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At least 721 records · Page 40

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NASA NTRS1998

Plants and somatic embryos in space: what have we learned?

Space provides a unique environment that can affect the interplay between cell cycle controls and environment and can thus modify the processes of cell division, development and growth. It is proposed that the chromosomal and nuclear abnormalities frequently encountered in cells of various plants exposed to space are due to a combination of factors including the biological status of the systems and the way in which they are grown, exposed to, and ultimately, the way in which they experience multiple stresses. The extent to which space-specific changes become manifest is dependent on the extent of pre-existing stresses in the system. This has become evident in a variety of plant species grown in space but has been particularly amenable to study using in vitro systems, especially in developing embryoids. The following observations allow us to harmonize disparate results from a variety of space experiments:- (a) the more completely developed a system, the less likely it is to show cell stress during growth; the less morphologically complex, the greater the vulnerability; (b) the size/"packaging" of the genome (karyotype) are significant experimental variables; plants with larger genomes (e.g. polyploids) seem to be more space-stress tolerant; (c) a single space-associated stress is inadequate to produce a significant adverse response unless the stress is severe, or a biological parameter necessary to 'amplify' it exists. On this view, an appropriate "stress match" with other non-equilibrium determinants, much like a 'tug of war', can result in genomic variations in space. All this emphasizes that fastidiously-controlled growing environments must be devised if one is to resolve the matter of direct versus indirect effects of space. Better understanding of the novel physico-chemical equilibrium phenomena associated with space will allow those interested in space cell and developmental biology to pick and choose procedures best suited to their exploitation for specific objectives.

Flight Experiment↗

DOE OSTI2020

Quality-Control Mechanism for Telomerase RNA Folding in the Cell

Long non-coding RNAs can often fold into different conformations. Telomerase RNA, an essential component of the telomerase ribonucleoprotein (RNP) enzyme, must fold into a defined structure to fulfill its function with the protein catalytic subunit (TERT) and other accessory factors. However, the mechanism by which the correct folding of telomerase RNA is warranted in a cell is still unknown. Here we show that La-related protein Pof8 specifically recognizes the conserved pseudoknot region of telomerase RNA and instructs the binding of the Lsm2-8 complex to its mature 3' end, thus selectively protecting the correctly folded RNA from exonucleolytic degradation. In the absence of Pof8, TERT assembles with misfolded RNA and produces little telomerase activity. Therefore, Pof8 plays a key role in telomerase RNA folding quality control, ensuring that TERT only assembles with functional telomerase RNA to form active telomerase. Our finding reveals a mechanism for non-coding RNA folding quality control.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, in this study, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2002

Radiation Effect on Human Tissue

Predicting the occurrence of human cancer following exposure of an epidemiologic population to any agent causing genetic damage is a difficult task. To an approximation, this is because the uncertainty of uniform exposure to the damaging agent, and the uncertainty of uniform processing of that damage within a complex set of biological variables, degrade the confidence of predicting the delayed expression of cancer as a relatively rare event within clinically normal individuals. This situation begs the need for alternate controlled experimental models that are predictive for the development of human cancer following exposures to agents causing genetic damage. Such models historically have not been of substantial proven value. It is more recently encouraging, however, that developments in molecular and cell biology have led to an expanded knowledge of human carcinogenesis, and of molecular markers associated with that process. It is therefore appropriate to consider new laboratory models developed to accomodate that expanded knowledge in order to assess the cancer risks associated with exposures to genotoxic agents. When ionizing radiation of space is the genotoxic agent, then a series of additional considerations for human cancer risk assessment must also be applied. These include the dose of radiation absorbed by tissue at different locations in the body, the quality of the absorbed radiation, the rate at which absorbed dose accumulates in tissue, the way in which absorbed dose is measured and calculated, and the alterations in incident radiation caused by shielding materials. It is clear that human cancer risk assessment for damage caused by ionizing radiation is a multidisciplinary responsibility, and that within this responsibility no single discipline can hold disproportionate sway if a risk assessment model of radiation-induced human cancer is to be developed that has proven value. Biomolecular and cellular markers from the work reported here are considered for use in assessing human cancer risk related to exposure to space radiation. This potential use must be integrated within the specified multidisciplinary context in order to create a new tool of molecular epidemiology that can hopefully then realistically assess this cancer risk.

Richmond, Robert C.↗

DOE OSTI2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Abstract DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

Yang, Yunqi↗

DOE OSTI2022

Rational Control of Off‐State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement**

Abstract Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non‐fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off ‐state conformations, trans1 and trans2 , located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off ‐state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high‐level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue‐ and red‐shifts of the absorption bands associated to trans1 and trans2 , respectively. Thus, due to elimination of trans2 , the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two‐fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2‐V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2002

Opportunities for nutritional amelioration of radiation-induced cellular damage

The closed environment and limited evasive capabilities inherent in space flight cause astronauts to be exposed to many potential harmful agents (chemical contaminants in the environment and cosmic radiation exposure). Current power systems used to achieve space flight are prohibitively expensive for supporting the weight requirements to fully shield astronauts from cosmic radiation. Therefore, radiation poses a major, currently unresolvable risk for astronauts, especially for long-duration space flights. The major detrimental radiation effects that are of primary concern for long-duration space flights are damage to the lens of the eye, damage to the immune system, damage to the central nervous system, and cancer. In addition to the direct damage to biological molecules in cells, radiation exposure induces oxidative damage. Many natural antioxidants, whether consumed before or after radiation exposure, are able to confer some level of radioprotection. In addition to achieving beneficial effects from long-known antioxidants such as vitamins E and C and folic acid, some protection is conferred by several recently discovered antioxidant molecules, such as flavonoids, epigallocatechin, and other polyphenols. Somewhat counterintuitive is the protection provided by diets containing elevated levels of omega-3 polyunsaturated fatty acids, considering they are thought to be prone to peroxidation. Even with the information we have at our disposal, it will be difficult to predict the types of dietary modifications that can best reduce the risk of radiation exposure to astronauts, those living on Earth, or those enduring diagnostic or therapeutic radiation exposure. Much more work must be done in humans, whether on Earth or, preferably, in space, before we are able to make concrete recommendations.

Review↗

NASA NTRS2003

Oxygen requirement of germinating flax seeds

Plant experiments in earth orbit are typically prepared on the ground and germinated in orbit to study gravity effects on the developing seedlings. Germination requires the breakdown of storage compounds, and this metabolism depends upon respiration, making oxygen one of the limiting factors in seed germination. In microgravity lack of run-off of excess water requires careful testing of water dispensation and oxygen availability. In preparation for a shuttle experiment (MICRO on STS-107) we studied germination and growth of flax (Linum usitatissimum L.) seedlings in the developed hardware (Magnetic Field Chamber, MFC). We tested between four to 32 seeds per chamber (air volume=14 mL) and after 36 h measured the root length. At 90 microliters O2 per seed (32 seeds/chamber), the germination decreased from 94 to 69%, and the root length was reduced by 20%, compared to 8 seeds per chamber. Based on the percent germination and root length obtained in controlled gas mixtures between 3.6 and 21.6% O2 we determined the lower limit of reliable germination to be 10 vol. % O2 at atmospheric pressure. Although the oxygen available in the MFC's can support the intended number of seeds, the data show that seed storage and microgravity-related limitations may reduce germination. c2003 Published by Elsevier Ltd on behalf of COSPAR.

NASA Discipline Plant Biology↗

DOE OSTI2020

Ambient Ion Trapping and Separations for High Throughput Structurally Selective Material Deposition

While ion mobility coupled to mass spectrometry (IMS/MS) has been increasingly adapted to biological analysis, the structural and molecular specificity offered by IMS/MS has untapped potential for creating novel materials (for energy, catalysis, biomolecular switches etc.) with rationally tailored properties by precisely controlling the chemical structure and composition of these materials. While electrochemical and catalytic properties of the bulk material are understood by mass-selective ion-soft-landing, different structures of one molecule can exhibit distinct properties from the bulk. Many biological phenomenon occur at interfaces and are highly structurally specific. IMS/MS offers means to separate molecules in a sample (which is first ionized and released to gas phase from the condensed phase) based on mass and structure. Species thus separated can potentially be deposited onto surfaces with molecular and structural specificity, to perform fundamental investigations for understanding critical interfacial phenomenon. Key performance metrics for IMS/MS analysis are resolution of separations and sensitivity. Recently developed Structures for Lossless Ion Manipulations (SLIM)4 enabled unprecedented resolution in IMS separations. In addition, high sensitivity was enabled in SLIM due to lossless confinement of ions using radio frequency fields. Thus, SLIM enabled extremely long path length separations (up to 0.1 km thus far) providing efficient separation of molecular ions never before achieved (e.g. isotopologues, D&L amino acids). While SLIM has unprecedented analytical separations power/utility, the use of SLIM platform for depositing mobility and mass selected molecular ions has two specific technological challenges: (a) Pulsed nature of IMS separations and their low duty cycle and (b) the need for a low vacuum of ~4 torr for lossless ion confinement. These limitations lead to long deposition times due to loss of ions generated from the sample. Enabling ion confinement at atmospheric pressure will be path-breaking contribution to the fundamental understanding of ion manipulations and separations and will also enable novel science currently precluded due to the inability of the present technologies to confine ions under ambient conditions. Traditionally used radio frequency fields are ineffective in confining ions at high pressures due to ion/neutral collisions. To address these, we propose to (a) develop methods for confining and manipulating ions for lossless IMS separations at atmospheric pressure enabling high sensitivity and throughput and (b) use the high specificity of IMS/MS and high throughput from ambient ion confinement to perform mobility and mass selective ion deposition at atmospheric pressure. Our goal is to enable the study of the fundamental properties of energy/catalysis materials and biomolecules. This project paves the way for high-throughput, mass and structure selective material deposition for highly specific surface creation/functionalization (discussed in Section 2 of the report). Further, the developments reported continue to push the boundaries of this process to ambient conditions (discussed in Section 3 of the report). We conclude with a list of specific intellectual property and publications which have been the outcome of this funded project.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth, provide nutrients, or confer pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and assembled stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. Here, this review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.

Clauer, Phillip [Massachusetts Inst. of Technology↗

DOE OSTI2021

Enhanced Diffusive Transport in Fluctuating Porous Media

Mass transport within porous structures is a ubiquitous process in biological, geological, and technological systems. Despite the importance of these phenomena, there is no comprehensive theory that describes the complex and diverse transport behavior within porous environments. While the porous matrix itself is generally considered a static and passive participant, many porous environments are in fact dynamic, with fluctuating walls, pores that open and close, and dynamically changing cross-links. While diffusion has been measured in fluctuating structures, notably in model biological systems, it is rarely possible to isolate the effect of fluctuations because of the absence of control experiments involving an identical static counterpart, and it is generally impossible to observe the dynamics of the structure. In this paper, we present a direct comparison of the diffusion of nanoparticles of various sizes within a trackable, fluctuating porous matrix and a geometrically equivalent static matrix, in conditions spanning a range of regimes from obstructed to highly confined. The experimental system comprised a close-packed layer of colloidal spheres that were either immobilized to a planar surface or allowed to fluctuate locally, within the space defined by their nearest neighbors. Interestingly, the effective long-time diffusion coefficient was approximately 35–65% greater in the fluctuating porous matrix than in the static one (depending on the size of the nanoparticle probes), regardless of the geometric regime. This was explained by considering the enhancing effects of matrix fluctuations on the short-time diffusion coefficient and cooperative “gate-opening” motions of matrix particles and nanoparticle probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Fast automated energy changes at synchrotron radiation beamlines equipped with transfocator or focusing mirrors

Algorithms and procedures to fully automate retuning of synchrotron radiation beamlines over wide energy ranges are discussed. The discussion is based on the implementation at the National Institute of General Medical Sciences and the National Cancer Institute Structural Biology Facility at the Advanced Photon Source. When a user selects a new beamline energy, software synchronously controls the beamline monochromator and undulator to maintain the X-ray beam flux after the monochromator, preserves beam attenuation by determining a new set of attenuator foils, changes, as needed, mirror reflecting stripes and the undulator harmonic, preserves beam focal distance of compound refractive lens focusing by changing the In/Out combination of lenses in the transfocator, and, finally, restores beam position at the sample by on-the-fly scanning of either the Kirkpatrick–Baez mirror angles or the transfocator up/down and inboard/outboard positions. The sample is protected from radiation damage by automatically moving it out of the beam during the energy change and optimization.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1998

Integration of GIS, Geostatistics, and 3-D Technology to Assess the Spatial Distribution of Soil Moisture

The spatial and temporal distribution of near surface soil moisture is of fundamental importance to many physical, biological, biogeochemical, and hydrological processes. However, knowledge of these space-time dynamics and the processes which control them remains unclear. The integration of geographic information systems (GIS) and geostatistics together promise a simple mechanism to evaluate and display the spatial and temporal distribution of this vital hydrologic and physical variable. Therefore, this research demonstrates the use of geostatistics and GIS to predict and display soil moisture distribution under vegetated and non-vegetated plots. The research was conducted at the Winfred Thomas Agricultural Experiment Station (WTAES), Hazel Green, Alabama. Soil moisture measurement were done on a 10 by 10 m grid from tall fescue grass (GR), alfalfa (AA), bare rough (BR), and bare smooth (BS) plots. Results indicated that variance associated with soil moisture was higher for vegetated plots than non-vegetated plots. The presence of vegetation in general contributed to the spatial variability of soil moisture. Integration of geostatistics and GIS can improve the productivity of farm lands and the precision of farming.

Betts, M.↗

NASA NTRS2000

Overview of Mars Sample Hazard Analysis (Requirements Workshop Series)

Samples returned from Mars should be contained and treated as though potentially hazardous until proven otherwise. If sample containment cannot be verified en route to Earth, the sample and spacecraft should either be sterilized in space or not returned to Earth. Integrity of sample containment should be maintained through reentry and transfer to a receiving facility. Controlled distribution of unsterilized materials should only occur if analyses determine the sample not to contain a biological hazard. Planetary protection measures adopted for the first sample return should not be relaxed for subsequent missions without thorough scientific review and concurrence by an appropriate independent body.

Rummel, John D.↗

NASA NTRS2001

Introduction to Mars Sample Handling Workshop Series: Overview of Mars Sample Hazard Analysis

Samples returned from Mars should be contained and treated as though potentially hazardous until proven otherwise If sample containment cannot be verified en route to Earth, the sample and spacecraft should either be sterilized in space or not returned to Earth. Integrity of sample containment should be maintained through reentry and transfer to a receiving facility. Controlled distribution of unsterilized materials should only occur if analyses determine the sample not to contain a biological hazard. Planetary protection measures adopted for the first sample return should not be relaxed for subsequent missions without thorough scientific review and concurrence by an appropriate independent body

Rummel, John D.↗

NASA NTRS2013

Methods and apparatus for microwave tissue welding for wound closure

Methods and apparatus for joining biological tissue together are provided. In at least one specific embodiment, a method for joining biological tissue together can include applying a biological solder on a wound. A barrier layer can be disposed on the biological solder. An antenna can be located in proximate spatial relationship to the barrier layer. An impedance of the antenna can be matched to an impedance of the wound. Microwaves from a signal generator can be transmitted through the antenna to weld two or more biological tissue pieces of the wound together. A power of the microwaves can be adjusted by a control circuit disposed between the antenna and the signal generator. The heating profile within the tissue may be adjusted and controlled by the placement of metallic microspheres in or around the wound.

Arndt, G. Dickey↗

DOE OSTI2021

Plants with enhanced yield and methods of construction

Transgenic plants having enhanced yield and having enhanced seed yield are disclosed. The transgenic plants are transformed with a transgenic polynucleotide encoding one or more metabolic enzymes. The metabolic enzymes can be from any biological source. The transgenic polynucleotide(s) comprises a nucleic acid sequences encoding the metabolic enzymes under the control of functional plant promoters, the one or more metabolic enzymes are targeted to the plastids by the addition of plastid targeting signals. Optionally the functional plant promoters are seed specific promoters and the metabolic enzymes are targeted to the plastids by the addition of plastid targeting peptide heterologous to the metabolic enzymes. Methods of making the transgenic plants and transgenic polynucleotides are disclosed. The magnitude of the increases in seed yield achieved with these transgenic plants are simply unprecedented.

Malik, Meghna↗

DOE OSTI2024

Plants with enhanced yield and methods of construction

Malik, Meghna↗