Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales.

BACKGROUND: The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS: We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS: The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.

General error analysis of matrix-operation-mode decomposition technique in few-mode fiber laser.

The mode decomposition based on matrix operation (MDMO) is one of the fastest mode decomposition (MD) techniques, which is important to the few-mode fiber laser characterization and its applications. In this paper, the general error of the MDMO technique was analyzed, where different influencing factors, such as position deviation of the optical imaging system, coordinate deviation of the image acquisition system, aberrations, and mode distortion were considered. It is found that the MDMO technique based on far-field intensity distribution is less affected by optical imaging system position deviation, coordinate deviation of the image acquisition system, and mode distortion than those based on direct near-field decomposition. But far-field decomposition is more affected by aberration than those based on near-field decomposition. In particular, the numerical results show that the deviation of the coordinate axis direction is an important factor limiting the accuracy of MD. In addition, replacing the ideal eigenmode basis with a distorted eigenmode basis can effectively suppress the decrease in mode decomposition accuracy caused by fiber bending. Moreover, based on detailed numerical analysis results, fitting formulas for estimating the accuracy of the MDMO technique with imperfections are also provided, which provides a comprehensive method for evaluating the accuracy of the MDMO technique in practical engineering operations.

Evaluation of the impact of weak end feedback on the SBS threshold in high-power narrow-linewidth fiber amplifiers.

In this work, we quantitatively investigate the SBS threshold in high-power narrow-linewidth fiber amplifiers seeded with phase-modulated single-frequency lasers in presence of weak end feedback. The impacts of the end feedback and spectral linewidths on the SBS threshold are demonstrated in detail through comparative experiments and numerical simulations, respectively. In the experiment, we have pointed out a practical method to estimate the end reflectivity in high-power fiber amplifiers. Based on this estimation, the SBS threshold characters of the high-power narrow-linewidth fiber amplifiers with different end reflectivity and seed linewidths are investigated. By reducing the end reflectivity, a 2.85 times SBS threshold enhancement has been achieved at the most susceptible linewidth (16.8 GHz). Furthermore, we propose a spectral evolution model to investigate the SBS threshold in high-power narrow-linewidth fiber amplifiers, which is even capable for calculating SBS thresholds of the systems with tens of GHz linewidth while weak end reflection is considered. The simulation results demonstrate that end reflection will obviously affect the SBS threshold when the linewidth of the seed laser is broadened beyond 5 GHz, especially for the spectral linewidth of seed lasers nearing the Brillouin frequency shift. Besides, when the end reflectivity is set to be stronger than -65 dB, the SBS threshold performs a tendency to decline and then rise with the growth of seed linewidth. The experiment and simulation results provide a new optimization sight for the SBS effect suppression in high-power narrow-linewidth fiber amplifiers.

The Pharus latifolius genome bridges the gap of early grass evolution.

The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. The ancestry of all grass genomes includes a shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance of ρ-WGD remains elusive. We sequenced the genome of Pharus latifolius, a grass species (producing a true spikelet) in the subfamily Pharoideae, a sister lineage to the core Poaceae including the (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) and Bambusoideae, Oryzoideae, and Pooideae (BOP) clades. Our results indicate that the P. latifolius genome has evolved slowly relative to cereal grass genomes, as reflected by moderate rates of molecular evolution, limited chromosome rearrangements and a low rate of gene loss for duplicated genes. We show that the ρ-WGD event occurred approximately 98.2 million years ago (Ma) in a common ancestor of the Pharoideae and the PACMAD and BOP grasses. This was followed by contrasting patterns of diploidization in the Pharus and core Poaceae lineages. The presence of two FRIZZY PANICLE-like genes in P. latifolius, and duplicated MADS-box genes, support the hypothesis that the ρ-WGD may have played a role in the origin and functional diversification of the spikelet, an adaptation in grasses related directly to cereal yields. The P. latifolius genome sheds light on the origin and early evolution of grasses underpinning the biology and breeding of cereals.

5†kW power-level 1050†nm narrow-linewidth fiber amplifier enabled by biconical-tapered active fiber.

Effective wavelength extension is vital in the applications of high-power narrow-linewidth fiber lasers. In this work, we demonstrate a 5-kW power-level narrow-linewidth fiber amplifier at 1050 nm utilizing a homemade biconical-tapered Yb-doped fiber (BT-YDF). Up to ∼4.96 kW fiber laser is achieved with a 3 dB linewidth of ∼0.54 nm and a beam quality factor of Mx 2 = 1.46, My 2 = 1.6. The experimental comparisons reveal that BT-YDF has the advantages of improving a stimulated Raman scattering threshold and balancing transverse mode instability suppression in the fiber amplifier. This work could provide a good reference for extending the operating wavelength of high-power fiber amplifiers.

A DFT Investigation of B-Doped C3 N as Single Atom Electrocatalysts for N2 -to-NH3 Conversion.

The NH3 synthesis from N2 plays an important role in the ecological cycle and industrial production. Different from industrial NH3 synthesis with high pollution and energy consumption, electrocatalytic NH3 synthesis is favored because of its environmental protection, energy saving, ambient reaction conditions and other characteristics. However, due to the low efficiency and poor reaction selectivity of the existing electrocatalysts, which can not be used actually, the development of new electrocatalysts for nitrogen reduction reaction (NRR) is particularly urgent. Herein, we designed a series of transition metal atoms anchored B-doped defective C3 N surface (TM@B2 C3 N) as single-atom catalysts. Through the screening process of N2 adsorption activation, N2 H formation and NH3 desorption, finally the excellent electrocatalysts with strong stability and high activity (Cr@B2 C3 N and Mn@B2 C3 N) were obtained. After simulating the entire pathway, it was found that the NRR process on Cr@B2 C3 N and Mn@B2 C3 N via consecutive and distal pathways with the lowest limiting potential of -0.42 and -0.52 V, which have the good ability to inhibit hydrogen evolution reaction. Finally, the electronic properties were analyzed, and the reason for their high catalytic activity was summarized. This work provides a new idea for the rational design of NRR electrocatalysts and promotes the practical application of electrocatalysts.

Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years.

Current biodiversity loss is generally considered to have been caused by anthropogenic disturbance, but it is unclear when anthropogenic activities began to affect biodiversity loss. One hypothesis suggests it began with the Industrial Revolution, whereas others propose that anthropogenic disturbance has been associated with biodiversity decline since the early Holocene. To test these hypotheses, we examined the unique vegetation of evergreen broadleaved forests (EBLFs) in East Asia, where humans have affected landscapes since the early Holocene. We adopted a genomic approach to infer the demographic history of a dominant tree (Litsea elongata) of EBLFs. We used Holocene temperature and anthropogenic disturbance factors to calculate the correlation between these variables and the historical effective population size of L. elongata with Spearman statistics and integrated the maximum-entropy niche model to determine the impact of climate change and anthropogenic disturbance on fluctuation in its effective population size. We identified 9 well-defined geographic clades for the populations of L. elongata. Based on the estimated historical population sizes of these clades, all the populations contracted, indicating persistent population decline over the last 11,000 years. Demographic history of L. elongata and human population change, change in cropland use, and change in irrigated rice area were significantly negatively correlated, whereas climate change in the Holocene was not correlated with demographic history. Our results support the early human impact hypothesis and provide comprehensive evidence that early anthropogenic disturbance may contribute to the current biodiversity crisis in East Asia.

Early Detection of Pipeline Natural Gas Leakage from Hyperspectral Imaging by Vegetation Indicators and Deep Neural Networks.

The timely detection of underground natural gas (NG) leaks in pipeline transmission systems presents a promising opportunity for reducing the potential greenhouse gas (GHG) emission. However, existing techniques face notable limitations for prompt detection. This study explores the utility of Vegetation Indicators (VIs) to reflect vegetation health deterioration, thereby representing leak-induced stress. Despite the acknowledged potential of VIs, their sensitivity and separability remain understudied. In this study, we employed ground vegetation as biosensors for detecting methane emissions from underground pipelines. Hyperspectral imaging from vegetation was collected weekly at both plant and leaf scales over two months to facilitate stress detection using VIs and Deep Neural Networks (DNNs). Our findings revealed that plant pigment-related VIs, modified chlorophyll absorption reflectance index (MCARI), exhibit commendable sensitivity but limited separability in discerning stressed grasses. A NG-specialized VI, the optimized soil-adjusted vegetation index (OSAVI), demonstrates higher sensitivity and separability in early detection of methane leaks. Notably, the OSAVI proved capable of discriminating vegetation stress 21 days after methane exposure initiation. DNNs identified the methane leaks following a 3-week methane treatment with an accuracy of 98.2%. DNN results indicated an increase in visible (VIS) and a decrease in near-infrared (NIR) in spectra due to methane exposure.

High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker.

After optimizing the original aptamer sequence by truncation strategy, a magnetic separation-assisted DNAzyme-driven 3D DNA walker fluorescent aptasensor was developed for detecting the food-borne pathogen Cronobacter species. Iron oxide magnetic nanoparticles (MNPs) modified with a hybrid of truncated aptamer probe and DNAzyme strand (AP-E1) denoted as MNPs@AP-E1, were employed as capture probes. Simultaneously, a DNAzyme-driven 3D-DNA walker was utilized as the signal amplification element. The substrate strand (Sub) was conjugated with the gold nanoparticles (AuNPs), resulting in the formation of AuNPs@Sub, which served as a 3D walking track. In the presence of the target bacteria and Mg2+, E1-DNAzyme was activated and moved along AuNPs@Sub, continuously releasing the signal probe. Under optimized conditions, a strong linear correlation was observed for Cronobacter sakazakii (C. sakazakii) in the concentration range 101 to 106 CFU mL-1, with a low detection limit of 2 CFU mL-1. The fluorescence signal responses for different Cronobacter species exhibited insignificant differences, with a relative standard deviation of 3.6%. Moreover, the aptasensor was successfully applied to determine  C. sakazakii in real samples with recoveries of 92.86%-108.33%. Therefore, the novel method could be a good candidate for ultra-sensitive and selective detection of Cronobacter species without complex manipulation.

Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change.

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs, to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into account studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 million years ago [Ma]), facilitated by the greenhouse warming. As a response to the cooling and drying climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.

Two-dimensional scanning of silicon-based focal plane array with field-of-view splicing technology.

All-solid-state beam scanning chip is ideal for next-generation LiDAR due to its reliability and small size. Here we propose a focal plane array chip for two-dimensional scanning using field-of-view splicing technology on silicon photonics platform. The chip has two rotationally symmetric structures, each including a 1 × 64 antenna array accompanied by a 1 × 64 micro-ring optical switch array. We demonstrate a two-dimensional scanning equivalent to an 8-line LiDAR with a field-of-view of 82° × 32°, a beam divergence angle of 0.07° × 0.07°, and a background suppression ratio of over 20 dB. Our chip works in such a simple way that only one optical switch needs to be turned on each time the beam is emitted. And the chip is scalable that a larger range of two-dimensional scanning can be achieved when using more antennas for field-of-view splicing and cascading more optical switches.

Analysis of an image noise sensitivity mechanism for matrix-operation-mode-decomposition and a strong anti-noise method.

Mode decomposition (MD) based on the matrix operation (MDMO) is one of the fastest mode decomposition methods in fiber laser which has great potential for optical communications, nonlinear optics and spatial characterization applications. However, we found that the image noise sensitivity is the main limit to the accuracy of the original MDMO method, but improving the decomposition accuracy by using conventional image filtering methods is almost ineffective. By using the norm theory of matrices, the analysis result shows that both the image noise and the coefficient matrix condition number determine the total upper-bound error of the original MDMO method. Besides, the greater the condition number, the more sensitive of MDMO method is to noise. In addition, it is found that the local error of each mode information solution in the original MDMO method is different, which depends on the L2-norm of each row vector of the inverse coefficient matrix. Moreover, a more noise-insensitive MD method is achieved by screening out the information corresponding to large L2-norm. In particular, selecting the higher accuracy among the original MDMO method and such noise-insensitive method as the result in a single MD process, a strong anti-noise MD method was proposed in this paper, which displays high MD accuracy in strong noise for both near-filed and far-filed MD cases.

Confined-doped fiber enabled kilowatt-level all-fiber laser with 1.28†GHz linewidth.

In this manuscript, a narrow linewidth fiber amplifier based on confined-doped fiber is established, and the power scaling and beam quality maintaining capabilities of this amplifier are investigated. Benefitted from the large mode area of the confined-doped fiber and precisely controlling the Yb-doped region in the fiber core, the stimulated Brillouin scattering (SBS) and transverse mode instability (TMI) effects are effectively balanced. As a result, a 1007 W signal laser with just 1.28 GHz linewidth is obtained by combining the advantages of confined-doped fiber, near-rectangular spectral injection, and 915 nm pump manner. As far as we know, this result is the first beyond kilowatt-level demonstration of all-fiber lasers with GHz-level linewidth, which could provide a well reference for simultaneously controlling spectral linewidth, suppressing the SBS and TMI effects in high-power, narrow-linewidth fiber lasers.

Wide field of view optical phased array with a high-directionality antenna.

Light detection and ranging (LiDAR) is a widely utilized technology for extracting information from the outside world in fields such as automotive, robotics, and aerospace. Optical phased array (OPA) is a promising solution for LiDAR technology, although its application is limited by loss and alias-free steering range. In this paper, we propose a dual-layer antenna that achieves a peak directionality of over 92%, thereby mitigating antenna loss and enhancing power efficiency. Based on this antenna, we design and fabricate a 256-channel non-uniform OPA that achieves 150° alias-free steering.

10 kW tandem pumping fiber amplifier with good beam quality based on tapered ytterbium-doped fiber.

In this paper, we established a high power tandem pumped fiber amplifier based on tapered ytterbium-doped fiber (TYDF). The TYDF is developed in-house with a core/inner cladding diameter of 30/250 µm at the small-core region and 48/400 µm at the large-core region. The key parameters of the amplifier in a co-pumped and counter-pumped configuration are experimentally investigated, such as slope efficiency, stimulated Raman scattering (SRS) threshold, and beam quality evolution. Up to 10.28 kW laser free of SRS or transverse mode instability is obtained from the counter-pumped amplifier, and the beam quality factor M2 is 2.29, which is significantly improved compared with the 48/400 µm uniform YDF. To the best of our knowledge, this is the highest average output power achieved so far based on the TYDF. This work could provide a solution for balancing the SRS suppression and high order modes control in high power tandem pumped YDF lasers.

Generating the 1.5†kW mode-tunable fractional vortex beam by a coherent beam combining system.

As an essential component of the vortex beam, the fractional vortex beam has significantly advanced various applications, such as optical imaging, optical communication, and particle manipulation. However, practical applications face a significant challenge as generating high average power fractional vortex beams remains difficult. Here, we proposed and experimentally demonstrated a high average power mode-tunable fractional vortex beam generator based on an internally sensed coherent beam combining (CBC) system. We presented the first, to the best of our knowledge, successful generation of a 1.5 kW continuous wave fractional vortex beam. Moreover, real-time tuning of the topological charge (TC) from -2/3 to +2/3 was easily achieved using the programmable liquid crystals (LCs). More importantly, the fractional vortex beam copier was presented as well, and the generated fractional vortex beam could be easily transformed into a fractional vortex beam array by changing the fill factor of the laser array. This work can pave the path for the practical implementation of high average power structured light beams.

Precipitation and local adaptation drive spatiotemporal variations of aboveground biomass and species richness in Tibetan alpine grasslands.

The Tibetan Plateau contains the highest and largest alpine pasture in the world, which is adapted to the cold and arid climate. It is challenging to understand how the vast alpine grasslands respond to climate change. We aim to test the hypothesis that there is local adaptation in elevational populations of major plant species in Tibetan alpine grasslands, and that the spatiotemporal variations of aboveground biomass (AGB) and species richness (S) can be mainly explained by climate change only when the effect of local adaptation is removed. A 7-year reciprocal transplant experiment was conducted among the distribution center (4950 m), upper (5200 m) and lower (4650 m) limits of alpine Kobresia meadow in central Tibetan Plateau. We observed interannual variations in S and AGB of 5 functional groups and 4 major species, and meteorological factors in each of the three elevations during 2012-2018. Relationships between interannual changes of AGB and climatic factors varied greatly with elevational populations within a species. Elevation of population origin generally had a greater or an equal contribution to interannual variation in AGB of the 4 major species, compared to temperature and precipitation effects. While the effect of local adaptation was removed by calculating differences in AGB and S between elevations of migration and origin, relative changes in AGB and S were mainly explained by precipitation change rather than by temperature change. Our data support the hypothesis, and further provide evidence that the monsoon-adapted alpine grasslands are more sensitive to precipitation change than to warming.

Over 30 W single-frequency all-fiber amplifier at 1120 nm with high ASE suppression.

A 1120 nm linearly polarized all-fiber single-frequency amplifier based on Yb-doped fiber (YDF) is reported. A maximum output power of 30 W is achieved by 976 nm clad-pumping and 1018 nm core-pumping, with corresponding slope efficiencies of 51.9% and 70.0%, respectively. With the 976 nm clad-pumping configuration, a signal to amplified spontaneous emission (ASE) ratio of more than 45 dB is realized at maximum output power. The polarization extinction ratio of the amplifier is measured to be more than 21 dB in the whole power scaling process. In addition, the intensity noise of the amplifier at maximum output power is also characterized to be around -130d B c/H z at frequencies above 2 kHz and is comparable to that of the seed laser. Moreover, the deterioration of frequency noise and linewidth of the amplified laser is negligible. To the best of our knowledge, this is the highest output power of a single-frequency all-fiber amplifier that exploits the fundamental transition of YDF at 1120 nm, even without any external intervention for suppressing ASE in the short wavelength range.

All-fiberized linearly polarized superfluorescent fiber source with 5 kW power output.

A superfluorescent fiber source (SFS) is a special fiber source that commonly possesses high temporal stability and a wide spectral linewidth. In this work, an all-fiberized linearly polarized SFS with, to our knowledge, record output power and near-diffraction-limited beam quality is presented. Up to 5.03 kW SFS is achieved at a pump power of 6.18 kW with a corresponding conversion efficiency of ∼81.1%. At maximum output power, the signal-to-noise ratio to background spectral noise is over 50 dB, the polarization extinction ratio is ∼17d B, and the beam quality factor is M x 2=1.49, M y 2=1.44. Further comparisons confirm the power scalability of fiber amplifiers employing SFSs as seed lasers. Overall, this work could provide a good reference for potential exploration of high-power fiber laser systems.

Molecular Docking Insight into the Label-Free Fluorescence Aptasensor for Ochratoxin A Detection.

Ochratoxin A (OTA) is the most common mycotoxin and can be found in wheat, corn and other grain products. As OTA pollution in these grain products is gaining prominence as a global issue, the demand to develop OTA detection technology has attracted increasing attention. Recently, a variety of label-free fluorescence biosensors based on aptamer have been established. However, the binding mechanisms of some aptasensors are still unclear. Herein, a label-free fluorescent aptasensor employing Thioflavin T (ThT) as donor for OTA detection was constructed based on the G-quadruplex aptamer of the OTA aptamer itself. The key binding region of aptamer was revealed by using molecular docking technology. In the absence of the OTA target, ThT fluorescent dye binds with the OTA aptamer to form an aptamer/ThT complex, and results in the fluorescence intensity being obviously enhanced. In the presence of OTA, the OTA aptamer binds to OTA because of its high affinity and specificity to form an aptamer/OTA complex, and the ThT fluorescent dye is released from the OTA aptamer into the solution. Therefore, the fluorescence intensity is significantly decreased. Molecular docking results revealed that OTA is binding to the pocket-like structure and surrounded by the A29-T3 base pair and C4, T30, G6 and G7 of the aptamer. Meanwhile, this aptasensor shows good selectivity, sensitivity and an excellent recovery rate of the wheat flour spiked experiment.