Radiotelemetric Investigation of the Ph Content in the Alimentary Canal
Radio telemetry study of ph of digestive system
RADIO TELEMETRY↗
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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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Study of the normal fecal bacterial flora of man quarterly progress report, oct. 1 - dec. 31, 1964
Human fecal bacteria culturing and isolation, and metabolic effects of nutrition in digestive tract
CULTURE TECHNIQUE↗
Study of the normal fecal bacterial flora of man quarterly progress report, jan. 1 - mar. 31, 1965
Human fecal bacteria isolation and metabolic studies for nutrition in digestive system
BACTERIA↗
Comparison of Select Food Waste Utilization Options
This document provides a comparison of several food waste utilization options: landfill gas capture, anaerobic digestion, and composting, across various metrics. These options are the most prevalent pathways for energy and resource recovery. Other options, not considered here, include food donation, animal feed, incineration, and gasification. The table below describes the differences or similarities between these processes and provides information about products, the number of current projects in the United States, capital and operation and maintenance (O&M) costs, job development potential, emissions, and incentives associated with each pathway, as well as other parameters, such as level of complexity, land requirement, and revenue type. Sources for the data in the table are listed in the references at the end of the document.
09 BIOMASS FUELS↗
Manipulating the Assembly and Architecture of Fibrillar Silk
Silk is a unique and exceptionally strong biological material. However, no synthetic method has yet come close to replicating the properties of natural silk. This shortfall is attributed to an insufficient understanding of both silk nanofibril structure and the mechanism of formation. Here in situ atomic force microscopy (AFM) and photo-induced force microscopy (PiFM) is utilized to investigate the formation process and define the basic structural paradigm of individual silk nanofibrils. By visualizing the multistage process of silk nanofibril formation, the importance of conformational transformations along the assembly pathway is revealed. Unfolded silk structures initially accumulate into amorphous clusters, which then evolve into crystal nuclei via conformational transformation into β-crystallites. Nanofibril elongation then occurs through the attachment of silk molecules at a single end of the nanofibril tip; this is facilitated through the formation of a new amorphous cluster that then repeats the aforementioned conformational transformation. However, enzymatic digestion of the amorphous regions leads to direct, rapid elongation of β-crystalline fibers. These findings imply that the energy landscape is characterized by shallow minima associated with intermediate states, which can be eliminated by introducing β-crystallites, and motivate research into the directed modification of the silk assembly pathway to select for features beneficial to specific applications.
36 MATERIALS SCIENCE↗
Investigation of the effects of ternary deep eutectic solvent composition on pretreatment of sorghum stover
Biomass‐derived deep eutectic solvents (DESs) have been introduced as promising pretreatment and fractionation solvents because of their mild processing conditions, easy synthesis, and green solvent components from biomass. In recent DES studies, solvent‐based third constituents like water, ethanol, and others improve the processibility of typical binary DESs. However, the impacts of these components are not well understood. Here, two solvent‐based constituents, including water and ethylene glycol, were applied to 3,4‐dihydroxybenzoic acid (DHBA)‐based DES system for improving the conversion efficiency of cellulose‐rich fraction and the properties of lignin fraction. Chemical composition, enzymatic digestibility, degree of polymerization of cellulose and physicochemical properties of lignin were used to evaluate the impact of each third constituent on biomass processing. Ternary ChCl‐DHBA DESs exhibited better performances in delignification, fermentable sugar production, and preservation of β‐O‐4 ether linkage in lignin compared with binary ChCl‐DHBA DES.
09 BIOMASS FUELS↗
A Glycan Array-Based Assay for the Identification and Characterization of Plant Glycosyltransferases
Growing plants with modified cell wall compositions is a promising strategy to improve resistance to pathogens, increase biomass digestibility, and tune other important properties. In order to alter biomass architecture, a detailed knowledge of cell wall structure and biosynthesis is a prerequisite. We report here a glycan array-based assay for the high-throughput identification and characterization of plant cell wall biosynthetic glycosyltransferases (GTs). We demonstrate that different heterologously expressed galactosyl-, fucosyl-, and xylosyltransferases can transfer azido-functionalized sugar nucleotide donors to selected synthetic plant cell wall oligosaccharides on the array and that the transferred monosaccharides can be visualized “on chip” by a 1,3-dipolar cycloaddition reaction with an alkynyl-modified dye. The opportunity to simultaneously screen thousands of combinations of putative GTs, nucleotide sugar donors, and oligosaccharide acceptors will dramatically accelerate plant cell wall biosynthesis research.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Algae to HEFA : Economics and potential deployment in the United States
Abstract To reach the goals set by the US Department of Energy's Sustainable Aviation Fuel (SAF) Grand Challenge, currently available feedstocks may be insufficient. Giving priority to developing, prototyping and reducing the cost of algal feedstock before investing and lining up locations is important. As the production of algal feedstocks advances, a simplified conversion approach using more mature technologies can help reduce the investment risk for algae‐based fuels. Reducing process complexity to the steps described here [namely, conversion of lipids to HEFA (hydroprocessed esters and fatty acids) fuels and relegating the remainder of the biomass to anaerobic digestion or food/feed production] enables the near‐term production of algal SAF but presents challenging economics depending on achievable cultivation costs and compositional quality. However, these economics can be improved by present‐day policy incentives. With these incentives, the modeled algae‐to‐HEFA pathway could reach a minimum fuel selling price as low as $4.7 per gasoline gallon equivalent depending on the carbon intensity reduction that can be achieved compared with petroleum. Uncertainty about algal feedstock production maturity in the current state of technology and the future will play a large role in determining the economic feasibility of building algae‐to‐HEFA facilities. For example, if immaturity increases the feedstock price by even 10%, SAF production in 2050 is about 58% of the production which could have been achieved with mature feedstock. Additionally, growth in this conversion pathway can be notably boosted through the inclusion of subsidies, and also through higher‐value coproducts or higher lipid yields beyond the scope of the process considered here.
09 BIOMASS FUELS↗
An overview of switchgrass phenotypes variability across diverse populations and their implications for conversion to fuels
There have been substantial changes to the human lifestyle over the past two centuries, which are reflected in the amount of fuel we consume to power our day-to-day needs. The way we use these resources has indeed manifested in an overdependence on non-renewable energy sources, such as coal and petroleum, for generating electricity and powering our transportation needs. There is a pressing need to explore alternative ways of fueling our current lifestyle without impacting the environment. Biofuels have long been touted as a sustainable solution for use as drop-in fuels in aviation and maritime applications. Still, they have yet to establish themselves as a competitive commercial alternative, necessitating further research and development. Lignocellulosic biomass is an underutilized resource that is widely accessible for the commercial processing of renewable biofuels. Bioenergy crops, such as switchgrass (Panicum virgatum L.), which can be cultivated on marginal lands with minimal competition for agricultural land, are an ideal and promising candidate for bulk-scale biofuel synthesis. Over the past 30 years, significant progress has been made in breeding and genetically modifying these grasses to enhance their drought resilience and subsequent yields. However, discrepancies in biomass composition can lead to irregular feedstocks for downstream operations, which in turn affect overall production targets for biofuels. Here, this review examines the variability in switchgrass (P. virgatum L.) biomass phenotypes across diverse populations and plant components, and their implications for biofuel conversion. The study highlights significant variations in biomass yield, composition, and cell wall chemistry both between switchgrass genotypes and within individual cultivars. Key findings include differences in cellulose, hemicellulose, and lignin content between leaves and stems, which affect biomass digestibility and ethanol yield. The review also discusses the impact of lignin chemistry, particularly the syringyl/guaicyl (S/G) ratio, on the efficiency of biomass saccharification. Furthermore, it explores how these variations respond differently to various pretreatment techniques, affecting overall biofuel production. We conclude that understanding and quantifying this variability is crucial for optimizing switchgrass as a feedstock for commercial biofuel production, thereby potentially addressing the pressing need for sustainable energy sources in sectors such as aviation.
Kousika, Rohit [Univ. of Tennessee, Knoxville, TN ↗
Activity–Based Protein Profiling of Bile Salt Hydrolysis in the Human Gut Microbiome with Beta–Lactam or Acrylamide–Based Probes
Microbial bile salt hydrolases (BSHs) found in the intestine catalyze the deconjugation of taurine– and glycine–linked bile salts produced in the liver. The resulting bile salts are biological detergents and are critical in aiding lipophilic nutrient digestion. Therefore, the activity of BSHs in the gut microbiome is directly linked to human metabolism and overall health. Bile salt metabolism has also been associated with disease phenotypes such as liver and colorectal cancer. In order to reshape the gut microbiome to optimize bile salt metabolism, tools to characterize and quantify these processes must exist to enable a much–improved understanding of how metabolism goes awry in the face of disease, and how it can be improved through an altered lifestyle and environment. Furthermore, it is necessary to attribute metabolic activity to specific members and BSHs within the microbiome. To this end, we have developed activity–based probes with two different reactive groups to target bile salt hydrolases. Finally, these probes bind similarly to the authentic bile salt substrates, and we demonstrate enzyme labeling of active bile salt hydrolases by using purified protein, cell lysates, and in human stool.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors**
The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2M Pro ) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1M Pro ), we have designed and synthesized a series of SC2M Pro inhibitors that contain β-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2M Pro active-site cysteine C145. All inhibitors display high potency with K i values at or below 100 nM. The most potent compound, MPI3, has as a K i value of 8.3 nM. Crystallographic analyses of SC2M Pro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 μM and A549/ACE2 cells at 0.16-0.31 μM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2M Pro inhibitors with ultra-high antiviral potency.
3C-like protease↗
Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform
Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis, response to environmental perturbation, pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool to study plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This protocol describes a recently-developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, with ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant tissue harvest, tissue preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells.
59 BASIC BIOLOGICAL SCIENCES↗
Improving the bioaccessibility of lipophilic ingredient in its oral intestinal delivery by ultrasound and biological cross‐linker
Abstract BACKGROUND Great efforts have been made to improve the oral bioaccessibility of lipophilic ingredients with multi‐functionalities. Achieving intestinal delivery of lipophilic ingredients and their encapsulation in micelles composed of bile salts and lipid hydrolysates (i.e. fatty acids) is critical for improving oral bioaccessibility. Therefore, oil‐core microcapsules are considered ideal carriers of lipophilic ingredients. Previous studies have reported oil‐core/zein‐shell microcapsules constructed by a one‐step anti‐solvent process. Still, its efficacy as an intestinal delivery system was limited because if the porous shell structure. RESULTS Zein solution was pretreated with ultrasound and tannic acid (TA) cross‐linking. Composite oil‐core microcapsule (COM) with a compact shell structure was successfully prepared by using modified zein solution in the anti‐solvent process. Fourier‐transform infrared spectroscopy and circular dichroism analyses indicated that ultrasound and TA synergistically promote the conformational transition of zein from α‐helix to β‐sheet and enhance the hydrophobic interactions among protein chains. The above changes contribute to the strengthen of shell zein network. Correspondingly, COM presents superior encapsulation efficiency and environmental stability over the simple oil‐core microcapsule (SOM) prepared without the use of ultrasound and TA. Furthermore, antioxidant activity of β‐carotene was well retained during the encapsulation process. In vitro studies indicated that COM was more resistant to digestibility and acid‐induced swelling. More than 87% of β‐carotene could be released in the intestine in a sustainable way. The controllable release behavior thus promoted a significant increase in bioaccessibility of β‐carotene encapsulated in COM compared to SOM (85.9% versus 48.5%). CONCLUSION The COM generated here shows potential for bioaccessibility improvement of lipophilic ingredients. © 2022 Society of Chemical Industry.
Wei, Yun‐Shan↗
Plastic glut down a microbial gut
Enzymes sequestered from microbes have demonstrated the ability to readily digest amorphous regions of polyethylene terephthalate (PET) in ambient conditions. Although nascent, enzymatic depolymerization can soon vie for commercialization and provide monomeric feedstock at rates comparable to petrochemical feedstock for repolymerization, achieving the coveted goal of cradle-to-cradle recycling. © 2022 The Authors. Polymer International published by John Wiley & Sons Ltd on behalf of Society of Industrial Chemistry.
59 BASIC BIOLOGICAL SCIENCES↗
BdGT43B2 functions in xylan biosynthesis and is essential for seedling survival in Brachypodium distachyon
Abstract Xylan is the predominant hemicellulose in the primary cell walls of grasses, but its synthesis and interactions with other wall polysaccharides are complex and incompletely understood. To probe xylan biosynthesis, we generated CRISPR/Cas9 knockout and amiRNA knockdown lines of BdGT43B2 , an ortholog of the wheat TaGT43‐4 xylan synthase scaffolding protein in the IRX14 clade, in Brachypodium distachyon . Knockout of BdGT43B2 caused stunting and premature death in Brachypodium seedlings. Immunofluorescence labeling of xylans was greatly reduced in homozygous knockout BdGT43B2 mutants, whereas cellulose labeling was unchanged or slightly increased. Biochemical analysis showed reductions in digestible xylan in knockout mutant walls, and cell size was smaller in knockout leaves. BdGT43B2 knockdown plants appeared morphologically normal as adults, but showed slight reductions in seedling growth and small decreases in xylose content in isolated cell walls. Immunofluorescence labeling of xylan and cellulose staining was both reduced in BdGT43B2 knockdown plants. Together, these data indicate that BdGT43B2 functions in the synthesis of a form of xylan that is required for seedling growth and survival in Brachypodium distachyon .
36 MATERIALS SCIENCE↗
Dissecting the structural heterogeneity of proteins by native mass spectrometry
Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Integrated structural model of the palladin–actin complex using XL ‐ MS , docking, NMR , and SAXS
Abstract Palladin is an actin‐binding protein that accelerates actin polymerization and is linked to the metastasis of several types of cancer. Previously, three lysine residues in an immunoglobulin‐like domain of palladin have been identified as essential for actin binding. However, it is still unknown where palladin binds to F‐actin. Evidence that palladin binds to the sides of actin filaments to facilitate branching is supported by our previous study showing that palladin was able to compensate for Arp2/3 in the formation of Listeria actin comet tails. Here, we used chemical crosslinking to covalently link palladin and F‐actin residues based on spatial proximity. Samples were then enzymatically digested, separated by liquid chromatography, and analyzed by tandem mass spectrometry. Peptides containing the crosslinks and specific residues involved were then identified for input to the HADDOCK docking server to model the most likely binding conformation. Small‐angle x‐ray scattering was used to provide further insight into palladin flexibility and the binding interface, and NMR spectra identified potential interactions between palladin's Ig domains. Our final structural model of the F‐actin:palladin complex revealed how palladin interacts with and stabilizes F‐actin at the interface between two actin monomers. Three actin residues that were identified in this study also appear commonly in the actin‐binding interface with other proteins such as myotilin, myosin, and tropomodulin. An accurate structural representation of the complex between palladin and actin extends our understanding of palladin's role in promoting cancer metastasis through the regulation of actin dynamics.
Sargent, Rachel [Department of Chemistry and Bioch↗
Carbonate clumped isotope analysis (Δ 47 ) of 21 carbonate standards determined via gas‐source isotope‐ratio mass spectrometry on four instrumental configurations using carbonate‐based standardization and multiyear data sets
Rationale Clumped isotope geochemistry examines the pairing or clumping of heavy isotopes in molecules and provides information about the thermodynamic and kinetic controls on their formation. The first clumped isotope measurements of carbonate minerals were first published 15 years ago, and since then, interlaboratory offsets have been observed, and laboratory and community practices for measurement, data analysis, and instrumentation have evolved. Here we briefly review historical and recent developments for measurements, share Tripati Lab practices for four different instrument configurations, test a recently published proposal for carbonate‐based standardization on multiple instruments using multi‐year data sets, and report values for 21 different carbonate standards that allow for recalculations of previously published data sets. Methods We examine data from 4628 standard measurements on Thermo MAT 253 and Nu Perspective IS mass spectrometers, using a common acid bath (90°C) and small‐sample (70°C) individual reaction vessels. Each configuration was investigated by treating some standards as anchors (working standards) and the remainder as unknowns (consistency standards). Results We show that different acid digestion systems and mass spectrometer models yield indistinguishable results when instrument drift is well characterized. For linearity correction, mixed gas‐and‐carbonate standardization or carbonate‐only standardization yields similar results. No difference is observed in the use of three or eight working standards for the construction of transfer functions. Conclusions We show that all configurations yield similar results if instrument drift is robustly characterized and validate a recent proposal for carbonate‐based standardization using large multiyear data sets. Δ 47 values are reported for 21 carbonate standards on both the absolute reference frame (ARF; also refered to as the Carbon Dioxide Equilibrated Scale or CDES) and the new InterCarb‐Carbon Dioxide Equilibrium Scale (I‐CDES) reference frame, facilitating intercomparison of data from a diversity of labs and instrument configurations and restandardization of a broad range of sample sets between 2006, when the first carbonate measurements were published, and the present.
58 GEOSCIENCES↗