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DOE OSTI2018

Enhancing hydrogen‐dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation

Abstract Synthesis gas (syngas) fermentation via the Wood–Ljungdahl pathway is receiving growing attention as a possible platform for the fixation of and renewable production of fuels and chemicals. However, the pathway operates near the thermodynamic limit of life, resulting in minimal adenosine triphosphate (ATP) production and long doubling times. This calls into question the feasibility of producing high‐energy compounds at industrially relevant levels. In this study, we investigated the possibility of co‐utilizing nitrate as an inexpensive additional electron acceptor to enhance ATP production during ‐dependent growth of Clostridium ljungdahlii , Moorella thermoacetica , and Acetobacterium woodii . In contrast to other acetogens tested, growth rate and final biomass titer were improved for C. ljungdahlii growing on a mixture of and when supplemented with nitrate. Transcriptomic analysis, labeling, and an electron balance were used to understand how electron flux was partitioned between and nitrate. We further show that, with nitrate supplementation, the ATP/adenosine diphosphate (ADP) ratio and acetyl‐CoA pools were increased by fivefold and threefold, respectively, suggesting that this strategy could be useful for the production of ATP‐intensive heterologous products from acetyl‐CoA. Finally, we propose a pathway for enhanced ATP production from nitrate and use this as a basis to calculate theoretical yields for a variety of products. This study demonstrates a viable strategy for the decoupling of ATP production from carbon dioxide fixation, which will serve to significantly improve the fixation rate and the production metrics of other chemicals from and in this host.

Emerson, David F.↗

DOE OSTI2015

Application of electroretinography (ERG) in early drug development for assessing retinal toxicity in rats

Retinal ocular toxicity is among the leading causes of drug development attrition in the pharmaceutical industry. Electroretinography (ERG) is a non-invasive functional assay used to assess neuro-retinal physiological integrity by measuring the electrical responses. To directly assess the utility of ERG, a series of studies was conducted following intravitreal and/or iv administration of pan-cyclin-dependent kinase inhibitors: AG-012,986 and AG-024,322 in rats. Both compounds have previously shown to induce retinal toxicity. Retinal injury was evaluated by ERG, histopathology and TUNEL staining. Intravitreal injection of AG-012,986 at ≥ 10 μg/eye resulted in decreases (60%) in ERG b-wave and microscopic changes of mild to moderate retinal degeneration, and at 30 μg/eye led to additional ophthalmic findings. Intravenous administration of AG-012,986 daily at ≥ 5 mg/kg resulted in dose-related decreases (25 to 40%) in b-wave and sporadic to intense positive TUNEL staining. Intravitreal injection of AG-024,322 at 30 μg/eye also resulted in decreases (50 to 60%) in b-wave, mild to marked retinal degeneration and mild vitreous debris. These experiments demonstrate that ERG can be used as a sensitive and reliable functional tool to evaluate retinal toxicity induced by test compounds in rats complementing other classical ocular safety measurements. - Highlights: • There were strong correlations of ERG readouts to in vivo ophthalmic exams, TUNEL assay, and histopathology. • ERG appears to be more sensitive and can detect retinal functional changes at a very early stage of pathogenesis. • ERG can be incorporated into routine exploratory toxicity study to identify compound ocular safety issues. • In drug discovery, ERG is a quick, non-invasive, sensitive and reliable tool in retinal toxicity de-risking.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Proton-Coupled Electron Transfer to a Molybdenum Ethylene Complex Yields a β-Agostic Ethyl: Structure, Dynamics and Mechanism

In this paper, the interconversion of molybdenum ethylene and ethyl complexes by proton-coupled electron transfer (PCET) is described, an unusual transformation in organometallic chemistry. The cationic molybdenum ethylene complex [( Ph Tpy)(PPh 2 Me) 2 Mo(C 2 H 4 )][BArF 24 ] ([1-C 2 H 4 ] + ; Ph Tpy = 4'-Ph-2,2',6',2"-terpyridine, ArF 24 = [C 6 H 3 -3,5-(CF 3 ) 2 ] 4 ) was synthesized, structurally characterized, and its electronic structure established by a combination of spectroscopic and computational methods. The overall electronic structure is best described as a molybdenum(III) complex with a metallacyclopropane and a redox neutral terpyridine ligand. Addition of the nonclassical ammine complex [( Ph Tpy)(PPh 2 Me) 2 Mo(NH 3 )][BArF 24 ] ([1-NH 3 ] + ) to [1-C 2 H 4 ] + resulted in a net C–H bond-forming PCET reaction to yield the molybdenum ethyl [( Ph Tpy)(PPh 2 Me) 2 Mo(CH 2 CH 3 )][BArF 24 ] ([1-CH 2 CH 3 ] + ) and amido [( Ph Tpy)(PPh 2 Me) 2 Mo(NH 2 )][BArF 24 ] ([1-NH 2 ] + ) compounds. The reaction was reversed by addition of 2,4,6-tritert-butylphenoxyl radical to [1-CH 2 CH 3 ] + . The solid-state structure of [1-CH 2 CH 3 ] + established a β-agostic ethyl ligand that is maintained in solution as judged by variable temperature 1 H and 13 C NMR experiments. A combination of variable-temperature NMR experiments and isotopic labeling studies were used to probe the dynamics of [1-CH 2 CH 3 ] + and established restricted β-agostic -CH 3 rotation at low temperature (ΔG ‡ = 9.8 kcal mol –1 at -86 °C) as well as ethyl isomerization by β-hydride elimination-olefin rotation-reinsertion (ΔH ‡ = 19.3 ± 0.6 kcal mol –1 ; ΔS ‡ = 3.4 ± 1.7 cal mol –1 K –1 ). The β-(C–H) bond-dissociation free energy (BDFE) in [1-CH 2 CH 3 ] + was determined experimentally as 57 kcal mol –1 (THF) supported by a DFT-computed value of 52 kcal/mol –1 (gas phase). Comparison of pK a and electrochemical data for the complexes [1-C 2 H 4 ] + and [1-NH 3 ] + in combination with a deuterium kinetic isotope effect (k H /k D ) of 3.5(2) at 23 °C support a PCET process involving initial electron transfer followed by protonation leading to the formation of [1-CH 2 CH 3 ] + and [1-NH 2 ] + or a concerted pathway. Lastly, the data presented herein provides a structural, thermochemical and mechanistic foundation for understanding the PCET reactivity of organometallic complexes with alkene and alkyl ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1983

Simulation of Viking biology experiments suggests smectites not palagonites, as martian soil analogues

An experimental comparison of palagonites and a smectite (montmorillonite) was performed in a simulation of the Viking Biology Labelled Release (LR) experiment in order to judge which mineral is a better Mars soil analog material (MarSAM). Samples of palagonite were obtained from cold weathering environments and volcanic soil, and the smectite was extracted from Wyoming Bentonite and converted to H or Fe types. Decomposition reaction kinetics were examined in the LR simulation, which on the Lander involved interaction of the martian soil with organic compounds. Reflectance spectroscopy indicated that smectites bearing Fe(III) in well-crystallized sites are not good MarSAMS. The palagonites did not cause the formate decomposition and C-14 emission detected in the LR, indicating that palagonites are also not good MarSAMS. Smectites, however, may be responsible for ion exchange, molecular adsorption, and catalysis in martian soil.

Banin, A.↗

DOE OSTI2017

Synthetic iron (hydr)oxide-glucose associations in subsurface soil: Effects on decomposability of mineral associated carbon

Soils are a globally important reservoir of organic carbon. There is a growing understanding that interactions with soil mineral phases contribute to the accumulation and retention of otherwise degradable organic matter (OM) in soils and sediments. However, the bioavailability of organic compounds in mineral-organic-associations (MOAs), especially under varying environmental conditions is not well known. To assess the impact of mineral association and warming on the decomposition of an easily respirable organic substrate (glucose), we conducted a series of laboratory incubations at different temperatures with field-collected soils from 10 to 20 cm, 50–60 cm, and 80–90 cm depth. We added 13 C-labeled glucose either directly to native soil or sorbed to one of two synthetic iron (hydr)oxide phases (goethite and ferrihydrite) that differ in crystallinity and affinity for sorbing glucose. Here, we found that: (1) association with the Fe (hydr)oxide minerals reduced the decomposition rate of glucose by > 99.5% relative to rate of decomposition for free glucose in soil; (2) the respiration rate per gram carbon did not differ appreciably with depth, suggesting a similar degree of decomposability for native C across depths and that under the incubation conditions total carbon availability represents the principal limitation on respiration under these conditions as opposed to reduced abundance of decomposers or moisture and oxygen limitations; (3) addition of free glucose enhanced native carbon respiration at all soil depths with the largest effect at 50–60 cm; (4) in general respiration of the organo-mineral complex (glucose and iron-(hydr)oxide) was less temperature sensitive than was respiration of native carbon; (5) the addition of organic free mineral decreased the rate of soil respiration in the intermediate 50–60 cm depth soil. The results emphasize the key role of MOAs in regulating the fluxes of carbon from soils to the atmosphere and in turn the stocks of soil carbon.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1972

Compounds of the organogenic elements in Apollo 11 and 12 lunar samples - A review.

Investigations of low molecular weight compounds of the organogenic elements on lunar samples are reviewed. The three general techniques of vacuum pyrolysis, acid hydrolysis, and crushing have been employed by most investigators. Vacuum pyrolysis of lunar fines produce a variety of gaseous species which are either: (1) indigenous, (2) solar wind products and/or (3) chemical reaction products of mineral phases found in the lunar samples. Acid hydrolysis of lunar fines using deuterium-labeled acids yields evidence for indigenous methane and ethane. Methane and ethane found in the lunar fines are largely derived from the solar wind with only trace amounts indigenous to the samples. Crushing experiments with lunar fines and breccias produce methane, ethane, hydrogen, nitrogen, hydrogen sulfide and the rare gases.

Gibson, E. K., Jr.↗

NASA NTRS1993

Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities

Intertidal marine microbial mats exhibited biologically mediated uptake of low molecular weight dissolved organic matter (DOM), including D-glucose, acetate, and an L-amino acid mixture at trace concentrations. Uptake of all compounds occurred in darkness, but was frequently enhanced under natural illumination. The photosystem 2 inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) generally failed to inhibit light-stimulated DOM uptake. Occasionally, light plus DCMU-amended treatments led to uptake rates higher than light-incubated samples, possibly due to phototrophic bacteria present in subsurface anoxic layers. Uptake was similar with either 3H- or 14C-labeled substrates, indicating that recycling of labeled CO2 via photosynthetic fixation was not interfering with measurements of light-stimulated DOM uptake. Microautoradiographs showed a variety of pigmented and nonpigmented bacteria and, to a lesser extent, cyanobacteria and eucaryotic microalgae involved in light-mediated DOM uptake. Light-stimulated DOM uptake was often observed in bacteria associated with sheaths and mucilage surrounding filamentous cyanobacteria, revealing a close association of organisms taking up DOM with photoautotrophic members of the mat community. The capacity for dark- and light-mediated heterotrophy, coupled to efficient retention of fixed carbon in the mat community, may help optimize net production and accretion of mats, even in oligotrophic waters.

NASA Discipline Exobiology↗

DOE OSTI2017

Environmental exposure to human carcinogens in teenagers and the association with DNA damage

Background: We investigated whether human environmental exposure to chemicals that are labeled as (potential) carcinogens leads to increased (oxidative) damage to DNA in adolescents. Material and methods: Six hundred 14–15-year-old youngsters were recruited all over Flanders (Belgium) and in two areas with important industrial activities. DNA damage was assessed by alkaline and formamidopyrimidine DNA glycosylase (Fpg) modified comet assays in peripheral blood cells and analysis of urinary 8-hydroxydeoxyguanosine (8-OHdG) levels. Personal exposure to potentially carcinogenic compounds was measured in urine, namely: chromium, cadmium, nickel, 1-hydroxypyrene as a proxy for exposure to other carcinogenic polycyclic aromatic hydrocarbons (PAHs), t,t-muconic acid as a metabolite of benzene, 2,5-dichlorophenol (2,5-DCP), organophosphate pesticide metabolites, and di(2-ethylhexyl) phthalate (DEHP) metabolites. In blood, arsenic, polychlorinated biphenyl (PCB) congeners 118 and 156, hexachlorobenzene (HCB), dichlorodiphenyltrichloroethane (DDT) and perfluorooctanoic acid (PFOA) were analyzed. Levels of methylmercury (MeHg) were measured in hair. Multiple linear regression models were used to establish exposure-response relationships. Results: Biomarkers of exposure to PAHs and urinary chromium were associated with higher levels of both 8-OHdG in urine and DNA damage detected by the alkaline comet assay. Concentrations of 8-OHdG in urine increased in relation with increasing concentrations of urinary t,t-muconic acid, cadmium, nickel, 2,5-DCP, and DEHP metabolites. Increased concentrations of PFOA in blood were associated with higher levels of DNA damage measured by the alkaline comet assay, whereas DDT was associated in the same direction with the Fpg-modified comet assay. Inverse associations were observed between blood arsenic, hair MeHg, PCB 156 and HCB, and urinary 8-OHdG. The latter exposure biomarkers were also associated with higher fish intake. Urinary nickel and t,t-muconic acid were inversely associated with the alkaline comet assay. Conclusion: This cross-sectional study found associations between current environmental exposure to (potential) human carcinogens in 14–15-year-old Flemish adolescents and short-term (oxidative) damage to DNA. Prospective follow-up will be required to investigate whether long-term effects may occur due to complex environmental exposures. - Highlights: • Exposure to (potential) carcinogens is associated with (oxidative) damage to DNA. • Most associations of exposures are with urinary 8-OHdG. • 1-Hydroxypyrene and chromium are associated with the comet assay and 8-OHdG. • PFOA is associated with higher levels of DNA damage in the alkaline comet assay.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots

Abstract Background Nitrate (NO 3 − ) is one of the two major forms of inorganic nitrogen absorbed by plant roots, and the tissue nitrate concentration in roots is considered important for optimizing developmental programs. Technologies to quantify the expression levels of nitrate transporters and assimilating enzymes at the cellular level have improved drastically in the past decade. However, a technological gap remains for detecting nitrate at a high spatial resolution. Using extraction-based methods, it is challenging to reliably estimate nitrate concentration from a small volume of cells (i.e., with high spatial resolution), since targeting a small or specific group of cells is physically difficult. Alternatively, nitrate detection with microelectrodes offers subcellular resolution with high cell specificity, but this method has some limitations on cell accessibility and detection speed. Finally, optical nitrate biosensors have very good ( in-vivo ) sensitivity (below 1 mM) and cellular-level spatial resolution, but require plant transformation, limiting their applicability. In this work, we apply Raman microspectroscopy for high-dynamic range in-vivo mapping of nitrate in different developmental zones of Arabidopsis thaliana roots in-situ . Results As a proof of concept, we have used Raman microspectroscopy for in-vivo mapping of nitrate content in roots of Arabidopsis seedlings grown on agar media with different nitrate concentrations. Our results revealed that the root nitrate concentration increases gradually from the meristematic zone (~ 250 µm from the root cap) to the maturation zone (~ 3 mm from the root cap) in roots grown under typical growth conditions used for Arabidopsis, a trend that has not been previously reported. This trend was observed for plants grown in agar media with different nitrate concentrations (0.5–10 mM). These results were validated through destructive measurement of nitrate concentration. Conclusions We present a methodology based on Raman microspectroscopy for in-vivo label-free mapping of nitrate within small root tissue volumes in Arabidopsis. Measurements are done in-situ without additional sample preparation. Our measurements revealed nitrate concentration changes from lower to higher concentration from tip to mature root tissue. Accumulation of nitrate in the maturation zone tissue shows a saturation behavior. The presented Raman-based approach allows for in-situ non-destructive measurements of Raman-active compounds.

Fernández González, Alma↗

NASA NTRS1988

Reaction mechanisms in the organometallic vapor phase epitaxial growth of GaAs

The decomposition mechanisms of AsH3, trimethylgallium (TMGa), and mixtures of the two have been studied in an atmospheric-pressure flow system with the use of D2 to label the reaction products which are analyzed in a time-of-flight mass spectrometer. AsH3 decomposes entirely heterogeneously to give H2. TMGa decomposes by a series of gas-phase steps, involving methyl radicals and D atoms to produce CH3D, CH4, C2H6, and HD. TMGa decomposition is accelerated by the presence of AsH3. When the two are mixed, as in the organometallic vapor phase epitaxial growth of GaAs, both compounds decompose in concert to produce only CH4. A likely model is that of a Lewis acid-base adduct that forms and subsequently eliminates CH4.

Larsen, C. A.↗

NASA NTRS2008

Nanoflow Separation of Amino Acids for the Analysis of Cosmic Dust

The delivery of amino acids to the early Earth by interplanetary dust particles, comets, and carbonaceous meteorites could have been a significant source of the early Earth's prebiotic organic inventory. Amino acids are central to modern terrestrial biochemistry as major components of proteins and enzymes and were probably vital in the origin of life. A variety of amino acids have been detected in the CM carbonaceous meteorite Murchison, many of which are exceptionally rare in the terrestrial biosphere including a-aminoisobutyric acid (AIB) and isovaline. AIB has also been detected in a small percentage of Antarctic micrometeorite grains believed to be related to the CM meteorites We report on progress in optimizing a nanoflow liquid chromatography separation system with dual detection via laser-induced-fluorescence time of flight mass spectrometry (nLC-LIF/ToF-MS) for the analysis of o-phthaldialdehydelN-acetyl-L-cysteine (OPA/NAC) labeled amino acids in cosmic dust grains. The very low flow rates (<3 micro-L/min) of nLC over analytical LC (>0.1 ml/min) combined with <2 micron column bead sizes has the potential to produce efficient analyte ionizations andchromatograms with very sharp peaks; both increase sensitivity. The combination of the selectivity (only primary amines are derivatized), sensitivity (>4 orders of magnitude lower than traditional GC-MS techniques), and specificity (compounds identities are determined by both retention time and exact mass) makes this a compelling technique. However, the development of an analytical method to achieve separation of compounds as structurally similar as amino acid monomers and produce the sharp peaks required for maximum sensitivity is challenging.

Martin, M. P.↗

DOE OSTI2024

CsO x Nanostructures on Au(111): Morphology- and Size-dependent Activity for the Water–Gas Shift Reaction

Alkali oxides are typically used as promoters of heterogeneous catalysts for the water–gas shift (WGS; H 2 O + CO → H 2 + CO 2 ) reaction. On Au(111), CsO x exhibits diverse nanostructures at varying coverages, as revealed by scanning tunneling microscopy. Clusters of cesium oxide (Cs 2 O 2 ) nucleate at elbow sites of the Au(111) herringbone when θ Cs is less than 0.1 ML. Subsequently, these clusters transform into two-dimensional (2D) islands (Cs 2 O, Cs 2 O 2 , CsO 2 ) as the cesium coverage increases (θ Cs > 0.1 ML). Both types of CsO x nanostructures enable the WGS process on Au(111). The highest activity was seen for the cesium oxide clusters which facilitated the partial dissociation of water and binding of CO. The CO ads and OH ads groups were not strongly bound and probably reacted to yield a short-lived HOCO intermediate that led to gaseous H 2 and CO 2 . The 2D islands of CsO x also enabled the WGS but their efficiency was reduced due to the formation of cesium hydroxide compounds (limiting mobility of OH groups) and the generation of CO 3 and C species (blocking of active centers). The fact that the performance of the CsO x /Au(111) catalysts changed dramatically with variations in the chemical properties of the CsO x nanostructures indicates that the alkali oxide was an integral part of the active phase, playing a central role in the activation and conversion of the reactants. To attach the label of “promoter” to CsO x is a simplification that does not help in the design and optimization of catalysts for C1 chemistry. In conclusion, to achieve a rational design, one must consider the structural and chemical properties of the alkali oxide.

36 MATERIALS SCIENCE↗

DOE OSTI2022

C fluxes from incubations of California upland soil with and without synthetic iron (hydr)oxide associations

There is a growing understanding that interactions with soil mineral phases contribute to the accumulation and retention of otherwise degradable organic matter in soils and sediments. However, the bioavailability of organic compounds in mineral-organic-associations, especially under varying environmental conditions is not well known. To assess the impact of mineral association and warming on the decomposition of an easily respirable organic substrate (glucose), we conducted a series of laboratory incubations at different temperatures with field-collected soils from 10 to 20 cm, 50–60 cm, and 80–90 cm depth at the Blodgett Forest Research Station. We added 13C-labeled glucose either directly to native soil or sorbed to one of two synthetic iron (hydr)oxide phases (goethite and ferrihydrite) that differ in crystallinity and affinity for sorbing glucose. We incubated the soils at 25 deg C. This dataset comprises the added glucose C and the cumulative fluxes over 72 and 1896 hours. We found that: (1) association with the Fe (hydr)oxide minerals reduced the decomposition rate of glucose by > 99.5% relative to rate of decomposition for free glucose in soil; (2) the respiration rate per gram carbon did not differ appreciably with depth, suggesting a similar degree of decomposability for native C across depths and that under the incubation conditions total carbon availability represents the principal limitation on respiration under these conditions as opposed to reduced abundance of decomposers or moisture and oxygen limitations; (3) addition of free glucose enhanced native carbon respiration at all soil depths with the largest effect at 50–60 cm; (4) in general respiration of the organo-mineral complex (glucose and iron-(hydr)oxide) was less temperature sensitive than was respiration of native carbon; (5) the addition of organic free mineral decreased the rate of soil respiration in the intermediate 50–60 cm depth soil. The results emphasize the key role of MOAs in regulating the fluxes of carbon from soils to the atmosphere and in turn the stocks of soil carbon.This dataset lists the glucose additions made to soils with and without added geothite or ferrihidrite and the C respired over the timespan of the incubations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are present in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13 C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13 C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

Advanced Automotive Fuels Research, Development, and Commercialization Cluster (OH) (Final Report)

Technical aspects of producing alternative fuels that may eventually supplement or replace conventional the petroleum-derived fuels that are presently used in vehicular transportation have been investigated. The work was centered around three projects: 1) deriving butanol as a fuel additive from bacterial action on sugars produced from decomposition of aqueous suspensions of wood cellulose under elevated temperature and pressure; 2) using highly ordered, openly structured molecules known as metal-organic framework (MOF) compounds as adsorbents for gas separations in fuel processing operations; and 3) developing a photocatalytic membrane for solar-driven water decomposition to generate pure hydrogen fuel. Several departments within the STEM College at YSU contributed to the effort: Chemistry, Biology, and Chemical Engineering. In the butanol project, sawdust was blended with water at variable pH and temperature (150 – 250 °C), and heated inside a pressure vessel for specified periods of time. Analysis of the extracts showed a wide variety of compounds, including simple sugars that bacteria are known to thrive upon. Samples of the cellulose hydrolysate were fed to colonies of Clostridium beijerinckii, which are known to convert sugars to a mixture of compounds, principally butanol. While the bacteria were active toward additions of pure sugar solutions, the cellulose extract appeared to inhibit butanol production, and furthermore encouraged the Clostridium to become dormant. Proteomic analysis showed that the bacteria had changed their genetic code to where it was becoming sporulated, i.e., the bacteria were trying to go dormant. This finding may be an opportunity, as it may be possible to genetically engineer bacteria that resist the butanol-driven triggering mechanism to stop further fuel production. Another way of handling the cellulosic hydrolysates was to simply add the enzymes responsible for butanol synthesis to the hydrolytic extract ex-vivo. These enzymes are generally not available commercially, however, and those that are can be quite expensive. Accordingly, the genes responsible for enzyme synthesis were inserted into other microorganisms in order to accelerate enzyme production. This was demonstrated for two of the required enzymes in the overall series. In the MOF project, a number of new MOF compounds were synthesized and characterized, as well as some common MOFs well-known for their adsorption properties. Selectivity for specific gases such as CO 2 and H 2 was demonstrated, although it was seen that water vapor would frequently act as an interferent. This work underscored the need to test MOF compounds under real world conditions, i.e., room temperature and above instead of liquid N 2 temperature, and testing adsorption using blends of gases instead of pure components. In the solar membrane project, thin films of CdTe and WO 3 were applied to steel substrates and used as p-type and n-type semiconductors, respectively, in the production of H 2 and O 2 . Testing with 2 H and 18 O isotopically labeled water enabled substantiation of net water-splitting.

08 HYDROGEN↗

DOE OSTI2021

Mapathons versus automated feature extraction: a comparative analysis for strengthening immunization microplanning

Background: Social instability and logistical factors like the displacement of vulnerable populations, the difficulty of accessing these populations, and the lack of geographic information for hard-to-reach areas continue to serve as barriers to global essential immunizations (EI). Microplanning, a population-based, healthcare intervention planning method has begun to leverage geographic information system (GIS) technology and geospatial methods to improve the remote identification and mapping of vulnerable populations to ensure inclusion in outreach and immunization services, when feasible. We compare two methods of accomplishing a remote inventory of building locations to assess their accuracy and similarity to currently employed microplan line-lists in the study area. Methods: The outputs of a crowd-sourced digitization effort, or mapathon, were compared to those of a machine-learning algorithm for digitization, referred to as automatic feature extraction (AFE). The following accuracy assessments were employed to determine the performance of each feature generation method: (1) an agreement analysis of the two methods assessed the occurrence of matches across the two outputs, where agreements were labeled as “befriended” and disagreements as “lonely”; (2) true and false positive percentages of each method were calculated in comparison to satellite imagery; (3) counts of features generated from both the mapathon and AFE were statistically compared to the number of features listed in the microplan line-list for the study area; and (4) population estimates for both feature generation method were determined for every structure identified assuming a total of three households per compound, with each household averaging two adults and 5 children. Results: The mapathon and AFE outputs detected 92,713 and 53,150 features, respectively. A higher proportion (30%) of AFE features were befriended compared with befriended mapathon points (28%). The AFE had a higher true positive rate (90.5%) of identifying structures than the mapathon (84.5%). The difference in the average number of features identified per area between the microplan and mapathon points was larger (t = 3.56) than the microplan and AFE (t = -2.09) (alpha = 0.05). Conclusions: Our findings indicate AFE outputs had higher agreement (i.e., befriended), slightly higher likelihood of correctly identifying a structure, and were more similar to the local microplan line-lists than the mapathon outputs. These findings suggest AFE may be more accurate for identifying structures in high-resolution satellite imagery than mapathons. However, they both had their advantages and the ideal method would utilize both methods in tandem.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Synthesis and properties of SiN coatings as stable fluorescent markers on vertically aligned carbon nanofibers

The growth of vertically aligned carbon nanofibers (VACNFs) in a catalytic dc ammonia/acetylene plasma process on silicon substrates is often accompanied by sidewall deposition of material that contains mostly Si and N. In fluorescent microscopy experiments, imaging VACNF interfacing to live cell cultures it turned out that this material is broadly fluorescent, which made VACNFs useful as spatial markers, or created nuisance when DNA-labeling got masked. In this paper we provide insight into nature of this silicon/nitrogen in situ coatings. Here we have proposed a potential mechanism for deposition of SiNx coating on the sidewalls of VACNFs during PECVD synthesis in addition to exploring the origin of the coatings fluorescence. It seems most likely that the substrate reacts with the process gases through both processes similar to reactive sputtering and CVD to form silane and other silicon bearing compounds before being deposited isotropically as a SiNx coating onto the VACNFs. The case for the presence of Si-NCs is made strong through a combination of the strong fluorescence and elemental analysis of the samples. These broadly luminescent fibers can prove useful as registry markers in fluorescent cellular studies.

Pearce, Ryan↗

DOE OSTI2025

DONUT: physics-aware machine learning for real-time X-ray nanodiffraction analysis

Coherent X-ray scattering techniques are critical for investigating the fundamental structural properties of materials at the nanoscale. While advancements have made these experiments more accessible, real-time analysis remains a significant bottleneck, often hindered by artifacts and computational demands. In scanning X-ray nanodiffraction microscopy, which is widely used to spatially resolve structural heterogeneities, this challenge is compounded by the convolution of the divergent beam with the sample’s local structure. To address this, we introduce DONUT (Diffraction with Optics for Nanobeam by Unsupervised Training), a physics-aware neural network designed for the rapid and automated analysis of nanobeam diffraction data. By incorporating a differentiable geometric diffraction model directly into its architecture, DONUT learns to predict crystal lattice strain and orientation in real-time. Crucially, this is achieved without reliance on labeled datasets or pre-training, overcoming a fundamental limitation for supervised machine learning in X-ray science. We demonstrate experimentally that DONUT accurately extracts all features within the data over 200 times more efficiently than conventional fitting methods.

Materials science↗