Showing papers by "United States Department of Energy published in 2018"

Prevalence of Autism Spectrum Disorder Among Children Aged 8 Years — Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States, 2014

Abstract: Problem/condition Autism spectrum disorder (ASD). Period covered 2014. Description of system The Autism and Developmental Disabilities Monitoring (ADDM) Network is an active surveillance system that provides estimates of the prevalence of autism spectrum disorder (ASD) among children aged 8 years whose parents or guardians reside within 11 ADDM sites in the United States (Arizona, Arkansas, Colorado, Georgia, Maryland, Minnesota, Missouri, New Jersey, North Carolina, Tennessee, and Wisconsin). ADDM surveillance is conducted in two phases. The first phase involves review and abstraction of comprehensive evaluations that were completed by professional service providers in the community. Staff completing record review and abstraction receive extensive training and supervision and are evaluated according to strict reliability standards to certify effective initial training, identify ongoing training needs, and ensure adherence to the prescribed methodology. Record review and abstraction occurs in a variety of data sources ranging from general pediatric health clinics to specialized programs serving children with developmental disabilities. In addition, most of the ADDM sites also review records for children who have received special education services in public schools. In the second phase of the study, all abstracted information is reviewed systematically by experienced clinicians to determine ASD case status. A child is considered to meet the surveillance case definition for ASD if he or she displays behaviors, as described on one or more comprehensive evaluations completed by community-based professional providers, consistent with the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision (DSM-IV-TR) diagnostic criteria for autistic disorder; pervasive developmental disorder-not otherwise specified (PDD-NOS, including atypical autism); or Asperger disorder. This report provides updated ASD prevalence estimates for children aged 8 years during the 2014 surveillance year, on the basis of DSM-IV-TR criteria, and describes characteristics of the population of children with ASD. In 2013, the American Psychiatric Association published the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5), which made considerable changes to ASD diagnostic criteria. The change in ASD diagnostic criteria might influence ADDM ASD prevalence estimates; therefore, most (85%) of the records used to determine prevalence estimates based on DSM-IV-TR criteria underwent additional review under a newly operationalized surveillance case definition for ASD consistent with the DSM-5 diagnostic criteria. Children meeting this new surveillance case definition could qualify on the basis of one or both of the following criteria, as documented in abstracted comprehensive evaluations: 1) behaviors consistent with the DSM-5 diagnostic features; and/or 2) an ASD diagnosis, whether based on DSM-IV-TR or DSM-5 diagnostic criteria. Stratified comparisons of the number of children meeting either of these two case definitions also are reported. Results For 2014, the overall prevalence of ASD among the 11 ADDM sites was 16.8 per 1,000 (one in 59) children aged 8 years. Overall ASD prevalence estimates varied among sites, from 13.1-29.3 per 1,000 children aged 8 years. ASD prevalence estimates also varied by sex and race/ethnicity. Males were four times more likely than females to be identified with ASD. Prevalence estimates were higher for non-Hispanic white (henceforth, white) children compared with non-Hispanic black (henceforth, black) children, and both groups were more likely to be identified with ASD compared with Hispanic children. Among the nine sites with sufficient data on intellectual ability, 31% of children with ASD were classified in the range of intellectual disability (intelligence quotient [IQ] 85). The distribution of intellectual ability varied by sex and race/ethnicity. Although mention of developmental concerns by age 36 months was documented for 85% of children with ASD, only 42% had a comprehensive evaluation on record by age 36 months. The median age of earliest known ASD diagnosis was 52 months and did not differ significantly by sex or race/ethnicity. For the targeted comparison of DSM-IV-TR and DSM-5 results, the number and characteristics of children meeting the newly operationalized DSM-5 case definition for ASD were similar to those meeting the DSM-IV-TR case definition, with DSM-IV-TR case counts exceeding DSM-5 counts by less than 5% and approximately 86% overlap between the two case definitions (kappa = 0.85). Interpretation Findings from the ADDM Network, on the basis of 2014 data reported from 11 sites, provide updated population-based estimates of the prevalence of ASD among children aged 8 years in multiple communities in the United States. The overall ASD prevalence estimate of 16.8 per 1,000 children aged 8 years in 2014 is higher than previously reported estimates from the ADDM Network. Because the ADDM sites do not provide a representative sample of the entire United States, the combined prevalence estimates presented in this report cannot be generalized to all children aged 8 years in the United States. Consistent with reports from previous ADDM surveillance years, findings from 2014 were marked by variation in ASD prevalence when stratified by geographic area, sex, and level of intellectual ability. Differences in prevalence estimates between black and white children have diminished in most sites, but remained notable for Hispanic children. For 2014, results from application of the DSM-IV-TR and DSM-5 case definitions were similar, overall and when stratified by sex, race/ethnicity, DSM-IV-TR diagnostic subtype, or level of intellectual ability. Public health action Beginning with surveillance year 2016, the DSM-5 case definition will serve as the basis for ADDM estimates of ASD prevalence in future surveillance reports. Although the DSM-IV-TR case definition will eventually be phased out, it will be applied in a limited geographic area to offer additional data for comparison. Future analyses will examine trends in the continued use of DSM-IV-TR diagnoses, such as autistic disorder, PDD-NOS, and Asperger disorder in health and education records, documentation of symptoms consistent with DSM-5 terminology, and how these trends might influence estimates of ASD prevalence over time. The latest findings from the ADDM Network provide evidence that the prevalence of ASD is higher than previously reported estimates and continues to vary among certain racial/ethnic groups and communities. With prevalence of ASD ranging from 13.1 to 29.3 per 1,000 children aged 8 years in different communities throughout the United States, the need for behavioral, educational, residential, and occupational services remains high, as does the need for increased research on both genetic and nongenetic risk factors for ASD.

Carbon capture and storage (CCS): the way forward

Abstract: Carbon capture and storage (CCS) is broadly recognised as having the potential to play a key role in meeting climate change targets, delivering low carbon heat and power, decarbonising industry and, more recently, its ability to facilitate the net removal of CO2 from the atmosphere. However, despite this broad consensus and its technical maturity, CCS has not yet been deployed on a scale commensurate with the ambitions articulated a decade ago. Thus, in this paper we review the current state-of-the-art of CO2 capture, transport, utilisation and storage from a multi-scale perspective, moving from the global to molecular scales. In light of the COP21 commitments to limit warming to less than 2 °C, we extend the remit of this study to include the key negative emissions technologies (NETs) of bioenergy with CCS (BECCS), and direct air capture (DAC). Cognisant of the non-technical barriers to deploying CCS, we reflect on recent experience from the UK's CCS commercialisation programme and consider the commercial and political barriers to the large-scale deployment of CCS. In all areas, we focus on identifying and clearly articulating the key research challenges that could usefully be addressed in the coming decade.

Earth BioGenome Project: Sequencing life for the future of life.

Abstract: Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project’s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

Probing magnetism in 2D van der Waals crystalline insulators via electron tunneling.

Abstract: Magnetic insulators are a key resource for next-generation spintronic and topological devices. The family of layered metal halides promises varied magnetic states, including ultrathin insulating multiferroics, spin liquids, and ferromagnets, but device-oriented characterization methods are needed to unlock their potential. Here, we report tunneling through the layered magnetic insulator CrI3 as a function of temperature and applied magnetic field. We electrically detect the magnetic ground state and interlayer coupling and observe a field-induced metamagnetic transition. The metamagnetic transition results in magnetoresistances of 95, 300, and 550% for bilayer, trilayer, and tetralayer CrI3 barriers, respectively. We further measure inelastic tunneling spectra for our junctions, unveiling a rich spectrum consistent with collective magnetic excitations (magnons) in CrI3.

Genomics of the origin and evolution of Citrus

Abstract: The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins This work provides a new evolutionary framework for the genus Citrus The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups

Enhancer redundancy provides phenotypic robustness in mammalian development

Abstract: Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers

Host-linked soil viral ecology along a permafrost thaw gradient

Abstract: Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Abstract: Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

Sustained climate warming drives declining marine biological productivity.

Abstract: Climate change projections to the year 2100 may miss physical-biogeochemical feedbacks that emerge later from the cumulative effects of climate warming. In a coupled climate simulation to the year 2300, the westerly winds strengthen and shift poleward, surface waters warm, and sea ice disappears, leading to intense nutrient trapping in the Southern Ocean. The trapping drives a global-scale nutrient redistribution, with net transfer to the deep ocean. Ensuing surface nutrient reductions north of 30°S drive steady declines in primary production and carbon export (decreases of 24 and 41%, respectively, by 2300). Potential fishery yields, constrained by lower–trophic-level productivity, decrease by more than 20% globally and by nearly 60% in the North Atlantic. Continued high levels of greenhouse gas emissions could suppress marine biological productivity for a millennium.

Phase Modulation of (1T-2H)-MoSe2/TiC-C Shell/Core Arrays via Nitrogen Doping for Highly Efficient Hydrogen Evolution Reaction.

Abstract: Tailoring molybdenum selenide electrocatalysts with tunable phase and morphology is of great importance for advancement of hydrogen evolution reaction (HER). In this work, phase- and morphology-modulated N-doped MoSe2 /TiC-C shell/core arrays through a facile hydrothermal and postannealing treatment strategy are reported. Highly conductive TiC-C nanorod arrays serve as the backbone for MoSe2 nanosheets to form high-quality MoSe2 /TiC-C shell/core arrays. Impressively, continuous phase modulation of MoSe2 is realized on the MoSe2 /TiC-C arrays. Except for the pure 1T-MoSe2 and 2H-MoSe2 , mixed (1T-2H)-MoSe2 nanosheets are achieved in the N-MoSe2 by N doping and demonstrated by spherical aberration electron microscope. Plausible mechanism of phase transformation and different doping sites of N atom are proposed via theoretical calculation. The much smaller energy barrier, longer HSe bond length, and diminished bandgap endow N-MoSe2 /TiC-C arrays with substantially superior HER performance compared to 1T and 2H phase counterparts. Impressively, the designed N-MoSe2 /TiC-C arrays exhibit a low overpotential of 137 mV at a large current density of 100 mA cm-2 , and a small Tafel slope of 32 mV dec-1 . Our results pave the way to unravel the enhancement mechanism of HER on 2D transition metal dichalcogenides by N doping.

Energy Management and Optimization Methods for Grid Energy Storage Systems

Abstract: Today, the stability of the electric power grid is maintained through real time balancing of generation and demand. Grid scale energy storage systems are increasingly being deployed to provide grid operators the flexibility needed to maintain this balance. Energy storage also imparts resiliency and robustness to the grid infrastructure. Over the last few years, there has been a significant increase in the deployment of large scale energy storage systems. This growth has been driven by improvements in the cost and performance of energy storage technologies and the need to accommodate distributed generation, as well as incentives and government mandates. Energy management systems (EMSs) and optimization methods are required to effectively and safely utilize energy storage as a flexible grid asset that can provide multiple grid services. The EMS needs to be able to accommodate a variety of use cases and regulatory environments. In this paper, we provide a brief history of grid-scale energy storage, an overview of EMS architectures, and a summary of the leading applications for storage. These serve as a foundation for a discussion of EMS optimization methods and design.

Material-based figure of merit for caloric materials

Abstract: The efficient use of reversible thermal effects in magnetocaloric, electrocaloric, and elastocaloric materials is a promising avenue that can lead to a substantially increased efficiency of refrigeration and heat pumping devices, most importantly, those used in household and commercial cooling applications near ambient temperature. A proliferation in caloric material research has resulted in a wide array of materials where only the isothermal change in entropy in response to a handful of different field strengths over a limited range of temperatures has been evaluated and reported. Given the abundance of such data, there is a clear need for a simple and reliable figure of merit enabling fast screening and down-selection to justify further detailed characterization of those material systems that hold the greatest promise. Based on the analysis of several well-known materials that exhibit vastly different magnetocaloric effects, the Temperature averaged Entropy Change is introduced as a suitable early indicator of the material's utility for magnetocaloric cooling applications, and its adoption by the caloric community is recommended.

A practical field guide to thermoelectrics: Fundamentals, synthesis, and characterization

Abstract: The study of thermoelectric materials spans condensed matter physics, materials science and engineering, and solid-state chemistry. The diversity of the participants and the inherent complexity of the topic mean that it is difficult, if not impossible, for a researcher to be fluent in all aspects of the field. This review, which grew out of a one-week summer school for graduate students, aims to provide an introduction and practical guidance for selected conceptual, synthetic, and characterization approaches and to craft a common umbrella of language, theory, and experimental practice for those engaged in the field of thermoelectric materials. This review does not attempt to cover all major aspects of thermoelectric materials research or review state-of-the-art thermoelectric materials. Rather, the topics discussed herein reflect the expertise and experience of the authors. We begin by discussing a universal approach to modeling electronic transport using Landauer theory. The core sections of the review are focused on bulk inorganic materials and include a discussion of effective strategies for powder and single crystal synthesis, the use of national synchrotron sources to characterize crystalline materials, error analysis, and modeling of transport data using an effective mass model, and characterization of phonon behavior using inelastic neutron scattering and ultrasonic speed of sound measurements. The final core section discusses the challenges faced when synthesizing carbon-based samples and the measuring or interpretation of their transport properties. We conclude this review with a brief discussion of some of the grand challenges and opportunities that remain to be addressed in the study of thermoelectrics.

Hydrogen at Scale (H2@Scale): Key to a Clean, Economic, and Sustainable Energy System

Abstract: Much of hydrogen's value to the energy-system lies in its ability to be cleanly and efficiently converted between chemical and electrical energy, while also possessing the high energy density and long-term storage potential of chemical bonds. For these reasons, hydrogen's importance is expected to grow substantially in the coming decades, providing cross-sector and cross-temporal impact through clean, efficient processes. Many of these processes are electrochemical in nature, such as electrolysis of water and electricity production using fuel cells. Hydrogen also offers significant flexibility in how it can integrate into the energy system as a function of scale (from W to GWs), source (fossil fuels, nuclear, biomass, solar, wind, thermal), and end use (grid, buildings, industry, transportation). This flexibility, along with the ability to be used as a dispatchable load or power generation source, allows hydrogen and hydrogen-based processes to couple with the overall energy system in an integrated or hybridized fashion, offering dramatic system optimization potential. However, achieving the scale necessary to have impact – the vision 'Hydrogen at Scale' (H2@Scale)" still has research challenges, many of which center around electrochemistry.

Probing magnetism in 2D van der Waals crystalline insulators via electron tunneling

Abstract: Magnetic insulators are a key resource for next-generation spintronic and topological devices The family of layered metal halides promises ultrathin insulating multiferroics, spin liquids, and ferromagnets, but new characterization methods are required to unlock their potential Here, we report tunneling through the layered magnetic insulator CrI3 as a function of temperature and applied magnetic field We electrically detect the magnetic ground state and inter-layer coupling and observe a field-induced metamagnetic transition The metamagnetic transition results in magnetoresistances of 95%, 300%, and 550% for bilayer, trilayer, and tetralayer CrI3 barriers, respectively We further measure inelastic tunneling spectra for our junctions, unveiling a rich spectrum of collective magnetic excitations (magnons) in CrI3 Our results establish vertical tunneling as a versatile probe of magnetism in atomically thin insulators

High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.

Abstract: Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Abstract: Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

Abstract: Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

Abstract: The regulatory specificity of enhancers and their interaction with gene promoters is thought to be controlled by their sequence and the binding of transcription factors. By studying Pitx1, a regulator of hindlimb development, we show that dynamic changes in chromatin conformation can restrict the activity of enhancers. Inconsistent with its hindlimb-restricted expression, Pitx1 is controlled by an enhancer (Pen) that shows activity in forelimbs and hindlimbs. By Capture Hi-C and three-dimensional modeling of the locus, we demonstrate that forelimbs and hindlimbs have fundamentally different chromatin configurations, whereby Pen and Pitx1 interact in hindlimbs and are physically separated in forelimbs. Structural variants can convert the inactive into the active conformation, thereby inducing Pitx1 misexpression in forelimbs, causing partial arm-to-leg transformation in mice and humans. Thus, tissue-specific three-dimensional chromatin conformation can contribute to enhancer activity and specificity in vivo and its disturbance can result in gene misexpression and disease.

Genome-reconstruction for eukaryotes from complex natural microbial communities.

Abstract: Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.

Abstract: Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.

Abstract: Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.