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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. Furthermore, these findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The structural OFF and ON states of myosin can be decoupled from the biochemical super- and disordered-relaxed states

Abstract There is a growing awareness that both thick-filament and classical thin-filament regulations play central roles in modulating muscle contraction. Myosin ATPase assays have demonstrated that under relaxed conditions, myosin may reside either in a high-energy-consuming disordered-relaxed (DRX) state available for binding actin to generate force or in an energy-sparing super-relaxed (SRX) state unavailable for actin binding. X-ray diffraction studies have shown that the majority of myosin heads are in a quasi-helically ordered OFF state in a resting muscle and that this helical ordering is lost when myosin heads are turned ON for contraction. It has been assumed that myosin heads in SRX and DRX states are equivalent to the OFF and ON states, respectively, and the terms have been used interchangeably. In this study, we use X-ray diffraction and ATP turnover assays to track the structural and biochemical transitions of myosin heads, respectively, induced with either omecamtiv mecarbil (OM) or piperine in relaxed porcine myocardium. We find that while OM and piperine induce dramatic shifts of myosin heads from the OFF to the ON state, there are no appreciable changes in the population of myosin heads in the SRX and DRX states in both unloaded and loaded preparations. Our results show that biochemically defined SRX and DRX can be decoupled from structurally defined OFF and ON states. In summary, while SRX/DRX and OFF/ON transitions can be correlated in some cases, these two phenomena are measured using different approaches, reflect different properties of the thick filament, and should be investigated and interpreted separately.

Jani, Vivek P. (ORCID:0000000238114973)↗
DOE OSTI2023

Integrated Process Optimization for Biochemical Conversion

This research is motivated by the challenges faced during biomass processing in bioenergy plants. It has been observed that variations in biomass characteristics, such as moisture, ash, and carbohydrate contents cause variations in feeding of the system which led to underutilization of equipment and the reactor. The objective of this research is to ensure a continuous flow of biomass to the reactor in plants that use the biochemical conversion process to generate liquid fuels. The overall goal is to lower the cost of producing biofuels, which could lead to improving US’s energy independency and growing US’s rural economy. The research team developed analytical models, such as discrete element method (DEM) models and mathematical models. The DEM models are unit-level models that explicitly capture biomass characteristics and quantify the impacts of biomass characteristics on bulk material properties and the performance of specific equipment. The mathematical models are system-level models that capture the impacts of system infeed rate, equipment processing rate, storage location and capacity, and biomass characteristics on system throughput. The functional relations predicting the bulk material properties from DEM models are incorporated to the mathematical models. The models developed were validated and evaluated using data collected at Idaho National Laboratory’s biomass processing facility. Via these models, we identified process control strategies that ensure a continuous flow of biomass to the reactor, while meeting the requirements of biochemical conversion process. Our analysis indicates that sequencing of biomass bales based on moisture level, and carbohydrate contents could have a positive impact on reducing processing time and inventory level and increasing throughput rate. Short bale sequences that repeat frequently, seem to have the greatest impact on improving system’s performance. Based on our experiments, the total annual system operating costs reduced by 20-30%, and the maximum inventory level reduced by 3 to 4 times. The operating costs include the annual equipment amortization cost and processing cost. The implementation of the models developed requires the use of standardized bale format, Radio Frequency Identification technology, sensing and real time monitoring of material attributes, automated material handling equipment, and automated process control. The scope of the model proposed can be extended to include the whole supply chain. The supply chain models help identify how many bales of different biomass feedstock to purchase given biomass availability in the region, biomass price and quality, and the biomass processing capabilities of the biorefinery. Thus, the outcomes of supply chain models can be used to inform the design of long-term contracts among farmers and the biorefinery.

09 BIOMASS FUELS↗
DOE OSTI2020

Application of Quantum Computing to Biochemical Systems: A Look to the Future

Chemistry is considered as one of the more promising applications to science of near-term quantum computing. Recent work in transitioning classical algorithms to a quantum computer has led to great strides in improving quantum algorithms and illustrating their quantum advantage. Because of the limitations of near-term quantum computers, the most effective strategies split the work over classical and quantum computers. There is a proven set of methods in computational chemistry and materials physics that has used this same idea of splitting a complex physical system into parts that are treated at different levels of theory to obtain solutions for the complete physical system for which a brute force solution with a single method is not feasible. These methods are variously known as embedding, multi-scale, and fragment techniques and methods. We review these methods and then propose the embedding approach as a method for describing complex biochemical systems, with the parts not only treated with different levels of theory, but computed with hybrid classical and quantum algorithms. Such strategies are critical if one wants to expand the focus to biochemical molecules that contain active regions that cannot be properly explained with traditional algorithms on classical computers. While we do not solve this problem here, we provide an overview of where the field is going to enable such problems to be tackled in the future.

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

Production of sugars from lignocellulosic biomass via biochemical and thermochemical routes

Sugars are precursors to the majority of the world’s biofuels. Most of these come from sugar and starch crops, such as sugarcane and corn grain. Lignocellulosic sugars, although more challenging to extract from biomass, represent a large, untapped, opportunity. In response to the increasing attention to renewable energy, fuels, and chemicals, we review and compare two strategies for extracting sugars from lignocellulosic biomass: biochemical and thermochemical processing. Biochemical processing based on enzymatic hydrolysis has high sugar yield but is relatively slow. Thermochemical processing, which includes fast pyrolysis and solvent liquefaction, offers increased throughput and operability at the expense of low sugar yields.

Energy & Fuels↗
DOE OSTI2025

Impact of shading following installation of agrivoltaic systems on eco-physiological and biochemical attributes of “Howes” cranberry in Massachusetts

Agrivoltaic (AV) systems, which integrate solar energy generation with crop production on the same piece of land, offer a sustainable solution for optimizing land-use efficiency. However, the impact of shading induced by solar panels on crop growth, physiology, and metabolic activities of cranberry is not known. Understanding these interactions is essential for assessing the feasibility of AV systems in cranberry production. In this study we evaluated eco-physiological and biochemical crop responses on a commercial ‘Howes’ cranberry bog grown under an agrivoltaics system using different row spacings in the year immediately following installation. Following installation of fixed tilt solar panels at a height of 3.0 m above the plant canopy, four shading treatments were evaluated: an uncovered control area and row spacings of 9.0 m, 7.0 m, and 5.0 m, corresponding to 30%, 35%, and 37% shading respectively. The shading effect was also evaluated at three different fruit developmental stages (green, blush, and full-red stage). Using microclimate sensors installed in the treatment areas, key eco-physiological and biochemical parameters, including leaf gas exchange, chlorophyll, anthocyanin, and antioxidant content, electrolyte leakage, proline and trehalose accumulation, were assessed. While moderate shading (30% and 35%) alleviated environmental stress, as reflected by improved leaf water status and reduced electrolyte leakage, these same treatments suppressed key physiological and metabolic functions, including photosynthetic activity, carbon reserve accumulation, and the biosynthesis of stress-related osmolytes and antioxidant compounds. Under higher shading (37%), these reductions were even more pronounced, indicating a potential threshold beyond which the benefits of shading are outweighed by declines in assimilate production and secondary metabolism. These findings highlight a trade-off between the stress-mitigating benefits of shading and the alterations in key physiological and metabolic processes under agrivoltaic systems. Minimizing these trade-offs by optimizing row spacing in agrivoltaics systems is critical to maintain cranberry physiological status. Since commercial cranberry is grown as a continuous plant canopy (no interrow spaces for equipment travel), damage caused by the installation process likely impacted crop response evaluated in the first year; multi-year studies are needed to fully understand the dynamics of a dual-use system. Notably, this work provides the first direct measurements of proline, trehalose content, and electrolyte leakage in cranberry grown under AV conditions, offering new insight into their physiological adjustments to shading.

14 SOLAR ENERGY↗
DOE OSTI2022

Biochemical responses of hairgrass (Deschampsia caespitosa) to hydrological change

Plant growth and development are closely related to water availability. Water deficit and water excess are detrimental to plants, causing a series of damage to plant morphology, physiological and biochemical processes. In the long evolutionary process, plants have evolved an array of complex mechanisms to combat against stressful conditions. In the present study, the duration-dependent changes in ascorbate (AsA) and glutathione (GSH) contents and activities of enzymes involved in the AsA-GSH cycle in hairgrass ( Deschampsia caespitosa ) in response to water stress was investigated in a pot trial using a complete random block design. The treatments were as follows: (1) heavily waterlogging, (2) moderate waterlogging, (3) light waterlogging, (4) light drought, (5) moderate drought, (6) heavily drought, and (7) a control (CK) with plant be maintained at optimum water availability. The hairgrass plants were subjected to waterlogging or drought for 7, 14, 21 and 28 days and data were measured following treatment. Results revealed that hairgrass subjected to water stress can stimulate enzymatic activities of ascorbate peroxidase (APX), glutathione peroxidase (GPX), glutathione reductase (GR), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR) and L-galactono-1, 4-lactone dehydrogenase (GalLDH), switched on the ascorbate-glutathione (AsA-GSH) cycle and the L-galactose synthesis, up-regulated the contents of AsA and GSH, and maintained higher ratios of ascorbate to dehydroascorbate (AsA/DHA) and reduced glutathione to oxidized glutathione (GSH/GSSG) to alleviate potential oxidative damage. However, the light waterlogging did not induce hairgrass under stress to switch on the AsA-GSH pathway. In general, the critic substances and enzyme activities in AsA-GSH metabolic pathway increased as the increase of water stress intensity. As the increase of exposure duration, the critic antioxidant substances content and enzyme activities increased first and then maintained a relatively stable higher level. Our findings provide comprehensive information on biochemical responses of hairgrass to hydrological change, which would be a major step for accelerating ecological restoration of degradation alpine marshes in the Qinghai-Tibetan Plateau.

Luo, Qiaoyu↗
DOE OSTI2024

RNA-seq and metabolomic analyses of beneficial plant phenol biochemical pathways in red alder

Red alder ( Alnus rubra ) has highly desirable wood, dye pigment, and (traditional) medicinal properties which have been capitalized on for thousands of years, including by Pacific West Coast Native Americans. A rapidly growing tree species native to North American western coastal and riparian regions, it undergoes symbiosis with actinobacterium Frankia via their nitrogen-fixing root nodules. Red alder’s desirable properties are, however, largely attributed to its bioactive plant phenol metabolites, including for plant defense, for its attractive wood and bark coloration, and various beneficial medicinal properties. Integrated transcriptome and metabolome data analyses were carried out using buds, leaves, stems, roots, and root nodules from greenhouse grown red alder saplings with samples collected during different time-points (Spring, Summer, and Fall) of the growing season. Pollen and catkins were collected from field grown mature trees. Overall plant phenol biochemical pathways operative in red alder were determined, with a particular emphasis on potentially identifying candidates for the long unknown gateway entry points to the proanthocyanidin (PA) and ellagitannin metabolic classes, as well as in gaining better understanding of the biochemical basis of diarylheptanoid formation, i.e. that help define red alder’s varied medicinal uses, and its extensive wood and dye usage.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1971

Physiological control - A physical view: Life and the biochemical oscillator.

The history and progress of physical interpretations of physiological control, viewing life as a biochemical oscillator, are surveyed. Special attention is given to the author's studies (1964, 1965, 1968 and 1969) and to studies of Katchalsky (1969) who demonstrated a 1,000-A scale which may provide a basis for a biochemical oscillator.

Iberall, A. S.↗
NASA NTRS1974

Biochemical responses of the Skylab crewman

The biochemical investigations of the Skylab crewmen were designed to study the physiological changes that were observed on flight crews returning from previous space flight missions as well as to study those changes expected to result from prolonged weightless exposure. These studies can be divided into two broad categories. One category included routine blood studies similar to those used in clinical medical practice. The second included research-type endocrine analyses used to investigate more thoroughly the metabolic/endocrine responses to the space flight environment. The premission control values indicated that all Skylab crewmen were healthy and were free from biochemical abnormalities. The routine results during and after flight showed slight but significant changes in electrolytes, glucose, total protein, osmolality, uric acid, cholesterol, and creatinine. Plasma hormal changes included adrenocorticotrophic hormone, cortisol, angiotensin I, aldosterone, insulin, and thyroxine. The 24-hour urine analyses results revealed increased excretion of cortisol, catecholamines, antidiuretic hormone, and aldosterone as well as excretion of significant electrolyte and uric acid during the Skylab flights.

Leach, C. S.↗
NASA NTRS1992

A linear spectral matching technique for retrieving equivalent water thickness and biochemical constituents of green vegetation

Over the last decade, technological advances in airborne imaging spectrometers, having spectral resolution comparable with laboratory spectrometers, have made it possible to estimate biochemical constituents of vegetation canopies. Wessman estimated lignin concentration from data acquired with NASA's Airborne Imaging Spectrometer (AIS) over Blackhawk Island in Wisconsin. A stepwise linear regression technique was used to determine the single spectral channel or channels in the AIS data that best correlated with measured lignin contents using chemical methods. The regression technique does not take advantage of the spectral shape of the lignin reflectance feature as a diagnostic tool nor the increased discrimination among other leaf components with overlapping spectral features. A nonlinear least squares spectral matching technique was recently reported for deriving both the equivalent water thicknesses of surface vegetation and the amounts of water vapor in the atmosphere from contiguous spectra measured with the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS). The same technique was applied to a laboratory reflectance spectrum of fresh, green leaves. The result demonstrates that the fresh leaf spectrum in the 1.0-2.5 microns region consists of spectral components of dry leaves and the spectral component of liquid water. A linear least squares spectral matching technique for retrieving equivalent water thickness and biochemical components of green vegetation is described.

Gao, Bo-Cai↗
NASA NTRS1992

Exploring the remote sensing of foliar biochemical concentrations with AVIRIS data

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data shows promise for the estimation of foliar biochemical concentrations at the scale of the canopy. There are, however, several problems associated with the use of AVIRIS data in this way and these are detailed in recent Plant Biochemical Workshop Report. The research reported was concentrated upon three of these problems: field sampling of forest canopies, wet laboratory assay of foliar chemicals, and the visualization of AVIRIS data.

Smith, Geoffrey M.↗
NASA NTRS1993

The effect of signal noise on the remote sensing of Foliar biochemical concentration

Spectral measurements made using an imaging spectrometer contain systematic and random noise, while the former can be corrected the latter remains a source of error in the remotely sensed signal. A number of investigators have tried to determine the signal-to-noise-ratio (SNR) of the instrument, or the resultant imagery. However, the level of noise at which spectra are too noisy to be useful is not usually determined. The first attempt was by Goetz and Calvin, who suggested that the depth of the absorption feature should be at least an order of magnitude greater than the noise and more recently Dekker suggested a SNR of around 600:1 was required in visible/near infrared wavelengths to measure a 1/gl change in chlorophyll a concentration water. The wide range of applications of imaging spectroscopy make it difficult to set SNR specifications as they are dependent on a number of factors, one of the most important being reflectance of a particular target. For example, the SNR of imagery for vegetated targets is relatively low simply because vegetation has a relatively low level of reflectance. The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) is being used to estimate the concentration of biochemicals within vegetation canopies. This paper reports a study undertaken to identify first, wavebands that were highly correlated with foliar biochemical concentration and second, to determine how sensitive these correlations were to sensor noise.

Smith, Geoffrey M.↗
NASA NTRS2002

Biochemical Composition of Dissolved Organic Matter Released During Experimental Diatom Blooms

An axenic culture of Skeletonema costatum was grown to late-log phase to examine the molecular weight distribution and the biochemical composition of high molecular weight dissolved organic matter released in the absence of actively growing bacteria. A second culture was grown in a 5 m(exp 3) mesocosm and placed in darkness for a period of 51 days to examine the impact of phytoplankton bloom dynamics and microbial decomposition on dissolved (DOM) and particulate organic matter (POM) composition. DOM was separated using tangential-flow ultrafiltration into three nominal size fractions: LDOM (less than 1 kDa DOM), HDOM (1-30 kDa) and VHDOM (30 kDa-0.2 micron) and characterized. Both axenic and mesocosm diatom blooms released 28-33% of net primary production as dissolved organic carbon (DOC). In the axenic culture, HDOM and LDOM each comprised about half of the diatom-released DOC with less than l% as VHDOM. Diatoms from both experiments released carbohydrate-rich high molecular weight DOM. Much of the axenic diatom-released high molecular weight DOC could be chemically characterized (61% of HDOM and 78% of VHDOM) with carbohydrates as the primary component (45% of HDOM and 55% of VHDOM). Substantial amounts of hydrolyzable amino acids (16% of HDOM and 22% of VHDOM) and small amounts of lipids (less than 1%) were also released. Proportions of recognizable biochemical components in DOM produced in the mesocosm bloom were lower compared to the axenic culture. The presence of bacterial fatty acids and peptidoglycan-derived D-amino acids within high molecular weight fractions from the mesocosm bloom revealed that bacteria contributed a variety of macromolecules to DOM during the growth and decay of the diatom bloom. Release of significant amounts of DOC by diatoms demonstrates that DOM excretion is an important component of phytoplankton primary production. Similarities in high molecular weight DOM composition in marine waters and diatom cultures highlight the importance of phytoplankton to DOM composition in the ocean.

Mannino, Antonio↗
NASA NTRS2002

Biochemical basis for the biological clock

NADH oxidases at the external surface of plant and animal cells (ECTO-NOX proteins) exhibit stable and recurring patterns of oscillations with potentially clock-related, entrainable, and temperature-compensated period lengths of 24 min. To determine if ECTO-NOX proteins might represent the ultradian time keepers (pacemakers) of the biological clock, COS cells were transfected with cDNAs encoding tNOX proteins having a period length of 22 min or with C575A or C558A cysteine to alanine replacements having period lengths of 36 or 42 min. Here we demonstrate that such transfectants exhibited 22, 36, or 40 to 42 h circadian patterns in the activity of glyceraldehyde-3-phosphate dehydrogenase, a common clock-regulated protein, in addition to the endogenous 24 h circadian period length. The fact that the expression of a single oscillatory ECTO-NOX protein determines the period length of a circadian biochemical marker (60 X the ECTO-NOX period length) provides compelling evidence that ECTO-NOX proteins are the biochemical ultradian drivers of the cellular biological clock.

NASA Discipline Cell Biology↗
NASA NTRS2004

Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

Dateo, Christopher E.↗
NASA NTRS1997

Biochemical markers in the assessment of bone disease

As the mean age of our population increases, increasing attention has been paid to the diseases associated with aging, including diseases of the skeleton such as osteoporosis. Effective means of treating and possibly preventing such skeletal disorders are emerging, making their early recognition an important goal for the primary care physician. Although bone density measurements and skeletal imaging studies remain of primary diagnostic importance in this regard, a large number of assays for biochemical markers of bone formation and resorption are being developed that promise to complement the densitometry measurements and imaging studies, providing an assessment of the rates of bone turnover and an earlier evaluation of the effects of therapy. In this review, emphasizing the recent literature, the major biochemical markers currently in use or under active investigation are described, and their application in a number of diseases of the skeleton including osteoporosis is evaluated.

Review↗
NASA NTRS1996

The effect of nonablative laser energy on joint capsular properties. An in vitro histologic and biochemical study using a rabbit model

The purpose of this study was to evaluate the effect of laser energy at nonablative levels on joint capsular histologic and biochemical properties in an in vitro rabbit model. The medial and lateral portions of the femoropatellar joint capsule from both stifles of 12 mature New Zealand White rabbits were used. Specimens were divided into three treatment groups (5 watts, 10 watts, and 15 watt) and one control group using a randomized block design. Specimens were placed in a 37 degrees bath of lactated Ringer's solution and laser energy was applied using a holmium:yttrium-aluminum-garnet laser in four transverse passes across the tissue at a velocity of 2 mm/sec with the handpiece set 1.5 mm from the synovial surface. Histologic analysis revealed thermal alteration of collagen (fusion) and fibroblasts (pyknosis) at all energy densities, with higher laser energy causing significantly greater morphologic changes over a larger area (P < 0.05). Application of laser energy did not significantly alter the biochemical parameters evaluated, including type I collagen content and nonreducible crosslinks (P > 0.05). This study demonstrated that nonablative laser energy caused significant thermal damage to the joint capsular tissue in an energy-dependent fashion, but type I collagen content and nonreducible crosslinks (P > 0.05). This study demonstrated that nonablative laser energy caused significant thermal damage to the joint capsular tissue in an energy-dependent fashion, but type I Collagen content and nonreducible corsslinks were not significantly altered.

NASA Discipline Musculoskeletal↗