Two insulin receptors determine alternative wing morphs in planthoppers.

Wing polyphenism is an evolutionarily successful feature found in a wide range of insects. Long-winged morphs can fly, which allows them to escape adverse habitats and track changing resources, whereas short-winged morphs are flightless, but usually possess higher fecundity than the winged morphs. Studies on aphids, crickets and planthoppers have revealed that alternative wing morphs develop in response to various environmental cues, and that the response to these cues may be mediated by developmental hormones, although research in this area has yielded equivocal and conflicting results about exactly which hormones are involved. As it stands, the molecular mechanism underlying wing morph determination in insects has remained elusive. Here we show that two insulin receptors in the migratory brown planthopper Nilaparvata lugens, InR1 and InR2, have opposing roles in controlling long wing versus short wing development by regulating the activity of the forkhead transcription factor Foxo. InR1, acting via the phosphatidylinositol-3-OH kinase (PI(3)K)-protein kinase B (Akt) signalling cascade, leads to the long-winged morph if active and the short-winged morph if inactive. InR2, by contrast, functions as a negative regulator of the InR1-PI(3)K-Akt pathway: suppression of InR2 results in development of the long-winged morph. The brain-secreted ligand Ilp3 triggers development of long-winged morphs. Our findings provide the first evidence of a molecular basis for the regulation of wing polyphenism in insects, and they are also the first demonstration--to our knowledge--of binary control over alternative developmental outcomes, and thus deepen our understanding of the development and evolution of phenotypic plasticity.

Efficacy and safety of Xiyanping injection in the treatment of COVID-19: A multicenter, prospective, open-label and randomized controlled trial.

Xiyanping (XYP) is a Chinese herbal medicine used in the clinic to treat respiratory infection and pneumonia. Recent evidence identified XYP as a potential inhibitor of severe acute respiratory syndrome coronavirus 2, implying XYP as a possible treatment for the coronavirus disease 2019 (COVID-19). Here, we conducted a prospective, multicenter, open-label and randomized controlled trial to evaluate the safety and effectiveness of XYP injection in patients with mild to moderate COVID-19. We consecutively recruited 130 COVID-19 patients with mild to moderate symptoms from five study sites, and randomized them in 1:1 ratio to receive XYP injection in combination with standard therapy or receive standard supportive therapy alone. We found that XYP injection significantly reduced the time to cough relief, fever resolution and virus clearance. Less patients receiving XYP injection experienced disease progression to the severe stage during the treatment process. No severe adverse events were reported during the study. Taken together, XYP injection is safe and effective in improving the recovery of patients with mild to moderate COVID-19. However, further studies are warranted to evaluate the efficacy of XYP in an expanded cohort comprising COVID-19 patients at different disease stages.

[Analysis of clinical application characteristics of Xiyanping Injection in 194 873 cases in real world].

To analyze the clinincal application characteristics of Xiyanping Injection in real world. The data of the patients came from the hospital information systerm(HIS) of 29 tertiary hospitals in China from 2006 to 2016. It included three parts about basic information, Western medicine diagnosis information, and doctor advice information. The exploration was conducted for the characteristics of the patients and disease distribution as well as the therapeutic regimen. Apriori algorithm was adopted to establish the models, and Clementing 12.0 was used for a correlation analysis of the comprehensive therapeutic regimen of Xiyanping Injection. There were 194 873 cases in the study. The male to female ratio was 1.44∶1. The median age was 4 years old. The median daily dosage was 200 mg. 46.68% of the patients were administered with 250-500 mg, and 33.07% were 50-100 mg one day. 47.08% of the patients were administered for 4-7 d, and 32.65% of the patients were 1-3 d. In the doctor advice information, the most frequently types of Western medicine, traditional Chinese medicine were mucilagin, heat-clearing agent. Second generation cephalosporins, third generation cephalosporins, compound penicillin were the most common types of antibiotic. Interferon, nucleoside and nucleotide, human immunoglobulin were the most common types of antiviral drug. The mining association rules results were analyzed, finding the application of Xiyanping Injection in severe infectious diseases. To improve respiratory symptoms, Xiyanping Injection treaments were Budesonide + Ipratropium Bromide + Ambroxol. To severe pulmonary infection, the treaments were Dopamine + Ambroxine. To severe hand, foot and mouth disease, the treatments were Namefen + Mannitol. To pulmonary heart failure, the treatments were Dobutamine + Heparin. Based on the results of the real world HIS, we could provide clinical application the idea, and a reference for further excavation of the applicable diseases of Xiyanping Injection.

[Real world analysis to explore Xiyanping injection combined with other drugs for hand-foot-mouth disease].

Integrated network analysis was used in this paper to analyze Xiyanping injection combined therapy for hand-foot-mouth disease based on the registered research data of 3 204 cases. It was found that the drug combination therapy was almost consistent with the guidelines for the diagnosis and treatment of hand foot mouth disease, but there were some problems to be noticed: there were too many applications of antibiotics, more than the need in preventing secondary infection; and ribavirin was not necessary for use. This article showed that the clinical antibacterial and antiviral values of Xiyanping injection has not been well recognized for hand-foot-mouth disease.

The 3DGD: a database of genome 3D structure.

UNLABELLED: The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions. AVAILABILITY AND IMPLEMENTATION: The 3DGD v1.1, data browser, downloadable files and documentation are available at: http://3dgd.biosino.org/.

Genome of a Bombyx mori nucleopolyhedrovirus strain isolated from India.

Bombyx mori nucleopolyhedrovirus (BmNPV), a member of the Baculoviridae, is a major pathogen of silkworm and has also been recently developed as an expression vector for heterologous gene expression in the silkworm larvae and pupae. To better understand the diversity of this important baculovirus, we sequenced the complete genome of the BmNPV strain isolated from India, where its host is available throughout the year due to its tropical climate. The genome of the Indian strain consists of 127,879 nucleotides, with a G+C content of 40.36%. There are 138 open reading frames (ORFs) encoding the predicted proteins of more than 50 amino acids. Genomic comparison of the Indian strain with 3 other reported BmNPV strains showed that the baculovirus repeat ORFs (bro) and homologous repeat regions (hr's) are highly variable. These results suggest that the BmNPV strain heterogeneity is mainly caused by single-nucleotide polymorphisms (SNPs) and changes in the hr's and bro genes.

Disruption of Bombyx mori nucleopolyhedrovirus ORF71 (Bm71) results in inefficient budded virus production and decreased virulence in host larvae.

The Bombyx mori nucleopolyhedrovirus (BmNPV) is a baculovirus that selectively infects domestic silkworm. BmNPV ORF71 (Bm71) is not a core set gene in baculovirus and shares 92 % amino acid sequence identity with Autographa californica multinucleocapsid NPV ORF88 (Ac88/cg30). Previously, it has been reported that virus lacking Ac88 had no striking phenotypes in cell lines or host larvae. However, the exact role of Bm71 during BmNPV life cycle remains unknown. In the present study, we constructed a Bm71-disrupted (Bm71-D) virus and assessed the effect of the Bm71 disruption on viral replication and viral phenotype throughout the viral life cycle. Results showed that the Bm71-D bacmid could successfully transfect Bm5 cell lines and produce infectious budded virus (BV). But the BV titer was 10- to 100-fold lower than that of the wild-type (WT) virus during infection, and the decreased BV titer was rescued by Bm71 gene repair virus (Bm71-R). A larval bioassay showed that Bm71-D virus took 7.5 h longer than the WT to kill Bombyx mori larvae. Transmission electron microscopy analysis indicated that the Bm71-D virus-infected cells had typical virogenic stroma, bundles of nucleocapsids and polyhedra. Taken together, these results suggest that Bm71 has important implications for determining BV yield and virulence in viral life cycle even though it is not an essential gene for replication of BmNPV.

PHDMF: A Flexible and Scalable Personal Health Data Management Framework Based on Blockchain Technology.

Currently, most of the personal health data (PHD) are managed and stored separately by individual medical institutions. When these data need to be shared, they must be transferred to a trusted management center and approved by data owners through the third-party endorsement technology. Therefore, it is difficult for personal health data to be shared and circulated over multiple medical institutions. On the other hand, the use of directly exchanging and sharing the original data has become inconsistent with the data rapid growth of medical institutions because of the need of massive data transferring across agencies. In order to secure sharing and managing the mass personal health data generated by various medical institutions, a federal personal health data management framework (PHDMF, https://hvic.biosino.org/PHDMF) has been developed, which had the following advantages: 1) the blockchain technology was used to establish a data consortium over multiple medical institutions, which could provide a flexible and scalable technical solution for member extension and solve the problem of third-party endorsement during data sharing; 2) using data distributed storage technology, personal health data could be majorly stored in their original medical institutions, and the massive data transferring process was of no further use, which could match up with the data rapid growth of these institutions; 3) the distributed ledger technology was utilized to record the hash value of data, given the anti-tampering feature of the technology, malicious modification of data could be identified by comparing the hash value; 4) the smart contract technology was introduced to manage users' access and operation of data, which made the data transaction process traceable and solved the problem of data provenance; and 5) a trusted computing environment was provided for meta-analysis with statistic information instead of original data, the trusted computing environment could be further applied to more health data, such as genome sequencing data, protein expression data, and metabolic profile data through combining the federated learning and blockchain technology. In summary, the framework provides a convenient, secure, and trusted environment for health data supervision and circulation, which facilitate the consortium establish over medical institutions and help achieve the value of data sharing and mining.

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Gene duplication is common in all three domains of life, especially in eukaryotic genomes. The duplicates provide new material for the action of evolutionary forces such as selection or genetic drift. Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons). We also constructed an internet-accessible Eukaryotic Paralog Group Database (EPGD; http://epgd.biosino.org/EPGD/). The database is gene-centered and organized by paralog family. It focuses on paralogs and evolutionary duplication events. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files. The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families.

Gene expression module-based chemical function similarity search.

Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of chemical related expression profiles, and introduced similarity comparison into chemical induced transcriptome analysis. Resembling sequence similarity alignment, expression pattern comparison among chemical intervention related expression profiles provides a new way for chemical function prediction and chemical-gene relation investigation. However, existing methods place more emphasis on comparing profile patterns globally, which ignore noises and marginal effects. At the same time, though the whole information of expression profiles has been used, it is difficult to uncover the underlying mechanisms that lead to the functional similarity between two molecules. Here a new approach is presented to perform biological effects similarity comparison within small biologically meaningful gene categories. Regarding gene categories as units, a reduced similarity matrix is generated for measuring the biological distances between query and profiles in library and pointing out in which modules do chemical pairs resemble. Through the modularization of expression patterns, this method reduces experimental noises and marginal effects and directly correlates chemical molecules with gene function modules.

A platform to standardize, store, and visualize proteomics experimental data.

With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database (IPED) as a platform for managing proteomics experimental data (both process and result data). IPED is based on the schema of the Proteome Experimental Data Repository (PEDRo), and complies with the General Proteomics Standard (GPS) drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform: the IPED client editor, IPED server software, and IPED web interface. The client editor collects experimental data and generates an extensible markup language (XML) data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database; and the web interface displays experimental results, to provide a convenient graphic representation of data. Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community. In its current release, IPED is available at http://www.biosino.org/iped2.

The contribution of cis-regulatory elements to head-to-head gene pairs' co-expression pattern.

Transcription regulation is one of the most critical pipelines in biological process, in which cis-elements play the role as gene expression regulators. We attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements. A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different conditions. Our discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

Efficacy of Weikang Pian in Patients with Functional Dyspepsia: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial.

BACKGROUND: FD (functional dyspepsia) is a common functional gastrointestinal disorder, which lacks effective and safe treatment. Chinese herbal medicine (CHM) has been applied in FD treatment for thousands of years with satisfactory clinical outcomes. Zhishi is a classical traditional Chinese medicine used to treat FD. Weikang pian (WKP) is made of flavonoids extracted from zhishi which could effectively alleviate the symptoms of FD. This research aimed to assess the efficacy and safety of WKP in FD treatment. METHODS: This was a randomized, double-blinded and placebo-controlled clinical trial. The patients were diagnosed as FD according to RomeIII criteria. Then, FD patients were selected and assigned randomly to either WKP or placebo group. The subjects randomly received WKP or placebo for 4 weeks with 4 tablets each time, 3 times daily. The single dyspepsia symptom (SDS) scale and the gastric emptying function were measured before and after the treatment. Moreover, the safety of the trial and patient compliance were evaluated. RESULTS: A total of 60 FD patients were eventually enrolled in the trial, among them 45 patients in the WKP group and 15 patients in the placebo group. The primary outcome was the SDS scale, including assessments of postprandial distension, early satiety, epigastric burning, and pain. The secondary outcome was the gastric emptying function. Compared with the placebo group, the symptoms of FD in the WKP group were relieved after 4 weeks of treatment (P < 0.05). Some minor changes appeared in the four groups, but there were no significant differences in gastric emptying parameters of GER (2-hour gastric emptying rate) and GET/2 (gastric semiempty time) (P > 0.05). Severe adverse events were absent. The compliance to treatment was 94%-96%, and there was no significant difference between the groups. CONCLUSION: WKP can relieve FD symptoms to some extent. This trial is registered with Chinese Clinical Trial Registry (ChiCTR): CTR 20132482.

Characteristics of the draft genome of "Candidatus Arsenophonus nilaparvatae", a facultative endosymbiont of Nilaparvata lugens.

There exists a kind of symbiotic bacterium named "Candidatus Arsenophonus nilaparvatae" in the brown planthopper (BPH), Nilaparvata lugens. After being filtered and assembled from the BPH genome sequencing project, the genome sequence of this bacterial symbiont was obtained. After initial analysis based on the genome, we have found its potential role to synthesize B vitamins for the host. In order to better understand the lifestyle and the genomic changes of this symbiotic bacterium after the symbiotic relationship was established, we further report the characteristics of this draft genome. Compared with several other related bacteria, "Candidatus Arsenophonus nilaparvatae" has proven to be a facultative endosymbiont at the genomic level. Concurrently, the presence of fimbriae and flagella formation related genes indicates this maternally transmitted endosymbiont is most likely to retain the capacity to invade new hosts. Through further analysis of annotated gene sets, we also find evidence of genome reduction in its secretion system and metabolic pathways. These findings reflect its evolutionary trend to be an obligate one and enable a deeper study of microbe-insect interactions.

Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle.

A number of sap-sucking insects harbor endosymbionts, which are thought to play an important role in the development of their hosts. One of the most important rice pests, the brown planthopper (BPH), Nilaparvata lugens (Stål), harbors an obligatory yeast-like symbiont (YLS) that cannot be cultured in vitro. Genomic information on this YLS would be useful to better understand its evolution. In this study, we performed genome sequencing of the YLS using both 454 and Illumina approaches, generating a draft genome that shows a slightly smaller genome size and relatively higher GC content than most ascomycete fungi. A phylogenomic analysis of the YLS supported its close relationship with insect pathogens. We analyzed YLS-specific genes and the categories of genes that are likely to have changed in the YLS during its evolution. The loss of mating type locus demonstrated in the YLS sheds light on the evolution of eukaryotic symbionts. This information about the YLS genome provides a helpful guide for further understanding endosymbiotic associations in hemiptera and the symbiotic replacement of ancient bacteria with a multifunctional YLS seems to have been a successful change.

Bicaudal-C plays a vital role in oogenesis in Nilaparvata lugens (Hemiptera: Delphacidae).

Bicaudal-C (Bic-C) was originally identified in a Drosophila melanogaster mutagenesis screen and plays vital roles in embryogenesis. In this study, we characterized the Bic-C gene in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae), an insect pest that undergoes incomplete metamorphosis. Our result showed that N. lugens Bic-C (NlBic-C) is a female-specific gene in this species. It is specifically expressed in developing oocytes and is not expressed in laid eggs. Ribonucleic acid interference (RNAi) of NlBic-C arrested the uptake of vitelline by oocytes, and resulted in undeveloped ovaries and the complete inhibition of oocyte growth in the ovarioles, suggesting that NlBic-C is required for oogenesis and oocyte maturation. NlBic-C is extremely highly sensitive to RNAi, suggesting that it may be a potential target in RNAi-based insect pest management.

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation.

BACKGROUND: The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. To better understand how a monophagous sap-sucking arthropod herbivore has adapted to its exclusive host selection and to provide insights to improve pest control, we analyzed the genomes of the brown planthopper and its two endosymbionts. RESULTS: We describe the 1.14 gigabase planthopper draft genome and the genomes of two microbial endosymbionts that permit the planthopper to forage exclusively on rice fields. Only 40.8% of the 27,571 identified Nilaparvata protein coding genes have detectable shared homology with the proteomes of the other 14 arthropods included in this study, reflecting large-scale gene losses including in evolutionarily conserved gene families and biochemical pathways. These unique genomic features are functionally associated with the animal's exclusive plant host selection. Genes missing from the insect in conserved biochemical pathways that are essential for its survival on the nutritionally imbalanced sap diet are present in the genomes of its microbial endosymbionts, which have evolved to complement the mutualistic nutritional needs of the host. CONCLUSIONS: Our study reveals a series of complex adaptations of the brown planthopper involving a variety of biological processes, that result in its highly destructive impact on the exclusive host rice. All these findings highlight potential directions for effective pest control of the planthopper.

A Metabolomics Profiling Study in Hand-Foot-and-Mouth Disease and Modulated Pathways of Clinical Intervention Using Liquid Chromatography/Quadrupole Time-of-Flight Mass Spectrometry.

Hand-foot-and-mouth disease (HFMD), with poorly understood pathogenesis, has become a major public health threat across Asia Pacific. In order to characterize the metabolic changes of HFMD and to unravel the regulatory role of clinical intervention, we have performed a metabolomics approach in a clinical trial. In this study, metabolites profiling was performed by liquid chromatography/quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) platform from the HFMD clinical patient samples. The outcome of this study suggested that 31 endogenous metabolites were mainly involved and showed marked perturbation in HFMD patients. In addition, combination therapy intervention showed normalized tendency in HFMD patients in differential pathway. Taken together, these results indicate that metabolomics approach can be used as a complementary tool for the detection and the study of the etiology of HFMD.

Molecular characterization of the flightin gene in the wing-dimorphic planthopper, Nilaparvata lugens, and its evolution in Pancrustacea.

Flightin was initially identified in Drosophila melanogaster. Previous work has shown that Drosophila flightin plays a key role in indirect flight muscle (IFM) function and has limited expression in the IFM. In this study, we demonstrated that flightin is conserved across the Pancrustacea species, including winged insects, non-winged insects, non-insect hexapods and several crustaceans. The brown planthopper (BPH), Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), a long-distance migration insect with wing dimorphism, is the most destructive rice pest in Asia. We showed that flightin was one of the most differentially expressed genes in macropterous and brachypterous BPH adults. In female BPHs, flightin was expressed in the IFM of macropterous adults, no expression was detected in brachypterous ones; while in male BPHs, flightin was not only expressed in the IFM of macropterous adults, but also in the dorsal longitudinal muscle (DLM) in the basal two abdominal segments of both macropterous and brachypterous ones. RNAi and transmission electron microscopy results showed that flightin played key roles in maintaining IFM and male DLM structure, which drive wing movements in macropterous adults and the vibration of the male-specific tymbal, respectively. Using Daphnia magna as an example of a crustacean species, we observed that flightin was expressed in juvenile instars and adults, and was localized in the antenna muscles. These results illustrate the functional variations of flightin in insects and other arthropod species and provide clues as to how insects with flight apparatuses evolved from ancient pancrustaceans.

Chitin synthase 1 gene and its two alternative splicing variants from two sap-sucking insects, Nilaparvata lugens and Laodelphax striatellus (Hemiptera: Delphacidae).

Chitin synthase (CHS) is an enzyme that is required for chitin formation in insect cuticles and other tissues. In this study, CHS genes from two destructive rice insect pests, the brown planthopper Nilaparvata lugens and the small brown planthopper Laodelphax striatellus, were cloned. Phylogenetic analysis showed that these genes belonged to class CHS1 of the CHS gene family. Most insects possess two CHS genes (CHS1 and CHS2); however, genome and transcriptome searches showed that N. lugens possibly possess only CHS1 in both databases. Two transcript variants (CHS1a and CHS1b) resulting from exclusively alternative splicing (exon 19a or 19b in N. lugens) were identified for each of the two rice planthopper CHS1s. Gene structure comparison using the genomes that are currently sequenced showed that the CHS1 genes in all insects except Acyrthosiphon pisum have two transcript variants. Transcription of NlCHS1a reached its highest level just after molting, whereas NlCHS1b reached its highest expression level 1-2 days before molting. Injection of the N. lugens nymphs with double-strand RNA (dsRNA) of CHS1, CHS1a and CHS1b reduced the corresponding variant transcript levels and exhibited subsequent phenotypes. Silencing of CHS1 and CHS1a resulted in elongated distal wing pads and the "wasp-waisted" or crimpled cuticle phenotypes and eventually died, whereas the phenotypes caused by injection of NlCHS1b dsRNA seem not so obvious although slightly increased mortality was observed. Our results suggest that N. lugens likely lacks CHS2 and CHS1 may be efficient target gene for RNAi-based N. lugens control.