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Evans, James E.

Publications and source records attributed to Evans, James E..

30 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Inactivation of Fluorescent Lipid Bilayers by Irradiation With 300 keV Electrons Using Liquid Cell Transmission Electron Microscopy

Liquid cell transmission electron microscopy allows for imaging of samples in a fully hydrated state at high resolution and has the potential for visualizing static or dynamic biological structures. However, the ionizing nature of the electron beam makes it difficult to discern real physiological dynamics from radiation induced artifacts within liquid cell samples. Electron flux thresholds for achieving high resolution structures from biological samples frozen in ice have been described extensively by the cryo-electron microscopy field, while electron flux thresholds which do not result in a functional change for biological samples within the hydrated environment of a transmission electron microscope liquid cell is less clear. Establishing these functional thresholds for biologically relevant samples is important for accurate interpretation of results from liquid cell experiments. Here we demonstrate the electron damage threshold of fluorescently tagged lipid bilayers by quantifying the change in fluorescence before and after electron exposure. We observe the reduction of fluorescent signal in bilayers by 25% after only 0.0005 e − /Å 2 and a reduction of over 90% after 0.01 e − /Å 2 . These results indicate that the loss of function occurs at irradiation thresholds far below a typical single high resolution (scanning) transmission electron microscopy image and orders of magnitude below fluxes used for preserving structural features with cryo-electron microscopy.

Moser, Trevor↗
DOE OSTI2021

Cryo nanomanipulator probe with integrated gas injection

A probe assembly for use with a charged particle instrument includes an elongate body having a proximal end for positioning outside of a charged particle instrument enclosed environment, a distal end for positioning within the enclosed environment and a longitudinal axis. A port interface is located on the body between the proximal and distal ends, and is coupleable to a nanomanipulator system of the charged particle instrument. A probe needle is positioned at a distal end of the body and is selectively positionable from outside the enclosed environment to contact a specimen within the enclosed environment. At least one gas injection needle is adjustably positioned near the probe needle. The gas injection needle is connectable to a source of pressurized gas to selectively inject gas in the area of the probe needle within the enclosed environment.

Perea, Daniel E.↗
DOE OSTI2021

Tunable Heteroassembly of a Plant Pseudoenzyme–Enzyme Complex

Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme–enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B 6 production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme–enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2–PDX1.3 pseudoenzyme–enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2–PDX1.3 interactions. In this work, our results provide a new model of pseudoenzyme–enzyme interactions and their native heterogeneity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Cellulosome Localization Patterns Vary across Life Stages of Anaerobic Fungi

Anaerobic fungi ( Neocallimastigomycota ) isolated from the guts of herbivores excel at degrading ingested plant matter, making them attractive potential platform organisms for converting waste biomass into valuable products, such as chemicals and fuels. Major contributors to their biomass-hydrolyzing power are the multienzyme cellulosome complexes that anaerobic fungi produce, but knowledge gaps in how cellulosome production is controlled by the cellular life cycle and how cells spatially deploy cellulosomes complicate the use of anaerobic fungi and their cellulosomes in industrial bioprocesses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Landsat 8 monitoring of multi-depth suspended sediment concentrations in Lake Erie’s Maumee River using machine learning

Satellite remote sensing has been widely used to map suspended sediment concentration (SSC) in waterbodies. However, due to the complexity of sediment-water interactions, it has been difficult to derive linear and non-linear regression equations to reliably predict SSC, especially when trying to estimate depth of integrated sediment. Herein, this study uses Landsat 8 OLI (Operational Land Imager) sensor to map SSC within the Maumee River in Ohio, USA, at multiple depth intervals (15, 61, 91, and 182 cm). Simple linear least squares regression (LLSR), and three common machine learning models: random forest (RF), support vector regression (SVR), and model averaged neural network (MANN) were used to estimate SSC at the depth intervals. All machine learning models significantly outperformed LLSR while RF performed the best. In both RF and MANN, R2 (coefficient of determination) increases with depth with a maximum R2 of 0.89 and 0.83, respectively, at a depth of 0–182 cm. The results show that machine learning models can implement nonlinear relationships that produce better predictions than traditional linear regression methods in estimating depth integrated SSC, especially when samples are limited.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Electron-beam-driven chemical processes during liquid phase transmission electron microscopy

Liquid phase (or liquid cell) transmission electron microscopy (LP-TEM) has been established as a powerful tool for observing dynamic processes in liquids at nanometer to atomic length scales. However, the simple act of observation using electrons irreversibly alters the nature of the sample. A clear understanding of electron beam-driven processes during LP-TEM is required to interpret in situ observations and utilize the electron beam as a stimulus to drive nanoscale dynamic processes. In this review, we discuss recent advances toward understanding, quantifying, mitigating, and harnessing electron beam-driven chemical processes occurring during LP-TEM. We will highlight progress in several research areas, including modeling electron beam-induced radiolysis near interfaces, electron beam-induced nanocrystal formation, and radiation damage of soft materials and biomolecules.

Woehl, Taylor J.↗
DOE OSTI2020

Aspartate Residues in a Forisome-Forming SEO Protein Are Critical for Protein Body Assembly and Ca 2+ Responsiveness

Forisomes are protein bodies known exclusively from sieve elements of legumes. Forisomes contribute to the regulation of phloem transport due to their unique Ca 2+ -controlled, reversible swelling. The assembly of forisomes from sieve element occlusion (SEO) protein monomers in developing sieve elements and the mechanism(s) of Ca 2+ -dependent forisome contractility are poorly understood because the amino acid sequences of SEO proteins lack conventional protein–protein interaction and Ca 2+ -binding motifs. Here we selected amino acids potentially responsible for forisome-specific functions by analyzing SEO protein sequences in comparison to those of the widely distributed SEO-related (SEOR), or SEOR proteins. SEOR proteins resemble SEO proteins closely but lack any Ca 2+ responsiveness. We exchanged identified candidate residues by directed mutagenesis of the Medicago truncatula SEO1 gene, expressed the mutated genes in yeast ( Saccharomyces cerevisiae ) and studied the structural and functional phenotypes of the forisome-like bodies that formed in the transgenic cells. We identified three aspartate residues critical for Ca 2+ responsiveness and two more that were required for forisome-like bodies to assemble. The phenotypes observed further suggested that Ca 2+ -controlled and pH-inducible swelling effects in forisome-like bodies proceeded by different yet interacting mechanisms. Finally, we observed a previously unknown surface striation in native forisomes and in recombinant forisome-like bodies that could serve as an indicator of successful forisome assembly. To conclude, this study defines a promising path to the elucidation of the so-far elusive molecular mechanisms of forisome assembly and Ca 2+ -dependent contractility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tip-Enhanced Raman Nanospectroscopy of Smooth Spherical Gold Nanoparticles

We record nanoscale-resolved chemical images of thiobenzonitrile (TBN)-functionalized smooth gold nanospheres on silicon via tip-enhanced Raman (TER) nano-spectroscopy. The recorded images trace the nascence of the familiar doughnut-shaped scattering profile of nanoparticles on silicon at its origin (the particle surface), which appears as a horseshoe-shaped scattering pattern under our experimental conditions. The local optical field maps are in agreement with their simulated finite-difference time-domain analogues. Analysis of the recorded spectra with the aid of ab initio molecular dynamics-based Raman spectral simulations further suggests that optical rectification and molecular charging take place throughout the course of atomic force microscopy-based TER nanoscale chemical imaging.

Bhattarai, Ashish↗
DOE OSTI2019

MicroED for rapid and comprehensive characterization of the unknown small molecule composition of crude plant and soil extracts

This project implemented at PNNL a method introduced recently for de novo structure elucidation of small organic molecules: Micro-Electron Diffraction (henceforth microED). Micro-ED is an alternative to X-ray diffraction (XRD) or Nuclear Magnetic Resonance (NMR) for atomic-resolution structure elucidation of small organic or biological molecules, and it can succeed in solving structures when these well-established methods fail. In particular, microED offers the possibility of determining structures from far smaller quantities of material than would be required for NMR or even XRD, or from substances that fail to form crystals suitable (i.e., large enough) for X-ray crystallography, because microED requires only microcrystalline samples: in principle, a single crystal with ca. 100 nm dimensions would be suitable. MicroED is performed typically with standard electron microscopy (EM) instrumentation. The substantial potential of microED has drawn significant attention and examples of its use to solve difficult structure elucidation problems where X-ray or NMR methods failed has been described recently.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1994

Ground-based wake vortex monitoring, prediction, and ATC interface

This talk will discuss three elements of a proposed Wake Vortex Advisory Service: monitoring, prediction and ATC interface. The monitoring element is needed to ensure safety by warning controllers of hazardous wake vortex conditions. Such conditions exist when wake vortices persist in the approach/departure flight paths due to advection or to atmospheric conditions which prevent their decay. The prediction element is needed to provide ATC supervisors with advance warning that wake vortex separation conditions are about to change (i.e., require increased or decreased wake vortex separation). The ATC interface element is needed to provide controllers with adaptive wake vortex separations. The use of these adaptive wake vortex separations would lead to increased airport capacity under most conditions, while maintaining safety under conditions of wake vortex hazard.

Campbell, Steven D.↗
NASA NTRS1988

The Federal Aviation Administration/Massachusetts Institute of Technology (FAA/MIT) Lincoln Laboratory Doppler weather radar program

The program focuses on providing real-time information on hazardous aviation weather to end users such as air traffic control and pilots. Existing systems will soon be replaced by a Next Generation Weather Radar (NEXRAD), which will be concerned with detecting such hazards as heavy rain and hail, turbulence, low-altitude wind shear, and mesocyclones and tornadoes. Other systems in process are the Central Weather Processor (CWP), and the terminal Doppler weather radar (TDWR). Weather measurements near Memphis are central to ongoing work, especially in the area of microbursts and wind shear.

Evans, James E.↗