ALBERT

Description: The Intelligent Systems and Robots Center at Sandia National Laboratories is developing technologies for the automation of processes associated with environmental remediation and information-driven manufacturing. These technologies, which focus on automated planning and programming and sensor-based and model-based control, are used to build intelligent systems which are able to generate plans of action, program the necessary devices, and use sensors to react to changes in the environment. By automating tasks through the use of programmable devices tied to computer models which are augmented by sensing, requirements for faster, safer, and cheaper systems are being satisfied. However, because of the need for rapid cost-effect prototyping and multi-laboratory teaming, it is also necessary to define a consistent approach to the construction of controllers for such systems. As a result, the Generic Intelligent System Controller (GISC) concept has been developed. This concept promotes the philosophy of producing generic tool kits which can be used and reused to build intelligent control systems.

Description: Agricultural ammonia (NH3) emissions are highly uncertain, with high spatiotemporal variability and a lack of widespread in situ measurements. Regional NH3 emission estimates using mass balance or emission ratio approaches are uncertain due to variable NH3 sources and sinks as well as unknown plume correlations with other dairy source tracers. We characterize the spatial distributions of NH3 and methane (CH4) dairy plumes using in situ surface and airborne measurements in the Tulare dairy feedlot region of the San Joaquin Valley, California, during the NASA Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality 2013 field campaign. Surface NH3 and CH4 mixing ratios exhibit large variability with maxima localized downwind of individual dairy feedlots. The geometric mean NH3:CH4 enhancement ratio derived from surface measurements is 0.15 +/- 0.03 ppmv ppmv1. Individual dairy feedlots with spatially distinct NH3 and CH4 source pathways led to statistically significant correlations between NH3 and CH4 in 68% of the 69 downwind plumes sampled. At longer sampling distances, the NH3:CH4 enhancement ratio decreases 20-30%, suggesting the potential for NH3 deposition as a loss term for plumes within a few kilometers downwind of feedlots. Aircraft boundary layer transect measurements directly above surface mobile measurements in the dairy region show comparable gradients and geometric mean enhancement ratios within measurement uncertainties, even when including NH3 partitioning to submicron particles. Individual NH3 and CH4 plumes sampled at close proximity where losses are minimal are not necessarily correlated due to lack of mixing and distinct source pathways. Our analyses have important implications for constraining NH3 sink and plume variability influences on regional NH3 emission estimates and for improving NH3 emission inventory spatial allocations.

Description: The San Joaquin Valley (SJV) of California experiences high concentrations of PM2.5 (particulate matter with aerodynamic diameter 2.5 m) during episodes of meteorological stagnation in winter. Modeling PM2.5 NH4NO3 during these episodes is challenging because it involves simulating meteorology in complex terrain under low wind speed and vertically stratified conditions, representing complex pollutant emissions distributions, and simulating daytime and nighttime chemistry that can be influenced by the mixing of urban and rural air masses. A rich dataset of observations related to NH4NO3 formation was acquired during multiple periods of elevated NH4NO3 during the DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) field campaign in SJV in January and February 2013. Here, NH4NO3 is simulated during the SJV DISCOVER-AQ study period with the Community Multiscale Air Quality (CMAQ) model version 5.1, predictions are evaluated with the DISCOVER-AQ dataset, and process analysis modeling is used to quantify HNO3 production rates. Simulated NO3- generally agrees well with routine monitoring of 24-h average NO3-, but comparisons with hourly average NO3- measurements in Fresno revealed differences at higher time resolution. Predictions of gas-particle partitioning of total nitrate (HNO3 + NO3-) and NHx (NH3 + NH4+) generally agreed well with measurements in Fresno, although partitioning of total nitrate to HNO3 was sometimes overestimated at low relative humidity in afternoon. Gas-particle partitioning results indicate that NH4NO3 formation is limited by HNO3 availability in both the model and ambient. NH3 mixing ratios are underestimated, particularly in areas with large agricultural activity, and the spatial allocation of NH3 emissions could benefit from additional work, especially near Hanford. HNO3 production via daytime and nighttime pathways is reasonably consistent with the conceptual model of NH4NO3 formation in SJV, and production peaked aloft between about 160 and 240 m in the model. During a period of elevated NH4NO3, the model predicted that the OH + NO2 pathway contributed 46% to total HNO3 production in SJV and the N2O5 heterogeneous hydrolysis pathway contributed 54%. The relative importance of the OH + NO2 pathway for HNO3 production is predicted to increase as NOx emissions decrease.

Description: Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve metaorganism identities and to disclose the various roles that microorganisms play in the biology of their hosts.

Description: Highlights: • All 3 animal MAPR families, PGRMC, NENF & NEUFC, were present in the common opisthokont ancestor. • Y-phosphorylated PGRMC1 Y139 & Y180 appeared concurrently with the gastrulation organiser. • The gastrulation organizer also appeared in the common ancestor of cnidarians and bilaterians. • PGRMC1 MIHIR has a predicted coiled-coil that would be disrupted by Y139 phosphorylation. • The C-terminus of each MAPR family was extended during the evolution from protists to animals. The membrane-associated progesterone receptor (MAPR) family consists of heme-binding proteins containing a cytochrome b5 (cytb5) domain characterized by the presence of a MAPR-specific interhelical insert region (MIHIR) between helices 3 and 4 of the canonical cytb5-domain fold. Animals possess three MAPR genes (PGRMC-like, Neuferricin and Neudesin). Here we show that all three animal MAPR genes were already present in the common ancestor of the opisthokonts (comprising animals and fungi as well as related single-celled taxa). All three MAPR genes acquired extensions C-terminal to the cytb5 domain, either before or with the evolution of animals. The archetypical MAPR protein, progesterone receptor membrane component 1 (PGRMC1), contains phosphorylated tyrosines Y139 and Y180. The combination of Y139/Y180 appeared in the common ancestor of cnidarians and bilaterians, along with an early embryological organizer and synapsed neurons, and is strongly conserved in all bilaterian animals. A predicted protein interaction motif in the PGRMC1 MIHIR is potentially regulated by Y139 phosphorylation. A multilayered model of animal MAPR function acquisition includes some pre-metazoan functions (e.g., heme binding and cytochrome P450 interactions) and some acquired animal-specific functions that involve regulation of strongly conserved protein interaction motifs acquired by animals (Metazoa). This study provides a conceptual framework for future studies, against which especially PGRMC1′s multiple functions can perhaps be stratified and functionally dissected.