Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic ...trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data.
We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline.
Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.
Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing ...technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species.
Carbon capture and utilization technology has been studied for its practical ability to reduce CO
emissions and enable economical chemical production. The main challenge of this technology is that a ...large amount of thermal energy must be provided to supply high-purity CO
and purify the product. Herein, we propose a new concept called reaction swing absorption, which produces synthesis gas (syngas) with net-zero CO
emission through direct electrochemical CO
reduction in a newly proposed amine solution, triethylamine. Experimental investigations show high CO
absorption rates (>84%) of triethylamine from low CO
concentrated flue gas. In addition, the CO Faradaic efficiency in a triethylamine supplied membrane electrode assembly electrolyzer is approximately 30% (@-200 mA cm
), twice higher than those in conventional alkanolamine solvents. Based on the experimental results and rigorous process modeling, we reveal that reaction swing absorption produces high pressure syngas at a reasonable cost with negligible CO
emissions. This system provides a fundamental solution for the CO
crossover and low system stability of electrochemical CO
reduction.
Reactive oxygen species (ROS) are a by-product of normal cell metabolism in plants; however, under stress conditions, the balance between production and elimination is disturbed. ROS rapidly ...inactivate enzymes, damage vital cellular organelles in plants, and destroy membranes by inducing the degradation of pigments, proteins, lipids and nucleic acids which ultimately results in cell death. In addition to degrading macromolecules, ROS act as a diffusible signal in signal transduction pathways and also as a secondary messenger in various developmental pathways in plants. Plants possess a complex battery of enzymatic and non-enzymatic antioxidative defense systems that can protect cells from oxidative damage and scavenge harmful ROS that are produced in excess of those normally required for various metabolic reactions. The mechanism by which ROS is generated in aerobic organisms is poorly understood. This review paper describes the generation, origin, and role of ROS in signal transduction and cell death, and the removal of ROS by antioxidative defense systems in plants during various developmental pathways.
To realize a hydrogen economy, many studies are being conducted regarding the development and analysis of hydrogen carriers. Recently, formic acid has been receiving attention as a potential hydrogen ...carrier due to its high volumetric energy density and relatively safe characteristics. However, hydrogen refueling systems using formic acid are very different from conventional hydrogen refueling stations, and quantitative risks assessments need to be conducted to verify their safe usage. In this study, a comparative safety analysis of a formic acid hydrogen refueling station (FAHRS) and a gaseous hydrogen refueling station (GHRS) was conducted. Since there is no FAHRS under operation, a process simulation model was developed and integrated with quantitative risk assessment techniques to perform safety analysis. Results of the analysis show that the FAHRS poses less risk than the GHRS, where the vapor cloud explosion occurring in the buffer tank is of greatest consequence. A GHRS poses a greater risk than an FAHRS due to the high pressure required to store hydrogen in the tube trailer. The mild operating conditions required for storage and dehydrogenation of formic acid contribute to the low risk values of an FAHRS. For risk scenarios exceeding the risk limit, risk mitigation measures were applied to design a safe process for GHRS. The results show that the installation of active safety systems for the GHRS allow the system to operate within acceptable safety regions.
Among two-dimensional (2D) layered van der Waals materials, ferromagnetic 2D materials can be useful for compact low-power spintronic applications. One promising candidate material is Fe3GeTe2 (FGT), ...which has a strong perpendicular magnetic anisotropy and relatively high Curie temperature. In this study, we confirmed that an oxide layer (O-FGT) naturally forms on top of exfoliated FGT and that an antiferromagnetic coupling (AFC) exists between FGT and O-FGT layers. From a first-principles calculation, oxide formation at the interface of each layer induces an AFC between the layers. An AFC causes a tailed hysteresis loop, where two-magnetization reversal curves are included, and a negative remanence magnetization at a certain temperature range.
In mammals, pain is regulated by the combination of an ascending stimulating and descending inhibitory pain pathway. It remains an intriguing question whether such pain pathways are of ancient origin ...and conserved in invertebrates. Here we report a new Drosophila pain model and use it to elucidate the pain pathways present in flies. The model employs transgenic flies expressing the human capsaicin receptor TRPV1 in sensory nociceptor neurons, which innervate the whole fly body, including the mouth. Upon capsaicin sipping, the flies abruptly displayed pain-related behaviors such as running away, scurrying around, rubbing vigorously, and pulling at their mouth parts, suggesting that capsaicin stimulated nociceptors in the mouth via activating TRPV1. When reared on capsaicin-containing food, the animals died of starvation, demonstrating the degree of pain experienced. This death rate was reduced by treatment both with NSAIDs and gabapentin, analgesics that inhibit the sensitized ascending pain pathway, and with antidepressants, GABAergic agonists, and morphine, analgesics that strengthen the descending inhibitory pathway. Our results suggest Drosophila to possess intricate pain sensitization and modulation mechanisms similar to mammals, and we propose that this simple, non-invasive feeding assay has utility for high-throughput evaluation and screening of analgesic compounds.
To meet the global climate goals agreed upon regarding the Paris Agreement, governments and institutions around the world are investigating various technologies to reduce carbon emissions and achieve ...a net-negative energy system. To this end, integrated solutions that incorporate carbon utilization processes, as well as promote the transition of the fossil fuel-based energy system to carbon-free systems, such as the hydrogen economy, are required. One of the possible pathways is to utilize CO2 as the base chemical for producing a liquid organic hydrogen carrier (LOHC), using CO2 as a mediating chemical for delivering H2 to the site of usage since gaseous and liquid H2 retain transportation and storage problems. Formic acid is a probable candidate considering its high volumetric H2 capacity and low toxicity. While previous studies have shown that formic acid is less competitive as an LOHC candidate compared to other chemicals, such as methanol or toluene, the results were based on out-of-date process schemes. Recently, advances have been made in the formic acid production and dehydrogenation processes, and an analysis regarding the recent process configurations could deem formic acid as a feasible option for LOHC. In this study, the potential for using formic acid as an LOHC is evaluated, with respect to the state-of-the-art formic acid production schemes, including the use of heterogeneous catalysts during thermocatalytic and electrochemical formic acid production from CO2. Assuming a hydrogen distribution system using formic acid as the LOHC, each of the production, transportation, dehydrogenation, and CO2 recycle sections are separately modeled and evaluated by means of techno-economic analysis (TEA) and life cycle assessment (LCA). Realistic scenarios for hydrogen distribution are established considering the different transportation and CO2 recovery options; then, the separate scenarios are compared to the results of a liquefied hydrogen distribution scenario. TEA results showed that, while the LOHC system incorporating the thermocatalytic CO2 hydrogenation to formic acid is more expensive than liquefied H2 distribution, the electrochemical CO2 reduction to formic acid system reduces the H2 distribution cost by 12%. Breakdown of the cost compositions revealed that reduction of steam usage for thermocatalytic processes in the future can make the LOHC system based on thermocatalytic CO2 hydrogenation to formic acid to be competitive with liquefied H2 distribution if the production cost could be reduced by 23% and 32%, according to the dehydrogenation mode selected. Using formic acid as a LOHC was shown to be less competitive compared to liquefied H2 delivery in terms of LCA, but producing formic acid via electrochemical CO2 reduction was shown to retain the lowest global warming potential among the considered options.
Abstract Background There is currently insufficient evidence to confirm the effect of ambient air pollution on mental disorders, especially among susceptible populations. This study investigated the ...short-term effect of ambient air pollution on the risk of depressive episode and the effect modification across disease subpopulations. Methods Subjects who visited the emergency department (ED) for depressive episode from 2005 to 2009 ( n =4985) in Seoul, Republic of Korea were identified from medical claims data. We conducted a time-stratified case-crossover study using conditional logistic regression. Subgroup analyses were conducted after the subjects were stratified by underlying disease (cardiovascular disease, diabetes mellitus, chronic obstructive pulmonary disease, asthma, and depressive disorder). The risk was expressed as an odds ratio (OR) per 1 standard deviation of each air pollutant. Results SO2 , PM10 , NO2 , and CO were positively associated with ED visits for depressive episode. The maximum risk was observed in the distributed lag 0–3 model for PM10 (OR, 1.120; 95% confidence interval, 1.067–1.176). PM10 , NO2 , and CO significantly increased the risks of ED visits for depressive episode in subjects with either underlying cardiovascular disease, diabetes mellitus, asthma, or depressive disorder. Limitations Our data may include a misclassification bias due to the validity of a diagnosis determined from medical services utilization data. Conclusions SO2 , PM10 , NO2 , and CO significantly increased the risk of ED visits for depressive episode, especially among individuals with pre-existing cardiovascular disease, diabetes mellitus, or asthma.
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