Long Term Potential Evapotranspiration and Evapotranspiration Data and Services at NASA GES DISC

Recently, the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has released global land 3-hourly Potential Evapotranspiration and Supporting Forcing Data Version-1 (PET_PU_3H025.001), at 0.25x0.25 degree spatial resolution, spanning the 23 year period from 1984 to 2006. The Version-2 will be released in the near future, covering longer time period. This dataset was generated by Professor Justin Sheffield through NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) project. Potential evapotranspiration (PET) is a representation of the environmental demand for evapotranspiration (ET). ET and PET are important part of the global water cycle estimation, and are also critical to advance our understanding of the climate system. NASA GES DISC archives and distributes various global and regional ET datasets from several projects, for example, Land Data Assimilation System (LDAS), Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2), other MEaSUREs Projects, such as Land Surface Atmospheric Boundary Interaction Product by William Rossow; and SRB/GEWEX evapotranspiration (Penman-Monteith) by Eric F. Wood. In this presentation, we will overview all available PET and ET datasets and services at GES DISC. As examples, climatology and some seasonal characteristics of PET and selected ET will be shown. The data can be accessed from NASA GES DISC (https://disc.gsfc.nasa.gov/) by searching keyword "evapotranspiration"

A Network of SCOP Hidden Markov Models and Its Analysis

<p>Abstract</p> <p>Background</p> <p>The Structural Classification of Proteins (SCOP) database uses a large number of hidden Markov models (HMMs) to represent families and superfamilies composed of proteins that presumably share the same evolutionary origin. However, how the HMMs are related to one another has not been examined before.</p> <p>Results</p> <p>In this work, taking into account the processes used to build the HMMs, we propose a working hypothesis to examine the relationships between HMMs and the families and superfamilies that they represent. Specifically, we perform an all-against-all HMM comparison using the HHsearch program (similar to BLAST) and construct a network where the nodes are HMMs and the edges connect similar HMMs. We hypothesize that the HMMs in a connected component belong to the same family or superfamily more often than expected under a random network connection model. Results show a pattern consistent with this working hypothesis. Moreover, the HMM network possesses features distinctly different from the previously documented biological networks, exemplified by the exceptionally high clustering coefficient and the large number of connected components.</p> <p>Conclusions</p> <p>The current finding may provide guidance in devising computational methods to reduce the degree of overlaps between the HMMs representing the same superfamilies, which may in turn enable more efficient large-scale sequence searches against the database of HMMs.</p

Ambient observations of dimers from terpene oxidation in the gas phase : Implications for new particle formation and growth

We present ambient observations of dimeric monoterpene oxidation products (C16-20HyO6-9) in gas and particle phases in the boreal forest in Finland in spring 2013 and 2014, detected with a chemical ionization mass spectrometer with a filter inlet for gases and aerosols employing acetate and iodide as reagent ions. These are among the first online dual-phase observations of such dimers in the atmosphere. Estimated saturation concentrations of 10(-15) to 10(-6)mu gm(-3) (based on observed thermal desorptions and group-contribution methods) and measured gas-phase concentrations of 10(-3) to 10(-2)mu gm(-3) (similar to 10(6)-10(7)moleculescm(-3)) corroborate a gas-phase formation mechanism. Regular new particle formation (NPF) events allowed insights into the potential role dimers may play for atmospheric NPF and growth. The observationally constrained Model for Acid-Base chemistry in NAnoparticle Growth indicates a contribution of similar to 5% to early stage particle growth from the similar to 60 gaseous dimer compounds. Plain Language Summary Atmospheric aerosol particles influence climate and air quality. We present new insights into how emissions of volatile organic compounds from trees are transformed in the atmosphere to contribute to the formation and growth of aerosol particles. We detected for the first time over a forest, a group of organic molecules, known to grow particles, in the gas phase at levels far higher than expected. Previous measurements had only measured them in the particles. This finding provides guidance on how models of aerosol formation and growth should describe their appearance and fate in the atmosphere.Peer reviewe

Estimates of the organic aerosol volatility in a boreal forest using two independent methods

The volatility distribution of secondary organic aerosols that formed and had undergone aging - i. e., the particle mass fractions of semi-volatile, low-volatility and extremely low volatility organic compounds in the particle phase - was characterized in a boreal forest environment of Hyytiala, southern Finland. This was done by interpreting field measurements using a volatility tandem differential mobility analyzer (VTDMA) with a kinetic evaporation model. The field measurements were performed during April and May 2014. On average, 40% of the organics in particles were semi-volatile, 34% were low-volatility organics and 26% were extremely low volatility organics. The model was, however, very sensitive to the vaporization enthalpies assumed for the organics (Delta H-VAP). The best agreement between the observed and modeled temperature dependence of the evaporation was obtained when effective vaporization enthalpy values of 80 kJ mol(-1) were assumed. There are several potential reasons for the low effective enthalpy value, including molecular decomposition or dissociation that might occur in the particle phase upon heating, mixture effects and compound-dependent uncertainties in the mass accommodation coefficient. In addition to the VTDMA-based analysis, semi-volatile and low-volatility organic mass fractions were independently determined by applying positive matrix factorization (PMF) to high-resolution aerosol mass spectrometer (HR-AMS) data. The factor separation was based on the oxygenation levels of organics, specifically the relative abundance of mass ions at m/z 43 (f43) and m/z 44 (f44). The mass fractions of these two organic groups were compared against the VTDMA-based results. In general, the best agreement between the VTDMA results and the PMF-derived mass fractions of organics was obtained when Delta H-VAP D 80 kJ mol(-1) was set for all organic groups in the model, with a linear correlation coefficient of around 0.4. However, this still indicates that only about 16% (R-2)of the variation can be explained by the linear regression between the results from these two methods. The prospect of determining of extremely low volatility organic aerosols (ELVOAs) from AMS data using the PMF analysis should be assessed in future studies.Peer reviewe

Lymphatic impairment leads to pulmonary tertiary lymphoid organ formation and alveolar damage

The lung is a specialized barrier organ that must tightly regulate interstitial fluid clearance and prevent infection in order to maintain effective gas exchange. Lymphatic vessels are important for these functions in other organs, but their roles in the lung have not been fully defined. In the present study, we addressed how the lymphatic vasculature participates in lung homeostasis. Studies using mice carrying a lymphatic reporter allele revealeded that, in contrast to other organs, lung lymphatic collecting vessels lack smooth muscle cells entirely, suggesting that forward lymph flow is highly dependent on movement and changes in pressure associated with respiration. Functional studies using CLEC2-deficient mice in which lymph flow is impaired due to loss of lympho-venous hemostasis or using inducible lung-specific ablation of lymphatic endothelial cells in a lung transplant model revealeded that loss of lymphatic function leads to an inflammatory state characterized by the formation of tertiary lymphoid organs (TLOs). In addition, impaired lymphatic flow in mice resulteds in hypoxia and features of lung injury that resemble emphysema. These findings reveal both a lung-specific mechanism of lymphatic physiology and a lung-specific consequence of lymphatic dysfunction that may contribute to chronic lung diseases that arise in association with TLO formation

An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications

The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generated an atlas of the rate of copy number changes (CNCs) in all the gene families of ten animal genomes. We grouped the gene families with similar CNC dynamics into rate pattern groups (RPGs) and annotated their function using a novel bottom-up approach. By comparing CNC rate patterns, we showed that most of the species-specific CNC rates groups are formed by gene duplication rather than gene loss, and most of the changes in rates of CNCs may be the result of adaptive evolution. We also found that the functions of many RPGs match their biological significance well. Our work confirmed the role of gene duplication in generating novel phenotypes, and the results can serve as a guide for researchers to connect the phenotypic features to certain gene duplications

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

<p>Abstract</p> <p>Background</p> <p>Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (<it>i.e.</it>, the random duplication model). However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (<it>i.e.</it>, the tandem duplication model).</p> <p>Results</p> <p>In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (<it>i.e.</it>, the so-called inparalogs), using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs), and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments, it is actually better than that of InParanoid in the simulation tests.</p> <p>Conclusions</p> <p>Our preliminary experimental results demonstrate that MSOAR 2.0 is a highly accurate tool for one-to-one ortholog assignment between closely related genomes. The software is available to the public for free and included as online supplementary material.</p

Adsorptive uptake of water by semisolid secondary organic aerosols

Aerosol climate effects are intimately tied to interactions with water. Here we combine hygroscopicity measurements with direct observations about the phase of secondary organic aerosol (SOA) particles to show that water uptake by slightly oxygenated SOA is an adsorption-dominated process under subsaturated conditions, where low solubility inhibits water uptake until the humidity is high enough for dissolution to occur. This reconciles reported discrepancies in previous hygroscopicity closure studies. We demonstrate that the difference in SOA hygroscopic behavior in subsaturated and supersaturated conditions can lead to an effect up to about 30% in the direct aerosol forcinghighlighting the need to implement correct descriptions of these processes in atmospheric models. Obtaining closure across the water saturation point is therefore a critical issue for accurate climate modeling.Peer reviewe

ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization

Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user’s configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem

Incorporation of Local Structural Preference Potential Improves Fold Recognition

Fold recognition, or threading, is a popular protein structure modeling approach that uses known structure templates to build structures for those of unknown. The key to the success of fold recognition methods lies in the proper integration of sequence, physiochemical and structural information. Here we introduce another type of information, local structural preference potentials of 3-residue and 9-residue fragments, for fold recognition. By combining the two local structural preference potentials with the widely used sequence profile, secondary structure information and hydrophobic score, we have developed a new threading method called FR-t5 (fold recognition by use of 5 terms). In benchmark testings, we have found the consideration of local structural preference potentials in FR-t5 not only greatly enhances the alignment accuracy and recognition sensitivity, but also significantly improves the quality of prediction models