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At least 1,297 records · Page 72

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Soil incubation methods lead to large differences in inferred methane production temperature sensitivity

Abstract Quantifying the temperature sensitivity of methane (CH 4 ) production is crucial for predicting how wetland ecosystems will respond to climate warming. Typically, the temperature sensitivity (often quantified as a Q 10 value) is derived from laboratory incubation studies and then used in biogeochemical models. However, studies report wide variation in incubation-inferred Q 10 values, with a large portion of this variation remaining unexplained. Here we applied observations in a thawing permafrost peatland (Stordalen Mire) and a well-tested process-rich model ( ecosys ) to interpret incubation observations and investigate controls on inferred CH 4 production temperature sensitivity. We developed a field-storage-incubation modeling approach to mimic the full incubation sequence, including field sampling at a particular time in the growing season, refrigerated storage, and laboratory incubation, followed by model evaluation. We found that CH 4 production rates during incubation are regulated by substrate availability and active microbial biomass of key microbial functional groups, which are affected by soil storage duration and temperature. Seasonal variation in substrate availability and active microbial biomass of key microbial functional groups led to strong time-of-sampling impacts on CH 4 production. CH 4 production is higher with less perturbation post-sampling, i.e. shorter storage duration and lower storage temperature. We found a wide range of inferred Q 10 values (1.2–3.5), which we attribute to incubation temperatures, incubation duration, storage duration, and sampling time. We also show that Q 10 values of CH 4 production are controlled by interacting biological, biochemical, and physical processes, which cause the inferred Q 10 values to differ substantially from those of the component processes. Terrestrial ecosystem models that use a constant Q 10 value to represent temperature responses may therefore predict biased soil carbon cycling under future climate scenarios.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2003

Insights into the Processing of Carbon by Early Microbial Ecosystems

Interactions between Earth and the biosphere that were crucial for early biological evolution also influenced substantially the processes that circulate C between its reservoirs in the atmosphere, ocean, crust and mantle. The C-13 C-12 values of crustal carbonates and organics have recorded changes both in biological discrimination and in the relative rates of burial of organics and carbonates. A full interpretation of these patterns needs further isotopic studies of microbial ecosystems and individual anaerobes. Thus we measured carbon isotope discrimination during autotrophic and heterotrophic growth of pure cultures of sulfate-reducing bacteria and archaea (SRB and SRA). Discrimination during CO2 assimilation is significantly larger than during heterotrophic growth on lactate or acetate. SRB grown lithoautotrophically consumed less than 3% of available CO2 and exhibited substantial discrimination, as follows: Desulfobacterium autotrophicum (alpha 1.0100 to 1.0123), Desulfobacter hydrogenophilus (alpha = 0.0138), and Desulfotomuculum acetoxidans (alpha = 1.0310). Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO2 resulted in biomass with delta C-13 composition intermediate to that of the substrates. We have recently extended these experiments to include the thermophilic SRA Archeoglobus spp. Ecological forces also influence isotopic discrimination. Accordingly, we quantified the flow of C and other constituents in modern marine cyanobacterial mats, whose ancestry extends back billions of years. Such ecosystem processes shaped the biosignatures that entered sediments and atmospheres. At Guerrero Negro, BCS, Mexico, we examined mats dominated by Microcoleus (subtidal) and Lyngbya (intertidal to supratidal) cyanobacteria. During 24 hour cycles, we observed the exchange of O2 and dissolved inorganic C (DIC) between mats and the overlying water. Microcoleus mats assimilated near-equal amounts of DIC during the day as they released at night, but Lyngbya mats typically showed net uptake of DIC over the diel cycle. Patterns of O2 daytime release and nighttime uptake mirrored these DIC trends in both mat types. Nighttime DIC effluxes from Microcoleus mats were equivalent in the presence versus absence of O2, whereas nighttime DIC effluxes from Lyngbya mats dropped markedly in the absence of O2. Thus aerobic diagenesis was more important in Lyngbya mats than in Microcoleus mats, perhaps because trapped O2 bubbles persist only in Lyngbya mats at night and thus sustain populations of aerbes. In both mat types, effluxes of H2, CH4 and short-chain fatty acids were much greater at night in the absence of 02, emphasizing the importance of fermentation. Differences observed between Microcoleus versus Lyngbya mats forecast differences in their microbial populations and in their patterns of gene expression.

DesMarais, D.↗

DOE OSTI2021

Multidimensional genome-wide screening in yeast provides mechanistic insights into europium toxicity

Abstract Europium is a lanthanide metal that is highly valued in optoelectronics. Even though europium is used in many commercial products, its toxicological profile has only been partially characterized, with most studies focusing on identifying lethal doses in different systems or bioaccumulation in vivo. This paper describes a genome-wide toxicogenomic study of europium in Saccharomyces cerevisiae, which shares many biological functions with humans. By using a multidimensional approach and functional and network analyses, we have identified a group of genes and proteins associated with the yeast responses to ameliorate metal toxicity, which include metal discharge paths through vesicle-mediated transport, paths to regulate biologically relevant cations, and processes to reduce metal-induced stress. Furthermore, the analyses indicated that europium promotes yeast toxicity by disrupting the function of chaperones and cochaperones, which have metal-binding sites. Several of the genes and proteins highlighted in our study have human orthologues, suggesting they may participate in europium-induced toxicity in humans. By identifying the endogenous targets of europium as well as the already existing paths that can decrease its toxicity, we can determine specific genes and proteins that may help to develop future therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Simulation of In Situ Bioremediation of Chromium (VI) Using Consortium Cultures and Column Studies - 19357

Chromium contaminated soil and ground water has become a serious problem caused by the rapid expansion of industries, leading to direct or indirect discharge of Cr(VI). The conventional methods that include pump and treat result into toxic byproducts and residual. Cr(VI) reducing bacteria in the contrary have been envisioned as an economically and ecologically friendly method to treat contaminated sites. Biological Cr(VI) reduction processes include biotransformation, biosorption which involve detoxification/ removal of hazardous substances and bioaccumulation. A continuous flow column system for Cr(VI) reduction was investigated in three different treatments and the control, using dried sludge and soil from target site. Cultures identified using effluent samples in the 16S rRNA sequencing showed a prominent of Exiguobacterium aestuarii species as it was identified from all column systems. Other cultures that showed 100% query cover included; Enterobacter aerogenes, Enterobacter kobei and Pseudomonas aeruginosa. More than 90% of Cr(VI) reduction was observed in all columns over a 60 day period at 40 mgL{sup -1}. Cr(VI) was reduced from 38.12 mgL{sup -1} to 0.39 mgL{sup -1}. A more unstable profile was observed at 60 mgL{sup -1} over 60 days. Subsequently, there was near complete reduction from System 1 and 3 of 1.152 mgL{sup -1} and 1.215 mgL{sup -1} Cr(VI) concentration, respectively. A Cr(VI) reduction profile along the column proved to be uniform at assumed quasi-steady state from the influent to the effluent for both 40 and 60 mgL{sup -1} Cr(VI) concentration. Biological remediation strategies for Cr(VI) contaminated soil and groundwater is an emerging field that has been proposed to successfully treat Cr(VI) contaminated sites using Cr(VI) reduction species of bacteria. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Accurate computational design of three-dimensional protein crystals

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here, in this study, we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Clock-like mutational processes in human somatic cells

During the course of a lifetime, somatic cells acquire mutations. Different mutational processes may contribute to the mutations accumulated in a cell, with each imprinting a mutational signature on the cell's genome. Some processes generate mutations throughout life at a constant rate in all individuals, and the number of mutations in a cell attributable to these processes will be proportional to the chronological age of the person. Using mutations from 10,250 cancer genomes across 36 cancer types, we investigated clock-like mutational processes that have been operating in normal human cells. Two mutational signatures show clock-like properties. Both exhibit different mutation rates in different tissues. However, their mutation rates are not correlated, indicating that the underlying processes are subject to different biological influences. For one signature, the rate of cell division may influence its mutation rate. This paper provides the first survey of clock-like mutational processes operating in human somatic cells.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1991

NASA spinoffs to bioengineering and medicine

Through the active transfer of technology, the National Aeronautics and Space Administration (NASA) Technology Utilization (TU) Program assists private companies, associations, and government agencies to make effective use of NASA's technological resources to improve U.S. economic competitiveness and to provide societal benefit. Aerospace technology from areas such as digital image processing, space medicine and biology, microelectronics, optics and electrooptics, and ultrasonic imaging have found many secondary applications in medicine. Examples of technology spinoffs are briefly discussed to illustrate the benefits realized through adaptation of aerospace technology to solve health care problems. Successful implementation of new technologies increasingly requires the collaboration of industry, universities, and government, and the TU Program serves as the liaison to establish such collaborations with NASA. NASA technology is an important resource to support the development of new medical products and techniques that will further advance the quality of health care available in the U.S. and worldwide.

Biomedical Engineering/instrumentation/trends↗

DOE OSTI2018

Development of Integrated Biomimetic Framework with Intelligent Monitoring, Cognition and Decision Capabilities for Control of Advanced Energy Plants

The objective of the project entitled “Development of Integrated Biomimetic Framework with Intelligent Monitoring, Cognition, and Decision Capabilities for Control of Advanced Energy Plants” is to develop algorithms and methodologies for designing a biomimetic control system for optimal control of advanced energy plants. Traditionally, control systems have been designed based on assumed a priori knowledge of the process system. A number of variables are manipulated to accomplish disturbance rejection and/or servo control performance. While it is possible to adapt the process model based on available data, the control structure and the controllers rarely change. Thus, the knowledge learnt during process operation is lost or remains underutilized. In addition, the business models of today, especially for power plants, are rapidly changing. The power plant operators are being pushed to the edge due to the penetration of renewable energy derived power to the grid, the demand for high efficiency, ever-tightening environmental regulations, and requirements for increased plant availability. Thus, power plant operations need to be agile and should adapt quickly to the dynamic requirements. A number of characteristics distinguish biological systems from the traditional process control systems. Self-organization, distributed intelligence, adaptability, intelligent monitoring, cognition, and decision capabilities are some of the powerful characteristics of the biological world that can be effectively utilized in process control. At the top, the central nervous system (CNS) integrates the information from and coordinates the activities of all parts of the bodies (for bilaterian animals). Inspired by these distinct characteristics, this project seeks to develop methodologies and algorithms to accomplish: (i) self-organization of the control structure for maximizing the plant’s operating profit by mimicking the function of the cortical areas in the human brain, (ii) distributed and adaptive controllers that mimic the rule of pursuit present in ants, (iii) intelligent monitoring of the controllers powered with cognition and decision capabilities that mimic the artificial immune systems, and (iv) seamless coordination and integration in the control system that mimics the CNS.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2018

Optimization of the radio frequency power, time and cooling water temperature for pasteurization of Salmonella Typhimurium in shell eggs

Here, radio frequency (RF) power, treatment time and cooling water temperature affect inactivation of Salmonella Typhimurium in shell eggs and internal quality. Eggs were processed using 40.68 MHz RF at 30–45 W, 2.5–8 min and 30–38 °C, followed by hot water (HW) treatment at 56.7 °C for 15 min. Five conditions achieved >5 log reduction of Salmonella without observable quality change. Analyses of the longest (8 min at 30 W and 30 °C) and shortest (4.5 min at 35 W and 38 °C) treatments indicated that combined RF/HW treatments significantly (P < 0.05) preserved quality better than HW pasteurization (56.7 °C for 60 min). No significant (P ≥ 0.05) difference in egg quality was observed between the longest and shortest treatment, except that the shortest resulted in greater albumen turbidity. As the longest treatment required 78% more time and 47% more energy than the shortest, industry may wish to use the shortest RF treatment time.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Evaluation of a Wave Powered Water Pump Performance by Ocean Field Testing and WEC-Sim Modeling

This submission from AMEC (the Atlantic Marine Energy Center) includes data from an ocean field deployment of a wave powered water pump in March 2023. The wave pump is an upweller device, designed to enhance macroalgal aquaculture. The wave pump device was deployed off the coast of Isles of Shoals Appledore Island in Maine, USA. The data were collected using a custom-built DAQ module comprised of Arduino Unos. GPS time stamp accompanies the data. The data are volumetric flow rate from the wave pump, and relative motion of the device between float and spar buoys. Flow rate is measured by flow meter, and relative motion is measured by lidar. Calibration data for the lidar and flow meter sensors are included. This data set also includes synchronous Sofar Spotter buoy data from a mooring approximately 300 feet away from the wave pump mooring. Video data from the deployment are included from both on-board the device sporadically throughout the deployment, and from a webcam for a short duration of the deployment. Hydrophone data were also taken co-currently, and are available by contacting Martin Wosnik at the University of New Hampshire. The Matlab code used to process the field data is incorporated. A biological assessment is included which aided the NEPA consultation process, prior to conducting the field deployment. A WEC-Sim numerical model of the wave pump, and a re-design effort are part of this work. Code used to validate the WEC-Sim model from the field data are also included.

16 TIDAL AND WAVE POWER↗

NASA NTRS1992

The design, fabrication, and test of a new VLSI hybrid analog-digital neural processing element

A hybrid analog-digital neural processing element with the time-dependent behavior of biological neurons has been developed. The hybrid processing element is designed for VLSI implementation and offers the best attributes of both analog and digital computation. Custom VLSI layout reduces the layout area of the processing element, which in turn increases the expected network density. The hybrid processing element operates at the nanosecond time scale, which enables it to produce real-time solutions to complex spatiotemporal problems found in high-speed signal processing applications. VLSI prototype chips have been designed, fabricated, and tested with encouraging results. Systems utilizing the time-dependent behavior of the hybrid processing element have been simulated and are currently in the fabrication process. Future applications are also discussed.

Deyong, Mark R.↗

NASA NTRS1997

Detection of chaotic determinism in time series from randomly forced maps

Time series from biological system often display fluctuations in the measured variables. Much effort has been directed at determining whether this variability reflects deterministic chaos, or whether it is merely "noise". Despite this effort, it has been difficult to establish the presence of chaos in time series from biological sytems. The output from a biological system is probably the result of both its internal dynamics, and the input to the system from the surroundings. This implies that the system should be viewed as a mixed system with both stochastic and deterministic components. We present a method that appears to be useful in deciding whether determinism is present in a time series, and if this determinism has chaotic attributes, i.e., a positive characteristic exponent that leads to sensitivity to initial conditions. The method relies on fitting a nonlinear autoregressive model to the time series followed by an estimation of the characteristic exponents of the model over the observed probability distribution of states for the system. The method is tested by computer simulations, and applied to heart rate variability data.

Non-NASA Center↗

DOE OSTI2019

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

Diterpenoids form a diverse class of small molecule natural products that are widely distributed across the kingdoms of life and have critical biological functions in developmental processes, interorganismal interactions, and environmental adaptation. Due to these various bioactivities, many diterpenoids are also of economic importance as pharmaceuticals, food additives, biofuels, and other bioproducts. Advanced genomics and biochemical approaches have enabled a rapid increase in the knowledge of diterpenoid-metabolic genes, enzymes, and pathways. However, the structural complexity of diterpenoids and the narrow taxonomic distribution of individual compounds in often only a single species remain constraining factors for their efficient production. Availability of a broader range of metabolic enzymes now provide resources for producing diterpenoids in sufficient titers and purity to facilitate a deeper investigation of this important metabolite group. Drawing on established tools for microbial and plant-based enzyme co-expression, we present an easily operated and customizable protocol for the enzymatic production of diterpenoids in either Escherichia coli or Nicotiana benthamiana, and the purification of desired products via silica chromatography and semi-preparative HPLC. Using the group of maize (Zea mays) dolabralexin diterpenoids as an example, we highlight how modular combinations of diterpene synthase (diTPS) and cytochrome P450 monooxygenase (P450) enzymes can be used to generate different diterpenoid scaffolds. Purified compounds can be used in various downstream applications, such as metabolite structural analyses, enzyme structure-function studies, and in vitro and in planta bioactivity experiments.

09 BIOMASS FUELS↗

DOE OSTI2023

Adapting enzymes to improve their functionality in plants: why and how

Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context (‘plantized’) even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can — or cannot — be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.

Biochemistry & Molecular Biology↗

DOE OSTI2017

Lipoxin A4 suppresses osteoclastogenesis in RAW264.7 cells and prevents ovariectomy-induced bone loss

Lipoxin A4 (LXA4; 5S, 6R, 15Strihydroxy- 7,9,13-trans-11-eicosatetraenoic acid) is a metabolic product of arachidonic acid under the action of lipoxidase. This lipid molecule plays important roles in several biological functions, especially inflammatory processes. In vivo, LXA4 regulates the inflammatory response through several signaling pathways. Its mechanism suggests that it might have an effect on osteoclastogenesis and bone loss. Using both in vitro and in vivo studies, it was here observed that LXA4 could significantly inhibit the formation and function of osteoclasts and these effects could be blocked by Boc-2, the specific inhibitor of FPR2/ALX (the receptor of LXA4). Meanwhile, LXA4 reduce the amount of ovariectomy-induced bone loss. These protective effects was found to be associated with inhibition of nuclear factor-κB (NF-κB), activator protein-1 (AP-1), PI3K-AKT, and p-38, ERK, and JNK in MAPKs. The expression of the receptor activator of the NF-κB ligand RANKL:osteoprotegerin ratio and serum levels of TNF-α, IL-1β, and IL-6 were decreased by LXA4. Moreover, LXA4 prevented the production of reactive oxygen species (ROS), the expression of osteoclast-specific genes, including tartrate-resistant acid phosphatase (TRAP), cathepsin K (CK), matrix metalloproteinase (MMP)-9, RANK, and osteoclastic related transcription factors of c-Fos, NFATc1 could also be significantly inhibited by LXA4 in a dose-dependent manner. Studies have demonstrated that LXA4 can inhibit the formation and function of osteoclasts through modulation of several pathways both upstream and downstream of RANKL signaling and FPR2/ALX was involved in the procedures. This shows that LXA4 may be used as a new strategy for the treatment of osteoclast-related diseases. - Highlights: • Lipoxin A4 can significantly inhibit the formation and function of osteoclasts. • Several pathways both upstream and downstream of RANKL signaling can be inhibit by Lipoxin A4. • Lipoxin A4 can alleviate ovariectomy-induced bone loss effectively.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Tandem chemocatalysis and biological funneling to valorize lignin

In 2014, Linger et al. presented a tandem process for lignin valorization by integrating chemical and biological catalysis. Chemical pretreatment of corn stover generated mixed lignocellulose-derived monomers that were converted to a single product, polyhydroxyalkanoates, by Pseudomonas putida. Tandem processes have since been developed for diverse feedstocks to support the bioeconomy.

09 BIOMASS FUELS↗

DOE OSTI2023

Estimating source-sink distributions and fluxes of reactive nitrogen and sulfur within a mixed forest canopy

The vertical source-sink distribution of air pollutants within and above forested canopies is necessary for describing the biological, physical, and chemical processes influencing the soil-vegetation-atmosphere exchange. Here, this study implemented inverse modeling methods to estimate the source-sink and flux profiles of reactive nitrogen (N) and sulfur (S) compounds from measurements of the mean concentration profiles of ammonia (NH 3 ), nitric acid (HNO 3 ), sulfur dioxide (SO 2 ), and particulate ammonium (NH 4 + ), nitrate (NO 3 − ), and sulfate (SO 4 2− ) at a forest site in the southern Appalachian Mountains. Three inverse approaches utilizing different approximations to scalar transport within the canopy were developed and evaluated against sensible heat flux measurements. The Eulerian model (EUL), which incorporates vertical velocity skewness, performed well in reproducing the turbulent heat fluxes and was subsequently used to calculate the chemical source-sink and flux profiles. Above-canopy fluxes of NH 3 were downward, indicating that the forest was a net sink of NH 3 . The soil/litter layer was both a source and a sink for NH 3 but the exchange rate at the forest floor was small. Fluxes of HNO 3 , SO 2 , NO 3 − , NH 4 + , and SO 4 2- were uni-directional (deposition only) between the air and the canopy/ground and increased monotonically from the forest floor to the canopy top. Crown foliage dominated the uptake of reactive N and S during the growing season, accounting for 80–90% of the total canopy-scale flux. Fluxes and canopy-ground partitioning estimated using the resistance-based Surface Tiled Aerosol and Gas Exchange (STAGE) model were generally comparable to EUL. The comparison highlights the need for improved parameterizations of litter exchange and NH 3 compensation points in resistance models for forest ecosystems. The findings here benefit the application of critical loads in forest ecosystems and guide further development of resistance-based exchange models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Preface

This special issue of Catalysis Today results from the Symposium in Catalysts and Catalytic Technologies for Conversion of Biomass and its Derivatives during the 252nd American Chemical Society National Meeting & Exposition held in Philadelphia, Pennsylvania on August 22 – 24, 2016. The topics of the three-day symposium covered (1) experimental and theory/computational methods for characterization and reactivity studies of biomass catalytic conversion; (2) novel catalytic materials for biomass processing: heterogeneous, homogeneous and biological catalysts; (3) catalytic technologies for biomass pretreatment and upgrading; and, (4) catalytic conversion of lignocellulose, starch, sugars and lipids to fuels and chemicals. The symposium consisted of 49 accepted presentations, with three keynote talks specifically on hydrogenation/hydrogenolysis of furans, thermochemical conversion of biomass and valorization of lignocellulosics to fuels, materials and chemicals.

Olarte, Mariefel V.↗