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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 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A synthetic co-culture for bioproduction of ammonia from methane and air

Abstract Fixed nitrogen fertilizers feed 50% of the global population, but most fixed nitrogen production occurs using energy-intensive Haber–Bosch-based chemistry combining nitrogen (N2) from air with gaseous hydrogen (H2) from methane (CH4) at high temperatures and pressures in large-scale facilities sensitive to supply chain disruptions. This work demonstrates the biological transformation of atmospheric N2 into ammonia (NH3) using CH4 as the sole carbon and energy source in a single vessel at ambient pressure and temperature, representing a biological “room-pressure and room-temperature” route to NH3 that could ultimately be developed to support compact, remote, NH3 production facilities amenable to distributed biomanufacturing. The synthetic microbial co-culture of engineered methanotroph Methylomicrobium buryatense (now Methylotuvimicrobium buryatense) and diazotroph Azotobacter vinelandii converted three CH4 molecules to l-lactate (C3H6O3) and powered gaseous N2 conversion to NH3. The design used division of labor and mutualistic metabolism strategies to address the oxygen sensitivity of nitrogenase and maximize CH4 oxidation efficiency. Media pH and salinity were central variables supporting co-cultivation. Carbon concentration heavily influenced NH3 production. Smaller-scale NH3 production near dispersed, abundant, and renewable CH4 sources could reduce disruption risks and capitalize on untapped energy resources. One-Sentence Summary Co-culture of engineered microorganisms Methylomicrobium buryatense and Azotobacter vinelandii facilitated the use of methane gas as a sole carbon feedstock to produce ammonia in an ambient temperature, atmospheric pressure, single-vessel system.

Biotechnology & Applied Microbiology↗
DOE OSTI2020

Unique contributions of chlorophyll and nitrogen to predict crop photosynthetic capacity from leaf spectroscopy

The photosynthetic capacity or the CO 2 -saturated photosynthetic rate (Vmax), chlorophyll, and nitrogen are closely linked leaf traits that determine C 4 crop photosynthesis and yield. Accurate, timely, rapid, and non-destructive approaches to predict leaf photosynthetic traits from hyperspectral reflectance are urgently needed for high-throughput crop monitoring to ensure food and bioenergy security. Therefore, this study thoroughly evaluated the state-of-the-art physically based radiative transfer models (RTMs), data-driven partial least squares regression (PLSR), and generalized PLSR (gPLSR) models to estimate leaf traits from leaf-clip hyperspectral reflectance, which was collected from maize (Zea mays L.) bioenergy plots with diverse genotypes, growth stages, treatments with nitrogen fertilizers, and ozone stresses in three growing seasons. The results show that leaf RTMs considering bidirectional effects can give accurate estimates of chlorophyll content (Pearson correlation r=0.95), while gPLSR enabled retrieval of leaf nitrogen concentration (r=0.85). Using PLSR with field measurements for training, the cross-validation indicates that V max can be well predicted from spectra (r=0.81). Here, the integration of chlorophyll content (strongly related to visible spectra) and nitrogen concentration (linked to shortwave infrared signals) can provide better predictions of V max (r=0.71) than only using either chlorophyll or nitrogen individually. This study highlights that leaf chlorophyll content and nitrogen concentration have key and unique contributions to V max prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25–30 plants h -1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH 4 NO 3 the benefit appears through N fixation, while at 0.5 mM NH 4 NO 3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Investigating biological nitrogen fixation via single-cell transcriptomics

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

Lotus japonicus↗
DOE OSTI2026

A Maize GT14 Family Glycosyltransferase Affects Cell Wall Composition and Carbohydrate Export from Source Leaves

Sucrose translocation from photosynthetic leaves to distant parts of a plant, such as seeds and roots, is a critical aspect of plant growth and development and a major determinant of crop yield. To identify genes contributing to this process in maize (Zea mays), we isolated four allelic mutants, carbohydrate partitioning defective7, 48, 49 (cpd7, cpd48, cpd49) and a UniformMu insertion (mu1049954), all of which exhibited reduced growth and fertility and hyperaccumulation of starch and soluble sugars in mature leaves. Consistent with carbohydrate accumulation, cpd7 mutants exhibited reduced sucrose export from mature leaves. Cpd7 encodes a Golgi-resident glucuronosyltransferase belonging to the Glycosyltransferase14 (GT14) family, which is involved in decoration of type II arabinogalactan proteins. No previously described GT14 mutants exhibit reduced sucrose transport or carbohydrate partitioning defects. Additionally, we show that mature leaves of cpd7 mutants have reduced cellulose content and an altered cell wall composition. Further, cpd7 mutants exhibit ectopic phloem lignification likely as a compensatory mechanism for reduced cell wall integrity. Collectively, our data suggest that Cpd7 functions to facilitate cell wall development in the phloem, which is required for efficient sucrose export from mature maize leaves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

A comprehensive overview of grain development in Brachypodium distachyon variety Bd21

A detailed and comprehensive understanding of seed reserve accumulation is of great importance for agriculture and crop improvement strategies. This work is part of a research programme aimed at using Brachypodium distachyon as a model plant for cereal grain development and filling. The focus was on the Bd21-3 accession, gathering morphological, cytological, and biochemical data, including protein, lipid, sugars, starch, and cell-wall analyses during grain development. This study highlighted the existence of three main developmental phases in Brachypodium caryopsis and provided an extensive description of Brachypodium grain development. In the first phase, namely morphogenesis, the embryo developed rapidly reaching its final morphology about 18 d after fertilization (DAF). Over the same period the endosperm enlarged, finally to occupy 80% of the grain volume. During the maturation phase, carbohydrates were continuously stored, mainly in the endosperm, switching from sucrose to starch accumulation. Large quantities of b-glucans accumulated in the endosperm with local variations in the deposition pattern. Interestingly, new b-glucans were found in Brachypodium compared with other cereals. Proteins (i.e. globulins and prolamins) were found in large quantities from 15 DAF onwards. These proteins were stored in two different sub-cellular structures which are also found in rice, but are unusual for the Pooideae. During the late stage of development, the grain desiccated while the dry matter remained fairly constant. Brachypodium exhibits some significant differences with domesticated cereals. Beta-glucan accumulates during grain development and this cell wall polysaccharide is the main storage carbohydrate at the expense of starch.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Formation of globular cluster candidates in merging proto-galaxies at high redshift: a view from the FIRE cosmological simulations

Using a state-of-the-art cosmological simulation of merging proto-galaxies at high redshift from the FIRE project, with explicit treatments of star formation and stellar feedback in the interstellar medium, we investigate the formation of star clusters and examine one of the formation hypotheses of present-day metal-poor globular clusters. Here, we find that frequent mergers in high-redshift proto-galaxies could provide a fertile environment to produce long-lasting bound star clusters. The violent merger event disturbs the gravitational potential and pushes a large gas mass of ≳ 10 5–6 M ⊙ collectively to high density, at which point it rapidly turns into stars before stellar feedback can stop star formation. The high dynamic range of the reported simulation is critical in realizing such dense star-forming clouds with a small dynamical time-scale, tff ≲ 3 Myr, shorter than most stellar feedback time-scales. Our simulation then allows us to trace how clusters could become virialized and tightly bound to survive for up to ~420 Myr till the end of the simulation. Finally, because the cluster's tightly bound core was formed in one short burst, and the nearby older stars originally grouped with the cluster tend to be preferentially removed, at the end of the simulation the cluster has a small age spread.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Aryl hydrocarbon receptor-dependent toxicity by retene requires metabolic competence

Polycyclic aromatic hydrocarbons (PAHs) are a class of organic compounds frequently detected in the environment with widely varying toxicities. Many PAHs activate the aryl hydrocarbon receptor (AHR), inducing the expression of a battery of genes, including xenobiotic metabolizing enzymes like cytochrome P450s (CYPs); however, not all PAHs act via this mechanism. We screened several parent and substituted PAHs in in vitro AHR activation assays to classify their unique activity. Retene (1-methyl-7-isopropylphenanthrene) displays Ahr2-dependent teratogenicity in zebrafish, but did not activate human AHR or zebrafish Ahr2, suggesting a retene metabolite activates Ahr2 in zebrafish to induce developmental toxicity. To investigate the role of metabolism in retene toxicity, studies were performed to determine the functional role of cyp1a, cyp1b1, and the microbiome in retene toxicity, identify the zebrafish window of susceptibility, and measure retene uptake, loss, and metabolite formation in vivo. Cyp1a-null fish were generated using CRISPR-Cas9. Cyp1a-null fish showed increased sensitivity to retene toxicity, whereas Cyp1b1-null fish were less susceptible, and microbiome elimination had no significant effect. Zebrafish required exposure to retene between 24 and 48 hours post fertilization (hpf) to exhibit toxicity. After static exposure, retene concentrations in zebrafish embryos increased until 24 hpf, peaked between 24 and 36 hpf, and decreased rapidly thereafter. We detected retene metabolites at 36 and 48 hpf, indicating metabolic onset preceding toxicity. This study highlights the value of combining molecular and systems biology approaches with mechanistic and predictive toxicology to interrogate the role of biotransformation in AHR-dependent toxicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

CO2 refixation is higher in leaves of woody species with high mesophyll and stomatal resistances to CO2 diffusion

Abstract The percentage of respiratory and photorespiratory CO2 refixed in leaves (Pr) represents part of the CO2 used in photosynthesis. The importance of Pr as well as differences between species and functional types are still not well investigated. In this study, we examine how Pr differs between six temperate and boreal woody species: Betula pendula, Quercus robur, Larix decidua, Pinus sylvestris, Picea abies and Vaccinium vitis-idaea. The study covers early and late successional species, deciduous broadleaves, deciduous conifers, evergreen conifers and evergreen broadleaves. We investigated whether some species or functional types had higher refixation percentages than others, whether leaf traits could predict higher Pr and whether these traits and their impact on Pr changed during growing seasons. Photosynthesis CO2 response (A/Ci)-curves, measured early, mid and late season, were used to estimate and compare Pr, mesophyll resistance (rm) and stomatal resistance (rs) to CO2 diffusion. Additionally, light images and transmission electron microscope images were used to approximate the fraction of intercellular airspace and cell wall thickness. We found that evergreens, especially late successional species, refixed a significantly higher amount of CO2 than the other species throughout the entire growing season. In addition, rm, rs and leaf mass per area, traits that typically are higher in evergreen species, were also significantly, positively correlated with Pr. We suggest that this is due to higher rm decreasing diffusion of (photo) respiratory CO2 out of the leaf. Cell wall thickness had a positive effect on Pr and rm, while the fraction of intercellular airspace had no effect. Both were significantly different between evergreen conifers and other types. Our findings suggest that species with a higher rm use a greater fraction of mitochondria-derived CO2, especially when stomatal conductance is low. This should be taken into account when modeling the overall CO2 fertilization effect for terrestrial ecosystems dominated by high rm species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Stand development and other intrinsic factors largely control fine-root dynamics with only subtle modifications from resource availability

Forest productivity depends on resource acquisition by ephemeral roots and leaves. A combination of intrinsic and environmental factors influences ephemeral organs; however, difficulties in studying belowground organs impede mechanistic understanding of fine-root production and turnover. To quantify factors controlling fine-root dynamics, we grew a deciduous hardwood (Populus deltoides Bartr.) and an evergreen conifer (Pinus taeda L.) with distinct soil moisture and nutrient availability treatments. We monitored fine-root dynamics with minirhizotrons for 6 years during early stand development and expressed results on a root length, biomass and mortality-risk basis. Stand development and other intrinsic factors consistently influenced both species in the same direction and by similar magnitude. Live-root length increased to a peak during establishment and slowly declined after roots of neighboring trees overlapped. Root longevity was highest during establishment and decreased thereafter. Root longevity consistently increased with depth of appearance and initial root diameter. Season of appearance affected root longevity in the following order: spring > summer > fall > winter. The influence of soil resource availability on fine-root dynamics was inconsistent between species, and ranked below that of rooting depth, initial diameter, stand development and phenology. Fine-root biomass either increased or was unaffected by greater resource availability. Fine-root production and live root length decreased with irrigation for both species, and increased with fertilization only for poplar. Fine-root mortality risk both increased and decreased depending on species and amendment treatment. Differing responses to soil moisture and nutrient availability between species suggests we should carefully evaluate generalizations about the response of fine-root dynamics to resource availability. Finally, while attempting to describe and explain carbon allocation to fine-root production and turnover, modelers and physiologists should first consider consistent patterns of allocation caused by different depth, diameter, stand development, phenology and species before considering allocation due to soil resource availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Over the past decades, crop yields have risen in parallel with increasing use of fossil-fuel derived nitrogen (N) fertilizers, but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic and endophytic plant growth promoting bacteria (PGPB) are known to stimulate plant growth. However, compared to the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix + ) or a fix - mutant strain (SmR54), compared to uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in situ laser ablation electrospray ionization mass spectrometry (LAESI-MS) to sample only those root segments at or adjacent to the sites of bacterial colonization. We report netabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix - strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix - strain, perhaps reflecting a plant defense response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Nitrogen fixation and resorption efficiency differences among twelve upland and lowland switchgrass cultivars

In nitrogen (N)-limited terrestrial ecosystems, plants employ various strategies to acquire and conserve N, including translocation of N in perennial tissues and stimulation of N fixation in roots and soils. Switchgrass (Panicum virgatum L.) is a genotypically and phenotypically diverse perennial grass with two distinct ecotypes (lowland and upland) and numerous genotypes. It grows well in low-N soils, likely because of its ability to translocate N and to associate with N-fixing microbes, but little is known about variation in these traits among cultivars or even ecotypes. We measured N translocation, N fixation potential in roots and soils, soil net N mineralization, soil net nitrification, and biomass yields in 12 switchgrass cultivars grown in a replicated block experiment in southwestern Michigan, USA. Lowland cultivars had higher yields, rates of N translocation, soil net N mineralization, and N fixation potentials on washed, non-sterile roots, while upland cultivars exhibited higher N fixation potentials in root-free soil. N resorption efficiencies averaged 53±5 [SE] % for lowland versus 29±3% for upland cultivars. Additionally, there were significant among-cultivar differences for all response variables except mineralization and nitrification, with differences likely explained by cultivar-specific physiologies and microbial communities. Here, the ideal cultivar for biofuels is one that can maintain high yields with minimal fertilizer addition and there appear to be several cultivars that meet these criteria. In addition, results suggest substantial N cycle differences among cultivars that might be exploited by breeders to create new or improved high-yielding, N-conserving switchgrass lines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Managing Plant Microbiomes for Sustainable Biofuel Production

The development of environmentally sustainable, economical, and reliable sources of energy is one of the great challenges of the 21st century. Large-scale cultivation of cellulosic feedstock crops (henceforth, bioenergy crops) is considered one of the most promising renewable sources for liquid transportation fuels. However, the mandate to develop a viable cellulosic bioenergy industry is accompanied by an equally urgent mandate to deliver not only cheap reliable biomass but also ecosystem benefits, including efficient use of water, nitrogen, and phosphorous; restored soil health; and net negative carbon emissions. Thus, sustainable bioenergy crop production may involve new agricultural practices or feedstocks and should be reliable, cost effective, and minimal input, without displacing crops currently grown for food production on fertile land. In this editorial perspective for the Phytobiomes Journal Focus Issue on Phytobiomes of Bioenergy Crops and Agroecosystems, we consider the microbiomes associated with bioenergy crops, the effects beneficial microbes have on their hosts, and potential ecosystem impacts of these interactions. We also address outstanding questions, major advances, and emerging biotechnological strategies to design and manipulate bioenergy crop microbiomes. This approach could simultaneously increase crop yields and provide important ecosystem services for a sustainable energy future.

09 BIOMASS FUELS↗
DOE OSTI2012

A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome

Spermatozoa are highly specialized cells that, when mature, are capable of navigating the female reproductive tract and fertilizing an oocyte. The sperm cell is thought to be largely quiescent in terms of transcriptional and translational activity. As a result, once it has left the male reproductive tract, the sperm cell is essentially operating with a static population of proteins. It is therefore theoretically possible to understand the protein networks contained in a sperm cell and to deduce its cellular function capabilities. To this end we have performed a proteomic analysis of mouse sperm isolated from the cauda epididymis and have confidently identified 2,850 proteins, which is the most comprehensive sperm proteome for any species reported to date. These proteins comprise many complete cellular pathways, including those for energy production via glycolysis, β-oxidation and oxidative phosphorylation, protein folding and transport, and cell signaling systems. This proteome should prove a useful tool for assembly and testing of protein networks important for sperm function.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2020

Phylogenetic conservation of soil bacterial responses to simulated global changes.

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Soil resistance and recovery during neotropical forest succession

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Wealth inequality in the prehispanic northern US Southwest: from Malthus to Tyche

Persistent differences in wealth and power among prehispanic Pueblo societies are visible from the late AD 800s through the late 1200s, after which large portions of the northern US Southwest were depopulated. In this paper we measure these differences in wealth using Gini coefficients based on house size, and show that high Ginis (large wealth differences) are positively related to persistence in settlements and inversely related to an annual measure of the size of the unoccupied dry-farming niche. We argue that wealth inequality in this record is due first to processes inherent in village life which have internally different distributions of the most productive maize fields, exacerbated by the dynamics of systems of balanced reciprocity; and second to decreasing ability to escape village life owing to shrinking availability of unoccupied places within the maize dry-farming niche as villages get enmeshed in regional systems of tribute or taxation. We embed this analytical reconstruction in the model of an ‘Abrupt imposition of Malthusian equilibrium in a natural-fertility, agrarian society’ proposed by Puleston et al. (Puleston C, Tuljapurkar S, Winterhalder B. 2014 PLoS ONE 9, e87541 (doi:10.1371/journal.pone.0087541)), but show that the transition to Malthusian dynamics in this area is not abrupt but extends over centuries. This article is part of the theme issue ‘Evolutionary ecology of inequality’.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant biology, showing distinct promoter methylation and evolution patterns (e.g., brain-specific genes evolve slowest, whereas testisspecific genes evolve fastest). Through integrative analyses of those tissue-specific genes with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle, including blood/immune system (e.g., CCDC88C) for male fertility, brain (e.g., TRIM46 and RAB6A) for milk production, and multiple growth-related tissues (e.g., FGF6 and CCND2) for body conformation. We validated these findings by using epigenomic data across major somatic tissues and sperm. Collectively, our findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and our transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.

59 BASIC BIOLOGICAL SCIENCES↗