Probabilistic models of species discovery and biodiversity comparisons
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Stewart M. Edie↗
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Stratospheric General Circulation with Chemistry Model (SGCCM)
In the past two years constituent transport and chemistry experiments have been performed using both simple single constituent models and more complex reservoir species models. Winds for these experiments have been taken from the data assimilation effort, Stratospheric Data Analysis System (STRATAN).
Rood, Richard B.↗
Mixing and combustion effects in a sliding-wedge ram accelerator with hydrogen injection
The ram accelerator concept has been envisioned as the basis of a ground-based flight-test facility concept in which the test section follows the ram-accelerated projectile, and allows hydrogen mixing/combustion experiments to be conducted when hydrogen carried by the projectile is injected into the freestream. A numerical simulation is presently conducted for such mixing and combustion; the chemical reactions in question are modeled using a seven-step, seven-species model. A grid-adaptation procedure is used to resolve flow features in areas of high fluid and species gradients.
Ramakrishnan, R.↗
Construction of analytically solvable models for interacting species
The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.
Rosen, G.↗
Implementation and verification of a model linearized multi-species collision operator in the COGENT code
We implement the multi-species linearized model collision operator, based on the approach proposed by Kolesnikov, in the full-f continuum gyrokinetic code COGENT. We describe the operator and use it in several COGENT simulations of highly collisional plasmas. We analyze simulation results with the Braginskii fluid model to illustrate that COGENT recovers both friction and thermal forces. Finally, we simulate the neoclassical transport of heavy impurities with COGENT and illustrate agreement with previously published theoretical results.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
CONDENSATION-EVAPORATION MODELING OF DRIFT FROM A MECHANICAL COOLING TOWER
Numerical studyfor investigatingthe phase change behavior of a drift from a mechanical draft cooling tower is presented. A k-ε turbulence model, discrete phase model, species transport equations, and a heat-mass exchange model are solved simultaneouslyto capture the heat and mass transfer effects of a drift condensing and evaporatingeffects. The simulation result is compared to an available real scale test data and its limitation is also discussed. A parametric study is carried out by varying the ambient dry bulb temperature, ambient relative humidity, wind speed, liquid droplet diameter, and the drift amount. It is found that by combining the evaporation and condensation models, a drift phase change phenomena is accurately depicted. A parametric study reveals that wind speed impact is affected by the ambient temperature and the number of liquid droplets and their size play a critical role in the phase change phen
Han, Kai↗
Dynamic-Chemical Coupling of the Upper Troposphere and Lower Stratosphere Region
The importance of the interaction of chemistry and dynamics in the upper troposphere and lower stratosphere for chemical species like ozone is investigated using two chemistry-climate models. Species emitted in the upper troposphere, like NOx (=NO+NO2) by lightning or aircraft, have the chance to be transported into the lowermost stratosphere. Trajectory calculations suggest that the main transport pathway runs via the Inter Tropical Convergence Zone, across the tropical tropopause and then to higher latitudes, i.e. into the lowermost stratosphere. Longer lifetimes of NOx in the lower stratosphere yield an accumulation of NO. there, which feeds back on upper troposphere chemistry. This effect has been estimated for lightning NO. emissions and reveals a contribution of at least 25% to 40% to the total northern hemisphere mid-latitude lightning increase of either NOx and ozone.
Grewe, Volker↗
Middle Atmosphere Program. Handbook for MAP. Volume 31: Reference models of trace species for the COSPAR international reference atmosphere
A set of preliminary reference atmosphere models of significant trace species which play important roles in controlling the chemistry, radiation budget, and circulation patterns of the atmosphere were produced. These models of trace species distributions are considered to be reference models rather than standard models; thus, it was not crucial that they be correct in an absolute sense. These reference models can serve as a means of comparison between individual observations, as a first guess in inversion algorithms, and as an approximate representation of observations for comparison to theoretical calculations.
Keating, G. M.↗
A Chromosome-Scale Genome Assembly of the Flax Rust Fungus Reveals the Two Unusually Large Effector Proteins, AvrM3 and AvrN
Rust fungi comprise thousands of species, many of which cause disease on important crop plants. The flax rust fungus Melampsora lini has been a model species for the genetic dissection of plant immunity since the 1940s; however, the highly fragmented and incomplete reference genome has so far hindered progress in effector gene discovery. Here, we generated a fully phased, chromosome-scale assembly of the two nuclear genomes of M. lini strain CH5, resolving an additional 320 Mbp of the sequence. The 482-Mbp dikaryotic genome is at least 79% repetitive, with a large proportion (approximately 40%) of the genome comprising young, highly similar transposable elements. The assembly resolves the known effector gene loci, some of which carry complex duplications that were collapsed in the previous assembly. Using a genetic map followed by manual correction of gene models, we identified the AvrM3 and AvrN genes, which encode unusually large fungal effector proteins and trigger defense responses when co-expressed with the corresponding resistance genes. We located the genes linked to the tetrapolar mating system on chromosomes 4 and 9, but in contrast to the cereal rusts that have one pheromone receptor gene per haplotype, in flax rust, three pheromone receptor genes were found, with two of them closely linked on one haplotype. Taken together, we show that a high-quality assembly is crucial for resolving complex gene loci, and given the increasing number of fungal effectors of large size, the commonly applied criterion for effector candidates of being small proteins needs to be reconsidered.
Melampsora↗
Discovering CO Adsorption and Desorption Pathways from Chemical Reaction Neural Network Modeling of Transient Kinetics Spectroscopy
Here, we demonstrate a data-driven approach to interpreting surface reactions by combining time-resolved gas pulsing infrared spectroscopy with chemical reaction neural networks (CRNNs). Using CO adsorption and desorption on Pd(111) at 460–490 K as a model system, we show how transient kinetic data can reveal detailed reaction mechanisms. Starting with a simple one-species model, we systematically evaluate increasingly complex mechanisms involving hollow and bridge site adsorption. Despite the similar goodness of fit to the same experimental absorbance data, our models predict distinct coverage dynamics for different adsorption sites. Through analysis of spectral peak stability and predicted dynamics, we identify a mechanism in which CO primarily adsorbs on bridge sites followed by rapid conversion to hollow sites as being the most physically consistent with experimental observations. This work provides a framework for extracting mechanistic insights from limited experimental data, demonstrating how machine learning can bridge the gap between transient kinetic measurements and a molecular-level understanding of surface reactions.
36 MATERIALS SCIENCE↗
Projecting the Local Impacts of Climate Change on a Central American Montane Avian Community
Significant changes in the climates of Central America are expected over the next century. Lowland rainforests harbor high alpha diversity on local scales (<1 km2), yet montane landscapes often support higher beta diversity on 10-100 km2 scales. Climate change will likely disrupt the altitudinal zonation of montane communities that produces such landscape diversity. Projections of biotic response to climate change have often used broad-scale modelling of geographical ranges, but understanding likely impacts on population viability is also necessary for anticipating local and global extinctions. We model species abundances and estimate range shifts for birds in the Tilaran Mountains of Costa Rica, asking whether projected changes in temperature and rainfall could be sufficient to imperil high-elevation endemics and whether these variables will likely impact communities similarly. We find that nearly half of 77 forest bird species can be expected to decline in the next century. Almost half of species projected to decline are endemic to Central America, and seven of eight species projected to become locally extinct are endemic to the highlands of Costa Rica and Panam . Logistic-regression modelling of distributions and similarity in projections produced by temperature and rainfall models suggest that changes in both variables will be important. Although these projections are probably conservative because they do not explicitly incorporate biological or climate variable interactions, they provide a starting point for incorporating more realistic biological complexity into community-change models. Prudent conservation planning for tropical mountains should focus on regions with room for altitudinal reorganization of communities comprised of ecological specialists.
Gasner, Matthew R.↗
Next-generation wildlife tracking devices and integrated sensors for measuring species-environment interactions and advancing conservation
Global land use and climate change have magnified the importance of collecting accurate animal movement and environmental data to improve our ability to model species interactions with the environment and promote effective conservation. Advanced animal tracking devices that couple cutting-edge technologies with our expanding need for ecological information is critical. In addition to further optimizing device size to monitor small, sensitive species, new paradigms for collecting, storing, and transmitting data about animals and their environments will propel wildlife tracking devices forward. Advanced telemetry capabilities will increase our ability to pair location and sensor data from tagged wildlife with remote sensing data. The USGS Western Ecological Research Center, NASA Ames Research Center, and collaborators have been developing new wildlife tracking devices and integrated environmental sensors to address these challenges. We describe a new, miniaturized solar GPS-enabled Globalstar satellite transmitter with accelerometer capability that is 20% lighter and 25% less expensive than existing commercially available tags. We also introduce a novel peer-to-peer, solar-powered network tag that uses long-range, low-power, wireless platform technology. Concurrently, we began adapting a carbon nanotube (CNT) sensor to detect dimethyl sulfide (DMS), a trace gas relevant to marine ecology and climate studies. CNT sensors offer a small, lightweight, and low-power technology that can detect changes in resistance across carbon nanotubes coated with adsorbent selected to specifically bind with a variety of reactive trace gasses. We flew a prototype sensor in a small UAS and sampled an apparent increase in DMS concentration consistent with a well-defined marine frontal boundary. Currently we are integrating project components to create a hybridized architecture of networked peer-to-peer and satellite tags with integrated CNT and additional on-board and remote sensors to advance animal tracking and to provide information for next generation wildlife conservation.
Ian G. Brosnan↗
Table and Charts of Equilibrium Normal-shock Properties for Pure Hydrogen with Velocities to 70 km/sec. Revised.
Errors found in the original edition are corrected. Refinement was made in procedures for solving the conservation relations for an incident (moving), standing, and reflected normal shock, as well as in computational methods for determining thermochemical-equilibrium hydrogen properties. A six-species hydrogen model replaces the original four-species model, and the heat of formation and spectroscopic constants used in this six-species model are listed in appendix A. In appendix B, comparisons are made between a number of methods for determining equilibrium thermodynamic properties for hydrogen for several values of pressure and temperatures to 50000 K. A comparison is also performed between the present method and a second method for determining thermodynamic properties and flow velocity behind an incident shock into pure hydrogen and behind a reflected shock.
Miller, C. G., III↗
Harmonized Emissions Component (HEMCO) 3.0 as a Versatile Emissions Component for Atmospheric Models: Application in the GEOS-Chem, NASA GEOS, WRF-GC, CESM2, NOAA GEFS-Aerosol, and NOAA UFS Models
Emissions are a central component of atmospheric chemistry models. The Harmonized Emissions Component (HEMCO) is a software component for computing emissions from a user-selected ensemble of emission inventories and algorithms. It allows users to re-grid, combine, overwrite, subset, and scale emissions from different inventories through a configuration file and with no change to the model source code. The configuration file also maps emissions to model species with appropriate units. HEMCO can operate in offline stand-alone mode, but more importantly it provides an online facility for models to compute emissions at runtime. HEMCO complies with the Earth System Modeling Framework (ESMF) for portability across models. We present a new version here, HEMCO 3.0, that features an improved three-layer architecture to facilitate implementation into any atmospheric model and improved capability for calculating emissions at any model resolution including multiscale and unstructured grids. The three-layer architecture of HEMCO 3.0 includes (1) the Data Input Layer that reads the configuration file and accesses the HEMCO library of emission inventories and other environmental data, (2) the HEMCO Core that computes emissions on the user-selected HEMCO grid, and (3) the Model Interface Layer that re-grids (if needed) and serves the data to the atmospheric model and also serves model data to the HEMCO Core for computing emissions dependent on model state (such as from dust or vegetation). The HEMCO Core is common to the implementation in all models, while the Data Input Layer and the Model Interface Layer are adaptable to the model environment. Default versions of the Data Input Layer and Model Interface Layer enable straightforward implementation of HEMCO in any simple model architecture, and options are available to disable features such as re-gridding that may be done by independent couplers in more complex architectures. The HEMCO library of emission inventories and algorithms is continuously enriched through user contributions so that new inventories can be immediately shared across models. HEMCO can also serve as a general data broker for models to process input data not only for emissions but for any gridded environmental datasets. We describe existing implementations of HEMCO 3.0 in (1) the GEOS-Chem “Classic” chemical transport model with shared-memory infrastructure, (2) the high-performance GEOS-Chem (GCHP) model with distributed-memory architecture, (3) the NASA GEOS Earth System Model (GEOS ESM), (4) the Weather Research and Forecasting model with GEOS-Chem (WRF-GC), (5) the Community Earth System Model Version 2 (CESM2), and (6) the NOAA Global Ensemble Forecast System – Aerosols (GEFS-Aerosols), as well as the planned implementation in the NOAA Unified Forecast System (UFS). Implementation of HEMCO in CESM2 contributes to the Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA) by providing a common emissions infrastructure to support different simulations of atmospheric chemistry across scales.
Haipeng Lin↗
The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses
Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.
59 BASIC BIOLOGICAL SCIENCES↗
Model Evaluation of Short-Lived Climate Forcers for the Arctic Monitoring and Assessment Programme: A Multi-Species, Multi-Model Study
While carbon dioxide is the main cause for global warming, modeling short-lived climate forcers (SLCFs) such as methane, ozone, and particles in the Arctic allows us to simulate near-term climate and health impacts for a sensitive, pristine region that is warming at 3 times the global rate. Atmospheric modeling is critical for understanding the long-range transport of pollutants to the Arctic, as well as the abundance and distribution of SLCFs throughout the Arctic atmosphere. Modeling is also used as a tool to determine SLCF impacts on climate and health in the present and in future emissions scenarios. In this study, we evaluate 18 state-of-the-art atmospheric and Earth system models by assessing their representation of Arctic and Northern Hemisphere atmospheric SLCF distributions, considering a wide range of different chemical species (methane, tropospheric ozone and its precursors, black carbon, sulfate, organic aerosol, and particulate matter) and multiple observational datasets. Model simulations over 4 years (2008-2009 and 2014-2015) conducted for the 2022 Arctic Monitoring and Assessment Programme (AMAP) SLCF assessment report are thoroughly evaluated against satellite, ground, ship, and aircraft-based observations. The annual means, seasonal cycles, and 3-D distributions of SLCFs were evaluated using several metrics, such as absolute and percent model biases and correlation coefficients. The results show a large range in model performance, with no one particular model or model type performing well for all regions and all SLCF species. The multi-model mean (mmm) was able to represent the general features of SLCFs in the Arctic and had the best overall performance. For the SLCFs with the greatest radiative impact (CH4, 03, BC, and SO(sup 2-)(sub 4)), the mmm was within ±25 % of the measurements across the Northern Hemisphere. Therefore, we recommend a multi-model ensemble be used for simulating climate and health impacts of SLCFs. Of the SLCFs in our study, model biases were smallest for C"4 and greatest for OA. For most SLCFs, model biases skewed from positive to negative with increasing latitude. Our analysis suggests that vertical mixing, long-range transport, deposition, and wildfires remain highly uncertain processes. These processes need better representation within atmospheric models to improve their simulation of SLCFs in the Arctic environment. As model development proceeds in these areas, we highly recommend that the vertical and 3-D distribution of SLCFs be evaluated, as that information is critical to improving the uncertain processes in models.
Arctic Monitoring and Assessment Programme↗
Estimation of skeletal muscle mass from body creatine content
Procedures have been developed for studying the effect of changes in gravitational loading on skeletal muscle mass through measurements of the body creatine content. These procedures were developed for studies of gravitational scale effects in a four-species model, comprising the hamster, rat, guinea pig, and rabbit, which provides a sufficient range of body size for assessment of allometric parameters. Since intracellular muscle creatine concentration varies among species, and with age within a given species, the concentration values for metabolically mature individuals of these four species were established. The creatine content of the carcass, skin, viscera, smooth muscle, and skeletal muscle was determined for each species. In addition, the skeletal muscle mass of the major body components was determined, as well as the total and fat-free masses of the body and carcass, and the percent skeletal muscle in each. It is concluded that these procedures are particularly useful for studying the effect of gravitational loading on the skeletal muscle content of the animal carcass, which is the principal weight-bearing organ of the body.
Pace, N.↗
Impact of irradiance and inorganic carbon availability on heterologous sucrose production in Synechococcus elongatus PCC 7942
Cyanobacteria have been proposed as a potential alternative carbohydrate feedstock and multiple species have been successfully engineered to secrete fermentable sugars. To date, the most productive cyanobacterial strains are those designed to secrete sucrose, yet there exist considerable differences in reported productivities across different model species and laboratories. In this study, we investigate how cultivation conditions (specifically, irradiance, CO 2 , and cultivator type) affect the productivity of sucrose-secreting Synechococcus elongatus PCC 7942. We find that S. elongatus produces the highest sucrose yield in irradiances far greater than what is often experimentally utilized, and that high light intensities are tolerated by S. elongatus , especially under higher density cultivation where turbidity may attenuate the effective light experienced in the culture. By increasing light and inorganic carbon availability, S. elongatus cscB / sps produced a total of 3.8 g L -1 of sucrose and the highest productivity within that period being 47.8 mg L -1 h -1 . This study provides quantitative description of the impact of culture conditions on cyanobacteria-derived sucrose that may assist to standardize cross-laboratory comparisons and demonstrates a significant capacity to improve productivity via optimizing cultivation conditions.
59 BASIC BIOLOGICAL SCIENCES↗