Radiotelemetric Investigation of the Ph Content in the Alimentary Canal
Radio telemetry study of ph of digestive system
RADIO TELEMETRY↗
SEARCH · Engineering Papers
Results for “DIGESTION”
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↗
Simulating Cellulose Structure, Properties, Thermodynamics, Synthesis, and Deconstruction with Atomistic and Coarse-Grain Models
Cellulose is still a mysterious polymer in many ways: structure of microfibrils, thermodynamics of synthesis and degradation, and interactions with other plant cell wall components. Our aim is to uncover the details and mechanisms of cellulose digestion and synthesis. We report the details of the structure of cellulose 1-beta under several temperature conditions and report here the results of these studies and connections to experimental measurements and the measurement in-silico the free energy of decrystallization of several morphologies of cellulose. In spatially large modeling, we show the most recent work of mapping atomistic and coarse-grain models into tomographic images of cellulose and extreme coarse-grain modeling of interactions of large cellulase complexes with microfibrils. We discuss the difficulties of modeling cellulose and suggest future work both experimental and theoretical to increase our understanding of cellulose and our ability to use it as a raw material for fuels and materials.
36 MATERIALS SCIENCE↗
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↗
A Study of autunite dissolution in the presence of Shewanella oneidensis MR1 and different bicarbonate concentrations - 15736
Remediation of uranium at Hanford Site 300 area via tripolyphosphate injections could sequester uranium (VI) in an insoluble form, creating different types of uranium phosphate minerals like autunite. The factors that influence the dissolution of such minerals come into question. Bacteria can play a significant role in the dissolution of minerals and the formation of secondary minerals. Formed autunite, as a phosphorus-containing mineral, can attract bacteria to liberate phosphorus, meeting their nutrient requirements and causing uranium release back into the environment. Previous studies have been conducted under aerobic conditions. This research was extended to investigate the stability of the autunite mineral under anaerobic conditions pertaining to the Hanford Site, and to study the effect of facultative anaerobic bacteria on the uranium (VI) release from autunite. Objectives: - Evaluate bacterial interactions with uranium (VI) by focusing on facultative anaerobic bacteria, Shewanella Oneidensis MR1. - Study the effect of bacteria on the dissolution of the uranyl phosphate solid phases created as a result of sodium tripolyphosphate injections into the subsurface at the Hanford 300 Area. - Evaluate the role of anaerobic bacteria as one of the factors affecting the outcome of environmental remediation. Experimental Approach: - 16 crimp-sealed bottles were prepared with 50 ml of media solution and 90 mg (4.4 mM of uranium VI) Ca-autunite mineral obtained from Hanford site. Bottles were inoculated with Shewanella Oneidensis MR1 strains when autunite was equilibrated with the media solutions. Bacteria was obtained from Pacific Northwestern National Laboratory (PNNL). - Solution media preparation: 20 mM NaHepes buffer: pH=7, 10 mM Lactate plus bicarbonate in four concentrations (0, 3, 5 and 10 of KHCO{sub 3}) and a bacteria-free control. Samples were taken from the supernatant solutions of the experimental and control bottles. Wet and dry digestion was performed until a white solid residue was acquired. Dilution was made on solid samples for KPA analysis to determine concentration of U (VI) as function of time. The results suggests that in the absence of HCO{sub 3}{sup -} there was a decrease in the of uranium (VI) concentration due to metal reducing bacteria Shewanella Oneidensis MR1, but for higher concentrations of HCO{sub 3}{sup -}, there is no significant difference in uranium (VI) reduction before and after inoculation with bacteria. - Although bottles were sealed, there is an hypothesis that it was oxygen restricted but not strictly performed under anaerobic conditions. For that matter there is a reason to repeat the experiment using the glove box to understand the uranium (VI) reduction mechanism and behavior of bacteria with oxic/anoxic interfaces. Conclusions: - Higher bicarbonate concentrations might interfere with uranium (VI) reduction by anaerobic bacteria. - It is necessary to reduce time of sampling before the inoculation and prolong sampling time after inoculation. - It might be necessary to increase concentration of lactate. Future Work: - Conduct experiment in strictly anaerobic conditions by using the glove box and evaluate if further reduction of uranium (VI) is obtained in the presence of carbonates (HCO{sub 3}{sup -}). - Finalize analysis of calcium and phosphorous via ICP instrument.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
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↗
Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase
Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. Here, we determined the high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed “pre-bound” molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygen activation. Our results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme–substrate complex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 ↗
Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production
Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this work briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. Finally, we also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.
59 BASIC BIOLOGICAL SCIENCES↗
Expanding the modular ester fermentative pathways for combinatorial biosynthesis of esters from volatile organic acids
ABSTRACT Volatile organic acids are byproducts of fermentative metabolism, for example, anaerobic digestion of lignocellulosic biomass or organic wastes, and are often times undesired inhibiting cell growth and reducing directed formation of the desired products. Here, we devised a general framework for upgrading these volatile organic acids to high‐value esters that can be used as flavors, fragrances, solvents, and biofuels. This framework employs the acid‐to‐ester modules, consisting of an AAT (alcohol acyltransferase) plus ACT (acyl CoA transferase) submodule and an alcohol submodule, for co‐fermentation of sugars and organic acids to acyl CoAs and alcohols to form a combinatorial library of esters. By assembling these modules with the engineered Escherichia coli modular chassis cell, we developed microbial manufacturing platforms to perform the following functions: (i) rapid in vivo screening of novel AATs for their catalytic activities; (ii) expanding combinatorial biosynthesis of unique fermentative esters; and (iii) upgrading volatile organic acids to esters using single or mixed cell cultures. To demonstrate this framework, we screened for a set of five unique and divergent AATs from multiple species, and were able to determine their novel activities as well as produce a library of 12 out of the 13 expected esters from co‐fermentation of sugars and (C2‐C6) volatile organic acids. We envision the developed framework to be valuable for in vivo characterization of a repertoire of not‐well‐characterized natural AATs, expanding the combinatorial biosynthesis of fermentative esters, and upgrading volatile organic acids to high‐value esters. Biotechnol. Bioeng. 2016;113: 1764–1776. © 2016 Wiley Periodicals, Inc.
Layton, Donovan S.↗
Encapsulin carrier proteins for enhanced expression of antimicrobial peptides
Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. To address these limitations, we have developed a novel AMP fusion protein system based on an encapsulin nanocompartment protein and have demonstrated its utility in enhancing expression of HBCM2, an AMP with activity against Gram–negative bacteria. Here, HBCM2 was fused to the N–terminus of several Encapsulin monomer (Enc) variants engineered with multiple TEV protease recognition site insertions to facilitate proteolytic release of the fused HBCM2. Fusion of HBCM2 to the Enc variants, but not other common carrier proteins, enabled robust overexpression in Escherichia coli C43(DE3) cells. Interestingly, variants with a TEV site insertion following residue K71 in Enc exhibited the highest overexpression and HBCM2 release efficiencies compared to other variants but were deficient in cage formation. HBCM2 was purified from the highest expressing variant following TEV protease digestion and was found to be highly active in inhibiting E. coli growth (MIC = 5 μg/ml). Our study demonstrates the potential use of the Enc system to enhance expression of AMPs for biomanufacturing and therapeutic applications.
59 BASIC BIOLOGICAL SCIENCES↗
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↗