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This project aims to study the microbial structure and potential functions of bacterial and fungal microbiomes in leaves, stems, roots, rhizospheres, and bulk soils of energy crops (oilcane) grown in greenhouses.
Repository for Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP can use K-FIT [2] input files. Example K-FIT input files are located in the K-FIT repository at https://github.com/maranasgroup/K-FIT.
Abstract not provided.
The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers.
Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.
Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra L.) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. Here, a similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Notably, for the site with pronounced local-scale functional legacies, there was much greater within-site variation in field-soil microsite moisture than at the site which did not exhibit functional legacies, suggesting that the extent of local-scale variation in microclimate may act as control on whether local-scale functional legacies are observed. Regardless of whether this mechanism does explain our findings, our observations do confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extend this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes are associated with microbial functional legacies.
Cross-slope climate differences in the midlatitudes are ecologically important, and impact vegetation-mediated water balance between the earth surface and the atmosphere. We made high-resolution in situ observations of air temperature, relative humidity, soil moisture, insolation, and sap velocity observations on 14 Pacific madrone trees (Arbutus menziesii) spanning adjacent north and south slopes at the University of California's Angelo Coast Range Reserve. To understand the cross-slope response of sap velocity, a proxy for transpiration, to microclimate, we modeled the sap velocity on each slope using a transpiration model driven by ambient environment and parameterized with a Markov Chain Monte Carlo parameter estimation process. The results show that trees on opposing slopes do not follow a shared pattern of physiological response to transpiration drivers. This means that the observed sap velocity differences are not due entirely to observed microclimate differences, but also due to population-level physiological differences, which indicates acclimation to inhabited microclimate. While our present data set and analytical tools do not identify mechanisms of acclimation, we speculate that differing proportions of sun-adapted and shade-adapted leaves, differences in stomatal regulation, and cross-slope root zone moisture differences could explain some of the observed and modeled differences.
Background Rural health disparities and access gaps may contribute to higher maternal and infant morbidity and mortality. Understanding and addressing access barriers for specialty women’s health services is important in mitigating risks for adverse childbirth events. The objective of this study was to investigate rural-urban differences in health care access for women of reproductive age by examining differences in past-year provider visit rates by provider type, and quantifying the contributing factors to these findings. Methods and findings Using a nationally-representative sample of reproductive age women (n = 37,026) from the Medical Expenditure Panel Survey (2010–2015) linked to the Area Health Resource File, rural-urban differences in past-year office visit rates with health care providers were examined. Blinder-Oaxaca decomposition analysis quantified the portion of disparities explained by individual- and county-level sociodemographic and provider supply characteristics. Overall, there were no rural-urban differences in past-year visits with women’s health providers collectively (65.0% vs 62.4%), however differences were observed by provider type. Rural women had lower past-year obstetrician-gynecologist (OB-GYN) visit rates than urban women (23.3% vs. 26.6%), and higher visit rates with family medicine physicians (24.3% vs. 20.9%) and nurse practitioners/physician assistants (NPs/PAs) (24.6% vs. 16.1%). Lower OB-GYN availability in rural versus urban counties (6.1 vs. 13.7 providers/100,000 population) explained most of the rural disadvantage in OB-GYN visit rates (83.8%), and much of the higher family physician (80.9%) and NP/PA (50.1%) visit rates. Other individual- and county-level characteristics had smaller effects on rural-urban differences. Conclusion Although there were no overall rural-urban differences in past-year visit rates, the lower OB-GYN availability in rural areas appears to affect the types of health care providers seen by women. Whether rural women are receiving adequate specialized women’s health care services, while seeing a different cadre of providers, warrants further investigation and has particular relevance for women experiencing high-risk pregnancies and deliveries.
Abstract. The southeastern Atlantic is home to an expansive smoke aerosol plume overlying a large cloud deck for approximately a third of the year. The aerosol plume is mainly attributed to the extensive biomass burning activities that occur in southern Africa. Current Earth system models (ESMs) reveal significant differences in their estimates of regional aerosol radiative effects over this region. Such large differences partially stem from uncertainties in the vertical distribution of aerosols in the troposphere. These uncertainties translate into different aerosol optical depths (AODs) in the planetary boundary layer (PBL) and the free troposphere (FT). This study examines differences of AOD fraction in the FT and AOD differences among ESMs (WRF-CAM5, WRF-FINN, GEOS-Chem, EAM-E3SM, ALADIN, GEOS-FP, and MERRA-2) and aircraft-based measurements from the NASA ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES) field campaign. Models frequently define the PBL as the well-mixed surface-based layer, but this definition misses the upper parts of decoupled PBLs, in which most low-level clouds occur. To account for the presence of decoupled boundary layers in the models, the height of maximum vertical gradient of specific humidity profiles from each model is used to define PBL heights. Results indicate that the monthly mean contribution of AOD in the FT to the total-column AOD ranges from 44 % to 74 % in September 2016 and from 54 % to 71 % in August 2017 within the region bounded by 25∘ S–0∘ N–S and 15∘ W–15∘ E (excluding land) among the ESMs. ALADIN and GEOS-Chem show similar aerosol plume patterns to a derived above-cloud aerosol product from the Moderate Resolution Imaging Spectroradiometer (MODIS) during September 2016, but none of the models show a similar above-cloud plume pattern to MODIS in August 2017. Using the second-generation High Spectral Resolution Lidar (HSRL-2) to derive an aircraft-based constraint on the AOD and the fractional AOD, we found that WRF-CAM5 produces 40 % less AOD than those from the HSRL-2 measurements, but it performs well at separating AOD fraction between the FT and the PBL. AOD fractions in the FT for GEOS-Chem and EAM-E3SM are, respectively, 10 % and 15 % lower than the AOD fractions from the HSRL-2. Their similar mean AODs reflect a cancellation of high and low AOD biases. Compared with aircraft-based observations, GEOS-FP, MERRA-2, and ALADIN produce 24 %–36 % less AOD and tend to misplace more aerosols in the PBL. The models generally underestimate AODs for measured AODs that are above 0.8, indicating their limitations at reproducing high AODs. The differences in the absolute AOD, FT AOD, and the vertical apportioning of AOD in different models highlight the need to continue improving the accuracy of modeled AOD distributions. These differences affect the sign and magnitude of the net aerosol radiative forcing, especially when aerosols are in contact with clouds.
Maximum likelihood estimation (MLE) has been used to produce perceptual scales from binary judgments of triads and quadruples. This method relies on Thurstone’s theory of a stochastic perceptual process where the perceived difference of two stimuli is the difference in their perceived strengths. It is possible that the perception of a suprathreshold difference is overestimated when adding smaller differences, a phenomenon referred to as diminishing returns. The current approach to construct a perceptual scale using MLE does not account for this phenomenon. We present a way to model the perception of differences using MLE and Thurstone’s theory, adapted to allow the possibility of diminishing returns. This method is validated using Monte Carlo simulated responses to experimental triads and can correctly model diminishing returns, the absence of diminishing returns, and the opposite of diminishing returns both in the cases when a perceptual scale is known and when the true perceived strengths of the stimuli are unknown. Additionally, this method was applied to empirical data sets to determine its feasibility in investigations of perception. Ultimately, it was found that this analysis allows for more accurate modeling of suprathreshold difference judgments, a more complete understanding of the perceptual processes underlying comparisons, and the evaluation of Thurstone’s theory of difference judgments.
Background: Investigations into the benefits of vagus nerve stimulation (VNS) through pre-clinical and clinical research have led to promising findings for treating several disorders. Despite proven effectiveness of VNS on conditions such as epilepsy and depression, understanding of off-target effects and contributing factors such as sex differences can be beneficial to optimize therapy design. New Methods: In this article, we assessed longitudinal effects of VNS on cardiovascular and immune systems, and studied potential sex differences using a rat model of longterm VNS. Rats were implanted with cuff electrodes around the left cervical vagus nerve for VNS, and wireless physiological monitoring devices for continuous monitoring of cardiovascular system using electrocardiogram (ECG) signals. ECG morphology and heart rate variability (HRV) features were extracted to assess cardiovascular changes resulting from VNS in short-term and long-term timescales. We also assessed VNS effects on expression of inflammatory cytokines in blood during the course of the experiment. Statistical analysis was performed to compare results between Treatment and Sham groups, and between male and female animals from Treatment and Sham groups. Results: Considerable differences between male and female rats in cardiovascular effects of VNS were observed in multiple cardiovascular features. However, the effects seemed to be transient with approximately 1-h recovery after VNS. While short-term cardiovascular effects were mainly observed in male rats, females in general showed more significant long-term effects even after VNS stopped. We did not observe notable changes or sex differences in systemic cytokine levels resulting from VNS. Comparison With Existing Methods: Compared to existing methods, our study design incorporated wireless physiological monitoring and systemic blood cytokine level analysis, along with long-term VNS experiments in unanesthetized rats to study sex differences. Conclusion: The contribution of sex differences for long-term VNS off-target effects on cardiovascular and immune systems was assessed using awake behaving rats. Although VNS did not change the concentration of inflammatory biomarkers in systemic circulation for male and female rats, we observed significant differences in cardiovascular effects of VNS characterized using ECG morphology and HRV analyses.
Durability assessment of materials exposed to natural weathering with expected service lifetimes of more than 20 years requires accelerated testing of the UV stability, especially for polymeric materials. Fraunhofer ISE organized an interlaboratory comparison for testing different back-sheets in various test laboratories using different UV sources. The five participating test laboratories used three different types of UV sources. The interaction of the UV radiation with the polymers used in PV modules is main subject of this round-robin. Laminates were produced by using solar glass and a suitable EVA encapsulant combined with 10 different back-sheets. The simultaneous usage of different optical filters allowed to investigate roughly the spectral sensitivity and the intensity impact. The degradation was followed by spectral reflectance and transmittance measurements and calculation of the yellowness index as degradation indicator. Clear differences in the degradation behavior of the different products were found.
Abstract We compare historical and end‐of‐century temperature and precipitation patterns over California from one dynamically downscaled simulation using the Weather Research and Forecast (WRF) model and two simulations statistically downscaled using Localized Constructed Analogs (LOCA). We uniquely separate causes of differences between dynamically and statistically based future climate projections into differences in historical climate (gridded observations versus regional climate model output) and differences in how these downscaling techniques explicitly handle future climate changes (numerical modeling versus analogs). In these methods, solutions between different downscaling techniques differ more in the future compared to the historical period. Changes projected by LOCA are insensitive to the choice of driving data. Only through dynamical downscaling can we simulate physically consistent regional springtime warming patterns across the Sierra Nevada, while the statistical simulations inherit an unphysical signal from their parent Global Climate Model (GCM) or gridded data. The results of our study clarify why these different techniques produce different outcomes and may also provide guidance on which downscaled products to use for certain impact analyses in California and perhaps other Mediterranean regimes.
ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.
Abstract Oilcane is a metabolically engineered sugarcane ( Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI 1 transgene. The WRI 1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.
Generally, passive gamma spectroscopy (PGS) is known as a useful technique for nondestructive measurement of burnup and nuclide production in normal spent nuclear fuel. However, PGS can be used not only for normal spent fuel, but also for molten fuel generated in severe accidents involving core meltdowns. In such cases, it is estimated by the radioactivity ratios of specific nuclides. At the time of the decommissioning of the Three Mile Island's unit 2 reactor, fission products (FPs) such as Cs{sup 134}, Cs{sup 137}, Ce{sup 144}, Eu{sup 154}, Ru{sup 106}, and Sb{sup 125} were concerned. The radioactivity ratios are estimated by numerical simulations. However, there are various uncertainties in numerical simulations. In this study, we evaluated the effect of the difference in fission yield data. We compared the productions of concerned nuclides of Three Mile Island's unit 2 reactor by using Tokyo-tech and JENDL FP Fission Yields Data File 2011(FPY- 2011). Tokyo-tech is newly created by Tsubakihara et al. at Tokyo Institute of Technology. FPY-2011 is currently the latest fission yield data in Japan. In the concerned nuclides, the relative difference (Tokyo-tech/FPY-2011 -1) in the production of Sb{sup 125} is 4.5% and that of Eu{sup 154} is -5.6%. The relative difference in the production of Sb{sup 125} is found to be caused by the difference in the independent yields of Sn{sup 125}, In{sup 125}, Cd{sup 125}, Ag{sup 125}, and Pd{sup 125}. The relative difference in Eu{sup 154} is found to be caused by the relative difference in the production of Sm{sup 152} and the relative difference in the cumulative yield of Eu{sup 153}.
Inhalation of uranium aerosols produced via human activities such as mining can pose a threat to human respiratory systems. Uranium oxide particulates emit short-range alpha particles that elicit DNA and direct damage, beyond associated physiochemical heavy-metal toxicity, to internal epithelial tissues. The availability of reliable in vitro models to study radiation exposure can greatly enhance our ability to understand and combat the biological impacts of exposure. However, the toxicological effects of alpha emissions and/or the oxidation states of uranium particulates vary across different human lung epithelial cell models and have not been systematically compared. We have endeavored to address this limitation by comparing impacts in three different human lung cell models: primary human bronchial and tracheal epithelial cells, primary human small airway epithelial cells, and human adenocarcinoma alveolar basal epithelial cells. Other studies have mainly investigated the toxicity of depleted uranium. Here, we compared the exposure of uranium oxide particulates (U 3 O 8 and UO 3 ) of different enrichment states on the chosen cell systems. Each cell model was exposed to 0.1, 1, 10, 50, 100, and 500 µg/mL of depleted U 3 O 8 , highly-enriched U 3 O 8 , and natural UO 3 particulates for 24 hours in submerged monolayer cultures. We compared viability and superoxide dismutase activity results across cell lines and uranium enrichment/ oxidative states. The results showed that 1) the oxide state of the particulates affected cell viability, implying that uranium’s different oxidation states contribute to different toxicological responses, and 2) each cell model reacts differently when exposed to uranium oxides, which may provide insights into the mechanistic processes associated with the exposure of radiological particulates on different biological systems. For instance, increased uranium enrichment corresponds to increased toxicity for the primary cells, but not for the immortalized cells. Our study shows that a holistic approach that incorporates similarities between model systems and types of radionuclides is required to truly develop empirical solutions for radiation exposure.
Basketball is a sport where shooting is one of the most important factors that determines the success or failure of the teams. Therefore, basketball players need to shoot the ball accurately. The present study aimed to evaluate whether different shooting conditions influence the visual behavior of athletes. For this, the Tobbi Pro Glasses 3 equipment was used to evaluate the time of the first fixation, the number of fixations, and the total time of fixations in the basket, during the shooting movement. Different distances to the basket, simulated gym audience noise, and shooting with opposition were considered. A group of 18 athletes with an average age of 22 ± 3.72 years and an average basketball practice experience of 12.5 ± 4.52 years performed 10 valid shots from different distances and different shooting angles, with different restrictions, namely, shooting with simulated opposition and gym audience noise. Statistically significant differences between shooting with opposition and baseline, in terms of the number of fixations and the total time of fixation, were found. Regarding shooting with gym audience noise, differences only occur for the total time of fixations in one position. Despite this, in all variables and positions, the values were lower in shooting with constraints compared to the baseline.