Splitting of surface defect partition functions and integrable systems

We study Bethe/gauge correspondence at the special locus of Coulomb moduli where the integrable system exhibits the splitting of degenerate levels. For this investigation, we consider the four-dimensional pure $\mathcal{N}=2$ supersymmetric $U(N)$ gauge theory, with a half-BPS surface defect constructed with the help of an orbifold or a degenerate gauge vertex. We show that the non-perturbative Dyson-Schwinger equations imply the Schr\"odinger-type and the Baxter-type differential equations satisfied by the respective surface defect partition functions. At the special locus of Coulomb moduli the surface defect partition function splits into parts. We recover the Bethe/gauge dictionary for each summand.Comment: 34 pages, 2 figures; v2. published versio

ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data

Abstract Background Insecticide resistance is a substantial problem in controlling agricultural and medical pests. Detecting target site mutations is crucial to manage insecticide resistance. Though PCR-based methods have been widely used in this field, they are time-consuming and inefficient, and typically have a high false positive rate. Acetylcholinesterases (Ace) is the neural target of the widely used organophosphate (OP) and carbamate insecticides. However, there is not any software available to detect insecticide resistance associated mutations in RNA-Seq data at present. Results A computational pipeline ACE was developed to detect resistance mutations of ace in insect RNA-Seq data. Known ace resistance mutations were collected and used as a reference. We constructed a Web server for ACE, and the standalone software in both Linux and Windows versions is available for download. ACE was used to analyse 971 RNA-Seq data from 136 studies in 7 insect pests. The mutation frequency of each RNA-Seq dataset was calculated. The results indicated that the resistance frequency was 30%–44% in an eastern Ugandan Anopheles population, thus suggesting this resistance-conferring mutation has reached high frequency in these mosquitoes in Uganda. Analyses of RNA-Seq data from the diamondback moth Plutella xylostella indicated that the G227A mutation was positively related with resistance levels to organophosphate or carbamate insecticides. The wasp Nasonia vitripennis had a low frequency of resistant reads (<5%), but the agricultural pests Chilo suppressalis and Bemisia tabaci had a high resistance frequency. All ace reads in the 30 B. tabaci RNA-Seq data were resistant reads, suggesting that insecticide resistance has spread to very high frequency in B. tabaci. Conclusions To the best of our knowledge, the ACE pipeline is the first tool to detect resistance mutations from RNA-Seq data, and it facilitates the full utilization of large-scale genetic data obtained by using next-generation sequencing

La Croix du Nord : supplément régional à la Croix de Paris ["puis" grand journal quotidien du Nord de la France]

27 janvier 19111911/01/27 (A22,N7391).Appartient à l’ensemble documentaire : NordPdeC

Additional file 4: Figure S3. of Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

Alternative splicing of identified lncRNAs in N. lugens. Most lncRNAs had only one isoforms. Only 19.9 % lncRNAs had multiple isoforms. (TIFF 63 kb

Additional file 14: Table S10. of Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

Primers used for RT-PCR and strand-specific PCR. Both two pairs of primers were used for RT-PCR validation. One pair of primers was used for strand-specific PCR for determining transcript orientations. *: the primer used for strand specific PCRs. (DOCX 24 kb

Additional file 7: Table S3. of Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

Specifically expressed lncRNAs in the fat body of TN1 strain of N. lugens. (XLSX 9 kb

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum

Abstract Background Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer). One striking phenomenon exhibited by M. cingulum is polyembryony, the formation of multiple genetically identical offspring from a single zygote. Moreover, M. cingulum employs a passive parasitic strategy by preventing the host’s immune system from recognizing the embryo as a foreign body. Thus, the embryos evade the host’s immune system and are not encapsulated by host hemocytes. Unfortunately, the mechanism of both polyembryony and immune evasion remains largely unknown. Results We report the genome of the parasitoid wasp M. cingulum. Comparative genomics analysis of M. cingulum and other 11 insects were conducted, finding some gene families with apparent expansion or contraction which might be linked to the parasitic behaviors or polyembryony of M. cingulum. Moreover, we present the evidence that the microRNA miR-14b regulates the polyembryonic development of M. cingulum by targeting the c-Myc Promoter-binding Protein 1 (MBP-1), histone-lysine N-methyltransferase 2E (KMT2E) and segmentation protein Runt. In addition, Hemomucin, an O-glycosylated transmembrane protein, protects the endoparasitoid wasp larvae from being encapsulated by host hemocytes. Motif and domain analysis showed that only the hemomucin in two endoparasitoids, M. cingulum and Venturia canescens, possessing the ability of passive immune evasion has intact mucin domain and similar O-glycosylation patterns, indicating that the hemomucin is a key factor modulating the immune evasion. Conclusions The microRNA miR-14b participates in the regulation of polyembryonic development, and the O-glycosylation of the mucin domain in the hemomucin confers the passive immune evasion in this wasp. These key findings provide new insights into the polyembryony and immune evasion

Additional file 1: of The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum

Figure S1. Flow cytometry estimation of the genome size for the M. cingulum. Figure S2. The distribution of 17-mer frequency in M. cingulum genome sequencing reads. Figure S3. Distribution of GC content, CpG Obs/ExpRatios of M. cingulum(Mcin), N. vitripennis(Nvit) and A. mellifera(Amel). Figure S4. COG function classification of the OGS in M. cingulum. Figure S5. KEGG pathway analysis of the OGS in M. cingulum. Figure S6. GO classification of the OGS in M. cingulum. Figure S7. Venn diagram of the homologous protein-coding genes among three wasps (M. cingulum, C. solmsi, N. vitripennis) and fruit fly (D. melanogaster). Figure S8. Phylogenetic relationship of CSP proteins from A. mellifera, C. floridanum, C. solmsi, M. cingulum, N.vitripennis, S.invicta. Figure S9. Phylogenetic relationship of GR proteins from A. mellifera, C. floridanum, C. solmsi, M. cingulum, N.vitripennis, S.invicta. Figure S10. Phylogenetic relationship of IR proteins from A. mellifera, C. floridanum, C. solmsi, M. cingulum, N.vitripennis, S.invicta. Figure S11. Phylogenetic relationship of OR proteins from C. floridanum, D. melanogaster and M. cingulum. Figure S12. Phylogenetic relationship of OBP proteins from A. mellifera, C. floridanum, C. solmsi, M. cingulum, N.vitripennis, S.invicta. Figure S13. Phylogenetic relationship of SNMP proteins from A.mellifera, C. floridanum, C. solmsi, M. cingulum, N.vitripennis, S.invicta. Figure S14. Phylogenetic relationship of GST proteins from A. mellifera, C. floridanum, C. solmsi, M. cingulum, N.vitripennis, S.invicta. Figure S15. Phylogenetic relationship of P450 proteins from N. vitripennis, D. melanogaster and M. cingulum. Figure S16. Phylogenetic relationship of ABC proteins from M. cingulum and D. melanogaster. Figure S17. Different expression levels of miR-14b in different developmental stages of M. cingulum.Table S1. Genome sequencing data of M. cingulum. Table S2. Estimation of M. cingulum genome size using K-mer analysis. Table S3. Summary of the M. cingulum genome assembly. Table S4. The published insect genomes. Table S5. The genome assembly assessment on different insects. Table S6. Classification of repeat sequences identified in the M. cingulum genome. Table S7. Genome features of the M. cingulum, N. vitripennis and A. mellifera. Table S8. Gene features of M. cingulum, N. vitripennis and A. mellifera. Table S9. The insects with OGSs in InsectBase. Table S10. Hemomucin genes in eight wasps. Table S11. The different gene expression of embryo and pseudogerm transcriptomes in KEGG pathway. Table S12. The differently expressed miRNAs in embryo and mixed embryo transcriptomes. Table S13. Comparison of gene numbers for chemoreception in A.mellifera, C. floridanum, C. solmsi, M. cingulum, N. vitripennis and S. invicta. Table S14. Comparison of gene numbers for Gene families associated with insecticide resistance and detoxification in D. melanogaster, A. mellifera, C. floridanum, C. solmsi, M. cingulum, N. vitripennis and S. invicta. Table S15. Comparison of gene numbers of insect immune in A. mellifera, C. floridanum, C. solmsi, M. cingulum, N. vitripennis and S. invicta. Table S16. The PCR primer for target genes of mci-miR-14b. (PDF 6076 kb