Characterization of a preclinical PET insert in a 7 tesla MRI scanner: beyond NEMA testing

[EN] This study evaluates the performance of the Bruker positron emission tomograph (PET) insert combined with a BioSpec 70/30 USR magnetic resonance imaging (MRI) scanner using the manufacturer acceptance protocol and the NEMA NU 4-2008 for small animal PET. The PET insert is made of 3 rings of 8 monolithic LYSO crystals (50 x 50 x 10 mm(3)) coupled to silicon photomultipliers (SiPM) arrays, conferring an axial and transaxial FOV of 15 cm and 8 cm. The MRI performance was evaluated with and without the insert for the following radiofrequency noise, magnetic field homogeneity and image quality. For the PET performance, we extended the NEMA protocol featuring system sensitivity, count rates, spatial resolution and image quality to homogeneity and accuracy for quantification using several MRI sequences (RARE, FLASH, EPI and UTE). The PET insert does not show any adverse effect on the MRI performances. The MR field homogeneity is well preserved (Diameter Spherical Volume, for 20 mm of 1.98 +/- 4.78 without and -0.96 +/- 5.16 Hz with the PET insert). The PET insert has no major effect on the radiofrequency field. The signal-to-noise ratio measurements also do not show major differences. Image ghosting is well within the manufacturer specifications (<2.5%) and no RF noise is visible. Maximum sensitivity of the PET insert is 11.0% at the center of the FOV even with simultaneous acquisition of EPI and RARE. PET MLEM resolution is 0.87 mm (FWHM) at 5 mm off-center of the FOV and 0.97 mm at 25 mm radial offset. The peaks for true/noise equivalent count rates are 410/240 and 628/486 kcps for the rat and mouse phantoms, and are reached at 30.34/22.85 and 27.94/22.58 MBq. PET image quality is minimally altered by the different MRI sequences. The Bruker PET insert shows no adverse effect on the MRI performance and demonstrated a high sensitivity, sub-millimeter resolution and good image quality even during simultaneous MRI acquisition.We acknowledge the KU Leuven core facility, Molecular Small Animal Imaging Center (MoSAIC), for their support with obtaining scientific data presented in this paper. This work was supported by Stichting tegen Kanker (2015-145, Christophe M. Deroose) and Hercules foundation (AKUL/13/029, Uwe Himmelreich) for the purchase of the PET and MRI equipment respectively. The work was supported by the following funding organizations: European Commission for the PANA project (H2020-NMP-2015-two-stage, grant 686009) and the European ERA-NET project 'CryptoView' (3rd call of the FP7 program Infect-ERA).Gsell, W.; Molinos, C.; Correcher, C.; Belderbos, S.; Wouters, J.; Junge, S.; Heidenreich, M.... (2020). Characterization of a preclinical PET insert in a 7 tesla MRI scanner: beyond NEMA testing. 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Journal of Nuclear Medicine, 59(3), 536-542. doi:10.2967/jnumed.116.187666Townsend, D. W. (2008). Combined Positron Emission Tomography–Computed Tomography: The Historical Perspective. Seminars in Ultrasound, CT and MRI, 29(4), 232-235. doi:10.1053/j.sult.2008.05.006Vandenberghe, S., & Marsden, P. K. (2015). PET-MRI: a review of challenges and solutions in the development of integrated multimodality imaging. Physics in Medicine and Biology, 60(4), R115-R154. doi:10.1088/0031-9155/60/4/r115Vaquero, J. J., & Kinahan, P. (2015). Positron Emission Tomography: Current Challenges and Opportunities for Technological Advances in Clinical and Preclinical Imaging Systems. Annual Review of Biomedical Engineering, 17(1), 385-414. doi:10.1146/annurev-bioeng-071114-040723Von Schulthess, G. K., & Schlemmer, H.-P. W. (2008). A look ahead: PET/MR versus PET/CT. 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Phylogenetic relationships and evolutionary history of the southern hemisphere genus Leptinella Cass. (Compositae, Anthemideae)

The genus Leptinella Cass. (Compositae, Anthemideae) is widely distributed in the southern hemisphere (Australia, Chatham Islands, New Guinea, New Zealand, South America, sub-Antarctic Islands). Leptinella comprises 42 taxa and consists of small perennial and predominantly procumbent herbs. The genus is characterised by a remarkable variety in sex expression: there are populations with monoecious, paradioecious, and dioecious plants. Additionally, Leptinella forms an impressive polyploid complex with chromosome numbers ranging from tetraploid to a chromosome set of 2n = 24x. In the present thesis, different molecular methods are used to reconstruct the phylogenies of the genus Leptinella and related genera. The obtained molecular phylogenies are then used to a) investigate the intergeneric and infrageneric relationships of Leptinella, b) elucidate the origin, the biogeography and the divergence time of the genus, and c) reconstruct the evolution of polyploidy and sex expression in Leptinella. Chapter 2 deals with the intergeneric relationships of Leptinella. One region from the nuclear (ITS) and the chloroplast genome (ndhF) were chosen for amplification and sequencing to reconstruct the molecular phylogeny of the southern hemisphere members of the tribe Anthemideae. The analyses show that the subtribes sensu Bremer and Humphries (1993) are polyphyletic. As a consequence of the non-monophyletic nature of these subtribes, an alternative generic grouping of the southern hemisphere Anthemideae is discussed (Osmitopsis, Cotula-group, Athanasia-grade, Pentzia-clade). The study shows that the genus Leptinella is a member of the basal Cotula-group which also contains seven southern African genera, the South American genus Soliva, and the widespread southern hemisphere genus Cotula. Chapter 3 and 4 deal with the infrageneric phylogeny of the genus Leptinella. For this purpose two different methods were used: DNA sequencing and AFLP fingerprinting. Both methods are suitable for the determination of taxon groups within Leptinella, but failed to resolve the relationships of single taxa. The extensive hybridization and polyploidization in combination with low genetic variation due the young age of Leptinella may be the main points to explain the observed patterns. In chapter 3, three different markers from the nuclear (ITS) and from the chloroplast genome (psbA-trnH, trnC-petN) were sequenced for Leptinella and other members of the Cotula-group. The analyses show that Leptinella is not monophyletic and the genus is nested within Cotula. However, Leptinella and Cotula alpina form a moderate support monophyletic clade in the combined dataset. In the cpDNA and nrDNA dataset this group is not monophyletic. The division of Leptinella into three subgenera according to Lloyd (1972c) is only partly supported by the molecular data. The genus Leptinella is split in two well supported groups: The filicula-group contains taxa from New Guinea and one taxon from Australia. The remaining taxa of Leptinella from New Zealand, South America, the Chatham Islands, the sub-Antarctic islands, and three further taxa from Australia belong to the Leptinella main clade. The latter group is divided into six further groups (dioica-, longipes-, minor-, plumosa-, pectinata-, pyrethrifolia-group). Within these groups most taxa are not monophyletic. The study shows that Leptinella has radiated in the Miocene to Pleistocene. The estimated divergence time for Leptinella is much younger as the supposed break-up of the Gondwana continent. Therefore, the current distribution of Leptinella could be explained only by long distance dispersal events. In chapter 4, AFLP fingerprinting was used to study the phylogeny of the Leptinella main group. The AFLP analysis resulted in three main groups (taxon group A-C) and several subgroups. These groups are partly congruent with the results of the sequencing analysis presented in chapter 3. The results indicate different evolutionary histories of group A and C. Taxon group C is characterised by extensive hybridization and polyploidization, whereas both processes are less frequent in taxon group A. Furthermore, new ploidy level estimations for Leptinella are provided this chapter. Chapter 5 focuses on the evolution of dimorphic sex expression and polyploidy in Leptinella. For this purpose, sex expression and ploidy levels are mapped on the phylogenetic tree of chapter 3. The study shows that monoecy is the ancestral sex expression in Leptinella and dimorphic sex expression (dioecy, paradioecy) has evolved independently at least four times from monoecy. Additionally, a weak correlation was found between dimorphic sex expression and polyploidy. However, neither of two diametrical hypotheses about the correlation of dioecy and polyploidy by Westergaard (1958; break down of dimorphic sex expression through polyploidization) and Miller and Venable (2000; polyploidy as a trigger of the evolution of dioecy) was able to explain the observed patterns in Leptinella

A new subtribal classification of the tribe Anthemideae (Compositae)

A new subtribal classification of the Compositae-Anthemideae is presented based on phylogenetic reconstructions for sequence information of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA) for 103 of the 111 accepted genera of the tribe. Results of the present analyses are compared with results from phylogenetic analyses based on cpDNA ndhF sequence variation and discussed in conjunction with morphological, anatomical, cytological, embryological and phytochemical evidence. As a result, 14 subtribes are circumscribed and described in detail, with information provided concerning the generic members and the geographical distribution of these entities. Four subtribes (i.e. Osmitopsidinae, Phymasperminae, Pentziinae and Leucanthemopsidinae) are described as new to science, for a further subtribe a new name (Glebionidinae, replacing the illegitimate Chrysantheminae) is validated

Characterization of preclinical PET insert for 7T: beyond NEMA testing.

status: publishe

Spectrum of DDC variants causing aromatic l-amino acid decarboxylase (AADC) deficiency and pathogenicity interpretation using ACMG-AMP/ACGS recommendations

Pathogenic variants in dopa decarboxylase (DDC), the gene encoding the aromatic l-amino acid decarboxylase (AADC) enzyme, lead to a severe deficiency of neurotransmitters, resulting in neurological, neuromuscular, and behavioral manifestations clinically characterized by developmental delays, oculogyric crises, dystonia, and severe neurologic dysfunction in infancy. Historically, therapy has been aimed at compensating for neurotransmitter abnormalities, but response to pharmacologic therapy varies, and in most cases, the therapy shows little or no benefit. A novel human DDC gene therapy was recently approved in the European Union that targets the underlying genetic cause of the disorder, providing a new treatment option for patients with AADC deficiency. However, the applicability of human DDC gene therapy depends on the ability of laboratories and clinicians to interpret the results of genetic testing accurately enough to diagnose the patient. An accurate interpretation of genetic variants depends in turn on expert-guided curation of locus-specific databases. The purpose of this research was to identify previously uncharacterized DDC variants that are of pathologic significance in AADC deficiency as well as characterize and curate variants of unknown significance (VUSs) to further advance the diagnostic accuracy of genetic testing for this condition. DDC variants were identified using existing databases and the literature. The pathogenicity of the variants was classified using modified American College of Medical Genetics and Genomics/Association for Molecular Pathology/Association for Clinical Genomic Science (ACMG-AMP/ACGS) criteria. To improve the current variant interpretation recommendations, in silico variant interpretation tools were combined with structural 3D modeling of protein variants and applied comparative analysis to predict the impact of the variant on protein function. A total of 422 variants were identified (http://biopku.org/home/pnddb.asp). Variants were identified on nearly all introns and exons of the DDC gene, as well as the 3' and 5' untranslated regions. The largest percentage of the identified variants (48%) were classified as missense variants. The molecular effects of these missense variants were then predicted, and the pathogenicity of each was classified using a number of variant effect predictors. Using ACMG-AMP/ACGS criteria, 7% of variants were classified as pathogenic, 32% as likely pathogenic, 58% as VUSs of varying subclassifications, 1% as likely benign, and 1% as benign. For 101 out of 108 reported genotypes, at least one allele was classified as pathogenic or likely pathogenic. In silico variant pathogenicity interpretation tools, combined with structural 3D modeling of variant proteins and applied comparative analysis, have improved the current DDC variant interpretation recommendations, particularly of VUSs

Spectrum of DDC variants causing aromatic l-amino acid decarboxylase (AADC) deficiency and pathogenicity interpretation using ACMG-AMP/ACGS recommendations

Pathogenic variants in dopa decarboxylase (DDC), the gene encoding the aromatic l-amino acid decarboxylase (AADC) enzyme, lead to a severe deficiency of neurotransmitters, resulting in neurological, neuromuscular, and behavioral manifestations clinically characterized by developmental delays, oculogyric crises, dystonia, and severe neurologic dysfunction in infancy. Historically, therapy has been aimed at compensating for neurotransmitter abnormalities, but response to pharmacologic therapy varies, and in most cases, the therapy shows little or no benefit. A novel human DDC gene therapy was recently approved in the European Union that targets the underlying genetic cause of the disorder, providing a new treatment option for patients with AADC deficiency. However, the applicability of human DDC gene therapy depends on the ability of laboratories and clinicians to interpret the results of genetic testing accurately enough to diagnose the patient. An accurate interpretation of genetic variants depends in turn on expert-guided curation of locus-specific databases. The purpose of this research was to identify previously uncharacterized DDC variants that are of pathologic significance in AADC deficiency as well as characterize and curate variants of unknown significance (VUSs) to further advance the diagnostic accuracy of genetic testing for this condition. DDC variants were identified using existing databases and the literature. The pathogenicity of the variants was classified using modified American College of Medical Genetics and Genomics/Association for Molecular Pathology/Association for Clinical Genomic Science (ACMG-AMP/ACGS) criteria. To improve the current variant interpretation recommendations, in silico variant interpretation tools were combined with structural 3D modeling of protein variants and applied comparative analysis to predict the impact of the variant on protein function. A total of 422 variants were identified (http://biopku.org/home/pnddb.asp). Variants were identified on nearly all introns and exons of the DDC gene, as well as the 3' and 5' untranslated regions. The largest percentage of the identified variants (48%) were classified as missense variants. The molecular effects of these missense variants were then predicted, and the pathogenicity of each was classified using a number of variant effect predictors. Using ACMG-AMP/ACGS criteria, 7% of variants were classified as pathogenic, 32% as likely pathogenic, 58% as VUSs of varying subclassifications, 1% as likely benign, and 1% as benign. For 101 out of 108 reported genotypes, at least one allele was classified as pathogenic or likely pathogenic. In silico variant pathogenicity interpretation tools, combined with structural 3D modeling of variant proteins and applied comparative analysis, have improved the current DDC variant interpretation recommendations, particularly of VUSs

Allelic phenotype values: a model for genotype-based phenotype prediction in phenylketonuria

PURPOSE The nature of phenylalanine hydroxylase (PAH) variants determines residual enzyme activity, which modifies the clinical phenotype in phenylketonuria (PKU). We exploited the statistical power of a large genotype database to determine the relationship between genotype and phenotype in PKU. METHODS A total of 9336 PKU patients with 2589 different genotypes, carrying 588 variants, were investigated using an allelic phenotype value (APV) algorithm. RESULTS We identified 251 0-variants encoding inactive PAH, and assigned APVs (0 = classic PKU; 5 = mild PKU; 10 = mild hyperphenylalaninaemia) to 88 variants in PAH-functional hemizygous patients. The genotypic phenotype values (GPVs) were set equal to the higher-APV allele, which was assumed to be dominant over the lower-APV allele and to determine the metabolic phenotype. GPVs for 8872 patients resulted in cut-off ranges of 0.0-2.7 for classic PKU, 2.8-6.6 for mild PKU and 6.7-10.0 for mild hyperphenylalaninaemia. Genotype-based phenotype prediction was 99.2% for classic PKU, 46.2% for mild PKU and 89.5% for mild hyperphenylalaninaemia. The relationships between known pretreatment blood phenylalanine levels and GPVs (n = 4217), as well as tetrahydrobiopterin responsiveness and GPVs (n = 3488), were significant (both P < 0.001). CONCLUSIONS APV and GPV are powerful tools to investigate genotype-phenotype associations, and can be used for genetic counselling of PKU families

MRI-based retrospective gating for PET reconstruction in rats: implementation and proof of principle study

status: publishe

MRI-based retrospective gating for PET reconstruction in rats: implementation and proof of principle study

status: publishe

ADP-dependent glucokinase regulates energy metabolism via ER-localized glucose sensing

Modulation of energy metabolism to a highly glycolytic phenotype, i.e. Warburg effect, is a common phenotype of cancer and activated immune cells allowing increased biomass-production for proliferation and cell division. Endoplasmic reticulum (ER)-localized ADP-dependent glucokinase (ADPGK) has been shown to play a critical role in T cell receptor activation-induced remodeling of energy metabolism, however the underlying mechanisms remain unclear. Therefore, we established and characterized in vitro and in vivo models for ADPGK-deficiency using Jurkat T cells and zebrafish. Upon activation, ADPGK knockout Jurkat T cells displayed increased cell death and ER stress. The increase in cell death resulted from a metabolic catastrophe and knockout cells displayed severely disturbed energy metabolism hindering induction of Warburg phenotype. ADPGK knockdown in zebrafish embryos led to short, dorsalized body axis induced by elevated apoptosis. ADPGK hypomorphic zebrafish further displayed dysfunctional glucose metabolism. In both model systems loss of ADPGK function led to defective N - and O-g lycosylation. Overall, our data illustrate that ADPGK is part of a glucose sensing system in the ER modulating metabolism via regulation of N - and O-glycosylation