Monitoring Wavepacket Dynamics at Conical Intersections by Entangled Two-Photon Absorption
Not provided.
Materials Science↗
Engineering topics
Chen, Feng
Publications and source records attributed to Chen, Feng.
Entangled two-photon absorption with Brownian-oscillator fluctuations
Here, we theoretically investigate the two-photon absorption signals of a three-band (g, e, f) system diagonally coupled to an over-damped Brownian oscillator bath, which induces random Gaussian modulations of energy levels with an arbitrary degree of correlation. For fast modulation, extra 2ω eg and 2ω fe peaks may obscure the g–f transitions in the classical two-photon absorption (CTPA) spectra for nearly resonant e states. These peaks arise from one-photon resonant g–e or e–f transitions. In the slow modulation limit, these peaks vanish because of the short tails of the Gaussian line shape. CTPA strongly depends on the correlations between energy fluctuations. In entangled two-photon absorption, the extra peaks are eliminated because of the broad one-photon but narrow two-photon spectrum of the twin photons. The variation of the coherences between f states with the correlation between energy fluctuations is explored.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Vibrational Hyper-Raman Molecular Spectroscopy with Entangled Photons
Not provided.
Materials Science↗
Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale
Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.
59 BASIC BIOLOGICAL SCIENCES↗
Review on dynamic modulus of coarse-grained soil filling for high-speed railway subgrade
Not Available
Ye, Yangsheng↗
Structural mechanism of DNA recognition by the p204 HIN domain
Explore the source record for details and available documents.
Fan, Xiaojiao↗
Differences in Mechanism and Rate of Zeolite-Catalyzed Cyclohexanol Dehydration in Apolar and Aqueous Phase
The rate of acid-base catalyzed dehydration of alcohols strongly depends on the solvent and the environment of the acid sites. In this work, we find that Brønsted acidic sites in large-pore zeolites, but not in medium-pore zeolites, catalyze cyclohexanol dehydration in decalin at significantly higher rates than hydrated hydronium ions in aqueous phase. Specifically, the difference in turnover rates between the two solvents amounts to two to three orders of magnitude on H-BEA and H-FAU, while being very modest (within a factor of 2) for H-MFI. Combining kinetic, isotopic tracer and 2H NMR measurements, it is established that cyclohexanol dehydration generally follows an E1-elimination pathway in decalin. A notable exception is the monomer dehydration route on H-MFI, which exhibits a much lower activation energy and a substantially negative activation entropy that appear to be associated with an E2-type mechanism. The C-O bond cleavage displays a dominant degree of rate control in decalin, which stands in contrast to deprotonation (C-H cleavage) being rate-limiting in aqueous-phase dehydration.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Directing the Rate‐Enhancement for Hydronium Ion Catalyzed Dehydration via Organization of Alkanols in Nanoscopic Confinements
Abstract Alkanol dehydration rates catalyzed by hydronium ions are enhanced by the dimensions of steric confinements of zeolite pores as well as by intraporous intermolecular interactions with other alkanols. The higher rates with zeolite MFI having pores smaller than those of zeolite BEA for dehydration of secondary alkanols, 3‐heptanol and 2‐methyl‐3‐hexanol, is caused by the lower activation enthalpy in the tighter confinements of MFI that offsets a less positive activation entropy. The higher activity in BEA than in MFI for dehydration of a tertiary alkanol, 2‐methyl‐2‐hexanol, is primarily attributed to the reduction of the activation enthalpy by stabilizing intraporous interactions of the C β ‐H transition state with surrounding alcohol molecules. Overall, we show that the positive impact of zeolite confinements results from the stabilization of transition state provided by the confinement and intermolecular interaction of alkanols with the transition state, which is impacted by both the size of confinements and the structure of alkanols in the E1 pathway of dehydration.
Shetty, Manish↗
Directing the Rate‐Enhancement for Hydronium Ion Catalyzed Dehydration via Organization of Alkanols in Nanoscopic Confinements
Abstract Alkanol dehydration rates catalyzed by hydronium ions are enhanced by the dimensions of steric confinements of zeolite pores as well as by intraporous intermolecular interactions with other alkanols. The higher rates with zeolite MFI having pores smaller than those of zeolite BEA for dehydration of secondary alkanols, 3‐heptanol and 2‐methyl‐3‐hexanol, is caused by the lower activation enthalpy in the tighter confinements of MFI that offsets a less positive activation entropy. The higher activity in BEA than in MFI for dehydration of a tertiary alkanol, 2‐methyl‐2‐hexanol, is primarily attributed to the reduction of the activation enthalpy by stabilizing intraporous interactions of the C β ‐H transition state with surrounding alcohol molecules. Overall, we show that the positive impact of zeolite confinements results from the stabilization of transition state provided by the confinement and intermolecular interaction of alkanols with the transition state, which is impacted by both the size of confinements and the structure of alkanols in the E1 pathway of dehydration.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Arabidopsis C‐terminal binding protein ANGUSTIFOLIA modulates transcriptional co‐regulation of MYB46 and WRKY33
Not Available
(hemi)biotrophic and necrotrophic pathogens↗
Proteogenomic Characterization of Endometrial Carcinoma
We undertook a comprehensive proteogenomic characterization of 95 endometrial carcinomas, of which 83 were endometrioid tumors and 12 were serous tumors. This analysis revealed new consequences of perturbations to the p53 and Wnt/ß-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new insights into proteomic markers of clinical and genomic tumor subgroups, some of which are in known druggable pathways. We performed a broad genome-wide acetylation survey, one of the first of its kind, yielding insights into regulatory mechanisms of histone acetylation. We also characterized the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, further our understanding of the molecular mechanisms underlying endometrial carcinoma, and identify new avenues for investigating potential therapeutic targets.
59 BASIC BIOLOGICAL SCIENCES↗
Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass ( Panicum virgatum L.)
Switchgrass ( Panicum virgatum L.), a perennial C4 grass, represents an important species in natural and anthropogenic grasslands of North America. Its resilience to abiotic and biotic stress has made switchgrass a preferred bioenergy crop. However, little is known about the mechanisms of resistance of switchgrass against pathogens and herbivores. Volatile compounds such as terpenes have important activities in plant direct and indirect defense. Here, we show that switchgrass leaves emit blends of monoterpenes and sesquiterpenes upon feeding by the generalist insect herbivore Spodoptera frugiperda (fall armyworm) and in a systemic response to the treatment of roots with defense hormones. Belowground application of methyl jasmonate also induced the release of volatile terpenes from roots. To correlate the emission of terpenes with the expression and activity of their corresponding biosynthetic genes, we identified a gene family of 44 monoterpene and sesquiterpene synthases (mono- and sesqui-TPSs) of the type-a, type-b, type-g, and type-e subfamilies, of which 32 TPSs were found to be functionally active in vitro. The TPS genes are distributed over the K and N subgenomes with clusters occurring on several chromosomes. Synteny analysis revealed syntenic networks for approximately 30–40% of the switchgrass TPS genes in the genomes of Panicum hallii, Setaria italica , and Sorghum bicolor , suggesting shared TPS ancestry in the common progenitor of these grass lineages. Eighteen switchgrass TPS genes were substantially induced upon insect and hormone treatment and the enzymatic products of nine of these genes correlated with compounds of the induced volatile blends. In accordance with the emission of volatiles, TPS gene expression was induced systemically in response to belowground treatment, whereas this response was not observed upon aboveground feeding of S. frugiperda . Our results demonstrate complex above and belowground responses of induced volatile terpene metabolism in switchgrass and provide a framework for more detailed investigations of the function of terpenes in stress resistance in this monocot crop
Plant Sciences↗
Modeling the Impacts of Urbanization on Summer Thermal Comfort: The Role of Urban Land Use and Anthropogenic Heat
Urban land use and anthropogenic heat (AH) emission can considerably influence the human thermal comfort during extreme heat events. In this study, a spatially heterogeneous AH emission data and updated urban land use data are integrated into the Weather Research and Forecasting model to simulate the physical processes of urban warming during summer. Simulations conducted in the Yangtze River Delta (YRD) of east China suggest that the mean urban heat island intensity reaches 1.49 °C in urbanized areas during summer, with AH emission making a considerable contribution. The warming effect due to urban land use is intensified during extremely hot days, but in contrast, the AH effects are slightly reduced. Urban development increases the total thermal discomfort hours by 27% in the urban areas of YRD, with AH and urban land use contributing nearly equal amount. By limiting the daytime latent heat release, urban land use reduces the daily maximum heat stress particularly during extremely hot days; however, such alleviations can be offset by the AH emission. We conclude strategies for mitigation of urban heat island effect and heat stress in cities should therefore include measures to reduce AH emission.
54 ENVIRONMENTAL SCIENCES↗
Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi
Fungi are essential eukaryotes of wide distribution. They are known as rich producers of secondary metabolites, especially terpenoids, which are crucial for fungi-environment interactions. Horizontal gene transfer (HGT) is an important mechanism contributing to genetic innovation of fungi. Yet, it remains unclear whether HGT has played a role in creating the enormous chemical diversity of fungal terpenoids. Here we report that fungi have acquired terpene synthase genes ( TPS s), which encode pivotal enzymes for terpenoid biosynthesis, from bacteria through HGT. Phylogenetic analysis placed the majority of fungal and bacterial TPS genes from diverse taxa into two clades, indicating ancient divergence. Nested in the bacterial TPS clade is a number of fungal TPS genes that are inferred as the outcome of HGT. These include a monophyletic clade of nine fungal TPS genes, designated as BTPSL for bacterial TPS -like genes, from eight species of related entomopathogenic fungi, including seven TPS s from six species in the genus Metarhizium. In vitro enzyme assays demonstrate that all seven BTPSL genes from the genus Metarhizium encode active enzymes with sesquiterpene synthase activities of two general product profiles. By analyzing the catalytic activity of two resurrected ancestral BTPSL s and one closely related bacterial TPS , the trajectory of functional evolution of BTPSL s after HGT from bacteria to fungi and functional divergence within Metarhizium could be traced. Using M. brunneum as a model species, both BTPSLs and typical fungal TPS s were demonstrated to be involved in the in vivo production of terpenoids, illustrating the general importance of HGT of TPS genes from bacteria as a mechanism contributing to terpenoid diversity in fungi.
59 BASIC BIOLOGICAL SCIENCES↗
Optimizing de novo genome assembly from PCR-amplified metagenomes
Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.
59 BASIC BIOLOGICAL SCIENCES↗