Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes.

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.

Photoelectron spectroscopy with entangled photons; enhanced spectrotemporal resolution.

In this theoretical study, we show how photoelectron signals generated by time-energy entangled photon pairs can monitor ultrafast excited state dynamics of molecules with high joint spectral and temporal resolutions, not limited by the Fourier uncertainty of classical light. This technique scales linearly, rather than quadratically, with the pump intensity, allowing the study of fragile biological samples with low photon fluxes. Since the spectral resolution is achieved by electron detection and the temporal resolution by a variable phase delay, this technique does not require scanning the pump frequency and the entanglement times, which significantly simplifies the experimental setup, making it feasible with current instrumentation. Application is made to the photodissociation dynamics of pyrrole calculated by exact nonadiabatic wave packet simulations in a reduced two nuclear coordinate space. This study demonstrates the unique advantages of ultrafast quantum light spectroscopy.

Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding.

Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.

The chromosome-level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis.

Coumarins are natural products with important medicinal values, and include simple coumarins, furanocoumarins and pyranocoumarins. Female ginseng (Angelica sinensis) is a renowned herb with abundant coumarins, originated in China and known for the treatment of female ailments for thousands of years. The molecular basis of simple coumarin biosynthesis in A. sinensis and the evolutionary history of the genes involved in furanocoumarin biosynthesis are largely unknown. Here, we generated the first chromosome-scale genome of A. sinensis. It has a genome size of 2.37 Gb, which was generated by combining PacBio and Hi-C sequencing technologies. The genome was predicted to contain 43 202 protein-coding genes dispersed mainly on 11 pseudochromosomes. We not only provided evidence for whole-genome duplication (WGD) specifically occurring in the Apioideae subfamily, but also demonstrated the vital role of tandem duplication for phenylpropanoid biosynthesis in A. sinensis. Combined analyses of transcriptomic and metabolomic data revealed key genes and candidate transcription factors regulating simple coumarin biosynthesis. Furthermore, phylogenomic synteny network analyses suggested prenyltransferase genes involved in furanocoumarin biosynthesis evolved independently in the Moraceae, Fabaceae, Rutaceae and Apiaceae after ζ and ε WGD. Our work sheds light on coumarin biosynthesis, and provides a benchmark for accelerating genetic research and molecular breeding in A. sinensis.

Manipulating Attosecond Charge Migration in Molecules by Optical Cavities.

The ultrafast electronic charge dynamics in molecules upon photoionization while the nuclear motions are frozen is known as charge migration. In a theoretical study of the quantum dynamics of photoionized 5-bromo-1-pentene, we show that the charge migration process can be induced and enhanced by placing the molecule in an optical cavity, and can be monitored by time-resolved photoelectron spectroscopy. The collective nature of the polaritonic charge migration process is investigated. We find that, unlike spectroscopy, molecular charge dynamics in a cavity is local and does not show many-molecule collective effects. The same conclusion applies to cavity polaritonic chemistry.

Scalar Breit interaction for molecular calculations.

Variational treatment of the Dirac-Coulomb-Gaunt or Dirac-Coulomb-Breit two-electron interaction at the Dirac-Hartree-Fock level is the starting point of high-accuracy four-component calculations of atomic and molecular systems. In this work, we introduce, for the first time, the scalar Hamiltonians derived from the Dirac-Coulomb-Gaunt and Dirac-Coulomb-Breit operators based on spin separation in the Pauli quaternion basis. While the widely used spin-free Dirac-Coulomb Hamiltonian includes only the direct Coulomb and exchange terms that resemble nonrelativistic two-electron interactions, the scalar Gaunt operator adds a scalar spin-spin term. The spin separation of the gauge operator gives rise to an additional scalar orbit-orbit interaction in the scalar Breit Hamiltonian. Benchmark calculations of Aun (n = 2-8) show that the scalar Dirac-Coulomb-Breit Hamiltonian can capture 99.99% of the total energy with only 10% of the computational cost when real-valued arithmetic is used, compared to the full Dirac-Coulomb-Breit Hamiltonian. The scalar relativistic formulation developed in this work lays the theoretical foundation for the development of high-accuracy, low-cost correlated variational relativistic many-body theory.

Correlated Dirac-Coulomb-Breit multiconfigurational self-consistent-field methods.

The fully correlated frequency-independent Dirac-Coulomb-Breit Hamiltonian provides the most accurate description of electron-electron interaction before going to a genuine relativistic quantum electrodynamics theory of many-electron systems. In this work, we introduce a correlated Dirac-Coulomb-Breit multiconfigurational self-consistent-field method within the frameworks of complete active space and density matrix renormalization group. In this approach, the Dirac-Coulomb-Breit Hamiltonian is included variationally in both the mean-field and correlated electron treatment. We also analyze the importance of the Breit operator in electron correlation and the rotation between the positive- and negative-orbital space in the no-virtual-pair approximation. Atomic fine-structure splittings and lanthanide contraction in diatomic fluorides are used as benchmark studies to understand the contribution from the Breit correlation.

Attosecond Charge Migration in Molecules Imaged by Combined X-ray and Electron Diffraction.

We show how ultrafast gas-phase X-ray and electron diffraction signals can be combined to generate real-space movies of charge migration dynamics in molecules. Charge migration denotes short time electronic charge redistribution upon photoexcitation of molecules where the nuclei are frozen. In this regime, we identify a mixed electronic-nuclear interference term that can be cleanly singled out. Using the ground-state nuclear structure as a reference, the phase information in this signal allows its inversion to real space and the capture of electronic charge density movies on the attosecond time scale.

miR-146a suppresses the expression of vascular endothelial growth factor and inflammatory responses in diabetic retinopathy.

This study was designed to explore the role of miR-146a in diabetic retinopathy (DR). 30 healthy control (HC), 50 patients with type 2 diabetes mellitus, and 48 DR patients were enrolled. Blood was collected and levels of miR-146a expression, vascular endothelial growth factor (VEGF), and three inflammatory cytokines (NF-κB, IL-1ß, and TNF-α) were detected. Moreover, ARPE-19 cells were treated with miR-146a mimic or inhibitor in the presence of high glucose to evaluate its effect in vitro. DR patients had the lowest level of miR-146a and the highest level of VEGF as well as the most severe inflammation among the three groups. In addition, the miR-146a level was negatively correlated with the expression of VEGF and three inflammatory cytokines, respectively in DR patients. Moreover, VEGF expression was positively correlated with these three inflammatory cytokines in DR patients. In summary, miR-146a could inhibit VEGF expression and inflammation in DR.

Metal-Organic Framework-Derived Three-Dimensional Macropore Nitrogen-Doped Carbon Frameworks Decorated with Ultrafine Ru-Based Nanoparticles for Overall Water Splitting.

Hydrogen energy with the advantages of green, sustainability, and high energy density has been considered as an alternative to fossil fuel energy. Water electrolysis to produce hydrogen is a promising energy conversion technology but limited to the large overpotential; thus, a highly efficient electrocatalyst is urgently needed. Herein, Ru-based electrocatalysts including an ultrathin Ru/three-dimensional (3D) macropore N-doped carbon framework (Ru/3DMNC) and ultrathin RuO2/3D macropore N-doped carbon framework (RuO2/3DMNC) are first prepared using a Zn-centered metal-organic framework (MOF, ZIF-8) as the precursor. The ultrathin 3D macropore framework structure together with N doping endows the as-synthesized Ru-based electrocatalysts with abundant exposed catalytic active sites, good electroconductivity, and excellent electron/mass transport, accomplishing improved activities for hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and overall water splitting. The Ru/3DMNC and RuO2/3DMNC present low overpotentials of 50.96 and 216.74 mV to reach a current density of 10 mA cm-2. Moreover, the overall water splitting device constructed by Ru/3DMNC and RuO2/3DMNC as the cathode and anode catalysts, respectively, affords a current density of 10 mA cm-2 only at 1.51 V, which is superior to the Pt/C||RuO2 cell (1.573 V). This work provides a rational strategy to design and construct the efficient framework structure electrocatalysts for water splitting using MOFs as the precursor.

Synergizing Cobalt Ruthenium Alloy with Chromium Oxyhydroxide for Highly Efficient Electrocatalytic Water Splitting.

Constructing a coupling interface of multicomponents with different functions is of considerable importance for designing an advanced bifunctional water splitting electrode. Particularly, designing and developing alloy/oxyhydroxide-integrated electrodes have emerged as a tendency yet remain a considerable challenge. In this work, a novel 3D nanostructure electrocatalyst assembled from CoRu nanoalloy and CrOOH nanosheets (denoted as CoRu-CrOOH/NF) was directly grown on nickel foam via a successive hydrothermal method. The unique synergy in CoRu-CrOOH/NF heterostructures is not only conducive to strengthening charge transfer capability and accelerating the reaction kinetics but also favors the redistribution of charge within the interface, thus improving the electrocatalytic performance. In view of the above-mentioned points, the resultant CoRu-CrOOH/NF displays outstanding catalytic performance with overpotentials of 26 and 272 mV at 10 mA cm-2 for hydrogen evolution reaction (HER) and 50 mA cm-2 for oxygen evolution reaction (OER). Remarkably, the symmetrical two-electrode cell using CoRu-CrOOH/NF only acquires 1.47 V at 10 mA cm-2 in 1.0 M KOH, which is superior to many other state-of-the-art overall water-splitting electrocatalysts. This holistic work provides a new insight to designing alloy/oxyhydroxide-integrated electrodes for high-efficiency overall water splitting.

Efficient evaluation of the Breit operator in the Pauli spinor basis.

The frequency-independent Coulomb-Breit operator gives rise to the most accurate treatment of two-electron interaction in the non-quantum-electrodynamics regime. The Breit interaction in the Coulomb gauge consists of magnetic and gauge contributions. The high computational cost of the gauge term limits the application of the Breit interaction in relativistic molecular calculations. In this work, we apply the Pauli component integral-density matrix contraction scheme for gauge interaction with a maximum spin- and component separation scheme. We also present two different computational algorithms for evaluating gauge integrals. One is the generalized Obara-Saika algorithm, where the Laplace transformation is used to transform the gauge operator into Gaussian functions and the Obara-Saika recursion is used for reducing the angular momentum. The other algorithm is the second derivative of Coulomb interaction evaluated with Rys-quadrature. This work improves the efficiency of performing Dirac-Hartree-Fock with the variational treatment of Breit interaction for molecular systems. We use this formalism to examine relativistic trends in the Periodic Table and analyze the relativistic two-electron interaction contributions in heavy-element complexes.

Rethinking the framework constructed by counterfactual functional model.

The causal inference represented by counterfactual inference technology breathes new life into the current field of artificial intelligence. Although the fusion of causal inference and artificial intelligence has an excellent performance in many various applications, some theoretical justifications have not been well resolved. In this paper, we focus on two fundamental issues in causal inference: probabilistic evaluation of counterfactual queries and the assumptions used to evaluate causal effects. Both of these issues are closely related to counterfactual inference tasks. Among them, counterfactual queries focus on the outcome of the inference task, and the assumptions provide the preconditions for performing the inference task. Counterfactual queries are to consider the question of what kind of causality would arise if we artificially apply the conditions contrary to the facts. In general, to obtain a unique solution, the evaluation of counterfactual queries requires the assistance of a functional model. We analyze the limitations of the original functional model when evaluating a specific query and find that the model arrives at ambiguous conclusions when the unique probability solution is 0. In the task of estimating causal effects, the experiments are conducted under some strong assumptions, such as treatment-unit additivity. However, such assumptions are often insatiable in real-world tasks, and there is also a lack of scientific representation of the assumptions themselves. We propose a mild version of the treatment-unit additivity assumption coined as M-TUA based on the damped vibration equation in physics to alleviate this problem. M-TUA reduces the strength of the constraints in the original assumptions with reasonable formal expression.

The Cotton Lignin Biosynthetic Gene Gh4CL30 Regulates Lignification and Phenolic Content and Contributes to Verticillium Wilt Resistance.

Verticillium wilt is a vascular disease causing tremendous damage to cotton production worldwide. However, our knowledge of the mechanisms of cotton resistance or susceptibility to this disease is very limited. In this study, we compared the defense transcriptomes of cotton (Gossypium hirsutum) cultivars Shidalukang 1 (Verticillium dahliae resistant, HR) and Junmian 1 (V. dahliae susceptible, HS) before and after V. dahliae infection, identified hub genes of the network associated with responses to V. dahliae infection, and functionally characterized one of the hub genes involved in biosynthesis of lignin and phenolics. We identified 6,831 differentially expressed genes (DEGs) between the basal transcriptomes of HR and HS; 3,685 and 3,239 of these DEGs were induced in HR and HS, respectively, at different time points after V. dahliae infection. KEGG pathway analysis indicated that DEGs were enriched for genes involved in lignin biosynthesis. In all, 23 hub genes were identified based on a weighted gene coexpression network analysis of the 6,831 DEGs and their expression profiles at different time points after V. dahliae infection. Knockdown of Gh4CL30, one of the hub genes related to the lignin biosynthesis pathway, by virus-induced gene silencing, led to a decreased content of flavonoids, lignin, and S monomer but an increased content of G monomer, G/S lignin monomer, caffeic acid, and ferulic acid, and enhanced cotton resistance to V. dahliae. These results suggest that Gh4CL30 is a key gene modulating the outputs of different branches of the lignin biosynthesis pathway, and provide new insights into cotton resistance to V. dahliae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Synergistically Integrating Nickel Porous Nanosheets with 5d Transition Metal Oxides Enabling Efficient Electrocatalytic Overall Water Splitting.

An integration hydrogen adsorption benign component such as a metal with an oxygen-containing reactant adsorption benign component such as metal oxide allows for efficient overall water splitting in alkaline solutions and yet remains a considerable challenge. Herein, 5d transition metal oxide WO2 and WO3 (denoted as WOx) nanoparticles are purposely integrated with a porous Ni nanosheet array grown on nickel foam (NF) to design a strongly coupled Ni/WOx/NF porous nanosheet array electrocatalyst. Through the anion exchange of Ni(OH)2 nanosheets with tungstate, followed by hydrogenation treatment, abundant Ni/WOx interfaces with strong coupling interaction are generated. Benefiting from the strong synergies between Ni and WOx and the unique nanostructure, Ni/WOx/NF only requires the overpotentials of 42 mV for hydrogen evolution reaction (HER) and 395.7 mV for oxygen evolution reaction (OER) to achieve the current densities of 10 and 100 mA cm-2, respectively. Furthermore, the Ni/WOx/NF can achieve a current density of 10 mA cm-2 at a low cell voltage of 1.54 V in a two-electrode system. This work opens a novel avenue for the design of high-performance but low-cost electrocatalysts for overall water splitting.

Interfacial engineering of CeO2 on NiCoP nanoarrays for efficient electrocatalytic oxygen evolution.

Transition metal phosphides (TMP)-based oxygen evolution reaction (OER) catalysts constructed by interface engineering strategy have a broad prospect due to their low cost and good performance. Herein, a novel CeO2/NiCoP nanoarray with intimate phosphide (NiCoP)-oxide (CeO2) interface was developed via in situ generation on nickel foam (NF). This structure is conducive to increasing active sites and accelerating charge transfer, and may be conducive to regulating electronic structure and adsorption energy. As expected, optimal 1.4-CeO2/NiCoP/NF delivers a low overpotential of 249 mV at the current density of 10 mA cm-2 with a Tafel slope of 77.2 mV dec-1. CeO2/NiCoP/NF boasts one of the best OER catalytic materials among recently reported phosphides (TMP)-based OER catalysts and composite catalysts involving CeO2. This work provides an effective strategy for the construction of hetero-structure with CeO2 with oxygen vacancies to improve the OER performance of phosphides.

Iron and chromium co-doped cobalt phosphide porous nanosheets as robust bifunctional electrocatalyst for efficient water splitting.

It is still a huge challenge to develop highly efficient and low-cost non-precious metal-based electrocatalysts for overall water splitting in alkaline electrolytes. Herein, Cr and Fe co-doped CoP porous mesh nanosheets (Mesh-CrFe-CoP NSs) were synthesized through hydrolysis reaction, ion exchange etching and subsequent low-temperature phosphating process. The Mesh-CrFe-CoP NSs provides overpotentials at a current density of 10 mA cm-2under alkaline electrolyte of 103.7 mV and 256.4 mV for HER and OER, respectively. Furthermore, when using Mesh-CrFe-CoP NSs as anode and cathode, the water splitting system could afford a current density of 10 mA cm-2at 1.55 V, which is better than an electrolytic cell composed of 20% Pt/C and RuO2. The excellent electrocatalytic performance of Mesh-CrFe-CoP NSs is attributed to the co-doping and porous nanostructure. Specifically, the Cr and Fe co-doped porous CoP nanosheets electrocatalyst not only provided abundant exposure active sites, accelerated the entry of liquid and the diffusion of gas, but also regulated the electronic environment of active sites, and thus enhanced the electrochemical performance. This work proposes a strategy for the rational design of highly efficient and stable non-precious metal co-doped phosphide electrocatalysts in the of electrochemical water splitting.

Specificity Enhancement of Deoxyribonucleic Acid Polymerization for Sensitive Nucleic Acid Detection.

Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic acid detection, DNA amplification, and gene cloning, require high specificity in DNA synthesis catalyzed by DNA polymerases. However, errors in DNA polymerization (such as mis-incorporation and mis-priming) can significantly jeopardize the specificity. Herein, we report our discovery that the specificity of DNA enzymatic synthesis can be substantially enhanced (up to 100-fold higher) by attenuating DNA polymerase kinetics via the phosphorothioate dNTPs. This specificity enhancement allows convenient and sensitive nucleic acid detection, polymerization, PCR, and gene cloning with complex systems (such as human cDNA and genomic DNA). Further, we found that the specificity enhancement offered higher sensitivity (up to 50-fold better) for detecting nucleic acids, such as COVID-19 viral RNAs. Our findings have revealed a simple and convenient strategy for facilitating specificity and sensitivity of nucleic acid detection, amplification, and gene cloning.

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance.

BACKGROUND: The function of 4-coumarate-CoA ligases (4CL) under abiotic stresses has been studied in plants, however, limited is known about the 4CL genes in cotton (G. hirsutum L.) and their roles in response to drought stress. RESULTS: We performed genome-wide identification of the 4CL genes in G. hirsutum and investigated the expression profiles of the identified genes in various cotton tissues and in response to stress conditions with an aim to identify 4CL gene(s) associated with drought tolerance. We identified 34 putative 4CL genes in G. hirsutum that were clustered into three classes. Genes of the same class usually share a similar gene structure and motif composition. Many cis-elements related to stress and phytohormone responses were found in the promoters of the Gh4CL genes. Of the 34 Gh4CL genes, 26 were induced by at least one abiotic stress and 10 (including Gh4CL7) were up-regulated under the polyethylene glycol (PEG) simulated drought stress conditions. Virus-induced gene silencing (VIGS) in cotton and overexpression (OE) in Arabidopsis thaliana were applied to investigate the biological function of Gh4CL7 in drought tolerance. The Gh4CL7-silencing cotton plants showed more sensitive to drought stress, probably due to decreased relative water content (RWC), chlorophyll content and antioxidative enzyme activity, increased stomatal aperture, and the contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Arabidopsis lines overexpressing Gh4CL7, however, were more tolerant to drought treatment, which was associated with improved antioxidative enzyme activity, reduced accumulation of MDA and H2O2 and up-regulated stress-related genes under the drought stress conditions. In addition, compared to their respective controls, the Gh4CL7-silencing cotton plants and the Gh4CL7-overexpressing Arabidopsis lines had a ~ 20% reduction and a ~ 10% increase in lignin content, respectively. The expression levels of genes related to lignin biosynthesis, including PAL, CCoAOMT, COMT, CCR and CAD, were lower in Gh4CL7-silencing plants than in controls. Taken together, these results demonstrated that Gh4CL7 could positively respond to drought stress and therefore might be a candidate gene for improvement of drought tolerance in cotton. CONCLUSION: We characterized the 4CL gene family in upland cotton and revealed a role of Gh4CL7 in lignin biosynthesis and drought tolerance.

Perspective on Kramers symmetry breaking and restoration in relativistic electronic structure methods for open-shell systems.

Without rigorous symmetry constraints, solutions to approximate electronic structure methods may artificially break symmetry. In the case of the relativistic electronic structure, if time-reversal symmetry is not enforced in calculations of molecules not subject to a magnetic field, it is possible to artificially break Kramers degeneracy in open shell systems. This leads to a description of excited states that may be qualitatively incorrect. Despite this, different electronic structure methods to incorporate correlation and excited states can partially restore Kramers degeneracy from a broken symmetry solution. For single-reference techniques, the inclusion of double and possibly triple excitations in the ground state provides much of the needed correction. Formally, however, this imbalanced treatment of the Kramers-paired spaces is a multi-reference problem, and so methods such as complete-active-space methods perform much better at recovering much of the correct symmetry by state averaging. Using multi-reference configuration interaction, any additional corrections can be obtained as the solution approaches the full configuration interaction limit. A recently proposed "Kramers contamination" value is also used to assess the magnitude of symmetry breaking.