Biomedical subjects

G Larry Bretthorst

Publications and source records attributed to G Larry Bretthorst.

8 recordsLinked to original sources

PubMed2006

Site-specific experiments on folding/unfolding of Jun coiled coils: thermodynamic and kinetic parameters from spin inversion transfer nuclear magnetic resonance at leucine-18.

The 32-residue leucine zipper subsequence, called here Jun-lz, associates in benign media to form a parallel two-stranded coiled coil. Studies are reported of its thermal unfolding/folding transition by circular dichroism (CD) on samples of natural isotopic abundance and by both equilibrium and spin inversion transfer (SIT) nuclear magnetic resonance (NMR) on samples labeled at the leucine-18 alpha-carbon with 99% 13C. The data cover a wide range of temperature and concentration, and show that Jun-lz unfolds below room temperature, being far less stable than some other leucine zippers such as GCN4. 13C-NMR shows two well-separated resonances. We ascribe the upfield one to 13C spins on unfolded single chains and the downfield one to 13C spins on coiled-coil dimers. Their relative intensities provide a measure of the unfolding equilibrium constant. In SIT NMR, the recovery of the equilibrium magnetization after one resonance is inverted is modulated in part by the unfolding and folding rate constants, which are accessible from the data. Global Bayesian analysis of the equilibrium and SIT NMR data provide values for the standard enthalpy, entropy, and heat capacity of unfolding, and show the latter to be unusually large. The CD results are compatible with the NMR findings. Global Bayesian analysis of the SIT NMR data yields the corresponding activation parameters for unfolding and folding. The results show that both reaction directions are activated processes. Activation for unfolding is entropy driven, enthalpy opposed. Activation for folding is strongly enthalpy opposed and somewhat entropy opposed, falsifying the idea that the barrier for folding is solely due to a purely entropic search for properly registered partners. The activation heat capacity is much larger for folding, so almost the entire overall change is due to the folding direction. This latter finding, if it applies to GCN4 leucine zippers, clears up an extant apparent disagreement between folding rate constants for GCN4 as determined by chevron analysis and NMR in differing temperature regimes.

Carbon Isotopes↗

PubMed2006

Modeling water diffusion anisotropy within fixed newborn primate brain using Bayesian probability theory.

An active area of research involves optimally modeling brain diffusion MRI data for various applications. In this study Bayesian analysis procedures were used to evaluate three models applied to phase-sensitive diffusion MRI data obtained from formalin-fixed perinatal primate brain tissue: conventional diffusion tensor imaging (DTI), a cumulant expansion, and a family of modified DTI expressions. In the latter two cases the optimum expression was selected from the model family for each voxel in the image. The ability of each model to represent the data was evaluated by comparing the magnitude of the residuals to the thermal noise. Consistent with previous findings from other laboratories, the DTI model poorly represented the experimental data. In contrast, the cumulant expansion and modified DTI expressions were both capable of modeling the data to within the noise using six to eight adjustable parameters per voxel. In these cases the model selection results provided a valuable form of image contrast. The successful modeling procedures differ from the conventional DTI model in that they allow the MRI signal to decay to a positive offset. Intuitively, the positive offset can be thought of as spins that are sufficiently restricted to appear immobile over the sampled range of b-values.

Animals↗

PubMed2005

Diffusion MR imaging characteristics of the developing primate brain.

Diffusion-based magnetic resonance imaging holds the potential to non-invasively demonstrate cellular-scale structural properties of brain. This method was applied to fixed baboon brains ranging from 90 to 185 days gestational age to characterize the changes in diffusion properties associated with brain development. Within each image voxel, a probability-theory-based approach was employed to choose, from a group of analytic equations, the one that best expressed water displacements. The resulting expressions contain eight or fewer adjustable parameters, indicating that relatively simple expressions are sufficient to obtain a complete description of the diffusion MRI signal in developing brain. The measured diffusion parameters changed systematically with gestational age, reflecting the rich underlying microstructural changes that take place during this developmental period. These changes closely parallel those of live, developing human brain. The information obtained from this primate model of cerebral microstructure is directly applicable to studies of human development.

Algorithms↗

PubMed2005

Sodium ion apparent diffusion coefficient in living rat brain.

The apparent diffusion coefficient (ADC) of Na(+) was determined in live rat brain. The brain extracellular-to-intracellular Na(+) content ratio is approximately 8:2, which is the inverse of that for water in these spaces. Consequently, the ADC of Na(+) is primarily affected by motion in the extracellular space, and Na(+) can be viewed as a reporter molecule for motion in that space. Likewise, water ADC is dominated by intracellular motion. The brain Na(+) ADC was 1.15 +/- 0.09 microm(2)/ms, which is 61% of the aqueous Na(+) free diffusion coefficient (D(free)) at 37 degrees C (1.9 microm(2)/ms), while the ADC for brain water is 28% of the water D(free) at 37 degrees C (3 microm(2)/ms). This suggests that the ADC of molecular species within the extracellular space is roughly twofold that within the intracellular space. In postmortem brain, both Na(+) and water decrease to 17% of the respective D(free) values. These results are consistent with Na(+) and water ADC values sharing the same biophysical determinants in postmortem brain. The observed difference between Na(+) and water ADC/D(free) ratios in living brain tissue may be attributable to the extracellular environment hindering molecular displacements twofold less than the intracellular environment.

Animals↗

PubMed2003

Equilibrium water exchange between the intra- and extracellular spaces of mammalian brain.

This report describes the measurement of water preexchange lifetimes and intra/extracellular content in intact, functioning mammalian brain. Intra- and extracellular water magnetic resonance (MR) signals from rat brain in vivo were quantitatively resolved in the longitudinal relaxation domain following administration of an MR relaxation agent into the extracellular space. The estimated intracellular water content fraction was 81% +/- 8%, and the intra- to extracellular exchange rate constant was 1.81 +/- 0.89 s(-1) (mean +/- SD, N = 9), corresponding to an intracellular water preexchange lifetime of approximately 550 ms. These results provide a temporal framework for anticipating the water exchange regime (fast, intermediate, or slow) underlying a variety of compartment-sensitive measurements. The method also supplies a means by which to evaluate membrane water permeability and intra/extracellular water content serially in intact tissue. The data are obtained in an imaging mode that permits detection of regional variations in these parameters.

Animals↗

PubMed2003

Sources of plasma glucose by automated Bayesian analysis of 2H NMR spectra.

Sources of blood glucose can be determined after oral ingestion of (2)H(2)O followed by isolation of plasma glucose and measurement of the relative (2)H enrichments in select positions within the glucose molecule. Typically, (2)H enrichments are obtained by mass spectrometry but (2)H NMR offers an alternative. Here it is demonstrated that the entire analysis may be automated by Bayesian analysis of a (2)H free induction decay signal of monoacetone glucose to obtain a direct readout of the relative contributions of glycogenolysis, glycerol, and phosphoenol pyruvate to plasma glucose production. Furthermore, Markov Chain Monte Carlo (MCMC) simulations of the posterior probability density provide uncertainties in all metabolic parameters from a single patient, thereby allowing comparisons in glucose metabolism from one individual to another. The combined MCMC Bayesian methodology is operationally simple and requires little intervention from the operator.

Autoanalysis↗

PubMed2003

Statistical model for diffusion attenuated MR signal.

A general statistical model that can describe a rather large number of experimental results related to the structure of the diffusion-attenuated MR signal in biological systems is introduced. The theoretical framework relies on a phenomenological model that introduces a distribution function for tissue apparent diffusion coefficients (ADC). It is shown that at least two parameters--the position of distribution maxima (ADC) and the distribution width (sigma)--are needed to describe the MR signal in most regions of a human brain. A substantial distribution width, on the order of 36% of the ADC, was found for practically all brain regions examined. This method of modeling the MR diffusion measurement allows determination of an intrinsic tissue-specific ADC for a given diffusion time independent of the strength of diffusion sensitizing gradients. The model accounts for the previously found biexponential behavior of the diffusion-attenuated MR signal in CNS.

Brain↗

PubMed2002

Quantitative in vivo assessment of lung microstructure at the alveolar level with hyperpolarized 3He diffusion MRI.

The study of lung emphysema dates back to the beginning of the 17th century. Nevertheless, a number of important questions remain unanswered because a quantitative localized characterization of emphysema requires knowledge of lung structure at the alveolar level in the intact living lung. This information is not available from traditional imaging modalities and pulmonary function tests. Herein, we report the first in vivo measurements of lung geometrical parameters at the alveolar level obtained with 3He diffusion MRI in healthy human subjects and patients with severe emphysema. We also provide the first experimental data demonstrating that 3He gas diffusivity in the acinus of human lung is highly anisotropic. A theory of anisotropic diffusion is presented. Our results clearly demonstrate substantial differences between healthy and emphysematous lung at the acinar level and may provide new insights into emphysema progression. The technique offers promise as a clinical tool for early diagnosis of emphysema.

Diffusion↗