the result of an analysis of parametric instability of a two-dimensional internal gravity wave as discussed by Yeh and Liu (1981) and Klostermeyer (1982), a group trajectory length scale for a gravity wave packet was determined, expressed in terms of the dominant vertical wavelenght and the degree of convective saturation. It is shown that this analysis justifies the Eikonal saturation method for relatively transient packets, that are well below the saturation amplitude, propagating in a slowly varying mean flow. Conversely, linear theory fails for persistent disturbances and trasient wave packets near convective saturation.

Dunkerton, Timothy J.↗

Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol

Farnesyl pyrophosphate synthase (FPPS) plays an important role in the synthesis of plant secondary metabolites, but its function and molecular regulation mechanism remain unclear in Pogostemon cablin . In this study, the full-length cDNA of the FPP synthase gene from P. cablin ( PcFPPS ) was cloned and characterized. The expressions of PcFPPS are different among different tissues (highly in P. cablin flowers). Subcellular localization analysis in protoplasts indicated that PcFPPS was located in the cytoplasm. PcFPPS functionally complemented the lethal FPPS deletion mutation in yeast CC25. Transient overexpression of PcFPPS in P. cablin leaves accelerated terpene biosynthesis, with an ~47% increase in patchouli alcohol. Heterologous overexpression of PcFPPS in tobacco plants was achieved, and it was found that the FPP enzyme activity was significantly up-regulated in transgenic tobacco by ELISA analysis. In addition, more terpenoid metabolites, including stigmasterol, phytol, and neophytadiene were detected compared with control by GC-MS analysis. Furthermore, with dual-LUC assay and yeast one-hybrid screening, we found 220 bp promoter of PcFPPS can be bound by the nuclear-localized transcription factor PcWRKY44. Overexpression of PcWRKY44 in P. cablin upregulated the expression levels of PcFPPS and patchoulol synthase gene ( PcPTS ), and then promote the biosynthesis of patchouli alcohol. Taken together, these results strongly suggest the PcFPPS and its binding transcription factor PcWRKY44 play an essential role in regulating the biosynthesis of patchouli alcohol.

Wang, Xiaobing↗

Variance of the Quantum Dwell Time for a Nonrelativistic Particle

Munoz, Seidel, and Muga [Phys. Rev. A 79, 012108 (2009)], following an earlier proposal by Pollak and Miller [Phys. Rev. Lett. 53, 115 (1984)] in the context of a theory of a collinear chemical reaction, showed that suitable moments of a two-flux correlation function could be manipulated to yield expressions for the mean quantum dwell time and mean square quantum dwell time for a structureless particle scattering from a time-independent potential energy field between two parallel lines in a two-dimensional spacetime. The present work proposes a generalization to a charged, nonrelativistic particle scattering from a transient, spatially confined electromagnetic vector potential in four-dimensional spacetime. The geometry of the spacetime domain is that of the slab between a pair of parallel planes, in particular those defined by constant values of the third (z) spatial coordinate. The mean Nth power, N = 1, 2, 3, . . ., of the quantum dwell time in the slab is given by an expression involving an N-flux-correlation function. All these means are shown to be nonnegative. The N = 1 formula reduces to an S-matrix result published previously [G. E. Hahne, J. Phys. A 36, 7149 (2003)]; an explicit formula for N = 2, and of the variance of the dwell time in terms of the S-matrix, is worked out. A formula representing an incommensurability principle between variances of the output-minus-input flux of a pair of dynamical variables (such as the particle s time flux and others) is derived.

Hahne, Gerhard↗

Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars

Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana ‘Zhonglin46’ (Pe1), P. euramericana ‘Guariento’ (Pe2), P. nigra ‘N179’ (Pn1), P. deltoides ‘Danhong’ (Pd1), and P. deltoides ‘Nanyang’ (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancement of the no-vent fill process

This paper presents an analytical and experimental evaluation of an enhanced techniques for no-vent fill. The method entails injecting liquid through the top of the receiver vessel, thereby increasing surface area and agitation of the ullage/liquid interface. Both of these factors promote condensation induced ullage collapse, and reduce compressive impedance to the incoming liquid. The enhanced process was analyzed by modifying the surface area algorithm of an existing tank thermodynamic code to model a downward-pointing, conical jet impringing on a steadily rising liquid surface. Transient pressure and temperature measurements from several tests with Freon-114 were input into the revised model to calculate condensation rate as a function of fill level. By expressing these rates in dimensionless form (i.e., in terms of Stanton number and Prandtl number), an empirical correlation similar to the submerged jet model of Brown and Sonin (1989) was derived. This provided a basis for developing an expression which relates top fill to bottom fill performance.

Vaughan, David A.↗

Particle irradiation induces FGF2 expression in normal human lens cells

Particle Irradiation Induces FGF2 Expression in Normal Human Lens Cells. Particle radiations, including both proton and helium-ion beams, have been used to successfully treat choroidal melanoma, but with the complication of radiation-induced cataract. We have investigated a role for radiation-induced changes in the expression of basic fibroblast growth factor (FGF2) gene expression as part of the mechanism(s) underlying lens cell injury associated with cataract. Normal human lens epithelial (HLE) cells were cultured in vitro on extracellular matrix (ECM) originated from bovine corneal endothelial cells. This study reports evidence for rapid but transient induction of FGF2 transcripts, an increase of between 5- and 8-fold, within 0.5 h after exposure to particle radiation, followed by another wave of increased transcription at 2-3 h postirradiation. Immunofluorescence results confirm the enhanced levels of FGF2 protein rapidly after exposure to protons or helium ions, followed by another wave of increased activity unique to helium at 6 h postirradiation. This second wave of increased immunoreactivity was not observed in the proton-irradiated samples. Total FGF2 protein analysis after helium-ion exposures shows induced expression of three FGF2 isoforms, with an increase of up to 2-fold in the 18-kDa low-molecular-weight species. Studies of the effects of protons on individual FGF2 protein isoforms are in progress. Several mechanisms involving a role for FGF2 in radiation-induced cataract are discussed.

NASA Discipline Radiation Health↗

Mechanically induced c-fos expression is mediated by cAMP in MC3T3-E1 osteoblasts

In serum-deprived MC3T3-E1 osteoblasts, mechanical stimulation caused by mild (287 x g) centrifugation induced a 10-fold increase in mRNA levels of the proto-oncogene, c-fos. Induction of c-fos was abolished by the cAMP-dependent protein kinase inhibitor H-89, suggesting that the transient c-fos mRNA increase is mediated by cAMP. Down-regulation of protein kinase C (PKC) activity by chronic TPA treatment failed to significantly reduce c-fos induction, suggesting that TPA-sensitive isoforms of PKC are not responsible for c-fos up-regulation. In addition, 287 x g centrifugation increased intracellular prostaglandin E2 (PGE2) levels 2.8-fold (P<0. 005). Since we have previously shown that prostaglandin E2 (PGE2) can induce c-fos expression via a cAMP-mediated mechanism, we asked whether the increase in c-fos mRNA was due to centrifugation-induced PGE2 release. Pretreatment with the cyclooxygenase inhibitors indomethacin and flurbiprofen did not hinder the early induction of c-fos by mechanical stimulation. We conclude that c-fos expression induced by mild mechanical loading is dependent primarily on cAMP, not PKC, and initial induction of c-fos is not necessarily dependent on the action of newly synthesized PGE2.

Non-NASA Center↗

Mixing Cell Model: A One-Dimensional Numerical Model for Assessment of Water Flow and Contaminant Transport in the Unsaturated Zone

This report describes the Mixing Cell Model code, a one dimensional model for water flow and solute transport in the unsaturated zone under steady state or transient flow conditions. The model is based on the principles and assumptions underlying mixing-cell model formulations. The unsaturated zone is discretized into a series of independent mixing cells. Each cell may have unique hydrologic, lithologic, and sorptive properties. Ordinary differential equations describe the material (water and solute) balance within each cell. Water-flow equations are derived from the continuity equation, assuming that unit gradient conditions exist at all times in each cell. Pressure gradients are considered implicitly through model discretization. Unsaturated hydraulic conductivity and moisture contents are determined by the material specific moisture-characteristic curves. Solute-transport processes include explicit treatment of advective processes, first order chain decay, and linear sorption reactions. Dispersion is addressed through implicit and explicit dispersion. Implicit dispersion is an inherent feature of all mixing-cell models and originates from the formulation of the problem in terms of mass balance around fully mixed volume elements. Expressions are provided that relate implicit dispersion to the physical dispersion of the system. Two FORTRAN codes were developed to solve the water flow and solute-transport equations: (1) the Mixing Cell Model for Flow (MCMF) solves transient water-flow problems and (2) the Mixing Cell Model for Transport (MCMT) solves the solute-transport problem. The transient water-flow problem is typically solved first by estimating the water flux through each cell in the model domain as a function of time using the MCMF code. These data are stored in either ASCII or binary files that are later read by the solute transport code (MCMT). Code output includes solute pore water concentrations, water and solute inventories in each cell and at each specified output time, and water and solute fluxes through each cell and specified output time. Computer run times for coupled transient water flow and solute transport were typically several seconds on a 2 GHz Intel Pentium IV desktop computer. The model was benchmarked against analytical solutions and finite element approximations to the partial differential equations (PDE) describing unsaturated flow and transport. Differences between the maximum solute flux estimated by the mixing cell model and the PDE models were typically less than two percent. This revision includes an option for a fixed concentration lower boundary condition for diffusive fluxes for versions 020321 and later.

54 ENVIRONMENTAL SCIENCES↗

Simulating transient heat transfer in graphene at finite Knudsen number via the Boltzmann transport equation and molecular dynamics

The phonon Boltzmann transport equation (BTE) with the relaxation time approximation (RTA) scattering model is used to calculate transient temperature profiles in graphene, and the results are compared to analogous molecular dynamics (MD) simulations. For the BTE calculations, the phonon dispersion relation and frequency-dependent scattering rates are obtained from a combination of MD data and semi-empirical power-law expressions for the normal and Umklapp phonon lifetimes. The dimensions and initial temperature conditions of graphene are varied to study the size and temperature dependence of thermal transport physics at the mesoscopic scale. Good quantitative agreement to within 5% is found between the BTE and MD results, over a wide range of temperatures and lengthscales of the temperature variation in the graphene sheet. Small differences are attributed to the inaccuracy of the RTA as applied to graphene, and to neglecting four-phonon scattering in the BTE simulations. The present results may further understanding in applications such as the transient heating of nanoelectronics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

eYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa × P. deltoides Clone ‘52-225’

Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone ‘52-225’ (P. trichocarpa × P. deltoides clone ‘52-225’). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.

59 BASIC BIOLOGICAL SCIENCES↗

Wave propagation in anisotropic medium due to an oscillatory point source with application to unidirectional composites

The far-field displacements in an infinite transversely isotropic elastic medium subjected to an oscillatory concentrated force are derived. The concepts of velocity surface, slowness surface and wave surface are used to describe the geometry of the wave propagation process. It is shown that the decay of the wave amplitudes depends not only on the distance from the source (as in isotropic media) but also depends on the direction of the point of interest from the source. As an example, the displacement field is computed for a laboratory fabricated unidirectional fiberglass epoxy composite. The solution for the displacements is expressed as an amplitude distribution and is presented in polar diagrams. This analysis has potential usefulness in the acoustic emission (AE) and ultrasonic nondestructive evaluation of composite materials. For example, the transient localized disturbances which are generally associated with AE sources can be modeled via this analysis. In which case, knowledge of the displacement field which arrives at a receiving transducer allows inferences regarding the strength and orientation of the source, and consequently perhaps the degree of damage within the composite.

Williams, J. H., Jr.↗

iSPECTRON: a simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software

We introduce iSPECTRON, an open source (under the Educational Community License version 2.0) program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained through quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The code capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Two levels of electronic structure theory, TDDFT (with NWChem) and RASSCF/RASPT2 (with OpenMolcas), are compared where possible. Acknowledgements: F.S., A.N., D.R.N., N.G., S.M, M.G. acknowledge support from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Award Nos. DE-SC0019484, KC-030103172684. The Spectron code was developed with support from the National Science Foundation (Grant CHE- 1953045). This research benefited from computational resources provided by EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at PNNL. PNNL is operated by Battelle Memorial Institute for the United States Department of Energy under DOE Contract No. DE-AC05-76RL1830.

Segatta, Francesco↗

Kinetics of the Reaction C2H + O2 from 193 to 350 K Using Laser Flash Kinetic Infrared Absorption Spectroscopy

Rate coefficients for the reaction C2H + O2 are measured from 193 to 350 K by using transient absorption spectroscopy with an infrared color center laser. Ethynyl radicals are produced by pulsed laser photolysis of C2H2 in a temperature variable flow cell and a tunable color center laser probes the transient removal Of C2H ((bar-X(sup 2))Sigma(+))(0,0,0)) in absorption. The rate coefficient has a slight negative temperature dependence over the range 193-350 K which can be expressed as k(O2) = (1.5 +/- 0.3) x 10(exp -11) exp((230 +/- 36)/T) Cu cm/(Molecule.s). The lack of a pressure dependence under our experimental conditions strongly suggests that the HCCOO* complex is short lived with respect to encountering a collision and rapidly dissociates to products without competition from collisional stabilization to HCCOO or collisionally induced dissociation to reactants.

Opansky, Brian J.↗

Capillary Flow in Containers of Polygonal Section: Theory and Experiment

An improved understanding of the large-length-scale capillary flows arising in a low-gravity environment is critical to that engineering community concerned with the design and analysis of spacecraft fluids management systems. Because a significant portion of liquid behavior in spacecraft is capillary dominated it is natural to consider designs that best exploit the spontaneous character of such flows. In the present work, a recently verified asymptotic analysis is extended to approximate spontaneous capillary flows in a large class of cylindrical containers of irregular polygonal section experiencing a step reduction in gravitational acceleration. Drop tower tests are conducted using partially-filled irregular triangular containers for comparison with the theoretical predictions. The degree to which the experimental data agree with the theory is a testament to the robustness of the basic analytical assumption of predominantly parallel flow. As a result, the closed form analytical expressions presented serve as simple, accurate tools for predicting bulk flow characteristics essential to practical low-g system design and analysis. Equations for predicting corner wetting rates, total container flow rates, and transient surfaces shapes are provided that are relevant also to terrestrial applications such as capillary flow in porous media.

Weislogel, Mark M.↗

Scaling of atomic layer etching of SiO 2 in fluorocarbon plasmas: Transient etching and surface roughness

Fabricating sub-10 nm microelectronics places plasma processing precision at atomic dimensions. Atomic layer etching (ALE) is a cyclic plasma process used in semiconductor fabrication that has the potential to remove a single layer of atoms during each cycle. In self-limiting ideal ALE, a single monolayer of a material is consistently removed in each cycle, typically expressed as EPC (etch per cycle). In plasma ALE of dielectrics, such as SiO 2 and Si 3 N 4 , using fluorocarbon gas mixtures, etching proceeds through deposition of a thin polymer layer and the process is not strictly self-terminating. As a result, EPC is highly process dependent and particularly sensitive to the thickness of the polymer layer. In this paper, results are discussed from a computational investigation of the ALE of SiO 2 on flat surfaces and in short trenches using capacitively coupled plasmas consisting of a deposition step (fluorocarbon plasma) and an etch step (argon plasma). We found that ALE performance is a delicate balance between deposition of polymer during the first half cycle and etching (with polymer removal) during the second half cycle. In the absence of complete removal of the overlying polymer in each cycle, ALE may be transient as the polymer thickness grows with each cycle with a reduction in EPC until the thickness is too large to enable further etching. Small and statistical amounts of polymer left from a previous cycle can produce statistical variation in polymer thickness on the next cycle, which in turn can lead to a spatially dependent EPC and ALE roughness. Based on synergy between T i (sputtering time) and T p (passivation time), dielectric ALE can be described as having three modes: deposition, roughening surface (transitioning to etch-stop), and smooth surface with steady-state EPC.

Materials Science↗

Advances in Cell Wall Matrix Research with a Focus on Mixed-Linkage Glucan

Mixed β(1,3;1,4)-linkage glucan (MLG) is commonly found in the monocot lineage, at particularly high levels in the Poaceae family, but also in the evolutionally distant genus, Equisetum. MLG has several properties that make it unique from other plant cell wall polysaccharides. It consists of β1,4-linked polymers of glucose interspersed with β1,3-linkages, but the presence of β1,3-linkages provides quite different physical properties compared to its closest form of the cell wall component, cellulose. The mechanisms of MLG biosynthesis have been investigated to understand whether single or multiple enzymes are required to build mixed linkages in the glucan chain. Currently, MLG synthesis by a single enzyme is supported by mutagenesis analyses of cellulose synthase-like F6, the major MLG synthase, but further investigation is needed to gather mechanistic insights. Because of transient accumulation of MLG in elongating cells and vegetative tissues, several hypotheses have been proposed to explain the role of MLG in the plant cell wall. Studies have been carried out to identify gene expression regulators during development and light cycles as well as enzymes involved in MLG organization in the cell wall. A role of MLG as a storage molecule in grains is evident, but the role of MLG in vegetative tissues is still not well understood. Characterization of a cell wall component is difficult due to the complex heterogeneity of the plant cell wall. Furthermore, as detailed in this review, recent exciting research has made significant impacts in the understanding of MLG biology in plants.

Transglucosylase/hydrolase (XTH)↗

Substructuring techniques

The substructure function generator program is discussed. Input to this program consists of a definition of a finite element model of a substructure, and specification of the type and number of displacement functions to be generated. Primary output is a substructure data file containing the substructure mass and stiffness matrices expressing kinetic and potential energies as quadratic forms in coefficients of the displacement functions, etc. The substructure synthesis program forms complete system mass, stiffness, and damping matrices, computes system modes and frequencies, and executes transient response calculations. Input to this program consists of the array of substructure data files generated by the function generator program for individual substructures, and data cards defining the position and interconnection of the substructures, damping data, forcing function details, and function control parameters.

Whetstone, W. D.↗