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At least 361 records · Page 20

Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C(5) and C(6) sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of -xylosidase xylD slowed the growth of T. saccharolyticum on birchwood xylan and led to an accumulation of short-chain xylo-oligomers, no other single deletion, including the deletion of the previously characterized endoxylanase XynA, had a phenotype distinct from that of the wild type. This result indicates a multiplicity of xylanase enzymes which facilitate xylan degradation in T. saccharolyticum. Growth on xylan was prevented only when a previously uncharacterized endoxylanase encoded by xynC was also deleted in conjunction with xynA. Sequence analysis of xynC indicates that this enzyme, a low-molecular-weight endoxylanase with homology to glycoside hydrolase family 11 enzymes, is secreted yet untethered to the cell wall. Together, these observations expand our understanding of the enzymatic basis of xylan hydrolysis by T. saccharolyticum.

Podkaminer, Kara K↗

Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002

Synechococcus sp. PCC 7002 was grown to steady state in optically thin turbidostat cultures under conditions for which light quantity and quality was systematically varied by modulating the output of narrow-band LEDs. Cells were provided photons absorbed primarily by chlorophyll (680 nm) or phycocyanin (630 nm) as the organism was subjected to four distinct mono- and dichromatic regimes. During cultivation with dichromatic light, growth rates displayed by Synechococcus sp. PCC 7002 were generally proportional to the total incident irradiance at values < 275 µmol photons m-2 s-1 and were not affected by the ratio of 630:680 nm wavelengths. Notably, under monochromatic light conditions, cultures exhibited similar growth rates only when they were irradiated with 630 nm light; cultures irradiated with only 680 nm light grew at rates that were 60 – 70% of those under other light quality regimes at equivalent irradiances. The functionality of photosystem II and associated processes such as maximum rate of photosynthetic electron transport, rate of cyclic electron flow, and rate of dark respiration generally increased as a function of growth rate. Nonetheless, some of the photophysiological parameters measured here displayed distinct patterns with respect to growth rate of cultures adapted to a single wavelength including phycobiliprotein content, which increased under severely light-limited growth conditions. Additionally, the ratio of photosystem II to photosystem I increased approximately 40% over the range of growth rates, although cells grown with 680 nm light only had the highest ratios. These results suggest the presence of effective mechanisms which allow acclimation of Synechococcus sp. PCC 7002 acclimation to different irradiance conditions.

chlorophyll↗

Identification of PAH Isomeric Structure in Cosmic Dust Analogs: The AROMA Setup

We developed a new analytical experimental setup called AROMA (Astrochemistry Research of Organics with Molecular Analyzer) that combines laser desorption/ionization techniques with ion trap mass spectrometry. We report here on the ability of the apparatus to detect aromatic species in complex materials of astrophysical interest and characterize their structures. A limit of detection of 100 femto-grams has been achieved using pure polycyclic aromatic hydrocarbon (PAH) samples, which corresponds to 2 × 10{sup 8} molecules in the case of coronene (C{sub 24}H{sub 12}). We detected the PAH distribution in the Murchison meteorite, which is made of a complex mixture of extraterrestrial organic compounds. In addition, collision induced dissociation experiments were performed on selected species detected in Murchison, which led to the first firm identification of pyrene and its methylated derivatives in this sample.

79 ASTRONOMY AND ASTROPHYSICS↗

Metabolic Suppression: A Promising Solution to Unlock the Future of Space Travel

Space tourism is no longer a distant dream but a present-day reality, with current excursions consisting of suborbital jaunts, and near future excursions to including lunar expeditions and, eventually, trips to Mars. Beneath the allure of weightlessness and cosmic views, however, lies a set of serious health risks for space travelers, including muscle and bone issues, heart problems, and cognitive impairment. In this mini review, we delve into the topic of metabolic suppression, an innovative approach to mitigating the deleterious effects of space travel that has been proposed for astronauts that may be appropriate for space tourists as well. Drawing inspiration from the survival strategies observed in hibernating animals and often depicted in sci-fi narratives where crews are in “suspended animation” throughout most of the voyage, this method involves inducing a reversible state of dormancy, akin to torpor, in human space travelers. The objective of metabolic suppression is to safeguard space travelers from the adverse impacts of extended exposure to microgravity and space radiation on long duration expeditions, so that on arrival at their destination, they can be healthy and ready to go. We shed light on ongoing research endeavors led by the National Aeronautics and Space Administration (NASA), the European Space Agency (ESA), and other prominent organizations dedicated to investing in and advancing metabolic suppression technologies for professional space travel, that may also enable space tourism to ever more distant destinations

Space Tourism↗

Integrating the Fields of Catalysis: Active Site Engineering in Metal Cluster, Metal Organic Framework and Metal Single Site

Research evolved using nanoparticles synthesized and characterized under reaction conditions opened the door to study all three fields of catalysis: heterogeneous, homogenous, and enzyme. Fundamental studies of catalytic reactions ranging from hydrogenation to understand Fischer-Tropsch synthesis and isomerization ultimately led to the integration of three fields of catalysis. Our recent work on bridging heterogeneous, homogenous, and enzymatic catalysis was present including functionalization of dendrimer encapsulated metal clusters surface for lactonization, active site engineering in metal organic framework catalysts for methanol production and oligomerization, and single site catalyst for hydrogen production. We envision that the combination of active site engineering and unifying fields of catalysis could be applied to solve practical issues of science-based technology and develop new fields useful in energy research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparative toxicity assessment of novel Si quantum dots and their traditional Cd-based counterparts using bacteria models Shewanella oneidensis and Bacillus subtilis

Quantum dots are crystalline semiconductor nanoparticles with unique optical properties due to quantum confinement effects. They have several advantages compared to traditional organic fluorescent dyes, such as high fluorescent brightness, photostability, and tunable emission wavelengths, dependent upon particle size. Their unique optical properties have led to an increased use in a variety of devices, including diode lasers and television displays, as well as in biomedical research. The most commonly used quantum dots (QDs) are made of cadmium selenide (CdSe) and have cadmium selenide core with zinc sulfide shell (CdSe/ZnS), containing inherently toxic cadmium. This work focuses on comparison of the toxic effects of conventional CdSe and CdSe/ZnS QDs and silicon QDs, which are emerging as a potentially benign alternative, using bacteria as model organisms. The bacteria models used for our studies are Shewanella oneidensis MR-1, a Gram-negative bacterium, and Bacillus subtilis SB 491, a Gram-positive bacterium. Furthermore, this research assesses changes in cell viability, respiration pattern, and cell membrane integrity in the presence of the nanoparticles using colony counting, respirometry and membrane integrity assays, respectively. The association of the QDs with bacterial cell membranes was investigated using transmission electron microscopy (TEM). Results indicate that the silicon QDs are benign to the bacteria considered, and they do not associate with the cell membranes. The CdSe cores exhibit significant toxicity to the bacterial cells, whereas the CdSe/ZnS QDs are comparatively less toxic.

54 ENVIRONMENTAL SCIENCES↗

Pyromellitic diimide based bipolar molecule for total organic symmetric redox flow battery

Non-aqueous redox flow batteries based on total organic electrolytes, consisting of earth-abundant elements, i.e., C, H, N, O, are regarded as a promising technology for sustainable and large-scale energy storage. In particular, bipolar redox-active organic materials (BROMs) are distinctly fascinating as electroactive species because they have multiple oxidation states and can undergo multiple redox processes. By virtue of this unique characteristic, BROMs can be utilized as both anolyte and catholyte in symmetric flow batteries, consequently, helping alleviate cross-contamination issues. Here, in this paper, we report an all-organic symmetric redox flow battery based on diimide molecule as a bipolar electroactive material. The potential interval between the cathodic peak and the inner and outer anodic peaks led to a promising cell voltage of 2.22 V. The symmetric battery can be operated at a current density of 20 mA cm -2 , with a coulombic efficiency of 90% for over 100 cycles. This work proposes an alternative approach to designing multi-electron organic redox active materials to facilitate the advancement of high-density symmetric flow batteries.

25 ENERGY STORAGE↗

Metal–Organic Frameworks as a Tunable Platform to Deconvolute Stereoelectronic Effects on the Catalytic Activity of Thioanisole Oxidation

The local environment of a metal active site plays an important role in affecting catalytic activity and selectivity. In re-cent studies, tailoring the behavior of a molybdenum-based active site via modulation of the first coordination sphere has led to improved thioanisole oxidation performance, but disentangling electronic effects from steric influences that arise from these modifications is nontrivial, especially in heterogeneous systems. To this end, the tunability of metal–organic frameworks (MOFs) makes them promising scaffolds for controlling the coordination sphere of a heterogene-ous, catalytically-active metal site while offering additional, attractive features such as crystallinity and high porosity. Herein, we report a variety of MOF-supported Mo species, which were investigated for catalytic thioanisole oxidation to methyl phenyl sulfoxide and/or methyl phenyl sulfone using tert-butyl hydroperoxide (tBHP) as the oxidant. In particular, MOFs of contrasting node architectures were targeted, presenting a unique opportunity to investigate ste-reoelectronic control of Mo active sites in a systematic manner. A Zr 6 -based MOF, NU-1000, was employed along with its sulfated analog Zr 6 -based NU-1000-SO 4 to anchor a dioxymolybdenum species, which enabled examination of sup-port-mediated active site polarizability on catalytic performance. In addition, a MOF containing a mixed metal node, Mo-MFU-4l, was used to probe the stereoelectronic impact of an N-donor ligand environment on the catalytic activity of the transmetalated Mo center. Furthermore, characterization techniques including single crystal X-ray diffraction, were concomi-tantly used with reaction kinetic profiles to better comprehend the dynamics of different Mo active sites, thus correlat-ing structural change with activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exchange interaction mechanisms in 1,3,5,7-tetramethyl-2,6-diazaadamantane N,N’-dioxyl biradical

The exchange interaction parameters were calculated and the spin density distribution over the organic skeleton of the 1,3,5,7-tetramethyl-2,6-diazaadamantane N,N’-dioxyl biradical was studied based on the results of quantum chemical modeling of the biradical structure by the DFT method using various hybrid functionals (UB3LYP, LC-wPBE, UCAM-B3LYP, UHSEH1PBE) with the 6-311++G(2d,2p) basis set and by the UHF method with the same basis set. The characteristics of the direct orbital overlap between the N atoms of the two nitroxide groups were determined. The values of the J constant, obtained using different calculation methods, were found to be similar to each other. It was established that there is ferromagnetic exchange interaction between the radical sites in the system in question, which occurs predominantly according to the spin polarization mechanism in the 2,6-diazaadamantane core, and the various spin density transfer pathways through the C atoms of the organic skeleton were found to be nonequivalent. The direct overlap of the upper singly-occupied МОs with localization on the nitroxide groups led to a noticeable additional contribution of the antiferromagnetic exchange interaction. Despite the latter factor, the total contribution of these two mechanisms (spin polarization and direct through-space exchange) resulted in the triplet ground state in the biradical studied.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies – two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy – and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

59 BASIC BIOLOGICAL SCIENCES↗

New Insights into Dynamics and Morphology of P3HT:PCBM Active Layers in Bulk Heterojunctions

Organic photovoltaics (OPVs) are topic of extensive research for their potential application in solar cells. Recent work has led to the development of a coarse-grained model for studying poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C 61 -butyric acid methyl ester (PCBM) blends with molecular simulations. Here we provide further validation of the force field and use it to study the thermal annealing process of P3HT:PCBM blends. A key finding of our study is that, in contrast to a previous report, the annealing process does not converge at the short time scales reported. Rather, we find that the self assembly of the blends is characterized by three rate dependent stages that require much longer simulations to approach convergence. Using state-of-the- art high performance computing, we are able to study annealing at length and time scales commensurate with devices used in experiments. Our simulations show different phase segregated morphologies dependent on the P3HT chain length and PCBM volume fraction in the blend. For short chain lengths, we observed a smectic morphology containing alternate P3HT and PCBM domains. In contrast, a phase segregated morphology containing domains of P3HT and PCBM distributed randomly in space is found for longer chain lengths. Theoretical arguments justifying stabilization of these morphologies due to shape anisotropy of P3HT (rod-like) and PCBM (sphere-like) are presented. Furthermore, results on structure factor, miscibility of P3HT and PCBM, domain spacing and kinetics of phase segregation in the blends are presented in detail. Qualitative comparison of these results with small-angle neutron scattering experiments from literature is presented and an excellent agreement is found.

14 SOLAR ENERGY↗

Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)

Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.

60 APPLIED LIFE SCIENCES↗

Development of an image converter of radical design

A long term investigation of thin film sensors, monolithic photo-field effect transistors, and epitaxially diffused phototransistors and photodiodes to meet requirements to produce acceptable all solid state, electronically scanned imaging system, led to the production of an advanced engineering model camera which employs a 200,000 element phototransistor array (organized in a matrix of 400 rows by 500 columns) to secure resolution comparable to commercial television. The full investigation is described for the period July 1962 through July 1972, and covers the following broad topics in detail: (1) sensor monoliths; (2) fabrication technology; (3) functional theory; (4) system methodology; and (5) deployment profile. A summary of the work and conclusions are given, along with extensive schematic diagrams of the final solid state imaging system product.

Irwin, E. L.↗

Space bio-technology in housing

Gas chromatography and mass spectrometry data obtained from monitoring atmospheric pollutants in Skylab spurred studies of indoor pollutants in terrestrial buildings. Subsequent studies of techniques for removing the pollutants from space habitats have led to building concepts which achieve the same purpose on earth. The Skylab data indicated that the synthesized organic materials used in many modern buildings, furnishings, personal clothing and aerosols add significant amounts of chemicals to the indoor atmosphere. Lowered circulation and ventilation rates to conserve energy have caused trapping of these substances in buildings. Studies of methods for space modules which will use plants and microbes to absorb airborne and wastewater pollutants have defined biotechnology designs which can be applied to remove pollutants from air and wastewater organically. Plant roots trap pollutants from wastewater and leaves readily absorb air pollutants, as well as improve the overall energy efficiency of buildings. Several designs which incorporate biotechnology to enhance both the aesthetics and efficiency of homes and office buildings are illustrated.

Wolverton, B. C.↗

Investigation of Strain/Vorticity and Large-Scale Flow Structure in Turbulent Nonpremixed Jet Flames

Our study will use the microgravity environment to investigate the underlying flow structure of turbulent nonpremixed round jet flames. In particular, we aim to investigate the large-scale turbulent structure using planar laser Mie scattering (PLMS), and the strain rate and vorticity fields using particle image velocimetry (PIV). This work is motivated by recent studies in our laboratory that have led to several interesting observations of nominally momentum-driven turbulent nonpremixed planar flames. First of all, the organized large-scale turbulent structures that are observed in nonreacting planar jets may be substantially modified or suppressed in nonpremixed planar jet flames. Furthermore, a recent study using PIV and planar laser-induced fluorescence of OH has shown that in transitional and turbulent nonpremixed planar jet flames the presence of the flame seems to greatly influence the underlying vorticity and strain fields, as compared to nonreacting jets. For example, the reaction zones in the jet flames are strongly correlated with regions of high vorticity. A related study has demonstrated that vorticity is not correlated in the same way with either iso-scalar surfaces or scalar dissipation layers in nonreacting planar jets. Furthermore, the relationship between strain and the reaction zone appears to be modified by the presence of high levels of heat release. In particular, the strain rate field in planar jet flames exhibits a preferred direction of principal compressive strain that apparently is related to strong shear across the reaction zone. This preferred direction of strain was not observed in nonreacting jets. One of the major problems encountered when conducting these types of studies is that it is difficult to know to what extent buoyancy influences the results. Therefore, the microgravity environment provides us with an excellent opportunity to explore these issues without the complicating effects of buoyancy. This is particularly the case when studying flames that are transitional between laminar and turbulent states. For example, the strong correlation of vorticity with the reaction zone (discussed above) was observed in both transitional and turbulent planar flames, but the effect was stronger for the transitional case. To date, the reason for the presence of the vorticity-reaction zone correlation is not known, although vorticity production via baroclinic torque is a likely cause. The microgravity environment will allow us to specifically determine whether the vorticity is produced by baroclinic torque resulting from the flame density gradient acting with the hydrostatic pressure gradient.AAdditional details of the planned experiments are provided.

Clemens, N. T.↗

Heating of the Solar Corona and its Loops

At several million degrees, the solar corona is more than two orders of magnitude hotter than the underlying solar surface. The reason for these extreme conditions has been a puzzle for decades and is considered one of the fundamental problems in astrophysics. Much of the coronal plasma is organized by the magnetic field into arch-like structures called loops. Recent observational and theoretical advances have led to great progress in understanding the nature of these loops. In particular, we now believe they are bundles of unresolved magnetic strands that are heated by storms of impulsive energy bursts called nanoflares. Turbulent convection at the solar surface shuffles the footpoints of the strands and causes them to become tangled. A nanoflare occurs when the magnetic stresses reach a critical threshold, probably by way of a mechanism called the secondary instability. I will describe our current state of knowledge concerning the corona, its loops, and how they are heated.

Klimchuk, James A.↗

British Petroleum's Deepwater Horizon Accident and the Thinking, Engaged Workforce - 13265

On April 20, 2010, hydrocarbons escaped from the Macondo well into Transocean's Deepwater Horizon, resulting in fire and multiple explosions. 11 people on the rig died. The billion dollar Deepwater Horizon sank. 4.9 M gallons of product flowed from the well for 87 days creating an environmental nightmare for communities bordering on the Gulf of Mexico. BP established a $20 B reserve to pay for damages. Investigations and legal culpability continue to this day. In September 2010, the Institute for Nuclear Power Operators (INPO) issued Significant Operating Experience Report (SOER) 10-2, Engaged, Thinking Organizations. The industry had experienced 11 events, 9 in US commercial nuclear utilities, and 2 international, that had disturbing trends. The underlying causes highlighted by INPO were inadequate recognition of risk, weaknesses in application of significant operating experience, tolerance of equipment and personnel problems, and a significant drift in standards. While the noted INPO problems and the Deepwater Horizon event appear to have nothing in common, they do exhibit similarities in a drift away from expected behavior on the part of front line workers and their supervisors. At the same time, hidden hazards are accumulating in the environment leading to error intolerant conditions. Without a good understanding of this concept, many organizations tend to focus on the person who 'touched it last', while missing the deeper organizational factors that led that individual to think that what they were doing was correct. An understanding of this failure model is important in reconstruction of events and crafting effective corrective actions. It is much more important, however, for leaders in high hazard industries to recognize when they are approaching error intolerant conditions and take steps immediately to add safety margin. (authors)

02 PETROLEUM↗