Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences.

The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few studies have been performed on using genomic data to infer phylogenetic relationships within Ranunculeae. In this study, the complete plastid genomes of nine species (eleven samples) from Ceratocephala, Halerpestes, and Ranunculus were de novo assembled using a next-generation sequencing method. Previously published plastomes of Oxygraphis and other related genera of the family were downloaded from GenBank for comparative analysis. The complete plastome of each Ranunculeae species has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The plastome structure of Ranunculeae samples is conserved in gene order and arrangement. There are no inverted repeat (IR) region expansions and only one IR contraction was found in the tested samples. This study also compared plastome sequences across all the samples in gene collinearity, codon usage, RNA editing sites, nucleotide variability, simple sequence repeats, and positive selection sites. Phylogeny of the available Ranunculeae species was inferred by the plastome data using maximum-likelihood and Bayesian inference methods, and data partitioning strategies were tested. The phylogenetic relationships were better resolved compared to previous studies based on Sanger sequencing methods, showing the potential value of the plastome data in inferring the phylogeny of the tribe.

Surface lattice resonances enhanced directional amplified spontaneous emission on plasmonic honeycomb nanocone array.

Plasmonic arrays have emerged as a promising platform for investigating light-matter interactions enhanced by surface lattice resonance (SLR) at the nanoscale, which exhibit superior properties in localized field enhancement, narrow linewidth, and effective radiation loss suppression. In this study, an Al nanocone array in a honeycomb arrangement served as an optical cavity with a tip effect to realize the directional and polarized amplified spontaneous emission (ASE) of R6G. Based on the optical feedback between the degenerated SLR mode of high local density of states (LDOS) and the emission of gain media, 140-fold enhanced ASE was observed at an emission angle of 25° under TM polarization when the pump power density exceeded the threshold of 197.8 W cm-2. Moreover, polarization-resolved iso-frequency images indicated that a specific polarization dependence of ASE was modulated by the SLR mode. This study clarifies the interaction between the gain media and plasmonic system, which is beneficial for the generation of nanolasing with directional emission and lays a foundation for the plasmonic device.

Direction- and polarization-tunable spontaneous emission beneficial from diffraction orders of a square R6G-nanopore array.

To meet the miniaturization and compatibility of current micro-nano optical devices, two-dimensional (2D) photonic crystals (PCs), which can manipulate the optical parameters and their propagation with more degree of freedom, have become more important in nano optics. In the case of 2D PCs, the specific symmetry of the microscopic lattice arrangement determines its macroscopic optical properties. In addition, beyond this key element of lattice arrangement, the unit cell of PCs is also a critical factor in modulating the far-field optical behaviors. This work explores the manipulation of spontaneous emission (SE) of rhodamine 6G (R6G) in a square lattice of anodic aluminum oxide (AAO) membrane. The directional and polarized emissions are observed to be related to the diffraction orders (DOs) of the lattice arrangement. By further tuning the size of unit cells, different DOs are triggered to overlap with the emission of R6G, resulting in an extended tuning for directions and polarizations of light emission. It exhibits the significance for the design and application of nano optics devices.

Entanglement generation by strong coupling between surface lattice resonance and exciton in an Al nanoarray-coated WS2 quantum emitter.

Strong light-matter interaction plays a central role in realizing quantum photonic technologies. The entanglement state, which results from the hybridization of excitons and cavity photons, forms the foundation of quantum information science. In this work, an entanglement state is achieved by manipulating the mode coupling between surface lattice resonance and quantum emitter into the strong coupling regime. At the same time, a Rabi splitting of 40 meV is observed. A full quantum model based on the Heisenberg picture is used to describe this unclassical phenomenon, and it perfectly explains the interaction and dissipation process. In addition, the observed concurrency degree of the entanglement state is 0.5, presenting the quantum nonlocality. This work effectively contributes to the understanding of nonclassical quantum effects arising from strong coupling and will intrigue more interesting potential applications in quantum optics.

Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data.

The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.

Directional amplified spontaneous emissions from Ag nanohole array with high diffraction orders.

Surface plasmon excitations in metallic hole arrays have been extensively studied in the context of light-matter interaction, since the generated Bloch surface plasmon polariton (Bloch-SPP) exhibits unique properties of nanoscale light confinement, near-field enhancements, and long-range metal surface propagation. In this work, we experimentally demonstrate a plasmonic device that exhibits highly directional emission in visible light; using Ag film with a thickness of 100 nm deposited on a subwavelength porous alumina array as a plasmonic cavity, four-level rhodamine 6G (R6G) is selected as the gain material. It is suggested that a Bloch-SPP with high diffraction orders on a Ag nanohole array can generate a strong local electric field and a high Purcell factor at a nanohole edge. Moreover, directional five-fold enhanced amplified spontaneous emission (ASE) with polarization dependence is observed under a low threshold of 199.9 W/cm2 in the visible light region, which comes from the optical feedback provided by the 2D periodic nanohole array. This work opens up a wide range of applications for real-time tunable wavelength, controlled multimode laser, fluorescence detection, etc.

Urchin-Like Structured MoO2 /Mo3 P/Mo2 C Triple-Interface Heterojunction Encapsulated within Nitrogen-Doped Carbon for Enhanced Hydrogen Evolution Reaction.

The development of highly efficient and cost-effective hydrogen evolution reaction (HER) catalysts is highly desirable to efficiently promote the HER process, especially under alkaline condition. Herein, a polyoxometalates-organic-complex-induced carbonization method is developed to construct MoO2 /Mo3 P/Mo2 C triple-interface heterojunction encapsulated into nitrogen-doped carbon with urchin-like structure using ammonium phosphomolybdate and dopamine. Furthermore, the mass ratio of dopamine and ammonium phosphomolybdate is found critical for the successful formation of such triple-interface heterojunction. Theoretical calculation results demonstrate that such triple-interface heterojunctions possess thermodynamically favorable water dissociation Gibbs free energy (ΔGH2O ) of -1.28 eV and hydrogen adsorption Gibbs free energy (ΔGH* ) of -0.41 eV due to the synergistic effect of Mo2 C and Mo3 P as water dissociation site and H* adsorption/desorption sites during the HER process in comparison to the corresponding single components. Notably, the optimal heterostructures exhibit the highest HER activity with the low overpotential of 69 mV at the current density of 10 mA cm-2 and a small Tafel slope of 60.4 mV dec-1 as well as good long-term stability for 125 h. Such remarkable results have been theoretically and experimentally proven to be due to the synergistic effect between the unique heterostructures and the encapsulated nitrogen-doped carbon.

Decorating Single-Atomic Mn Sites with FeMn Clusters to Boost Oxygen Reduction Reaction.

The regulation of electron distribution of single-atomic metal sites by atomic clusters is an effective strategy to boost their intrinsic activity of oxygen reduction reaction (ORR). Herein we report the construction of single-atomic Mn sites decorated with atomic clusters by an innovative combination of post-adsorption and secondary pyrolysis. The X-ray absorption spectroscopy confirms the formation of Mn sites via Mn-N4 coordination bonding to FeMn atomic clusters (FeMnac /Mn-N4 C), which has been demonstrated theoretically to be conducive to the adsorption of molecular O2 and the break of O-O bond during the ORR process. Benefiting from the structural features above, the FeMnac /Mn-N4 C catalyst exhibits excellent ORR activity with half-wave potential of 0.79 V in 0.5 M H2 SO4 and 0.90 V in 0.1 M KOH as well as preeminent Zn-air battery performance. Such synthetic strategy may open up a route to construct highly active catalysts with tunable atomic structures for diverse applications.

Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae).

Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa.

Water-activated formation of porous graphitic carbon nitride with carbon vacancies to boost photocatalytic hydrogen peroxide production.

A facile water-activated method is developed for preparing porous graphitic carbon nitride with carbon vacancies by co-pyrolysis of melamine and water at a relatively low temperature under an Ar atmosphere, resulting in an increased specific surface area and the efficient separation of photo-generated electrons and holes. As expected, the optimal catalyst exhibited a high H2O2 yield of 180 µM within 4 h and good cycling stability. The reported template-free method may provide a reference for the preparation of high-performance photocatalysts in a facile way.

A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae.

The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using these data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.

Corrigendum: Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae.

[This corrects the article DOI: 10.3389/fgene.2021.730495.].

Mid-long wavelength infrared absorptance of hyperdoped silicon via femtosecond laser microstructuring.

Hyperdoped silicon (hSi) fabricated via femtosecond laser irradiation has emerged as a promising photoelectric material with strong broadband infrared (IR) absorption. In this work, we measured the optical absorptance of the hSi in the wavelength of 0.3-16.7 µm. Unlike the near to mid wavelength IR absorption, the mid-long wavelength IR (M-LWIR) absorption is heavily dependent on the surface morphology and the dopants. Furthermore, calculations based on coherent potential approximation (CPA) reveal the origin of free carrier absorption, which plays an important role in the M-LWIR absorption. As a result, a more comprehensive picture of the IR absorption mechanism is drawn for the optoelectronic applications of the hSi.

Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae.

The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.

An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene.

Convergent evolution, often viewed as the inevitable outcome of natural selection, has received special attention since the time of Darwin. Clematis is well known for its climbing habit, but it has some shrubby species, known as sect. Fruticella s.l. The shrubby Clematis species are distributed in the dry habitats of Central Asia and adjacent areas showing possible convergent evolution. In this study, we assembled the complete plastome and nuclear ribosomal DNA (nrDNA) sequences of 56 Clematis species, representing most sections and covering most of the shrubby species, to reconstruct their evolutionary histories. Using both maximum likelihood and Bayesian methods, the plastome and nrDNA datasets generated similar, but not identical, phylogenetic relationships, which are better resolved than in previous studies. Then, molecular dating, historical range reconstruction, and character optimization analyses were conducted based on this updated phylogenetic framework. All the morphological characters widely used for taxonomy were shown to have evolved multiple times. Molecular dating inferred that Clematis diverged from its sister in the mid Miocene, and all six major clades of Clematis originated during the late Miocene, with a species radiation during the Pliocene to Pleistocene. The results clearly showed that the shrubby habit evolved independently in four lineages of Clematis in Asia. We also revealed that the shrubby lineages have emerged since the very beginning of Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby Clematis in Central Asia and adjacent dry areas.

Application of boundary electro-osmotic pulse to reduce sludge-to-wall adhesion.

Adhesion is one of the main features of sewage sludge. This paper aims at reducing sludge-to-wall adhesion through formation of a water layer induced by boundary electro-osmotic pulse (BEOP) which is characterized by distributing anodes and cathodes on one surface and exerting a pulsating current. The effects of the related parameters, including current intensity, exerting time, frequency, duty cycle (DTC), and the ratio of cathodic surface area to anodic surface area (C/A), on the adhesive stress of sewage sludge with different moisture content were thoroughly studied. The results indicated that, under the optimal conditions of BEOP, the adhesive stress of sludge with moisture content of 35%, 45%, 60% and 70% was reduced by 40.4%, 54.5%, 31%, and 24.4%, respectively. The migrations of water, ions and organic matters were also investigated to explore the functional mechanism of BEOP. The results showed that the water migrated from the anode side to the cathode side, whereas the organic matters migrated in the opposite direction. The increment of the sludge moisture content on the cathode surface was reduced with the increase of distance away from the anode. Based on theoretical modeling, the distributions of current density and temperature in sludge cake were obtained. The current flowed from anode to cathode and decayed quickly with the increase of the flowing distance, which well explained the moisture content distribution in sludge cake.

Atomic scale study of stress-induced misaligned subsurface layers in KDP crystals.

We carried out ab initio calculations to study the atomic configuration, band structure and optical absorption of the lattice misalignment structure (LMS) in a subsurface layer of a machined KH2PO4 (KDP) crystal. By varying the different degrees of misalignment, the changes in the corresponding atomic position and bond and energy are obtained, and their correlations are analysed in detail. The results indicate that in the LMS evolution, the variation in the proton distribution around the oxygen atoms plays an important role, and many local stable LMSs appear. Interestingly, at a certain misalignment value, the total system energy of the local stable LMS is near that of a perfect KDP crystal. For some local stable LMSs, the electronic and optical properties related to the laser damage threshold (LDT) of KDP are further studied. The results show that in comparison with a perfect KDP crystal, the band gaps of local stable LMSs at some certain misalignment values become narrow, and their optical absorption curves produce an obvious redshift. These facts demonstrate that the emergence of the LMS could have a significant impact on the optical absorption of the KDP material and thus affect the LDT of KDP under certain working conditions.

Crystallinity and Sub-Band Gap Absorption of Femtosecond-Laser Hyperdoped Silicon Formed in Different N-Containing Gas Mixtures.

Femtosecond (fs)-laser hyperdoped silicon has aroused great interest for applications in infrared photodetectors due to its special properties. Crystallinity and optical absorption influenced by co-hyperdoped nitrogen in surface microstructured silicon, prepared by fs-laser irradiation in gas mixture of SF6/NF3 and SF6/N2 were investigated. In both gas mixtures, nitrogen and sulfur were incorporated at average concentrations above 1019 atoms/cm³ in the 20-400 nm surface layer. Different crystallinity and optical absorption properties were observed for samples microstructured in the two gas mixtures. For samples prepared in SF6/N2, crystallinity and light absorption properties were similar to samples formed in SF6. Significant differences were observed amongst samples formed in SF6/NF3, which possess higher crystallinity and strong sub-band gap absorption. The differing crystallinity and light absorption rates between the two types of nitrogen co-hyperdoped silicon were attributed to different nitrogen configurations in the doped layer. This was induced by fs-laser irradiating silicon in the two N-containing gas mixtures.

Composition-dependent band gaps and indirect-direct band gap transitions of group-IV semiconductor alloys.

We used the coherent potential approximation to investigate the band structures of group-IV semiconductor alloys, including Si(x)Ge(1-x), Ge(1-y)Sn(y) and Si(x)Ge(1-x-y)Sn(y). The calculations for Si(x)Ge(1-x) prove the reliability and accuracy of the method we used. For Ge(1-y)Sn(y), the direct band gap optical bowing parameter we obtained is 2.37 eV and the indirect-direct band gap transition point is at y = 0.067, both consistent with the existing experimental data. For Si(x)Ge(1-x-y)Sn(y), with the increase of the Si concentration, the compositional dependency of the band gap becomes complex. An indirect-direct band gap transition is found in Si(x)Ge(1-x-y)Sn(y) in the range of 0 < x≤ 0.20, and the indirect-direct crossover line in the compositional space has the quadratic form of y = 3.4x(2) + 1.11x + 0.07, not the linear form as suggested before. Furthermore, for the Ge lattice-matched alloy Ge(1-x()Si0.79Sn0.21)(X), our results show that those with 0.18 < X < 0.253 have band gaps larger than 0.8 eV at room temperature.

Feature importance analysis in guide strand identification of microRNAs.

MicroRNA (miRNA) is the negative regulator of gene expression, also known as guide strand of transient miRNA:miRNA* duplex. It is critical in maintaining the normal physiological processes such as development, differentiation, and apoptosis in many organisms. With increasing miRNA data, it is desirable to design methods to identify guide strand based on machine learning algorithms. In this study, the random forest models based on local sequence-structure features were proposed to identify miRNA in four species. The accuracies achieved were 86.51% for Homo sapiens, 81.66% for Ornithorhynchus anatinus, 82.33% for Mus musculus and 85.71% for Schmidtea mediterranea, respectively. Furthermore, the important analysis of feature elements was carried out by using the conditional feature importance strategy. The analysis results revealed that most of the significant elements were related to guanine-cytosine (GC) base pair. We believed that our method could be beneficial to annotate the function of miRNA and help the further understanding of the RNA interference mechanism.