Tarim University

Bismuth-rich bismuth oxyhalides (Bi–O–X; X = Cl, Br, I) display high photocatalytic reduction activity due to the promoting conduction band potential. In this work, two Bi5O7I nanosheets with different dominant facets were synthesized using either molecular precursor hydrolysis or calcination. Crystal structure characterizations, included X-ray diffraction patterns (XRD), field emission electron microscopy and fast Fourier transformation (FFT) images, showed that hydrolysis and calcination resulted in the dominant exposure of {100} and {001} facets, respectively. Photocatalytic data revealed that Bi5O7I–001 had a higher activity than Bi5O7I–100 for N2 fixation and dye degradation. Photoelectrochemical data revealed that Bi5O7I–001 had higher photoinduced carrier separation efficiency than Bi5O7I–100. The band structure analysis also used to explain the underlying photocatalytic mechanism based on the different conduction band position. This work presents the first report about the facet-dependent photocatalytic performance of bismuth-rich Bi–O–X photocatalysts.

Abstract Ternary NiCoFe‐layered double hydroxide (NiCo III Fe‐LDH) with Co 3+ is grafted on nitrogen‐doped graphene oxide (N‐GO) by an in situ growth route. The array‐like colloid composite of NiCo III Fe‐LDH/N‐GO is used as a bifunctional catalyst for both oxygen evolution/reduction reactions (OER/ORR). The NiCo III Fe‐LDH/N‐GO array has a 3D open structure with less stacking of LDHs and an enlarged specific surface area. The hierarchical structure design and novel material chemistry endow high activity propelling O 2 redox. By exposing more amounts of Ni and Fe active sites, the NiCo III Fe‐LDH/N‐GO illustrates a relatively low onset potential (1.41 V vs reversible hydrogen electrode) in 0.1 mol L −1 KOH solution under the OER process. Furthermore, by introducing high valence Co 3+ , the onset potential of this material in ORR is 0.88 V. The overvoltage difference is 0.769 V between OER and ORR. The key factors for the excellent bifunctional catalytic performance are believed to be the Co with a high valence, the N‐doping of graphene materials, and the highly exposed Ni and Fe active sites in the array‐like colloid composite. This work further demonstrates the possibility to exploit the application potential of LDHs as OER and ORR bifunctional electrochemical catalysts.

Diet polyphenols-primarily categorized into flavonoids (e.g., flavonols, flavones, flavan-3-ols, anthocyanidins, flavanones, and isoflavones) and nonflavonoids (with major subclasses of stilbenes and phenolic acids)-are reported to have health-promoting effects, such as antioxidant, antiinflammatory, anticarcinoma, antimicrobial, antiviral, and cardioprotective properties. However, their applications in functional foods or medicine are limited because of their inefficient systemic delivery and poor oral bioavailability. Epigallocatechin-3-gallate, curcumin, and resveratrol are the well-known representatives of the bioactive diet polyphenols but with poor bioavailability. Food macromolecule based nanoparticles have been fabricated using reassembled proteins, crosslinked polysaccharides, protein-polysaccharide conjugates (complexes), as well as emulsified lipid via safe procedures that could be applied in food. The human gastrointestinal digestion tract is the first place where the food grade macromolecule nanoparticles exert their effects on improving the bioavailability of diet polyphenols, via enhancing their solubility, preventing their degradation in the intestinal environment, elevating the permeation in small intestine, and even increasing their contents in the bloodstream. We contend that the stability and structure behaviors of nanocarriers in the gastrointestinal tract environment and the effects of nanoencapsulation on the metabolism of polyphenols warrant more focused attention in further studies.

Long noncoding RNAs (lncRNAs), a recently discovered class of cellular RNAs, play important roles in the regulation of many cellular developmental processes. Although lncRNAs have been systematically identified in various systems, most of them have not been functionally characterized in vivo in animal models. In this study, we identified 128 testis-specific Drosophila lncRNAs and knocked out 105 of them using an optimized three-component CRISPR/Cas9 system. Among the lncRNA knockouts, 33 (31%) exhibited a partial or complete loss of male fertility, accompanied by visual developmental defects in late spermatogenesis. In addition, six knockouts were fully or partially rescued by transgenes in a trans configuration, indicating that those lncRNAs primarily work in trans Furthermore, gene expression profiles for five lncRNA mutants revealed that testis-specific lncRNAs regulate global gene expression, orchestrating late male germ cell differentiation. Compared with coding genes, the testis-specific lncRNAs evolved much faster. Moreover, lncRNAs of greater functional importance exhibited higher sequence conservation, suggesting that they are under constant evolutionary selection. Collectively, our results reveal critical functions of rapidly evolving testis-specific lncRNAs in late Drosophila spermatogenesis.

The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.

Nickel-iron layered double hydroxide (NiFe-LDH) nanosheets have shown optimal oxygen evolution reaction (OER) performance; however, the role of the intercalated ions in the OER activity remains unclear. In this work, we show that the activity of the NiFe-LDHs can be tailored by the intercalated anions with different redox potentials. The intercalation of anions with low redox potential (high reducing ability), such as hypophosphites, leads to NiFe-LDHs with low OER overpotential of 240 mV and a small Tafel slope of 36.9 mV/dec, whereas NiFe-LDHs intercalated with anions of high redox potential (low reducing ability), such as fluorion, show a high overpotential of 370 mV and a Tafel slope of 80.8 mV/dec. The OER activity shows a surprising linear correlation with the standard redox potential. Density functional theory calculations and X-ray photoelectron spectroscopy analysis indicate that the intercalated anions alter the electronic structure of metal atoms which exposed at the surface. Anions with low standard redox potential and strong reducing ability transfer more electrons to the hydroxide layers. This increases the electron density of the surface metal sites and stabilizes their high-valence states, whose formation is known as the critical step prior to the OER process.

By reviewing the development history of stimulation techniques for deep/ultra-deep oil and gas reservoirs, the new progress in this field in China and abroad has been summed up, including deeper understanding on formation mechanisms of fracture network in deep/ultra-deep oil and gas reservoir, performance improvement of fracturing fluid materials, fine stratification of ultra-deep vertical wells, and mature staged multi-cluster fracturing technique for ultra-deep and highly deviated wells/horizontal wells. In light of the exploration and development trend of ultra-deep oil and gas reservoirs in China, the requirements and technical difficulties in ultra-deep oil and gas reservoir stimulation are discussed: (1) The research and application of integrated geological engineering technology is difficult. (2) The requirements on fracturing materials for stimulation are high. (3) It is difficult to further improve the production in vertical profile of the ultra-deep and hugely thick reservoirs. (4) The requirements on tools and supporting high-pressure equipment on the ground for stimulation are high. (5) It is difficult to achieve efficient stimulation of ultra-deep, high-temperature and high-pressure wells. (6) It is difficult to monitor directly the reservoir stimulation and evaluate the stimulation effect accurately after stimulation. In line with the complex geological characteristics of ultra-deep oil and gas reservoirs in China, seven technical development directions are proposed: (1) To establish systematic new techniques for basic research and evaluation experiments; (2) to strengthen geological research and improve the operational mechanism of integrating geological research and engineering operation; (3) to develop high-efficiency fracturing materials for ultra-deep reservoirs; (4) to research separated layer fracturing technology for ultra-deep and hugely thick reservoirs; (5) to explore fracture-control stimulation technology for ultra-deep horizontal well; (6) to develop direct monitoring technology for hydraulic fractures in ultra-deep oil and gas reservoirs; (7) to develop downhole fracturing tools with high temperature and high pressure tolerance and supporting wellhead equipment able to withstand high pressure.

Soil salinization is a global issue resulting in soil degradation, arable land loss and ecological environmental deterioration. Over the decades, multispectral and hyperspectral remote sensing have enabled efficient and cost-effective monitoring of salt-affected soils. However, the potential of hyperspectral sensors installed on an unmanned aerial vehicle (UAV) to estimate and map soil salinity has not been thoroughly explored. This study quantitatively characterized and estimated field-scale soil salinity using an electromagnetic induction (EMI) equipment and a hyperspectral camera installed on a UAV platform. In addition, 30 soil samples (0~20 cm) were collected in each field for the lab measurements of electrical conductivity. First, the apparent electrical conductivity (ECa) values measured by EMI were calibrated using the lab measured electrical conductivity derived from soil samples based on empirical line method. Second, the soil salinity was quantitatively estimated using the random forest (RF) regression method based on the reflectance factors of UAV hyperspectral images and satellite multispectral data. The performance of models was assessed by Lin’s concordance coefficient (CC), ratio of performance to deviation (RPD), and root mean square error (RMSE). Finally, the soil salinity of three study fields with different land cover were mapped. The results showed that bare land (field A) exhibited the most severe salinity, followed by dense vegetation area (field C) and sparse vegetation area (field B). The predictive models using UAV data outperformed those derived from GF-2 data with lower RMSE, higher CC and RPD values, and the most accurate UAV-derived model was developed using 62 hyperspectral bands of the image of the field A with the RMSE, CC, and RPD values of 1.40 dS m−1, 0.94, and 2.98, respectively. Our results indicated that UAV-borne hyperspectral imager is a useful tool for field-scale soil salinity monitoring and mapping. With the help of the EMI technique, quantitative estimation of surface soil salinity is critical to decision-making in arid land management and saline soil reclamation.

Compared with traditional technological innovation modes, green technology innovation is more targeted for low carbon development and critical support for countries worldwide to combat climate change. The impact of green technology innovation on carbon emissions is considered in terms of fixed effect and mediating effect models through industrial structure upgrading. For this purpose, the sample dataset of 30 provincial administrative areas in China from 2008 to 2020 is employed. The results demonstrate that green technology innovation exerts significantly inhibitory effects on carbon emissions, whose conclusion still holds after removing municipalities and replacing the dependent variable. Industrial structure upgrading is vital for green technology innovation to diminish carbon emissions. There is significant regional heterogeneity in the effects of green technology innovation on carbon emissions, i.e., the direct and indirect impact of green technology innovation on carbon emission reduction is significant in the eastern-central area, but its effect is insignificant in the western region. Therefore, it is essential to realize carbon emission reduction by further bolstering green technology innovation and accelerating industrial structure upgrading to fulfill the synergy of technology and structure.

Exploration of highly efficient bifunctional electrocatalysts for optimal hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) has been widely carried out, though it still remains a big challenge. Herein, a hierarchical CoO–Co4N@NiFe-LDH (layered-double-hydroxides) heterostructure electrode anchored on nickel foam (NF) is prepared via a developed three-step hydrothermal–nitridation–electrodeposition pathway. The fabricated CoO–Co4N@NiFe-LDH/NF electrode needs low overpotential values of 66 and 231 mV to supply a current density value of 10 mA cm–2 in aqueous solution of KOH (1 M) for HER and OER, respectively. The Tafel slopes and electrochemical impedance spectroscopy results display favorable reaction kinetics throughout the electrolysis process. Subsequently, an alkaline electrolyzer is assembled with CoO–Co4N@NiFe-LDH/NF, which serves both as the anode and cathode, yielding 10 mA cm–2 with a small voltage of 1.529 V and showing a robust stability for 28 h. Impressively, a urine-mediated electrolysis cell shows efficient catalytic activity as well, allowing to mount the sluggish OER during water splitting. To drive the urine-mediated electrolysis cell containing 0.33 M urea, a low voltage of 1.393 V is required, which is about 136 mV lower compared to the urea-free electrolysis cell. This work presents a solid step for the electrocatalytic generation of hydrogen through water splitting by harvesting low energy.

Abiotic stresses such as drought and salinity constantly threaten food security. Biochar as a soil amendment has the potential to ameliorate soil and alleviate drought and salinity stress. Multiple studies have been conducted to evaluate the effect of biochar in alleviating independent drought or salinity stress. However, the potential of biochar in mitigating the combined drought and salinity stress on plants has not been studied so far. Therefore, a pot experiment was conducted in the climate-controlled chamber with the objective to investigate the effect of biochar on growth, physiology, and yield of quinoa under independent and combined drought and salinity stress. Quinoa plants were subjected to three irrigation treatments i.e., full irrigation (FI), deficit irrigation (DI), and alternate root-zone drying irrigation (ARD), two saline water treatments (0 and 400 mM) and two levels of biochar (0% and 5% by weight). In the FI treatment, plants were irrigated daily to maintain pot water-holding capacity. In limited irrigation treatments, 70% water of FI was applied either to the whole pot in DI or to one side of the pot alternating in ARD, respectively. The results showed that combined drought and salinity stress drastically affected growth and performance of quinoa compared to the independent drought or salinity stress. However, soil amendment with biochar had positive effect in mitigating both independent and combined effect of drought and salinity on quinoa plants. Furthermore, biochar amendment in ARD under salinity significantly enhanced plant height, shoot biomass, and grain by 11.7%, 18.8%, and 10.2% as compared with DI under salinity, respectively. In addition, leaf photosynthetic rate (An) and stomatal conductance (gs) decreased under limited saline irrigation. Moreover, the interactive effect of biochar and ARD efficiently adjusted the balance between chemical signal (leaf ABA) and hydraulic signal (leaf water potential). Thus, intrinsic water use efficiency (WUEi) and yield in ARD were significantly enhanced compared to DI, especially under salinity stress. Overall, biochar in combination with ARD might be a wise approach for sustaining crop productivity in salt affected and drought stressed areas of the world to ensure food security.

BACKGROUND: Wintersweet (Chimonanthus praecox), an important ornamental plant, has evolved unique fragrant aroma and winter-flowering properties, which are critical for its successful sexual reproduction. However, the molecular mechanisms underlying these traits are largely unknown in this species. In addition, wintersweet is also a typical representative species of the magnoliids, where the phylogenetic position of which relative to eudicots and monocots has not been conclusively resolved. RESULTS: Here, we present a chromosome-level wintersweet genome assembly with a total size of 695.36 Mb and a draft genome assembly of Calycanthus chinensis. Phylogenetic analyses of 17 representative angiosperm genomes suggest that Magnoliids and eudicots are sister to monocots. Whole-genome duplication signatures reveal two major duplication events in the evolutionary history of the wintersweet genome, with an ancient one shared by Laurales, and a more recent one shared by the Calycantaceae. Whole-genome duplication and tandem duplication events have significant impacts on copy numbers of genes related to terpene and benzenoid/phenylpropanoid (the main floral scent volatiles) biosynthesis, which may contribute to the characteristic aroma formation. An integrative analysis combining cytology with genomic and transcriptomic data reveals biological characteristics of wintersweet, such as floral transition in spring, floral organ specification, low temperature-mediated floral bud break, early blooming in winter, and strong cold tolerance. CONCLUSIONS: These findings provide insights into the evolutionary history of wintersweet and the relationships among the Magnoliids, monocots, and eudicots; the molecular basis underlying floral scent biosynthesis; and winter flowering, and highlight the utility of multi-omics data in deciphering important ornamental traits in wintersweet.

Based on well cores and thin section observations of more than 300 wells from major exploration target areas and formations in the Tarim, Sichuan and Ordos Basins, combined with seismic, well logging and testing data, the types and characteristics of carbonate reservoirs as well as the geologic conditions for their extensive development are analyzed systematically, and their distribution features are summarized. All varieties of marine carbonate reservoirs are developed in China, including three types of large-scale effective reservoirs, which are (1) depositional reef-shoal and dolomite reservoirs, (2) epigenetic dissolution-percolation reservoirs and (3) deep burial-hydrothermal altered reservoirs. Besides sedimentary facies, paleoclimate and paleogeomorphy, other factors controlling the development of deep large-scale effective reservoirs include interstratal and intrastratal dissolution-percolation and burial dolomitization which can be impacted by hydrothermal processes. Large effective reservoirs in deep carbonate rocks are distributed along unconformities and hiatuses in sedimentation, while reservoirs of epigenetic dissolution-percolation type extend from paleohigh uplift zones to lower slope reliefs. The reservoirs are widely distributed in stratified planar forms, and are superposed by multi-stage karstification processes vertically and have obvious heterogeneity controls. Burial dolomitization is restricted by primary sedimentary facies, and can form extensive effective reservoirs in deep layers in layered or stratified shapes. Hydrothermal related reservoirs are always distributed along deep, large faults, forming effective reservoirs in the form of a bead string in vertical direction and band-rod horizontally, which are not restricted by burial depth.

As a product of asexual reproduction in plants, the somatic embryo (SE) differentiates into a new plantlet via a zygotic embryogenesis-like process. Here, we present the phenotypic and cellular differences between SEs and zygotic embryos (ZEs) revealed by histological section scanning using three parallel development stages of the two types of embryos of cotton (Gossypium hirsutum cv. YZ1), including globular, torpedo and cotyledonary-stages. To identify the molecular characteristics of SE development in cotton, the digital gene expression system was used to profile the genes active during SE and ZE development. A total of 4242 differentially expressed genes (DEGs) were identified in at least one developmental stage. Expression pattern and functional classification analysis based on these DEGs reveals that SE development exhibits a transcriptional activation of stress responses. RT-PCR analysis further confirmed enhanced expression levels of stress-related genes in SEs than in ZEs. Experimental stress treatment, induced by NaCl and ABA, accelerated SE development and increased the transcription of genes related to stress response, in parallel with decelerated proliferation of embryogenic calluses under stress treatment. Our data reveal that SE development involves the activation of stress responses, which we suggest may regulate the balance between cell proliferation and differentiation. These results provide new insight into the molecular mechanisms of SE development and suggest strategies that can be used for regulating the developmental processes of somatic embryogenesis.

Accurate monitoring of soil salinization plays a key role in the ecological security and sustainable agricultural development of arid regions. As a branch of artificial intelligence, machine learning acquires new knowledge through self-learning and continuously improves its own performance. The purpose of this study is to combine Sentinel-2 Multispectral Imager (MSI) data and MSI-derived covariates with measured soil salinity data and to apply three machine learning algorithms in modeling to estimate and map the soil salinity in the study sample area. According to the convenient transportation conditions, the study area and sampling quadrat were set up, and the 5-point method was used to collect the soil mixed samples, and 160 soil mixed samples were collected. Kennard–Stone (K–S) algorithm was used for sample classification, 70% for modeling and 30% for verification. The machine learning algorithm uses Support Vector Machines (SVM), Artificial Neural Network (ANN), and Random Forest (RF). The results showed that (1) the average reflectance of each band of the MSI data ranged from 0.21–0.28. According to the spectral characteristics corresponding to different soil electrical conductivity (EC) levels (1.07–79.6 dS m−1), the spectral reflectance of salinized soil in the MSI data ranged from 0.09–0.35. (2) The correlation coefficient between the MSI data and MSI-derived covariates and soil EC was moderate, and the correlation between certain MSI data sets and soil EC was not significant. (3) The SVM soil EC estimation model established with the MSI data set attained a higher performance and accuracy (R2 = 0.88, root mean square error (RMSE) = 4.89 dS m−1, and ratio of the performance to the interquartile range (RPIQ) = 1.96, standard error of the laboratory measurements to the standard error of the predictions (SEL/SEP) = 1.11) than those attained with the soil EC estimation models established with the RF and ANN models. (4) We applied the SVM soil EC estimation model to map the soil salinity in the study area, which showed that the farmland with higher altitudes discharged a large amount of salt to the surroundings due to long-term irrigation, and the secondary salinization of the farmland also caused a large amount of salt accumulation. This research provides a scientific basis for the simulation of soil salinization scenarios in arid areas in the future.

This work studied the antifungal mechanism of dill seed essential oil (DSEO) against Candida albicans. Flow cytometric analysis and inhibition of ergosterol synthesis were performed to clarify the mechanism of action of DSEO on C. albicans. Upon treatment of cells with DSEO, propidium iodide penetrated C. albicans through a lesion in its plasma membrane. DSEO also significantly reduced the amount of ergosterol. These findings indicate that the plasma membrane of C. albicans was damaged by DSEO. The effect of DSEO on the functions of the mitochondria in C. albicans was also studied. We assayed the mitochondrial membrane potential (mtΔψ) using rhodamine 123 and determined the production of mitochondrial dysfunction-induced reactive oxygen species (ROS) via flow cytometry. The effects of the antioxidant l-cysteine (Cys) on DSEO-induced ROS production and the antifungal effect of DSEO on C. albicans were investigated. Exposure to DSEO increased mtΔψ. Dysfunctions in the mitochondria caused ROS accumulation in C. albicans. This increase in the level of ROS production and DSEO-induced decrease in cell viability were prevented by the addition of Cys, indicating that ROS are an important mediator of the antifungal action of DSEO. These findings indicate that the cytoplasmic membrane and mitochondria are the main anti-Candida targets of DSEO.

Summary Soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), available potassium (AK) and pH are key chemical properties for evaluating soil fertility and quality. This study involved the integration of four soil sensors, visible near‐infrared (vis – NIR) spectrometer, mid‐infrared (mid‐IR) spectrometer, portable X‐ray fluorescence (PXRF) analyser and laser‐induced breakdown spectroscopy (LIBS), to achieve rapid measurement of these soil properties. A genetic algorithm and partial least‐squares regression (GA – PLSR) were used to select characteristic bands to reduce data redundancy. We then calibrated models from three aspects: models using partial least‐squares regression (PLSR) based on single sensor data, models using PLSR based on fused sensor data, involving data combined from the four sensors into a new dataset to create a data fusion (DF) model, and models with Bayesian model averaging (BMA) based on prediction results of fused sensor data, involving prediction results combined from the four sensors into a new dataset to form the BMA model. The results showed the following. (i) For the single sensor, the predictive performance decreased as follows: mid‐IR > vis–NIR > LIBS > PXRF. (ii) Compared with the single sensor approach, the DF approach slightly improved or even reduced prediction accuracy and caused a large amount of redundancy. We suggest that this approach is not able to improve predictive ability. (iii) The BMA approach achieved the best prediction for the six soil properties. Our findings suggest that model averaging of vis – NIR, mid‐IR and LIBS could be a reliable and stable approach for the fast measurement of soil properties. Highlights We used four proximal soil sensors to evaluate six key properties for evaluating soil fertility and quality. GA–PLSR was used to select characteristic bands. We compared predictions of six soil properties from single sensor, DF and BMA approaches. BMA predictions were more accurate than predictions from single and fused sensor data.

As an allotetraploid, most genes have multiple copies that belong to At and Dt subgenomes in cotton (Gossypium hirsutum). Allotetraploid cotton genome is very complex (AADD, 2n = 4x = 52) with a large genome size of 2.5 Gb. As a result, different types of genome editing tools are desirable to improve the functional genomic research in cotton. CRISPR/Cpf1 (Cas12a) is a novel member of the CRISPR/Cas system from Alicyclobacillus acidoterrestris, and currently, three kinds of Cpf1 are commonly used in genome editing, namely AsCpf1, LbCpf1 and FnCpf1. In 2015, type V CRISPR/Cpf1 (Cas12a) was applied in human cells to create gene knockout mutation for the first time (Zetsche et al., 2015). Several applications in rice showed that LbCpf1 exhibited higher genome editing efficiency than AsCpf1 and spCas9 (Tang et al., 2017, 2018). The LbCpf1 used in this study is from Lachnospiraceae bacterium ND2006 (LbCpf1, NCBI accession number: NZ_JNKS01000011; gene locus_tag: T521_RS08385) consisting of 1228 amino acids (Zhong et al., 2018). Unlike the Cas9 requiring higher G/C content in PAM sites, the PAM sequence of Cpf1 is 5′-TTTV-3′, which prefers genes with higher A/T content. The crRNA of Cpf1 is 23 nt in length (the PAM sequence is upstream of the target sites). The editing process of Cpf1 does not require the participation of tracrRNA, and the pre-crRNA can be self-modified into a mature crRNA. The Cpf1 binds to the mature crRNA to form a binary complex, and then, this complex binds to the target DNA to form a ternary complex (Xu et al., 2018). Recently, several groups have successfully applied the CRISPR/Cpf1 system in plant species such as rice, soya bean, tobacco and maize (Lee et al., 2019; Tang et al., 2017, 2019). Notably, no off-target mutations were detected at the potential off-target sites in the LbCpf1-edited rice plant, suggesting that LbCpf1 is a robust and precise genome editing tool after the Cas9 system (Tang et al., 2018). However, this promising system has not been tested in cotton yet. Here, we established an efficient CRISPR/LbCpf1 system to expand the scope of genome editing in allotetraploid cotton for the first time. To test the efficiency of LbCpf1 system in cotton, we constructed an LbCpf1 plasmid vector that harbors 23-nt crRNA to target the cotton endogenous gene cloroplastos alterados (GhCLA). A previous work has shown that tRNA-sgRNA transcription unit is very effective to enhance the sgRNA transcription in CRISPR/Cas9 system for cotton genome editing (Wang et al., 2018). Therefore, we designed the crRNA following our previous work and conducted a vector named pGhRBE3-Cpf1-GhCLA1 targeting GhCLA1 gene (Figure 1a). Several independent regenerated plants were obtained through Agrobacterium-mediated transformation following our previous protocol (Wang et al., 2018). In total, 92 independent regenerated plants were obtained in the T0 generation after the genetic transformation containing LbCpf1 plasmid vector. Mutations in the generated transgenic plants were detected by high-throughput (Hi-Tom) sequencing and Sanger sequencing (Liu et al., 2019). The targeted region of GhCLA1 was amplified by PCR using site-specific primers and used for mutation detection. The PCR products of the 92 T0 plants containing the target sites were pooled and purified to conduct high-throughput sequencing, whereas Sanger sequencing results showed that 80 out of 92 (87% efficiency) independent T0 plants were detected with mutations at the target site, suggesting the robust editing activity of LbCpf1 in cotton plants. On the other hand, Hi-TOM data (original data have been submitted to http://gsa.big.ac.cn/) revealed that each individual plant contained diverse editing extent. Samples with target mutation ratio (the reads with target mutations/total reads of the target site) lower than 1% were considered as negative (no edition at the target site), whereas those samples with mutation ratio > 1% accounted as mutated in which mutations truly occurred at the target site. Based on this criterion, 12 individuals of the 92 independent plants were negative without any obvious targeted mutations, which are completely consistent with the Sanger sequencing data. The remaining 80 individuals were edited with mutation extent ranging from 1% to 94.12% (Figure 1b). Those plants (8 out of 80 T0 plants) with higher target mutations ratio (around 80% mutation ratio revealed by Hi-TOM, indicated with red arrow in Figure 1b) exhibited homozygous phenotype (albino seedlings), while the plantlets with <80% mutation ratio were chimeric mutants with white spots in the leaves and the stems. The editing extent per plant was mainly concentrated in 20%–60% (Figure 1b). In summary, the CRISPR/Cpf1 system has high gene editing efficiency in cotton. Most of the generated T0 plants have been mutated at the target site. The editing window and profiling of CRISPR/Cpf1 system in the edited T0 plants were systematically analysed in this report. Since no target mutation occurs preceding the PAM sequence and within the PAM sequence, we investigated the editing downstream of the PAM sequence. The main editing window of CRISPR/Cpf1 ranged between the +13 and +25 downstream of the PAM sequence (Figure 1c). Comparing with base substitution and insertion, the CRISPR/Cpf1 system prefers to induce DNA deletion at the target sites rather than base substitution or insertion. Only deletions were detected at the crRNA target sites in all the 80 T0 plants. Among them, 68 samples were edited in At and Dt subgenomes simultaneously, and the rest of the samples were edited only in At or Dt subgenome (Figure 1d). Deletion size and proportion of each target mutation in T0 plants were also analysed and are shown in Figure 1e. The deletion sizes ranged from 3 to 28 bp in length, and the deletion size of majority is from 5 to 12 bp (Figure 1e), which are larger than the average deletion size (1–5 bp) induced by CRISPR/Cas9 in cotton genome (Wang et al., 2018). Therefore, we speculate that the CRISPR/Cpf1 system prefers to generate large size deletions in cotton genome editing. Generally, GhCLA1-mutated plants (homozygous mutants) should be albino if the GhCLA1 gene was completely knocked out. However, in this report, all the analysed T0 plants exhibited chimeric phenotype (with white spots in the leaves and stems) (Figure 1f, upper panel) because the homozygous mutants of GhCLA1 cannot survive in the soil. The chimeric phenotype in the T0 generation was also very common in the CRISPR/Cas9-edited cotton plants due to the gene redundancy. Each gene in the allotetraploid cotton genome has almost four loci at At and Dt subgenomes, and to obtain the homozygous mutants, all the gene loci should be edited simultaneously (Wang et al., 2018). For further determination of whether the target sites of the GhCLA1 gene in the heterozygous plants were edited or not, the following three types of leave samples were analysed: a whole piece of leaf with white and green parts (Chimeric-1 and 2), a full white leaf piece (White-1) and full green leaf piece (Green-1), and all these samples were taken from the same T0 plant (S6). The Sanger sequencing data showed that only one copy of GhCLA1 at At or Dt subgenome was mutated in Chimeric-1 and 2 samples and in the White-1 sample, and all the loci at At and Dt subgenomes gained the target mutations. Obviously, there are no target mutations in At nor Dt subgenomes of the Green-1 sample (Figure 1g, upper panel). To detect the inheritance of the editing from T0 to T1 generation, the phenotype of T1 progeny from 4 chimeric T0 plants was recorded and all these four T1 lines exhibited inherited mutations at the target sites. As shown in line S6, some of the progeny were homozygous with completely albino seedlings and all the loci in the At and Dt subgenomes were mutated simultaneously, but their growth was significantly stunted. Notably, almost half of T1 plants from line S6 still showed chimeric phenotype just like their parental T0 plants with white spots scattered in the green leaves. The Sanger sequencing data reveal the same genotype in T1 progeny (White-1 and White-2) as the chimeric samples (Chimeric-1 and 2) from the T0 parental plant (S6) with partial mutation in the At or Dt subgenome, and no target mutation was detected in the green T1 plant (sample Green-1) (Figure 1f, lower panel). The other three T1 lines showed similar phenotypes with line S6 (some plants are homozygous and others are chimeric). Depending on the genotype profiling of T1 plants, most editing types in T0 plants were faithfully inherited to all the T1 progenies (Albino plants, chimeric plants and green plants) and confirmed by Sanger sequencing (Figure 1g, lower panel). In addition to the on-target editing of the CRISPR/Cpf1 in cotton, the off-target effects were also investigated in this report. We identified the most six potential off-target sites based on the method described in sgRNAcas9_3.0.5 software and our recent report (Xie et al., 2014). These potential off-target sites of T1 plants were tasted by Sanger sequencing using their site-specific PCR products. Sequencing results showed that no off-target effects were detected in all the predicted off-target sites (Figure 1h–i), concluding that CRISPR/Cpf1 system is highly specific and can be a good option for cotton genome editing. Overall, in this study, we successfully built a site genome editing in allotetraploid cotton with 87% editing efficiency and no off-target effects using CRISPR/Cpf1 system. Our results are comparable with the editing efficiency in rice and maize (Lee et al., 2019; Tang et al., 2017; Xu et al., 2018). More importantly, the phenotypic and the genetic edition occurred in the T0 generation were inherited faithfully to their progenies and some homozygous mutants were obtained in the T1 generation. In the future, whole-genome sequencing (WGS) will be applied to evaluate the off-target of CRISPR/Cpf1 system in cotton. These results support the finding that the CRISPR/Cpf1 system is a highly specific and efficient system in plant genome editing, which will be a very promising alternative of the CRISPR/Cas9 system in cotton. This work was supported by a grant from National Key Research and Development Plan (2016YFD0100203-9), a grant from National R&D Project of Transgenic Crops of Ministry of Science and Technology of China (2018ZX08010-05B) and Fundamental Research Funds for the Central Universities (2013PY064, 2662015PY028, 2662015PY091 and 0900206328). The authors declare no conflicts of interest.

Gut microbiota plays multiple important roles in intestinal and physiological homeostasis, and using fecal microbiota transplantation (FMT) to reprogram gut microbiota has demonstrated promise for redressing intestinal and physiological disorders. This study tested the alterations in reprogramming efficiency caused by different gut preparation procedures and explored the associated underlying mechanisms. We prepared the guts of mice for FMT by administering one of the three most-clinically used pretreatments [antibiotics, bowel cleansing (BC) solution, or no pretreatment], and we found that preparing the gut with antibiotics induced a more efficient modification of the gut bacterial community than was induced by either of the other two pretreatment types. The increased efficiency of antibiotic treatment appeared to occur via increasing the xenomicrobiota colonization. Further analysis demonstrated that antibiotic treatment of mice induced intestinal microbiota disruption, mostly by expelling antibiotic-sensitive bacteria, while the indigenous microbiota was maintained after treatment with a BC solution or in the absence of pretreatment. The amount of antibiotic-resistant bacteria increased shortly after antibiotics usage but subsequently decreased after FMT administration. Together, these results suggest that FMT relied on the available niches in the intestinal mucosa and that preparing the gut with antibiotics facilitated xenomicrobiota colonization in the intestinal mucosa, which thus enhanced the overall gut microbiota reprogramming efficiency.

Phytohemical investigation on the heartwood of Dalbergia odorifera resulted in the isolation of nine flavonoids. Their structures were elucidated as sativanone (1), (3R)-vestitone (2), (3R)-2',3',7-trihydroxy-4'-methoxyisoflavanone (3), (3R)-4'-methoxy-2',3,7-trihydroxyisoflavanone (4), carthamidin (5), liquiritigenin (6), isoliquiritigenin (7), (3R)-vestitol (8), and sulfuretin (9) based on their spectral data. All compounds were evaluated for their inhibitory activity against Ralstonia solanacearum. This is the first report about anti-R. solanacearum activity of the compounds from D. odorifera.