Scientific and Technical Assistance for the Deployment of a Flexible Airborne Spectrometer System During C-MAPExp and COMEX

The COMEX (CO2 and MEthane eXperiment) campaign supports the mission definition of CarbonSat and HyspIRI (Hyperspectral Infrared Imager) by providing representative airborne remote sensing data MAMAP (Methane Airborne MAPper) for CarbonSat; the Airborne Visual InfraRed Imaging Spectrometer (Classic & Next Generation) AVIRISC/AVIRISNG for HyspIRI as well as ground-based and airborne insitu data. The objectives of the COMEX campaign activities are (see Campaign Implementation Plan (RD4)): 1. Investigate spatial/spectral resolution tradeoffs for CH4 anomaly detection and flux inversion by comparison of MAMAPderived emission estimates with AVIRIS/AVIRISNG derived data. 2. Evaluate sunglint observation geometry on CH4 retrievals for marine sources. 3. Characterize the effect of Surface Spectral Reflectance (SSR) heterogeneity on trace gas retrievals of CO2 and CH4 for medium and lowresolution spectrometry. 4. Identify benefits from joint SWIR/TIR (ShortWave InfraRed/Thermal InfraRed ) data for trace gas detection and retrieval by comparison of MAMAP and AVIRIS/AVIRISNG NIR/SWIR data with MAKO (Aerospace Corp.)TIR data. The ability to derive emission source strength for a range of strong emitting targets by remote sensing will be evaluated from combined AVIRISNG and MAMAP data, adding significant value to the HyspIRI campaign AVIRISNG dataset. The data will be used to quantify anomalies in atmospheric CO2 and CH4 from strong local greenhouse gas sources e.g. localized industrial complexes, landfills, etc. and to derive CO2 and CH4 emissions estimates from atmospheric gradient measurements. The original campaign concept was developed by University of Bremen and BRI. The COMEX campaign is funded bilaterally by NASA and ESA (European Space Agency). Whereas NASA funds the US part of the project via a contract with Dr. Ira Leifer, BRI (Bubbleology Research International), the contribution of MAMAP to the COMEX campaign is funded by ESA within the COMEXE project and NASA with respect to a 50 percent contribution to the flight-related costs of flying MAMAP on a US aircraft. The Data Acquisition Report (RD9) describes the instrumentation used, the measurements made by the team during the COMEX campaign in May/June 2014 and August/September 2014 in California, and an initial assessment of the data quality

Involvement of A pertussis Toxin Sensitive G-Protein in the Inhibition of Inwardly Rectifying K+ Currents by Platelet-Activating Factor in Guinea-Pig Atrial Cardiomyocytes

Platelet-activating factor (PAF) inhibits single inwardly rectifying K+ channels in guinea-pig ventricular cells. There is currently little information as to the mechanism by which these channels are modulated. The effect of PAF on quasi steady-state inwardly rectifying K+ currents (presumably of the IK1 type) of auricular, atrial and ventricular cardiomyocytes from guinea-pig were studied. Applying the patch-clamp technique in the whole-cell configuration, PAF (10 nM) reduced the K+ currents in all three cell types. The inhibitory effect of PAF occurred within seconds and was reversible upon wash-out. It was almost completely abolished by the PAF receptor antagonist BN 50730. Intracellular infusion of atrial cells with guanine 5′-(β-thio)diphosphate (GDPS) or pretreatment of cells with pertussis toxin abolished the PAF dependent reduction of the currents. Neither extracellularly applied isoproterenol nor intracellularly applied adenosine 3′,5′-cyclic monophosphate (cyclic AMP) attenuated the PAF effect. In multicellular preparations of auricles, PAF (10 nM) induced arrhythmias. The arrhythmogenic activity was also reduced by BN 50730. The data indicate that activated PAF receptors inhibit inwardly rectifying K+ currents via a pertussis toxin sensitive G-protein without involvement of a cyclic AMP-dependent step. Since IK1 is a major component in stabilizing the resting membrane potential, the observed inhibition of this type of channel could play an important role in PAF dependent arrhythmogenesis in guinea-pig heart

Defining an olfactory receptor function in airway smooth muscle cells

Pathways that control, or can be exploited to alter, the increase in airway smooth muscle (ASM) mass and cellular remodeling that occur in asthma are not well defined. Here we report the expression of odorant receptors (ORs) belonging to the superfamily of G-protein coupled receptors (GPCRs), as well as the canonical olfaction machinery (G olf and AC3) in the smooth muscle of human bronchi. In primary cultures of isolated human ASM, we identified mRNA expression for multiple ORs. Strikingly, OR51E2 was the most highly enriched OR transcript mapped to the human olfactome in lung-resident cells. In a heterologous expression system, OR51E2 trafficked readily to the cell surface and showed ligand selectivity and sensitivity to the short chain fatty acids (SCFAs) acetate and propionate. These endogenous metabolic byproducts of the gut microbiota slowed the rate of cytoskeletal remodeling, as well as the proliferation of human ASM cells. These cellular responses in vitro were found in ASM from non-asthmatics and asthmatics, and were absent in OR51E2-deleted primary human ASM. These results demonstrate a novel chemo-mechanical signaling network in the ASM and serve as a proof-of-concept that a specific receptor of the gut-lung axis can be targeted to treat airflow obstruction in asthma.open0

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Background: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. Results: Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Background: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. Results: Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future

Evaluation of simulated CO₂ power plant plumes from six high-resolution atmospheric transport models

Global anthropogenic CO2 sources are dominated by power plants and large industrial facilities. Quantifying the emissions of these point sources is therefore one of the main goals of the planned constellation of anthropogenic CO2 monitoring satellites (CO2M) of the European Copernicus program. Atmospheric transport models may be used to study the capabilities of such satellites through observing system simulation experiments and to quantify emissions in an inverse modelling framework. How realistically the CO2 plumes of power plants can be simulated and how strongly the results may depend on model type and resolution, however, is not well known due to a lack of observations available for benchmarking. Here, we use the unique data set of aircraft in-situ and remote sensing observations collected during the CoMet measurement campaign down-wind of the coal fired power plants at Bełchatów in Poland and Jaenschwalde in Germany in 2018 to evaluate the simulations of six different atmospheric transport models

The International Virus Bioinformatics Meeting 2023

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting

A Framework for Exploring Functional Variability in Olfactory Receptor Genes

BACKGROUND: Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, OR genes are classified into families and subfamilies, a classification that is believed to be a proxy for OR gene functional variability. However, the assumption that overall protein sequence diversity is a good proxy for functional properties is untested. METHODOLOGY: Here, we propose an alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach is based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region. CONCLUSIONS: Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regions. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability