Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “electrophoresis”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Membrane Profiling by Free Flow Electrophoresis and SWATH-MS to Characterize Subcellular Compartment Proteomes in Mesembryanthemum crystallinum

The study of subcellular membrane structure and function facilitates investigations into how biological processes are divided within the cell. However, work in this area has been hampered by the limited techniques available to fractionate the different membranes. Free Flow Electrophoresis (FFE) allows for the fractionation of membranes based on their different surface charges, a property made up primarily of their varied lipid and protein compositions. In this study, high-resolution plant membrane fractionation by FFE, combined with mass spectrometry-based proteomics, allowed the simultaneous profiling of multiple cellular membranes from the leaf tissue of the plant Mesembryanthemum crystallinum. Comparisons of the fractionated membranes’ protein profile to that of known markers for specific cellular compartments sheds light on the functions of proteins, as well as provides new evidence for multiple subcellular localization of several proteins, including those involved in lipid metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Detection of Polar Compounds Condensed on Particulate Matter Using Capillary Electrophoresis-Mass Spectrometry

A new analytical method to aid in the understanding of the organic carbon (OC) phase of particulate matter (PM) from advanced compression ignition (ACI) operating modes, is presented. The presence of NO2 and unburned fuel aromatics in ACI emissions, and the low exhaust temperatures that result from this low temperature combustion strategy, provide the right conditions for the formation of carboxylic acids and nitroaromatic compounds. These polar compounds contribute to OC in the PM and are not typically measured using nonpolar solvent extraction methods such as the soluble organic fraction (SOF) method. The new extraction and detection method employs capillary electrophoresis with electrospray ionization mass spectrometry (CE-ESI MS) and was specifically developed to determine polar organic compounds in the ACI PM emissions. The new method identified both nitrophenols and aromatic carboxylic acids in the ACI PM. The ACI air-fuel stratification mode and NOx emissions were found to correlate with the presence and amount of the individual polar species identified.

Lewis Sr, Samuel↗
DOE OSTI2021

Volumetric micro-injector for capillary electrophoresis

A volumetric microfluidic injector for capillary electrophoresis (CE) for highly repeatable sample injection has been designed and built to eliminate known injection bias in hydrodynamic injection. A defined volume from 1-10 nL or 0.1-100 nL of sample is confined in a defined region of a micro-valve PDMS microfluidic injector chip and electrophoretic potential is applied to drive sample into a separation device such as an embedded fused silica capillary for separation and detection. Using a 75 μm ID capillary, the RSD of an absorbance peak area as low as 1.32% (n=11) is obtained. As a comparison, the time-dependent injection was tested using the same chip which resulted in an inferior repeatability.

Ha, Noel Seunghyun↗
DOE OSTI2022

Ligand-Assisted Separation of Rare Earth Elements via Capillary Electrophoresis

Rare earth elements (REEs) are a class of critical materials vital in applications such as EVs, batteries, and defense weapons systems. These elements are found primarily in ores, and due to their similar chemical behavior, the challenge remains to find an effective means of separation. The addition of ligands of varying charge, size, denticity, etc. can help to increase separation, yet the mechanistic behavior and factors influencing separation are still poorly understood. Here, iminodiacetic acid (IDA) is used to exploit and maximize differences in electrophoretic mobilities between adjacent REEs. Mobilities and diffusion coefficients of REEs in aqueous media are measured via CE and are compared to MD and FEM simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2020

3D RNA nanocage for encapsulation and shielding of hydrophobic biomolecules to improve the in vivo biodistribution

Ribonucleic acid (RNA) nanotechnology platforms have the potential of harboring therapeutics for in vivo delivery in disease treatment. However, the nonspecific interaction between the harbored hydrophobic drugs and cells or other components before reaching the diseased site has been an obstacle in drug delivery. In this work, we report an encapsulation strategy to prevent such nonspecific hydrophobic interactions in vitro and in vivo based on a self-assembled three-dimensional (3D) RNA nanocage. By placing an RNA three-way junction (3WJ) in the cavity of the nanocage, the conjugated hydrophobic molecules were specifically positioned within the nanocage, preventing their exposure to the biological environment. The assembly of the nanocages was characterized by native polyacrylamide gel electrophoresis (PAGE), atomic force microscopy (AFM), and cryogenic electron microscopy (cryo-EM) imaging. The stealth effect of the nanocage for hydrophobic molecules in vitro was evaluated by gel electrophoresis, flow cytometry, and confocal microscopy. The in vivo sheathing effect of the nanocage for hydrophobic molecules was assessed by biodistribution profiling in mice. The RNA nanocages with hydrophobic biomolecules underwent faster clearance in liver and spleen in comparison to their counterparts. Therefore, this encapsulation strategy holds promise for in vivo delivery of hydrophobic drugs for disease treatment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Proteomic Analysis of Pecan ( Carya illinoinensis ) Nut Development

Pecan (Carya illinoinensis) nuts are an economically valuable crop native to the United States and Mexico. A proteomic summary from two pecan cultivars at multiple time points was used to compare protein accumulation during pecan kernel development. Patterns of soluble protein accumulation were elucidated using qualitative gel-free and label-free mass-spectrometric proteomic analyses and quantitative (label-free) 2-D gel electrophoresis. Two-dimensional (2-D) gel electrophoresis distinguished a total of 1267 protein spots and shotgun proteomics identified 556 proteins. Rapid overall protein accumulation occurred in mid-September during the transition to the dough stage as the cotyledons enlarge within the kernel. Pecan allergens Car i 1 and Car i 2 were first observed to accumulate during the dough stage in late September. While overall protein accumulation increased, the presence of histones diminished during development. Twelve protein spots accumulated differentially based on 2-D gel analysis in the weeklong interval between the dough stage and the transition into a mature kernel, while eleven protein spots were differentially accumulated between the two cultivars. These results provide a foundation for more focused proteomic analyses of pecans that may be used in the future to identify proteins that are important for desirable traits, such as reduced allergen content, improved polyphenol or lipid content, increased tolerance to salinity, biotic stress, seed hardiness, and seed viability.

2D-gel↗
DOE OSTI2025

SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides

Capillary zone electrophoresis (CZE) is gaining attention in the field of single-cell proteomics for its ultralow-flow and high-resolution separation abilities. Even more sample-limited yet rich in biological information are phosphoproteomics experiments, as the phosphoproteome composes only a fraction of the whole cellular proteome. Rapid analysis, high sensitivity, and maximization of sample utilization are paramount for single-cell analysis. Some challenges of coupling CZE analysis with mass spectrometry analysis (MS) of complex mixtures include 1. sensitivity due to volume loading limitations of CZE and 2. incompatibility of MS duty cycles with electropherographic time scales. Here, we address these two challenges as applied to singlecell- equivalent phosphoproteomics experiments by interfacing a microchip-based CZE device integrated with a solid-phaseextraction (SPE) bed with the Orbitrap Astral mass spectrometer. Using 225 phosphorylated peptide standards and phosphorylated peptide-enriched mouse brain tissue, we investigate microchip-based SPE-CZE functionality, quantitative performance, and complementarity to nano-LC-MS (nLC-MS) analysis. We highlight unique SPE-CZE separation mechanisms that can empower fitfor- purpose applications in single-cell-equivalent phosphoproteomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Comparison of genotyping assays for detection of targeted CRISPR/Cas mutagenesis in highly polyploid sugarcane

Sugarcane (Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Genetic Fusion of Thermoresponsive Polypeptides with UCST‐type Behavior Mediates 1D Assembly of Coiled‐Coil Bundlemers

Abstract Thermoresponsive resilin‐like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil‐forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature‐triggered phase separation of the RLP units. Their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet‐visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic‐transmission electron microscopy and coarse‐grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.

Patkar, Sai S.↗
DOE OSTI2023

Genetic Fusion of Thermoresponsive Polypeptides with UCST–type Behavior Mediates 1D Assembly of Coiled–Coil Bundlemers

Thermoresponsive resilin-like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil-forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature-triggered phase separation of the RLP units. Furthermore, their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet-visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic-transmission electron microscopy and coarse-grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Can Charge Transfer Across C─H⋅⋅⋅O Hydrogen Bonds Stabilize Oil Droplets in Water?

Oil-water emulsions resist aggregation due to the presence of negative charges at their surface that leads to mutual repulsion between droplets, but the molecular origin of oil charge is currently under debate. Although much evidence has suggested that ionic species must accumulate at the interface, an alternative perspective attributes the negative charge on the oil droplet to charge transfer of electron density from water to oil molecules. Although the charge transfer mechanism is consistent with the correct sign of oil charge, it is just as important to provide good estimates of the charge magnitude to explain emulsion stability and electrophoresis experiments. Here, we show using energy decomposition analysis that the amount of net flow of charge from water to oil is negligibly small due to nearly equal forward and backward charge transfer through weak oil-water interactions, such that oil droplets would be unstable and coalesce, contrary to experiment. The lack of charge transfer also explains why vibrational sum frequency scattering reports a blue shift in the oil C-H frequency when forming emulsions with water, which arises from Pauli repulsion due to localized confinement at the interface. Finally, unlike ions, neither charge transfer nor dynamic polarization can produce a finite conductivity needed to couple to electric fields that would explain electrophoretic mobility.

Zhao, Ruoqi↗
DOE OSTI2022

Triptycene-Based Molecular Rods for Langmuir-Blodgett Monolayers

In this report we introduce fully modular synthesis leading to three representative examples of rigid molecular rods that are intended to form sturdy monolayers on various surfaces. These molecules contain two triptycene units that are designed to interlock into a compact "double-decker" structure. Two of the three final products provided suitable crystals for X-ray diffraction (analyzed on synchrotron), allowing deeper insight into packing in the 3-D crystal lattice. The acidity of all three compounds were determined by capillary electrophoresis, and the pK a values ranged between 2.06-2.53. All three rigid rods easily formed Langmuir-Blodgett monolayers (LBMs) on the water-air interfaces, with the area per molecule equal to 55-59 Å 2 /molecule, suggesting tight intermolecular packing. The thickness of all three films reached ~19 Å after transfer to a gold (111) surface, meaning that individual molecules are tilted maximally 38° from the axis perpendicular to the surface. The structure of one of these films on a gold (111) surface was visualized by AFM. These geometrically unique molecules represent promising platforms with a wide scope of applicability in the supramolecular architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Mitigating the allergenicity of peanut allergen Ara h 1 by cold atmospheric pressure argon plasma jet

Abstract BACKGROUND Peanut allergy is recognized as a major food allergy that triggers severe and even fatal symptoms. Avoidance of peanuts in the diet is the main option for current safety management. Processing techniques reducing peanut allergenicity are required to develop other options. Cold plasma is currently considered as a novel non‐thermal approach to alter protein structure and has the potential to alleviate immunoreactivity of protein allergen. RESULTS The application of a cold argon plasma jet to peanut protein extract could reduce the amount of a 64 kDa protein band corresponding to a major peanut allergen Ara h 1 using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, but the overall protein size distribution did not change significantly. A decrease in peanut protein solubility was a possible cause that led to the loss of protein content in the soluble fraction. Immunoblotting and enzyme‐linked immunosorbent assay elucidated that the immunoreactivity of Ara h 1 was significantly decreased with the time treated with plasma. Ara h 1 antigenicity reduced by 38% after five scans (approximately 3 min) of cold argon plasma jet treatment, and the reduction was up to 66% after approximately 15 min of treatment. CONCLUSION The results indicate that cold argon plasma jet treatment could be a suitable platform for alleviating the immunoreactivity of peanut protein. This work demonstrates an efficient, compact, and rapid platform for mitigating the allergenicity of peanuts, and shows great potential for the plasma platform as a non‐thermal technique in the food industry. © 2023 Society of Chemical Industry.

Hsu, Fu‐Chiun↗
DOE OSTI2025

Evaluating size exclusion chromatography for nucleic acid removal in Klebsiella pneumoniae cell surface polysaccharide purification

Cell surface-associated polysaccharides in Klebsiella are major virulence determinants and crucial targets for developing vaccines. Traditionally, the purification of these cell surface polysaccharides from Klebsiella pneumoniae involves a multi-step process comprising phenol extraction, nuclease digestion, ultracentrifugation, and repeated ethanol extractions. In this study, we evaluated size exclusion chromatography for effectively eliminating nucleic acid contamination while purifying high molecular weight cell surface-associated polysaccharides. Post-initial extraction, the nucleic acid content remains significantly elevated, and kinetic analysis reveals that DNase I and RNase A digestion is neither economically viable nor effective for removing these contaminants. Employing an appropriate size exclusion resin removes over 99 % of nucleic acid contamination, as confirmed by nucleic acid content analysis and agarose gel electrophoresis. Purity and structural analysis using 1H 1D-NMR and 2D-NMR demonstrate that the cell surface-associated polysaccharide purified with this study is highly homogeneous and identified as antigenic O-polysaccharide. This approach streamlines the purification process by removing the need for nuclease digestion and additional ethanol precipitation steps.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

The spore coat is essential for Bacillus subtilis spore resistance to pulsed light, and pulsed light treatment eliminates some spore coat proteins

Microbial surface contamination of equipment or of food contact material is a recurring problem in the food industry. Spore-forming bacteria are far more resistant to a wide variety of treatments than their vegetative forms. Understanding the mechanisms underlying decontamination processes is needed to improve surface decontamination strategies against endospores potentially at the source of foodborne diseases or food-spoilage. Pulsed light (PL) with xenon lamps delivers high-energy short-time pulses of light with wavelengths in the range 200 nm-1100 nm and a high UV-C fraction. Bacillus subtilis spores were exposed to either PL or to continuous UV-C. Gel electrophoresis and western blotting revealed elimination of various proteins of the spore coat, an essential outer structure that protects spores from a wide variety of environmental conditions and inactivation treatments. Proteomic analysis confirmed the elimination of some spore coat proteins after PL treatment. Transmission electron microscopy of PL treated spores revealed a gap between the lamellar inner spore coat and the outer spore coat. Overall, spores of mutant strains with defects in genes coding for spore coat proteins were more sensitive to PL than to continuous UV-C. This study demonstrates that radiations delivered by PL contribute to specific damage to the spore coat, and overall to spore inactivation. Keywords Decontamination, UV, proteins, proteomics, microscopy Journal Pre-proof

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The congenital APOA1 K107del mutation disrupts the lipid-free conformation of monomeric APOA1 and impairs oligomerization

Apolipoprotein A-I (APOA1) oligomerization is thought to be essential for high-density lipoprotein (HDL) formation and metabolism. Naturally occurring mutations can disrupt normal APOA1 folding and self-association, leading to dysfunctional HDL formation and cardiovascular disease. The congenital APOA1 variant p.K131del (APOA1 K107del ) has been associated with cardiovascular pathologies such as low HDL-cholesterol levels and aortic amyloidosis, and multiple studies indicate structural changes in APOA1 conformation underlie associated dysfunction. In the current study, we confirmed that APOA1 K107del exhibits no notable defect in lipid-binding. However, using polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC), we found that loss of lysine 107 resulted in a remarkable shift in the distribution of APOA1 oligomers with a much higher proportion of monomers present in APOA1 K107del compared to wild-type APOA1. Further investigation using quantitative cross-linking revealed a major disruption of interactions in helical regions reported to participate in domain swaps necessary for proper self-association. This structural disruption appears to impair N- and C-termini interactions and dynamics that lead to non-specific aggregation. In conclusion, these findings support the hypothesis that lysine 107 is critical for proper folding and self-association of lipid-free APOA1 which could impact HDL biogenesis.

APOA1 (p.K131del)↗