Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping.

MOTIVATION: Primer design is a routine practice for modern molecular biology labs. Bioinformatics tools like primer3 and primer-blast have standardized the primer design for a specific region. However, large-scale primer design, especially for genome-wide screening, is still a labor-intensive job for most wet-lab researchers using these pipelines. RESULTS: Here, we present the primerdiffer pipeline, which can be used to batch design primers that differentiate haplotypes on a large scale with precise false priming checking. This command-line interface (CLI) pipeline includes greedy primer search, local and global in silico PCR-based false priming checking, and automated best primer selection. The local CLI application provides flexibility to design primers with the user's own genome sequences and specific parameters. Some species-specific primers designed to genotype the hybrid introgression strains from Caenorhabditis briggsae and Caenorhabditis nigoni have been validated using single-worm PCR. This pipeline provides the first CLI-based large-scale primer design tool to differentiate haplotypes in any targeted region. AVAILABILITY AND IMPLEMENTATION: The open-source python modules are available at github (https://github.com/runsheng/primerdiffer, https://github.com/runsheng/primervcf) and Python package index (https://pypi.org/project/primerdiffer/, https://pypi.org/project/primervcf/).

Least Absolute Shrinkage and Selection Operator-Based Prediction of the Binding Constant of p-Sulfonatocalix[6]/[8]arenes with Alkaloids.

p-Sulfonatocalix[n]arenes (SCnA) have demonstrated great potential for drug encapsulation through host-guest complexation to improve solubility, stability, and bioavailability. In this study, the solubilization effect of SCnA (n = 4, 6, 8) on 95 active compounds derived from traditional Chinese medicine (TCM) was investigated. Based on the significant solubilization effect on alkaloids, SC6A/SC8A and 76 alkaloids were selected as the host and guest, respectively, to determine the binding constant by competitive fluorescence titration. LASSO regression was adopted to investigate the mechanism of the complex of SCnA with alkaloids. The binding constant of alkaloids-SC6A and alkaloids-SC8A was related to the alkaloid alkalinity. Also, the electronegativity, polarization, first ionization potential, hydrogen bond potential, the molecular size, and shape of alkaloids are critical properties to determine alkaloids-SC6A binding constant as well as electronegativity, polarization, hydrophobicity, and the molecular size and shape of alkaloids play an important role for the alkaloids-SC8A binding constant.

Chemometrics-based Chemical Analysis of Myrrh and Its Vinegar-processed Products by UPLC-MS/MS.

Myrrh is widely used in clinical practice but accompanied by obvious toxicity. According to traditional Chinese medicines theory, processing with vinegar can effectively reduce its toxicity. However, the detoxification processing technology of Myrrh and the corresponding mechanism have been unclear. The objective of this study is to systematically analyze the variation in chemical composition of raw Myrrh and its processed products using UPLC-Q-TOF-MS/MS coupled with chemometrics. A total of 75 compounds including 56 sesquiterpenoids, 2 diterpenoids, 15 triterpenoids and 2 other types were identified. Raw Myrrh and its processed products were divided into two major groups, and 14 chemical markers were selected out by principal component analysis and partial least square discriminant analysis. Additionally, the exact content of 5 representative chemical markers was determined to be significantly reduced after vinegar-processing by UPLC-QQQ-MS/MS. Moreover, multivariate statistical analysis and the quantitative results comprehensively indicated that the optimized processing method was processing at a ratio of 200 : 5 (Myrrh:vinegar). This research provides not only a reliable foundation for the study of Myrrh, but also a scientific reference for clinical use of this herb.

Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development.

Massively parallel sequencing of the polyadenylated RNAs has played a key role in delineating transcriptome complexity, including alternative use of an exon, promoter, 5' or 3' splice site or polyadenylation site, and RNA modification. However, reads derived from the current RNA-seq technologies are usually short and deprived of information on modification, compromising their potential in defining transcriptome complexity. Here, we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in Caenorhabditis elegans We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts. To utilize the full-length transcripts in defining transcriptome complexity, we devised a method to classify the long reads as the same as existing transcripts or as a novel transcript using sequence mapping tracks rather than existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. The sets of genes with differential expression versus differential isoform usage over development are largely different, implying a fine-tuned regulation at isoform level. We also observed an unexpected increase in putative RNA modification in all bases in the coding region relative to the UTR, suggesting their possible roles in translation. The RNA reads and the method for read classification are expected to deliver new insights into RNA processing and modification and their underlying biology in the future.

Genetically encoded protein sensors for metal ion detection in biological systems: a review and bibliometric analysis.

Metal ions are indispensable elements in living organisms and are associated with regulating various biological processes. An imbalance in metal ion content can lead to disorders in normal physiological functions of the human body and cause various diseases. Genetically encoded fluorescent protein sensors have the advantages of low biotoxicity, high specificity, and a long imaging time in vivo and have become a powerful tool to visualize or quantify the concentration level of biomolecules in vivo and in vitro, temporal and spatial distribution, and life activity process. This review analyzes the development status and current research hotspots in the field of genetically encoded fluorescent protein sensors by bibliometric analysis. Based on the results of bibliometric analysis, the research progress of genetically encoded fluorescent protein sensors for metal ion detection is reviewed, and the construction strategies, physicochemical properties, and applications of such sensors in biological imaging are summarized.

Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization.

To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.

A comprehensive quality evaluation method of different medicinal parts of Physalis Calyx seu Fructus by fingerprints, chemometrics, antioxidant activity, network pharmacology and molecular docking.

Physalis Calyx seu Fructus (PCF) is a herb widely used in China for its function of clearing heat and detoxifying, benefitting the pharynx and reducing phlegm, both in health care and in tea drinking. However, the quality of its fruit and calyx is uneven and the storage period is short. Therefore, it is crucial to develop other parts of PCF with longer storage periods and obvious medicinal effects. Firstly, high-performance liquid chromatography was used to develop the fingerprint of different parts of PCF, and various chemometric analyses were conducted to screen out chemical markers. The calyxes of PCF were found to cluster together, distinct from the fruits, roots, stems and leaves. The active components of PCF were concentrated in the persistent calyxes, and flavonoids were mainly found in the persistent calyxes and leaves. Secondly, the extraction of persistent calyxes showed the strongest scavenging ability of DPPH and ABTS. Finally, the important chemical markers were verified by network pharmacological analysis and molecular docking. It provides a reference for the clinical application of PCF, and the obtained chemical markers offer a scientific basis for quality evaluation.

Analysis of Bitter Almonds and Processed Products Based on HPLC-Fingerprints and Chemometry.

In the processing field, there is a saying that "seed drugs be stir-fried". Bitter almond (BA) is a kind of seed Chinese medicine. BA need be used after being fried. To distinguish raw bitter almonds (RBA) from processed products and prove the rationality of "seed drugs be stir-fried", we analyzed the RBA and five processed products (scalded bitter almonds, fried bitter almonds, honey fried bitter almonds, bran fried bitter almonds, bitter almonds cream) using RP-HPLC fingerprints and chemometric methods. The similarity between RBA and processed products was 0.733∼0.995. Hierarchically clustered heatmap was used to evaluate the changes in components. Principal component analysis (PCA) was used for classification, and all samples are distinguished according to RBA and five processing methods. Six chemical markers were obtained by partial least squares discriminant analysis (PLS-DA). The content and degradation rate of amygdalin and ß-glucosidase activity were determined. Compared with RBA, the content and degradation rate of amygdalin, and ß-glucosidase activity were increased in bitter almonds cream. The content and degradation rate were decreased, and ß-glucosidase was inactivated in other processed products. The above results showed that stir-frying had the best effect. The results showed that processing can ensure the stability of RBA quality, and the saying "seed drugs be stir-fried" is reasonable.

Species Differentiation and Quality Evaluation for Atractylodes Medicinal Plants by GC/MS Coupled with Chemometric Analysis.

The utilization of rhizomes from the genus Atractylodes has been challenging due to their closely related origins. In this study, we developed an analytical strategy to differentiate Atractylodes lancea (A. lancea), Atractylodes chinensis (A. chinensis), Atractylodes japonica (A. japonica), and Atractylodes macrocephala (A. macrocephala), and compared their volatile compositions. Gas chromatography-mass spectrometry (GC/MS) was used to analyze the volatile profiles of essential oils extracted from 59 batches of samples. Chemometric methods enabled a better understanding of the differences in volatile oils between the four species and identified significant components affecting their classification and quality. A total of 50 volatile components were identified from the essential oils by GC/MS. Unsupervised and supervised chemometric analyses accurately distinguished A. lancea, A. chinensis, A. japonica, and A. macrocephala. Furthermore, five characteristic chemical markers, namely hinesol, ß-eudesmol, atractylon, atractylodin and atractylenolide I, were obtained, and their respective percentage contents in individual species and samples were determined. This study provides a valuable reference for the quality evaluation of medicinal plants with essential oils and holds significance for species differentiation and the rational clinical application of Atractylodes herbs.

Discrimination of Polygonati Rhizoma Species: An Investigation Utilizing High-Performance Liquid Chromatography Fingerprints and Chemometrics.

Polygonati Rhizoma has been a famous traditional Chinese medicine (TCM) for two thousand years. It is increasingly being used not just as a traditional herbal medicine but also as a popular functional food. In this study, qualitative and quantitative analysis of PR from three different origins were initially performed using chemical fingerprint and chemometrics methods. Hierarchical cluster analysis (HCA) and Principal component analysis (PCA) were used to classify 60 PR samples from three different origins. The results revealed that the PR samples fell into three clusters related to the origins. In addition, pairwise comparison of varying PR and obtaining chemical markers between different species through the establishment of partial least squares discriminant analysis. Finally, chemical markers 9,13 and 17 were identified by LC/MS as disporopsin, 5,7-dihydroxy-3-(4'-hydroxybenzyl)-6,8-dimethylchroman-4-one and (3R)-5,7-dihydroxy-3-(4'-hydroxybenzyl)-6-methylchroman-4-one or isomer, respectively. In conclusion, these methods can be applied to identify and distinguish the quality of PR with other original plants and provide novel ideas for evaluating herbal products used in TCM.

A (Traditional Chinese Medicine) TCM-Inspired Doxorubicin Resistance Reversing Strategy: Preparation, Characterization, and Application of a Co-loaded pH-Sensitive Liposome.

In this study, nano-strategy for combined medication of active compounds from traditional Chinese medicine herbs was proposed to achieve the synergistic effects of inhibiting the doxorubicin (DOX) resistance, reducing the cardio-toxicity, and improving the treatment efficacy simultaneously. Dihydroartemisinin (DHA) and tetrandrine (TET) were co-delivered for the first time to treat DOX resistance of breast cancer with multi-pathway mechanism. Tumor micro-environment sensitivity prescription was adopted to enhance the reversal effect of DOX resistance nearly 50 times (resistance index, RI was 46.70) and uptake ability. The DHA-TET pH-sensitive liposomes (DHA-TET pH-sensitive LPs) had a good spherical structure and a uniform dispersion structure with particle size, polydispersity index (PDI), and zeta potential of 112.20 ± 4.80 nm, 0.20 ± 0.02, and - 8.63 ± 0.74 Mv, and was stable until 14 days under the storage environment of 4°C and for 6 months at room temperature environment. With the DOX resistance reversing ability increased, the inhibition effect of DHA-TET pH-sensitive LPs on both MCF-7/ADR cells and MCF-7 cells was significantly enhanced; meanwhile, the toxicity on cardiac cell (H9c2) was lowered. Ferroptosis induced by the DHA was investigated showing that the intracellular reactive oxygen species (ROS) and lipid peroxidation were increased to promote the synergistic effect through the due-loaded nano-carrier, providing a promising alternative for future clinical application.

Genomic architecture of 5S rDNA cluster and its variations within and between species.

BACKGROUND: Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. RESULTS: Here we generate ultra-long Oxford Nanopore Technologies (ONT) and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA's repeating units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform assembly of the cluster by taking advantage of the long reads that carry these units, which led to an assembly of 5S rDNA cluster consisting of up to 167 consecutive 5S rDNA units in the N2 strain. The ordering and copy number of various rDNA units are consistent with the separation time between strains. Surprisingly, we observed a drastically reduced level of variation in the unit composition in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than in the C. elegans N2 strain, suggesting that N2, a widely used reference strain, is likely to be defective in maintaining the 5S rDNA cluster stability compared with other wild isolates of C. elegans or C. briggsae. CONCLUSIONS: The results demonstrate that Nanopore DNA sequencing reads are capable of generating assembly of highly repetitive sequences, and rDNA units are highly dynamic both within and between population(s) of the same species in terms of sequence and copy number. The detailed structure and variation of the 5S rDNA units within the rDNA cluster pave the way for functional and evolutionary studies.

Characteristic profiling of Aconiti Lateralis Radix for distinguishing it from compatible herbal pair using UPLC-Q-TOF-MS coupled with chemometrics.

A method combining ultra-high-performance liquid chromatograph/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and chemometrics was established to evaluate the differences in chemical composition between Aconiti Lateralis Radix (Fuzi in Chinese) before and after combination with Glycyrrhizae Radix et Rhizoma (Gancao in Chinese). UPLC-Q-TOF-MS was used to characterize the chemical components before and after the combination of Fuzi with Gancao, and genetic algorithm selection variables were applied to extract important variables. Partial least square discriminant analysis was used to verify the reliability of the variables obtained by genetic algorithm selection in differentiating Fuzi and combinations with Gancao, and nine potential chemical markers were obtained. The changes in content of chemical markers in Fuzi before and after combination were visualized using a heat map and hierarchical cluster analysis. Based on the chemical markers, characteristic profiling of UPLC-Q-TOF-MS data was developed, then unsupervised principal components analysis and a supervised counter-propagation artificial neural network were used to validate the characteristic profiling approach and showed that it performed well in differentiating between Fuzi and combinations with Gancao.

Comprehensive Quality Evaluation of the Root Bark of Morus alba L. Based on High-Performance Liquid Chromatography Fingerprinting and Chemometric Analyses.

The quality of the root bark of Morus alba L. (SBP) herbs currently circulating in the market is variable. In order to ensure clinical effectiveness, a high-performance liquid chromatography (HPLC) fingerprinting method combined with chemical pattern recognition should be established to control the quality of SBP herbs. The differences of 23 batches of SBP were analyzed by exploratory cluster analysis based on shared fingerprint peak data, and the results indicated that the processing method to remove the cork layer from SBP materials is an important influencing factor on SBP quality. Principal component analysis indicated that SBP samples with the cork layer removed can be clearly distinguished from samples without cork layer removal. The potential chemical markers (kuwanon G, morusin and oxyresveratrol) were screened by partial least squares discriminant analysis. Finally, the contents of the main components were determined, indicating that the processing method of SBP materials can affect content of bioactive ingredients and that cork layer removal leads to a more uniform chemometric profile. The HPLC-based chemometrics approach described here will support the development of quality standards in SBP products.

Discovery of potential Q-marker of traditional Chinese medicine based on chemical profiling, chemometrics, network pharmacology, and molecular docking: Centipeda minima as an example.

INTRODUCTION: The characteristics of chemical components or groups of chemical components in traditional Chinese medicines (TCMs) determine their clinical efficacy. Quality markers (Q-markers) is of great significance for standardizing the quality control system of TCM. OBJECTIVES: We aimed to develop a new strategy to discover potential Q-markers of TCM by integrating chemometrics, network pharmacology, and molecular docking, using Centipeda minima (also known as ebushicao [EBSC]) as an example. MATERIALS AND METHODS: First, fingerprints of different batches of EBSC and its counterfeit Arenaria oreophila (also known as zaozhui [ZZ]) were established. Second, chemometric analysis was conducted to determine the influence of varying authenticity/batches of herbs on quality and the chemical markers were screened out. Third, network pharmacology and molecular docking simulations were used to verify the relationship between active ingredients and targets. Lastly, potential Q-markers were selected based on TCM theory. RESULTS: The chemical profiles of EBSC and ZZ were investigated. It was found that different batches of EBSC have differences in chemical composition. Based on our chemometric analysis, chlorogenic acid, rutin, isochlorogenic acid A, quercetin, arnicolide D, and brevilin A were selected as candidate active ingredients. ATIL6, EGFR, CASP3, MYC, HIF1A, and VEGFA were the main targets. Molecular docking was used to verify the binding ability. Based on the concept of Q-marker, arnicolide D and brevilin A were identified as potential Q-markers for EBSC. CONCLUSIONS: Our strategy could be used as a practical approach to discover Q-markers of TCM to evaluate overall chemical consistency.

An innovative extraction strategy for herbal medicine by adopting p-sulphonatocalix[6]/[8]arenes.

INTRODUCTION: Alkaloids exist in various herbal medicine widely and exhibit diverse biological and pharmacological activities. p-Sulphonatocalix[6]arenes (SC6A) and p-sulphonatocalix[8]arenes (SC8A) are water-soluble supramolecular macrocycles and are applied to the extraction of alkaloids from herbal products. OBJECTIVE: In this study, an innovative method of SC6A/SC8A assisted extraction of the alkaloids from herbs was established. METHODS: SC6A and SC8A were designed to extract 27 alkaloids from seven herbal medicines. Based on the significant solubilisation and extraction effect, Stephaniae Tetrandrae Radix (Fangji, FJ) was selected to obtain the optimal extraction process by adopting single factor test and orthogonal experiment. Then, the alkaloids and SC6A/SC8A were separated by one-step alkalisation and SCnA were reused. The host-guest complexes between alkaloids and SCnA were determined by competitive fluorescence titration, differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) and proton nuclear magnetic resonance (1 H-NMR) analysis. RESULTS: The optimum condition for SC6A assisted extraction was 5:1:80 (g/g/mL) for herbs/SC6A/solution ratio, 355-250 µm particle size and ultrasonicate 0.5 h, whilst 10:1:40 (g/g/mL) for herbs/SC8A/solution ratio, 355-250 µm particle size and ultrasonicate 0.5 h for SC8A assisted extraction. The total yield of alkaloids (fangchinoline and tetrandrine) from FJ was increased by 4.87 times and 5.97 times with SC6A and SC8A. Moreover, a good reusability of SC6A/SC8A was achieved by alkalisation dissociation. Host-guest complexes were determined by competitive fluorescence titration at a molar ratio of 1:1 between most alkaloids (25/27, except evodiamine and rutaecarpine) and SC6A/SC8A. The complex structure was proved by DSC, FTIR and 1 H-NMR analysis. CONCLUSION: The study provided an effective eco-friendly and energy-saving extraction method of alkaloids from herbal medicine.

An eco-friendly extraction and purification method of nuciferine from Folium nelumbinis with p-sulfonatocalix[6]arenes.

INTRODUCTION: Folium nelumbinis is used as vegetable, functional food and herbal medicine in Asia. p-Sulfonatocalix[6]arene (SC6A) is a water-soluble supramolecular macrocycle and has never been applied to the extraction of herbal products. OBJECTIVE: In this study, SC6A-assisted extraction of nuciferine from Folium nelumbinis has been carried out to develop an eco-friendly extraction process with high extraction efficacy and easy operation. METHODS: Single-factor experiments were adopted to obtain the optimal conditions for the SC6A-assisted extraction of nuciferine from Folium nelumbinis, and then nuciferine and SC6A were separated easily by one-step alkalization. The host-guest complexes between nuciferine and SC6A were analyzed by competitive fluorescence titration, DSC, FT-IR and 1 H-NMR. RESULTS: The optimal SC6A/Folium nelumbinis/solution ratio for extraction was 0.4:1:20 (g/g/mL), with a granulometric fraction below 180 µm and an extraction time of 1 h with soaking. The purity and recovery of nuciferine extracted with SC6A were increased 29.24 and 35.73 times compared with extraction with aqueous solution, respectively. Moreover, a good reusability of SC6A in the extraction of nuciferine was demonstrated. Competitive fluorescence titration, DSC, FT-IR and 1 H-NMR characterization indicated that SC6A could form host-guest complexes with nuciferine at a ratio of 1:1. CONCLUSION: The study provided an eco-friendly, safe and effective nuciferine extraction method, which can be used for the development of nutrition supplements containing nuciferine.

Comparative investigation of raw and processed products of Gardeniae Fructus and Gardenia jasminoides var. radicans using HPLC coupled with chemometric methods.

As a commonly used traditional Chinese medicine (TCM), Gardeniae Fructus (GF) and its processed products, GF (stir-baked) and GF Praeparatus, have important medicinal value in clinical practice. Gardenia jasminoides var. radicans (GJVR) is a variant of GF, and because of the naming GJVR is often confused in the clinic with GF, resulting in medical misprescriptions. To distinguish GF and GJVR and study the changes before and after processing, the fingerprints of GF and GJVR are presented using HPLC, followed by hierarchical cluster analysis (HCA), principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA). GF has purging and choleretic effects, and in this study, we determined the content of main active ingredients to preliminarily assess the GF and GJVR quality from the perspective of material basis. For PCA score plot, the samples fell into six clusters, the cross-validity Q2 (cum) = 0.842 and the cumulative contribution rate R2 x (cum) = 0.988, indicating that the model has a good precision. The results were then corroborated by HCA and PLS-DA method, showing that this methodology can distinguish GF and GJVR and can be used for the comparison of raw and two processed products. According to the model established by PLS-DA, eight components were identified as the most significant variables for discrimination. The results obtained by multiple model methods are consistent and verified by each other, providing a scientific reference for further clarification of the medicinal properties of GF and GJVR.

Comparative Investigation for Raw and Processed Products of Euodiae Fructus Based on High-Performance Liquid Chromatography Fingerprints and Chemical Pattern Recognition.

As a traditional Chinese medicine, Euodiae Fructus is widely used due to its analgesic, anti-inflammatory, and antihypertensive effects. However, Euodiae Fructus has also been documented to be toxic, and the toxic effects can be reduced by processing. To distinguish Euodiae Fructus from its processes products and study the changes of raw and processed products before and after processing, we evaluated four auxiliary material processing methods including vinegar, Zingiberis Rhizoma, Coptidis Rhizoma, and Glycyrrhizae Radix et Rhizoma. The raw Euodiae Fructus and four processed Euodiae Fructus samples were analyzed and compared based on the high-performance liquid chromatography (HPLC) fingerprints combined with chemometrics, including principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and principal component analysis-class (PCA-Class). A total of 27 common peaks were obtained by fingerprint analysis. The fingerprint similarity of raw and processed samples was between 0.86-0.999. We also determined the contents of the main active ingredients - Evodiamine and Rutaecarpine. PCA and PLS-DA analyses were used to distinguish between the raw and processed samples of Euodiae Fructus, and 14 chemical markers were screened out. Four kinds of processed products were further analyzed and the results showed that they could be successfully distinguished under the established models, and 12 chemical markers were labeled. PCA-Class results revealed that the classification models constructed in this study had adequate discrimination ability. The method combined with HPLC fingerprinting and multi-component chemical pattern recognition technology could be used to differentiate raw and processed Euodiae Fructus with adequate predictive power. Our findings confirmed the rationality of the pharmacopoeial method and provided a reference for the quality control of the Glycyrrhizae Radix et Rhizoma processed Euodiae Fructus.

Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni.

DNA recombination is required for effective segregation and diversification of genomes and for the successful completion of meiosis. Recent studies in various species hybrids have demonstrated a genetic link between DNA recombination and speciation. Consistent with this, we observed a striking suppression of recombination in the hybrids between two nematodes, the hermaphroditic Caenorhabditis briggsae and the gonochoristic C. nigoni. To unravel the molecular basis underlying the recombination suppression in their hybrids, we generated a C. nigoni genome with chromosome-level contiguity and produced an improved C. briggsae genome with resolved gaps up to 2.8 Mb. The genome alignment reveals not only high sequence divergences but also pervasive intra- and inter-chromosomal sequence re-arrangements between the two species, which are plausible culprits for the observed suppression. Comparison of recombination boundary sequences suggests that recombination in the hybrid requires extensive sequence homology, which is rarely seen between the two genomes. The new genomes and genomic libraries form invaluable resources for studying genome evolution, hybrid incompatibilities and sex evolution for this pair of model species.