Diffusion microscopic MRI of the mouse embryo: Protocol and practical implementation in the splotch mouse model.
ABSTRACT: Advanced methodologies for visualizing novel tissue contrast are essential for phenotyping the ever-increasing number of mutant mouse embryos being generated. Although diffusion microscopic MRI (?MRI) has been used to phenotype embryos, widespread routine use is limited by extended scanning times, and there is no established experimental procedure ensuring optimal data acquisition.We developed two protocols for designing experimental procedures for diffusion ?MRI of mouse embryos, which take into account the effect of embryo preparation and pulse sequence parameters on resulting data. We applied our protocols to an investigation of the splotch mouse model as an example implementation.The protocols provide DTI data in 24 min per direction at 75 ?m isotropic using a three-dimensional fast spin-echo sequence, enabling preliminary imaging in 3 h (6 directions plus one unweighted measurement), or detailed imaging in 9 h (42 directions plus six unweighted measurements). Application to the splotch model enabled assessment of spinal cord pathology.We present guidelines for designing diffusion ?MRI experiments, which may be adapted for different studies and research facilities. As they are suitable for routine use and may be readily implemented, we hope they will be adopted by the phenotyping community.
Project description:Given the restricted total scanning time for clinical neuroimaging, it is unclear whether clinical diffusion MRI protocols would benefit more from higher spatial resolution or higher angular resolution. In this work, we investigated the relative benefit of improving spatial or angular resolution in diffusion MRI to separate two parallel running white matter tracts that are targets for deep brain stimulation: the anterior thalamic radiation and the supero-lateral branch of the medial forebrain bundle. Both these tracts are situated in the ventral anterior limb of the internal capsule, and recent studies suggest that targeting a specific tract could improve treatment efficacy. Therefore, we scanned 19 healthy volunteers at 3T and 7T according to three diffusion MRI protocols with respectively standard clinical settings, increased spatial resolution of 1.4 mm, and increased angular resolution (64 additional gradient directions at b = 2200s/mm2). We performed probabilistic tractography for all protocols and quantified the separability of both tracts. The higher spatial resolution protocol improved separability by 41% with respect to the clinical standard, presumably due to decreased partial voluming. The higher angular resolution protocol resulted in increased apparent tract volumes and overlap, which is disadvantageous for application in precise treatment planning. We thus recommend to increase the spatial resolution for deep brain stimulation planning to 1.4 mm while maintaining angular resolution. This recommendation complements the general advice to aim for high angular resolution to resolve crossing fibers, confirming that the specific application and anatomical considerations are leading in clinical diffusion MRI protocol optimization.
Project description:BACKGROUND:Neuroscience research in brain development and disorders can benefit from an in vivo animal model that portrays normal white matter (WM) development trajectories and has a sufficiently large cerebrum for imaging with human MRI scanners and protocols. NEW METHOD:Twelve three-month-old Sinclair™ miniature pigs (Sus scrofa domestica) were longitudinally evaluated during adolescent development using advanced diffusion weighted imaging (DWI) focused on cerebral WM. Animals had three MRI scans every 23.95?±?3.73?days using a 3-T scanner. The DWI imaging protocol closely modeled advanced human structural protocols and consisted of fifteen b-shells (b?=?0-3500?s/mm2) with 32-directions/shell. DWI data were analyzed using diffusion kurtosis and bi-exponential modeling that provided measurements that included fractional anisotropy (FA), radial kurtosis, kurtosis anisotropy (KA), axial kurtosis, tortuosity, and permeability-diffusivity index (PDI). RESULTS:Significant longitudinal effects of brain development were observed for whole-brain average FA, KA, and PDI (all p?<?0.001). There were expected regional differences in trends, with corpus callosum fibers showing the highest rate of change. COMPARISON WITH EXISTING METHOD(S):Pigs have a large, gyrencephalic brain that can be studied using clinical MRI scanners/protocols. Pigs are less complex than non-human primates thus satisfying the "replacement" principle of animal research. CONCLUSIONS:Longitudinal effects were observed for whole-brain and regional diffusion measurements. The changes in diffusion measurements were interepreted as evidence for ongoing myelination and maturation of cerebral WM. Corpus callosum and superficial cortical WM showed the expected higher rates of change, mirroring results in humans.
Project description:Diffusion-weighted Magnetic Resonance Imaging (dMRI) has relevant applications in the microstructural characterization of the spinal cord, especially in neurodegenerative diseases. Animal models have a pivotal role in the study of such diseases; however, in vivo spinal dMRI of small animals entails additional challenges that require a systematical investigation of acquisition parameters. The purpose of this study is to compare three acquisition protocols and identify the scanning parameters allowing a robust estimation of the main diffusion quantities and a good sensitivity to neurodegeneration in the mouse spinal cord. For all the protocols, the signal-to-noise and contrast-to noise ratios and the mean value and variability of Diffusion Tensor metrics were evaluated in healthy controls. For the estimation of fractional anisotropy less variability was provided by protocols with more diffusion directions, for the estimation of mean, axial and radial diffusivity by protocols with fewer diffusion directions and higher diffusion weighting. Intermediate features (12 directions, b = 1200 s/mm2) provided the overall minimum inter- and intra-subject variability in most cases. In order to test the diagnostic sensitivity of the protocols, 7 G93A-SOD1 mice (model of amyotrophic lateral sclerosis) at 10 and 17 weeks of age were scanned and the derived diffusion parameters compared with those estimated in age-matched healthy animals. The protocols with an intermediate or high number of diffusion directions provided the best differentiation between the two groups at week 17, whereas only few local significant differences were highlighted at week 10. According to our results, a dMRI protocol with an intermediate number of diffusion gradient directions and a relatively high diffusion weighting is optimal for spinal cord imaging. Further work is needed to confirm these results and for a finer tuning of acquisition parameters. Nevertheless, our findings could be important for the optimization of acquisition protocols for preclinical and clinical dMRI studies on the spinal cord.
Project description:We previously observed a complex pattern of differences in white matter (WM) microstructure between preterm-born (PT) and full-term-born (FT) children and adolescents age 9-17 years. The aim of this study was to determine if the same differences exist as early as age 6 years.We obtained diffusion MRI (dMRI) scans in children born PT at age 6 years (n = 20; 11 males) and FT (n = 38; 14 males), using two scanning protocols: 30 diffusion directions (b = 1000 s/mm2) and 96 diffusion directions (b = 2500 s/mm2). We used deterministic tractography and analyzed fractional anisotropy (FA) along bilateral cerebral WM pathways that demonstrated differences in the older sample.Compared to the FT group, the PT group showed (1) significantly decreased FA in the uncinate fasciculi and forceps major and (2) significantly increased FA in the right anterior thalamic radiation, inferior fronto-occipital fasciculi, and inferior longitudinal fasciculi. This pattern of group differences resembles findings in the previous study of older PT and FT participants. Group differences were similar across dMRI acquisition protocols.The underlying neurobiology driving the pattern of PT-FT differences in FA is present as early as age 6 years. Generalization across dMRI acquisition protocols demonstrates the robustness of group differences in FA. Future studies will use quantitative neuroimaging techniques to understand the tissue properties that give rise to this consistent pattern of WM differences after PT birth.
Project description:Spina bifida is one of the most common of all human structural birth defects. Despite considerable effort over several decades, the causes and mechanisms underlying this malformation remain poorly characterized.To better understand the pathogenesis of this abnormality, we conducted a microarray study using Mouse Whole Genome Bioarrays which have ~36,000 gene targets, to compare gene expression profiles between two mouse models; CXL-Splotch and FKBP8(Gt(neo)) which express a similar spina bifida phenotype. We anticipated that there would be a collection of overlapping genes or shared genetic pathways at the molecular level indicative of a common mechanism underlying the pathogenesis of spina bifida during embryonic development.A total of 54 genes were determined to be differentially expressed (25 downregulated, 29 upregulated) in the FKBP8Gt((neo)) mouse embryos; whereas 73 genes were differentially expressed (56 downregulated, 17 upregulated) in the CXL-Splotch mouse relative to their wild-type controls. Remarkably, the only two genes that showed decreased expression in both mutants were v-ski sarcoma viral oncogene homolog (Ski), and Zic1, a transcription factor member of the zinc finger family. Confirmation analysis using quantitative real-time (qRT)-PCR indicated that only Zic1 was significantly decreased in both mutants. Gene ontology analysis revealed striking enrichment of genes associated with mesoderm and central nervous system development in the CXL-Splotch mutant embryos, whereas in the FKBP8(Gt(neo)) mutants, the genes involved in dorsal/ventral pattern formation, cell fate specification, and positive regulation of cell differentiation were most likely to be enriched. These results indicate that there are multiple pathways and gene networks perturbed in mouse embryos with shared phenotypes.
Project description:Diffusion microstructural imaging techniques have attracted great interest in the last decade due to their ability to quantify axon diameter and volume fraction in healthy and diseased human white matter. The estimates of compartment size and volume fraction continue to be debated, in part due to the lack of a gold standard for validation and quality control. In this work, we validate diffusion MRI estimates of compartment size and volume fraction using a novel textile axon ("taxon") phantom constructed from hollow polypropylene yarns with distinct intra- and extra-taxonal compartments to mimic white matter in the brain. We acquired a comprehensive set of diffusion MRI measurements in the phantom using multiple gradient directions, diffusion times and gradient strengths on a human MRI scanner equipped with maximum gradient strength (Gmax) of 300?mT/m. We obtained estimates of compartment size and restricted volume fraction through a straightforward extension of the AxCaliber/ActiveAx frameworks that enables estimation of mean compartment size in fiber bundles of arbitrary orientation. The voxel-wise taxon diameter estimates of 12.2?±?0.9??m were close to the manufactured inner diameter of 11.8?±?1.2??m with Gmax?=?300?mT/m. The estimated restricted volume fraction demonstrated an expected decrease along the length of the fiber bundles in accordance with the known construction of the phantom. When Gmax was restricted to 80?mT/m, the taxon diameter was overestimated, and the estimates for taxon diameter and packing density showed greater uncertainty compared to data with Gmax?=?300?mT/m. In conclusion, the compartment size and volume fraction estimates resulting from diffusion measurements on a human scanner were validated against ground truth in a phantom mimicking human white matter, providing confidence that this method can yield accurate estimates of parameters in simplified but realistic microstructural environments. Our work also demonstrates the importance of a biologically analogous phantom that can be applied to validate a variety of diffusion microstructural imaging methods in human scanners and be used for standardization of diffusion MRI protocols for neuroimaging research.
Project description:Risk of neural tube defects (NTDs) is determined by genetic and environmental factors, among which folate status appears to play a key role. However, the precise nature of the link between low folate status and NTDs is poorly understood, and it remains unclear how folic acid prevents NTDs. We investigated the effect of folate level on risk of NTDs in splotch (Sp(2)(H)) mice, which carry a mutation in Pax3. Dietary folate restriction results in reduced maternal blood folate, elevated plasma homocysteine and reduced embryonic folate content. Folate deficiency does not cause NTDs in wild-type mice, but causes a significant increase in cranial NTDs among Sp(2)(H) embryos, demonstrating a gene-environment interaction. Control treatments, in which intermediate levels of folate are supplied, suggest that NTD risk is related to embryonic folate concentration, not maternal blood folate concentration. Notably, the effect of folate deficiency appears more deleterious in female embryos than males, since defects are not prevented by exogenous folic acid. Folate-deficient embryos exhibit developmental delay and growth retardation. However, folate content normalized to protein content is appropriate for developmental stage, suggesting that folate availability places a tight limit on growth and development. Folate-deficient embryos also exhibit a reduced ratio of s-adenosylmethionine (SAM) to s-adenosylhomocysteine (SAH). This could indicate inhibition of the methylation cycle, but we did not detect any diminution in global DNA methylation, in contrast to embryos in which the methylation cycle was specifically inhibited. Hence, folate deficiency increases the risk of NTDs in genetically predisposed splotch embryos, probably via embryonic growth retardation.
Project description:Diffusion magnetic resonance imaging (MRI) in combination with functional MRI promises a whole new vista for scientists to investigate noninvasively the structural and functional connectivity of the human brain-the human connectome, which had heretofore been out of reach. As with other imaging modalities, diffusion MRI data are inherently noisy and its acquisition time-consuming. Further, a faithful representation of the human connectome that can serve as a predictive model requires a robust and accurate data-analytic pipeline. The focus of this paper is on one of the key segments of this pipeline-in particular, the development of a sparse and optimal acquisition (SOA) design for diffusion MRI multiple-shell acquisition and beyond.The authors propose a novel optimality criterion for sparse multiple-shell acquisition and quasimultiple-shell designs in diffusion MRI and a novel and effective semistochastic and moderately greedy combinatorial search strategy with simulated annealing to locate the optimum design or configuration. The goal of the optimality criteria is threefold: first, to maximize uniformity of the diffusion measurements in each shell, which is equivalent to maximal incoherence in angular measurements; second, to maximize coverage of the diffusion measurements around each radial line to achieve maximal incoherence in radial measurements for multiple-shell acquisition; and finally, to ensure maximum uniformity of diffusion measurement directions in the limiting case when all the shells are coincidental as in the case of a single-shell acquisition. The approach taken in evaluating the stability of various acquisition designs is based on the condition number and the A-optimal measure of the design matrix.Even though the number of distinct configurations for a given set of diffusion gradient directions is very large in general-e.g., in the order of 10(232) for a set of 144 diffusion gradient directions, the proposed search strategy was found to be effective in finding the optimum configuration. It was found that the square design is the most robust (i.e., with stable condition numbers and A-optimal measures under varying experimental conditions) among many other possible designs of the same sample size. Under the same performance evaluation, the square design was found to be more robust than the widely used sampling schemes similar to that of 3D radial MRI and of diffusion spectrum imaging (DSI).A novel optimality criterion for sparse multiple-shell acquisition and quasimultiple-shell designs in diffusion MRI and an effective search strategy for finding the best configuration have been developed. The results are very promising, interesting, and practical for diffusion MRI acquisitions.
Project description:BACKGROUND:Tumours growing in organs of different vascular environment could exhibit diverse responses to vascular disrupting agent (VDA). This study was aimed to identify in vivo imaging biomarkers for evaluation of pancreatic and hepatic tumours and comparison of their responses to a VDA Combretastatin A4 Phosphate (CA4P) using multiparametric MRI. METHODS:Male WAG/Rij rats were used for orthotopic pancreatic head tumour and hepatic tumour implantation; tumour growth was monitored by 3D isotropic MRI using a 3.0-T clinic scanner. Therapeutic intervention using CA4P was investigated by in vivo quantitative MRI measurements including T2/T1 relaxation mapping, diffusion kurtosis imaging and dynamic contrast-enhancement (DCE) imaging. Animals were scarified 10?h after CA4P treatment for ex vivo validation using microangiography and histomorphology. RESULTS:State-of-the-art clinical MRI protocols were successfully adapted for imaging small animal tumour with high reliability. One hour after CA4P injection, marked vascular shutdown was detected with DCE MRI in both pancreatic and hepatic tumours. However, 10?h later, therapeutic necrosis was limited in pancreatic tumours compared with that in hepatic tumours (P<0.01). Heterogeneous therapeutic changes were depicted in tumour lesions using pixel-wise Tofts model, which was generated from dynamic T1 mapping. In addition, tumour responses including haemorrhage, oedema and necrosis were detected using quantitative T2/T1 relaxation maps and diffusion kurtosis images, and were validated using histomorphology. CONCLUSIONS:Using multiparametric imaging biomarkers, hepatic tumours were found to be significantly more responsive to CA4P than pancreatic tumours, which could be of reference for designing future clinical trials on this agent.
Project description:Mouse embryo imaging is conventionally carried out on ex vivo embryos excised from the amniotic sac, omitting vital structures and abnormalities external to the body. Here, we present an in amnio MR imaging methodology in which the mouse embryo is retained in the amniotic sac and demonstrate how important embryonic structures can be visualised in 3D with high spatial resolution (100 µm/px). To illustrate the utility of in amnio imaging, we subsequently apply the technique to examine abnormal mouse embryos with abdominal wall defects. Mouse embryos at E17.5 were imaged and compared, including three normal phenotype embryos, an abnormal embryo with a clear exomphalos defect, and one with a suspected gastroschisis phenotype. Embryos were excised from the mother ensuring the amnion remained intact and stereo microscopy was performed. Embryos were next embedded in agarose for 3D, high resolution MRI on a 9.4T scanner. Identification of the abnormal embryo phenotypes was not possible using stereo microscopy or conventional ex vivo MRI. Using in amnio MRI, we determined that the abnormal embryos had an exomphalos phenotype with varying severities. In amnio MRI is ideally suited to investigate the complex relationship between embryo and amnion, together with screening for other abnormalities located outside of the mouse embryo, providing a valuable complement to histology and existing imaging methods available to the phenotyping community.