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Zhang, Yu

Publications and source records attributed to Zhang, Yu.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Altered Expression of Two Small Secreted Proteins (ssp4 and ssp6) Affects the Degradation of a Natural Lignocellulosic Substrate by Pleurotus ostreatus

Pleurotus ostreatus is a white-rot fungus that can degrade lignin in a preferential manner using a variety of extracellular enzymes, including manganese and versatile peroxidases (encoded by the vp1-3 and mnp1-6 genes, respectively). This fungus also secretes a family of structurally related small secreted proteins (SSPs) encoded by the ssp1-6 genes. Using RNA sequencing (RNA-seq), we determined that ssp4 and ssp6 are the predominant members of this gene family that were expressed by P. ostreatus during the first three weeks of growth on wheat straw. Downregulation of ssp4 in a strain harboring an ssp RNAi construct (KDssp1) was then confirmed, which, along with an increase in ssp6 transcript levels, coincided with reduced lignin degradation and the downregulation of vp2 and mnp1. In contrast, we observed an increase in the expression of genes related to pectin and side-chain hemicellulose degradation, which was accompanied by an increase in extracellular pectin-degrading capacity. Genome-wide comparisons between the KDssp1 and the wild-type strains demonstrated that ssp silencing conferred accumulated changes in gene expression at the advanced cultivation stages in an adaptive rather than an inductive mode of transcriptional response. Based on co-expression networking, crucial gene modules were identified and linked to the ssp knockdown genotype at different cultivation times. Based on these data, as well as previous studies, we propose that P. ostreatus SSPs have potential roles in modulating the lignocellulolytic and pectinolytic systems, as well as a variety of fundamental biological processes related to fungal growth and development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination

Abstract The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate Salix in tissue culture, previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea . Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP‐Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea , contributing to a regulatory system that is notably different from that of its sister genus Populus . Evidence was also obtained for the roles of two transcription factors, an AP2 / ERF family gene and a homeodomain‐like transcription factor, in downstream regulation of sex dimorphism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A versatile high-average-power ultrafast infrared driver tailored for high-harmonic generation and vibrational spectroscopy

We report on an ultrafast infrared optical parametric chirped-pulse amplifier (OPCPA), pumped by a 200-W thin-disk Yb-based regenerative amplifier at a repetition rate of 100 kHz. The OPCPA is tunable in the spectral range 1.4–3.9 μm, generating up to 23 W of < 100-fs signal and 13 W of < 200-fs idler pulses for infrared spectroscopy, with additional spectral filtering capabilities for Raman spectroscopy. The OPCPA can also yield 19 W of 49-fs 1.75- μm signal or 5 W of 62-fs 2.8- μm idler pulses with active carrier-to-envelope-phase (CEP) stabilisation for high-harmonic generation (HHG). We illustrate the versatility of the laser design, catering to various experimental requirements for probing ultrafast science.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Patterned OLEDs: effect of substrate corrugation pitch and height

Abstract An ongoing OLED challenge is cost-effective enhancement of light extraction, i.e., increasing the external quantum efficiency ( EQE ∼20% in conventional devices). OLEDs on corrugated substrates often show enhanced EQE s providing insight into light emission processes. In particular, patterned plastic substrates directly imprinted easily at room temperature and amenable to low-cost R2R production are ideal for studying/optimizing various structures, further elucidating the extraction process. We show new semi-quantitative data of the effect of the pitch ( a ) and height/depth ( h ) of plastic substrate patterns on the OLEDs’ stack and EQE , focusing on new designs, interestingly, some showing surprisingly enhanced EQE s that were neither reported nor discussed before. These includ e : ( i ) shallow ( h < 200 nm) convex polycarbonate with a ∼ 750 versus ∼400 nm, where the h gradually decreases as the OLED stack is built and ( ii ) concave PET/CAB with large a (∼2.8 and ∼7.8 μ m), where the EQE enhancement of conformal OLEDs may be due largely to scattering. EQE s of green, blue, and white phosphorescent OLEDs were measured. OLEDs on substrates with narrow a ∼ 400 nm and low h < 200 nm s h owed no enhancement, resembling flat devices. In contrast, OLEDs on substrates with comparable or smaller h , but larger a ∼ 750 nm show signific a nt EQE enhancement despite h reduction across the stack. Green OLEDs with a ∼ 750 nm and h ∼ 160 to ∼180 nm, showed EQE s ∼30%, reaching ∼58% with substrate mode extraction. Surprisingly, fully conformal OLEDs on a PET/CAB substrate with a ∼ 7.8 μ m showed blue a nd white EQE s reaching ∼33%, without substrate mode extraction. The enhancing patterns increase the OLEDs’ EQE by reducing surface plasmon excitation and internal waveguiding. The experimental results for OLEDs on substrates with a < 2 μ m are supported by scattering matrix simulations that assume conformal stacks, incorporating diffraction for internal losses reduction. EQE enhancement not predicted by simulations may be due additionally to scattering mostly for substrates with a signific a ntly larger than the emitting wavelength.

42 ENGINEERING↗
DOE OSTI2023

IMA genome-F18

Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Nucleon-Pair Shell Model within a Symmetry Broken Basis

The nucleon-pair shell model (NPSM) within the framework of a broken symmetry basis is studied. The results demonstrate the validity of such a scheme, which in turn leads to a significant reduction in the dimensionality of the multi-pair configuration space. Specifically, in the case of an axially-deformed basis, the results yield a satisfactory description of the low-lying spectrum, even without the need for applying the projection procedure. In the case of a triaxially-deformed basis, the result of variation after angular momentum projection suggest a potential for using the NPSM to find exact solutions in a semi-magic system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Structural changes induced by electric currents in a single crystal of Pr 2 CuO 4

We demonstrate an approach to the structural and electronic property modification of perovskites, focusing on Pr 2 CuO 4 , an undoped parent compound of a class of electron-doped copper-oxide superconductors. Currents were passed parallel or perpendicular to the copper oxygen layers with the voltage ramped up until a rapid drop in the resistivity was achieved, a process referred to as “flash.” The current was then further increased tenfold in current-control mode. This state was quenched by immersion into liquid nitrogen. Flash can drive many compounds into different atomic structures with new properties, whereas the quench freezes them into a long-lived state. Single-crystal neutron diffraction of as-grown and modified Pr 2 CuO 4 revealed a √10 ×√10 superlattice due to oxygen-vacancy order. The diffraction peak intensities of the superlattice of the modified sample were significantly enhanced relative to the pristine sample. Raman-active phonons in the modified sample were considerably sharper. Measurements of electrical resistivity, magnetization, and two-magnon Raman scattering indicate that the modification affected only the Pr-O layers, but not the Cu-O planes. These results point to enhanced oxygen-vacancy order in the modified samples well beyond what can be achieved without passing electrical current. Our work opens a new avenue toward electric field/quench control of structure and properties of layered perovskite oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models

Here, a shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born–Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born–Oppenheimer molecular dynamics (BOMD). XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO 2 ) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born–Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Perpendicular in-plane negative magnetoresistance in ZrTe 5

The unique band structure in topological materials frequently results in unusual magneto-transport phenomena, one of which is in-plane longitudinal negative magnetoresistance (NMR) with the magnetic field aligned parallel to the electrical current direction. This NMR is widely considered as a hallmark of chiral anomaly in topological materials. Here we report the observation of in-plane NMR in the topological material ZrTe 5 when the in-plane magnetic field is both parallel and perpendicular to the current direction, revealing an unusual case of quantum transport beyond the chiral anomaly. We find that a general theoretical model, which considers the combined effect of Berry curvature and orbital moment, can quantitatively explain this in-plane NMR. In conclusion, our results provide new insights into the understanding of in-plane NMR in topological materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Virion glycosylation influences mycobacteriophage immune recognition

Glycosylation of eukaryotic virus particles is common and influences their uptake, trafficking, and immune recognition. In contrast, glycosylation of bacteriophage particles has not been reported; phage virions typically do not enter the cytoplasm upon infection, and they do not generally inhabit eukaryotic systems. We show here that several genomically distinct phages of Mycobacteria are modified with glycans attached to the C terminus of capsid and tail tube protein subunits. These O-linked glycans influence antibody production and recognition, shielding viral particles from antibody binding and reducing production of neutralizing antibodies. Glycosylation is mediated by phage-encoded glycosyltransferases, and genomic analysis suggests that they are relatively common among mycobacteriophages. Putative glycosyltransferases are also encoded by some Gordonia and Streptomyces phages, but there is little evidence of glycosylation among the broader phage population. The immune response to glycosylated phage virions in mice suggests that glycosylation may be an advantageous property for phage therapy of Mycobacterium infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Coupled effects of future rainfall and land use on urban stormwater drainage system in Tampa, Florida (USA)

Future rainfall and land use are two important factors for flood management since they both directly and indirectly affect the functionality and performance of urban stormwater drainage infrastructures. Although some studies have already examined the coupled effects of future rainfall and land use conditions, they have not concluded how such effects on both surface runoff and flood areas would change with regional surface elevation variation and infrastructure conditions. This paper analyzed the coupled effects of future rainfall and land use on urban drainage systems in terms of surface runoff quantity and flood area changes using EPA SWMM. Future downscaled and bias-corrected precipitation projections for 2040–2060 and 2080–2099 from “Downscaled CMIP3 and CMIP5 Climate and Hydrology Projections” Archive and future land use for 2050 s and 2090 s from EPA ICLUS project were used for the City of Tampa in Florida (USA). It was shown that potential runoff volume and flood area changes ranged from –40% to 160%, and –40% to 400% due to rainfall change, while potential changes induced by land use change ranged from 0% to 3.5%, and 0% to 18% respectively. Additionally, this study examined the coupled effects of future rainfall and land use changes on flood area variations, considering the capacity of drainage infrastructure and elevation variation of study site. Results showed that flood area variations are not solely influenced by runoff quantity changes due to the two external drivers, but also by other factors. Specifically, in low-relief areas with inadequate drainage infrastructure and less elevation variation, these two drivers have no additive effects on the percentage of flood area changes. In contrast, in areas with adequate drainage infrastructure and greater surface elevation variation, there are additive effects from rainfall and land use changes on flood area expansions. These findings have important implications for stakeholders involved in city planning and flooding control, particularly for urban areas facing future precipitation and urbanization challenges.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

GRAF-Plan for Vietnam

Evaluates the reserve requirements for power system balancing areas based on variability and uncertainty of load as well as wind and solar generation scenarios. The tool uses minute‐by‐minute site‐specific generation and load information, as well as information from generation and load forecasting algorithms used in the balancing areas. The Balancing‐Plan Tool can be used directly by utility planners and operators to aid in the integration of intermittent renewable resources. The tool provides reserve requirements of various kinds, such as day‐ahead, load following and regulation, as well as estimates the capacity of the generation fleet to provide the require reserves.

Campbell, Allison↗
DOE OSTI2023

Simulation of compound flooding in Japan using a nationwide model

For this study, a high-resolution, summit-to-sea unstructured-grid model was used to simulate two compound flooding events in different geomorphic settings in Japan: the July 2012 flood in Kumamoto city and July 2018 flood in Okayama City, both caused by a torrential rainfall during seasonal Meiyu front but otherwise exhibiting quite different compound flood characteristics. The model shows good performance in simulating flooding extent; e.g., the Hit Rate for the inundation event in 2018 exceeds 0.9. Sensitivity tests were conducted to determine the roles/significance of levee structures along major rivers in coastal regions. Our results indicate that riverine and oceanic factors as well as levees significantly contribute to the observed flooding extents, and we are able to quantify the contributions from each factor at different locations. The model has been implemented operationally as the first nationwide 3-day compound flooding forecast system for Japan.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Seeded stimulated X-ray emission at 5.9 keV

X-ray free-electron lasers (XFELs) provide intense pulses that can generate stimulated X-ray emission, a phenomenon that has been observed and studied in materials ranging from neon to copper. Two schemes have been employed: amplified spontaneous emission (ASE) and seeded stimulated emission (SSE), where a second color XFEL pulse provides the seed. Both phenomena are currently explored for coherent X-ray laser sources and spectroscopy. Here, we report measurements of ASE and SSE of the 5.9 keV Mn K α 1 fluorescence line from a 3.9 molar NaMnO 4 solution, pumped with 7 femtosecond FWHM XFEL pulses at 6.6 keV. We observed ASE at a pump pulse intensity of 1.7×10 19 W/cm 2 , consistent with earlier findings. We observed SSE at dramatically reduced pump pulse intensities down to 1.1×10 17 W/cm 2 . These intensities are well within the range of many existing XFEL instruments, which supports the experimental feasibility of SSE as a tool to generate coherent X-ray pulses, spectroscopic studies of transition metal complexes, and other applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner

Filamentous fungi degrade complex plant material to its monomeric building blocks, which have many biotechnological applications. Transcription factors play a key role in plant biomass degradation, but little is known about their interactions in the regulation of polysaccharide degradation. Here, we deepened the knowledge about the storage polysaccharide regulators AmyR and InuR in Aspergillus niger. AmyR controls starch degradation, while InuR is involved in sucrose and inulin utilization. In our study, the phenotypes of A. niger parental, ΔamyR, ΔinuR and ΔamyRΔinuR strains were assessed in both solid and liquid media containing sucrose or inulin as carbon source to evaluate the roles of AmyR and InuR and the effect of culture conditions on their functions. In correlation with previous studies, our data showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active. In contrast, growth profiles and transcriptomic data showed that the deletion of amyR in the ΔinuR background strain resulted in more pronounced growth reduction on both substrates, mainly evidenced by data originating from solid cultures. Overall, our results show that submerged cultures do not always reflect the role of transcription factors in the natural growth condition, which is better represented on solid substrates. Importance: The type of growth has critical implications in enzyme production by filamentous fungi, a process that is controlled by transcription factors. Submerged cultures are the preferred setups in laboratory and industry and are often used for studying the physiology of fungi. In this study, we showed that the genetic response of A. niger to starch and inulin was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment did not fully match the behavior of the fungus in a solid environment. These results have direct implications in enzyme production and would help industry choose the best approaches to produce specific CAZymes for industrial purposes.

59 BASIC BIOLOGICAL SCIENCES↗