PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants.

N 6-methyladenosine (m6A), which is the mostly prevalent modification in eukaryotic mRNAs, is involved in gene expression regulation and many RNA metabolism processes. Accurate prediction of m6A modification is important for understanding its molecular mechanisms in different biological contexts. However, most existing models have limited range of application and are species-centric. Here we present PEA-m6A, a unified, modularized and parameterized framework that can streamline m6A-Seq data analysis for predicting m6A-modified regions in plant genomes. The PEA-m6A framework builds ensemble learning-based m6A prediction models with statistic-based and deep learning-driven features, achieving superior performance with an improvement of 6.7% to 23.3% in the area under precision-recall curve compared with state-of-the-art regional-scale m6A predictor WeakRM in 12 plant species. Especially, PEA-m6A is capable of leveraging knowledge from pretrained models via transfer learning, representing an innovation in that it can improve prediction accuracy of m6A modifications under small-sample training tasks. PEA-m6A also has a strong capability for generalization, making it suitable for application in within- and cross-species m6A prediction. Overall, this study presents a promising m6A prediction tool, PEA-m6A, with outstanding performance in terms of its accuracy, flexibility, transferability, and generalization ability. PEA-m6A has been packaged using Galaxy and Docker technologies for ease of use and is publicly available at https://github.com/cma2015/PEA-m6A.

IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study.

The advent of high-throughput sequencing technologies has led to the production of a significant amount of omics data in plants, which serves as valuable assets for conducting cross-species multi-omics comparative analysis. Nevertheless, the current dearth of comprehensive platforms providing evolutionary annotation information and multi-species multi-omics data impedes users from systematically and efficiently performing evolutionary and functional analysis on specific genes. In order to establish an advanced plant multi-omics platform that provides timely, accurate, and high-caliber omics information, we collected 7 distinct types of omics data from 6 monocots, 6 dicots, and 1 moss, and reanalyzed these data using standardized pipelines. Additionally, we furnished homology information, duplication events, and phylostratigraphic stages of 13 species to facilitate evolutionary examination. Furthermore, the integrative plant omics platform (IPOP) is bundled with a variety of online analysis tools that aid users in conducting evolutionary and functional analysis. Specifically, the Multi-omics Integration Analysis tool is available to consolidate information from diverse omics sources, while the Transcriptome-wide Association Analysis tool facilitates the linkage of functional analysis with phenotype. To illustrate the application of IPOP, we conducted a case study on the YTH domain gene family, wherein we observed shared functionalities within orthologous groups and discerned variations in evolutionary patterns across these groups. To summarize, the IPOP platform offers valuable evolutionary insights and multi-omics data to the plant sciences community, effectively addressing the need for cross-species comparison and evolutionary research platforms. All data and modules within IPOP are freely accessible for academic purposes (http://omicstudio.cloud:4012/ipod/).

Genome optimization via virtual simulation to accelerate maize hybrid breeding.

The employment of doubled-haploid (DH) technology in maize has vastly accelerated the efficiency of developing inbred lines. The selection of superior lines has to rely on genotypes with genomic selection (GS) model, rather than phenotypes due to the high expense of field phenotyping. In this work, we implemented 'genome optimization via virtual simulation (GOVS)' using the genotype and phenotype data of 1404 maize lines and their F1 progeny. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' or 'advantageous alleles' in a genetic pool. Such a virtually optimized genome, although can never be developed in reality, may help plot the optimal route to direct breeding decisions. GOVS assists in the selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. The assumption is that the more fragments of optimal genotypes a line contributes to the assembly, the higher the likelihood of the line favored in the F1 phenotype, e.g. grain yield. Compared to traditional GS method, GOVS-assisted selection may avoid using an arbitrary threshold for the predicted F1 yield to assist selection. Additionally, the selected lines contributed complementary sets of advantageous alleles to the virtual genome. This feature facilitates plotting the optimal route for DH production, whereby the fewest lines and F1 combinations are needed to pyramid a maximum number of advantageous alleles in the new DH lines. In summary, incorporation of DH production, GS and genome optimization will ultimately improve genomically designed breeding in maize. Short abstract: Doubled-haploid (DH) technology has been widely applied in maize breeding industry, as it greatly shortens the period of developing homozygous inbred lines via bypassing several rounds of self-crossing. The current challenge is how to efficiently screen the large volume of inbred lines based on genotypes. We present the toolbox of genome optimization via virtual simulation (GOVS), which complements the traditional genomic selection model. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' in a breeding population, and then assists in selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. Availability of GOVS (https://govs-pack.github.io/) to the public may ultimately facilitate genomically designed breeding in maize.

Global hypermethylation of the N6-methyladenosine RNA modification associated with apple heterografting.

Grafting can facilitate better scion performance and is widely used in plants. Numerous studies have studied the involvement of mRNAs, small RNAs, and epigenetic regulations in the grafting process. However, it remains unclear whether the mRNA N6-methyladenosine (m6A) modification participates in the apple (Malus x domestica Borkh.) grafting process. Here, we decoded the landscape of m6A modification profiles in 'Golden delicious' (a cultivar, Gd) and Malus prunifolia 'Fupingqiuzi' (a unique rootstock with resistance to environmental stresses, Mp), as well as their heterografted and self-grafted plants. Interestingly, global hypermethylation of m6A occurred in both heterografted scion and rootstock compared with their self-grafting controls. Gene Ontology (GO) term enrichment analysis showed that grafting-induced differentially m6A-modified genes were mainly involved in RNA processing, epigenetic regulation, stress response, and development. Differentially m6A-modified genes harboring expression alterations were mainly involved in various stress responses and fatty acid metabolism. Furthermore, grafting-induced mobile mRNAs with m6A and gene expression alterations mainly participated in ABA synthesis and transport (e.g. carotenoid cleavage dioxygenase 1 [CCD1] and ATP-binding cassette G22 [ABCG22]) and abiotic and biotic stress responses, which might contribute to the better performance of heterografted plants. Additionally, the DNA methylome analysis also demonstrated the DNA methylation alterations during grafting. Downregulated expression of m6A methyltransferase gene MdMTA (ortholog of METTL3) in apples induced the global m6A hypomethylation and distinctly activated the expression level of DNA demethylase gene MdROS1 (REPRESSOR OF SILENCING 1) showing the possible association between m6A and 5mC methylation in apples. Our results reveal the m6A modification profiles in the apple grafting process and enhance our understanding of the m6A regulatory mechanism in plant biological processes.

Long-range, high-precision optical calibration path based on an optoelectronic oscillator.

We propose a laser ranging calibration optical path system using multiple optoelectronic oscillators (OEOs) that provides long range, high precision, low cost and high stability. A phase locked loop is used to control the length of the calibration optical path, which is measured with high precision by alternating the oscillations between the measurement loop and the reference loop. The calibration optical path length exceeds 9000 m with the stability of 6.8 µm during 3 minutes, and the relative measurement accuracy of the calibration optical path reaches 6.9 × 10-10.

Efficiently tuning the electrical performance of PBTTT-C14 thin film viainsitucontrollable multiple precursors (Al2O3:ZnO) vapor phase infiltration.

Conjugated polymer-based organic/inorganic hybrid materials become the current research frontier and show great potential to integrate flexible polymers and rigid solid materials, which have been widely used in the field of various flexible electronics and optical devices. In this study, based on the multiple vapor phase infiltration (VPI) process, various precursor molecules (diethylzinc DEZ, trimethylaluminum TMA, H2O) are applied for thein situmodification of PBTTT-C14 films. The conductivity of the PBTTT-C14/Al2O3:ZnO (AZO) film is significantly enhanced, and the maximum value of conductivity is 1.16 S cm-1, which is eight orders of magnitude higher than the undoped PBTTT-C14 thin film. Here, the change of morphologies and crystalline states are analyzed via SEM, AFM, and XRD. And the chemical changes during the VPI process of PBTTT-C14 are characterized through Raman, XPS, and UV-vis. During the AZO VPI process, the formation of new ZnS matrix in the polymer subsurface can generate new additional electron conduction pathways through the crosslinking of polymer chains with inorganic materials, and the addition of Al2O3can bring about the increase of average grain size of ZnO crystals, which is also benefit to the conductivity increase of PBTTT-C14 thin film. Generally, the synergistic effect between the inorganic and polymer constituents results in the significantly enhancement of the conductivity of PBTTT-C14/AZO thin films.

Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.).

The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.

Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants.

Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the evolutionary role of DNA modifications, and little is understood about the influence of posttranscriptional RNA modifications on genome evolution. To explore the evolutionary significance of RNA modifications, we generated transcriptome-wide profiles of N6-methyladenosine (m6A), the most prevalent internal modification of mRNA, for 13 representative plant species spanning over half a billion years of evolution. These data reveal the evolutionary conservation and divergence of m6A methylomes in plants, uncover the preference of m6A modifications on ancient orthologous genes, and demonstrate less m6A divergence between orthologous gene pairs with earlier evolutionary origins. Further investigation revealed that the evolutionary divergence of m6A modifications is related to sequence variation between homologs from whole-genome duplication and gene family expansion from local-genome duplication. Unexpectedly, a significant negative correlation was found between the retention ratio of m6A modifications and the number of family members. Moreover, the divergence of m6A modifications is accompanied by variation in the expression level and translation efficiency of duplicated genes from whole- and local-genome duplication. Our work reveals new insights into evolutionary patterns of m6A methylomes in plant species and their implications, and provides a resource of plant m6A profiles for further studies of m6A regulation and function in an evolutionary context.

Changes in m6A RNA methylation are associated with male sterility in wolfberry.

BACKGROUND: N6-methyladenosine (m6A) modification is the most abundant type of RNA modification in eukaryotic cells, playing pivotal roles in multiple plant growth and development processes. Yet the potential role of m6A in conferring the trait of male sterility in plants remains unknown. RESULTS: In this study, we performed RNA-sequencing (RNA-Seq) and m6A-sequencing (m6A-Seq) of RNAs obtained from the anther tissue of two wolfberry lines: 'Ningqi No.1' (LB1) and its natural male sterile mutant 'Ningqi No.5' (LB5). Based on the newly assembled transcriptome, we established transcriptome-wide m6A maps for LB1 and LB5 at the single nucleus pollen stage. We found that the gene XLOC_021201, a homolog of m6A eraser-related gene ALKBH10 in Arabidopsis thaliana, was significantly differentially expressed between LB1 and LB5. We also identified 1642 and 563 m6A-modified genes with hypermethylated and hypomethylated patterns, respectively, in LB1 compared with LB5. We found the hypermethylated genes significantly enriched in biological processes related to energy metabolism and lipid metabolism, while hypomethylation genes were mainly linked to cell cycle process, gametophyte development, and reproductive process. Among these 2205 differentially m6A methylated genes, 13.74% (303 of 2205) were differentially expressed in LB1 vis-à-vis LB5. CONCLUSIONS: This study constructs the first m6A transcriptome map of wolfberry and establishes an association between m6A and the trait of male sterility in wolfberry.

Low Dimensional, Metal-Free, Hydrazinium Halide Perovskite-Related Single Crystals and Their Use as X-Ray Detectors.

Metal-free halide perovskites (MFHaPs) have garnered significant attention in recent years due to their desirable properties, such as low toxicity, light weight, chemical versatility, and potential for optoelectronics. MFHaPs with the formula A2+ B+ X-3 (where A is a large organic divalent cation, B+ is typically NH4 + , and X is a halide) have been studied extensively, but few studies have examined alternative cations at the B position. This paper reports the synthesis of three MFHaP-related single crystals, DABCO-N2 H5 -X3 (DABCO = N-N-diazabicyclo[2.2.2]octonium, X = Br and I) and (DABCO)3 -N2 H5 (NH4 )2 Cl9 , which feature hydrazinium (N2 H5 ) at the B position. The crystals have a perovskite-like, one-dimensional, edge-connected structure and exhibit optical and band structure properties. The crystals were then tested as X-ray detectors, where they showed excellent photoresponsivity, stability, and low background noise, owing to the large semi-gap that dictates long lifetimes. The detectors exhibited sensitivity as high as 1143 ± 10 µC Gyair -1 cm-2 and a low detection limit of 2.68 µGy s-1 at 10 V. The researchers suggest that the stronger hydrogen bonding in N2 H5 + compounds compared to NH4 + MFHaPs may contribute to the detectors' enhanced stability.

Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS.

Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal or other dimensions. TS has been associated with human diseases, plant development and stress responses. Its investigation is often hampered by a lack of suitable tools allowing comprehensive and flexible TS analysis for high-throughput RNA sequencing (RNA-Seq) data. Here, we present deepTS, a user-friendly web-based implementation that enables a fully interactive, multifunctional identification, visualization and analysis of TS events for large-scale RNA-Seq datasets from pairwise, temporal and population experiments. deepTS offers rich functionality to streamline RNA-Seq-based TS analysis for both model and non-model organisms and for those with or without reference transcriptome. The presented case studies highlight the capabilities of deepTS and demonstrate its potential for the transcriptome-wide TS analysis of pairwise, temporal and population RNA-Seq data. We believe deepTS will help research groups, regardless of their informatics expertise, perform accessible, reproducible and collaborative TS analyses of large-scale RNA-Seq data.

High-precision micro-displacement sensing based on an optical filter and optoelectronic oscillators.

High-precision micro-displacement sensing based on an optical filter and optoelectronic oscillators (OEOs) is proposed and experimentally demonstrated. In this scheme, an optical filter is utilized to separate the carriers of the measurement and reference OEO loops. Through the optical filter, the common path structure can be consequently achieved. The two OEO loops share all optical/electrical components, except for the micro-displacement to be measured. Measurement and reference OEOs are alternately oscillated by using a magneto-optic switch. Therefore, self-calibration is achieved without additional cavity length control circuits, greatly simplifying the system. A theoretical analysis of the system is developed, and this analysis is then demonstrated with experiments. Regarding the micro-displacement measurements, we achieved a sensitivity of 312.058 kHz/mm and a measurement resolution of 356 pm. The measurement precision is less than 130 nm over a measurement range of 19 mm.

Giant muscle hydatid in lower extremity: a rare case with neurological symptoms as the first manifestation.

BACKGROUND: Human hydatid disease typically occurs in organs such as the liver and kidney. Primary solitary intramuscular hydatid disease, however, is rare. CASE PRESENTATION: We report a case of a giant muscle hydatid in the lower extremity, with neurological symptoms as the first manifestation. The symptoms specifically manifested as intermittent pain in the right lower extremity and numbness in the sole of the right foot. However, there were no obvious abnormalities detected in electromyography and lumbar MRI. Subsequent ultrasonography and calf MRI showed that the patient had cystic lesions in the calf. The patient was initially diagnosed with a muscle hydatid cyst. Treatment involved complete surgical excision of the lesion, and the diagnosis of a hydatid cyst was confirmed through macroscopic and microscopic histopathological examination after the mass was excised. The patient was given oral albendazole, and no recurrence was observed during the 12 months of follow-up. CONCLUSIONS: This case underscores the need to consider hydatid disease when diagnosing soft tissue masses in muscles, particularly in endemic areas. Patients may initially present with atypical symptoms like peripheral nerve issues.

Complications associated with single-level bone transport for the treatment of tibial bone defects caused by fracture-related infection.

BACKGROUND: The purpose of this study was to report the outcomes of single-level bone transport with a unilateral external fixator for treatment of proximal, intermediate and distal tibial bone defects caused by fracture-related infection (FRI) and compare their complications. METHODS: The clinical records and consecutive X-ray photographs of patients with tibial bone defects treated by single-level bone transport using a unilateral external fixator (Orthofix Limb Reconstruction System) were analyzed retrospectively, from January 2012 to December 2018. Patients were divided into the proximal group (P, n = 19), intermediate group (I, n = 25), and distal group (D, n = 18) according to the location of the tibial bone defect. The Association for the Study and Application of the Method of Ilizarov (ASAMI) standard was applied to assess the bone and functional outcomes and postoperative complications evaluated by the Paley classification. RESULTS: A total of 62 participants were included in this study, with a median age of 36 ± 7.14 years. Sixty patients with tibial bone defects caused by FRI were successfully treated by single-level bone transport using a unilateral external fixator, with a mean bone union time (BUT) of 7.3 ± 1.71 months. According to the ASAMI criteria, there were statistical differences in bone and function results between the three groups (P vs. I vs. D, P < 0.001). The excellent and good rate of bone result in the intermediate group was higher than the other (P vs. I vs. D, 73.6% vs. 84% vs. 66.7%), and the excellent and good rate of function result in the proximal group was the highest (P vs. I vs. D, 84.2% vs. 80% vs. 73.3%). Complications were observed in 29 out of 62 patients (46.7%), with pin tract infection being the most common (14.8%), followed by axial deviation (14.8%), muscle contractures (12.7%), joint stiffness (12.7%), and soft tissue incarceration (12.7%). Other complications included delayed consolidation (12.7%), delayed union (6.3%), nonunion (4.2%), and neurological injury (8.5%). Two patients (3.2%) required below-knee amputation due to uncontrollable infection and previous surgery failure. CONCLUSIONS: Pin tract infection was the most common complication in tibial bone transport using an external fixator. Complications of distal tibial bone transport are more severe and occur at a higher rate than in other parts. Axial deviation mostly occurred in the intermediate tibial bone transport.

Influence mechanism of awns on wheat grain Pb absorption: Awns' significant contribution to grain Pb was mainly originated from their direct absorption of atmospheric Pb at the late grain-filling stage.

The spike is the organ that contributes the most to lead (Pb) accumulation in wheat grains. However, as an important photosynthetic and transpiration tissue in spike, the role of awn in wheat grain Pb absorption remains unknown. A field experiment was conducted to investigate the influence mechanism of awn on grain Pb accumulation through two comparative treatments: with and without awns (de-awned treatment). The de-awned treatment decreased wheat yield by 4.1 %; however, it significantly lowered the grain Pb accumulation rate at the late filling stage (15 days after anthesis) and led to a 22.8 % decrease in grain Pb concentration from 0.57 to 0.44 mg·kg-1. Moreover, the relative contribution of awn-to-grain Pb accumulation gradually increased with the filling process, finally reaching 26.6 % at maturity. In addition, Pb isotope source analysis indicated that the Pb in the awn and grain mainly originated from atmospheric deposition, and the de-awned treatment decreased the proportion of grain Pb from atmospheric deposition by 8.9 %. Microstructural observations further confirmed that the contribution of awns to grain Pb accumulation mainly originated from their direct absorption of atmospheric Pb. In conclusion, awns play an important role in wheat grain Pb absorption at the late grain-filling stage; planting awnless or short-awn wheat varieties may be the simplest and effective environmental management measure to reduce the health risks of Pb in wheat in regions with serious atmospheric Pb contamination.

Responses of maize (Zea mays L.) seedlings growth and physiological traits triggered by polyvinyl chloride microplastics is dominated by soil available nitrogen.

As a burgeoning pollutant, microplastics (MPs) has elicited global concern. However, ecological effects and mechanisms of MPs on plant-soil system are still poorly understood. In the present study, the impacts of polyvinyl chloride microplastics (PVC-MPs) on maize (Zea mays L.) seedlings growth and physiological traits and soil properties were discussed through a 30-day pot experiment. Results showed that PVC-MPs had greater toxicity effect on seedlings shoot biomass than root biomass. To defense the impact of PVC-MPs, the superoxide dismutase and catalase activities in seedlings leaf were stimulated. Moreover, the adhesion of MPs on soil particles increased, and soil microorganism, enzymes, and nutrients were altered significantly with increasing content of PVC-MPs. Notably, soil nitrate nitrogen decreased significantly with increasing content of PVC-MPs, whereas soil ammonium nitrogen was promoted under lower contents (0.1% and 1%) of PVC-MPs. Redundancy analysis indicated that soil nitrate nitrogen and ammonium nitrogen can explain 87.4% and 7.7% of variation in maize seedlings growth and physiological traits, respectively. These results display that maize seedlings shoot is more susceptible to the impact of PVC-MPs and soil available nitrogen is the primary limiting factor on maize seedlings growth and physiological traits triggered by PVC-MPs. Impacts of PVC-MPs on maize seedlings growth and physiological traits by nitrogen depletion lead to the possible yield and economic loess and potential risks due to the over use of nitrogen fertilizers.

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.

A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, resulting in the loss of significant biological information and insights. To fill this gap, we present Comprehensive Assembly and Functional annotation of Unmapped RNA-Seq data (CAFU), a Galaxy-based framework that can facilitate the large-scale analysis of unmapped RNA sequencing (RNA-Seq) reads from single- and mixed-species samples. By taking advantage of machine learning techniques, CAFU addresses the issue of accurately identifying the species origin of transcripts assembled using unmapped reads from mixed-species samples. CAFU also represents an innovation in that it provides a comprehensive collection of functions required for transcript confidence evaluation, coding potential calculation, sequence and expression characterization and function annotation. These functions and their dependencies have been integrated into a Galaxy framework that provides access to CAFU via a user-friendly interface, dramatically simplifying complex exploration tasks involving unmapped RNA-Seq reads. CAFU has been validated with RNA-Seq data sets from wheat and Zea mays (maize) samples. CAFU is freely available via GitHub: https://github.com/cma2015/CAFU.

High-precision micro-displacement measurement method based on alternately oscillating optoelectronic oscillators.

We propose a high-precision micro-displacement measurement method based on alternately oscillating optoelectronic oscillators (OEOs). This method uses a reference loop to compensate for the change in the measuring loop length except for the displacement to be measured. Therefore, self-calibration is realized without using a phase-locked loop to control the loop length, greatly simplifying the system. The measurement range is 20 mm, and the measurement precision is <300 nm, which is limited by the incomplete consistency between the reference and the measuring loops, with the exception of the displacement to be measured and environmental disturbances resulting from the spatial optical path.

Greatly increased electrical conductivity of PBTTT-C14 thin film via controllable single precursor vapor phase infiltration.

Doping is an important strategy for effectively regulating the charge carrier concentration of semiconducting materials. In this study, the electronic properties of organic-inorganic hybrid semiconducting polymers, synthesized viain situcontrolled vapor phase infiltration (VPI) of poly[2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT-C14) with the metal precursors molybdenum pentachloride (MoCl5) and titanium tetrachloride (TiCl4), were altered and characterized. The conductivities of the infiltration-doped PBTTT-C14 thin films were enhanced by up to 9 and 4 orders of magnitude, respectively. The significantly improved electrical properties may result from interactions between metal atoms in the metal precursors and sulfur of the thiophene rings, thus forming new chemical bonds. Importantly, VPI doping has little influence on the structure of the PBTTT-C14 thin films. Even if various dopant molecules infiltrate the polymer matrix, the interlayer spacing of the films will inevitably expand, but it has negligible effects on the overall morphology and structure of the film. Also, Lewis acid-doped PBTTT-C14 thin films exhibited excellent environmental stability. Therefore, the VPI-based doping process has great potential for use in processing high-quality conductive polymer films.

The crystal structure of Cpf1 in complex with CRISPR RNA.

The CRISPR-Cas systems, as exemplified by CRISPR-Cas9, are RNA-guided adaptive immune systems used by bacteria and archaea to defend against viral infection. The CRISPR-Cpf1 system, a new class 2 CRISPR-Cas system, mediates robust DNA interference in human cells. Although functionally conserved, Cpf1 and Cas9 differ in many aspects including their guide RNAs and substrate specificity. Here we report the 2.38 Å crystal structure of the CRISPR RNA (crRNA)-bound Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1). LbCpf1 has a triangle-shaped architecture with a large positively charged channel at the centre. Recognized by the oligonucleotide-binding domain of LbCpf1, the crRNA adopts a highly distorted conformation stabilized by extensive intramolecular interactions and the (Mg(H2O)6)(2+) ion. The oligonucleotide-binding domain also harbours a looped-out helical domain that is important for LbCpf1 substrate binding. Binding of crRNA or crRNA lacking the guide sequence induces marked conformational changes but no oligomerization of LbCpf1. Our study reveals the crRNA recognition mechanism and provides insight into crRNA-guided substrate binding of LbCpf1, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.