David H. Johnson

Overexpression of the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) in skeletal muscle repatterns energy metabolism in the mouse

Transgenic mice, containing a chimeric gene in which the cDNA for phosphoenolpyruvate carboxykinase (GTP) (PEPCK-C) (EC 4.1.1.32) was linked to the α-skeletal actin gene promoter, express PEPCK-C in skeletal muscle (1-3 units/g). Breeding two founder lines together produced mice with an activity of PEPCK-C of 9 units/g of muscle (PEPCK-Cmus mice). These mice were seven times more active in their cages than controls. On a mouse treadmill, PEPCK-Cmus mice ran up to 6 km at a speed of 20 m/min, whereas controls stopped at 0.2 km. PEPCK-Cmus mice had an enhanced exercise capacity, with a VO2max of 156 ± 8.0 ml/kg/min, a maximal respiratory exchange ratio of 0.91 ± 0.03, and a blood lactate concentration of 3.7 ± 1.0 mm after running for 32 min at a 25° grade; the values for control animals were 112 ± 21 ml/kg/min, 0.99 ± 0.08, and 8.1 ± 5.0 mm respectively. The PEPCK-Cmus mice ate 60% more than controls but had half the body weight and 10% the body fat as determined by magnetic resonance imaging. In addition, the number of mitochondria and the content of triglyceride in the skeletal muscle of PEPCK-Cmus mice were greatly increased as compared with controls. PEPCK-Cmus mice had an extended life span relative to control animals; mice up to an age of 2.5 years ran twice as fast as 6-12-month-old control animals. We conclude that overexpression of PEPCK-C repatterns energy metabolism and leads to greater longevity.

Reproducible MRI measurement of adipose tissue volumes in genetic and dietary rodent obesity models

To develop ratio MRI [lipid/(lipid+water)] methods for assessing lipid depots and compare measurement variability with biological differences among lean controls (spontaneously hypertensive rats [SHRs]), dietary obese rats (SHR‐DOs), and genetic/dietary obese rats (SHROBs).

Improved fat–water reconstruction algorithm with graphics hardware acceleration

To develop a fast and robust Iterative Decomposition of water and fat with Echo Asymmetry and Least‐squares (IDEAL) reconstruction algorithm using graphics processor unit (GPU) computation.

Fast Lipid And Water Levels by Extraction with Spatial Smoothing (FLAWLESS): Three-dimensional volume fat/water separation at 7 Tesla

To quickly and robustly separate fat/water components of 7T MR images in the presence of field inhomogeneity for the study of metabolic disorders in small animals.

A Fast Iterated Conditional Modes Algorithm for Water–Fat Decomposition in MRI

Decomposition of water and fat in magnetic resonance imaging (MRI) is important for biomedical research and clinical applications. In this paper, we propose a two-phased approach for the three-point water-fat decomposition problem. Our contribution consists of two components: 1) a background-masked Markov random field (MRF) energy model to formulate the local smoothness of field inhomogeneity; 2) a new iterated conditional modes (ICM) algorithm accounting for high-performance optimization of the MRF energy model. The MRF energy model is integrated with background masking to prevent error propagation of background estimates as well as improve efficiency. The central component of our new ICM algorithm is the stability tracking (ST) mechanism intended to dynamically track iterative stability on pixels so that computation per iteration is performed only on instable pixels. The ST mechanism significantly improves the efficiency of ICM. We also develop a median-based initialization algorithm to provide good initial guesses for ICM iterations, and an adaptive gradient-based scheme for parametric configuration of the MRF model. We evaluate the robust of our approach with high-resolution mouse datasets acquired from 7T MRI.

Quantification of adipose tissue in a rodent model of obesity

Obesity is a global epidemic and a comorbidity for many diseases. We are using MRI to characterize obesity in rodents, especially with regard to visceral fat. Rats were scanned on a 1.5T clinical scanner, and a T1W, water-spoiled image (fat only) was divided by a matched T1W image (fat + water) to yield a ratio image related to the lipid content in each voxel. The ratio eliminated coil sensitivity inhomogeneity and gave flat values across a fat pad, except for outlier voxels (> 1.0) due to motion. Following sacrifice, fat pad volumes were dissected and measured by displacement in canola oil. In our study of 6 lean (SHR), 6 dietary obese (SHR-DO), and 9 genetically obese rats (SHROB), significant differences in visceral fat volume was observed with an average of 29±16 ml increase due to diet and 84±44 ml increase due to genetics relative to lean control with a volume of 11±4 ml. Subcutaneous fat increased 14±8 ml due to diet and 198±105 ml due to genetics relative to the lean control with 7±3 ml. Visceral fat strongly correlated between MRI and dissection (R2 = 0.94), but MRI detected over five times the subcutaneous fat found with error-prone dissection. Using a semi-automated images segmentation method on the ratio images, intra-subject variation was very low. Fat pad composition as estimated from ratio images consistently differentiated the strains with SHROB having a greater lipid concentration in adipose tissues. Future work will include in vivo studies of diet versus genetics, identification of new phenotypes, and corrective measures for obesity; technical efforts will focus on correction for motion and automation in quantification.

Statistical modeling and MAP estimation for body fat quantification with MRI ratio imaging

We are developing small animal imaging techniques to characterize the kinetics of lipid accumulation/reduction of fat depots in response to genetic/dietary factors associated with obesity and metabolic syndromes. Recently, we developed an MR ratio imaging technique that approximately yields lipid/{lipid + water}. In this work, we develop a statistical model for the ratio distribution that explicitly includes a partial volume (PV) fraction of fat and a mixture of a Rician and multiple Gaussians. Monte Carlo hypothesis testing showed that our model was valid over a wide range of coefficient of variation of the denominator distribution (c.v.: 0-0:20) and correlation coefficient among the numerator and denominator (&rgr; 0-0.95), which cover the typical values that we found in MRI data sets (c.v.: 0:027-0:063, &rgr;: 0:50-0:75). Then a maximum a posteriori (MAP) estimate for the fat percentage per voxel is proposed. Using a digital phantom with many PV voxels, we found that ratio values were not linearly related to PV fat content and that our method accurately described the histogram. In addition, the new method estimated the ground truth within +1.6% vs. +43% for an approach using an uncorrected ratio image, when we simply threshold the ratio image. On the six genetically obese rat data sets, the MAP estimate gave total fat volumes of 279 ± 45mL, values ≈ 21% smaller than those from the uncorrected ratio images, principally due to the non-linear PV effect. We conclude that our algorithm can increase the accuracy of fat volume quantification even in regions having many PV voxels, e.g. ectopic fat depots.

MICE : A mouse imaging collaboration environment

With the ever-increasing complexity of science and engineering, many important research problems are being addressed by collaborative, multidisciplinary teams. We present a web-based collaborative environment for small animal imaging research, called the Mouse Imaging Collaboration Environment (MICE). MICE provides an effective and user-friendly tool for managing and sharing of the terabytes of high-resolution and high-dimension image data generated at small animal imaging core facilities. We describe the design of MICE and our experience in the implementation and deployment of a beta-version baseline-MICE. The baseline-MICE provides an integrated solution from image data acquisition to end-user access and long-term data storage at our UH/Case Small Animal Imaging Resource Center. As image data is acquired from scanners, it is pushed to the MICE server which automatically stores it in a directory structure according to its DICOM metadata. The directory structure reflects imaging modality, principle investigators, animal models, scanning dates and study details. Registered end-users access this imaging data through an authenticated web-interface. Thumbnail images are created by custom scripts running on the MICE server while data down-loading is achieved through standard web-browser ftp. MICE provides a security infrastructure that manages user roles, their access privileges such as read/write, and the right to modify the access privileges. Additional data security measures include a two server paradigm with the Web access server residing outside a network firewall to provide access through the Internet, and the imaging data server - a large RAID storage system supporting flexible backup policies - residing behind the protected firewall with a dedicated link to the Web access server. Direct network link to the RAID storage system outside the firewall other than this dedicated link is not permitted. Establishing the initial image directory structure and letting the project leader manage data access through a web-interface represent Phase I implementation. In Phase II, features for uploading image analysis scripts and results back to the MICE server will be implemented, as well as mechanisms facilitating asynchronous and synchronous discussion, annotation, and analysis. Most of MICE features are being implemented in the Plone5 object-oriented database environment which greatly shortens developmental time and effort by the reuse of a variety of Plones open-source modules for Content Management Systems.7, 8 The open-source modules are well suited as an implementation basis of MICE and provide data integration as a built-in primitive.