Genetic Structure of Cydia pomonella Granulovirus Isolates and their Potential in Overcoming Resistance in Codling Moth

Cydia pomonella granulovirus (CpGV) is a highly virulent pathogen of codling moth (CM, Cydia pomonella L.) larvae. It has been developed to one of the most successful commercial baculovirus biocontrol agents used on hundred thousands of hectares of pome fruit production worldwide. In recent years, however, three types (I to III) of field resistance to CpGV as well as the existence of resistance-breaking CpGV isolates have been discovered, providing an ideal model for studying baculovirus-host adaptation. This thesis aims to elucidate the potential of recently collected isolates of CpGV from northwest China to infect susceptible and resistant CM colonies and to study the stability and restoration of type I resistance in laboratory rearing by mass-crossing and selection. To further explore the genotypic and biological differences of CpGV, the population structure of 20 CpGV isolates was analyzed on the basis of Illumina next generation sequence (NGS) data. The isolates included seven new Chinese CpGV isolates, termed CpGV-ZY, -JQ, -ALE, -KS1, -KS2, -ZY2 and -WW, the re-sequenced isolates CpGV-M, -S, -E2, -I12 and the Iranian isolate CpGV-I0X, as well as the active ingredients of commercial virus selections from MadexPlus, MadexMAX, MadexTOP (V15), V14, V34, V45 and Carpovirusine EVO2. First, resistance testing or full range bioassays were conducted to determine the resistance-breaking capacity or the median lethal concentration (LC50) of the Chinese CpGV isolates against susceptible and three resistant CM strains, representing type I to III resistance (Chapter 2). The isolates were further screened for the presence of the additional 2×12 bp repeat insertion in CpGV gene pe38 (ORF24), which had been proposed to be the target of type I resistance in the Mexican isolate CpGV-M. It was found that the isolates CpGV-JQ, -KS1 and -ZY2 could break type I resistance, though a distinct delay was observed in the infection process. The isolates followed the previously established “pe38 model” of resistance-breaking, except CpGV-WW, which lacked the 2×12 bp repeat involved in resistance-breaking but failed to overcome type I resistance. However, CpGV-WW was able to overcome type II and type III resistance. Correlation of bioassay results and the isolates’ pe38 repeat structure were in agreement with the potential role of pe38 as the major target for resistance in CpRR1, except for CpGV-WW. Second, resistance tests with CpGV-M revealed a certain decline of the resistance level of CM strain CpRR1, expressing type I resistance, after it had been reared for several years without virus pressure (Chapter 3). Therefore, two newly selected lines, CpRR1_F5 and CpRR1_F7, were established by mass crossing experiments combined with virus selection on CpGV-M. Resistance level of the newly selected lines was determined by full range bioassays. The successful selection process resulted in a 15- to 160-fold increase of the LC50 of CpRR1_F5 resistance compared to CpRR1, suggesting that the rearing in absence of virus selection was most likely the main factor involved the observed resistance decline of CpRR1. Additionally, some fitness costs of fecundity were recorded in the re-selected CpRR1_F5. Single-pair crossing of CpRR1_F5 and CpRR1-F7 with susceptible CM, followed by a resistance testing with a discriminating concentration of CpGV-M occlusion bodies, revealed a dominant but not fully sex-linked inheritance arguing for a partial change of previous genetic traits in CpRR1. Third, in Chapter 4 the genomic difference among seven new Chinese CpGV isolates could provide some answers for the virulence difference observed in bioassays. After Illumina NGS sequencing, the genome annotation and phylogenetic analyses of these isolates indicated that the genomes were highly conserved and related to known CpGV isolates, despite a considerable geographic distance. However, two new phylogenetic lineages, termed genome groups F (CpGV-JQ and -ZY2) and G (CpGV-ALE), were proposed in addition to previous phylogenetic genome groups A to E. The genetic composition of the isolates was further quantified on the basis of previously identified genome group specific single nucleotide polymorphisms (SNPs). In addition of 223 new SNP positions out of total 563 SNPs were detected against CpGV-M reference sequence, which represented virus characteristics of Chinese isolates. Whereas CpGV-WW was proposed to be genetically highly homogeneous, belonging to genome group E, the other six isolates were mixtures of at least two genotypes. Thereof CpGV-ZY, -KS1 and -KS2 were highly similar and were composed of variable ratios of genome group A (CpGV-M) and genome group E (CpGV-WW). Detailed quantification of the 12 bp repeat unit of pe38 corresponded to the results obtained from PCR and Sanger sequence analyses (Chapter 2). Fourth, to achieve a fully comprehensive perspective of CpGVs of different origin, 20 CpGV isolates, including twelve natural isolates from different geographic locations and eight selected CpGV strains, were analyzed together for the distribution and frequency of single nucleotide polymorphisms (SNPs) in NGS genome data and for the abundance of the 12 bp repeat unit in pe38 (Chapter 5). The results indicated that CpGV-M, -WW, -S and MadexPlus were genetically highly homogenous isolates with a low rate of polymorphisms, while other isolates were composed of two or more genome groups at different ratios. Based on hierarchical clustering on principal components (HCPC) analysis, six distinct clusters were proposed, which represents the previously proposed main phylogenetic lineages, though the insertions and deletions were not included in cluster analysis. Relative location of different isolates in HCPC further reflected the ratio of variable compositions of different genome groups. For the quantification of the proportions of 1-5×12 bp repeat units in the different CpGV isolates a “read counting” method was developed and showed a high diversity and less conserved characteristics in pe38 than literature reported before. The established methods for SNP quantification and HCPC analysis provide novel tools to decipher the molecular complexity of genome mixtures in virus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than genome consensus based analyses. In summary, the results in this thesis showed that resistance loss in CpRR1 is developing in laboratory under continuous rearing without virus pressure. Newly discovered CpGV isolates exhibited high potential for control of known types of field resistance of CM. The established methods to determine positional SNP distribution can be easily extended to other (baculo)viruses to assess isolate composition and genetic diversity and to study quality and stability of virus mixtures during propagation. It can be further applied to determine its potential for control of resistant CM on molecular level, since CpGV isolates with the similar virulence patterns were found to be grouped together considering their spatial location in factor map of HCPC. Understanding CpGV population structure and the genetic adaption between baculovirus and host insect give a crucial blueprint to improve current strategies of CpGV resistance management in the field

DRL-GAN: dual-stream representation learning GAN for low-resolution image classification in UAV applications.

Identifying tiny objects from extremely low resolution (LR) UAV-based remote sensing images is generally considered as a very challenging task, because of very limited information in the object areas. In recent years, there have been very limited attempts to approach this problem. These attempts intend to deal with LR image classification by enhancing either the poor image quality or image representations. In this paper, we argue that the performance improvement in LR image classification is affected by the inconsistency of the information loss and learning priority on Low-Frequency (LF) components and High-Frequency (HF) components. To address this LF-HF inconsistency problem, we propose a Dual-Stream Representation Learning Generative Adversarial Network (DRL-GAN).The core idea is to produce super image representations optimal for LR recognition by simultaneously recovering the missing information in LF and HF components, respectively, under the guidance of high-resolution (HR) images. We evaluate the performance of DRL-GAN on the challenging task of LR image classification. A comparison of the experimental results on the LR benchmark, namely HRSC and CIFAR-10, and our newly collected “WIDER-SHIP” dataset demonstrates the effectiveness of our DRL-GAN, which significantly improves the classification performance, with up to 10% gain on average

Lattice marginal reconstruction enabled high ambient-tolerance Perovskite Quantum Dots phototransistors

Perovskite quantum dots (PeQDs) have been developed rapidly as photoactive materials in hybrid phototransistors because of their strong light absorption, broad bandgap customizability, and defect-tolerance in charge-transport properties. The solvent treatment has been well recognized as a practical approach for improving the charge transport of PeQDs and the photoresponsivity of PeQD phototransistors. However, there is a lack of fundamental understanding of the origin of its impacts on the material’s ambient stability as well as phototransistor’s operational lifetime. Especially, the relationship between surface ligands dissociation and their microstructural reconstruction has not been fully elucidated so far. Herein, we report that a simultaneous enhancement of photoresponsivity and ambient tolerance for PeQD-based hybrid phototransistors can be realized via medium-polarity-solvent treatment on solid-state PeQDs. Our comprehensive optoelectronic characterization and electron microscopic study reveals that the crystal morphology, instead of surface ligands, is the dominating factor that results in the PeQD’s stability enhancement associated with the preservation of optical property and quantum confinement. Besides, we unveil a marginal reconstruction process occurred during solvent treatment, which opens up a new route for facets-oriented attachment of PeQDs along the zone axis to suppress the damage from water molecules penetration. Our study yields a new understanding of the solvent impact on PeQD microstructures reconstruction and suggests new routes for perovskite materials and corresponding device operational stability enhancement

Lattice Marginal Reconstruction Enabled High Ambient-Tolerance Perovskite Quantum Dots Phototransistors

Perovskite quantum dots (PeQDs) have been developed rapidly as photoactive materials in hybrid phototransistors because of their strong light absorption, broad bandgap customizability, and defect-tolerance in charge-transport properties. The solvent...</p

Partial Loss of Inheritable Type I Resistance of Codling Moth to Cydia pomonella granulovirus

Current knowledge of the field resistance of codling moth (CM, Cydia pomonella, L) against Cydia pomonella granulovirus (CpGV) is based mainly on the interaction between the Mexican isolate CpGV-M and CpRR1, a genetically homogeneous CM inbreed line carrying type I resistance. The resistance level of laboratory-reared CpRR1 to CpGV-M was recently found to have decreased considerably, compared to the initially high resistance. To understand the background of this phenomenon, CpRR1 larvae were exposed over several generations to CpGV-M for re-selection of the original resistance level. After five and seven generations of selection, new CpRR1_F5 and CpRR1_F7 lines were established. The resistance ratio of these selected lines was determined by full range bioassays. The CpRR1_F5 strain regained a higher level of resistance against CpGV up to 104-fold based on LC50 values compared to susceptible larvae (CpS), which indicated that the absence of virus selection had resulted in a reduction of resistance under laboratory rearing conditions. In addition, some fitness costs of fecundity were observed in CpRR1_F5. Single-pair crossings between CpRR1_F5 or CpRR1_F7 with susceptible CpS moths revealed a dominant but not fully sex-linked inheritance, which suggests a partial loss of previous resistance traits in CpRR1

Non-Probabilistic Reliability Bounds Method for Series Structural Systems Considering Redundant Failure Modes

Non-probabilistic structural reliability analysis is based on the convex model and more applicable for practical engineering problems with limited samples. Recently, the authors proposed a non-probabilistic reliability bounds method (NRBM) for series structural systems as an effective means for the assessment of systems’ non-probabilistic reliability. A novel non-probabilistic reliability bounds method considering redundant failure modes is proposed in this paper for series structural systems to further improve the efficiency and accuracy of the NRBM. By decomposing the system into several subsystems with two or three failure modes, three identification criteria for redundant failure modes are developed for these subsystems. A bounding formula for the system’s non-probabilistic failure degree is then derived after removing the redundant failure modes. An investigation of three numerical examples indicates that the proposed method has a higher efficiency and at least equivalent accuracy compared to the NRBM

Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses

Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool &ldquo;bacsnp&rdquo;, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample