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Reconfiguring Plant Metabolism for Biodegradable Plastic Production
For decades, plants have been the subject of genetic engineering to synthesize novel, value-added compounds. Polyhydroxyalkanoates (PHAs), a large class of biodegradable biopolymers naturally synthesized in eubacteria, are among the novel products that have been introduced to make use of plant acetyl-CoA metabolic pathways. It was hoped that renewable PHA production would help address environmental issues associated with the accumulation of nondegradable plastic wastes. However, after three decades of effort synthesizing PHAs, and in particular the simplest form polyhydroxybutyrate (PHB), and seeking to improve their production in plants, it has proven very difficult to reach a commercially profitable rate in a normally growing plant. This seems to be due to the growth defects associated with PHA production and accumulation in plant cells. Here, we review major breakthroughs that have been made in plant-based PHA synthesis using traditional genetic engineering approaches and discuss challenges that have been encountered. Then, from the point of view of plant synthetic biology, we provide perspectives on reprograming plant acetyl-CoA pathways for PHA production, with the goal of maximizing PHA yield while minimizing growth inhibition. Specifically, we suggest genetic elements that can be considered in genetic circuit design, approaches for nuclear genome and plastome modification, and the use of multiomics and mathematical modeling in understanding and restructuring plant metabolic pathways.
Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as “prime editing,” has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
Digital Twin Empowered PV Power Prediction
The accurate prediction of photovoltaic (PV) power generation is significant to ensure the economic and safe operation of power systems. To this end, the paper proposes a new digital twin (DT) empowered PV power prediction framework that is capable of ensuring reliable data transmission and employing the DT to achieve high accuracy of power prediction. With this framework, considering potential data contamination in the collected PV data, a generative adversarial network is employed to restore the historical data set, which offers a prerequisite to ensure accurate mapping from the physical space to the digital space. Further, a new DT empowered PV power prediction method is proposed. Therein, we model a DT that encompasses a digital physical model for reflecting the physical operation mechanism and a neural network model (i.e., a parallel network of convolution and bidirectional long-short-term memory model) for capturing the hidden spatial-temporal features. The proposed method enables the use of the DT to take advantages of the digital physical model and the neural network model, resulting in enhanced prediction accuracy. Finally, a real data set is conducted to access the effectiveness of the proposed method.
NEAR-CONTACT BINARIES IZ MONOCEROTIS AND AR DRACONIS
We present multi-color photometric observations for two neglected near-contact binaries, IZ Mon (P=0--AMP--fd;77980) and AR Dra (P=0--AMP--fd;67584). By the aid of the updated W-D analysis code, the photometric solutions were deduced from the multi-color light curves (LCs). IZ Mon is a semi-detached binary with a mass ratio of q=0.388(±0.002), while AR Dra is a detached star with a mass ratio of q=0.652(±0.002). The asymmetric LCs of IZ Mon were modeled by a hot spot on the secondary’s surface, which may be attributed to mass transfer from the primary. Based on all collected eclipse times for two systems, we constructed their timing residual curves. The orbital period for IZ Mon may be continuously decreasing at a rate of dP/dt=−2.06(±0.04) days yr{sup −1}, which may result from mass and angular momentum loss from the central system. For AR Dra, there exists a cyclic variation with a period of P{sub 3}=104.9(±2.9) yr due to light-time orbit effect via the presence of the third body, whose mass is more than 0.28(±0.02) M{sub ⊙}. Finally, two near-contact binaries, IZ Mon and AR Dra, will evolve into contact binaries.
PHOTOMETRIC PROPERTIES OF SELECTED ALGOL-TYPE BINARIES. IX. V548 CYGNI
We present a new UV light curve of the Algol eclipsing binary V548 Cyg obtained with the Lunar Ultraviolet Telescope. We model the UV light curve together with two previously published (B and V) light curves, primary star radial velocities, and eclipse timings in a unified multi-data-type solution and determine orbital parameters and absolute dimensions. Timing residuals hint at the presence of a third star in the system. This star is possibly the source of the third light that is needed to obtain a good fit to each of the light curves simultaneously. The light–time oscillation in the timing residuals has a period of either ≈19 or ≈46 years. The third body orbit inclination would have to be low (23{sup ∘} or 15{sup ∘}, respectively) for the third star to have a mass of ≈1.5 M{sub ⊙}, which would be expected for a main-sequence star of color B−V≈0.32, as determined from the light curve solution. In an H–R diagram, the mass-gaining, primary component of V548 Cyg is located between the zero-age and terminal-age main sequence for solar composition stars, and close to the 0.4 Gyr isochrone.
X-ray spectral and temporal analysis of narrow line Seyfert 1 galaxy Was 61
We present an analysis of spectrum and variability of the bright reddened narrow line Seyfert 1 galaxy Was 61 using 90 ks archival XMM-Newton data. The X-ray spectrum in 0.2–10 keV can be characterized by an absorbed power-law plus soft excess and an Fe Kα emission line. The power-law spectral index remains constant during the flux variation. The absorbing material is mildly ionized, with a column density of 3.2 × 10{sup 21} cm{sup −2}, and does not appear to vary during the period of the X-ray observation. If the same material causes the optical reddening (E(B–V) ≃ 0.6 mag), it must be located outside the narrow line region with a dust-to-gas ratio similar to the average Galactic value. We detect significant variations of the Fe Kα line during the observational period. A broad Fe Kα line at ≃6.7 keV with a width of ∼0.6 keV is detected in the low flux segment of the first 40 ks exposure, and is absent in the spectra of other segments; a narrow Fe Kα emission line ∼6.4 keV with a width of ∼0.1 keV is observed in the subsequent 20 ks segment, which has a count rate 35% higher and is in the next day. We believe this is due to the change in geometry and kinematics of the X-ray emitting corona. The temperature and flux of soft X-ray excess appear to correlate with the flux of the hard power-law component. Comptonization of disc photons by a warm and optically thick inner disk is preferred to interpret the soft excess, rather than the ionized reflection.
Long fading mid-infrared emission in transient coronal line emitters: dust echo of a tidal disruption flare
The sporadic accretion following the tidal disruption of a star by a super-massive black hole (TDE) leads to a bright UV and soft X-ray flare in the galactic nucleus. The gas and dust surrounding the black hole responses to such a flare with an echo in emission lines and infrared emission. In this paper, we report the detection of long fading mid-IR emission lasting up to 14 years after the flare in four TDE candidates with transient coronal lines using the WISE public data release. We estimate that the reprocessed mid-IR luminosities are in the range between 4×10{sup 42} and 2×10{sup 43} erg s{sup −1} and dust temperature in the range of 570–800 K when WISE first detected these sources three to five years after the flare. Both luminosity and dust temperature decrease with time. We interpret the mid-IR emission as the infrared echo of the tidal disruption flare. We estimate the UV luminosity at the peak flare to be 1 to 30 times 10{sup 44} erg s{sup −1} and that for warm dust masses to be in the range of 0.05–1.3 M{sub ⊙} within a few parsecs. Our results suggest that the mid-infrared echo is a general signature of TDE in the gas-rich environment.
A self-consistent and spatially dependent model of the multiband emission of pulsar wind nebulae
A self-consistent and spatially dependent model is presented to investigate the multiband emission of pulsar wind nebulae (PWNe). In this model, a spherically symmetric system is assumed and the dynamical evolution of the PWN is included. The processes of convection, diffusion, adiabatic loss, radiative loss, and photon–photon pair production are taken into account in the electron’s evolution equation, and the processes of synchrotron radiation, inverse Compton scattering, synchrotron self-absorption, and pair production are included for the photon’s evolution equation. Both coupled equations are simultaneously solved. The model is applied to explain observed results of the PWN in MSH 15–52. Our results show that the spectral energy distributions (SEDs) of both electrons and photons are all a function of distance. The observed photon SED of MSH 15–52 can be well reproduced in this model. With the parameters obtained by fitting the observed SED, the spatial variations of photon index and surface brightness observed in the X-ray band can also be well reproduced. Moreover, it can be derived that the present-day diffusion coefficient of MSH 15–52 at the termination shock is κ{sub 0}=6.6×10{sup 24} cm{sup 2} s{sup −1}, the spatial average has a value of κ-bar =1.4×10{sup 25} cm{sup 2} s{sup −1}, and the present-day magnetic field at the termination shock has a value of B{sub 0}=26.6 μG and the spatial averaged magnetic field is B-bar =14.9 μG. The spatial changes of the spectral index and surface brightness at different bands are predicted.
The DESI One-Percent Survey: Constructing Galaxy–Halo Connections for ELGs and LRGs Using Auto and Cross Correlations
In the current Dark Energy Spectroscopic Instrument (DESI) survey, emission line galaxies (ELGs) and luminous red galaxies (LRGs) are essential for mapping the dark matter distribution at z ~ 1. We measure the auto and cross correlation functions of ELGs and LRGs at 0.8 < z ≤ 1.0 from the DESI One-Percent survey. Following Gao et al., we construct the galaxy–halo connections for ELGs and LRGs simultaneously. With the stellar–halo mass relation for the whole galaxy population (i.e., normal galaxies), LRGs can be selected directly by stellar mass, while ELGs can also be selected randomly based on the observed number density of each stellar mass, once the probability P sat of a satellite galaxy becoming an ELG is determined. We demonstrate that the observed small scale clustering prefers a halo mass-dependent P sat model rather than a constant. With this model, we can well reproduce the auto correlations of LRGs and the cross correlations between LRGs and ELGs at r p > 0.1 Mpc h –1 . We can also reproduce the auto correlations of ELGs at r p > 0.3 Mpc h –1 (s > 1 Mpc h –1 ) in real (redshift) space. Although our model has only seven parameters, we show that it can be extended to higher redshifts and reproduces the observed auto correlations of ELGs in the whole range of 0.8 < z ≤ 1.6, which enables us to generate a lightcone ELG mock for DESI. With the above model, we further derive halo occupation distributions for ELGs, which can be used to produce ELG mocks in coarse simulations without resolving subhalos.
The DESI One-Percent Survey: A Concise Model for the Galactic Conformity of Emission-line Galaxies
Galactic conformity is the phenomenon whereby a galaxy of a certain physical property is correlated with its neighbors of the same property, implying a possible causal relationship. Here, the observed auto correlations of emission-line galaxies (ELGs) from the highly complete DESI One-Percent Survey exhibit a strong clustering signal on small scales, providing clear evidence for the conformity effect of ELGs. Building upon the original subhalo abundance-matching (SHAM) method developed by Gao et al., we propose a concise conformity model to improve the ELG–halo connection. In this model, the number of satellite ELGs is boosted by a factor of ~5 in the halos whose central galaxies are ELGs. We show that the mean ELG satellite number in such central halos is still smaller than 1 and that the model does not significantly increase the overall satellite fraction. With this model, we can well recover the ELG auto correlations to the smallest scales explored with the current data (i.e., r p > 0.03 Mpc h –1 in real space and at s > 0.3 Mpc h –1 in redshift space), while the cross correlations between luminous red galaxies and ELGs are nearly unchanged. Although our SHAM model has only eight parameters, we further verify that it can accurately describe the ELG clustering in the entire redshift range from z = 0.8 to 1.6. We therefore expect that this method can be used to generate high-quality ELG lightcone mocks for DESI.
Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons
The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases ( KCS ), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions. Random Forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Additionally, amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a Helitron transposon. A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays. Long-read generated telomere-to-telomere assemblies of P. trichocarpa chromosome 10 revealed large-effect loci critical to genetic studies that are unattainable from short-reads. This new resource produced novel insights into genome structure and function, and a novel mechanism for generating tandem gene duplication. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.
AttentionFire_v1.0: interpretable machine learning fire model for burned-area predictions over tropics
Abstract. African and South American (ASA) wildfires account for more than 70 % of global burned areas and have strong connection to local climate for sub-seasonal to seasonal wildfire dynamics. However, representation of the wildfire–climate relationship remains challenging due to spatiotemporally heterogenous responses of wildfires to climate variability and human influences. Here, we developed an interpretable machine learning (ML) fire model (AttentionFire_v1.0) to resolve the complex controls of climate and human activities on burned areas and to better predict burned areas over ASA regions. Our ML fire model substantially improved predictability of burned areas for both spatial and temporal dynamics compared with five commonly used machine learning models. More importantly, the model revealed strong time-lagged control from climate wetness on the burned areas. The model also predicted that, under a high-emission future climate scenario, the recently observed declines in burned area will reverse in South America in the near future due to climate changes. Our study provides a reliable and interpretable fire model and highlights the importance of lagged wildfire–climate relationships in historical and future predictions.
Performance of the h, p and h-p versions
There are three basic versions of the finite element method, called the h, p and h-p versions. They are characterized by the way in which the finite element meshes and polynomial degree of elements are chosen. They differ in computer implementation (program architecture) and mathematical analysis. The manner in which the meshes and polynomial degree of the elements affect the accuracy of finite element solutions is examined. The approach is to fix certain parameters and increase the number of degrees of freedom so that the finie element solutions converge to the exact solution. Such a systematic increase of the number of degrees of freedom is called extension because it can be interpreted as a systematic extension of finite element spaces.
Residual stresses in continuous graphite fiber Al metal matrix composites
The residual stresses in graphite fiber reinforced aluminum (Gr/Al) composites with various thermal histories are measured using X-ray diffraction (XRD) methods. The XRD stress analysis is based on the determination of lattice strains by precise measurements of the interplanar spacings in different directions of the sample. The sample is a plate consisting of two-ply P 100 Gr/Al 6061 precursor wires and Al 6061 overlayers. Prior to XRD measurement, the 6061 overlayers are electrochemically removed. In order to calibrate the relationship between stress magnitude and lattice spacing shift, samples of Al 6061 are loaded at varying stress levels in a three-point bend fixture, while the stresses are simultaneously determined by XRD and surface-attached strain gages. The stresses determined by XRD closely match those determined by the strain gages. Using these calibrations, the longitudinal residual stresses of P 100 Gr/Al 6061 composites are measured for various heat treatments, and the results are presented.
Fiber-matrix interface failures
Interface fractures of aluminum-graphite composites under transverse loading are expected to occur within the graphite fibers, but very near the interface. Residual stresses in aluminum, reinforced with the new high modulus pitch-based fibers, are much lower than would be expected based on simple elasticity calculations. The excess stress may be relaxed by shearing internal to the fibers or at the interface rather than by plastic flow of the matrix. The internal shearing also occurs during repeated thermal cycling of these composites; the fibers are repeatedly intruded, then extruded, during repeated temperature excursions.
Modeling of chemical vapor infiltration for ceramic composites reinforced with layered, woven fabrics
A homogeneous model is developed for the chemical vapor infiltration by one-dimensional diffusion into a system of layered plies consisting of woven tows containing bundles of filaments. The model predictions of the amount of deposition and the porosity of the sample as a function of time are compared with the predictions of a recent nonhomogeneous model with aligned holes formed by the weave. The nonhomogeneous model allows for diffusion through the aligned holes, into the spaces between plies, and into the gaps around filaments; i.e., three diffusion equations apply. Relative to the nonhomogeneous results, the homogeneous model underestimates the amount of deposition, since the absence of holes and spaces allows earlier occlusion of gaps around filaments and restricts the vapor infiltration.
The H(sub infinity) optimal controller design and reduction for the inertial hold mode of the attitude control system of the XTE spacecraft
The Inertial Hold Mode (IHM) is one mode of the attitude control system of the X-ray Timing Explorer spacecraft that is disturbed by both parametric uncertainties and external torque disturbance. The IHM model is modified into a typical H-infinity mixed-sensitivity problem through choosing suitable weighting functions W(sub 1)(s) and W(sub 3)(s). The controller is designed by the H-infinity optimization technique with the transformation of shifting the imaginary axis. It can stabilize the plant with uncertainties from the natural frequencies of the flexible body. The gain margin and phase margin of the system are 24.03 db and 55.04 deg, respectively. The step response attenuates to zero within 150 seconds. These show that the controller satisfies the specified requirements. Since the order of the controller appears high, it is reduced to fourth order one. The results show that the stability and the performance of the system with the reduced controller are retained perfectly.