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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Oxygen vacancy migration and impact on high voltage DC polarization in 0.8BaTiO 3 –0.2BiZn 0.5 Ti 0.5 O 3

Electrical polarization and defect transport are examined in 0.8BaTiO 3 –0.2BiZn 0.5 Ti 0.5 O 3 , an attractive capacitor material for high power electronics. Oxygen vacancies are suggested to be the majority charge carrier at or below 250°C with a grain conduction hopping activation energy of 0.97 eV and 0.92 eV for thermally stimulated depolarization current (TSDC) and impedance spectroscopy measurements, respectively. At higher temperature, thermally generated electronic conduction with an activation energy of 1.6 eV is dominant. Significant oxygen vacancy concentration is indicated (up to ~1%) due to cation vacancy formation (i.e., acceptor defects) from observed Bi (and likely Zn) volatility. Oxygen vacancy diffusivity is estimated to be 10 -12.8 cm 2 /s at 250°C. Low diffusivity and high activation energies are indicative of significant defect interactions. Dipolar oxygen vacancy defects are also indicated, with an activation energy of 0.59 eV from TSDC measurements. In conclusion, the large oxygen vacancy content leads to a short lifetime during high voltage (30 kV/cm), high temperature (250°C) direct current (DC) electrical measurements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Nonspecific phospholipase C6 increases seed oil production in oilseed Brassicaceae plants

Summary Plant oils are valuable commodities for food, feed, renewable industrial feedstocks and biofuels. To increase vegetable oil production, here we show that the nonspecific phospholipase C6 (NPC6) promotes seed oil production in the Brassicaceae seed oil species Arabidopsis, Camelina and oilseed rape. Overexpression of NPC6 increased seed oil content, seed weight and oil yield both in Arabidopsis and Camelina, whereas knockout of NPC6 decreased seed oil content and seed size. NPC6 is associated with the chloroplasts and microsomal membranes, and hydrolyzes phosphatidylcholine and galactolipids to produce diacylglycerol. Knockout and overexpression of NPC6 decreased and increased, respectively, the flux of fatty acids from phospholipids and galactolipids into triacylglycerol production. Candidate‐gene association study in oilseed rape indicates that only BnNPC6.C01 of the four homeologues NPC6s is associated with seed oil content and yield. Haplotypic analysis indicates that the BnNPC6.C01 favorable haplotype can increase both seed oil content and seed yield. These results indicate that NPC6 promotes membrane glycerolipid turnover to accumulate TAG production in oil seeds and that NPC6 has a great application potential for oil yield improvement.

Cai, Guangqin↗
DOE OSTI2022

Thick filament activation is different in fast- and slow-twitch skeletal muscle

The contractile properties of fast-twitch and slow-twitch skeletal muscles are primarily determined by the myosin isoform content and modulated by a variety of sarcomere proteins. X-ray diffraction studies of regulatory mechanisms in muscle contraction have focused predominately on fast- or mixed-fibre muscle with slow muscle being much less studied. Here, we used time-resolved X-ray diffraction to investigate the dynamic behaviour of the myofilament proteins in relatively pure slow-twitch-fibre rat soleus (SOL) and pure fast-twitch-fibre rat extensor digitorum longus (EDL) muscle during twitch and tetanic contractions at optimal length. During twitch contractions the diffraction signatures indicating a transition in the myosin heads from ordered OFF states, where heads are held close to the thick filament backbone, to disordered ON states, where heads are free to bind to thin filaments, were found in EDL and not in SOL muscle. During tetanic contraction, changes in the disposition of myosin heads as active tension develops is a quasi-stepwise process in EDL muscle whereas in SOL muscle this relationship appears to be linear. The observed reduced extensibility of the thick filaments in SOL muscle as compared to EDL muscles indicates a molecular basis for this behaviour. These data indicate that for the EDL, thick filament activation is a cooperative strain-induced mechano-sensing mechanism, whereas for the SOL, thick filament activation has a more graded response. Further, these different approaches to thick filament regulation in fast- and slow-twitch muscles may be adaptations for short-duration, strong contractions versus sustained, finely controlled contractions, respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Challenges in atomic layer etching of gallium nitride using surface oxidation and ligand-exchange

Two atomic layer etching (ALE) methods were studied for crystalline GaN, based on oxidation, fluorination, and ligand exchange. Etching was performed on unintentionally doped GaN grown by hydride vapor phase epitaxy. For the first step, the GaN surfaces were oxidized using either water vapor or remote O 2 -plasma exposure to produce a thin oxide layer. Removal of the surface oxide was addressed using alternating exposures of hydrogen fluoride (HF) and trimethylgallium (TMG) via fluorination and ligand exchange, respectively. Several HF and TMG super cycles were implemented to remove the surface oxide. Each ALE process was monitored in situ using multiwavelength ellipsometry. X-ray photoelectron spectroscopy was employed for the characterization of surface composition and impurity states. Additionally, the thermal and plasma-enhanced ALE methods were performed on patterned wafers and transmission electron microscopy (TEM) was used to measure the surface change. The x-ray photoelectron spectroscopy measurements indicated that F and O impurities remained on etched surfaces for both ALE processes. Ellipsometry indicated a slight reduction in thickness. TEM indicated a removal rate that was less than predicted. In conclusion, we suggest that the etch rates were reduced due to the ordered structure of the oxide formed on crystalline GaN surfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Melt-grown semi-insulating Mn:β-Ga 2 O 3 single crystals exhibiting unique visible absorptions and luminescence

In this study, several acceptor dopants have been explored in β-Ga 2 O 3 to produce semi-insulating substrates and epitaxial films. Fe and Mg make up the majority of research thus far; however, other transition metals provide potential alternatives for optimized performance. β-Ga 2 O 3 bulk single crystals were grown by the Czochralski and vertical gradient freeze methods with a nominal dopant concentration of 0.25 at. % Mn. Ultraviolet-visible-near infrared spectroscopy and photoluminescence revealed polarization- and orientation-dependent optical absorptions (pleochroism) coupled with an orange luminescence. All samples were electrically insulating, on the order of 10 9 –10 11 ohm cm at room temperature, indicative of acceptor doping. Actual dopant concentrations of the intentionally doped transition metal and background impurities were determined via glow discharge mass spectrometry, indicating the macroscale segregation behavior. High-temperature resistivity measurements indicated an experimental acceptor level of 1.7 ± 0.2 eV. Hydrogenation of samples resulted in an increase in the orange luminescence and O–H stretching modes observable in the infrared spectrum. Density functional theory calculations were performed to determine the likely site-occupancy and acceptor level of Mn in the bandgap.

36 MATERIALS SCIENCE↗
DOE OSTI2022

All topological bands of all nonmagnetic stoichiometric materials

Topological quantum chemistry and symmetry-based indicators have facilitated large-scale searches for materials with topological properties at the Fermi energy ( E F ). We report the implementation of a publicly accessible catalog of stable and fragile topology in all of the bands both at and away from E F in the 96,196 processable entries in the Inorganic Crystal Structure Database. Our calculations, which represent the completion of the symmetry-indicated band topology of known nonmagnetic materials, have enabled the discovery of repeat-topological and supertopological materials, including rhombohedral bismuth and Bi 2 Mg 3 . We find that 52.65% of all materials are topological at E F , roughly two-thirds of bands across all materials exhibit symmetry-indicated stable topology, and 87.99% of all materials contain at least one stable or fragile topological band.

Science & Technology - Other Topics↗
DOE OSTI2022

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Fecal microbiota transplantation ameliorates type 2 diabetes via metabolic remodeling of the gut microbiota in db/db mice

Gut microbiome (GM) deregulation has been implicated in major conditions such as obesity and type 2 diabetes (T2DM). Our previous prospective study indicated that fecal microbiota transplantation (FMT) successfully improved patients with T2DM. We hypothesized that FMT may be a potential therapeutic method for T2DM, but its precise mechanisms in T2DM remains to be elucidated. Eight db/m mice were FMT donors and control mice, and 16 genetically diabetic db/db mice were equally divided into two groups (db/db+phosphate-buffered saline (PBS) group, db/db+FMT group). The db/db+FMT group was administered fresh fecal suspension (0.2 mL/mice) daily for 4 weeks. Analysis of the GM and serum metabolome was carried out by 16S ribosomal RNA sequencing and liquid chromatogram-mass spectrometry, respectively. Effects of FMT on the gut barrier and pancreas were assessed using protein assays, messenger RNA, immunohistology and clinical indicators testing. Our results showed that FMT treatment of db/db mice relieves a series of clinical indicators, including fasting plasma glucose, serum insulin and oral glucose tolerance test among others. Compared with non-diabetic control mice, db/db+PBS mice exhibited decreased abundance of Ruminococaceae, Porphyromonadaceae and increased abundance of Rikenellaceae and Lactobacillaceae. FMT treatment reversed this effect on the microbiome. Eleven metabolites were changed between the db/db+PBS and db/db+FMT groups. Correlation analysis showed that the structural changes of the GM were correlated with host metabolite levels. We further showed that FMT treatment of db/db mice improved intestinal barrier function, reduced inflammation and caused an alteration in the number of circulating immune cells. FMT-mediated changes in the GM, serum metabolites, intestinal epithelial barrier, inflammation and circulating immune cells play an important role in the efficacy of FMT on T2DM disease progression.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Experimental Study of TCP Throughput Profiles and Dynamics Over Dedicated Connections

A throughput profile expressed as a function of the round-trip times of a data transport infrastructure is a critical indicator of its level of optimization, particularly, over dedicated connections. We study the throughput profiles of eleven TCP versions using measurements collected over dedicated hardware-emulated connections with distances spanning round the earth. Among them, BBR has overall higher temporal variations and lower throughput profiles compared to five loss-based TCP versions, and the comparison with other TCP versions is mixed. Using the Poincare map regions of throughput time traces, we show that the richer dynamics of BBR are correlated with its lower throughput profiles. We present basic analytical results that indicate that higher temporal variations of TCP methods lead to lower throughput profiles, thereby establishing the underlying causality. Under external losses, BBR achieves sustained high throughput compared to others as the loss rate is increased. Overall, our results provide insights into the relationship between time dynamics and throughput profiles of TCP versions, in particular, show that limited time traces can be indicative of global properties of throughput profiles.

Rao, Nageswara↗
DOE OSTI2022

A Systematic Review and Meta-Analysis of Tai Chi Training in Cardiorespiratory Fitness of Elderly People

Objectives. The purpose of this study was to investigate the influence of Tai Chi on cardiorespiratory fitness (CRF) in elderly people using meta-analysis. Methods. This study used seven electronic databases and data retrieved from randomized controlled trials (RCTs) investigating the role of Tai Chi on CRF in the elderly. All these 24 RCTs were screened and selected from 7 literature databases. The Stata 11.2 software (StataCorp, USA) was used for the meta-analysis, subgroup analysis, and bias test, while the Cochrane Collaboration’s tool was used for the assessment of the risk of bias (RoB). 4 researchers independently participated in sample selection, data extraction, and RoB assessment. Results. Following the inclusion criteria, 24 eligible studies were included in our analysis. The meta-analysis indicated that Tai Chi practice significantly increased the maximum rate of oxygen consumption (VO2 max) (weighted mean difference (WMD) = 3.76, 95% CI: 1.25 to 6.26, P < 0.1 ), leading to an overall reduction in the heart rate (HR) (WMD = −1.84, 95% CI: −2.04 to −1.63, P ≤ 0.001 ) and an increase in the O2 pulse (WMD = 0.94, 95% CI: 0.60 to 1.28, P ≤ 0.001 ) in individuals who practiced Tai Chi regularly compared with those who did not. The subgroup analysis suggested that overall in those who practiced Tai Chi, males (WMD = 1.48, 95% CI: 0.85 to 2.12, P ≤ 0.001 ) had higher O2 pulse than females (WMD = 0.73, 95% CI: 0.33 to 1.12, P ≤ 0.001 ). The subgroup analysis also showed an increase in the vital capacity (VC) (WMD = 316.05, 95% CI: 239.74 to 392.35, P ≤ 0.001 ) in individuals practicing Tai Chi. When the samples were further stratified by Tai Chi practicing time, the subgroup analysis suggested that individuals practicing Tai Chi over a period of 24 weeks showed no significant difference in VC (WMD = 82.95, 95% CI: -98.34 to 264.23, P = 0.370 ), while those practicing Tai Chi over a period of 48 weeks showed a significant increase (WMD = 416.62, 95% CI: 280.68 to 552.56, P ≤ 0.001 ). Furthermore, the subgroup analysis demonstrated that the increase in VC is significantly correlated with the Tai Chi practicing time (WMD = 344.97, 95% CI: 227.88 to 442.06, P ≤ 0.001 ). Conclusion. Regular Tai Chi practice could improve the CRF in the elderly, as indicated by significant improvement in indicators including VO2max, O2pulse, VC, and HR. However, gender and practice time might influence the overall beneficial outcomes.

Tan, Tianyang↗
DOE OSTI2023

Climate Services for Agriculture: Tools for Informing Decisions Relating to Climate Change and Climate Variability in the Wine Industry

Australia’s changing climate is already impacting the agriculture sector and will continue to do so in the future. To help respond to these impacts, the Climate Services for Agriculture (CSA) platform presents readily accessible climate data, including future climate projections, relevant to specific agricultural commodities. This wine industry example aims to demonstrate the functionality and utility of the CSA for national use across a broad range of commodities. Methods and Results. The platform includes commodity-relevant climate indices designed in consultation with experts to ensure that they are as salient to producers as possible; the wine-grape specific indices include measures of growing season temperature, rainfall, extreme heat, and frost. Here, we describe the research behind the wine-grape specific indices and present sample outputs from the CSA platform for a site within a selected winegrowing region. We note the CSA platform has been developed through an extensive and continuing user engagement initiative, ensuring it meets the needs of the agriculture community as they grapple with how to make decisions based on longer term climate projections. Conclusions. Provision of past, seasonal outlook, and future climate information for Australia and for a range of important agricultural commodities can help improve on-farm planning and decision-making to respond to climate risks. The wine industry provides a leading example of how to use these data for decision-making, noting ongoing adjustments will be needed. Significance of the Study. The CSA platform brings together historical climate data, seasonal climate outlooks, and future climate projections to assist agricultural producers to better manage climate variability and climate change. It aims to nationalise this information for all major agricultural commodities in Australia. We use wine production as a demonstration case here.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Understanding Predictability of Daily Southeast U.S. Precipitation Using Explainable Machine Learning

Abstract We investigate the predictability of the sign of daily southeastern U.S. (SEUS) precipitation anomalies associated with simultaneous predictors of large-scale climate variability using machine learning models. Models using index-based climate predictors and gridded fields of large-scale circulation as predictors are utilized. Logistic regression (LR) and fully connected neural networks using indices of climate phenomena as predictors produce neither accurate nor reliable predictions, indicating that the indices themselves are not good predictors. Using gridded fields as predictors, an LR and convolutional neural network (CNN) are more accurate than the index-based models. However, only the CNN can produce reliable predictions that can be used to identify forecasts of opportunity. Using explainable machine learning we identify which variables and grid points of the input fields are most relevant for confident and correct predictions in the CNN. Our results show that the local circulation is most important as represented by maximum relevance of 850-hPa geopotential heights and zonal winds to making skillful, high-probability predictions. Corresponding composite anomalies identify connections with El Niño–Southern Oscillation during winter and the Atlantic multidecadal oscillation and North Atlantic subtropical high during summer.

Pegion, Kathy↗
DOE OSTI2021

AMOC stability and diverging response to Arctic sea ice decline in two climate models

This study compares the impacts of Arctic sea ice decline on the Atlantic meridional overturning circulation (AMOC) in two configurations of the Community Earth System Model with different horizontal resolution. In a suite of model experiments, we impose radiative imbalance at the ice surface, replicating a loss of sea ice cover comparable to that observed during 1979–2014, and we find dramatic differences in the AMOC response between the two models. In the lower-resolution configuration, the AMOC weakens by about one-third over the first 100 years, approaching a new quasi-equilibrium. By contrast, in the higher-resolution configuration, the AMOC weakens by ~10% during the first 20–30 years followed by a full recovery driven by invigorated deep water formation in the Labrador Sea and adjacent regions. We investigate these differences using a diagnostic AMOC stability indicator, which reflects the AMOC freshwater transport in and out of the basin and hence the strength of the basin-scale salt-advection feedback. This indicator suggests that the AMOC in the lower-resolution model is less stable and more sensitive to surface perturbations, as confirmed by hosing experiments mimicking Arctic freshening due to sea ice decline. Differences between the models’ mean states, including the Atlantic Ocean mean surface freshwater fluxes, control the differences in AMOC stability. Our results demonstrate that the AMOC stability indicator is indeed useful for evaluating AMOC sensitivity to perturbations. We emphasize that, despite the differences in the long-term adjustment, both models simulate a multidecadal AMOC weakening caused by Arctic sea ice decline, relevant to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The Importance of Convective Stage on Out-of-Cloud Convectively Induced Turbulence from High-Resolution Simulations

Turbulence (clear-air, mountain wave, convectively induced) is an aviation hazard that is a challenge to forecast due to the coarse resolution ultilized in operational weather models. Turbulence indices are commonly used to aid pilots in avoiding turbulence, but these indices have been designed and calibrated for midlatitude clear-air turbulence prediction (e.g., the Ellrod index). A significant limitation with current convectively induced turbulence (CIT) prediction is the lack of storm stage dependency. In this study, six high-resolution simulations of tropical oceanic and midlatitude continental convection are performed to characterize the turbulent environment near various convective types during the developing and mature stages. Second-order structure functions, a diagnostic commonly used to identify turbulence in turbulence prediction systems, are used to characterize the probability of turbulence for various convective types. Turbulence likelihood was found to be independent of region (i.e., tropical vs midlatitude) but dependent on convective stage. The probability of turbulence increased near developing convection for the majority of cases. Additional analysis of static stability and vertical wind shear, indicators of turbulence potential, showed that the convective environment near developing convection was more favorable for turbulence production than mature convection. Near developing convection, static stability decreased and vertical wind shear increased. Vertical wind shear near mature and developing convection was found to be weakly correlated to turbulence intensity in both the tropics and the midlatitudes. Finally, this study emphasizes the need for turbulence avoidance guidelines for the aviation community that are dependent on convective stage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Parametric evaluation of ducted fuel injection in an optically accessible mixing-controlled compression-ignition engine with two- and four-duct assemblies

Ducted fuel injection (DFI) is a strategy to improve fuel/charge-gas mixing in direct-injection compression-ignition engines. DFI involves injecting fuel along the axis of a small tube in the combustion chamber, which promotes the formation of locally leaner mixtures in the autoignition zone relative to conventional diesel combustion. Previous work has demonstrated that DFI is effective at curtailing engine-out soot emissions across a wide range of operating conditions. This study extends previous investigations, presenting engine-out emissions and efficiency trends between ducted two-orifice and ducted four-orifice injector tip configurations. For each configuration, parameters investigated include injection pressure, injection duration, intake manifold pressure, intake manifold temperature, start of combustion timing, and intake-oxygen mole fraction. For both configurations and across all parameters, DFI reduced engine-out soot emissions compared to conventional diesel combustion, with little effect on other emissions and engine efficiency. Emissions trends for both configurations were qualitatively the same across the parameters investigated. The four-duct configuration had higher thermal efficiency and indicated-specific engine-out nitrogen oxide emissions but lower indicated-specific engine-out hydrocarbon and carbon monoxide emissions than the two-duct assembly. Both configurations achieved indicated-specific engine-out emissions for both soot and nitrogen oxides that comply with current on- and off-road heavy-duty regulations in the United States without exhaust-gas aftertreatment at an intake-oxygen mole fraction of 12%. High-speed in-cylinder imaging of natural soot luminosity shows that some conditions include a second soot-production phase late in the cycle. The probability of these late-cycle events is sensitive to both the number of ducted sprays and the operating conditions.

Yraguen, Boni Frances↗
DOE OSTI2023

Knock-limited combustion of ethanol-, isobutanol-, and 2-methyl-3-buten-2-ol-gasoline blends in a direct-injected spark-ignition engine

Knock-limited combustion of alcohol-gasoline fuel blends was studied in a direct-injection spark-ignition engine. Ethanol, isobutanol (2-methyl-1-propanol), and methylbutenol (2-methyl-3-buten-2-ol) were splash-blended with a blendstock for oxygenate blending (BOB) gasoline. Ethanol was blended in fractions of 10%, 20%, and 30% by volume (E10, E20, and E30). Isobutanol and methylbutenol were blended to match the oxygen weight percentage of the ethanol blends, resulting in blends of 16%, 32%, and 49% (I16, I32, and I49) isobutanol by volume and 18%, 37%, and 56% (M18, M37, and M56) methylbutenol by volume. Neat BOB and gasoline primary reference fuels (PRF) with octane numbers (ON) of 87 (PRF87) and 100 (PRF100) were included for reference. The engine was operated at fixed speed, equivalence ratio, and injection timing while knock-limited spark advance was located across a range of intake pressures. Low-level alcohol blends E10 and M18 had similar knocking behavior and appeared to be slightly more knock-resistant than I16. For mid-level blends, E20 showed further improvement over I32 while M37 showed noticeably better knock resistance, able to match the knock-resistance of PRF100 for loads above 1000 kPa gross indicated mean effective pressure (GIMEP). For high-level blends, the difference between E30 and I49 was similar to their mid-level counterparts. However, M56 showed significant improvement over E30 and I49 throughout the entire range of loads tested. M56 exceeded the knock-resistance of PRF100 for loads above 700 kPa GIMEP. The improved knock-resistance combined with the increased volumetric energy density of methylbutenol resulted in improved fuel consumption and indicated efficiency. The overall results of this study indicate that the order of knock-resistance of these three alcohols, for direct-injection operation with injection during the intake stroke, is isobutanol < ethanol < methylbutenol when compared on an equal oxygen weight basis.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2020

Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species. However, as with any trait, comparing gene expression across species can be confounded by the non-independence of species due to shared ancestry, making standard hypothesis testing inappropriate. We compared RNA-Seq data across 18 fungal species using a multivariate Brownian Motion phylogenetic comparative method (PCM), which allowed us to quantify coevolution between protein pairs while directly accounting for the shared ancestry of the species. Our work indicates proteins which physically-interact show stronger signals of coevolution than randomly-generated pairs. Interactions with stronger empirical and computational evidence also showing stronger signals of coevolution. We examined the effects of number of protein interactions and gene expression levels on coevolution, finding both factors are overall poor predictors of the strength of coevolution between a protein pair. Simulations further demonstrate the potential issues of analyzing gene expression coevolution without accounting for shared ancestry in a standard hypothesis testing framework. Furthermore, our simulations indicate the use of a randomly-generated null distribution as a means of determining statistical significance for detecting coevolving genes with phylogenetically-uncorrected correlations, as has previously been done, is less accurate than PCMs, although is a significant improvement over standard hypothesis testing. These methods are further improved by using a phylogenetically-corrected correlation metric. Our work highlights potential benefits of using PCMs to detect gene expression coevolution from high-throughput omics scale data. This framework can be built upon to investigate other evolutionary hypotheses, such as changes in transcription regulatory mechanisms across species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Composition and yield of non-cellulosic and cellulosic sugars in soluble and particulate fractions during consolidated bioprocessing of poplar biomass by Clostridium thermocellum

Abstract Background Terrestrial plant biomass is the primary renewable carbon feedstock for enabling transition to a sustainable bioeconomy. Consolidated bioprocessing (CBP) by the cellulolytic thermophile Clostridium thermocellum offers a single step microbial platform for production of biofuels and biochemicals via simultaneous solubilization of carbohydrates from lignocellulosic biomass and conversion to products. Here, solubilization of cell wall cellulosic, hemicellulosic, and pectic polysaccharides in the liquor and solid residues generated during CBP of poplar biomass by C. thermocellum was analyzed. Results The total amount of biomass solubilized in the C. thermocellum DSM1313 fermentation platform was 5.8, 10.3, and 13.7% of milled non-pretreated poplar after 24, 48, and 120 h, respectively. These results demonstrate solubilization of 24% cellulose and 17% non-cellulosic sugars after 120 h, consistent with prior reports. The net solubilization of non-cellulosic sugars by C. thermocellum (after correcting for the uninoculated control fermentations) was 13 to 36% of arabinose (Ara), xylose (Xyl), galactose (Gal), mannose (Man), and glucose (Glc); and 15% and 3% of fucose and glucuronic acid, respectively. No rhamnose was solubilized and 71% of the galacturonic acid (GalA) was solubilized. These results indicate that C. thermocellum may be selective for the types and/or rate of solubilization of the non-cellulosic wall polymers. Xyl, Man, and Glc were found to accumulate in the fermentation liquor at levels greater than in uninoculated control fermentations, whereas Ara and Gal did not accumulate, suggesting that C. thermocellum solubilizes both hemicelluloses and pectins but utilizes them differently. After five days of fermentation, the relative amount of Rha in the solid residues increased 21% indicating that the Rha-containing polymer rhamnogalacturonan I (RG-I) was not effectively solubilized by C. thermocellum CBP, a result confirmed by immunoassays. Comparison of the sugars in the liquor versus solid residue showed that C. thermocellum solubilized hemicellulosic xylan and mannan, but did not fully utilize them, solubilized and appeared to utilize pectic homogalacturonan, and did not solubilize RG-I. Conclusions The significant relative increase in RG-I in poplar solid residues following CBP indicates that C. thermocellum did not solubilize RG-I. These results support the hypothesis that this pectic glycan may be one barrier for efficient solubilization of poplar by C. thermocellum .

09 BIOMASS FUELS↗