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At least 1,603 records · Page 89

MicroED for rapid and comprehensive characterization of the unknown small molecule composition of crude plant and soil extracts

This project implemented at PNNL a method introduced recently for de novo structure elucidation of small organic molecules: Micro-Electron Diffraction (henceforth microED). Micro-ED is an alternative to X-ray diffraction (XRD) or Nuclear Magnetic Resonance (NMR) for atomic-resolution structure elucidation of small organic or biological molecules, and it can succeed in solving structures when these well-established methods fail. In particular, microED offers the possibility of determining structures from far smaller quantities of material than would be required for NMR or even XRD, or from substances that fail to form crystals suitable (i.e., large enough) for X-ray crystallography, because microED requires only microcrystalline samples: in principle, a single crystal with ca. 100 nm dimensions would be suitable. MicroED is performed typically with standard electron microscopy (EM) instrumentation. The substantial potential of microED has drawn significant attention and examples of its use to solve difficult structure elucidation problems where X-ray or NMR methods failed has been described recently.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Structure of the Human BK Ion Channel in Lipid Environment

Voltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage sensing, ligand binding, and channel opening, the structures of ion channels in various functional states and in lipid membrane environments need to be determined. Here, the random spherically constrained (RSC) single-particle cryo-EM method was employed to study human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure was determined at 3.5 Å resolution in the absence of Ca 2+ . Instead of the common fourfold symmetry observed in ligand-modulated ion channels, a twofold symmetry was observed in hBK in liposomes. Compared with the structure of isolated hSlo1 Ca 2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits also moved downwards relative to the two other subunits.

59 BASIC BIOLOGICAL SCIENCES↗

Laboratory and field studies of ice-nucleating particles from open-lot livestock facilities in Texas

Abstract. In this work, an abundance of ice-nucleating particles (INPs) from livestock facilities was studied through laboratory measurements from cloud-simulation chamber experiments and field investigation in the Texas Panhandle. Surface materials from two livestock facilities, one in the Texas Panhandle and another from McGregor, Texas, were selected as dust proxies for laboratory analyses. These two samples possessed different chemical and biological properties. A combination of aerosol interaction and dynamics in the atmosphere (AIDA) measurements and offline ice spectrometry was used to assess the immersion freezing mode ice nucleation ability and efficiency of these proxy samples at temperatures above −29 ∘C. A dynamic filter processing chamber was also used to complement the freezing efficiencies of submicron and supermicron particles collected from the AIDA chamber. For the field survey, periodic ambient particle sampling took place at four commercial livestock facilities from July 2017 to July 2019. INP concentrations of collected particles were measured using an offline freezing test system, and the data were acquired for temperatures between −5 and −25 ∘C. Our AIDA laboratory results showed that the freezing spectra of two livestock dust proxies exhibited higher freezing efficiency than previously studied soil dust samples at temperatures below −25 ∘C. Despite their differences in composition, the freezing efficiencies of both proxy livestock dust samples were comparable to each other. Our dynamic filter processing chamber results showed on average approximately 50 % supermicron size dominance in the INPs of both dust proxies. Thus, our laboratory findings suggest the importance of particle size in immersion freezing for these samples and that the size might be a more important factor for immersion freezing of livestock dust than the composition. From a 3-year field survey, we measured a high concentration of ambient INPs of 1171.6 ± 691.6 L−1 (average ± standard error) at −25 ∘C for aerosol particles collected at the downwind edges of livestock facilities. An obvious seasonal variation in INP concentration, peaking in summer, was observed, with the maximum at the same temperature exceeding 10 000 L−1 on 23 July 2018. The observed high INP concentrations suggest that a livestock facility is a substantial source of INPs. The INP concentration values from our field survey showed a strong correlation with measured particulate matter mass concentration, which supports the importance of size in ice nucleation of particles from livestock facilities.

58 GEOSCIENCES↗

OSSA Space Station Freedom science utilization plans

Long duration exposure to an essentially zero-gravity environment is a phenomenon exclusive to the Space Station Freedom that cannot be duplicated on Earth. The Freedom Station will offer periods of time on orbit extending to weeks and months rather than hours or days, allowing for in-depth space based research and analysis to a degree never before achieved. OSSA remains committed to exploiting the unique capabilities provided by the Space Station as well as other space-based facilities to study the nature of physical, chemical, and biological processes in a low-gravity environment and to apply these studies to advance science and applications in such fields as biomedical research, plant and animal physiology, exobiology, biotechnology, materials science, fluid physics, and combustion science. The OSSA focus is on progressive science investigations, many requiring hands-on scientist involvement using sophisticated experiment hardware. OSSA science utilization planning for the Freedom Station is firmly established. For this presentation, this planning is discussed in three general areas: OSSA goals and overall approach, the current and on-going program, and plans for space station utilization. In the first area, OSSA addresses its overall approach to space science research, its commitment to transition to Space Station Freedom, and its top-level strategy for the utilization of Freedom. The current and on-going program is next discussed, focusing on the various Spacelab series of missions which are providing the stepping-stones to Space Station Freedom. Selected science results from SLS-1 and USML-1 are cited which underline the value of properly outfitted laboratories in space in which crew-intensive experiment interactions are possible. The presentation is concluded with a discussion of top-level goals and strategies for utilizing the Freedom Station by OSSA's Life Sciences Division and its Microgravity Science and Applications Division.

Cressy, Philip J.↗

Considerations for Life Science experimentation on the Space Shuttle

The conduct of Life Science experiments aboard the Shuttle Spacelab presents unaccustomed challenges to scientists. Not only is one confronted with the challenge of conducting an experiment in the unique microgravity environment of a orbiting spacecraft, but there are also the challenges of conducing experiments remotely, using equipment, techniques, chemicals, and materials that may differ from those standardly used in ones own laboratory. Then there is the question of "controls." How does one study the effects of altered gravitational fields on biological systems and control for other variables like vibration, acceleration, noise, temperature, humidity, and the logistics of specimen transport? Typically, the scientist new to space research has neither considered all of these potential problems nor has the data at hand with which to tackle the problems. This paper will explore some of these issues and provide pertinent data from recent Space Shuttle flights that will assist the new as well as the experienced scientist in dealing with the challenges of conducting research under spaceflight conditions.

Flight Experiment↗

Radiation exposure for human Mars exploration

One major obstacle to human space exploration is the possible limitations imposed by the adverse effects of long-term exposure to the space environment. Even before human space flight began, the potentially brief exposure of astronauts to the very intense random solar energetic particle events was of great concern. A new challenge appears in deep-space exploration from exposure to the low-intensity heavy-ion flux of the galactic cosmic rays since the missions are of long duration, and accumulated exposures can be high. Because cancer induction rates increase behind low to moderate thicknesses of aluminum shielding, according to available biological data on mammalian exposures to galactic cosmic ray-like ions, aluminum shield requirements for a Mars mission may be prohibitively expensive in terms of mission launch costs. Alternative materials for vehicle construction are under investigation to provide lightweight habitat structures with enhanced shielding properties. In the present paper, updated estimates for astronaut exposures on a Mars mission are presented and shielding properties of alternative materials are compared with aluminum.

NASA Center LaRC↗

Ultrasonic wave velocity measurement in small polymeric and cortical bone specimens

A system was refined for the determination of the bulk ultrasonic wave propagation velocity in small cortical bone specimens. Longitudinal and shear wave propagations were measured using ceramic, piezoelectric 20 and 5 MHz transducers, respectively. Results of the pulse transmission technique were refined via the measurement of the system delay time. The precision and accuracy of the system were quantified using small specimens of polyoxymethylene, polystyrene-butadiene, and high-density polyethylene. These polymeric materials had known acoustic properties, similarity of propagation velocities to cortical bone, and minimal sample inhomogeneity. Dependence of longitudinal and transverse specimen dimensions upon propagation times was quantified. To confirm the consistency of longitudinal wave propagation in small cortical bone specimens (< 1.0 mm), cut-down specimens were prepared from a normal rat femur. Finally, cortical samples were prepared from each of ten normal rat femora, and Young's moduli (Eii), shear moduli (Gij), and Poisson ratios (Vij) were measured. For all specimens (bone, polyoxymethylene, polystyrene-butadiene, and high-density polyethylene), strong linear correlations (R2 > 0.997) were maintained between propagation time and distance throughout the size ranges down to less than 0.4 mm. Results for polyoxymethylene, polystyrene-butadiene, and high-density polyethylene were accurate to within 5 percent of reported literature values. Measurement repeatability (precision) improved with an increase in the wave transmission distance (propagating dimension). No statistically significant effect due to the transverse dimension was detected.

Non-NASA Center↗

Deep cytoplasmic rearrangements in ventralized Xenopus embryos

Following fertilization in Xenopus, dramatic rearrangements of the egg cytoplasm relocalize maternally synthesized egg components. During the first cell cycle the vegetal yolk mass rotates relative to the egg surface, toward the sperm entry point (SEP) (J. P. Vincent, G. F. Oster, and J. C. Gerhart, 1986, Dev. Biol. 113, 484-500), while concomitant deep cytoplasmic rearrangements occur in the animal hemisphere (M. V. Danilchik and J. M. Denegre, 1991, Development 111, 845-856). In this paper we examine the role of vegetal yolk mass rotation in producing the animal cytoplasmic rearrangements. We inhibited rotation by uv-irradiating embryos during the first cell cycle, a treatment that yields an extremely ventralized phenotype. Both uv-irradiated embryos and unirradiated control embryos show cytoplasmic rearrangements in the animal hemisphere during the first cell cycle. Cytoplasmic rearrangements on the SEP side of the embryo associated with the path of the sperm pronucleus, plus a swirl on the anti-SEP (dorsal) side, are seen, whether or not yolk mass rotation has occurred. This result suggests a role for the expanding sperm aster in directing animal hemisphere cytoplasmic movements. In unirradiated control embryos the anti-SEP (dorsal) swirl is larger than that in uv-irradiated embryos and often extends into the vegetal hemisphere, consistent with the animal cytoplasm having been pulled dorsally and vegetally by the sliding vegetal yolk mass. Thus the yolk mass rotation may normally enhance the dorsalward cytoplasmic movement, begun by the sperm aster, enough to induce normal axis formation. We extended our observations of unirradiated control and uv-irradiated embryos through early cleavages. The vegetal extent of the anti-SEP (dorsal) swirl pattern seen in control embryos persists through the early cleavage period, such that labeled animal cytoplasm extends deep into dorsal third-tier blastomeres at the 32-cell stage. Significantly, in uv-irradiated embryos, which have not undergone vegetal rotation, most of this labeled material remains more equatorial.

Non-NASA Center↗

Connecting research and teaching introductory cell and molecular biology using an Arabidopsis mutant screen

A complex research project was translated into a Course-based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth-inhibiting, lipid-derived plant hormone and mutagenized this line. Students in the CURE cultured the mutagenized plant population and selected and characterized suppressor mutants. They learned to observe phenotypes related to the biosynthesis and perception of the plant hormone and explored the genetic and biochemical basis of these phenotypes. As the students studied the relevant genetic, molecular and biochemical concepts during this CURE, they were able to translate this knowledge into practice and develop scientific arguments. This CURE was a successful collaboration between the teaching lab and the research lab. It benefited both parties as the students had a real-life, deep learning experience in scientific methodology, while the research lab gathered data and materials for further studies

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds

The current extraction and use of fossil fuels has been linked to extensive negative health and environmental outcomes. Lignocellulosic biomass-derived biofuels and bioproducts are being actively considered as renewable alternatives to the fuels, chemicals, and materials produced from fossil fuels. A major challenge limiting large-scale, economic deployment of second-generation biorefineries is the insufficient product yield, diversity, and value that current conversion technologies can extract from lignocellulose, in particular from the underutilized lignin fraction. Rhodococcus opacus PD630 is an oleaginous gram-positive bacterium with innate catabolic pathways and tolerance mechanisms for the inhibitory aromatic compounds found in depolymerized lignin, as well as native or engineered pathways for hexose and pentose sugars found in the carbohydrate fractions of biomass. As a result, R. opacus holds potential as a biological chassis for the conversion of lignocellulosic biomass into biodiesel precursors and other value-added products. This review begins by examining the important role that lignin utilization will play in the future of biorefineries and by providing a concise survey of the current lignin conversion technologies. The genetic machinery and capabilities of R. opacus that allow the bacterium to tolerate and metabolize aromatic compounds and depolymerized lignin are also discussed, along with a synopsis of the genetic toolbox and synthetic biology methods now available for engineering this organism. Finally, we summarize the different feedstocks that R. opacus has been demonstrated to consume, and the high-value products that it has been shown to produce. Engineered R. opacus will enable lignin valorization over the coming years, leading to cost-effective conversion of lignocellulose into fuels, chemicals, and materials.

09 BIOMASS FUELS↗

Design of materials with supramolecular polymers

One hundred years ago Hermann Staudinger was strongly criticized by his scientific peers for his macromolecular hypothesis, but today it is hard to imagine a world without polymers. His hypothesis described polymers as macromolecules composed of large numbers of structural units connected by covalent bonds. In the 1990s the concept of supramolecular polymers emerged in the scientific literature as discrete entities of large molar mass comparable to that of classical polymers but built through non-covalent bonds among monomers. Supramolecular polymers exist in biological systems, and potentially blend the physical properties of covalent polymers with unique features such as high degrees of internal order within the polymeric structure, defined shapes, and novel dynamics. This trend article provides a summary of seminal contributions in supramolecular polymerization and provides recent examples from the Stupp laboratory to demonstrate the potential applications of an exciting class of materials composed fully or partially of supramolecular polymers. Finally, in closing, we provide our perspective on future opportunities provided by this field at the onset of a second century of polymers. It is our objective here to demonstrate that this second century could be as prosperous, if not more so, than the preceding one.

36 MATERIALS SCIENCE↗

EPA's Suite of Tools for Managing Waste Following a Large-Scale Incident - 19420

Large-scale disasters have the potential to generate a significant amount of waste. For example, Hurricane Katrina and the Joplin Missouri tornado resulted in 100 million and 1.5 million cubic yards of waste respectfully. Man-made chemical, biological, radiological or nuclear (CBRN) incidents either by way of terrorism, war, or accidents have the potential to generate as much or more hazardous waste. Recovery is profoundly impacted by waste management issues. The quantification, segregation, transportation, and storage of waste can be an arduous and costly undertaking. Furthermore, these processes are intricately linked with decisions made throughout the recovery timeline. Therefore, the remediation, including waste management, must be holistically considered. Understanding these complex interactions can be facilitated by using models and tools that adhere to the 'system-of-systems' approach. To better understand and predict waste management issues the Environmental Protection Agency's (EPA's) Homeland Security Research Program (HSRP) is developing a suite of tools and resources for planning and recovery purposes. The waste management suite consists of four tools: - Incident Waste Decision Support Tool (I-WASTE): characterizes and produces order-of-magnitude estimates for the weight and volume of waste materials that may require management and/or disposal, as well as identifies and locates potential treatment and disposal facilities. - Waste Estimation Support Tool (WEST): estimates waste generated from remediation and cleanup activities following a wide-area radiological or biological incident; - Waste Storage and Staging Tool: identifies and prioritizes potential locations for staging and storing waste; - Waste Logistics Tool: estimates optimal routes with consideration to cost, time, and logistical requirements (e.g., resource demand, transportation type, access limitations, etc.) associated with transporting large volumes of waste from disaster-stricken areas to intermediate waste staging/temporary storage/on-site processing sites to off-site waste management facilities; and This paper will present EPA's waste management suite of tools, their purpose and application to large-scale incidents, and a case study demonstrating their use in a hypothetical scenario. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Targeted evolution of pinning landscapes for large superconducting critical currents

The ability of type II superconductors to carry large amounts of current at high magnetic fields is a key requirement for future design innovations in high-field magnets for accelerators and compact fusion reactors, and largely depends on the vortex pinning landscape comprised of material defects. The complex interaction of vortices with defects that can be grown chemically, e.g., self-assembled nanoparticles and nanorods, or introduced by postsynthesis particle irradiation precludes a priori prediction of the critical current and can result in highly nontrivial effects on the critical current. Here, we borrow concepts from biological evolution to create a vortex pinning genome based on a genetic algorithm, naturally evolving the pinning landscape to accommodate vortex pinning and determine the best possible configuration of inclusions for two different scenarios: a natural evolution process initiating from a pristine system and one starting with preexisting defects to demonstrate the potential for a postprocessing approach to enhance critical currents. Furthermore, the presented approach is even more general and can be adapted to address various other targeted material optimization problems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Thermodynamic and Kinetic Transitions of Liquids in Nanoconfinement

Core principles of chemistry are ubiquitously invoked to shed light on the nature of molecular level interactions in nanoconfined fluids, which play a pivotal role in a wide range of processes in geochemistry, biology, and engineering. A detailed understanding of the physicochemical processes involved in the flow, structural transitions, and freezing or melting behavior of fluids confined within nanometer-sized pores of solid materials is thus of enormous importance for both basic research and technological applications. This Account provides a perspective on new insights into the thermodynamic and kinetic transitions of nanoconfined fluids in their stable and metastable forms. After briefly introducing the unique properties of mesoporous silicas from the SBA, MCM, and FDU families that serve as the confinement matrices, combining highly ordered single and bimodal mesopore architectures with tunable pore sizes in the ~2-15 nm range and narrow size distributions, recent studies on melting/freezing behavior of water confined in these host matrices are reviewed. While differential scanning calorimetry (DSC) reveals a linear relationship between melting point depression and pore size (independent of the pore shape), as predicted by the Gibbs-Thomson relation, variable temperature 2 H wide-line nuclear magnetic resonance (NMR) spectroscopy studies confirm the core-shell model of water and give evidence for a layer-by-layer freezing mechanism, which gives rise to an apparent fragile-to-strong transition in the solidification dynamics. In contrast to the freezing/melting behavior of water, the effect of nanoconfinement on the glass transition of supercooled liquids is nonuniversal and the glass transition temperature T g can either increase or decrease with the dimensionality and extent of confinement. This nonuniversal behavior is exemplified by the two glass-forming molecular liquids, glycerol and ortho-terphenyl (OTP). While glycerol shows an increase in T g and a pronounced slowdown of the rotational dynamics of the constituent molecules due to a change in the molecular packing between the bulk and the confined liquid, OTP displays a linear and confining-media-dependent depression of T g with increased confinement that is strongly influenced by the pore-liquid interface characteristics. This Account concludes with a focus on recent experimental evidence of extreme spatial and dynamical heterogeneity in both freezing and glass transition processes. This discovery was enabled by the unique mesoporous structures of SBA-16 and FDU-5, possessing bimodal architectures with two interconnected pore types of different size and shape (spherical and cylindrical). For the very first time, two melting points for water and two glass transitions for supercooled OTP, corresponding to a specific pore type, were observed. Collectively, these observations strongly suggest a close mechanistic connection between the local fluctuations in the structure and dynamics of nanoconfined liquids. Finally, while the findings reviewed in this Account provide new insights into thermodynamic and kinetic transitions of fluids, there remain many unanswered questions regarding the effects of nanoconfinement on the fundamental properties of fluids, which offer exciting future opportunities in chemical research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cellulose hydrolysis by Clostridium thermocellum is agnostic to substrate structural properties in contrast to fungal cellulases

The native recalcitrance of lignocellulosic biomass hinders its effective deconstruction for biological conversion to fuel ethanol. However, once cellulose is physically available to enzymes/microbes, i.e., macro-accessible, cellulose micro-accessibility, i.e., the accessibility as influenced by cellulose properties, further affects cellulose conversion. Here, we performed a comparative study of the effect of cellulose micro-accessibility on cellulose conversion by two biological approaches of potential commercial interest: consolidated bioprocessing (CBP) using Clostridium thermocellum and cell-free saccharification mediated by fungal enzymes. Commercially available cellulosic substrates, Avicel® PH-101, Sigmacell Cellulose Type 50, cotton linters, Whatman™ 1 milled filter paper, and α-cellulose were employed to constitute different cellulose micro-accessibilities. Physiochemical characterization was performed on these substrates to determine key morphological and chemical differences. Biological conversion of these substrates showed that C. was unaffected overall by cellulose structural properties, i.e., micro-accessibility, and achieved similar solids solubilization and metabolite production from these structurally different materials. However, fungal enzymes digested these substrates to different extents. Specifically, glucan conversion of these substrates diminished in the following order: milled filter paper > Avicel > Sigmacell and α-cellulose > cotton linters. Here, we propose that C. thermocellum digestion of lignocellulosic biomass is primarily controlled by the physical availability of cellulose in the lignocellulosic matrix and largely unaffected by cellulose properties once cellulose is made macro-accessible. Finally, in contrast, fungal enzymes require cellulose to be physically accessible, i.e., macro-accessible, as well as have properties amenable to digestion, i.e., micro-accessible.

09 BIOMASS FUELS↗

Genome organization and botanical diversity

Abstract The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes—both in content and in dynamics—has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.

Biochemistry & Molecular Biology↗

Compressive properties of silicone Bouligand structures

Abstract This article presents an examination of silicone, Bouligand lattices in compression. Appearing frequently in biological organisms and manufacturing design, Bouligand structures comprise layers of parallel strands or fibers oriented in a helical fashion. They can exhibit exceptional fracture resistance when composed of rigid or composite materials. The behavior of elastomeric Bouligand structures, however, is less well understood. Additively manufactured (AM) elastomeric lattices have applications in stress mitigation, medical devices, and soft robotics. This article demonstrates that Bouligand structures are a useful addition to the design space of AM elastomers. By adjusting the layer-rotation parameters, lattice stress can increase by more than 300% without altering the porosity. Additionally, we introduce path length metrics that help explain the observed relationship between layer rotation and compression response. Impact statement Additive manufacturing (AM) continues to push the boundary of manufacturable structures and enhance the ability to robustly design for specific properties and behaviors. The more we understand the design space of a novel AM microstructure, the greater its application range. In this article, we describe the mechanical behavior of helicoidal, elastomeric lattices and introduce path length metrics to help explain their stress response. We show that these structures can exhibit a large range of mechanical behaviors in compression, making them well suited for applications such as stress mitigation and impact absorption. Additionally, the path length metrics could become useful design tools and may be applicable to a larger set of cellular structures. These findings expand our ability to rapidly design materials with highly specific and customizable properties to meet the needs of modern engineering challenges. Graphical abstract

Van Meerbeek, I. M. (ORCID:000000021258132X)↗