Novel types of resistance of codling moth to Cydia pomonella granulovirus

The Cydia pomonella granulovirus (CpGV, Baculoviridae) is an important biological control agent to control codling moth (CM; Cydia pomonella, L.) in organic and integrated pome fruit and walnut production. The CpGV is highly host-specific and supremely virulent for early larval stages of CM, additionally safe for the environment and other animals and humans. Since 2005, resistance against the widely used Mexican isolate (CpGV-M) has been reported from different countries in Europe. Until now, over 40 apple orchards with resistance to CpGV-M based products were identified. For several CM field populations in Europe a Z-linked, monogenetic and dominant inheritance was proposed suggesting a highly similar mode of resistance, termed type I resistance. Type I resistance is targeted only against the isolate CpGV-M and specific the 24 bp insertion in its viral gene pe38. Some other CpGV isolates collected from infected larvae of different geographical regions, lacking this 24 bp repetitive insertion in their pe38 gene and caused virus infection in resistant larvae. Some of these isolates, e.g. CpGV-S, were eventually registered to re-establish the efficient control of CM larvae in the field. Recently, two CM field populations, called NRW-WE and SA-GO, with an untypically high resistance level against CpGV-M and other CpGV isolates, were identified and a novel resistance type II was proposed. This thesis focuses on the elucidation of their mode of inheritance and their cellular mechanism. For generating genetically homogenous resistant strains out of the field population NRW-WE, larvae were selected by repeated mass crosses and selection under virus pressure, using the two isolates CpGV-M and CpGV-S, respectively. The resulting strains CpR5M and CpR5S showed a clear cross-resistance to both CpGV-M and CpGV-S. By crossing and backcrossing experiments between CpR5M or CpR5S and susceptible CM strain (CpS) an autosomal dominant and monogenetic inheritance of resistance was elucidated. The autosomal inheritance mode supported the evidence of a second type (type II) of resistance. Initially, an interchromosomal rearrangement involving the Z chromosome was hypothesized to explain the translocation from a Z-chromosomal to an autosomal inheritance. This hypothesis, however, could be clearly ruled out because a highly conserved synteny of all probed Z-linked genes was observed for different resistant CM strains when fluorescence in situ hybridization with marker genes (BAC-FISH) was applied. Considering the cross-resistance in type II resistance, CM larvae were treated with single or mixtures of the isolates CpGV-M and CpGV-S. For these treatments no virus infection was observed but a recombinant of CpGV-M containing the pe38 gene of CpGV-S caused high mortality. The results indicated that beyond the known pe38 related mechanism of type I resistance against CpGV-M, a second mechanism seemed to exist in type II resistance. With CpR5M and CpS budded viruses injections, circumventing initial midgut infection, gave further evidence that resistance against CpGV-S is midgut-related. A fluoresecence-quenching assay using rhodamin-18 labeled occlusion derived viruses could not fully elucidate whether receptor binding or an intercellular midgut factor is involved in type II resistance. The results led to the model of two different but genetically linked resistance mechanisms in the type II resistant CM larvae: resistance against CpGV-M is systemic and targeted against the pe38 gene, whereas resistance against CpGV-S is based on an unidentified midgut factor, inhibiting initiation of infection. A further CM field population, termed SA-GO, was also investigated for the biological and genetic background of CpGV resistance. Crossing experiments between CpS and field collected larvae of SA-GO, followed by resistance testing with two CpGV isolates revealed differences in the susceptibility and the mode of inheritance compared to the one found in type I or type II resistance of CM. Single-pair inbreeding generated the genetically more homogenous resistant strain CpRGO. Reciprocal hybrid crosses and backcrosses between individuals of CpRGO and susceptible CpS observed a dominant and polygenic inheritance of resistance in the majority of crosses. Resistance to CpGV-S appeared to be autosomal and dominant for larval survivorship but recessive when success of pupation of the hybrids was considered. Resistance of CpRGO to CpGV-M however, is proposed to be both autosomal and Z-linked inherited, since only male larvae were able to pupate, similar to the type I resistance. CpRGO was therefore termed type III resistance. When the efficacy of different CpGV isolates classified to all known CpGV genome groups (A - E) was tested with neonates of all resistant strains. CpGV isolates of the genome groups B and C were able to cause significant mortality in larvae of all resistance types. In addition, CpGV of genome group D caused high mortality in type III resistant CM strain, whereas type I resistance was broken by all known CpGV genome groups, except group A. When isolates of commercial CpGV products were tested in the resistant CM strains, it was found that the commercially used CpGV isolates R5 and 0006 did break only type I and type III resistance, whereas isolate V15 was able to cause high mortality in all resistant types. In conclusion, two types of CpGV resistance, type II and type III were identified and showed a high heterogeneity in their mode of inheritance, mode of action and response to CpGV isolates of different genome groups. The major finding of this thesis is that field resistance of CM to CpGV is genetically and functionally variable and needs to be carefully addressed when resistance management strategies are developed for CM control in the field

Chronostratigraphy of two Late Pleistocene loess-palaeosol sequences in the Rhône Valley (southeast France)

International audienceA sedimentological and chronostratigraphical investigation was carried out on two loess sections located in the Mediterranean area in southeast France along the Rhône River (Lautagne) and the lower reach of a tributary of the Rhône River (Collias). High-resolution sampling (5–20 cm) for magnetic susceptibility, grain size distribution (including non-parametric end-member modelling), colour reflectance and geochemistry was performed. The chronology was based on luminescence dating of quartz grains and radiocarbon dating of small gastropod shells, coupled with hierarchical Bayesian modelling. The Collias section (~8 m thick) records the whole last climatic cycle. It comprises a thick red basal pedocomplex S1 developed during the Last Interglacial and the Early Glacial, similar to that observed elsewhere in southern and southeastern Europe. Loess deposition occurred during the Lower (L1L2) and the Upper Pleniglacial (L1L1). It was interrupted by soil formation during the Middle Pleniglacial, of which a brown Bwk horizon has been preserved (L1S1). By contrast, the ~5 m thick Lautagne section provides a detailed record of the Upper Pleniglacial. Weakly developed hydromorphic soils are correlated with the Greenland Interstadials GI-4 to GI-2, while the main period of coarse loess sedimentation corresponds to the Greenland Stadials GS-5 to GS-2. At a regional scale, the time of loess deposition ranges between 38.5 ka and 12 ka, with a peak at ~28–24 ka, overlapping with the maximal advance of the Alpine Ice Sheet (AIS). This strongly suggests that regional glacier dynamics was the main driver of loess sedimentation

Application of an artificial intelligence-based tool in [18F]FDG PET/CT for the assessment of bone marrow involvement in multiple myeloma

Purpose: [18F]FDG PET/CT is an imaging modality of high performance in multiple myeloma (MM). Nevertheless, the inter-observer reproducibility in PET/CT scan interpretation may be hampered by the different patterns of bone marrow (BM) infiltration in the disease. Although many approaches have been recently developed to address the issue of standardization, none can yet be considered a standard method in the interpretation of PET/CT. We herein aim to validate a novel three-dimensional deep learning-based tool on PET/CT images for automated assessment of the intensity of BM metabolism in MM patients. Materials and methods: Whole-body [18F]FDG PET/CT scans of 35 consecutive, previously untreated MM patients were studied. All patients were investigated in the context of an open-label, multicenter, randomized, active-controlled, phase 3 trial (GMMG-HD7). Qualitative (visual) analysis classified the PET/CT scans into three groups based on the presence and number of focal [18F]FDG-avid lesions as well as the degree of diffuse [18F]FDG uptake in the BM. The proposed automated method for BM metabolism assessment is based on an initial CT-based segmentation of the skeleton, its transfer to the SUV PET images, the subsequent application of different SUV thresholds, and refinement of the resulting regions using postprocessing. In the present analysis, six different SUV thresholds (Approaches 1–6) were applied for the definition of pathological tracer uptake in the skeleton [Approach 1: liver SUVmedian 7 1.1 (axial skeleton), gluteal muscles SUVmedian 7 4 (extremities). Approach 2: liver SUVmedian 7 1.5 (axial skeleton), gluteal muscles SUVmedian 7 4 (extremities). Approach 3: liver SUVmedian 7 2 (axial skeleton), gluteal muscles SUVmedian 7 4 (extremities). Approach 4: ≥ 2.5. Approach 5: ≥ 2.5 (axial skeleton), ≥ 2.0 (extremities). Approach 6: SUVmax liver]. Using the resulting masks, subsequent calculations of the whole-body metabolic tumor volume (MTV) and total lesion glycolysis (TLG) in each patient were performed. A correlation analysis was performed between the automated PET values and the results of the visual PET/CT analysis as well as the histopathological, cytogenetical, and clinical data of the patients. Results: BM segmentation and calculation of MTV and TLG after the application of the deep learning tool were feasible in all patients. A significant positive correlation (p < 0.05) was observed between the results of the visual analysis of the PET/CT scans for the three patient groups and the MTV and TLG values after the employment of all six [18F]FDG uptake thresholds. In addition, there were significant differences between the three patient groups with regard to their MTV and TLG values for all applied thresholds of pathological tracer uptake. Furthermore, we could demonstrate a significant, moderate, positive correlation of BM plasma cell infiltration and plasma levels of β2-microglobulin with the automated quantitative PET/CT parameters MTV and TLG after utilization of Approaches 1, 2, 4, and 5. Conclusions: The automated, volumetric, whole-body PET/CT assessment of the BM metabolic activity in MM is feasible with the herein applied method and correlates with clinically relevant parameters in the disease. This methodology offers a potentially reliable tool in the direction of optimization and standardization of PET/CT interpretation in MM. Based on the present promising findings, the deep learning-based approach will be further evaluated in future prospective studies with larger patient cohorts

Chromatin accessibility dynamics across C. elegans development and ageing.

An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here, we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one Caenorhabditis elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.The work was supported by Wellcome Trust Senior Research Fellowships to JA (054523 and 101863), a Wellcome Trust PhD fellowship to JJ (097679), a Sir Robert Edwards Scholarship from Churchill College, an English Speaking Union Graduate Scholarship, and funding from the Cambridge Trust to MS, a Medical Research Council DTP studentship to JS, and a Thouron award to CW. This study was also supported by the European Sequencing and Genotyping Infrastructure (funded by the EC, FP7/2007-2013) under Grant Agreement 26205 (ESGI) as part of the transnational access program. We thank Drs. Hans Lehrach and Marie-Laure Yaspo for generous support of the ESGI project, Dr. Marc Sultan for setting up sequencing technology platforms, and Mathias Linser and the rest of the sequencing team of the Department of Vertebrate Genomics at the Max Planck Institute for Molecular Genetics for technical assistance. We also acknowledge core support from the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492)

Optimizing expert and patient input in pediatric trial design : lessons learned and recommendations from a collaboration between conect4children and European Patient‐CEntric ClinicAl TRial PLatforms

Advice from multiple stakeholders is required to design the optimal pediatric clinical trial. We present recommendations for acquiring advice from trial experts and patients/caregivers, derived from advice meetings that were performed through a collaboration of the Collaborative Network for European Clinical Trials for Children (c4c) and the European Patient‐CEntric ClinicAl TRial PLatforms (EU‐PEARL). Three advice meetings were performed: (1) an advice meeting for clinical and methodology experts, (2) an advice meeting for patients/caregivers, and (3) a combined meeting with both experts and patients/caregivers. Trial experts were recruited from c4c database. Patients/caregivers were recruited through a patient organization. Participants were asked to provide input on a trial protocol, including endpoints, outcomes, and the assessment schedule. Ten experts, 10 patients, and 13 caregivers participated. The advice meetings resulted in modification of eligibility criteria and outcome measures. We have provided recommendations for the most effective meeting type per protocol topic. Topics with limited options for patient input were most efficiently discussed in expert advice meetings. Other topics benefit from patient/caregiver input, either through a combined meeting with experts or a patients/caregivers‐only advice meeting. Some topics, such as endpoints and outcome measures, are suitable for all meeting types. Combined sessions profit from synergy between experts and patients/caregivers, balancing input on protocol scientific feasibility and acceptability. Both experts and patients/caregivers provided critical input on the presented protocol. The combined meeting was the most effective methodology for most protocol topics. The presented methodology can be used effectively to acquire expert and patient feedback