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Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

Past research at the Advanced Light Source (ALS) provided a proof-of-principle demonstration that deep learning methods could be effectively employed to compensate for the significant perturbations to the transverse electron beam size induced by user-controlled adjustments of the insertion devices. However, incorporating these methods into the ALS' daily operations has faced notable challenges. The complexity of the system's operational requirements and the significant upkeep demands has restricted their sustained application during user operation. Here, we introduce the development of a more robust neural network (NN)-based algorithm that utilizes a novel online fine-tuning approach and its systematic integration into the day-to-day machine operations. Our analysis emphasizes the process of NN model selection, demonstrates the superior performance of the NN-based method over traditional feedback methods, and examines the effectiveness and resilience of the new algorithm during user-operation scenarios.

Most of Earths trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earths land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

The beamline optics and endstations at branch B of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source are described. B07-B provides medium-flux X-rays in the range 45-2200 eV from a bending magnet source, giving access to local electronic structure for atoms of all elements from Li to Y. It has an endstation for high-throughput X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) measurements under ultrahigh-vacuum (UHV) conditions. B07-B has a second endstation dedicated to NEXAFS at pressures from UHV to ambient pressure (1 atm). The combination of these endstations permits studies of a wide range of interfaces and materials. The beamline and endstation designs are discussed in detail, as well as their performance and the commissioning process.

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

Fourth-generation storage rings enabled by multi-bend achromat lattices are being inaugurated worldwide and many more are planned for the next decade. These sources deliver stable ultra-high brightness radiation with unmatched levels of transverse coherence by virtue of their highly advanced magnetic lattices. Optimization of these challenging and strongly nonlinear lattices with many degrees of freedom bounded by extensive sets of constraints and multiple often conflicting optimization goals is highly demanding and requires application of the most advanced numerical tools available to the community. While multi-objective genetic algorithms have been very successful in supporting these optimization efforts, the algorithms suffer from a fundamental limitation of their stochastic nature: an exceedingly vast number of candidate lattices, most of which eventually are rejected, has to be fully evaluated. This comes at immense computational cost and thus drives excessive runtime despite use of large supercomputing clusters. We therefore propose to employ deep learning techniques and iterative retraining of neural networks to massively accelerate such lattice evaluation, thereby allowing lattice optimization to rely on far fewer a priori assumptions, open up to larger search ranges, and include right from the start and in parallel multiple error distributions to find truly global optima, all while completing a full optimization campaign in weeks rather than months. In this paper we present the neural network designs, the deep learning approach, iterative retraining procedures, and demonstrate how these machine learning techniques can be incorporated into existing state-of-the-art optimization workflows with only minimal changes applied to the optimization pipeline itself and none at all to the employed tracking codes.

The ALS-U is the upgrade of the existing Lawrence Berkeley National Laboratory Advanced Light Source to a diffraction-limited soft x-ray light source. Here we present the lattice correction studies and commissioning simulations demonstrating that the proposed machine design can be expected to deliver the intended performance when realistic errors and perturbations are fully accounted for. Critical to this demonstration are the high-fidelity, realistic simulations of the beam-based alignment process (both in turn-by-turn mode during early commissioning and with stored beam) that are now made possible by the Toolkit for Simulated Commissioning. In addition to presenting a statistical performance analysis based on a large number of lattice error realizations, we also study the range of further improvements that can be obtained by fine-tuning the correction chain to individual error seeds, mimicking the approach one would follow once the machine is built.

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles.

We examine the effect of higher-harmonic passive cavities (HHCs) on the beam response to rf noise. Upon invoking certain assumptions to make the problem tractable, we employ Vlasov methods to show that when the dipole approximation applies the HHCs have a generally limited impact. Beam loading in the main cavity is included in the analysis. We illustrate our results and the limitations of our model in application to the Lawrence Berkeley National Laboratory ALS (Advanced Light Source) and the future ALS Upgrade (ALS-U) offering validation against macroparticle simulations.

The Advanced Light Source Upgrade (ALS-U) is a 4th generation diffraction-limited soft x-ray radiation source, consisting of a new accumulator ring (AR) and a new storage ring (SR). In both rings coupling-impedance driven instabilities need careful evaluation to ensure meeting the machine's high-performance goals. This paper presents the workflow followed in building the impedance models and the beam-stability analysis based on those models. We follow the commonly accepted approach of separating the resistive-wall and the geometric parts of the impedance; the former is obtained by analytical formulas, the latter by numerical electro-magnetic codes (primarily CST Studio software) with perfectly-conducting boundary conditions. Impedance budgets are established and pseudo-Green functions calculated to be used in beam dynamics studies. We also present various ways to cross-check simulation results for reliable impedance modeling. Finally, the crucial single-bunch instability current thresholds for various operation modes are determined and discussed.

The Advanced Light Source Upgrade will implement on axis single-train swap-out injection employing an accumulator between the booster and storage rings. The accumulator ring (AR) design is a twelve period triple-bend achromat that will be installed along the inner circumference of the storage-ring tunnel. A nonconventional injection scheme will be utilized for top-off off axis injection from the booster into the AR meant to accommodate a large ∼300 nm emittance beam into a vacuum-chamber with a limiting horizontal aperture radius as small as 8 mm. The scheme incorporates three dipole kickers distributed over three sectors, with two kickers perturbing the stored beam and the third affecting both the stored and the injected beam trajectories. This paper describes this "3DK"injection scheme and how it fits the AR's particular requirements. We describe the design and optimization process, and how we evaluated its fitness as a solution for booster-to-accumulator ring injection.

DNMT3A encodes an enzyme that carries out de novo DNA methylation, which is essential for the acquisition of cellular identity and specialized functions during cellular differentiation. DNMT3A is the most frequently mutated gene in age-related clonal hematopoiesis. As such, mature immune cells harboring DNMT3A mutations can be readily detected in elderly persons. Most DNMT3A mutations associated with clonal hematopoiesis are heterozygous and predicted to cause loss of function, indicating that haploinsufficiency is the predominant pathogenic mechanism. Yet, the impact of DNMT3A haploinsufficiency on the function of mature immune cells is poorly understood. Here, we demonstrate that DNMT3A haploinsufficiency impairs the gain of DNA methylation at decommissioned enhancers, while simultaneously and unexpectedly impairing DNA demethylation of newly activated enhancers in mature human myeloid cells. The DNA methylation defects alter the activity of affected enhancers, leading to abnormal gene expression and impaired immune response. These findings provide insights into the mechanism of immune dysfunction associated with clonal hematopoiesis and acquired DNMT3A mutations.

The ALS-U light source will implement on-axis single-train swap-out injectionemploying an accumulator between the booster and storage rings. The accumulatorring design is a twelve period triple-bend achromat that will be installedalong the inner circumference of the storage-ring tunnel. A non-conventionalinjection scheme will be utilized for top-off off-axis injection from thebooster into the accumulator ring meant to accommodate a large $\sim 300$~nmemittance beam into a vacuum-chamber with a limiting horizontal aperture radiusas small as $8$ mm. The scheme incorporates three dipole kickers distributedover three sectors, with two kickers perturbing the stored beam and the thirdaffecting both the stored and the injected beam trajectories. This paperdescribes this ``3DK'' injection scheme and how it fits the accumulator ring'sparticular requirements. We describe the design and optimization process, andhow we evaluated its fitness as a solution for booster-to-accumulator ringinjection.

The ALS-U light source will implement on-axis single-train swap-out injectionemploying an accumulator between the booster and storage rings. The accumulatorring design is a twelve period triple-bend achromat that will be installedalong the inner circumference of the storage-ring tunnel. A non-conventionalinjection scheme will be utilized for top-off off-axis injection from thebooster into the accumulator ring meant to accommodate a large $\sim 300$~nmemittance beam into a vacuum-chamber with a limiting horizontal aperture radiusas small as $8$ mm. The scheme incorporates three dipole kickers distributedover three sectors, with two kickers perturbing the stored beam and the thirdaffecting both the stored and the injected beam trajectories. This paperdescribes this ``3DK'' injection scheme and how it fits the accumulator ring'sparticular requirements. We describe the design and optimization process, andhow we evaluated its fitness as a solution for booster-to-accumulator ringinjection.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.

The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.

The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We identify five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The missense variant Val94Met (rs17151919) in LEP was common in individuals of African ancestry only, and its association with lower leptin concentrations was specific to this ancestry (P = 2 × 10-16, n = 3,901). Using in vitro analyses, we show that the Met94 allele decreases leptin secretion. We also show that the Met94 allele is associated with higher BMI in young African-ancestry children but not in adults, suggesting that leptin regulates early adiposity.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Floral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in adjacent fields by 16% on average. However, effects on crop pollination and yield were more variable. Our synthesis identifies several important drivers of variability in effectiveness of plantings: pollination services declined exponentially with distance from plantings, and perennial and older flower strips with higher flowering plant diversity enhanced pollination more effectively. These findings provide promising pathways to optimise floral plantings to more effectively contribute to ecosystem service delivery and ecological intensification of agriculture in the future.

We study the effect of a passive harmonic cavity, introduced to cause bunch lengthening, in an electron storage ring. We derive a formula for the induced voltage from such a cavity with high Q, excited by a sequence of bunches, allowing for arbitrary gaps in the sequence and arbitrary currents. Except for a minor term that can be determined iteratively, the voltage is given in terms of a single mode of the Fourier transforms of the bunch forms, namely, the mode at the resonant frequency of the cavity. Supposing that the only wakefield is from the harmonic cavity, we derive a system of coupled Haïssinski equations which determine the bunch positions and profiles in the equilibrium state. The number of unknowns in the system is only twice the number of bunches, and it can be solved quickly by a Newton iteration, starting with a guess determined by path following from a solution at a weak current. We explore the effect of the fill pattern on the bunch lengthening and also the dependence on the shunt impedance and detuning of the cavity away from the third harmonic of the main accelerating cavity. We consider two measures to reduce the effects of gaps: (i) distribution of the gaps around the ring to the greatest extent allowed and (ii) "guard bunches"with higher charges adjacent to the gaps, compensating for the charge missing in gaps. Results for parameters of the forthcoming Advanced Light Source upgrade are presented.

We study the effect of a passive harmonic cavity, introduced to cause bunch lengthening, in an electron storage ring. We derive a formula for the induced voltage from such a cavity with high Q, excited by a sequence of bunches, allowing for arbitrary gaps in the sequence and arbitrary currents. Except for a minor term that can be determined iteratively, the voltage is given in terms of a single mode of the Fourier transforms of the bunch forms, namely, the mode at the resonant frequency of the cavity. Supposing that the only wakefield is from the harmonic cavity, we derive a system of coupled Haïssinski equations which determine the bunch positions and profiles in the equilibrium state. The number of unknowns in the system is only twice the number of bunches, and it can be solved quickly by a Newton iteration, starting with a guess determined by path following from a solution at a weak current. We explore the effect of the fill pattern on the bunch lengthening and also the dependence on the shunt impedance and detuning of the cavity away from the third harmonic of the main accelerating cavity. We consider two measures to reduce the effects of gaps: (i) distribution of the gaps around the ring to the greatest extent allowed and (ii) "guard bunches"with higher charges adjacent to the gaps, compensating for the charge missing in gaps. Results for parameters of the forthcoming Advanced Light Source upgrade are presented.

The concept of using a single nonlinear kicker (NLK) to inject electron beams into a storage ring has been proposed and tested in several synchrotron radiation light source facilities. Different from pulsed dipole kicker magnets used in a conventional local-bump injection, the single nonlinear kicker provides a nonlinear distribution of magnetic fields which has a maximum value off axis where the injected beam arrives and a zero or near-zero value at the center where the stored beam passes by. Therefore, the injected beam will receive a kick from the NLK and lose its transverse momentum, and will be eventually captured by the storage ring. In the meantime the stored beam at the center will receive no kick or less kick, which significantly reduces the injection perturbations on the stored beam. In addition, the NLK injection requires less space for the kicker and removes the complications of synchronizing four pulsed kicker magnets. Because of these advantages, several light source facilities are either proposing or already using this NLK injection as a replacement of the conventional local-bump injection scheme. In this paper, we will discuss the working principal of this NLK injection, and use both Advanced Light Source and Advanced Light source Upgrade as examples to optimize the NLK injections. By optimizing the NLK design and injection conditions, we could achieve maximum injection efficiencies for both facilities with a large injected beam from the existing ALS booster.

The concept of using a single nonlinear kicker (NLK) to inject electron beams into a storage ring has been proposed and tested in several synchrotron radiation light source facilities. Different from pulsed dipole kicker magnets used in a conventional local-bump injection, the single nonlinear kicker provides a nonlinear distribution of magnetic fields which has a maximum value off axis where the injected beam arrives and a zero or near-zero value at the center where the stored beam passes by. Therefore, the injected beam will receive a kick from the NLK and lose its transverse momentum, and will be eventually captured by the storage ring. In the meantime the stored beam at the center will receive no kick or less kick, which significantly reduces the injection perturbations on the stored beam. In addition, the NLK injection requires less space for the kicker and removes the complications of synchronizing four pulsed kicker magnets. Because of these advantages, several light source facilities are either proposing or already using this NLK injection as a replacement of the conventional local-bump injection scheme. In this paper, we will discuss the working principal of this NLK injection, and use both Advanced Light Source and Advanced Light source Upgrade as examples to optimize the NLK injections. By optimizing the NLK design and injection conditions, we could achieve maximum injection efficiencies for both facilities with a large injected beam from the existing ALS booster.

We present a new accelerator toolbox (AT)-based toolkit for simulating the commissioning of light-source storage rings. The toolkit provides a framework for supporting high-level scripts to represent with realism the various procedures (e.g., orbit and optics correction, beam-based alignment, etc.) encountered during commissioning and is designed to mirror as closely as possible the reality as seen from the control room. Emphasis is placed on the inclusion of a comprehensive set of error sources and faithful modeling of beam diagnostics. The toolkit capabilities are demonstrated in an application to the recent design and commissioning studies of the Advanced Light Source Upgrade (ALS-U) Accumulator Ring, a short-time successful commissioning of which will be critical to the overall ALS-U project success.

We present a new accelerator toolbox (AT)-based toolkit for simulating the commissioning of light-source storage rings. The toolkit provides a framework for supporting high-level scripts to represent with realism the various procedures (e.g., orbit and optics correction, beam-based alignment, etc.) encountered during commissioning and is designed to mirror as closely as possible the reality as seen from the control room. Emphasis is placed on the inclusion of a comprehensive set of error sources and faithful modeling of beam diagnostics. The toolkit capabilities are demonstrated in an application to the recent design and commissioning studies of the Advanced Light Source Upgrade (ALS-U) Accumulator Ring, a short-time successful commissioning of which will be critical to the overall ALS-U project success.

Circulating levels of adiponectin, an adipocyte-secreted protein associated with cardiovascular and metabolic risk, are highly heritable. To gain insights into the biology that regulates adiponectin levels, we performed an exome array meta-analysis of 265,780 genetic variants in 67,739 individuals of European, Hispanic, African American, and East Asian ancestry. We identified 20 loci associated with adiponectin, including 11 that had been reported previously (p < 2 × 10-7). Comparison of exome array variants to regional linkage disequilibrium (LD) patterns and prior genome-wide association study (GWAS) results detected candidate variants (r2 > .60) spanning as much as 900 kb. To identify potential genes and mechanisms through which the previously unreported association signals act to affect adiponectin levels, we assessed cross-trait associations, expression quantitative trait loci in subcutaneous adipose, and biological pathways of nearby genes. Eight of the nine loci were also associated (p < 1 × 10-4) with at least one obesity or lipid trait. Candidate genes include PRKAR2A, PTH1R, and HDAC9, which have been suggested to play roles in adipocyte differentiation or bone marrow adipose tissue. Taken together, these findings provide further insights into the processes that influence circulating adiponectin levels.

With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.

We introduce a perturbation-theory, mode-analysis method for longitudinal multibunch instabilities driven by the higher harmonic cavity (HHC) fundamental mode. The method, based on the exact solution of the unperturbed particle motion in the rf bucket and suitable for modeling the effect of cavities with general settings, is applied to study the feasibility of reutilizing the existing Advanced Light Source (ALS) HHCs in the ALS Upgrade (ALS-U). We find that with ALS cavities the ALS-U would be susceptible to a fast =1 mode instability. Interestingly, the instability is driven by the imaginary rather than the real part of the cavity fundamental-mode impedance.

We introduce a perturbation-theory, mode-analysis method for longitudinal multibunch instabilities driven by the higher harmonic cavity (HHC) fundamental mode. The method, based on the exact solution of the unperturbed particle motion in the rf bucket and suitable for modeling the effect of cavities with general settings, is applied to study the feasibility of reutilizing the existing Advanced Light Source (ALS) HHCs in the ALS Upgrade (ALS-U). We find that with ALS cavities the ALS-U would be susceptible to a fast =1 mode instability. Interestingly, the instability is driven by the imaginary rather than the real part of the cavity fundamental-mode impedance.

The ALS upgrade into a diffraction-limited soft x-rays light source requires a small emittance, which is achieved by much stronger focusing than in the present ALS. Very strong focusing elements and a relatively small vacuum chamber make the required rapid commissioning a significant challenge. This paper will describe the progress towards a start-to-end simulation of the machine commissioning and present first simulation results.

The effect of rf harmonic cavities on the transverse mode-coupling instability (TMCI) is still not very well understood. We offer a fresh perspective on the problem by proposing a new numerical method for mode analysis and investigating a regime of potential interest to the new generation of light sources where resistive wall is the dominant source of transverse impedance. When the harmonic cavities are tuned for maximum flattening of the bunch profile we demonstrate that at vanishing chromaticities the transverse single-bunch motion is unstable at any current, with growth rate that in the relevant range scales as the 6th power of the current. With these assumptions and radiation damping included, we find that for machine parameters typical of 4th-generation light sources the presence of harmonic cavities could reduce the instability current threshold by more than a factor two.

The effect of rf harmonic cavities on the transverse mode-coupling instability (TMCI) is still not very well understood. We offer a fresh perspective on the problem by proposing a new numerical method for mode analysis and investigating a regime of potential interest to the new generation of light sources where resistive wall is the dominant source of transverse impedance. When the harmonic cavities are tuned for maximum flattening of the bunch profile we demonstrate that at vanishing chromaticities the transverse single-bunch motion is unstable at any current, with growth rate that in the relevant range scales as the 6th power of the current. With these assumptions and radiation damping included, we find that for machine parameters typical of 4th-generation light sources the presence of harmonic cavities could reduce the instability current threshold by more than a factor two.

The ALS-U upgrade promises to deliver diffraction limited performance throughout the soft x-ray range by lowering the horizontal emittance to about 50 pm resulting in 2-3 orders of brightness increase for soft x-rays compared to the current ALS. The design utilizes a multi bend achromat lattice with on-axis swap-out injection and an accumulator ring. One central design goal is to install and commission ALS-U within a short dark period. This paper summarizes the status of the conceptual design of the accelerator, as well as some results of the R&D program that has been ongoing for the last 3 years.

The shot-noise driven microbunching instability can significantly degrade electron beam quality in x-ray free electron laser light sources. Experiments were carried out at the Linac Coherent Light Source (LCLS) to study this instability. In this paper, we present start-to-end simulations of the shot-noise driven microbunching instability experiment at the LCLS using the real number of electrons. The simulation results reproduce the measurements quite well. A microbunching self-heating mechanism is also illustrated in the simulation, which helps explain the experimental observation.

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

The shot-noise driven microbunching instability can significantly degrade electron beam quality in x-ray free electron laser light sources. Experiments were carried out at the Linac Coherent Light Source (LCLS) to study this instability. In this paper, we present start-to-end simulations of the shot-noise driven microbunching instability experiment at the LCLS using the real number of electrons. The simulation results reproduce the measurements quite well. A microbunching self-heating mechanism is also illustrated in the simulation, which helps explain the experimental observation.

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.

Excessive alcohol consumption is a major public health problem worldwide. Although drinking habits are known to be inherited, few genes have been identified that are robustly linked to alcohol drinking. We conducted a genome-wide association metaanalysis and replication study among >105,000 individuals of European ancestry and identified β-Klotho (KLB) as a locus associated with alcohol consumption (rs11940694; P = 9.2 × 10-12). β-Klotho is an obligate coreceptor for the hormone FGF21, which is secreted from the liver and implicated in macronutrient preference in humans. We show that brain-specific β-Klotho KO mice have an increased alcohol preference and that FGF21 inhibits alcohol drinking by acting on the brain. These data suggest that a liver-brain endocrine axis may play an important role in the regulation of alcohol drinking behavior and provide a unique pharmacologic target for reducing alcohol consumption.

Excessive alcohol consumption is a major public health problem worldwide. Although drinking habits are known to be inherited, few genes have been identified that are robustly linked to alcohol drinking. We conducted a genome-wide association metaanalysis and replication study among >105,000 individuals of European ancestry and identified β-Klotho (KLB) as a locus associated with alcohol consumption (rs11940694; P = 9.2 × 10-12). β-Klotho is an obligate coreceptor for the hormone FGF21, which is secreted from the liver and implicated in macronutrient preference in humans. We show that brain-specific β-Klotho KO mice have an increased alcohol preference and that FGF21 inhibits alcohol drinking by acting on the brain. These data suggest that a liver-brain endocrine axis may play an important role in the regulation of alcohol drinking behavior and provide a unique pharmacologic target for reducing alcohol consumption.

The need to operate an rf-gun-based electron photoinjector with a beam emitted away from the cathode center can occur under various circumstances. First, in some cases the cathode can be affected by ion back-bombardment that progressively reduces the quantum efficiency (QE) in its center, making off-axis operation mandatory; second, in some cases the drive laser intensity can be sufficiently high to generate QE depletion in the cathode area illuminated by the laser, forcing off-axis operation; last, in cathodes with nonuniform QE distribution it could be convenient to operate off axis to exploit a better QE. However, operation in this mode may lead to growth of the projected transverse beam emittances due to correlations between the transverse and longitudinal degrees of freedom that are introduced within the gun and downstream rf cavities. A strategy is described to mitigate this emittance growth by allowing the beam to propagate along a carefully tuned off-axis trajectory in downstream rf cavities to remove the time-dependent rf kicks introduced in the gun. Along this trajectory, short range wakefields do not degrade the emittance, and long range wakefields degrade the emittance for very high repetition rate only.

The buildup of low energy electrons in an accelerator, known as electron cloud, can be severely detrimental to machine performance. Under certain beam conditions, the beam can become resonant with the cloud dynamics, accelerating the buildup of electrons. This paper will examine two such effects: multipacting resonances, in which the cloud development time is resonant with the bunch spacing, and cyclotron resonances, in which the cyclotron period of electrons in a magnetic field is a multiple of bunch spacing. Both resonances have been studied directly in dipole fields using retarding field analyzers installed in the Cornell Electron Storage Ring. These measurements are supported by both analytical models and computer simulations.

The buildup of low energy electrons in an accelerator, known as electron cloud, can be severely detrimental to machine performance. Under certain beam conditions, the beam can become resonant with the cloud dynamics, accelerating the buildup of electrons. This paper will examine two such effects: multipacting resonances, in which the cloud development time is resonant with the bunch spacing, and cyclotron resonances, in which the cyclotron period of electrons in a magnetic field is a multiple of bunch spacing. Both resonances have been studied directly in dipole fields using retarding field analyzers installed in the Cornell Electron Storage Ring. These measurements are supported by both analytical models and computer simulations.

Using a 1D steady-state free-space coherent synchrotron radiation (CSR) model, we identify a special design setting for a triple-bend isochronous achromat that yields vanishing emittance growth from CSR. When a more refined CSR model with transient effects is included in the analysis, numerical simulations show that the main effect of the transients is to shift the emittance growth minimum slightly, with the minimum changing only modestly.

Using a 1D steady-state free-space coherent synchrotron radiation (CSR) model, we identify a special design setting for a triple-bend isochronous achromat that yields vanishing emittance growth from CSR. When a more refined CSR model with transient effects is included in the analysis, numerical simulations show that the main effect of the transients is to shift the emittance growth minimum slightly, with the minimum changing only modestly.