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Enantioselective Direct anti-Selective Mannich-type Reactions Catalyzed by 3-Pyrrolidinecarboxylic Acid in the Presence of Potassium Carbonate: Addition of Potassium Carbonate Improves Enantioselectivities
Get PDFMannich-type reactions of cyclohexanone and related six-membered-ring ketones with N-p-methoxyphenyl-protected imines of arylaldehydes catalyzed by 3-pyrrolidinecarboxylic acid in the presence of K2CO3 that afford anti-isomers of the Mannich products with high diastereo- and enantioselectivities are reported. Addition of K2CO3 improved the enantioselectivities of the reactions catalyzed by 3-pyrrolidinecarboxylic acid while retaining the anti-selectivity of the reaction. Thus, the use of K2CO3 expands the scope of these organocatalytic reactions for providing the products with high enantioselectivities.journal articl
One-Step Growth of Core–Shell (PtPd)@Pt and (PtPd)@Pd Nanoparticles in the Gas Phase
Get PDFPt–Pd nanoparticles are grown in the gas phase by a magnetron-sputtering source and characterized by electron microscopy techniques for both Pt-rich and Pd-rich compositions of the metallic vapor. It is shown that this growth procedure can produce different types of core–shell nanoparticles, in one step, with sizes in the range of 4–10 nm, according to the composition of the vapor being rich either in Pt or in Pd. In all cases, the nanoparticles present intermixed cores containing both Pt and Pd and shells made of the majority element, i.e., of (PtPd)@Pt structure for the Pt-rich vapor and (PtPd)@Pd structure for the Pd-rich vapor. Global searches of the optimal chemical ordering show that none of these structures correspond to equilibrium configurations. On the contrary, these core–shell structures are strongly out-of-equilibrium, being the result of kinetic trapping phenomena. This is verified by molecular dynamics growth simulations which are able to reproduce both the different types of chemical ordering and the variety of geometric shapes found in the experiments.journal articl
Storm moisture and landfalling hurricanes
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyWhen a hurricane strikes land, it can cause immense destruction to humans and other terrestrial life. Despite its importance, few studies have focused on the dynamics of hurricanes past landfall. By contrast, how hurricanes originate and grow over warm oceans has been extensively studied. Over oceans, moisture from the ocean fuels the intense winds of a hurricane heat engine. Past landfall, the hurricane is severed from this heat source, and its intensity decays. It is generally thought that this decay is a non-thermodynamic process that is dominated by the frictional drag with the land surface — crucially, moisture from the ocean plays no role in this process. Challenging this notion, we argue that the "storm moisture" — the stock of moisture which a hurricane carries as it strikes land — constitutes a source of heat that modulates the decay of intensity and shapes the internal structure of hurricanes past landfall. The critical, albeit unrecognized, role of storm moisture forms the leitmotif of this thesis, which consists of three parts. First, we analyze intensity data for North Atlantic landfalling hurricanes to show that the timescale of hurricane decay has increased in direct proportion to a contemporaneous rise in the sea-surface temperature over the past 50 years. Second, we show that a landfalling hurricane generates a cold-core in its eye that is distinct from the cold-core in an extratropical cyclone. Third, we show that as the cold-core grows past landfall, its competition with Ekman pumping restructures the secondary flow in the hurricane and can lead to the splitting of the hurricane. In all three cases, we show, using a blend of theory, computational simulations, and field observations, that storm moisture dictates the hurricane dynamics past landfall
In situ TEM oxidation study of Fe thin-film transformation to single-crystal magnetite nanoparticles
Get PDFIn this work, we present an in situ transmission electron microscopy (TEM) study of Fe thin films to Fe nanoparticle formation and their oxidation to single-crystal magnetite nanoparticles. Amorphous Fe thin films were prepared by sputtering on TEM carbon grids. The thin Fe films were continuously heated in situ from room temperature to 700 °C under vacuum (4 × 10–4 Pa). With the increase in temperature, the continuity of the thin film starts breaking, and Fe nanoparticle nucleation centers are formed. At 600 °C, the thin film transforms into metallic Fe nanoparticles (NPs) with a small presence of different Fe oxide NPs. Further increase in the temperature to 700 °C resulted in the full oxidation of the NPs (i.e., no core–shell were found). Zero-loss energy filtered diffraction and HRTEM analysis of the lattice spacing reveals that all NPs have fully transformed into single-phase magnetite NPs. The structural study of the magnetite NPs shows that magnetite NPs are free of antiphase domain boundary defects. This work demonstrates that under low partial pressure of oxygen at elevated temperatures a complete oxidation of Fe NPs into magnetite single-crystal nanoparticles can be achieved.journal articl
RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
Get PDFMammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure.journal articl
DNA barcoding and community assembly—A simple solution to a complex problem
Get PDFIdentifying the current and past processes driving community assembly is critical in the effort to understand the Earth's biodiversity and its response to future environmental change. But while studies on community assembly often emphasize the role of contemporary ecological drivers, it has been particularly challenging to account for the effects of past processes in shaping present-day communities. In this issue of Molecular Ecology, Hao et al. (2020) provide a holistic analysis of factors driving the assembly of diverse communities of Lepidoptera in two mountain ranges in northeastern China. The authors use an impressively large data set and exceptionally comprehensive analyses to test how processes of range expansion and gene flow, speciation and extinction, dispersal limitation, environmental filtering and competition have led to present-day diversity patterns. A key novelty of this work is the exhaustive use of DNA barcodes, relatively simple yet powerful molecular markers, to tackle complex biological questions. The authors elegantly show the utility of DNA barcoding data for research beyond simple taxonomic assignment. Their approach is remarkable as it manages to integrate population genetics, phylogenetic history, species diversity and ecology into a well-rounded picture of community assembly. With this work, Hao et al. demonstrate the great promise of DNA barcoding for exhaustive community analysis of even highly diverse and complex systems, raising the bar for future research.journal articl
Macroevolutionary integration of phenotypes within and across ant worker castes
Get PDFPhenotypic traits are often integrated into evolutionary modules: sets of organismal parts that evolve together. In social insect colonies, the concepts of integration and modularity apply to sets of traits both within and among functionally and phenotypically differentiated castes. On macroevolutionary timescales, patterns of integration and modularity within and across castes can be clues to the selective and ecological factors shaping their evolution and diversification. We develop a set of hypotheses describing contrasting patterns of worker integration and apply this framework in a broad (246 species) comparative analysis of major and minor worker evolution in the hyperdiverse ant genusPheidole. Using geometric morphometrics in a phylogenetic framework, we inferred fast and tightly integrated evolution of mesosoma shape between major and minor workers, but slower and more independent evolution of head shape between the two worker castes. Thus,Pheidoleworkers are evolving as a mixture of intracaste and intercaste integration and rate heterogeneity. The decoupling of homologous traits across worker castes may represent an important process facilitating the rise of social complexity.journal articl
Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes
Get PDFThe genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.journal articl
Reef influence quantification in light of the 1771 Meiwa tsunami
Get PDFWhile interactions between regular wave driven flooding and reefs have been widely studied due to climate change pressure, the effects of reefs on tsunami flooding have less been investigated. From studies of historical events, reefs can behave as buffers or as amplifiers of inundation, depending upon the location. Interactions between reefs and tsunamis have generally been analyzed with idealized models, and there have been only few studies of specific reefs and their characteristics. Using numerical NonLinear Shallow Water models, this study characterizes the influence of the Southeast Ishigaki Island reef during the 1771 tsunami that hit the Yaeyama Islands. In this work, we modified reef topography in silico and then, measured the impact of these changes using a new parameter, the Reef Impact Factor (RIF). First, a reference model was built, simulating the real event with an accurate reef representation and using run-up data to calibrate bottom friction. This calibration highlights the difficulty of representing reef friction with a homogeneous coefficient. Second, a model without a reef was compared to the reference model. The impact of reef removal varies considerably along the coastline and maximum wave heights at the shore were strongly affected, with a increase on average. Overall, this suggests a protective role of the reef along most of the coast. However, at local scale, channels that break the continuity of the front reef, increased wave heights by up to on the proximate coast, revealing their strong focusing influence. Finally, changes in tide level, which regulates reef depth, were investigated, showing a global positive correlation between sea level and maximum wave height at the coast. However, the impact of the reef depth appeared weak compared to the impact of incident wave parameters. This study contributes to a global effort to understand tsunami-reef interactions in a non-idealized framework, suggesting a Reef Impact Factor for inter-reef/study comparisons. Moreover, vulnerable and exposed coasts were identified at Ishigaki Island, which may help to improve inundation forecasting, resulting in more appropriate management of these vulnerable sections of the coast.journal articl
Synthetic Symbiosis under Environmental Disturbances
Get PDFBy virtue of complex ecologies, the behavior of mutualisms is challenging to study and nearly impossible to predict. However, laboratory engineered mutualistic systems facilitate a better understanding of their bare essentials. On the basis of an abstract theoretical model and a modifiable experimental yeast system, we explore the environmental limits of self-organized cooperation based on the production and use of specific metabolites. We develop and test the assumptions and stability of the theoretical model by leveraging the simplicity of an artificial yeast system as a simple model of mutualism. We examine how one-off, recurring, and permanent changes to an ecological niche affect a cooperative interaction and change the population composition of an engineered mutualistic system. Moreover, we explore how the cellular burden of cooperating influences the stability of mutualism and how environmental changes shape this stability. Our results highlight the fragility of mutualisms and suggest interventions, including those that rely on the use of synthetic biology.
IMPORTANCE The power of synthetic biology is immense. Will it, however, be able to withstand the environmental pressures once released in the wild. As new technologies aim to do precisely the same, we use a much simpler model to test mathematically the effect of a changing environment on a synthetic biological system. We assume that the system is successful if it maintains proportions close to what we observe in the laboratory. Extreme deviations from the expected equilibrium are possible as the environment changes. Our study provides the conditions and the designer specifications which may need to be incorporated in the synthetic systems if we want such "ecoblocs" to survive in the wild.journal articl