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At least 361 records · Page 20

Topological Signature of Stratospheric Poincaré-Gravity Waves

The rotation of Earth breaks time-reversal and reflection symmetries in an opposite sense north and south of the equator, leading to a topological origin for certain atmospheric and oceanic equatorial waves. Away from the equator, the rotating shallow-water and stably stratified primitive equations exhibit Poincaré inertia–gravity waves that have nontrivial topology as evidenced by their strict superinertial time scale and a phase singularity in frequency–wavevector space. This nontrivial topology then predicts, via the principle of bulk-interface correspondence, the existence of two equatorial waves along the equatorial interface, the Kelvin and Yanai waves. To directly test the nontrivial topology of Poincaré-gravity waves in observations, we examine ERA5 data and study cross correlations between the wind velocity and geopotential height of the midlatitude stratosphere at the 50 hPa height. We find the predicted vortex and antivortex in the relative phase of the geopotential height and velocity at the high frequencies of the waves. By contrast, lower-frequency planetary waves are found to have trivial topology also as expected from theory. These results demonstrate a new way to understand stratospheric waves and provide a new qualitative tool to investigate waves in other components of the climate system.

54 ENVIRONMENTAL SCIENCES↗

Role of Tropical Variability in Driving Decadal Shifts in the Southern Hemisphere Summertime Eddy-Driven Jet

The Southern Hemisphere summertime eddy-driven jet and storm tracks have shifted poleward over the recent few decades. In previous studies, explanations have mainly stressed the influence of external forcing in driving this trend. Here we examine the role of internal tropical SST variability in controlling the austral summer jet’s poleward migration, with a focus on interdecadal time scales. The role of external forcing and internal variability are isolated by using a hierarchy of Community Earth System Model version 1 (CESM1) simulations, including the pre-industrial control, large ensemble, and pacemaker runs. Model simulations suggest that in the early twenty-first century, both external forcing and internal tropical Pacific SST variability are important in driving a positive southern annular mode (SAM) phase and a poleward migration of the eddy-driven jet. Tropical Pacific SST variability, associated with the negative phase of the interdecadal Pacific oscillation (IPO), acts to shift the jet poleward over the southern Indian and southwestern Pacific Oceans and intensify the jet in the southeastern Pacific basin, while external forcing drives a significant poleward jet shift in the South Atlantic basin. In response to both external forcing and decadal Pacific SST variability, the transient eddy momentum flux convergence belt in the middle latitudes experiences a poleward migration due to the enhanced meridional temperature gradient, leading to a zonally symmetric southward migration of the eddy-driven jet. This mechanism distinguishes the influence of the IPO on the midlatitude circulation from the dynamical impact of ENSO, with the latter mainly promoting the subtropical wave-breaking critical latitude poleward and pushing the midlatitude jet to higher latitudes.

54 ENVIRONMENTAL SCIENCES↗

Persistent ocean anomalies as a response to Northern Hemisphere heating induced by biomass burning variability

Biomass burning aerosol (BBA) emissions in the Coupled Model Intercomparison Project Phase 6 (CMIP6) historical forcing fields have enhanced temporal variability during the years 1997–2014 compared to earlier periods. Recent studies document that the corresponding inhomogeneous shortwave forcing over this period can cause changes in clouds, permafrost, and soil moisture, which contribute to a net terrestrial Northern Hemisphere warming relative to earlier periods. Here, we investigate the ocean response to the hemispherically asymmetric warming, using a 100-member ensemble of the Community Earth System Model version 2 Large Ensemble forced by two different BBA emissions (CMIP6 default and temporally smoothed over 1990–2020). Differences between the two subensemble means show that ocean temperature anomalies occur during periods of high BBA variability and subsequently persist over multiple decades. In the North Atlantic, surface warming is efficiently compensated for by decreased northward oceanic heat transport due to a slowdown of the Atlantic Meridional Overturning Circulation. In the North Pacific, surface warming is compensated for by an anomalous cross-equatorial cell (CEC) that reduces northward oceanic heat transport. The heat that converges in the South Pacific through the anomalous CEC is shunted into the subsurface and contributes to formation of long-lasting ocean temperature anomalies. The anomalous CEC is maintained through latitude-dependent contributions from narrow western boundary currents and basin-wide near-surface Ekman transport. Furthermore, these results indicate that interannual variability in forcing fields may significantly change the background climate state over long timescales, presenting a potential uncertainty in CMIP6-class climate projections forced without interannual variability.

54 ENVIRONMENTAL SCIENCES↗

Fibrous anisotropy and mineral gradients within the radula stylus of chiton: Controlled stiffness and damage tolerance in a flexible biological composite

Over hundreds of millions of years, organisms have evolved architected structures via precise control over hierarchically assembled components, including the integration of dissimilar materials. One such example is found in the radula system of chitons, intertidal mollusks that feed on algae growing on the rock. Their radula consists of multiple rows of ultrahard teeth, each integrated with a foldable belt-like substrate via a stiff, yet flexible stylus, which is essential for efficient rasping during the feeding process. Here, we investigate the nano and micro-scale components and architectures as well as regional mechanical properties of the stylus, and their subsequent role during the rasping of Cryptochiton stelleri. Three important factors were determined to contribute to the regio-specific stiffness of the stylus: the presence of mineral components, highly oriented chitinous fibers, and a chemically cross-linked protein matrix. All these factors are varied throughout the stylus. There is a high mineral content on the trailing edge close to the tooth and a cross-linked matrix on the leading edge, both with orientational specific oriented chitin fibers that provide force transduction to the tooth. Conversely, there is a significant lack of mineral or cross-linked matrix in the proximal end as well as a low degree of fiber orientation, resulting in a flexible region that can accommodate torsion and flexure during rasping. Understanding the graded composite structure of the stylus and applying this unique design to various engineering fields such as soft robotics, biotechnology, and the medical industry, can inspire the production of high-performance materials.

Lee, Jung-Eun↗

Field evaluation of transgenic hybrid poplars with desirable wood properties and enhanced growth for biofuel production by bicistronic expression of PdGA20ox1 and PtrMYB3 in wood-forming tissue

Background: To create an ideotype woody bioenergy crop with desirable growth and biomass properties, we utilized the viral 2A-meidated bicistronic expression strategy to express both PtrMYB3 ( MYB46 ortholog of Populus trichocarpa , a master regulator of secondary wall biosynthesis) and PdGA20ox1 (a GA20-oxidase from Pinus densiflora that produces gibberellins) in wood-forming tissue (i.e., developing xylem). Results: Transgenic Arabidopsis plants expressing the gene construct DX15::PdGA20ox1-2A-PtrMYB3 showed a significant increase in both stem fresh weight (threefold) and secondary wall thickening (1.27-fold) relative to wild-type (WT) plants. Transgenic poplars harboring the same gene construct grown in a greenhouse for 60 days had a stem fresh weight up to 2.6-fold greater than that of WT plants. In a living modified organism (LMO) field test conducted for 3 months of active growing season, the stem height and diameter growth of the transgenic poplars were 1.7- and 1.6-fold higher than those of WT plants, respectively, with minimal adverse growth defects. Although no significant changes in secondary wall thickening of the stem tissue of the transgenic poplars were observed, cellulose content was increased up to 14.4 wt% compared to WT, resulting in improved saccharification efficiency of the transgenic poplars. Moreover, enhanced woody biomass production by the transgenic poplars was further validated by re-planting in the same LMO field for additional two growing seasons. Conclusions: Taken together, these results show considerably enhanced wood formation of our transgenic poplars, with improved wood quality for biofuel production.

09 BIOMASS FUELS↗

Enhanced thermoelectric performance of SnSe by controlled vacancy population

Abstract The thermoelectric performance of SnSe strongly depends on its low-energy electron band structure that provides high density of states in a narrow energy window due to the multi-valley valence band maximum (VBM). Angle-resolved photoemission spectroscopy measurements, in conjunction with first-principles calculations, reveal that the binding energy of the VBM of SnSe is tuned by the population of Sn vacancy, which is determined by the cooling rate during the sample growth. The VBM shift follows precisely the behavior of the thermoelectric power factor, while the effective mass is barely modified upon changing the population of Sn vacancies. These findings indicate that the low-energy electron band structure is closely correlated with the high thermoelectric performance of hole-doped SnSe, providing a viable route toward engineering the intrinsic defect-induced thermoelectric performance via the sample growth condition without an additional ex-situ process. Graphical Abstract

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Controlling structure and interfacial interaction of monolayer TaSe2 on bilayer graphene

Abstract Tunability of interfacial effects between two-dimensional (2D) crystals is crucial not only for understanding the intrinsic properties of each system, but also for designing electronic devices based on ultra-thin heterostructures. A prerequisite of such heterostructure engineering is the availability of 2D crystals with different degrees of interfacial interactions. In this work, we report a controlled epitaxial growth of monolayer TaSe 2 with different structural phases, 1 H and 1 T , on a bilayer graphene (BLG) substrate using molecular beam epitaxy, and its impact on the electronic properties of the heterostructures using angle-resolved photoemission spectroscopy. 1 H -TaSe 2 exhibits significant charge transfer and band hybridization at the interface, whereas 1 T -TaSe 2 shows weak interactions with the substrate. The distinct interfacial interactions are attributed to the dual effects from the differences of the work functions as well as the relative interlayer distance between TaSe 2 films and BLG substrate. The method demonstrated here provides a viable route towards interface engineering in a variety of transition-metal dichalcogenides that can be applied to future nano-devices with designed electronic properties.

36 MATERIALS SCIENCE↗

Topological surface states of semimetal TaSb 2

Topological surface states, protected by the global symmetry of the materials, are the keys to understanding various novel electrical, magnetic, and optical properties. TaSb 2 is a newly discovered topological material with unique transport phenomena, including negative magnetoresistance and resistivity plateau, whose microscopic understanding is yet to be reached. In this study, we investigate the electronic band structure of TaSb 2 using angle-resolved photoemission spectroscopy and density functional theory. Our analyses reveal distinct bulk and surface states in TaSb 2 , providing direct evidence of its topological nature. Notably, surface states predominate the electronic contribution near the Fermi level, while bulk bands are mostly located at higher binding energies. Our study underlines the importance of systematic investigations into the electronic structures of topological materials, offering insights into their fundamental properties and potential applications in future technologies.

36 MATERIALS SCIENCE↗

Application of physics-informed neural networks (PINNs) solution to coupled thermal and hydraulic processes in silty sands

Abstract The accurate modeling of water and heat transport in soils is crucial for both geo-environmental and geothermal engineering. Traditional modeling methods are problematic because they require well-defined boundaries and initial conditions. Recently, physics-informed neural networks (PINNs), which incorporate partial differential equations (PDEs) to solve forward and inverse problems, have attracted increasing attention in machine learning research. In this study, we applied PINNs to tackle hydraulic and thermal transport coupling forward problems in silty sands. A fully connected deep neural network was utilized for training. This neural network model leverages automatic differentiation to apply the governing equations as constraints, based on the mathematical approximations established by the neural network itself. We conducted forward problems and compared the solutions derived from PINNs with those from Finite Element Method (FEM) simulations. The forward problem results demonstrate the PINNs model’s capability in predicting hydraulic transport, heat transport, and thermal–hydraulic coupling in silty sands under various boundary conditions. The PINNs exhibited great performance in simulating the thermal–hydraulic coupling problem. The accuracy of the PINNs solutions shows its potential for simulation in geotechnical engineering.

Feng, Yuan↗

Time-dependent probability density function analysis of H-mode transitions

Abstract The first application of time-dependent probability density function (PDF) analysis to the L-H transition in fusion plasmas is presented. PDFs are constructed using Doppler Backscattering data of perpendicular fluctuation velocity, , and turbulence from the edge region of the DIII-D tokamak. These raw time-series data are sliced into millisecond-long sliding time-windows to create PDFs. During the transition, the PDFs develop strong right tails, indicative of turbulence-suppressing localised flows in the plasma edge; such features and other subtle behaviours are explored using novel information geometry techniques. This letter examines the applicability of these techniques to predict L-H transitions and investigate predator-prey self-regulation theories between turbulence and perpendicular velocity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Data for System Analysis of Lipomyces starkeyi During Growth on Various Plant‑Based Sugars

Oleaginous yeasts have received significant attention due to their substantial lipid storage capability. The accumulated lipids can be utilized directly or processed into various bioproducts and biofuels. Lipomyces starkeyi is an oleaginous yeast capable of using multiple plant-based sugars, such as glucose, xylose, and cellobiose. It is, however, a relatively unexplored yeast due to limited knowledge about its physiology. In this study, we have evaluated the growth of L. starkeyi on different sugars and performed transcriptomic and metabolomic analyses to understand the underlying mechanisms of sugar metabolism. Principal component analysis showed clear differences resulting from growth on different sugars. We have further reported various metabolic pathways activated during growth on these sugars. We also observed non-specific regulation in L. starkeyi and have updated the gene annotations for the NRRL Y-11557 strain. This analysis provides a foundation for understanding the metabolism of these plant-based sugars and potentially valuable information to guide the metabolic engineering of L. starkeyi to produce bioproducts and biofuels.

Conversion↗

Data for Genome-Wide Association and Genomic Prediction for Yield and Component Traits of Miscanthus sacchariflorus

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus .

Biomass Analytics↗

Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids

This dataset contains all data used in the paper "Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids". The dataset includes genotypes and phenotypic data from two autotetraploid species Miscanthus sacchariflorus and Vaccinium corymbosum that was used used for genome wide association studies and genomic prediction and the scripts used in the analysis. In this V2, 2 files have the raw data are added: "Miscanthus_sacchariflorus_RADSeq.vcf" is the VCF file with the raw SNP calls of the Miscanthus sacchariflorus data used for genotype calling using the 6 genotype calling methods. "Blueberry_data_read_depths.RData" is the a RData file with the read depth data that was used for genotype calling in the Blueberry dataset.

allelic dosage↗

Data from Enhanced 2′-Fucosyllactose Production by Engineered Saccharomyces cerevisiae using Xylose as a Co-Substrate

2′-Fucosyllactose (2′-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli , Saccharomyces cerevisiae , Corynebacterium glutamicum , and Bacillus subtilis have been engineered to produce 2′-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2′-FL, but accumulation of by-products due to overflow metabolism of glucose hampered efficient production of 2′-FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidative metabolism, for the production of 2′-FL by engineered yeast. Specifically, we modified an engineered S. cerevisiae strain capable of assimilating xylose to produce 2′-FL from a mixture of xylose and lactose. First, a lactose transporter (Lac12) from Kluyveromyces lactis was introduced. Second, a heterologous 2′-FL biosynthetic pathway consisting of enzymes Gmd, WcaG, and WbgL from E. coli was introduced. Third, we adjusted expression levels of the heterologous genes to maximize 2′-FL production. The resulting engineered yeast produced 25.5 g/L of 2′-FL with a volumetric productivity of 0.35 g/L∙h in a fed-batch fermentation with lactose and xylose feeding to mitigate the glucose repression. Interestingly, the major location of produced 2′-FL by the engineered yeast can be changed using different culture media. While 72% of the produced 2′-FL was secreted when a complex medium was used, 82% of the produced 2′-FL remained inside the cells when a minimal medium was used. As yeast extract is already used as food and animal feed ingredients, 2′-FL enriched yeast extract can be produced cost-effectively using the 2′-FL-accumulating yeast cells.

Conversion↗

Data for Integrating Transcriptomic and Metabolomic Analysis of the Oleaginous Yeast Rhodosporidium toruloides IFO0880 During Growth under Different Carbon Sources

Rhodosporidium toruloides is an oleaginous yeast capable of producing a variety of biofuels and bioproducts from diverse carbon sources. Despite numerous studies showing its promise as a platform microorganism, little is known about its metabolism and physiology. In this work, we investigated the central carbon metabolism in R. toruloides IFO0880 using transcriptomics and metabolomics during growth on glucose, xylose, acetate, or soybean oil. These substrates were chosen because they can be derived from plants. Significant changes in gene expression and metabolite concentrations were observed during growth on these four substrates. We mapped these changes onto the governing metabolic pathways to better understand how R. toruloides reprograms its metabolism to enable growth on these substrates. One notable finding concerns xylose metabolism, where poor expression of xylulokinase induces a bypass leading to arabitol production. Collectively, these results further our understanding of central carbon metabolism in R. toruloides during growth on different substrates. They may also help guide the metabolic engineering and development of better models of metabolism for R. toruloides .

Conversion↗

Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.

60 APPLIED LIFE SCIENCES↗

Structure of puromycin-sensitive aminopeptidase and polyglutamine binding

Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Å. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of an in vitro three-dimensional HepaRG spheroid model for genotoxicity testing using the high-throughput CometChip platform

Three-dimensional (3D) culture systems are increasingly being used for genotoxicity studies due to improved cell-to-cell interactions and tissue-like structures that are limited or lacking in 2D cultures. The present study optimized a 3D culture system using metabolically competent HepaRG cells for in vitro genotoxicity testing. 3D HepaRG spheroids, formed in 96- or 384-well ultra-low attachment plates, were exposed to various concentrations of 34 test articles, including 8 direct-acting and 11 indirect-acting genotoxicants/carcinogens as well as 15 compounds that show different genotoxic responses in vitro and in vivo. DNA damage was evaluated using the high-throughput CometChip assay with concurrent cytotoxicity assessment by the ATP assay in both 2D and 3D cultures. 3D HepaRG spheroids maintained a stable phenotype for up to 30 days with higher levels of albumin secretion, cytochrome P450 gene expression, and enzyme activities compared to 2D cultures. 3D spheroids also demonstrated a higher sensitivity than 2D cultures for detecting both direct- and indirect-acting genotoxicants/carcinogens, indicating a better prediction of in vivo genotoxicity responses. When DNA damage dose-response data were quantified using PROAST software, 3D spheroids generally had lower or similar benchmark dose values compared to 2D HepaRG cells and were more comparable with primary human hepatocytes. These results demonstrate that 3D models can be adapted to the CometChip technology for high-throughput genotoxicity testing and that 3D HepaRG spheroids may be used as a reliable and pragmatic in vitro approach to better support the hazard identification and risk assessment of potential human genotoxic carcinogens.

60 APPLIED LIFE SCIENCES↗