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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The Sustainability Index: a new tool to breed for reduced greenhouse-gas emissions intensity in Australian dairy cattle

Context The Australian dairy industry has a target to reduce greenhouse-gas (GHG) emissions intensity by 30% between 2015 and 2030. At the animal level, apart from nutritional modifications and other management practices, selecting animals that emit less GHG can be a cost-effective and long-term strategy. Given the world’s demand for protein is increasing, selecting for animals with lower GHG emissions per unit of production, i.e. emissions intensity, is a realistic approach that addresses the key issue of emissions reduction while maintaining farm productivity. Aim To develop a selection index for Australian dairy cattle to breed for reduced emissions intensity. Methods The Sustainability Index was built based on the existing Balanced Performance Index (BPI) but placed greater emphasis on production, survival, health and feed efficiency. Key results In August 2022, DataGene released the Sustainability Index that can be used by dairy farmers to select animals with lower environmental footprints. Compared with BPI, the weights for protein, fat, survival, mastitis resistance and feed efficiency increased by 2.6-, 1.4-, 2.8-, 1.3- and 3.8-fold respectively. It is expected that with the use of the Sustainability Index, emissions intensity will be reduced by 7.64%, 8.96% and 5.52% respectively in Holstein, Jersey and Red breeds by 2050, compared with the 2015 level. The corresponding values when selecting for BPI were 6.34%, 7.91% and 5.23% respectively. However, the trade-off in BPI when using the Sustainability Index will be AUD0.79, AUD0.83, AUD0.22 per cow per year for Holstein, Jersey and Red breeds respectively. Conclusions The current profit index BPI has contributed to reduction in emissions intensity. To enhance the rate of improvement in emissions intensity, the Sustainability Index can be used with minimal impacts on profit. Implications To breed for lower emissions intensity, farmers can select animals with high Sustainability Index values that are published on DataVat (datavat.com.au) and the Good Bulls App. To lower gross emissions, combinations of additional measures such as management of diet, adjustment to animal numbers, management of stored manure, and appropriate use of carbon neutral fertiliser, renewable fuels and energy, will need to be adopted on farms.

Agriculture↗
DOE OSTI2020

Bioavailable soil Pb minimized by in situ transformation to plumbojarosite

Exposure to lead (Pb) during early life has persistent adverse health effects. During childhood, ingestion of bioavailable Pb in contaminated soils can be a major route of Pb absorption. Remediation to alter physiochemical properties of soil-borne Pb can reduce Pb bioavailability. Our laboratory-based approach for soil Pb remediation uses addition of iron (Fe) sulfate and application of heat to promote formation of plumbojarosite (PLJ), a sparingly soluble Pb-Fe hydroxysulfate mineral. We treated two soils with anthropogenic Pb contamination and samples of clean topsoil spiked with various Pb compounds (i.e., carbonate, chloride, phosphate [P], or sulfate) to convert native Pb species to PLJ and used a mouse assay to assess relative bioavailability (RBA) of Pb in untreated (U) and remediated soils. Bone and blood Pb levels were significantly lower (P < 0.001, Student's t test) in mice that consumed diets amended with remediated soils than with U soils. Estimated RBA for Pb in both remediated natural soils and Pb-mineral spiked soils were reduced by >90% relative to Pb RBA for U soils, which is substantially more effective than other soil amendments, including P. X-ray absorption spectroscopy showed that >90% of all Pb species in remediated soils were converted to PLJ, and ingested PLJ was not chemically transformed during gastrointestinal tract transit. Post treatment neutralization of soil pH did not affect PLJ stability, indicating the feasibility in field conditions. These results suggest that formation of PLJ in contaminated soils can reduce the RBA of Pb and minimize this medium’s role as a source of Pb exposure for young children.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Investigating genomic prediction strategies for grain carotenoid traits in a tropical/subtropical maize panel

Abstract Vitamin A deficiency remains prevalent on a global scale, including in regions where maize constitutes a high percentage of human diets. One solution for alleviating this deficiency has been to increase grain concentrations of provitamin A carotenoids in maize (Zea mays ssp. mays L.)—an example of biofortification. The International Maize and Wheat Improvement Center (CIMMYT) developed a Carotenoid Association Mapping panel of 380 inbred lines adapted to tropical and subtropical environments that have varying grain concentrations of provitamin A and other health-beneficial carotenoids. Several major genes have been identified for these traits, 2 of which have particularly been leveraged in marker-assisted selection. This project assesses the predictive ability of several genomic prediction strategies for maize grain carotenoid traits within and between 4 environments in Mexico. Ridge Regression-Best Linear Unbiased Prediction, Elastic Net, and Reproducing Kernel Hilbert Spaces had high predictive abilities for all tested traits (β-carotene, β-cryptoxanthin, provitamin A, lutein, and zeaxanthin) and outperformed Least Absolute Shrinkage and Selection Operator. Furthermore, predictive abilities were higher when using genome-wide markers rather than only the markers proximal to 2 or 13 genes. These findings suggest that genomic prediction models using genome-wide markers (and assuming equal variance of marker effects) are worthwhile for these traits even though key genes have already been identified, especially if breeding for additional grain carotenoid traits alongside β-carotene. Predictive ability was maintained for all traits except lutein in between-environment prediction. The TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) Genomic Selection plugin performed as well as other more computationally intensive methods for within-environment prediction. The findings observed herein indicate the utility of genomic prediction methods for these traits and could inform their resource-efficient implementation in biofortification breeding programs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Prey-switching to fishery discards does not compensate for poor natural foraging conditions in breeding albatross

Abstract Fishery discards supplement food for many seabirds, but the impacts of declining discards are poorly understood. Discards may be beneficial for some populations but have negative impacts by increasing bycatch risk or because they are junk-food. The Falkland Islands support > 70% of global black-browed albatross Thalassarche melanophris populations, which feed on discards. However, the effect of discards on population demographics, and implications of fishery management changes, are unknown. We analysed stomach contents of black-browed albatross chicks across eight breeding seasons (2004–2020) from New Island, Falkland Islands, to assess variation in discard consumption and how this relates to foraging conditions and breeding success. Across years, 68%–98% of samples contained natural prey, whilst 23%–88% of samples contained fishery discards. Discard consumption was positively related to fishery catches of hoki Macruronus magellanicus and sea surface temperature anomalies SSTA (°C), and negatively related to breeding success. These results suggest a diet-switching behaviour for Falkland Islands albatrosses, whereby birds switch from preferred natural prey to suboptimal discards when environmental conditions, and hence natural feeding opportunities, are unfavourable. Crucially, this study highlights that fishery discards do not compensate for poor natural foraging conditions for breeding albatrosses in the long term.

Kuepfer, Amanda (ORCID:0000000235598802)↗
DOE OSTI2023

Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5′-monophosphate as the biological substrate

Abstract Eukaryotic life benefits from—and ofttimes critically relies upon—the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5′-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Lipid droplet-associated proteins in alcohol-associated fatty liver disease: A proteomic approach

The earliest manifestation of alcohol-associated liver disease (ALD) is steatosis characterized by deposition of fat in specialized organelles called lipid droplets (LDs). While alcohol administration causes a rise in LD numbers in the hepatocytes, little is known regarding their characteristics that allow their accumulation and size to increase. The aim of the present study is to gain insights into underlying pathophysiological mechanisms by investigating the ethanol-induced changes in hepatic LD proteome as a function of LD size. Adult male Wistar rats (180–200 g BW) were fed with ethanol liquid diet for 6 weeks. At sacrifice, large-, medium-, and small-sized hepatic LD subpopulations (LD1, LD2, and LD3, respectively) were isolated and subjected to morphological and proteomic analyses. Morphological analysis of LD1-LD3 fractions of ethanol-fed rats clearly demonstrated that LD1 contained larger LDs compared with LD2 and LD3 fractions. Our preliminary results from principal component analysis showed that the proteome of different-sized hepatic LD fractions was distinctly different. Proteomic data analysis identified over 2000 proteins in each LD fraction with significant alterations in protein abundance among the three LD fractions. Among the altered proteins, several were related to fat metabolism, including synthesis, incorporation of fatty acid, and lipolysis. Ingenuity pathway analysis revealed increased fatty acid synthesis, fatty acid incorporation, LD fusion, and reduced lipolysis in LD1 compared to LD3. Overall, the proteomic findings indicate that the increased level of protein that facilitates fusion of LDs combined with an increased association of negative regulators of lipolysis dictates the generation of large-sized LDs during the development of alcohol-associated hepatic steatosis. Several significantly altered proteins were identified in different-sized LDs isolated from livers of ethanol-fed rats. Ethanol-induced increases in specific proteins that hinder LD lipid metabolism led to the accumulation and persistence of large-sized LDs in the liver.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Generating Ectropis obliqua axenic larvae in support of functional microbiome studies

Abstract Ectropis obliqua Prout (Lepidoptera: Geometridae) is a serious leaf‐eating pest in tea gardens throughout China, with rich bacterial communities in the larval gut. Few studies have investigated whether these bacteria play an important role in growth, development, and adaptability of E. obliqua . Axenic larval models are a useful tool for the study of interactions between gut bacteria and host insects. At present, artificial diet and antibiotics are typically used to remove larval gut bacteria for study; however, this method may change the natural food of insects and the habitat provided by their host plants, and cannot completely eliminate insect gut bacteria. Therefore, in order to establish an axenic insect feeding model, we first investigated the effects of egg age, different disinfectant concentration, and treatment time on the eggs of E. obliqua through orthogonal experiments. Next, we fed E. obliqua larvae tissue‐cultured tea seedlings under aseptic conditions. Thus, we successfully generated a feeding model of gut axenic larvae in the laboratory. Based on it, we then compared the mortality of axenic and non‐axenic E. obliqua larvae infected with the entomopathogenic fungus Beauveria bassiana (Balsamo) Vuill. These results demonstrated the feasibility of this axenic larval model and that B. bassiana is a broad‐spectrum entomogenous fungus with a toxic effect on E. obliqua .

Su, Qingqing↗
DOE OSTI2021

Testing effects of invasive fire ants and disturbance on ant communities of the longleaf pine ecosystem

Invasive species and habitat disturbance are among the most important drivers of biodiversity loss and ecological change. Their individual effects, however, are difficult to disentangle because invasion and disturbance are often intimately linked. Here we test alternative hypotheses to determine if the invasive red imported fire ant, Solenopsis invicta, is a ‘driver’ or simply a ‘passenger’ of ecological change in a longleaf pine ecosystem. We randomly assigned treatments of (1) unmanipulated, (2) soil disturbance, (3) fire ant removal and (4) soil disturbance + fire ant removal to experimental blocks and measured how ant communities changed over 2 years in thirty-six 15-m 2 plots. Additionally, fire ant abundance in removal plots averaged 42% lower in pitfall traps and 95% lower on baits compared to unmanipulated, control plots. Species richness of co-occurring ants also decreased 42% in removal plots, with significant changes in community composition. Soil disturbance alone did not affect ant communities. Fire ant diet breadth—measured using carbon and nitrogen stable isotopes—increased up to 4.7-fold in soil disturbance + removal plots (i.e. 0.84‰ 2 to 3.94‰ 2 ). While non-target impacts of the fire ant removal treatment complicate interpretation, our results suggest fire ants follow an alternative ‘interacting drivers’ model in which partial recovery of some species occurs when populations of an invasive species are reduced. Further recovery of native ants may be limited by persisting, landscape-level effects of fire ants suppressing co-occurring ants below historical levels.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

3,3’-Diindolylmethane Exhibits Significant Metabolism After Oral Dosing in Humans

3,3’-Diindolylmethane (DIM), a major phytochemical derived from ingestion of cruciferous vegetables such as Brussels sprouts, is also a dietary supplement. In preclinical models, DIM is an effective cancer chemopreventive agent and has been studied in a number of clinical trials. Previous pharmacokinetic studies in preclinical and clinical models have not reported DIM metabolites in plasma or urine following oral dosing and the pharmacological actions of DIM on target tissues is assumed to be solely via the parent compound. Seven subjects (6 males and 1 female) ranging from 26-65 years of age, on a cruciferous vegetable-restricted diet prior to and during the study, took 2 BioResponse-DIM® 150 mg capsules (45.3 mg DIM/capsule) in the evening for one week with a final dose the morning of the first blood draw. A complete time course was performed with plasma and urine collected over 48 hours and analyzed by UPLC-MS/MS. In addition to parent DIM, two mono-hydroxylated (2-ox- and 3-methylenehydroxy-DIM) and 1 dihydroxylated (3-methylenehydroxy-2-ox-DIM) metabolites, along with their sulfate and glucuronide conjugates, were present in both plasma and urine. The results reported here are indicative of significant phase 1 and phase 2 metabolism and differ from previous pharmacokinetic studies in rodents and humans which reported only parent DIM present following oral administration.

Vermillion-Maier, Monica↗
DOE OSTI2023

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

ABSTRACT The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made toward identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N = N-R’), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azoreductase activity was controlled by the fumarate and nitrate reduction ( fnr ) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Furthermore, we found that FNR indirectly regulates this process through the small noncoding regulatory RNA fnrS . Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical groups found in both dietary and pharmaceutical compounds. IMPORTANCE This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Immunomodulation by cannabidiol in bovine primary ruminal epithelial cells

Ruminant livestock experience a number of challenges, including high concentrate diets, weaning and transport, which can increase their risk of disorders such as ruminal acidosis, and the associated inflammation of the ruminal epithelium. Cannabidiol (CBD), a phytochemical from hemp (Cannabis sativa), is a promising target as a therapy for gastrointestinal inflammation, and may be extremely valuable as either a treatment or prophylactic. However, the effects of CBD in the the ruminant gastrointestinal tract have not been explored, in part due to the restrictions on feeding hemp to livestock. Therefore, the objective of this study was to investigate the immunomodulatory properties of CBD using a model of inflammation in primary ruminal epithelial cells (REC). In addition, CBD dose was evaluated for possible cytotoxic effects. Negative effects on cell viability were not observed when REC were exposed to 10 μM CBD. However, when the dose was increased to 50 μM for 24 h, there was a significant cytotoxic effect. When 10 μM CBD was added to culture media as treatment for inflammation induced with lipopolysaccharide (LPS), expression of genes encoding for pro-inflammatory cytokine IL1B was less compared to LPS exposure alone, and CBD resulted in a down-regulation of IL6. As a pre-treatment, prior to LPS exposure, REC had decreased expression of IL6 and CXCL10 while CBD was present in the media, but not when it was removed prior to addition of LPS. Results suggest that CBD may reduce cytokine transcription both during LPS-induced inflammation and when used preventatively, although these effects were dependent on its continued presence in the culture media. Overall, these experiments provide evidence of an immunomodulatory effect by CBD during a pro-inflammatory response in primary REC in culture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Criterion validity of wrist accelerometry for assessing energy intake via the intake-balance technique

Background: Intake-balance assessments measure energy intake (EI) by summing energy expenditure (EE) with concurrent change in energy storage (ΔES). Prior work has not examined the validity of such calculations when EE is estimated via open-source techniques for research-grade accelerometry devices. The purpose of this study was to test the criterion validity of accelerometry-based intake-balance methods for a wrist-worn ActiGraph device. Methods: Healthy adults (n = 24) completed two 14-day measurement periods while wearing an ActiGraph accelerometer on the non-dominant wrist. During each period, criterion values of EI were determined based on ΔES measured by dual X-ray absorptiometry and EE measured by doubly labeled water. A total of 11 prediction methods were tested, 8 derived from the accelerometer and 3 from non-accelerometry methods (e.g., diet recall; included for comparison). Group-level validity was assessed through mean bias, while individual-level validity was assessed through mean absolute error, mean absolute percentage error, and Bland–Altman analysis. Results: Mean bias for the three best accelerometry-based methods ranged from -167 to 124 kcal/day, versus -104 to 134 kcal/day for the non-accelerometry-based methods. The same three accelerometry-based methods had mean absolute error of 323–362 kcal/day and mean absolute percentage error of 18.1-19.3%, versus 353–464 kcal/day and 19.5-24.4% for the non-accelerometry-based methods. All 11 methods demonstrated systematic bias in the Bland–Altman analysis. Conclusions: Accelerometry-based intake-balance methods have promise for advancing EI assessment, but ongoing refinement is necessary. We provide an R package to facilitate implementation and refinement of accelerometry-based methods in future research (see paulhibbing.com/IntakeBalance).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans

Abstract Background Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism. Results 13 CO 2 breath tests with germ-free C57BL/6 mice gavaged with 13 C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance ofAgathobacter rectalisandBilophila wadsworthiain cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice.Escherichia coliandEnterocloster clostridioformiswere identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although someE. clostridioformisgenomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derivedE. clostridioformisstrain. Conclusions Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.

Microbiology↗
DOE OSTI2024

Estimating Sparse Direct Effects in Multivariate Regression With the Spike-and-Slab LASSO

The multivariate regression interpretation of the Gaussian chain graph model simultaneously parametrizes (i) the direct effects of p predictors on q outcomes and (ii) the residual partial covariances between pairs of outcomes. We introduce a new method for fitting sparse versions of these models with spike-and-slab LASSO (SSL) priors. We develop an Expectation Conditional Maximization algorithm to obtain sparse estimates of the p × q matrix of direct effects and the q × q residual precision matrix. Our algorithm iteratively solves a sequence of penalized maximum likelihood problems with self-adaptive penalties that gradually filter out negligible regression coefficients and partial covariances. Because it adaptively penalizes individual model parameters, our method is seen to outperform fixed-penalty competitors on simulated data. We establish the posterior contraction rate for our model, buttressing our method’s excellent empirical performance with strong theoretical guarantees. Using our method, we estimated the direct effects of diet and residence type on the composition of the gut microbiome of elderly adults.

EM algorithm↗
DOE OSTI2020

Quantile-dependent expressivity of postprandial lipemia

“Quantile-dependent expressivity” describes an effect of the genotype that depends upon the level of the phenotype (e.g., whether a subject’s triglycerides are high or low relative to its population distribution). Prior analyses suggest that the effect of a genetic risk score (GRS) on fasting plasma triglyceride levels increases with the percentile of the triglyceride distribution. Postprandial lipemia is well suited for testing quantile-dependent expressivity because it exposes each individual’s genotype to substantial increases in their plasma triglyceride concentrations. Ninety-seven published papers were identified that plotted mean triglyceride response vs. time and genotype, which were converted into quantitative data. Separately, for each published graph, standard least-squares regression analysis was used to compare the genotype differences at time t (dependent variable) to average triglyceride concentrations at time t (independent variable) to assess whether the genetic effect size increased in association with higher triglyceride concentrations and whether the phenomenon could explain purported genetic interactions with sex, diet, disease, BMI, and drugs.

59 BASIC BIOLOGICAL SCIENCES↗